賀志理，男，博士，中山大學環境科學與工程學院教授、博士生導師。
基本介紹
- 中文名：賀志理
- 畢業院校：澳大利亞國立大學
- 學位/學歷：博士
- 專業方向：環境、人類、植物微生物組學等
- 任職院校：中山大學
人物經歷,教育經歷,工作經歷,研究方向,學術成果,科研項目,學術論文,
人物經歷
教育經歷
1982.9-1986.7湖南師範大學 理學學士
1986.9-1989.7中科院上海植物生理研究所 理學碩士
1994.2-1998.7 澳大利亞國立大學 哲學博士
1999.1-2001.10 加拿大圭爾夫大學文學學士
工作經歷
1989.08-1994.02中科院上海植物生理研究所 助理研究員
1997.12-1998.09日本地球創新技術研究所 研究員
1998.10-2002.12加拿大圭爾夫大學 博士後
2003.02-2005.08美國能源部橡樹嶺國家實驗室 博士後
2005.09-2005.09 美國能源部橡樹嶺國家實驗室 助理教授
2005.10-2007.08美國俄克拉荷馬大學環境基因組研究所助理教授/副所長
2007.09-2011.08美國俄克拉荷馬大學環境基因組研究所 副教授/副所長
2011.09-2017.02美國俄克拉荷馬大學環境基因組研究所 教授/副所長
2017.03--至今 中山大學教授 環境微生物組研究中心負責人
研究方向
（1）環境、人類、植物微生物組學（微生物多樣性、組成、結構、功能、演替及其與環境/宿主的關係）
（2）環境微生物生態學（使用高通量組學、基因組學的方法分析全球環境變化、環境壓力以及生物修復相關的微生物學）
（4）開發生物技術和生物信息學工具（功能基因晶片GeoChip、人類微生物基因晶片HuMiChip等）
學術成果
科研項目
起止時間 項目來源 負責的具體任務
2011/2-2014/1 美國俄克拉荷馬州OCAST基金主持，負責人體微生物組基因晶片的設計、研發和評估，其產品為HuMiChip 1.0和2.0。
2010/6-2011/3 美國能源部 主持，負責套用amoA基因研究土壤微生物群落中硝化細菌的多樣性。
2008/1-2011/12 美國俄克拉荷馬州政府基金 主持，負責研究高效產乙醇系統中微生物群落的構建和相互作用及其調節網路。
2006/10-2009/9 美國俄克拉荷馬州OCAST基金主持，負責研發GeoChip設計、研發和評估工具和數據處理系統及項目匯報，其產品為GeoChip 3.0，獲得美國《R&D》雜誌2009 年頒發的“R&D 100 Award”獎。
2014/1-2017/12 NSFC-廣東聯合重點基金 參與，負責微生物方面的研究，利用高通量的宏基因組探索海洋水體和底泥微生物群落結構與功能。
2013/9-2016/8 美國能源部 參與並協調多個參與單位，負責美國俄克拉荷馬州和阿拉斯加州升溫實驗場地土壤微生物群落的宏基因組學研究。
2013/9-2015/8 美國能源部 參與，負責土壤微生物群落的宏基因組學研究和研發基於KBase的生物信息學工具。
2012/1-2015/12 中國國家自然科學基金 參與，負責河流物修復系統中水體和底泥微生物群落的宏基因組學研究，評估生物治理技術的效果。
2011/9-2013/8 美國國家自然科學基金EPSCoR 參與並協調多個俄克拉荷馬州大學和研究機構（共30多人參加，總經費為1500萬美元），
（俄克拉荷馬州） 主持其中一子項目：建立高效產乙醇微生物菌群及其表征。
2010/7-2014/7 美國能源部 參與，負責微生物群落功能過程的GeoChip和宏基因組分析，協調多個參與單位。
2008/10-2017/9 美國能源部 主持地下水微生物群落的宏基因組學研究，同時套用GeoChip分析和測序的技術研究微生物群落中硫酸鹽還原、
金屬還原和有機污染物降解過程。
2008/7-2010/12 美國康菲石油公司 參與並協調與美國康菲石油公司的研究計畫，負責套用GeoChip研究油田微生物群落結構與功能，評估生物治理技術的效果。
2008/6-2012/8 美國能源部 參與，負責分析微生物群落結構和功能。
2008/1-2011/12 美國俄克拉荷馬州政府基金 參與並協調該項目實施，負責GeoChip在土壤微生物種群研究中的套用。
2008/1-2011/12 美國俄克拉荷馬州政府基金 參與，負責一種特殊真菌產乙醇功能表征和工藝最佳化研究。
2007/3-2012/3 美國能源部 參與並協調多個參與單位，負責套用GeoChip研究美國橡樹嶺鈾污染場地地下水樣品。
2007/9-2012/8 美國農業部 參與並協調BioCON實驗，負責草地土壤微生物群落結構與功能研究。
2005/9-2008/9 美國能源部 參與，負責Desulfovibriovulgaris基因晶片的構建、評估及其套用。
學術論文
截至2016年底，發表環境微生物組及生物信息學方面相關論文210餘篇，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；總影響因子＞900，總引用次數＞12,000(Google Scholar)，H index ＞ 54。
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.
