School of Geography and Oceanography
Nanjing University
About Professor Jonathan Adams
I am from England, in the UK, and graduated from Oxford University for my Bachelors and University of Aix-Marseille II for my PhD, followed by postdoctoral research at the University of Cambridge (UK) and Oak Ridge National Laboratory (USA). I have taught at University of Adelaide (Australia), Rutgers University (USA) and Seoul National University (South Korea) before coming to Nanjing University in 2019.
In my group, we mainly study the patterns in community structure and diversity of the countless lifeforms – such as bacteria, fungi, archaea, protozoa and small soil animals - that are too small to see with the naked eye. We use DNA gathered from soil, plant roots, or water to detect them and make sense of their patterns.
We study the microbial ecology of both natural and agricultural systems.
If you are interested in joining us, as a graduate student, postdoc or intern, please contact Prof Jonathan Adams at jonadams@nju.edu.cn or at geog.ecol@gmail.com
Current research areas include:
1) Differences in microbiome between traditional and modern crop cultivars, and their significance for crop health
2) Influences of land use change on the microbial ecology
3) Influence of dispersal limitation on microbial functions in the environment
4) Role of stochasticity (chance) in microbial community structuring
5) Effects of global change and pollutants on soil and crop microbiomes
6) The effects of ocean CO2 acidification on the microbiomes on rocks, sediments and polluting plastics
(Above) Collaborations of Jonathan Adams around the world in last 5 years. Size of circle indicates roughly the relative amount of collaborative work being done.
Teaching
I teach three courses most years.
Earth System Science (also called ‘Earth Surface Processes’ on the course rosters): Graduate level course
Biogeochemical Cycles (undergraduate)
Global Change (undergraduate)
Our lab: The Laboratory of Geographical Microbiology
Our lab includes standard DNA lab equipment – PCR machine, gel doc, centrifuges, fume cupboard etc, autoclave, plus a plate reader, and also a growth cabinet for growing plants.
(above) Inauguration Day of the newly opened Adams Lab, 2020.
Present and recent projects:
(above) Studying global change (raised CO2 and temperature) effects of crop root microbiome, in collaboration with the CAS Black Soils Institute, Harbin.
(above left) Sampling rice plants to study the effect of different farming systems, soil types and climates on the root microbiome. (above right) pH map of our sampling area in Jiangsu and Zhejiang Provinces. + symbols indicate our sampling locations.
(Above) On fieldwork at Dai Zhuang organic farming village, Jiangsu, with local village officials
(Above) Growing rice plants under controlled conditions to compare the influence of different cultivars (traditional and modern types) on the rhizosphere microbiome.
(above) Experiment to study differences in microbial community of biofilms building up on plastic bottle ‘waste’ in areas of ocean enriched in CO2, off southern Japan
(above) Imaging of soil enzyme activity in the rice rhizosphere – effects of microplastics addition to the soil.
(Above) Study of the soil microbial ecology of high elevation ecosystems in Gansu Province
(Above) Effect on soil gene composition of conversion of natural steppe to agricultural land in north-eastern China’s ‘black soil’ belt.
Google Scholar page of Jonathan Adams: https://scholar.google.com/citations?user=KI0OP5QAAAAJ&hl=en
The full list of publications since the lab was set up in 2019 (up to May 2024) is shown here. Most graduate students have produced multiple publications in international journals during their time in the lab.
Gao Y, … Adams J.M.*, Yang L. Rice rhizosphere microbiome is more diverse but less variable along environmental gradients compared to bulk soil. Plant and Soil (in press, May 2024)
Bin Song, Yue Xue, Zhenhua Yu, Yucheng He, Zihao Liu, Jie Fang, Yuchao Wang, Jonathan M. Adams*, Youning Hu, Bahar S. Razavi (2024). Toxic metal contamination effects mediated by hotspot intensity of soil enzymes and microbial community structure, Journal of Hazardous Materials, 2024, 133556,. ISSN 0304-3894,. https://doi.org/10.1016/j.jhazmat.2024.133556.. IF = 13.8
Yucheng He, Binu M Tripathi, Jie Fang, Zihao Liu, Yaping Guo, Yue Xue, Jonathan M Adams* (2023). Bacterial community network complexity and role of stochasticity decrease during primary succession. Soil Ecology Letters 6, 230218.
