基本信息English
基本信息




教育经历
1978-1981 中国湖南农业大学植物病理学与昆虫学 学士1982-1984 中国湖南农业大学数学生态学 硕士1989-1993 美国华盛顿州立大学分子生物学 博士


工作经历
1985－1986 中国 湖南农业大学 讲师1986－1988 中国 中国科学院动物所/生态环境研究中心 助理研究员 (攻读博士学位)1988 加拿大 加拿大卡尔加里大学（University of Calgary, Calgary, Alberta, Canada）访问学者（Visiting Scientist）1993－1995 美国 国家自然科学基金会微生物生态研究中心（NSF Center for Microbial Ecology）博士后（Postdoctoral Research Associate）1996－1997 美国 橡树岭国家实验室（Oak Ridge National Lab）博士后（Alexander Hollaender Distinguished Postdoctoral Fellow）1997－2000 美国 橡树岭国家实验室环境科学部（Environmental Sciences Division, Oak Ridge National Lab）研究员（Staff Scientist）2001－2002 美国 橡树岭国家实验室（Oak Ridge National Lab）高级研究员（Senior Staff Scientist）2000－2004 美国 橡树岭国家实验室（Oak Ridge National Lab）环境基因学科带头人（Science Leader for Environmental Genomics Program）2003－2005 美国 橡树岭国家实验室（Oak Ridge National Lab）资深研究员（Distinguished R&D Staff Scientist）2005－今 美国 俄克拉荷马大学植物学与微生物学系环境基因研究所（Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma University of Oklahoma）首席教授（ Presidential Professor），所长（Director）2006－今 美国 劳伦斯-伯克利国家实验室（Lawrence Berkeley National Laboratory）兼职高级研究员（Adjunct Senior Scientist）2012年－今，哈尔滨工业大学兼职教授


研究领域
环境基因组学和功能基因组学系统生物学和生物信息学微生物生态学和群落生态学


奖项成果
1996 Alexander Hollaender杰出博士后奖（Alexander Hollaender Distinguished Postdoctoral Fellow）（此奖项由美国能源部设立，是美国最具声望的博士后奖项）1998橡树岭国家实验室杰出成果奖（Research Accomplishment Award）1999 橡树岭国家实验室杰出成就奖（Superior Performance Award）2001 美国能源部青年科学家奖 (DOE Office of Science’s 2001 Early Career Award for Scientists and Engineers2001 美国青年科学家总统奖（Presidential Early Career Award for Scientists and Engineers from the President of the United State of America）（美国青年科学家最高荣誉）2004 中国国家基金委海外杰青2005 联邦实验室联盟技术转化杰出奖（Federal Laboratory Consortium award for Excellence in Technology Transfer）2006 俄克拉荷马大学首席教授（Presidential Professor）2009 环境功能基因芯片（Geochip）研发获全球百大创新技术研发奖（R&D 100 Award，2009年全球最具科学创新和技术突破，并且具有极高商业化前景的100项科技成果，研发杂志评选，有极高的国际影响力）2009 俄克拉荷马亚洲协会杰出亚裔美国人（Outstanding Asian American for the Asia Society of Oklahoma）


发表文章
2013
1.

Sul, Woo Jun, Stella Asuming-Brempong, Qiong Wang, Dieter M. Tourlousse, C. Ryan Penton, Ye Deng, Jorge LM Rodrigues et al. 2013. Tropical agricultural land management influences on soil microbial communities through its effect on soil organic carbon. Soil Biology and Biochemistry.


2.

Aifen Zhou, Edward Baidoo, Zhili He, Aindrila Mukhopadhyay, Jason K Baumohl, Peter Benke, Marcin P Joachimiak, Ming Xie, Rong Song, Adam P Arkin, Terry C Hazen, Jay D Keasling, Judy D Wall, David A Stahl and Jizhong Zhou. 2013. Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution. The ISME Journal doi:10.1038/ismej.2013.60.


3.

