Assistant Project Scientist
Assistant Project Scientist
Maggie is currently an assistant project scientist and a soil microbiologist at UC Berkeley. She earned her Bachelor’s degree in Environmental Engineering from Tsinghua University in Beijing, China in 2011, and got her Ph.D. in Microbiology from the University of Oklahoma in 2017, advised by Professors Jizhong Zhou and Boris Wawrik. Then she joined Professor Mary Firestone’s lab at UC Berkeley as a postdoc. Her research areas include microbial ecology, soil microbiology, and climate change microbiology.
Ph.D. Microbiology, University of Oklahoma, 2017
B.E. Environmental Engineering, Tsinghua University, 2011
Microbial ecology
Soil microbiology
Climate change biology
I am interested in exploring how things work in nature - started off counting phytoplanktons collected from urban wetlands to figure out how eutrophication affects freshwater life, I became fascinated about the tiny but mighty microorganisms in soil, one of the most heterogeneous habitat on earth. I probe into who’s there, what they are capable of doing, what they actually do, and how do microbial functions affect human-relevant soil processes in the context of different soil niches under ever-changing environment. Growing evidence indicates that soil functions are often outcomes of groups of microbes interacting each other. My recent focus is thus to capture these interactions, especially those between fungi and bacteria, in grassland soils.
Bacteria and fungi are the two most dominant groups of microorganisms that drive many essential biogeochemical cycles on the planet. However, it is only recently that complex, multitrophic, cross-domain interactions among soil organisms have been explored in depth; yet our mechanistic understanding of these interactions, especially among bacteria and fungi, and the outcomes of these interactions in the context of soil nutrient cycling are far from understood. Our team seeks to understand the fundamentals of bacterial-fungal interactions in their native soil environment, and how they determine the availability and fate of C across the complexity of soil niches, in different soil mineralogies and under reduced water availability. We use multi-comics, stable isotope probing, network analysis, modeling, and combine experiments scale from microcosms to the field to understand soil microbes and their functions.
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2023
Jiang M, Delgado-Baquerizo M, Yuan M, Ding J, Yergeau E, Zhou J, Crowther T, Liang Y. Home-based microbial solution to boost crop growth in low-fertility soil. New Phytologist (in press)
Zhang Y, Ning D, Wu L, Yuan M, Zhou X, Guo X, Hu Y, Jian S, Yang Z, Han S, Feng J, Kuang J, Cornell C, Bates C, Fan Y, Michael J, Ouyang Y, Guo J, Gao Z, Shi Z, Xiao N, Fu Y, Zhou A, Wu L, Liu X, Yang Y, Tiedje J and Zhou J. Experimental Warming Leads to Convergent Succession of Grassland Archaeal Community. Nature Climate Change (accepted)
Yu P, Huang D, Yuan M, Chen J, Zheng X, Wong D, and Alvarez P, The association of prokaryotic antiviral systems and symbiotic phage communities in drinking water microbiomes, ISME Communications (accepted)
Ji M, Fan X, Cornell CR, Zhang Y, Yuan M, Tian Z, Sun K, Gao R, Liu Y and Zhou J. Tundra soil viruses mediate responses of microbial communities to climate warming. mbio, e03009-22. DOI: https://doi.org/10.1128/mbio.03009-22
2022
Guo X, Yuan M*, Lei J, Shi Z, Zhou X, Li J, Deng Y, Yang Y, Wu L, Luo Y, Tiedje J and Zhou J. Climate warming restructures seasonal dynamics of grassland soil microbial communities. mLife. https://doi.org/10.1002/mlf2.12035
