Zhili He
Environmental Microbiomics Research Center
School of Environmental Science and Engineering
Sun Yat-Sen University
Address: 132 East Circle, University Town, Guangzhou, China510006
Phone: +86-20-3106-5837
Email: hezhili@mail.sysu.edu.cn
Website: http://sese.sysu.edu.cn/node/4014
WeChat: zhilihe65
Education and Certificates
Bioinformatics Certified Bioinformatics Specialist (CBS) and Master (CBM) 2002
BA Computing and Information Science, University of Guelph, ON, Canada 2001
PhD Research School of Biological Sciences, Australian National University, Australia 1998
MS Shanghai Institute of Plant Physiology, the Chinese Academy of Science, China 1989
BS Department of Biology, Hunan Normal University, China 1986
Interests
• Environmental/human/animal/plant/ microbiomes in terms of diversity, composition, structure, function, dynamics, interaction and their relationships with host (e.g., nutrition, growth, health, disease) and environmental drivers
• Microbial ecology related to global change, stress responses, and bioremediation using (meta)genomics approaches
• Synthetic microbial ecology, systems microbiology and microbial functional genomics to understanding the gene function, regulation and interaction for culturable microorganisms
• Single cell genomics to understand microbial ecology, physiology and evolution for not-yet cultivated microorganisms
• Development of biotechnologies (e.g., microbiome engineering) and bioinformatic tools for environmental applications, data analysis and modelling, and ecosystem functioning predictions
Professional Experience
Professor, Environmental Microbiomics Research Center
School of Environmental Science and Engineering Mar 2017– present
Sun Yat-Sen University, Guangzhou, China
Professor/ Research Scientist, Department of Microbiology and Plant Biology
Associate Director, Institute for Environmental Genomics Sep 2011– Feb 2017
University of Oklahoma, Norman OK, USA
Associate Professor/ Research Scientist, Department of Botany and Microbiology
Associate Director, Institute for Environmental Genomics Sep 2007 – Aug 2011
University of Oklahoma, Norman OK, USA
Assistant Professor/ Research Scientist, Department of Botany and Microbiology
Associate Director, Institute for Environmental Genomics Oct 2005 – Aug 2006
University of Oklahoma, Norman OK, USA
Research Assistant Professor & Bioinformatics Team Leader Jul 2005 – Sep 2005
University of Tennessee/ORNL, Oak Ridge, Tennessee, USA
Postdoctoral Associate & Bioinformatics Team Leader Feb 2003 – Jun 2005
Oak Ridge National Laboratory (ORNL), Oak Ridge, Tennessee, USA
Postdoctoral Research Associate
University of Guelph, Guelph, Ontario, Canada Oct 1998 - Dec 2002
Researcher Dec 1997 – Sep 1998
Research Institute of Innovative Technology for the Earth, Kyoto, Japan
Junior Researcher/Research Scientist Aug 1989 - Mar 1994
Shanghai Institute of Plant Physiology, the Chinese Academy of Sciences, Shanghai, China
Selected Publications: 2019 and 2020 Highly Cited Researcher (Clarivate/Web of Science): ~300 publications, H index = 75, and a total of > 17,000 citations (Google Scholar, up to December 31, 2020).
2021
1. Yu X, Zhou J, Song W, Xu M, He Q, Peng Y, Tian Y, Wang C, Shu L, Wang S, Yan Q, Liu J, Tu Q*, and He Z*. 2021. SCycDB: A curated functional gene database for metagenomic profiling of sulfur cycling pathways. Mol Ecol Resour 21: 924–940.
2. Xu K, Li Z, Juneau P, Xiao F, Lian Y, Zhang W, Shu L, Jiang H, Zhang K, Wang C, Wang S, Yan Q, and He Z*. 2021. Toxic and protective mechanisms of cyanobacterium Synechocystis sp. in response to titanium dioxide nanoparticles. Environ Pollut 274: 116508.
3. Li Z, Deng T, Yan L, Zhou J, He Z, Deng Y and Xu M. 2021. Elevated nitrate simplifies microbial community compositions and interactions in sulfide-rich river sediments. Sci Tot Environ 750: 141513 (DOI: 10.1016/j.scitotenv.2020.141513).
4. Liang Z, Fang W, Luo Y, Lu Q, Juneau P, He Z, and Wang S. 2021. Mechanistic insights into organic carbon-driven water blackening and odorization of urban rivers. J Hazard Mat 405: 124663.
5. Qian Y, Xu M, Deng T, Hu W, He Z, Yang X, Wang B, Song D, Chen L, Huang Y, and Sun G. 2021. Synergistic interactions of Desulfovibrio and Petrimonas for sulfate-reduction coupling polycyclic aromatic hydrocarbon degradation. J Hazard Mat 407: 124385 (https://doi.org/10.1016/j.jhazmat.2020. 124385).
6. Shi Y, Queller D, Tian Y, Zhang S, Yan Q, He Z, He ZZ, Wu C, Wang C, and Shu L. 2021. The Ecology and Evolution of Amoeba-Bacterium Interactions. Appl Environ Microbiol 87: e01866.
7. Wu B, Liu F, Fang W, Yang T, Chen G, He Z, and Wang S. 2021. Microbial sulfur metabolism and environmental implications. Sci Tot Environ 778: 146085.
8. Xiao F, Zhu W, Yu Y, He Z, Wu B, Wang C, Shu L, Li X, Yin H, Wang J, Juneau P, Zheng X, Wu Y, Li J, Chen X, Hou D, Huang J, He J, Xu G, Xie L, Huang J, and Yan Q. 2021. Host development overwhelms environmental dispersal in governing the ecological succession of zebrafish gut microbiota. npj Biofilms Microbomes 7: 5.
9. Xiao F, Liao L, Xu Q, He Z, Xiao T, Wang J, Huang J, Yu Y, Wu B, and Yan Q. 2021. Host–microbiota interactions and responses to grass carp reovirus infection in Ctenopharyngodon idellus. Environ Microbiol 23: 431-447.
10. Yu H, Zheng X, Weng W, Yan X, Chen P, Liu X, Peng T, Zhong Q, Xu K, Wang C, Shu L, Yang T, Xiao F, He Z, and Yan Q. 2021. Synergistic effects of antimony and arsenic contaminations on bacterial, archaeal and fungal communities in the rhizosphere of Miscanthus sinensis: Insights for nitrification and carbon mineralization. J Hazard Mat 411:125094.
11. Zhang N, Juneau P, Huang R, He Z, Sun B, and Zhou J. 2021. Coexistence between antibiotic resistance genes and metal resistance genes in manure-fertilized soils. Geoderma 382: 114760 (DOI: 10.1016/j.Geoderma.2020.114760).
12. Zheng X, Zhang K, Yang T, He Z, Shu L, Xiao F, Wu Y, Wang B, Yu H, Blaoco J, and Yan Q. 2021. Sediment resuspension drives protist metacommunity structure and assembly in grass carp (Ctenopharyngodon idella) aquaculture ponds. Sci Tot Environ 764: 142840.
2020
13. He Z*#, Deng Y#, Xu M#, Liang J, Xiong J, Yu H, Wu L, Xue K, Shi S, Wu B, Van Nostrand JD, Hobbie SE, Reich PB, Schadt CW, Kent A, Pendall E, Wallenstein M, Luo Y, and Yan Q*, Zhou J*. 2020. Microbial gene abundances reveal consistent effects of elevated carbon dioxide on ecosystem functioning. Environ Intl 144: 106068 (DOI: 10.1016/j.envint.2020.106068, #co-first authors, *corresponding author).
14. Wu B, Liu F, Zhou A, Li J, Shu L, Kempher M, Yang X, Ning D, Pan F, Zane G, Wall J, Van Nostrand JD, Juneau P, Chen S*, Yan Q*, Zhou J* and He Z*. 2020. Experimental evolution reveals nitrate tolerance mechanisms in Desulfovibrio vulgaris. ISME J 14: 2862–2876 (DOI: 10.1038/s41396-020-00753-5).
15. Yu X, Yang X, Wu Y, Peng Y, Yang T, Xiao F, Zhong Q, Xu K, Shu L, He Q, Tian Y, Yan Q, Wang C*, Wu B*, and He Z*. 2020. Sonneratia apetala introduction alters methane cycling microbial communities and increases methane emissions in mangrove ecosystems. Soil Biol Biochem 144: 107775 (DOI: 10.1016/j.soilbio.2020.107775).
16. Zhuang W, Yu X, Hu R, Luo Z, Liu X, Zheng X, Xiao F, Peng Y, He Q, Tian Y, Yang C, Wang S, Shu L, Yan Q, Wang C*, and He Z*. 2020. Diversity, function and assembly of mangrove root-associated microbial at a continuous fine scale. npj Biofilms Microbiomes 6: 52 (10.1038/s41522-020-00164-6).
17. Li Z, Juneau P, Lian Y, Zhang W, Wang S, Wang C, Shu L, Yan Q, He Z* and Xu K*. 2020. Effects of titanium dioxide nanoparticles on photosynthetic and antioxidative processes of Scenedesmus obliquus. Plants 9: 1748.