Bai S, Li J, He Z, Van Nostrand JD, Tian Y, Lin G, Zhou J, Zheng T. 2013. GeoChip-based analysis of the functional gene diversity and metabolic potential of soil microbial communities of mangroves. Appl Microbiol Biotechnol. 2013 Aug;97(15):7035-48.


4.

Kai Xue, Liyou Wu, Ye Deng, Zhili He, Joy Van Nostrand, Philip G. Robertson, Thomas M. Schmidt and Jizhong Zhou. 2013. Functional Gene Differences in Soil Microbial Communities from Conventional, Low-Input, and Organic Farmlands. Appl. Environ. Microbiol. 2013, 79(4):1284.


5.

Meiying Xu, Zhili He, Ye Deng, Liyou Wu, Joy D van Nostrand, Sarah E Hobbie, Peter B Reich and Jizhong Zhou. 2013. Elevated CO2 influences microbial carbon and nitrogen cycling. BMC Microbiology 2013, 13:124.


6.

Tu Q, He Z, Deng Y, Zhou J. 2013. Strain/Species-specific probe design for microbial identification microarrays. Appl Environ Microbiol. 79(16):5085-8. doi: 10.1128/AEM.01124-13.


7.

Yuki Chan, Joy D. Van Nostrand, Jizhong Zhou, Stephen B. Pointing, and Roberta L. Farrell. 2013. Functional ecology of an Antarctic Dry Valley. PNAS doi: 10.1073/pnas.**.


8.

Zhou J, Liu W, Deng Y, Jiang Y, Xue K, He, Van Nostrand JD, Wu L, Yang Y, and Wang A. 2013. Stochastic Assembly Leads to Alternative Communities with Distinct Functions in a Bioreactor Microbial Community. mBio 4(2):e00584-12.


2012
1.

Michelle Q. Carter, Kai Xue, Maria T. Brandl, Feifei Liu, Liyou Wu, Jacqueline W. Louie, Robert E. Mandrell, Jizhong Zhou . 2012. Functional Metagenomics of Escherichia coli O157:H7 Interactions with Spinach Indigenous Microorganisms during Biofilm Formation. PLoS ONE 7(9): e44186.


2.

Beazley MJ, Robert J. Martinez, Suja Rajan, Jessica Powell, Yvette M. Piceno, Lauren M. Tom, Gary L. Andersen, Terry C. Hazen, Joy D. Van Nostrand, Jizhong Zhou, Behzad Mortazavi, Patricia A. Sobecky. 2012. Microbial Community Analysis of a Coastal Salt Marsh Affected by the Deepwater Horizon Oil Spill. PLoS ONE 7(7): e41305.


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.


4.

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.


5.

He, Z., Y. Deng, and J.-Z. Zhou. 2012. Development of functional gene microarrays for microbial community analysis. Curr.Opin. Microbiol., 23: 49-55


6.

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.


7.

He, Z.L., J. D. Van Nostrand, and J.-Z. Zhou. 2012. Applications of functional gene microarrays for profiling microbial communities. Curr.Opin. Microbiol. doi.org/10.1016/j.copbio.2011.12.021.


8.

Huang, W., and J.-Z. Zhou. 2012. When single cell technology meets omics, the new toolbox of analytical biotechnology is emerging. Curr.Opin. Microbiol., 23:1.


9.

Joy D. Van Nostrand, Zhili He, Jizhong Zhou. 2012. Use of functional gene arrays for elucidating in situ biodegradation. Frontiers in Microbiology. doi: 10.3389/fmicb.2012.00339.


10.

Lara Rajeev, Kristina L. Hillesland, Grant M. Zane, Aifen Zhou, Marcin P. Joachimiak, Zhili He, Jizhong Zhou, Adam P. Arkin, Judy D. Wall and David A. Stahl. 2012. Deletion of the Desulfovibrio vulgaris Carbon Monoxide Sensor Invokes Global Changes in Transcription. J Bacteriol. 194(21):5783-93.


11.

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.


12.

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.


13.

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.


14.

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 doi: 10.1038/ismej.2011.91.


15.

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.


16.

Van Nostrand, J. D, Terry J. Gentry, and J.-Z. Zhou. 2012. 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).


17.

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.


18.

