基本情况
贺志理，男，教授，博士生导师
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联系方式
地址：广州市大学城外环东路132号，中山大学环境科学与工程学院，510006
电话：
E-mail：hezhili@mail.sysu.edu.cn
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教育经历
1982.9-1986.7??? 湖南师范大学? 理学学士
1986.9-1989.7??? 中科院上海植物生理研究所? 理学硕士
1994.2-1998.7? ? 澳大利亚国立大学? 哲学博士
1999.1-2001.10 ? 加拿大圭尔夫大学? 文学学士
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工作经历
1989.08-1994.02?? 中科院上海植物生理研究所? 助理研究员
1997.12-1998.09?? 日本地球创新技术研究所? 研究员
1998.10-2002.12?? 加拿大圭尔夫大学? 博士后
2003.02-2005.08?? 美国能源部橡树岭国家实验室? 博士后
2005.09-2005.09 ? 美国能源部橡树岭国家实验室? 助理教授
2005.10-2007.08?? 美国俄克拉荷马大学环境基因组研究所? 助理教授/副所长
2007.09-2011.08?? 美国俄克拉荷马大学环境基因组研究所? 副教授/副所长
2011.09-2017.02?? 美国俄克拉荷马大学环境基因组研究所? 教授/副所长
2017.03--至今???? ? 中山大学教授? 环境微生物组研究中心负责人
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研究方向
（1）环境、人类、植物微生物组学（微生物多样性、组成、结构、功能、演替及其与环境/宿主的关系）
（2）?环境微生物生态学（使用高通量组学、基因组学的方法分析全球环境变化、环境压力以及生物修复相关的微生物学）?
（3）系统微生物学以及微生物功能基因研究（分析纯培养或合成微生物群落，了解基因功能、调控和互作网络）
（4）开发生物技术和生物信息学工具（功能基因芯片GeoChip、人类微生物基因芯片HuMiChip等）
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科研项目
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? 起止时间 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ??项目来源 ? ? ? ? ? ? ? ? ? ? ? ?负责的具体任务
2011/2-2014/1 ? ? ? ? ? ? ? ?美国俄克拉荷马州OCAST基金 ? ? ? ? ??主持，负责人体微生物组基因芯片的设计、研发和评估，其产品为HuMiChip ? 1.0和2.0。
2010/6-2011/3 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ??美国能源部 ? ? ? ? ? ? ? ? ? ? ? ?主持，负责应用amoA基因研究土壤微生物群落中硝化细菌的多样性。
2010/6-2011/3 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 美国能源部 ? ? ? ? ? ? ? ? ? ? ? ?主持，负责应用dsrA/B基因研究地下微生物群落中硫酸盐还原细菌的多样性。
2008/1-2011/12 ? ? ? ? ? ? ? ??美国俄克拉荷马州政府基金 ? ? ? ? ? ? ?主持，负责研究高效产乙醇系统中微生物群落的构建和相互作用及其调节网络。
2006/10-2009/9 ? ? ? ? ? ? ?美国俄克拉荷马州OCAST基金 ? ? ? ? ??主持，负责研发GeoChip设计、研发和评估工具和数据处理系统及项目汇报，其产品为GeoChip ? 3.0，获得美国《R&D》杂志2009 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?年颁发的“R&D ? 100 Award”奖。
2014/1-2017/12 ? ? ? ? ? ? ? ? ??NSFC-广东联合重点基金 ? ? ? ? ? ? ? 参与，负责微生物方面的研究，利用高通量的宏基因组探索海洋水体和底泥微生物群落结构与功能。
2013/9-2016/8 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ??美国能源部 ? ? ? ? ? ? ? ? ? ? ? ?参与并协调多个参与单位，负责美国俄克拉荷马州和阿拉斯加州升温实验场地土壤微生物群落的宏基因组学研究。
2013/9-2015/8 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ??美国能源部 ? ? ? ? ? ? ? ? ? ? ? ?参与，负责土壤微生物群落的宏基因组学研究和研发基于KBase的生物信息学工具。
2012/1-2015/12 ? ? ? ? ? ? ? ? ? ? ??中国国家自然科学基金 ? ? ? ? ? ? ??参与，负责河流物修复系统中水体和底泥微生物群落的宏基因组学研究，评估生物治理技术的效果。
2011/9-2013/8 ? ? ? ? ? ??美国国家自然科学基金EPSCoR ? ? ? ? ? ?参与并协调多个俄克拉荷马州大学和研究机构（共30多人参加，总经费为1500万美元），
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?（俄克拉荷马州） ? ? ? ? ? ? ? ? ? ? ?主持其中一子项目：建立高效产乙醇微生物菌群及其表征。
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2011/8-2015/7 ? ? ? ? ? ? ? ? ? ? ? ? 美国国家自然科学基金 ? ? ? ? ? ? ? ?参与并协调多个参与单位，主持微生物子项目，研究森林生态系统中微生物群落的多样性。
2010/7-2014/7 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?美国能源部 ? ? ? ? ? ? ? ? ? ? ? ??参与，负责微生物群落功能过程的GeoChip和宏基因组分析，协调多个参与单位。
2008/10-2017/9 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?美国能源部 ? ? ? ? ? ? ? ? ? ? ? ??主持地下水微生物群落的宏基因组学研究，同时应用GeoChip分析和测序的技术研究微生物群落中硫酸盐还原、
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?金属还原和有机污染物降解过程。
2008/7-2010/12 ? ? ? ? ? ? ? ? ? ? ? ? ? 美国康菲石油公司 ? ? ? ? ? ? ? ? ??参与并协调与美国康菲石油公司的研究计划，负责应用GeoChip研究油田微生物群落结构与功能，评估生物治理技术的效果。
2008/6-2012/8 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?美国能源部 ? ? ? ? ? ? ? ? ? ? ? ??参与，负责分析微生物群落结构和功能。
2008/1-2011/12 ? ? ? ? ? ? ? ? ?美国俄克拉荷马州政府基金 ? ? ? ? ? ? 参与并协调该项目实施，负责GeoChip在土壤微生物种群研究中的应用。
2008/1-2011/12 ? ? ? ? ? ? ? ? ?美国俄克拉荷马州政府基金 ? ? ? ? ? ??参与，负责一种特殊真菌产乙醇功能表征和工艺优化研究。
2007/3-2012/3 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ??美国能源部 ? ? ? ? ? ? ? ? ? ? ? ? ?参与并协调多个参与单位，负责应用GeoChip研究美国橡树岭铀污染场地地下水样品。
2007/9-2012/8 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ??美国农业部 ? ? ? ? ? ? ? ? ? ? ? ? ?参与并协调BioCON实验，负责草地土壤微生物群落结构与功能研究。
2005/9-2008/9 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 美国能源部 ? ? ? ? ? ? ? ? ? ? ? ? ??参与，负责Desulfovibrio ? vulgaris基因芯片的构建、评估及其应用。
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学术论文（*通讯；#并列第一）
截至 2016 年底，发表环境微生物组及生物信息学方面相关论文 210 余篇， 主要包括 Nature Climate Change，Nature Reviews Microbiology，Nature Communications，PNAS，Ecology Letters，The ISME Journal，Nucleic Acids Research，Global Change Biology，Environmental Microbiology 等；总影响因子 >900，总引用次数 > 12,000(Google Scholar)，H index > 54。
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2017
1.??????????? Tu Q, Li J, Shi Z, Chen Y, Lin L, Li J, Wang H, Yan J, Zhou Q, Li X, Li L, Zhou J, He Z*. 2017. HuMiChip2 for strain level identification and functional profilingof human microbiomes. Appl Environ Microbiol101: 423-435.
2.??????????? Tu Q, He Z, Wu L, Xue K, Xie G, Chain P, Reich PB, Hobbie SE, and Zhou J. 2017. Metagenomic reconstruction of nitrogen cycling pathways in a CO2-enriched grassland ecosystem. Soil Biol Biochem106: 99-108.
3.??????????? Li H, Yang S, Xu Z, Yan Q, Li X, van Nostrand J. He Z, Yao F, Han X, Zhou J, Deng Y, Jiang Y. 2017. Responses of soil microbial functional genes to global changes are indirectly influenced by aboveground plant biomass variation. Soil Biol Biochem104: 18-29.
4.??????????? Yao M, Rui J, Niu H, Heděnec P, Li J, He Z, Wang J, Cao W, and Li X. 2017. The differentiation of soil bacterial communities along a precipitation and temperature gradient in the eastern Inner Mongolia steppe. CATENA152: 47-56.?
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2016
5.??????????? Deng Y, He Z*, Xiong J, Yu H, Xu M, Hobbie SE, Reich PB, Schadt CW, Kent A, Pendall E, Wallenstein M, and Zhou J. 2016. Elevated carbon dioxide accelerates the spatial turnover of soil microbial communities. Glob Change Biol 22:957–964.
