Skip Navigation

Research

Skip Side Navigation

IEG Research Interests


The mission of IEG is to advance scientific research and education in environmental genomics and stimulate bio-economic development. We aim to address scientific challenges related to (i) defining gene function, (ii) delineating gene regulatory networks (iii) developing a systems-level understanding of biological systems beyond individual cells, and (iv) creating computational simulations of biological systems. 

Research Interests

The Institute for Environmental Genomics has research interests in functional and comparative genomics, microbial ecology and community genomics, and development of metagenomic and bioinformatic tools.  Our current projects include the experimental evolution of Desulfovibrio vulgaris Hildenborough under a variety of stress conditions, developing gene manipulation tools using the CRISPR-Cas9 system, examining the impact of climate change on microbial communities and the global carbon cycle, understanding the global water microbiome, examining the response of microbial communities to contaminants (U, nitrate, pH, Cr) important to the U.S. DOE, designing bioinformatics tools for ‘big data’ analysis, and developing and expanding high-throughput metagenomic tools and techniques such as microarrays, sequencing, and single cell genomics to examine microbial communities.

Microbial Ecology and Community Genomics

Another key research direction at IEG is to use genomic technology to understand microbial community diversity, composition, structure, function and dynamics and determine the mechanisms controlling microbial community diversity.  Microorganisms inhabit almost every imaginable environment on earth and play a large part in global geochemical cycles, yet the extent of microbial diversity and what mechanism control microbial communities are largely unknown.  We use a variety of metagenomics approaches, such as functional gene arrays, high-throughput sequencing, and single cell genomics to address these areas.  This work examines a variety of systems and environmental perturbations including global change, bioremediation, land use, bioenergy, and agricultural practices as well as across spatial and temporal differences.

CLIMATE CHANGE

Climate change is an ongoing concern as the average temperature of Earth continues to rise and weather patterns become more extreme.  Understanding the responses, adaptations and feedback mechanisms of biological communities to climate change is critical in order to predict the future state of Earth and climate systems.  Although a great deal is known regarding the feedbacks of aboveground communities to climate change, the response of belowground microbial communities is still poorly understood.  Thus, it is important to advance system-level predictive understanding of the feedbacks of belowground microbial communities to multiple climate change factors and their impacts on soil carbon (C) cycling.  We have been examining microbial responses from several angles.

 In in a tall grass prairie ecosystem, we have been characterizing community changes resulting from warming and clipping (harvest of plant tops), a practice commonly used in agriculture and for biofuels feedstock harvesting. 

Microbial decomposition of permafrost C is one of the most likely potential positive feedbacks from terrestrial ecosystems to the atmosphere in a warmer world, so we have been studying microbial communities from a tundra warming experiment in Alaska. 

Another area of research is examining how microbial communities impact plant growth and what functions are responsible for improved plant growth.  This could have important implications to biofuels feedstock growth and harvesting.

GROUNDWATER BIOREMEDIATION

We are involved in several projects involving the U. S. DOE Oak Ridge Integrated Field Research Challenge site.  Oak Ridge was part of the Manhattan Project and has high levels of U, nitrate, and very low pH.  Our focus is to understand the factors and mechanisms shaping microbial community structure at this contaminated site.  Understanding the mechanisms controlling microbial community composition and function is extremely important because the knowledge gained may provide novel approaches to the manipulation of microbial communities for desired functions, and will be critical for successful bioaugmentation and biostimulation.

Because the Oak Ridge site has been the subject of so much study and there are decades worth of data related to the site geology, geochemistry, hydrology as well as microbial studies, it is an ideal site to study the stability, resilience, resistance, and evolution of microorganisms and mechanisms that influence their assembly and performance.  Samples from over 100 sampling wells have been collected to better understand the response of microbial communities to environmental conditions.  Ongoing studies include characterizing the diversity of protists and fungi in groundwater and examining the relationship between functional diversity and phylogenetic diversity.  Shotgun sequencing is being employed to determine the diversity and metabolic capacity of the subsurface microbial communities.  Mechanisms of community assembly for free-living and particle-associated bacteria are also being determined.

