Mechanisms underlying the structural and functional evolution of microbial communities in response to disturbance;

Microbial transformation and degradation of soil pollutants.

Dr. Yuan Ge is a Professor at the Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (RCEES, CAS). He received his Ph.D. degree from the RCEES, CAS in 2009. Then he was appointed as an Assistant Specialist and Associate Specialist at the University of California, Santa Barbara from 2009 to 2015. He was appointed as a Professor at the RCEES, CAS and University of Chinese Academy of Sciences, and was funded by the CAS Outstanding Oversea Talent Program in 2015. Dr. Ge’s research has been published in many esteemed journals including PNAS, ISME Journal, Environmental Science & Technology, mBio, Journal of Ecology, Molecular Ecology, and Environmental Microbiology, etc.

2016-, Frontiers in Soil Biology, for graduate students
2015-, Soil Biology, for graduate students

Selected Publications (#Equal contribution; *Corresponding author)

2023

1)           Sai Qu; Congcong Shen; Lin Zhang; Jichen Wang; Li-Mei Zhang; Baodong Chen; Guo-Xin Sun; Yuan Ge*. Dispersal limitation and host selection drive geo-specific and plant-specific differentiation of soil bacterial communities in the Tibetan alpine ecosystem. Science of the Total Environment, 2023, 863: 160944.

2)           Yao‑Qin Sun; Yuan Ge*. Relic DNA effects on the estimates of bacterial community composition and taxa dynamics in soil. Applied Microbiology and Biotechnology, 2023, doi: 10.1007/s00253-023-12576-3.

3)           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, 307: 3033–3045.

4)           Yongli Xu#; Liyao Zhu#; Raja Vukanti; Jichen Wang; Congcong Shen; Yuan Ge*. Nano-Nd2O3 reduced soil bacterial community function by altering the relative abundance of rare and sensitive taxa. Environmental Science and Pollution Research, 2023, doi: 10.1007/s11356-023-27979-y.

5)           Dong-Hui Zhao; Cong-Cong Shen; Zhi-Ming Zhang; Si-Yi Liu; Bao-Dong Chen; Dong-Li Sun; Ji-Chen Wang; Yuan Ge*. Coupling relationship between soil functions and environmental factors along an altitudinal gradient: a case study of the Meili Mountain. Environmental Science (in Chinese with English abstract), 2023, 44(2): 924-931. 赵冬辉; 申聪聪; 张志明; 刘四义; 陈保冬; 孙东丽; 王继琛; 葛源*. 土壤功能与环境因素在海拔梯度上的耦合关系: 以梅里雪山为例. 环境科学, 2023, 44(2): 924-931.

6)           Bo-Jian Li; Cong-Cong Shen; Si-Yi Liu; Hua-Yong Wu; Ji-Chen Wang; Dong-Hui Zhao; Yuan Ge*. Horizontal variation characteristics of alpine grassland soil function and vertical changes along soil genetic horizons in the Three-River Headwaters region. Environmental Science (in Chinese with English abstract) , 2023, 44(3): 1562-1571. 李柏键; 申聪聪; 刘四义; 吴华勇; 王继琛; 赵冬辉; 葛源*.三江源地区高寒草地土壤功能的水平分异特征及其沿发生层的垂直变化. 环境科学, 2023, 44(3): 1562-1571.

2022

1)           Yan Li#; Jiang Wang#; Congcong Shen; Jichen Wang; Brajesh K. Singh; Yuan Ge*. Plant diversity improves resistance of plant biomass and soil microbial communities to drought. Journal of Ecology, 2022, 110: 1656-1672.

2)           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.

3)           Zhongwang Jing#; Jiang Wang#; Yi Bai; Yuan Ge*. Faunal communities mediate the effects of plant richness, drought, and invasion on ecosystem multifunctional stability. Communications Biology, 2022, 5:527.

4)           Congcong Shen; Jiang Wang; Zhongwang Jing; Neng-Hu Qiao; Chao Xiong; Yuan Ge*. Plant diversity enhances soil fungal network stability indirectly through the increase of soil carbon and fungal keystone taxa richness. Science of the Total Environment, 2022, 818: 151737.

5)           Bojian Li#; Congcong Shen#; Hua-Yong Wu; Li-Mei Zhang; Jichen Wang; Siyi Liu; Zhongwang Jing; Yuan Ge*. Environmental selection dominates over dispersal limitation in shaping bacterial biogeographical patterns across different soil horizons of the Qinghai-Tibet Plateau. Science of the Total Environment, 2022, 838: 156177.