18. Avila-Jimenez ML, Burns G, He Z, Zhou J, Hodson A, Avila-Jimenez JL, and Pearce D. 2020. Functional associations and resilience in microbial communities. Microorganisms 8: 951 (DOI:10.3390/Microorganisms8060951).
19. Feng J, Wang C, Lei J, Yang Y, Yan Q, Zhou X, Tao X, Ning D, Yuan M, Qin Y, Shi Z, Guo X, He Z, Van Nostrand JD, Wu L, Bracho-Garillo RG, Penton CR, Cole JR, Konstantinidis KT, Luo Y, Schuur EAG, Tiedje JM, and Zhou J. 2020. Warming-induced permafrost thaw exacerbates tundra soil carbon decomposition mediated by microbial community. Microbiome 8: 3 (doi: 10.1186/s40168-019-0778-3).
20. Gao Q, Wang G, Xue K, Yang Y, Xie J, Yu H, Bai S, Liu F, He Z, Ning D, Hobbie SE, Reich PB, and Zhou J. 2020. Stimulation of soil respiration by elevated CO2 is enhanced under nitrogen limitation in a decade-long grassland study. Proc Natl Acad Sci USA 117: 33317-33324 (DOI：10.1073/pnas.2002780117).
21. Guo X, Gao Q, Yuan M, Wang G, Zhou S, Feng J, Shi Z, Hale L, Wu LH, Zhou A, Tian R, Liu F, Wu B, Chen L, Jung CG, Niu S, Li D, Xu X, Jiang L, Escalas A, Wu LY, He Z, Van Nostrand JD, Ning D, Liu X, Yang Y, Schuur E, Konstantinidis K, Cole J, Penton CR, Luo Y, Tiedje JM and Zhou J. 2020. Gene-informed decomposition model predicts lower soil carbon loss due to persistent microbial adaptation to warming. Nat Commun 11: 4897 (DOI: 10.1038/s41467-020-18706-z).
22. Li M, Fang A, Yu X, Zhang K, He Z, Wang C, Peng Y, Xiao F, Yang T, Zhuang W, Zheng X, Zhong Q, Liu X and Yan Q. 2020. Microbially-driven sulfur cycling microbial communities in different mangrove sediments. Chemosphere (DOI: 10.1016/j. Chemosphere.2020.128597).
23. Li J, Li C, Kou Y, Yao M, He Z, and Li X. 2020. Distinct mechanisms shape soil bacterial and fungal co-occurrence networks in Mountain Gongga. FEMS Microbiol Ecol 96: fiaa030 (DOI: 10.1093/femsec/fiaa030).
24. Liang Z, Shi J, Wang C, Li J, Liang D, Yong EL, He Z, and Wang S. 2020. Genome-centric metagenomic insights into the impact of alkaline/acid and thermal sludge pre-treatment on digestion sludge Microbiome. Appl Environ Microbiol 86: e01920-20 (doi: 10.1128/AEM.01920-20).
25. Liu X, Yang C, Yu X, Yu H, Zhuang W, Gu H, Xu K, Zheng X, Wang C, Xiao F, Wu B, He Z, and Yan Q. 2020. Revealing structure and assembly for rhizophyte-endophyte diazotrophic community in mangrove ecosystem after introduced Sonneratia apetala and Laguncularia racemose. Sci Tot Environ 721: 137807 (DOI: 10.1016/j.scitotenv.2020.137807).
26. Luo H, Yang Y, Wang Q, Wu Y, He Z, and Yu W. 2020. Protection of Siganus oramin, rabbitfish, from heavy metal toxicity by the selenium-enriched seaweed Gracilaria lemaneiformis. Ecotox Environ Safe 206: 111183 (DOI: 10.1016/j.ecoenv.2020.111183).
27. Pressler Y, Zhou J, He Z, Van Nostrand JD, and Smith AP. 2020. Post-agricultural tropical forest regeneration shifts soil microbial functional potential for carbon and nutrient cycling. Soil Biol Biochem 145: 107784 (DOI: 10.1016/j.soilbio.2020.107784).
28. Qiu L, Fang W, He H, Liang Z, Zhan Y, Lu Q, Liang D, He Z, Mai B, and Wang S. 2020. Organohalide-respiring bacteria in polluted urban rivers employ novel bifunctional reductive dehalogenases to dechlorinate polychlorinated biphenyls and tetrachloroethene. Environ Sci Technol 54: 8791-8800 (doi: 10.1021/acs.est.0c01569).
29. Shen R, Yu L, Xu P, Liang Z, Lu Q, Liang D, He Z, and Wang S. 2020. Water content as a primary parameter determines microbial reductive dechlorination activities in soil. Chemosphere 267: 3 (DOI: 10.1016/j.Chemosphere.2020.129152).
30. Tian R, Ning D, He Z, Zhang P, Spencer SJ, Gao S, Shi W, Wu L, Zhang Y, Yang Y, Adams BG, Rocha AM, Detienne BL, Lowe KA, Joyner DC, Klingeman DM, Arkin AP, Fields MW, Hazen TC, Stahl DA, Alm EJ, and Zhou J. 2020. Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity. Microbiome 8: 51 (DOI: 10.1186/s40168-020-00825-w).
31. Tu Q, Yan Q, Deng Y, Michaletz ST, Buzzard S, Weiser MD, Waide R, Ning D, Wu L, He Z, and Zhou J. 2020. Biogeographic patterns of microbial co-occurrence ecological networks in six American forests. Soil Biol Biochem 148: 107897 (DOI: 10.1016/j.soilbio.2020.107897).
32. Wang B, Zheng X, Zhang H, Xiao F, Gu H, Zhang K, He Z, Liu X, and Yan Q. 2020. Bacterial community responses to tourism development in the Xixi National Wetland Park, China. Sci Tot Environ 720: 137570 (DOI: 10.1016/j.scitotenv.2020.137570).
33. Wang B, Zheng X, Zhang H, Xiao F, He Z and Yan Q. 2020. Keystone taxa of water Microbiome respond to environmental quality and predict water contamination. Environ Res 187: 109666 (DOI: 10.1016/j.envres.2020.109666).
34. Wang C, Hu R, Strong P, Zheng W, Huang W, Luo Z, Yan Q, He Z, Shu L. 2020. Prevalence of antibiotic resistance genes and bacterial pathogens along the soil–mangrove root continuum. J Hazard Mat 408: 124985.
35. Wang Y, Zheng H, Yang Y, Liang Y, Zhou J, He Z, Chen F, Ouyang Z, 2020. Microbial functional gene diversity in natural secondary forest Ultisols. Acta Oecologica 105: 103575 (DOI: 10.1016/j.actao.2020.103575).
36. Wu Y, Xiao F, Wang C, Shu L, Zheng X, Xu K, Yu X, Zhang K, Luo H, Yang Y, He Z and Yan Q. 2020. The beta-diversity of Siganus fuscescens-associated microbial communities from different habitats increases with body weight. Front Microbiol 11: 1562 (doi: 10.3389/fmicb.2020.01562).
37. Yu H, Yan X, Zheng X, Xu K, Zhong Q, Yang T, Liu F, Wang C, Shu L, He Z, Xiao F and Yan Q. 2020. Differential distribution of and similar biochemical responses to different species of arsenic and antimony in Vetiveria zizanioides. Environ Geochem Health 42: 3995-4010 (doi: 10.1007/s10653-020-00658-4).
38. Zhang K, Zheng X, He Z, Yang T, Shu L, Xiao F, Wu Y, Wang B, Li Z, Chen P, Yan Q. 2020. Fish growth enhances microbial sulfur cycling in aquaculture pond sediments. Microb Biotechnol 13: 1597–1610 (DOI:10.1111/1751-7915.13622).
39. Zheng X, Wang Y, Yang T, He Z, and Yan Y. 2020. Size-fractioned aggregates within phycosphere define functional bacterial communities related to Microcystis aeruginosa and Euglena sanguinea blooms. Aqua Ecol 54: 609–623 (DOI: 10.1007/s10452-020-09762-0).
40. Zhong Q, Xue D, Chen H, Liu L, He Y, Zhu D, and He Z. 2020. Structure and distribution of nitrite-dependent anaerobic methane oxidation bacteria vary with water tables in Zoige peatlands. FEMS Microbiol Ecol 96: fiaa039 (DOI: 10.1093/femsec/fiaa039).
41. Zou Y, Ning D, Huang Y, Liang Y, Wang H, Dua L, Yuan T, He Z, Yang Y, Xue K, Van Nostrand JD, and Zhou J. 2020. Functional structures of soil microbial community relate to contrasting N2O emission patterns from a highly acidified forest. Sci Tot Environ 725: 138504 (DOI: 10.1016/j.scitotenv.2020.138504).
2019
42. Zhang S, He Z, and Meng F. 2019. Floc-size effects of the pathogenic bacteria in a membrane bioreactor plant. Environ Intl 127: 645-652.
43. Feng J, Penton R, He Z, Van Nostrand JD, Yuan M, Wu L, Wang C, Qin Y, Shi Z, Guo X, Schuur EAG, Luo Y, Bracho R, Konstantinnidis KT, Cole JR, Tiedje JM, Yang Y, and Zhou J. 2019. Long-term warming in Alaska enlarges the diazotrophic community in deep soils. mBio 10: e02521-18 (DOI: 10.1128/mBio.02521-18).