Santos-Medellín C, Estera-Molina K, Yuan M, Pett-Ridge J, Firestone M and Emerson J. Spatial turnover of soil viral populations and genotypes overlain by cohesive responses to moisture in grasslands. PNAS, 119(45): e2209132119. https://www.pnas.org/doi/10.1073/pnas.2209132119
Wu L, Zhang Y, Guo X, Ning D, Zhou X, Feng J, Yuan M, Liu S, Guo J, Gao Z, Ma J, Kuang J, Jian S, Han S, Yang Z, Ouyang Y, Fu Y, Xiao N, Liu X, Wu L, Zhou A, Yang Y, Tiedje J and Zhou J. Reduction of microbial diversity in grassland soil is driven by long-term climate warming. Nature Microbiology, 7(7), 1054-1062. https://www.nature.com/articles/s41564-022-01147-3
Xiao N, Zhou A, Kempher M, Zhou B, Shi Z, Yuan M, Guo X, Wu L, Ning D, Van Nostrand J, Firestone M and Zhou J. Disentangling direct from indirect relationships in association networks. PNAS, 119(2):e2109995119. https://www.pnas.org/doi/10.1073/pnas.2109995119
Fossum C, Estera-Molina K, Yuan M, Herman D, Chu-Jacoby I, Nico P, Morrison K, Pett-Ridge J and Firestone M. Belowground allocation and dynamics of recently fixed plant carbon in a California annual grassland soil. Soil Biology and Biochemistry, 165, 108519. https://doi.org/10.1016/j.soilbio.2021.108519
Ma X, Wang T, Shi Z, Chiariello N, Docherty K, Field C, Gutknecht J, Gao Q, Gu Y, Guo X, Hungate B, Lei J, Niboyet A, Le Roux X, Yuan M, Yuan T, Zhou J and Yang Y. Long-term nitrogen deposition enhances microbial capacities in soil carbon stabilization but reduces network complexity. Microbiome, 10, 112. https://doi.org/10.1186/s40168-022-01309-9
Escalas A, Paula F, François Guilhaumon F, Yuan M, Yang Y, Wu L, Liu F, Feng J, Zhang Y and Zhou J. Macroecological relationships highlight the functional differences between rare and common microbial genes. ISME J, 16:726–737. https://www.nature.com/articles/s41396-021-01120-8
2021
Yuan M*, Guo X, Wu L, Zhang Y, Xiao N, Ning D, Shi Z, Zhou X, Wu L, Yang Y, Tiedje J and Zhou J. Climate warming enhances microbial network complexity and stability. Nature Climate Change, 11, 343–348. https://www.nature.com/articles/s41558-021-00989-9. ESI Top 1% highly cited
Yuan M*, Kakouridis A, Starr E, Nguyen N, Shi S, Pett-Ridge J, Nuccio E, Zhou J and Firestone M. (2021) Fungal-bacterial co-occurrence patterns differ between AMF and non-mycorrhizal fungi across soil niches. mBio, 12:e03509-20. https://journals.asm.org/doi/full/10.1128/mBio.03509-20
Cheng J, Yang Y, Yuan M, Gao Q, Wu L, Qin Z, Shi Z, Schuur E, Cole J, Tiedje J and Zhou J. Winter warming rapidly increases carbon degradation capacities of fungal communities in tundra soil: potential consequences on carbon stability. Molecular Ecology, 30:926-937. https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.15773
Gao Y, Ding J, Yuan M, Chiariello N, Docherty K, Field C, Gao Q, Gu B, Gutknecht J, Hungate B, Le Roux X, Niboyet A, Qi Q, Shi, Z, Zhou J and Yang Y. Long-term warming in a Mediterranean-type grassland affects soil bacterial functional potential but not bacterial taxonomic composition, Biofilms and Microbiomes, 7:17. https://www.nature.com/articles/s41522-021-00187-7
Ceja-Navarro J, Wang Y, Ning D, Arellano A, Ramanculova L, Yuan M, Byer A, Craven K, Saha M, Brodie E, Pett-Ridge J and Firestone M. Protist diversity and community complexity in the rhizosphere of switchgrass are dynamic as plants develop. Microbiome, 9, 96. https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-021-...
