2022/3-至今 南方海洋科学与工程广东省实验室（珠海） 首席科学家

2017/3 -2022/2 中山大学 教授

2011/9 - 2017/2 美国俄克拉荷马大学 教授/研究员

2007/9 - 2011/8 美国俄克拉荷马大学 副教授/研究员

2005/10 - 2007/8 美国俄克拉荷马大学 助理教授/研究员

2003/2 - 2005/9 美国橡树岭国家实验室 博士后（课题组组长） 合作导师：周集中

1998/10 – 2002/12 圭尔夫大学，圭尔夫，安大略，加拿大 博士后

1997/12 – 1998/9 地球创新技术研究所，京都，日本 研究员

1989/8 – 1994/3 中国科学院上海植物生理研究所，上海，中国 初级研究员





Academic Refereeing Activities学术评审（时间倒序）

• 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

承担的科研项目

Fundings：

国家自然科学基金面上项目，31770539，使用合成反硝化菌群探索微生物生态系统稳定性机制2017/01-2020/12，62万元，在研，主持。



1.国家自然科学基金水圈微生物重大研究计划集成项目,96251306,典型海陆交汇关键带微生物驱动碳氮硫循环的机制与碳源汇效应集成研究,2023/01-2024/12,242.3万(主持课题)，在研

2.国家自然科学基金水圈微生物重大研究计划重点项目,91951207,河口红树林湿地甲烷厌氧氧化及其与碳氮硫循环的耦合机制,2020/01-2023/12,306万，在研,主持

3.国家自然科学基金面上项目，31770539，使用合成反硝化菌群探索微生物生态系统稳定性机制，2018/01-2021/12，62万，在研，主持

4.广东省财政配套科研经费，QR计划入选者省财政配套科研工作经费，2020/04-2022/12, 100万, 在研，主持

5.南方海洋科学与工程广东省实验室（珠海）自主项目，南海典型生态系统碳汇过程与碳指纹标识体系研发，2021/01-2023/12, 150万，在研，主持

6.南方海洋科学与工程广东省实验室（珠海）创新团队项目,海洋生命过程与生物资源利用, 2021/01-2021/12, 160万，在研，主持课题

7.南方海洋科学与工程广东省实验室（珠海）创新团队项目,海洋生命过程与生物资源利用, 2020/01-2020/12, 170万，已结题，主持课题

8.南方海洋科学与工程广东省实验室（珠海）创新团队项目,海洋生命过程与生物资源利用, 2019/01-2019/12, 110万，已结题，主持课题

9.中山大学十三五优先发展领域专项，红树林微生物多样性形成、维持和丧失机制及其与生态系统功能的关系， 2017/07-2019/07, 100万, 已结题，主持

10.国家自然科学基金-广东联合重点基金，U1301235，大型海藻龙须菜栽培生态系统结构功能与关键生物地球化学过程，2014/01-2017/12，270万元，已结题，参加

2023

1. Feng J, Zhang T, Yan W, Sun J, Tian S, He Z* and Xiong Y*. 2023. Piezocatalytic activities of SnO2 /t-BaTiO3 film towards pollutant degradation: Understanding the performance of piezo-current response. Separation and Purification Technology 307: 122834.

2. Wang B, Ma B, Stirling E, He Z, Zhang H and Yan Q. 2023. Freshwater trophic status mediates microbial community assembly and interdomain network complexity. Environ Pollu 316: 120690.



2022

3. He Z*, Lin L, Wang X, Qin W and Zhang C. 2022. Editorial: Carbon storage by marine microorganisms for carbon neutrality. Front Mar Sci 9: 1018397 (doi: 10.3389/fmars.2022.1018397).

4. Yang X, Yu X, He Q, Deng T, Guan X, Lian Y, Xu K, Shu L, Wang C, Yan Q, Yang Y, Wu B* and He Z*. 2022. Niche diferentiation among comammox (Nitrospira inopinata) and other metabolically distinct nitrifiers. Front Microbiol 13: 956860 (DOI: 10.3389/fmicb.2022.956860).

5. Zeng J, Tu Q, Yu X, Qian L, Wang C, Shu L, Liu F, Liu S, Huang Z, He J, Yan Q*, and He Z*. 2022. PCycDB: a comprehensive and accurate database for fast analysis of phosphorus cycling genes. Microbiome (in press, *corresponding author).

