1. 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, doi.org/10.1016/j.scib.2021.01.021
2. 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
3. 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
4. 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
5. 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
6. 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, DOI: 10.3389/fmicb.2021.629852
9. 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, accepted
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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,2019,38(11): 1-12
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
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, 4: 1839-1850
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
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
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.
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.
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.
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
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.
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.
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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
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.
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Deng lab, Metagenomics for Environmental Microbiology