1. (New!) Xi Peng, Shang Wang, Miaoxiao Wang, Kai Feng, Qing He, Xingsheng Yang, Weiguo Hou, Fangru Li, Yuxiang Zhao, Baolan Hu, Xiao Zou, Ye Deng*. Metabolic interdependencies in thermophilic communities are revealed using co-occurrence and complementarity networks. Nature Communications, 2024, 15: 8166 Read More
  2. (New!) Xi Peng, Kai Feng*, Xingsheng Yang, Qing He, Bo Zhao, Tong Li, Shang Wang, Ye Deng*. iNAP 2.0: Harnessing metabolic complementarity in microbial network analysis. iMeta, 2024, 4: 235 Read More
  3. Xingsheng Yang, Kai Feng, Shang Wang, Mengting Maggie Yuan, Xi Peng, Qing He, Danrui Wang, Wenli Shen, Bo Zhao, Xiongfeng Du, Yingcheng Wang, Linlin Wang, Dong Cao, Wenzong Liu, Jianjun Wang, Ye Deng* . Unveiling the deterministic dynamics of microbial meta-metabolism: a multi-omics investigation of anaerobic biodegradation. Microbiome, 2024, 12: 166 Read More
  4. Kai Feng, Shang Wang, Qing He, Michael Bonkowski, Mohammad Bahram, Etienne Yergeau, Zhujun Wang, Xi Peng, Danrui Wang, Shuzhen Li, Yingcheng Wang, Zhicheng Ju, Xiongfeng Du, Chengliang Yan, Songsong Gu, Tong Li, Xingsheng Yang, Wenli Shen, Ziyan Wei, Qiulong Hu, Pengfei Li, Yanmei Zhu, Guangxin Lu, Clara Qin, Gengxin Zhang, Chunwang Xiao, Yunfeng Yang, Jizhong Zhou, Ye Deng*. CoBacFM: Core Bacteria Forecast Model for Global Grassland pH Dynamics under Future Climate Warming Scenarios. One Earth, 2024, 7(7): 1275-1287 Read More
  5. Tong Li, Kai Feng, Shang Wang, Xingsheng Yang, Xi Peng, Qichao Tu, Ye Deng*. Beyond Water and Soil: Air Emerges as a Major Reservoir of Human Pathogens. Environment International, 2024, 190: 108869 Read More
  6. Bo Zhao, Zhaojing Zhang, Kai Feng, Xi Peng, Danrui Wang, Weiwei Cai, Wenzong Liu, Aijie Wang, Ye Deng*. Inoculum source determines the stress resistance of electroactive functional taxa in biofilms: A metagenomic perspective. Science of the Total Environment, 2024, 945: 174018 Read More
  7. Yong-Chao Wang, Ya-Hui Lv, Can Wang*, Ye Deng*, Yu-Ting Lin, Guan-Yu Jiang, Xu-Rui Hu, John C Crittenden. Stochastic processes shape microbial community assembly in biofilters: Hidden role of rare taxa. Bioresource Technology, 2024, 402: 130838 Read More
  8. Shuping Wang#, Songsong Gu#, Yaqun Zhang, Ye Deng*, Wenhui Qiu, Qianhang Sun, Tianxu Zhang, Pengyuan Wang, Zhenguang Yan*. Microeukaryotic plankton community dynamics under ecological water replenishment:Insights from eDNA metabarcoding. Environmental Science and Ecotechnology, 2024, 20: 100409 Read More
  9. Jing Tian#*, Jennifer Dungait#*, Ruixing Hou#, Ye Deng#, Iain Hartley, Yunfeng Yang, Yakov Kuzyakov, Fusuo Zhang*, M. Francesca Cotrufo*, Jizhong Zhou*. Microbially mediated mechanisms underlie soil carbon accrual by conservation agriculture under decade-long warming. Nature Communications, 2024, 15: 377 Read More
  10. Yang Yu, Yong Zhou, Ivan Janssens, Ye Deng, Xiaojia He, Lingli Liu, Yin Yi, Nengwen Xiao, Xiaodong Wang, Chao Li, Chunwang Xiao. Divergent rhizosphere and non-rhizosphere soil microbial structure and function in long-term warmed steppe due to altered root exudation. Global Change Biology, 2024, 30(1): e17111 Read More
  11. Wei Wei, Jing Li, Boyu Tang, Ye Deng, Yan Li, Qianming Chen. Metabolomics and Metagenomics Reveal the Impact of γδ T Inhibition on Gut Microbiota and Metabolism in Periodontitis-Promoting OSCC. mSystems, 2024, DOI: 10.1128/msystems.00777-23 Read More
  12. Zheng Hao, Qianhong Wang, Jianjun Wang, Ye Deng, Zaisheng Yan, Linqi Tian, Helong Jiang. Water Level Fluctuations Modulate the Microbiomes Involved in Biogeochemical Cycling in Floodplains. Microbial Ecology, 2024, 87(1): 24 Read More
  13. Zhang Yang, Zhipeng Xiao, Lin Tan, Can Wang, Pengfei Li, Ye Deng, Huiya Xie, Shaolong Wu, Qiulong Hu. Interdomain ecological network analysis infers the endophytic bacteria protect against Fusarium root rot invasion. Plant Stress, 2024, 11: 100358 Read More
  14. Xingxing Zhang, Yiwei Wang, Pengbo Jiao, Ming Zhang, Ye Deng, Chengying Jiang, Xian-Wei Liu, Liping Lou, Yongmei Li, Xu-Xiang Zhang, Liping Ma*. Microbiome-functionality in Anaerobic Digesters: A Critical Review. Water Research, 2024, 249: 120891 Read More
  15. Linqi Tian, Ye Deng, Helong Jiang*. Comparing the benthic nitrogenase activity and diazotrophic community assembly of three large river-connected freshwater lakes in eastern China. Journal of Environmental Sciences, 2024, 150: 134-148 Read More
  16. Hao-Jie Huang, Xi Zhang, Xin-Wei Sun, Biao Chen, Xiu-Tong Li, Nan Zhou, Rashidin Abdugheni, Qiu-Yin Cheng, Tie-Jun Zhang, Yao Liu, Yong Jiang, Ye Deng, Shuang-Jiang Liu*, Cheng-Ying Jiang*. Xiashengella succiniciproducens gen. nov., sp. nov., a succinate-producing bacterium isolated from an anaerobic digestion tank in the family Marinilabiliaceae of the order Bacteroidales. Archives of Microbiology, 2024, 206: 141 Read More
  17. Xingyun Yi, Kristian Koefoed Brandt, Shudan Xue, Jingjing Peng, Yifei Wang, Meng Li, Ye Deng, Guilan Duan*. Niche differentiation and biogeography of Bathyarchaeia in paddy soil ecosystems: a case study in eastern China. Environmental Microbiome, 2024, 19: 13 Read More
  18. Zongrui Lai, Zhen Liu, Ye Deng, Wei Feng, Yuanyuan Zhao, Shugao Qin, Yanfei Sun*. Distinguishing the effects of micro- and macro-habitats on plant-associated microbiomes in the Qinghai-Tibetan Qaidam Basin. Land Degradation & Development, 2024, 35(10): 3344-3361 Read More
  19. Enzhao Wang, Bing Yu, Jiayin Zhang, Songsong Gu, Yunfeng Yang, Ye Deng, Xue Guo, Buqing Wei, Jingjing Bi, Miaomiao Sun, Huaqi Feng, Alin Song*, Fenliang Fan. Low Carbon Loss from Long-Term Manure-Applied Soil during Abrupt Warming Is Realized through Soil and Microbiome Interplay. Environmental Science & Technology, 2024, 58(22): 9658-9668 Read More
  20. Yunyun Gao, Kai Peng, Defeng Bai, Xiao-Ye Bai, Yujing Bi, Anqi Chen, Baodong Chen, Feng Chen, Juan Chen, Lei Chen, Tong Chen, Wei Chen, Xu Cheng, Yanfen Cheng, Jie Cui, Jingjing Dai, Junbiao Dai, Zhaolai Dai, Ye Deng, Yi-Zhen Deng, Wei Ding, Zhencheng Fang, Wei Fu, Hanbing Gao, Shaohua Gu, Xue Guo, Xuguang Guo, Dongfei Han, Lele He, Yatao He, Hui-Yu Hou, Baolei Jia, Gengjie Jia, Shuo Jiao, Wei Jin, Feng Ju, Zhicheng Ju, Siyuan Kong, Canhui Lan, Bing Li, Da Li, Diyan Li, Jingdi Li, Meng Li, Qi Li, Qiang Li, Wen-Jun Li, Xiaofang Li, Xuemeng Li, Yahui Li, You-Gui Li, Zhibin Liang, Ning Ling, Fufeng Liu, Qing Liu, Shuang-Jiang Liu, Hongye Lu, Qi Lu, Guangwen Luo, Hao Luo, Yuheng Luo, Hujie Lyu, Chuang Ma, Liyuan Ma, Tengfei Ma, Jinfeng Ni, Ziqin Pang, Xiaojing Qiang, Yuan Qin, Qingyue Qu, Chao Ran, Shuqiang Ren, Haitao Shang, Luyang Song, Linyang Sun, Weimin Sun, Liping Tang, Jian Tian, Kai Wang, Mengzhi Wang, Ming-Ke Wang, Tao Wang, Xiao-Yan Wang, Yao Wang, Yiwen Wang, Youshan Wang, Hailei Wei, Hong Wei, Zhong Wei, Tao Wen, Jiqiu Wu, Linhuan Wu, Linkun Wu, Jiao Xi, Bo Xie, Guofang Xu, Jun Xu, Shanshan Xu, Qing Xue, Liping Yan, Haifei Yang, Jun Yang, Junbo Yang, Ruifu Yang, Yalin Yang, Ying-Jie Yang, Xiaofang Yao, Yanpo Yao, Salsabeel Yousuf, Ke Yu, Zhengrong Yuan, Zhilin Yuan, Dong Zhang, Tianyuan Zhang, Weipeng Zhang, Yunzeng Zhang, Zhaonan Zhang, Zhen Zhang, Zhi-Feng Zhang, Shengguo Zhao, Wei Zhao, Maosheng Zheng, Ziqiang Zheng, Xin Zhou, Yuanping Zhou, Zhigang Zhou, Mo Zhu, Yong-Guan Zhu, Haiyan Chu*, Yang Bai*, Yong-Xin Liu*. The Microbiome Protocols eBook initiative: Building a bridge to microbiome research. iMeta, 2024, 3(2): e182 Read More
  21. Songsong Gu, Shaolong Wu, Weiai Zeng, Ye Deng, Gongwen Luo, Pengfei Li, Yishuai Yang, Zhengqiang Wang, Qiulong Hu*, Lin Tan*. High-elevation-induced decrease in soil pH weakens ecosystem multifunctionality by influencing soil microbiomes. Environmental Research, 2024, 257: 119330 Read More
  22. Juanjuan Xiao, Deying Wang, Banerjee Sinchan, Ryan Mushinski, Decai Jin, Ye Deng. Response patterns of the microbiome during hexavalent chromium remediation by Tagetes erecta L.. Science of the Total Environment, 2024, 935: 173413 Read More
  23. Xun Wang, Peifang Wang*, Ye Deng, Xiaolei Xing, Qiusheng Yuan, Chenggong Du, Jiawen Gan, Yuran Zheng, Yunxin Liu, Yufan Xia, Yuan Fang. Impacts of cascade hydropower development on river ecosystem homeostasis: A review. Journal of Hydrology, 2024, 638: 131484 Read More
  24. Zhenyan Zhang, Qi Zhang, Bingfeng Chen, Yitian Yu, Tingzhang Wang, Nuohan Xu, Xiaoji Fan, Josep Penuelas, Zhengwei Fu, Ye Deng, Yong-Guan Zhu, Haifeng Qian*. Global biogeography of microbes driving ocean ecological status under climate change. Nature Communications, 2024, 15: 4657 Read More
  25. Yunpeng Zhao, Chengzhu Liu, Enze Kang, Xingqi Li, Ye Deng, Xiaojuan Feng*. Plant–microbe interactions underpin contrasting enzymatic responses to wetland drainage. Nature Climate Change, 2024, https://doi.org/10.1038/s41558-024-02101-3 Read More
  26. Xuefeng Zhu, Kaikai Min, Kai Feng, Hongtu Xie, Hongbo He, Xudong Zhang, Ye Deng, Chao Liang . Microbial necromass contribution to soil carbon storage via community assembly processes. Science of the Total Environment, 2024, 951: 175749 Read More
  27. Ben Ma, Mengting Chu, Haihan Zhang*, Kaige Chen, Fengrui Li, Xiang Liu, Dmitry B. Kosolapov, Wei Zhi, Zhongbing Chen, Jun Yang, Ye Deng, Raju Sekark, Tao Liu, Xiaoyan Liu, Tinglin Huang. Mixotrophic aerobic denitrification facilitated by denitrifying bacterial-fungal communities assisted with iron in micro-polluted water: Performance, metabolic activity, functional genes abundance, and community co-occurrence. Journal of Hazardous Materials, 2024, 476: 135057 Read More
  28. Hao Yu, Qi Huang, Jianan Men, Jian Wang, Juanjuan Xiao, Decai Jin*, Ye Deng. Chromium contamination affects the fungal community and increases the complexity and stability of the network in long-term contaminated soils. Environmental Research, 2024, 262: 119946 Read More
  29. Zi-Yan Wei, Min Feng, Ding-Xi Zhang, Cheng-Ying Jiang, Ye Deng, Zhu-Jun Wang, Kai Feng, Yang Song, Nan Zhou, Yu-Lin Wang, Shuang-Jiang Liu*. Deep insights into the assembly mechanisms, co-occurrence patterns, and functional roles of microbial community in wastewater treatment plants. Environmental Research, 2024, 263: 120029 Read More
  30. Lingfang Ni, Jiaping Wu, Hongyue Dang, Carlos M. Duarte, Kai Feng, Ye Deng, Daoqiong Zheng, Dongdong Zhang*. Stand age-related effects of mangrove on archaeal methanogenesis in sediments: Community assembly and co-occurrence patterns. Science of the Total Environment, 2024, 954: 176596 Read More
