Community Organization and Metagenomics of Bacterial Assemblages Across Local Scale pH Gradients in Northern Forest Soil
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SOIL MICROBIOLOGY
Community Organization and Metagenomics of Bacterial Assemblages Across Local Scale pH Gradients in Northern Forest Soils Joseph B. Yavitt 1
&
C. Armanda Roco 2 & Spencer J. Debenport 3 & Samuel E. Barnett 3 & James P. Shapleigh 2
Received: 18 May 2020 / Accepted: 25 September 2020 # Springer Science+Business Media, LLC, part of Springer Nature 2020
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. Keywords Acidity . Community assembly . Ecological diversity . Shotgun metagenomics . Soil microbiome
Introduction Bacteria are sensitive to their environmental pH [1], and differences in soil pH have been used to explain variation in community composition, ecological diversity, community assembly, and the genotype of bacteria at different pH levels [2–4]. It is generally held that acidic soil conditions select Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00248-020-01613-7) contains supplementary material, which is available to authorized users. * Joseph B. Yavitt [email protected] 1
Department of Natural Resources, Cornell University, 226 Mann Drive, Fernow Hall, Ithaca, NY 14853, USA
2
Department of Microbiology, Cornell University, 123 Wing Drive, Wing Hall, Ithaca, NY 14853, USA
3
School of Integrative Plant Science, Cornell University, 306 Tower Road, Bradfield Hall, Ithaca, NY 14853, USA
for members of the Acidobacteria and cause an overall decrease in bacterial diversity [5, 6]. However, the proximate environmental cues that in
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