• Falkowski PG, Fenchel T, Delong EF. The microbial engines that drive Earth’s biogeochemical cycles. Science. 2008;320(5879):1034–9. https://doi.org/10.1126/science.1153213.

    CAS 
    Article 
    PubMed 

    Google Scholar
     

  • Delgado-Baquerizo M, Maestre FT, Reich PB, Jeffries TC, Gaitan JJ, Encinar D, et al. Microbial diversity drives multifunctionality in terrestrial ecosystems. Nat Commun. 2016. https://doi.org/10.1038/ncomms10541.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Delgado-Baquerizo M, Reich PB, Trivedi C, Eldridge DJ, Abades S, Alfaro FD, et al. Multiple elements of soil biodiversity drive ecosystem functions across biomes. Nat Ecol Evol. 2020;4(2):210–20. https://doi.org/10.1038/s41559-019-1084-y.

    Article 
    PubMed 

    Google Scholar
     

  • Delgado-Baquerizo M, Oliverio AM, Brewer TE, Benavent-González A, Eldridge DJ, Bardgett RD, et al. A global atlas of the dominant bacteria found in soil. Science. 2018;359(6373):320–5. https://doi.org/10.1126/science.aap9516.

    CAS 
    Article 
    PubMed 

    Google Scholar
     

  • Banerjee S, Schlaeppi K, Van Der Heijden MGA. Keystone taxa as drivers of microbiome structure and functioning. Nat Rev Microbiol. 2018;16(9):567–76. https://doi.org/10.1038/s41579-018-0024-1.

    CAS 
    Article 
    PubMed 

    Google Scholar
     

  • Toju H, Peay KG, Yamamichi M, Narisawa K, Hiruma K, Naito K, et al. Core microbiomes for sustainable agroecosystems. Nat Plants. 2018;4(5):247–57. https://doi.org/10.1038/s41477-018-0139-4.

    Article 
    PubMed 

    Google Scholar
     

  • Walters WA, Jin Z, Youngblut N, Wallace JG, Sutter J, Zhang W, et al. Large-scale replicated field study of maize rhizosphere identifies heritable microbes. Proc Natl Acad Sci U S A. 2018;115(28):7368–73. https://doi.org/10.1073/pnas.1800918115.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Egidi E, Delgado-Baquerizo M, Plett JM, Wang J, Eldridge DJ, Bardgett RD, et al. A few Ascomycota taxa dominate soil fungal communities worldwide. Nat Commun. 2019;10(1):2369. https://doi.org/10.1038/s41467-019-10373-z.

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Stegen JC, Bottos EM, Jansson JK. A unified conceptual framework for prediction and control of microbiomes. Curr Opin Microbiol. 2018;44:20–7. https://doi.org/10.1016/j.mib.2018.06.002.

    Article 
    PubMed 

    Google Scholar
     

  • Singh BK, Trivedi P, Egidi E, Macdonald CA, Delgado-Baquerizo M. Crop microbiome and sustainable agriculture. Nat Rev Microbiol. 2020;18(11):601–2. https://doi.org/10.1038/s41579-020-00446-y.

    CAS 
    Article 
    PubMed 

    Google Scholar
     

  • Tilman D, Balzer C, Hill J, Befort BL. Global food demand and the sustainable intensification of agriculture. Proc Natl Acad Sci U S A. 2011;108(50):20260–4. https://doi.org/10.1073/pnas.1116437108.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Dai ZM, Su WQ, Chen HH, Barberan A, Zhao HC, Yu MJ, et al. Long-term nitrogen fertilization decreases bacterial diversity and favors the growth of Actinobacteria and Proteobacteria in agro-ecosystems across the globe. Glob Change Biol. 2018;24(8):3452–61. https://doi.org/10.1111/gcb.14163.

    Article 

    Google Scholar
     

  • Hartmann M, Frey B, Mayer J, Mader P, Widmer F. Distinct soil microbial diversity under long-term organic and conventional farming. ISME J. 2015;9(5):1177–94. https://doi.org/10.1038/ismej.2014.210.

    Article 
    PubMed 

    Google Scholar
     

  • Feng YZ, Chen RR, Hu JL, Zhao F, Wang JH, Chu HY, et al. Bacillus asahii comes to the fore in organic manure fertilized alkaline soils. Soil Biol Biochem. 2015;81:186–94. https://doi.org/10.1016/j.soilbio.2014.11.021.

