Falkowski PG, Tom F, Delong EF. The microbial engines that drive Earth’s biogeochemical cycles. Science. 2008;320:1034–9.
Patricia B, Pfisterer AB, Nina B, Jing-Shen H, Tohru N, David R, et al. Quantifying the evidence for biodiversity effects on ecosystem functioning and services. Ecol Lett. 2010;9:1146–56.
Griffiths BS, Laurent P. Insights into the resistance and resilience of the soil microbial community. FEMS Microbiol Rev. 2013;37:112–29.
Tripathi BM, Stegen JC, Kim M, Dong K, Adams JM, Lee YK. Soil pH mediates the balance between stochastic and deterministic assembly of bacteria. ISME J. 2018;12:1072–83.
Shade A, Peter H, Allison SD, Baho D, Berga M, Buergmann H, et al. Fundamentals of microbial community resistance and resilience. Front Microbiol. 2012;3:417.
Jurburg SD, Nunes I, Brejnrod A, Jacquiod S, Priemé A, Sørensen SJ, et al. Legacy effects on the recovery of soil bacterial communities from extreme temperature perturbation. Front Microbiol. 2017;8:1832.
de Nijs EA, Hicks LC, Leizeaga A, Tietema A, Rousk J. Soil microbial moisture dependences and responses to drying-rewetting: the legacy of 18 years drought. Glob Chang Biol. 2019;25:1005–15.
Fuhrman JA, Cram JA, Needham DM. Marine microbial community dynamics and their ecological interpretation. Nat Rev Microbiol. 2015;13:133–46.
Wertz S, Degrange V, Prosser JI, Poly F, Commeaux C, Guillaumaud N, et al. Decline of soil microbial diversity does not influence the resistance and resilience of key soil microbial functional groups following a model disturbance. Environ Microbiol. 2007;9:2211–9.
Cruz Martã Nez K, Suttle KB, Brodie EL, Power ME, Andersen GL, Banfield JF. Despite strong seasonal responses, soil microbial consortia are more resilient to long-term changes in rainfall than overlying grassland. ISME J. 2009;3:738–44.
Girvan MS, Campbell CD, Killham K, Prosser JI, Glover LA. Bacterial diversity promotes community stability and functional resilience after perturbation. Environ Microbiol. 2005;7:301–13.
Loreau M, De MC. Biodiversity and ecosystem stability: a synthesis of underlying mechanisms. Ecol Lett. 2013;16:106–15.
Gamfeldt L, Lefcheck JS, Byrnes JEK, Cardinale BJ, Duffy JE, Griffin JN. Marine biodiversity and ecosystem functioning: what’s known and what’s next? Oikos. 2015;124:252–65.
Bardgett RD, van der Putten WH. Belowground biodiversity and ecosystem functioning. Nature. 2014;515:505–11.
Schimel J, Schaeffer SM. Microbial control over carbon cycling in soil. Front Microbiol. 2012;3:348.
Banerjee S, Kirkby CA, Schmutter D, Bissett A, Kirkegaard JA, Richardson AE. Network analysis reveals functional redundancy and keystone taxa amongst bacterial and fungal communities during organic matter decomposition in an arable soil. Soil Biol Biochem. 2016;97:188–98.
Banerjee S, Walder F, Büchi L, Meyer M, Held AY, Gattinger A, et al. Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots. ISME J. 2019;13:1722–36.
Banerjee S, Schlaeppi K, van der Heijden MGA. Keystone taxa as drivers of microbiome structure and functioning. Nat Rev Microbiol. 2018;16:567–76.
Niu B, Paulson JN, Zheng X, Kolter R. Simplified and representative bacterial community of maize roots. Proc Natl Acad Sci U S A. 2017;114:2450–9.
Faust K, Raes J. Microbial interactions: from networks to models. Nat Rev Microbiol. 2012;10:538–50.
Zhang J, Liu Y-X, Zhang N, Hu B, Jin T, Xu H, et al. NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice. Nat Biotechnol. 2019;37:676–84.
Ramirez KS, Knight CG, de Hollander M, Brearley FQ, Constantinides B, Cotton A, et al. Detecting macroecological patterns in bacterial communities across independent studies of global soils. Nat Microbiol. 2018;3:189–96.
Schluter J, Foster KR. The evolution of mutualism in gut microbiota via host epithelial selection. PLoS Biol. 2012;10:e1001424.
