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Institute for Environmental Genomics / Publications

Publications

In press
  1. Baker, N. R., K. Zhalnina, M. Yuan, D. Herman, J. A. Ceja-Navarro, J. Sasse, J. S. Jordan, B. P. Bowen, L. Wu, C. Fossum, A. Chew, Y. Fu, M. Saha, J. -Z. Zhou, J. Pett-Ridge, T. R. Northen, and M. K. Firestone (2024). "Nutrient and moisture limitations reveal keystone metabolites linking rhizosphere metabolomes and microbiomes". Proceedings of the National Academy of Sciences of the United States of America. In press.
2024
 
 
  1. Feng, K., S. Wang, Q. He, M. Bonkowski, M. Bahram, E. Yergeau, Z. J. Wang, X. Peng, D. R. Wang, S. Z. Li, Y. C. Wang, Z. C. Ju, X. F. Du, C. L. Yan, S. S. Gu, T. Li, X. S. Yang, W. L. Shen, Z. Y. Wei, Q. L. Hu, P. F. Li, Y. M. Zhu, G. X. Lu, C. Qin, G. X. Zhang, C. W. Xiao, Y. F. Yang, J. Z. Zhou and Y. Deng (2024). "CoBacFM: Core bacteria forecast model for global grassland pH dynamics under future climate warming scenarios." One Earth 7(7), 1275-1287. Suppl (zip)
  2. Hu, H., J. Chen, F. Zhou, M. Nie, D. Hou, H. Liu, M. Delgado-Baquerizo, H. Ni, W. Huang, J.-Z.  Zhou, X. Song, X. Cao, B. Sun, J. Zhang, T. Crowther and Y. Liang (2024). "Relative increases in CH4 and CO2 emissions from wetlands under global warming dependent on soil carbon substrates." Nature Geoscience 17(1). Suppl 1 (pdf), suppl 2 (zip), suppl 3 (zip)
  3. Hunt, K. A., A. V. Carr, A. E. Otwell, J. J. Valenzuela, K. S. Walker, E. R. Dixon, L. M. Lui, T. N. Nielsen, S. Bowman, F. von Netzer, J.-W. Moon, C. W. Schadt, M. Rodriguez Jr, K. Lowe, D. Joyner, K. J. Davis, X. Wu, R. Chakraborty, M. W. Fields, J.-Z. Zhou, T. C. Hazen, A. P. Arkin, S. D. Wankel, N. S. Baliga and D. A. Stahl (2024). "Contribution of Microorganisms with the Clade II Nitrous Oxide Reductase to Suppression of Surface Emissions of Nitrous Oxide." Environmental Science & Technology, .58(16), 7056–7065. Suppl (pdf).
  4. Lei, J., Y. Su, S. Jian, X. Guo, M. Yuan, C. T. Bates, Z. J. Shi, J. Li, Y. Su, D. Ning, L. Wu, J.-Z.  Zhou and Y. Yang (2024). "Warming effects on grassland soil microbial communities are amplified in cool months." ISME Journal 18(1): wrae088. Suppl (pdf)
  5. Li, S., M. Delgado-Baquerizo, J. X. Ding, H. Hu, W. G. Huang, Y. S. Sun, H. W. Ni, Y. Y. Kuang, M. M. Yuan, J.- Z. Zhou, J. B. Zhang and Y. T. Liang (2024). "Intrinsic microbial temperature sensitivity and soil organic carbon decomposition in response to climate change." Global Change Biology 30(6), e17395;  https://doi.org/10.1111/gcb.17395. Suppl (docx)
  6. Jian, S., J. Li, G. Wang, J.-Z.  Zhou, C. W. Schadt and M. A. Mayes (2024). "Generalizing Microbial Parameters in Soil Biogeochemical Models: Insights From a Multi-Site Incubation Experiment." Journal of Geophysical Research-Biogeosciences 129(4), e2023JG007825., https://doi.org/10.1029/2023JG007825.. Suppl (docx).
  7. Liang, Z., X. Guo, S. Liu, Y. Su, Y. Zeng, C. Xie, Q. Gao, J. Lei, B. Li, M. Wang, T. Dai, L. Ma, F. Fan, Y. Yang, X. Liu and J. Zhou (2024). "Microbial mediation of soil carbon loss at the potential climax of alpine grassland under warming." Soil Biology & Biochemistry 192. Suppl (docx).
  8. Liu, X. J. A., S. Han, S. D. Frey, J. M. Melillo, J._Z. Zhou and K. M. Deangelis (2024). "Microbial responses to long-term warming differ across soil microenvironments." ISME Communications 4(1), doi.org/10.1093/ismeco/ycae051. Suppl (docx)
  9. Ma, Z., S. Jiao, K. Zheng, H. Ni, D. Li, N. Zhang, Y. Yang, J. Zhou, B. Sun and Y. Liang (2024). "Multiple spatial scales of bacterial and fungal structural and functional traits affect carbon mineralization." Molecular Ecology 33(3). Suppl (pdf).
  10. Michael, J. P., A. D. Putt, Y. Yang, B. G. Adams, K. R. McBride, Y. Fan, K. A. Lowe, D. Ning, S. Jagadamma, J. W. Moon, D. M. Klingeman, P. Zhang, Y. Fu, T. C. Hazen and J. Zhou (2024). "Reproducible responses of geochemical and microbial successional patterns in the subsurface to carbon source amendment." Water Research 255. Suppl (zip).
  11. Ning, D., Y. Wang, Y. Fan, J. Wang, J. D. Van Nostrand, L. Wu, P. Zhang, D. J. Curtis, R. Tian, L. Lui, T. C. Hazen, E. J. Alm, M. W. Fields, F. Poole, M. W. W. Adams, R. Chakraborty, D. A. Stahl, P. D. Adams, A. P. Arkin, Z. He and J. Zhou (2024). "Environmental stress mediates groundwater microbial community assembly." Nature Microbiology 9(2). Suppl (pdf).
  12. Qiao, M., R. Sun, Z. Wang, K. Dumack, X. Xie, C. Dai, E. Wang, J. Zhou, B. Sun, X. Peng, M. Bonkowski and Y. Chen (2024). "Legume rhizodeposition promotes nitrogen fixation by soil microbiota under crop diversification." Nature Communications 15(1). Suppl 1 (pdf), suppl 2 (zip).
  13. Qin, H. L., Y. Liu, C. L. Chen, A. L. Chen, Y. T. Liang, C. R. Cornell, X. Guo, E. Bai, H. J. Hou, D. Wang, L. Y. Zhang, J. Y. Wang, D. L. Yao, X. M. Wei, J. -Z. Zhou, Z. L. Tan and B. L. Zhu (2024). "Differential contribution of microbial and plant-derived organic matter to soil organic carbon sequestration over two decades of natural revegetation and cropping." Science of the Total Environment 949, , 174960, https://doi.org/10.1016/j.scitotenv.2024.174960. Suppl (zip)
  14. Qin, W., S. P. Wei, Y. Zheng, E. Choi, X. Li, J. Johnston, X. Wan, B. Abrahamson, Z. Flinkstrom, B. Wang, H. Li, L. Hou, Q. Tao, W. W. Chlouber, X. Sun, M. Wells, L. Ngo, K. A. Hunt, H. Urakawa, X. Tao, D. Wang, X. Yan, D. Wang, C. Pan, P. K. Weber, J. Jiang, J. Zhou, Y. Zhang, D. A. Stahl, B. B. Ward, X. Mayali, W. Martens-Habbena and M.-K. H. Winkler (2024). "Ammonia-oxidizing bacteria and archaea exhibit differential nitrogen source preferences." Nature Microbiology 9(2). Suppl 1 (pdf).
  15. Qiu, Z., L. Yuan, C.-A. Lian, B. Lin, J. Chen, R. Mu, X. Qiao, L. Zhang, Z. Xu, L. Fan, Y. Zhang, S. Wang, J. Li, H. Cao, B. Li, B. Chen, C. Song, Y. Liu, L. Shi, Y. Tian, J. Ni, T. Zhang, J. Zhou, W.-Q. Zhuang and K. Yu (2024). "BASALT refines binning from metagenomic data and increases resolution of genome-resolved metagenomic analysis." Nature Communications 15(1). Suppl 1 (pdf), suppl 2 (xlsx).
  16. Shi, Z., F. M. Hoffman, M. Xu, U. Mishra, S. D. Allison, J.-Z. Zhou and J. T. Randerson (2024). "Global-Scale Convergence Obscures Inconsistencies in Soil Carbon Change Predicted by Earth System Models." AGU Advances 5(2), e2023AV001068, doi.org/10.1029/2023AV001068. Suppl (docx).
  17. Tao, X., Z. Yang, J. Feng, S. Jian, Y. Yang, C. T. Bates, G. Wang, X. Guo, D. Ning, M. L. Kempher, X. J. A. Liu, Y. Ouyang, S. Han, L. Wu, Y. Zeng, J. Kuang, Y. Zhang, X. Zhou, Z. Shi, W. Qin, J. Wang, M. K. Firestone, J. M. Tiedje and J. Zhou (2024). "Experimental warming accelerates positive soil priming in a temperate grassland ecosystem." Nature Communications 15(1). Suppl (pdf).
  18. Tian, J., J. A. J. Dungait, R. Hou, Y. Deng, I. P. Hartley, Y. Yang, Y. Kuzyakov, F. Zhang, M. F. Cotrufo and J. Zhou (2024). "Microbially mediated mechanisms underlie soil carbon accrual by conservation agriculture under decade-long warming." Nature Communications 15(1). Suppl (pdf).
  19. Tian, R., J. Z. Zhou and B. Imanian (2024). "PlasmidHunter: accurate and fast prediction of plasmid sequences using gene content profile and machine learning." Briefings in Bioinformatics 25(4). Suppl (docx)
  20. Wang, D., P. Candry, K. A. Hunt, Z. Flinkstrom, Z. Shi, Y. Liu, N. Q. Wofford, M. J. McInerney, R. S. Tanner, K. B. De Leon, J.-Z. Zhou, M.-K. H. Winkler, D. A. Stahl and C. Pan (2024). "Metaproteomics-informed stoichiometric modeling reveals the responses of wetland microbial communities to oxygen and sulfate exposure." npj Biofilms and Microbiomes 10(1): 55. doi.org/10.1038/s41522-024-00525-5. Suppl (pdf)
  21. Zeng, Y., X. Guo, J. Lei, Y. Shi, X. Liu, T. Dai, Q. Zhang, Q. Gao, H. Chu, Y. Liu, J. Zhou and Y. Yang (2024). "Regional microbial biogeography linked to soil respiration." Science of the Total Environment 929. Suppl (docx)
  22. Zhang, L., R. Huang, Z. Ma, S. Li, J. Ding, W. Huang, C. Liu, Y. Sui, J. Zhou, J. Zhang and Y. Liang (2024). "Warming Leads to Changes in Soil Organic Carbon Molecules Due to Decreased Mineral Protection." Journal of Agricultural and Food Chemistry 72(14), 7765-7773, doi.org/10.1021/acs.jafc.3c09657. Suppl (pdf).
  23. Zhang, Y., Y. Deng, C. Wang, S. Li, F. T. K. Lau, J. Zhou and T. Zhang (2024). "Effects of operational parameters on bacterial communities in Hong Kong and global wastewater treatment plants." Msystems 9(3). Suppl 1 (pdf), suppl 2 (xlsx).
  24. Zheng, Y., B. Wang, P. Gao, Y. Yang, B. Xu, X. Su, D. Ning, Q. Tao, Q. Li, F. Zhao, D. Wang, Y. Zhang, M. Li, M.-K. H. Winkler, A. E. Ingalls, J. Zhou, C. Zhang, D. A. Stahl, J. Jiang, W. Martens-Habbena and W. Qin (2024). "Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments." Isme Journal 18(1). Suppl (docx).
  25. Zhang, Z., L. Zhang, L. Zhang, H. Chu, J. Zhou and F. Ju (2024). "Diversity and distribution of biosynthetic gene clusters in agricultural soil microbiomes." Msystems. Suppl 1 (pdf), suppl 2 (xlsx).
  26. Zheng, Y., B. Wang, P. Gao, Y. Yang, B. Xu, X. Su, D. Ning, Q. Tao, Q. Li, F. Zhao, D. Wang, Y. Zhang, M. Li, M.-K. H. Winkler, A. E. Ingalls, J. Zhou, C. Zhang, D. A. Stahl, J. Jiang, W. Martens-Habbena and W. Qin (2024). "Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments." Isme Journal 18(1). Suppl (docx)
  27. Zhu, L., L. Luan, Y. Chen, X. Wang, S. Zhou, W. Zou, X. Han, Y. Duan, B. Zhu, Y. Li, W. Liu, J.-Z. Zhou, J. Zhang, Y. Jiang and B. Sun (2024). "Community assembly of organisms regulates soil microbial functional potential through dual mechanisms." Global Change Biology 30(2), e17160, doi.org/10.1111/gcb.17160. Suppl (docx).

 

2023
  1. Cornell, C.R., Y. Zhang, D. Ning, N. Xiao, P. Wagle, X. Xiao and J. Zhou (2023). "Land use conversion increases network complexity and stability of soil microbial communities in a temperate grassland". Isme Journal. Suppl (pdf) doi:10.1038/s41396-023-01521-x.
  2. Huang, L. and J. Zhou (2023). A successful start for mLife, vol 2, p 1-1. Wiley Online Library. mLife 1(1).
  3. Ji, M. Z., X. Y. Fan, C. R. Cornell, Y. Zhang, M. M. Yuan, Z. Tian, K. L. Sun, R. F. Gao, Y. Liu and J. Z. Zhou (2023). "Tundra Soil Viruses Mediate Responses of Microbial Communities to Climate Warming." Mbio. suppl 1 (pdf), suppl 2 (xlsx)
  4. Jiang, M., M. Delgado-Baquerizo, M. M. Yuan, J. Ding, E. Yergeau, J. Zhou, T. W. Crowther and Y. Liang (2023). "Home-based microbial solution to boost crop growth in low-fertility soil." New Phytologist. Suppl (pdf)
  5. Liang, Q.-Y., J.-Y. Zhang, D. Ning, W.-X. Yu, G.-J. Chen, X. Tao, J. Zhou, Z.-J. Du and D.-S. Mu (2023). "Niche Modification by Sulfate-Reducing Bacteria Drives Microbial Community Assembly in Anoxic Marine Sediments." Mbio. Suppl 1 (pdf), suppl 2 (xlsx)
  6. Liao, H., X. Hao, F. Qin, M. Delgado-Baquerizo, Y. Liu, J. Zhou, P. Cai, W. Chen and Q. Huang (2023). "Microbial autotrophy explains large-scale soil CO2 fixation." Global Change Biology 29(1): 231-242. Suppl (docx)
  7. Liu, C., M. Jiang, M.M. Yuan, E. Wang, Y. Bai, T.W. Crowther, J. Zhou, Z. Ma, L. Zhang, Y. Wang, J. Ding, W. Liu, B. Sun, R. Shen, J. Zhang and Y. Liang (2023). "Root microbiota confers rice resistance to aluminium toxicity and phosphorus deficiency in acidic soils". Nature Food doi:10.1038/s43016-023-00848-0. Suppl 1 (pdf), suppl 2 (xlsx)
  8. Ma, Z., S. Jiao, K. Zheng, H. Ni, D. Li, N. Zhang, Y. Yang, J. Zhou, B. Sun and Y. Liang (2023). "Multiple spatial scales of bacterial and fungal structural and functional traits affect carbon mineralization". Molecular Ecology doi:10.1111/mec.17235. Suppl (pdf)
  9. Peng, Q., L. Lin, Q. Tu, X. Wang, Y. Zhou, J. Chen, N. Jiao and J. Zhou (2023). "Unraveling the roles of coastal bacterial consortia in degradation of various lignocellulosic substrates". Msystems doi:10.1128/msystems.01283-22. Suppl 1 (docx), Suppl 2 (xlsx), Suppl 3 (xlsx), Suppl 4 (xlsx)
  10. Qin, Y., L. Wu, Q. Zhang, C. Wen, J.D. Van Nostrand, D. Ning, L. Raskin, A. Pinto and J. Zhou (2023). "Effects of error, chimera, bias, and GC content on the accuracy of amplicon sequencing". Msystems doi:10.1128/msystems.01025-23. Suppl 1 (pdf), suppl 2 (xslx), suppl 3 (xlsx)
  11. Shi, K., H. Cheng, C. R. Cornell, H. Wu, S. Gao, J. Jiang, T. Liu, A. Wang, J. Zhou and B. Liang (2023). "Micro-aeration assisted with electrogenic respiration enhanced the microbial catabolism and ammonification of aromatic amines in industrial wastewater." Journal of Hazardous Materials 448. Suppl (docx)
  12. Shi, K., B. Liang, K. Feng, D. Ning, C. R. Cornell, Y. Zhang, W. Xu, M. Zhou, Y. Deng, J. Jiang, T. Liu, A. Wang and J. Zhou (2023). "Electrostimulation triggers an increase in cross-niche microbial associations toward enhancing organic nitrogen wastewater treatment." Journal of Environmental Management 331. Suppl (docx)
  13. Tao, X., J.S. Morgan, J. Liu, M.L. Kempher, T. Xu and J. Zhou (2023). "Target integration of an exogenous β-glucosidase enhances cellulose degradation and ethanol production in Clostridium cellulolyticum". Bioresource Technology doi:org/10.1016/j.biortech.2023.128849.
  14. Tao, X., H. Ouyang, A. Zhou, D. Wang, H. Matlock, J.S. Morgan, A.T. Ren, D. Mu, C. Pan, X. Zhu, A. Han and J. Zhou (2023). "Polyethylene Degradation by a Rhodococcous Strain Isolated from Naturally Weathered Plastic Waste Enrichment". Environmental Science & Technology 57:13901-13911. Suppl (pdf)
  15. Wang, D., K. A. Hunt, P. Candry, X. Tao, N. Q. Wofford, J. Zhou, M. J. McInerney, D. A. Stahl, R. S. Tanner, A. Zhou, M. Winkler and C. Pan (2023). "Cross-Feedings, Competition, and Positive and Negative Synergies in a Four-Species Synthetic Community for Anaerobic Degradation of Cellulose to Methane." Mbio. Suppl (pdf)
  16. Wang, M., X. Sun, B. Cao, N.R. Chiariello, K.M. Docherty, C.B. Field, Q. Gao, J.L.M. Gutknecht, X. Guo, G. He, B.A. Hungate, J. Lei, A. Niboyet, X. Le Roux, Z. Shi, W. Shu, M. Yuan, J. Zhou and Y. Yang (2023). "Long-term elevated precipitation induces grassland soil carbon loss via microbe-plant-soil interplay". Global Change Biology doi:10.1111/gcb.16811. Suppl (docx), Suppl 2 (xlsx)
  17. Wang, H., H. Cui, X. Ma, C. R. Cornell, L. Zhang, Y. Ren, M. Li, Y. Liu, S.-H. Gao, Z. Li, A.-J. Wang, J. Zhou and B. Liang (2023). "Molecular mechanism of adsorbing triclocarban by the activated sludge in wastewater treatment systems." Chemical Engineering Journal 463. Suppl (docx)
  18. Wang, Y., R. Zhang, Y. Yang, Q. Tu, J. Zhou and N. Jiao (2023). "Ocean acidification altered microbial functional potential in the Arctic Ocean". Limnology and Oceanography doi:10.1002/lno.12375. Suppl (pdf)
  19. Wu, L., Y. Yang, D. Ning, Q. Gao, H. Yin, N. Xiao, B.Y. Zhou, S. Chen, Q. He and J. Zhou (2023). "Assessing mechanisms for microbial taxa and community dynamics using process models". mLife. Suppl (docx)
  20. Wu, Y., C. Fu, C.L. Peacock, S.J. Sorensen, M.A. Redmile-Gordon, K.-Q. Xiao, C. Gao, J. Liu, Q. Huang, Z. Li, P. Song, Y. Zhu, J. Zhou and P. Cai (2023). "Cooperative microbial interactions drive spatial segregation in porous environments". Nature Communications 14. Suppl (pdf)
  21. Xiao, X., M. Delgado-Baquerizo, H. Shen, Z. Ma, J. Zhou, B. Sun and Y. Liang (2023). "Microbial Interactions Related to N2O Emissions and Temperature Sensitivity from Rice Paddy Fields." Mbio. Suppl (pdf)
  22. Xiao, X., Z. Ma, J. Zhang, B. Sun, J. Zhou and Y. Liang (2023). "Coupling temperature-dependent spatial turnover of microbes and plants using the metabolic theory of ecology." New Phytologist: Vol. 238 Issue 1 Pages 383-392
    . Suppl (pdf)
  23. Xu, T., X. Tao, H. He, M. L. Kempher, S. Zhang, X. Liu, J. Wang, D. Wang, D. Ning, C. Pan, H. Ge, N. Zhang, Y.-X. He and J. Zhou (2023). "Functional and structural diversification of incomplete phosphotransferase system in cellulose-degrading clostridia." Isme Journal. Suppl (pdf)
  24. Yang, Y. and J. Zhou (2023). "Unveiling the hidden world of microorganisms and their impact on the Earth's ecosystems". Mlife 2:339-340.
  25. Zhang, L., X. Huang, J. Zhou and F. Ju (2023). "Active predation, phylogenetic diversity, and global prevalence of myxobacteria in wastewater treatment plants." Isme Journal. Suppl (docx)
  26. Zhang, Y., D. Ning, L. Wu, M. M. Yuan, X. Zhou, X. Guo, Y. Hu, S. Jian, Z. Yang, S. Han, J. Feng, J. Kuang, C. R. Cornell, C. T. Bates, Y. Fan, J. P. Michael, Y. Ouyang, J. Guo, Z. Gao, Z. Shi, N. Xiao, Y. Fu, A. Zhou, L. Wu, X. Liu, Y. Yang, J. M. Tiedje and J. Zhou (2023). "Experimental warming leads to convergent succession of grassland archaeal community." Nature Climate Change. Suppl 1 (pdf), suppl 2 (docx)
  27. Zhang, Y., Y. Wang, M. Tang, J. Zhou and T. Zhang (2023). "The microbial dark matter and "wanted list" in worldwide wastewater treatment plants". Microbiome 11. Suppl (docx)
  28. Zhou, J., W. Qin, X. Lu, Y. Yang, D. Stahl, N. Jiao, J. Zhou, J. Liu and Q. Tu (2023). "The diversity and ecological significance of microbial traits potentially involved in B12 biosynthesis in the global ocean". bioRxiv:2023.2008. 2019.553841.
  29. Zhu, L., Y. Chen, R. Sun, J. Zhang, L. Hale, K. Dumack, S. Geisen, Y. Deng, Y. Duan, B. Zhu, Y. Li, W. Liu, X. Wang, B.S. Griffiths, M. Bonkowski, J. Zhou and B. Sun (2023). "Resource-dependent biodiversity and potential multi-trophic interactions determine belowground functional trait stability". Microbiome 11. Suppl 1 (docx), Suppl 2 (xlsx), Suppl 3 (xlsx), Suppl 4 (xlsx), Suppl 5 (xlsx), Suppl 6 (xlsx)
  30. Zhuang, J., R. Zhang, Y. Zeng, T. Dai, Z. Ye, Q. Gao, Y. Yang, X. Guo, G. Li and J. Zhou (2023). "Petroleum pollution changes microbial diversity and network complexity of soil profile in an oil refinery". Frontiers in Microbiology 14. Suppl (zp)
 
2022
  1. Bates CT, Escalas A, Kuang JL, Hale L, Wang Y, Herman D, et al. Conversion of marginal land into switchgrass conditionally accrues soil carbon but reduces methane consumption. Isme Journal. 2022;16(1):10-25. Suppl (zip)
  2. Cornell, C. R. et al. Temporal Dynamics of Bacterial Communities along a Gradient of Disturbance in a US Southern Plains Agroecosystem. Mbio, doi:10.1128/mbio.03829-21 (2022). Suppl info 1 (tif), 2 (docx)
  3. Dai, T. et al. Nutrient supply controls the linkage between species abundance and ecological interactions in marine bacterial communities. Nature communications 13, 1-9 (2022). Suppl info (pdf)
  4. Duan Y, Wu X, Yang Y, Gu L, Liu L, Yang Y, et al. Marked shifts in gut microbial structure and neurotransmitter metabolism in fresh inmates revealed a close link between gut microbiota and mental health: A case-controlled study. International Journal of Clinical and Health Psychology. 2022;22(3). Suppl (docx)
  5. Escalas A, Paula FS, Guilhaumon F, Yuan MT, Yang YF, Wu LW, et al. Macroecological distributions of gene variants highlight the functional organization of soil microbial systems. Isme Journal. 2022;16(3):726-37. Suppl (pdf)
  6. Goff, J. L., L. M. Lui, T. N. Nielsen, M. P. Thorgersen, E. G. Szink, J.-M. Chandonia, F. L. Poole, II, J. Zhou, T. C. Hazen, A. P. Arkin and M. W. W. Adams (2022). "Complete Genome Sequence of Bacillus cereus Strain CPT56D-587-MTF, Isolated from a Nitrate-and Metal-Contaminated Subsurface Environment." Microbiology Resource Announcements 11(5).
  7. Goff JL, Szink EG, Thorgersen MP, Putt AD, Fan Y, Lui LM, et al. Ecophysiological and genomic analyses of a representative isolate of highly abundant Bacillus cereus strains in contaminated subsurface sediments. Environmental Microbiology. 2022. Suppl (zip)
  8. Guo X, Yuan M, Lei J, Shi Z, Zhou X, Li J, et al. Climate warming restructures seasonal dynamics of grassland soil microbial communities. mLife. 2022;1(3):245-56. Suppl (pdf)
  9. Guo, Y., X. Xiao, Y. Zhao, J. Liu, J. Zhou, B. Sun and Y. Liang (2022). "Antibiotic resistance genes in manure-amended paddy soils across eastern China: Occurrence and influencing factors." Frontiers of Environmental Science & Engineering 16(7). Suppl info (pdf)
  10. He, H., A. L. L. Carlson, P. H. Nielsen, J. Zhou and G. T. T. Daigger (2022). "Comparative analysis of floc characteristics and microbial communities in anoxic and aerobic suspended growth processes." Water Environment Research 94(12). Suppl (docx)
  11. Huang L, Zhou J. mLife: Your journal for cutting-edge research in all microbiological disciplines. mLife. 2022;1(1):1-2.
  12. Kuang J, Deng D, Han S, Bates CT, Ning D, Shu W-s, Zhou J. 2022. Resistance potential of soil bacterial communities along a biodiversity gradient in forest ecosystems. mLife 1:399-411. Suppl (pdf)
  13. Liao H, Hao X, Qin F, Delgado-Baquerizo M, Liu Y, Zhou J, et al. Microbial autotrophy explains large-scale soil CO2 fixation. Global Change Biology. 2022. Suppl (docx)
  14. Liu, W. et al. Long-Term Effects of Soil Remediation with Willow Short Rotation Coppice on Biogeographic Pattern of Microbial Functional Genes. Microorganisms 10, doi:10.3390/microorganisms10010140 (2022). Suppl info (zip)
  15. Liu, Y. et al. Microbial Community Structure and Ecological Networks during Simulation of Diatom Sinking. Microorganisms 10, doi:10.3390/microorganisms10030639 (2022). Suppl (zip)
  16. Ma X, Wang T, Shi Z, Chiariello NR, Docherty K, Field CB, et al. Long-term nitrogen deposition enhances microbial capacities in soil carbon stabilization but reduces network complexity. Microbiome. 2022;10(1). Suppl (docx)
  17. Mu, P. et al. Genomic Features and Pervasive Negative Selection in Rhodanobacter Strains Isolated from Nitrate and Heavy Metal Contaminated Aquifer. Microbiology spectrum 10, e02591-02521 (2022). Suppl info (zip)
  18. Paradis CJ, Miller JI, Moon JW, Spencer SJ, Lui LM, Van Nostrand JD, et al. Sustained Ability of a Natural Microbial Community to Remove Nitrate from Groundwater. Groundwater. 2022;60(1):99-111.
  19. Qi Q, Zhao J, Tian R, Zeng Y, Xie C, Gao Q, et al. Microbially enhanced methane uptake under warming enlarges ecosystem carbon sink in a Tibetan alpine grassland. Global Change Biology. 2022. Suppl (docx)
  20. Qin, Z., Q. Gao, Q. Dong, J. D. Van Nostrand, Q. Qi, Y. Su, S. Liu, T. Dai, J. Cheng, J. Zhou and Y. Yang (2022). "Antibiotic resistome mostly relates to bacterial taxonomy along a suburban transmission chain." Frontiers of Environmental Science & Engineering 16(3). Suppl info (pdf)
  21. Song, W., J. Liu, W. Qin, J. Huang, X. Yu, M. Xu, D. Stahl, N. Jiao, J. Zhou and Q. Tu (2022). "Functional Traits Resolve Mechanisms Governing the Assembly and Distribution of Nitrogen-Cycling Microbial Communities in the Global Ocean." Mbio 13(2). Suppl 1 (pdf), 2 (xlsx)
  22.  Sun, J., Z. Lin, D. Ning, H. Wang, Z. Zhang, Z. He and J. Zhou (2022). "Functional microbial community structures and chemical properties indicated mechanisms and potential risks of urban river eco-remediation." Science of the Total Environment 803. Suppl info (docx)
  23. Tiedje, J. M. et al. Microbes and Climate Change: a Research Prospectus for the Future. Mbio, doi:10.1128/mbio.00800-22 (2022).
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  25. Tao X, Zhou A, Kempher ML, Liu J, Peng M, Li Y, et al. Development of a Markerless Deletion Mutagenesis System in Nitrate-Reducing Bacterium Rhodanobacter denitrificans. Applied and Environmental Microbiology. 2022. Suppl (pdf)
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  28. Wang, J. et al. Embracing mountain microbiome and ecosystem functions under global change. New Phytologist, doi:10.1111/nph.18051 (2022). Suppl info 1 (pdf), 2 (xlsx)
  29. Wu, L. W. et al. Permafrost thaw with warming reduces microbial metabolic capacities in subsurface soils. Molecular Ecology 31, 1403-1415, doi:10.1111/mec.16319 (2022). Suppl Info 1(docx), 2(xlsx)
  30. Wu, L., Y. Zhang, X. Guo, D. Ning, X. Zhou, J. Feng, M. M. Yuan, S. Liu, J. Guo, Z. Gao, J. Ma, J. Kuang, S. Jian, S. Han, Z. Yang, Y. Ouyang, Y. Fu, N. Xiao, X. Liu, L. Wu, A. Zhou, Y. Yang, J. M. Tiedje and J. Zhou (2022). "Reduction of microbial diversity in grassland soil is driven by long-term climate warming." Nature Microbiology. Suppl (pdf)
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  33. Yang L, Ning D, Yang Y, He N, Li X, Cornell CR, et al. Precipitation balances deterministic and stochastic processes of bacterial community assembly in grassland soils. Soil Biology and Biochemistry. 2022(168):1-13. Suppl (docx)
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2021

 

 

  1. Cao LF, L Lin, HY Sui, H Wang, ZC Zhang, NZ Jiao, and JZ Zhou. 2021. Efficient extracellular laccase secretion via bio-designed secretory apparatuses to enhance bacterial utilization of recalcitrant lignin. Green Chem. 23:20179-2094. Suppl Info (pdf), 2 (pdf)
  2. Chen QY, YL Yuan, YL Hu, J Wand, GC Si, R Xu, JZ Zhou, CW Xi, A Hu, and GX Zhang. 2021. Excessive nitrogen addition accelerates N assimilation and P utilization by enhancing organic carbon decomposition in a Tibetan alpine steppe. Sci Tot Envrion. 764:142848. Suppl Info
  3. Chen, L., M. Zhang, D. Ning, J. D. Van Nostrand, Y. Yang, J. Zhou and J. Zuo (2021). "Behaviors of Homologous Antibiotic Resistance Genes in a Cephalosporin WWTP, Subsequent WWTP and the Receiving River." Frontiers in Environmental Science 9. Suppl info (zip)
  4. Cheng J, Z Han, J Cong, J Yu, J Zhou, M Zhao, and Y Zhang. 2021. Edaphic variables are better indicators of soil microbial functional structure than plant-related ones in subtropical broad-leaved forests. Sci Tot Environ. 773:145630. Suppl Info (pdf)
  5. Cheng J, Y Yang, MM Yuan, Q Gao, L Wu, Z Qin, ZJ Shi, EAG Schuur, JR Colre, JM Tiedje, and J Zhou.  2021. Winter warming rapidly increases carbon degradation capacities of fungal communities in tundra soil: potential consequences on carbon stability. Mol Ecol. 30:926-937. Suppl Info (docx)
  6. Ding J, W Seow, JZ Zhou, RJ Zeng, J Gu, and Y Zhou. 2021. Effects of Fe(II) on anammox community activity and physiologic response. Front Environ Sci Engineer. 15:7.
  7. Deng, J., S. Frolking, R. Bajgain, C. R. Cornell, P. Wagle, X. Xiao, J. Zhou, J. Basara, J. Steiner and C. Li (2021). "Improving a Biogeochemical Model to Simulate Microbial-Mediated Carbon Dynamics in Agricultural Ecosystems." Journal of Advances in Modeling Earth Systems 13(11).
  8. Gao Q, S Gao, C Bates, Y Zeng, J Lei, H Su, Q Dong, Z Qin, J Zhao, Q Zhang, D Ning, Y Huang, J Zhou, and Y Yang. The microbial network property as a bio-indicator of antibiotic transmission in the environment. Sci Tot Environ. 758:143712. doi.org/10.1016/j.scitotenv.2020.143712
  9. Gao Y, J Ding, M Yuan, N Chiariello, K Docherty, C Field, Q Gao, B Gu, J Gutknecht, BA Hungate, X Le Roux, A Niboyet, Q Qi, Z Shi, J Zhou, and Y Yang. 2021. Long-term warming in a Mediterranean-type grassland affects soil bacterial functional potential but not bacterial taxonomic composition. Biofilms Microbiomes. 7:17.
  10. Han S, M Delgado-Baquerizo, X Luo, Y Liu, JD Van Nostrand, W Chen, J Zhou, and Q Huang. 2021. Soil aggregate size-dependent relationships between microbial functional diversity and multifunctionality. Soil Biol Biochem. 154:108143. Suppl Info (docx)
  11. Han S, X Luo, X Hao, Y Ouyang, L Zeng, L Wang, S Wen, B Wang, JD Van Nostrand, W Chen, J Zhou, and Q Haung. Microscale heterogeneity of the soil nitrogen cycling microbial functional structure and potential metabolism. Environ Microbiol. doi.org/10.1111/1462-2920.15348. Suppl Info (docx)
  12. Huang, M., L. Chai, D. Jiang, M. Zhang, W. Jia, Y. Huang and J. Zhou (2021). "Dissolved organic matter (DOM) quality drives biogeographic patterns of soil bacterial communities and their association networks in semi-arid regions." Fems Microbiology Ecology 97(7). Suppl info (docx)
  13. Huang, Z., D. Hou, R. Zhou, S. Zeng, C. Xing, D. Wei, X. Deng, L. Yu, H. Wang, Z. Deng, S. Weng, D. Ning, C. Xiao, Q. Yan, J. Zhou, Z. He and J. He (2021). "Environmental Water and Sediment Microbial Communities Shape Intestine Microbiota for Host Health: The Central Dogma in an Anthropogenic Aquaculture Ecosystem." Frontiers in Microbiology 12. Suppl info (zip)
  14. Kuang, J., C. T. Bates, X. Wan, D. Ning, D. Deng, W. Shu and J. Zhou (2021). "High historical variability weakens the effects of current climate differentiation on microbial community dissimilarity and assembly." Global Change Biology 27(22): 5963-5975. Suppl info (pdf)
  15. Lei J, X Guo, Y Zeng, J.-Z. Zhou, Q Gao, and Y Yang. 2021. Temporal changes of global soil respiration since 1987. Nat. Comm. 12:403. Suppl Info (pdf)
  16. Li D, HW Ni, S Jiao, YH Lu, JZ Zhou, B Sun, and YT Liang. 2021. Coexistence patterns of soil methanogens are closely tied to methane generation and community assembly in rice paddies. Microbiome. 9:20. Suppl Info (docx)
  17. Li, E., T. Deng, L. Yan, J.-Z. Zhou, Z. He, Y. Deng, M. Xu. 2021. Elevated Nitrate Simplifies Microbial Community Compositions and Interactions in Sulfide-rich River Sediments. Sci Tot Environ. 750:141513. Suppl Fig (link)
  18. Li Y, K Wang, B Zhang, Q Tu, Y Yao, B Cui, B Ren, J He, X Shen, JD Van Nostrand, J Zhou, W Shi, L Xiao, C Lu, and X Zhou. 2021. Mycobiome dysbiosis in oral lichen planus. In: Zhou X and Y Li (eds) Atlas of Oral Microbiology: From Healthy Microflora to Disease. Springer, Singapore.