44. Feng K, Zhang Y, He Z, Ning D and Deng Y. 2019. Interdomain ecological networks between Plants and microbes. Mol Ecol Resour 19: 1565-1577 (DOI: 10.1111/1755-0998.13081).
45. Luo H, Wang Q, He Z, Wu Y, Long A, and Yang Y. 2019. Protection of dietary selenium-enriched seaweed Gracilaria lemaneiformis against cadmium toxicity to abalone Haliotis discus hannai.Ecotox Environ Safe 171: 398-405.
46. Johnston ER, Hatt JK, He Z, Wu L, Guo X, Luo Y, Schuur EAG, Diedje JM, Zhou J, and Konstantinidis KT. 2019. Responses of tundra soil microbial communities to half a decade of experimental warming at two critical depths. Proc Natl Acad Sci USA 116: 15096-15105.
47. Qin H, Wang S, Feng K, He Z, Virta M, Hou W, Dong H, and Deng Y. 2019. Unraveling the diversity of sedimentary sulfate-reducing prokaryotes (SRP) across Tibetan saline lakes using epicPCR. Microbiome 7: 71 (DOI: 10.1186/s40168-019-0688-4).
48. Buzzard V, Michaletz ST, Deng Y, He Z, Ning D, Shen L, Tu Q, Van Nostrand JD, Voordeckers JW, Wang J, Weiser MD, Kaspari M, Waide RB, Zhou J and Enquist BJ. 2019. Continental scale structuring of forest and soil diversity via functional traits. Nat Ecol Evol 3:1298–1308.
49. Tu Q, Lin L, Cheng L, Deng Y and He Z. 2019. NCycDB: a curated integrative database for fast and accurate metagenomic profiling of nitrogen cycling genes. Bioinformatics 35: 1040–1048 (DOI:10.1093/bioinformatics/bty741).
50. Xu K, Racine F, He Z, and Juneau P. 2019. Impacts of hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor (mesotrione) on photosynthetic processes in Chlamydomonas reinhardtii. Environ Pollu 244: 295-303.
51. Lin X, Hetharua B, Lin L, Xu H, Zheng T, He Z, and Tian Y. 2019. Mangrove Sediment Microbiome: Adaptive Microbial Assemblages and Their Routed Biogeochemical Processes in Yunxiao Mangrove National Nature Reserve, China. Microb Ecol 78: 57-69.
52. Xiao F, Bi Y, Li X, Huang J, Yu Y, Xie Z, Fang T, Cao X, He Z, Juneau P, and Yan Q. 2019. The impact of anthropogenic disturbance on bacterioplankton communities during the construction of Donghu Tunnel (Wuhan, China). Microb Ecol 77: 277-287.
53. Weiser MD, Ning D, Buzzard V, Michaletz ST, He Z, Enquist BJ, Waide RB, J Zhou, and Kaspari M. 2019. Thermal disruption of soil bacterial assemblages decreases diversity and assemblage similarity. Ecosphere 10: ecs2.2598 (DOI: 10.1002/ecs2.2598).
54. Guo X, Zhou X, Hale L, Yuan M, Ning D, Feng J, Shi Zhou, Li Z, Feng B, Gao Q, Wu W, Shi W, Zhou A, Fu Y, Wu L, He Z, Van Nostrand JD, Qiu G, Liu X, Luo Q, Tiedje JM, Yang Y, and Zhou J. 2019. Climate warming accelerates temporal scaling of grassland soil microbial biodiversity. Nat Ecol Evol 3: 1-8 (DOI: 10.1038/s41559-019-0848-8).
55. Wu L, Ning D, Zhang B, Li Y, Zhang P, Shan X, Zhang Q, Brown M, Li Z, Van Nostrand JD, Ling F, Xiao N, Zhang Y, Vierheilig J, Wells G, Yang Y, Deng Y, Tu Q, Wang A, Zhang T, He Z, Keller J, Nielsen PH, Alvarez P, Criddle C, Wagner M, Tiedje J, He Q, Curtis T, Stahl D, Alvarez-Cohen L, Rittman B, Wen X, and Zhou J. 2019. Global Diversity and Biogeography of Bacterial Communities in Wastewater Treatment Plants. Nat Microbiol 4: 1 (DOI: 10.1038/s41564-019-0426-5).
56. Shi JZ, Yin H, Van Nostrand JD, Voordeckers JW, Tu Q, Deng Y, Yuan MM, Zhou A, Zhang P, Xiao N, Ning D, He Z, Wu L, and Zhou J. 2019. Functional gene array-based ultrasensitive and quantitative detection of microbial populations in complex communities. mSystems 4: e00296-19 (DOI: 10.1128/mSystems.00296-19).
2018
57. He Z*, Zhang P, Wu LW, Rocha AM, Tu Q, Shi Z, Qin Y, Wang J, Curtis D, Ning D, Wu B, Van Nostrand JD, Wu LY, Yang Y, Elias DA, Watson DB, Adams MWW, Fields MW, Alm EJ, Hazen TC, Adams PD, Arkin AP, and Zhou J*. 2018. Microbial functional gene diversity predicts groundwater contamination and ecosystem functioning. mBio 9: e02435-17 (*corresponding author).
58. Wu B, Liu F, Weiser MD, Ning D, Okie JG, Shen L, Li J, Chai B, Deng Y, Feng K, Wu L, Chen S*, Zhou J*, and He Z*. 2018. Temperature determines the diversity and structure of N2O-reducing microbial assemblages. Func Ecol 32: 1867-1878 (*corresponding author).
59. Yu H, He Z*, Wang A, Xie J, Wu L, Van Nostrand JD, Jin D, Shao Z, Schadt CW, Zhou J*, and Deng Y*. 2018. Divergent responses of forest soil microbial communities under elevated CO2 in different depths of upper layers. Appl Environ Microbiol 84: e01694-17 (*corresponding author).
60. Yu H, He Z, Van Nostrand JD, Wang S, Jin D, Wang A, Wu L, Wang D, Tai X, Zhou J, and Deng Y. 2018. Elevated CO2 and warming altered grassland microbial communities in soil top-layers. Front Microbiol 9:1790.
61. Chai Z, He Z, DengY, Yang Y, and Tang Y. 2018. Cultivation of seaweed Gracilaria lemaneiformis enhanced biodiversity in a eukaryotic plankton community as revealed via metagenomic analyses. Mol Ecol 27: 1081-1093).
62. Li K, Cai D, Wang Z, He Z, and Chen S. 2018. Development of an efficient genome editing tool in Bacillus licheniformis using CRISPR-Cas9 nickase. Appl Environ Microbiol 84: e02608-17.
63. Li B, Cai D, Hu S, Zhu A, He Z, and Chen S. 2018. Enhanced synthesis of poly-gamma-glutamic acid by increasing the intracellular reactive oxygen species in the Bacillus licheniformis Δ1-pyrroline-5-carboxylate dehydrogenase gene ycgN deficient strain. Appl Microbiol Biotechnol 102: 10127-10137.
64. Deng Y, Ning D, Qin Y, Xue K, Wu L, He Z, Yin H, Liang Y, Buzzard V, Michaletz ST, and Zhou J. 2018. Spatial scaling of forest soil microbial communities across a temperature gradient. Environ Microbiol 20: 3504-3513.
65. Shi S, Herman DJ, He Z, Pett-Ridge J, Wu L, Zhou J, and Firestone MK. 2018. Plant roots alter microbial functional genes supporting root litter decomposition. Soil Biol Biochem 127: 90-99.
66. Guo X, Zhou X, Hale L, Yuan M, Feng J, Ning D, Shi Z, Qin Y, Liu F, Wu L, He Z, Van Nostrand JD, Liu X, Luo Y, Tiedje JM and Zhou J. 2018. Taxonomic and functional responses of soil microbial communities to annual removal of aboveground plant biomass. Front Microbiol 9: 954 (doi: 10.3389/fmicb.2018.00954).
67. Guo X, Feng J, Shi Z, Zhou X, Yuan M, Tao X, Hale L, Yuan T, Wang J, Qin Y, Zhou A, Fu Y, Wu L, He Z, Van Nostrand JD, Ning D, Liu X, Luo Y, Tiedje J, Yang Y, and Zhou J2018. Climate warming leads to divergent succession of grassland microbial communities. Nat Clim Change 8: 813–818 (DOI: 10.1038/s41558-018-0254-2).
68. Sun W, Cai Y, Wang Q, Tang S, Cao X, Luo H, He Z, Hu X, Nie X, Yang Y, and Wang T. 2018. Proteogenomic Analyses Revealed Favorable Metabolism Pattern Alterations in Rotifer Brachionus plicatilis Fed with Selenium-rich Chlorella. J Agri Food Chem 66: 6699–6707 (DOI: 10.1021/acs.jafc.8b00139).
69. Wang S, Qiu L, Liu X, Xu G, Siegert M, Lu Q, Juneau P, Yu L, Liang D, He Z, and Qiu R. 2018. Electron transport chains in organohalide-respiring bacteria and bioremediation implications. Biotechnol Advances 36: 1194-1206 (doi:10.1016/j.biotechadv.2018.03.018).
