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Institute for Environmental Genomics

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Institute for Environmental Genomics

Mission


The mission of IEG is to advance scientific research and education in environmental genomics and stimulate bio-economic development in the State of Oklahoma in order 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. 

Current Research

Three research themes are pursued at IEG:

(i) functional and comparative genomics for understanding gene function, regulation, network and evolution,

(ii) microbial ecology and community genomics for analysis of diversity, composition, structure, function and dynamics of microbial communities related to global change, bioremediation, land use, bioenergy, and agricultural practices using metagenomics approaches, such as functional gene arrays (e.g., GeoChip), high-throughput sequencing, and single cell genomics, and

(iii) development of metagenomic and bioinformatic tools for big data analysis to understand and model ecosystem functioning and stability.

Read more

IEG Highlights


Dr. Jizhong Zhou is a George Lynn Cross Research Professor and a Presidential Professor in the Department of Microbiology and Plant Biology and Director for the Institute for Environmental Genomics, University of Oklahoma, Norman, OK; Visiting Senior Scientist at Lawrence Berkeley National Laboratory; and Adjunct Professor at Tsinghua University, Beijing, China. His expertise is in molecular biology, microbial genomics, microbial ecology, theoretical ecology and genomic technologies. His laboratory has pioneered the development and use of genomic technologies for environmental studies for which GeoChip won an R&D 100 Award in 2009. He received a Presidential Early Career Award for Scientists and Engineers in 2001. He received an Ernest Orlando Lawrence Award in 2014. He is a former Editor for Applied and Environmental Microbiology, a current Editor for mBio and a Senior Editor for The ISME Journal. He is a Fellow of the American Academy of Microbiology and the American Association for the Advancement of Science.

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Ernest Orlando Lawrence Award recognizes exceptional US scientists and engineers preforming research supporting the Energy Department mission. IEG Director, Jizhong Zhou, was selected as one of nine recipients in 2015.

Jizhong (Joe) Zhou (University of Oklahoma) - Biological and Environmental Sciences Honored for his outstanding accomplishments in environmental genomics and microbial ecology, including the development of innovative metagenomics technologies for environmental sciences, for groundbreaking discoveries to understand the feedbacks, mechanisms, and fundamental principles of microbial systems in response to environmental change, and for transformative leadership to elucidate microbial ecological networks and to link microbial biodiversity with ecosystem functions.

Congressional Record of Award (pdf)

News and Announcements

May, 2019

OU-Led Study Expands Understanding of Bacterial Communities for Global Next-Generation Wastewater Treatment and Reuse Systems

IEG has a new publication in Nature Microbiology, "Global diversity and biogeography of bacterial communities in wastewater treatment plants". (link to publisher's website)

Microorganisms in wastewater treatment plants (WWTPs) are essential for water purification to protect public and environmental health. However, the diversity of microorganisms and the factors that control it are poorly understood. Using a systematic global-sampling effort, we analysed the 16S ribosomal RNA gene sequences from ~1,200 activated sludge samples taken from 269 WWTPs in 23 countries on 6 continents. Our analyses revealed that the global activated sludge bacterial communities contain ~1 billion bacterial phylotypes with a Poisson lognormal diversity distribution. Despite this high diversity, activated sludge has a small, global core bacterial community (n = 28 operational taxonomic units) that is strongly linked to activated sludge performance. Meta-analyses with global datasets associate the activated sludge microbiomes most closely to freshwater populations. In contrast to macroorganism diversity, activated sludge bacterial communities show no latitudinal gradient. Furthermore, their spatial turnover is scale-dependent and appears to be largely driven by stochastic processes (dispersal and drift), although deterministic factors (temperature and organic input) are also important. Our findings enhance our mechanistic understanding of the global diversity and biogeography of activated sludge bacterial communities within a theoretical ecology framework and have important implications for microbial ecology and wastewater treatment processes.

OU Press Release

Global Water Microbiome Consortium website

 

April, 2019

IEG Members Selected for ESA Contributed Talks

Several IEG member were selected to present their research at the 2019 Ecological Society of America/United States Society for Ecological Economics Joint Meeting in Louisville, Kentucky.  The meeting will be held August 11-16 at the Kentucky International Convention Center.

Colin Bates, a graduate student, will present his research, "Conversion of Natural Grassland into Biofuel Crops (Switchgrass, Panicum virgatum L.) is Associated with a Reduction in Methane Consumption"

Jailiang Kuang, a postdoctoral fellow, will present his research, "Ecological effects of deep-rooted perennial grass systems on soil carbon sequestration in marginal lands"

Qi Qi, a visiting scholar, will present her research, "Quantifying microbial and plant determinants of soil carbon flux responses to various climate changes"

Xiaoling Wan, a visiting scholar, will present her research, "Depth-related spatial distribution of microbial composition in marginal soils”

Gangsheng Wang, a research scientist, will present his research, "Costs and Benefits to Assimilate Microbial Data into Ecosystem Modeling"

Linwei Wu, a postdoctoral fellow, and Daliang Ning, a research scientist, organized the session, Macro-View of Microbes: Treasure and Challenges in Continental- and Global-Scale Microbial Ecology Researches (Tues Aug 13, 3:30-5:00 pm). Linwei will moderate the session and Dr.  Zhou will present during the session.

Newest Publications

  1. Ning D, Y Deng, JM Tiedje, and J Zhou. 2019. A general framework for quantitatively assessing ecological stochasticity. Proc Nat Acad Sci. doi.org/10.1073/pnas.1904623116
  2. 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. https://doi.org/10.1128/MRA.00456-19.
  3. 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
  4. 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.
  5. 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. doi.org/10.1111/gcb.14750. Suppl Material (docx)
  6. 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 depthsProc. Nat. Acad. Sci. 116:15096-15105. Suppl Material (pdf); Suppl Data 1 (txt)2 (txt)3 (txt)4 (txt)
  7. 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 communitiesmSystems. 4:e00296-19. Suppl Material: Text (pdf), GeoChip 5 Table (pdf), Tables/Figures (pdf)
  8. Wakelin S, P Maclean , V Cave, J Zhou, GA Grelet, and D Whitehead. 2019. Characterising the soil ecosystem phenotype associated with relatively low nitrate-N concentrationsAppl Soil Sci. 142:189-198. Suppl Material: Text (docx), Data (xlsx)
  9. 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 plantsNat Microbiol, 4:1183-1195. Suppl Material: Tables S1S3S11S12
  10. 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 gyreJ Geophys Res: Biogeosci. 124:1001-1017. doi.org/10.1029/2018JG004707. Suppl MaterialNormalized Miicroarray Data (zip)