  31. (New!) Hualiang Zhang, Dongsheng Guo, Yuting Lei, Jose L. Lozano-Torres, Ye Deng, Jianming Xu, Lingfei Hu*. Cover crop rotation suppresses root-knot nematode infection by shaping soil microbiota. New Phytologist, 2024, DOI: 10.1111/nph.20220 Read More
  32. 于皓, 刘琦, 邓晔*, 顾松松, 芦光新, 周学丽. 补播和施肥对高寒退化草地根际细菌群落的影响. 环境科学, 2024 in press Read More
  33. 王尚, 冯凯, 李瞳, 王洁, 顾松松, 杨兴盛, 李春格, 邓晔*. 环境病原微生物研究数据库及数据挖掘方法. 生物技术通报, 2024 in press Read More
  1. Danrui Wang, Jiangtao Li, Lei Su, Wenli Shen, Kai Feng, Xi Peng, Zhujun Wang, Bo Zhao, Zheng Zhang, Zhaojing Zhang, Étienne Yergeau, Ye Deng. Phylogenetic diversity of functional genes in deep-sea cold seeps: a novel perspective on metagenomics. Microbiome, 2023, 11: 276 Read More
  2. Songsong Gu, Xueli Zhou, Hao Yu*, Huilin Yan, Yingcheng Wang, Yue Liu, Zhihui Wang, Kai Feng, Xiongfeng Du, Guangxin Lu, Ye Deng*. Microbial and chemical fertilizers for restoring degraded alpine grassland. Biology and Fertility of Soils, 2023, 10.1007/s00374-023-01759-9 Read More
  3. Qing He, Shang Wang*, Kai Feng, Sean T Michaletz, Weiguo Hou, Wenhui Zhang, Fangru Li, Yidi Zhang, Danrui Wang, Xi Peng, Xingsheng Yang, Ye Deng*. High speciation rate of niche specialists in hot springs. The ISME Journal, 2023, doi.org/10.1038/s41396-023-01447-4 Read More
  4. Haijuan Zhang†, Kaifu Zheng†, Songsong Gu, Yingcheng Wang, Xueli Zhou, Huilin Yan, Kun Ma, Yangan Zhao, Xin Jin, Guangxin Lu*,  Ye Deng*. Grass–Legume Mixture with Rhizobium Inoculation Enhanced the Restoration Effects of Organic Fertilizer. Microorganisms, 2023, 11(5), 1114 Read More
  5. Zheng Zhang, Jiang Li*, Hongjun Li, Linlin Wang, Yuqi Zhou, Shuzhen Li, Zhaojing Zhang, Kai Feng, Ye Deng*. Environmental DNA metabarcoding reveals the influence of human activities on microeukaryotic plankton along the Chinese coastline. Water Research, 2023, 233: 119730 Read More
  6. Xiongfeng Du, SongSong Gu, Zheng Zhang, Shuzhen Li, Yuqi Zhou, Zhaojing Zhang, Qi Zhang, Linlin Wang, Zhicheng Ju, Chengliang Yan, Tong Li, Danrui Wang, Xingsheng Yang, Xi Peng, Ye Deng*. Spatial distribution patterns across multiple microbial taxonomic groups. Environmental Research, 2023, 223: 115470  Read More
  7. Huilin Yan†, Xueli Zhou†, Kaifu Zheng, Songsong Gu, Hao Yu, Kun Ma, Yangan Zhao, Yingcheng Wang,Hua Zheng, Hanjiang Liu, Dejun Shi, Guangxin Lu*, Ye Deng*. Response of Organic Fertilizer Application to Soil Microorganisms and Forage Biomass in Grass–Legume Mixtures. Agronomy, 2023, 13(2): 481 Read More
  8. Yingcheng Wang†, Ning Dang†, Kai Feng, Junbang Wang, Xin Jin, Shiting Yao, Linlin Wang, Songsong Gu, Hua Zheng, Guangxin Lu*, Ye Deng*. Grass-microbial inter-domain ecological networks associated with alpine grassland productivity. Frontiers in Microbiology, 2023, 14:1109128 Read More
  9. Linlin Wang, Mingliang Zhao, Xiongfeng Du, Kai Feng, Songsong Gu, Yuqi Zhou, Xingsheng Yang, Zhaojing Zhang, Yingcheng Wang, Zheng Zhang, Qi Zhang, Baohua Xie, Guangxuan Han, Ye Deng*. Fungi and cercozoa regulate methane-associated prokaryotes in wetland methane emissions. Frontiers in Microbiology, 2023, 13: 1076610, doi: 10.3389/fmicb.2022.1076610 Read More
  10. Lingzhan Miao, Wanyi Li, Tanveer M. Adyel, Yu Yao, Ye Deng*, Jun Wu, Yongqiang Zhou, Yue Yu, Jun Hou*. Spatio-temporal succession of microbial communities in plastisphere and their potentials for plastic degradation in freshwater ecosystems. Water Research, 2023, doi.org/10.1016/j.watres.2022.119406 Read More
  11. Mengyue Sun, Mingcong Li, Yuqi Zhou, Jiai Liu, Wenchong Shi, Xiaoliang Wu, Baohua Xie*, Ye Deng*, Zheng Gao*. Nitrogen deposition enhances the deterministic process of the prokaryotic community and increases the complexity of the microbial co-network in coastal wetlands. Science of the Total Environment, 2023, doi.org/10.1016/j.scitotenv.2022.158939 Read More
  12. Ke Shi, Bin Liang*, Kai Feng, Daliang Ning, Carolyn R. Cornell, Yanqing Zhang, Wenbin Xu, Min Zhou, Ye Deng, Jiandong Jiang, Tiejun Liu, Aijie Wang, Jizhong Zhou. Electrostimulation triggers an increase in cross-niche microbial associations toward enhancing organic nitrogen wastewater treatment. Journal of Environmental Management, 2023, 331: 117301 Read More
  13. Xiu-Tong Li, Zhong-Sheng Huang, Ye Huang, Zhen Jiang, Zong-Lin Liang, Hua-Qun Yin, Guang-Ji Zhang, Yan Jia, Ye Deng, Shuang-Jiang Liu*, Cheng-Ying Jiang*. Responses of microbial community to geochemical parameters on vertical depth in bioheap system of low-grade copper sulfide. Science of the Total Environment, 2023, 869: 161752 Read More
  14. Yi Sun, Hongjun Li*, Xiaocheng Wang, Hongbo Li, Ye Deng. Kelp culture enhances coastal biogeochemical cycles by maintaining bacterioplankton richness and regulating bacterioplankton interactions. mSystems, 2023, 10.1128/msystems.00002-23 Read More
  15. Shiting Dai, Qing He, Ziming Han, Wenli Shen, Ye Deng, Yang Wang, Wei Qiao, Min Yang, Yu Zhang*. Uncovering the diverse hosts of tigecycline resistance gene tet(X4) in anaerobic digestion systems treating swine manure by epicPCR. Water Research X, 2023, doi.org/10.1016/j.wroa.2023.100174 Read More
  16. Shiqing Nie, Zhongwang Jing, Jichen Wang, Ye Deng, Yingshuang Zhang, Zheng Ye* & Yuan Ge*. The link between increased Desulfovibrio and disease severity in Parkinson’s disease. Applied Microbiology and Biotechnology, 2023, 107, 3033–3045 Read More
  17. Lioba Rüger, Kai Feng, Yan Chen, Ruibo Sun, Bo Sun, Ye Deng, Doris Vetterlein, Michael Bonkowski*. Responses of root architecture and the rhizosphere microbiome assembly of maize (Zea mays L.) to a soil texture gradient. Soil Biology and Biochemistry, 2023, 10.1016/j.soilbio.2023.109026 Read More
  18. Lingyue Zhu, Yan Chen*, Ruibo Sun, Jiabao Zhang*, Lauren Hale, Kenneth Dumack, Stefan Geisen, Ye Deng, Yinghua Duan, Bo Zhu, Yan Li, Wenzhao Liu, Xiaoyue Wang, Bryan S. Griffiths, Michael Bonkowski, Jizhong Zhou, Bo Sun*. Resource-dependent biodiversity and potential multi-trophic interactions determine belowground functional trait stability. Microbiome, 2023, 11: 95 Read More
  19. Chunge Li*, Ye Deng, Jingguo Wang, Weibin Ruan, Shang Wang and Weidong Kong. Effects of p-Hydroxyphenylacetic Acid and p-Hydroxybenzoic Acid on Soil Bacterial and Fungal Communities. Sustainability, 2023, 15(12), 9285 Read More
  20. Yao Guo, Songsong Gu, Kaixuan Wu, Andrew J. Tanentzap, Junqi Yu, Xiangfen Liu, Qianzheng Li, Peng He, Dongru Qiu, Ye Deng, Pei Wang, Zhenbin Wu, Qiaohong Zhou. Temperature-mediated microbial carbon utilization in China’s lakes. Global Change Biology, 2023, doi.org/10.1111/gcb.16840 Read More
  21. Yuxiang Zhao, Zishu Liu, Baofeng Zhang, Jingjie Cai, Xiangwu Yao, Meng Zhang, Ye Deng, Baolan Hu*. Inter-bacterial mutualism promoted by public goods in a system characterized by deterministic temperature variation. Nature Communications, 2023, 14:5394 Read More
  22. Li Wang, Chunang Lian, Wenjie Wan, Zhiguang Qiu, Xuesong Luo, Qiaoyun Huang, Ye Deng, Tong Zhang, Ke Yu. Salinity-triggered homogeneous selection constrains the microbial function and stability in lakes. Applied Microbiology and Biotechnology, 2023, DOI: 10.1007/s00253-023-12696-w Read More
  23. Luyao Kang, Leiyi Chen, Ziliang Li, Jianjun Wang, Kai Xue, Ye Deng, Manuel Delgado-Baquerizo, Yutong Song, Dianye Zhang, Guibiao Yang, Wei Zhou, Xuning Liu, Futing Liu, Yuanhe Yang*. Patterns and drivers of prokaryotic communities in thermokarst lake water across Northern Hemisphere. Global Ecology and Biogeography, 2023, doi.org/10.1111/geb.13764 Read More
  24. Mikhail Semenov, Hui Li, Yu Luo, Ye Deng, Yakov Kuzyakov. Editorial: Microbial regulation of soil carbon cycling in terrestrial ecosystems. Frontiers in Microbiology, 2023, doi.org/10.3389/fmicb.2023.1295624 Read More
  25. Songsong Gu, Ye Deng, Pengyuan Wang, Chenhong Li, Dejun Shi, Shuping Wang*. Assessing riverine fish community diversity and stability by eDNA metabarcoding. Ecological Indicators, 2023, 157: 111222 Read More
  26. 于皓, 刘悦, 邓晔, 芦光新, 颜珲璘, 王英成. 天然高寒草地转变为混播人工草地对土壤微生物群落特征的影响. 环境科学, 2023, 44(5):2928-2935 Read More
  1. Zheng Zhang, Hongjun Li, Wenli Shen, Kai Feng, Shuzhen Li, Songsong Gu, Yuqi Zhou, Xi Peng, Xiongfeng Du, Qing He, Linlin Wang, Zhaojing Zhang, Danrui Wang, Zhujun Wang, Ye Deng*. The stability of phyto-zooplanktonic networks varied with zooplanktonic sizes in Chinese coastal ecosystem. mSystems, 2022, doi.org/10.1128/msystems.00821-22 Read More
  2. Zhujun Wang, Kai Feng, Ziyan Wei, Yueni Wu, Kazuo Isobe, Keishi Senoo, Xi Peng, Danrui Wang, Qing He, Xiongfeng Du, Shuzhen Li, Yan Li, Ye Deng*. Evaluation and redesign of the primers for detecting nitrogen cycling genes in environments. Methods in Ecology and Evolution, 2022, doi.org/10.1111/2041-210X.13946 Read More 
  3. Huilin Yan, Songsong Gu, Shuzhen Li, Wenli Shen, Xueli Zhou, Hao Yu, Kun Ma, Yangan Zhao, Yingcheng Wang, Hua Zheng, Ye Deng*, Guangxin Lu*. Grass-legume mixtures enhance forage production via the bacterial community. Agriculture Ecosystems & Environment, 2022, doi.org/10.1016/j.agee.2022.108087 Read More
  4. Lin Tan, Yansong Xiao, Wei-ai Zeng, Songsong Gu, Zhengguang Zhai, Shaolong Wu, Pengfei Li, Kai Feng, Ye Deng*, Qiulong Hu*, Network analysis reveals the root endophytic fungi associated with Fusarium root rot invasion. Applied Soil Ecology, 2022, doi.org/10.1016/j.apsoil.2022.104567 Read More
  5. Danrui Wang, Shang Wang, Xiongfeng Du, Qing He, Yue Liu, Zhujun Wang, Kai Feng, Yan Li, Ye Deng*. ddPCR surpasses classical qPCR technology in quantitating bacteria and fungi in the environment. Molecular Ecology Resources, 2022, doi.org/10.1111/1755-0998.13644 Read More
  6. Shuzhen Li, Wenli Shen, Shenyang Lian, Yueni Wu, Yuanyuan Qu, Ye Deng*. DARHD: a sequence database for aromatic ring-hydroxylating dioxygenase analysis and primer evaluation. Journal of Hazardous Materials, 2022, doi.org/10.1016/j.jhazmat.2022.129230 Read More
  7. Kun Ma, Yingcheng Wang, Xin Jin, Yangan Zhao, Huilin Yan, Haijuan Zhang, Xueli Zhou, Guangxin Lu*, Ye Deng*, Application of Organic Fertilizer Changes the Rhizosphere Microbial Communities of a Gramineous Grass on Qinghai-Tibet Plateau. Microorganisms, 2022, doi.org/10.3390/microorganisms10061148 Read More
  8. Xingsheng Yang, Zhaojing Zhang, Shuzhen Li, Qing He, Xi Peng, Xiongfeng Du, Kai Feng, Shang Wang*, Ye Deng*. Fungal dynamics and potential functions during anaerobic digestion of food waste. Environmental Research, 2022, doi.org/10.1016/j.envres.2022.113298 Read More
  9. Ziyan Wei, Wenli Shen, Kai Feng, Youzhi Feng, Zhili He, Yan Li, Chengying Jiang, Shuangjiang Liu, Yong-Guan Zhu, Ye Deng*. Organic fertilizer potentiates the transfer of typical antibiotic resistance gene among special bacterial species. Journal of Hazardous Materials, 2022, doi.org/10.1016/j.jhazmat.2022.128985 Read More