70. Chen C, Hemme C, Beleno J, Shi Z, Ning D, Qin Y, Tu Q, Jorgensen M, He Z, Wu L, and Zhou J. 2018. Oral microbiota of periodontal health and disease and their changes after nonsurgical periodontal therapy. ISME J 12: 1210–1224.
71. Li H, Xu Z, Yan Q, Yang S, van Nostrand JD, Wang Z, He Z, Zhou J, Jiang Y, and Deng Y. 2018. Soil microbial beta-diversity is linked with compositional variation in aboveground plant biomass in a semi-arid grassland. Plant Soil 423: 465–480 (DOI:10.1007/s11104-017-3524-2).
72. Yuan MM, Zhang J, Xue K, Wu L, Deng Y, J Deng, Hale L, Zhou X, He Z, Yang Y, Van Nostrand JD, Schuur EAG, Konstantinidis KT, Penton CR, Cole JR, Tiedje JM, Luo Y, and Zhou J. 2018. Microbial functional diversity covaries with permafrost thaw-induced environmental heterogeneity in tundra soil. Glob Change Biol 24: 297-307 (DOI: 10.1111/gcb.13820).
73. Weiser MD, Michaletz ST, Buzzard V, Deng Y, He Z, Shen L, Enquist BJ, Waide RB, J Zhou, and Kaspari M. 2018. Toward a theory for diversity gradients: the abundance – adaptation hypothesis. Ecography 41: 255-264 (doi: 10.1111/ecog.02314).
2017
74. Xie X, He Z*, Hu X, Yin H, Liu X, and Yang Y*. 2017. Largescale seaweed cultivation diverges water and sediment microbial communities in the coast of Nan'ao Island, South China Sea. Sci Tot Environ 598: 97–108 (*corresponding author).
75. Zhu C, Xiao F, Qiu Y, Wang Q, He Z*, and Chen S*. 2017. Lichenysin production is improved in codY null Bacillus licheniformis by addition of precursor amino acids. Appl Microbiol Biotechnol 101: 6375-6383 (10.1007/s00253-017-8352-z, *corresponding author).
76. Tu Q, Li J, Shi Z, Chen Y, Lin L, Li J, Wang H, Yan J, Zhou Q, Li X, Li L, Zhou J*, and He Z*. 2017. HuMiChip2 for strain level identification and functional profiling of human Microbiomes. Appl Microbiol Biotechnol 101: 423-435 (*corresponding authors, DOI: 10.1007/s00253-016-7910-0).
77. Feng K, Zhang Z, Cai W, Liu W, Xu M, Yin H, Wang A, He Z, and Deng Y. 2017. Biodiversity and species competition regulate the resilience of microbial biofilm community. Mol Ecol 26: 6170-6182.
78. Hou D, Huang Z, Zeng S, Liu J, Wei D, Deng X, Wen S, He Z, and He J. 2017. Environmental factors shape water microbial community structure and function in shrimp culture ecosystems. Front Microbiol 8: 2359 (doi: 10.3389/fmicb.2017.02359).
79. 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 Biochem 106: 99-108 (DOI: 10.1016/j.soilbio.2016.12.017).
80. Zhang P, He Z, Van Nostrand JD, Qin Y, Deng Y, Wu L, Tu Q, Wang J, Schadt CW, Fields MW, Hazen TC, Arkin AP, Stahl DA, and Zhou J. 2017. Dynamic succession of groundwater sulfate-reducing communities during prolonged reduction of uranium in a contaminated aquifer. Environ Sci Technol 51: 3609–3620.
81. Yan Z, He Y, Cai H, Van Nostrand JD, He Z, Zhou J, Krumholz LR, and Jiang H. 2017. Interconnection of key microbial functional genes for enhanced benzo[a]pyrene biodegradation in sediments by microbial electrochemistry. Environ Sci Technol 51: 8519-8529 (DOI: 10.1021/acs.est.7b00209).
82. Yan Q, Stegen J, Yu Y, Deng Y, Li X, Wu S, Dai L, Zhang X, Li J, Wang C, Ni J, Li X, Hu H, Xiao F, Feng W, Ning D, He Z, van Nostrand JD, Wu L, Zhou J. 2017. Nearly a decade-long repeatable seasonal diversity patterns of bacterioplankton communities in the eutrophic Lake Donghu (Wuhan, China). Mol Ecol 26: 3839-3850.
83. Lu Q, Yu L, Liang Z, Yan Q, He Z, Luan T, Liang DW, Wang S. 2017. Dehalococcoides as a potential biomarker evidence for uncharacterized organohalides in environmental samples. Front Microbiol 8: 1677.
84. 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. 2017. Correspondence: Reply to ‘Analytical flaws in a continental-scale forest soil microbial diversity study'. Nat Comm 8: 15583 (DOI: 10.1038/ncomms15583).
85. Wang Y, Zhang R, He Z, Van Nostrand JD, Zheng Q, Zhou J, and Jiao N. 2017. Functional gene diversity and metabolic potential of the microbial community in an estuary-shelf environment. Front Microbiol 8: 1153 (DOI: 10.3389/fmicb.2017.01153).
86. Ni J, Li X, He Z, and Xu M. 2017. A novel method to determine the minimum number of sequences required for reliable microbial community analysis. J Microbiol Methods 139: 196-201.
87. Wu L, Yang Y, Chen S, Shi J, Zhao M, Zhu Z, Yang S, Qu Y, Ma Q, Z He, Zhou J, and He Q. 2017. Microbial functional trait of rRNA operon copy numbers increases with organic levels in anaerobic digesters. ISME J 11: 2874–2878 (doi: 10.1038/ismej.2017.135).
88. Wu L, Yang Y, Wang S, Yue H, Lin Q, Hu Y, He Z, Van Nostrand JD, Hale L, Li X, Gilbert GA, and Zhou J. 2017. Alpine soil carbon is vulnerable to rapid microbial decomposition under climate cooling. ISME J 11: 2102-2111 (DOI:10.1038/ismej.2017.75).
89. Zhou A, Lau R, Baran R, Ma J, von Netzer F, Shi W, Gorman-Lewis D, Kempher ML, He Z, Qin Y, Shi Z, Zane GM, Wu L, Bowen BP, Northen TR, Hillesland KL, Stahl DA, Wall JD, Arkin AP, Zhou J. 2017. Key metabolites and mechanistic changes for salt tolerance in an experimentally evolved sulfate-reducing bacterium Desulfovibrio vulgaris. mBio 8: e01780-17.
90. Cheng L, Zhang N, Yuan M, Xiao J, Qin Y, Deng Y, Tu Q, Xue K, Van Nostrand JD, Wu L, He Z, Zhou X, Leigh MB, Konstantinidis KT, Schuur EAG, Luo Y, Tiedje JM， and Zhou J. 2017. Warming enhances old organic carbon decomposition through altering functional microbial communities. ISME J 11: 1825–1835.
91. Gu Y, Van Nostrand JD, Wu L, He Z, Qin Y, Zhao F, and Zhou J. 2017. Bacterial community and arsenic functional genes diversity in arsenic contaminated soils from different geographic locations. PLoS ONE 12: e0176696.
92. 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. CATENA 152: 47–56.
93. Hu X, Wen G, Cao Y, Gong Y, Li Z, He Z, and Yang Y. 2017. Metabolic and phylogenetic profiles of microbial communities from a mariculture base on the Chinese Guangzhou coast. Fish Sci 83: 465-477 (doi:10.1007/s12562-017-1073-5).
94. Li H, Yang S, Xu Z, Yan Q, Li X, Van Nostrand JD, He Z, Yao F, Han X, Zhou J, Deng Y, and Jiang Y. 2017. Responses of soil microbial functional genes to global changes are indirectly influenced by aboveground plant biomass variation. Soil Biol Biochem 104: 18-29.
95. Zhang H, Wang R, Chen S, Qi G, He Z, and Zhao X. 2017. Microbial taxa and functional genes shift in degraded soil with bacterial wilt. Sci Rep 7: 39911 (DOI: 10.1038/srep39911).
2016
96. 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 (*corresponding author).
97. 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 (*corresponding author).
98. 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. Ecotoxicology 10: 1759-1770 (#co-first authors, DOI: 10.1007/s10646-016-1719-6).
99. 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 J 10: 1527-1539 (DOI: 10.1038/ismej.2015.201).
100. Shi S, Nuccio EE, Shi Z, He Z, Zhou J, and Firestone MK. 2016. The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages. Ecol Lett 19: 926-936 (DOI: 10.1111/ele.12630).
101. 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 Ecol 71: 604-615 (DOI:10.1007/s00248-015-0659-7).
102. 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 Change 6: 595-600 (doi:10.1038/nclimate2940).
103. 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 Microbiol 18: 205–218 (DOI:10.1111/1462-2920.12981).
104. 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 Comm 7: 12083.
105. 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 Microbiol 18: 4739-4754 (DOI: 10.1111/1462-2920.13365).
106. 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 Ecol 25: 2937-2948 (DOI: 10.1111/mec.13651).
107. 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. Geoderma 268: 119–127.
108. 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 Rep 6: 34744.
109. 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 Rep 6: 34645 (DOI: 10.1038/srep34645).