Zihao Liu, Fang Jie, Bin Song, Jonathan M. Adams* (2023). A regional metadata study reveals comparative patterns in diversity of M-AMF and G-AMF across China. Science of The Total Environment. 912:168907 (DOI:10.1016/j.scitotenv.2023.168907) IF = 9.8
D Kerfahi, Y Guo, K Dong, Q Wang, JM Adams* (2023). pH is the major predictor of soil microbial network complexity in Chinese forests along a latitudinal gradient. Catena 234, 107595. IF = 6.3
Junjie Liu1, Yaping Guo,,Haidong Gu, Zhuxiu Liu, Xiaojing Hu, Zhenhua Yu, Yansheng Li, Lujun Li, Yueyu Sui, Jian Jin, Xiaobing Liu, Jonathan M. Adams *, Conversion of steppe to cropland increases spatial heterogeneity of soil functional genes. The ISME Journal 17 (11), 1872-1883. https://doi.org/10.1038/s41396-023-01496-9 IF = 11.2
Zihao Liu, Zhenhua Yu, Bin Song, Yansheng Li, Jie Fang, Yaping Guo, Jian Jin, Jonathan M. Adams*. (2023). Elevated CO2 and temperature increase arbuscular mycorrhizal fungal diversity, but decreases root colonization, in maize and wheat. Science of The Total Environment. 873, 162321. IF = 10.75
B Song, S Shang, FM Cai, Z Liu, J Fang, JM Adams*, BS Razavi (2023). Microbial resistance in rhizosphere hotspots under biodegradable and conventional microplastic amendment: Community and functional sensitivity Soil Biology and Biochemistry 180, 108989. IF = 9.5
Within-species plant phylogeny drives ectomycorrhizal fungal community composition in tree roots along a timberline (2023). T Yang, L Song, HY Lin, K Dong, X Fu, GF Gao, JM Adams, H Chu. Soil Biology and Biochemistry 176, 108880. IF = 9.5
J Fang, J.M. Adams, Y Deng, X Zhu, M Hernández, Y Liu (2022). Propagule limitation affects the response of soil methane oxidizer community to increased salinity. Geoderma. 426, 116082 IF = 7.6
Zihao Liu, Jie Fang, Bin Song, Ying Yang, Zhi Yu, Junli Hu, Ke Dong, Koichi Takahashi, Jonathan M Adams* (2023). Stochastic processes dominate soil arbuscular mycorrhizal fungal community assembly along an elevation gradient in central Japan. Science of The Total Environment. 855, 158941 IF = 10.75
D Kerfahi, KK. Newsham, K. Dong, Song HK, M Tibbett, JM Adams*. (2022) Enduring legacy of coal mining on the fungal community in a High Arctic soil after five decades. Pedosphere 32 (5), 698-706 IF = 5.2
D Kerfahi, Shi Yu, Wang Baozhan, Song H, Chu Haiyan, JM Adams* (2023). Environmental similarity is more important than distance in community structuring processes of AOA in agricultural soils Pedosphere (in press) IF = 5.5
Xu S., Dong K., Lee S, MC Ogwu, S Undrakhbold, D Singh, D Ariunzaya, O Enkhmandel, LA Spence, Anarmaa Sharkhuu, BB Casper, JM Adams*, B Boldgiv (2022). Metagenetics of fairy rings reveals complex and variable fungal communities.
