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Differential roles of deterministic and stochastic processes in structuring soil bacterial ecotypes across terrestrial ecosystems

Author

Listed:
  • Mia Riddley

    (Virginia Tech)

  • Shannon Hepp

    (Virginia Tech)

  • FNU Hardeep

    (Virginia Tech)

  • Aruj Nayak

    (Virginia Tech)

  • Meimei Liu

    (Virginia Tech)

  • Xin Xing

    (Virginia Tech)

  • Hailong Zhang

    (Virginia Tech)

  • Jingqiu Liao

    (Virginia Tech
    Virginia Tech
    Virginia Tech)

Abstract

Soil bacteria are vital to ecosystem resilience and resistance, yet ecological attributes and the drivers governing their composition and distribution, especially for taxa varying in ecological traits and inhabiting different ecosystems, are not fully understood. Here, we analyzed a large-scale bacterial community and environmental dataset of 622 soil samples systematically collected by us from six major terrestrial ecosystems across the United States. We show that soil bacterial diversity and composition significantly differ among ecotypes and ecosystems, partially determined by a few universal abiotic factors (e.g., soil pH, calcium, and aluminum) and several ecotype- or ecosystem-specific ecological drivers. Co-occurrence network analysis suggests that rare taxa have stronger ecological relevance to the community than abundant taxa. Ecological models revealed that deterministic processes shape assembly of abundant taxa and generalists, while stochastic processes played a greater role in rare taxa and specialists. Also, bacterial communities in the shrubland ecosystem appear to be more sensitive to environmental changes than other ecosystems, evidenced by the lowest diversity, least connected community network, and strongest local environmental selection driven by surrounding land use. Overall, this study reveals ecological mechanisms underlying the bacterial biogeography in terrestrial ecosystems nationwide and highlights the need to preserve rare biosphere and shrubland ecosystems amid environmental disturbance.

Suggested Citation

  • Mia Riddley & Shannon Hepp & FNU Hardeep & Aruj Nayak & Meimei Liu & Xin Xing & Hailong Zhang & Jingqiu Liao, 2025. "Differential roles of deterministic and stochastic processes in structuring soil bacterial ecotypes across terrestrial ecosystems," Nature Communications, Nature, vol. 16(1), pages 1-13, December.
  • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-57526-x
    DOI: 10.1038/s41467-025-57526-x
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    References listed on IDEAS

    as
    1. Zachary D Kurtz & Christian L Müller & Emily R Miraldi & Dan R Littman & Martin J Blaser & Richard A Bonneau, 2015. "Sparse and Compositionally Robust Inference of Microbial Ecological Networks," PLOS Computational Biology, Public Library of Science, vol. 11(5), pages 1-25, May.
    2. Ying-Xian Goh & Sai Manohar Balu Anupoju & Anthony Nguyen & Hailong Zhang & Monica Ponder & Leigh-Anne Krometis & Amy Pruden & Jingqiu Liao, 2024. "Evidence of horizontal gene transfer and environmental selection impacting antibiotic resistance evolution in soil-dwelling Listeria," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
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