Bucci V, Bradde S, Biroli G, Xavier JB. Social interaction, noise and antibiotic-mediated switches in the intestinal microbiota. PLoS Computat Biol. 2012;8:e1002497.
Coyte KZ, Schluter J, Foster KR. The ecology of the microbiome: networks, competition, and stability. Science. 2015;350:663–6.
Nichols D, Cahoon N, Trakhtenberg EM, Pham L, Mehta A, Belanger A, et al. Use of ichip for high-throughput in situ cultivation of “uncultivable” microbial species. Appl Environ Microbiol. 2010;76:2445–50.
Gavrish E, Bollmann A, Epstein S, Lewis K. A trap for in situ cultivation of filamentous actinobacteria. J Microbiol Methods. 2008;72:257–62.
Chen S-K, Edwards CA. A microcosm approach to assess the effects of fungicides on soil ecological processes and plant growth: comparisons of two soil types. Soil Biol Biochem. 2001;33:1981–91.
Yan Y, Kuramae EE, de Hollander M, Klinkhamer PGL, van Veen JA. Functional traits dominate the diversity-related selection of bacterial communities in the rhizosphere. ISME J. 2017;11:56–66.
Philippot L, Spor A, Hénault C, Bru D, Bizouard F, Jones CM, et al. Loss in microbial diversity affects nitrogen cycling in soil. ISME J. 2013;7:1609–19.
Calderón K, Spor A, Breuil M-C, Bru D, Bizouard F, Violle C, et al. Effectiveness of ecological rescue for altered soil microbial communities and functions. ISME J. 2017;11:272–83.
Xun W, Li W, Xiong W, Ren Y, Liu Y, Miao Y, et al. Diversity-triggered deterministic bacterial assembly constrains community functions. Nat Commun. 2019;10:3833.
Rowell DL. Soil science: methods & applications. New York: Longman Scientific & Technical; 1994.
McNamara NP, Black HIJ, Beresford NA, Parekh NR. Effects of acute gamma irradiation on chemical, physical and biological properties of soils. Appl Soil Ecol. 2003;24:117–32.
Xun W, Li W, Huang T, Ren Y, Xiong W, Miao Y, et al. Long-term agronomic practices alter the composition of asymbiotic diazotrophic bacterial community and their nitrogen fixation genes in an acidic red soil. Biol Fertil Soils. 2018;54:329–39.
Walters WA, Caporaso JG, Lauber CL, Berg-Lyons D, Fierer N, Knight R. PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers. Bioinformatics. 2011;27:1159–61.
Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods. 2013;10:996–8.
Peng Y, Leung HCM, Yiu SM, Chin FYL. IDBA – a practical iterative de bruijn graph de novo assembler. Lect Notes Comput Sc. 2010;6044:426–40.
Noguchi H, Park J, Takagi T. MetaGene: prokaryotic gene finding from environmental genome shotgun sequences. Nucleic Acids Res. 2006;34:5623–30.
Gu S, Fang L, Xu X. Using SOAPaligner for short reads alignment. Curr Protoc Bioinformatics. 2013;44(11.11):1–17.
Jiang G, Wang W. Error estimation based on variance analysis of k -fold cross-validation. Pattern Recogn. 2017;69:94–106.
Rodríguez-Pérez R, Fernández L, Marco S. Overoptimism in cross-validation when using partial least squares-discriminant analysis for omics data: a systematic study. Anal Bioanal Chem. 2018;410:5981–92.
Therneau T, Atkinson B, Ripley B. Recursive partitioning and regression trees. R package version 4.1-15. 2019; Available online: https://cran.pau.edu.tr/web/packages/rpart/rpart.pdf
Esteban A, Matias G, Noelia G. Applies multiclass AdaBoost.M1, SAMME and Bagging. R package version 4.1. 2015; Available online: https://ufal.mff.cuni.cz/~holub/2016/docs/adabag.pdf
Schliep K, Hechenbichler K, Lizee A. Weighted k-nearest neighbors. R package version 1.3.1. 2016; Available online: http://ftp5.gwdg.de/pub/misc/cran/web/packages/kknn/kknn.pdf
Karatzoglou A, Smola A, Hornik K, Maniscalco MA., Teo CH. Kernel-based machine learning lab. R package version 0.9-29. 2019; Available online: http://cran.rediris.es/web/packages/kernlab/kernlab.pdf
Breiman L, Cutler A, Liaw A, Matthew W. Breiman and Cutler’s random forests for classification and regression. R package version 4.6-7. 2012; Available online: https://ufal.mff.cuni.cz/~holub/2014/docs/randomForest.manual.pdf
Ripley B, Venables W. Feed-forward neural networks and multinomial log-linear models. R package version 7.3-12. 2016; Available online: https://mran.microsoft.com/snapshot/2016-06-17/web/packages/nnet/nnet.pdf
Hausmann B, Pelikan C, Herbold CW, Köstlbacher S, Albertsen M, Eichorst SA, et al. Peatland Acidobacteria with a dissimilatory sulfur metabolism. ISME J. 2018;12:1729–42.