Pedosphere 33 (4), 567-578
Y Guo, B Song, A Li, Q Wu, H Huang, N Li, Y Yang, JM Adams*, L Yang (2022). Higher pH is associated with enhanced co‐occurrence network complexity, stability and nutrient cycling functions in the rice rhizosphere microbiome. Environmental Microbiology 24 (12), 6200-6219 IF = 5.5
Y Yang, Y Shi, J Fang, H Chu, J.M. Adams* (2022). Soil microbial network complexity varies as a continuum, not a threshold, across the North China Plain. Frontiers in Microbiology. 13. IF = 6.06
Dorsaf Kerfahi, Ben P Harvey, Hyoki Kim, Ying Yang, Jonathan M Adams*, Jason M Hall-Spencer (2022). Whole community and functional gene changes of biofilms on marine plastic debris in response to ocean acidification. Microbial Ecology IF = 4.2
Zhihuang Xie, Zhenhua Yu, Yansheng Li, Guanghua Wang, Xiaobing Liu, Caixian Tang, Tengxiang Lian, Jonathan Adams, Junjie Liu, Judong Liu, Stephen J Herbert, Jian Jin (2022). Soil microbial metabolism on carbon and nitrogen transformation links the crop-residue contribution to soil organic carbon. npj Biofilms and Microbiomes 8 (1), 1-10
Ke Dong, Zhi Yu, Dorsaf Kerfahi, Sang-seob Lee, Nan Li, Teng Yang, Jonathan M Adams* (2022). Soil microbial co-occurrence networks become less connected with soil development in a high Arctic glacier foreland succession. Science of The Total Environment 813, 152565. IF = 10.75
J Zhang, Z Yu, Y Li, G Wang, X Liu, C Tang, J Adams, J Liu, J Liu (2022). Co–elevation of CO2 and temperature enhances nitrogen mineralization in the rhizosphere of rice. Biology and Fertility of Soils, 1-13. IF = 6.6.
Hao Li, Fang Nie, Lele Zhu, Menghua Mu, Ruixiao Fan, Jingyao Li, Aaqib Shaheen, Yifan Liu, Can Li, Wenjuan Liu, Huihui Liang, Xinpeng Zhao, Shenglong Bai, Guanghui Guo, Zheng Li, Yiheng Hu, Yuannian Jiao, Jonathan Adams, Assaf Distelfeld, Guiling Sun, Suoping Li, Yun Zhou, Chun-Peng Song (2022). New insights into the dispersion history and adaptive evolution of taxon Aegilops tauschii in China. Journal of Genetics and Genomics 49 (3), 185-194
Zhi Yu, Shuqi Zou, Nan Li, Dorsaf Kerfahi, Changbae Lee, Jonathan Adams, Hyun Jeong Kwak, Jinsoo Kim, Sang‐Seob Lee, Ke Dong (2021). Elevation-related climatic factors dominate soil free-living nematode communities and their co-occurrence patterns on Mt. Halla, South Korea. Ecology and Evolution. 11 (24), 18540-18551
Ying Yang, Yu Shi, Dorsaf Kerfahi, Matthew C Ogwu, Jianjun Wang, Ke Dong, Koichi Takahashi, Itumeleng Moroenyane, Jonathan M Adams* (2021). Elevation-related climate trends dominate fungal co-occurrence network structure and the abundance of keystone taxa on Mt. Norikura, Japan. Science of the Total Environment. 799, 149368. IF = 10.75
X Liu, T Yang, Y Shi, Y Zhu, M He, Y Zhao, JM Adams, H Chu (2021). Strong partitioning of soil bacterial community composition and co-occurrence networks along a small-scale elevational gradient on Zijin Mountain. Soil Ecology Letters 3 (4), 290-302 IF = 4.2
FQ Brearley, H Song, BM Tripathi, K Dong, NM Zin, AR Abdul Rachman, Kalan Ickes, Jonathan M Adams*, Matthew S Luskin (2021).Wild pigs mediate far-reaching agricultural impacts on tropical forest soil microbial communities. bioRxiv, 2021.09. 10.459828
E Haruna, NM Zin, H Cho, JM Adams* (2021). Alternate states dominate the bacterial endophyte community of a tropical tree. Environmental Sustainability 4 (4), 785-796
X Liu, T Yang, Y Shi, Y Zhu, M He, Y Zhao, JM Adams, H Chu (2021). Strong partitioning of soil bacterial community composition and co-occurrence networks along a small-scale elevational gradient on Zijin Mountain. Soil Ecology Letters 3 (4), 290-302. IF = 4.2
Teng Yang, Leho Tedersoo, Xiao Fu, Chang Zhao, Xu Liu, Guifeng Gao, Liang Cheng, Jonathan M Adams, Haiyan Chu (2021). Saprotrophic fungal diversity predicts ectomycorrhizal fungal diversity along the timberline in the framework of island biogeography theory. ISME Communications. IF = 10.3
Z Deng, S Chen, P Zhang, X Zhang, JM Adams, Q Luo, X Lin (2021). Dynamics of Free-Living and Attached Bacterial Assemblages in Skeletonema sp. Diatom Cultures at Elevated Temperatures. Frontiers in Marine Science. 8 IF = 4.43
D Kerfahi, K Dong, Y Yang, H Kim, K Takahashi, J Adams* (2021). Elevation trend in bacterial functional gene diversity decouples from taxonomic diversity Catena 199, 105099. IF = 6.28
Xiang X, Adams J.M., et al. (2021). Nutrient improvement and soil acidification inducing contrary effects on bacterial community structure following application of hairy vetch (Vicia villosa Roth L.) in Ultisol. Agriculture, Ecosystems & Environment 312, 107348. IF = 5.57
Q Lin, L Li, JM Adams, P Heděnec, B Tu, C Li, T Li, X Li (2021). Nutrient resource availability mediates niche differentiation and temporal co-occurrence of soil bacterial communities. Applied Soil Ecology. 163, 103965.