    CAS 
    Article 

    Google Scholar
     

  • Fierer N, Wood SA, Bueno De Mesquita CP. How microbes can, and cannot, be used to assess soil health. Soil Biol Biochem. 2021. https://doi.org/10.1016/j.soilbio.2020.108111.

    Article 

    Google Scholar
     

  • Guerra CA, Bardgett RD, Caon L, Crowther TW, Delgado-Baquerizo M, Montanarella L, et al. Tracking, targeting, and conserving soil biodiversity. Science. 2021;371(6526):239–41. https://doi.org/10.1126/science.abd7926.

    CAS 
    Article 
    PubMed 

    Google Scholar
     

  • Shade A, Handelsman J. Beyond the Venn diagram: the hunt for a core microbiome. Environ Microbiol. 2012;14(1):4–12. https://doi.org/10.1111/j.1462-2920.2011.02585.x.

    CAS 
    Article 
    PubMed 

    Google Scholar
     

  • Chernov TI, Zhelezova AD. The dynamics of soil microbial communities on different timescales: a review. Eurasian Soil Sci. 2020;53(5):643–52. https://doi.org/10.1134/S106422932005004x.

    Article 

    Google Scholar
     

  • Liu W, Graham EB, Zhong L, Zhang J, Li S, Lin X, et al. Long-term stochasticity combines with short-term variability in assembly processes to underlie rice paddy sustainability. Front Microbiol. 2020;11:873. https://doi.org/10.3389/fmicb.2020.00873.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rasche F, Knapp D, Kaiser C, Koranda M, Kitzler B, Zechmeister-Boltenstern S, et al. Seasonality and resource availability control bacterial and archaeal communities in soils of a temperate beech forest. ISME J. 2011;5(3):389–402. https://doi.org/10.1038/ismej.2010.138.

    CAS 
    Article 
    PubMed 

    Google Scholar
     

  • Lauber CL, Ramirez KS, Aanderud Z, Lennon J, Fierer N. Temporal variability in soil microbial communities across land-use types. ISME J. 2013;7(8):1641–50. https://doi.org/10.1038/ismej.2013.50.

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Fierer N, Jackson RB. The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci U S A. 2006;103(3):626–31. https://doi.org/10.1073/pnas.0507535103.

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Fan KK, Delgado-Baquerizo M, Guo XS, Wang DZ, Zhu YG, Chu HY. Biodiversity of key-stone phylotypes determines crop production in a 4-decade fertilization experiment. ISME J. 2021;15(2):550–61. https://doi.org/10.1038/s41396-020-00796-8.

    CAS 
    Article 
    PubMed 

    Google Scholar
     

  • Jiao S, Xu Y, Zhang J, Hao X, Lu Y. Core microbiota in agricultural soils and their potential associations with nutrient cycling. mSystems. 2019. https://doi.org/10.1128/mSystems.00313-18.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Takahashi M, Nakanishi H, Kawasaki S, Nishizawa NK, Mori S. Enhanced tolerance of rice to low iron availability in alkaline soils using barley nicotianamine aminotransferase genes. Nat Biotechnol. 2001;19(5):466–9. https://doi.org/10.1038/88143.

    CAS 
    Article 
    PubMed 

    Google Scholar
     

  • Berdugo M, Delgado-Baquerizo M, Soliveres S, Hernandez-Clemente R, Zhao YC, Gaitan JJ, et al. Global ecosystem thresholds driven by aridity. Science. 2020;367(6479):787–90. https://doi.org/10.1126/science.aay5958.

    CAS 
    Article 
    PubMed 

    Google Scholar
     

  • Slessarev EW, Lin Y, Bingham NL, Johnson JE, Dai Y, Schimel JP, et al. Water balance creates a threshold in soil pH at the global scale. Nature. 2016;540(7634):567–9. https://doi.org/10.1038/nature20139.

    CAS 
    Article 
    PubMed 

    Google Scholar
     

  • Lobell DB, Field CB. Global scale climate—crop yield relationships and the impacts of recent warming. Environ Res Lett. 2007. https://doi.org/10.1088/1748-9326/2/1/014002.

    Article 

    Google Scholar
     

  • Meng L, Ding W, Cai Z. Long-term application of organic manure and nitrogen fertilizer on N2O emissions, soil quality and crop production in a sandy loam soil. Soil Biol Biochem. 2005;37(11):2037–45. https://doi.org/10.1016/j.soilbio.2005.03.007.

