Manipulating soil microbial communities to unravel biotic interactions
Abstract
The importance of microbial communities and the complex functional roles they perform is
becoming increasingly evident. Yet, we know little about the ecological processes driving the
assembly of these communities in the environment. In this context, our objectives were to
unravel how biotic interactions within complex microbial communities determine microbial
community assembly and functioning. For building a predictive understanding of community
assembly, we used a manipulation approach to remove or enrich targeted groups in a soil
microbial community. Soil suspensions were either subjected to antibiotic, antimicrobial
peptide, heat or osmotic shock as well as directed enrichment treatments before being
inoculated in a total of 325 sterile soil microcosms(n=25). Interactions between microbial taxa
were evidenced 45 days after recolonization of the sterilized soils by sequencing the bacterial
16S rRNA gene and the fungal ITS region using Illumina Miseq sequencing. Causal effects of
microbial community manipulations for soil functioning were assessed by measuring a range
of activities related to C and N cycling. A model-based biclustering approach allowed the
identification of strong associations between specific microbial groups and applied
treatments. We also identified keystone species conserved between the different treatments
using comparative analysis of OTU-based co-occurrence networks. Large differences in
community composition were related to changes in C and N cycling. By explicitly testing biotic
interactions using a manipulation approach, this study provides insights into the role of
interactions between bacterial taxa in the assembly of soil microbial communities.
Domains
Environmental SciencesOrigin | Files produced by the author(s) |
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