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The chosen few—variations in common and rare soil bacteria across biomes

  • 1.

    Nemergut DR, Schmidt SK, Fukami T, O’Neill SP, Bilinski TM, Stanish LF, et al. Patterns and processes of microbial community assembly. Microbiol Mol Biol Rev. 2013;77:342–56.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 2.

    Jousset A, Bienhold C, Chatzinotas A, Gallien L, Gobet A, Kurm V, et al. Where less may be more: how the rare biosphere pulls ecosystems strings. ISME J. 2017;11:853–62.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 3.

    Rivett DW, Bell T. Abundance determines the functional role of bacterial phylotypes in complex communities. Nat Microbiol. 2018;3:767–72.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 4.

    Bell T, Newman JA, Silverman BW, Turner SL, Lilley AK. The contribution of species richness and composition to bacterial services. Nature. 2005;436:1157–60.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 5.

    Starke R, Capek P, Morais D, Callister SJ, Jehmlich N. The total microbiome functions in bacteria and fungi. J Proteom. 2020;213:1–5.

    Article 
    CAS 

    Google Scholar 

  • 6.

    Saleem M, Hu J, Jousset A. More than the sum of its parts: microbiome biodiversity as a driver of plant growth and soil health. Annu Rev Ecol Evol Syst. 2019;50:145–68.

    Article 

    Google Scholar 

  • 7.

    Wagg C, Schlaeppi K, Banerjee S, Kuramae EE, Heijden van der MGA. Fungal-bacterial diversity and microbiome complexity predict ecosystem functioning. Nat Commun. 2019;10:1–10.

    CAS 
    Article 

    Google Scholar 

  • 8.

    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;7:1–8.

    Article 
    CAS 

    Google Scholar 

  • 9.

    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;4:210–20.

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 10.

    Aanderud ZT, Jones SE, Fierer N, Lennon JT. Resuscitation of the rare biosphere contributes to pulses of ecosystem activity. Front Microbiol. 2015;6:1–11.

    Article 

    Google Scholar 

  • 11.

    Song H-K, Song W, Kim M, Tripathi BM, Kim H, Jablonski P, et al. Bacterial strategies along nutrient and time gradients, revealed by metagenomic analysis of laboratory microcosms. FEMS Microbiol Ecol. 2017;93:1–13.

    Article 
    CAS 

    Google Scholar 

  • 12.

    Jiao S, Chen W, Wei G. Biogeography and ecological diversity patterns of rare and abundant bacteria in oil-contaminated soils. Mol Ecol. 2017;26:5305–5317.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 13.

    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;359:320–5.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 14.

    Yu X, Polz MF, Alm EJ. Interactions in self-assembled microbial communities saturate with diversity. ISME J. 2019;13:1602–17.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 15.

    Li P, Liu J, Jiang C, Wu M, Liu M, Li Z. Distinct successions of common and rare bacteria in soil under humic acid amendment—a microcosm study. Front Microbiol. 2019;10:1–14.

    Article 

    Google Scholar 

  • 16.

    Nemergut DR, Costello EK, Hamady M, Lozupone C, Jiang L, Schmidt SK, et al. Global patterns in the biogeography of bacterial taxa. Environ Microbiol. 2011;13:135–44.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 17.

    Bickel S, Chen X, Papritz A, Or D. A hierarchy of environmental covariates control the global biogeography of soil bacterial richness. Sci Rep. 2019;9:1–10.

    CAS 
    Article 

    Google Scholar 

  • 18.

    Clarke RT, Murphy JF. Effects of locally rare taxa on the precision and sensitivity of RIVPACS bioassessment of freshwaters. Freshw Biol. 2006;51:1924–40.

    Article 

    Google Scholar 

  • 19.

    Kurm V, Putten WH, van der, Boer W, de, Naus‐Wiezer S, Hol WHG. Low abundant soil bacteria can be metabolically versatile and fast growing. Ecology. 2017;98:555–64.

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 20.

    Kurm V, Putten WH, van der, Hol WHG. Cultivation-success of rare soil bacteria is not influenced by incubation time and growth medium. PLoS ONE. 2019;14:1–14.

