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Co-occurrence networks reveal more complexity than community composition in resistance and resilience of microbial communities

Author

Listed:
  • Cheng Gao

    (Chinese Academy of Sciences
    University of California)

  • Ling Xu

    (University of California
    China Agricultural University)

  • Liliam Montoya

    (University of California)

  • Mary Madera

    (University of California)

  • Joy Hollingsworth

    (University of California Kearney Agricultural Research & Extension Center)

  • Liang Chen

    (Chinese Academy of Sciences)

  • Elizabeth Purdom

    (University of California)

  • Vasanth Singan

    (Department of Energy Joint Genome Institute)

  • John Vogel

    (University of California
    Department of Energy Joint Genome Institute)

  • Robert B. Hutmacher

    (University of California West Side Research & Extension Center)

  • Jeffery A. Dahlberg

    (University of California Kearney Agricultural Research & Extension Center)

  • Devin Coleman-Derr

    (University of California
    Plant Gene Expression Center, US Department of Agriculture-Agricultural Research Service)

  • Peggy G. Lemaux

    (University of California)

  • John W. Taylor

    (University of California)

Abstract

Plant response to drought stress involves fungi and bacteria that live on and in plants and in the rhizosphere, yet the stability of these myco- and micro-biomes remains poorly understood. We investigate the resistance and resilience of fungi and bacteria to drought in an agricultural system using both community composition and microbial associations. Here we show that tests of the fundamental hypotheses that fungi, as compared to bacteria, are (i) more resistant to drought stress but (ii) less resilient when rewetting relieves the stress, found robust support at the level of community composition. Results were more complex using all-correlations and co-occurrence networks. In general, drought disrupts microbial networks based on significant positive correlations among bacteria, among fungi, and between bacteria and fungi. Surprisingly, co-occurrence networks among functional guilds of rhizosphere fungi and leaf bacteria were strengthened by drought, and the same was seen for networks involving arbuscular mycorrhizal fungi in the rhizosphere. We also found support for the stress gradient hypothesis because drought increased the relative frequency of positive correlations.

Suggested Citation

  • Cheng Gao & Ling Xu & Liliam Montoya & Mary Madera & Joy Hollingsworth & Liang Chen & Elizabeth Purdom & Vasanth Singan & John Vogel & Robert B. Hutmacher & Jeffery A. Dahlberg & Devin Coleman-Derr & , 2022. "Co-occurrence networks reveal more complexity than community composition in resistance and resilience of microbial communities," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-31343-y
    DOI: 10.1038/s41467-022-31343-y
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    1. Christopher R. Schwalm & William R. L. Anderegg & Anna M. Michalak & Joshua B. Fisher & Franco Biondi & George Koch & Marcy Litvak & Kiona Ogle & John D. Shaw & Adam Wolf & Deborah N. Huntzinger & Kev, 2017. "Global patterns of drought recovery," Nature, Nature, vol. 548(7666), pages 202-205, August.
    2. Mengting Maggie Yuan & Xue Guo & Linwei Wu & Ya Zhang & Naijia Xiao & Daliang Ning & Zhou Shi & Xishu Zhou & Liyou Wu & Yunfeng Yang & James M. Tiedje & Jizhong Zhou, 2021. "Climate warming enhances microbial network complexity and stability," Nature Climate Change, Nature, vol. 11(4), pages 343-348, April.
    3. Franciska T. Vries & Rob I. Griffiths & Mark Bailey & Hayley Craig & Mariangela Girlanda & Hyun Soon Gweon & Sara Hallin & Aurore Kaisermann & Aidan M. Keith & Marina Kretzschmar & Philippe Lemanceau , 2018. "Soil bacterial networks are less stable under drought than fungal networks," Nature Communications, Nature, vol. 9(1), pages 1-12, December.
    4. Franciska T. de Vries & Mira E. Liiri & Lisa Bjørnlund & Matthew A. Bowker & Søren Christensen & Heikki M. Setälä & Richard D. Bardgett, 2012. "Land use alters the resistance and resilience of soil food webs to drought," Nature Climate Change, Nature, vol. 2(4), pages 276-280, April.
    5. Ragan M. Callaway & R. W. Brooker & Philippe Choler & Zaal Kikvidze & Christopher J. Lortie & Richard Michalet & Leonardo Paolini & Francisco I. Pugnaire & Beth Newingham & Erik T. Aschehoug & Cristin, 2002. "Positive interactions among alpine plants increase with stress," Nature, Nature, vol. 417(6891), pages 844-848, June.
    6. De Boeck, Paul & Bakker, Marjan & Zwitser, Robert & Nivard, Michel & Hofman, Abe & Tuerlinckx, Francis & Partchev, Ivailo, 2011. "The Estimation of Item Response Models with the lmer Function from the lme4 Package in R," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 39(i12).
    7. Cameron Wagg & Klaus Schlaeppi & Samiran Banerjee & Eiko E. Kuramae & Marcel G. A. Heijden, 2019. "Fungal-bacterial diversity and microbiome complexity predict ecosystem functioning," Nature Communications, Nature, vol. 10(1), pages 1-10, December.
    8. Omri M. Finkel & Isai Salas-González & Gabriel Castrillo & Jonathan M. Conway & Theresa F. Law & Paulo José Pereira Lima Teixeira & Ellie D. Wilson & Connor R. Fitzpatrick & Corbin D. Jones & Jeffery , 2020. "A single bacterial genus maintains root growth in a complex microbiome," Nature, Nature, vol. 587(7832), pages 103-108, November.
    9. Kevin E. Trenberth & Aiguo Dai & Gerard van der Schrier & Philip D. Jones & Jonathan Barichivich & Keith R. Briffa & Justin Sheffield, 2014. "Global warming and changes in drought," Nature Climate Change, Nature, vol. 4(1), pages 17-22, January.
    10. Cheng Gao & Liliam Montoya & Ling Xu & Mary Madera & Joy Hollingsworth & Elizabeth Purdom & Vasanth Singan & John Vogel & Robert B. Hutmacher & Jeffery A. Dahlberg & Devin Coleman-Derr & Peggy G. Lema, 2020. "Fungal community assembly in drought-stressed sorghum shows stochasticity, selection, and universal ecological dynamics," Nature Communications, Nature, vol. 11(1), pages 1-14, December.
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    1. Shuan Jia & Yongcheng Chen & Rongzheng Huang & Yuxin Chai & Chunhui Ma & Fanfan Zhang, 2023. "Study on Phyllosphere Microbial Community of Nettle Leaf during Different Seasons," Agriculture, MDPI, vol. 13(6), pages 1-15, June.
    2. Yuxiang Zhao & Zishu Liu & Baofeng Zhang & Jingjie Cai & Xiangwu Yao & Meng Zhang & Ye Deng & Baolan Hu, 2023. "Inter-bacterial mutualism promoted by public goods in a system characterized by deterministic temperature variation," Nature Communications, Nature, vol. 14(1), pages 1-12, December.

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