  19. Li, Y., J.-S. He, H. Wang, J. Zhou, Y. Yang and H. Chu (2021). "Lowered water table causes species substitution while nitrogen amendment causes species loss in alpine wetland microbial communities." Pedosphere 31(6): 912-922. Suppl info (docs)
  20. Lui LM, ELW Majumder , HJ Smith, HK Carlson, F von Netzer, MW Fields, DA Stahl, JZ Zhou, TC Hazen, NS Baliga, PD Adams, and AP Arkin. 2021. Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology. Front Microbiol. 12:642422. Suppl Info (docx)
  21. Liu SY, JC Dai, HH Wei, SY Li, P Wang, TB Zhu, JZ Zhou, and DR Qiu. 2021. Dissimilatory nitrate reduction to ammonium (DNRA) and denitrification pathways are leveraged by cyclic AMP receptor protein (CRP) paralogues based on electron donor/acceptor limitation in Shewanella loihica PV-4. Appl Environ Micro. 87:e01964-20. Suppl Info (pdf)
  22. Ma B, E Stirling, YH Jiu, KK Zhao, JZ Zhou, BK Singh, CX Tang, RA Dahlgren, and JM Xu. 2021. Soil biogeochemical cycle couplings inferred from a function-taxon network. Research 2021:7102769. Suppl Info (docx)
  23. Ouyang Y, D Chen, Y Fu, W Shi, T Provon, A Han, E van Shaik, JE Samuel, P De Figueiredo, A Zhou, and J Zhou. 2021. Direct cell extraction from fresh and stored soil samples: Impact on microbial viability and community compositions. Soil Biol Biochem. 155:108178. Suppl Info
  24. Pett-Ridge J, S Shi, K Estera-Molina, E Nuccio, M Yuan, R Rijkers, T Swenson, K Zhalnina, T Northen, J Zhou, and MK Firestone. 2021. Rhizosphere Carbon Turnover from Cradle to Grave: The Role of Microbe–Plant Interactions. In: Gupta V., Sharma A. (eds) Rhizosphere Biology: Interactions Between Microbes and Plants. Rhizosphere Biology. Springer, Singapore. doi.org/10.1007/978-981-15-6125-2_2
  25. Qi Q, H Yue, Z Zhang, JD Van Nostrand, L Wu, X Guo, J Feng, M Wang, S Yang, J Zhao, Q Gao, Q Zhang, M Zhao, C Xie, Z Ma, J He, H Chu, Y Huang, J.-Z. Zhou, and Y Yang, Microbial functional responses explain alpine soil carbon fluxes under future climate scenarios. mBio. Doi: 10.1128/mBio.00761-20. Suppl Info
  26. Ren, L., Y. Liu, T. L. Lauridsen, M. Sondergaard, B. Han, J. Wang, E. Jeppesen, J. Zhou and Q. L. Wu (2021). "Warming exacerbates the impact of nutrient enrichment on microbial functional potentials important to the nutrient cycling in shallow lake mesocosms." Limnology and Oceanography 66(6): 2481-2495. Suppl info (pdf)
  27. Shi, W., Q. Ma, F. Pan, Y. Fan, M. L. Kempher, D. Ning, Y. Qu, J. D. Wall, A. Zhou and J. Zhou (2021). "Genetic Basis of Chromate Adaptation and the Role of the Pre-existing Genetic Divergence during an Experimental Evolution Study with Desulfovibrio vulgaris Populations." Msystems 6(3). Suppl info 1 (pdf), 2 (xlsx)
  28. Shu D, Y Guo, B Zhang, C Zhang, JD Van Nostrand, Y Lin, J Zhou, and G Wei. 2021. Rare prokaryotic sub-communities dominate the complexity of ecological networks and soil multinutrient cycling during long-term secondary succession in China's Loess Plateau. Sci Tot Environ. 774:145737.  Suppl Info (docx)
  29. Somenahally, A. C., R. H. Loeppert, J. Zhou and T. J. Gentry (2021). "Niche Differentiation of Arsenic-Transforming Microbial Groups in the Rice Rhizosphere Compartments as Impacted by Water Management and Soil-Arsenic Concentrations." Frontiers in Microbiology 12. Suppl info (docx)
  30. Sun, C., B. Zhang, D. Ning, Y. Zhang, T. Dai, L. Wu, T. Li, W. Liu, J. Zhou and X. Wen (2021). "Seasonal dynamics of the microbial community in two full-scale wastewater treatment plants: Diversity, composition, phylogenetic group based assembly and co-occurrence pattern." Water Research 200. Suppl info (zip)
  31. Teng, J., J. Tian, R. Barnard, G. Yu, Y. Kuzyakov and J. Zhou (2021). "Aboveground and Belowground Plant Traits Explain Latitudinal Patterns in Topsoil Fungal Communities From Tropical to Cold Temperate Forests." Frontiers in Microbiology 12. Suppl info (docx)
  32.  Tian J, N Zong, IP Hartleuy, J Zhang, J Zhou, Y Kuzyakov, F Zhang, G Yu, and JAJ Dungait. 2021. Microbial metabolic response to winter warming stabilizes soil carbon. Glob Change Biol. DOI:10.1111/gcb.15538. Suppl Info (docx)
  33. Turkarslan, S., N. Stopnisek, A. W. Thompson, C. E. Arens, J. J. Valenzuela, J. Wilson, K. A. Hunt, J. Hardwicke, A. L. G. de Lomana, S. Lim, Y. M. Seah, Y. Fu, L. Wu, J. Zhou, K. L. Hillesland, D. A. Stahl and N. S. Baliga (2021). "Synergistic epistasis enhances the co-operativity of mutualistic interspecies interactions." Isme Journal 15(8): 2233-2247. Suppl info (pdf)
  34. Wang XP, L Lin, and JZ Zhou. 2021. Links among extracellular enzymes, lignin degradation and cell growth establish the models to identify marine lignin-utilizing bacteria. Environ Microbiol. 23:1. Suppl Info (docx)
  35.  Wang, A., K. Shi, D. Ning, H. Cheng, H. Wang, W. Liu, S. Gao, Z. Li, J. Han, B. Liang and J. Zhou (2021). "Electrical selection for planktonic sludge microbial community function and assembly." Water Research 206. Suppl info (docx)
  36. Wang, S., X. Bao, K. Feng, Y. Deng, W. Zhou, P. Shao, T. Zheng, F. Yao, S. Yang, S. Liu, R. Shi, Z. Bai, H. Xie, J. Yu, Y. Zhang, Y. Zhang, L. Sha, Q. Song, Y. Liu, J. Zhou, Y. Zhang, H. Li, Q. Wang, X. Han, Y. Zhu and C. Liang (2021). "Warming-driven migration of core microbiota indicates soil property changes at continental scale." Science Bulletin 66(19): 2025-2035.
  37. Xiao X, N Zhang, H Ni, Y Yang, J Zhou, B Sun, and Y Liang. A latitudinal gradient of microbial β‐diversity in continental paddy soils. Glob Ecol Biogeography.  doi.org/10.1111/geb.13267. Suppl Info
  38. Yu H, Y Deng, Z He, E Pendall, Y Carrillo, S Wang, D Jin, L Wu, A Wang, B Liu, X  Tai, and J Zhou. 2021. Stimulation of soil microbial functioning by elevated CO2 may surpass effects mediated by irrigation in a semiarid grassland. Geoderma. 401:115162. Suppl Inf (docx)
  39. Yuan MM, X Guo, L Wu, Y Zhang, N Xiao, D Ning, Z Shi, X Zhou, L Wu, Y Yang, JM Tiedje, and J Zhou. 2021. Climate warming enhances microbial network complexity and stability. Nat Clim Change. https://doi.org/10.1038/s41558-021-00989-9. Suppl Info: 1(xlsx), 2(xlsx), 3(xlxs), 4(xlsx), 5(xlsx), 6(xlsx), 7(xlsx), 8(xlsx), 9(xlsx)
  40. Yuan MM, A Karkouridid, E Starr, N Nguyen, S Shi, J Peet-Ridge, E Nuccio, J Zhou, and M Firestone. Fungal-bacterial cooccurrence patterns differ between arbuscular mycorrhizal fungi and nonmycorrhizal fungi across soil niches. mBio. 12:e03509-20. DOI: 10.1128/mBio.03509-20. Suppl Info (pdf)
  41. Yuan, L., Y. Wang, L. Zhang, A. Palomo, J. Zhou, B. F. Smets, H. Burgmann and F. Ju (2021). "Pathogenic and Indigenous Denitrifying Bacteria are Transcriptionally Active and Key Multi-Antibiotic-Resistant Players in Wastewater Treatment Plants." Environmental Science & Technology 55(15): 10862-10874. Suppl info 1 (pdf), 2 (xlsx)
  42. Zhang B, D Ning, JD Van Nostrand, C Sun, Y Yang, J Zhou, and X Wen. 2021. The call for regional design code from the regional discrepancy of microbial communities in activated sludge. Environ Poll. 273:116487.
  43. Zhang N, P Juneau, RL Huang, ZL He, B Sun, JZ Zhou, and YT Liang. 2021. Coexistence between antibiotic resistance genes and metal resistance genes in manure-fertilized soils. Geoderma. 382:114760. Suppl Info (docx)
  44. Zhang, C., X. Xiao, Y. Zhao, J. Zhou, B. Sun and Y. Liang (2021). "Patterns of microbial arsenic detoxification genes in low-arsenic continental paddy soils." Environmental Research 201.
  45. Zhang, N., N. Nunan, P. R. Hirsch, B. Sun, J. Zhou and Y. Liang (2021). "Theory of microbial coexistence in promoting soil-plant ecosystem health." Biology and Fertility of Soils 57(7): 897-911.
  46. Zhao M, J Zhao, L Hale, T Wen, Q Huang, JM Vivanco, J Zhou, GA Kowalchuk, and Q Shen. 2021. Root exudates drive soil‐microbe‐nutrient feedbacks in response to plant growth. Plant Cell Environ. 44:613-628. Suppl infor 1 (docx), 2 (xlsx)
  47. Zhou, J., X. Yu, J. Liu, W. Qin, Z. He, D. Stahl, N. Jiao, J. Zhou and Q. Tu (2021). "VB(12)Path for Accurate Metagenomic Profiling of Microbially Driven Cobalamin Synthesis Pathways." Msystems 6(3). Suppl info (pdf)
2020
  1. Avila-Jimenez ML, G Burns, Z He, J Zhou, A Hodson, JL Avila-Jimenez, and D Pearce. 2020. Functional associations and resilience in microbial communities. Microorganisms. 8:951.
  2.  Cagle G, Q Lin, SA Graham, I Mendelssohn, JW Fleeger, D Deis, DS Johnson, J Zhou, and A Hou. 2020. Planting Spartina alterniflora in a salt marsh denuded of vegetation by an oil spill induces a rapid response in the soil microbial community. Ecol. Engineer. 151:105815. Suppl Info (zip)
  3. Chen Q, B Niu, Y Hu, J Wang, T Lei, R Xu, J Zhou, and G Zhang. 2020. Multilevel nitrogen additions alter chemical composition and turnover of the labile fraction soil organic matter via effects on vegetation and microorganisms. JGR Biogeosciences. 125:e2019JG005316. Suppl Info (docx)
  4. Cheng J, M Zhao, J Cong, Q Qi, Y Xiao, W Cong, Y Deng, J Zhou, and Y Zhang. 2020. Soil pH exerts stronger impacts than vegetation type and plant diversity on soil bacterial community composition in subtropical broad-leaved forests. Plant Soil. 450:273-286. Suppl Info (docx)
  5. De Vrieze J, T De Mulder, S Matassa, J Zhou, LT Angenent, N Boon, and W Verstraete. 2020. Stochasticity in microbiology: managing unpredictability to reach the Sustainable Development Goals. Microbial Biotechnol. 13:829-843. doi.org/10.1111/1751-7915.13575
  6. Ding J, W Seow, JZ Zhou , RJ Zeng, J Gu, and Y Zhou. 2020. Effects of Fe(II) on anammox community activity and physiologic response. Front Environ Sci Engineer. 15:7.
  7. Feng JJ, C Wang, JS Lei, YF Yang, QY Yan, XS Zhou, XY Tao, DL Ning, MTM Yuan, Y Qin, , ZJ Shi, X Guo, Z He, JD Van Nostrand, L Wu, RG Bracho-Garillo, CR Penton, JR Cole, KT Konstantinidis, Y Luo, EAG Schuur, JM Tiedje, and J Zhou. 2020. Warming-induced permafrost thaw exacerbates tundra soil carbon decomposition mediated by microbial community. Microbiome. 8:3. Suppl Info (docx)
  8. Gao Q, Q Dong , L Wu, Y Yang, L Hale, Z Qin, C Xie, Q Zhang, JD Van Nostrand, and J Zhou. 2020. Environmental antibiotics drives the genetic functions of resistome dynamics. Environment Internat. 135:105398. Suppl Material (doc)
  9. Gao Q, G Wang, K Xue, Y Yang, J Xie, H Yu, S Bai, F Liu, Z He, D Ning, SE Hobbie, PB Reich, and J Zhou. 2020. Stimulation of soil respiration by elevated CO2 is enhanced under nitrogen limitation in a decade-long grassland study. Proc Nat Acad Sci. 117:33317-33324. Suppl Info (pdf)
  10. Guo X, Q Gao, M Yuan, G Wang, X Zhou, J Feng, Z Shi, L Hale, L Wu, A Zhou, R Tian, F Liu, B Wu, L Chen, CG Jung, S Niu, D Li, X Xi, L Jiang, A Excalas, L Wu, Z He, JD Van Nostrand, D Ning, X Liu, Y Yang, EAG Schuur, KT Konstandtinidis, JR Cole, CT Penton, Y Luo, JM Tiedje, and J Zhou. 2020. Gene-informed decomposition model predicts lower soil carbon loss due to persistent microbial adaptation to warming. Nat Commun 11, 4897 (2020). https://doi.org/10.1038/s41467-020-18706-z. Suppl Info (pdf) Microarray data (txt)
  11. He Z, Y Deng,  M Xu, J Li, J Liang, J Xiong, H Yu, B Wu, L Wu, K Xue, S Shi, Y Carrillo, JD Van Nostrand, SE Hobbie, PB Reich, CW Schadt, AD Kent, E Pendall, M Wallenstein, Y Luo, Q Yan, and J Zhou. 2020. Microbial functional genes commonly respond to elevated carbon dioxide. Environ Internat. 144:106068. Suppl Info (docx)
  12. Hu A, J Wang, H Sun, B Niu, G Si, J Wang, C-F Yeh, X Zhu, X Lu, J Zhou, Y Yang, M Ren, Y Hu, H Dong and G Zhang. 2020. Mountain biodiversity and ecosystem functions: interplay between geology and contemporary environments. ISME J. 14:931-944. Suppl Info (docx)
  13. Huang Z, S Zeng, J Xiong, D Hou, R Zhou, C Xing, D Wei, X Deng, L Yu, H Wang, Z Deng, S Weng, S Kriengkrai, Dg Ning, J Zhou, and J He. 2020. Microecological Koch’s postulates reveal that intestinal microbiota dysbiosis contributes to shrimp white feces syndrome. Microbiome 8:32. Suppl Info: Tables (xlsx), Figures (docx)
  14. Kempher ML, X Tao, R Song , B Wu, DA Stahl, JD Wall, AP Arkin, A Zho and J Zhou. 2020. Effects of genetic and physiological divergence on the evolution of a sulfate-reducing bacterium under conditions of elevated temperature. mBio. DOI: 10.1128/mBio.00569-20. Suppl Info 1 (docx),  Suppl Info 2 (docx),  Suppl Info 3 (docx),  Suppl Info 4 (docx), Suppl Info 5 (tiff), Suppl Info 6 (docx)
  15. Li YC, YF Li, MK Yang, SX Chang, JL Qi, CX Tang, ZL Wen, Z hong, TY Yang, ZL Ma, Q Gao, JZ Zhou, YF Yang and YH Yang. 2020. Changes of microbial functional capacities in the rhizosphere contribute to aluminum tolerance by genotype-specific soybeans in acid soils. Biol Fertility Soils. Doi.10.1007/s00374-020-01451-2. Suppl Info (docx)
  16. Liang Y, X Xiao, EE Nuccio, M Yuan, N Zhang, K Xue, FM Cohan, J Zhou, and B Sun. Differentiation strategies of soil rare and abundant microbial taxa in response to changing climatic regimes. Environ Microbiol. 22:1327-1340. Suppl Info (docx)
  17. Liang Y, D Ning, Z Lu, N Zhang, L Hale, L Wu, IM Clark, SP McGrath, J Storkey, PR Hirsch, B Sun, and J Zhou. 2020. Century long fertilization reduces stochasticity controlling grassland microbial community succession. Soil Biol Biochem. 151:108023. Suppl Info (zip)
  18. Mu DS, S Wang, QY Liang, ZZ Du, RM Tian, Y Ouyang, XP Wang, AF Zhou, Y Gong, GJ Chen, J Van Nostrand, YF Yang, JZ Zhou, and ZJ Du. 2020. Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments. Microbiome. 8:126. Suppl Info: Text and Figures (docx), Tables 1 (xlsx), 2 (xlsx), 3 (xlsx), 4 (xlsx), 5 (xlsx), 6 (docx), 7 (docx)
  19. Ning, D., M. Yuan, L. Wu, Y. Zhang, X. Guo, X. Zhou, Y. Yang, A. P. Arkin, M. K. Firestone, and J.-Z. Zhou. 2020. A quantitative framework reveals ecological drivers of grassland soil microbial community assembly in response to warming. Nat Comm, 11:4717. Suppl Info (pdf)
  20. Nuccia EE, E Starr, U Karaoz ,  EL Brodie, J Zhou, S Tringe, RR Malmstrom, T Woyke, JF Banfield, MK Firestone, and J Pett-Ridge. Niche differentiation is spatially and temporally regulated in the rhizosphere. ISME J. 14:999-1014. Suppl Info (docx), 1 (xlsx), 2 (xlsx), , 3 (xlsx), 4 (xlsx), 5 (xlsx), 6 (xlsx), 7 (xlsx)
  21. Picazo F, A Vilmi, J Aalto, J Soininen, EO Casamayou, Y Liu, Q Wu, L Ren, J Zhou, J Shen, and J Wang. 2020. Climate mediates continental scale patterns of stream microbial functional diversity. Microbiome 8:92. doi.org/10.1186/s40168-020-00873-2. Suppl Info (docx)
  22. Pressler Y, J Zhou, Z He, JD Van Nostrand, and AP Smith. 2020. Post-agricultural tropical forest regeneration shifts soil microbial functional potential for carbon and nutrient cycling. Soil Biol Biochem. 145:107784.
  23.  Qin W, Y Zheng, F Zhao, Y Wang, H Urakawa, W Martens-Habbena, H Liu, X Huang, X Zhang, T Nakagawa, DR Mende, A Bollmann, B Wang, Y Zhang, SA Amin, JL Nielsen, K Mori, R Takahashi, EV.Armbrust, MKH Winkler, EF DeLong, M Li, P Lee, JZ Zhou, C Zhang, T Zhang, DA Stahl, and AE Ingalls. Alternative strategies of nutrient acquisition and energy conservation map to the biogeography of marine ammonia-oxidizing archaea. ISME J.  DOI: 10.1038/s41396-020-0710-7. Suppl Tables: S1, S2, S3, S4, S5, S6 (xlxs)
  24. Sher Y, NR Baker, D Herman, C Fossum, L Hale, X Zhang, E Nuccio, M Saha, J Zhou, J Pett-Ridge, and M Firestone. 2020. Microbial extracellular polysaccharide production and aggregate stability controlled by Switchgrass (Panicum virgatum) root biomass and soil water potential. Soil Biol Biochem. 143:107742. Suppl Info (zip)
  25. Sidhu JPS, VVSR Gupta, C Stange, J Ho, N Harris, K Barry, D Gonzalez, JD Van Nostrand, J Zhou, D Page, A Tiehm, and S Toze. 2020. Prevalence of antibiotic resistance and virulence genes in the biofilms from an aquifer recharged with stormwater. Water Res. 185:116269. Suppl Info (zip)
  26. Tao X, J Feng, Y Yang, G Wang, R Tian, F Fan, D Ning, CT Bates, L Hale, MM Yuan, L Wu, Q Gao, J Lei, EAG Schuur, J Yu, R Bracho, Y Luo, KT Konstantinidis, ER Johnston, JR Cole, CR Penton, JM Tiedje, and J Zhou. 2020. Winter warming in Alaska accelerates lignin decomposition contributed by Proteobacteria. Microbiome 8:84. doi.org/10.1186/s40168-020-00838-5. Suppl Info: Figs (docx),  MAGS (xlsx)
  27. Tao X, T Xu, ML Kempher, J Liu and J Zhou. 2020.  Precise promoter integration improves cellulose bioconversion and thermotolerance in Clostridium cellulolyticum. Metabolic Engineer. 60:110-118. Suppl Info (zip)
  28. Tian R, D Ning, Z He, P Zhang, SJ Spencer, S Gao, W Shi, L Wu, Y Zhang, Y Yang, BG Adams, AM Rocha, BL Detienne, KA Lowe, DC Joyner, DM Klingeman, AP Arkin, MW Fields, TC Hazen, DA Stahl, EJ Alm, and J Zhou. 2020. Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity. Microbiome. 8:51. Suppl Info (docx)
  29. Tu Q, Q Yan, Y Deng, ST Michaletz, V Buzzard, MD Weiser, R Waide, D Ning, L Wu, Z He, and J Zhou. 2020. Biogeographic patterns of microbial co-occurrence ecological networks in six American forests. Soil Biol Biochem. 148:107897. Suppl Info (docx)
  30. Wan X, Q Gao, J Zh ao, J Feng, JD van Nostrand, Y Yang, and J Zhou. Biogeographic patterns of microbial association networks in paddy soil within Eastern China. Soil Biol Biochem. doi.org/10.1016/j.soilbio.2019.107696. Suppl Info (docx)
  31. Wang GS, HJ  Huang, GY Zhou, MA Mayes, and JZ Zhou. 2020. Modeling the processes of soil moisture in regulating microbial and carbon-nitrogen cycling. J Hydrology. 585:124777.
  32. Wang JJ, P Legendre, J Soininen, CF Yeh, E Graham, J Stegen, EO Casamayor, JZ Zhou, J Shen, FY Pan. 2020. Temperature drives local contributions to beta diversity in mountain streams: Stochastic and deterministic processes. Glob Ecol Biogeography. 29:420-432. DOI: 10.1111/geb.13035. Suppl Info (docx)
  33. Wang PD, SP Li, X Yang, JZ Zhou, WS Shu, and L Jiang. 2020. Mechanisms of soil bacterial and fungal community assembly differ among and within islands. Environ Microbiol. 22:1559-1571. DOI: 10.1111/1462-2920.14864. Suppl Info (docx)
  34. Wang Y, H Zheng, FL Chen, J Zeng, JZ Zhou, and ZY Ouyang. 2020. Stabilities of soil organic carbon and carbon cycling genes are higher in natural secondary forests than in artificial plantations in southern China. Land Degrad Develop. 31:2986-2995.
  35. Wang Y, H Zheng, Y Yang, Y Liang, J Zhou, Z He, F Chen, and Z Ouyang. 2020. Microbial functional gene diversity in natural secondary forest Ultisols. Acta Oecologia. 105:103575.
  36. Wilpiszeski RL, CM Gionfriddo, AM Wymore, JW Moon, KA Lowe, M Podar, S Rafie, MW Fields, TC Hazen, X Ge, F Poole, MWW Adams, R Chakraborty, Y Fan, JD Van Nostrand, J Zhou, AP Arkin, DA Elias. 2020. In-field bioreactors demonstrate dynamic shifts in microbial communities in response to geochemical perturbations. PLoS One. 15:e0232437. https://doi.org/10.1371/journal.pone.0232437. Suppl Info (docx)
  37. Wu B, F Lie, A Zhou, J Li, L Shu, ML Kempher, X Yang, D Ning, F Pan, GM Zane, JD Wall, JD Van Nostrand, P Juneau, S Chen, Q Yan, J Zhou, and Z He. 2020. Experimental evolution reveals nitrate tolerance mechanisms in Desulfovibrio vulgaris. ISME J. https://doi.org/10.1038/s41396-020-00753-5. Suppl Info (pdf)
  38. Wu LW, XY Shan, S Chen, QT Zhang, Q Qi, ZY Qin, ZY Qin, HQ Yin, JZ Zhou, Q He, and YF Yang. 2020. Progressive microbial community networks with incremental organic loading rates underlie higher anaerobic digestion performance. mSystems. 5:e00357-19. Suppl Info: 1 (tiff), 2 (tiff), 3 (docx), 4 (tiff)
  39. Wu R, B Chai, JR Cole, SK Gunturu, X Guo, R Tian, J Gu, J Zhou, and JM Tiedje. 2020. Targeted assemblies of cas1 suggest CRISPR-Cas’s response to soil warming. ISME J. 14:1651-1662. doi.org/10.1038/s41396-020-0635-1. Suppl Info 2 (docx), 3 (xlsx), 4 (xlsx), 5 (xlsx), 6 (xlsx), 7 (docx)
  40. Xue K, JD Van Nostrand, J Zhou, S Neu, I Muller, L Giagnoni, and G Renella. 202. Phytomanagement reduces metal availability and microbial metal resistance in a metal contaminated soil. Front Microbio. doi.org/10.3389/fmicb.2020.01899.  GeoChip data (csv), Suppl Info (docx)
  41. Yang, S., Q. Zheng, Y. Yang, M. Yuan, X. Ma, N. R. Chiariello, K. M. Docherty, C. B. Field, J. L. M. Gutknecht, B. A. Hungate, A. Niboyet, X. Le Roux, and J.-Z. Zhou. 2020. Fire affects the taxonomic and functional composition of soil microbial communities, with cascading effects on grassland ecosystem functioning. Glob. Chang. Biol. 26:431-442. Suppl Info (docx)
  42. Zhang B, D Ning, JD Van Nostrand C Sun, Y Yand, J Zhou, and X Wen. 2020. The biogeography and assembly of microbial communities in wastewater treatment plants in China. Environ Sci Tech. 54:5884-5892. Suppl Info (pdf), 2 (xlsx)
  43. Zhang B, D Ning, Y Yang, JD Van Nostrand, J Zhou, and X Wen. 2020. Biodegradability of wastewater determines microbial assembly mechanisms in full-scale wastewater treatment plants. Wat Res. 169:115276. doi.org/10.1016/j.watres.2019.115276. Suppl Material (zip)
  44. Zhao M, J Cong, J Cheng, Q Qi, Y Sheng, D Ning, H Lu, KN Wyckoff, Y Deng, D Li, J Zhou, and Y Zhang. 2020. Soil Microbial Community Assembly and Interactions Are Constrained by Nitrogen and Phosphorus in Broadleaf Forests of Southern China. Forests 11:285. Suppl Info (pdf)
  45. Zhou YY, L Lin, H Wang, ZC Zhang, JZ Zhou, NZ Jiao. 2020. Development of a CRISPR/Cas9n-based tool for metabolic engineering of Pseudomonas putida for ferulic acid-to-polyhydroxyalkanoate bioconversion. Comm Biol. 3:98. Suppl Info: 1 (pdf), 2 (xlsx), 3 (xlsx), 4 (xlsx), 5 (xlsx), 6 (xlsx)
  46. Zou Y, D Ning, Y Huang, Y Liang, H Wang, L Duan, T Yuan, Z He, Y Yang, K Xue, JD Van Nostrand, and J Zhou. 2020. Functional structures of soil microbial community relate to contrasting N2O emission patterns from a highly acidified forest. Sci Tot Envrion. 725:138504. Suppl Info (docx)
2019
  1. Buzzard, V., S. T. Michaletz, Y. Deng, Z. He, D. Ning, L. Shen, Q. Tu, J. Van Nostrand, J. W. Voordeckers, J. Wang, M. D. Weiser, M. Kaspari, R. B. Waide, J.-Z. Zhou, and B. J. Enquist. Continental scale structuring of forest and soil diversity via functional traits. 2019. Nature Ecol. & Evol. 3:1298-1308.  Suppl Material: File 1 (csv), File 2 (csv), File 3 (csv), File 4 (zip), File 5 (pdf)
  2. Dai J, Y Liu, S Li u, S Li, N Gao, J Wang, J Zhou and D Qiu. 2019. Differential gene content and gene expression for bacterial evolution and speciation of Shewanella in terms of biosynthesis of heme and heme-requiring proteins. BMC Microbiol. 19:173 doi.org/10.1186/s12866-019-1549-9. Suppl Material
  3. Day LA, De León KB, Kem pher ML, Zhou J, Wall JD. 2019. Complete genome sequence of Desulfovibrio desulfuricans IC1, a sulfonate-respiring anaerobe. Microbiol Resour Announc 8:e00456-19. doi.org/10.1128/MRA.00456-19.
  4. Escalas, A., L. Hale, J. W. Voordeckers, Y. Yang, M. K. Firestone, L. Alvarez-Cohen, and J.-Z. Zhou. 2019. Microbial functional diversity: From concepts to applications. Ecol Evol, 9:12000-12016. doi.org/10.1002/ece3.5670. Suppl Material: Legends (docx), Table S1 (xls), Table S2 (xls)
  5. Feng J, CR Penton, Z He, JD Van Nostrand, MM Yuan, L Wu, C Wang, Y Qin, Z Shi, X Guo, EAG Schuur, Y Luo, R Bracho, KT Konstantinidis, JR Cole, JM Tiedje, Y Yang, and JZ Zhou. 2019. Long-term winter warming in Alaska enlarges the diazotrophic community in deep soils. mBio, DOI:10.1128/mBio.02521-18, e02521-18. Suppl Material (pdf)
  6. Gao, Q., Y. Yang, J. Feng, R. Tian, X. Guo, D. Ning, L. Hale, M. Wang, J. Cheng, L. Wu, M. Zhao, J. Zh ao, L .Wu, Y. Qin, Q. Qi, Y. Liang, B. Sun, H. Chu, and J.-Z. Zhou. 2019. The spatial scale-dependency of diazotrophic and bacterial community assembly in paddy soil. Glob Ecol Biogeography, doi.org/10.1111/geb.12917. Suppl Material (docx)
  7. Gao, S., J. Ho, L. Fan, A. Nouwens, R. D. Hoelzle, B. Schulz, J. Guo, J.-Z. Zhou, Z. Yuan, and P. L. Bond. 2019. A comparative proteomic analysis of Desulfovibrio vulgaris Hildenborough in response to the antimicrobial agent free nitrous acid. Sci Tot Environ, 672:625-633. Suppl Material
  8. Guo X, X Zhou, L Hale, M Yuan, D Ning, J Feng, Z Shi, Z Li, B Feng, Q Gao, L Wu, W Shi, A Zhou, Y Fu, L Wu, Z He, JD Van Nostrand, G Qiu, X Liu, Y Luo, JM Tiedje, Y Yang, and JZ Zhou. 2019. Climate warming accelerates temporal scaling of grassland soil microbial biodiversity. Nat Ecol Evol., 3:612-619.
  9. Hale, L., W. Feng, H. Yin, X. Guo, X. Zhou, R. Bracho, E. Pegoraro, C. R. Penton, L. Wu, J. Cole, K. T. Konstantinidis, Y. Luo, J. M. Tiedje, E. A. G. Schuur, and J.-Z. Zhou. 2019. Tundra microbial community taxa and traits predict decomposition parameters of stable, old soil organic carbon. ISME J. doi.org/10.1038/s41396-019-0485-x. Suppl Material
  10. Hu Y, Z Zhang, L Huang, Q Qi, L Liu, Y Zhao, Z Wang, H Zhou, X Lv, Z Mao, Y Yang, J Zhou, and P Kardol. 2019. Shifts in soil microbial community functional gene structure across a 61-year desert revegetation chronosequence. Geoderma. 347:126-134. Suppl Material (docx)
  11. Huang RL, SP McGrath, PR Hirsch, IM Clark, J Storkey, LY Wu, JZ Zhou, and Liang YT. 2019. Plant-microbe networks in soil are weakened by century-long use of inorganic fertilizers. Microbial Biotechnol. 12:1464-1475.
  12. Johnston, E. R., J.  K. Hatt, Z. He, L. Wu, X. Guo; Y. Luo, E. A. G Schuur, J. M. Tiedje, J.-Z. Zhou, and K. T. Konstantinidis. 2019. Responses of tundra soil microbial communities to half a decade of experimental in-situ warming at two critical depths. Proc. Nat. Acad. Sci. 116:15096-15105. Suppl Material (pdf); Suppl Data 1 (txt), 2 (txt), 3 (txt), 4 (txt)
  13. Li Y, B Zhang, K Wang, Q Tu, B Cui, B Ren, J He, X Shen, JD Van Nostrand, J Zhou, W Shi, L Xiao, C Lu, X Zhou, and Y Yao. Salivary mycobiome dysbiosis and its potential impact on bacteriome shifts and host immunity in oral lichen planus. Int J Oral Sci. 11:3. Suppl Material (docx)
  14. Liang B, JC Ma, WW Cai, ZL Li, WZ Liu, MY Qi, YK Zhao, XD Ma, Y Deng, AJ Wang, and JZ Zhou. 2019. Response of chloramphenicol-reducing biocathode resistome to continuous electrical stimulation. Wat Res. 148:398-406. Suppl Material (docx)
  15. Ma X, Q Zhang, M Zheng, Y Gao, T Yuan, L Hale, JD Van Nostrand, JZ Zhou, S Wan and Y Yang. 2019. Microbial functional traits are sensitive indicators of mild disturbance by lamb grazing. ISME J., 13:1370-1373. Suppl Material (docx)
  16. Ning D, Y Deng, JM Tie dje, and J Zhou. 2019. A general framework for quantitatively assessing ecological stochasticity. Proc Nat Acad Sci. 116:16893-16898.