GLOBAL WATER MICROBIOME CONSORTIUM

To facilitate international collaboration and communication on research and education related to global water microbiome studies, the Global Water Microbiome Consortium (GWMC) was founded in 2014 by IEG and scientists from China and Europe. Since its establishment, GWMC has gown to include more than 100 research groups from over 25 countries. IEG is leading the sampling campaign, microbiome analyses, and data integration for all GWMC initiatives. The first initiative of the GWMC focused on Municipal Wastewater Microbiomes. As a systematic global-sampling effort, we have analyzed microbiomes from ~1,200 activated sludge samples taken from 269 WWTPs in 23 countries on 6 continents. We have also launched another global initiative on anaerobic digester microbiomes. 

Functional and Comparative Genomics

This research area focuses on functional analysis of microorganisms important in environmental cleanup and bioenergy, particularly anaerobic microorganisms to understand gene function, regulation, networks and evolution.

A major challenge in microbiology is linking phenotype (functional traits) and genotypes (genes responsible for that trait) because phenotypes are often controlled by multiple genes and correlated to environmental conditions.  Microbial experimental evolution can provide direct evidence of gene function in both essential and non-essential genes as well as non-coding regions.  In this approach, microbial populations are propagated under controlled laboratory conditions and the underlying genomic changes are identified by sequencing the whole genomes of the evolved strain(s) or populations and aligning to the reference genome sequences of the ancestral strain.

Currently, the functional genomics studies are centered on the sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough, and a denitrifier, Rhodanobacter denitrificans. Both species exist in contaminated field sites, but Rhodanobacter is dominant in ground water ecosystems with low pH and high heavy metal concentrations. We use genome sequencing, gene expression microarrays, qPCR, transposon libraries, and mutagenesis to analyze the function of genes involved in energy metabolism under different growth conditions, characterize stress response and global gene expression regulation, and examine their interactions with other species in artificial communities under various environmental conditions.

Targeted genome editing is critical for both fundamental molecular biology and applied genetic engineering, but genome editing is challenging in many microorganism due to the lack of efficient editing tools. The CRISPR-Cas9 system has been shown to be a powerful and versatile option for foreign gene knock-in and gene inactivation in eukaryotes, however, its application in microorganisms has been limited. Our lab has developed a single nick-triggered homologous recombination strategy using the Cas9 nickase and successfully edited specific genome loci in Clostridium cellulolyticum.  Currently we are in the process of expanding the application of this powerful tool for use in other bacteria and as a high-throughput process.

Development of Experimental Metagenomic Technologies

IEG researchers have pioneered the development and application of functional gene arrays (e.g., GeoChip), and metagenomic sequencing (e.g., MiSeq sequencing of phylogenetic and functional gene amplicons) for microbial community and quantitative analysis.  Current research directions include the establishment of a Raman-based single cell genomics facility and methods for analyzing ‘big data’.

GeoChip microarra ys are the most comprehensive FGAs available to date.  Using Agilent microarray technology, we currently have two versions of the latest GeoChip design, 5S and 5M.  GeoChip 5S contains approximately 60,000 probes per array and was designed for general microbial ecology studies.  It covers genes involved in the core biogeochemical cycles (C, N, S, and P), and metal and antibiotic resistance genes that alter the metal or antibiotic (oxidation, reduction, degradation)  GeoChip 5M is a larger array, containing ~180,000 probes for functional genes involved in C, N, S, and P cycles, degradation genes for environmental contaminants (organic solvents, pesticides, BTEX, etc.), metal homeostasis, antibiotic resistance, stress response, electron transport, microbial defense, as well as several other categories (virulence, viral and protist genes, etc).  These versions greatly expanded the overall gene and sequence coverage of previous versions by adding more than 1,000 new gene families covering a total of 1,447 gene families.  New categories include microbial defense, plant growth promotion, pigments and protist phylogenetic markers. We continue to expand the number and coverage of functional gene groups, develop and improve on software and algorithms used for sequence selection, probe design, and data processing, improve on sample preparation and hybridization protocols, and develop new uses for the microarray technology. We anticipate having the GeoChip 6 available later this year. 

