Publication

2024

  • Baker N, Zhalnina K, Yuan M, Herman D, Ceja-Navarro J, Sasse J, Jordan J, Bowen B, Wu L, Fossum C, Chew A, Fu Y, Saha M, Zhou J, Pett-Ridge J, Northen T, Firestone M. Nutrient and moisture limitations reveal keystone metabolites linking rhizosphere metabolomes and microbiomes. PNAS 121(32): e2303439121. https://doi.org/10.1073/pnas.2303439121
  • Kakouridis A, Yuan M, Nuccio E, Hagen A, Fossum C, Moore M, Estera-Molina K, Nico P, Weber P, Pett-Ridge J, and Firestone M. Arbuscular mycorrhiza convey significant plant carbon to a diverse hyphosphere microbial food web and mineral-associated organic matter. New Phytologist 242: 1661–1675. doi: 10.1111/nph.19560
  • Li S, Delgado‐Baquerizo M, Ding J, Hu H, Huang W, Sun Y, Ni H, Kuang Y, Yuan M, Zhou J, Zhang J, Liang Y. Intrinsic microbial temperature sensitivity and soil organic carbon decomposition in response to climate change. Global Change Biology 30(6):e17395. https://doi.org/10.1111/gcb.17395
  • Lei J, Su Y, Jian S, Guo X, Yuan M, Bates C, Shi Z, Li J, Su Y, Ning D, Wu L, Zhou J, Yang Y. Warming effects on grassland soil microbial communities are amplified in cool months. The ISME Journal 18(1): wrae088. https://doi.org/10.1093/ismejo/wrae088

2023

  • Liu C, Jiang M, Yuan M, Wang E, Bai Y, Crowther T, Zhou J, Ma Z, Zhang L, Wang Y, Ding J, Liu W, Sun B, Shen R, Zhang J. Root microbiota confers rice resistance to aluminum toxicity and phosphorus deficiency in acidic soils. Nature Food 4, 912–924. https://doi.org/10.1038/s43016-023-00848-0
  • 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 239(2): 752-765. https://doi.org/10.1111/nph.18943
  • 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 13, 561–569. https://doi.org/10.1038/s41558-023-01664-x
  • Huang D, Yuan M, Chen J, Zheng X, Wong D, and Alvarez P, Yu P. The association of prokaryotic antiviral systems and symbiotic phage communities in drinking water microbiomes, ISME Communications 3(1):46. https://doi.org/10.1038/s43705-023-00249-1
  • 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