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. Str?poc, and A.V. Callaghan. 2012. Field and laboratory studies on the bioconversion of coal to methane in the San Juan Basin. FEMS Microb. Ecol. DOI: 10.1111/j.1574-6941.2011.01272.x.


19.

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.


20.

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 Biol. 18(5):1648-1656.


21.

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.


22.

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(4):1168-1177.


23.

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. doi:10.1038/nclimate1331.


2011
1.

He, Z., D. J. Van Nostrand, Y. Deng, and Z.-J. 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. China 5: 1-20.


2.

He. Q, Christopher L. Hemme, Helong Jiang, Zhili He, Jizhong Zhou. 2011. Mechanisms of enhanced cellulosic bioethanol fermentation by co-cultivation of Clostridium and Thermoanaerobacter spp. Bioresource Technology 102 (2011) 9586–9592.


3.

Hemme, CL, Matthew W. Fields, Qiang He, Ye Deng, Lu Lin, Qichao Tu, Housna Mouttaki, Aifen Zhou, Xueyang Feng, Zheng Zuo, Bradley D. Ramsay, Zhili He, Liyou Wu, Joy Van Nostrand, Jian Xu, Yinjie J. Tang, Juergen Wiegel, Tommy J. Phelps, and Jizhong Zhou. 2011. Correlation of Genomic and Physiological Traits of Thermoanaerobacter Species with Biofuel Yields. Appl. Environ. Microbiol, 77:7998-8008.


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.


5.

Liang, Y.T. J. D. van Nostrand, Y. Deng, Z.H. He, L.Y. Wu, X. Zhang, G.H. Li and J.-Z. Zhou. 2011. Functional gene diversity of soil microbial communities from five oil-contaminated fields in China. The ISME J. 5, 403-413.


6.

Lin, L., H. Song, Q. Tu, Y. Qin, A. Zhou, W. Liu, Z. He, J.-Z. Zhou, and J. Xu. 2011. The Thermoanaerobacter Glycobiome Reveals Mechanisms of Pentose and Hexose Co-Utilization in Bacteria. PLoS Genetics, 7(10): e**.


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.


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. Shewanella oneidensis MR-1 Sensory Box Protein Involved in Aerobic and Anoxic Growth. Appl. Environ. Microbiol 77: 4647-4656.


9.

Van Nostrand, J. D., S. Kang, Y. Deng, Y. Liang, Z. He, and J.-Z. Zhou. 2011. Monitoring Microbial Activity with GeoChip. In: Microbial Metal and Metalloid Metabolism: Advances and Applications. In: J.F. Stolz and R.S. Oremland (eds). Microbial Metal and Metalloid Metabolism: Advances and Applications.ASM Press, Washington DC, (Invited book chapter).


10.

Van Nostrand, J. D., Z. He, and J.-Z. Zhou. 2011. 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.


11.

Van Nostrand, J.D. and J. Zhou. 2011. Application of functional gene arrays (GeoChips) in monitoring carbon cycling. In: N. Jiao, F. Azam, and S. Sander (eds) Biological Carbon Pump (booklet). AAAS. pp 64-65.


12.

Van Nostrand, J.D., L.Y. Wu*,W.-M. Wu, Z.J. Huang, T. J. Gentry, Y. Deng, J. Carley, S. Carroll, Z.-H. 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.


13.

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..


14.

Van Nostrand,J.D., Z. He, and 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, 509-520.


15.

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.H. He, and J.-Z. Zhou. 2011. Isolation and Characterization of Shigella flexneri G3, Capable of Effective Cellulosic Saccharification under Mesophilic Conditions. Appl. Environ. Microbiol, 77: 517-523.


16.

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.


17.

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.


18.

Xie, J.P. Z.H. 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.


19.

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.


20.

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. The ISME J. 5: 1303-1313.


21.

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.


22.

Zhou. J, Ye Deng, Feng Luo, Zhili He, and Yunfeng Yang. 2011. Phylogenetic Molecular Ecological Network of Soil Microbial Communities in Response to Elevated CO2. mBio 2(4):e00122-11.