    CAS 
    Article 

    Google Scholar
     

  • Gong W, Yan X-Y, Wang J-Y, Hu T-X, Gong Y-B. Long-term manuring and fertilization effects on soil organic carbon pools under a wheat–maize cropping system in North China Plain. Plant Soil. 2008;314(1–2):67–76. https://doi.org/10.1007/s11104-008-9705-2.

    CAS 
    Article 

    Google Scholar
     

  • Liang YT, Ning DL, Lu ZM, Zhang N, Hale L, Wu LY, et al. Century long fertilization reduces stochasticity controlling grassland microbial community succession. Soil Biol Biochem. 2020. https://doi.org/10.1016/j.soilbio.2020.108023.

    Article 

    Google Scholar
     

  • Schwieger F, Tebbe CC. A new approach to utilize PCR-single-strand-conformation polymorphism for 16S rRNA gene-based microbial community analysis. Appl Environ Microbiol. 1998;64(12):4870–6. https://doi.org/10.1128/AEM.64.12.4870-4876.1998.

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods. 2013;10(10):996–8. https://doi.org/10.1038/Nmeth.2604.

    CAS 
    Article 
    PubMed 

    Google Scholar
     

  • Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007;73(16):5261–7. https://doi.org/10.1128/Aem.00062-07.

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7(5):335–6. https://doi.org/10.1038/nmeth.f.303.

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Smith MB, Rocha AM, Smillie CS, Olesen SW, Paradis C, Wu LY, et al. Natural bacterial communities serve as quantitative geochemical biosensors. MBio. 2015. https://doi.org/10.1128/mBio.00326-15.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hermans SM, Buckley HL, Case BS, Curran-Cournane F, Taylor M, Lear G. Using soil bacterial communities to predict physico-chemical variables and soil quality. Microbiome. 2020. https://doi.org/10.1186/s40168-020-00858-1.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Archer E. rfPermute: estimate permutation p-values for random forest importance metrics. 2020.

  • Benjamini Y, Hochberg Y. Controlling the false discovery rate—a practical and powerful approach to multiple testing. J R Stat Soc B. 1995;57(1):289–300. https://doi.org/10.1111/j.2517-6161.1995.tb02031.x.

    Article 

    Google Scholar
     

  • Widder S, Besemer K, Singer GA, Ceola S, Bertuzzo E, Quince C, et al. Fluvial network organization imprints on microbial co-occurrence networks. Proc Natl Acad Sci U S A. 2014;111(35):12799–804. https://doi.org/10.1073/pnas.1411723111.

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Barberan A, Bates ST, Casamayor EO, Fierer N. Using network analysis to explore co-occurrence patterns in soil microbial communities. ISME J. 2012;6(2):343–51. https://doi.org/10.1038/ismej.2011.119.

    CAS 
    Article 
    PubMed 

    Google Scholar
     

  • R Core Team. R: a language and environment for statistical computing. Vienna: R Foundation for Statistical Computing; 2013. http://www.R-project.org/.

  • De Menezes AB, Prendergast-Miller MT, Richardson AE, Toscas P, Farrell M, Macdonald LM, et al. Network analysis reveals that bacteria and fungi form modules that correlate independently with soil parameters. Environ Microbiol. 2015;17(8):2677–89. https://doi.org/10.1111/1462-2920.12559.

    CAS 
    Article 
    PubMed 

    Google Scholar
     

  • Bastian M, Heymann S, Jacomy M. Gephi: an open source software for exploring and manipulating networks. In: Proceedings of the international AAAI conference on web and social media; 2009. https://www.aaai.org/ocs/index.php/ICWSM/09/paper/view/154.

  • Gloor GB, Macklaim JM, Pawlowsky-Glahn V, Egozcue JJ. Microbiome datasets are compositional: and this is not optional. Front Microbiol. 2017;8:2224. https://doi.org/10.3389/fmicb.2017.02224.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Peschel S, Müller CL, Von Mutius E, Boulesteix A-L, Depner M. NetCoMi: network construction and comparison for microbiome data in R. Brief Bioinform. 2021;22(4):bbaa290. https://doi.org/10.1093/bib/bbaa290.

    Article 
    PubMed 

    Google Scholar
     

  • Kurtz ZD, Müller CL, Miraldi ER, Littman DR, Blaser MJ, Bonneau RA. Sparse and compositionally robust inference of microbial ecological networks. PLoS Comput Biol. 2015;11(5): e1004226. https://doi.org/10.1371/journal.pcbi.1004226.

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol. 2014;64:346–51. https://doi.org/10.1099/ijs.0.059774-0.