6.??????????? Wu B, Wang X, Yang L, Yang H, Zeng H, Qiu Y, Wang C, Yu J, Li J, Xu D, He Z*, and Chen S*. 2016. Effects of Bacillus amyloliquefaciens ZM9 on bacterial wilt and rhizosphere microbial communities of tobacco. Appl Soil Ecol 103:1–12.
7.??????????? Yu Z#, He Z#, Tao X, Zhou J, Yang Y, Zhao M, Zhang X, Zheng Z, Yuan T, Liu P, Chen Y, Nolan V, and Li X. 2016. The shifts of sediment microbial community phylogenetic and functional structures during chromium (VI) reduction. Ecotoxicology25: 1750-1770.
8.??????????? Deng Y, Zhang P, Qin Y, Tu Q, Yang Y, He Z, Schadt CW, and Zhou J. 2016. Network succession reveals the importance of competition in response to emulsified vegetable oil amendment for uranium bioremediation. Environ Microbiol18: 205-218.
9.??????????? Tu Q, Zhou X, He Z, Xue K, Wu L, Reich PB, Hobbie SE, and Zhou J. 2016. The diversity and co-occurrence patterns of N2-fixing communities in a CO2-enriched grassland ecosystem. Microb Ecol71: 604-615.
10.??????? Kuang J, Huang L, He Z, Chen L, Hua Z, Jia P, Li S, Liu J, Li J, Zhou J, and Shu W. 2016. Predicting taxonomic and functional structure of microbial communities in acid mine drainage. ISME J10: 1527-1539.
11.??????? Shi S, Nuccio EE, Shi Z, He Z, Zhou J, and Firestone MK. 2016. The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages. Ecol Lett19: 926-936.
12.??????? Xue K, Yuan MM, Shi Z, Qin Y, Deng Y, Cheng L, Wu L, He Z, Van Nostrand JD, Bracho R, Natali S, Schurr EAG, Luo C, Konstantinidis KT, Wang Q, Cole JR, Tiedje JM, Luo Y, and Zhou J. 2016. Tundra soil carbon is vulnerable to rapid microbial decomposition under climate warming. Nat Clim Change6: 595.
13.??????? Zhou J, Deng Y, Shen L, Wen C, Yan Q, Ning D, Qin Y, Xue K, Wu L, He Z, Voordeckers JW, Van Nostrand JD, Buzzard V, Michaletz ST, Enquist BJ, Weiser MD, Kaspari M, Waide R, Yang Y, and Brown JH. 2016. Temperature mediates continental-scale diversity of microbes in forest soils. Nat Comm7: 12083.
14.??????? Yan Q, Li J, Yu Y, Wang J, He Z, Van Nostrand JD, Kempher ML, Wu L, Wang Y, Liao L, Li X, Wu S, Ni J, Wang C, and Zhou J. 2016. Environmental filtering decreases with fish development for the assembly of gut microbiota. Environ Microbiol18: 4739-4754.
15.??????? Tu Q, Deng Y, Yan Q, Shen L, Lin L, He Z, Wu L, Van Nostrand JD, Buzzard V, Michaletz ST, Enquist BJ, Weiser MD, Kaspari M, Waide R, Brown JH, and Zhou J. 2016. Biogeographic patterns of soil diazotrophic communities across six forests in North America. Mol Ecol25: 2937-2948.
16.??????? Morrison E. Newman S, Bae HS, He Z, Zhou J, Reddy KR, and Ograma A. 2016. Microbial genetic and enzymatic responses to an anthropogenic phosphorus gradient within a subtropical peatland. Geoderma268: 119–127.
17.??????? Niu J, Deng J, Xiao Y, He Z, Zhang X, Van Nostrand JD, Liang Y, Deng Y, Liu X, and Yin H. 2016. The shift of microbial communities and their roles in sulfur and iron cycling in a copper ore bioleaching system. Sci Rep6: 34744.?
18.??????? Yang C, Li Y, Zhou Y, Lei X, Zheng W, Tian Y, Van Nostrand JD, He Z, Wu L, Zhou J, and Zheng T. 2016. A comprehensive insight into functional profiles of free-living microbial community responses to a toxic Akashiwo sanguinea bloom. Sci Rep6: 34645.
19.??????? Qiu D, Xie M, Dai J, An W, Wei H, Tian C, Kempher ML, Zhou A, He Z, Gu B, and Zhou J. 2016. Differential regulation of the two ferrochelatase paralogues in Shewanella loihica PV-4 in response to environmental stresses. Appl Environ Microbiol82: 5077-5088.
20.??????? Hemme CL, Green ST, Rishishwar L, Prakash O, Pettenato A, Chakraborty R, Deutchbauer AM,? Van Nostrand JD, Wu L, He Z, Jordan IK, Hazen TC, Arkin AP, Adams P, Kostka JE, and Zhou J. 2016. Marked lateral gene transfer in a heavy metal-contaminated groundwater microbial community. mBio 7: e02234-15.
21.??????? Johnston ER, Rodriguez-R LM, Luo C, Yuan MM, Wu L, He Z, Schuur EAG, Luo Y, Tiedje JM, Zhou J, and Konstantinidis KT. 2016. Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity Across the Alaska Tundra Ecosystem. Front Microbiol 7: 579.
22.??????? Shen C, Shi Y, Ni Y, Deng Y, Van Nostrand JD, He Z, Zhou J, and Chu H. 2016. Dramatic increases of soil microbial functional gene diversity at the treeline ecotone of Changbai Mountain. Front Microbiol 7:7994.
23.??????? Wu L, Yang Y, Chen S, Zhao M, Zhu Z, Yang S, Qu Y, Ma Q, He Z, Zhou J, and He Q. 2016. Long-term successional dynamics of microbial association networks in anaerobic digestion processes. Water Res104:1-10..
24.??????? Xue K, Xie J, Zhou A, Liu F, Li D, Wu L, Deng Y, He Z, Van Nostrand JD, Luo Y, and Zhou J. 2016. Warming alters expressions of microbial functional genes important to ecosystem functioning. Front Microbiol7: 668.
25.??????? Xue K, Yuan MM, Xie J, Li D, Qin Y, Hale LE, Wu L, Deng Y, He Z, Van Nostrand JD, Luo Y, Tiedje JM, Zhou J. 2016. Annual removal of aboveground plant biomass alters soil microbial responses to warming. mBio7: e00976-16.
26.??????? Van Nostrand JD, Yin H, He Z, and Zhou J. 2016. Hybridization of Environmental Microbial Community Nucleic Acids by GeoChip. In: (FM Martin and S Uroz, eds) Methods in Molecular Biology - Microbial Environmental Genomics. Springer Press.
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2015
27.??????? Xiong J, He Z*, Shi S, Kent A, Deng Y, Wu L, Van Nostrand JD, and Zhou J*. 2015. Elevated CO2 shifts the functional structure and metabolic potentials of soil microbial communities in a C4 agroecosystem. Sci Rep5: 9316.
28.??????? Zhou J, He Z, Yang Y, Deng Y, Tringe SG, and Alvarez-Cohen L. 2015. High-throughput metagenomic technologies for complex microbial community analysis: open and closed formats. mBio6: 02288-14.
29.??????? Xu M, He Z, Zhang Q, Liu J, Guo J, Sun G, and Zhou J. 2015. Responses of aromatic-degrading microbial communities to elevated nitrate in sediments. Environ Sci Technol49: 12422-12431.
30.??????? Tu Q, Yuan M, He Z, Deng Y, Xue K, Wu L, Hobbie SE, Reich PB, and Zhou J. 2015. Fungal communities respond to long-term elevated CO2elevation by community reassembly. Appl Environ Microbiol81: 2445-2454.
31.??????? Zhou A, Hillesland K, He Z, Schackwitz W, Tu Q, Zane G, Ma Q, Qu Y, Stahl DA, Wall J, Arkin AP, Hazen TC, Fields MW, and Zhou J. 2015. Rapid selective sweep of pre-existing polymorphismss and slow fixation of new mutations in Desulfovibrio vulgaris. ISME J9: 2360–2372.
32.??????? Azarbad H, Niklińska M, Laskowski R, Van Straalen N, Van Gestel C, Zhou J, He Z, Wen C, and R?ling W. 2015. Microbial community composition and functions are resilient to metal pollution along two forest soil gradients. FEMS Microbiol Ecol91:1-11.
33.??????? Deng J, Gu Y, Zhang J, Xue K, Qin Y, Yuan M, Yin H, He Z, Wu L, Schuur AG, Tiedje JM, and Zhou J. 2015. Shifts of tundra bacterial and archaeal communities along a permafrost thaw gradient in Alaska. Mol Ecol24: 222–234.