Hokyung Song, Dorsaf Kerfahi, Koichi Takahashi, Sophie L Nixon, Binu Mani Tripathi, Hyoki Kim, Ryunosuke Tateno, Jonathan Adams* (2020) Metagenomic analysis reveals rapid development of soil biota on fresh volcanic ash. Scientific Reports 10 (1), 1-15
Kerfahi, D., Ogwu, M.C., Ariunzaya, D. et al. Adams J.M.* (2020). Metal-Tolerant Fungal Communities Are Delineated by High Zinc, Lead, and Copper Concentrations in Metalliferous Gobi Desert Soils. Microbial Ecology 79, 420–431. https://doi.org/10.1007/s00248-019-01405-8
Tirza Doniger, Jonathan M Adams*, Eugene Marais, Gillian Maggs-Kölling, Chen Sherman, Dorsaf Kerfahi, Ying Yang, Yosef Steinberger (2020). The fertile island effect of Welwitschia plants on soil microbiota is influenced by plant gender. FEMS Microbiology Ecology. 96: 11, fiaa186, https://doi.org/10.1093/femsec/fiaa186
GF Gao, D Peng, Y Zhang, Y Li, K Fan, BM Tripathi, JM Adams, H Chu (2020). Dramatic change of bacterial assembly process and co-occurrence pattern in Spartina alterinflora salt marsh. Science of the Total Environment 755, 142546
Nan Li, …Adams Jonathan, Zhao Huaxin (2020). Stochastic processes dominate marine free living Vibrio community assembly in a subtropical gulf. FEMS Microbiology Ecology.
Xing Chen, …Jonathan M. Adams, et al. (2020). Patterns and drivers of Vibrio isolates: phylogenetic diversity in Beibu Gulf, China. Journal of Microbiology 58 (12), 998-1009
BP Harvey, D Kerfahi, YG Jung, JH Shin, JM Adams*, JM Hall-Spencer (2020). Ocean acidification alters bacterial communities on marine plastic debris. Marine Pollution Bulletin 161, 111749
Feixue Shen, Lin Yang*, Xianglin He, Chenghu Zhou & Jonathan M. Adams (2020) Understanding the spatial–temporal variation of human footprint in Jiangsu province, China, its anthropogenic and natural drivers and potential implications. Scientific Reports,10:13316
Liyan Zhang, Marc G. Dumont, Paul L. Bodelier, Jonathan M. Adams, Dan He, Haiyan Chu (2020). DNA stable-isotope probing highlights the effects of temperature on functionally active methanotrophs in natural wetlands. Soil Biology & Biochemistry (in press).