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  11. Zheng Zhang, Hongjun Li, Wenli Shen, Xiongfeng Du, Shuzhen Li, Ziyan Wei, Zhaojing Zhang, Kai Feng, Ye Deng*. The large-scale spatial patterns of ecological networks between phytoplankton and zooplankton in coastal marine ecosystems. Science of The Total Environment, 2022, doi.org/10.1016/j.scitotenv.2022.154285 Read More
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  19. Shanghua Wu, Yuzhu Dong, Ye Deng, Lijuan Cui, Xuliang Zhuang*. Protistan consumers and phototrophs are more sensitive than bacteria and fungi to pyrene exposure in soil. Science of The Total Environment, 2022, doi.org/10.1016/j.scitotenv.2022.153539 Read More
  20. Luyao Kang, Leiyi Chen, Dianye Zhang, Yunfeng Peng, Yutong Song, Dan Kou, Ye Deng, Yuanhe Yang*. Stochastic processes dominate belowground community assembly in alpine grasslands on the Tibetan Plateau. Environmental Microbiology, 2022, doi.org/10.1111/1462-2920.15827 Read More
  21. Xianzhe Gong, Zhiyi Chen, Ye Deng, Duo Zhao, Ping Gao, Liang Zhang, Qichao Tu, Lingyun Qu, Liwen Zheng, Yong Zhang, Chao Song, Jihua Liu*. Contrasting archaeal and bacterial community assembly processes and the importance of rare taxa along a depth gradient in shallow coastal sediments. 2022, 852: 158411 Read More
  22. Jinshan Lian,  Huiying Wang,  Ye Deng,  Minggang Xu,  Shutang Liu,  Baoku Zhou,  Kamlesh Jangid,  Yinghua Duan*. Impact of long-term application of manure and inorganic fertilizers on common soil bacteria in different soil types. Agriculture Ecosystems & Environment. 2022, 337: 108044 Read More
  23. Wei Wei, Jia Li, Xin Shen, Jinglu Lyu, Caixia Yan, Boyu Tang, Wenjuan Ma, Huixu Xie, Lei Zhao, Lei Cheng, Ye Deng, Yan Li*. Oral Microbiota from Periodontitis Promote Oral Squamous Cell Carcinoma Development via γδ T Cell Activation. mBio. 2022, doi.org/10.1128/msystems.00469-22 Read More
  24. Kenneth Dumack*, Kai Feng, Sebastian Flues, Melanie Sapp, Susanne Schreiter, Rita Grosch, Laura E. Rose, Ye Deng, Kornelia Smalla, Michael Bonkowski. What Drives the Assembly of Plant-associated Protist Microbiomes? Investigating the Effects of Crop Species, Soil Type and Bacterial Microbiomes. Protist. 2022, doi.org/10.1016/j.protis.2022.125913 Read More
  25. Songsong Gu, Xingyao Xiong, Lin Tan, Ye Deng, Xiongfeng Du, Xingxing Yang, Qiulong Hu*. Soil microbial community assembly and stability are associated with potato (Solanum tuberosum L.) fitness under continuous cropping regime. Frontiers in Plant Science. 2022,  doi.org/10.3389/fpls.2022.1000045 Read More
  26. Shiqing Nie, Jichen Wang, Ye Deng, Zheng Ye, Yuan Ge*. Inflammatory microbes and genes as potential biomarkers of Parkinson’s disease. NPJ Biofilms and Microbiomes, 2022, 8: 101 Read More
  27. 彭玺, 冯凯, 厉舒祯, 邓晔*, 宏基因组学技术与微生物群落多样性分析方法, 科技导报, 2022 Read More
  28. 赵阳安, 芦光新*, 邓晔*, 王英成, 马坤, 颜珲璘, 张海娟, 周学丽, 窦声云, 根瘤菌拌种对两种苜蓿生长及根际微生物多样性的影响, 草地学报, 2022 Read More
  29. 马坤, 芦光新*, 邓晔*, 颜珲璘, 王英成, 赵阳安, 张海娟, 周学丽, 窦声云, 有机肥对垂穗披碱草根际微生物及土壤理化性质的影响, 草地学报, 2022 Read More
  30. 张琪，邓晔，邵宗泽，王万鹏*，潮间带沉积物厌氧烃降解细菌的多样性及Desulfovibrio subterraneus ND17的分离鉴定，海洋学报，2022 Read More
  1. Zhicheng Ju, Xiongfeng Du, Kai Feng, Shuzhen Li, Songsong Gu, Decai Jin*, Ye Deng*. The Succession of Bacterial Community Attached on Biodegradable Plastic Mulches During the Degradation in Soil. Frontiers in Microbiology, 2021. https://doi.org/10.3389/fmicb.2021.785737 Read More
  2. Yuqi Zhou#, Baoyu Sun#, Baohua Xie, Kai Feng, Zhaojing Zhang, Zheng Zhang, Shuzhen Li, Xiongfeng Du, Qi Zhang, Songsong Gu, Wen Song, Linlin Wang, Jianyang Xia, Guangxuan Han*, Ye Deng*. Warming reshaped the microbial hierarchical interactions. Global Change Biology, 2021. doi.org/10.1111/gcb.15891 Read More
  3. Ziyan Wei, Kai Feng, Zhujun Wang, Yu Zhang, Min Yang, Yong-Guan Zhu, Marko P. J. Virta, and Ye Deng*. High-Throughput Single-Cell Technology Reveals the Contribution of Horizontal Gene Transfer to Typical Antibiotic Resistance Gene Dissemination in Wastewater Treatment Plants. Environmental Science & Technology, 2021, DOI: 10.1021/acs.est.1c01250 Read More
  4. Lin Tan, Wei-Ai Zeng, Yansong Xiao, Pengfei Li, Songsong Gu, Shaolong Wu, Zhengguang Zhai, Kai Feng, Ye Deng*, Qiulong Hu*. Fungi-bacteria associations in wilt diseased rhizosphere and endosphere by interdomain ecological network analysis. Frontiers in Microbiology, 2021, doi: 10.3389/fmicb.2021.722626 Read More
  5. Shuzhen Li, Xiongfeng Du, Kai Feng, Yueni Wu, Qing He, Zhujun Wang, Yangying Liu, Danrui Wang, Xi Peng, Zhaojing Zhang, Arthur Escalas, Yuanyuan Qu, Ye Deng*. Assessment of microbial α-diversity in one meter squared topsoil. Soil Ecology Letters, 2021, https://doi.org/10.1007/s42832-021-0111-5 Read More
  6. Yingcheng Wang, Guangxin Lu, Hao Yu, Xiongfeng Du, Qing He, Shiting Yao, Lirong Zhao, Caixia Huang, Xiaocheng Wen, Ye Deng*. Meadow degradation increases spatial turnover rates of the fungal community through both niche selection and dispersal limitation. Science of The Total Environment, 2021, https://doi.org/10.1016/j.scitotenv.2021.149362. Read More
  7. Shang Wang#, Xuelian Bao#, Kai Feng#, Ye Deng*, Wenjun Zhou, Pengshuai Shao, Tiantian Zheng, Fei Yao, Shan Yang, Shengen Liu, Rongjiu Shi, Zhen Bai, Hongtu Xie, Jinghua Yu, Ying Zhang, Yiping Zhang, Liqing Sha, Qinghai Song, Yuntong Liu, Jizhong Zhou, Yuguang Zhang, Hui Li, Qingkui Wang, Xingguo Han, Yongguan Zhu, Chao Liang*. Warming-driven migration of core microbiota projects soil property changes at continental scale. Science Bulletin, 2021, 10.1016/j.scib.2021.01.021 Read More
  8. Xiongfeng Du, Ye Deng*, Shuzhen Li, Arthur Escalas, Kai Feng, Qing He, Zhujun Wang, Yueni Wu, Danrui Wang, Xi Peng, Shang Wang. Steeper spatial scaling patterns of subsoil microbiota are shaped by deterministic assembly process. Molecular Ecology, 2021, 30(4): 1072-1085 Read More
  9. Shuzhen Li, Ye Deng*, Xiongfeng Du, Kai Feng, Yueni Wu, Qing He, Zhujun Wang, Yangying Liu, Danrui Wang, Xi Peng, Zhaojing Zhang, Arthur Escalas, Yuanyuan Qu. Sampling cores and sequencing depths affected the measurement of microbial diversity in soil quadrats. Science of the Total Environment, 2021, 767: 144966 Read More
  10. Shang Wang, Weiguo Hou, Hongchen Jiang, Liuqin Huang, Hailiang Dong, Shu Chen, Bin Wang, Yongcan Chen, Binliang Lin, Ye Deng*. Microbial diversity accumulates in a downstream direction in the Three Gorges Reservoir. Journal of Environmental Sciences, 2021, 101:156-167 Read More
  11. Qing He, Shang Wang*, Weiguo Hou, Kai Feng, Fangru Li, Wanming Hai, Yidi Zhang, Yuxuan Sun, Ye Deng. Temperature and microbial interactions drive the deterministic assembly processes in sediments of hot springs. Science of the Total Environment, 2021, 772: 145465 Read More
  12. Pei Wang, Xiao Kong, Hongsong Chen, Youlun Xiao, Huijun Liu, Xiaojuan Li, Zhuo Zhang, Xingqiu Tan, Diandong Wang, Decai Jin*, Ye Deng, Tomislav Cernava. Exploration of intrinsic microbial community modulators in the rice endosphere indicates a key role of distinct bacterial taxa across different cultivars. Frontiers in Microbiology, 2021, 12: 629852 Read More
  13. Shang Wang, Weiguo Hou, Hongchen Jiang, Hailiang Dong, Liuqin Huang, Shu Chen, Bin Wang, Yongcan Chen, Binliang Lin, Ye Deng*. The Lifestyle-Dependent Microbial Interactions Vary Between Upstream and Downstream of the Three Gorges Dam. Frontiers in Ecology and Evolution, 2021, 10.3389/fevo.2021.624476 Read More
  14. Hao Yu, Ye Deng*, Zhili He, Elise Pendall*, Yolima Carrillo, Shang Wang, Decai Jin, Liyou Wu, Aijie Wang, Ying Xu, Baoyong Liu, Xin Tai, Jizhong Zhou. Stimulation of soil microbial functioning by elevated CO2 may surpass effects mediated by irrigation in a semiarid grassland. Geoderma, 2021, 401: 115162 Read More
  15. Lioba Rüger*, Kai Feng, Kenneth Dumack, Jule Freudenthal, Yan Chen, Ruibo Sun, Monica Wilson, Peng Yu, Bo Sun, Ye Deng, Frank Hochholdinger, Doris Vetterlein, Michael Bonkowski. Assembly Patterns of the Rhizosphere Microbiome Along the Longitudinal Root Axis of Maize (Zea mays L.). Frontiers in Microbiology, 2021, 12: 614501 Read More
  16. Enze Li, Tongchu Deng, Lei Yan, Jizhong Zhou, Zhili He, Ye Deng, Meiying Xu*. Elevated nitrate simplifies microbial community compositions and interactions in sulfide-rich river sediments. Science of the Total Environment, 2021, 750: 141513 Read More
  17. Hui Li, Shan Yang, Mikhail Semenov, Fei Yao, Ji Ye, Rencang Bu, Ruiao Ma, Junjie Lin, Irina Kurganova, Xugao Wang, Ye Deng, Irina Kravchenko, Yong Jiang*, Yakov Kuzyakov. Temperature sensitivity of SOM decomposition is linked with a K-selected microbial community. Global Change Biology, 2021, 10.1111/gcb.15593 Read More
  18. Dong Yuzhu, Wu Shanghua, Deng Ye, Wang Shijie, Fan Haonan, Li Xianglong, Bai Zhihui, Zhuang Xuliang. Distinct Functions and Assembly Mechanisms of Soil Abundant and Rare Bacterial Taxa Under Increasing Pyrene Stresses. Frontiers in Microbiology, 2021, 10.3389/fmicb.2021.689762 Read More
  19. Weiwei Cai, Bo Wang, Wenzong Liu, Hong Yao, Ye Deng, Aijie Wang. Sessile methanogens dominated cathodic biofilm: Distribution and network in physiological transitions. Science of The Total Environment, 2021, 10.1016/j.scitotenv.2021.148724 Read More
  20. Liu, Nana, Huifeng Hu, Wenhong Ma, Ye Deng, Qinggang Wang, Ao Luo, Jiahui Meng, Xiaojuan Feng, and Zhiheng Wang. 2021. Relative Importance of Deterministic and Stochastic Processes on Soil Microbial Community Assembly in Temperate Grasslands. Microorganisms 9, no. 9: 1929. https://doi.org/10.3390/microorganisms9091929 Read More
  21. 杨兴盛, 王尚*, 何晴, 王朱珺, 张照婧, 姜成英, 马黎萍, 刘贤伟, 胡宝兰, 李咏梅, 邓晔*. 典型有机固废厌氧消化微生物研究现状与发展方向[J]. 生物工程学报, 2021,37(10): 3425~3438 Read More
  22. 周煜琦，张照婧，位光山，张政，邓晔*. 全球变化下海岸带微生物生态研究进展. 微生物学报, 2021, 61(06): 1743-1760 Read More
  23. 沈文丽，王尚*，邓晔. 细胞内融合基因技术（epicPCR）测定功能微生物类群多样性. Bio-protocol, DOI: 10.21769/BioProtoc.2003724 Read More
  24. 张照婧，王尚*，邓晔. 环境样本中的细菌总量测定——流式细胞法. Bio-protocol, DOI: 10.21769/BioProtoc.2003700 Read More
  25. 何晴，王尚，邓晔*. 环境样本中原核生物的总量测定—16SrRNA基因荧光定量PCR(SYBR Green染料法). Bio-protocol, DOI: 10.21769/BioProtoc.2003691 Read More
  26. 王朱珺，王尚*，邓晔. 从环境样本中提取高质量DNA-研磨加DNeasy试剂盒方法. Bio-protocol, DOI: 10.21769/BioProtoc.2003696 Read More
  27. 鞠志成，金德才*，邓晔. 土壤中塑料与微生物的相互作用及其生态效应. 中国环境科学，2021, 41(5): 2352-2361 Read More
  28. 王英成，芦光新*，赵丽蓉，邓晔，王军邦. 高寒草甸退化对土壤电导率变化影响的研究. 干旱区研究，DOI: 10.13866/j.azr.2021.01.12 Read More
  29. 姚世庭，芦光新*，邓晔，党宁，王英成，张海娟，颜珲璘，模拟增温对土壤真菌群落组成及多样性的影响，生态环境学报，2021, 10.16258/j.cnki.1674-5906.2021.07.009 Read More