34.??????? Dopheide A, Lear G, He Z, Zhou J, and Lewis GD. 2015. Functional Gene Composition, Diversity and Redundancy in Microbial Stream Biofilm Communities. PLoS ONE10: e**.
35.??????? Hemme CL, Tu Q, Shi Z, Qin Y, Gao W, Deng Y, Van Nostrand JD, Wu L, He Z, Chain PSG, Tringe SG, Fields MW, Rubin EM, Tiedje JM, Hazen TC, Arkin AP, and Zhou J. 2015. Comparative metagenomics reveals impact of contaminants on groundwater microbiomes. Front Microbiol6: 1205.
36.??????? Li X, Zhang Y, Ding C, Jia Z, He Z, Zhang T, Wang X. 2015. Declined soil suppressiveness to Fusarium oxysporum by rhizosphere microflora of cotton in soil sickness. Biol Fertil Soils51: 935–946.
37.??????? Liang Y, Wu L, Clark IM, Xue K, Yang Y, Van Nostrand JD, Deng Y, He Z, McGrath S, Storkey J, Hirsch PR, Sun B, and Zhou J. 2015. Over 150 years long-term fertilization alters spatial scaling of microbial biodiversity. mBio6: e00240-15.
38.??????? Liu S, Wang F, Xue K, Sun B, Zhang Y, He Z, Van Nostrand JD, Zhou J, and Yang Y. 2015. The interactive effects of soil transplant into colder regions and cropping on soil microbiology and biogeochemistry. Envion Microbiol17: 566–576.
39.??????? Qu Y, Ma Q, Deng J, Shen W, Zhang X, He Z, Van Nostrand JD, Zhou J, and Zhou J. 2015. Responses of Microbial Communities to Single-Walled Carbon Nanotubes in Phenol Wastewater Treatment Systems. Environ Sci Technol49: 4627-4635.
40.??????? Qu Y, Zhang X, Ma Q, Deng J, Deng Y, Van Nostrand JD, Wu L, He Z, Qin Y, Zhou J, and Zhou J. 2015. Microbial community dynamics and activity link to indigo production from indole in bioaugmented activated sludge systems. PLoS ONE 10: e**.
41.??????? Rui J, Li J, Wang S, An J, Liu WT, Lin Q, Yang Y, He Z and Li X. 2015. Responses of bacterial communities to simulated climate changes in alpine meadow soil of Qinghai-Tibet plateau. Appl Environ Microbiol81: 6070-6077.
42.??????? Saxena G, Marzinelli EM, Naing NN, He Z, Liang Y, Tom L, Ping H, Joshi UM, Reuben S, Mynampati KC, Mishra S, Umashankar S, Mitra S, Zhou J, Andersen G, Kjelleberg S, and Swarup S. 2015. Ecogenomics reveals metals and land-use pressures on microbial communities in the waterways of a megacity. Environ Sci Technol 49: 1462-1471.
43.??????? Shi S, Nuccio E., Herman DJ, Rijkers R, Estera K, Li J, da Rocha UN, He Z, Pett-Ridge J, Brodie E, Zhou J, and Firestone M. 2015. Successional trajectories of rhizosphere bacterial communities over consecutive seasons. mBio6: e007746-15.
44.??????? Smith MB, Rocha AM, Smillie CS, Olesen SW, Paradis C, Wu L, Campbell JH, Fortney JL, Mehlhorn TL, Lowe KA, [...], Watson DB, Zhang P, He Z, Dubinsky EA, Adams PD, Arkin AP, Fields MW, Zhou J, Alm EJ, and Hazen TC. 2015. Natural bacterial communities serve as quantitative geochemical biosensors. mBio6: e00326-15.
45.??????? Xu T, Li Y, Shi Z, Hemme CL, Li Y, Zhu Y, Van Nostrand JD, He Z, Zhou J. 2015. Efficient genome editing in Clostridium cellulolyticum via CRISPR-Cas9 nickase. Appl Environ Microbiol81: 4423-4431.
46.??????? Xiao Y, Xu Y, Dong W, Liang Y, Fan F, Zhang X, Zhang X, Niu J, Ma S, She S, He Z, Liu X, and Yin H. 2015. The complicated substrates enhance the microbial diversity and zinc leaching efficiency in sphalerite bioleaching system. Appl Microbiol Biotechnol99: 10311-10322.
47.??????? Yan Q, Bi Y, Deng Y, He Z, Wu L, Van Nostrand JD, Shi Z, Li J, Wang X, Hu Z, Yu Y, and Zhou J. 2015. Impacts of the Three Gorges Dam on microbial structure and potential function. Sci Rep 5: 8605.
48.??????? Yang Y, Chai Z, Wang Q, Chen W, He Z, and Jiang S. 2015. Cultivation of seaweed Gracilaria in Chinese coastal waters and its contribution to environmental improvements. Algal Res9: 236–244.
49.??????? Yang C, Ili Y, Zhou B, Zhou Y, Zheng W, Tian Y, Van Nostrand JD, Wu L, He Z, Zhou J, and Zheng T. 2015. llumina sequencing-based analysis of free-living bacterial community dynamics during an Akashiwo sanguine bloom in Xiamen sea, China. Sci Rep5: 8476.
50.??????? Yin, H., J. Niu, Y. Ren, J. Cong, X. Zhang, F. Fan, Y. Xiao, X. Zhang, J. Deng, M. Xie, Z. He, J.-Z. Zhou, Y. Liang, and X. Liu. 2015. An integrated insight into the response of sedimentary microbial communities to heavy metal contamination. Sci Rep5: 14266.
51.??????? Yue H, Wang M, Wang S, Gilbert J, Sun X, Wu L, Lin Q, Hu Y, Li X, He Z, Zhou J, and Yang Y. 2015. The microbe-mediated mechanisms affecting topsoil carbon stock in Tibetan grasslands. ISME J9: 2012–2020.
52.??????? Zhang P, Van Nostrand JD, He Z, Chakraborty R, Deng Y, Curtis D, Fields MW, Hazen TC, Arkin AP, and Zhou J. 2015. A slow-release substrate stimulates groundwater microbial communities for long-term in situ Cr(VI) reduction. Environ Sci Technol49: 12922–12931.
53.??????? Zhang P, Wu W, Van Nostrand JD, Deng Y, He Z, Gihring T, Zhang G, Schadt CW, Watson D, Jardine P. Criddle CS, Brooks S, Marsh TL, Tiedje JM, Arkin AP, and Zhou J. 2015. Dynamic succession of groundwater functional microbial communities in response to emulsified vegetable oil amendment during sustained in situ U(VI) reduction. Appl Environ Microbiol81: 4164-4172.
54.??????? Zhang Z, Wang H, Zhou J, Li H, He Z, Van Nostrand JD, Wang Z, and Xu X. 2015. Redox potential and microbial functional gene diversity in wetland sediments under simulated warming conditions: implications for phosphorus mobilization. Hydrobiologia743: 221-235.
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2014
57.??????? He Z (Ed.) 2014.Microarrays: Current Technology, Innovation and Applications. Caister Academic Press, Norwich, UK (http://www.horizonpress.com/microarrays2). It has 13 chapters with a focus on current microarray technologies and their applications in the analysis of microbial communities from different habitats and resources.
58.??????? He Z*, Xiong J, Kent AD, Deng Y, Xue K, Wang G, Wu Y, Van Nostrand JD, and Zhou J*.? 2014. Distinct responses of soil microbial communities to elevated CO2 and O3 in a soybean agroecosystem. ISME J8: 714-726.
59.??????? Tu Q, He Z*, and Zhou J*. 2014. Strain/Species identification in metagenomes using genome-specific markers. Nucleic Acid Res42: e67.
60.??????? Xu M*, Zhang Q, Xia C, Zhong Y, Sun G, Guo J, Yuan T, Zhou J, and He Z*. Elevated nitrate enriches microbial functional genes for potential bioremediation of complexly contaminated sediments. ISME J8: 1932–1944.
61.??????? Tu Q, Yu H, He Z, Deng Y, Wu L, Van Nostrand JD, Zhou A, Voordeckers J, Lee Y-J, Qin Y,??? Hemme CL, Shi Z, Xue K, Yuan T, Wang A, and Zhou J. 2014. GeoChip 4: a functional gene arrays-based high throughput environmental technology for microbial community analysis. Mol Ecol Resour14: 914–928.
62.??????? Tu Q, He Z*, Li Y, Chen Y, Deng Y, Lin L, Hemme CL, Yuan T, Van Nostrand JD, Wu L, Zhou X, Shi W, Li L, Xu J, and Zhou J*. 2014. Development of HuMiChip for Functional Profiling of Human Microbiomes. PLoS ONE9: e90546.