110. 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 Microbiol 82: 5077-5088 (DOI: 10.1128/AEM.00203-16).
111. 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.
112. 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 (DOI: 10.3389/fmicb.2016.00579).
113. 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 (DOI: 10.3389/fmicb.2016.01184).
114. 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 Res 104: 1-10 (DOI: 10.1016/j.watres.2016.07.072).
115. 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 Microbiol 7: 668 (DOI: 10.3389/fmicb.2016.00668).
116. 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. mBio 7: e00976-16 (doi:10.1128/mBio.00976-16).
117. 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
118. 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 Rep 5: 9316 (DOI: 10.1038/srep09316, *corresponding author).
119. 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. mBio 6: 02288-14 (doi:10.1128/mBio.02288-14).
120. 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 Technol 49: 12422-12431 (DOI:10.1021/acs.est.5b03442).
121. 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 CO2 by community reassembly. Appl Environ Microbiol 81: 2445-2454 (doi:10.1128/AEM.04040-14).
122. 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 J 9: 2360–2372.
123. 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 Ecol 91: 1-11 (DOI: 10.1093/femsec/fiu003)
124. 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 Ecol 24: 222–234.
125. Dopheide A, Lear G, He Z, Zhou J, and Lewis GD. 2015. Functional Gene Composition, Diversity and Redundancy in Microbial Stream Biofilm Communities. PLoS ONE 10: e0123179 (DOI:10.1371/journal.pone.0123179).
126. 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 Microbiol 6: 1205 (doi:10.3389/fmicb.2015.01205).
127. 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 Soils 51: 935–946.
128. 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. mBio 6: e00240-15 (doi:10.1128/mBio.00240-15).
129. 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 Microbiol 17: 566–576 (DOI: 10.1111/1462-2920.12398).
130. 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 Technol 49: 4627-4635 (DOI: 10.1021/es5053045).
131. 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: e0138455 (DOI:10.1371/journal.pone.0138455).
132. 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 Microbiol 81: 6070-6077 (DOI:10.1128/AEM.00557-15).
133. 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 (DOI: 10.1021/es504531s).
134. 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. mBio 6: e007746-15.
135. 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. mBio 6: e00326-15 (DOI:10.1128/mBio.00326-15).
136. 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 Microbiol 81: 4423-4431 (DOI:10.1128/AEM.00873-15).
137. 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 Biotechnol 99: 10311-10322 (DOI:10.1007/s00253-015-6881-x).
138. 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 (doi:10.1038/srep08605).
139. 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 Res 9: 236–244.
140. 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 Rep 5: 8476 (doi:10.1038/srep08476).
141. Yin H, Niu J, Ren Y, Cong J, Zhang X, Fan F, Xiao Y, Deng J, Xie M, He Z, Zhou J, Liang Y, and Liu X. 2015. An integrated insight into the response of sedimentary microbial communities to heavy metal contamination. Sci Rep 5: 14266 (DOI: 10.1038/srep14266).
142. 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 J 9: 2012–2020.
143. 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 Technol 49: 12922–12931.
144. 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 Microbiol 81: 4164-4172.
145. 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. Hydrobiologia 743: 221-235.
2014
146. 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.
147. 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 J 8: 714-726 (*Corresponding author).
148. Tu Q, He Z*, and Zhou J*. 2014. Strain/Species identification in metagenomes using genome-specific markers. Nucleic Acid Res 42: e67 (*corresponding author).
149. 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 ONE 9: e90546 (*Corresponding author).
150. 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 J 8: 1932–1944 (*corresponding author).
151. 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 Resour 14: 914–928.
152. 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.
153. 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 Microbiol 14: 179.
154. 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 China 13: 857-864.
155. 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 Biofuels 7: 25.
156. 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 ONE 9: e112609.
157. Xu T, Li Y, He Z, and Zhou J. 2014. Dockerin-containing protease inhibitor protects key cellulosomal cellulases from proteolysis in Clostridium cellulolyticum. Mol Microbiol 91: 694–705.
158. 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 Microbiol 80: 1544-1552.
159. 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 Microbiol 80: 1777-1786.
160. 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 Microbiol 16: 2408–2420.
161. 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.
162. 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.
163. 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.
164. 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 Energy 39: 222-4233.
165. 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 Genomics 15: 753.
166. 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 ONE 9: e104427.
167. Yao M, Rui J, Li J, Dai Y, Bai Y, Hedene P, 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 Biochem 79: 81-90.
168. 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 Data 2: 132–134.
169. 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: 166–169.
170. 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.
171. 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.
172. 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.
173. Deng Y and He Z. 2014. Microarray data analysis. In: Z. He (ed) Microarrays: Current Technology, Innovations and Applications. Caister Academic Press, Norwich, UK.
174. 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.
175. 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.
2013
176. 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 J 7: 660-71 (*corresponding author).
177. Tu Q, He Z*, Deng Y, and Zhou J*. 2013. Strain/species-specific probe design for microbial identification microarrays. Appl Environ Microbiol 79: 5085-5088 (*corresponding authors).
178. 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.
179. 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 Microbiol 13: 124.
180. 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 Hildenborough through experimental evolution. ISME J 7: 1790–1802.
181. 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 Technol 47: 9841−9849 (DOI:10.1021/es4018656).
182. 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 ONE 8: e70686.
183. 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.
184. 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 Biochem 66: 130-138.
185. 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 Technol 47: 9950−9958 (DOI: 10.1021/es402228x).
186. 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 Ecol 86: 200-214.
187. 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 J 7: 1974–1984 (doi:10.1038/ismej.2013.88).
188. 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 Microbiol 79: 5050-5257.
189. 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.
190. 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.
191. 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 Microbiol 79: 1284-1292.
192. 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 Microbiol 79: 1191-1199.
193. 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 Biol 19: 637-648.
194. 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 Biochem 57: 675-682.
195. 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 Biotechnol 97: 7035-7048 (doi: 10.1007/s00253-012-4496-z).
196. 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 Microbiol 13: 72 (doi:10.1186/1471-2180-13-72).
197. 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.
198. 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. Geobiology 11: 356-376.
199. 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. mBio 4: e00584-12.
200. 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.
2012
201. He Z, Van Nostrand JD, and Zhou J. 2012. Applications of functional gene microarrays for profiling microbial communities. Curr Opin Biotechnol 23: 460–466 (Invited review).
202. He Z*, Deng Y, and Zhou J. 2012. Development of functional gene microarrays for microbial community analysis. Curr Opin Biotechnol 23: 49–55 (*corresponding author, invited review).
203. 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.
204. 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 Microbiol 78: 2991-2995 (#co-first authors).
205. 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.
206. 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 ONE 7: e50507.
207. Van Nostrand JD, He Z, and Zhou J. 2012. Use of functional gene arrays for elucidating in situ biodegradation. Front Microbiol 3: 339 (doi: 10.3389/fmicb.2012.00339, invited review).
208. 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 Ecol 82: 148-156.
209. 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 J 6: 2107-2118.
210. 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.
211. 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 Bacteriol 194: 5783-5793.
212. 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 Univ 19: 3055−3063.
213. 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.
214. 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 Genomics 13: 138 (doi:10.1186/1471-2164-13-138).
215. 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.
216. Deng Y, Jiang Y, Yang Y, He Z, Luo F, and Zhou J. 2012. Molecular ecological network analysis. BMC Bioinformatics 13: 113 (doi:10.1186/1471-2105-13-113).
217. 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 Microbiol 194: 473–482.
218. 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.
219. 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.
220. 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.
221. 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 (doi:10.1038/nclimate1331).
2011
222. 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 China 5: 1-20 (Invited Feature Article).
223. 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.
224. 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.
225. 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 Genet 7: e1002318 (doi:10.1371/journal.pgen.1002318).
226. 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 Chem 401: 2003–2011.
227. 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.
228. 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.
229. 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.
230. 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. mBio 2: e00122-11.
231. 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.
232. 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 J 5: 1303–1313.
233. 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.
234. 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 J 5: 403-413.
235. 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.
236. 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 (Invited book chapter).
237. 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.
238. 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.
239. 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.
2010
240. 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 Lett 13: 564-575.
241. 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 J 4: 1167-1179.
242. 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 Microbiol 76: 1574–1586.
243. 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 (#co-first authors).
244. Zhou J, He Z, Van Nostrand JD, Wu L, and Deng Y. 2010. Applying GeoChip analysis to disparate microbial communities. Microbe 5: 60-65 (Invited review).
245. 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.
246. 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.
247. Zhou J, Deng Y, Luo F, He Z, Tu Q, and Zhi X. 2010. Functional molecular ecological networks. mBio 1: e00169-10.
248. 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 Microbiol 10: 291.
249. 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.
250. 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.
251. 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.
252. 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 ONE 5: e12919.
253. 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 ONE 5: e12582.
254. 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 Biotechnol 3: 455-466.
255. 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.
256. 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.
257. 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.
258. 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.
259. 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 (Invited book chapter).
2009
260. 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 (Invited review).
261. 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.
262. 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.
263. 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.
264. 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.
265. 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.
266. 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.
267. 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.
268. 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 USA 106: 4840–4845.
269. 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 (Invited book chapter).
270. 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.