1. Shuzhen Li, Zhujun Wang, Yuanyuan Wang, Maoyong Song, Guangxin Lu, Ning Dang, Huaqun Yin, Yuanyuan Qu, Ye Deng*. Effects of graphene oxide on PCR amplification for microbial community survey. BMC Microbiology, 2020, 20: 278 Read More

2. Yueni Wu, Kai Feng, Ziyan Wei, Zhujun Wang, Ye Deng*. ARDEP, a Rapid Degenerate Primer Design Pipeline Based on k-mers for Amplicon Microbiome Studies. International Journal of Environmental Research and Public Health, 2020, 17: 5958 Read More

3. Zhili He#,*, Ye Deng#, Meiying Xu#, Juan Li, Junyi Liang, Jinbo Xiong, Hao Yu, Bo Wu, Liyou Wu, Kai Xue, Shengjing Shi, Yolima Carrillo, Joy D. Van Nostrand, Sarah E. Hobbie, Peter B. Reich, Christopher W. Schadt, Angela D. Kent, Elise 6 Pendall, Matthew Wallenstein, Yiqi Luo, Qingyun Yan*, Jizhong Zhou*. Microbial functional genes commonly respond to elevated carbon dioxide. Environment International, 2020, 144: 106068 Read More

4. Kai Feng, Shang Wang, Ziyan Wei, Zhujun Wang, Zhaojing Zhang, Yueni Wu, Yuguang Zhang, Ye Deng*. Niche width of above- and belowground organisms varied in predicting biodiversity profiling along a latitudinal gradient. Molecular Ecology, 2020, 29(10): 1890-1902 Read More

5. Shuzhen Li, Ye Deng*, Zhujun Wang, Zhaojing Zhang, Xiao Kong, Wenjun Zhou, Yanyun Yi, Yuanyuan Qu*. Exploring the accuracy of amplicon-based internal transcribed spacer (ITS) markers for fungal community. Molecular Ecology Resources, 2020, 20: 170-184 Read More

6. Zhaojing Zhang, Yuanyuan Qu*, Shuzhen Li, Kai Feng, Weiwei Cai, Huaqun Yin, Shang Wang, Wenzong Liu, Aijie Wang, Ye Deng*. Florfenicol restructured the microbial interaction network for wastewater treatment by microbial electrolysis cells. Environmental Research, 2020, 183: 1-11 Read More

7. Qiulong Hu, Lin Tan, Songsong Gu, Yansong Xiao, Xingyao Xiong, Wei-ai Zeng, Kai Feng, Zhong Wei, Ye Deng*. Network analysis infers the wilt pathogen invasion associated with non-detrimental bacteria. NPJ Biofilms and Microbiomes, 2020, 6: 8 Read More

8. Xin Tai, Rui Li, Bao Zhang, Hao Yu, Xiao Kong, Zhihui Bai, Ye Deng, Lan Jia, Decai Jin*. Pollution Gradients Altered the Bacterial Community Composition and Stochastic Process of Rural Polluted Ponds. Microorganisms, 2020, 8:311 Read More

9. Qiulong Hu, Lin Tan, Xingxing Yang, Ye Deng, Songsong Gu, Jiren Chen, Liu Cai, Qian Zhou, Xinxi Hu, Yuzhi Qin, Xingyao Xiong*. The divergence of bacterial communities among continuous cropping, rotational cropping and new planting potato soils. International Journal of Agriculture & Biology, 2020, 23:721–729 Read More

10. Mengxin Zhao, Jing Cong, Jingmin Cheng, Qi Qi, Yuyu Sheng, Daliang Ning, Hui Lu, Kristen Wyckoff, Ye Deng, Diqiang Li, Jizhong Zhou, Yuguang Zhang*. Nitrogen and phosphorus limitations constrain soil microbial community assembly and interaction in broadleaf forests of southern China. Forests, 2020, 11(3), 285 Read More

11. Shengyang Lian, Yuanyuan Qu*, Shuzhen Li, Zhaojing Zhang, Henglin Zhang, Chunxiao Dai, Ye Deng. Interaction of graphene-family nanomaterials with microbial communities in sequential batch reactors revealed by high-throughput sequencing. Environmental Research, 2020, 184: 109392 Read More

12. Song-Can Chen, Guo-Xin Sun, Yu Yan, Konstantinos Konstantinidis, Si-Yu Zhang, Ye Deng, Xiao-Min Li, Hui-Ling Cui, Florin Musat, Denny Popp, Barry P. Rosen, Yong-Guan Zhu*. The Great Oxidation Event expanded the genetic repertoire of arsenic metabolism and cycling. Proceedings of the National Academy of Sciences of the United States of America, 2020, 117 (19) 10414-10421 Read More

13. Jingmin Cheng, Mengxin Zhao, Jing Cong, Qi Qi, Ye Xiao, Wei Cong, Ye Deng, Jizhong Zhou, Yuguang Zhang*. Soil pH exerts stronger impacts than vegetation type and plant diversity on soil bacterial community composition in subtropical broad-leaved forests. Plant and soil, 2020, 450: 273–286 Read More

14. Qichao Tu, Qingyun Yan, Ye Deng, Sean T. Michaletz, Vanessa Buzzard, Michael D. Weiser, Robert Waide, Daliang Ning, Luguang Wu, Zhili He, Jizhong Zhou*. Biogeographic patterns of microbial co-occurrence ecological networks in six American forests. Soil Biology & Biochemistry, 2020, 148: 107897 Read More

15. 吴悦妮，冯凯，厉舒祯，王朱珺，张照婧，邓晔*. 16S-18S-ITS扩增子高通量测序引物的生物信息学评估和改进. 微生物学通报, 2020, 47(9): 2897-2912 Read More

16. 王丹蕊，沈文丽，魏子艳，王尚，邓晔*. 单细胞测序技术在微生物生态领域中的应用. 生物技术通报, 2020, 36(10): 1-7 Read More

17. 杜雄峰，厉舒祯，冯凯，何晴，王朱珺，吴悦妮，王丹蕊，彭玺，王尚，邓晔*. 农牧交错带草地土壤剖面微生物总量、多样性和互作网络的垂直分布特征. 微生物学通报, 2020, 47(9): 2789-2806 Read More
 