63.??????? Li Y, He J, He Z, Zhou Y, Yuan M, Xu X, Sun F, Liu C, Li J, Xie W, Deng Y, Qin Y,? VanNostrand JD, Xiao L, Wu L, Zhou J, Shi W, and Zhou X. 2014. Phylogenetic and functional gene structure shifts of the oral microbiomes in periodontitis patients. ISME J 8:1879–1891.
64.??????? Yin H, Zhang X, Li X, He Z, Liang Y, Guo X, Hu Q, Xiao Y, Cong J, Ma L, Niu J, and Liu X. 2014. Whole-genome sequencing reveals novel insights into sulfur oxidation in the extremophile Acidithiobacillus thiooxidans. BMC Microbiol14: 179.
65.??????? Hu X, Liu Q, Li Z, He Z, Gong Y, Cao Y, and Yang Y. 2014. Metabolic and phylogenetic profile of bacterial community in Guishan coastal water (Pearl River Estuary), South China Sea. J Ocean Univ China13: 857-864.
66.??????? Li Y.C., Xu T, Tschaplinski TJ, Engle NL, Yang Y, Graham DE, He Z, and Zhou J. 2014. Improvement of cellulose catabolism in Clostridium cellulolyticum by sporulation abolishment and carbon alleviation. Biotechnol Biofuels7: 25.
67.??????? Li X, Rui J, Xiong J, Li J, He Z, Zhou J, Yannarell AC, and Mackie RI. 2014. Functional potential of soil microbial communities in the maize rhizosphere. PLoS ONE9: e112609.
68.??????? Xu T, Li Y, He Z, and Zhou J. 2014. Dockerin-containing protease inhibitor protects key cellulosomal cellulases from proteolysis in Clostridium cellulolyticum. Mol Microbiol91:? 694–705.
69.??????? Xu T, Li Y, Van Nostrand JD, He Z, and Zhou J. 2014. CRISPR-based tools for targeted genome editing and transcriptional control. Appl Environ Microbiol80: 1544-1552.
70.??????? Luo C, Rodriguez-R LM, Johnston ER, Wu L, Cheng L, Xue K, Tu Q, Deng Y, He Z, Shi Z, Yuan M, Rebecca SA, Li D, Luo Y, Schuur EAG, Chain P, Tiedje JM, Zhou J, and Konstantinidis KT. 2014. Soil microbial community responses to a decade of warming as revealed by comparative metagenomics. Appl Environ Microbiol80: 1777-1786.
71.??????? Singh B, Quince C, Macdonald CA, Thomas N, Al-Soud WA, S?rensen SJ, He Z, White D, Sinclair A, Crooks B, Zhou J, and Campbell CD. 2014. Loss of biodiversity in soil is coincident with reductions in some specialised functions. Environ Microbiol16: 2408–2420.
72.??????? Yang F, Ning K, Chang X, Yuan X, Tu Q, Tong Y, Deng Y, Hemme CL, Van Nostrand JD, Cui X, He Z, Chen Z, Guo D, Yu J, Zhang Y, Zhou J, and Xu J. 2014. Saliva microbiota carry caries-specific functional gene signatures. PLoS ONE 9: e76458.
73.??????? Yang Y, Gao Y, Wang S, Xu D, Yu H, Wu L, Lin Q, Hu Y, Li X, He Z, Deng Y, and Zhou J. 2013. The microbial gene diversity along an elevation gradient of the Tibetan grassland. ISME J 8: 430–440.
74.??????? Zhou J, Deng Y, Zhang P, Xue K, Liang Y, Van Nostrand JD, Yang Y, He Z, Wu L, Stahl DA, Hazen TC, Tiedje JM, and Arkin AP. 2014. Stochasticity, succession and environmental perturbations in a fluidic ecosystem. Proc Natl Acad Sci USA 111: E836-E845.
75.??????? Varrone C, Van Nostrand JD, Liu W, Zhou B, Wang Z, Liu F, He Z, Wu L, Zhou J and Wang A. 2014. Metagenomic-based analysis of biofilm communities for electrohydrogenesis: From wastewater to hydrogen. Intl J Hydrogen Energy39: 222-4233.
76.??????? Chen Y, Qin N, Guo J, Qian G, Fang D, Shi D, Xu M, Yang F, He Z, Van Nostrand JD, Yuan T, Deng Y, Zhou J, and Li L. 2014. Functional gene arrays-based analysis of fecal microbiomes in patients with liver cirrhosis. BMC Genomics15: 753.
77.??????? Vigneron A, Cruaud P, Roussel EG, Pignet P, Caprais JC, Callac N, Ciobanu MC, Godfroy A, Cragg BA, Parkes JR, Van Nostrand JD, He Z, Zhou J and Toffin L. 2014. Phylogenetic and functional diversity of microbial communities associated with subsurface sediments of the sonora margin, guaymas basin. PLoS ONE9: e104427.
78.??????? Yao M, Rui J, Li J, Dai Y, Bai Y, HedeneP, Wang J, Zhang S, Pei K, Liu C, Wang Y, He Z, Frouz J, and Li X. 2014. Rate-specific responses of prokaryotic diversity and structure to nitrogen deposition in the Leymus chinensis steppe. Soil Biol Biochem79: 81-90.
79.??????? Gao Y, Wang S, Xu D, Yu H, Wu L, Lin Q, Hu Y, Li X, He Z, Deng Y, Zhou J, and Yang Y. 2014. GeoChip as a Metagenomics Tool to Analyze the Microbial Gene Diversity along an Elevation Gradient. Genomics Data2: 132–134.
80.??????? Zhao M, Wang F, Liu S, Xue K, Liang Y, Bai S, He Z, Van Nostrand JD, Zhou J, Yang Y and Sun B. 2014. GeoChip profiling of microbial community in response to global changes simulated by soil transplant and cropping. Genomics Data 2: Genomics Data 2: 166–169.
81.??????? He Z and Zhou J. 2014. Microarrays for microbial community analysis at a glance. In: Z. He (ed) Microarrays: Current Technology, Innovations and Applications. Caister Academic Press, Norwich, UK.
82.??????? Probst AJ, Lum PK, John B, Dubinsky EA, Piceno YM, Tom LM, Andersen GL, He Z, and DeSantis TD. Microarray of 16S rRNA gene probes for quantifying population differences across microbiome samples. In: Z. He (ed) Microarrays: Current Technology, Innovations and Applications. Caister Academic Press, Norwich, UK.
83.??????? Tu Q, Deng Y, Zhou J, and He Z. 2014. Development and evaluation of functional gene arrays with GeoChip as an example. In: Z. He (ed) Microarrays: Current Technology, Innovations and Applications. Caister Academic Press, Norwich, UK.
84.??????? Deng Y and He Z. 2014. Microarray data analysis.In: Z. He (ed) Microarrays: Current Technology, Innovations and Applications. Caister Academic Press, Norwich, UK.
85.??????? Xue K, He Z, Van Nostrand, and Zhou J. 2014. GeoChip Analysis of Soil Microbial Community Responses to Global Change.In: Z. He (ed) Microarrays: Current Technology, Innovations and Applications. Caister Academic Press, Norwich, UK.
86.??????? Xue K, Van Nostrand JD, He Z and Zhou J. 2014. Functional Molecular Analysis of Microbial Nitrogen Cycle by Microarray-based GeoChip: Insights for Climate Change, Agriculture and Other Ecological Studies. In: D. Marco (ed) Metagenomics of the Microbial Nitrogen Cycle: Theory, Methods and Applications. Caister Academic, Poole, UK.
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2013
87.??????? Li X, Deng Y, Li Q, Lu C, Wang J, Zhang H, Zhu J, Zhou J, and He Z*. 2013. Shifts of functional gene representation in wheat rhizosphere microbial communities under elevated ozone. ISME J7: 660-71.
88.??????? Tu Q, He Z*, Deng Y, and Zhou J*. 2013. Strain/species-specific probe design for microbial identification microarrays. Appl Environ Microbiol79: 5085-5088.
89.??????? He Z, Van Nostrand JD, and Zhou J. 2013. GeoChip-based metagenomics technologies for analyzing microbial community functional structure and activities. Encyclopedia of Metagenomics, edited by Karen E. Nelson.
90.??????? Xu M, He Z, Deng Y, Wu L, Van Nostrand JD, Hobbie SE, Reich PB, and Zhou J. 2013. Elevated CO2 influences microbial carbon and nitrogen cycling. BMC Microbiol13: 124.
91.??????? Zhou A, Baidoo E, He Z, Mukhopadhyay A, Baumohl JK, Benke P, Joachimiak MP, Xie M, Song R, Arkin AP, Hazen TC, Keasling JD, Wall JD, Stahl DA, and Zhou J. 2013. Characterization of NaCl-tolerance in Desulfovibrio vulagris Hildenboroughthrough experimental evolution. ISME J7: 1790–1802.
