Publications

Zhang Y, J Xie, M Liu, Z Tian, Z He, JD Van Nostrand, L Ren, J Zhou, M Yang. 2013. Microbial community functional structure in response to antibiotics in pharmaceutical wastewater treatment systems. Water Research. doi.org/10.1016/j.watres.2013.08.003.

Chan, Yuki; Joy D. Van Nostrand, Jizhong Zhou, Stephen B. Pointing, and Roberta L. Farrell. 2013. Functional ecology of an Antarctic Dry Valley. PNAS. 110:8990-8995.

He, Zhili; Jinbo Xiong, Angela D Kent, Ye Deng, Kai Xue, Gejiao Wang, Liyou Wu, Joy D Van Nostrand, and Jizhong Zhou. 2013. Distinct responses of soil microbial communities to elevated CO2 and O3 in a soybean agro-ecosystem. The ISME Journal 1-13.

Li, Xinyu, Ye Deng, Qi Li, Caiyan Lu, Jingjing Wang, Huiwen Zhang, Jianguo Zhu, Jizhong Zhou, and Zhili He. 2013. Shifts of functional gene representation in wheat rhizosphere microbial communities under elevated ozone. The ISME journal.

Lu, Zhenmei, Zhili He, Victoria A. Parisi, Sanghoon Kang, Ye Deng, Joy D. Van Nostrand, Jason R. Masoner, Isabelle M. Cozzarelli, Joseph M. Suflita, and Jizhong Zhou. 2013. GeoChip-based analysis of microbial functional gene diversity in a landfill leachate-contaminated aquifer. Environmental science & technology, 46(11), 5824-5833.

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.

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.

He, Z.H., 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.

Wang, F., H. Zhou, J. Meng, X.T. Peng, L. Jiang, P. Sun, C. Zhang, J.D.VanNostrand , 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.

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.

Antony-Babu, A, A Deveau, J Van Nostrand, J Zhou, F Le Tacon, C Robin, P Frey-Klett, and S Uroz. 2013. Black truffle-associated bacterial communities during the development and maturation of Tuber melanosporum ascocarps and putative functional roles. Environ Microbiol. In press.

Kang, S., J.D. Van Nostrand, H.L. Gough, Z. He, T.C. Hazen, D.A. Stahl, J. Zhou. 2013. Functional gene array-based analysis of microbial communities in heavy metals contaminated lake sediments. FEMS Microbiol. Ecol. DOI: 10.1111/1574-6941.12152.

Zhang Y, J Xie, M Liu, Z Tian, Z He, JD Van Nostrand, L Ren, J Zhou, M Yang. 2013. Microbial community functional structure in response to antibiotics in pharmaceutical wastewater treatment systems. Water Research. doi.org/10.1016/j.watres.2013.08.003.

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):7035-7048.

Chan, Yuki; Joy D. Van Nostrand, Jizhong Zhou, Stephen B. Pointing, and Roberta L. Farrell. 2013. Functional ecology of an Antarctic Dry Valley. PNAS. 110:8990-8995.

Eisenlord, Sarah D., Zachary Freedman, Donald R. Zak, Kai Xue, Zhili He, and Jizhong Zhou. 2013. Microbial mechanisms mediating increased soil C storage under elevated atmospheric N deposition. Applied and environmental microbiology 79, no. 4 (2013): 1191-1199.

He, Zhili; Jinbo Xiong, Angela D Kent, Ye Deng, Kai Xue, Gejiao Wang, Liyou Wu, Joy D Van Nostrand, and Jizhong Zhou. 2013. Distinct responses of soil microbial communities to elevated CO2 and O3 in a soybean agro-ecosystem. The ISME Journal 1-13.

Li, Xinyu, Ye Deng, Qi Li, Caiyan Lu, Jingjing Wang, Huiwen Zhang, Jianguo Zhu, Jizhong Zhou, and Zhili He. 2013. Shifts of functional gene representation in wheat rhizosphere microbial communities under elevated ozone. The ISME journal.

Lu, Zhenmei, Zhili He, Victoria A. Parisi, Sanghoon Kang, Ye Deng, Joy D. Van Nostrand, Jason R. Masoner, Isabelle M. Cozzarelli, Joseph M. Suflita, and Jizhong Zhou. 2013. GeoChip-based analysis of microbial functional gene diversity in a landfill leachate-contaminated aquifer. Environmental science & technology, 46(11), 5824-5833.

Wakelin, Steven A., Barbara IP Barratt, Emily Gerard, Adrienne L. Gregg, Eoin L. Brodie, Gary L. Andersen, Todd Z. DeSantis et al. 2013. Shifts in the phylogenetic structure and functional capacity of soil microbial communities follow alteration of native tussock grassland ecosystems. Soil Biology and Biochemistry.

Xu, Meiying; 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.

Xue, Kai; 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. 79(4):1284-1294.

Zhang, Yuguang, Zhenmei Lu, Shanshan Liu, Yunfeng Yang, Zhili He, Zuohua Ren, Jizhong Zhou, and Diqiang Li. 2013. Geochip-based analysis of microbial communities in alpine meadow soils in the Qinghai-Tibetan plateau. BMC microbiology, 13(1), 72.

Zhang, Zhenyi, Xuan Zhao, Yuting Liang, Guanghe Li, and Jizhong Zhou. 2013. Microbial functional genes reveal selection of microbial community by PAHs in polluted soils. Environmental Chemistry Letters, 11(1), 11-17.