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 Biol22:957–964.
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 ofBacillus amyloliquefaciensZM9 on bacterial wilt and rhizosphere microbial communities of tobacco.Appl Soil Ecol103:1–12.
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 toxicAkashiwo sanguineabloom.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 inShewanella loihicaPV-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.mBio7: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 Microbiol7: 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 Microbiol7:7994.
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.
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 inDesulfovibrio 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 Röling 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:e0123179.
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 toFusarium oxysporumby 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 ONE10: e0138455.
41.Rui J, Li J, Wang S, An J, Liu WT, Lin Q, Yang Y,He Zand 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 Technol49:1462-1471.
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 Rep5: 8605.
48.Yang Y, Chai Z, Wang Q, Chen W,He Z,and Jiang S. 2015. Cultivation of seaweedGracilariain 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-termin situCr(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 sustainedin situU(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.
2014
57.He Z (Ed.)2014.Microarrays: Current Technology, Innovation and Applications.Caister Academic Press, Norwich, UK.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, andHe 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 J8:1879–1891.
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 extremophileAcidithiobacillus 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 inClostridium cellulolyticumby 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 inClostridium 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, Sørensen 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 ONE9: 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 J8:430–440.
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 USA111: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 theLeymus chinensissteppe.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 Data2: Genomics Data2:166–169.
81.He Zand 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, andHe 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 andHe 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 Zand 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.
2013
87.Li X, Deng Y, Li Q, Lu C, Wang J, Zhang H, Zhu J, Zhou J, andHe 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 inDesulfovibrio vulagrisHildenboroughthrough 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 inThermoanaerobacter.Biotechnol Biofuels6:103.
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 ofShewanella putrefaciensW3-18-1.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 Microbiol79:1580-1589.
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 Res47:6298-6308.
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.mBio4: e00324-13.
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 J6:259-272.
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 Microbiol78:7652-7661.
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 elucidatingin situbiodegradation.Front Microbiol3:339.
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 J6:2045-2055.
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 theDesulfovibrio vulgariscarbon 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 Technol46:5824−5833.
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 ofDesulfovibrio vulgarisbiofilms: 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 J6:363-383.
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 ofShewanella 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 J6:451-460.
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 Microbiol78:2966-2972.
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 inDesulfovibrio vulgarisHildenborough.Appl Environ Microbiol78:1168-117.
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 Change2:106–110.
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 Microbiol77:991-999.
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 ofThermoanaerobacterspecies with biofuel yields.Appl Environ Microbiol77:7998-8008.
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:e1002318.
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 ofClostridiumandThermoanaerobacterspp.Bioresour Technol102: 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 Microbiol77:4241–4245.
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 duringin situbioremediation of a uranium-contaminated aquifer.Appl Environ Microbiol77:3860–3869.
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 Microbiol9:452-466.
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 ofShigella flexneriG3 for effective cellulosic saccharification under mesophilic conditions.Appl Environ Microbiol77:517-523.
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 NostrandJD,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 NostrandJD, 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 NostrandJD,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.
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 ofDesulfovibrio vulgarisHildenborough 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 Microbiol76:1088-1094.
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 inDesulfovibrio vulgarisHildenborough.Environ Microbiol12:2645–2657.
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 J4:1386-1397.
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 inShewanella 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 Technol44:7729-7735.