High-throughput sequencing has enabled microbiologists to address many previously unanswerable research questions and sequencing amplified gene markers to determine phylogenetic and functional diversity is becoming a common approach.  The Illumina platform, particularly the MiSeq, has become an attractive sequencing option due to lower cost, rapid analysis, and higher accuracy.  IEG is equipped with a MiSeq benchtop sequencer.  A major challenge for MiSeq amplicon sequencing is the so-called low sequence diversity or unbalanced base composition in template DNA sequences.  We have optimized protocols for de novo sequencing of 16S rRNA gene for bacteria and archaea and developed a novel phasing amplicon sequencing approach to overcome this issue by shifting sequencing phases among different community samples by adding spacers consisting of 0-7 bases.  We continue to improve our sequencing protocols to increase quality and reduce cost and to increase available primer sets to allow sequencing of more genes.

In addition to the above, IEG is expanding into single cell genomics using Raman sorting.  A great challenge in single cell genomics is identifying the isolated cells for subsequent sequencing.  Raman sorting allows for the identification of specific bacterial species based on their spectral pattern.  The spectra can also provide information on physiological differences, growth phase of particular cells, and incorporation of stable isotopes.  We are currently working on setting up protocols and methods for this new project.

Development of Computational Technologies

Although the rapidly expanding genomic technologies provide powerful analysis tools, as data sets become larger and larger, it is increasingly more difficult to analyze this ‘big data’.  IEG has been working on development and implementing bioinformatics tools for processing this data.  

For microbial community studies, we have developed the Molecular Ecological Network Analysis Pipeline (MENAP). This novel mathematical and bioinformatics framework can be used to construct ecological association networks, referred to as molecular ecological networks (MENs), using the Random Matrix Theory (RMT). RMT allows for the automatic definition of the network and is robust to noise, thus providing an excellent solution to several common issues associated with high-throughput metagenomics data analysis. MENAP also incorporates network analysis tools that are commonly encountered in microbial ecological studies. 

For microarray and sequencing data analysis, we have developed a series of pipelines tailored for different application scenarios. We have developed microarray data processing pipelines to allow users to upload, process, and analyze the data (normalization, quality filtering, designate signal cutoffs). The pipeline can also accept other types of data such as amplicon sequencing data. We also have developed a dedicated sequencing analysis pipeline to process raw amplicon sequencing data. It can be used to remove control and artifact sequences , sort, trim, and combine sequences, convert the sequences to FASTA format, and then generate OTU tables. For automatic analysis of metagenomic sequencing data from an ecological function perspective, we have developed EcoFun-MAP, which includes two manually-curated functional gene databases specifically tailored for this application. EcoFun-MAP allows profiling of large amounts of raw reads to the functional OTU level, and provides annotation into hierarchical ecological functional categories. 

We have also developed a Microbial ENzyme Decomposition model (MEND) pipeline to model mechanistic details about microbial decomposition, including adsorption and desorption of dissolved organic carbon, active microbial biomass, and enzymes. 

All these pipelines are available for public access on our Data Analysis Pipeline webpage. 

Funding

Since moving to OU in 2006, Dr. Zhou has secured  >$42M in funding for 38 projects in genomics and microbial ecology.

While at Oak Ridge National Lab (1996-2006), Dr. Zhou secured $26M in funding for 36 projects.

Currently Funded Projects

MTM 2: Searching for General Rules Governing Microbiome Dynamics using Anaerobic Digesters as Model Systems. National Science Foundation. Zhou (PI) with Alan Hastings, Mathew Leibold, Qiang He, and Daling Ning, $3M in total, ~$1.3M for J. Zhou and D. Ning (October 1, 2020, September 30, 2025). 