6. Qian L, Yu X, Zhou J, Gu H, Ding J, Peng Y, He Q, Tian Y, Liu J, Wang S, Wang C, Shu L, Yan Q, Liu G*, Tu Q* and He Z*. 2022. MCycDB: a curated database for comprehensively profiling methane cycling processes of environmental microbiomes. Mol Ecol Resour (DOI: 10.1111/1755-0998.13589).

7. Zhang S, He Zz, Wu C, Wang Z, Mai Y, Hu R, Zhang X, Huang W, Tian Y, Xia D, Wang C, Yan Q, He Z* and Shu L*. 2022. Complex bilateral interactions determine the fate of polystyrene micro- and nano-plastics and soil protists: implications from a soil amoeba. Environ Sci Technol (DOI: 10.1021/acs.est.1c06178, in press).

8. Yu H, Zhong Q, Peng Y, Zheng X, Xiao F, Wu B, Yu X, Luo Z, Shu L, Wang C, Yan Q* and He Z*. 2022. Environmental filtering by pH and salinity jointly drives prokaryotic community assembly in coastal wetland sediments. Front Mar Sci 8: 792294 (DOI: 10.3389/fmars.2021.792294).

9. Liang Z, Abdillah A, Fang W, Qiu R, Mai B, He Z, Juneau P, Gomes MP, Priadi CR, Wang S. 2022. Unique microbiome in organic matter–polluted urban rivers. Glob Change Biol (DOI: 10.1111/gcb.16472).

10. Hu R, Liu S, Huang W, Nan Q, Strong PJ, Saleem M, Zhou Z, Luo Z, Shu F, Yan Q, He Z and Wang C. 2022. Evidence for Assimilatory Nitrate Reduction as a Previously Overlooked Pathway of Reactive Nitrogen Transformation in Estuarine Suspended Particulate Matter. Environ Sci Technol 56: 14852-14866 (DOI: 10.1021/acs.est.2c04390).

11. Hu R, Liu S, Saleem M, Xiong Z, Zhou Z, Luo Z, Shu L, He Z and Wang C. 2022. Environmentally induced reconstruction of microbial communities alters particulate carbon flux of deep chlorophyll maxima in the South China sea. Func Ecol (DOI: 10.1111/1365-2435.14154).

12. Zhang C，Shi T, Liu J, He Z, Thomas H, Dong H, Rinkevich B, Wang Y, Hyun J-H, Weinbauer M, López-Abbatek C, Tu Q, Xie S, Yamashita Y, Tishchenko P, Chen Q, Zhang R and Jiao N. 2022. Eco-engineering approaches for ocean negative carbon emission. Sci Bull (https://doi.org/10.1016/j.scib.2022.11.016).

13. Wu Y, Zhang Y, Yang X, Li K, Mai B, He Z and Wu R. 2022. Deterministic processes shape bacterial community assembly in a karst river across dry and wet seasons. Front Microbiol 13 (DOI: 10.3389/fmicb.2022.938490).

14. Yu H, Yan X, Weng W, Xu S, Xu G, Gu T, Guan X, Liu S, Chen P, Wu Y, Xiao F, Wang C, Shu L, Wu B, Qiu D, He Z and Yan Q. 2022. Extracellular proteins of Desulfovibrio vulgaris as adsorbents and redox shuttles promote biomineralization of antimony. J Hazard Mat 426: 127795 (DOI: 10.1016/j.jhazmat.2021.127795).

15. Zhang M, Dai Y, Dai P, Sun Z, Lin X, He Z and Tian Y. 2022. Finding the pieces for the anaerobic methane oxidation jigsaw puzzle in mangrove wetlands. Intl Biodeterior Biodegrad 168: 105375 (DOI: 10.1016/j.ibiod.2022.105375).

16. Wu B, Zhou L, Liu S, Liu F, Saleem M, Han X, Shu L, Yu X, Hu R, He Z, and Wang C. 2022. Biogeography of soil protistan consumer and parasite is contrasting and linked to microbial nutrient mineralization in forest soils at a wide-scale. Soil Biol Biochem 165: 108513 (DOI: 10.1016/j.soilbio.2021.108513).