  17. Pegoraro E, M Mauritz, R Bracho, C Ebert, P Dijkstra, BA Hungate, KT Konstantinidis, Y Luo, C Schädel, JM Tiedje, J Zhou, and EAG Schuur. 2019. Glucose addition increases the magnitude and decreases the age of soil respired carbon in a long-term permafrost incubation study. Soil Biol Biochem. 129:201-211. Suppl Material 1 (docx) Suppl Material 2 (xml)
  18. Shi X, J Zhao, L Chen, J Zuo, Y Yang, Q Zhang, Z Qin, and J Zhou. 2019. Genomic dynamics of full-scale temperature-phased anaerobic digestion treating waste activated sludge: Focusing on temperature differentiation. Waste Manag. 87:621-628.
  19. Shi Z, H Yin, JD Van Nostran d, JW Voordeckers, Q Tu, Y Deng, M Yuan, A Zhou, P Zhang, N Xiao, D Ning, Z He, L Wu, and J Zhou. 2019. Functional gene array-based ultrasensitive and quantitative detection of microbial populations in complex communities. mSystems. 4:e00296-19. Suppl Material: Text (pdf), GeoChip 5 Table (pdf), Tables/Figures (pdf)
  20. Song, D., X. Chen, M. Xu, R. Hai, A. Zhou, R. Tian, J. D. Van Nostrand, M. L. Kempher, J. Guo, G. Sun, and J.-Z. Zhou. 2019. Evolution of Sphingobium hydrophobicum C1T in Electronic Waste Contaminated River Sediment. Front Microbiol, doi: 10.3389/fmicb.2019.02263. Suppl Material (zip)
  21. Tang L, L Zhong, K Xue, S Wang, Z Xu, Q Lin, C Luo, Y Rui, X Li, M Li, W Liu, Y Yang, J Zhou, and Y Wang. 2019. Warming counteracts grazing effects on the functional structure of the soil microbial community in a Tibetan grassland. Soil Biol Biochem. 134:113-121. Suppl Material (docx)
  22. Tian J, AJ Dunga it, X Lu, Y Yang, IP Hartley, W Zhang, J Mo. G Yu, J Zhou, and Y Kuzyakov. Long‐term nitrogen addition modifies microbial composition and functions for slow carbon cycling and increased sequestration in tropical forest soil. Glob Change Biol. 25:3267-3281. Suppl Material (docx)
  23. Wakelin S, P Maclean , V Cave, J Zhou, GA Grelet, adn D Whitehead. 2019. Characterising the soil ecosystem phenotype associated with relatively low nitrate-N concentrations. Appl Soil Sci. 142:189-198. Suppl Material: Text (docx), Data (xlsx)
  24. Wang P, Y Chen, Y Sun, S Tan, S Zhang, Z Wang, JZ Zhou, G Zhang, W Shu, C Luo, and J Kuang. 2019.  Distinct biogeography of different fungal guilds and their associations with plant species richness in forest ecosystems. Front Ecol Evol. 7:216, doi: 10.3389/fevo.2019.00216. Suppl Info (zip)
  25. Wang XB, J Yao, HY Zhang, XG Wang, KH Li, XT Lu, ZW Wang, JZ Zhou, and XG Han. 2019. Environmental and spatial variables determine the taxonomic but not functional structure patterns of microbial communities in alpine grasslands. Sci Tot Environ. 654:960-968. Suppl Material (docx)
  26. Wang Y, H Zheng, F Chen, Y Yang, J Zeng, J Van Nostrand, JZ Zhou, and Z Ouyang. 2019. Artificial reforestation produces less diverse soil nitrogen-cycling genes than natural restoration. Ecosphere. 10:e02562. https://doi.org/10.1002/ecs2.2562. Suppl Material (pdf)
  27. Weiser MD, D Ning, V Buzzard, ST Michaletz, Z He, BJ Enquist, RB Waide, JZ Zhou, and M Kaspari. 2019. Thermal disruption of soil bacterial assemblages decreases diversity and assemblage similarity. Ecosphere, doi.org/10.1002/ecs2.2598. Suppl Material (pdf)
  28. Wu L, D Ning, B Zhang, Y Li, P Zhang, X Shan, Q Zhang, M Brown, Z Li, JD Van Nostrand, F Ling, N Xiao, Y Zhang, J Vierheilig, GF Wells, Y Yang, Y Deng, Q Tu, A Wang, Global Water Microbiome Consortium, T Zhang, Z He, J Keller, PH Nielsen, PJJ Alvarez, CS Criddle, M Wagner, JM Tiedje, Q He, TP Curtis, DA Stahl, L Alvarez-Cohen, BE Rittmann, X Wen, and JZ Zhou. 2019. Global diversity and biogeography of the bacterial communities in wastewater treatment plants. Nat Microbiol, 4:1183-1195. Suppl Material: Tables S1, S3, S11, S12
  29. Xia X, Y Wang , Y Yang, T Luo, JD Van Nostrand, J Zhou, N Jiao, R Zhang . Ocean acidification regulates the activity, community structure and functional potential of heterotrophic bacterioplankton in an oligotrophic gyre. J Geophys Res: Biogeosci. 124:1001-1017. doi.org/10.1029/2018JG004707. Suppl Material, Normalized Miicroarray Data (zip)
  30. Yang S, Q Zheng, Myuan, Z Shi, NR Chiariello, KM Docherty, S Dong, CB Field, Y Gu, J Gutknecht, BA Hungate, X Le Roux, X Ma, A Niboyet, T Yuan, J Zhou, and Yu Yang. 2019. Long-term elevated CO2 shifts composition of soil microbial communities in a Californian annual grassland, reducing growth and N utilization potentials. Sci Tot Environ. 652:1474-1481. Suppl Material (doc)
  31. Zelaya AJ, AE Pa rker, KL Bailey, P Zhang, JD Van Nostrand, D Ning, DA Elias, J Zhou, TC Hazen, AP Arkin, and MW Fields. High spatiotemporal variability of bacterial diversity over short time scales with unique hydrochemical associations within a shallow aquifer. Water Res. 164:114917. Suppl Material (pdf)
  32. Zhang Q, M Wang, X Ma, Q Gao, T Wang, X shi, J Zhou, J Zuo, and Y Yang. 2019. High variations of methanogenic microorganisms drive full-scale anaerobic digestion process. Environ Internat. 126:543-551. Suppl Material (docx)
  33. Zhao J, Q Gao, J Zhou, M Wang, Y Liang, B Sun, H Chu, and Y Yang. 2019. The scale dependence of fungal community distribution in paddy soil driven by stochastic and deterministic processes. Fungal Ecol. 42:100856
  34. Zhao M, X Lu, H Zhao, Y Yang, L Hale, Q Gao, W Liu, J Guo, Q Li, J Zhou, and F Wan. 2019. Ageratina adenophora invasions are associated with microbially mediated differences in biogeochemical cycles. Sci Tot Environ. 677:47-56. Suppl Material (docx)
  35. Zhao M, B Sun, L Wu, F Wang, C Wen, M Wang, Y Liang, L Hale, J Zhou, and Y Yang. 2019. Dissimilar responses of fungal and bacterial communities to soil transplantation simulating abrupt climate changes. Mol Ecol. 28:1842-1856. Suppl Material (docx)
  36. Zhu CM, JY Zhang, R Guan, L Hale, N Chen, M Li, ZH Lu, QY Ge, YF Yang, JZ Zhou, and T Chen. 2019. Alternate succession of aggregate-forming cyanobacterial genera correlated with their attached bacteria by co-pathways. Sci Total Environ 688:867-879. Suppl Material (zip)
2018
  1. Brandon AM, S Ga o, R Tian, D Ning, S Yang, J Zhou, W Wu, and CS Criddle. 2018. Biodegradation of polyethylene and plastic mixtures in mealworms (larvae of Tenebrio molitor) and effects on the gut microbiome. Environ. Sci Technol52:6526-6533. Suppl Material (pdf)
  2. Chen C, C Hemme, J Beleno, ZJ Shi, D Ning, Y Qin, Q Tu, M Jorgenson, Z He, L Wu, and J Zhou. 2018. Oral microbiota of periodontal health and disease and their changes after nonsurgical periodontal therapy. ISME J. 12:1210–1224. Suppl Material (pdf)
  3. Christensen GA, J Moon, AM Veach, JJ Mosher, AM Wymore, JD Van Nostrand, J Zhou, TC Hazen, AP Arkin, and DA Elias. 2018. Use of in-field bioreactors demonstrate groundwater filtration influences planktonic bacterial community assembly, but not biofilm composition. PLoS ONE 13(3): e0194663. Suppl Material (zip)
  4. Deng Y, D Ning, Y Qin, K Xue, L Wu, Z He, H Yin, Y Liang, V Buzzard, ST Michaletz, and J Zhou. 2018. Spatial scaling of forest soil microbial communities across a temperature gradient. Environ Microbiol. 20:3504-3513. Supplemental Information; Supplmental Data: R code R file; Suppl Material (pdf) 
  5. Dignam BEA , O’Callaghan M, Condron LM, Kowalchuk GA, Van Nostrand JD, Zhou J, and SA Wakelin. 2018. Effect of land use and soil organic matter quality on the structure and function of microbial communities in pastoral soils: Implications for disease suppression. PLoS ONE 13: e0196581. Suppl Material (zip)
  6. Guo X, J Feng, Z Shi, X Zhou, M Yuan, X Tao, L Hale, T Yuan, J Wang, Y Qin, A Zhou, Y Fu, L Wu, Z He, J Van Nostrand, D Ning, X Liu, Y Luo, J Tiedje, Y Yang, and J Zhou. 2018. Climate warming leads to divergent succession of grassland microbial communities. Nat Clim Change. 8:813-818. Suppl Material (pdf)
  7. Guo X, X Zhou, L Hale, M Yuan, D Ning, Z Shi, Y Qin, F Liu, L Wu, Z He, J Van Nostrand, X Liu, Y Luo, JM Tiedje, and J Zhou. Taxonomic and functional responses of soil microbial communities to annual removal of aboveground plant biomass. Front. Microbio. 9:954. Suppl. Material. (zip)
  8. He J, Q Tu, Y Ge, Y Qin, B Cui, X Hu, Y Wang, Y Deng, K Wang, JD Van Nostrand, J Li, J Zhou, Y Li, X Zhou. 2018. Taxonomic and functional analyses of the supragingival microbiome from caries-affected and caries-free hosts.Microbial Ecol. 75:543-554. Suppl Material: Figures (doc), Tables (xls)
  9. He Z, P Zhang, L Wu, AM Rocha, Q Tu, Z Shi, B Wu, Y Qin, J Wang, Q Yan, D Curtis, JD Van Nostrand, L Wu, Y Yang, DA Elias, DB Watson, MWW Adams, MW Fields, EJ Alm, TC Hazen, PD Adams, AP Arkin, and J-Z Zhou. 2018. Microbial functional gene diversity predicts groundwater contamination and ecosystem functioning. mBio. 9:e02435-17. Supplementary Information (csv); Suppl Material (pdf)
  10. Hou Y, C Yang, A Zhou, W Liu, C Liu, W Cai, J Zhou, and J Zhou. 2018. Microbial community response and SDS-PAGE reveal possible mechanism of waste activated sludge acidification enhanced by microaeration coupled thermophilic pretreatment. Process Biochem. 64:1-8. Suppl Material (doc)
  11. Karna RR, GM Hettiarachchi, JD Van Nostrand, T Yuan, CW Rice, YM Assefa, and J Zhou. Microbial population dynamics and the role of sulfur reducing bacteria genes in stabilizing Pb, Zn and Cd in the terrestrial subsurface. Soil Systems. 2:60. 
  12. Li H, Z X u, Q Yan, S Yang, JD Van Nostrand, Z Wang, Z He, J Zhou, Y Jiang, and Y Deng. Soil microbial beta-diversity is linked with compositional variation in aboveground plant biomass in a semi-arid grassland. Plant Soil. 423:465-480. Suppl Material (pdf)
  13. Li Y, Y Li, SX Chang, Y Yang, S Fu, P Jiang, Y Luo, M Yang, Z Chen, S Hu, M Zhao, X Liang, Q Xu, G Zhou, and J Zhou. 2018. Biochar reduces soil heterotrophic respiration in a subtropical plantation through increasing soil organic carbon recalcitrancy and decreasing carbon-degrading microbial activity.Soil Biol Biochem. 122:173-185. Suppl Material (doc)
  14. Liang J, J Xia , Z Shi, L Jiang, S Ma, X Lu, M Mauritz, SM Natali, E Pegoraro, CR Penton, C Plaza, VG Salmon, G Celis, JR Cole, KT Konstantinidis, JM Tiedje, J Zhou, EAG Schuur, and Y Luo. 2018. Biotic responses buffer warming‐induced soil organic carbon loss in Arctic tundra. Glob Change Biol. 24:4946-4959. Suppl Material (doc)
  15. Liang J, Z Zhou, C Huo, Z Shi, JR Cole, L Huang, KT Konstantinidis, X Li, B Liu, Z Luo, CR Penton, EA Schuur, JM Tiedje, YP Wang, L Wu, J Xia, J Zhou, and Y Luo. 2018. More replenishment than priming loss of soil organic carbon with additional carbon input. Nat Comm. 8:3175. Suppl Material: Figures (pdf), Tables (xls)
  16. Reyes VC, PB Gedalanga , N Merino, JD Van Nostrand, SP Keely, SK De Long, J Zhou, and S Mahendra. 2018. Differential sensitivity of wetland-derived nitrogen cycling microorganisms to copper nanoparticles. ACS Sustainable Chem Eng. 6:11642-11652. Suppl Material (pdf)
  17. Sheng Z, JD Van Nostrand, J Zhou, and Y Liu. 2018. Contradictory effects of silver nanoparticles on activated sludge wastewater treatment. J Haz Mat. 341:448-456.
  18. Shi S, DJ Herman, Z He, J Pett-Ridge, L Wu, J Zhou, and MK Firestone. Plant roots alter microbial functional genes supporting root litter decomposition. Soil Biol Biochem. 127:90-99. Suppl Material (doc)
  19. Shi Z, Y Lin, KR Wilcox, L Souza, L Jiang, J Jiang, CG Jung, X Xu, M Yuan, X Guo, L Wu, J Zhou, and Y Luo. Successional change in species composition alters climate sensitivity of grassland productivity. Glob Change Biol. 24:4993-5003. Suppl Material (doc)
  20. Tian J, N He, L Hale, S Niu, G Yu, Y Liu, E Blagodatskaya, Y Kuzyakov, Q Gao, and J Zhou. 2018. Soil organic matter availability and climate drive latitudinal patterns in bacterial diversity from tropical to cold-temperate forests. Funct Ecol. 32:61-70. Suppl Material (pdf)
  21. Tian J, N He, W Kong, Y Deng, K Feng, SM Green, X Wang, J Zhou, Y Kuzyakov, and G Yu. 2018. Deforestation decreases spatial turnover and alters the network interactions in soil bacterial communities. Soil Biol Biochem. 123:80-86. Suppl Material (doc)
  22. Vishnivetska ya TA, H Hu, JD Van Nostrand, AM Wymore, X Xu, G Qiu, X Feng, J Zhou, SD Brown, CC Brandt, M Podar, B Gu and DA Elias. 2018. Microbial community structure with trends in methylation gene diversity and abundance in mercury-contaminated rice paddy soils in Guizhou, China. Environ. Sci. Process Impacts. 20:673.  Suppl Material (pdf)
  23. Wang M, J Ding , B Sun, J Zhang, KN Wyckoff, H Yue, M Zhao, Y Liang, X Wang, C Wen, J Zhou, and Y Yang. Microbial responses to inorganic nutrient amendment overridden by warming: Consequences on soil carbon stability. Environ Microbiol. 20:2509-2522. Suppl Material (doc)
  24. Weiser, M., S. Michaletz, V. Buzzard, Y. Deng, Z. He, L. Shen, B. Enquist, R. Waide, J.-Z. Zhou, and M. Kaspari. 2018. Toward a theory for diversity gradients: the abundance-adaptation hypothesis. Ecography. 41:255-264.
  25. Weiser M D, NG Swenson, BJ Enquist, ST Michaletz, RB Waide, J Zhou, and M Kaspari. 2018. Taxonomic decomposition of the latitudinal gradient in species diversity of North American floras. J Biogeography. 45:418–428. Suppl Material: Appendix 1 (doc), Appendix 2 (csv)
  26. Whitman T, R Neurath, A Perera, I Chu‐Jacoby, D Ning, J Zhou, P Nico, J Pett‐Ridge, and M Firestone. Microbial community assembly differs across minerals in a rhizosphere microcosm. Environ Microbiol. doi.org/10.1111/1462-2920.14366. Suppl Material: Figures (doc), Table 1 (xls), Table 2 (xls)
  27. Wu B, F Liu, MD Weiser, D Ning, JG Okie, L Shen, J Li, B Chai, Y Deng, K Feng, L Wu, S Chen, J Zhou, and Z He. 2018. Temperature determines the diversity and structure of N2O-reducing microbial assemblages. Funct. Ecol. 32:1867-1878. Suppl Material (pdf)
  28. Wu X, L Wu , Y Liu, P Zhang, Q Li, J Zhou, N Hess, TC Hazen, W Yang and R Chakraborty. 2018. Microbial interactions with dissolved organic matter drive carbon dynamics and community succession. Front Microbiol. doi: 10.3389/fmicb.2018.01234. 9:1234. Suppl Material (doc)
  29. Xiao, J., F. Yu, W. Zhu, C. Xu, K. Zhang, Y. Luo, J. M. Tiedje, J.-Z. Zhou, L. Cheng. 2018. Comment on “The whole-soil carbon flux in response to warming”.Science, 359:eaao0218. DOI: 10.1126/science.aao0218
  30. Xing W, J Li, P Li, C Wang, Y Cao, D Li, Y Yang, J Zhou, and J Zuo. 2018. Effects of residual organics in municipal wastewater on hydrogenotrophic denitrifying microbial communities. J Envrion Sci. 65:262-270. Suppl Material (doc)
  31. Xue K, J Zhou, J Van Nostrand, M Mench, C Bes, L Giagnoni, and G Renella. 2018. Functional activity and functional gene diversity of a Cu-contaminated soil remediated by aided phytostabilization using compost, dolomitic limestone and a mixed tree stand. Environ Poll. 242(A):229-238. Suppl Material (doc)
  32. Yang S, AM Brandon, JCA Flanagan, J Yang, D Ning, S Cai, H Fan, Z Wang, J Ren, E Benbow, N Ren, RM Waymouth, J Zhou, CS Criddle, and W Wu. 2018. Biodegradation of polystyrene wastes in yellow mealworms (larvae of Tenebrio molitor Linnaeus): Factors affecting biodegradation rates and the ability of polystyrene-fed larvae to complete their life cycle. Chemosphere. 191:979-989. Suppl Material (doc)
  33. Yang S, Wu WM, Brandon AM, Fan HQ, Receveur JP, Li Y, Wang ZY, Fan R, McClellan RL, Gao SH, Ning D, Phillips DH, Peng BY, Wang H, Cai SY, Li P, Cai WW, Ding LY, Yang J, Zheng M, Ren J, Zhang YL, Gao J, Xing D, Ren NQ, Waymouth RM, Zhou J, Tao HC, Picard CJ, Benbow ME, Criddle CS. 2018. Ubiquity of polystyrene digestion and biodegradation within yellow mealworms, larvae of Tenebrio molitor Linnaeus (Coleoptera: Tenebrionidae). Chemosphere. 212:262-271. Suppl Material (pdf)
  34. Yu H, Z He, J Van Nostrand, S Wang, D Jin, A Wang, L Wu, D Wang, X Tai, J Zhou, and Y Deng. 2018. Elevated CO2 and warming altered grassland microbial communities in soil top-layers. Front Microbiol. 9:1790. Suppl Material (zip)
  35. Yu H, Z He, A Wang, J Xie, L Wu, JD Van Nostrand, D Jin, Z Shao, CW Schadt, J Zhou, and Y Deng. 2018. Divergent responses of forest soil microbial communities under elevated CO2 in different depths of upper soil layers. Appl. Environ Microbiol. 84:e01698-17. Suppl Material (pdf)
  36. Yuan M, J Zhang, K Xue, L Wu, Y Deng, J Deng, L Hale, X Zhou, Z He, Y Yang, JD Van Nostrand, EAG Schuur, KT Kostantinidis, CR Penton, JR Cole, JM Tiedje, Y Luo, and J Zhou. 2018. Microbial functional diversity covaries with permafrost thaw-induced environmental heterogeneity in tundra soil. Glob Change Bio.24:297-307. Suppl Material (doc)
2017
  1. Cheng L, N Zhang , M Yuan, J Xiao, Y Qin, Y Deng, Q Tu, K Xue, J Van Nostrand, L Wu, Z He, X Zhou, MB Leigh, K Konstantinidis, E Schuur, Y Luo, J Tiedje, and J Zhou.2017. Warming enhances old organic carbon decomposition through altering functional microbial communities. ISME J. 11:1825-1835. doi: 10.1038/ismej.2017.48. Suppl Material: Appendix 1 (pdf); Appendix 2 (xlsx); Figures (pdf)
  2. Colin Y, O Nicolitch, JD Van Nostrand, JZ Zhou, MP Turpault, S Uroz. 2017. Taxonomic and functional shifts in the beech rhizosphere microbiome across a natural soil toposequence. Sci Rep. 7:9604. Doi:10.1038/s41598-017-07639-1. Suppl Material
  3. Escalas, A., Troussellier, M., Tong, Y., Bouvier, T., Bouvier, C., Mouchet, M. A., Flores hernandez, D., Ramos miranda, J., Zhou, J. and Mouillot, D. Functional diversity and redundancy across fish gut, sediment, and water bacterial communities. Environ. Microbiol. 19:3268-3282. Suppl Material: Appendix 1 (doc); Appendix 2 (doc); Appendix 3 (xls)
  4. Feng W, Liang J, Hale LE, Jung CG, Chen J, Zhou J, Xu M, Yuan M, Wu L, Bracho R, Pegoraro E, Schuur EAG, and Luo Y. 2017. Enhanced decomposition of stable soil organic carbon and microbial catabolic potentials by long-term field warming. Glob Change Biol. https://doi.org/10.1111/gcb.13755. Suppl Material: Figure S1 (tif); Figure S2 (tif); Method (pdf)
  5. Gu Y, JD Van Nostrand, L Wu, Z He, Y Qin, F Zhao, and J Zhou. 2017. Bacterial communities and arsenic functional genes diversity in arsenic contaminated soils from different geographic locations. PloS One, 12(5): e0176696. doi.org/10.1371/journal.pone.0176696.  Supplementary Data: Fasta files (zip); Suppl Material (docx)
  6. Hou Y, B Zhang , H Yun, Z Yang, J Han, J Zhou, A Wang, and H Cheng. Palladized cells as suspension catalyst and electrochemical catalyst for reductively degrading aromatics contaminants: Roles of Pd size and distribution. Wat Res. doi.org/10.1016/j.watres.2017.08.055
  7. Huang C, Q Liu, C Chen, F Chen, YK Zhao, LF Gao, WZ Liu, JZ Zhou, ZL Li, AJ Wang. Elemental sulfur recovery and spatial distribution of functional bacteria and expressed genes under different carbon/nitrate/sulfide loadings in up-flow anaerobic sludge blanket reactors. J Haz Mat. 324A:48-53.
  8. Kaspari, M ., Bujan, J., Weiser, M. D., Ning, D., Michaletz, S. T., Zhili, H., Enquist, B. J., Waide, R. B., Zhou, J., Turner, B. L. and Wright, S. J. 2017. Biogeochemistry drives diversity in the prokaryotes, fungi, and invertebrates of a Panama forest. Ecology. 98:2019-2028. Suppl Material (pdf)
  9. King AJ, SP Preheim, KL Bailey, MS Robeson, TR Chowdhury, BR Crable, RA Hurt Jr, T Mehlhorn, KA Lowe, TJ Phelps, AV Palumbo, CC Brandt, SD Brown, M Podar, P Zhang, WA Lancaster, F Poole, DB Watson, MW Fields, JM Chandonia, EJ Alm, J Zhou, MWW Adams, TC Hazen, AP Arkin, and DA Elias. 2017. Temporal dynamics of in-field bioreactor populations reflect the groundwater system and respond predictably to perturbation. Environ. Sci. Technol., 51(5):2879–2889. Suppl Material (pdf)
  10. Kuang J, Cadotte MW, Chen Y, Shu H, Liu J, Chen L, Hua Z, Shu W, Zhou J and Huang L 2017. Conservation of species- and trait-based modeling network interactions in extremely acidic microbial community assembly. Front. Microbiol. 8:1486. doi: 10.3389/fmicb.2017.01486. Suppl Material (link)
  11. Li H, S Yang, Z Xu, Q Yan, X Li, JD Van Nostrand, Z He, F Yao, X Han, J Zhou, Y Deng, Y Jiang. 2017. Responses of soil microbial functional genes to global changes are indirectly influenced by aboveground plant biomass variation. Soil Biol Biochem. 104:18-29. Suppl Material (docx)
  12. Li P, Z Jiang, Y Wang, Y Deng, JD Van Nostrand, T Yuan, H Liu, D Wei, and J Zhou. 2017. Analysis of the functional gene structure and metabolic potential of microbial community in high arsenic groundwater. Water Res. 123:268-276. Suppl Material (docx)
  13. Lindsay, MR, C Anderson, N Fox, G Scofield, J Allen, E Anderson, L Bueter, S Poudel, K Sutherland, JH Munson-McGee, JD Van Nostrand, J Zhou, JR Spear, BK Baxter, DR Lageson, and ES Boyd. Microbialite response to an anthropogenic salinity gradient in Great Salt Lake, Utah. Geobiology. 15:131-145. DOI: 10.1111/gbi.12201. Suppl Material (docs)
  14. Lyles, CN, VA Parisi, W H Beasley, JD Van Nostrand, J Zhou, and JM Suflita. Elucidation of the methanogenic potential from coalbed microbial communities amended with volatile fatty acids. FEMS Microbiol Ecol 93(4):fix040 doi: 10.1093/femsec/fix040. Suppl Material (zip)
  15. Ma, X., Zhao, C., Gao, Y., Liu, B., Wang, T., Yuan, T., Hale, L., Van Nostrand, J. D., Wan, S., Zhou, J. and Yang, Y. Divergent taxonomic and functional responses of microbial communities to field simulation of aeolian soil erosion and deposition. Mol Ecol. 26:4186-4196. Suppl Material (docx)
  16. Navarrete, AA, EV Mellis, A Escalas, LN Lemos, J Lavres Jr, JA Quaggio, J Zhou, SM Tsai. 2017. Zinc concentration affects the functional groups of microbial communities in sugarcane-cultivated soil. Agricult. Ecosys. Environment 236:187-197. Suppl Material (docx)
  17. Qi Q, M Zhao, S Wang, X Ma, Y Wang, Y Gao, Q Lin, X Li, B Gu, G Li, J Zhou, and Y Yang. 2017. The biogeographic pattern of microbial functional genes along an altitudinal gradient of the Tibetan pasture. Front. Microbiol. doi.org/10.3389/fmicb.2017.00976. Suppl Material (docx)
  18. Tu Q, Z He, L Wu, K Xue, G Xie, P Chain, PB Reich, SE Hobbie, and J Zhou. 2017. Metagenomic reconstruction of nitrogen cycling pathways in a CO2-enriched grassland ecosystem. Soil Biol Biochem. 106:99-108. Suppl Material (docx)
  19. Tu Q, J Li, Z Shi, Y Chen, L Lin, J Li, H Wang, J Yan, Q Zhou, X Li, L Li, J Zhou, Z He. 2017. HuMiChip2 for strain level identification and functional profiling of human microbiomes. Appl Microbiol Biotechnol. 101:423-435. Suppl Material (xlsx)
  20. Wang, H, L Yu, Z Zhang, W Liu, L Chen, G Cao, H Yue, J Zhou, Y Yang, Y Tang and J He. 2017. Molecular mechanisms of water table lowering and nitrogen deposition in affecting greenhouse gas emissions from a Tibetan alpine wetland. Global Change Biol. 23, 815–829. Suppl Material (xlsx)
  21. Wang, J., Meier, S., Soininen, J., Casamayor, E. O., Pan, F., Tang, X., Yang, X., Zhang, Y., Wu, Q., Zhou, J. and Shen, J. 2017, Regional and global elevational patterns of microbial species richness and evenness. Ecography, 40: 393–402. doi:10.1111/ecog.02216
  22. Wang, X., X. Lü, J. Yao, Z. Wang, Y. Deng, W. Cheng, J.-Z. Zhou, X. Han. 2017. Habitat-specific patterns and drivers of bacterial β-diversity in China’s drylands. ISME J. 11:1345-1358. Suppl Material (doc)
  23. Wang, Y., R Zhang, Z He, JD Van Nostrand, Q Zheng, J Zhou, and N Jiao. 2017. Functional gene diversity and metabolic potential of the microbial community in an estuary-shelf environment. Front. Microbiol. 8:1153, DOI: 10.3389/fmicb.2017.01153  Supplementary Data: Microarray data - original signal (txt); Microarray data - Relative Signal (csv); Suppl Material (pdf)
  24. Wen C, L Wu, Y Qin, JD Van Nostrand, S Bo, K Xue, Y Deng, F Liu, and J Zhou. 2017. Evaluation of the Reproducibility of Amplicon Sequencing with Illumina MiSeq Platform. PLoS One, 12(4):e0176716. doi: 10.1371/journal.pone.0176716. Suppl Material (zip)
  25. Wu L, Y Yang, S Chen , J Shi, M Zhao, Z Zhu, S Yang, Y Qu, Q Ma, Z He, J Zhou, and Q He. Microbial functional trait of rRNA operon copy numbers increases with organic levels in anaerobic digesters. ISME J doi: 10.1038/ismej.2017.135. Suppl Material (doc)
  26. Wu L, Y Yang , S Wang, H Yue, Q Lin, Y Hu, Z He, JD Van Nostrand, L Hale, X Li, JA Gilbert, and J Zhou. 2017. Alpine soil carbon is vulnerable to rapid microbial decomposition under climate cooling. ISME J. 11:2102-2111. Suppl Material (doc)
  27. Xu T, Y Li, Z He, JD Van Nostrand, and J Zhou. Cas9 nickase-assisted RNA repression enables stable and efficient manipulation of essential metabolic genes in Clostridium cellulolyticum. Front. Microbiol. 8:1744. doi: 10.3389/fmicb.2017.01744. Suppl Material (pdf)
  28. Yan, Q., J. Stegen, Y. Yu, Y. Deng, X. Li, S. Wu, L. Dai, X. Zhang, J. Li, C. Wang, J. Ni, X. Li, H. Hu, F. Xiao, W. Feng, D. Ning, Z. He, J. D. van Nostrand, L. Wu, and J.-Z. Zhou. 2017. Nearly a decade-long repeatable seasonal diversity patterns of bacterioplankton communities in the eutrophic Lake Donghu (Wuhan, China). Mol. Ecol. 26:3839-3850. Suppl Material (pdf)
  29. Yan Z, Y He, H Cai, J Van Nostrand, Z He, J Zhou, L Krumholz, H Jiang. 2017. Interconnection of key microbial functional genes for enhanced benzo[a]pyrene biodegradation in sediments by microbial electrochemistry. Environ Sci Technol. 51:8519-8529. Suppl Material (pdf)
  30. Yang, S., Y. Zhang, J. Cong, M. Wang, M. Zhao, H. Lu, C. Xie, C. Yang, T. Yuan, D. Li, J.-Z. Zhou, B. Gu, Y. Yang. 2017. Variations of soil microbial community structures beneath broadleaved forest trees in temperate and subtropical climate zones. Front. Microbiol. doi: 10.3389/fmicb.2017.00200. Suppl Material (doc)
  31. Yang Z, S Yang, J Van Nostrand, J Zhou, W Fang, Q Qi, Y Liu, L Liang, SD Wullschleger, DE Graham, Y Yang, and B Gu. Microbial community and functional gene changes in Arctic tundra soils in a microcosm warming experiment. Front. Microbiol. 8:1741. Suppl Material (doc)
  32. Yu D, M Xia, L Zhang, Y Song, Y Duan, T Yuan, M Yao, L Wu, C Tian, Z Wu, X Li, J Zhou and D Qiu. RpoN (σ54) is required for floc formation but not for extracellular polysaccharide biosynthesis in a floc-forming Aquincola tertiaricarbonis strain. Appl Environ Microbiol. doi: 10.1128/AEM.00709-17. Suppl Material (pdf)
  33. Zeng, F., Z. Wang, Y. Wang, J.-Z. Zhou, and T. Chen. 2017. Large-scale 16S gene assembly using metagenomics shotgun sequences. Bioinformatics, 33:1447-1456. DOI:10.1093/bioinformatics/btx018. Suppl Material (zip)
  34. Zhang J, Q Gao, Q Zhang, T Wang, H Yue, L Wu, J Shi, Z Qin, J Zhou, J Zuo and Y Yang. 2017. Bacteriophage–prokaryote dynamics and interaction within anaerobic digestion processes across time and space. Microbiome. 5:57. Suppl Material (doc)
  35. Zhang, P., Z. He, J. Van Nostrand, Y. Qin, Y. Deng, L. Wu, Q., Tu, J. Wang, C. Schadt, M. Fields, T. Hazen, A. Arkin, D. Stahl, and J.-Z. Zhou. 2017. Dynamic succession of groundwater sulfate-reducing communities during prolonged reduction of uranium in a contaminated aquifer. Environ. Sci. & Technol.51(7):3609–3620. Suppl Material (pdf)
  36. Zhang Y, X Liu, J Cong, H Lu, T Sheng, X Wang, D Li, X Liu, H Yin, J Zhou, and Y Deng. The microbially-mediated soil organic carbon loss under degenerative succession in an alpine meadow. Mol Ecol. 26:3676-3686. Suppl Material: Figures (doc), Table 1 (xls), Table 2 (xls)
  37. Zhang Y, Q Yang, J Ling, JD Van Nostrand, Z Shi, J Zhou, and J Dong. 2017. Diversity and structure of diazotrophic communities in mangrove rhizosphere, revealed by high-throughput sequencing. Front. Microbiol. 8:2031. doi.org/10.3389/fmicb.2017.02032. Suppl Material: Tables (doc) Figure (ppt)
  38. Zhou A, R Lau, R Baran, J Ma, F von Netzer, W Shi, D Gorman-Lewis, ML Kempher, Z He, Y Qin, Z Shi, GM Zane, L Wu, BP Bowen, TR Northen, KL Hillesland, DA Stahl, JD Wall, AP Arkin, J Zhou. 2017. Key metabolites and mechanistic changes for salt tolerance in an experimentally evolved sulfate-reducing bacterium, Desulfovibrio vulgaris. mBio. 8: e01780-17. Suppl Material (pdf)
  39. Zhou J, Y Deng, L Shen, C Wen, Q Yan, D Ning, Y Qin, K Xue, L Wu, Z He, J Voordeckers, J Van Nostrand, V Buzzard, S Michaletz, B Enquist, M Weiser, M Kaspari, R Waide, Y Yang, and J Brown. 2017. Correspondence: Reply to 'Analytical flaws in a continental-scale forest soil microbial diversity study'. Nat Comm. 8:15583.