92.??????? Zhou A, He Z, Qin Y, Lu Z, Deng Y, Tu Q, Hemme CL, Van Nostrand JD, Wu L, Hazen TC, Arkin AP, and Zhou J. 2013. StressChip as a high-Throughput tool for assessing microbial community responses to environmental stresses. Environ Sci Technol47: 9841?9849.
93.??????? Yang Y, Xu M, He Z, Guo J, Sun G, and Zhou J. 2013. Microbial electricity generation enhances anaerobic degradation of decabromodiphenyl ether (BDE-209). PLoS ONE8: e70686.
94.??????? Lin L, Ji Y, Tu Q, Huang R, Teng L, Zeng X, Song H, Wang K, Zhou Q, Li Y, Cui Q, He Z, Zhou J, and Xu J. 2013. Microevolution from shock to adaptation revealed strategies improving ethanol tolerance and production in Thermoanaerobacter. Biotechnol Biofuels 6: 103.
95.??????? Freedman Z, Eisenlord SD, Zak DR, Xue K, He Z, and Zhou J. 2013. Towards a molecular understanding of N cycling in northern hardwood forests under future rates of N deposition. Soil Biol Biochem66: 130-138.
96.??????? Li M, Mathieu J, Yang Y, Fiorenza S, Deng Y, He Z, Zhou J, and Alvarez PJJ. 2013. Widespread Distribution of Soluble Di-iron Monooxygenase (SDIMO) Genes in Arctic Groundwater Impacted by 1,4-Dioxane. Environ Sci Technol47: 9950?9958.
97.??????? Kang S, Van Nostrand JD, Gough H, He Z, Hazen TC, Stahl D, and Zhou J. Functional gene array-based analysis of microbial communities in heavy metals contaminated lake sediments. FEMS Microbiol Ecol86: 200-214.
98.??????? Lee Y-J, Van Nostrand JD, Tu Q, Lu Z, Cheng L, Yuan T, Deng Y, Carter MQ, He Z, Wu L, Yang F, Xu J, and Zhou J. 2013. The PathoChip, a functional gene array for assessing pathogenic properties of diverse microbial communities. ISME J7: 1974–1984.
99.??????? Qiu D, Wei H, Tu Q, Yang Y, Xie M, Chen J, Pinkerton M, Liang Y, He Z, and Zhou J. 2013. Combined genomics and experimental analyses of respiratory characteristics of Shewanella putrefaciens W3-18-1.Appl Environ Microbiol79: 5050-5257.
100.??? Deng Y, Yang Y, He Z, and Zhou J. 2013. Molecular Ecological Network of Soil Microbial Communities. Encyclopedia of Metagenomics, edited by Karen E. Nelson.
101.??? Jiang H, He Q, He Z, Hemme CL, Wu L, and Zhou J. 2013. Continuous Cellulosic Bioethanol Fermentation by Cyclic Fed-Batch Co-Cultivation. Appl Environ Microbiol 79: 1580-1589.
102.??? Xue K, Wu L, Deng Y, He Z, Van Nostrand JD, Robertson P, Schmidt T, and Zhou J. 2013. Functional gene differences in soil microbial communities from conventional, low-input and organic farmlands. Appl Environ Microbiol79: 1284-1292.
103.??? Eisenlord S, Freedman Z, Zak D, Xue K, He Z, and Zhou J. 2013. Microbial mechanisms mediating increased soil C storage under elevated atmospheric N deposition. Appl Environ Microbiol79: 1191-1199.
104.??? Yang Y, Wu L, Lin Q, Yuan M, Xu D, Yu H, Hu Y, Duan J, Li X, He Z, Xue K, Van Nostrand JD, Wang S, and Zhou J. 2013. Responses of the functional structure of soil microbial community to livestock grazing in the Tibetan alpine grassland. Glob Change Biol19: 637-648.
105.??? Wakelin SA, Barratt BIP, Gerard E, Gregg AL, Brodie EL, Andersen GL, DeSantis TZ, He Z, Zhou J, Kowalchuk GA, and O’Callaghan M. 2013. Shifts in the phylogenetic structure and functional capacity of soil microbial communities follow alteration of native tussock grassland ecosystems. Soil Biol Biochem57: 675-682.
106.??? Bai S, Li J, He Z, Van Nostrand JD, Tian Y, Lin G, Zhou J, and Zheng T. 2013. GeoChip-based analysis of the functional gene diversity and metabolic potential of mangroves soil microbial communities. Appl Microbiol Biotechnol97: 7035-7048.
107.??? Zhang Y, Lu Z, Liu S, Yang Y, He Z, Ren Z, Zhou J, and Li D. 2013. GeoChip-based analysis of microbial communities in alpine meadow soils in the Qinghai-Tibetan plateau. BMC Microbiol13: 72.
108.??? Zhang Y, Xie J, Liu M, Tian Z, He Z, Van Nostrand JD, Ren L, Zhou J, and Yang M. 2013. Microbial community functional structure in response to antibiotics in pharmaceutical wastewater treatment systems. Water Res 47: 6298-6308.
109.??? Siering PL, Wolfe GV, Wilson MS, Yip AN, Carey CM, Wardman CD, Shapiro RS, Stedman KM, Kyle J, Yuan T, Van Nostrand JD, He Z, and Zhou J. 2013. Microbial biogeochemistry of boiling springs lake: a physically dynamic, oligotrophic, low-pH geothermal ecosystem. Geobiology11: 356-376.
110.??? Zhou J，Liu W，Deng Y, Jiang YH, Xue K, He Z, Van Nostrand JD, Wu L, Yang Y，Wang A. 2013. Stochastic assembly leads to alternative communities with distinct functions in a bioreactor microbial community. mBio4: e00584-12.
111.??? Zhou J, Jiang YH, Deng Y, Shi Z, Zhou BY, Xue K, Wu L, He Z, and Yang Y. 2013. Random sampling process leads to overestimation of β-diversity of microbial communities. mBio 4: e00324-13.
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2012
112.??? He Z, Van Nostrand JD, and Zhou J. 2012. Applications of functional gene microarrays for profiling microbial communities. ?Curr Opin Biotechnol23: 460–466.
113.??? He Z*, Deng Y, and Zhou J. 2012. Development of functional gene microarrays for microbial community analysis. Curr Opin Biotechnol23: 49–55.
114.??? He Z, Piceno Y, Deng Y, Xu M, Lu Z, DeSantis T, Andersen G, Hobbie SE, Reich PB, and Zhou J. 2012. The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide. ISME J 6: 259-272.
115.??? Deng Y#, He Z#, Xu M, Qin Y, Van Nostrand JD, Wu L, Roe BA, Wiley G, Hobbie SE, Reich PB, and Zhou J. 2012. Elevated carbon dioxide alters the structure of soil microbial communities. Appl Environ Microbiol78: 2991-2995.
116.??? Wang H, He Z, Lu Z, Zhou J, Van Nostrand JD, Xu X, and Zhang Z. 2012. Genetic linkage of sediment carbon pools and microbial functions in subtropical freshwater wetlands responding to experimental warming. Appl Environ Microbiol 78: 7652-7661.
117.??? Xiong J, He Z, Van Nostrand JD, Luo G, Tu S, Zhou J, and Wang G. 2012. Assessing the microbial community and functional genes in a vertical soil profile with long-term arsenic contamination. PLoS ONE7: e50507.
118.??? Van Nostrand JD, He Z, and Zhou J. 2012. Use of functional gene arrays for elucidating in situ biodegradation. Front Microbiol 3:339.
119.??? Ding G, Heuer H, He Z, Xie J, Zhou J, Smalla K. 2012. More functional genes and convergent overall functional patterns detected by GeoChip in phenanthrene spiked soils. FEMS Microbiol Ecol82: 148-156.
120.??? Reith F, Brugger J, Zammit CM, Gregg AL, Goldfarb KC, Andersen GL, DeSantis TZ, Piceno YM, Brodie EL, Lu Z, He Z, Zhou J, and Wakelin SA. 2012. Influence of geogenic factors on microbial communities in metallogenic Australian soils. ISME J6: 2107-2118.
121.??? Walker CB, Redding-Johanson AM, Baidoo EE, Rajeev L, He Z, Hendrickson EL, Joachimiak MP, Stolyar S, Arkin AP, Leigh JA, Zhou J, Keasling JD, Mukhopadhyay A, and Stahl DA. 2012. Functional responses of methanogenic archaea to syntrophic growth. ISME J 6: 2045-2055.
122.??? Rajeev L, Hillesland K, Zane G, Zhou A, Joachimiak M, He Z, Zhou J, Arkin AP, Wall JD, and Stahl DA. 2012. Deletion of the Desulfovibrio vulgaris carbon monoxide sensor invokes global changes in transcription. J Bacteriol194: 5783-5793.