Mus F, Crook MB, Garcia K, Costas AG, Geddes BA, Kouri ED, et al. Symbiotic nitrogen fixation and the challenges to its extension to nonlegumes. Appl Environ Microbiol. 2016;82:3698–710.
Chen J, Zhou HC, Pan Y, Shyla FS, Tam NF-Y. Effects of polybrominated diphenyl ethers and plant species on nitrification, denitrification and anammox in mangrove soils. Sci Total Environ. 2016;553:60–70.
Lever MA. A new era of methanogenesis research. Trends Microbiol. 2016;24:84–6.
Zhu G, Zhou L, Wang Y, Wang S, Guo J, Long X-E, et al. Biogeographical distribution of denitrifying anaerobic methane oxidizing bacteria in Chinese wetland ecosystems. Environ Microbiol Rep. 2014;7:128–38.
Crits-Christoph A, Diamond S, Butterfield CN, Thomas BC, Banfield JF. Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis. Nature. 2018;558:440–4.
Singh BK, Quince C, Macdonald CA, Khachane A, Thomas N, Al-Soud WA, et al. Loss of microbial diversity in soils is coincident with reductions in some specialized functions. Environ Microbiol. 2014;16:2408–20.
Gianfreda L, Rao MA. Soil microbial and enzymatic diversity as affected by the presence of xenobiotics. In: Hashmi MZ, Kumar V, Varma A, editors. Xenobiotics in the soil environment: monitoring, toxicity and management. Switzerland: Springer International Publishing; 2017. p. 153–69.
Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B. 1995;57:289–300.
Erdös P, Rényi A. On the evolution of random graphs. T Am Math Soc. 2011;286:257–74.
Xun W, Huang T, Li W, Ren Y, Xiong W, Ran W, et al. Alteration of soil bacterial interaction networks driven by different long-term fertilization management practices in the red soil of South China. Appl Soil Ecol. 2017;120:128–34.
Olesen JM, Bascompte J, Dupont YL, Jordano P. The modularity of pollination networks. Proc Natl Acad Sci U S A. 2007;104:19891–6.
Revelle WR. psych: Procedures for personality and psychological research. Evanston: Northwestern University; 2017. Version = 1.8.12. Available online: https://CRANR-project.org/package=psych
Bastian M, Heymann S, Jacomy M. Gephi: an open source software for exploring and manipulating networks. Proc 3rd Intl ICWSM Conf; 2009. p. 361–2.
Oksanen JF, Blanchet G, Friendly M, Kindt R, Legendre P, McGlinn D. vegan: Community Ecology Package. R package version 2.4-1; 2016.
Hamady M, Lozupone C, Knight R. Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J. 2010;4:17–27.
Kembel SW, Cowan PD, Helmus MR, Cornwell WK, Morlon H, Ackerly DD, et al. Picante: R tools for integrating phylogenies and ecology. Bioinformatics. 2010;26:1463–4.
Feng K, Zhang Z, Cai W, Liu W, Xu M, Yin H, et al. Biodiversity and species competition regulate the resilience of microbial biofilm community. Mol Ecol. 2017;26:6170–82.
Nannipieri P, Ascher J, Ceccherini MT, Landi L, Pietramellara G, Renella G. Microbial diversity and soil functions. Eur J Soil Sci. 2003;54:655–70.
Allison SD, Martiny JBH. Resistance, resilience, and redundancy in microbial communities. Proc Natl Acad Sci U S A. 2008;105:11512–9.
Rogers BF, Tate RL. Temporal analysis of the soil microbial community along a toposequence in Pineland soils. Soil Biol Biochem. 2001;33:1389–401.