    Article 
    CAS 

    Google Scholar 

  • 21.

    Meyer KM, Memiaghe H, Korte L, Kenfack D, Alonso A, Bohannan BJM. Why do microbes exhibit weak biogeographic patterns? ISME J. 2018;12:1404–13.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 22.

    Escalas A, Hale L, Voordeckers JW, Yang Y, Firestone MK, Alvarez‐Cohen L, et al. Microbial functional diversity: from concepts to applications. Ecol Evol. 2019;9:12000–16.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 23.

    Barberán A, Ramirez KS, Leff JW, Bradford MA, Wall DH, Fierer N. Why are some microbes more ubiquitous than others? Predicting the habitat breadth of soil bacteria. Ecol Lett. 2014;17:794–802.

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 24.

    Dee LE, Cowles J, Isbell F, Pau S, Gaines SD, Reich PB. When do ecosystem services depend on rare species? Trends Ecol Evol. 2019;34:746–58.

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 25.

    Pueyo S, He F, Zillio T. The maximum entropy formalism and the idiosyncratic theory of biodiversity. Ecol Lett. 2007;10:1017–28.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 26.

    Bahram M, Hildebrand F, Forslund SK, Anderson JL, Soudzilovskaia NA, Bodegom PM, et al. Structure and function of the global topsoil microbiome. Nature. 2018;560:233–7.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 27.

    Zhou J, Deng Y, Shen L, Wen C, Yan Q, Ning D, et al. Temperature mediates continental-scale diversity of microbes in forest soils. Nat Commun. 2016;7:1–10.

    Google Scholar 

  • 28.

    Thompson LR, Jex AR, Campbell AH, Linz AM, Berry A, Williams AE, et al. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature. 2017;551:457–63.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 29.

    Bickel S, Or D. Soil bacterial diversity mediated by microscale aqueous-phase processes across biomes. Nat Commun. 2020;11:1–9.

    Google Scholar 

  • 30.

    Xu X, Thornton PE, Post WM. A global analysis of soil microbial biomass carbon, nitrogen and phosphorus in terrestrial ecosystems. Glob Ecol Biogeogr. 2013;22:737–49.

    Article 

    Google Scholar 

  • 31.

    Serna-Chavez HM, Fierer N, van Bodegom PM. Global drivers and patterns of microbial abundance in soil: global patterns of soil microbial biomass. Glob Ecol Biogeogr. 2013;22:1162–72.

    Article 

    Google Scholar 

  • 32.

    Wang G, Or D. A hydration-based biophysical index for the onset of soil microbial coexistence. Sci Rep. 2012;2:1–5.

    Google Scholar 

  • 33.

    Li CH, Lee CK. Minimum cross entropy thresholding. Pattern Recognit. 1993;26:617–625.

    Article 

    Google Scholar 

  • 34.

    Walt S, van der, Schönberger JL, Nunez-Iglesias J, Boulogne F, Warner JD, Yager N, et al. scikit-image: image processing in Python. PeerJ. 2014;2:1–18.

    Google Scholar 

  • 35.

    Homem-de-Mello T, Rubinstein RY. Estimation of rare event probabilities using cross-entropy. Proc Winter Simul Conf. 2002;1:310–19.

    Article 

    Google Scholar 

  • 36.

    Murali A, Bhargava A, Wright ES. IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences. Microbiome. 2018;6:1–14.

    Article 

    Google Scholar 

  • 37.

    Šťovíček A, Kim M, Or D, Gillor O. Microbial community response to hydration-desiccation cycles in desert soil. Sci Rep. 2017;7:1–9.

    Article 
    CAS 

    Google Scholar 

  • 38.

    Zhao M, Heinsch FA, Nemani RR, Running SW. Improvements of the MODIS terrestrial gross and net primary production global data set. Remote Sens Environ. 2005;95:164–76.

    Article 

    Google Scholar 

  • 39.

