Bacteria utilising plant-derived carbon in the rhizosphere of <em>Triticum aestivum</em> change in different depths of an arable soil.

Abstract

Root exudates shape microbial communities at the plant soil interface. Here we compared bacterial communities that utilise plant-derived carbon in the rhizosphere of wheat in different soil depths, including topsoil, as well as two subsoil layers up to 1 m depth. The experiment was performed in a green house using soil monoliths with intact soil structure taken from an agricultural field. To identify bacteria utilizing plant derived carbon, (13) C-CO2 labelling of plants was performed for two weeks at the EC50 stage, followed by stable isotope probing of extracted DNA from the rhizosphere combined with 16S rRNA gene-based amplicon sequencing. Our findings suggest substantially different bacterial key players and interaction mechanisms between plants and bacteria utilising plant-derived carbon in the rhizosphere of subsoils and topsoil. Among the three soil depths, clear differences were found in (13) C enrichment pattern across abundant operational taxonomic units (OTUs). Whereas OTUs linked to Proteobacteria were enriched in (13) C mainly in the topsoil, in both subsoil layers OTUs related to Cohnella, Paenibacillus, Flavobacterium showed a clear (13) C signal, indicating an important, so far overseen role of Firmicutes and Bacteriodetes in the subsoil rhizosphere