Pett-Ridge J, Shi S, Estera-Molina K, Nuccio E, Yuan M, Rijkers R, Swenson T, Zhalnina K, Northen T, Zhou J and Firestone M. Rhizosphere carbon turnover from cradle to grave: the role of microbe–plant interactions. In: Gupta V, Sharma A. (eds) Rhizosphere Biology: Interactions Between Microbes and Plants. Rhizosphere Biology, Springer, Singapore. https://link.springer.com/chapter/10.1007/978-981-15-6125-2_2
2020
Guo X, Gao Q, Yuan M*, Wang G, Zhou X, Feng J, Shi J, Hale L, Wu L, Zhou A, Tian R, Liu F, Wu B, Chen L, Jung C, Niu S, Li D, Xu X, Jiang L, Escalas A, Wu L, He Z, Van Nostrand J, Ning D, Liu X, Yang Y, Schuur E, Konstantinidis K, Cole J, Penton C, Luo Y, Tiedje J and Zhou J. Gene-informed decomposition model predicts lower soil carbon loss due to persistent microbial adaptation to warming. Nature Communications, 11, 4897. https://www.nature.com/articles/s41467-020-18706-z
Yang S, Zheng Q, Yang Y, Yuan M, Ma X, Chiariello N, Docherty K, Field C, Gutknecht J, Hungate B, Niboyet A, Le Roux X and Zhou J. Fire affects the taxonomic and functional composition of soil microbial communities, with cascading effects on grassland ecosystem functioning. Global Change Biology, 26:431-442. https://onlinelibrary.wiley.com/doi/abs/10.1111/gcb.14852
Liang Y, Xiao X, Nuccio E, Yuan M, Zhang N, Xue K, Cohan F, Zhou J and Sun B. Differentiation strategies of soil rare and abundant microbial taxa in response to changing climatic regimes. Environmental Microbiology, 22:1327-1340. https://ami-journals.onlinelibrary.wiley.com/doi/abs/10.1111/1462-2920.1...
Ning D, Yuan M, Wu L, Zhang Y, Guo X, Zhou X, Yang Y, Arkin A, Firestone M and Zhou J. A quantitative framework reveals ecological drivers of grassland soil microbial community assembly in response to warming. Nature Communications, 11:4717. https://www.nature.com/articles/s41467-020-18560-z
Tao X, Feng J, Yang Y, Wang G, Tian R, Fan F, Ning D, Bates C, Hale L, Yuan M, Wu L, Gao Q, Lei J, Schuur E, Yu J, Bracho-Garillo R, Luo Y, Konstantinidis K, Johnston E, Cole J, Penton C, Tiedje J and Zhou J. Winter warming in Alaska accelerates lignin decomposition contributed by Proteobacteria. Microbiome, 8:84. https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-020-...
Feng J, Wang C, Yang Y, Yan Q, Zhou X, Tao X, Ning D, Yuan M, Qin Y, Shi Z, Guo X, He Z, Van Nostrand J, Wu L, Bracho-Garillo R, Penton C, Cole J, Konstantinidis K, Luo Y, Schuur E, Tiedje J and Zhou J. Warming-induced permafrost thaw exacerbates tundra soil carbon decomposition mediated by microbial community. Microbiome, 8:3. https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-019-...