Xun W, Yan R, Ren Y, Jin D, Xiong W, Zhang G, et al. Grazing-induced microbiome alterations drive soil organic carbon turnover and productivity in meadow steppe. Microbiome. 2018;6:170.
Zhou J, Deng Y, Luo F, He Z, Tu Q, Zhi X. Functional molecular ecological networks. Mbio. 2010;1:1592–601.
Krause AE, Frank KA, Mason DM, Ulanowicz RE, Taylor WW. Compartments revealed in food-web structure. Nature. 2003;426:282–5.
Wagg C, Schlaeppi K, Banerjee S, Kuramae EE, van der Heijden MGA. Fungal-bacterial diversity and microbiome complexity predict ecosystem functioning. Nat Commun. 2019;10:4841.
Morgan K, Martucci N, Kozlowska A, Gamal W, Brzeszczyński F, Treskes P, et al. Chlorpromazine toxicity is associated with disruption of cell membrane integrity and initiation of a pro-inflammatory response in the HepaRG hepatic cell line. Biomed Pharmacother. 2019;111:1408–16.
Marijuán PC, Navarro J, del Moral R. How prokaryotes ‘encode’ their environment: systemic tools for organizing the information flow. Biosystems. 2018;164:26–38.
Cutler DR, Edwards TC, Beard KH, Adele C, Hess KT, Jacob G, et al. Random forests for classification in ecology. Ecology. 2007;88:2783–92.
Cardenas E, Kranabetter JM, Hope G, Maas KR, Hallam S, Mohn WW. Forest harvesting reduces the soil metagenomic potential for biomass decomposition. ISME J. 2015;9:2465–76.
Huang X, Zhou X, Zhang J, Cai Z. Highly connected taxa located in the microbial network are prevalent in the rhizosphere soil of healthy plant. Biol Fertil Soils. 2019;55:299–312.
Lupatini M, Suleiman AKA, Jacques RJS, Antoniolli ZI, de Siqueira FA, Kuramae EE, et al. Network topology reveals high connectance levels and few key microbial genera within soils. Front Environ Sci. 2014;2:10.
Ma B, Wang H, Dsouza M, Lou J, He Y, Dai Z, et al. Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China. ISME J. 2016;10:1891–901.
Altmann D, Stief P, Amann R, Beer DD, Schramm A. In situ distribution and activity of nitrifying bacteria in freshwater sediment. Environ Microbiol. 2003;5:798–803.
Kits KD, Sedlacek CJ, Lebedeva EV, Han P, Bulaev A, Pjevac P, et al. Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle. Nature. 2017;549:269–72.
van Velzen R, Holmer R, Bu F, Rutten L, van Zeijl A, Liu W, et al. Comparative genomics of the nonlegume Parasponia reveals insights into evolution of nitrogen-fixing rhizobium symbioses. Proc Natl Acad Sci U S A. 2018;115:E4700–9.
Porter SS, Faber-Hammond J, Montoya AP, Friesen ML, Sackos C. Dynamic genomic architecture of mutualistic cooperation in a wild population of Mesorhizobium. ISME J. 2019;13:301–15.
Yang FC, Chen YL, Tang SL, Yu CP, Wang PH, Ismail W, et al. Integrated multi-omics analyses reveal the biochemical mechanisms and phylogenetic relevance of anaerobic androgen biodegradation in the environment. ISME J. 2016;10:1967–83.
Banerjee S, Baah-Acheamfour M, Carlyle CN, Bissett A, Richardson AE, Siddique T, et al. Determinants of bacterial communities in Canadian agroforestry systems. Environ Microbiol. 2016;18:1805–16.
Chao Y, Liu W, Chen Y, Chen W, Zhao L, Ding Q, et al. Structure, variation, and co-occurrence of soil microbial communities in abandoned sites of a rare earth elements mine. Environ Sci Technol. 2016;50:11481–90.
Yang C, Wang Q, Simon PN, Liu J, Liu L, Dai X, et al. Distinct network interactions in particle-associated and free-living bacterial communities during a Microcystis aeruginosa bloom in a Plateau lake. Front Microbiol. 2017;8:1202.
Xue L, Ren H, Li S, Leng X, Yao X. Soil bacterial community structure and co-occurrence pattern during vegetation restoration in karst rocky desertification area. Front Microbiol. 2017;8:2377.
Rivett DW, Bell T. Abundance determines the functional role of bacterial phylotypes in complex communities. Nat Microbiol. 2018;3:767–72.