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 Bacteriol192: 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 plantPteris vittataL.Appl Environ Microbiol76:7277–7284.
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 ofShewanella onedensisc-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 J4:1060-1070.
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 J4:660-672.
168.Andersen G,He Z,DeSantis T, Brodie E, andZhou J. 2010.The Use of Microarrays in Microbial Ecology inEnvironmental 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. InHandbook 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) inGeomicrobiology: Molecular and Environmental Perspective, pp109-126. Springer, New York.
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 Ecol70:324-333.
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 Microbiol11:2611-2626.
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 grownDesulfovibrio vulgaris.J Bacteriol191:5793-5801.
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 toDesulfovibrio vulgarisgenome plasticity.Environ Microbiol11:2244-2252.
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 inThermoanaerobacter sp. strain X514 via isotopomer-assisted metabolite analysis.Appl Environ Microbiol75:5001-5008.
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 China19:700-706.
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 Technol43:3529-3534.
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 Zand Zhou J. 2009. Detection and characterization of uncultivated microorganisms using microarrays. InUncultivated Microorganisms (Microbiology Monographs)Vol.10:35-58, Epstein, Slava S. (Ed.) Springer-Verlag Berlin Heidelberg.
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182.He Zand Zhou J. 2008. Empirical evaluation of a new method for calculating signal-to-noise ratio for microarray data analysis.Appl Environ Microbiol74:2957-2966.
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 China18:1319-1327.
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 anExiguobacterium sibiricumstrain isolated from 3 million year old permafrost: A genome and transcriptome approach.BMC Genomics9:547.
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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 J1:67-77.
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 ofDesulfovibrio vulgaristo 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 J1:163-179.
189.Butler J, He Q, Nevin PK,He Z,Zhou J, and Lovley D. 2007.Genomic and microarray analysis of aromatics degradation inGeobacter metallireducensand comparison to aGeobacterisolate from a contaminated field site.BMC Genomics8:180.
190.Caffrey SM, Park HS, Voordouw JK,He Z,Zhou J, and Voordouw G. 2007. Function of periplasmic hydrogenases in the sulfate-reducing bacteriumDesulfovibrio vulgarisHildenborough.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 ofDesulfovibrio vulgarisHildenborough.Appl Environ Microbiol73:5389-5400.
192.BrownSD, Raman B, McKeown CK, Kale SP,He Zand Mielenz JR. 2007.Construction and evaluation of aClostridium thermocellumATCC 27405 whole-genome oligonucleotide microarray.Appl Biochem Biotechnol137-140:663-674.
193.Gentry TJ, Schadt CW,He Z, and ZhouJ. 2007.Functional gene arrays for microbial community analysis. InManual of Environmental Microbiology(Third edition), pp1052-1062 (Hurst CJ et al., eds), ASM Press, Washington DC, USA.
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194.Gentry TJ, Wickham JS, Schadt CW,He Z, and ZhouJ. 2006.Microarray applications in microbial ecology research.Microb Ecol52:159-175.
195.Walker CB, Stolyar SS, Pinel N, Yen HC,He Z,Zhou J, Wall JD,Stahl DA. 2006.Recovery of temperateDesulfovibrio vulgarisbacteriophage using a novel host strain.Environ Microbiol8: 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 asDesulfovibrio vulgarisHildenborough transitions into stationary phase during electron donor depletion.Appl Environ Microbiol72:5578-5588.
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 inDesulfovibrio vulgarisHildenborough: 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 inDesulfovibrio vulgarisHildenborough inferred from global transcriptional analysis.Appl Environ Microbiol72:4370-4381.
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 inDesulfovibrio vulgarisHildenborough.J Bacteriol188:1817-1828.
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 Microbiol72:1688-1691.
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201.He Z,Wu L, Li X, Fields MW and Zhou J. 2005. Empirical establishment of oligonucleotide probe design criteria.Appl Environ Microbiol71: 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 Microbiol71:5154-5162.
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. InMethods in MicrobiologyVolume34:329-365. (Savidge T. and H. Pothulakis, eds) Academic Press, London, UK.
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206.Andrews TJ, von Caemmerer S,He Z,Hudson GS. 1998. Rubisco catalysisin vitroandin vivo.Photosynthesis: Mechanisms and Effects5:3307.
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.
