MEM

2019

1. 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, 2019, in press

2. Kai Feng, Yuguang Zhang, Zhili He, Daliang Ning, Ye Deng*. Interdomain ecological networks between plants and microbes. Molecular Ecology Resources, 2019, https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.13081

3. 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, https://doi.org/10.1016/j.soilbio.2019.107532

4. 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

5. 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

6. 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

7. 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

8. 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

9. 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, 10.1007/s00203-019-01683-3

10. 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, www.pnas.org/cgi/doi/10.1073/pnas.1904623116

11. 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

12. 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

13. 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

14. 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

15. 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

16. 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

17. 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, 10.1039/C9EW00423H

18. 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, https://doi.org/10.1038/s41559-019-0954-7

19. 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

20. 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

21. 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

22. 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 new

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

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，微生物学通报，2019，59(6): 996-1011

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

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，in press

2018

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, DOI: 10.1111/1462-2920.14303

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

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, DOI: 10.1039/C8EW00357B.

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

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.

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.

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.

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, 628:969–978 2018.

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

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

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

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

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

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.

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.

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.

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, 1-2, Doi:10.1111/1365-2435.13091.

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, 10.1111/1462-2920.14128

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

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

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.

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

2017

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.

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.

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.

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.

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.

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.

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.

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.

9. Cheng L, Zhang N, Yuan M, Xiao J, Qin Y, Deng Y, Tu Q, Xue K, Van Nostrand JD, Wu L, He Z, Zhou X, Leigh MB, Konstantinidis KT, Schuur EA, Luo Y, Tiedje JM, Zhou J. Warming enhances old organic carbon decomposition through altering functional microbial communities. The ISME Journal, 2017, 11:1825-1835.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

2016

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.

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.

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.

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; doi:10.3390/ijms17071012.

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.

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, doi: 10.3389/fmicb.2016.00668.

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. doi:10.1128/mBio.00976-16.

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.

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.

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, DOI: 10.1007/s11368-016-1462-x.

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, DOI: 10.1111/1462-2920.13337.

12. Wang Y., Zhang R., Zheng Q., Deng Y., Van Nostrand J.D., Zhou J.*, Jiao N.*, Bacterioplankton community resilience to ocean acidification: evidence from microbial network analysis. ICES Journal of Marine Science, 2016, 73(3): 865-875.

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, doi: 10.3389/fmicb.2016.00060

14. Weiss S., Van Treuren W., Lozupone C., Faust K., Friedman J., Ye Deng., Xia L.C., Xu Z.Z., Ursell L., Alm E., Birmingham A., Cram J., Fuhrman J.A., Rae J., Sun F., Jizhong Zhou., Knight R.*, Correlation detection strategies in microbial datasets vary widely in sensitivity and precision. The ISME Journal, 2016, 10(7): 1669-1681, doi:10.1038/ismej.2015.235

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

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, doi:10.3389/fmicb.2016.01894.

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, DOI: 10.1038/srep28819.

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, doi:10.1016/j.jhazmat.2016.06.055.

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, doi: 10.3389/fmicb.2016.01184

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, http://dx.doi.org/10.3389/fmicb.2016.01447

21. YuzhanYang, Ye Deng, LeiCao*. Characterising the interspecific variations and convergence of gut microbiota in Anseriformes herbivores at wintering areas. Scientific Report, 2016, 6: 32655, doi: 10.1038/srep32655

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.

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, DOI: 10.1111/1758-2229.12485

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, doi:10.1038/srep34744.

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)

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

2015

1. Jin D., Kong X., Li Y., Bai Z.*, Zhuang G., Zhuang X., Deng Y.* 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.

2. Ma J., Deng Y., Yuan T., Zhou J., Alvarez P.J.*, 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.

3. Ding J., Zhang Y., Deng Y., Cong J., Lu H., Sun X., Yang C., Yuan T., Van Nostrand J.D., Li D., Zhou J., Yang Y.*, Integrated metagenomics and network analysis of soil microbial community of the forest timberline. Scientific Reports, 2015, 5, 7994-7803.

4. Yan Q, Bi Y, Deng Y, He Z, Wu L, Van Nostrand JD, Shi Z, Li J, Wang X, Hu Z, Yu Y*, Zhou J*. Impacts of the Three Gorges Dam on microbial structure and potential function. Scientific Reports, 2015, 5, 8605.

5. Xiong J, He Z*, Shi S, Kent A, Deng Y, Wu L, Van Nostrand JD, Zhou J*. Elevated CO2 shifts the functional structure and metabolic potentials of soil microbial communities in a C4 agroecosystem. Scientific Reports, 2015, 5, 9316.