2019
Shi Z, Yin H, Van Nostrand J, Voordeckers J, Tu Q, Deng Y, Yuan M, Zhou A, Zhang P, Xiao N, Ning D, He Z, Wu L and Zhou J. Functional gene array-based ultra-sensitive and quantitative detection of microbial populations in complex communities. mSystems, 4:e00296-19. https://journals.asm.org/doi/10.1128/mSystems.00296-19
Guo X., Zhou X, Hale L, Yuan M, Ning D, Feng J, Shi Z, Li Z, Feng B, Gao Q, Wu L, Shi W, Zhou A, Fu Y, Wu L, He Z, Van Nostrand J, Qiu G, Liu X, Luo Y, Tiedje J, Yang Y and Zhou J. Climate warming accelerates temporal scaling of grassland soil microbial biodiversity. Nature Ecology & Evolution, 3, 612–619. https://www.nature.com/articles/s41559-019-0848-8
Feng J, Penton C, He Z, Van Nostrand J, Yuan M, Wu L, Wang C, Qin Y, Shi Z, Guo X, Schuur E, Luo Y, Bracho R, Konstantinidis K, Cole J, Tiedje J, Yang Y and Zhou J. Long-term warming in Alaska enlarges the diazotrophic community in deep soils. mBio, 10:e02521-18. https://journals.asm.org/doi/10.1128/mBio.02521-18
Yang S, Zheng Q, Yuan M, Shi Z, Chiariello N, Docherty K, Dong S, Field C, Gu Y, Gutknecht J, Hungate B, Le Roux X, Ma X, Niboyet A, Yuan T, Zhou J and Yang Y. Long-term elevated CO2 shifts composition of soil microbial communities in a Californian annual grassland, reducing growth and N utilization potentials. Science of the Total Environment. 652: 1474-1481. https://doi.org/10.1016/j.scitotenv.2018.10.353
Wang, Z., Lu, G., Yuan M, Yu, H., Wang, S., Li, X., Deng, Y. Elevated temperature overrides the effects of N amendment in Tibetan grassland on soil microbiome. Soil Biology and Biochemistry, 136, https://doi.org/10.1016/j.soilbio.2019.107532
2018
Yuan M*, Zhang J, Xue K, Wu L, Deng Y, Deng, J, Hale L, Zhou X, He Z, Yang Y, Van Nostrand J, Schuur E, Konstantinidis K, Penton C, Cole J, Tiedje J, Luo Y and Zhou J. Microbial functional diversity covaries with permafrost thaw-induced environmental heterogeneity in tundra soil. Global Change Biology, 24(1), 297-307. https://onlinelibrary.wiley.com/doi/abs/10.1111/gcb.13820
Shi Z, Wu L, Lin Y, Wilcox K, Souza L, Jiang L, Jiang J, Jung C, Xu X, Yuan M, Guo X, Wu L, Zhou J and Luo Y. Successional change in species composition alters climate sensitivity of grassland productivity. Global Change Biology, 24: 4993-5003. https://onlinelibrary.wiley.com/doi/abs/10.1111/gcb.14333
Guo X, Feng J, Shi Z, Zhou X, Yuan M, Tao X, Hale L, Yuan T, Wang J, Qin Y, Zhou A, Fu Y, Wu L, He Z, Van Nostrand J, Ning D, Liu X, Luo Y, Tiedje J, Yang Y and Zhou J. Climate Warming leads to divergent succession of grassland microbial communities. Nature Climate Change, 8:813-818. https://www.nature.com/articles/s41558-018-0254-2
Guo X, Zhou X, Hale L, Yuan M, Ning D, Shi Z, Qin Y, Liu F, Wu L, He Z, Van Nostrand J, Liu X, Luo Y, Tiedje J and Zhou J. Taxonomic and functional responses of soil microbial communities to annual removal of aboveground plant biomass. Frontiers in Microbiology, 9:954. https://doi.org/10.3389/fmicb.2018.00954
2017
Feng W, Liang J, Hale L, Jung C, Chen J, Zhou J, Xu M, Yuan M, Wu L, Bracho R, Pegoraro E, Schuur E and Luo Y. Enhanced decomposition of stable soil organic carbon and microbial catabolic potentials by long-term field warming. Global Change Biology, 23:4765-4776. https://onlinelibrary.wiley.com/doi/abs/10.1111/gcb.13755
Cheng L, Zhang N, Yuan M, Xiao J, Qin Y, Deng Y, Tu Q, Xue K, Van Nostrand J, Wu L, He Z, Zhou X, Leigh M, Konstantinidis K, Schuur E, Luo Y, Tiedje J and Zhou J. Warming enhances old organic carbon decomposition through altering functional microbial communities. ISME J, 11:1825-1835. https://www.nature.com/articles/ismej201748
2016
Xue K, Yuan M*, Shi Z, Qin Y, Deng Y, Cheng L, Wu L, He Z, Van Nostrand J, Bracho R, Natali S, Schuur E, Luo C, Konstantinidis K, Wang Q, Cole J, Tiedje J, Luo Yand Zhou J. Tundra soil carbon is vulnerable to rapid microbial decomposition under climate warming. Nature Climate Change, 6, 595. https://www.nature.com/articles/nclimate2940. Highlight by the Washington Post.