出版著作
Zhou, J.-Z., D.K. Thompson, Y. Xu, and James M. Tiedje. 2004. Microbial Functional Genomics. 624pp. John Wiley & Sons, Hoboken, New Jersey.


Education background
BS 1978-1981 Plant Pathology & Entomology, Hunan Agricultural University, Changsha, ChinaMS 1982-1984 Mathematical Ecology, Hunan Agricultural University, Changsha, China,Ph.D candidate 1986-1988 System Ecology, Eco-Environmental Research Center, Chinese Academy of Sciences, Beijing ChinaPh.D 1990-1993 Molecular Biology, Washington State University, Pullman, WA


Experience
1982-1984 Teaching and Research Assistant, Department of Plant Pathology and Entomology, Hunan Agricultural University, Changsha, China1985-1986 Lecturer in the Department of Plant Pathology and Entomology, Hunan Agricultural University, Changsha, China1986-1988 Research Associate, Eco-Environmental Research Center, Chinese Academy of Sciences, Beijing, China1988 Visiting Scientist, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada1989 Graduate Research and Teaching Assistant, Laboratory of Dr. Alan Berryman, Department of Entomology, Washington State University, Pullman, WA1990-1993 Graduate Research and Teaching Assistant, Laboratory of Dr. AndrisKleinhofs, Department of Genetics and Cell Biology, Washington State University, Pullman, WA1993-1995 Research Associate, Laboratory of Dr. James M. Tiedje, NSF Center for Microbial Ecology, Michigan State University, East Lansing, MI. Bioreactor Subgroup Leader of the Community Analysis Group1996-1997 Alexander Hollaender Distinguished Postdoctoral Fellow, Environmental Sciences Division, ORNL1997-2000 Staff Scientist, Environmental Sciences Division, ORNL2000-2001 Science Team Leader for Microbial Genomics and Ecology, Environmental Sciences Division, ORNL2001-2002 Senior Staff Scientist, Environmental Sciences Division, ORNL2002-2004 Science Leader for Environmental Genomics Program, Biological and Environmental Sciences Directorate, ORNL2003-2005 Distinguished R&D Staff Scientist, Environmental Sciences Division, ORNL2004-2005 Member of Science Council, Biological and Environmental Sciences Directorate, ORNL2005-present Director of the Institute for Environmental Genomics (IEG), University of Oklahoma, Norman, OK2005-present Presidential Professor, Department of Botany and Microbiology, University of Oklahoma, Norman, OK2006-present Adjunct Senior Scientist, Lawrence Berkeley National Laboratory (LBL)2011-present Director for Environmental Technology for ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies), a large scale Genomics: GTL Foundational Science Program at Lawrence Berkeley National Laboratory.2012-present Adjunct Professor, Harbin Institute of Technology


Areas of Research Interests/ Research Projects
Environmental Genomics and Functional GenomicsSystems Biology and BioinformaticsMicrobial Ecology and Community Ecology


Published Books
Zhou, J.-Z., D.K. Thompson, Y. Xu, and James M. Tiedje. 2004. Microbial Functional Genomics. 624pp. John Wiley & Sons, Hoboken, New Jersey.


PUBLICATIONS


2013
1.

Sul, Woo Jun, Stella Asuming-Brempong, Qiong Wang, Dieter M. Tourlousse, C. Ryan Penton, Ye Deng, Jorge LM Rodrigues et al. 2013. Tropical agricultural land management influences on soil microbial communities through its effect on soil organic carbon. Soil Biology and Biochemistry.


2.

Aifen Zhou, Edward Baidoo, Zhili He, Aindrila Mukhopadhyay, Jason K Baumohl, Peter Benke, Marcin P Joachimiak, Ming Xie, Rong Song, Adam P Arkin, Terry C Hazen, Jay D Keasling, Judy D Wall, David A Stahl and Jizhong Zhou. 2013. Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution. The ISME Journal doi:10.1038/ismej.2013.60.


3.

