Genomic fingerprints of the world’s soil ecosystems

Graham, Emily B.; Garayburu-Caruso, Vanessa A.; Wu, Ruonan; Zheng, Jianqiu; McClure, Ryan S.; Jones, Gerrad D.

doi:10.1128/msystems.01112-23

Title: Genomic fingerprints of the world’s soil ecosystems

Journal Article · 09 May 2024 · mSystems

DOI: https://doi.org/10.1128/msystems.01112-23 · OSTI ID:2468653

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Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); Washington State Univ., Pullman, WA (United States)
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
Oregon State Univ., Corvallis, OR (United States)

Despite the explosion of soil metagenomic data, we lack a synthesized understanding of patterns in the distribution and functions of soil microorganisms. These patterns are critical to predictions of soil microbiome responses to climate change and resulting feedbacks that regulate greenhouse gas release from soils. To address this gap, we assay 1,512 manually curated soil metagenomes using complementary annotation databases, read-based taxonomy, and machine learning to extract multidimensional genomic fingerprints of global soil microbiomes. Our objective is to uncover novel biogeographical patterns of soil microbiomes across environmental factors and ecological biomes with high molecular resolution. We reveal shifts in the potential for (i) microbial nutrient acquisition across pH gradients; (ii) stress-, transport-, and redox-based processes across changes in soil bulk density; and (iii) greenhouse gas emissions across biomes. We also use an unsupervised approach to reveal a collection of soils with distinct genomic signatures, characterized by coordinated changes in soil organic carbon, nitrogen, and cation exchange capacity and in bulk density and clay content that may ultimately reflect soil environments with high microbial activity. Genomic fingerprints for these soils highlight the importance of resource scavenging, plant-microbe interactions, fungi, and heterotrophic metabolisms. Across all analyses, we observed phylogenetic coherence in soil microbiomes—more closely related microorganisms tended to move congruently in response to soil factors. Collectively, the genomic fingerprints uncovered here present a basis for global patterns in the microbial mechanisms underlying soil biogeochemistry and help beget tractable microbial reaction networks for incorporation into process-based models of soil carbon and nutrient cycling.

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Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE Laboratory Directed Research and Development (LDRD) Program

Grant/Contract Number:: AC05-76RL01830

OSTI ID:: 2468653

Report Number(s):: PNNL-SA--191207

Journal Information:: mSystems, Journal Name: mSystems Journal Issue: 6 Vol. 9; ISSN 2379-5077

Publisher:: American Society for MicrobiologyCopyright Statement

Country of Publication:: United States

Language:: English

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