Cross-Kingdom Interactions: the Foundation for Nutrient Cycling in Grassland Soils. Department of Energy, Co-PI with Mary Firestone et al, $340K for J. Zhou (October1, 2019 - September 30, 2022)

iSENTRY: An integrated Microfluidics-enabled system for phenotypic detection of biothreat agents. Department of Defense, DARPA program, Co-PI with James Samuel, Arum Han and Paul de Figueiredo etc., $880K for J. Zhou (December 1, 2018 to November 30, 2022).

Multi-scale analysis of microbe-climate interactions in greenhouse gas emissions from grasslands and croplands with livestock and manure use. Department of Agriculture, Co-PI with Xiangming Xiao et al, $3M, ~$360K for J. Zhou (March 1, 2016 – February 28, 2021).

Establishment to senescence: plant-microbe and microbe-microbe interactions mediate switchgrass sustainability, Department of Energy, Co-PI with Mary Firestone et al, ~$15M,  $2500K for J. Zhou (October1, 2015 - September 30, 2021)

From Genomes to Ecosystems: Systems-Level Mechanistic Understanding of Microbial Stress Responses at Chromium Contaminated Sites. Department of Energy. PI, $3,500K (Oct 1. 2017-September 30, 2022) (This project is changed from previous VIMSS project (2002-2007) to LBL SFA, i.e. ENIGMA- Ecosystems and Networks Integrated with Genes and Molecular Assemblies. Paul Adams and Adam Arkin are the Program Directors).

Completed Projects

Directing traffic in the rhizosphere: how phage and fauna shape the flow and fate of root carbon through microbial pathways, Department of Energy, Co-PI with Mary Firestone et al, $570K for J. Zhou (October1, 2016 - September 30, 2020)

From Structure to Functions: Metagenomics-Enabled Predictive Understanding of Soil Microbial Feedbacks to Climate Change, Department of Energy, PI (Zhou, Tiedje, Schuur, Luo, Konstantinidis) $3,595K (October1, 2013 - September 30, 2018) (OU’s portion: $2,069K).

Microbial biogeography of soil communities in paddy fields. PI, Chinese NSF, ¥3.6M (October 1, 2014 - September 30, 2019)

Plant Stimulation of Soil Microbial Community Succession: How Sequential Expression Mediates Soil Carbon Stabilization and Turnover, Department of Energy, Co-PI with Mary Firestone et al, $620K for J. Zhou (October1, 2013 - September 30, 2017)

Experimental Macroecology: Effects of Temperature on Biodiversity.  NSF Macrosystems Biology, Co-PI with James Brown, Mike Kaspari, Brian Enquist, et al ($4.5M in total, $1.8M for J. Zhou) (July 1, 2011 to June 30, 2016).

The Fund for Foreign Scholars in University Research and Teaching Programs supported by The Ministry of Education of China and The State Administration of Foreign Experts Affairs of China, ¥10M Chinese yuan (equivalent to ~$770K) (January 1, 2007--- December 31, 2016) (This has been funded by Chinese Government to support research activity within China)

Development of Microarrays-based Metagenomics Technology for Monitoring Sulfate-Reducing Bacteria in Subsurface Environments. PI, DOE STTR/SBIR Phase II, $750K (June 19, 2011- March 18, 2014)

Development of Novel Random Network Theory-Based Approaches to Identify Network Interactions Among Nitrifying Bacteria. PI, DOE STTR/SBIR Phase I, $750K (June 19, 2011- March 18, 2014)

HuMiChip to detect and characterize the human microbiome.  Co-PI with He.  OCAST, $300K (February 1, 2011 to January 31, 2014)

From Community Structure to Functions: Metagenomics-Enabled Predictive Understanding of Temperature Sensitivity of Soil Carbon Decomposition to Climate Warming, Department of Energy, PI (Zhou, Tiedje, Schuur, Luo, Konstantinidis) $3M (July 1, 2010 - June 30, 2014) (OU’s portion: $1,946K).