17. Chen P, Huang J, Rao L, Zhu W, Yu Y, Xiao F, Yu H, Wu Y, Hu R, Liu X, He Z, and Yan Q. 2022. Environmental effects of nanoparticles on the ecological succession of gut microbiota across zebrafish development. Sci Tot Environ 806: 150963 (DOI: 10.1016/j.scitotenv.2021.150963).

18. Fang W, Lin M, Shi J, Liang Z, Tu X, He Z, Qiu R and Wang S. 2022. Organic carbon and eukaryotic predation synergistically change resistance and resilience of aquatic microbial communities. Sci Tot Environ 830: 154386 (DOI: 10.1016/j.scitotenv.2022.154386).

19. Liu S, Yu H, Yu Y, Huang J, Zhou Z, Zeng J, Chen P, Xiao F, He Z and Yan Q. 2022. Ecological stability of microbial communities in Lake Donghu regulated by keystone taxa. Ecol Indi 136: 108695 (DOI: 10.1016/j.ecolind.2022.108695).

20. Wei Z, Shen W, Feng K, Feng Y, He Z, Li Y, Jiang C, Liu S, Zhu Y, Deng Y. 2022. Organic fertilizer potentiates the transfer of typical antibiotic resistance gene among special bacterial species. J Hazard Mat 435: 128985 (DOI: 10.1016/j.jhazmat.2022.128985).

21. Xuan Y, Mai Y, Xu Y, Zheng J, He Z, Shu L, and Cao Y. 2022. Enhanced microbial nitrification-denitrification processes in a subtropical metropolitan river network. Water Res 222: 118857 (DOI: /10.1016/j.watres.2022.118857).

22. Ye S, Li Y, Huang H, Xu Y, Du S, Wan F, Xie R, Huang P, Liu B, Dong T, He Z, Leung DYC. 2022. Fast and deep disinfection for face masks recycle using vacuum ultraviolet irradiation. J Clean Prod (in press, doi: 10.1016/j.jclepro.2022.133221).

23. Zhang D, Li M, Yang Y, Yu H, Xiao F, Mao C, Huang J, Yu Y, Wang Y, Wu B, Wang C, Shu L, He Z and Yan Q. 2022. Nitrite and nitrate reduction drive sediment microbial nitrogen cycling in a eutrophic lake. Water Res 220: 118637 (DOI: 10.1016/j.watres.2022.118637).

24. 丁吉娟, 刘飞, 顾航, 于晓莉，贺志理*. 2022. 甲烷代谢古菌分离培养研究进展. 微生物学通报 (DOI:10.13344/j.microbiol.china.210895).



2021

25. 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. (*corresponding author).

26. 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 Pollu 274:  116508.

27. Zhao L, Xu K, Juneau P, Huang P, Lian Y, Zheng X, Zhong Q, Zhang W, Xiao F, Wu B, Yan Q and He Z*. 2021. Light modulates the effect of antibiotic norfloxacin on photosynthetic processes of Microcystis aeruginosa. Aqua Toxicol 235: 105826 (DOI: 10.1016/j.aquatox.2021.105826).

28. Huang Z*, Hou D, Zhou R, Zeng S,Xing C, Wei D, Deng X, Yu L, Wang H,Deng Z, Weng S, Ning D, Xiao C,Yan Q, Zhou J, He Z* and He J*. 2021. Environmental water and sediment microbial communities shape intestine microbiota for host health: the central dogma in an anthropogenic aquaculture ecosystem. Front Microbiol 12: 772149 (DOI: 10.3389/fmicb.2021.772149).

29. Luo Z, Zhong Q, Han X, Hu R, Liu X, Xu W, Wu Y, Huang W, Zhou Z, Zhuang W, Yan Q, He Z, and Wang C. 2021. Depth-dependent variability of biological nitrogen fixation and diazotrophic communities in mangrove sediments. Microbiome 9: 212.

30. Shu L, He ZZ, Guan X, Yang X, Tian Y, Zhang S, Wu C, He Z, Yan Q, Wang C, Shi Y. 2021. A dormant amoeba species can selectively sense and predate on different soil bacteria. Func Ecol 35 (DOI: 10.1111/1365-2435.13824).

