Bacterial community composition in agricultural soils under long-term organic and conventional management

Organic row cropping systems utilize diverse management regimes, but share required practices, including biological fertility sources, diverse rotations, incorporation of organic matter, and lack of synthetic pesticides. The practices can alter the composition of functionally significant soil microbes relative to conventional practices. We used 16S rRNA sequencing to profile soil bacterial communities at five locations where long-term organic and conventional row cropping were practiced in close proximity on the same underlying soil type. Location effects, reflecting soil characteristics, were stronger than effects of organic vs. conventional management or corn (Zea mays L.) vs. soybean [Glycine max (L.) Merr.] cropping on the relative abundance of bacterial taxa. A core subset of 1,300 operational taxonomic units (OTUs) were detected in all sampled soils. Firmicutes made up a smaller portion of core OTUs than total OTUs, indicating that taxa in this group were more likely to be found only in specific environments. Conversely, Actinobacteria OTUs were more highly represented in the core than the full OTU set, indicating wide distribution of these taxa across environments. The genus Streptomyces comprised a five-fold–greater proportion of core OTUs than of total OTUs. We identified 303 OTUs whose abundance differed with management system. Of those, members of the phyla Bacteroidetes and Planctomycetes tended to be more abundant under organic management, whereas members of the Actinobacteria and Verrucomicrobia tended to be more abundant in conventional. This multi-site study contributes to identification of bacterial community members most affected by organic practice adoption across soil types and practices.