Impacts of agroecological practices on soil microbial communities in experimental open-field market-gardens

Aims: The aim of the present study was to identify the impact of a set of agroecological practices on the composition and diversity of edaphic bacterial and fungal communities. Methods and Results: We designed two experimental agroecological vegetable cropping systems and we analyzed effects of these two systems on soil microbial communities by a metagenomic approach. Our results showed an increase of bacterial OTUs in the two experimental systems compared to bare soil, particularly for Actinobacteria phylum that represents one of the most important group of bacteria with benefits for soil properties. Simultaneously, a significantly decrease of proportions of Xanthomonadales and Burkholderiales families OTUs was observed in the two experimental systems compared to bare soil. These two bacteria families include many pathogenic species. Conclusion: In the two experimental systems, the change in food quality and quantity (mulch, vermicompost, plant diversity) has modified the abundance and diversity of microbial communities. Significant and Impact of the Study: Overall, our two experimental agroecological systems seem to have a positive impact on soil microbial communities particularly bacterial communities. In fact, these new vegetable cropping systems rather promoted the development of beneficial soil bacteria and limit development of pathogenic ones.