31. Wang C, Hu R, Strong P, Zheng W, Huang W, Luo Z, Yan Q, He Z, Shu L. 20201. Prevalence of antibiotic resistance genes and bacterial pathogens along the soil–mangrove root continuum. J Hazard Mat 408: 124985.

32. 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.

33. 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.

34. 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.

35. 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.

36. 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.

37. Hu R, Zhao H, Xu X, Wang Z, Yu K, Shu L, Yan Q, Wu B, Mo C, He Z and Wang C. 2021. Bacteria-driven phthalic acid ester biodegradation: Current status and emerging opportunities. Environ Intl 154: 106560 (DOI: 10.1016/j.envint.2021.106560).

38. 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.

39. Yu H, Liu X, Yang C, Peng Y, Yu X, Gu H, Zheng X, Wang C, Xiao F, Shu L, He Z, Wu B and Yan Q. 2021. Co-symbiosis of arbuscular mycorrhizal fungi (AMF) and diazotrophs promote biological nitrogen fixation in mangrove ecosystems. Soil Biol Biochem 161: 108382 (DOI: 10.1016/j.soilbio.2021.108382).

40. Wang B, Zheng X, Zhang H, Yu X, Lian Y, Yang X, Yu H, Hu R, He Z, Xiao F and Yan Q. 2021. Metagenomic insights into the effects of submerged plants on functional potential of microbial communities in wetland sediments. Marine Life Sci Technol (DOI: 10.1007/s42995-021-00100-3).

41. Liang Y, Lu Q, Liang Z, Liu X, Fang W, Liang D, Kuang J, Qiu R, He Z and Wang S. 2021. Substrate-dependent competition and cooperation relationships between Geobacter and Dehalococcoides for their organohalide respiration. ISME Commun 1:23 (DOI: 10.1038/s43705-021-00025-z).

42. 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.

43. Lu Q, Liang Y, Fang W, Guan K, Huang C, Liang Z, Qi X, Zeng Y, Luo X, Mai B, He Z and Wang S. 2021. Spatial Distribution, Bioconversion and Ecological Risk of PCBs and PBDEs in the Surface Sediment of Contaminated Urban Rivers: A Nationwide Study. Environ Sci Technol 55: 9579–9590 (DOI: 10.1021/acs.est.1c01095).

44. 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).

45. Li J, Xie T, Zhu H, Zhou J, Li C, Xiong W, Xu L, Wu Y, He Z and Li X. 2021. Alkaline phosphatase activity mediates soil organic phosphorus mineralization in a subalpine forest ecosystem. Geoderma 404: 115376.

46. Zhou J, Yu X, Liu J, Qin W, He Z, Stahl D, Jiao N, Zhou J, Tu Q. 2021. VB12 Path for accurate metagenomic profiling of microbially driven cobalamin synthesis pathways. mSystems 6: e00497-21 (DOI: 10.1128/mSystems.00497-21).

47. Sun J, Lin Z, Ning D, Wang H, Zhang Z, He Z and Zhou J. 2021. Functional microbial community structures and chemical properties indicated mechanisms and potential risks of urban river eco-remediation. Sci Tot Environ 803: 149868.

48. Yu H, Deng Y, He Z, Pendall E, Carrillo Y, Wang S, Jin D, Wu L, Wang A, Xu Y, Liu B, Tai X and Zhou J. Stimulation of soil microbial functioning by elevated CO2 may surpass effects mediated by irrigation in a semiarid grassland. Geoderma 401: 115162 (DOI: 10.1016/j.geoderma.2021.115162).

49. Wang B, Stirling E, He Z, Ma B, Zhang H, Zheng X, Xiao F and Yan Q. Pollution alters methanogenic and methanotrophic communities and increases dissolved methane in small ponds. Sci Tot Environ 801: 149723 (DOI: 10.1016/j.scitotenv.2021.149723).

50. 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).

51. 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 (DOI: 10.1016/j.jhazmat.2020. 124385).

52. Shen R, Yu L, Xu P, Liang Z, Lu Q, Liang D, He Z, and Wang S. 2021. Water content as a primary parameter determines microbial reductive dechlorination activities in soil. Chemosphere 267: 3 (DOI: 10.1016/j.chemosphere.2020.1291).