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2016
  1. Bouskill, NJ, TE Wood, R Baran, Z Ye, BP Bowen, H-C Lim, J Zhou, JD Van Nostrand, P Nico, TR Northen, WL Silver, and EL Brodie. 2016. Belowground response to drought in a tropical forest soil. I. Changes in microbial functional potential and metabolism (pdf). Front. Microbiol. 7:525. doi: 10.3389/fmicb.2016.00525. Suppl Material (doc)
  2. Bracho R, S Natali , E Pegoraro, KG Crummer, C Schädel, G Celis, L Hale, L Wu, H Yin, JM Tiedje, KT Konstantinidis, Y Luo, J Zhou, EAG Schuur. 2016. Temperature sensitivity of organic matter decomposition of permafrost-region soils during laboratory incubations. Soil Biol Biochem. 97:1-14. Suppl Material (pdf)
  3. Deng Y, Z He, J Xiong, H Yu, MY Xu, SE Hobbie, PB Reich, CW Schadt, A Kent, E Pendall, M Wallenstein, and J-Z Zhou. 2016. Elevated carbon dioxide accelerates the spatial turnover of soil microbial communities. Glob Change Biol. 22:957-964. Suppl Material (doc)
  4. Deng Y, P Zhang, Y Qin, Q Tu, Y Yand, Z He, CW Schadt, and J-Z Zhou. 2016. Network succession reveals the importance of competition in response to emulsified vegetable oil amendment for uranium bioremediation. Environ Microbiol. 18:205-218. Suppl Material (zip)
  5. Feng W, Z Shi, J Jiang, J Xia, J Liang, J Zhou, and Y Luo. 2016. Methodological uncertainty in estimating carbon turnover times of soil fractions. Soil Biol Biochem. 100:118–124. Suppl Material: Additional References (doc); Tables 1 (xls), Tables 2 (xls)
  6. Hemme, CL, SJ Green, L Rishishwar, O Prakash, A Pettenato, R Chakraborty, AM Deutchbauer, JD Van Nostrand, L Wu, Z He, IK Jordan, TC Hazen, AP Arkin, JE Kostka, and J-Z Zhou. 2016. Lateral Gene Transfer in a Heavy Metal-Contaminated Groundwater Microbial Community (pdf). mBio, 7:e02234-15. Suppl Material (pdf)
  7. Herath, A., B. Wawrik, Y. Qin, J.-Z . Zhou, and A.V. Callaghan. 2016. Transcriptional response of Desulfatibacillum alkenivorans AK-01 to growth on alkanes: insights from RT-qPCR and microarray analyses. FEMS Microbiology Ecology, 92: fiw062; DOI: 10.1093/femsec/fiw062. Suppl Material (zip)
  8. Hou Y, H Liu, J Han, W Cai, J Zhou, A Wang, and H Cheng. 2016. Electroactive Biofilm Serving as the Green Synthesizer and Stabilizer for in Situ Fabricating 3D Nanopalladium Network: An Efficient Electrocatalyst. ACS Sustainable Chem Engineer. 4:5392-5397.
  9. Hwang C, Copeland A, Lucas S, Lapidus A, Barry K, Detter JC, Glavina del Rio T, Hammon N, Israni S, Dalin E, Tice H, Pitluck S, Chertkov O, Brettin T, Bruce D, Han C, Schmutz J, Larimer F, Land ML, Hauser L, Kyrpides N, Mikhailova N, Ye Q, Zhou J, Richardson P, Fields MW. 2016. Complete genome sequence of Alkaliphilus metalliredigens strain QYMF, an alkaliphilic and metal-reducing bacterium isolated from borax-contaminated leachate ponds. Genome Announc 4(6):e01226-16. doi:10.1128/genomeA.01226-16.
  10. Huang C, Z Lia, F Chena, Q Liua, Y Zhao, L Gao, C Chena, J-Z Zhou, and A Wang. 2016. Efficient regulation of elemental sulfur recovery through optimizing working height of upflow anaerobic sludge blanket reactor during denitrifying sulfide removal process. Bioresource Technol. 200:1019-1023.
  11. Jiang Y, Y Liang, C Li, F Wang, YSui, N Suvannang, J Zhou, and B Sun. 2016. Crop rotations alter bacterial and fungal diversity in paddy soils across East Asia. Soil Biol. Biochem. 95:250-261. Suppl Material (doc)
  12. Jiang Z, P Li, J Van Nostrand, P Zhang, J-Z Zhou, Y Wang, X Dai, R Zhang, D Jiang, and Y Wang. 2016. Microbial communities and arsenic biogeochemistry at the outflow of an alkaline sulfide-rich hot spring (pdf). Sci Reports. 6:25262. doi:10.1038/srep25262. Suppl Material (pdf)
  13. Johnston, ER, LM Rodriguez-R, C Luo, MM Yuan, L Wu, Z He, EAG Schuur, Y Luo, JM Tiedje, J Zhou, and KT Konstantinidis. 2016. Metagenomics reveals pervasive bacterial populations and reduced community diversity across the Alaska tundra ecosystem Front. Microbiol. 7:579. Suppl Material (doc)
  14. Kuang J, L Huang, Z He, L Chen, Z Hua, P Jia, S Li, J Liu, J Li, J Zhou, and W Shu. 2016. Predicting taxonomic and functional structure of microbial communities in acid mine drainage (pdf). ISME J. 10:1527–1539.  Supplementary data: Microarray data; Suppl Material (pdf)
  15. Liang B, D Kong, J Ma, C Wen, T Yuan, DJ Lee, J Zhou, A Wang. 2016. Low temperature acclimation with electrical stimulation enhance the biocathode functioning stability for antibiotics detoxification. Water Res. 100:157-168. Suppl Material (doc)
  16. Liang Y., H. Zhao, Y. Deng, J.-Z. Zhou, G. Li, and B. Sun. 2016. Long-term oil contamination alters the molecular ecological networks of soil microbial functional genes (pdf). Front. Microbiol. 7:60. doi:10.3389/fmicb.2016.00060. Supplemental Data: Microarray data; Suppl Material (doc)
  17. Michaletz ST, MD Weiser, NG McDowell, J Zhou, M Kaspari, BR Helliker, and BJ Enquist. 2016. The energetic and carbon economic origins of leaf thermoregulation. Nat Plants 2:16129. Suppl Material (pdf)
  18. Morrison E, S Newman , HS Bae, Z He, J Zhou, KR Reddy, A Ogram. 2016. Microbial genetic and enzymatic responses to an anthropogenic phosphorus gradient within a subtropical peatland. Geoderma. 268:119-127. Suppl Material (pdf)
  19. Penton, C.R., C. Yang, L. Wu, Q. Wang, J. Zhang, F. Liu, Y. Qin, Y. Deng, C. L Hemme, T. Zheng, E. A.G. Schuur, J. M. Tiedje, and J.-Z. Zhou. 2016. NifH- Harboring Bacterial Community Composition Across an Alaskan Permafrost Thaw Gradient. Front. Microbiol. 7:1894. doi: 10.3389/fmicb.2016.01894. Suppl Material (pdf)
  20. Qiu D, M Xie, J Dai, W An, H Wei, C Tian, ML Kempher, A Zhou, Z He, B Gu and J Zhou. 2016. Differential regulation of the two ferrochelatase paralogues in Shewanella loihica PV-4 in response to environmental stresses. Appl Environ Microbiol 82:5077-5088. Suppl Material (pdf)
  21. Shen C, Y Shi, Y Ni, Y Deng, J Van Nostrand, Z He, J Zhou, and H Chu. 2016. Dramatic increases of soil microbial functional gene diversity at the treeline ecotone of Changbai Mountain. Front. Microbiol. doi.org/10.3389/fmicb.2016.01184. Suppl Material (doc)
  22. Shi S, EE Nuccio , ZJ Shi, Z He, J Zhou, and MK Firestone. 2016. The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages. Ecol Lett, 19: 926–936. Suppl Material (pdf)
  23. Sun Y, Y Shen, P Liang, J Zhou, Y Yang, and X Huang. 2016. Multiple antibiotic resistance genes distribution in ten large-scale membrane bioreactors for municipal wastewater treatment. Bioresouce Technol 222:100-106. Suppl Material
  24. Trivedi P, M Delgado-Baquerizo, C Trivedi, H Hu, IC Anderson, TC Jeffries, J Zhou, and BK Singh. 2016. Microbial regulation of the soil carbon cycle: evidence from gene–enzyme relationships. ISME J. 10:2593-2604. Suppl Material: Figures (pdf), Tables (doc)
  25. Tu Q, Y Deng, Q Yan, L Shen, L Lin, Z He, L Wu, JD Van Nostrand, V Buzzard, S Michaletz, B Enquist, M Weiser, M Kaspari, R Waide, J Brown, and J Zhou. 2016. Biogeographic Patterns of Soil Diazotrophic Communities across Six Forests in the North America. Mol Ecol. 25:2937-2948. Suppl Material  (doc)
  26. Tu, Q, X Zhou, Z He, K Xue, L Wu, P Reich, S Hobbie, J-Z Zhou. 2016. The diversity and co-occurrence patterns of N2-fixing communities in a CO2-enriched grassland ecosystem. Microbial Ecol. 71:604-615. Suppl Material (doc)
  27. Utturkar SM, Bayer EA, Borovok I, Lamed R, Hurt RA, Land ML, Klingeman DM, Elias D, Zhou J, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Ngan CY, Daum C, Shapiro N, Markowitz V, Ivanova N, Kyrpides N, Woyke T, Brown SD. 2016. Application of long sequence reads to improve genomes for Clostridium thermocellum AD2, Clostridium thermocellum LQRI, and Pelosinus fermentans R7. Genome Announc 4(5):e01043-16. doi:10.1128/genomeA.01043-16.
  28. Van Nostrand, JD, H Yin, Z He and J-Z Zhou. 2016. Hybridization of Environmental Microbial Community Nucleic Acids by GeoChip. In: (FM Martin and S Uroz, eds) Methods in Molecular Biology - Microbial Environmental Genomics. Springer Press.
  29. Van Nostrand, JD , A Zhou, and J-Z Zhou. 2016 StressChip for monitoring microbial stress response in the environment. In: (FJ De Bruijn, ed) Environmental Control of Gene Expression and Adaptation in Bacteria.Wiley-Blackwell.
  30. Wakelin SA, VM Cave, BE Dignam, C D’Ath, M Tourna, LM Condron, J Zhou, JD Van Nostrand & M O’Callaghan. 2016. Analysis of soil eDNA functional genes: potential to increase profitability and sustainability of pastoral agriculture. New Zealand J Agri Res. 59:333-350. Suppl Material (xlsx)
  31. Wang J, S Meier, J Soininen, EO Casamayor, F Pan, X Tang, X Yang, Y Zhang, Q Wu, J Zhou, and J Shen. 2016. Regional and global elevational patterns of microbial species richness and evenness. Ecography. 39:001-010. DOI: 10.1111/ecog.02216. Suppl Material (pdf)
  32. Wang K, W Lu, Q Tu, Y Ge, J He, Y Zhou, Y Gou, JD Van Nostrand, Y Qin, J Li, J Zhou, Y Li, L Xiao, and X Zhou. 2016. Preliminary analysis of salivary microbiome and their potential roles in oral lichen planus. Sci Rep. 2016; 6: 22943. Suppl Material (doc)
  33. Wang M, S Wang, L Wu, D Xu, Q Lin, Y Hu, X Li, J Zhou, Y Yang. 2016. Evaluating the lingering effect of livestock grazing on functional potentials of microbial communities in Tibetan grassland soils. Plant Soil. 407:385-399. Suppl Material (docx)
  34. Wang X, X Wen , Y Deng, X Xia, Y Yang, and J Zhou. Distance-decay relationship in biological wastewater treatment plants Appl Environ Microbiol.82:4860-4866. Suppl Material (pdf)
  35. Webster TM, RR Reddy, JY Tan, JD Van Nostrand, J Zhou, KF Hayes, and L Raskin. 2016. Anaerobic Disposal of Arsenic-Bearing Wastes Results in Low Microbially Mediated Arsenic Volatilization. Environ Sci Technol. 50:10951-10959. Suppl Material (pdf)
  36. Wei H, J Dai, M Xia, MF Romine , L Shi, A Beliav, JM Tiedje, KH Nealson, JK Fredrickson, J Zhou, D Qiu. 2016. Functional roles of CymA and NapC in reduction of nitrate and nitrite by Shewanella putrefaciens W3-18-1. Microbiology. 162:930-941. Suppl Material (pdf)
  37. Wei S, DC Lacap-Bugler , M Lau, T Caruso, S Rao, A de los Rios, S Archer, JM Chiu, C Higgins, JD Van Nostrand, J Zhou, D Hopkins, SB Pointing. 2016. Taxonomic and functional diversity of soil and hypolithic microbial communities in Miers Valley, McMurdo Dry Valleys, Antarctica. Front. Microbiol.http://dx.doi.org/10.3389/fmicb.2016.01642. Suppl Material (pdf)
  38. Weiss, S ., W. Van Treuren, C. Lozupone, K. Faust, J. Friedman, Y. Deng, L. C. Xia, Z. Z. Xu, L. Ursell, E. J. Alm, A. Birmingham, J. Cram, J. A. Fuhrman, J. Raes, F. Sun, J.-Z. Zhou, and R. Knight. 2016. Correlation detection strategies in microbial datasets vary widely in sensitivity and precision. ISME J, 10:1669-1681. Suppl Material: Figures (pdf), Tables 1 (xls), 2 (xls), 3 (xls)
  39. Wu L, Y Yang, S Chen, M Zhao, Z Zhu, S Yang, T Qu, Q Ma, Z He, J Zhou, and Q He. 2016. Long-term successional dynamics of microbial association networks in anaerobic digestion processes. Water Res. 104:1-10. Suppl Material (doc)
  40. Xia, Y., M. Hu, X. Wen, X. Wang, Y. Yang, and J.-Z. Zhou. 2016. Diversity and interactions of microbial functional genes under differing environmental conditions: insights from a membrane bioreactor and an oxidation ditch. Sci Reports. 6: 18509. DOI: 10.1038/srep18509. Suppl Material (doc)
  41. Xu, X., Z. Shi, D. Li, A. Rey, H. Ruan, J. M. Craine, J. Liang, J.-Z. Zhou, and Y. Luo. 2016. Soil properties control decomposition of soil organic carbon: Results from data-assimilation analysis. Geoderma. 262: 235-242. Suppl Material (doc)
  42. Xue K, M Yuan , Z Shi, Y Qin, Y Deng, L Cheng, L Wu, Z He, J Van Nostrand, R Bracho, S Natali, E Schuur, C Luo, K Konstantinidis, Q Wang, J Cole, J Tiedje, Y Luo, and J-Z Zhou. 2016. Tundra soil carbon is vulnerable to rapid microbial decomposition under climate warming. Nat Clim Change. 6:595-600. Suppl Material (pdf)
  43. Xue K, J Xie , A Zhou, F Liu, D Li, L Wu, Y Deng, Z He, JD Van Nostrand, Y Luo, J Zhou. 2016. Warming alters expressions of microbial functional genes important to ecosystem functioning. Front Microbiol. 7:668. Supplementary Data: Raw Geochip data (Tab delimited txt); Normalized GeoChip data (csv); Suppl Material (doc)
  44. Xue K, MM Yuan, J Xie, D Lic , Y Qin, LE Hale, L Wu, Y Deng, Z He, JD Van Nostrand, Y Luo, JM Tiedje, and J Zhou. 2016. Annual removal of aboveground plant biomass alters soil microbial responses to warming. mBio 7:e00976-16. Supplementary Data: Raw Geochip data (Tab delimited txt); Normalized GeoChip data (csv); Suppl Material (pdf)
  45. Yan Q, J Li, J Wang, Z He, JD Van Nostrand, ML Kempher, L Wu, Y Wang, L Liao, X Li, S Wu, J Ni, C Wang, J Zhou. 2016. Environmental filtering decreases with fish development for the assembly of gut microbiota. Environ Microbiol.18:4739-4754. Suppl Material (pdf)
  46. Yang C, Y Li, Y Zhou, X Lei, W Zheng, Y Tian, JD Van Nostrand, Z He, L Wu, J Zhou, and T Zheng. 2016. A comprehensive insight into functional profiles of free-living microbial community responses to a toxic Akashiwo sanguinea bloom. Sci Rep 6:34645. Suppl Material (pdf)
  47. Yu Z, Z He, X Tao, J Zhou, Y Yang, M Zhao, X Zhang, Z Zheng, T Yuan, P Liu, Y Chen, V Nolan, and X Li. 2016. The shifts of sediment microbial community phylogenetic and functional structures during chromium (VI) reduction. Ecotoxicology 25:1759-1770. Suppl Material: Figures (pdf), Table 1 (xls), Table 2 (xls)
  48. Zhang B, Y Xia, X Wen, X Wang, Y Yang, J Zhou, and Y Zhang. 2016. The Composition and Spatial Patterns of Bacterial Virulence Factors and Antibiotic Resistance Genes in 19 Wastewater Treatment Plants. PLoS ONE 11(12): e0167422. doi:10.1371/journal.pone.0167422. Suppl Material (zip)
  49. Zhang Y, Y Li, B Xie, X Chen, Q Yao, X Zhang, ML Kempher, J Zhou, A Oren, and Q Qin. 2016. Nascent Genomic Evolution and Allopatric Speciation of Myroides profundi D25 in Its Transition from Land to Ocean. mBio. 7:e01945-15. Suppl Material (pdf)
  50. Zhang Y, Q Yang, J Ling, JD Van Nostrand, Z Shi, J Zhou, J Dong. 2016. The shifts of diazotrophic communities in spring and summer associated with coral Galaxea astreata, Pavona decussata and Porites lutea. Front. Microbiol. 7:1870. Suppl Material (pdf)
  51. Zhao M, B Sun, L Wu, Q Gao, F Wang, C Wen, M Wang, Y Liang, L Hale, J Zhou, and Y Yang. 2016. Zonal soil type determines soil microbial responses to maize cropping and fertilization. mSystems. 1(4):e00075-16. DOI: 10.1128/mSystems.00075-16. Suppl Material (pdf)
  52. Zhou JZ, Y Deng, L Shen, C Wen , Q Yan, D Ning, Y Qin, K Xue, L Wu, Z He, JW Voordeckers, JD Van Nostrand, V Buzzard, ST Michaletz, BJ Enquist, MD Weiser, M Kaspari, R Waide, Y Yang, JH Brown. 2016. Temperature mediates continental-scale diversity of microbes in forest soils. Nat Comm. 7:12083. doi:10.1038/ncomms12083. Supplementary Data: OTU Table (zip); Suppl Material (pdf)
  53. Zhu YG, JQ Su , Z Cao, K Xue, J Quensen, GX Guo, YF Yang, J Zhou, HY Chu, and JM Tiedje. 2016. A buried Neolithic paddy soil reveals loss of microbial functional diversity after modern rice cultivation. Sci. Bull. 61:1052-1061. Suppl Material (doc)
  54. Zhang, Y., J. Cong, H. Lu, Y. Deng, X. Liu, J.-Z. Zhou, and D. Li. 2016. Soil bacterial endemism and potential functional redundancy in natural broadleaf forest along a latitudinal gradient. Scientific report, 6: article number 28819; DOI: 10.1038/srep28819.
2015
  1. Azarbad, H, A., M. Niklińska, R. Laskowski, N. van Straalen, C. van Gestel, J.-Z. Zhou, Z. He, C. Wen, and W. Röling. 2015. Microbial community composition and functions are resilient to metal pollution along two forest soil gradients. FEMS Microbiology Ecology, 91:1-11, doi.org/10.1093/femsec/fiu003. Suppl Material (zip)
  2. Cai, M., Y. Nie, C. Chi, Y. Tang, Y. Li, X. Wang, Z. Liu, Y. Yang, J.-Z. Zhou, and X. L. Wu. 2015. Crude oil as a microbial seed bank with unexpected functional potentials. Sci. Reports, 5:16057, doi:10.1038/srep16057. Suppl Material (pdf)
  3. Cong J, Y Yang, X Liu, H Lu, X Liu, J-Z Zhou, D Li, H Yin, J Ding, and Y Zhang. 2015. Analyses of soil microbial community compositions and functional genes reveal potential consequences of natural forest succession. Scientific Reports. 5:10007. Suppl Material (doc)
  4. Dai, J, H Wei, C Tian, FH Damron, J-Z Zhou, and D Qiu. 2015. An extracytoplasmic function sigma factor-dependent periplasmic glutathione peroxidase is involved in oxidative stress response of Shewanella oneidensis. BMC Microbiol 15:34, doi:10.1186/s12866-015-0357-0. Suppl Material (doc)
  5. Deng, J, Y Gu, J Zhang, K Xue, Y Qin, M Yuan, H Yin, Z He, L Wu, EAG Schuur, JM Tiedje, and J-Z Zhou. 2015. Shifts of tundra bacterial and archaeal communities along a permafrost thaw gradient in Alaska. Mol Ecol. 24:222-234. Suppl Material (doc)
  6. Ding, J., Y. Zhang, Y. Deng, C. Yang, T. Yuan, J. D Van Nostrand, D. Li, J.-Z. Zhou, and Yunfeng Yang. 2015. Integrated metagenomics and network analysis of soil microbial community of the forest timberline. Scientific Reports, 5:7994, doi10.1038/srep07994. Suppl Material (pdf)
  7. Ding J, Y Zhang, MM Wang, X Sun, J Cong, Y Deng, H Lu, T Yuan, JD Van Nostrand, D Li, J-Z Zhou and Y Yang. Soil organic matter quantity and quality shape microbial community compositions of subtropical broadleaved forests.Mol Ecol. 24: 5175-5185. Suppl Material (doc)
  8. Dopheide, A, G Lear, Z He, J-Z Zhou, GD Lewis. 2015. Functional gene composition, diversity and redundancy in microbial stream biofilm communities. PLOS One, 10(4): e0123179. Suppl Material (zip)
  9. Hemme CL, Q Tu, Z Shi, Y Qin, W Gao, Y Deng, JD Van Nostrand, L Wu, Z He, PSG Chain, S Green Tringe, MW Fields, E Rubin, JM. Tiedje, TC Hazen, A Arkin, J-Z Zhou. 2015. Comparative metagenomics reveals impact of contaminants on groundwater microbiomes. Front in Microbiol, 6:doi.org/10.3389/fmicb.2015.01205. Suppl Material (pdf)
  10. Huang C, Z Li, F Chen, Q Liu, Y Zhao, J-Z Zhou, and A Wang. 2015. Microbial community structure and function in response to the shift of sulfide/nitrate loading ratio during the denitrifying sulfide removal process. Bioresource Technol. 197:227-234. Suppl Material (pdf)
  11. Huang, C, Y Zhao, Z Lia, Y Yuan, C Chen, W Tan, S Gao, L Gao, J-Z Zhou, A Wang. 2015. Enhanced elementary sulfur recovery with sequential sulfate-reducing, denitrifying sulfide-oxidizing processes in a cylindrical-type anaerobic baffled reactor. Bioresource Tech. 192:478-785.
  12. Leigh, M. B., W.M. Wu, E. Cardenas, O. Uhlik, S. Carroll, T. Gentry, T. L. Marsh, J.-Z. Zhou, P. Jardine, C. S. Ceiddle, J. M. Tiedje. 2015. Microbial communities biostimulated by ethanol during uranium (VI) bioremediation in contaminated sediment as shown by stable isotope probing. Front. Environ. Sci. Engineer., 9:453-464, DOI 10.1007/s11783-014-0721-6
  13. Li X, PL Bond, JD Van Nostrand, J-Z Zhou and L Huang. 2015. From lithotroph- to organotrophdominant: directional shift of microbial community in sulphidic tailings during phytostabilization. Sci Reports. 5:12978, DOI: 10.1038/srep12978. Suppl Material (pdf)
  14. Liang, J, D Li, Z Shi, JM Tiedje, J-Z Zhou, EAG Schuur, KT Konstantinidis, and Y Luo. 2015. Methods for estimating temperature sensitivity of soil organic matter based on incubation data: A comparative evaluation. Soil Biol Biochem. 80:127-135. Suppl Material (pdf)
  15. Liang Y, Y Jiang, F Wang, C Wen, Y Deng, K Xue, Y Qin, Y Yang, L Wu, J-Z Zhou and B Sun. 2015. Long-term soil transplant simulating climate change with latitude significantly alters microbial temporal turnover. ISME J. 9:2561-2572. Suppl Material (pdf)
  16. Liang Y, Wu L, Clark IM, Xue K, Yang Y, Van Nostrand JD, Deng Y, He Z, McGrath S, Storkey J, Hirsch PR, Sun B, Zhou J. 2015. Over 150 years of long-term fertilization alters spatial scaling of microbial biodiversity. mBio6(2):e00240-15. doi:10.1128/mBio.00240-15. Suppl Material (pdf)
  17. Liang, Y, X Zhang, J-Z Zhou, and G Li. 2015. Long-term oil contamination increases deterministic assembly processes in soil microbes. Ecol Applications.25:1235-1243. Supplementary Information (xls)
  18. Lin, J, J Chen, J He, J Chen, Q Yan, J-Z Zhou, and P Xie. 2015. Effects of microcystin-LR on bacterial and fungal functional genes profile in rat gut. Toxicon. 96:50-56. Suppl Material (doc), 
  19. Liu, S., Wang, K. Xue, B. Sun, Y. Zhang, Z. He, J. D. Van Nostrand, J.-Z. Zhou and Y. Yang. The interactive effects of soil transplant into colder regions and cropping on soil microbiology and biogeochemistry, Env. Microbiol. 17:566-576. Suppl Material (doc)
  20. Ma, J, Y Deng, T Yuan, J-Z Zhou, and PJJ Alvarez. 2015. Succession of microbial functional communities in response to a pilot-scale ethanol-blended fuel release throughout the plume life cycle. Environ Poll. 198:154-160. Suppl Material (doc)
  21. MacDonald, CA, MJ Crawley, DJ Wright, J Kuczynski, L Robinson, R knight, WA Al-Soud, SJ Sorenson, Y Deng, J-Z Zhou, and BK Singh. 2015. Identifying qualitative effects of different grazing types on below-ground communities and function in a long-term field experiment. Environ. Microbiol. 17:841-854. Suppl Material (doc)
  22. Michaletz ST, MD Weiser, J-Z Zhou, M Kaspari, BR Helliker, and BJ Enquist. 2015. Plant Thermoregulation: Energetics, Trait–Environment Interactions, and Carbon Economics. Trends in Ecol Evol. 30:714-724. Suppl Material (pdf)
  23. Myung J, WM Galega, JD Van Nostrand, T Yuan, J-Z Zhou, and CS Criddle. Long-term cultivation of a stable Methylocystis-dominated methanotrophic enrichment enabling tailored production of poly(3-hydroxybutyrate-co-3-hydroxyvalerate). Biores Technol. 198:811-818.
  24. Myung J, Z Wang, T Yuan, P Zhang, JD Van Nostrand, J-Z Zhou, and CS Criddle. 2015. Production of nitrous oxide from nitrite in stable Type II methanotrophic enrichments. Environ Sci Technol. 49:10969-10975. Suppl Material (pdf)
  25. Penton, CR, D St. Louis, A Pham, JR Cole, L Wu, Y Luo, EAG Schuur, J-Z Zhou and JM Tiedje. 2015. Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils. Front. Microbiol.6:746. Doi:10.3389/fmicb.2015.00746.  Suppl Material (pdf)
  26. Qu, Y, Q Ma, J Deng, W Shen, X Zhang, Z He, JD Van Nostrand, J Zhou, and J-Z Zhou. 2015. Responses of microbial communities to single-walled carbon nanotubes in phenol wastewater treatment systems. Environ Sci Technol49:4627-4635. Suppl Material (pdf)
  27. Qu Y, X Zhang, Q Ma, J Deng, Y Deng, JD Van Nostrand, L Wu, Z He, Y Qin, J Zhou, and J-Z Zhou. 2015. Microbial community dynamics and activity link to indigo production from indole in bioaugmented activated sludge systems. PLoS ONE, 10(9): e0138455. Suppl Material (pdf)
  28. Saxena, G., E. M. Marzinelli, N. N. Naing, Z. He, Y. Liang, Y. Piceno, S. Mitra, H. Ping, U. M. Joshi, S.Reuben, K. C. Mynampati, S. Mishra, S. Umashankar, .J.-Z. Zhou, G. Andersen, S. Kjelleberg, and S. Swarup. 2015. Ecogenomics reveals metals and land-use pressures on microbial communities in the waterways of a megacity. Environ. Sci & Tech., 49:1462-1472. Suppl Material (pdf)
  29. Sheng, Z, JD Van Nostrand, J-Z Zhou, and Y Liu. 2015. The effects of silver nanoparticles on intact wastewater biofilms. Front. Microbiol. 6:680. doi: 10.3389/fmicb.2015.00680. Suppl Material (pdf)
  30. Shi S, E Nuccio, DJ Herman, R Rijkers, K Estera, J Li, U Nunes da Rocha, Z He, J Pett-Ridge, EL Brodie, J-Z Zhou, and M Firestone. 2015. Successional trajectories of rhizosphere bacterial communities over consecutive seasons. mBio6(4):e00746-15. Suppl Material (pdf)
  31. Shi Y, P Grogan, H Sun, J Xiong, Y Yang, J-Z Zhou, H Chu. 2015. Multi-scale variability analysis reveals the importance of spatial distance in shaping Arctic soil microbial functional communities. Soil Biol Biochem. 86:126-1347. Suppl Material (doc)
  32. Smith MB, AM Rocha, CS Smillie, SW Olesen, C Paradis, L Wu, JH Campbell, JL Fortney, TL Mehlhorn, KA Lowe, JE Earles, J Phillips, SM Techtmann, DC Joyner, DA Elias, KL Bailey, RA Hurt Jr, SP Preheim, MC Sanders, J Yang, MA Mueller, S Brooks, DB Watson, P Zhang, Z He, EA Dubinsky, PD Adams, AP Arkin, MW Fields, J-Z Zhou, EJ Alm, TC Hazen. 2015. Natural bacterial communities serve as quantitative geochemical biosensors. mBio 6: e00326-15. Suppl Material (pdf)
  33. Su, J. Q., L.J. Ding, K. Xue, H. Y. Yao, J. Quensen, S. Bai, W. X. Wei, J.S. Wu, J.-Z. Zhou, J. M. Tiedje, and Y.G. Zhu. 2015. Long-term balanced fertilization increases the soil microbial functional diversity in a phosphorus-limited paddy soil. Mol. Ecol., 24:136-150. Suppl Material (doc)
  34. Trivedi, P., I.J. Rochester, C. Trivedi, J.D. Van Nostrand, J.-Z. Zhou, S. Karunaratne, I.C. Anderson, B.K. Singh. 2015. Soil aggregate size mediates the impacts of cropping regimes on soil carbon and microbial communities. Soil Biol Biochem. 91: 169-181. Suppl Material (pdf)
  35. Tu, Q., M. Yuan, Z. He, Y. Deng, K. Xue, L. Wu, S. Hobbie, P. Reich, and J.-Z. Zhou. 2015. Fungal communities respond to long-term elevated CO2 by community reassembly. Appl. Environ. Microbiol., 81:5445-2454. Suppl Material (pdf)
  36. Wang F, Y Liang, Y Jiang, Y Yang, K Xue, J Xiong, J-Z Zhou, and B Sun. 2015. Planting increases the abundance and structure complexity of soil core functional genes relevant to carbon and nitrogen cycling. Sci Rep. 5:14345. Suppl Material (pdf)
  37. Wang, M., S. Liu, F. Wang, B. Sun, J.-Z. Zhou., and Y. Yang. 2015. Microbial responses to southward and northward Cambisol soil transplant. MicrobiologyOpen, 4:931-940. Suppl Material (doc)
  38. Wang, X, JD Van Nostrand, Y Deng, X Lu, C Wang, J-Z Zhou and X Han. 2015. Scale-dependent effects of climate and geographic distance on bacterial diversity patterns across northern China’s grasslands. FEMS Microbiol Ecol. 91(12). doi: 10.1093/femsec/fiv133. Suppl Material (zip) 
  39. Wang Y, R Zhang, Q Zheng, Y Deng, JD Van Nostrand, J-Z Zhou, and N Jiao. 2015. Bacterioplankton community resilience to ocean acidification: evidence from microbial network analysis. ICES J Mar Sci. 73:865-875.  Suppl Material (zip)
  40. Wei, STS, MA Fernandez-Martinez, Y Chan, JD Van Nostrand, A de los Rios-Murillo, JMY Chiu, AM Ganeshram, SC Cary, J-Z Zhou, and SB Pointing. 2015. Diverse metabolic and stress-tolerance pathways in chasmoendolithic and soil communities of Miers Valley, McMurdo Dry Valleys, Antarctica. Polar Biol. 38:433-443
  41. Wood, S. A., M. Almaraz, M. A. Bradford, K. L. McGuire, S. Naeem, C. Neill, C. A. Palm, K. L. Tully, and J.-Z. Zhou. 2015. Farm management, not soil microbial diversity, controls nutrient loss from smallholder tropical agriculture. Frontiers in Microbiology, 6:90. doi: 10.3389/fmicb.2015.00090. Suppl Material (doc)
  42. Wood, S.A., M. A. Bradford, J. A. Gilbert, K. L. McGuire, C. A. Palm, K. L. Tully, J.-Z. Zhou, and S. Naeem. 2015. Agricultural intensification and the functional capacity of soil microbes on smallholder African farms. J. Applied Ecol. 52:744-752. Suppl Material (doc)
  43. Wu L, C Wen, Y Qin, H Yin, Q Tu, JD Van Nostrand, T Yuan, M Yuan, Y Deng, and J-Z Zhou. 2015. Phasing amplicon sequencing on Illumina Miseq for robust environmental microbial community analysis. BMC Microbiol. 15:125. DOI 10.1186/s12866-015-0450-4. Suppl Material: Figures, Tables, Methods (pdf); Tables 2 (xls)
  44. Xiong, J, Z He, S Shi, A Kent, Y Deng, L Wu, JD Van Nostrand, and J-Z Zhou. 2015. Elevated CO2 shifts the functional structure and metabolic potentials of soil microbial communities in a C4 agroecosystem. Scientific Reports. 5:9316. Suppl Material (pdf)
  45. Xu M, Z He, Q Zhang, J Liu, J Guo, G Sun, and J-Z Zhou. 2015. Responses of aromatic-degrading microbial communities to elevated nitrate in sediments.Environ Sci Technol 49:12422–12431. Suppl Material (pdf)
  46. Xu, T., Y. Li, Z. Shi, C.L. Hemme, Y. Li, Y. Zhu, J.D. Van Nostrand, Z. He, and J.-Z. Zhou. 2015. Efficient Genome Editing in Clostridium cellulolyticum via CRISPR-Cas9 Nickase. Appl. Environ. Microbiol. 81:4423–4431. Suppl Material (pdf)
  47. Xue K, JD Van Nostrand, J Vangronsveld, N Witters, JO Janssen, J Kumpiene, G Siebielec, R Galazka, L Giagnoni, M Arenella, JZ Zhou, G Renella. 2015. Management with willow short rotation coppice increase the functional gene diversity and functional activity of a heavy metal polluted soil. Chemosphere, 138:469-477. Suppl Material (doc)
  48. Yan Q, Y Bi, Y Deng, Z He, L Wu, JD Van Nostrand, Z Shi, J Li, X Wang, Z Hu, Y Yu, and J-Z Zhou. 2015. Impacts of the Three Gorges Dam on microbial structure and potential function. Sci Rep 5:8605. doi:10.1038/srep08605. Suppl Material (pdf)
  49. Yang, C., Y. Li, B.Y. Zhou, Y. Zhou, W. Zheng, Y. Tian, J.D. Van Nostrand, L. Wu, Z. He, J.-Z. Zhou, and T. Zheng. 2015. Illumina sequencing-based analysis of bacterial community dynamics during Akashiwo sanguine bloom in Xiamen sea, China. Sci Rep, 5: doi:10.1038/srep08476. 