    Article 
    PubMed 

    Google Scholar
     

  • Letunic I, Bork P. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 2019;47(W1):W256–9. https://doi.org/10.1093/nar/gkz239.

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Pohl S, Harwood CR. Heterologous protein secretion by Bacillus species: from the cradle to the grave. In: Laskin AI, Sariaslani S, Gadd GM, editors. Advances in applied microbiology. London: Academic Press; 2010. p. 1–25.


    Google Scholar
     

  • Jing ZW, Chen RR, Wei SP, Feng YZ, Zhang JB, Lin XG. Response and feedback of C mineralization to P availability driven by soil microorganisms. Soil Biol Biochem. 2017;105:111–20. https://doi.org/10.1016/j.soilbio.2016.11.014.

    CAS 
    Article 

    Google Scholar
     

  • Dourado MN, Neves AAC, Santos DS, Araujo WL. Biotechnological and agronomic potential of endophytic pink-pigmented methylotrophic Methylobacterium spp. Biomed Res Int. 2015. https://doi.org/10.1155/2015/909016.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hsu SH, Shen MW, Chen JC, Lur HS, Liu CT. The photosynthetic bacterium Rhodopseudomonas palustris strain PS3 exerts plant growth-promoting effects by stimulating nitrogen uptake and elevating auxin levels in expanding leaves. Front Plant Sci. 2021. https://doi.org/10.3389/fpls.2021.573634.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Alonso-Ayuso M, Gabriel JL, Quemada M. Nitrogen use efficiency and residual effect of fertilizers with nitrification inhibitors. Eur J Agron. 2016;80:1–8. https://doi.org/10.1016/j.eja.2016.06.008.

    CAS 
    Article 

    Google Scholar
     

  • Gao DC, Bai E, Li MH, Zhao CH, Yu KL, Hagedorn F. Responses of soil nitrogen and phosphorus cycling to drying and rewetting cycles: a meta-analysis. Soil Biol Biochem. 2020. https://doi.org/10.1016/j.soilbio.2020.107896.

    Article 

    Google Scholar
     

  • Pohl S, Harwood CR. Heterologous protein secretion by Bacillus species: from the cradle to the grave. Adv Appl Microbiol. 2010;73:1–25. https://doi.org/10.1016/S0065-2164(10)73001-X.

    CAS 
    Article 
    PubMed 

    Google Scholar
     

  • Berry C. The bacterium, Lysinibacillus sphaericus, as an insect pathogen. J Invertebr Pathol. 2012;109(1):1–10. https://doi.org/10.1016/j.jip.2011.11.008.

    Article 
    PubMed 

    Google Scholar
     

  • Fan KK, Delgado-Baquerizo M, Guo XS, Wang DZ, Wu YY, Zhu M, et al. Suppressed N fixation and diazotrophs after four decades of fertilization. Microbiome. 2019. https://doi.org/10.1186/s40168-019-0757-8.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Blake L, Goulding KWT, Mott CJB, Johnston AE. Changes in soil chemistry accompanying acidification over more than 100 years under woodland and grass at Rothamsted Experimental Station, UK. Eur J Soil Sci. 1999;50(3):401–12. https://doi.org/10.1046/j.1365-2389.1999.00253.x.

    CAS 
    Article 

    Google Scholar
     

  • Blake L, Goulding KWT, Mott CJB, Poulton PR. Temporal changes in chemical properties of air-dried stored soils and their interpretation for long-term experiments. Eur J Soil Sci. 2000;51(2):345–53. https://doi.org/10.1046/j.1365-2389.2000.00307.x.

    CAS 
    Article 

    Google Scholar
     

  • Benucci GMN, Rennick B, Bonito G. Patient propagules: do soil archives preserve the legacy of fungal and prokaryotic communities? PLoS ONE. 2020. https://doi.org/10.1371/journal.pone.0237368.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tzeneva VA, Salles JF, Naumova N, De Vos WA, Kuikman PJ, Dolfing J, et al. Effect of soil sample preservation, compared to the effect of other environmental variables, on bacterial and eukaryotic diversity. Res Microbiol. 2009;160(2):89–98. https://doi.org/10.1016/j.resmic.2008.12.001.

    CAS 
    Article 
    PubMed 

    Google Scholar
     

  • Schmidt JE, Kent AD, Brisson VL, Gaudin ACM. Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling. Microbiome. 2019. https://doi.org/10.1186/s40168-019-0756-9.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

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