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.

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.

Carter, Michelle Q; 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.

Ding, Guo-Chun, Holger Heuer, Zhili He, Jianping Xie, Jizhong Zhou, and Kornelia Smalla. 2012. More functional genes and convergent overall functional patterns detected by geochip in phenanthrene-spiked soils. FEMS microbiology ecology 82, no. 1 (2012): 148-156.

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.

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.

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.

Reith, Frank, Joel Brugger, Carla M. Zammit, Adrienne L. Gregg, Katherine C. Goldfarb, Gary L. Andersen, Todd Z. DeSantis et al. 2012. Influence of geogenic factors on microbial communities in metallogenic Australian soils. The ISME Journal, 6(11), 2107-2118.

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.

Wang, Hang, Zhili He, Zhenmei Lu, Jizhong Zhou, Joy D. Van Nostrand, Xinhua Xu, and Zhijian Zhang. 2012. Genetic linkage of soil carbon pools and microbial functions in subtropical freshwater wetlands in response to experimental warming. Applied and environmental microbiology, 78(21), 7652-7661.

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. 81:26-42. DOI: 10.1111/j.1574-6941.2011.01272.x.

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.

Xiong, Jinbo, Zhili He, Joy D. Van Nostrand, Guosheng Luo, Shuxin Tu, Jizhong Zhou, and Gejiao Wang. 2012. Assessing the Microbial Community and Functional Genes in a Vertical Soil Profile with Long-Term Arsenic Contamination. PloS one, 7(11), e50507.

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.

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.

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.

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.

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.

Epelde, L., J. M. Becerril, G. A. Kowalchuk, Y. Deng, J.-Z. Zhou, and C. Garbisu. 2010. Impact of Metal Pollution and Thlaspi caerulescens Growth on Soil Microbial Communities. APPLIED AND ENVIRONMENTAL MICROBIOLOGY 76(23): 7843-7853.

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.

He, Z., Y. Deng, J. D. Van Nostrand, Q. Tu, M. Xu, C.L. Hemme, X. Li, L. Wu, T.J. Gentry, Y. Yin, J. Leibich, T.C. Hazen, and J. Zhou. 2010. GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity. ISME J. 4: 1167-1179.

He, Z.H., 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.

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.

Liu, W.Z., A.J. Wang, Sh. Cheng, B. E. Logan, H. Yu, Y. Deng, J. D. van Nostrand, L.Y. Wu, Z.H. 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.

Parnell JJ, Rompato G, Latta LC IV, Pfrender ME, Van Nostrand JD, He J, Zhou J, Andersen G, Champine P, Ganesan B, Weimer BC. 2010. Functional Biogeography as Evidence of Gene Transfer in Hypersaline Microbial Communities. PLoS ONE 5(9): e12919.

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. The ISME J. 4: 1099-1107.

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.

Xiong, J.B., L.Y. Wu, S.X. Tu, J. D. van Nostrand, Z.H. 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-Hyperaccumulating Plant Pteris vittata L. Appl. Environ. Microbiol, 76: 7277-7284.

Xu Meiying, Wei-Min Wu, Liyou Wu, Zhili He, Joy D Van Nostrand, Ye Deng, Jian Luo, Jack Carley, Matthew Ginder-Vogel, Terry J Gentry, Baouhua Gu, David Watson, Philip M Jardine, Terence L Marsh, James M Tiedje, Terry Hazen, Craig S Criddle and Jizhong Zhou. 2010. Responses of microbial community functional structures to pilot-scale uranium in situ bioremediation. The ISME Journal. 4: 1060-1070.

Wang, F., H. Zhou, J. Meng, X.T. Peng, L. Jiang, P. Sun, C. Zhang, J.D.VanNostrand , 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.

Jost Liebich, Thorsten Wachtmeister, Jizhong Zhou and Peter Burauel. 2009. Degradation of Diffuse Pesticide Contaminants: Screening for Microbial Potential Using a Functional Gene Microarray. VADOSE ZONE JOURNA, 8 : 703-710.

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 during ozonation and biodegradation of crude oil. Chemosphere, 75: 193-199.

Liang, YT; Li, GH; Van Nostrand, JD, et al.. 2009. Microarray-based analysis of microbial functional diversity along an oil contamination gradient in oil field. FEMS MICROBIOLOGY ECOLOGY, 70(2):324-333..

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 insights into their role in biogeochemical cycling in marine basalts. ISME J, 3: 231-242.

Tas, N., M. H.A. van Eekert, G. Schraa, J.-Z. Zhou, W. M. de Vos, and H. Smidt. 2009. Tracking Functional Guilds: "Dehalococcoides" spp. in European River Basins Contaminated with Hexachlorobenzene . Appl. Environ. Microbiol. 75: 4696-4704.

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 during the reoxidation of a bioreduced uranium-contaminated aquifer. Environ. Microbiol., 11: 2611-2626.

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.

Wu, Liyou*, Laurie Kellogg, Allan H. Devol, Anothy V. Palumbo, James M. Tiedje, and Jizhong 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.

Zhou, J.-Z*, Sanghoon Kang*, Christopher W. Schadt, and Charles T. Garten, Jr. 2008. Spatial Scaling of Functional Gene Diversity across Various Microbial Taxa. Proc Nat. Acad. Sci, 105: 7768-7773. *equal contribution.