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Environmental and biotic drivers of soil microbial β‐diversity across spatial and phylogenetic scales

Citation

Chalmandrier, Loïc et al. (2020), Environmental and biotic drivers of soil microbial β‐diversity across spatial and phylogenetic scales, Dryad, Dataset, https://doi.org/10.5061/dryad.m905qftwt

Abstract

Soil microbial communities play a key role in ecosystem functioning but still little is known about the processes that determine their turnover (β-diversity) along ecological gradients. Here, we characterize soil microbial β-diversity at two spatial scales and at multiple phylogenetic grains to ask how archaeal, bacterial and fungal communities are shaped by abiotic processes and biotic interactions with plants. We characterized microbial and plant communities using DNA metabarcoding of soil samples distributed across and within eighteen plots along an elevation gradient in the French Alps. The recovered taxa were placed onto phylogenies to estimate microbial and plant β-diversity at different phylogenetic grains (i.e. resolution). We then modeled microbial β-diversities with respect to plant β-diversities and environmental dissimilarities across plots (landscape scale) and with respect to plant β-diversities and spatial distances within plots (plot scale). At the landscape scale, fungal and archaeal β-diversities were mostly related to plant β-diversity, while bacterial β-diversities were mostly related to environmental dissimilarities. At the plot scale, we detected a modest covariation of bacterial and fungal β-diversities with plant β-diversity; as well as a distance–decay relationship that suggested the influence of ecological drift on microbial communities. In addition, the covariation between fungal and plant β-diversity at the plot scale was highest at fine or intermediate phylogenetic grains hinting that biotic interactions between those clades depends on early-evolved traits. Altogether, we show how multiple ecological processes determine soil microbial community assembly at different spatial scales and how the strength of these processes change among microbial clades. In addition, we emphasized the imprint of microbial and plant evolutionary history on today’s microbial community structure.

Methods

Details about the methods are available in the article Chalmandrier et al. Environmental and biotic drivers of soil microbial β-diversity across spatial and phylogenetic scales. Ecography

This dataset contains:

- environmental DNA data for 378 soil samples of subalpine/alpine grasslands (Valloire, France, 2012) for four clades: Archaea, Tracheophyta, Fungi and Bacteria

- associated environmental conditions

- Fasta files for the four clades.

Furthermore the analysis procedure used to do the analysis is included.

Funding

Agence Nationale de la Recherche, Award: 11-BSV7-0020

Agence Nationale de la Recherche, Award: ANR-16-CE02-0009

Agence Nationale de la Recherche, Award: ANR-15-IDEX-02

Agence Nationale de la Recherche, Award: ANR-10-LABX-56

Agence Nationale de la Recherche, Award: ANR-10-LABX-25-01

European Research Council, Award: 281422

European Research Council, Award: FP7/2007-2013

Labex, Award: ANR10 LABX56