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RESEARCH PRODUCT

Deciphering Biotic Interactions and Their Role in Soil Microbial Community Assembly and Functions

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description

Microbial communities play a key role in ecosystem functioning as well as in plant, animal, and human welfare. Their assembly relies on different processes commonly referred to as abiotic and biotic filters. Despite the widespread emphasis on abiotic filters in terrestrial ecosystems, a growing body of evidence suggests that interactions between microorganisms play a critical role in community assembly. However, the contribution of these interactions to microbial community assembly and the factors influencing them have not been clearly established. In most cases, biotic interactions between microorganisms have been investigated based on cocultures of a handful of strains, completely overlooking the high complexity of microbial communities in nature.This thesis objectives were to decipher biotic interactions occurring between microbial community members and to assess the role of these interactions in the assembly of complex communities. Thereby, we used three top-down experiments based on the manipulation of native soil microbial communities and their reinoculation in sterile soil microcosms allowing them to reassemble during soil recolonisation.Our results suggest that between 15% and 28% of the bacterial community could be subjected to negative interactions during soil recolonization. Proteobacteria and Firmicutes exhibited a recurrent negative correlation, indicating that competition between them might be a rule governing microbial community assembly. Our approach also uncovered the importance of density-dependent interactions in microbial community assembly, the competitiveness of individuals strongly depending on the density and identity of surrounding neighbours. Furthermore, we showed that coalescence (mixing of manipulated and control communities) could also restore -at least partly- community diversity and soil functions. While the diversity of the coalesced communities was related to that of the source communities, their structure was mostly influenced by the density and the composition of the source communities.Altogether, we bring here additional evidence that community manipulation could become a standard tool to decipher microbial interactions in complex communities, their contribution to community assembly, and the links between community structure and function. Furthermore, our work highlights the potential of using community manipulation to design new microbial engineering strategies allowing to steer microbial communities in situ, without adding non-endemic species, by using the interactions occurring between the native community members.