Plant Stimulation of Soil Microbial Community Succession: How Sequential Expression Mediates Soil Carbon Stabilization and Turnover, Department of Energy, Co-PI with Mary Firestone et al, $0.5M for J. Zhou (July 1, 2010 - June 30, 2014)

Center for Advanced Microbial Ecology, Tsinghua University, Beijing, China, ¥6M Chinese (Yuan equivalent to ~$940K) (January 1, 2011 December 30, 2013). (This has been funded by Chinese Government to support research activity within China)

Oklahoma EPSCoR Research Infrastructure Improvement Plan, Building Oklahoma’s Leadership Role in Cellulosic Bioenergy. NSF EPSCoR Program ($8.7M in total), PI with Ray Huhnke (Director) et al, $2,117K for J. Zhou (Oct 1, 2008-Dec 30, 2013)

Integrated genome-based studies of Shewanella ecophysiology. DOE Genomics:GTL program ($15M) PI with  J. Fredrickson (Director), K. Nealson, J.M Tiedje,  and et al.), $1000K for J. Zhou (October 1, 2006– September 30, 2009). DOE Genomics:GTL program, October 1, 2006– March 30, 2012.

Rapid Deduction of Stress Response Pathways in Metal and Radionuclide Reducing Bacteria Phase 2: Molecular Determinants of Community Activity, Stability and Ecology (MDCASE) (ESPP 2),  DOE Genomics:GTL Program ($35M in total), PI with Adam Arkins (Director), Terry Hazen, Judy Wall, David Stahl, et al, $4,000K (October 1, 2007 – September 30, 2012) 

Metagenomics-enabled understanding of the functions and activities of microbial communities at ERSP Field Research Center at Oak Ridge, TN. Co-PI with Tiedje and Marsh. DOE NABIR program, ~ $1500 K (October 1, 2006  March 30, 2012), $750K for J. Zhou.

MO: A Genomics-enabled FACE Microbial Observatory: Changes in Microbial Diversity and Functions in responding to elevated CO2, Nitrogen Deposition and Plant Diversity. NSF-USDA Microbial Observatories Program, PI with Zhili He, $866K (July 1, 2007 – August 13, 2012).

Trajectories of microbial community function in response to accelerated remediation of subsurface metal contaminants. Co-PI with Mary Firestone et al. DOE ERSP program, ~ $1350 K (October 1, 2007  May 30, 2012), $210K for J. Zhou.

Microbial Enhanced Hydrocarbon Recovery (MEHR) Systems Biology Program. Energy BioSciences Institute, Co-PI with Hazen et al, $600K for J. Zhou (Oct 1, 2008 – Sept 30, 2012). 

Isolation and characterization of novel microbial catalysts for direct fermentation of lignocellulose to ethanol. PI with Liyou Wu, Zhili He, Oklahoma Bioenergy Center, $400K (February 1, 2008, January 31, 2011)

Multiscale Investigations on the Rates and Mechanisms of Targeted Immobilization and Natural Attenuation of Metal, Radionuclide and Co-Contaminants in the Subsurface. Co-PI with Jardine, Watson, Criddle, Gu et al. $15M, (October 1, 2006 --- September 30, 2011), $150K for Zhou.

Genomics-enabled understanding of microbial interactions and regulatory networks of microbial consortia for efficient cellulosic ethanol production. Co-PI with Zhili He, Liyou Wu et al, Oklahoma Bioenergy Center, $830K (February 1, 2008, January 31, 2011)

Linking community structure to functions: Metagenomic analysis of Feedstock-Related Microbial Communities using GeoChip and Pyrosequencing. Co-PI with Liyou Wu, Zhili He, Yiqi Luo, Oklahoma Bioenergy Center, $1,030K (February 1, 2008, January 31, 2011)

Whole genome DNA arrays for bacterial identification and detection, Co-PI with Wu et al.  OCAST, $300K (February 1, 2008 to January 31, 2011)