  50. Yin H, J Niu, Y Ren, J Cong, X Zhang, F Fan, Y Xiao, X Zhang, J Deng, M Xie, Z He, J-Z Zhou, Y Liang, and X Liu. 2015. An integrated insight into the response of sedimentary microbial communities to heavy metal contamination. Sci Rep. 5:14266. Suppl Material: Figures (pdf); Tables (xls)
  51. Yue, H., M. Wang, S. Wang, J. A. Gilbert, X. Sun, L. Wu, Q. Lin, Y. Hu, X. Li, Z. He, J.-Z. Zhou, and Y. Yang. The microbe-mediated mechanisms affecting topsoil carbon stock in Tibetan grasslands. ISME J, 9:2012-2020. Suppl Material (doc)
  52. Zhang, P, JD Van Nostrand, Z He, R Chakraborty, Y Deng, D Curtis, M Fields, TC Hazen, AP Arkin, and J-Z Zhou. A slow-release substrate stimulates groundwater microbial communities for long-term in-situ Cr(VI) reduction. Eviron Sci Technol. 49:12922-12931. Suppl Material (pdf)
  53. Zhang, P, WM Wu, JD Van Nostrand, Y Deng, Z He, T Gihring, G Zhang, CW Schadt, D Watson, P Jardine, CS Criddle, S Brooks, TL Marsh, JM Tiedje, AP Arkin, and J-Z Zhou. 2015. Dynamic succession of groundwater functional microbial communities in response to emulsified vegetable oil amendment during sustained in situ U(VI) reduction. Appl Environ Microbiol. 81:4164-4172. Suppl Material (pdf)
  54. Zhang, Y, J Cong, H Lu, G Li, Y Xue, Y Deng, H Li, J-Z Zhou and D Li. 2015. Soil bacterial diversity patterns and drivers along an elevational gradient on Shennongjia Mountain, China. Microbial Biotech. 8:739-746. Supplementary Data: Fastq files (zip) - Forward, Reverse, Barcodes; Suppl Material (doc)
  55. Zhang, Y., J. Ling, Q.S. Yang, C. Q. Wen, Q.Y. Yan, H.Y. Sun, J. Van Nostrand, Z. Shi, J.-Z. Zhou, J.D. Dong. 2015. The functional gene composition and metabolic potential of coral-associated microbial communities. Sci Report. 5: 16191. Suppl Material (pdf)
  56. Zhang, Y, Z Tian, M Liu, ZJ Shi, L Hale, J-Z Zhou, and M Yang. 2015. High concentrations of the antibiotic spiramycin in wastewater lead to high abundance of ammonia-oxidizing archaea in nitrifying populations. Environ Sci Technol. 49:9124-9132. Suppl Material (pdf)
  57. Zhang, Z, H Wang, J-Z Zhou, H Li, Z He, JD Van Nostrand, Z Wang, and X Xu. 2015. Redox potential and microbial functional gene diversity in wetland sediments under simulated warming conditions: implications for phosphorus mobilization. Hydrobiolia. 743:221-235. Suppl Material (doc)
  58. Zhou, A, KL Hillesland, Z He, W Schackwitz, Q Tu, GM Zane, Q Ma, Y Qu, DA Stahl, JD Wall, TC Hazen, MW Fields, AP Arkin, and J-Z Zhou. 2015. Rapid selective sweep of pre-existing polymorphisms and slow fixation of new mutations in experimental evolution of Desulfovibrio vulgaris. ISME J. 9:2360-2372. Suppl Material (pdf)
  59. Zhou, J., Z. He, Y. Yang, Y. Deng, S.G. Tringe and L. Alvarez-Cohen. 2015. High-throughput metagenomic technologies for complex microbial community analysis: Open and closed formats. mBio, 6:1e02288-14
2014
  1. Antony-Babu, S., A. Deveau, J. D Van Nostrand, J.-Z. Zhou, F. L. Tacon, C. Robin, P. Frey-Klett, S. Uroz. 2014. Selection of specific bacterial communities by the Black truffle Tuber melanosporum during its development and ascocarp maturation. Environ. Microbiol., 16:2831-2847. Supplementary Data: GeoChip data (xls); Suppl Material: Tables1 (xls), Tables2 (xls), Figures and Tables (pdf)
  2. Bartley, L, T Xu, C Zhang, H Nguyen, and J-Z Zhou. 2014. Switchgrass biomass content, synthesis, and biochemical conversion to biofuels. In: H Luo, Y Wu, and C Kole (eds) Compendiou of Bioenergy Plants: Switchgrass. CRC Press
  3. Chen, Y., J. S. Pettis, M. Corona, W. Chen, C. Li, M. Spivak, P. K. Visscher, G. DeGrandi-Hoffman, H. Boncristiani, Y. Zhao, D. van Engelsdorp, K. Delaplane, L. Solter, F. Drummond, M. Kramer, W. I. Lipkin , G. Palacios, M. C. Hamilton, B. Smith, S. Huang, H. Zheng, J. Li , X. Zhang, A. Zhou, L. Wu, J.-Z. Zhou, M.-L. Lee, E. W. Teixeira, Z. Li, JD. Evans. 2014. Israeli acute paralysis virus: epidemiology, pathogenesis and implications for honey bee health. PLoS Pathogens, 10(7):e1004261.  Suppl Material (zip)
  4. Chen Y, N Qin, J Guo, G Qian, D Fang, D Shi, M Xu, F Yang, Z He, JD Van Nostrand, T Yuan, Y Deng, J-Z Zhou and L Li. 2014. Functional gene arrays-based analysis of fecal microbiomes in patients with liver cirrhosis. BMC Genomics. 15:753. Suppl Material (pdf)
  5. Chu, H., S. Wang, H. Yue, Q. Lin, Y. Hu, X. Li, J.-Z. Zhou and Y. Yang. Contrasting soil microbial community structures in two major landscapes of the Tibetan alpine meadow, Microbiology Open, 3(5):585-594. Suppl Material (doc)
  6. Deng, Y and Z He. 2014. Microarray data analysis. In: Z He (ed) Microarrays: Current Technology, Innovations and Applications, Caister Academic Press
  7. Diaz, M. R., J. D. Van Nordstrand, G.P. Eberli, A. M. Piggot, J.-Z. Zhou, and J. S. Klaus. 2014. Functional Gene Diversity of Oolitic Sands from Great Bahama Bank. Geobiology, 12: 231-249. Suppl Material (pdf)
  8. Gao, Y. S. Wang, D. Xu, H. Yu, L. Wu, Q. Lin, Y. Hu, X. Li, Z. He, Y. Deng, J.-Z. Zhou, and Y. Yang. 2014. GeoChip as a Metagenomics Tool to Analyze the Microbial Gene Diversity along an Elevation Gradient, Genomics Data, 2:132-134. Supplementary Data: Microarray data (txt)
  9. He, Z.; J. Xiong, A. D Kent, Y. Deng, K. Xue, G. Wang, L. Wu, J. D Van Nostrand, and J.-Z. Zhou. 2014. Distinct responses of soil microbial communities to elevated CO2 and O3 in a soybean agro-ecosystem. ISME J 8:714-726. Suppl Material (pdf)
  10. He, Z and J-Z Zhou. 2014. Microarrays for microbial community analysis at a glance. In: Z He (ed) Microarrays: Current Technology, Innovations and Applications, Caister Academic Press
  11. Hillesland, KL, S Lim, JJ Flowers, S Turkarslan, N Pinel, GM Zane, N Elliott, Y Qin, L Wu, NS Baliga, J-Z Zhou, JD Wall and DA Stahl. 2014. Erosion of functional independence early in the evolution of a microbial mutualism. Proc Nat Acad Sci USA. 111(4):14822-14827. Suppl Material (pdf)
  12. Jia, X., X. Zhou, Y. Luo, K Xue, X. Xue, X. Xu, Y. Yang, L. Wu, and J.-Z. Zhou. 2014. Effects of substrate addition on soil respiratory carbon release under long-term warming and clipping in a tallgrass prairie. PLosOne, 9:e114203, doi: 10.1371/journal.pone.0114203
  13. Kappell, A.D., Y. Wei, R. J. Newton, J. D. Van Nostrand, J.-Z. Zhou, S. L. McLellan, and K. R. Hristova. 2014. The polycyclic aromatic hydrocarbon degradation potential of Gulf of Mexico native coastal microbial communities after the Deepwater Horizon oil spill. Front. Microbiol., 5:205. Supplementary Data: Microarray Data (xlsx); Suppl Material (pdf)
  14. Kuramae, E.E., J. Z. Zhou, G. A. Kowalchuk, and J. A. van Veen. 2014. Soil-borne microbial functional structure across different land uses. Scientific World J. vol. 2014, Article ID 216071, 8 pages, doi:10.1155/2014/216071
  15. Levy, O., B. A. Ball, B. Bond-Lamberty, K. S. Cheruvelil, A. O. Finley, N. Lottig, S. W. Punyasena, J. Xiao, J.-Z. Zhou, L. B. Buckley, C. T. Filstrup, T. Keitt, J. R. Kellner12, Alan K. Knapp, A. D. Richardson, C. Stow, D. Tcheng, M. Toomey, R. Vargas, J. W. Voordeckers, T. Wagner, and J. W. Williams. 2014. Approaches for advancing scientific understanding of macrosystems. Front. Ecol. Environ. 12: 15–23. Suppl Material (pdf)
  16. Li, X., J. Rui, J. Xiong, J. Li, Z. He, J.-Z. Zhou, A. C. Yannarell, and R. I. Mackie. 2014. Functional potential of soil microbial communities 1 in the maize rhizosphere. PlosOne, DOI: 10.1371/journal.pone.0112609, 9(11):e112609. Suppl Material (zip)
  17. Li Y, J He, Z He, Y Zhou, M Yuan, X Xu, F Sun, C Liu, J Li, W Xie, Y Deng, Y Qin, JD Van Nostrand, L Xiao, L Wu, J-Z Zhou, W Shi, and X Zhou. 2014. Phylogenetic and functional gene structure shifts of the oral microbiomes in periodontitis patients. ISME J. 8:1879-1891. Suppl Material ( pdf)
  18. Li, Y., T. Xu, T. J. Tschaplinski, N. L. Engle, Y. Yang, D. E. Graham, Z. He, and J.-Z. Zhou. 2014. Improvement of cellulose catabolism in Clostridium cellulolyticum by sporulation abolishment and carbon alleviation. Biotechnol Biofuels., 7:25. DOI: 10.1186/1754-6834-7-25. Suppl Material (pdf)
  19. Liang, B., H. Cheng, J. D. Van Nostrand, J. Ma, H. Yu, D. Kong, W. Liu, N. Ren, L. Wu, A. Wang, D. Lee, and J.-Z. Zhou. 2014. Microbial Community Structure and Function of Nitrobenzene Reduction Biocathode in Response to Carbon Source Switchover. Water Res., 54:137-48. Suppl Material (docx)
  20. Liang Y, H Zhao, X Zhang, J-Z Zhou, and G Li. 2014. Contrasting microbial functional genes in two distinct saline-alkali and slightly acidic oil-contaminated sites. Sci Tot Environ. 487:272-278.
  21. Luo, C., L. M. Rodriguez-R, E. R. Johnston, L. Wu, L. Cheng, K. Xue, Q. Tu, Y. Deng, Z. He, J. Z. Shi, M. M. Yuan, S. A. Rebecca, D. Li, Y. Luo, E. A.G. Schuur, P. Chain, J. M. Tiedje, J.-Z. Zhou, and K. T. Konstantinidis. 2014. Soil microbial community responses to a decade of warming as revealed by comparative metagenomics. Appl. Environ. Microbiol. 80: 1777-1786. Suppl Material (pdf)
  22. Paula, F. S., J. L. M. Rodrigues, J.-Z. Zhou, L. Wu, R. C. Mueller, B. S. Mirza, B. J. M. Bohannan, Klaus Nüsslein, Y. Deng, J. M. Tiedje, and V. H. Pellizari. 2014. Land use change alters functional gene diversity, composition and abundance in Amazon forest soil microbial communities. Mol. Ecol. 23:2988-2999. Supplementary Data: Microarray data (xlsx); Suppl Material (pdf)
  23. Probst, AJ, PY Lum, B John, EA Dubinsky, YM Piceno, LM Tom, GL Andersen, Z He and TZ DeSantis. 2014. Microarray of 16S rRNA gene probes for quantifying population differences across microbiome samples. In: Z He (ed) Microarrays: Current Technology, Innovations and Applications, Caister Academic Press
  24. Qin, Q.L., B. Xie, X. Zhang, X. Chen, B. Chen, J.-Z. Zhou, A. Oren, and Y. Zhang. 2014. A proposed genus boundary for the prokaryotes based on genomic insights. J. Bacteriol. 96: 2210-2215. Suppl Material (pdf)
  25. Singh, B., C. Quince, C. A. Macdonald, A. Khachane, W. A. Al-Soud, N. Thomas, S. J Sørensen, Z. He, D. White, A.Sinclair, B. Crooks J.-Z. Zhou and C. D. Campbell. 2014. Loss of microbial biodiversity in soils is coincident with reductions in some specialized functions. Environ. Microbiol. 16(8):2408-2402. Suppl Material (pdf)
  26. Sun, Y., Y. Shen, P. Liang, J.-Z. Zhou, Y. Yang and X. Huang, 2014, Linkages between microbial functional potential and wastewater constituents in large-scale membrane bioreactors for municipal wastewater treatment, Water Research, 56: 162-171. Suppl Material (pdf)
  27. Tu, Q, Y Deng, J-Z Zhou, and Z He. 2014. Development and evaluation of functional gene arrays with GeoChip as an example. In: Z He (ed) Microarrays: Current Technology, Innovations and Applications, Caister Academic Press
  28. Tu, Q., H. Yu, Z. He, Y. Deng, L. Wu, J. D. Van Nostrand, A. Zhou, J. Voordeckers, Y.-J. Lee, Y. Qin, C. Hemme, Z. Shi, K. Xue, T. Yuan, A. Wang, and J.-Z. Zhou. 2014. GeoChip 4: a functional gene arrays-based high throughput environmental technology for microbial community analysis. Mol. Ecol. Resource 14(5):914-928. Supplementary Data: Microarray data (zip); List of gene families (xlsx); Suppl Material (doc)
  29. Tu, Q., Z. He, Y. Li, Y. Chen, Y. Deng, L. Lin, C. L. Hemme, T. Yuan, J. D. Van Nostrand, L. Wu, X. Zhou, W. Shi, L. Li, J. Xu, and J.-Z. Zhou. 2014. Development of HuMiChip for Functional Profiling of Human Microbiomes. PLoSOne, 9: e90546. doi:10.1371/journal.pone.0090546. Supplementary data: HumiChip data (zip); Suppl Material (zip)
  30. Tu, Q., Z. He, and J.-Z. Zhou. 2014. Strain/Species identification in metagenomes using genome-specific markers. Nucl. Acid Res., 42: E67-E67 (Editor picks by Genomeweb). Suppl Material (zip)
  31. Van Nostrand J and J-Z Zhou. 2014. Applications of functional gene microarrays for profiling microbial communities. In, V Garcia-Canas, A Cifuentes, and C Simo, eds, Comprehensive Analytical Chemistry: Applications of Advanced Omics Technologies: From Genes to Metabolites, Elsevier, Amsterdam, The Netherlands
  32. Van Nostrand, JD and J-Z Zhou. 2014. GeoChip applications in bioremediation studies. In: Z He (ed) Microarrays: Current Technology, Innovations and Applications, Caister Academic Press
  33. Varrone*, C., J. D. Van Nostrand*, W. Liu, B. Y. Zhou, Z. Wang, F. Liu, Z. He, L. Wu, J.-Z. Zhou, and A. Wang. 2014. Metagenomic-based analysis of biofilm communities for electrohydrogenesis: From wastewater to hydrogen. Intl. J. of Hydrogen Energy. 39: 222-4233 (*Equal contribution) Suppl Material (docx)
  34. Vigneron, A, P Cruaud, P Pignet, J-C Caprais, N Callac, M Ciobanu, A Godfroy, EG Roussel, BA Cragg, RJ Parkes, JD Van Nostrand, Z He, J-Z Zhou, and L Toffin. 2014. Phylogenetic and functional diversity of microbial communities associated with subsurface sediments of the Sonora Margin, Guaymas Basin.PLOS One, 9(8): e104427. Suppl Material (zip)
  35. Wakelin, S. E. Gerard, A. Black, K. Hamonts, L. Condron, T. Yuan, J. van Nostrand, J.-Z. Zhou, and Maureen O’Callaghan. 2014. Mechanisms of pollution induced community tolerance in a soil microbial community exposed to Cu. Environmental Pollution, 190: 1-9.
  36. Wang, C, X Wang, D Liu, H Wu, X Lu, Y Fang, W Cheng, W Luo, P Jiang, J Shi, H Yin, J-Z Zhou, X Han and E Bai. 2014. Aridity threshold in controlling ecosystem nitrogen cycling in arid and semi-arid grasslands. Nature Comm. 5:4799. DOI: 10.1038/ncomms5799. Suppl Material (pdf)
  37. Wang, F. J.-Z. Zhou, and B. Sun. 2014. Structure of functional ecological networks of soil microbial communities for nitrogen transforming and its response to cropping in major soils in Eastern China. Chinese Science Bulletin, 59: 387-396 (In Chinese)
  38. Wang, X., X. Yu, X. Wen, Y. Yang, and J.-Z. Zhou. 2014. Microbial community functional structures in wastewater treatment plants as characterized by GeoChip. PLoS One, 9: e93422. doi:10.1371/journal.pone.0093422. Suppl Material (doc)
  39. Xia, Y., X. Wang, X. Wen, K. Ding, J.-Z. Zhou, Y. Yang, and Y. Zhang. 2014. Overall functional gene diversity of microbial communities in three full-scale activated sludge bioreactors, Appl. Microbiol. Biotechnol. DOI: 10.1007/s00253-014-5791-7, 98(16):7233-7242. Suppl Material (pdf)
  40. Xu, M., Q. Zhang, C. Xia, Y. Zhong, G. Sun, J. Guo, T. Yuan, J.-Z. Zhou, and Z. He. 2014. Elevated nitrate enriches microbial functional genes for potential bioremediation of complexly contaminated sediments. ISME J. 8:1932-1944. Suppl Material (pdf)
  41. Xu, T., Y. Li, Z. He, and J.-Z. Zhou. 2014. Dockerin-containing protease inhibitor protects key cellulosomal cellulases from proteolysis in Clostridium cellulolyticum. Mol. Microbiol., 91: 694-705. Suppl Material (docx)
  42. Xu, T., Y. Li, J. D. Van Nostrand, Z. He, and J.-Z. Zhou. 2014. Cas9-Based Tools for Targeted Genome Editing and Transcriptional Control. Appl. Environ. Microbiol. 80: 1544-1552. (Review) Suppl Material (pdf)
  43. Xu, X, C Chen, A Wang, H Yu, X Zhou, H Guo, Y Yuan, D Lee, J-Z Zhou, N Ren. 2014. Bioreactor performance and functional gene analysis of microbial community in a limited-oxygen fed bioreactor for co-reduction of sulfate and nitrate with high organic input. J Haz Mat 278:250-257. Suppl Material (docx)
  44. Xue, K Z He, JD Van Nostrand, and J-Z Zhou. 2014. GeoChip analysis of soil microbial community responses to global change. In: Z He (ed) Microarrays: Current Technology, Innovations and Applications, Caister Academic Press,
  45. Xue, K., J. D. Van Nostrand, Z. He and J.-Z. Zhou. 2014. Functional Molecular Analysis of Microbial Nitrogen Cycle by Microarray-based GeoChip: Insights for Climate Change, Agriculture and Other Ecological Studies. In: D. Marco (ed) Metagenomics of the Microbial Nitrogen Cycle: Theory, Methods and Applications. Caister Academic, Poole, UK. (out Sept. 2014)
  46. Yang F, Ning K, X. Chang, X. Yuan, Q. Tu, Y. Tong, Y. Deng, C. L. Hemme, J. Van Nostrand, X. Cui, Z. He, Z. Chen, D. Guo, J. Yu, Y. Zhang, J.-Z. Zhou, and J. Xu. 2014. Saliva microbiota carry caries-specific functional gene signatures.PLoS One, 9(2):e76458  Supplementary Data: HumiChip data (xls); Suppl Material (zip)
  47. Yang, Y., Y. Gao, Q. Lin, D. Xu, H. Yu, L. Wu, Y. Hu, X. Li, Z. He, Y. Deng, S. Wang and J.-Z. Zhou. 2014. The microbial gene diversity along an elevation gradient of the Tibetan grassland, ISME J, 8: 430-440. Suppl Material (pdf)
  48. Yu, H, C Chen, J Ma, W Liu, J-Z Zhou, D Lee, N Ren, A Wang. 2014. GeoChip-based analysis of the microbial community functional structures in simultaneous desulfurization and denitrification process. J Environ Sci. 26:1375-1382.
  49. Yuan, Y, C Chen, B Liang, C Huang, Y Zhao, X Xu, W Tan, X Zhou, S Gao, D Sun, D Lee, J-Z Zhou, and A Wang. 2014. Fine-tuning key parameters of an integrated reactor system for the simultaneous removal of COD, sulfate and ammonium and elemental sulfur reclamation, J Haz Mat. 269:56-67.  Suppl Material (doc)
  50. Zhang, Y, J Cong, H Lu, G Li, Y Qu, X Su, J-Z Zhou, and D Li. 2014. Community structure and elevational diversity patterns of soil Acidobacteria. J Environ Sci.26(8):1717-1724. Suppl Material (doc)
  51. Zhang Y., J. Cong, H. Lu, C. Yang, Y. Yang, J.-Z. Zhou, and D. Li. 2014. An integrated study to analyze soil microbial community structure and metabolic potential in two forest types. PLoS One, 9: e93773. doi:10.1371/journal.pone.0093773. Suppl Material (zip)
  52. Zhao, J, J Zuo, X Wang, J Lin, Y Yang, J-Z Zhou, H Chu, and P Li. 2014. GeoChip-based analysis of microbial community of a combined nitritation-anammox reactor treating anaerobic digestion supernatant. Water Res.67:345-354. Suppl Material (doc)
  53. Zhao, M., F. Wang, S. Liu, K. Xue, Y. Liang, S. Bai, Z. He, J.D. van Nostrand, J.-Z. Zhou, and Y. Yang, B Sun. GeoChip profiling of microbial community in response to global changes simulated by soil transplant and cropping, Genomics Data, 2:166-169.
  54. Zhao, M., K. Xue, F. Wang, S. Liu, S. Bai, B. Sun, J.-Z. Zhou and Y. Yang. Microbial mediation of biogeochemical cycles revealed by simulation of global changes with soil transplant and cropping, ISME J. 8(10):2045-2055. Suppl Material (doc)
  55. Zhou, J.-Z., Y. Deng, P. Zhang, K. Xue, Y. Liang, J. D. Van Nostrand, Y. Yang, Z. He, L. Wu, D. A. Stahl, T. C. Hazen, J. M Tiedje, and A. P. Arkin. 2014. Stochasticity, Succession and Environmental Perturbations in a Fluidic Ecosystem. Proc. Nat. Acad. Sci. USA, 111: E836-E845,  doi:10.1073/pnas.1324044111 (Selected as an Editors’ Pick, http://www.pnas.org/site/media/current.xhtml#processes) (Also Editor picks by Genomeweb). Suppl Material (pdf)
  56. Zimmerman, N., J. Izard, C. Klatt, and J.-Z. Zhou and E. Aronson. 2014. The Unseen World: environmental microbial sequencing and identification methods for ecologists. Front Ecol Environ, 12: 224-231. Supplementary Information (pdf)
2013
  1. Bai, S. J. Li, Z. He, J.D. van Nostrand, Y. Tian, G. Lin, J.-Z. Zhou and T. Zheng. 2013. GeoChip-based analysis of the functional gene diversity and metabolic potential of soil microbial communities of mangroves. Appl. Microbiol. Biotech. 97: 7035-7048. Supplementary Information (doc).
  2. Bartley, L.E., M. L. Peck, S. R. Kim, B. Ebert, C. Manisseri, D. M. Chiniquy, R. Sykes, L. Gao, C. Rautengarten, M. E. Vega-Sánchez, P. I. Benke, P. E. Canlas, P. Cao, S. Brewer, F. Lin, W. L. Smith, X. Zhang, R. E. Jentoff, S. B. Foster, J.-Z. Zhou, A. Ziebell, G. An, H. V. Scheller, P. C. Ronald. 2013. Overexpression of a BAHD Acyltransferase, OsAt10, alters rice cell wall hydroxycinnamic acid content and saccharification. Plant Physiology, 161: 1615-1633. Suppl Material: Table S1 (xls), Tables (pdf), Figures (pdf)
  3. Chan, Y., J. D. Van Nostrand3, J.-Z. Zhou, S. B. Pointing, and R. L. Farrell. 2013. Functional ecology of an Antarctic Dry Valleys landscape. Proc. Nat. Acad. Sci, 110: 8990-8995. doi: 10.1073/pnas.1300643110. Supplementary Data: Microarray data (xls), Suppl Material (pdf)
  4. Deng Y., Yang Y., He Z., Zhou J. 2013. Molecular ecological network of microbial communities. In: Nelson K. (Ed.) Encyclopedia of Metagenomics: SpringerReference (www.springerreference.com). Springer-Verlag Berlin Heidelberg, 2013. 2013-03-06 15:51:49 UTC
  5. Eisenlord, S., Z. Freedman, D. Zak, K. Xue, Z. He, and J.-Z Zhou. 2013. Microbial mechanisms mediating increased soil C storage under elevated atmospheric N deposition. Appl. Environ. Microbiol., 79: 1191-1199. Suppl Material (pdf)
  6. Freedman, Z., S. D. Eisenlord, K. Xue, D. R. Zak, and J.-Z. Zhou. 2013. Towards a molecular understanding of N cycling in northern hardwood forests under future rates of N deposition. Soil Biol. Biochem., 66:130-138. Suppl Material (pdf)
  7. He Z., Van Nostrand J., Zhou J. 2013. GeoChip-based metagenomics technologies for analyzing microbial community functional structure and activities. In: Nelson K. (Ed.) Encyclopedia of Metagenomics: SpringerReference (www.springerreference.com). Springer-Verlag Berlin Heidelberg, 2013. 2013-03-06 15:48:27 UTC
  8. He, Z., J. Xiong, A. D. Kent, G. Wang, L. Wu, J. D. Van Nostrand, and J.-Z. Zhou. 2013. Distinct responses of soil microbial communities to elevated CO2 and O3 in a soybean agro-ecosystem. ISME J, 8: 714-726, doi:10.1038/ismej.2013.177. Suppl Material (pdf)
  9. Jiang, H. Q. He, Z. He, C. L. Hemme, L. Wu, and J.-Z. Zhou. 2013. Continuous Cellulosic Bioethanol Fermentation by Cyclic Fed-Batch Co-Cultivation. Appl. Environ. Microbiol., 79: 1580-1589. Suppl Material (pdf)
  10. Kang*, S.K., J. Van Nostrand*, H. Gough, Z. He, T. C. Hazen, D.A. Stahl, and J.-Z. Zhou. 2013. Functional gene array-based analysis of microbial communities in heavy metals contaminated lake sediments. FEMS Microbiology Ecology, 86: 200-214.*Authors contributed equally to this work. Supplementary Data: Microarray data (xlsx); Suppl Material: Tables (xls), Figures (pdf), Info (doc)
  11. Lee, Y.-J., J. D. van Nostrand, Q. Tu, Z. Lu, L. Cheng, T. Yuan, Y. Deng, M. Q. Carter, Z. He, L. Wu, F. Yang, J. Xu, and J.-Z. Zhou. 2013. The PathoChip, a functional gene array for assessing pathogenic properties of diverse microbial communities. ISME J., 7: 1974-84, doi: 10.1038/ismej.2013.88. Suppl Material: Info (pdf), Figures (pdf)
  12. Li, D., C. Schadel, R., M.L. Haddix, E.A. Paul, R. Conant, J.W. Li, J.Z. Zhou, and Y.Q. Luo. 2013. Differential responses of soil organic carbon fractions to warming: Results from an analysis with data assimilation. Soil Biol. & BioChem., 67: 24-30. Suppl Material (pdf)
  13. Li, D., X. Zhou, L. Wu, J.-Z. Zhou, and Y. Luo. 2013. Contrasting responses of heterotrophic and autotrophic respiration to experimental warming in a winter annual-dominated prairie. Glob Change Biol, 19;3553–3564, doi:10.1111/gcb.12273. Suppl Material (docx)
  14. Li, M.; J. Mathieu, Y. Yang, Yu; S. Fiorenza, Y. Deng, Z. He, J.-Z. Zhou, P. Alvarez. 2013. Widespread distribution of soluble di-iron monooxygenase (SDIMO) genes in Arctic groundwater impacted by 1,4-dioxane. Environ. Sci & Technol., 47:9950-9958. Suppl Material (pdf)
  15. Li, X.Y., Y. Deng, Q. Li, C. Lu, J. Wang, H.W. Zhang, J.G Zhu, J.-Z. Zhou, and Zhili He. 2013. Shifts of functional gene representation in rhizosphere microbial communities under elevated ozone. The ISME J, 7: 660-71. Suppl Material (pdf)
  16. Lin, L, Y. Ji, Q. Tu, R. Huang, L.Teng, X. Zeng, H. Song, K. Wang, Q. Zhou, Y. Li, Q. Qiu, Z. He, J.-Z. Zhou, J. Xu. 2013. Microevolution from Shock to Adaptation Revealed Strategies Improving Ethanol Tolerance and Production in Thermoanaerobacter. Biotechnol Biofuels, 6:103 doi:10.1186/1754-6834-6-103. Suppl Material: Figures (pdf), Tables 1 (xls), 2 (xls), 3 (xls), 4 (xls) 
  17. Penton, C.R., D. St. Louis, Y. Luo, J. Cole, L. Wu, J.-Z. Zhou, T. Schuur, J.-M. Tiedje. 2013. Fungal diversity in permafrost and tallgrass prairie soils under experimental warming. Appl. Environ. Microbiol., 79: 7063-7072. Suppl Material (pdf)
  18. Qiu, D., H. Wei, Q. Tu, Y. Yang, M. Xie, J. Chen, M. H. Pinkerton, Y. Liang, Z. He, and J.-Z. Zhou. 2013. Combined genomics and experimental analyses of respiratory characteristics of Shewanella putrefaciens W3-18-1. Appl. Environ. Microbiol., 79: 5250-5257. Suppl Material (pdf)
  19. Siering, P.L., G. V. Wolfe, M. S. Wilson, A. N. Yip, C. M. Carey, C. D. Wardman, R. S. Shapiro, K. M. Stedman, J. Kyle, T. Yuan, J. D. Van Nostrand, Z. He, and J.-Z. Zhou. 2013. Microbial biogeochemistry of boiling springs lake: a physically dynamic, oligotrophic, low pH geothermal ecosystem. Geomicrobiology, 11: 356-376. Suppl Material: Figures (pdf), Videos (link)
  20. Somenahally, A.C., J. J. Mosher, T. Yuan, M. Podar, T. J. Phelps, S. D. Brown, Z. K. Yang, T. C. Hazen, A. P. Arkin, A. V. Palumbo, J. D. Van Nostrand, J.-Z. Zhou, and D. A. Elias. 2013. Hexavalent chromium reduction under fermentative conditions with lactate stimulated native microbial communities. PLoS One, 8: 8(12): e83909 DOI: 10.1371/journal.pone.0083909. Suppl Material (docx)
  21. Sul, W. J., S. Asuming-Brempong, Q. Wang, D. M. Tourlousse, C. R. Penton, Y. Deng, J. L. M. Rodrigues, S. G.K. Adiku, J. W. Jones, J.-Z. Zhou, J. R. Cole, and J. M. Tiedje. 2013. Tropical agricultural land management influences on soil microbial communities through its effect on soil organic carbon. Soil Biol. & Biochem., 65:33-38. Suppl Material (docx)
  22. Tu Q, Z. He, Y. Deng, and J.-Z. Zhou. 2013. Strain/species-specific probe design for microbial identification microarrays. Appl Environ Microbiol. 79: 5085-5088. Suppl Material: Table 1 (xls), Table 2 (xls)
  23. Van Nostrand, J. D, T. J. Gentry, and J.-Z. Zhou. 2013. Microarray-Based Microbial Identification and Characterization. In Y.-W. Tang and C. W. Stratton (eds) Advanced Techniques in Diagnostic Microbiology, 2nd ed., Springer, New York, NY (Invited).
  24. Wakelin, S.A., B.I.P. Barratt, E. Gerard; A. L. Gregg, E. L. Brodie, G. L. Andersen, T. Z. DeSantis, J.-Z. Zhou, Z.H. He, G. A. Kowalchuk, M. O’Callaghan. 2013. Shifts in the phylogenetic structure and functional capacity of soil microbial communities follow alteration of native tussock grassland ecosystems. Soil Biology & Biochemistry, 57:675-682. DOI:10.1016/j.soilbio.2012.07.003. Suppl Material: Figures (pdf), Table 1 (xls), Table 2 (xls)
  25. Xu, C., R. Huang, L. Teng, D. Wang, C. L. Hemme, I. Borovok, Q. He, R.l Lamed, E. A. Bayer, J.-Z. Zhou, and J. Xu. 2013. Structure and regulation of the cellulose degradome in Clostridium cellulolyticum. Biotechnology for Biofuels. 6:73 DOI: 10.1186/1754-6834-6-73. Suppl Material: Figures (pdf), Tables 1 (xls), 2 (xls), 3 (xls), 4 (xls) 
  26. Xu, M., Z. He, Y. Deng, L. Wu, J.D. van Nostrand, S. E. Hobbie, P. B. Reich, and J.-Z. Zhou. 2013. Elevated CO2 influences microbial carbon and nitrogen cycling. BMC Microbiology, 13:124. DOI: 10.1186/1471-2180-13-124. Suppl Material (pdf)
  27. Xu M, Y. Fang, J. Liu, X. Chen, G. Sun, J. Guo, Z. Hua, Q. Tu, L. Wu, J.-Z. Zhou, X. Liu. 2013. Draft genome sequence of Shewanella decolorationis S12, adye-degrading bacterium isolated from a water treatment plant. Genome Announce. 1(6):e00993-13. doi:10.1128/genomeA.00993-13.