18. 段云峰, 王升跃, 陈禹保, 杨瑞馥, 李后开, 朱怀球, 童贻刚, 杜文斌, 付钰, 胡松年, 王军, 辛玉华, 赵方庆, 鲍一明, 张雯, 李娟, 曾明, 牛海涛, 周欣, 李岩, 崔生辉, 袁静, 李俊桦, 王加义, 刘东来, 倪铭, 孙青, 邓晔, 朱宝利. 微生物组测序与分析专家共识. 生物工程学报, 2020, 36(12):2516-2524 Read More

1. Kai Feng, Yuguang Zhang, Zhili He, Daliang Ning, Ye Deng*. Interdomain ecological networks between plants and microbes. Molecular Ecology Resources, 2019, 19(6): 1565-1577 Read More

2. Zhujun Wang#, Guangxin Lu#, Mengting Yuan, Hao Yu, Shang Wang, Xin Li, Ye Deng*. Elevated temperature overrides the effects of N amendment in Tibetan grassland on soil microbiome. Soil Biology and Biochemistry, 2019, 136: 107532 Read More

3. Huayu Qin, Shang Wang, Kai Feng, Zhili He, Marko P. J. Virta, Weiguo Hou, Hailiang Dong, Ye Deng*. Unraveling the diversity of sedimentary sulfate-reducing prokaryotes (SRP) across Tibetan saline lakes using epicPCR. Microbiome, 2019, 7:71 Read More

4. Ziyan Wei, Yueni Wu, Kai Feng, Min Yang, Yu Zhang, Qichao Tu, Jun Wang, Ye Deng*. ARGA, a pipeline for primer evaluation on antibiotic resistance genes. Environment International, 2019, 128:137-145 Read More

5. Xiao Kong, Decai Jin*, Xin Tai, Hao Yua, Guilan Duan, Xiulan Yan, Jiangang Pan, Junhua Song, Ye Deng. Bioremediation of dibutyl phthalate in a simulated agricultural ecosystem by Gordonia sp. strain QH-11 and the microbial ecological effects in soil. Science of The Total Environment, 2019, 667: 691-700 Read More

6. Zhaojing Zhang, Ye Deng*, Kai Feng, Weiwei Cai, Shuzhen Li, Huaqun Yin, Meiying Xu, Daliang Ning, Yuanyuan Qu*. Deterministic assembly and diversity gradient altered the biofilm community performances of bioreactors. Environmental Science & Technology, 2019, 53(3): 1315-1324 Read More

7. Xiao Kong, Decai Jin*, Xinxin Wang, Fengsong Zhang, Guilan Duan, Huijun Liu, Minghong Jia, Ye Deng. Dibutyl phthalate contamination remolded the fungal community in agro-environmental system. Chemosphere, 2019, 215: 189-198 Read More

8. Zhuo Zhang, Xiao Kong, Decai Jin*, Hao Yu, Xun Zhu, Xiaofeng Su, Pei Wang, Ruiyong Zhang, Minghong Jia, Ye Deng. Euonymus japonicus phyllosphere microbiome is significantly changed by powdery mildew. Archives of Microbiology, 2019, 201: 1099-1109 Read More

9. Daliang Ning, Ye Deng, James M. Tiedje, Jizhong Zhou*. A General Framework for Quantitatively Assessing Ecological Stochasticity. Proceedings of the National Academy of Sciences of the United States of America, 2019, 116(34): 16892-16898 Read More

10. Qichao Tu*, Lu Lin*, Lei Cheng, Ye Deng, Zhili He. NCycDB: a curated integrative database for fast and accurate metagenomic profiling of nitrogen cycling genes. Bioinformatics, 2019, 35(6): 1040-1048 Read More

11. Weiwei Cai, Wenzong Liu*, Zhaojing Zhang, Kai Feng, Ge Ren, Chuanliang Pu, Jiaqi Li, Ye Deng, Aijie Wang. Electro-driven methanogenic microbial community diversity and variability in the electron abundant niche. Science of The Total Environment, 2019, 661: 178-186 Read More

12. Bin Liang, Jincai Ma, Weiwei Cai, Zhiling Li, Wenzong Liu, Mengyuan Qi, Youkang Zhao, Xiaodan Ma, Ye Deng, Aijie Wang, Jizhong Zhou. Response of chloramphenicol-reducing biocathode resistome to continuous electrical stimulation. Water Research, 2019, 148: 398-406 Read More

13. Yuzhan Yang, Yangchun Gao, Xuena Huang, Ping Ni, Yueni Wu, Ye Deng, Aibin Zhan. Adaptive shifts of bacterioplankton communities in response to nitrogen enrichment in a highly polluted river. Environmental Pollution, 2019, 245: 290-299 Read More

14. Linwei Wu#, Daliang Ning#, Bing Zhang#, Yong Li, Ping Zhang, Xiaoyu Shan, Qiuting Zhang, Mathew Brown, Zhenxin Li, Joy D. Van Nostrand, Fangqiong Ling, Naijia Xiao, Ya Zhang, Julia Vierheilig, George F. Wells, Yunfeng Yang, Ye Deng, Qichao Tu, Aijie Wang, Global Water Microbiome Consortium, Tong Zhang, Zhili He, Jurg Keller, Per H. Nielsen, Pedro J. J. Alvarez, Craig S. Criddle, Michael Wagner, James M. Tiedje, Qiang He*, Thomas P. Curtis*, David A. Stahl, Lisa Alvarez-Cohen, Bruce E. Rittmann, Xianghua Wen*, Jizhong Zhou*. Global Diversity and Biogeography of Bacterial Communities in Wastewater Treatment Plants. Nature Microbiology, 2019, 4: 1183-1195 Read More

15. Zhou Shi, Huaqun Yin, Joy D. Van Nostrand, James W. Voordeckers, Qichao Tu, Ye Deng, Mengting Yuan, Aifen Zhou, Ping Zhang, Naijia Xiao, Daliang Ning, Zhili He, Liyou Wu, Jizhong Zhou*. Functional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities. mSystems, 2019, 245: 290-299 Read More

16. Tingting Zhu, Weiwei Cai, Bo Wang, Wenzong Liu*, Kai Feng, Ye Deng, Aijie Wang. Enhanced nitrate removal in an Fe0-driven autotrophic denitrification system using hydrogen-rich water. Environmental Science: Water Research & Technology, 2019, 5: 1380-1388 Read More

17. Sean Michaletz, Ye Deng, Zhili He, Daliang Ning, Lina Shen, Qichao Tu, Joy Van Nostrand, James Voordeckers, Jianjun Wang, Michael Weiser, Michael Kaspari, Robert Waide, Jizhong Zhou, Brian Enquist*. Continental scale structuring of forest and soil diversity via functional traits. Nature Ecology & Evolution, 2019, 3: 1298-1308 Read More

18. Haishu Sun, Shengjun Xu, Shanghua Wu, Rui Wang, Guoqiang Zhuang, Zhihui Bai, Ye Deng, Xuliang Zhuang*. Enhancement of facultative anaerobic denitrifying communities by oxygen release from roots of the macrophyte in constructed wetlands. Journal of Environmental Management, 2019, 246:157-163 Read More

19. Songsong Gu, Qiulong Hu, Yuqi Cheng, Lianyang Bai, Zhonghua Liu, Wenjun Xiao, Zhihua Gong, Yueni Wu, Kai Feng, Ye Deng, Lin Tan*. Application of organic fertilizer improves microbial community diversity and alters microbial network structure in tea (Camellia sinensis) plantation soils. Soil & Tillage Research, 2019, 195: 104356 Read More

20. Lin Tan, Songsong Gu, Shi Li, Zuohua Ren, Ye Deng, Zhonghua Liu, Zhihua Gong, Wenjun Xiao, Qiulong Hu*. Responses of Microbial Communities and Interaction Networks to Different Management Practices in Tea Plantation Soils. Sustainability, 2019, 11: 4428 Read More

21. Nana Liu, Huifeng Hu, Wenhong Ma, Ye Deng, Yuqing Liu, Baihui Hao, Xinying Zhang, Dimitar Dimitrov, Xiaojuan Feng*, Zhiheng Wang*. Contrasting Biogeographic Patterns of Bacterial and Archaeal Diversity in the Top- and Subsoils of Temperate Grasslands. mSystems, 2019, 4(5): e00566-19 Read More

22. Mukan Ji, Weidong Kong*, Linyan Yue, Junbo Wang, Ye Deng, Liping Zhu. Salinity reduces bacterial diversity, but increases network complexity in Tibetan Plateau lakes. FEMS Microbiology Ecology, 2019, 95(12): 1-10 Read More

23. Yangying Liu, Shang Wang, Zhujun Wang, Zhaojing Zhang, Huayu Qin, Ziyan Wei, Kai Feng, Shuzhen Li, Yueni Wu, Huaqun Yin, Hui Li, Ye Deng*. Soil microbiome mediated nutrients decline during forest degradation process. Soil Ecology Letter, 2019, 1(1-2):59-71 Read More

24. 何晴，王尚*，邓晔. 分子生物学技术在热泉地质微生物学研究中的应用，微生物学报，2019，59(6): 996-1011 Read More

25. 厉舒祯,邓晔*,张照婧,曲媛媛. 生物降解芳香族化合物的分子检测技术研究进展，中国环境科学，2019，39(6)：2577-2587 Read More

26. 杜雄峰,于皓,王尚,邓晔*. 宏基因组方法揭示草地土壤微生物群落响应全球变化，生态学杂志，2019，38(11): 1-12 Read More

1. Ye Deng*, Daliang Ning, Yujia Qin, Kai Xue, Liyou Wu, Zhili He, Huaqun Yin, Yuting Liang, Vanessa Buzzard, Sean T. Michaletz, Jizhong Zhou*. Spatial scaling of forest soil microbial communities across a temperature gradient. Environmental Microbiology, 2018, 20(10): 3504-3513 Read More

2. Hao Yu, Ye Deng*, Zhili He, Joy D. Van Nostrand, Shang Wang, Decai Jin, Aijie Wang, Liyou Wu, Daohan Wang, Xin Tai, Jizhong Zhou. Elevated CO2 and Warming Altered Grassland Microbial Communities in Soil Top-Layers. Frontiers in Microbiology, 2018,9:1790 Read More

3. Wenzong Liu, Yongjian Piao, Fugui Zhang, Lin Liu, Dongfang Meng, Jun Nan, Ye Deng*, Aijie Wang*. Hydrogen consumption and methanogenic community evolution in anodophilic biofilms in single chamber microbial electrolysis cells under different startup modes. Environmental Science: Water Research & Technology, 2018, 4: 1839-1850 Read More

4. Ziyan Wei, Kai Feng, Shuzhen Li, Yu Zhang, Hongrui Chen, Huaqun Yin, Meiying Xu, Ye Deng*. Exploring abundance, diversity and variation of a widespread antibiotic resistance gene in wastewater treatment plants. Environment International, 2018, 117:186-195 Read More

5. Hao Yu, Zhili He*, Aijie Wang, Jianping Xie, Liyou Wu, Joy D. Van Nostrand, Decai Jin, Zhimin Shao, Christopher W. Schadt, Jizhong Zhou, Ye Deng*. Divergent responses of forest soil microbial communities under elevated CO2 in different depths of upper soil layers. Applied and Environmental Microbiology, 2018, 84:e01694-17 Read More

6. Hui Li, Zhuwen Xu, Qingyun Yan, Shan Yang, Joy D. Van Nostrand, Zhirui Wang, Zhili He, Jizhong Zhou, Yong Jiang*, Ye Deng*. Soil microbial beta-diversity is linked with compositional variation in aboveground plant biomass in a semi-arid grassland. Plant and soil, 2018, 423: 465–480 Read More

7. Shang Wang, Xiaobo Wang, Xingguo Han, Ye Deng*. Higher precipitation strengthens the microbial interactions in semi-arid grassland soils. Global Ecology and Biogeography, 2018, 27(5): 570-580 Read More

8. Ziyan Wei, Yangying Liu, Kai Feng, Shuzhen Li, Shang Wang, Decai Jin, Yu Zhang, Hongrui Chen, Huaqun Yin, Meiying Xu, Ye Deng*. The divergence between fungal and bacterial communities in seasonal and spatial variations of wastewater treatment plants. Science of the Total Environment, 2018, 628:969–978 Read More

9. Xiao Kong, Decai Jin*, Shulan Jin, Zhigang Wang, Huaqun Yin, Meiying Xu, Ye Deng*. Responses of bacterial community to dibutyl phthalate (DBP) pollution in a soil-vegetable ecosystem. Journal of Hazardous Materials, 2018, 353: 142-150 Read More