Bai S, Li J, He Z, Van Nostrand JD, Tian Y, Lin G, Zhou J, Zheng T. 2013. GeoChip-based analysis of the functional gene diversity and metabolic potential of soil microbial communities of mangroves. Appl Microbiol Biotechnol. 2013 Aug;97(15):7035-48.


4.

Kai Xue, Liyou Wu, Ye Deng, Zhili He, Joy Van Nostrand, Philip G. Robertson, Thomas M. Schmidt and Jizhong Zhou. 2013. Functional Gene Differences in Soil Microbial Communities from Conventional, Low-Input, and Organic Farmlands. Appl. Environ. Microbiol. 2013, 79(4):1284.


5.

Meiying Xu, Zhili He, Ye Deng, Liyou Wu, Joy D van Nostrand, Sarah E Hobbie, Peter B Reich and Jizhong Zhou. 2013. Elevated CO2 influences microbial carbon and nitrogen cycling. BMC Microbiology 2013, 13:124.


6.

Tu Q, He Z, Deng Y, Zhou J. 2013. Strain/Species-specific probe design for microbial identification microarrays. Appl Environ Microbiol. 79(16):5085-8. doi: 10.1128/AEM.01124-13.


7.

Yuki Chan, Joy D. Van Nostrand, Jizhong Zhou, Stephen B. Pointing, and Roberta L. Farrell. 2013. Functional ecology of an Antarctic Dry Valley. PNAS doi: 10.1073/pnas.**.


8.

Zhou J, Liu W, Deng Y, Jiang Y, Xue K, He, Van Nostrand JD, Wu L, Yang Y, and Wang A. 2013. Stochastic Assembly Leads to Alternative Communities with Distinct Functions in a Bioreactor Microbial Community. mBio 4(2):e00584-12.


2012
1.

Michelle Q. Carter, Kai Xue, Maria T. Brandl, Feifei Liu, Liyou Wu, Jacqueline W. Louie, Robert E. Mandrell, Jizhong Zhou . 2012. Functional Metagenomics of Escherichia coli O157:H7 Interactions with Spinach Indigenous Microorganisms during Biofilm Formation. PLoS ONE 7(9): e44186.


2.

Beazley MJ, Robert J. Martinez, Suja Rajan, Jessica Powell, Yvette M. Piceno, Lauren M. Tom, Gary L. Andersen, Terry C. Hazen, Joy D. Van Nostrand, Jizhong Zhou, Behzad Mortazavi, Patricia A. Sobecky. 2012. Microbial Community Analysis of a Coastal Salt Marsh Affected by the Deepwater Horizon Oil Spill. PLoS ONE 7(7): e41305.


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.


4.

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.


5.

He, Z., Y. Deng, and J.-Z. Zhou. 2012. Development of functional gene microarrays for microbial community analysis. Curr.Opin. Microbiol., 23: 49-55


6.

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.


7.

He, Z.L., J. D. Van Nostrand, and J.-Z. Zhou. 2012. Applications of functional gene microarrays for profiling microbial communities. Curr.Opin. Microbiol. doi.org/10.1016/j.copbio.2011.12.021.


8.

Huang, W., and J.-Z. Zhou. 2012. When single cell technology meets omics, the new toolbox of analytical biotechnology is emerging. Curr.Opin. Microbiol., 23:1.


9.

Joy D. Van Nostrand, Zhili He, Jizhong Zhou. 2012. Use of functional gene arrays for elucidating in situ biodegradation. Frontiers in Microbiology. doi: 10.3389/fmicb.2012.00339.


10.

Lara Rajeev, Kristina L. Hillesland, Grant M. Zane, Aifen Zhou, Marcin P. Joachimiak, Zhili He, Jizhong Zhou, Adam P. Arkin, Judy D. Wall and David A. Stahl. 2012. Deletion of the Desulfovibrio vulgaris Carbon Monoxide Sensor Invokes Global Changes in Transcription. J Bacteriol. 194(21):5783-93.


11.

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.


12.

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.


13.

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.


14.

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 doi: 10.1038/ismej.2011.91.


15.

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.


16.

Van Nostrand, J. D, Terry J. Gentry, and J.-Z. Zhou. 2012. 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).


17.

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.