2008
271. 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.
272. He Z*, Van Nostrand JD, Wu L, and Zhou J. 2008. Development and application of functional gene arrays for microbial community analysis. Trans Nonferrous Metals Soc China 18: 1319-1327 (Invited review, *corresponding author).
273. Deng Y, He Z*, Van Nostrand JD, Zhou J*. 2008. Design and analysis of mismatch probes for long oligonucleotide microarrays. BMC Genomics 9: 491 (*corresponding author).
274. 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 Genomics 9: 547.
2007
275. 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 (News Release by Nature Press Office: http://www.nature.com/ismej/press_releases/index.html).
276. 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 Bacteriol 189: 8944-8952.
277. 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.
278. 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.
279. 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 Bacteriol 189: 6159-6167.
280. 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 Microbiol 73: 5389-5400.
281. Brown SD, 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.
282. Gentry TJ, Schadt CW, He Z, and Zhou J. 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.
2006
283. Gentry TJ, Wickham JS, Schadt CW, He Z, and Zhou J. 2006. Microarray applications in microbial ecology research. Microb Ecol 52: 159-175.
284. 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.
285. 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.
286. 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 Bacteriol 188: 4068-4078.
287. 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.
288. 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.
289. 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.
2005
290. 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 (One of the top 20 papers most requested in 2005 by AEM).
291. 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.
292. Li X#, He Z# and Zhou J. 2005. Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation (#co-first author). Nucleic Acids Res 33: 6114-6123.
293. 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.
294. 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.
2004 and before
295. Andrews TJ, von Caemmerer S, He Z, Hudson GS. 1998. Rubisco catalysis in vitro and in vivo. Photosynthesis: Mechanisms and Effects 5: 3307.
296. 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 Physiol 115: 1569–1580.
297. He Z, Tang Z. 1994. An Increased 66-kD Polypeptide associated with stimulation of K+ uptake in sorghum roots under PEG stress. Chinese Science Bulletin 39: 587–591.
298. 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 TongBao 38: 2190-2193.
299. He Z, Li J, and Tang Z. 1993. Stimulative Effect of osmotic stress on the K+ accumulation in sorghum roots. Acta Phytophysiol Sinica 19: 379–386.
300. 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 Physiol Commun 28: 330–334.
301. He Z, and Wang H. 1991. Emergence of salt-induced proteins in alfalfa under NaCl stress. Acta Phytophysiol Sinica 17: 71–79.
Awards
• A Patent Award by The University of Oklahoma for the patent “Methods of producing protoporphyrin IX and bacterial mutants therefor (NO. 9,273,334)” by Zhou J, Qiu D, He Z, and M Xie (2016).
• An Innovator of the Year 2010 Award by The Journal Record for the development of GeoChip and associated technologies in Oklahoma. This program recognizes businesses, organizations and individuals who embrace both the entrepreneurialism and innovation that make Oklahoma such a special place to live and work (2010).
• 2009 R&D 100 Award by R&D Magazine for OU GeoChip developed by Jizhong Zhou, Zhili He, Liyou Wu, Joy D. Van Nostrand, and Ye Deng at the Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma. This is a prestigious award for providing a mark of excellence known to industry, government, and academia as proof that the product is one of the most innovative ideas of the year (2009).
Patents
Zhou J, Qiu D, He Z, and M Xie (approved in March 2016). Methods of producing protoporphyrin IX and bacterial mutants therefor (Patent NO. NO. 9,273,334).
Professional Services and Memberships
• An Associate Editor of Microbiome and Environmental Microbiome
• An editor of PLoS ONE and Scientific Reports
• A review editor of Frontiers in Environmental Science (Soil Process)
• A member of the Editorial Board of Applied Environmental Microbiology (2007-2016), Agricultural Science and The Scientific World Journal (Genomics)
• The American Society for Microbiology (ASM)
• The International Society for Microbial Ecology (ISME)
• The Ecological Society of America (ESA)
• Reviewer for a variety of journals, including PNAS, The ISME Journal (ISME J), Microbiome, Ecology Letters, npj Biofilmes and Microbiomes, Environmental Microbiology (EM), Applied and Environmental Microbiology (AEM), Environmental Science and Technology (EST), Water Research, BMC Genomics，BMC Bioinformatics, Bioinformatics, mBio and Applied Microbiology Biotechnology.
• Reviewer of US DOE, NIH and NSF proposals
Biotechnologies and bioinformatic tools
1. MCycDB: The methane cycling database (MCycDB) contains 298 methane cycling gene families covering 10 methane metabolic pathways with 651,098 representative sequences and 20,616 homologous orthology groups, and associated reference sequences from the NCBI RefSeq database were also integrated in MCycDB with 43 phyla and 2355 genera, and 5 phyla and 115 genera for bacteria and archaea, respectively. Also, homologous groups from public orthology databases were identified and included in MCycDB to reduce false positive assignments (Qian et al., unpublished).
2. SCycDB: SCycDB is a curated database to analyze microbial sulfur cycling functional genes/pathways for metagenome sequencing data. It contains 207 gene families and 585,055 representative sequences affiliated with 52 phyla and 2684 genera of bacteria/archaea as well as 20,761 homologous orthology groups. This work was submitted to Molecular Ecology Resources (Yu et al., 2021).
3. NCycDB: NCycDB is a curated database to analyze microbial nitrogen cycling functional genes/pathways for metagenome sequencing data. It contains 68 gene (sub)families and covers eight N cycle processes with 84759 representative sequences and 1958 homologous orthology groups. This was published in Bioinformatics (Tu et al., 2019).
4. GSmer: GSmer is a novel k-mer-based approach to identify genome-specific markers (GSMs) from currently sequenced microbial genomes, and then is used for strain-/species-level identification in metagenome, thus characterizing metagenomes. This was published in Nucleic Acids Research (Tu et al., 2014).
5. SSPD. It is a de novo Strain-Specific Probe Design (SSPD) software tool to design strain-specific oligonucleotide probes for microarray construction. Those probes are expected to specifically identify sequenced microbial species and strains from any environmental samples. This was published in Applied and Environmental Microbiology (Tu et al., 2013).
6. Molecular Ecological Network Analysis (MENA). This pipeline uses Random Matrix Theory (RMT)-based methods to construct and analyze molecular ecological networks (MENs). It was published in BMC Bioinformatics (Deng et al., 2012).
7. GeoChip 2.0. This GeoChip contains 24,243 probes covering more than 10,000 functional gene variants in 150 functional gene categories. It was published in The ISME Journal (He et al., 2007).
8. GeoChip 3.0. This GeoChip is more comprehensive than GeoChip 2.0, containing 28,000 probes and covering about 57,000 functional gene variants in 292 functional categories. It was published in The ISME Journal (He et al., 2010). GeoChip 3.0-based OU GeoChip won an R&D 100 Award in 2009.
9. GeoChip 4.0. The currently used GeoChip 4.0 is constructed by the Roche NimbleGen in 135 K x 12 format. It is more comprehensive than GeoChip 3.0, containing 120,000 functional gene probes and covering >152,000 functional gene variants in 410 functional categories. A manuscript was published in Molecular Ecology Resources (Tu et al., 2014).
10. GeoChip 5.0. GeoChip 5.0 has four versions with the Agilent platform with small (60 K x 8, 8 arrays with 60,000 probes each on one slide), middle (180 K x 4), large (400K x2) and extra large (1.0 M x 1) formats. It is the current version in use, and its middle format contains 167,044 distinct probes, covering 395,894 coding sequences (CDS) from ~1500 functional gene families involved in microbial carbon (degradation, fixation, methane), nitrogen, sulfur, and phosphorus cycling, energy metabolism, metal homeostasis, organic remediation, secondary metabolism (e.g. antibiotic metabolism, pigments), stress responses, viruses (both bacteriophages and eukaryotic viruses), and virulence. This work was published in mSystems (Shi et al., 2019).
11. HuMiChip 1.0. The first version of human Microbiome chip (HuMiChip) contains 36,062 probes and covering 47,979 functional gene variants in 139 functional categories. HuMiChip is used to study human Microbiomes from different body sites, including oral, gut, and air way. A manuscript was published in PLoS ONE (Tu et al., 2014).
12. HuMiChip 2.0. Updated from HuMiChip 1.0 and developed on the Agilent platform with a 180 K x 4 with strain-level identification features: (i) 30,396 strain-specific probes to identify > 2063 sequenced reference strains, (ii) 83,518 functional gene probes targeting 423,898 protein coding sequences for 139 key genes/enzymes involved in 19 pathways, and (iii) 36,449 functional gene probes for representative metagenomes targeting 56,253 protein coding sequences for 139 key functional gene families, and other functional processes important for the human Microbiome, such as antibiotic resistance and stress response. It was published in Applied Microbiology and Biotechnology (Tu et al., 2017).
13. StressChip 1.0. The first version of microbial stress response chip (StressChip) contains 22,855 probes and covering 79,628 functional gene variants in 46 functional categories involved in response to temperature, oxygen, salinity, osmolarity and nutrition. StressChip is used to analyze the response of microbial communities to different environmental stresses. This paper was published in Environmental Science and Technology (Zhou et al., 2013).