  28. Xue, K. L. Wu, Y. Deng, Z. He, J. Van Nostrand, G. P. Robertson, T. M. Schmidt, and J.-Z. Zhou. 2013. Functional gene differences in soil microbial communities from conventional, low-input and organic farmlands. Appl. Environ. Microbiol., 79:1284-1294. Suppl Material (pdf)
  29. Yang, Y.F., L. W. Wu, Q. Lin, M.Y. Yuan, D.P Xu, H. Yu, Y.G. Hu, J.C. Duan, X.Z. Li, Z.L. He, K. Xue, S.P. Wang, and J.-Z. Zhou. 2013. Responses of the functional structure of soil microbial community to livestock grazing in the Tibetan alpine grassland, Glob Change Biol, 19: 637–648. Supplementary Data: GeoChip Data (xls); Suppl Material (docx)
  30. Yang, Y., J. Chen, D. Qiu, and J.-Z. Zhou. 2013. Roles of UndA and MtrC of Shewanella putrefaciens W3-18-1 in iron reduction. BMC Microbiol, 13:267. DOI: 10.1186/1471-2180-13-267. Suppl Material (docs)
  31. Yang, Y., M. Xu, Z. He, J. Guo, G. Sun, J.-Z. Zhou. 2013. Microbial electricity generation enhances decabromodiphenyl ether (BDE-209) degradation. PLoS One, 8:e70686. doi: 10.1371/journal.pone.0070686. Suppl Material (docx)
  32. Zhao, F.-J., E. Harris, J. Yan; J. C. Ma, L.Y. Wu, W.J. Liu, S. McGrath, J.-Z. Zhou, Y.G. Zhu. 2013. Arsenic methylation in soils and its relationship with microbial arsM abundance and diversity, and As speciation in rice. Environ. Sci.& Technol., 47: 7147-7154. Suppl Material (pdf)
  33. Zhang Y, J. Xie, M. Liu, Z. Tian, Z. He, J.D. Van Nostrand, L. Ren, J.-Z. Zhou, and M Yang. 2013. Microbial community functional structure in response to antibiotics in pharmaceutical wastewater treatment systems. Water Research. 47:6298-6308. doi.org/10.1016/j.watres.2013.08.003. Supplementary Data: Microarray Data (xlsx); Suppl Material (docx)
  34. Zhang, Y., Z. Lu, S. Liu, Y. Yang, Z. Ren, J.-Z. Zhou, D Li, and Z. He. 2013. GeoChip-based analysis of microbial communities in alpine meadow soils in the Qinghai-Tibetan plateau. BMC Microbiology. 13:72. DOI: 10.1186/1471-2180-13-720. Suppl Material (pdf)
  35. Zhang, Z., X. Zhao, Y.T. Liang, G.H. Li, and J.-Z. Zhou. 2013. Microbial functional genes reveal selection of microbial community by PAHs in polluted soils. Environmental Chemistry Letters, 11: 11-17.
  36. Zhou, A., Z. He, Y. Qin, Z. Lu, Y. Deng, Q. Tu, C. L. Hemme, J. D. Van Nostrand, L. Wu, T. C. Hazen, A. P. Arkin, and J.-Z. Zhou. 2013. StressChip as a High Throughput Tool for Assessing Microbial Community. Environ Sci Tech., 47:9841-9849. Supplemental Data: StressChip data (xlsx); Suppl Material (pdf)
  37. Zhou, A., E. Baidoo, Z. He, A. Mukhopadhyay, J. K. Baumohl, P. Benke, M. P. Joachimiak, M. Xie, R. Song, A. P. Arkin, T. C. Hazen, J. D Keasling, J. D. Wall, D. A. Stahl, and J.-Z. Zhou. 2013. Characterization of NaCl-tolerance in Desulfovibrio vulagris Hildenborough through experimental evolution. The ISME J., 7: 1790-1802., doi: 10.1038/ismej.2013.60. Suppl Material (docx)
  38. Zhou, J.-Z., Y.H. Jiang, Y. Deng, Z. Shi, B.-Y. Zhou, K. Xue, L. Wu, Z. He, and Y. Yang. 2013. Random Sampling Process Leads to Overestimation of β-Diversity of Microbial Communities. mBio 4: e00324-13 (doi:10.1128/mBio.00324-13) (selected as an Editors’ Pick). Supplemental Data: R codes (R format) for predicting overlap with 2 replicates and 3 replicates and for predicting sampling effort; Suppl Material (pdf)
  39. Zhou, J.-Z., W. Liu, Y. Deng, Y. Jiang, K. Xue, Z. He, J. D. Van Nostrand, L. Wu, Y. Yang, and A. Wang. 2013. Stochastic assembly leads to alternative communities with distinct functions. mBio, 4: e00584-12. Suppl Material: Figures and Tables (pdf), Info (pdf)
2012
  1. Beazley, M. J., R. J. Martinez, S. Rajan, J. Powell, Y. M. Piceno, L. M. Tom, G. L. Andersen, T. C. Hazen, J. D. Van Nostrand, J.-Z. Zhou, B. Mortazavi, and P. A. Sobecky. 2012. Microbial Community Analysis of a Coastal Salt Marsh Impacted by the Deepwater Horizon Oil Spill. PLoS One, 7: e41305 DOI: 10.1371/journal.pone.0041305. Suppl Material (zip)
  2. Carter, M. Q., K. Xue, M. T. Brandl, F.F. Liu, J. W. Louie, L.Y. Wu, and J.-Z. Zhou. 2012. Functional metagenomics of Escherichia coli O157:H7 interactions with spinach indigenous microorganisms during biofilm formation, PLoSOne, 7: e44186 DOI: 10.1371/journal.pone.0044186 Supplementary Data: Microarray Data (xls), Suppl Material (zip)
  3. Clark, M. E., Z. He, A. M. Redding, M.P. Joachimiak, J.D. Keasling, J.-Z. Zhou, A.P. Arkin, A. Mukhopadhyay, and M. W. Fields. 2012. Transcriptomic and Proteomic Analyses of Desulfovibrio vulgaris Biofilms: Carbon and Energy Flow Contribute to the Distinct Biofilm Growth State. BMC Genomics, 13:138. Suppl Material (pdf)
  4. Dassa, B., Ilya Borovok, R. Lamed, B. Henrissat, P. Coutinho, C. L. Hemme, Y. Huang, J.-Z. Zhou and E. A. Bayer. 2012. Genome-wide analysis of Acetivibrio cellulolyticus provides a blueprint of an elaborate cellulosome system. BMC Genomics, 13:210. Suppl Material (doc)
  5. Deng, Y., Y. Jiang, Y. Yang, Z. He, F. Luo, and J.-Z. Zhou. 2012. Molecular Ecological Network Analyses. BMC Bioinformatics, 13:113
  6. Deng, Y., Z. He, M. Xu, Y. Qin, J. D. Van Nostrand, L. Wu, B. A. Roe, G. Wiley, S. E. Hobbie, P. B. Reich, and J.-Z, Zhou. 2012. Elevated Carbon Dioxide Alters the Structure of Soil Microbial Communities. Appl. Environ. Microbiol., 78:2991-2995. Supplemental Data: Fasta files (zip), Suppl Material (pdf)
  7. Ding, G. C., H. Heuer, Z. He, J. Xie, J.-Z. Zhou, K. Smalla. 2012. More functional genes and convergent overall functional patterns detected by GeoChip in phenanthrene spiked soils. FEMS Microbiol. Ecol. 82: 148-156. DOI: 10.1111/j.1574-6941.2012.01413.x
  8. He, Z., Y. Deng, and J.-Z. Zhou. 2012. Development of functional gene microarrays for microbial community analysis. Curr.Opin. Biotechnol., 23: 49-55. Supplementary Information.
  9. He, Z., Y. Piceno, Y. Deng, M. Xu, Z. Lu, T. DeSantis, G. Andersen, S. E. Hobbie, P. B. Reich, and J.-Z. Zhou. 2012. The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide. ISME J, 6: 259-272. Supplementary Information.
  10. He, Z.L., J. D. Van Nostrand, and J.-Z. Zhou. 2012. Applications of functional gene microarrays for profiling microbial communities. Curr.Opin. Biotechnol., 23:460–466
  11. Huang, W., and J.-Z. Zhou. 2012. Editorial Overview: When single cell technology meets omics, the new toolbox of analytical biotechnology is emerging. Curr. Opin. Biotechnol., 23:1
  12. Liang, Y. H. Gao, X. Guo, J. Chen, G. Qiu, Z. He, J.-Z. Zhou, and X. Liu. 2012. Transcriptome analysis of pellicle formation of Shewanella oneidensis. Archives Of Microbiology, 194: 473-482. Suppl Material (pdf)
  13. Liang, Y., J. D. Van Nostrand, L. A. N’Guessan, A. D. Peacock, Y. Deng, P. E. Long, C. T. Resch, L. Wu, Z. He, G. Li, T. C. Hazen, D. R. Lovley, and J.-Z. Zhou. 2012. Microbial Functional Gene Diversity with a Shift of Subsurface Redox Condition during in situ Uranium Reduction. Appl. Environ. Microbiol., 78:2966-2972. Supplemental Data: Microarray data (xls), Suppl Material: Figures (pdf), Tables (pdf)
  14. Liu, W.Z., A. Wang, Aijie, D. Sun, Dan, N. Ren, Nanqi, Y. Zhang, J.-Z. Zhou. 2012. Characterization of microbial communities during anode biofilm reformation in a two-chambered microbial electrolysis cell (MEC). J. Biotechnol. 157: 628-632.
  15. Lomax, C., W. Liu, L. Wu, K. Xue, J. Xiong, J.-Z. Zhou, S. P. McGrath, A. A. Meharg, A. J. Miller, and F-J. Zhao. 2012. Methylated arsenic species in plants originate from soil microorganisms. New Phytologist, 193:665-672. Suppl Material (pdf)
  16. Lu, Z.M., Z. He, V. A. Parisi, S. Kang, Y. Deng, J. D. Van Nostrand, J. R. Masoner, I. M. Cozzarelli, J. M. Suflita, and J.-Z. Zhou. 2012. GeoChip-based analysis of microbial functional gene diversity in a landfill leachate-contaminated aquifer. Environ. Sci. Technol., 46: 5824-5833 Supplemental Data: Microarray data (xlsx), Suppl Material (pdf)
  17. Lu, Z.-M., Y. Deng, J. D. Van Nostrand, Z. He, J. Voordeckers, A. Zhou, Y.-J. Lee, O. Mason, E. Dubinsky, K. Chavarria, L. Tom, J. Fortney, R. Lamendella, J. K. Jansson, P. D’haeseleer, T. C. Hazen, and J.-Z. Zhou. 2012. Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume. ISME J., 6: 451-460. Supplementary Information (doc) (Highlighted by Science for Environment Policy, http://ec.europa.eu/environment/integration/research/research_alert_en.htm, the European Commission's environmental news service for policy makers, titled Microbes degrade oil from Deepwater Horizon spill)
  18. Mason, O. U., T. C. Hazen, S. Borglin, P. S. G. Chain, E. A. Dubinsky, J. L. Fortney, J. Han, H.Y N. Holman, J. Hultman, R. Lamendella, R. Mackelprang, S. Malfatti, L. M. Tom, S. G. Tringe, T. Woyke, J.-Z. Zhou, E. M. Rubin, and J. K. Jansson. 2012. Metagenomics, metatranscriptomics and single cell genomics reveal functional response of active Oceanospirillales to Gulf oil spill. The ISME J., 6: 1715-1727. Suppl Material (pdf)
  19. Rajeev, L., K. Hillesland, G. Zane, A. Zhou, M. Joachimiak, Z. He, J.-Z. Zhou, A. P. Arkin, J. D. Wall, and D.A. Stahl. 2012. Deletion of the Desulfovibrio vulgaris carbon monoxide sensor invokes global changes in transcription. J. Bacteriol., 194: 5783-93.
  20. Reith, F., R., J. Brugger, C. M. Zammit, A. L. Gregg, K. C. Goldfarb, G. L. Andersen, T. Z. DeSantis, Y. M Piceno, E. L. Brodie, Z. Lu, Z. He, J.-.Z. Zhou, and S. A. Wakelin. 2012. Influence of geogenic factors on microbial communities in metallogenic Australian soils. The ISME J. 6: 2107-2118. Suppl Material (link)
  21. Trivedi, P., Z. He, J. D. Van Nostrand, Gene Albrigo, J.-Z. Zhou, and N. Wang. 2012. Huanglongbing alters the structure and functional diversity of microbial communities associated with citrus rhizosphere. ISME J, 6: 363-383. Supplementary Information.
  22. Van Nostrand, J. D., Z. He, and J.-Z. Zhou. 2012. Use of functional gene arrays for elucidating in situ biodegradation. New Frontiers in Microbiology, 3:339.
  23. Walker, C.B. A.M. Redding-Johanson, E. E. Baidoo, L. Rajeev, Z. He, E.L, Hendrickson5, M.P. Joachimiak, S. Stolyar, A. P Arkin, J.A. Leigh, J.-Z. Zhou, J.D. Keasling, A. Mukhopadhyay, and D.A. Stahl. 2012. Functional Responses of Methanogenic Archaea to Syntrophic Growth. Th ISME J., 6: 2045–2055. Suppl Material:  Figures (doc), Tables (xls)
  24. Wang, Y., H. Zheng, F. Chen, J. Zeng, S. Chen, J.-Z. Zhou, and Z. Ouyang. 2012. Methane metabolic microbial community in soils of slash pine plantation and Masson pine plantation. Acta Ecologica Sinica, 32:2-7. (Chinese, DOI:10.5846/stxb201103080280)
  25. Wang, H., Z. He, Z.M. Lu, J.-Z. Zhou, J. D. Van Nostrand, X.H. Xu, and Z.J. Zhang. 2012. Genetic linkage of sediment carbon pools and microbial functions in subtropical freshwater wetlands responding to experimental warming. Appl. Environ. Microbiol., 78: 7652-7661. Suppl Material (pdf)
  26. Wawrik, B., M. Mendivelso, V.A. Parisi, J.M. Suflita, I.A. Davidova, C.R. Marks, J.D. Van Nostrand, Y. Liang, J.-Z. Zhou, B.J. Huizinga, D. Strąpoć, and A.V. Callaghan. 2012. Field and laboratory studies on the bioconversion of coal to methane in the San Juan Basin. FEMS Microb. Ecol., 81: 26-42, DOI: 10.1111/j.1574-6941.2011.01272.x. Suppl Material (pdf)
  27. Wawrik, B., W. Boling, J. Van Nostrand, J.P. Xie, J.-Z. Zhou,D. A. Bronk. 2012. Assimilatory Nitrate Utilization by Bacteria on the West Florida Shelf as Determined by Stable Isotope Probing and Functional Microarray Analysis. FEMS Microbiology Ecology, 79:400-411.
  28. Xie, J, L Wu, JD Van Nostrand, Z He, Z Lu, H Yu, J Xiong, X Liu, and J-Z Zhou. 2012. Improvements on environmental DNA extraction and purification procedures for metagenomics analysis. J Cent South Univ. 19:3055-3063.
  29. Xiong J, Z. He, J.D. Van Nostrand, G. Luo, S. Tu, J.-Z. Zhou, and G. Wang. 2012. Assessing the Microbial Community and Functional Genes in a Vertical Soil Profile with Long-Term Arsenic Contamination. PLoS ONE 7(11): e50507. doi:10.1371/journal.pone.0050507. Suppl Material (zip)
  30. Xu, X., S. Niu, R. A. Sherry, X. Zhou, J.-Z. Zhou, Y. Luo. 2012. Interannual variability in responses of belowground NPP and NPP partitioning to long-term warming and clipping in a tallgrass prairie. Global Change Biology, 18:1648-1656.
  31. Xu, X., Y. Luo, J.-Z. Zhou. 2012. Carbon Quality And The Temperature Sensitivity Of Soil Organic Carbon Decomposition In A Tallgrass Prairie. Soil Biol. & Biochem, 50: 142-148. Doi.org/10.1016/j.soilbio.2012.03.007.
  32. Xu, X. R. A. Sherry, S. Niu, J.-Z. Zhou, Yiqi Luo. 2012. Long-term experimental warming decreased labile soil organic carbon in a tallgrass prairie. Plant and Soil, 50: 142-148. DOI: 10.1007/s11104-012-1265-9
  33. Yergeau, E., S. Bokhorst, S. Kang, J.-Z. Zhou, C. W. Greer, R. Aerts, G. A. Kowalchuk. 2012. Shifts in soil microorganisms in response to warming are consistent across a range of Antarctic environments. ISME J, 6: 692-702. Supplementary Information (doc)
  34. Zhou, A.F., Y.I. Chen, G. M. Zane, Z.H. He, C. L. Hemme, M. P. Joachimiak, J. Baumohl, Q. He, M. W. Fields, A. P. Arkin, J. D. Wall, T. C. Hazen, and J.-Z. Zhou. 2012. Functional characterization of Crp/Fnr-type global transcriptional regulators in Desulfovibrio vulgaris Hildenborough. Appl. Environ. Microbiol., 78:1168-1177. Suppl Material (doc)
  35. Zhou, J.-Z., K. Xue, J.-P. Xie, Y. Deng, L.Y. Wu, X.L. Cheng, S.F. Fei, S.P. Deng, Z.-H. He, J.D. van Nostrand, and Y.Q. Luo. 2012. Microbial Mediation of Carbon Cycle Feedbacks to Climate Warming. Nature Climate Change, 2:106-110. (Ranked by Faculty 1000 as the top 2% of the published articles in biology and medicine). Supplemental Information (pdf)
2011
  1. He, Q., C. L. Hemme, H. Jiang, Z. He, and J.-Z. Zhou. 2011. Mechanisms of Enhanced Cellulosic Bioethanol Fermentation by Co-Cultivation of Clostridium and Thermoanaerobacter spp. BioResource Tech, 102: 9586-9592
  2. He, Z., J. D. Van Nostrand, Y. Deng, and J.-Z. Zhou. 2011. Development and applications of functional gene microarrays in the analysis of the functional diversity, composition, and structure of microbial communities. Front. Environ. Sci. Engin. 5: 1-20.
  3. Hemme, C. L., M. W. Fields, Q. He, Y. Deng, L. Lin, Q. Tu, H. Mouttaki, A. Zhou, X. Feng, Z. Zuo, B.D. Ramsey, Z. He, L. Wu, J. Van D. Nostrand, J. Xu, Y. Tang, J. Wiegel, T. J. Phelps, and J.-Z. Zhou. 2011. Correlation of genomic and physiological traits to biofuel yields in Thermoanaerobacter species. Appl. Environ. Microbial., 77: 7998–8008. Suppl Material (doc)
  4. Li, B., W.G. Cao, J.-Z. Zhou, and F. Luo. 2011. Understanding and predicting synthetic lethal genetic interactions in Saccharomyces cerevisiae using domain genetic interactions. BMC Systems Biology 5:73. Suppl Material (pdf)
  5. Liang, Y.T. J. D. Van Nostrand, Y. Deng, Z. He, L.Y. Wu, X. Zhang, G.H. Li and J.-Z. Zhou. 2011. Functional gene diversity of soil microbial communities from oil-contaminated fields in China. ISME J. 5: 403-413. Suppl Material: Figures (ppt), Tables (doc), Information (oc)
  6. Lin, L., H. Song, Q. Tu, Y. Qin, A. Zhou, W. Liu, Z. He, J.-Z. Zhou, and J. Xu. 2011. The thermoanaerobic Glycobiome Reveals Mechanisms of Pentose and Hexose Co-utilization in Bacteria. PLoS Genetics, 7(10): e1002318. doi:10.1371/journal.pgen.1002318. Suppl Material (zip)
  7. Liu, A.H., L. Wu, Z.L. He, and J.-Z. Zhou. 2011. Development of highly fluorescent silica nanoparticles chemically doped with organic dye for sensitive DNA microarray detection. Anal Bioanal Chem, 401:2003–2011. Suppl Material (pdf)
  8. Sundararajan, A., J. Kurowski, T. Yan, D. M. Klingman, M.P. Joachimiak, J.-Z. Zhou, B. Naranjo, J. A. Gralnick, and M. W. Fields. 2011. A Shewanella oneidensis MR-1 Sensory Box Protein Involved in Aerobic and Anoxic Growth. Appl. Environ. Microbiol. 77: 4647-4656, doi:10.1128/AEM.03003-10).
  9. Van Nostrand, J.D., Z. He and J. Zhou. 2011. Dynamics of Microbes in the Natural Setting: Development of the GeoChip.  in Environmental Microbiology: Current Technology and Water Applications (Edited by: Keya Sen and Nicholas J. Ashbolt). Caister Academic Press, U.K.
  10. Van Nostrand, J.D., Z. He, J.-Z. Zhou. 2011. GeoChip: A high throughput metagenomics technology for dissecting microbial community functional structure. In: F.J. de Bruijn (ed) Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats. John Wiley & Sons, New Jersey, pp 509-520.
  11. Van Nostrand, J.D., Z. He, and J.-Z. Zhou. 2011. New developments and applications of microarrays for microbial community analysis in natural and impacted ecosystems. In: M. Moo-Young (ed) Comprehensive Biotechnology, 2e. Elsevier, Amsterdam, The Netherlands.
  12. Van Nostrand, J.D., Z.L. He, and J.-Z. Zhou. 2011. Metagenomics analysis of below-ground microbial communities using microarrays. In: D. Marco (ed) Metagenomics: Current Innovations and Future Trends, Caister Academic. pp 265-288.
  13. Van Nostrand, J. D., Z. He, and J.-Z. Zhou. 2011. Microarray analysis of environmental samples. In: Environmental Microbiology: Current Technology and Water Applications. Horizon Scientific, Norwich, UK.
  14. Van Nostrand, J. D., S. Kang, Y. Deng, Y. Liang, Z. He, and J.-Z. Zhou. 2011. Monitoring Microbial Activity with GeoChip. In: J.F. Stolz and R.S. Oremland (eds) Microbial Metal and Metalloid Metabolism: Advances and Applications. ASM Press, Washington DC.
  15. Van Nostrand*, J.D., L.Y. Wu*, W.-M. Wu, Z.J. Huang, T. J. Gentry, Y. Deng, J. Carley, S. Carroll, Z. He, B.H. Gu, J. Luo, C. S. Criddle, D. B. Watson, P. M. Jardine, T. L. Marsh, J.M. Tiedje, T. C. Hazen, and J.-Z. Zhou. 2011. Dynamics of Microbial Community Composition and Function during In Situ Bioremediation of a Uranium-Contaminated Aquifer. Appl. Environ. Microbiol, 77:3860-3869 (*Equal distribution). Supplementary Data: Microarray Data (xlsx); Suppl Material: Table (xls), Figures (doc)
  16. Van Nostrand, J.D., and J.-Z. Zhou. 2011. Application of GeoChips in monitoring Carbon cycling. In: N. Jiao, F. Azam, and S. Sander (eds) Microbial Carbon Pump in the Ocean (booklet). AAAS. pp 64-65.
  17. Wang, J., J. D. Van Nostrand, L. Wu, Z. He, G. Li, and J.-Z. Zhou. 2011. Microarray-Based Evaluation of Whole-Community Genome DNA Amplification Methods. Appl. Environ. Microbiol. 77: 4241-4245, (doi:10.1128/AEM.01834-10). Supplementary Information.
  18. Wang, A.J., L.F. Gao, N.Q. Ren, J.F. Xu, C. Liu, G.-L Cao, H. Yu, W.Z. Liu, C. L. Hemme, Z. He, and J.-Z. Zhou. 2011. Isolation and characterization of Shigella flexneri G3 for effective cellulosic saccharification under mesophilic conditions. Appl. Environ. Microbiol. 77: 517-523. Supplementary Information (doc)
  19. Wu, WM, J. Carley, D. Watson , B.H. Gu, S. Brooks, S. S. Kelly, K. Kemner, J. D. van Nostrand , L. Wu, M. Xu, J.-Z. Zhou, J. Luo, E. Cardenas, C. Hwang, M. W. Fields, T. L. Marsh, J. M. Tiedje, S. J. Green, J. E. Kostka, P. K. Kitanidis, P. M. Jardine, C. S. Criddle. 2011. Bioreduction and immobilization of uranium in situ: a case study at a USA Department of Energy radioactive waste site, Oak Ridge, Tennessee. Acta Scientiae Circumstaniae. 3: 449-459. (Chinese)
  20. Xie, J.P., H.C., Jiang, X.X. Liu, X.D. Liu, J.-Z. Zhou, and G. Z. Qiu. 2011. 16s rDNA based microbial diversity analysis of eleven acid mine drainages obtained from three Chinese copper mines. Journal of Central South University of Technology, 18: 1930-1939.
  21. Xie, J.P. Z. He, X.X. Liu, X.D. Liu, J. D. Van Nostrand, Y. Deng, L.Y. Wu, J.-Z. Zhou, and G.-Z. Qiu. 2011. GeoChip-based analysis of the functional gene diversity and metabolic potential of microbial communities in acid mine drainage. Appl. Environ. Microbiol. 77: 991-999. Suppl Material (doc)
  22. Zhou, J.-Z.*, Y. Deng*, F. Luo, Z. He, and Y.F. Yang. 2011. Phylogenetic Molecular Ecological Network of Soil Microbial Communities in Response to Elevated CO2. mBio, 2(4): doi:10.1128/mBio.00122-11. (*Equal contribution). Supplementary Data:  Fasta Files (zip), OTU distribution (xlsx), Perl script (zip), Module Eigenvalues Analyses (pdf), Suppl Figures (pdf)
  23. Zhou, J., Q. He, C. L. Hemme, A. Mukhopadhyay, K. Hillesland, A. Zhou, Z. He, J. D. Van Nostrand, T. C. Hazen, D. A. Stahl, J. D. Wall, and A. P. Arkin. 2011. How sulphate-reducing microorganisms cope with stress: lessons from systems biology. Nature Review in Microbiology. 9:452-466. Supplementary Information (pdf)
  24. Zhou, J-.Z. *, L.-Y. Wu*, Y. Deng, X.-Y. Zhi, Y.-H. Jiang, Q.-C. Tu, J.-P. Xie, J. D. Van Nostrand, Z.-H. He, and Y.-F. Yang. 2011. Reproducibility and Quantitation of Amplicon Sequencing-Based Detection. ISME J. 5:1303-1313, *Equal distribution). Supplementary Data: Fasta files (zip) Suppl Material (link)
2010
  1. Andersen, G. L., Z. He, T.Z. DeSantis, E. L. Brodie, J.-Z. Zhou. 2010. The Use of Microarrays in Microbial Ecology. In: Environmental Molecular Microbiology (Liu, WT; Jansson, JK, eds), pp. 87-109, Caister Academic Press, Wymondham, UK.
  2. Cardenas, E., W.-M. Wu, M. B. Leigh, J. Carley, S. Carroll, T. Gentry, J. Luo, D. Watson, B. Gu, M. Ginder-Vogel, P. K. Kitanidis, P. M. Jardine, J.-Z. Zhou, C. S. Criddle, T. L. Marsh, and J. M. Tiedje. 2010. Significant Association between Sulfate-Reducing Bacteria and Uranium-Reducing Microbial Communities as Revealed by a Combined Massively Parallel Sequencing-Indicator Species Approach. Appl. Environ. Microbiol. 76: 6778-6786. Suppl Material: Legends (pdf); Table S1 (xls); Fig S1 (tif)
  3. Epelde, L., J. M. Becerril, G. A. Kowalchuk, Y. Deng, J.-Z. Zhou, and C. Garbisu. 2010. Impact of metal pollution and thlaspi caerulescens phytoextraction on soil microbial communities. Appl. Environ. Microbiol. 76: 7843-7853.
  4. Gao, H., X. Wang, Z.K. Yang, J. Chen, Y. Liang, H. Chen, T. Palzkill, and J.-Z. Zhou. 2010. Physiological roles of ArcA, Crp, and EtrA and their interactive control on aerobic and anaerobic respiration in Shewanella oneidensis. PLoS ONE, e15295 (DOI:10.1371/journal.pone.0015295). Suppl Material (zip)
  5. Gao, H., S. Barua, Y. Liang, L. Wu, Y. Dong, S. Reed, J. Chen, D. Culley, D. Kennedy, Y. Yang, Z. He, K. H. Nealson, J. K. Fredrickson, J. M. Tiedje, M. Romine4 and J.-Z. Zhou. 2010. Impacts of Shewanella oneidensis c-type cytochromes on aerobic and anaerobic respiration. Microb. Biotech. 3(4): 455-466. Suppl Material: Tables S1 and S2 (doc); Table S3 (xls)
  6. Gao, W.M., T. J.Gentry, T. L. Mehlhorn, S. L. Carroll, P. M. Jardine, and J.-Z. Zhou. 2010. Characterization of Co(III) EDTA reducing bacteria in metal- and radionuclide-contaminated groundwater. Geomicrobiol. J., 27: 93-100.
  7. Gihring, T.M., C.W. Schadt, G.-L. Zhang, Z. Yang, S. Carroll, K. Lowe, T.-L. Mehlhorn, P. Jardine, D. Watson, S.C. Brooks, W. Wu, J.E. Kostka, W. Overholt, S.J. Green, J.-Z. Zhou, P. Zhang, J. D. Van Nostrand. 2010. Changes in microbial community structure and activity during amendment with long-term electron donor sources for bioreduction of groundwater contaminants. Geochimica et Cosmochimica Acta. 74: A329-A329. Suppl Material (pdf)
  8. Hazen, T. C., E. Dubinsky, T. DeSantis, G. Andersen, Y. Piceno, N. Singh, J. Jansson, A. Probst, S. Borglin, J. Fortney, W. Stringfellow, M. Bill, M. Conrad, L. Tom, K. Chavarria, T. Alusi, R. Lamendella, D. Joyner, C. Spier, J. Baelum, M. Auer, M. Zemla, R. Chakraborty, E. Sonnenthal, P. D'haeseleer, H.-Y. Holman, S. Osman, Z.M. Lu, J. van Nostrand, Y. Deng, J.Z. Zhou, and O. U. Mason. 2010. Deep-sea oil plume enriches Indigenous oil-degrading bacteria. Science 330: 204-208. Suppl Information.
  9. He, Q., Z. He, D. C. Joyner, M. Joachimiak, M. N. Price, Z. K. Yang, H.-C. B. Yen, C. L. Hemme, R. Chakraborty, W. Chen, M. M. Fields, D. A. Stahl, J. D. Keasling, M. Keller, A. P. Arkin, T. C. Hazen, J. D. Wall, and J.-Z. Zhou. 2010. Impact of elevated nitrate on sulfate-reducing bacteria: Implications of inhibitory mechanisms in addition to osmotic stress. ISME J. 4: 1386-1397. Suppl Material (link)
  10. He, Z., Y. Deng, J. D. Van Nostrand, Q. Tu, M. Xu, C. Hemme, X. Li, L. Wu, T. J. Gentry, Y.F. Yin, J. Liebich, T. C. Hazen, and J-Z. Zhou. 2010. GeoChip 3.0 as a high throughput tool for analyzing microbial community structure, composition, and functional activity. ISME J. 4: 1167-1179. Supplementary Information (doc)
  11. He, Z., M. Xu, D. Ye, S. Kang, L. Kellogg, L.Y. Wu, J. D. Van Nostrand, S. E. Hobbie, P. B. Reich, and J.-Z. Zhou. 2010. Metagenomic analysis reveals a marked divergence in the structure of belowground microbial communities at elevated CO2. Ecol. Lett. 13: 564-575 (Highlighted by Science as an example of the frontier of integrative biodiversity studies, Naeem et al. 2012. Science: 336: 1401-1406). Supplementary Information (doc)
  12. He, Z., A.F. Zhou, E. Baidoo, Q. He, M. P. Joachimiak, P. Benke, R. Phan, A. Mukhopadhyay, K. Huang, E. J. Alm, M. W. Fields, J. Wall, D. Stahl, T. C. Hazen, J. D. Keasling, A. P. Arkin, and J.-Z. Zhou. 2010. Global transcriptional, physiological and metabolite analyses of Desulfovibrio vulgaris Hildenborough responses to salt adaptation. Appl. Environ. Microbiol. 76:1574-1586. Supplementary Information.
  13. Hemme, C. L., H. Mouttaki, Y.-J. Lee, L. Goodwin, S. Lucas, A. Copeland, A. Lapidus, T. G. d. Rio, H. Tice, E. Saunders, T. Brettin, J. C. Detter, C. S. Han, S. Pitluck, M. L. Land, L. J. Hauser, N. Krypides, N. Mikhailova, Z. He, L. Wu, J. D. V. Nostrand, B. Henrissat, Q. He, P. A. Lawson, R. S. Tanner, L. R. Lynd, J. Wiegel, M. W. Fields, A. P. Arkin, C. W. Schadt, B. S. Stevenson, M. J. McInerney, Y. Yang, H. Dong, Denfeng Xing, Nanqi Ren, Aijie Wang, R. L. Huhnke, J. R. Mielenz, S.-Y. Ding, M. E. Himmel, S. Taghavi, D. v. d. Lelie, E. M. Rubin, and J.-Z. Zhou. 2010. Sequencing of Multiple Clostridia Genomes Related to Biomass Conversion and Biofuels Production. Journal of Bacteriology, 192: 6494-6496.
  14. Hemme, C. L., Y. Deng, T. J. Gentry, M. W. Fields, L. Wu, Z. Fang, S. Barua, K. Barry, S. Green-Tringe, D. B. Watson, Z. He, T. C. Hazen, J. M. Tiedje, E. M. Rubin and J.-Z Zhou. 2010. Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community. ISME J.5: 660-672. (Highlighted by The Scientist, http://www.the-scientist.com/blog/display/57342/) Supplementary Information.
  15. Huang, Y., W.M. Zong, X. Yan, R.F. Wang, C.L. Hemme, J.-Z. Zhou, Z.H. Zhou. 2010. Succession of the Bacterial Community and Dynamics of Hydrogen Producers in a Hydrogen-Producing Bioreactor. Appl. Environ. Microbiol. 76: 3387-3390. Supplementary Information (doc)
  16. Kimes, N. E., J. D.Van Nostrand, E.Weil, J.-Z. Zhou, and P.J. Morris. 2010. Microbial functional structure of Montastraea faveolata, an important Caribbean reef-building coral, differs between healthy and yellow-band diseased colonies. Environ. Microbiol. 12: 541-556.
  17. Liang, Y., H. Gao, J. Chen, Y. Dong, L. Wu, Z. He, X. Liu, G. Qiu, and J.-Z. Zhou. 2010. Pellicle formation in Shewanella oneidensis. BMC Microbiol. 10: 291 (DOI: 10.1186/1471-2180-10-291). Suppl Material (pdf)
  18. Liang. Y.T., Z. He, L. Y. Wu, Y. Deng, G.H. Li, and J.-Z. Zhou. 2010. Development of a common oligo reference standard (CORS) for microarray data normalization and comparison across different microbial communities. Appl. Environ. Microbiol. 76: 1088-1094.
  19. Lin L., H.H. Song, Y.T. Ji, Z. He, Y.T. Pu, J.-Z. Zhou, and J. Xu. 2010. Ultrasound-mediated DNA transformation in thermophilic Gram-positive anaerobes. PLoS One 5(9): e12582 (doi:10.1371/journal.pone.0012582). Suppl Material (zip)
  20. Liu, W.Z., A.J. Wang, S. Cheng, B. E. Logan, H. Yu, Y. Deng, J. D. van Nostrand, L.Y. Wu, Z. He and J.-Z. Zhou. 2010. GeoChip-based functional gene analysis of anodophilic communities in microbial electrolysis cells under different operational modes. Environ. Sci. Technol. 44: 7729-7735. Supplementary Information.
  21. Mason, O. U., T. Nakagawa, M. Rosner, J. D. Van Nostrand, J.-Z. Zhou, A. Maruyama, M. R. Fisk, S. J. Giovannoni. 2010. First Investigation of the Microbiology of the Deepest Layer of Ocean Crust. PLoS ONE 5(11): e15399 (doi:10.1371/journal.pone.0015399). Suppl Material (zip)
  22. Parnell, J. J., G. Rompato, L. C. Latta IV, M. E. Pfrender, D. Naftz, J. VanNostrand, Z. He, J.-Z. Zhou, G. Andersen, P. Champine, B. Ganesan, and B. C. Weimer. 2010. Functional Biogeography as Evidence of Gene Transfer in Hypersaline Microbial Communities. PLoS ONE 5: e12919 (doi:10.1371/journal.pone.0012919). Suppl Material (zip)
  23. Reeve, J., C. W. Schadt, L. Carpenter-Boggs, S.H. Kang, J.-Z. Zhou, and J. P. Reganold. 2010. Effects of soil type and farm management on soil ecological functional genes and microbial activities. ISME J. 4: 1099-1107. Suppl Material (link)
  24. Reganold, J.P., P.K. Andrews, J.R. Reeve, L. Carpenter-Boggs, C.W. Schadt, J.R. Alldredge, C.F. Ross, N.M. Davies, and J.-Z. Zhou. 2010. Fruit and soil quality of organic and conventional strawberry agroecosystems. PLoS ONE 5: e12346 (doi:10.1371/journal.pone.0012346). Suppl Material (zip)
  25. Van Nostrand, J. D., Z. He, and J.-Z. Zhou. 2010. Analysis of microbial communities by functional gene arrays. In: L. Barton, M. Mandl and A. Loy (eds) Geomicrobiology: Molecular and Environmental Perspective. Springer, New York. Pp 109-126.
