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Community Organization and Metagenomics of Bacterial Assemblages Across Local Scale pH Gradients in Northern Forest Soils

  • Soil Microbiology
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Abstract

Soil pH has shown to predict bacterial diversity, but mechanisms are still poorly understood. To investigate how bacteria distribute themselves as a function of soil pH, we assessed community composition, diversity, assembly, and gene abundance across local (ca. 1 km) scale gradients in soil pH from ~ 3.8 to 6.5 created by differences in soil parent material in three northern forests. Plant species were the same on all sites, with no evidence of agriculture in the past. Concentrations of extractable calcium, iron, and phosphorus also varied significantly across the pH gradients. Among taxa, Alphaproteobacteria and Acidobacteria were more common in soils with acidic pH values. Overall richness and diversity of OTUs peaked at intermediate pH values. Variations in OTU richness and diversity also had a quadratic fit with concentrations of extractable calcium and phosphorus. Community assembly was via homogeneous deterministic processes in soils with acidic pH values, whereas stochastic processes dominated in soils with near-neutral pH values. Although we expected selection via genes for acid tolerance response in acidic soils, genes for genetic information processing were more selective. Taxa in higher pH soils had differential abundance of transporter genes, suggesting adaptation to acquire metabolic substrates from soils. Soil bacterial communities in northern forest soils are incredibly diverse, and we still have much to learn about how soil pH and co-varying soil parameters directly drive gene selection in this critical component of ecosystem structure.

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Acknowledgments

This work was supported by a US Department of Agriculture (USDA), National Institute of Food and Agriculture (NIFA), Hatch project. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of NIFA or the USDA. We thank the ad hoc reviewers for comments and suggestions that greatly improved the clarity of the presentation.

Funding

This work was supported by a US Department of Agriculture (USDA), National Institute of Food and Agriculture (NIFA), Hatch project (1007286). Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of NIFA or the USDA.

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Authors and Affiliations

  1. Department of Natural Resources, Cornell University, 226 Mann Drive, Fernow Hall, Ithaca, NY, 14853, USA

    Joseph B. Yavitt

  2. Department of Microbiology, Cornell University, 123 Wing Drive, Wing Hall, Ithaca, NY, 14853, USA

    C. Armanda Roco & James P. Shapleigh

  3. School of Integrative Plant Science, Cornell University, 306 Tower Road, Bradfield Hall, Ithaca, NY, 14853, USA

    Spencer J. Debenport & Samuel E. Barnett

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  1. Joseph B. Yavitt
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Correspondence to Joseph B. Yavitt.

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Yavitt, J.B., Roco, C.A., Debenport, S.J. et al. Community Organization and Metagenomics of Bacterial Assemblages Across Local Scale pH Gradients in Northern Forest Soils. Microb Ecol 81, 758–769 (2021). https://doi.org/10.1007/s00248-020-01613-7

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