123.??? Xie J, Wu L, van Nostrand JD, He Z, Lu Z, Yu H, Xiong J, Liu X, and Zhou J. 2012. Improvements on environmental DNA extraction and purification procedures for matagenomic analysis. J Cent South Univ19: 3055?3063.
124.??? Lu Z, He Z, Parisi V, Kang S, Deng Y, Van Nostrand JD, Masoner J, Cozzarelli I, Suflita JM, and Zhou J. 2012. GeoChip-based analysis of microbial functional gene diversity in a landfill leachate-contaminated aquifer. 2012. Environ Sci Technol 46: 5824?5833.
125.??? Clark ME, He Z, Redding AM, Joachimiak MP, Keasling JD, Zhou J, Arkin AP, Mukhopadhyay A, and Fields MW. 2012. Transcriptomic and proteomic analyses of Desulfovibrio vulgaris biofilms: carbon and energy flow contribute to the distinct biofilm growth state. BMC Genomics13: 138.
126.??? Trivedi P, He Z, Van Nostrand JD, Zhou J, Albrigo G, and Wang N. 2012. Huanglongbing alters the structure and functional diversity of microbial communities associated with citrus rhizosphere. ISME J 6: 363-383.
127.??? Deng Y, Jiang Y, Yang Y, He Z, Luo F, and Zhou J. 2012. Molecular ecological network analysis. BMC Bioinformatics13: 113.
128.??? Liang Y, Gao H, Guo X, Chen J, Qiu G, He Z, Zhou J, Liu X. 2012. Transcriptome analysis of pellicle formation of Shewanella oneidensis. Arch Microbiol194: 473–482.
129.??? Lu Z, Deng Y, Van Nostrand JD, He Z, Voordeckers J, Zhou A, Lee YJ, Mason OU Dubinsky? EA,? Chavarria KL, Tom LM, Fortney JL, Lamendella R, Jansson JK, D'haeseleer P, Hazen TC, and Zhou J. 2012. Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume.ISME J 6: 451-460.
130.??? Liang Y, Van Nostrand JD, N’Guessan LA, Peacock AD, Deng Y, Long PE, Resch T, Wu L, He Z, Li G, Hazen, Lovley DR, and Zhou J. 2012. Microbial functional gene diversity with a shift of subsurface redox condition. Appl Environ Microbiol 78: 2966-2972.
131.??? Zhou A, Chen Y, Zane GM, He Z, Hemme CL, Joachimiak MP, Baumoh J, He Q, Fields MW, Arkin AP, Wall JD, Hazen TC, and Zhou J. 2012. Functional characterization of Crp/Fnr-type global transcriptional regulators in Desulfovibrio vulgaris Hildenborough. Appl Environ Microbiol 78:1168-117.
132.??? Zhou J, Xue K, Xie J, Deng Y, Wu L, Cheng X, Fei S, Deng S, He Z, Van Nostrand JD, and Luo Y. 2012. Microbial mediation of carbon cycle feedbacks to climate warming. Nat Clim Change 2: 106–110.
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2011
133.??? He Z, Van Nostrand JD, Deng Y, and Zhou J. 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 China5: 1-20.
134.??? Xie J, He Z, Liu X, Liu X, Van Nostrand JD, Deng Y, Wu L, Zhou J, and Qiu G. 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.
135.??? Hemme CL, Fields MW, He Q, Deng Y, Lin L, Tu Q, Mouttaki H, He Z, Barry K, Saunders E, Sun H, Land M, Hauser L, Lapidus A, Han CS, Xu J, Wiegel J, Phelps TJ, Rubin E, and Zhou J. 2011. Correlation of genomic and physiological traits of Thermoanaerobacter species with biofuel yields. Appl Environ Microbiol 77: 7998-8008.
136.??? Lin L, Song H, Tu Q, Qin Y, Zhou A, Liu W, He Z, Zhou J, and Xu J. 2011. Thermoanaerobic glycobiome reveals mechanisms of pentose and hexose co-utilization in bacteria. PLoS Genet7: e**.
137.??? Liu A, Wu L, He Z, and Zhou J. 2011. Development of highly fluorescent silica nanoparticles chemically doped with organic dye for sensitive DNA microarray detection. Anal Bioanal Chem401: 2003–2011.
138.??? He Q, Hemme CL, Jiang H, He Z, and Zhou J. 2011. Mechanisms of enhanced cellulosic bioethanol fermentation by co-cultivation of Clostridium and Thermoanaerobacter spp. Bioresour Technol 102: 9586–9592.
139.??? Wang J, Van Nostrand JD, Wu L, He Z, Li G, and Zhou J. 2011. Microarray-based evaluation of whole-community genome DNA amplification methods. Appl Environ Microbiol 77: 4241–4245.
140.??? Van Nostrand JD, Wu L, Wu W, Huang Z, Gentry TJ, Deng Y, Carley J, Carroll S, He Z, Gu B, Luo J, Criddle CS, Watson DB, Jardine PM, Marsh TL, Tiedje JM, Hazen TC, and Zhou J. 2011. Dynamics of microbial community composition and function during in situ bioremediation of a uranium-contaminated aquifer. Appl Environ Microbiol 77: 3860–3869.
141.??? Zhou J, Deng Y, Luo F, He Z, and Yang Y. 2011. Phylogenetic molecular ecological network of soil microbial communities in response to elevated CO2. mBio2: e00122-11.
142.??? Zhou J, He Q, Hemme CL, Mukhopadhyay A, Hillesland K., Zhou A, He Z, Van Nostrand JD, Hazen TC, Stahl DA, Wall JD, and Arkin AP. 2011. How sulphate-reducing microorganisms cope with stress: lessons from systems biology. Nat Rev Microbiol 9: 452-466.
143.??? Zhou J, Wu L, Deng Y, Zhi X, Jiang YH, Tu Q, Xie J, Van Nostrand JD, He Z, and Yang Y. 2011. Reproducibility and quantitation of amplicon sequencing-based detection. ISME J5: 1303–1313.
144.??? Wang A, Gao L, Ren N, Xu J, Liu C, Gao G, Yu H, Liu W, Hemme CL, He Z, and Zhou J. 2011. Isolation and characterization of Shigella flexneri G3 for effective cellulosic saccharification under mesophilic conditions. Appl Environ Microbiol 77: 517-523.
145.??? Liang Y, Van Nostrand JD, Deng Y, He Z, Wu L,? Zhang X, Li G, and Zhou J. 2011. Functional gene diversity of soil microbial communities from oil-contaminated fields in China. ISME J5: 403-413.
146.??? Trivedi P, He Z, Van Nostrand JD, Zhou J, Albrigo G, and Wang N. 2011. Effect of Huanglongbing on the structure and functional diversity of microbial communities associated with citrus rhizosphere. Phytopathology 101: S178-S178.
147.??? Van Nostrand JD, Kang S, Deng Y, Liang Y, He Z, and Zhou J. 2011. Monitoring microbial activity with GeoChip. In JF Stolz and RS Oremland (eds), Microbial Metal and Metalloid Metabolism: Advances and Applications, pp261-282. ASM Press, Washington DC.
148.??? Van Nostrand JD, He Z, and Zhou J. 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.
149.??? Van Nostrand JD, He Z, and Zhou J. 2011. New developments and applications of microarrays for microbial community analysis in natural and impacted ecosystems. In: M. Moo-Young (ed) Comprehensive Biotechnology, 2e. Elsevier, Amsterdam, The Netherlands.
150.??? Van Nostrand JD, He Z, Zhou J. 2011. GeoChip: A high throughput metagenomics technology for dissecting microbial community functional structure. In: F.J. de Bruijn (ed) Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats. John Wiley & Sons, New Jersey, pp 509-520.
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2010
151.??? He Z, Xu M, Deng Y, Kang S, Kellogg L, Wu L, Van Nostrand JD, Hobbie SE, Reich PB, and Zhou J. 2010. Metagenomic analysis reveals a marked divergence in the structure of belowground microbial communities at elevated CO2. Ecol Lett13: 564-575.
152.??? He Z, Deng Y, Van Nostrand JD, Tu Q, Xu M, Hemme CL, Li X, Wu L, Hazen TC, and Zhou J. 2010. GeoChip 3.0 as a high throughput tool for analyzing microbial community composition, structure, and functional activity. ISME J4: 1167-1179.
153.??? He Z, Zhou A, Baidoo E, He Q, Joachimiak MP, Benke P, Phan R, Mukhopadhyay A, Hemme CL, Huang K, Alm EJ, Fields MW, Wall JD, Stahl D, Hazen TC, Keasling JD, Arkin, AP, and Zhou J. 2010. Global transcriptional, physiological and metabolite analyses of Desulfovibrio vulgaris Hildenborough responses to salt adaptation.? Appl Environ Microbiol76: 1574–1586.