6. Zhang P, Van Nostrand JD, He Z, Chakraborty R, Deng Y, Curtis D, Fields MW, Hazen TC, Arkin AP, Zhou J*. A slow-release substrate stimulates groundwater microbial communities for long-term in-situ Cr(VI) reduction. Environmental science & technology, 2015, 49(21):12922-12931.

7. Zhang P, Wu WM, Van Nostrand JD, Deng Y, He Z, Gihring T, Zhang G, Schadt C, Watson D, Jardine P, Criddle C, Brooks S, Marsh T, Tiedje J, Arkin A, Zhou J*. 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.

8. Liang Y, Wu L, Clark IM, Xue K, Yang Y, Van Nostrand JD, Deng Y, He Z, McGrath S, Storkey J, Hirsch PR, Sun B, Zhou J*. Over 150 Years of Long-Term Fertilization Alters Spatial Scaling of Microbial Biodiversity. mBio, 2015, 6(2):e00240-15.

9. Cong J, Liu X, Lu H, Xu H, Li Y, Deng Y, Li D, Zhang Y*. Available nitrogen is the key factor influencing soil microbial functional gene diversity in tropical rainforest. BMC Microbiology, 2015, 15:167.

10. Ding J, Zhang Y, Wang M, Sun X, Cong J, Deng Y, Lu H, Yuan T, Yang Y, Van Nostrand JD, Li D, Zhou J, Yang Y*. Soil organic matter quantity and quality shape microbial community compositions of subtropical broadleaved forests. Molecular Ecology, 2015, 24(20): 5175-5185.

11. Zhou J.*, He Z., Yang Y., Deng Y., Tringe S.G., Alvarez-Cohen L., High-Throughput Metagenomic Technologies for Complex Microbial Community Analysis: Open and Closed Formats. mBio, 2015, 6(1), e02288-14.

12. Tu Q, Yuan M, He Z, Deng Y, Xue K, Wu L, Hobbie SE, Reich PB, Zhou J*. Fungal communities respond to long-term elevated CO2 by community reassembly. Applied and Environmental Microbiology, 2015, 81(7): 2445-2454.

13. Zhang Y*, Cong J, Lu H, Li G, Xue Y, Deng Y, Li H, Zhou J, Li D. Soil bacterial diversity patterns and drivers along an elevational gradient on Shennongjia Mountain, China. Microbial Biotechnology, 2015, 8(4):739-46.

14. Liang Y., Jiang Y., Wang F., Wen C., Deng Y., Xue K., Qin Y., Yang Y., Wu L., Zhou J.*, Sun B.*, Long-term soil transplant simulating climate change with latitude significantly alters microbial temporal turnover. The ISME Journal, 2015, 9, 2561–2572.

15. Wu L., Wen C., Qin Y., Yin H., Tu Q., Van Nostrand J.D., Tong Y., Yuan M., Deng Y., Zhou J.*, Phasing amplicon sequencing on Illumina Miseq for robust environmental microbial community analysis. BMC Microbiology, 2015, 15:125

16. Yang B., Kong X., Cui B., Jin D., Deng Y., Zhuang X., Zhuang G., Bai Z.*, Impact of Rural Domestic Wastewater Irrigation on Physicochemical and Microbiological Properties of Pakchoi and Soil. Water, 2015, 7(5), 1825-1839.

17. Qu Y, Zhang X, Ma Q, Deng J, Deng Y, Van Nostrand J.D, Wu L, He Z, Qin Y, Zhou J, Zhou J. Microbial Community Dynamics and Activity Link to Indigo Production from Indole in Bioaugmented Activated Sludge Systems. Plos One, 2015, 10(9): e0138455.

18. Hemme C.L.*, Tu Q., Shi Z., Qin Y., Gao W., Deng Y., Van Nostrand J.D., Wu L., He Z., Chain P.S.G., Tringe S.G., Fields M.W., Rubin E., Tiedje J.M., Hazen T.C., Zhou J*. Comparative metagenomics reveals impact of contaminants on groundwater microbiomes. Frontiers in Microbiology, 2015, 6:1205.

19. Wang X., Van Nostrand J.D., Deng Y., Lu X., Wang C., Zhou J., Han X.*, Scale-dependent effects of climate and geographic distance on bacterial diversity patterns across northern China’s grasslands. FEMS Microbiology Ecology, 2015, 91(12), doi: 10.1093/femsec/fiv133

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.

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.

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.

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.

2014

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

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

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

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

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.

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

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

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.

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.

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.

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.

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.