soil metagenome Raw sequence reads. soil metagenome

Land plants are engaged in intricate communities with soil bacteria and fungi indispensable for plant survival and growth. The plant-microbial interactions are largely governed by specific metabolites. Here, we employed a combination of lipid-fingerprinting, enzyme activity assays, high-throughput DNA sequencing and isolation of cultivable microorganisms to uncover the dynamics of the bacterial and fungal community structures in the soil after exposure to isothiocyanates, toxic glucosinolate catabolites from rapeseed and other Brassicaceae. We show that rapeseed-derived isothiocyanates drastically diminish diversity of bacteria and fungi. After isothiocyanate exposure, only few bacterial taxa of the Gammaproteobacteria (Acinetobacter, Thermomonas), Bacteriodetes (Flavobacterium) and Acidobacteria (Geothrix) proliferated while Trichosporon (Zygomycota) dominated the fungal soil community. Thus, the inclusion of Brassica cover crops for biofumigation, and the intensive cultivation of Brassica species in agriculture cause extreme losses within the microbial community structure with a strong impact on the cultivation of subsequent crops during crop rotation.