  26. Van Nostrand, J. D, Y. Liang, Z. He, G. Li, and J.-Z. Zhou. 2010. GeoChip: A high throughput genomic tool for linking community structure to functions. In: K. N. Timmis (ed) Handbook of Hydrocarbon and Lipid Microbiology, vol 4, Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids. Springer, New York, pp 2677-2685.
  27. Van Nostrand, J. D, L. Wu, Z. He, and J.-Z. Zhou. 2010. GeoChips for analysis of microbial functional communities. In: J. R. van der Meer (ed) Handbook of Hydrocarbon and Lipid Microbiology, vol 5, Experimental Protocols and Appendices. Springer, New York, pp 4039-4050.
  28. Wang, A.J., W.Z., Liu WZ, N. Q. Ren, J.-Z. Zhou, and A.A. Cheng. 2010. Key factors affecting microbial anode potential in a microbial electrolysis cell for H2 production. International Journal of Hydrogen Energy 35: 13481-13487.
  29. Wu, M.-M., J. Carley, S. J. Green, J. Luo, S. D. Kelly, J. D. van Nostrand, K. Lowe, T. Mehlhorn, S. Carroll, B. Boonchayanant, F.E. Löfller, D. Watson, K.M. Kemner, J.-Z. Zhou, P. K. Kitanidis, J. E. Kostka, P. M. Jardine, and C. S. Criddle. 2010. Effects of nitrate on the stability of uranium in a bioreduced region of the subsurface. Environ. Sci. Technol. 44: 5104-5111. Supplementary Information (pdf)
  30. Wu, WM, J. Carley, D. Watson, B.H. Gu, S. Brooks, S. S. Kelly, K. Kemner, J. D. Van Nostrand, L. Wu, M. Xu, J.-Z. Zhou, J. Luo, E. Cardenas, C. Hwang, M. W. Fields, T. L. Marsh, J. M. Tiedje, S. J. Green, J. E. Kostka, P. K. Kitanidis, P. M. Jardine, C. S. Criddle. 2010. Bioreduction and immobilization of uranium in situ: a case study at a USA Department of Energy radioactive waste site, Oak Ridge, Tennessee. Acta Scientiae Circumstaniae. 31:449-459. (Chinese)
  31. Xiong, J.B., L.Y. Wu, S.X. Tu, J. D. van Nostrand, Z. He, J.-Z. Zhou, and G.J. Wang. 2010. Microbial Communities and Functional Genes Associated with Soil Arsenic Contamination and the rhizosphere of the arsenic hyper-accumulating plant Pteris vittata L. Appl. Environ. Microbiol 76: 7277-7284. Suppl Material (pdf)
  32. Xu, M.Y., W.-M. Wu, L.Y. Wu, Z. He, J.D. Van Nostrand, Y. Deng, J. Luo, J. Carley, M. A. Ginder-Vogl, T. Gentry, B. Gu, D. Watson, P. M. Jardine, C. S. Criddle, and J.-Z. Zhou. 2010. Responses of microbial community functional structures to pilot-scale uranium in situ bioremediation. ISME J. 4: 1060-1070. Supplementary Information (doc)
  33. Yang, Y., L. A. McCue, A. B. Parsons, C. X. Guan, S. Feng and J.-Z. Zhou. 2010. The tricarboxylic acid cycle in Shewanella oneidensis is independent of Fur and RyhB control. BMC Microbiology 10:264 (DOI: 10.1186/1471-2180-10-264).
  34. Zhou, A.-F, Z. He, A. M. Redding, A. Mukhopadhyay, C. L. Hemme, M. P. Joachimiak, K. S. Bender, J. D. Keasling, D. A. Stahl, M. W Fields, T. C. Hazen, A. P. Arkin, J. D. Wall, and J.-Z. Zhou. 2010. Hydrogen peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough. Environ. Microbiol. 12: 2645-2657. Suppl Material
  35. Zhou*, J.-Z., Y. Deng*, F. Luo, Z.-H. He, Q. Tu, and X.Y. Zhi. 2010. Functional Molecular Ecological Networks. mBio 1(4):e00169-10 (doi:10.1128/mBio.00169-10, *equal contribution). Suppl Material: Tables (doc), Figures (pdf)
  36. Zhou, J.-Z., Z. He, J. D. Van Nostrand, L.Y. Wu, and Y. Deng. 2010. Applying GeoChip Analysis to Disparate Microbial Communities. Microbe, 5:60-64.
2009
  1. Feng, X.Y., H. Mouttaki, L. Lin, R. Huang, B. Wu, C. L. Hemme, Z. He, B. Zhang, L. Hicks, J. Xu, J.-Z. Zhou, and Y. J. Tang. 2009. Characterization of the Central Metabolic Pathways in Thermoanaerobacter sp. X514 via Isotopomer-Assisted Metabolite Analysis. Appl. Environ. Microbiol. 75: 5001-5008. Supplemental Information (doc)
  2. Gao, H., Z.K Yang, S. Barua, S. B. Reed, M. F. Romine, K. H. Nealson, J. K. Fredrickson, J. M. Tiedje, and J.-Z. Zhou. 2009. Reduction of nitrate in Shewanella oneidensis depends on atypical NAP and NRF systems with NapB as a preferred electron transport protein from CymA to NapA. ISME J. 3: 966-976. Suppl Material (pdf)
  3. Gentry TJ, He Z and Zhou J. 2009. Detection and characterization of uncultivated microorganisms using microarrays. In Uncultivated Microorganisms (Microbiology Monographs) Vol. 10: 179-202, Epstein, Slava S. (Ed.) Springer-Verlag Berlin Heidelberg (Invited review).
  4. He, Q., P. M. Lokken, and J.-Z. Zhou. 2009. Characterization of the Impact of Acetate and Lactate on Ethanolic Fermentation by Thermoanaerobacter ethanolicus. Bioresource Technology 100: 5955-5965.
  5. Hwang, C., W. Wu, T.J. Gentry, J. Carley, S.L. Carroll, D. Watson, P.M. Jardine, J.-Z Zhou, C.S. Criddle, and M.W. Fields. 2009. Bacterial Community Succession During in situ Uranium Bioremediation: Spatial Similarities Along Controlled Flow Paths. ISME J. 3: 47-64. Suppl Material (pdf)
  6. Liang, Y.L., Z.L. He, H.C. Gao HC, G.Z. Qiu, J.-Z. Zhou, and X.-D. Liu. 2009. Characterization of cytochrome mutants for pellicle formation in Shewanella oneidensis MR-1. Trans. Nonferrous Met. Soc. China 19: 700-706.
  7. Liang, Y.T, G. Li, J. D. Van Nostrand, Z. He, L.Y. Wu, Y. Deng, X. Zhang, and J.-Z. Zhou. 2009. Microarray-based analysis of microbial functional diversity along an oil contamination gradient in oil field. FEMS Microbiol. Ecol. 70: 324-333. Suppl. Info.
  8. Liang, Y., J. Wang, J. D. Van Nostrand, J.-Z. Zhou, X. Zhang, G. Li. 2009. Microarray-based functional gene analysis of soil microbial communities in ozonation and biodegradation of crude oil. Chemosphere, 75: 193-199.
  9. Liebich, J. T. Wachtmeister, J.-Z. Zhou, and P. 2009. Degradation of Diffuse Pesticide Contaminants: Screening for Microbial Potential Using a Functional Gene Microarray. Vadose Zone Journal 8: 703-710.
  10. Luo, W.S., S. D. Kelly, K. M. Kemner, D. Watson , J.-Z. Zhou, P.M. Jardine, and B.H. Gu. 2009. Sequestering Uranium and Technetium through Co-Precipitation with Aluminum in a Contaminated Acidic Environment. Environ. Sci. Technol. 43: 7516-7522. Suppl. Info.
  11. Mason, O. U., C. A DiMeo-Savoie, J. D. Van Nostrand, J.-Z. Zhou, M. R. Fisk, and S. J. Giovannoni. 2009. Prokaryotic diversity, distribution, and preliminary insights into their role in biogeochemical cycling in marine basalts. ISME J. 3: 231-242. Suppl. Info.
  12. Ning, J., J. Liebich, M. Kastner, J.-Z Zhou, A. Schaffer, P. and Burauel. 2009. Different influences of DNA purity indices and quantity on PCR-based DGGE and functional gene microarray in soil microbial community study. Appl. Microbiol. Biotechnol. 82: 983-993
  13. Singh BK, CD Campbell, SJ Sorenson, and J Zhou. 2009. Soil genomics. Nat. Rev Microbiol. 7:756
  14. Tas, N., M. H.A. van Eekert, G. Schraa, J.-Z. Zhou, W. M. de Vos, and H. Smidt. 2009. 2009. Tracking Functional Guilds: Dehalococcoides spp. in European River Basins Contaminated with Hexachlorobenzene. Appl. Environ. Microbiol. 75: 4696-4704. Supplementary Information (doc)
  15. Van Nostrand, J. D, W.-M. Wu, L. Wu, Y. Deng, J. Carley, S. Carroll, Z. He, B. Gu, J. Luo, C. Criddle, P. Jardine, J. M. Tiedje, T. C. Hazen, J.-Z. Zhou. 2009. GeoChip-based analysis of functional microbial communities in a bioreduced uranium-contaminated aquifer during reoxidation by oxygen. Environ. Microbiol. 11: 2611-2626. Supplementary Information (doc)
  16. Waldron, P. J., J. D.Van Nostrand, D. B. Watson, Z. He, L. Wu, P. M. Jardine, T. C. Hazen, and J.-Z. Zhou. 2009. Functional Gene Array-Based Analysis of Microbial Community Structure in Groundwaters with a Gradient of Contaminant Levels. Environ. Sci. Technol. 43: 3529-3534. Suppl. Info.
  17. Walker, C. B., Z. He, Z. K. Yang, J. A. Ringbauer, Jr., J.-Z. Zhou, G. Voordouw, J. D. Wall, A. P. Arkin, T.C. Hazen, S. Stolyar, and D. A. Stahl. 2009. The Electron Transfer System of Syntrophically Grown Desulfovibrio vulgaris. J. Bacteriol. 191: 5793-5801. Suppl Material: Tables (pdf), Figures (pdf)
  18. Walker, C, S. S. Stolyar, D. Chivian, N. Pinel, J. A. Gabster, P. S. Dehal, Z. He, Z. K. Yang, H. B. Yen, J.-Z. Zhou, J. D. Wall, T. C. Hazen, A. P. Arkin, D. A. Stahl. 2009. Contribution of mobile genetic elements to Desulfovibrio vulgaris genome plasticity. Environ. Microbiol. 11: 2244-2252. Suppl Material: Tables S1-7 (pdf); Table S6 (pdf), Figures S1 (tif), S2 (tif), S3 (tif), S4 (tif), S5 (tif)
  19. Wang, A.J., W. Z., Liu, S.A. Cheng, D.F. Xing, J.-Z. Zhou, and B. E. Logan. 2009. Source of methane and methods to control its formation in single chamber microbial electrolysis cells. International J Hydrogen Energy 34: 3653-3658.
  20. Wang, F., H. Zhou, J. Meng, X.T. Peng, L. Jiang, P. Sun, C. Zhang, J. D. Van Nostrand , Y. Deng, Z. He, L. Wu, J.-Z. Zhou, X. Xiao. 2009. GeoChip-based Analysis of Metabolic Diversity of Microbial Communities at the Juan de Fuca Ridge Hydrothermal Vent. Proc Nat. Acad. Sci, 106: 4840-4845. Suppl. Info. (pdf)
  21. Yang Y. , D. P. Harris, F. Luo, W. Xiong, M. Joachimiak, L. Wu, P. Dehal. J. Jacobsen, Z. Yang, A. V. Palumbo, A. P. Arkin, and J.-Z. Zhou. 2009. Snapshot of Iron Response in Shewanella oneidensis by Gene Network Reconstruction. BMC Genomics 10:131. Suppl Material (jpeg)
  22. Zhou, J.-Z., 2009. Predictive Microbial Ecology. Microb. Biotechnol. 2: 154–156
  23.  Brajesh K. Singh, B.K., C. D. Campbell, S. J. Sorenson, and J.-Z. Zhou. 2009. Soil genomics is the way forward. Nat. Rev. Microbiol. 7: 10 (DOI: 10.1038/nrmicro2119-c1).
2008
  1. Cardenas, E., W. Wu, M.B. Leigh, J. Carley, S. Carroll, T. Gentry, J. Luo, D. Watson, B. Gu, M. Ginder-Vogel, P. K. Kitanidis, P.M. Jardine, J.-Z.,Zhou, C.S. Criddle, T.L. Marsh and J.M. Tiedje. 2008. Microbial Communities in Contaminated Sediments Associated with Bioremediation of Uranium to Submicromolar Levels. Appl. Environ. Microbiol. 74: 3718-3729.
  2. Deng, Y., Z. He, J. D. Van Nostrand, J.-Z. Zhou. 2008. Design and analysis of mismatch probes for long oligonucleotide microarrays. BMC Genomics, 9:491 (doi:10.1186/1471-2164-9-491). Supplemental Information (xls)
  3. Gao, H.C., X.H. Wang, Z.K. Yang, T. Palzkill, and J.-Z. Zhou. 2008. Probing Regulon of ArcA in Shewanella oneidensis MR-1 by Integrated Genomic Analyses. BMC Genomics 9: 42. Suppl Material: File 1 (ppt); File 2 (doc); File 3 (doc); File 4 (doc); File 5 (doc)
  4. Gao, H., D. Pattison, T. Yan, D. M. Klingeman, X. Wang, J. Petrosino, L. Hemphill, X. Wan, A.B. Leaphart, G. Weinstock, T. Palzkill, and J.-Z. Zhou. 2008. Generation and Validation of a Shewanella oneidensis MR-1 Clone Set for Protein Expression and Phage Display. PLoS One 3(8): e2983. Supplementary Information (xls).
  5. He, Z., and J.-Z. Zhou. 2008. Empirical determination of signal to noise ratio (SNR) thresholds for microarray analysis. Appl. Environ. Microbiol. 74: 2957–2966. Suppl Material (doc)
  6. He, Z., and J.-Z. Zhou. 2008. Selection of oligonucleotide probes for microarrays. In: Molecular Microbial Ecology Manual 2nd, Springer Netherlands. pp1880-1891. (Invited review).
  7. He, Z, J. D.Van Nostrand, L. Wu, and J.-Z. Zhou. 2008. Development and application of functional gene arrays for microbial community analysis. Trans. Nonferrous Met. Soc. China 18: 1319-1327 (Invited review).
  8. Pereira, P.M. Q. He, A.V. Xavier, J.-Z. Zhou, I.A. C. Pereira and R. O. Louro. 2008. Transcriptional Response of Desulfovibrio vulgaris Hildenborough to Oxidative Stress Mimicking Environmental Conditions. Archives of Microbiology, 189: 451-461. Suppl Material (doc)
  9. Pereira, P. M., Q. He, F. M. A. Valente, A. V. Xavier, J.-Z. Zhou, I. A. C. Pereira & R. O. Louro. 2008. Energy metabolism in Desulfovibrio vulgaris Hildenborough: insights from transcriptome analysis. Antonie van Leeuwenhoek International Journal of General and Molecular Microbiology, 93:347-362.
  10. Rodrigues, D. F., N. Ivannova, Z. He, M. Huebner, J.-Z. Zhou and J. M. Tiedje. 2008. Architecture of thermal adaptation in an Exiguobacterium sibiricum strain isolated from 3 million year old permafrost: A genome and transcriptome approach. BMC Genomics 9:547 (doi:10.1186/1471-2164-9-547). Supplementary Information (doc)
  11. Wang, X., H. Gao, Y. Shen, G. M. Weinstock, J.-Z. Zhou, and T. Palzkill. 2008. A High-throughput Percentage-of-Binding Strategy to Measure Binding Energies in DNA-Protein Interactions: Application to Genome Scale Site Discovery. Nucleic Acids Res. 36: 4863-4871. Supplementary Information (doc)
  12. Wu, L. Y., X.D. Liu, M.W. Fields, D.K. Thompson, C.E. Bagwell, J.M. Tiedje, T.C. Hazen, and J.-Z. Zhou. 2008. Microarray-based whole-genome hybridization as a tool for determining prokaryotic species relatedness. ISME J. 2, 642–655. Suppl Material (doc)
  13. Wu*, L., L. Kellogg, A.H. Devol, A.V. Palumbo, J.M. Tiedje, and J.-Z. Zhou*. 2008. Microarray-Based Characterization of Microbial Community Functional Structure and Heterogeneity in Marine Sediments From the Gulf of Mexico. Appl. Environ. Microbiol. 74: 4516-4529 (*equal contribution). Suppl Material: Table S1 (zip)
  14. Yang, Y.F., D.P. Harris, F. Luo, L.Y. Wu, A.B. Parsons, A. V. Palumbo and J.-Z. Zhou. 2008. Characterization of the Shewanella oneidensis Fur Gene: Roles in Iron and Acid Tolerance Response. BMC Genomics 9(Suppl 1):S11. Suppl Material: Figures S1 (jpg) and S2 (jpg)
  15. Yang, Y., M. Zhu, L. Wu, and J.-Z. Zhou. 2008. Assessment of Data Processing to Improve Reliability of Microarray Experiments Using Genomic DNA Reference. BMC Genomics 9(Suppl 2):S5 (doi:10.1186/1471-2164-9-S2-S5).
  16. Yin, H., G. Qiu, L. Wu, M. Xie, J. Zhou, Z. Dai, D. Wang, L. Kellogg, L. Cao and X. Liu (2008). "Microbial community diversity and changes associated with a mine drainage gradient at the Dexing copper mine, China". Aquatic Microbial Ecology 51:67-76.
  17. Yin, H. Q., L. Cao, G. Qiu, D. Wang, L. Kellogg, J.-Z. Zhou, X. Liu, Z. Dai, J. Ding, X. Liu. 2008. Molecular diversity of 16S rRNA and gyrB genes in copper mines. Archives of Microbiology, 189: 101-110.
  18. Yin, H., L. Cao, M. Xie, Q. Chen, G. Qiu, J.-Z. Zhou, L. Wu, D. Wang, X. Liu. 2008. Bacterial diversity based on 16S rRNA and gyrB genes at Yinshan mine, China. Syst. Appl. Microbiol. 31: 302-311.
  19. Zhou, J.-Z*, S. Kang*, C. W. Schadt, and C.T. Garten, Jr. 2008. Spatial Scaling of Functional Gene Diversity across Various Microbial Taxa. Proc. Nat. Acad. Sci, 105: 7768-7773 (*equal contribution). Supplementary Informaiton (pdf)
2007
  1. Amos, B. K., Y. Sung, K. E. Fletcher, T. J. Gentry, J.-Z. Zhou, and F. E. Löffler. 2007. Detection and Quantification of Geobacter lovleyi Strain SZ: Implications for Bioremediation at Tetrachloroethene- (PCE-) and Uranium-Impacted Sites. Appl. Environ. Microbiol. 73: 6898-6904.  Suppl text.
  2. Bender, K.S., H. Yen, C. L. Hemme, Z Yang, Z. He, Q. He, J.-Z. Zhou, K. Huang, E. J. Alm, T. C. Hazen, A. P. Arkin, and J. D. Wall. 2007. Analysis of a Ferric Uptake Regulator (Fur) Mutant of Desulfovibrio vulgaris Hildenborough. Appl. Environ. Microbiol. 73: 5389-5400.
  3. Bretschger, O., A Obraztsova, C. A. Sturm, I. Chang, Y. A. Gorby, S. B. Reed, D. E. Culley, C. L. Reardon, S.Barua, M.F. Romine, J.-Z. Zhou, A.S. Beliaev, R. Bouhenni, D. Saffarini, F. Mansfeld, B.H. Kim, J. K. Fredrickson, and K.H. Nealson. 2007. Current production and metal oxide reduction by Shewanella oneidensis MR-1 wild type and mutants. Appl. Environ. Microbiol. 73:7003-7012. Suppl Material: Methods (doc); Fig S1 (doc)
  4. Butler, J. E., Q. He, K. P. Nevin, Z. He, J.-Z. Zhou, D. R. Lovley. 2007. Genomic and microarray analysis of aromatics degradation in Geobacter metallireducens and comparison to a Geobacter isolate from a contaminated field site. BMC Genomics 8:180.
  5. Caffrey, S., H. S. Park, J. Voordouw, Z. He, J.-Z. Zhou, and Gerrit Voordouw. 2007. Function of Periplasmic Hydrogenases in the Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough. J. Bacteriol. 89: 6159–6167. Supplementary Information (xls)
  6. Gao, H., Z. K. Yang, T. J. Gentry, L.Wu, C. W. Schadt, and J.-Z. Zhou. 2007. Microarray-based Analysis of Microbial Community RNAs by Whole Community RNA Amplification (WCRA). Appl. Environ. Microbiol. 73: 563-571. (The 8th of the top 20 papers most requested in 2007 (January to March) by AEM).
  7. Garten, C.T., S. Kang, D.J. Brice, C. W. Schadt, and J.-Z. Zhou. 2007. Variability in Soil Properties at Different Spatial Scales (1 m to 1 km) in a Deciduous Forest Ecosystem. Soil Biol. Biochem. 39: 2621-2627.
  8. Gentry,T., C. Schadt, and J.-Z. Zhou. 2007. Functional gene array for microbial community analysis. Pp. 1052-1062. In Hurst, C.J, Crawford, R. L., Mills, A. L., Garland, J.L., Stetzenbach, L. D., and Lipson, D. A. (eds), The 3rd edition of the ASM Manual of Environmental Microbiology, (Invited), ASM Press, Washington DC.
  9. He, Z., T. J. Gentry, C. W. Schadt, L. Wu, J. Liebich, S. C. Chong, W.M. Wu, B. Gu, P. Jardine, C. Criddle, and J.-Z. Zhou. 2007. GeoChip: A comprehensive microarray for investigating biogeochemical, ecological, and environmental processes. The ISME Journal, 1: 67-77 (News Release by Nature Press Office: (http://www.nature.com/ismej/press_releases/index.html) (One of the top few highly cited in this Journal). Supplementary Information: Suppl1 (doc); Table of all probes (xls)
  10. Huang, Z., C. Zhang, B.P. Hedlund, J. Wiegel, J.-Z. Zhou. 2007. Molecular phylogeny of uncultivated Crenarchaeota in Great Basin hot springs of moderately elevated temperature. Geomicrobiology J. 24: 535-542.
  11. Leigh, M.B., V.H. Pellizari, O. Uhlik, R. Sutka, J. Rodrigues, N. E. Ostrom, J.-Z. Zhou, and J. M. Tiedje, 2007. Biphenyl-utilizing bacteria and their functional genes in a pine root zone contaminated with polychlorinated biphenyls (PCBs). ISME J. 1: 134-148.
  12. Luo, F., Y. Yang, C. Chen, J.-Z. Zhou, R. H. Scheuermann. 2007. Modular Organization of Protein Interaction Networks. Bioinformatics. 23: 207-214.
  13. Luo, W., W. Wu, T. Yan, C. S. Criddle, P. M. Jardine, J.-Z. Zhou, and B, Gu. 2007. Influence of Bicarbonate, Sulfate, and Electron Donors on Biological reduction of Uranium and Microbial Community Composition. Appl.Microbiol. Biotechnol. 77: 713-721.
  14. Luo*, F., D. Yang*, J. Zhong, H. Gao, L. Khan, D. K. Thompson and J.-Z. Zhou. 2007. Constructing gene co-expression networks and predicting functions of unknown genes by random matrix theory. BMC Bioinformatics, 8:299 (*Equal contribution). Suppl Material: Figures (pdf); RMT Notes (pdf); Tables (pdf)
  15. Mukhopadhyay A., A.M. Redding, M.P. Joachimiak, A.P. Arkin, S.E. Borglin, P.S. Dehal, R. Chakraborty, J.T. Geller, T.C. Hazen, Q.He, D.C. Joyner, V.J. J. Martin, J.D. Wall, Z. K. Yang, J.-Z. Zhou, and J.D. Keasling. 2007. Cell wide responses to low oxygen exposure in Desulfovibrio vulgaris Hildenborough. J. Bacteriol. 189:5996-6010. Suppl Material: ITRAQ Data (zip); Figure S1 (zip); Table S1 (zip
  16. Stolyar, S., Q. He, M.P. Joachimiak, Z. He, Z. K. Yang, S. E. Borglin, D.C. Joyner, K. Huang, E. Alm, T. C. Hazen, J.-Z. Zhou, J.D. Wall, A.P. Arkin, and D.A. Stahl. 2007. Response of Desulfovibrio vulgaris to alkaline stress. J. Bacteriol. 189: 8944-8952. Suppl Material: Tables S1 (zip), S2 (zip), S3 (zip); Figure S1 (zip
  17. Van Nostrand, J. D., T.V. Khijniak, T.J. Gentry, M.T. Novak, A.G. Sowder, J.-Z. Zhou, P.M. Bertsch and P.J. Morris. 2007. Isolation and Characterization of Four Gram-Positive Nickel-Tolerant Microorganisms from Contaminated Riparian Sediments. Microb. Ecol. 53: 670-682.
  18. Wagner M., H. Smidt, A. Loy, J.-Z. Zhou. 2007. Unravelling Microbial Communities with DNA-Microarrays: Challenges and Future Directions. Microbial Ecol. 53:498-506
  19. Wu, W., J. Carley, J. Luo, M. A Ginder-Vogel, E. Cardenas, M.B. Leigh, C.C. Hwang, S. D. Kelly, C. Ruan, L.Wu, J. Van Nostrand, T. Gentry , K. Lowe, T. Mehlhorn, S. Carroll, M. W. Fields, B. Gu, D. Watson, K. M. Kemner, T. Marsh, J.M. Tiedje, J.-Z. Zhou, Scott Fendorf, Peter K. Kitanidis, Philip M. Jardine, and Craig S. Criddle. 2007. In Situ Bioreduction of Uranium (VI) to Submicromolar Levels and Reoxidation by Dissolved Oxygen. Environ. Sci. Technol. 41: 5716-5723. Supplementary Information (pdf)
  20. Yang Y., M.Wan, W. Shi, H. Peng, G. Qiu, J.-Z. Zhou, X. Liu. 2007. Bacterial diversity and community structure in acid mine drainage from Dabaoshan Mine, China. Aquatic Microb. Ecol 47: 141-151.
  21. Yergeau, E., S. Kang, Z. He, J.-Z., Zhou, and G. A. Kowalchuk. 2007. Functional microarray analysis of nitrogen and carbon cycling genes across an Antarctic latitudinal transect. ISME J. 1: 163-179. Supplementary Information (pdf)
  22. Yin, H., L. Cao, G. Qiu, D. Wang, L. Kellogg, J.-Z. Zhou, Z. Dai, X. Liu, 2007. Development and evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in Acid Mine Drainages and bioleaching systems. J. Microbiol. Methods 70: 165-178.
  23. Zhang, Y., X. Zhang, X. Liu, Y. Xiao, L. Qu, L. Wu, J.-Z. Zhou, 2007. Microarray-based analysis of changes in diversity of microbial genes involved in organic carbon decomposition following land use/cover changes. FEMS Microbiol. Lett. 266: 144-151.
  24. Zhou, X., and J.-Z. Zhou. 2007. Antibody-microarrays on hybrid polymeric thin film-coated slides for multiple-protein Immunoassays., In: Rampal, JB (ed), Microarrays: Volume 2: Applications and Data Analysis, Vol. 382, Methods in Molecular Biology, The Humana Press Inc, New Jersey, USA Pp. 257-270. (Invited).
2006
  1. Bagwell, C. E., X. Liu, L. Wu, and J.-Z. Zhou. 2006. Effects of legacy nuclear waste on the compositional diversity and distributions of sulfate-reducing bacteria in a terrestrial subsurface aquifer. FEMS Microbiol. Ecol. 55:424-431.
  2. Brown, S. D., M. Martin, K. Huang, E. Alm, Y. Yang, A. Arkin, J.-Z. Zhou, and D. K. Thompson. 2006. Cellular Response of Shewanella oneidensis to Strontium Stress. Appl. Environ. Microbiol. 72: 890-900. Supplemental Material.
  3. Brown, S. D., M. R. Thompson, N. C. VerBerkmoes, K. Chourey, M. Shah, J.-Z. Zhou, R. L. Hettich, and D. K. Thompson. 2006. Molecular Dynamics of the Shewanella oneidensis Response to Chromate Stress. Molecular and Cellular Proteomics 5: 1054-1071. Suppl Material (link)
  4. Chhabra, S.R., Q. He, K. H. Huang, S. P. Gaucher, E. J. Alm, Z. He, M. Z. Hadi, T.C. Hazen, J. D. Wall, J.-Z. Zhou, A. P. Arkin, and A.K. Singh. 2006. Global Analysis of Heat Shock Response in Desulfovibrio vulgaris Hildenborough. J. Bacteriol. 188: 1817-1828. Suppl Material: Table S1 (zip); Table S2 (zip)
  5. Cho, C. M., T. Yan, X. Liu, L. Wu, J.-Z. Zhou, and L.Y. Stein. 2006. Transcriptome of Nitrosomonas europaea with a disrupted nitrite reductase (nirK) gene. Appl. Environ. Microbiol. 70:4450-4454. Supplemental Information (xls)
  6. Chourey, K., M. Thompson, J. Morrell-Falvey, N. C. VerBerkmoes, S. D. Brown, M. Shah, J.-Z. Zhou, M. Doktycz, R. L. Hettich, and D. K. Thompson. 2006. Global molecular and morphological effects of 24-hour chromium (VI) exposure on Shewanella oneidensis MR-1. Appl. Environ. Microbiol. 72: 6331-6344
  7. Clark, M.E., Q. He, Z. He, K. Huang, E.J. Alm, X. Wan, T.C. Hazen, A.P. Arkin, J.D. Wall, J.-Z. Zhou, and M.W. Fields. 2006. Temporal transcriptomic analysis of Desulfovibrio vulgaris Hildenborough transition into stationary phase growth during electron donor depletion. Appl. Environ. Microbiol. 72: 5578-5588. Supplementary Material.
  8. Fields, M.W., J. Schryver, C. C. Brandt, T. Yan, J.-Z. Zhou, and A.V. Palumbo. 2006. Confidence intervals for similarity values achieved from direct sequence determination of cloned SSU rRNA genes from environmental samples. J. Microbiol. Methods, 65: 144-152.
  9. Fields, M.F., C.E. Bagwell, S.L. Carroll, T. Yan, X. Liu, D.B. Watson, P.M. Jardine, C.S. Criddle, T.C. Hazen, and J.-Z. Zhou. 2006. Phylogenetic and functional biomarkers as indicators of bacterial community responses to mixed-waste contamination. Environ. Sci. Technol. 40: 2601-2607.
  10. Gao, H., Z. K. Yang, L. Wu, D. K. Thompson, and J.-Z. Zhou. 2006. Global Transcriptome Analysis of the Cold Shock Response of Shewanella oneidensis MR-1 and mutational analysis of its classical cold-shock proteins. J. Bacteriol. 188:4560-4569. Suppl Material: Figure S1 (doc); Table S1 (doc)
  11. Gao, H., A. Obraztova, N. Stewart, R. Popa, J. K. Fredrickson, J. M. Tiedje, K., H. Nealson, and J.-Z. Zhou. 2006. Shewanella loihica sp. nov., isolated from iron-rich microbial mats in Pacific Ocean. Int. J. Syst. Evol. Microbiol. 56: 1911-1916. Supplementary Material.
  12. Gao, W., Y. Liu, C. S. Giometti, L. Wu, X. Liu, T. Yan, D. Stanek, D. Xu, Y. Xu, M. W. Fields, and J.-Z. Zhou. 2006. Knock-out of SO1377 gene, which encodes the member of a conserved hypothetical bacterial protein family COG2268, results in alteration of iron metabolism, increased spontaneous mutation and hydrogen peroxide sensitivity in Shewanella oneidensis MR-1. BMC Genomics 7:76.
  13. Gentile, M, T. Yan, S. M. Tiquia, M. W. Fields, J. Nyman, J.-Z. Zhou, and C. S. Criddle. 2006. Stability and Resilience in a Denitrifying Fluidized Bed Reactor. Microb. Ecol. 52: 311-321.
  14. Gentry, T., Wickham, G.S, C.W. Schadt, and J.-Z. Zhou. 2006. Microarray applications in microbial ecology research. Microb. Ecol., 52:159-175 (Invited).
  15. Gentry, T., and J.-Z. Zhou. 2006. Microarrays-based microbial detection and characterization. In Advanced Techniques in Diagnostic Microbiology, Edited by Yi-Wei Tang and Charles W. Stratton, pp 276-290. Springer, New York, NY (Invited).
  16. He, Q., K. Huang, Z. He, E. Alm, M. W. Fields, T. C. Hazen, A. Arkin, J. D. Wall, and J.-Z. Zhou. 2006. Energetic Consequences of Nitrite Stress in Desulfovibrio vulgaris Hildenborough Inferred from Global Transcriptional Analysis. Appl. Environ. Microbiol. 72:4370-4381. Supplementary Information 1 (xls); 2 (xls); 3 (pdf)
  17. Hwang, C., W. Wu, T. J. Gentry, J. Carley, S. L. Carroll, C. Schadt, D. Watson, P. M. Jardine, J.-Z. Zhou, R. F. Hickey, C. S. Criddle, and M.W. Fields. 2006. Changes in bacterial community structure correlate with initial operating conditions of a field­scale denitrifying fluidized bed reactor. Appl. Microbiol. Biotechnol. 71：748-760.
  18. Leaphart, A. B., D. K. Thompson, K. Huang, E. Alm, X. Wan, A. Arkin, S. D. Brown, L. Wu, T. Yan, X. Liu, G. S. Wickham, and J.-Z. Zhou. 2006. Transcriptome Profiling of Shewanella oneidensis Gene Expression Following Exposure to Acidic and Alkaline pH. J. Bacteriol. 188:1633-42. Suppl Material: Table S1 (zip); Table S2 (doc)
  19. Liebich, J., S. C. Chong, C. Schadt, Z. He, and J.-Z. Zhou. 2006. Improvement of oligonucleotide probe design criteria for the development of functional gene microarrays for environmental applications. Appl. Environ. Microbiol. 72:1688-1691. Supplemental Material (doc)
  20. Luo, F., J. Zhong, Y. Yang, J.-Z. Zhou. 2006. Application of Random Matrix Theory to Microarray Profiles for Discovering Functional Gene Modules. Physical Review E 73 (031924), 1-5.
  21. Luo, F., J. Zhong, Y. Yang, R. H. Scheuermann, and J.-Z. Zhou. 2006. Application of random matrix theory to biological networks. Physics Lett. A: 357: 420-423.