Characterization of an H2 Producing Biological System operating at 1 nM H2 Concentration. Co-PI with Krumholtz et al ($900K in total). DOE BES, $250K for J. Zhou (Oct 1, 2008-Sept 30, 2011)

Extending Knowledge of Anaerobic Hydrocarbon Metabolism: Linking Metabolism, Functional Gene Molecular Markers and the GeoChip. ConoPhilipps, Co-PI with Joseph Suflita et a ($2 M in total), $ $403K for J. Zhou (Oct 1, 2008 –December 30, 2010)

Development of Microarrays-based Metagenomics Technology for Monitoring Sulfate-Reducing Bacteria in Subsurface Environments. PI, DOE STTR/SBIR Phase I, $100K (June 19, 2010- March 18, 2011)

Development of Novel Random Network Theory-Based Approaches to Identify Network Interactions Among Nitrifying Bacteria. PI, DOE STTR/SBIR Phase I, $100K (June 19, 2010- March 18, 2011)

Institute for Environmental Genomics, PI with Z.L. He, $200K (January 1, 2008 --- December 31, 2010).

The Joint BioEnergy Institute (JBEI) ($125M in total), $400K for J. Zhou (October 1, 2007  September 30, 2012).

Development of Comprehensive Functional Gene Arrays for Microbial Community Analysis, Co-PI with He.  OCAST, $300K (October 1, 2006 to Sept 30, 2009)

Microarray analysis and functional assays to assess microbial ecology and disease suppression in soils under organic or sustainable management. Co-PI with Louws and Hu, USDA,  $160K (October 1, 2006 ---September 30, 2008)

Development of microbial consortia for efficient ethanol production from plant biomass, PI, Department of Energy, Oklahoma, $200K (April 1, 2007  ---  March 31, 2009)

Special award for Oversea Young Scientist, ¥120K Chinese Yuan (July 1, 2004 --- June 30, 2007). (This was funded by Chinese Government to support research activities within China)

Identification of Molecular and Cellular Responses of Desulfovibrio vulgaris Biofilms under Culture Conditions Relevant to Field Conditions for Bioreduction of Heavy Metals, Co-PI with Matthew Fields, Judy Wall, DOE ERSP Program, $300K (October 1, 2005 to Sept 30, 2008).

Deduction and analysis of the interacting stress response pathways of metal/radionuclide-reducing bacteria, DOE Genomics:GTL Program, PI with Adam Arkins (Director), Terry Hazen, Judy Wall, David Stahl, et al ($30M in total), $5,010K for J. Zhou (July 1, 2002 – September 30, 2007).

Molecular Approaches to Understanding C and N Dynamics and their Role in the Global Carbon Cycle. Co-PI, with Tiedje, Devol, and Massol-Deya, DOE Biotechnological Investigations  Ocean Margin Program. ~ $1,500 K (October 1, 2003 – September 30, 2006). $600K for J. Zhou.

Towards Understanding Population Dynamics of Metal and Radionuclide Reducers at Field Remediation Sites. Co-PI with Tiedje and Treves. DOE NABIR program, ~ $900 K (October 1, 2003  September 30, 2006), $450K for J. Zhou.

Development and Use of Integrated Microarray-based Genomic Technologies for Assessing Microbial Community Composition and Dynamics. PI, DOE NABIR program, ~ $900 K (October 1, 2003  September 30, 2006). 

Elucidating the Molecular Basis of Chromium(VI) Reduction by Shewanella oneidensis MR-1 and Resistance to Metal Toxicity Using Integrated Biochemical, Proteomic, and Comparative Genomics Approaches. Co-PI with Thompson and Hettich. DOE NABIR program, ~ $820 K (October 1, 2003  September 30, 2006). 

Integrated analysis of protein complexes and regulatory networks involved in anaerobic energy metabolism of Shewanella oneidensis MR-1, PI, with Larimer, Nealson, Thompson, et al., DOE Microbial Cell Project, $4,500K (October 1, 2001– September 30, 2006).