14. CommOligo series. Oligonucleotide probe design software tools, which can design specific oligonucleotide probes for microbial genomes, individual functional genes, and metagenomes for constructing microarrays. The earliest version of CommOligo was published in Nucleic Acids Research (Li, He and Zhou, 2005).
15. Functional Gene Array Data Analysis Systems (FGADAS). This pipeline is developed to analyze GeoChip-based microarray data, and contains a series of statistical analysis tools. It can be used to analyze GeoChips 2.0-4.0, HuMiChip 1.0-2.0, or StressChip 1.0 data sets.
Grants
Since 2006, a total of more than 30 projects have been funded with more than US$23 million received as PI or Co-PI from USA. Since 2017, about 20 million RMB was secured to establish the Environmental Microbiomics Research Center at Sun Yat-sen University.
1. Natural National Science Foundation of China, Hydrosphere Microbial Project, 91951207, Anaerobic methane oxidation and its coupling mechanisms with carbon, nitrogen and sulfur cycling in estuarine mangrove wetlands,2020/01-2023/12,3,060,000 RMB，current, PI
2. Natural National Science Foundation of China, 31770539，Exploring the mechanism of ecosystem stability using synthetic denitrifying communities，2018/01-2021/12，620,000 RMB，current, PI
3. Sothern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Open Project: Development of detection technologies for carbon sink processes and carbon fingerprinting of typical ecosystems in South China Sea，2021/01-2023/12, 1,500,000 RMB，current, PI
4. Sothern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Innovation Team Project: Marine life processes and biological resource utilization, 2020/01-2020/12, 1,700,000 RMB，completed, PI
5. Sothern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Innovation Team Project: Marine life processes and biological resource utilization, 2019/01-2019/12, 1,100,000 RMB，completed, PI
6. Sun Yat-Sen University, Mechanisms for microbial community diversity formation, maintenance and loss and their relationships with ecosystem functioning,2017/07-2019/07, 1,000,000 RMB，completed, PI
7. Natural National Science Foundation of China-Guangdong,U1301235，Biogeochemical roles of microorganisms in Gracilania lemaneiformis cultivation systems，2014/01-2017/12，2,700,000 RMB，completed, Co-PI
|
Supporting agency |
US DOE |
|
Project title |
Directing traffic in the rhizosphere: how phage and fauna shape the flow and fate of root carbon through microbial pathways |
|
Total award amount |
$3,000,000 for four years |
|
Role and responsibility |
Co-PI with Mary Firestone (PI) et al. at the University of California at Berkeley (e.g., ViruChip, high throughput sequencing analysis of soil microbial communities |
|
Period covered |
10/1/2016 - 9/30/2020 |
|
Effort |
5% (annual) |
|
Location of research |
The University of Oklahoma |
|
Status |
Completed
|
|
Supporting agency |
USDA NIFA AFRI |
|
Project title |
Multi-scale analysis of microbe-climate interactions in greenhouse gas emissions from grasslands and croplands with livestock and manure use |
|
Total award amount |
$3,000,000 for four years |
|
Role and responsibility |
Co-PI with Xiangming Xiao (PI) et al. at the University of Oklahoma for metagenomic analysis (e.g., GeoChip, high throughput sequencing) of soil microbial communities in response to greenhouse gas emissions grasslands and croplands with livestock and manure use |
|
Period covered |
2/1/2016 - 1/31/2020 |
|
Effort |
10% (annual) |
|
Location of research |
The University of Oklahoma |
|
Status |
Completed
|
|
Supporting agency
|
DOE ENIGMA Program (a Science Focus Area from the Lawrence Berkeley National Laboratory) |
|
Project title |
From Genomes to Ecosystems: Systems-Level Mechanistic Understanding of Microbial Stress Responses at Oak Ridge Contaminated Sites |
|
Total award amount |
$2,100,000 for OU for three years |
|
Role and responsibility |
Co-PI with Jizhong Zhou (PI) et al. at the University of Oklahoma for metagenomic analysis (e.g., GeoChip, high throughput sequencing) of groundwater microbial communities from the Oak Ridge Integrated Field-scale Research Challenges (OR-IFRC) site |
|
Period covered |
10/1/2014 - 9/30/2017 |
|
Effort |
10% (annual) |
|
Location of research |
The University of Oklahoma |
|
Status |
Completed
|
|
Supporting agency |
DOE Genomic Science |
|
Project title |
From Structure to Functions: Metagenomics-Enabled Predictive Understanding of Soil Microbial Feedbacks to Climate Change |
|
Total award amount |
$2,069,549 for OU for three years (A total of $3,595,722) |
|
Role and responsibility |
Co-PI with Jizhong Zhou (PI) et al. at the University of Oklahoma for metagenomic analysis (e.g., GeoChip, high throughput sequencing) of soil microbial communities from Oklahoma and Alaska experimental warming sites |
|
Period covered |
9/1/2013 - 8/31/2016 |
|
Effort |
10% (annual) |
|
Location of research |
The University of Oklahoma |
|
Status
|
Completed
|
|
Supporting agency |
DOE Genomic Science |
|
Project title |
Mapping soil carbon from cradle to grave: drafting a molecular blueprint for carbon transformation from roots to stabilized soil organic carbon |
|
Total award amount |
$600,000 for three years |
|
Role and responsibility |
Co-PI with Mary Firestone (PI) at the University of California, Berkeley for metagenomic analysis (e.g., GeoChip, high throughput sequencing) of soil microbial communities, and development of bioinformatics tools for KBase |
|
Period covered |
9/1/2013 - 8/31/2016 |
|
Effort |
5% (annual) |
|
Location of research |
The University of Oklahoma |
|
Status |
Completed
|
|
Supporting agency |
NSF Macrosystems Biology |
|
Project title |
Experimental Macroecology: effects of temperature on biodiversity |
|
Total award amount |
$1,491,192 for the first two year (A total of $2,799,999 for four years) |
|
Role and responsibility |
Co-PI with James Brown (PI) at the University of New Mexico for metagenomic analysis (e.g., GeoChip, pyrosequencing, metagenome sequencing) of microbial communities from six forest ecosystems distributed along a geographic gradient of increasing temperature from cold temperate to warm tropical regions |
|
Period covered |
8/1/2011 - 7/31/2016 |
|
Effort |
5% (annual) |
|
Location of research |
The University of Oklahoma |
|
Status |
Completed
|
|
Supporting agency |
Oklahoma State (OCAST OARS Program) |
|
Project title |
HuMiChip to Detect and Characterize the Human Microbiome |
|
Total award amount |
$293,017 for three years |
|
Role and responsibility |
PI with Co-PI Jizhong Zhou at the University of Oklahoma for development of a microarray-based technology human microbiome chip (HuMuChip) design, construction, data analysis, and evaluation as well as commercialization |
|
Period covered |
02/1/2011-01/31/2014 |
|
Effort |
10% (annual) |
|
Location of research |
The University of Oklahoma |
|
Status |
Completed |
|
Supporting agency |
US DOE (GTL:Genomics Program) |
|
|
From Community Structure to Functions: Metagenomics-Enabled Predictive Understanding of Temperature Sensitivity of Soil Carbon Decomposition to Climate Warming |
|
Total award amount |
$1,998,713 for first two years (A total of $2,998,405 for three years) |
|
Role and responsibility |
Co-PI with PI Jizhong Zhou at the University of Oklahoma for GeoChip analysis, metagenome sequencing, pyrosequencing of targeted gene, and analysis of functional processes |
|
Period covered |
7/15/2010-7/14/2013 |
|
Effort |
5% (annual) |
|
Location of research |
The University of Oklahoma |
|
Status |
Completed |
|
|
|
Supporting agency |
US DOE (ERSP Program) |
|
Project title |
Tractable Controls on Microbial Community Trajectories: Phylogeny and Function Underlying Subsurface Metal Remediation |
|
Total award amount |
$195,300 extended to four years |
|
Role and responsibility |
Co-PI with PI Mary Firestone at University of California, Berkeley for GeoChip analysis |
|
Period covered |
6/1/2008 - 8/31/2013 |
|
Effort |
5% (annual) |
|
Location of research |
The University of Oklahoma |
|
Status |
Completed |
|
|
|
Supporting agency |
US DOE (Genomics:GTL Program) |
|
Project title |
Rapid Deduction of Stress Response Pathways in Metal and Radionuclide Reducing Bacteria Phase 2: Molecular Determinants of Community Activity, Stability and Ecology (MDCASE) (ESPP 2) |
|
Total award amount |
$2,920,251 for four years |
|
Role and responsibility |
Co-PI with PIs Adam Arkin and Terry Hazen at the Lawrence Berkeley National Laboratory for stress responses of sulfate-reducing bacteria, GeoChip analysis of microbial communities related to sulfate reduction, metal reduction, and organic contaminant degradation |
|
Period covered |
6/5/2011 - 9/30/2014 |
|
Effort |
15% (annual) |
|
Location of research |
The University of Oklahoma |
|
Status |
Completed |
|
|
|
Supporting agency |
NSF (EPSCoR Program) |
|
Project title |
Oklahoma EPSCoR Research Infrastructure Improvement Plan - Building Oklahoma’s Leadership Role in Cellulosic Bioenergy |