  22. Mukhopadhyay A., Z. He , E. J. Alm, A.P. Arkin, E.E. Baidoo, S.C. Borglin, W.Chen, T.C. Hazen, Q. He, H.Y.Holman, K. Huang, R. Huang, D.C. Joyner, N. Katz, M. Keller, P. Oeller, A. Redding, J. Sun, J. D. Wall, J. Wei, Z. M Yang, H. Yen , J.-Z. Zhou and J.D. Keasling. 2006. Salt stress in Desulfovibrio vulgaris Hildenborough: An integrated genomics approach. J. Bacteriol. 188: 4068-4078.
  23. Qiu, X., M. J. Daly, A. Vasilenko, M. V. Omelchenko, E. K. Gaidamakova, L. Wu, J.-Z. Zhou, G. W. Sundin and J. M. Tiedje. 2006. Transcriptome Analysis Applied to Survival of Shewanella oneidensis MR-1 Exposed to Ionizing Radiation and Comparison to Deinococcus radiodurans. J. Bacteriol. 188:1199-1204.
  24. Rodríguez-Martínez, E.M., E. X. Pérez, C.W. Schadt, J.-Z. Zhou, and A.A. Massol-Deyá. 2006. Microbial Diversity and Bioremediation of a Hydrocarbon-Contaminated Aquifer in Vega Baja, Puerto Rico. International Journal of Environmental Research and Public Health: 3:292-300.
  25. Roh, Y., H. Gao, H. Vali, D. W. Kennedy, Z. K. Yang, W. Gao, A. C. Dohnalkova, R. D. Stapleton, J. W. Moon, T. J. Phelps, J. K. Fredrickson, and, J.-Z. Zhou. 2006. Metal Reduction and Iron Biomineralization by a Psychrotolerant Fe(III)-Reducing Bacterium Shewanella sp. PV-4. Appl. Environ. Microbiol. 72:3236-3244.
  26. Schadt C. W., and J.-Z. Zhou. 2006. Advances in Microarrays for Soil Microbial Community Analyses. In: Soil Biology Volume 8: Nucleic Acids and Proteins in Soil (Nannipieri, P. & Smalla K., eds). Springer-Verlag, Pp189-203.
  27. Walker, C. B., S. S. Stolyar, N. Pinel, H. Yen, Z. He, J.-Z. Zhou, J. D. Wall, D. A. Stahl. 2006. Recovery of temperate Desulfovibrio vulgaris bacteriophage using a novel host strain. Environ. Microbiol. 8:1950-1959. Supplementary Material.
  28. Wan, X., J.- Z. Zhou, and D. Xu. 2006. CodonO: a new informatics method for measuring synonymous codon usage bias within and across genomes. International Journal of General Systems 35:109-125.
  29. Wei, X., T. Yan, N. G. Hommes, X. Liu, L. Wu, C. McAlvin, M.G. Klotz, L.A. Sayavedra-Soto, J.-Z. Zhou, and D. J. Arp. 2006. Transcript profile of Nitrosomonas europaea during growth and ammonia/carbonate deprivation. FEMS Microbiology Lett. 257:76-83.
  30. Windt, W.D, H. Gao, W. Krömer, J. Dick, N. Boon, J.-Z. Zhou, and W. Verstraete. 2006. AggA is required for aggregation and increased biofilm formation of a hyper-aggregating mutant of Shewanella oneidensis MR-1. Microbiology 152: 721-729. Suppl Material (pdf)
  31. Wu*, L., X. Liu, C. W. Schadt, and J.-Z. Zhou*. 2006. Microarray-based analysis of sub-nanogram quantities of microbial community DNAs using Whole Community Genome Amplification (WCGA). Appl. Environ. Microbiol. 72:4931-4941. Suppl Material: file 1 (pdf); file 2 (pdf); file 3 (doc) (*equal contribution, The 11th of the top 20 papers most requested in 2006 October to December by AEM).
  32. Wu, W.M., J. Carley, T. Gentry, M. A. Ginder-Vogel, M. Fienen, T. Mehlhorn, H. Yan, S. Caroll, J. Nyman, J. Luo, M. E. Gentile, M. W. Fields, R. F. Hickey, D. Watson, S. Fendorf, J.-Z. Zhou, P. Kitanidis, P. M. Jardine, and C. S. Criddle. 2006. Pilot-scale in situ bioremedation of uranium in a highly contaminated aquifer. 2. Reduction of U(VI) and geochemical control of U(VI) bioavailability. Environ. Sci. Technol. 40: 3986-3995. Supplementary Information (pdf). (Most-Cited Article Published in 2006, Thomson Scientific (ISI) Essential Science Indicators, most citations through the period ending December 31, 2007: “Hot Paper” Achievement 2008, Thomson Scientific (ISI) Essential Science Indicators, most citations in a two-month period for a paper published within the past two years).
  33. Yan, T., J.-Z. Zhou, and C. Zhang. 2006. Diversity of functional genes for methanotrophs in sediments associated with gas hydrates and hydrocarbon seeps in the Gulf of Mexico. FEMS Microbiol.Ecol. 57: 251-259.
  34. Zhou, X., and J.-Z. Zhou. 2006. Oligosaccharide microarrays fabricated on aminooxyacetyl functionalized glass surface for characterization of carbohydrate-protein interaction. Biosensors & Bioelectronics. Biosensors & Bioelectronics 21: 1451-1458.
  35. Zhou, X., J.-Z. Zhou. 2006. Protein microarrays on hybrid polymeric thin films prepared by self-assembly of polyelectrolytes for multiple-protein immunoassays. Proteomics, 6:1415-1426.
  36. Zhu, M., Q. Wu, Y. Yang, J.-Z. Zhou. 2006. A New Approach to Identify Functional Modules Using Random Matrix Theory. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology 1:117-123.
2005
  1. Beliaev, A. S., D. M. Stanek, J. A. Klappenbach, L. Wu, D. A. Saffarini, M. F. Romine, K. H. Nealson, J. K. Fredrickson, and J.-Z. Zhou. 2005. Global transcriptome analysis of Shewanella oneidensis MR-1 exposed to different terminal electron acceptors. J. Bacteriol. 187:7138-7145. Suppl Material: Tables S1-2 (zip); Tables S3-12 (zip)
  2. Bencheikh-Latmani, R., S. M. Williams, L. Haucke, C. S. Criddle, L. Wu, J.-Z. Zhou, B. M. Tebo. 2005. Global Transcriptional Profiling of Shewanella oneidensis MR-1 During Cr(VI) and U(VI) Reduction. Appl. Environ. Microbiol. 71:7453-7460. Suppl Material (pdf)
  3. Fields, M.W., T. Yan, S. K. Rhee, S. L. Carroll, P. Jardine, C. S. Criddle and J.-Z. Zhou. 2005. Impacts on microbial communities and cultivable isolates from ground water contaminated with high levels of nitric acid–uranium waste. FEMS Microbiol. Ecol. 53: 417–428
  4. Gao, W., Y. Liu, J.-Z. Zhou, and H. Pan. 2005. Effects of a Strong Static Magnetic Field on Bacterium Shewanella oneidensis: An Assessment by Using Whole Genome Microarray. Bioelectromagnetics, 26:2-6.
  5. Gu, B., W. Wu, M. A. Ginder-Vogel, H. Yan, M. W. Fields, J.-Z. Zhou, S. Fendorf, C. S. Criddle, and P. M. Jardine. 2005. Bioreduction of Uranium in a Contaminated Soil Column. Environ. Sci. Technol. 39: 4841-4847.
  6. He, Z., L. Wu, M. W. Fields, J.-Z. Zhou. 2005. Use of Microarrays with Different Probe Sizes for Monitoring Gene Expression. Appl. & Environ. Microbiol. 71: 5154–5162. Supplementary Information (xls)
  7. He, Z., L. Wu, X. Li, M. W. Fields, J.-Z. Zhou. 2005. Empirical establishment of oligonucleotide probe design criteria using perfect match and mismatch probes and artificial targets. Appl. & Environ. Microbiol, 71:3753-3760. Suppl Material: Figure S1 (zip); Tables (doc) (Listed as one of the top 20 papers most requested in 2005 by AEM).
  8. Kataeva, I., J. Chang, H. Xu, C. Luan, J.-Z. Zhou, V. N. Uversky, D. Lin, P. Horanyi, Z. Liu, L. G. Ljungdahl, J. Rose, M. Luo, and B. Wang. 2005. Improving solubility of Shewanella oneidensis MR-1 and Clostridium thermocellum JW-20 proteins expressed into Esherichia coli. J. Proteome Res. 4:1942-1951.
  9. Kolker, E., A. F. Picone, M. Y. Galperin, M. F. Romine, R. Higdon, K. S. Makarova, N. Kolker, G. A. Anderson, K. J. Auberry, G. Babnigg, A. S. Beliaev, P. Edlefsen, D. A. Elias, Y. Gorby, T. Holzman, J. Klappenbach, K. T. Konstantinidis, M. L. Land, M. S. Lipton, L. McCue, M. Monroe, L. Pasa-Tolic, G. Pinchuk, S. Purvine, X Qiu, M. Serres, S. Tsapin, B. A. Zakrajsek, W. Zhu, J.-Z. Zhou, F. W. Larimer, C. Lawrence, M. Riley, F. R. Collart, J. R. Yates, III, R. D. Smith, C. Giometti, K. Nealson, J. K. Fredrickson, and J. M. Tiedje. 2005. Global Profiling of Shewanella oneidensis MR-1: Expression of ‘Hypothetical’ Genes and Improved Functional Annotations. Proc. Nat. Acad. Sci.USA 102: 2099-2104. Suppl Material (link)
  10. Li, X., Z. He, and J.-Z. Zhou. 2005. Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation. Nucleic Acids Res. 33:6114-6123.
  11. Liu, Y., W. Gao, T. Yan, L. Wu, X. Liu, E. Alm, S. Wang, A. Arkin, M. W. Fields, D. K. Thompson, and J.-Z. Zhou. 2005. Transcriptome Analysis of Shewanella oneidensis MR-1 in Response to Elevated Salt Conditions. J. Bacteriol. 187: 2901-2907.
  12. Oda, Y., S. K. Samanta, L. Wu, X. Liu, T. Yan, J.-Z. Zhou, C. S. Harwood. 2005. A functional genomic analysis of three nitrogenase isozymes in the photosynthetic bacterium Rhodopseudomonas palustris. J. Bacteriol. 187: 7784-7794. Supplementary Information (pdf)
  13. Qiu, X., G. W. Sundin, L. Wu, J.-Z. Zhou, and J. M. Tiedje. 2005. Comparative analysis of differentially expressed genes in Shewanella oneidensis MR-1 following UVA-, UVB- and UVC exposure. J. Bacteriol. 187: 3556-3564. Suppl Material: Text (doc); Figures (ppt)
  14. Stapleton, R., Z. L. Sabree, A. V. Palumbo, C. Moyer, A. Devol, Y. Roh, and J.-Z. Zhou. 2005. Metal reduction at cold temperatures by Shewanella isolates from various marine environments. Aquatic Microbiol. 38: 81–91.
  15. Wu, W., B. Gu, M. W. Fields, M. Gentile,Y. Ku, H. Yan, S. Tiquia, T. Yan, J. Nyman, J.-Z. Zhou, P.M. Jardine, C. S. Criddle. 2005. Uranium (VI) Reduction by Denitrifying Biomass. Bioremediation J., 9:49-61.
2004
  1. Gao, H., Y. Wang, X. Liu, T. Yan, L. Wu, E. Alm, A. Arkin, D. K. Thompson, and J.-Z. Zhou. 2004. Global Transcriptome Analysis of the Heat Shock Response of Shewanella oneidensis. J. Bacteriol., 186: 7796-7803. SupplMat: Figure (doc), Table (xls)
  2. Liu, Y., A. Venkateswaran, and J.-Z. Zhou, 2004. Functional Genomic Analysis of Deinococcus radiodurans Resistance to Ionizing Radiation. European Symposium on Environmental Biotechnology on April 25-28, 2004.
  3. Luo, F., L. Khan, F. Bastani, I. Yen and J.-Z. Zhou. 2004. A Dynamically Growing Self-organizing Tree (DGSOT) for Hierarchical Clustering Gene Expression Profiles. Bioinformatics 20: 2605-2617.
  4. Palumbo, A.V., J. Schryver, M. Fields, C. Bagwell, and J.-Z. Zhou, T. Yan, X. Liu, and C. T. Brandt. 2004. Coupling of Functional Gene Diversity and Geochemical Data from Environmental Samples. Appl. Environ. Microbiol. 70:6525-6534.
  5. Post, V.M, R.C. Izaurralde, J.D. Jastrow, B.A. McCarl, J.E. Amonette, V.L. Bailey, P.M. Jardine, T.O. West, J.-Z. Zhou. 2004. Enhancement of Carbon Sequestration in U.S. Soils. BioScience 54: 895-908.
  6. Qiu, X., R. A. Hurt, L.. Wu, C. Chen, J. M. Tiedje, and J.-Z. Zhou. 2004. Detection and quantification of copper-denitrifying bacteria by quantitative competitive PCR. J. Microbiol. Methods 59:199-210.
  7. Rhee*, S.K, X. Liu, L. Wu, S. C. Chong, X. Wan and J.-Z. Zhou*. 2004. Detection of genes involved in biodegradation and biotransformation in microbial communities using 50-mer oligonucleotide microarrays. Appl. Environ. Microbiol. 70:4303-4317 (*Equal contribution).
  8. Schadt, C. W., J. Liebich, S. C. Chong, T. J. Gentry, Z. He, H. Pan and J.-Z. Zhou. 2004. Design and Use of Functional Gene Microarrays (FGAs) for the Characterization of Microbial Communities. In: Savidge T, Pothulakis H (eds) Methods in Microbiology V34: Microbial Imaging, pp331-368, Academic Press, London (Invited).
  9. Tiquia, S.M., M.W. Fields, and J.-Z. Zhou. 2004. Oligonucleotide-based functional gene arrays for analysis of microbial communities in the environment. In: Molecular Microbial Ecology Manual. Kowalchuk, G.G.; de Bruijn, F.J.; Head, I.M.; Akkermans, A.D.; van Elsas, J.D. (Eds.), Kluwer Academic Publishers, pp. 1743-1763.
  10. Tiquia, S.M., L.Wu, S.C. Chong, S. Passovets, D. Xu, Y. Xu, and J.-Z. Zhou. 2004. Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples. Biotechniques. 36: 664-675.
  11. Wan, X., N.C. VerBerkmoes, L. A. McCue, D. Stanek, H. Connelly, L. Wu, X. Liu, T. Yan, A. Leaphart, R. L. Hettich, J.-Z. Zhou, and D. K. Thompson. 2004. Transcriptomic and proteomic characterization of the fur modulon in the metal-reducing bacterium Shewanella oneidensis. *Equal contribution. J. Bacteriol. 186: 8385-8400.
  12. Wan, X., D. Xu, A. Kleinhofs and J.-Z. Zhou. 2004. Quantitative relationship between synonymous codon usage bias and GC composition across the unicellular genomes. BMC Evolutionary Biology 2004, 4:19.
  13. Wu, L., D. K. Thompson, X. Liu, M. W. Fields, C. E. Bagwell, J. M. Tiedje, and J.-Z. Zhou. 2004. Development and evaluation of microarray-based whole-genome hybridization for detection of microorganisms within the context of environmental applications. Environ. Sci. Technol. 38: 6775-6782. Supplementary Information (pdf)
  14. Ye, Q., Y. Roh, S. L. Carroll, B. Blair, J.-Z. Zhou, C. Zhang and M. W. Fields. 2004. Alkaline, anaerobic respiration: isolation and characterization of a novel, alkaliphilic, metal-reducing bacterium. Appl. Environ. Microbiol. 70: 5595-5602.
  15. Zhou, X., and J.-Z. Zhou. 2004. Improving the signal sensitivity and photostability of DNA hybridizations on microarrays by using dye-doped core-shell silica nanoparticles. Anal. Chem. 76:5302-5312.
  16. Zhou, J.-Z., and D. K. Thompson. 2004. Microarray technology and applications in environmental microbiology. Vol 82. In: Sparks D.L. (Editor-in-Chief), Advances in Agronomy. Academic Press, New York pp 183-268 (Invited). http://onlinelibrary.wiley.com/book/10.1002/0471647527
  17. Zhou, J.-Z., D.K. Thompson, Y. Xu, and James M. Tiedje. 2004. Microbial Functional Genomics. 624pp. John Wiley & Sons, Hoboken, New Jersey. (First comprehensive book in this field)
  18. Zhou, J.-Z., B. Xia, H. Huang, A.V. Palumbo, and J. M. Tiedje. 2004. Microbial diversity and heterogeneity in sandy subsurface soils. Appl. Environ. Microbiol. 70: 1723-1734.
  19. Zhou, X., L. Wu, J.-Z. Zhou. 2004. Fabrication of DNA microarrays on nanoengineered polymeric ultrathin film prepared by self-assembly of polyelectrolyte multilayers. Langmuir 20: 8877-8885.
2003
  1. Liu, X., C. Bagwell, L. Wu, A. H. Devol, and J.-Z. Zhou. 2003. Molecular Diversity of Sulfate-Reducing Bacteria from Two Different Continental Margin Habitats. Appl. Environ. Microbiol. 69:6073-6081 (*Equal contribution).
  2. Liu, X., S. M. Tiquia, G. Holguin, L. Wu, S. C. Nold, A. H. Devol, K. Luo, A. V. Palumbo, J. M. Tiedje, and J.-Z. Zhou. 2003. Molecular diversity of denitrifying genes in continental margin sediments within the oxygen deficient zone of the Pacific Coast of Mexico. Appl. Environ. Microbiol. 69:3549-3560.
  3. Liu*, Y., J.-Z. Zhou*, M. Omelchenko, A. Beliaev, A. Venkateswaran, J. Stair, L. Wu, D. K. Thompson, D. Xu, I. B. Rogozin, E. K. Gaidamakova, M. Zhai, K. S. Makarova, E. V. Koonin, and M. J. Daly. 2003. Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation. PNAS, 100: 4191-4196. *equal contribution. (Commentary by Jeremy S.Edwards and John R. Battista. 2003. TRENDS in Biotechnology: 21: 381-382).  Supplemental Information (website)
  4. Palumbo, A.V., S. Fisher, J. R. Tarver, W. L. Daniels, Z. Yang, S. M. Tiquia, L. Wu, and J.-Z. Zhou, and J. Amonette,. 2003. Issues with the Use of Fly Ash for Carbon Sequestration Proceedings of the Second National Conference on Carbon Sequestration. Hilton Mark Center, Alexandria, Virginia. May 5-8, 2003.
  5. Roh, Y., C. Zhang, H. Vali, R.J. Lauf, J.-Z. Zhou, and T. J. Phelps. 2003. Biogeochemical and environmental factors in Fe biomineralization: magnetite and siderite formation. Clays and Clay Minerals. 51: 83-95.
  6. Treves, D. S., B. Xia, J.-Z. Zhou and J. M. Tiedje. 2003. A Two-Species Test of the Hypothesis That Spatial Isolation Influences Microbial Diversity in Soil. Microb. Ecol. 45:20-8.
  7. Wan, X., D. Xu, and J.-Z. Zhou. 2003. A new informatics method for measuring synonymous codon usage bias. In: Intelligent engineering systems through artificial neural networks, vol 13, eds. Dagli et al., p1101-1018. New York, NY: ASME Press
  8. Yan, T., M. W. Fields, L. Wu, Y. Zu, J. M. Tiedje and J.-Z. Zhou. 2003. Molecular diversity and characterization of nitrite reductase gene fragments (nirK and nirS) from nitrate- and uranium-contaminated groundwater. Environ. Microbiol. 5:13-24 (*equal contribution).
  9. Yost, C., L. Hauser, F. Larimer, D.K. Thompson, A. Beliaev, J.-Z. Zhou, Y. Xu, and D. Xu. 2003. A computational study of Shewanella oneidensis MR-1: Structural prediction and functional inference of hypothetical proteins. Omics 7:177-191.
  10. Zhou, J.-Z. 2003. Microarrays for bacterial detection and microbial community analysis. Curr. Opion. Microbiol. 6:288-294 (Invited).
  11. Zhou, J.-Z., and D. K. Thompson. 2003. Microarrays: Application in environmental microbiology. p. 1968-1979. Bitton, G. (Editor in Chief), The Encyclopedia in Environmental Microbiology, John Wiley & Sons, New York. (Invited)
  12. Zhou, J.-Z., B. Xia, H. Huang, D. S. Treves, L. J. Hauser, R. J. Mural, A. V. Palumbo, and J. M. Tiedje. 2003. Bacterial phylogenetic diversity and a novel candidate division of two humid region, sandy surface soils. Soil Biol. Biochem. 35:915-924.
2002
  1. Beliaev, A. S., D. K. Thompson, C. S. Giometti, G. Li, J. Yates III, K. H. Nealson, J.M. Tiedje, J. F. Heidelberg, and J.-Z. Zhou. 2002. Gene and Protein Expression Profiles of Shewanella oneidensis During Anaerobic Growth with Different Electron Acceptors. Omics: A Journal of Integrative Biology 6: 39-60.
  2. Beliaev, A. S., D. K. Thompson, M. Fields, L. Wu, D. P. Lies, K. H. Nealson, and J.-Z. Zhou. 2002. Microarray Transcription Profiling of a Shewanella oneidensis etrA Mutant. J. Bacteriol. 184: 4612-4616.
  3. Gu, B., D. B. Watson, L. Wu, D. H. Phillips, D. C. White, and J.-Z Zhou. 2002. Microbiological characteristics in a zero-valent iron reactive barrier. Environ. Monitoring Assessment: 77: 293-309.
  4. Palumbo A. V., J.-Z. Zhou, C. Zhang, R. D. Stapleton, B. L. Kinsall, and T. M. Phelps. 2002. Biotransformations and biodegradation in extreme environments. P. 549-571. In Biotransformations: Bioremediation Technology for Health and Environmental Protection (eds. Singh, V. P. and Stapleton, R. D.). Elsevier, London.
  5. Roh, Y., S. Liu, G. Li, H. Huang, T. J. Phelps, and J.-Z. Zhou. 2002. Isolation and characterization of metal-reducing Thermoanaerobacter strains from deep subsurface environments. Appl. Environ. Microbiol., 68:6013-6020.
  6. Schut, G. J., J.-Z. Zhou, and M. W. Adams. 2002. DNA microarray analysis of the hyperthermophilic archaeon Pyrococcus furiosus: Evidence for a new type of sulfur-reducing enzyme complex. J. Bacteriology 183: 7027-7036.
  7. Taranenko N. I., R. Hurt, J.-Z. Zhou, N. R. Isola, H. Huang, S.H. Lee, C. H. Chen. 2002. Laser desorption mass spectrometry for microbial DNA analysis. J. Microbiol. Methods 48: 101-106.
  8. Thompson, D.K., A. S. Beliaev, C. S. Giometti, S. L. Tollaksen, T. Khare, D. P. Lies, K. H. Nealson, H. Lim, J. Yates III, C. C. Brandt, J. M. Tiedje, and J.-Z. Zhou. 2002. Transcriptional and Proteomic Analysis of a Ferric Uptake Regulator (Fur) Mutant of Shewanella oneidensis: Possible Involvement of Fur in Energy Metabolism, Transcriptional Regulation, and Oxidative Stress. Appl. Environ. Microbiol. 68:881-892.
  9. Xu, D., G. Li, L. Wu, J.-Z. Zhou, and Y. Xu. 2002. PRIMEGENS: A Computer Program for Robust and Efficient Design of Gene-Specific Targets on Microarrays. Bioinformatics, 18:1432-1437, 2002.
  10. Zhou, J.-Z., and J. H. Miller. 2002. Microbial genomics, challenges and opportunities, The 9th International Conference on Microbial Genomes. J. Bacteriol. 184: 4327-4333 (Invited).
  11. Zhou, J.-Z., and D. K. Thompson. 2002. Challenges in applying microarrays to environmental studies. Curr. Opion. Biotech. 13:204-207. (Invited)
  12. Zhou, J.-Z., and J. M. Tiedje. 2002. New DOE program expands dramatically beyond microbial genomics. ASM News: 68:110-111 (Invited).
  13. Zhou, J.-Z., B. Xia, D. S. Treves, T. L. Marsh, R. V. O’Neill, L. Wu, A. V. Palumbo and J. M. Tiedje. 2002. Spatial and resource factors influencing high soil microbial diversity. Appl. Environ. Microbiol. 68: 326-334.
2001
  1. Gruntzig, V., S. C. Nold, J.-Z. Zhou, and J. M. Tiedje. 2001. Pseudomonas stutzeri nitrite reductase gene abundance in environmental samples measured by real-time PCR. Appl. Environ. Microbiol. 67: 760-768.
  2. Hurt, R. A., X. Qiu, L. Wu, Y. Roh, A. V. Palumbo, J. M. Teidje, and J.-Z. Zhou. 2001. Simultaneous Extraction of RNA and DNA from Environmental Samples. Appl. Environ. Microbiol. 67: 4495-4503.
  3. Murray, A. E., D. Lies, G. Li, K. Nealson, J.-Z. Zhou, J. M. Tiedje. 2001. DNA:DNA hybridization to microarrays reveals gene-specific differences between closely related microbial genomes. Proc. Natl. Sci. Acad. USA 98: 9853-9858. Supplemental Information: Table 2 (xls), Fig 4 (website), Fig 5 (website)
  4. Qiu, X., L. Wu, H. Huang, P. E. McDonel, A.V. Palumbo, J. M. Tiedje, and J.-Z. Zhou. 2001. Evaluation of PCR-generated chimeras, mutations, and heteroduplexes with 16S rRNA gene-based cloning. Appl. Environ. Microbiol. 67: 880-887.
  5. Schut, G. J., J.-Z. Zhou, and M. W. W. Adams. 2001. DNA microarray analysis of the hyperthermophilic archaeon Pyrococcus furiosus: Evidence for a new type of sulfur-reducing enzyme complex. J. Bacteriology 183: 7027-7036
  6. Sepulveda-Torres, L. C., J.-Z. Zhou, C. Guasp, J. Lalucat, D. Knaebel, J. L. Plank and C. S. Criddle. 2001. Pseudomonas strain KC represents a new genomovar within Pseudomonas stutzeri. Int. Syst. J. Bact. 51: 2013-2019.
  7. Tiedje, JM, JC Cho, A Murray, D Treves, B Xia, and J Zhou. Soil teeming with life: new frontiers for soil science. In: (eds RM Rees, BC Ball, CD Campbell, CA Watson) Sustainable Management of Soil Organic Matter. CAB International.
  8. Wu, L., D. Thompson, G. Li, R. Hurt, H. Huang, J. M. Tiedje, and J.-Z. Zhou. 2001. Development and Evaluation of Functional Gene Arrays for Detection of Selected Genes in the Environment. Appl. Environ. Microbiol. 67: 5780-5790.
  9. Xia, B., D. S. Treves, J.-Z. Zhou, J. M. Tiedje. 2001. Soil microbial community diversity and driving mechanisms. Prog. Nat. Sci. 11: 818-824.
  10. Zhang, C., J. Horita, D. R. Cole, J.-Z. Zhou, D. R. Lovley, and T. J. Phelps. 2001. Temperature-dependent oxygen and carbon isotope fractions of biogenic siderite. Geochimica et Cosmochimica Acta. 65: 2257-2271.
  11. Zhou, J.-Z., S. Liu, B. Xia, C. Zhang, A. V. Palumbo, and T. J. Phelps. 2001. Molecular characterization and diversity of thermophilic iron-reducing enrichment cultures from deep subsurface environments. J. Appl. Microbiol. 90: 96-105.
2000
  1. Braker, G., J.-Z. Zhou, L. Wu, A. H. Devol, and J. M. Tiedje. 2000. Nitrite Reductase Genes (nirK and nirS) as Functional Markers to Investigate Diversity of Denitrifying Bacteria in Marine Sediment Communities. Appl. Environ. Microbiol. 66: 2096-2104.
  2. Nold, S. C., J.-Z. Zhou, A. H. Devol, and J. M. Tiedje. 2000. Pacific Northwest marine sediments contain-Proteobacterial ammonia oxidizing bacteria. Appl. Environ. Microbiol. 66: 4532-4535.
  3. Xia, B., J.-Z. Zhou, J. M. Tiedje. 2000, Structure of bacterial community in soil environment and its ecological characteristics, Acta Ecologica Sinica 20(4): 1201-1209.
  4. Xu, D., Y. Xu, G. Li, and J.-Z. Zhou. 2000. A computer program for generating gene-specific fragments for microarrays. P. 3-4, In Miyano, S., R. Shamir, and T. Takagi (eds), Currents in Computational Molecular Biology, Universal Academy Press, Inc, Tokyo, Japan.
  5. Zhou, J.-Z. and A. V. Palumbo. 2000. Sequence to function: The 7th Conference on Small Genomes. Genetica 108: vii-ix.
  6. Zhou, J.-Z., B. Xia, L. Wu, R. V. O’Neill, A. V. Palumbo, and J. M. Tiedje. 2000. Unusual diversity in soil microbial communities. The 6th Chinese Society of Ecology. P. 29-40 (Invited).
1986-1999
  1. Li, G., and J.-Z Zhou. 1999. Genomics, microarray-based genomic technology and potential ecological applications. The 3rd Conference on Molecular Ecology, Beijing, P. 29-40 (Invited).
  2. Palumbo, A. V., J.-Z. Zhou, T. J. Phelps, B. Kinsall, C. Zhang, E. L. Majer, J. E. Peterson, T. Griffin, S. M. Pfiffner. 1999. Ecology and bioremediation: a staged approach to site characterization. Uzochukwu and Reddy (eds), Proceedings of the 1998 National Conference on Environmental Remediation Science and Technology. Battelle Press, pp. 195-202.
  3. Song, B., M. M. Haggblom, J.-Z. Zhou, J. M. Tiedje, and N. J. Palleroni. 1999. Taxonomic characterization of aromatics-degrading denitrifying bacteria: Description of Azoarcus sp. nov. and Azoarcus sp. nov. Int. Syst. J. Bact. 49: 1129-1140.
  4. Zhang C., R. Stapleton, J.-Z. Zhou, A. V. Palumbo, and T. J. Phelps. 1999. Iron reduction by psychrophilic enrichment cultures. FEMS Microb. Ecol. 30: 367-371.
  5. Zhou. J.-Z., A. V. Palumbo and J. M. Strong-Gunderson. 1999. Phylogenetic characterization of a mixed microbial community capable of degrading carbon tetrachloride. Appl. Biochem. Biotechnol. 80: 243-253.
  6. Dedysh, S. N., N. S. Panikov, W. Liesack, R. Grobkopf, J.-Z. Zhou, and J. M. Tiedje. 1998. Isolation of acidophilic methane-oxidizing bacteria from northern peat wetlands. Science 282: 281-284.
  7. Xia, B., J.-Z. Zhou, J. M. Tiedje 1998. Effect of vegetation on structure of soil microbial community. Chinese Journal of Applied Ecology 9(3): 296-300
  8. Xia, B., J.-Z. Zhou, J. M. Tiedje. 1998. Application of molecular methods in microbial ecology. Acta Scientiarum Naturalium Universitatis Sunyatseni 37(2): 97-101
  9. Xia, B., J.-Z. Zhou, J. M. Tiedje. 1998. Effect of overlying vegetation on soil microbial community structure and their activity. Acta Scientiarum Naturalium Universitatis Sunyatseni 37(3): 94-98
  10. Zhou, J.-Z., S. V. Liu, C., Zhang, A. V. Palumbo, and T. J. Phelps. 1998. Extremophilic iron-reducing bacteria: Their implications for possible life in extraterrestrial environments. The Third Symposium of Chinese Young Scientists, p. 47-52, Beijing, P. R. China.
  11. Liu, S., J.-Z. Zhou, C. Zhang, D. R. Cole and T. J. Phelps. 1997. Thermophilic Fe(III)-reducing bacteria from the deep subsurface: The evolutionary implications. Science 277: 1106-1109.
  12. Massol-Deya, A., R. Weller, L. Rio-Hernandez, J.-Z. Zhou, R. F. Hickey, and J. M. Tiedje. 1997. Succession and convergence of biofilm communities in fixed-film reactors treating aromatic hydrocarbons in groundwater. Appl. Environ. Microbiol. 63: 270-276.
  13. Tiedje, J.M., K. Nüsslein, J.-Z. Zhou, B. Xia, C. Moyer, and F. Dazzo. 1997. The vast world of microbial diversity. In The 5th International Symposium on New Frontiers in Microbiology by the Japan Science and Technology Corporation. January 30-31, 1997, Tokyo, Japan.
  14. Tiedje, J. M., J.-Z. Zhou, K. Nusslein, C. Moyer and R. R. Fulthorpe. 1997. Extent and patterns of soil microbial diversity. P. 35-41. In Martins, M. T. et al. (eds). Progress in Microbial Ecology, Brazilian Society for Microbiology, Sao Paulo.
  15. Zhou, J.-Z., M. E. Davey, J. B. Figueras, E. Rivkina, D. Gilichinsky, and J. M. Tiedje. 1997. Phylogenetic diversity of a bacterial community determined from Siberian tundra soil DNA. Microbiology 143:3913-3919.
  16. Zhou, J.-Z., A. V. Palumbo, and J. M. Tiedje. 1997. Sensitive detection of a novel class of toluene-degrading denitrifiers, Azoarcus tolulyticus using SSU rRNA primers and probes. Appl. Environ. Microbiol. 63: 2384-2390.
  17. Chee-Sanford, J.C., J. W. Frost, M. R. Fries, J.-Z. Zhou, and J. M. Tiedje. 1996. Evidence for acetyl coenzyme A and cinnamoyl coenzyme A in the anaerobic toluene mineralization pathway in Azoarcus tolulyticus Tol-4. Appl. Environ. Microbiol. 62: 964-973.
  18. Shih, C. C., M. E. Davey, J.-Z. Zhou, J. M. Tiedje, and C. S. Criddle. 1996. Effects of phenol feeding pattern on microbial community structure and cometabolism of trichloroethylene. Appl. Environ. Microbiol. 62: 2953-2960.
  19. Tiedje, J. M., and J.-Z. Zhou. 1996. Analysis of non-culturable bacteria. pp. 53-65. In Methods for the examination of organismal diversity in soils and sediments, (G. S. Hall, ed). CAB International, New York.
  20. Zhou, J.-Z., and A. Kleinhofs. 1996. Molecular evolution of nitrate reductase genes. J. Mol. Evol. 42: 432-442.
  21. Zhou, J.-Z., M. A. Bruns, and J. M. Tiedje. 1996. DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62: 316-322. (Among the most highly cited 20 papers for all papers published in Applied and Environmental Microbiology, since January, 2008)
  22. Zhou, J.-Z., S. Ma, and G. W. Hinman. 1996. Ecological exergy analysis: A new method for ecological energetics study. Ecological Modeling 84: 291-303.
  23. Zhou, J.-Z., M. R. Fries, J. C. Chee-Sanford, and J. M. Tiedje. 1995. Phylogenetic analyses of a new group of denitrifiers capable of anaerobic growth on toluene: Description of Azoarcus tolulyticus sp. nov. Int. J. Syst. Bacterol. 45: 500-506.
  24. Zhou, J.-Z., A. Kilian, R. L. Warner, and A. Kleinhofs. 1995. Variation of nitrate reductases genes in grass species. Genome 38: 919-927.
  25. Zhou, J.-Z., and J. M. Tiedje. 1995. Gene transfer from a bacterium injected into an aquifer to an indigenous bacterium. Mol. Ecol. 4: 613-638.
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