Xue K, Yuan M*, Xie J, Li D, Qin Y, Hale L, Wu L, Deng Y, He Z, Van Nostrand J, Luo Y, Tiedje J and Zhou J. Annual removal of aboveground plant biomass alters soil microbial responses to warming. mBio, 7(5):e00976-00916. https://journals.asm.org/doi/10.1128/mBio.00976-16
Johnston E, Rodriguez-R L, Luo C, Yuan M, Wu L, He Z, Schuur E, Luo Y, Tiedje J, Zhou J and Konstantinidis K. Metagenomics reveals pervasive bacterial populations and reduced community diversity across the Alaska tundra ecosystem. Frontiers in Microbiology, 7(579). https://doi.org/10.3389/fmicb.2016.00579
2015 and before
Tu Q, Yuan M, He Z, Deng Y, Xue K, Wu L, Hobbie S, Reich P and Zhou J. (2015) Fungal communities respond to long-term CO2 elevation by community reassembly. Applied and Environmental Microbiology, 81(7), 2445-2454. https://journals.asm.org/doi/10.1128/AEM.04040-14
Deng J, Gu Y, Zhang J, Xue K, Qin Y, Yuan M, Yin H, He Z, Wu L, Schuur E, Tiedje J and Zhou J. (2015) Shifts of tundra bacterial and archaeal communities along a permafrost thaw gradient in Alaska. Molecular Ecology, 24(1), 222-234.
Wu L, Wen C, Qin Y, Yin H, Tu Q, Van Nostrand J, Yuan T, Yuan M, Deng Y and Zhou J. (2015) Phasing amplicon sequencing on Illumina Miseq for robust environmental microbial community analysis. BMC Microbiology, 15(1), 125. https://onlinelibrary.wiley.com/doi/10.1111/mec.13015
Luo C, Rodriguez-R L, Johnston E, Wu L, Cheng L, Xue K, Tu Q, Deng Y, He Z, Shi Z, Yuan M, Rebecca S, Li D, Luo Y, Schuur E, Chain P, Tiedje J, Zhou J and Konstantinidis K. (2014) Soil microbial community responses to a decade of warming as revealed by comparative metagenomics. Applied Environmental Microbiology, 80:1777-1786. https://journals.asm.org/doi/10.1128/AEM.03712-13. (Picked up as AEM Spotlight)
Li Y, He J, He Z, Zhou Y, Yuan M, Xu X, Sun F, Liu C, Li J, Xie W, Deng Y, Qin Y, Van Nostrand J, Xiao L, Wu L, Zhou J, Shi W and Zhou X. (2014) Phylogenetic and functional gene structure shifts of the oral microbiomes in periodontitis patients. ISME J, 8, 1879. https://www.nature.com/articles/ismej201428
Yang Y, Wu L. Lin Q, Yuan M, Xu D, Yu H, Hu Y, Duan J, Li X, He Z, Xue K, Van Nostrand J, Wang S and Zhou J. (2013) Responses of the functional structure of soil microbial community to livestock grazing in the Tibetan alpine grassland. Global Change Biology, 19:637–648. https://onlinelibrary.wiley.com/doi/abs/10.1111/gcb.12065
Institute for Environmental Genomics (IEG) Excellent Student Award, 2017
George L. and Cleo Cross Graduate Student Endowed Scholarship, University of Oklahoma, 2016
American Society of Microbiology Student Travel Grant, 2014
Contact details
Mengting "Maggie" Yuan
CV-Yuan Mengting-Mar2023-web.pdf 442 Energy Biosciences Building
2151 Berkeley way
Berkeley, CA 94704.