10. Decai Jin, Xiao Kong, Jie Wang, Jiajun Sun, Xiangyang Yu, Xuliang Zhuang, Ye Deng*, Zhihui Bai*. Chitinophaga caeni sp. nov., isolated from activated sludge. International Journal of Systematic and Evolutionary Microbiology, 2018, 68: 2209-2213 Read More

11. Decai Jin*, Xiao Kong, Bingjian Cui, Shulan Jin, Yunfeng Xie, Xingrun Wang, Ye Deng*. Bacterial communities and potential waterborne pathogens within the typical urban surface waters. Scientific Reports, 2018, 8: 13368 Read More

12. Yueni Wu, Yuzhan Yang, Lei Cao, Huaqun Yin, Meiying Xu, Zhujun Wang, Yangying Liu, Xin Wang, Ye Deng*. Habitat environments impacted the gut microbiome of long-distance migratory swan geese but central species conserved. Scientific Reports, 2018, 8: 13314 Read More

13. Shengjun Xu, Shugeng Feng, Haishu Sun, Shanghua Wu, Guoqiang Zhuang, Ye Deng, Zhihui Bai, Chuanyong Jing, Xuliang Zhuang. Linking N2O Emissions from Biofertilizer-Amended Soil of Tea Plantations to the Abundance and Structure of N2O-Reducing Microbial Communities. Environmental Science & Technology, 2018, 52 (19), 11338–11345 Read More

14. Jinzhi He, Qichao Tu, Yichen Ge, Yujia Qin, Bomiao Cui, Xiaoyu Hu, Yuxia Wang, Ye Deng, Kun Wang, Joy D. Van Nostrand, Jiyao Li, Jizhong Zhou*, Yan Li*, Xuedong Zhou*. Taxonomic and Functional Analyses of the Supragingival Microbiome from Caries-Affected and Caries-Free Hosts. Microbial Ecology, 2018, 75:543-554 Read More

15. Shengen Liu, Hang Wang, Ye Deng, Peng Tian, Qingkui Wang*. Forest conversion induces seasonal variation in microbial β-diversity. Environmental Microbiology, 2018, 20:111-123 Read More

16. Weiwei Cai, Wenzong Liu*, Zhaojing Zhang, Kai Feng, Ge Ren, Chuanliang Pu, HaishuSun, Jiaqi Li, Ye Deng, Aijie Wang**. mcrA sequencing reveals the role of basophilic methanogens in a cathodic methanogenic community. Water Research, 2018, 136:192-199 Read More

17. Bo Wu, Feifei Liu, Michael D. Weiser, Daliang Ning, Jordan G. Okie, Lina Shen, Juan Li, Benli Chai, Ye Deng, Kai Feng, Liyou Wu, Shouwen Chen*, Jizhong Zhou*, Zhili He*. Temperature determines the diversity and structure of N2O‐reducing microbial assemblages. Functional Ecology, 2018, 32(7): 1867-1878 Read More

18. Ge Ren, Anzhou Ma, Yanfen Zhang, Ye Deng, Guodong Zheng, Xuliang Zhuang, Guoqiang Zhuang, Danielle Fortin. Electron acceptors for anaerobic oxidation of methane drive microbial community structure and diversity in mud volcanoes: Electron acceptors drive microbial communities. Environmental Microbiology, 2018, 20(7): 2370-2385 Read More

19. Michael D. Weiser*, Sean Michaletz, Vanessa Buzzard, Ye Deng, Zhili He, Lina Shen, Brian J. Enquist, Robert B. Waide, Jizhong Zhou, Michael Kaspari. Toward a theory for diversity gradients: the Abundance-Adaptation Hypothesis. Ecography, 2018, 41(2): 255-264 Read More

20. Jing Tian, Nianpeng He, Weidong Kong, Ye Deng, Kai Feng, Sophie M. Green, Xiaobo Wang, Jizhong Zhou, Yakov Kuzyakov, and Guirui Yu*. Deforestation Decreases Spatial Turnover and Alters the Network Interactions in Soil Bacterial Communities. Soil Biology & Biochemistry, 2018, 123: 80-86 Read More

21. Mengting M. Yuan, Jin Zhang, Kai Xue, Liyou Wu, Ye Deng, Jie Deng, Lauren Hale, Xishu Zhou, Zhili He, Yunfeng Yang, Joy D. Van Nostrand, Edward A. G. Schuur, Konstantinos T. Konstantinidis, C. Ryan Penton, James R. Cole, James M. Tiedje, Yiqi Luo, Jizhong Zhou*. Microbial functional diversity covaries with permafrost thaw-induced environmental heterogeneity in tundra soil. Global Change Biology, 2018, 24:297-307 Read More
 
22.王朱珺，王尚，刘洋荧，冯凯，邓晔*，2018. 宏基因组技术在氮循环功能微生物分子检测研究中的应用，生物技术通报，34(1): 1-14 Read More

1. Hui Li, Shan Yang, Zhuwen Xu, Qingyun Yan, Xiaobin Li, Joy D. van Nostrand, Zhili He, Fei Yao, Xingguo Han, Jizhong Zhou, Ye Deng*, Yong Jiang*. Responses of soil microbial functional genes to global changes are indirectly influenced by aboveground plant biomass variation. Soil Biology & Biochemistry, 2017, 104: 18-29 Read More

2. Xiaoxia Zhang, Ruijie Zhang, Jusheng Gao, Xiucheng Wang, Fenliang Fan, Xiaotong Ma, Huaqun Yin, Caiwen Zhang, Kai Feng, Ye Deng*. Thirty-one years of rice-rice-green manure rotations shape the rhizosphere microbial community and enrich beneficial bacteria. Soil Biology & Biochemistry, 2017,104: 208-217 Read More

3. Yuguang Zhang*, Xiao Liu, Jing Cong, Hui Lu, Yuyu Sheng, Xiulei Wang, Diqiang Li, Xueduan Liu, Huaqun Yin, Jizhong Zhou, Ye Deng*. The microbially-mediated soil organic carbon loss under degenerative succession in an alpine meadow. Molecular Ecology, 2017, 26:3676-3686 Read More

4. Zhaojing Zhang, Yuanyuan Qu*, Shuzhen Li, Kai Feng, Shang Wang, Weiwei Cai, Yuting Liang, Hui Li, Meiying Xu, HuaqunYin, Ye Deng*. Soil bacterial quantifcation approaches coupling with relative abundances reflecting the changes of taxa. Scientific Reports, 2017, 7:4837 Read More

5. Jizhong Zhou*, Ye Deng*, Lina Shen, Chongqing Wen, Qingyun Yan, Daliang Ning, Yujia Qin, Kai Xue, Liyou Wu, Zhili He, James W. Voordeckers, Joy van Nostrand, Vanessa Buzzard, Sean T. Michaletz, Brian J. Enquist, Michael D. Weiser, Michael Kaspari, Robert Waide, Yunfeng Yang, James H. Brown. Correspondence: Reply to “Analytical flaws in a continental-scale forest soil microbial diversity study”. Nature Communications, 2017, 8:15583 Read More

6. Kai Feng, Zhaojing Zhang, Weiwei Cai, Wenzong Liu, Meiying Xu, Huaqun Yin, Aijie Wang, Zhili He, Ye Deng*. Biodiversity and species competition regulate the resilience of microbial biofilm community. Molecular Ecology, 2017, 26:6170-6182 Read More

7. Decai Jin, Xiao Kong, Minghong Jia, Xiangyang Yu, Xinxin Wang, Xuliang Zhuang, Ye Deng*, Zhihui Bai*. Gordonia phthalatica sp. nov., a di-n-butyl phthalate-degrading bacterium isolated from activated sludge. International Journal of Systematic and Evolutionary Microbiology, 2017, 67(12): 5128-5133 Read More

8. Qingyun Yan, James C. Stegen, Yuhe Yu, Ye Deng, Xinghao Li, Shu Wu, Lili Dai, Xiang Zhang, Jinjin Li, Chun Wang, Jiajia Ni, Xuemei Li, Hongjuan Hu, Fanshu Xiao, Weisong Feng, Daliang Ning, Zhili He, Joy D. Van Nostrand, Liyou Wu, Jizhong Zhou. Nearly a decade-long repeatable seasonal diversity patterns of bacterioplankton communities in the eutrophic Lake Donghu (Wuhan, China). Molecular Ecology, 2017, 26:3839-3850 Read More

9. Lei Cheng*, Naifang Zhang, Mengting Yuan, Jing Xiao, Yujia Qin, Ye Deng, Qichao Tu, Kai Xue, Joy D Van Nostrand, Liyou Wu, Zhili He, Xuhui Zhou, Mary Beth Leigh, Konstantinos T Konstantinidis, Edward AG Schuur, Yiqi Luo, James M Tiedje & Jizhong Zhou*. Warming enhances old organic carbon decomposition through altering functional microbial communities. The ISME Journal, 2017, 11:1825-1835 Read More

10. Honggui Wang, Zhong Wei, Lijuan Mei, Jingxin Gu, Suisui Yin, Karoline Faust, Jeroen Raes, Ye Deng, Yulong Wang, Qirong Shen, Shixue Yin*. Combined use of network inference tools identifies ecologically meaningful bacterial associations in a paddy soil. Soil Biology & Biochemistry, 2017,105: 227-235 Read More

11. Yong-Liang Chen, Tian-Le Xu, Stavros D. Veresoglou, Hang-Wei Hu, Zhi-Peng Hao, Ya-Jun Hu, Lei Liu, Ye Deng, Matthias C. Rillig, Bao-Dong Chen. Plant diversity represents the prevalent determinant of soil fungal community structure across temperate grasslands in northern China. Soil Biology & Biochemistry, 2017,110: 12-21 Read More

12. Ren Bai, Jun-Tao Wang, Ye Deng, Ji-Zheng He, Kai Feng, Li-Mei Zhang*. Microbial Community and Functional Structure Significantly Varied among Distinct Types of Paddy Soils But Responded Differently along Gradients of Soil Depth Layers. Frontiers in Microbiology, 2017, 8:945 Read More

13. Chongqing Wen, Liyou Wu*, Yujia Qin, Joy D. Van Nostrand, Daliang Ning, Bo Sun, Kai Xue, Feifei Liu, Ye Deng, Yuting Liang, Jizhong Zhou*. Evaluation of the reproducibility of amplicon sequencing with Illumina MiSeq platform. PLoS One, 2017; 12(4):e0176716 Read More

14. Quan Zhen, Ye Deng, Yaqing Wang, Xiaoke Wang, Hongxing Zhang, Xu Sun, Zhiyun Ouyang. Meteorological factors had more impact on airborne bacterial communities than air pollutants. Science of The Total Environment, 2017, 601, 703–712 Read More

15. Xiao-Bo Wang, Xiao-Tao Lü, Jing Yao, Zheng-Wen Wang, Ye Deng, Wei-Xin Cheng, Ji-Zhong Zhou, Xing-Guo Han. Habitat-specific patterns and drivers of bacterial β-diversity in China’s drylands. The ISME Journal, 2017, 11: 1345-1358 Read More

16. Wenfang Dai, Jinjie Zhang, Qichao Tu, Ye Deng, Qiongfen Qiu, Jinbo Xiong*. Bacterioplankton assembly and interspecies interaction indicating increasing coastal eutrophication. Chemosphere, 2017, 177: 317-325 Read More

17. Ping Li*, Zhou Jiang, Yanhong Wang, Ye Deng, Joy D. Van Nostrand, Tong Yuan, Han Liu, Dazhun Wei, Jizhong Zhou. Analysis of the functional gene structure and metabolic potential of microbial community in high arsenic groundwater. Water Research, 2017, 123:268-276 Read More

18. Song-Can Chen, Guo-Xin Sun, Barry P. Rosen, Si-Yu Zhang, Ye Deng, Bo-Kai Zhu, Christopher Rensing, Yong-Guan Zhu. Recurrent horizontal transfer of arsenite methyltransferase genes facilitated adaptation of life to arsenic. Scientific Reports, 2017, 7:7741 Read More

19. Ping Zhang, Zhili He, Joy D. Van Nostrand, Yujia Qin, Ye Deng, Liyou Wu, Qichao Tu, Jianjun Wang, Christopher W. Schadt, Matthew W. Fields, Terry C. Hazen, Adam P. Arkin, David A. Stahl, and Jizhong Zhou. Dynamic succession of groundwater sulfate-reducing communities during prolonged reduction of uranium in a contaminated aquifer. Environmental science & technology, 2017, 51:3609-3620 Read More