154.??? Liang Y#, He Z#, Wu L, Deng Y, Li G, and Zhou J.? 2010. Development of a common oligonucleotide reference standard for microarray data normalization and comparison across different microbial communities. Appl Environ Microbiol 76: 1088-1094.?
155.??? Zhou J, He Z, Van Nostrand JD, Wu L, and Deng Y. 2010. Applying GeoChip analysis to disparate microbial communities. Microbe5: 60-65.
156.??? Zhou A, He Z, Redding AM,? Mukhopadhyay A, Hemme CL, Joachimiak MP, He Q, Bender KS, Keasling JD, Stahl D, Fields MW, Hazen TC, Arkin, AP, Wall JD, and Zhou J. 2010. Hydrogen peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough. Environ Microbiol 12: 2645–2657.
157.??? He Q, He Z, Joyner DC, Price MN, Yang ZK, Yen HB, Chakraborty R, Chen W, Keller M, Arkin AP, Hazen TC, Wall JD, and Zhou J. 2010. Impact of elevated nitrate on sulfate-reducing bacteria: implications of inhibitory mechanisms in addition to osmotic stress. ISME J 4: 1386-1397.?
158.??? Zhou J, Deng Y, Luo F, He Z, Tu Q, and Zhi X. 2010. Functional molecular ecological networks. mBio1: e00169-10.?
159.??? Liang Y, Gao H, Chen J, Dong Y, Wu L, He Z, Liu X, Qiu G, and Zhou J. 2010. Pellicle formation in Shewanella oneidensis. BMC Microbiol10: 291.
160.??? Liu W, Wang A, Cheng S, Logan B, Yu H, Deng Y, Van Nostrand JD, Wu L, He Z, and? Zhou J. 2010. GeoChip-based functional gene analysis of anodophilic communities in microbial electrolysis cells under different operational modes. Environ Sci Technol 44: 7729-7735.
161.??? Hemme CL, Mouttaki H, Lee YJ, Goodwin L, Lucas S, Copeland A,? Lapidus A, del Rio TG, Tice H, Saunders E, Brettin T, Detter JC, Han CS, Pitluck S, Land ML, Hauser LJ, Krypides N, Mikhailova N, He Z, Wu L, Van Nostrand JD, Henrissat B, He Q, Lawson PA, Tanner RS, Lynd LR, Wiegel J, Fields MW, Arkin AP, Schadt CW, Stevenson BS, McInerney MJ, Yang Y, Dong H, Huhnke RL, Mielenz JR, Ding SY, Himmel ME, Taghavi S, van der Lelie D, Rubin EM, and Zhou J. 2010. Genome announcement: sequencing of multiple Clostridia genomes related to biomass conversion and biofuels production. J Bacteriol 192: 6494-6496.?
162.??? Xiong J, Wu L, Tu S, Van Nostrand JD, He Z, Zhou J, and Wang G. 2010. Microbial communities and functional genes associated with soil arsenic contamination and rhizosphere of the arsenic hyper-accumulating plant Pteris vittata L. Appl Environ Microbiol 76: 7277–7284.
163.??? Parnell JJ, Rompato G, Latta LC IV, Pfrender ME, Van Nostrand JD, He Z, Zhou J, Andersen G, Champine P, Ganesan B, and Weimer1BC. 2010. Functional Biogeography as Evidence of Gene Transfer in Hypersaline Microbial Communities. PLoS ONE5: e12919.
164.??? Lin L,? Song H,? Ji Y,? He Z,? Pu Y,? Zhou J, and Xu J. 2010. Ultrasound-mediated DNA transformation in thermophilic Gram-positive anaerobes. PLoS ONE5: e12582.
165.??? Gao H, Barua S, Liang Y, Wu L, Dong Y, Reed S, Chen J, Culley D, Kennedy D, Yang Y, He Z, Nealson KH, Fredrickson JK, Tiedje JM, Romine M, and J Zhou. 2010. Impacts of Shewanella onedensis c-type cytochromes on aerobic and anaerobic respiration. Microb Biotechnol3: 455-466.
166.??? Xu M, Wu W, Wu L, He Z, Van Nostrand JD, Deng Y, Luo J, Carley J, Ginder-Vogel M,? Gentry TJ, Gu B, Watson D, Jardine PM, Marsh TL, Tiedje JM, Hazen TC, Criddle CS, and Zhou J. 2010. Functional understanding of microbial community structures in contaminated sediments during in situ bioremediation/immobilization of uranium. ISME J 4: 1060-1070.
167.??? Hemme CL, Wu L, Deng Y, Gentry TJ, Fields MW, Fang Z, Barua S, Watson D, He Z, Richardson P, Hazen TC, Tiedje JM, Rubin E, and Zhou J. 2010. Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community. ISME J 4: 660-672.
168.??? Andersen G, He Z, DeSantis T, Brodie E, and Zhou J. 2010. The Use of Microarrays in Microbial Ecology in Environmental Molecular Microbiology, pp87-110 (Edited by Wen-Tso Liu and Janet K. Jansson), Caister Academic Press, Norfolk, UK.
169.??? Van Nostrand JD, Liang Y, He Z, Li G, and Zhou J. 2010. GeoChip: A high throughput genomic tool for linking community structure to functions. In Handbook of Hydrocarbon and Lipid Microbiology, Kenneth N. Timmis (ed.), pp.2677-2685. Springer Berlin Heidelberg, Germany.
170.??? Van Nostrand, JD, He Z, and Zhou J. 2010. Analysis of microbial communities by functional gene Arrays. In: L. Barton, M. Mandl and A. Loy (eds) in Geomicrobiology: Molecular and Environmental Perspective, pp109-126. Springer, New York.
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2009
171.??? He Z, and Zhou J. 2009. Selection of oligonucleotide probes for microarrays. Molecular Microbial Ecology Manual 2nd, A. D. L. Akkermans, F. J. de Bruijn, I. M. Head, G. A. Kowalchuk, and J. D. van Elsas (ed.), pp1880-1891. Springer Netherlands.
172.??? Liang Y, Li G, Van Nostrand JD, He Z, Wu L, Deng Y, Zhang X, and Zhou J. 2009. Microarray-based analysis of microbial functional diversity along an oil contamination gradient in oil field. FEMS Microb Ecol 70: 324-333.
173.??? Van Nostrand JD, Wu W, Wu L, Deng Y, Carley J, Carroll S, He Z, Gu B, Luo J, Criddle CS, Watson DB, Jardine PM, Marsh TL, Tiedje JM, Hazen TC, and Zhou J. 2009. GeoChip-based analysis of functional microbial communities in a bioreduced uranium-contaminated aquifer during reoxidation by oxygen. Environ Microbiol 11: 2611-2626.
174.??? Walker CB, He Z, Yang ZK, Stolyar SS, Jacobsen J, Ringbauer Jr JA, Wall JD, Zhou J, Arkin AP, and Stahl DA. 2009. The electron transfer system of syntrophically grown Desulfovibrio vulgaris. J Bacteriol 191: 5793-5801.
175.??? Walker CB, Stolyar S, Chivian D, Pinel N, Gabster JA, Dehal PS, He Z, Yang ZK, Yen HCB, Zhou J, Wall JD, Hazen TC, Arkin AP, and Stahl DA. 2009. Contribution of mobile genetic elements to Desulfovibrio vulgaris genome plasticity. Environ Microbiol 11: 2244-2252.
176.??? Feng X, Mouttaki H, Lin L, Huang R, Wu B, Hemme CL, He Z, Zhang B, Hicks LM, Xu J, Zhou J, and Tang YJ. 2009. Characterization of the central metabolic pathways in Thermoanaerobacter sp. strain X514 via isotopomer-assisted metabolite analysis. Appl Environ Microbiol 75: 5001-5008.
177.??? Liang Y, He Z, Gao H, Qiu G, Zhou J and Liu X. 2009. Characterization of cytochrome mutants for pellicle formation in Shewanella onedensis MR-1. Trans Nonferrous Met Soc China 19:700-706.
178.??? Waldron PJ, Wu L, Van Nostrand JD, Schadt CW, He Z, Watson DB, Jardine PM, Palumbo AV, Hazen TC, Zhou J. 2009. Functional gene array-based analysis of microbial community structure in groundwaters with a gradient of contaminant levels. Environ Sci Technol 43: 3529-3534.
179.??? Wang F, Zhou H, Meng J, Peng X, Jiang L, Sun P, Zhang C, Van Nostrand JD, Deng Y, He Z, Wu L, Zhou J, and Xiao X. GeoChip-based analysis of metabolic diversity of microbial communities at the Juan de Fuca Ridge hydrothermal vent. Proc Natl Acad Sci USA106:4840–4845.