6)           Junnan Fang; Xue-Ting Bai; Lin Qi; Raja Vukanti; Yuan Ge*. Rare-earth metal oxide nanoparticles decouple the linkage between soil bacterial community structure and function by selectively influencing potential keystone taxa. Environmental Pollution, 2022, 298: 118863.

7)           Jichen Wang; Jiang Wang; Ji-Zheng He; Zhongwang Jing; Yongli Xu; Yuan Ge*. Arbuscular mycorrhiza fungi increase soil denitrifier abundance relating to vegetation community. Applied Soil Ecology, 2022, 171(16): 104325.

8)           Jiang Wang#; Yuan Ge#; Johannes H. C. Cornelissen; Xiao‑Yan Wang; Song Gao; Yi Bai; Tong Chen; Zhong‑Wang Jing; Chong‑Bang Zhang; Wen‑Li Liu; Jun‑Min Li; Fei‑Hai Yu*. Litter nitrogen concentration changes mediate effects of drought and plant species richness on litter decomposition. Oecologia, 2022, 198:507-518. 

2021

1)           Yuan Ge#*; Zhongwang Jing#; Qingyun Diao; Ji-Zheng He; Yong-Jun Liu*. Host species and geography differentiate honeybee gut bacterial communities by changing the relative contribution of community assembly processes. mBio, 2021, 12(3): e00751-21.

2)           Yan Li#; Yuan Ge#*; Jichen Wang; Congcong Shen; Jianlei Wang; Yong-Jun Liu. Functional redundancy and specific taxa modulate the contribution of prokaryotic diversity and composition to multifunctionality. Molecular Ecology, 2021, 30(12): 2915-2930.

3)           Jichen Wang#; Jiang Wang#; Ji-Zheng He; Yong-Guan Zhu; Neng-Hu Qiao; Yuan Ge*. Arbuscular mycorrhizal fungi and plant diversity drive restoration of nitrogen-cycling microbial communities. Molecular Ecology, 2021, 30(16): 4133-4146.

4)           Congcong Shen#; Jiang Wang#; Ji-Zheng He; Fei-Hai Yu; Yuan Ge*. Plant diversity enhances soil fungal diversity and microbial resistance to plant invasion. Applied & Environmental Microbiology, 2021, 87(11): e00251-21.

5)           Congcong Shen; Ji-Zheng He; Yuan Ge*. Seasonal dynamics of soil microbial diversity and functions along elevations across the treeline. Science of the Total Environment, 2021, 794: 148644.

6)           Yan Yue; Yong-Jun Liu; Jichen Wang; Raja Vukanti; Yuan Ge*. Enrichment of potential degrading bacteria accelerates removal of tetracyclines and their epimers from cow manure biochar amended soil. Chemosphere, 2021, 278: 130358.

7)           Yao-Qin Sun; Yuan Ge*. Temporal changes in the function of bacterial assemblages associated with decomposing earthworms. Frontiers in Microbiology, 2021, 12: 682224.

8)           Yong-Jun Liu#*; Zhongwang Jing#; Xue-Ting Bai#; Qing-Yun Diao; Jichen Wang; Yan-Yan Wu; Qing Zhao; Tian Xia; Baoshan Xing; Patricia A. Holden; Yuan Ge*. Nano-La2O3 induces honeybee (Apis mellifera) death and enriches for pathogens in honeybee gut bacterial communities. Frontiers in Microbiology, 2021, 12: 780943.

9)           Jianlei Wang#; Qingkang Li#; Congcong Shen#; Fengting Yang; Jichen Wang; Yuan Ge*. Significant dose effects of fertilizers on soil diazotrophic diversity, community composition, and assembly processes in a long-term paddy field fertilization experiment. Land Degradation & Development, 2021, 32(1): 420-429.

10)        Xue-Ting Bai; Jichen Wang; Hailiang Dong; Jia-Min Chen; Yuan Ge*. Relative importance of soil properties and heavy metals/metalloids to modulate microbial community and activity at a smelting site. Journal of Soils and Sediments, 2021, 21(1): 1-12.

11)        Xiao-Yan Wang#; Yuan Ge#; Song Gao; Tong Chen; Jiang Wang*; Fei-Hai Yu*. Evenness alters the positive effect of species richness on community drought resistance via changing complementarity. Ecological Indicators, 2021, 133: 108464.