20. Haishu Sun, Feng Liu, Shengjun Xu, Shanghua Wu, Guoqiang Zhuang, Ye Deng, Shui Jin Wu*, Xuliang Zhuang*. Myriophyllum aquaticum constructed wetland effectively removes nitrogen in swine wastewater. Frontiers in Microbiology, 2017, 8:1932 Read More

21. Yong-Liang Chen, Ye Deng, Jin-Zhi Ding, Hang-Wei Hu,Tian-Le Xu, Fei Li, Gui-Biao Yang, Yuan-He Yang*. Distinct microbial communities in the active and permafrost layers on the Tibetan Plateau. Molecular Ecology. 2017, 26:6608-6620 Read More

22. Wei Zheng, Dongmei Xue*, Xiangzhen Li, Ye Deng, Junpeng Rui, Kai Feng, Zhong-liang Wang. The responses and adaptations of microbial communities to salinity in farmland soils A molecular ecological network analysis. Applied Soil Ecology, 2017, 120: 239-246 Read More
 
23. 刘洋荧, 王尚, 厉舒祯, 邓晔*, 2017. 基于功能基因的微生物碳循环分子生态学研究进展, 微生物学通报, 44(7): 1676-1689 Read More

1. Ye Deng, Zhili He*, Jinbo Xiong, Hao Yu, Meiying Xu, Sarah E. Hobbie, Peter B. Reich, Christopher W. Schadt, Angela Kent, Elise Pendall, Matthew Wallenstein, Jizhong Zhou*, Elevated carbon dioxide accelerates the spatial turnover of soil microbial communities. Global Change Biology, 2016, 22(2):957-964 Read More

2. Ye Deng, Ping Zhang, Yujia Qin, Qichao Tu, Yunfeng Yang, Zhili He, Christopher Warren Schadt, Jizhong Zhou*, Network succession reveals the importance of competition in response to emulsified vegetable oil amendment for uranium bioremediation. Environmental Microbiology, 2016, 18(1): 205-218 Read More

3. Jizhong Zhou*, Ye Deng*, Lina Shen, Chongqing Wen, Qingyun Yan, Daliang Ning, Yujia Qin, Kai Xue, Liyou Wu, Zhili He, James W. Voordeckers, Joy van Nostrand, Vanessa Buzzard, Sean T. Michaletz, Brian J. Enquist, Michael D. Weiser, Michael Kaspari, Robert Waide, Yunfeng Yang, James H. Brown. Temperature mediates continental-scale diversity of microbes in forest soils. Nature Communications, 2016, 7:12083 Read More

4. Decai Jin, Xiao Kong, Huijun Liu, Xinxin Wang, Ye Deng*, Minghong Jia*, Xiangyang Yu. Characterization and Genomic Analysis of a Highly Efficient Dibutyl Phthalate-Degrading Bacterium Gordonia sp. Strain QH-12. International Journal of Molecular Sciences, 2016, 17(7): 1012 Read More

5. Decai Jin, Xiao Kong, Honghong Li, Luyun Luo, Xuliang Zhuang, Guoqiang Zhuang, Ye Deng*, Zhihui Bai*. Patulibacter brassicae sp. nov., isolated from rhizosphere soil of Chinese cabbage (Brassica campestris). International Journal of Systematic and Evolutionary Microbiology, 2016, 66(12): 5056-5060 Read More

6. Kai Xue, Jianping Xie, Aifen Zhou, Feifei Liu, Dejun Li, Liyou Wu, Ye Deng, Zhili He, Joy Van Nostrand, Yiqi Luo, Jizhong Zhou*. Warming alters expressions of microbial functional genes important to ecosystem functioning. Frontiers in Microbiology, 2016, 7:668 Read More

7. Kai Xue, Mengting. Yuan, Jianping Xie, Dejun Li, Yujia Qin, Lauren E. Hale, Liyou Wu, Ye Deng, Zhili He, Joy D. Van Nostrand, Yiqi Luo, James M. Tiedje, Jizhong Zhou*. Annual Removal of Aboveground Plant Biomass Alters Soil Microbial Responses to Warming. mBio, 2016, 7(5):e00976-16 Read More

8. Qichao Tu, Ye Deng, Qingyun Yan, Lina Shen, Lu Lin, Zhili He, Liyou Wu, Joy Van Nostrand, Vanessa Buzzard, Sean T Michaletz, Brian J. Enquist, Michael D. Weiser, Michael Kaspari, Robert Waide, James H. Brown, Jizhong Zhou*. Biogeographic patterns of soil diazotrophic communities across six forests in the North America. Molecular Ecology, 2016, 25:2937-2948 Read More

9. Xiaohui Wang, Xiang-hua Wen*, Ye Deng, Yu Xia, Yunfeng Yang, Jizhong Zhou. Distance-Decay Relationship for Biological Wastewater Treatment Plants. Applied and environmental microbiology, 2016, 82:4860-4866 Read More

10. Hai-Yan Yuan, Long-Jun Ding, Ning Wang, Song-Can Chen, Ye Deng, Xiao-Ming Li, Yong-Guan Zhu*. Geographic distance and amorphous iron affect the abundance and distribution of Geobacteraceae in paddy soils in China. Journal of Soils and Sediments, 2016, 16:2657-2665 Read More

11. Sebastien Olivier Leclercq, Chao Wang, Zhihai Sui, Hai Wu, Baoli Zhu, Ye Deng, Jie Feng*. A multi-player game: Species of Clostridium, Acinetobacter, and Pseudomonas are responsible for the persistence of antibiotic resistance genes in manure-treated soils. Environmental Microbiology, 2016, 18(10):3494-3508 Read More

12. Yu Wang, Rui Zhang, Qiang Zheng, Ye Deng, Joy D. Van Nostrand, Jizhong Zhou*, Nianzhi Jiao*. Bacterioplankton community resilience to ocean acidification: evidence from microbial network analysis. ICES Journal of Marine Science, 2016, 73(3): 865-875 Read More

13. Yuting Liang, Huihui Zhao, Ye Deng, Jizhong Zhou, Guanghe Li, Bo Sun*. Long-Term oil contamination alters the molecular ecological networks of soil microbial functional genes. Frontiers in Microbiology, 2016, 7:60 Read More

14. Sophie Weiss, Will Van Treuren, Catherine Lozupone, Karoline Faust, Jonathan Friedman, Ye Deng, Li Charlie Xia, Zhenjiang Zech Xu, Luke Ursell, Eric J Alm, Amanda Birmingham, Jacob A Cram, Jed A Fuhrman, Jeroen Raes, Fengzhu Sun, Jizhong Zhou, Rob Knight*. Correlation detection strategies in microbial datasets vary widely in sensitivity and precision. The ISME Journal, 2016, 10(7): 1669-1681 Read More

15. Kai Xue, Mengting M. Yuan, Zhou J. Shi, Yujia Qin, Ye Deng, Lei Cheng, Liyou Wu, Zhili He, Joy D. Van Nostrand, Rosvel Bracho, Susan Natali, Edward A.G. Schuur, Chengwei Luo, Konstantinos T. Konstantinidis, Qiong Wang, James R. Cole, James M. Tiedje, Yiqi Luo, Jizhong Zhou*. Tundra soil carbon is vulnerable to rapid microbial decomposition under climate warming. Nature Climate Change, 2016, 6:595-600 Read More

16. Ryan Penton, Caiyun Yang, Liyou Wu, Qiong Wang, Jin Zhang, Feifei Liu, Yujia Qin, Ye Deng, Christopher L. Hemme, Tianling Zheng, Edward A.G. Schuur, James Tiedje and Jizhong Zhou. Nifh-Harboring Bacterial Community Composition Across an Alaskan Permafrost Thaw Gradient. Frontiers in Microbiology, 2016, 7:1894 Read More

17. Yuguang Zhang*, Jing Cong, Hui Lu, Ye Deng, Xiao Liu, JizhongZhou, Diqiang Li. Soil bacterial endemism and potential functional redundancy in natural broadleaf forest along a latitudinal gradient. Scientific Report, 2016, 6:28819 Read More

18. Jian-Kang Zhao, Xiao-Ming Li, Guo-Min Ai, Ye Deng, Shuang-Jiang Liu*, Cheng-Ying Jiang*. Reconstruction of metabolic networks in a fluoranthene-degrading enrichments from polycyclic aromatic hydrocarbon polluted soil. Journal of Hazardous Materials, 2016, 318:90-98 Read More

19. Congcong Shen, Yu Shi, Yingying Ni, Ye Deng, Joy D. Van Nostrand, Zhili He, Jizhong Zhou and Haiyan Chu*. Dramatic Increases of Soil Microbial Functional Gene Diversity at the Treeline Ecotone of Changbai Mountain. Frontiers in Microbiology, 2016, 7:1184 Read More

20. Qianhui Zu, Linghao Zhong, Ye Deng, Yu Shi, Baozhan Wang, Zhongjun Jia, Xiangui Lin and Youzhi Feng*. Geographical Distribution of Methanogenic Archaea in Nine Representative Paddy Soils in China. Frontiers in Microbiology, 2016, 7:1447 Read More

21. Yuzhan Yang, Ye Deng, Lei Cao*. Characterising the interspecific variations and convergence of gut microbiota in Anseriformes herbivores at wintering areas. Scientific Report, 2016, 6: 32655 Read More

22. Weiwei Cai, Zhaojing Zhang, Ge Ren, Qiuxuan Shen, Yanan Hou, Anzhou Ma, Ye Deng, Aijie Wang*, Wenzong Liu*. Quorum sensing alters the microbial community of electrode-respiring bacteria and hydrogen scavengers toward improving hydrogen yield in microbial electrolysis cells. Applied Energy, 2016, 183(1): 1133-1141 Read More

23. Tianle Xu, Stavros D. Veresoglou, Yongliang Chen, Matthias C. Rillig, Dan Xiang, Daniel Ondrej, Zhipeng Hao, Lei liu, Ye Deng, Yajun Hu, Weiping Chen, Juntao Wang, Jizheng He, Baodong Chen*. Plant community, geographic distance and abiotic factors play different roles in predicting AMF biogeography at the regional scale in northern China. Environmental Microbiology Reports, 2016, 8(6):1048-1057 Read More

24. Jiaojiao Niu, Jie Deng, Yunhua Xiao, Zhili He, Xian Zhang, J. D. Van Nostrand, Yili Liang, Ye Deng, Xueduan Liu, Huaqun Yin*. The shift of microbial communities and their roles in sulfur and iron cycling in a copper ore bioleaching system. Scientific Reports, 2016, 6:34744 Read More

25.邓晔*,冯凯,魏子艳,刘文宗,梁玉婷,金德才,2016. 宏基因组学在环境工程领域的应用及研究进展，环境工程学报，10(7): 3373-3382 (封面文章) Read More

26. Decai Jin, Ying Zhu, Xinxin Wang, Xiao Kong, Huijun Liu, Yafeng Wang, Ye Deng*, Minghong Jia*, 2016. Draft Genome Sequence of Sphingobium yanoikuyae TJ, a Halotolerant Di-n-Butyl-Phthalate-Degrading Bacterium. Genome Announcements, 4(3): e00569-16 Read More

1. Decai Jin, Xiao Kong, Yujie Li, Zhihui Bai*, Guoqiang Zhuang, Xuliang Zhuang, Ye Deng*. Biodegradation of di-n-Butyl Phthalate by Achromobacter sp. Isolated from Rural Domestic Wastewater. International Journal of Environmental Research and Public Health, 2015, 12(10), 13510-13522 Read More

2. Jie Ma, Ye Deng, Tong Yuan, Jizhong Zhou, Pedro J.J. Alvarez*. Succession of microbial functional communities in response to a pilot-scale ethanol-blended fuel release throughout the plume life cycle. Environmental Pollution, 2015, 198,154-160 Read More

3. Junjun Ding, Yuguang Zhang, Ye Deng, Jing Cong, Hui Lu, Xin Sun, Caiyun Yang, Tong Yuan, Joy D. Van Nostrand, Diqiang Li, Jizhong Zhou, Yunfeng Yang*. Integrated metagenomics and network analysis of soil microbial community of the forest timberline. Scientific Reports, 2015, 5, 7994-7803 Read More

4. Qingyun Yan, Yonghong Bi, Ye Deng, Zhili He, Liyou Wu, Joy D. Van Nostrand, Zhou Shi, Jinjin Li, Xi Wang, Zhengyu Hu, Yuhe Yu*, Jizhong Zhou*. Impacts of the Three Gorges Dam on microbial structure and potential function. Scientific Reports, 2015, 5, 8605 