53. 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. 2021. Microbially-driven sulfur cycling microbial communities in different mangrove sediments. Chemosphere (DOI: 10.1016/j.chemosphere.2020.128597).

54. Chen P, Huang J, Rao L, Zhu W, Yu Y, Xiao F, Chen X, Yu H, Wu Y, Xu K, Zheng X, Hu R, He Z, and Yan Q. 2021. Resistance and resilience of fish gut microbiota to silver. mSystems (DOI: 10.1128/mSystems.00630-21).

55. Zhou Z, Hu R, Ni Y, Zhuang W, Luo Z, Huang W, Yan Q, He Z, Zhong Q, and Wang C. 2021. Genetic elucidation of quorum sensing and cobamide biosynthesis in divergent bacterial-fungal associations across the soil-mangrove root interface. Front Microbiol (DOI: 10.3389/fmicb.2021.698385).

56. 赵立斌，徐魁*，连英丽，颜庆云，贺志理*. 2021. 原绿球藻对环境胁迫的生理和分子响应机制. 微生物学报 61: 1143-1159.

57. 焦念志，刘纪化, 石拓, 张传伦, 张永雨, 郑强, 陈泉睿, 汤凯, 王誉泽, 董海良, 唐剑武, 叶思源, 董双林, 高坤山, 张继红, 薛强, 李琦, 贺志理, 屠奇超, 王法明, 黄小平, 白雁, 潘德炉. 2021. 实施海洋负排放践行碳中和战略. 中国科学: 地球科学 51: 1–14 (doi: 10.1360/SSTe-2020-0358).

58. 杨宇峰，罗洪添，王庆，贺志理，龙爱民. 2021.大型海藻规模栽培是增加海洋碳汇和解决近海环境问题的有效方法. 中国科学院院刊 36: 259-269 (DOI：10.16418/j.issn.1000-3045.20210217103).



2020

59. 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).

60. 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).

61. 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).

62. 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).

63. 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.

64. 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).

65. 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).

66. 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).

67. 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).

68. 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).

69. 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).

70. 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).

71. 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).

72. 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).

73. 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).

74. 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).

75. 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).

76. 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).

77. 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).

78. 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).

79. 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).

80. 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.

81. 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).

82. 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).

83. 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).

84. 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).

85. 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).

86. 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).

87. 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).

88. 方安琪，贺志理，王成，杨超，颜庆云. 2020. 红树林沉积物中微生物驱动硫循环研究进展. 微生物学报 60: 1-13.

89. 邓婷，关晓彤，吴波*，贺志理*. 2020. 数学模型在合成微生物群落构建中的应用.应用与环境生物学报 (Doi: 10.19675/j.cnki.1006-687x.2020.01009).



2019

90. 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.

91. 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).

92. 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).

93. 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.

94. 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.

95. 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).

96. 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.

97. 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).

98. 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.

99. 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.

100. 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.

101. 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).

102. 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).

103. 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).

104. 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).

105. 王彬浩,关晓彤,颜庆云,贺志理*. 2019. 含氟有机废水处理过程活性污泥微生物群落研究进展.微生物学通报46: 2020−2037 (“活性污泥主题刊”被邀综述).

106. 庄炜，杨雪琴，于晓莉，颜庆云，连英丽，王成，钟秋萍，贺志理*．2019. 微生物驱动的滨海湿地N2O产生及其机制研究进展．微生物学通报 (https://doi.org/10.13344/j.microbiol.china.190130).



2018

107. 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).

108. 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).

109. 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).

110. 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.

111. 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).

112. 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.

113. 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.

114. 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.

115. 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.

116. 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).

117. 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).

118. 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).

119. 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).

120. 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.

121. 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).

122. 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).

123. 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).

124. 杨雪琴，连英丽，颜庆云*，贺志理*. 2018. 滨海湿地生态系统微生物驱动的氮循环研究进展. 微生物学报 58: 1-16.

125. 顾航，肖凡书，贺志理，颜庆云*. 2018. 湿地微生物介导的甲烷排放机制. 微生物学报 58: 618-632.



2017

126. 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).

127. 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).

128. 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).

129. 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.

130. Hou D, Huang Z, Zen