2020

1)           Yong-Jun Liu#; Neng-Hu Qiao#; Qing-Yun Diao; Zhongwang Jing; Raja Vukanti; Ping-Li Dai; Yuan Ge*. Thiacloprid exposure perturbs the gut microbiota and reduces the survival status in honeybees. Journal of Hazardous Materials, 2020, 389: 121818.

2)           Congcong Shen#; Anna Gunina#; Yu Luo*; Jianjun Wang; Ji-Zheng He; Yakov Kuzyakov; Andreas Hemp; Aimée T. Classen; Yuan Ge*. Contrasting patterns and drivers of soil bacterial and fungal diversity across a mountain gradient. Environmental Microbiology, 2020, 22(8): 3287-3301.

3)           Yan Yue; Lin Qi; Yan Li; Jichen Wang; Congcong Shen; Yuan Ge*. Negative effects of rare earth oxide nanoparticles of La2O3, Nd2O3, and Gd2O3 on the ammonia-oxidizing microorganisms. Journal of Soils and Sediments, 2020, 20: 3114-3123.

2019

1)           Yan Li#; Zhan Chen#; Ji-Zheng He; Qing Wang; Congcong Shen; Yuan Ge*. Ectomycorrhizal fungi inoculation alleviates simulated acid rain effects on soil ammonia oxidizers and denitrifiers in Masson pine forest. Environmental Microbiology, 2019, 21(1): 299-313.

2)           Lin Qi#; Yuan Ge#*; Tian Xia; Ji-Zheng He; Congcong Shen; Jianlei Wang; Yong-Jun Liu. Rare earth oxide nanoparticles promote soil microbial antibiotic resistance by selectively enriching antibiotic resistance genes. Environmental Science: Nano, 2019, 6(2): 456-466.

3)           Yan Yue; Congcong Shen; Yuan Ge*. Biochar accelerates the removal of tetracyclines and their intermediates by altering soil properties. Journal of Hazardous Materials, 2019, 380: 120821.

4)           Jichen Wang; Jianlei Wang; Geoff Rhodes; Ji-Zheng He; Yuan Ge*. Adaptive responses of comammox Nitrospira and canonical ammonia oxidizers to long-term fertilizations: Implications for the relative contributions of different ammonia oxidizers to soil nitrogen cycling. Science of the Total Environment, 2019, 668: 224-233.

5)           Yao-Qin Sun; Jiang Wang; Congcong Shen; Ji-Zheng He; Yuan Ge*. Plant evenness modulates the effect of plant richness on soil bacterial diversity. Science of the Total Environment, 2019, 662: 8-14.

6)           Congcong Shen; Yu Shi; Kunkun Fan; Jin-Sheng He; Jonathan M. Adams; Yuan Ge*; Haiyan Chu*. Soil pH dominates elevational diversity pattern for bacteria in high elevation alkaline soils on the Tibetan Plateau. FEMS Microbiology Ecology, 2019, 95(2): fiz003.

7)           Congcong Shen; Dawei Ma; Ruibo Sun; Benyao Zhang; Delin Li; Yuan Ge*. Long-term stacking coal promoted soil bacterial richness associated with increased soil organic matter in coal yards of power plants. Journal of Soils and Sediments, 2019, 19(10): 3442-3452.

2018 and before

1)           Yuan Ge; Congcong Shen; Ying Wang; Yao-Qin Sun; Joshua P. Schimel; Jorge L. Gardea-Torresdey; Patricia A. Holden*. Carbonaceous nanomaterials have higher effects on soybean rhizosphere prokaryotic communities during the reproductive growth phase than during vegetative growth. Environmental Science & Technology, 2018, 52(11): 6636-6646.

2)           Yuan Ge; John H. Priester; Monika Mortimer; Chong Hyun Chang; Zhaoxia Ji; Joshua P. Schimel; Patricia A. Holden*. Long-term effects of multiwalled carbon nanotubes and graphene on microbial communities in dry soil. Environmental Science & Technology, 2016, 50(7): 3965-3974.

3)         Yuan Ge; Allison M. Horst; Junyeol Kim; John H. Priester; Zoe S. Welch; Patricia A. Holden. Toxicity of manufactured nanomaterials to microorganisms. In Baoshan Xing; Chad D. Vecitis; Nicola Senesi (Eds), Engineered Nanoparticles and the Environment: Biophysicochemical Processes and and Biotoxicity (pp. 320-346), John Wiley & Sons, 2016, Chapter 17.

4)           孙耀琴; 申聪聪; 葛源*. 典型纳米材料的土壤微生物效应研究进展. 生态毒理学报, 2016, 11(5): 2-13.