5. Jinbo Xiong, Zhili He*, Shengjing Shi, Angela Kent, Ye Deng, Liyou Wu, Joy D. Van Nostrand, Jizhong Zhou*. Elevated CO2 shifts the functional structure and metabolic potentials of soil microbial communities in a C4 agroecosystem. Scientific Reports, 2015, 5, 9316 Read More

6. Ping Zhang, Joy D. Van Nostrand, Zhili He, Romy Chakraborty, Ye Deng, Daniel Curtis, Matthew W. Fields, Terry C. Hazen, Adam P. Arkin, Jizhong Zhou*. A slow-release substrate stimulates groundwater microbial communities for long-term in-situ Cr(VI) reduction. Environmental science & technology, 2015, 49(21):12922-12931 Read More

7. Ping Zhang, Wei-Min Wu, Joy D. Van Nostrand, Ye Deng, Zhili He, Thomas Gihring, Gengxin Zhang, Chris W. Schadt, David Watson, Phil Jardine, Craig S. Criddle, Scott Brooks, Terence L. Marsh, James M. Tiedje, Adam P. Arkin, Jizhong Zhou*. Dynamic succession of groundwater functional microbial communities in response to emulsified vegetable oil amendment during sustained in situ U(VI) reduction. Applied and environmental microbiology, 2015, 81(12): 4164-4172 Read More

8. Yuting Liang, Liyou Wu, Ian M. Clark, Kai Xue, Yunfeng Yang, Joy D. Van Nostrand, Ye Deng, Zhili He, Steve McGrath, Jonathan Storkey, Penny R. Hirsch, Bo Sun, Jizhong Zhou*. Over 150 Years of Long-Term Fertilization Alters Spatial Scaling of Microbial Biodiversity. mBio, 2015, 6(2):e00240-15 Read More

9. Jing Cong, Xueduan Liu, Hui Lu, Han Xu, Yide Li, Ye Deng, Diqiang Li, Yuguang Zhang*. Available nitrogen is the key factor influencing soil microbial functional gene diversity in tropical rainforest. BMC Microbiology, 2015, 15:167 Read More

10. Junjun Ding, Yuguang Zhang, Mengmeng Wang, Xin Sun, Jing Cong, Ye Deng, Hui Lu, Tong Yuan, Joy D. Van Nostrand, Diqiang Li, Jizhong Zhou, Yunfeng Yang*. Soil organic matter quantity and quality shape microbial community compositions of subtropical broadleaved forests. Molecular Ecology, 2015, 24(20): 5175-5185 Read More

11. Jizhong Zhou*, Zhili He, Yunfeng Yang, Ye Deng, Susannah G. Tringe, Lisa Alvarez-Cohen. High-Throughput Metagenomic Technologies for Complex Microbial Community Analysis: Open and Closed Formats. mBio, 2015, 6(1), e02288-14 Read More

12. Qichao Tu, Mengting Yuan, Zhili He, Ye Deng, Kai Xue, Liyou Wu, Sarah E. Hobbie, Peter B. Reich, Jizhong Zhou*. Fungal communities respond to long-term elevated CO2 by community reassembly. Applied and Environmental Microbiology, 2015, 81(7): 2445-2454 Read More

13. Yuguang Zhang*, Jing Cong, Hui Lu, Guangliang Li, Yadong Xue, Ye Deng, Hui Li, Jizhong Zhou, Diqiang Li. Soil bacterial diversity patterns and drivers along an elevational gradient on Shennongjia Mountain, China. Microbial Biotechnology, 2015, 8(4):739-46 Read More

14. Yuting Liang, Yuji Jiang, Feng Wang, Chongqing Wen, Ye Deng, Kai Xue, Yujia Qin, Yunfeng Yang, Liyou Wu, Jizhong Zhou*, Bo Sun*. Long-term soil transplant simulating climate change with latitude significantly alters microbial temporal turnover. The ISME Journal, 2015, 9, 2561–2572 Read More

15. Liyou Wu, Chongqing Wen, Yujia Qin, Huaqun Yin, Qichao Tu, Joy D. Van Nostrand, Tong Yuan, Menting Yuan, Ye Deng, Jizhong Zhou*. Phasing amplicon sequencing on Illumina Miseq for robust environmental microbial community analysis. BMC Microbiology, 2015, 15:125 Read More

16. Bo Yang, Xiao Kong, Bingjian Cui, Decai Jin, Ye Deng, Xuliang Zhuang, Guoqiang Zhuang, Zhihui Bai*. Impact of Rural Domestic Wastewater Irrigation on Physicochemical and Microbiological Properties of Pakchoi and Soil. Water, 2015, 7(5), 1825-1839 Read More

17. Yuanyuan Qu*, Xuwang Zhang, Qiao Ma, Jie Deng, Ye Deng, Joy D. Van Nostrand, Liyou Wu, Zhili He, Yujia Qin, Jiti Zhou, Jizhong Zhou. Microbial Community Dynamics and Activity Link to Indigo Production from Indole in Bioaugmented Activated Sludge Systems. Plos One, 2015, 10(9): e0138455 Read More

18. Christopher L. Hemme*, Qichao Tu, Zhou Shi, Yujia Qin, Weimin Gao, Ye Deng, Joy D. Van Nostrand, Liyou Wu, Zhili He, Patrick S. G. Chain, Susannah G. Tringe, Matthew W. Fields, Edward M. Rubin, James M. Tiedje, Terry C. Hazen, Adam P. Arkin, Jizhong Zhou*. Comparative metagenomics reveals impact of contaminants on groundwater microbiomes. Frontiers in Microbiology, 2015, 6:1205 Read More

19. Xiaobo Wang, Joy D. Van Nostrand, Ye Deng, XiaotaoLü, Chao Wang, Jizhong Zhou, Xingguo Han*. Scale-dependent effects of climate and geographic distance on bacterial diversity patterns across northern China’s grasslands. FEMS Microbiology Ecology, 2015, 91(12) Read More

20. Catriona A. Macdonald, Michael J. Crawley, Denis J. Wright, Justin Kuczynski, Lucinda Robinson, Rob Knight, Waleed Abu Al-Soud, Søren J. Sørensen, Ye Deng, Jizhong Zhou, Brajesh K. Singh*. Identifying qualitative effects of different grazing types on below-ground communities and function in a long-term field experiment. Environmental Microbiology, 2015, 17(3): 841-854 Read More

21.魏子艳,金德才,邓晔*,2015.环境微生物宏基因组学研究中的生物信息学方法.微生物学通报，42（5）：890-901 Read More

22.张照婧,厉舒祯,邓晔,李会杰,李端行,刘紫嫣,王经伟,沈文丽,马桥,曲媛媛*,周集体,2015.合成微生物群落及其生物处理应用研究新进展, 应用与环境生物学报. 21(6): 981-986 Read More

23.孔晓，崔丙健，金德才*，吴尚华，杨波，邓晔*，庄国强，庄绪亮，2015. 农村污水膜生物反应器系统中微生物群落解析，环境科学，36（9）：211-220 Read More

1. Hongchen Jiang#, Liuqin Huang#, Ye Deng#, Shang Wang, Yu Zhou, Li Liu, Hailiang Dong*. Latitudinal Distribution of Ammonia-Oxidizing Bacteria and Archaea in the Agricultural Soils of Eastern China. Applied and environmental microbiology, 2014, 80 (18): 5593-5602 Read More

2. Zhili He*, Jinbo Xiong, Angela D Kent, Ye Deng, Kai Xue, Gejiao Wang, Liyou Wu, Joy D Van Nostrand, Jizhong Zhou*. Distinct responses of soil microbial communities to elevated CO2 and O3 in a soybean agroecosystem. ISME Journal, 2014, 8 (3), 714-726 Read More

3. Fang Yang, Kang Ning, Xingzhi Chang, Xiao Yuan, QichaoTu, Tong Yuan, Ye Deng, Christopher L. Hemme, Joy Van Nostrand, Xinping Cui, Zhili He, Zhenggang Chen, Dawei Guo, Jian Xu*. Saliva microbiota carry caries-specific functional gene signatures. PloS One, 2014, 9 (2), e76458 Read More
 
4. Qichao Tu, Hao Yu, Zhili He, Ye Deng, Liyou Wu, Joy D. Van Nostrand, Aifen Zhou, James Voordeckers, Yong-Jin Lee, Yujia Qin, Christopher L. Hemme, Zhou Shi, Kai Xue, Tong Yuan, Aijie Wang, Jizhong Zhou*. GeoChip 4: a functional gene-array-based high-throughput environmental technology for microbial community analysis. Molecular ecology resources, 2014, 14 (5), 914-928 Read More
 
5. Qichao Tu, Zhili He*, Yan Li, Yanfei Chen, Ye Deng, Lu Lin, Christopher L. Hemme, Tong Yuan, Joy D. Van Nostrand, Liyou Wu, Xuedong Zhou, Wenyuan Shi, Lanjuan Li, Jian Xu, Jizhong Zhou*. Development of HuMiChip for Functional Profiling of Human Microbiomes. PloS One,2014,9 (3), e90546 Read More

6. Fabiana S. Paula*, Jorge L. M. Rodrigues, Jizhong Zhou, Liyou Wu, Rebecca C. Mueller, Babur S. Mirza, Brendan J. M. Bohannan, Klaus Nüsslein, Ye Deng, James M. Tiedje, Vivian H. Pellizari. Land use change alters functional gene diversity, composition and abundance in Amazon forest soil microbial communities. Molecular ecology, 2014, 23 (12), 2988-2999 Read More

7. Yanfei Chen, Nan Qin, Jing Guo, Guirong Qian, Daiqiong Fang, Ding Shi, Min Xu, Fengling Yang, Zhili He, Joy D Van Nostrand, Tong Yuan, Ye Deng, Jizhong Zhou*,Lanjuan Li*. Functional gene arrays-based analysis of fecal microbiomes in patients with liver cirrhosis. BMC Genomics, 2014, 15 (1), 753 Read More

8. Chengwei Luo, Luis M. Rodriguez-R, Eric R. Johnston, Liyou Wu, Lei Cheng, Kai Xue, Qichao Tu, Ye Deng, Zhili He, Jason Zhou Shi, Mengting Maggie Yuan, Rebecca A. Sherry, Dejun Li, Yiqi Luo, Edward A. G. Schuur, Patrick Chain, James M. Tiedje, Jizhong Zhou, Konstantinos T. Konstantinidis*. Soil microbial community responses to a decade of warming as revealed by comparative metagenomics. Applied and environmental microbiology, 2014, 80 (5), 1777-1786 Read More

9. Yan Li, Jinzhi He, Zhili He, Yuan Zhou, Mengting Yuan, Xin Xu, Feifei Sun, Chengcheng Liu, Jiyao Li, Wenbo Xie, Ye Deng, Yujia Qin, Joy D Van Nostrand, Liying Xiao, Liyou Wu, Jizhong Zhou, Wenyuan Shi*, Xuedong Zhou*. Phylogenetic and functional gene structure shifts of the oral microbiomes in periodontitis patients. The ISME Journal, 2014, 8 (9), 1879-1891 Read More

10. Jizhong Zhou*, Ye Deng, Ping Zhang, Kai Xue, Yuting Liang, Joy D. Van Nostran, Yunfeng Yang, Zhili He, Liyou Wu, David A. Stahl, Terry C. Hazen, James M. Tiedje, Adam P. Arkin. Stochasticity, succession, and environmental perturbations in a fluidic ecosystem. Proceedings of the National Academy of Sciences of the United States of America, 2014,110(9): E836–E845 Read More

11. Yunfeng Yang*, Ying Gao, Shiping Wang, Depeng Xu, Hao Yu, Linwei Wu, Qiaoyan Lin, Yigang Hu, Xiangzhen Li, Zhili He, Ye Deng, Jizhong Zhou. The microbial gene diversity along an elevation gradient of the Tibetan grassland. The ISME Journal, 2014, 8 (2), 430-440 Read More

12. Deng Y., He Z.. 2014. Microarray data analysis. In Zhili He. ed. Microarrays: Current Technology, Innovations and Applications.Horizon Scientific Press. Invited book chapter.
 
13. Deng Y. 2014. Molecular ecological network analysis. In Nelson K. ed. Encyclopedia of Metagenomics. Springer. Invited book chapter.