|
Total award amount |
$513,996 for the first two years (A total of $2,116,524 for five years) |
|
Role and responsibility |
Co-PI with the PI Ray Huhnke at Oklahoma State University for microbial conversion of biomass to biofuels with mixed cultures: establishment and characterization of microbial consortia with high yield ethanol |
|
Period covered |
9/1/2008-8/31/2013 |
|
Effort |
5% (annual) |
|
Location of research |
The University of Oklahoma |
|
Status |
Completed |
|
Supporting agency |
US DOE (NABIR Program) |
|
Project title |
Identification of Molecular and Cellular Responses of Desulfovibrio vulgaris Biofilms under Culture Conditions Relevant to Field Conditions for Bioreduction of Heavy Metals |
|
Total award amount |
$1,241,000 for three years |
|
Role and responsibility |
Co-PI with PI Matthew Fields at Miami University for Desulfovibrio vulgaris microarray construction and associated analyses of gene expression under different conditions |
|
Period covered |
1/1/2006-12/31/2008 |
|
Effort |
10% (annual) |
|
Location of research |
The University of Oklahoma |
|
Status |
Completed |
|
Supporting agency |
Oklahoma State (OCAST/OARS Program) |
|
Project title |
Development of Comprehensive Functional Gene Arrays for Microbial Community Analysis |
|
Total award amount |
$299,519 for three years |
|
Role and responsibility |
PI with Co-PI Jizhong Zhou at University of Oklahoma for probe design software development, GeoChip design, and development of GeoChip analysis pipeline including databases |
|
Period covered |
10/1/2006-9/30/2009 |
|
Effort |
10% (annual) |
|
Location of research |
The University of Oklahoma |
|
Status |
Completed |
|
Supporting agency |
US DOE (Genomics:GTL Program) |
|
Project title |
Integrated Genome-Based Studies of Shewanella Ecophysiology |
|
Total award amount |
$1, 004, 000 for five years |
|
Role and responsibility |
Co-PI with Jim Fredrickson at Pacific Northwest National Laboratory for study of Shewanella species in terms of gene function, regulation and network and their ecophysiology |
|
Period covered |
4/1/2007 – 3/31/2012 |
|
Effort |
10% (annual) |
|
Location of research |
The University of Oklahoma |
|
Status |
Completed |
|
Supporting agency |
NSF-USDA (MO Program) |
|
Project title |
A Genomics-enabled FACE Microbial Observatory: Changes in Microbial Diversity and Functions in responding to elevated CO2, Nitrogen Deposition and Plant Diversity |
|
Total award amount |
$859,630 for five years |
|
Role and responsibility |
Co-PI with PI Jizhong Zhou at the University of Oklahoma for phylogenetic and functional diversity of soil microbial communities in a grassland, effects of elevated CO2, nitrogen deposition, and plant diversity on soil microbial communities using GeoChip, pyrosequencing, PLFA and other approaches |
|
Period covered |
9/15/2007 - 9/14/2012 |
|
Effort |
15% (annual) |
|
Location of research |
The University of Oklahoma |
|
Status |
Completed |
|
Supporting agency |
US DOE (ERSP program) |
|
Project title |
Metagenomics-Enabled Understanding of the Functions and Activities of Microbial Communities at ERSP Field Research Center at Oak Ridge, TN |
|
Total award amount |
$748,387.00 for four years |
|
Role and responsibility |
Co-PI with PI James Tiedje at Michigan State University for GeoChip update, and analysis of underground water samples from the Oak Ridge FRC site using updated GeoChip |
|
Period covered |
3/15/2007-3/14/2011 |
|
Effort |
10% (annual) |
|
Location of research |
The University of Oklahoma |
|
Status |
Completed |
|
Supporting agency |
Oklahoma State (Oklahoma Bioenergy Center) |
|
Project title |
Genomics-Enabled Understanding of Microbial Interactions and Regulatory Networks of Microbial Consortia for Efficient Cellulosic Ethanol Production |
|
Total award amount |
$697,410 for four years |
|
Role and responsibility |
PI with Co-PIs Michael McInerney, Christopher Hemme, and Jizhong Zhou at the University of Oklahoma for construction and analysis of interactions and regulatory networks of microbial consortia for ethanol production |
|
Period covered |
1/1/2008 - 12/31/2010 |
|
Effort |
5% (annual) |
|
Location of research |
The University of Oklahoma |
|
Status |
Completed |
|
Supporting agency |
Oklahoma State (Oklahoma Bioenergy Center) |
|
Project title |
Genomics-Enabled Understanding of Microbial Interactions and Regulatory Networks of Microbial Consortia for Efficient Cellulosic Ethanol Production (Renewed) |
|
Total award amount |
$215,402 for two and half years |
|
Role and responsibility |
PI with Co-PIs Michael McInerney, Christopher Hemme, and Jizhong Zhou at the University of Oklahoma for construction and analysis of interactions and regulatory networks of microbial consortia for ethanol production |
|
Period covered |
01/01/2010 - 12/31/2012 |
|
Effort |
5% (annual) |
|
Location of research |
The University of Oklahoma |
|
Status |
Completed |
|
Supporting agency |
Oklahoma State (Oklahoma Bioenergy Center) |
|
Project title |
Isolation and characterization of novel microbial catalysts for direct fermentation of lignocellulose to ethanol |
|
Total award amount |
$294,089 for two years |
|
Role and responsibility |
Co-PI with PI Jizhong Zhou at the University of Oklahoma for functional characterization and performance improvements of a novel fungus for ethanol production |
|
Period covered |
1/1/2008 - 12/31/2009 |
|
Effort |
5% (annual) |
|
Location of research |
The University of Oklahoma |
|
Status |
Completed |
|
Supporting agency |
Oklahoma State (Oklahoma Bioenergy Center) |
|
Project title |
Improvement of the Performance of Novel Microbial Catalysts for Direct Fermentation of Lignocellulose to Ethanol (renewed) |
|
Total award amount |
$221,611 for two and half years |
|
Role and responsibility |
Co-PI with PI Jizhong Zhou at the University of Oklahoma for functional characterization and performance improvements of a novel fungus for ethanol production |
|
Period covered |
7/1/2010 - 12/31/2011 |
|
Effort |
5% (annual) |
|
Location of research |
The University of Oklahoma |
|
Status |
Completed |
|
Supporting agency |
Oklahoma State (Oklahoma Bioenergy Center) |
|
Project title |
Linking community structure to function: Metagenomic analysis of feedstock-related microbial communities |
|
Total award amount |
$761,982 for two years |
|
Role and responsibility |
Co-PI with PI Liyou Wu for development and applications of GeoChip for analysis of soil microbial communities |
|
Period covered |
1/1/2008 - 12/31/2009 |
|
Effort |
5% (annual) |
|
Location of research |
The University of Oklahoma |
|
Status |
Completed |
|
Supporting agency |
Oklahoma State (Oklahoma Bioenergy Center) |
|
Project title |
Systems-Level Understanding of Factors Controlling Feedstock Productivity and Sustainability (Renewed) |
|
Total award amount |
$250,000 for two and half years |
|
Role and responsibility |
Co-PI with PI Liyou Wu for development and applications of GeoChip for analysis of soil microbial communities |
|
Period covered |
7/1/2009 - 12/31/2011 |
|
Effort |
5% (annual) |
|
Location of research |
The University of Oklahoma |
|
Status |
Completed |
|
Supporting agency |
ConocoPhillips |
|
Project title |
Extending Knowledge of Anaerobic Hydrocarbon Metabolism: Linking Metabolism, Functional Gene Molecular Markers and the GeoChip |
|
Total award amount |
$999,299 for three years |
|
Role and responsibility |
Co-PI with the PI Joseph Suflita at the University of Oklahoma for GeoChip development for oil fields and associated analysis |
|
Period covered |
7/1/2008 - 12/31/2010 |
|
Effort |
5% (annual) |
|
Location of research |
The University of Oklahoma |
|
Status |
Completed |
|
Supporting agency |
US DOE (STTR Phase I Program) |
|
Project title |
MSB: Development of Novel Random Network Theory-Based Approaches to Identify Network Interactions in Microbial Communities Among Nitrifying Bacteria |
|
Total award amount |
$48,251 for nine months |
|
Role and responsibility |
PI with Glomics Inc. for examination of the diversity of nitrifying bacteria by pyrosequencing of amoA genes in soil microbial communities |
|
Period covered |
6/19/2010-03/18/2011 |
|
Effort |
5% (annual) |
|
Location of research |
The University of Oklahoma |
|
Status |
Completed |
|
Supporting agency |
US DOE (STTR Phase I Program) |
|
Project title |
Development of Microarrays-based Metagenomics Technology for Monitoring Sulfate-Reducing Bacteria in Subsurface Environments |
|
Total award amount |
$47,423 for nine months |
|
Role and responsibility |
Co-PI with Glomics Inc. for examination of the diversity of sulfate-reducing bacteria by pyrosequencing of dsrA/B genes in subsurface environments, construction and evaluation of the proposed functional gene array for SRB characterization |
|
Period covered |
6/19/2010-03/18/2011 |
|
Effort |
5% (annual) |
|
Location of research |
The University of Oklahoma |
|
Status |
Completed |