Analysis report and associated Rmarkdown for Metagenomics reveals contrasted responses of microbial communities to wheat straw amendment in cropland and grassland soils

Rmarkdown analytical report for article: Metagenomics reveals contrasted responses of microbial communities to wheat straw amendment in cropland and grassland soils ABSTRACT Soil microbial communities respond quickly to natural and/or anthropic-induced changes in environmental conditions, with potential impacts in terms of soil functioning. However, most studies are limited to specific microbial groups, mainly bacteria and fungi, thus the in situ dynamics of the whole microbial community remains to be documented. Here, we investigated the response of the soil microbial community (archaea, bacteria, fungi, protists and viruses) to wheat straw input in a 4-month in-situ field study. We employed global metagenomics to characterise the whole soil microbial diversity, and compared the results with those previously obtained using high throughput amplicon sequencing on the same soil samples. Taxonomic patterns at the community, phyla and genus levels, were concordant between the two methodologies but global metagenomics was more sensitive and allowed studying all the microbial groups simultaneously, showing the considerable potential of this approach for the fine analysis of microbial population dynamics in situ. Microorganisms from each taxonomic group were affected directly or indirectly by the amendment. Land-use histories impacted the soil communities and their responses to amendment. Lastly, both inter and intra-domain trophic interactions could be inferred from our dataset. In particular, we observed the multiplication of viral sequences in the early phase of straw decomposition, in parallel to that of copiotrophic bacteria, suggesting a “kill-the-winner” dynamic that, to our knowledge, had not been observed before in soils. Our study highlights that top-down regulation by microbial predators or viruses might play a key role in soil microbiota dynamics and structure.