Name

He Zhili

Gender

Male

Year of birth

1965

Titles

Professor, Ph.D.

Position/Group job

Once deputy director of the American Institute of Environmental Genomics, international authoritative expert in the field of environmental microbiology, editors of several authoritative international magazines

Research direction

Interdisciplinary research in Environmental Microbiology, Systems Microbiology and Bioinformatics

Recruiting doctoral subjects

Crop Cultivation and Farming System

Contact Email

Hezhili@mail.sysu.edu.cn

Resume

Professor, Lifelong Fellow of Department of Microbiology, University of Oklahoma, USA, Deputy Director, Institute of Environmental Genomics, Ph.D. in Botany, School of Biological Sciences, Australian National University. Currently special professor of Hunan Agricultural University and Sun Yat-sen University.

Science &Teaching

Research

Projects

Nearly 30 scientific research projects at all levels, including the National Natural Science Foundation, the National Natural Science Foundation of the United States and the Department of Energy of the United States.

Papers and Works

More than 250 papers on Environmental Microbiology and bioinformatics published, includingNature Climate Change,Nature Reviews Microbiology,Nature Communications, PNAS, Ecology Letters, The ISME Journal, Nucleic Acids Research, Global Change Biology, Environmental Microbiology, etc. References > 10,000 (Google Scholar), H index > 56. Major papers are listed as follows,

1. 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).

2. 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. Funct Ecol 32: 1867-1878 (DOI:10.1111/1365-2435.13091, *corresponding author).

3. 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 (doi:10.1128/AEM.01694-17, *corresponding author).

4. 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.

5. 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 (DOI: 10.1111/mec.14496).

6. 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 (DOI: 10.1128/AEM.02608-17, in press).

7. Tu Q, Lin L, Cheng L, Deng Y and He Z. 2018. NCycDB: a curated integrative database for fast and accurate metagenomic profiling of nitrogen cycling genes. Bioinformatics (DOI:10.1093/bioinformatics/bty741).

8. Chen S, Li B, Cai D, Hu S, Zhu A and He Z. 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 (DOI: 10.1101/337402).

9. 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 (DOI: 10.1111/1462-2920.14303).

10. 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).

11. 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).

12. 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).

13. 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).

14. 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 (DOI: 10.1038/s41396-017-0037-1, in press).

15. Xiao F, Bi Y, Li X, Huang J, Yu Y, Xie Z, Fang T, Cao X, He Z, Juneau P, and Yan Q. 2018. The Impact of Anthropogenic Disturbance on Bacterioplankton Communities During the Construction of Donghu Tunnel (Wuhan, China). Microb Ecol (in press, DOI: 10.1007/s0024).

16. 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).

17. 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).

18. 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).

19. 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).

20. 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).

21. 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).

22. 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.

23. 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).

24. 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).

25. 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.

26. 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).

27. 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.

28. 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.

29. 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).

30. 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).

31. 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.

32. 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).

33. 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).

34. 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.

35. 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.

36. 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.

37. 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.

38. 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).

39. 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.

40. 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).

41. 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).

42. 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).

43. 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).

44. 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).

45. 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).

46. 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).

47. 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).

48. 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).

49. 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.

50. 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).

51. 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).

52. 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.

53. 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.

54. 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).

55. 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).

56. 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.

57. 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).

58. 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).

59. 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).

60. 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).

61. 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).

62. 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.

63. 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).

64. 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).

65. 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).

66. 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).

67. 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.

68. 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)

69. 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.

70. 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).

71. 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).

72. 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.

73. 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).

74. 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).

75. 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).

76. 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).

77. 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).

78. 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).

79. 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.

80. 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).

81. 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).

82. 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).

83. 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).

84. 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.

85. 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).

86. 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).

87. 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.

88. 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.

89. 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.

90. 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.

91. He Z (Ed.) 2014. Microarrays: Current Technology, Innovation and Applications. Caister Academic Press, Norwich, (http://www.horizonpress.com/microarrays2).

92. 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).

93. Tu Q, He Z*, and Zhou J*. 2014. Strain/Species identification in metagenomes using genome-specific markers. Nucleic Acid Res 42: e67 (*corresponding author).

94. 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.

95. 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).

96. 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).

97. 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.

98. 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.

99. 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.

100. 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.

101. 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.

102. 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.

103. 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.

104. 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.

105. 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.

106. 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.

107. 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.

108. 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.

109. 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.

110. 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.

111. 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.

112. 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.

113. 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.

114. 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.

115. 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.

116. 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.

117. 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.

118. Deng Y and He Z. 2014. Microarray data analysis. In: Z. He (ed) Microarrays: Current Technology, Innovations and Applications. Caister Academic Press, Norwich, UK.

119. 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.

120. 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.

121. 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).

122. 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).

123. 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.

124. 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.

125. 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.

126. 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).

127. 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.

128. 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.

129. 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.

130. 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).

131. 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.

132. 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).

133. 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.

134. 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.

135. 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.

136. 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.

137. 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.

138. 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.

139. 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.

140. 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).

141. 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).

142. 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.

143. 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.

144. 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.

145. 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.

146. 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).

147. 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).

148. 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.

149. 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).

150. 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.

151. 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.

152. 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).

153. 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.

154. 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.

155. 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.

156. 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.

157. 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.

158. 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.

159. 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).

160. 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.

161. 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).

162. 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.

163. 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.

164. 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.

165. 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.

166. 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).

167. 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).

168. 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.

169. 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.

170. 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).

171. 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.

172. 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.

173. 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.

174. 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.

175. 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.

176. 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.

177. 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.

178. 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.

179. 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.

180. 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.

181. 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).

182. 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.

183. 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.

184. 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.

185. 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.

186. 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.

187. 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.

188. 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).

189. 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).

190. 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.

191. 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.

192. Zhou J, Deng Y, Luo F, He Z, Tu Q, and Zhi X. 2010. Functional molecular ecological networks. mBio 1: e00169-10.

193. 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.

194. 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.

195. 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.

196. 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.

197. 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.

198. 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.

199. 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.

200. 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.

201. 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.

202. 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.

203. 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.

204. 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).

205. 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).

206. 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.

207. 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.

208. 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.

209. 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.

210. 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.

211. 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.

212. 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.

213. 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.

214. 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).

215. 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.

216. 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.

217. 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).

218. 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).

219. 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.

220. 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).

221. 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.

222. 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.

223. 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.

224. 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.

225. 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.

226. 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.

227. 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.

228. Gentry TJ, Wickham JS, Schadt CW, He Z, and Zhou J. 2006. Microarray applications in microbial ecology research. Microb Ecol 52: 159-175.

229. 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.

230. 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.

231. 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.

232. 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.

233. 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.

234. 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.

235. 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).

236. 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.

237. 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.

238. 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.

239. 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.

240. Andrews TJ, von Caemmerer S, He Z, Hudson GS. 1998. Rubisco catalysis in vitro and in vivo. Photosynthesis: Mechanisms and Effects 5: 3307.

241. 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.

242. 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.

243. 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.

244. 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.

245. 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.

246. He Z, and Wang H. 1991. Emergence of salt-induced proteins in alfalfa under NaCl stress. Acta Phytophysiol Sinica 17: 71–79.