Tateno, R; Tatsumi, C; Nakayama, M; Takahashi, K; Kerfahi, D; Adams, J*(2019). Temperature effects on the first three years of soil ecosystem development on volcanic ash. Catena, 172:1-10, DOI: 10.1016/j.catena.2018.08.009
Kerfahi, D; Tripathi, BM; Dong, K; Kim, M; Kim, H; Slik, JWF; Go, R; Adams, JM* (2019). From the High Arctic to the Equator: Do Soil Metagenomes Differ According to Our Expectations?. Microbial Ecology, 77(1):168-185, DOI: 10.1007/s00248-018-1215-z
Song,Ho-Kyung; Shi,Yu; Yang,Teng; Chu,Haiyan; He, Jin-Sheng; Kim, Hyoki; Jablonski, Piotr*; Adams, Jonathan M*(2019). Environmental filtering of bacterial functional diversity along an aridity gradient. Scientific Reports, 9:866, DOI:10.1038/s41598-018-37565-9
Kerfahi, D; Tripathi, BM; Slik, JWF; Sukri, RS; Jaafar, S;Dong, K; Ogwu, MC; Kim, HK; Adams, JM*(2019). Soil Metagenome of Tropical White Sand Heath Forests in Borneo: What Functional Traits Are Associated with an Extreme Environment Within the Tropical Rainforest?. Pedosphere, 29(1):12-23, DOI:10.1016/S1002-0160(18)60054-2
Hokyung Song, Dharmesh Singh, Kyle W Tomlinson, Xiaodong Yang, Matthew Chidozie Ogwu, J W Ferry Slik, Jonathan M Adams*, (2019) Tropical forest conversion to rubber plantation in southwest China results in lower fungal beta diversity and reduced network complexity, FEMS Microbiology Ecology, Volume 95, Issue 7, July 2019, fiz092, https://doi.org/10.1093/femsec/fiz092
Shen, CC; Shi, Y; Fan, KK; He, JS; Adams, JM; Ge, Y*; Chu, HY*(2019). Soil pH dominates elevational diversity pattern for bacteria in high elevation alkaline soils on the Tibetan Plateau. FEMS Microbiology Ecology, 95(2): fiz003, DOI:10.1093/femsec/fiz003
Cho, HJ; Tripathi, BM*; Moroenyane, I; Takahashi, K; Kerfahi, D; Dong, K; Adams, JM*(2019). Soil pH rather than elevation determines bacterial phylogenetic community assembly on Mt. Norikura. FEMS Microbiology Ecology, 95(3):fiy216, DOI:10.1093/femsec/fiy216
Sherman, C; Marais, E; Maggs-Kolling, G; Adams, J; Steinberger, Y*(2019). Abiotic and plant gender effects on the structure and function of soil microbial communities associated with Acanthosicyos horridus (Nara) in the Namibian sand-dune desert ecosystem. Journal of Arid Environments,163:50-58, DOI: 10.1016/j.jaridenv.2019.01.009
Singh, Dharmesh; Slik, J. W. Ferry; Jeon, Yoon-Seong; Tomlinson, Kyle W.; Yang, Xiaodong; Wang, Jin; Kerfahi, Dorsaf; Porazinska, Dorota L.; Adams, Jonathan M*(2019). Tropical forest conversion to rubber plantation affects soil micro- & mesofaunal community & diversity. Scientific Reports,9:5893, DOI:10.1038/s41598-019-42333-4
Ogwu, Matthew Chidozie; Takahashi, Koichi; Dong, Ke*; Song, Ho-Kyung; Moroenyane, Itumeleng; Waldman, Bruce; Adams, Jonathan M*(2019). Fungal Elevational Rapoport pattern from a High Mountain in Japan. Scientific Reports,9:6570, DOI:10.1038/s41598-019-43025-9
Zhang, LY; Adams, JM; Dumont, MG; Li, YT; Shi, Y; He, D; He, JS; Chu, HY*(2019). Distinct methanotrophic communities exist in habitats with different soil water contents. Soil Biology & Biochemistry,132:143-152, DOI:10.1016/j.soilbio.2019.02.007
Ogwu, Matthew Chidozie; Kerfahi, Dorsaf; Song, HoKyung; Dong, Ke; Seo, Hoseong; Lim, Sangyong; Srinivasan, Sathiyaraj; Kim, Myung Kyum*; Waldman, Bruce; Adams, Jonathan M*(2019). Changes in soil taxonomic and functional diversity resulting from gamma irradiation. Scientific Reports, 9:7894, DOI:10.1038/s41598-019-44441-7