5)           Yuan Ge; John H. Priester; Laurie C. Van De Werfhorst; Sharon L. Walker; Roger M. Nisbet; Youn-Joo An; Joshua P. Schimel; Jorge L. Gardea-Torresdey; Patricia A. Holden*. Soybean plants modify metal oxide nanoparticle effects on soil bacterial communities. Environmental Science & Technology, 2014, 48(22): 13489-13496.

6)           Yuan Ge; Joshua P. Schimel; Patricia A. Holden*. Analysis of run-to-run variation of bar-coded pyrosequencing for evaluating bacterial community shifts and individual taxa dynamics. PLoS One, 2014, 9(6): e99414.

7)           Jiang Wang; Yuan Ge*; Tong Chen; Yi Bai; Bao Ying Qian; Chong Bang Zhang. Facilitation drives the positive effects of plant richness on trace metal removal in a biodiversity experiment. PLoS One, 2014, 9(4): e93733.

8)           Yuan Ge; John H. Priester; Laurie C. Van De Werfhorst; Joshua P. Schimel; Patricia A. Holden*. Potential mechanisms and environmental controls of TiO2 nanoparticle effects on soil bacterial communities. Environmental Science & Technology, 2013, 47(24): 14411-14417.

9)           Jiang Wang; Yuan Ge*; Chong B. Zhang; Yi Bai; Zhao K. Du. Dominant functional group effects on the invasion resistance at different resource levels. PLoS One, 2013, 8(10): e77220.

10)        Yuan Ge; Joshua P. Schimel; Patricia A. Holden*. Identification of soil bacteria susceptible to TiO2 and ZnO nanoparticles. Applied and Environmental Microbiology, 2012, 78(18): 6749-6758.

11)        John H. Priester; Yuan Ge; Randall E. Mielke; Allison M. Horst; Shelly Cole Moritz; Katherine Espinosa; Jeff Gelb; Sharon L. Walker; Roger M. Nisbet; Youn-Joo An; Joshua P. Schimel; Reid G. Palmer; Jose A. Hernandez-Viezcas; Lijuan Zhao; Jorge L. Gardea-Torresdey; Patricia A. Holden*. Soybean susceptibility to manufactured nanomaterials with evidence for food quality and soil fertility interruption. Proceedings of the National Academy of Sciences of the United States of America, 2012, 109(37): E2451-E2456.

12)        Yuan Ge; Joshua P. Schimel; Patricia A. Holden*. Evidence for negative effects of TiO2 and ZnO nanoparticles on soil bacterial communities. Environmental Science & Technology, 2011, 45(4): 1659-1664.

13)        Yuan Ge; Chengrong Chen*; Zhihong Xu; Ram Oren; Ji-Zheng He*. The spatial factor, rather than elevated CO2, controls the soil bacterial community in a temperate forest ecosystem. Applied and Environmental Microbiology, 2010, 76(22): 7429-7436.

14)        Yuan Ge; Chengrong Chen*; Zhihong Xu; Simon M. Eldridge; Kwong Yin Chan; Yan He; Ji-Zheng He*. Carbon/nitrogen ratio as a major factor for predicting the effects of organic wastes on soil bacterial communities assessed by DNA-based molecular techniques. Environmental Science and Pollution Research, 2010, 17(3): 807-815.

15)        Ji-Zheng He#*; Yuan Ge#; Zhihong Xu; Chengrong Chen. Linking soil bacterial diversity to ecosystem multifunctionality using backward-elimination boosted trees analysis. Journal of Soils and Sediments, 2009, 9(6): 547-554.

16)        Yuan Ge; Ji-Zheng He*; Yong-Guan Zhu; Jia-Bao Zhang; Zhihong Xu; Li-Mei Zhang; Yuan-Ming Zheng. Differences in soil bacterial diversity: driven by contemporary disturbances or historical contingencies?. The ISME Journal, 2008, 2(3): 254-264.

17)        Yuan Ge; Jia-Bao Zhang; Li-Mei Zhang; Min Yang; Ji-Zheng He*. Long-term fertilization regimes affect bacterial community structure and diversity of an agricultural soil in northern China. Journal of Soils and Sediments, 2008, 8(1): 43-50.

18)        贺纪正*; 葛源. 土壤微生物生物地理学研究进展. 生态学报, 2008, 28(11): 5571-5582.

19)        葛源; 贺纪正*; 郑袁明; 张丽梅; 朱永官. 稳定性同位素探测技术在微生物生态学研究中的应用. 生态学报, 2006, 26(5): 1574-1582.