Identifying the Active Microbiome Associated with Roots and Rhizosphere Soil of Oilseed Rape

RNA stable isotope probing and high-throughput sequencing were used to characterize the active microbiomes of bacteria and fungi colonizing the roots and rhizosphere soil of oilseed rape to identify taxa assimilating plant-derived carbon following13 CO2 labeling. Root- and rhizosphere soil-associated communities of both bacteria and fungi differed from each other, and there were highly significant differences between their DNA- and RNA-based community profiles.Verrucomicrobia ,Proteobacteria ,Planctomycetes ,Acidobacteria ,Gemmatimonadetes ,Actinobacteria , andChloroflexi were the most active bacterial phyla in the rhizosphere soil.Bacteroidetes were more active in roots. The most abundant bacterial genera were well represented in both the13 C- and12 C-RNA fractions, while the fungal taxa were more differentiated.Streptomyces ,Rhizobium , andFlavobacterium were dominant in roots, whereasRhodoplanes andSphingomonas (Kaistobacter ) were dominant in rhizosphere soil. “Candidatus Nitrososphaera” was enriched in13 C in rhizosphere soil.Olpidium andDendryphion were abundant in the12 C-RNA fraction of roots;Clonostachys was abundant in both roots and rhizosphere soil and heavily13 C enriched.Cryptococcus was dominant in rhizosphere soil and less abundant, but was13 C enriched in roots. The patterns of colonization and C acquisition revealed in this study assist in identifying microbial taxa that may be superior competitors for plant-derived carbon in the rhizosphere ofBrassica napus .IMPORTANCE This microbiome study characterizes the active bacteria and fungi colonizing the roots and rhizosphere soil ofBrassica napus using high-throughput sequencing and RNA-stable isotope probing. It identifies taxa assimilating plant-derived carbon following13 CO2 labeling and compares these with other less active groups not incorporating a plant assimilate.Brassica napus is an economically and globally important oilseed crop, cultivated for edible oil, biofuel production, and phytoextraction of heavy metals; however, it is susceptible to several diseases. The identification of the fungal and bacterial species successfully competing for plant-derived carbon, enabling them to colonize the roots and rhizosphere soil of this plant, should enable the identification of microorganisms that can be evaluated in more detailed functional studies and ultimately be used to improve plant health and productivity in sustainable agriculture.