Field-scale evaluation of biostimulation for remediation of uranium–contaminated groundwater at a proposed NABIR Field research center in Oak Ridge TN, Co-PI, with Criddle, Jardine,  Kitanidis, Hopkins. DOE NABIR program, ~ $3,250 K (October 1, 2000  September 30, 2004). $540K for J. Zhou.

Center for research on enhancing carbon sequestration in terrestrial ecosystems (Co-PI, with Jacobs et al.) ($10M in total), $900K for J. Zhou (October 1, 1999  September 30, 2005).

The Rhodopseudomonas palustris Microbial Cell Project, Co-PI, with Tabita, Thompson, et al., DOE Microbial Cell Project ($2.1M in total), $150K for J. Zhou (October 1, 2001– September 30, 2006).

The dynamics of cellular stress responses in Deinococcus radiodurans, Co-PI, with Mike Daly et al., DOE Microbial Cell Project ($900K in total), $240K (October 1, 2001– September 30, 2004).

Microbially mediated immobilization of contaminants through in situ biostimulation: Scale up of EMSP project 55267, Co-PI with Jardine and Brooks, DOE EM Science Program, $1,427K (October 1, 2000  September 30, 2004). $140K for J. Zhou.

Use of DNA Microarrays for Understanding the Genetic and Metabolic Regulation of Carbon Dioxide Fixation and Hydrogen Production in Rhodopseudomonas palustris. Co-PI with Harwood and Thompson. DOE Microbial Genome Program ($1.8M in total), $750K for J. Zhou (October 1, 2001– September 30, 2004).

Gene Expression Profiles in Nitrosomonas europaea, an Obligate Chemolitho- autotroph. Co-PI with Arp and Klotz, DOE Microbial Genome Program, $600K for J. Zhou (October 1, 2001– September 30, 2004).

Genomic Characterization of Belowground Ecosystem Responses to Climate Change. Co-PI with DiFazio, Fields, et al., ORNL Laboratory Directed Development and Research Program, $545K (October 1, 2002– September 30, 2004).

Community-Wide Analysis of Unique Sequences and Functions from Uncultured Microorganisms, Co-PI with Fields, ORNL Laboratory Directed Development and Research Program, $500K, (October 1, 2001– September 30, 2003).

Coupling process and microbial community studies to understand the mechanisms controlling carbon preservation and nitrogen loss in marine sediments. Co-PI, with Tiedje, Devol, Massol-Deya and Palumbo, DOE Biotechnological Investigations  Ocean Margin Program. ~ $1,650 K (October 1, 2000 – September 30, 2003). $600K for J. Zhou.

Understanding the roles of spatial isolation and carbon in microbial community structure dynamics, and activity for bioremediation, Co-PI with Tiedje and Treves. DOE NABIR program, ~ $1,250 K (October 1, 2000  September 30, 2003), $650K for J. Zhou.

Development and use of 16S rRNA gene-based oligonucleotide microarrays for Assessing Microbial Community Composition and Dynamics. PI with Thompson, Hurt, Xu and Xu, DOE NABIR program, ~ $1,200 K (October 1, 2000  September 30, 2003). $900K for J. Zhou.

Enhancing carbon sequestration and reclamation of degraded lands with fossil fuel combustion byproducts, Co-PI with Palumbo et al., DOE Fossil Energy Program, ~1,100K (October 1, 2000 – September 30, 2003).

Computational structure characterization of metal-reduction proteins in microbe, Co-PI with Ying Xu, Dong Xu et al., DOE Experimental and Computational Structural Biology, ~ $1,100K (October 1, 2000 – September 30, 2003).

Shewanella putrefaciens: Regulation of the genes and proteins involved in metal reduction pathways, Co-PI with Carol Giometti, DOE NABIR Program, $210K (October 1, 1999  September 30, 2002). 