180.??? Van Nostrand JD, Wu L, He Z, and Zhou J. 2009. GeoChips for analysis of microbial functional communities. In: J. R. van der Meer (ed) Handbook of Hydrocarbon and Lipid Microbiology, Vol. 4: Experimental Protocols and Appendices. Springer, New York, pp 4039-4050.
181.??? Gentry TJ, He Z and Zhou J. 2009. Detection and characterization of uncultivated microorganisms using microarrays. In Uncultivated Microorganisms (Microbiology Monographs) Vol. 10: 35-58, Epstein, Slava S. (Ed.) Springer-Verlag Berlin Heidelberg.
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2008
182.??? He Z and Zhou J. 2008. Empirical evaluation of a new method for calculating signal-to-noise ratio for microarray data analysis. Appl Environ Microbiol 74: 2957-2966.
183.??? He Z*, Van Nostrand JD, Wu L, and Zhou J. 2008. Development and application of functional gene arrays for microbial community analysis. Transactions of Nonferrous Metals Society of China 18:1319-1327.
184.??? Deng Y, He Z*, Van Nostrand JD, Zhou J*. 2008.Design and analysis of mismatch probes for long oligonucleotide microarrays. BMC Genomics9: 491.
185.??? Rodrigues DF, Ivanova N, He Z, Huebner M, Zhou J, and Tiedje JM. 2008. Architecture of thermal adaptation in an Exiguobacterium sibiricum strain isolated from 3 million year old permafrost: A genome and transcriptome approach. BMC Genomics9: 547.
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2007
186.??? He Z, Gentry TJ, Schadt CW, Wu L, Liebich J, Chong SC, Huang Z, Wu W, Gu B, Jardine P, Criddle C, and Zhou J. 2007. GeoChip: A comprehensive microarray for investigating biogeochemical, ecological, and environmental processes. ISME J 1: 67-77.
187.??? Stolyar S, He Q, Joachimiak MP, He Z, Yang ZK, Borglin SE, Joyner DC, Huang K, Alm E, Hazen TC, Zhou J, Wall JD, Arkin AP, and Stahl DA. 2007. Response of Desulfovibrio vulgaris to alkaline stress. J Bacteriol189: 8944-8952.
188.??? Yergeau E, Kang S, He Z, Zhou J, and Kowalchuk GA. 2007. Functional microarray analysis of nitrogen and carbon cycling genes across an Antarctic latitudinal transect. ISME J 1: 163-179.
189.??? Butler J, He Q, Nevin PK, He Z, Zhou J, and Lovley D. 2007. Genomic and microarray analysis of aromatics degradation in Geobacter metallireducens and comparison to a Geobacter isolate from a contaminated field site.BMC Genomics 8: 180.
190.??? Caffrey SM, Park HS, Voordouw JK, He Z, Zhou J, and Voordouw G. 2007. Function of periplasmic hydrogenases in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. J Bacteriol189: 6159-6167.
191.??? Bender KS, Yen BCB, Hemme CL, Yang Z, He Z, He Q, Zhou J, Huang KH, Alm EJ, Hazen TC, Arkin AP, and Wall JD. 2007. Analysis of a ferric uptake regulator (Fur) mutant of Desulfovibrio vulgaris Hildenborough. Appl Environ Microbiol73: 5389-5400.
192.??? BrownSD, Raman B, McKeown CK, Kale SP, He Z and Mielenz JR. 2007. Construction and evaluation of a Clostridium thermocellum ATCC 27405 whole-genome oligonucleotide microarray. Appl Biochem Biotechnol 137-140: 663-674.
193.??? Gentry TJ, Schadt CW, He Z, and ZhouJ. 2007.Functional gene arrays for microbial community analysis. In Manual of Environmental Microbiology(Third edition), pp1052-1062 (Hurst CJ et al., eds), ASM Press, Washington DC, USA.
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2006
194.??? Gentry TJ, Wickham JS, Schadt CW, He Z, and ZhouJ. 2006.Microarray applications in microbial ecology research. Microb Ecol 52: 159-175.
195.??? Walker CB, Stolyar SS, Pinel N, Yen HC, He Z, Zhou J, Wall JD, Stahl DA. 2006.Recovery of temperate Desulfovibrio vulgaris bacteriophage using a novel host strain. Environ Microbiol 8: 1950-1959.
196.??? Clark ME, He Q, He Z, Huang KH, Alm EJ, Wan X, Hazen TC, Arkin AP, Wall JD, Zhou J, and Fields MW. 2006. Temporal transcriptomic analysis as Desulfovibrio vulgaris Hildenborough transitions into stationary phase during electron donor depletion. Appl Environ Microbiol 72: 5578-5588.
197.??? Mukhopadhyay A, He Z, Yen HC, Alm EJ, He Q, Huang K, Baidoo EE, Chen W, Borglin SC,? Redding A, Holman HY, Sun J, Joyner DC, Keller M, Zhou J, Arkin AP, Hazen TC, Wall JD, and Keasling JD. 2006. Salt stress in Desulfovibrio vulgaris Hildenborough: an integrated genomics approach. J Bacteriol188: 4068-4078.
198.??? He Q, Huang KH, He Z, Alm EJ, Fields MW, Hazen TC, Arkin AP, Wall JD, and Zhou J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl Environ Microbiol 72: 4370-4381.
199.??? Chhabra SR, He Q, Huang KH, Gaucher SP, Alm EJ, He Z, Hadi MZ, Hazen TC, Wall JD, Zhou, J, Arkin AP and Singh AK. 2006. Global analysis of heat shock response in Desulfovibrio vulgaris Hildenborough. J Bacteriol 188: 1817-1828.
200.??? Liebich J, Schadt CW, Chong SC, He Z, Rhee SK and Zhou J. 2006. Improvement of oligonucleotide probe design criteria for functional gene microarrays in environmental applications. Appl Environ Microbiol 72: 1688-1691.
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2005
201.??? He Z, Wu L, Li X, Fields MW and Zhou J. 2005. Empirical establishment of oligonucleotide probe design criteria. Appl Environ Microbiol 71: 3753-3760.
202.??? He Z, Wu L, Fields MW and Zhou J. 2005. Use of microarrays with different probe sizes for monitoring gene expression. Appl Environ Microbiol 71: 5154-5162.
203.??? Li X#, He Z#andZhou J. 2005. Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation. Nucleic Acids Res33:6114-6123.
204.??? Schadt CW, Liebich J, Chong SC, Gentry TJ, He Z, Pan H and Zhou J. 2005.? Design and use of functional gene microarrays (FGAs) for the characterization of microbial communities.? In Methods in Microbiology Volume 34: 329-365. (Savidge T. and H. Pothulakis, eds) Academic Press, London, UK.
205.??? Mukhopadhyay A, He Z, Alm E, He Q, Yen B, Huang K, Baidoo E, Chen W, Borglin S, Redding A, Holman HY, Sun J, Joyner D, Katz N, Keller M, Zhou J, Arkin AP, Hazen TC, Wall J, and Keasling JD. 2005. The anatomy of salt stress in Desulfovibrio vulgaris hildenborough. Mol Cell Proteomics 4: S384-S384.
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1991-1998
206.??? Andrews TJ, von Caemmerer S, He Z, Hudson GS. 1998. Rubisco catalysis in vitro and in vivo. Photosynthesis: Mechanisms and Effects 5: 3307.
207.??? He Z, von Caemmerer S, Hudson GS, Price GD, Badger MR, Andrews TJ. 1997. Ribulose-1, 5-bisphosphate carboxylase/oxygenase activase deficiency delays senescence of ribulose-1, 5-bisphosphate carboxylase/oxygenase but progressively impairs its catalysis during tobacco leaf development. Plant Physiol115: 1569–1580.
208.??? He Z, Tang Z. 1994. An Increased 66-kD Polypeptide associated with stimulation of K+ uptake in sorghum roots under PEG stress. Chinese Science Bulletin39: 587–591.
209.??? He Z, Tang Z. 1993. Relationship between increase in 66-kD polypeptide content and stimulation of K+ uptake in sorghum roots under drought stress. Kexue TongBao38: 2190-2193.
210.??? He Z, Li J, and Tang Z. 1993. Stimulative Effect of osmotic stress on the K+ accumulation in sorghum roots. Acta Phytophysiol Sinica19: 379–386.
211.??? He Z, and Wang H. 1992. Effect of NaCl Pretreatment on the accumulation and distribution of Na+, Cl- and proline in alfalfa under salt stress. Plant Physiology Communications28: 330–334.
212.??? He Z, and Wang H. 1991. Emergence of salt-induced proteins in alfalfa under NaCl stress. Acta Phytophysiol Sinica17: 71–79.
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