    Fick SE, Hijmans RJ. WorldClim 2: new 1-km spatial resolution climate surfaces for global land areas: new climate surfaces for global land areas. Int J Climatol. 2017;37:4302–15.

    Article 

    Google Scholar 

  • 40.

    Schoolfield RM, Sharpe PJH, Magnuson CE. Non-linear regression of biological temperature-dependent rate models based on absolute reaction-rate theory. J Theor Biol. 1981;88:719–31.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 41.

    Beck HE, Wood EF, Pan M, Fisher CK, Miralles DG, van Dijk AIJM, et al. MSWEP V2 Global 3-hourly 0.1° precipitation: methodology and quantitative assessment. Bull Am Meteorol Soc. 2019;100:473–500.

    Article 

    Google Scholar 

  • 42.

    Wang G, Or D. Hydration dynamics promote bacterial coexistence on rough surfaces. ISME J. 2013;7:395–404.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 43.

    Kim M, Or D. Individual-based model of microbial life on hydrated rough soil surfaces. PLoS ONE. 2016;11:1–31.

    Google Scholar 

  • 44.

    Hermsen R, Okano H, You C, Werner N, Hwa T. A growth-rate composition formula for the growth of E.coli on co-utilized carbon substrates. Mol Syst Biol. 2015;11:1–6.

    Article 
    CAS 

    Google Scholar 

  • 45.

    García FC, Bestion E, Warfield R, Yvon-Durocher G. Changes in temperature alter the relationship between biodiversity and ecosystem functioning. Proc Natl Acad Sci. 2018;115:10989–94.

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 

  • 46.

    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;540:567–9.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 47.

    Treves DS, Xia B, Zhou J, Tiedje JM. A two-species test of the hypothesis that spatial isolation influences microbial diversity in soil. Micro Ecol. 2003;45:20–8.

    CAS 
    Article 

    Google Scholar 

  • 48.

    Campbell BJ, Yu L, Heidelberg JF, Kirchman DL. Activity of abundant and rare bacteria in a coastal ocean. Proc Natl Acad Sci. 2011;108:12776–81.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 49.

    Stauffer D. Scaling theory of percolation clusters. Phys Rep. 1979;54:1–74.

    Article 

    Google Scholar 

  • 50.

    Scher H, Zallen R. Critical density in percolation processes. J Chem Phys. 1970;53:3759–61.

    CAS 
    Article 

    Google Scholar 

  • 51.

    Hengl T, de Jesus JM, Heuvelink GB, Gonzalez MR, Kilibarda M, Blagotić A, et al. SoilGrids250m: global gridded soil information based on machine learning. PloS ONE. 2017;12:1–40.

    Article 
    CAS 

    Google Scholar 

  • 52.

    Chase AB, Arevalo P, Brodie EL, Polz MF, Karaoz U, Martiny JBH. Maintenance of sympatric and allopatric populations in free-living terrestrial bacteria. mBio. 2019;10:1–11.

    Article 

    Google Scholar 

  • 53.

    Fisher CK, Mehta P. The transition between the niche and neutral regimes in ecology. Proc Natl Acad Sci. 2014;111:13111–6.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 54.

    Ratzke C, Barrere J, Gore J. Strength of species interactions determines biodiversity and stability in microbial communities. Nat Ecol Evol. 2020;4:376–83.

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 55.

    Doud DFR, Bowers RM, Schulz F, Raad MD, Deng K, Tarver A, et al. Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere. ISME J. 2020;14:659–75.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 56.

    Shade A, Jones SE, Caporaso JG, Handelsman J, Knight R, Fierer N, et al. Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity. mBio. 2014;5:1–9.

    Article 
    CAS 

    Google Scholar 

  • 57.

    Kaminsky R, Morales SE. Conditionally rare taxa contribute but do not account for changes in soil prokaryotic community structure. Front Microbiol. 2018;9:1–6.

    Article 

    Google Scholar 

  • 58.

    Price PB, Sowers T. Temperature dependence of metabolic rates for microbial growth, maintenance, and survival. Proc Natl Acad Sci U S A. 2004;101:4631–6.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 


  • Source: Ecology - nature.com

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