18.

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. Str?poc, and A.V. Callaghan. 2012. Field and laboratory studies on the bioconversion of coal to methane in the San Juan Basin. FEMS Microb. Ecol. DOI: 10.1111/j.1574-6941.2011.01272.x.


19.

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.


20.

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 Biol. 18(5):1648-1656.


21.

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.


22.

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(4):1168-1177.


23.

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. doi:10.1038/nclimate1331.


2011
1.

He, Z., D. J. Van Nostrand, Y. Deng, and Z.-J. 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. China 5: 1-20.


2.

He. Q, Christopher L. Hemme, Helong Jiang, Zhili He, Jizhong Zhou. 2011. Mechanisms of enhanced cellulosic bioethanol fermentation by co-cultivation of Clostridium and Thermoanaerobacter spp. Bioresource Technology 102 (2011) 9586–9592.


3.

Hemme, CL, Matthew W. Fields, Qiang He, Ye Deng, Lu Lin, Qichao Tu, Housna Mouttaki, Aifen Zhou, Xueyang Feng, Zheng Zuo, Bradley D. Ramsay, Zhili He, Liyou Wu, Joy Van Nostrand, Jian Xu, Yinjie J. Tang, Juergen Wiegel, Tommy J. Phelps, and Jizhong Zhou. 2011. Correlation of Genomic and Physiological Traits of Thermoanaerobacter Species with Biofuel Yields. Appl. Environ. Microbiol, 77:7998-8008.


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.


5.

Liang, Y.T. J. D. van Nostrand, Y. Deng, Z.H. He, L.Y. Wu, X. Zhang, G.H. Li and J.-Z. Zhou. 2011. Functional gene diversity of soil microbial communities from five oil-contaminated fields in China. The ISME J. 5, 403-413.


6.

Lin, L., H. Song, Q. Tu, Y. Qin, A. Zhou, W. Liu, Z. He, J.-Z. Zhou, and J. Xu. 2011. The Thermoanaerobacter Glycobiome Reveals Mechanisms of Pentose and Hexose Co-Utilization in Bacteria. PLoS Genetics, 7(10): e**.


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.


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. Shewanella oneidensis MR-1 Sensory Box Protein Involved in Aerobic and Anoxic Growth. Appl. Environ. Microbiol 77: 4647-4656.


9.

Van Nostrand, J. D., S. Kang, Y. Deng, Y. Liang, Z. He, and J.-Z. Zhou. 2011. Monitoring Microbial Activity with GeoChip. In: Microbial Metal and Metalloid Metabolism: Advances and Applications. In: J.F. Stolz and R.S. Oremland (eds). Microbial Metal and Metalloid Metabolism: Advances and Applications.ASM Press, Washington DC, (Invited book chapter).


10.

Van Nostrand, J. D., Z. He, and J.-Z. Zhou. 2011. 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.


11.

Van Nostrand, J.D. and J. Zhou. 2011. Application of functional gene arrays (GeoChips) in monitoring carbon cycling. In: N. Jiao, F. Azam, and S. Sander (eds) Biological Carbon Pump (booklet). AAAS. pp 64-65.


12.

Van Nostrand, J.D., L.Y. Wu*,W.-M. Wu, Z.J. Huang, T. J. Gentry, Y. Deng, J. Carley, S. Carroll, Z.-H. 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.


13.

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..


14.

Van Nostrand,J.D., Z. He, and 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, 509-520.


15.

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.H. He, and J.-Z. Zhou. 2011. Isolation and Characterization of Shigella flexneri G3, Capable of Effective Cellulosic Saccharification under Mesophilic Conditions. Appl. Environ. Microbiol, 77: 517-523.


16.

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.


17.

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.


18.

Xie, J.P. Z.H. 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.


19.

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.


20.

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. The ISME J. 5: 1303-1313.


21.

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.


22.

Zhou. J, Ye Deng, Feng Luo, Zhili He, and Yunfeng Yang. 2011. Phylogenetic Molecular Ecological Network of Soil Microbial Communities in Response to Elevated CO2. mBio 2(4):e00122-11.