Linking genomics to cellular responses and mechanisms for radiation resistance in Deinococcus radiodurans, PI, with Hettich, Burlage, Beliaev, and Thompson, Laboratory Directed Research and Development Program, Oak Ridge National Laboratory, $867K (October 1, 2000 – September 30, 2002).

Development of microchip-based detection methods: a high throughput microbial detection tool for bioremediation and carbon sequestration. PI, Seed Money Program, Oak Ridge National Laboratory, 100K (February 1, 2000  September 30, 2001).

Exploring whole genome sequence information for defining the functions of unknown genes and regulatory networks in dissimilatory metal reduction pathways. PI, with Nealson and Tiedje, DOE Microbial Genome Program, $1,350K (October 1, 1998  September 30, 2001).

Noncompetitive diversity patterns in soils: their causes and implications. Co-PI with Tiedje, O’Neill and Palumbo, DOE NABIR program, ~ $1,100 K (October 1, 97  September 30, 2000)

Linking process and population studies to understand the nitrogen loss mechanisms of Pacific Northwest marine sediments. Co-PI with Tiedje, Devol, Massol-Deya and Palumbo, DOE Biotechnological Investigations  Ocean Margin Program. ~ $1,300 K (October 1, 1997  September 30, 2000).

Rapid gene probe for microorganisms monitoring by novel MS approaches. Co-PI with W. Chen, DOE NABIR program, ~ $800 K (October 1, 1999  September 30, 2002).

Isolation of Proteins Involved in Metal Reduction from Shewanella oneidensis MR-1 with Mass Spectrometry, LDRD Program, Oak Ridge National Laboratory, $50K (March 1, 2000  September 30, 2000)

Development and testing of molecular probes that distinguish effective TCE-cooxidizers from ineffective TCE-cooxidizers: a potential tool for site assessment and management. Co-PI with Tiedje, Department of Defense, $150K (September 1, 1996 to September 1, 1998).

Enzymes from extremophiles in bioremediation and bioprocessing. Co-PI with Woodward and Palumbo et al., Oak Ridge National Laboratory, ~ $800K (September 1, 1996 to August 31, 1998).

Development of gene probes for nitrate reductase in environmental media: a tool to evaluate nitrogen retention in watersheds. Co-PI with Mulholland and Garten, Oak Ridge National Laboratory, 92K (January 1, 1998 to December 30, 1998).

Genome Sequencing Projects

Genomic Sequencing of Multiple Species of Class Clostridia Relevant to the Production of Bioethanol from Cellulosic Feedstocks. 2006. (PI with Hemme, He et al). The genome will be sequenced by DOE Joint Genome Institute.

Sequencing Clostridium cellulolyticum to advance understanding plant biomass degradation and energy production, 2005. (Qing He, and J.-Z. Zhou).  The genome will be sequenced by DOE Joint Genome Institute. 

Genome sequencing of multiple Anaeromyxobacter species:  comparative genomics for insight into the ecophysiology, genetics and evolution of metal-reducing and halorespiring bacteria. 2005. (Robert A. Sanford, Matthew W. Fields, Frank E. Löffler, John R. Kirby, J.-Z. Zhou, James K. Fredrickson, and Alexander S. Beliaev).   Three genomes will be sequenced by DOE Joint Genome Institute.  

Genome-level understanding of the diversity and structure of a groundwater microbial community in the NABIR Research Field Research Center. 2004. (Zhou, PI, Fields, co-PI). The entire community with about 20 species in highly contaminated site will be sequenced by DOE Joint Genome Institute in 2005.

Whole-genome sequence determination of novel, extremophilic, metal-reducing bacteria important to bioremediation and energy production. 2003. (Fields, Zhou). 3 gram-positive extremophilic iron-reducing bacteria isolated at ORNL are under sequencing. 

Sequence multiple strains of Shewanella to advance understanding their metal-reducing physiology and ecological potential. 2004. (Fredrickson, Nealson, DiChristina, Tiedje, Zhou et al.). 16 Shewanella strains are under sequencing by JGI. Two of these strains were isolated at ORNL.