Abstract
Microbial communities play important roles in all ecosystems and yet a comprehensive understanding of the ecological processes governing the assembly of these communities is missing. To address the role of biotic interactions between microorganisms in assembly and for functioning of the soil microbiota, we used a top-down manipulation approach based on the removal of various populations in a natural soil microbial community. We hypothesized that removal of certain microbial groups will strongly affect the relative fitness of many others, therefore unraveling the contribution of biotic interactions in shaping the soil microbiome. Here we show that 39% of the dominant bacterial taxa across treatments were subjected to competitive interactions during soil recolonization, highlighting the importance of biotic interactions in the assembly of microbial communities in soil. Moreover, our approach allowed the identification of microbial community assembly rule as exemplified by the competitive exclusion between members of Bacillales and Proteobacteriales. Modified biotic interactions resulted in greater changes in activities related to N- than to C-cycling. Our approach can provide a new and promising avenue to study microbial interactions in complex ecosystems as well as the links between microbial community composition and ecosystem function.
Highlights
Microbial communities in nature exist in complex and dynamic consortia of populations that are central to all major biogeochemical cycles, and influence plant, animal, and human welfare [1,2,3]
We show here that 39% of the dominant bacterial taxa across treatments were subjected to competitive interactions during soil recolonization, experimentally showing for the first time the importance of negative interactions between microorganisms for community assembly in a complex environment
We found weak to non-significant effects of the depletion of different operational taxonomic units (OTUs), of which some are assumed to have removal treatments on fungal communities with only zero to two positive or negative interactions with the remaining OTUs
Summary
Microbial communities in nature exist in complex and dynamic consortia of populations that are central to all major biogeochemical cycles, and influence plant, animal, and human welfare [1,2,3]. Using the 16S rRNA gene copy number in the original soil to cases of negative interactions for which both competing strains calculate a maximal bacterial density in the inoculum before were affected by the removal treatments or causing a decreased relative fitness (example 3, Fig. 1b) could not be determined in our analysis.
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