Bacterial communities of soil and earthworm casts of native Palouse Prairie remnants and no-till wheat cropping systems

Abstract

Earthworms are important ecosystem engineers and modify the physical and chemical properties of soils. However, less is known about how earthworms impact soil microbial communities. We compared bacterial communities of the bulk soil and earthworm casts in native prairie remnants and wheat cropped fields in the Palouse of eastern Washington using next-generation sequencing. Communities among prairie sites were similar, indicating a consistent prairie community. The bulk soil and earthworm casts of native prairie locations had higher richness compared to agricultural sites, but similar diversity. Diversity tended to be higher in bulk soil than earthworm casts in native prairies but not agricultural soils. In native prairies, earthworm casts were enriched in the families Caulobacteraceae, Cellulomonadaceae, Cytophagaceae, and Microbacteriaceae, and the genera Flavobacterium, Caulobacter, Burkholderia, Brevundimonas, compared to the bulk soil. In agricultural soils, Geodermatophilaceae, Flavobacterium and Pseudomonas were relatively more abundant in casts, whereas bulk soil harbored greater relative abundances of taxa related to Acidobacteria GP1. Casts from prairies had higher abundances of Actinobacteria, including Cellulomonas, Pseudonocardia, Geodermatophilaceae, and Propionibacteraceae, whereas casts from agricultural habitats were especially enriched in Flavobacterium and Pseudomonas. Fresh casts from Aporrectodea trapezoides from agricultural sites were highly enriched in Flavobacteriaceae, Pseudomonadaceae, Nocardioidaceae and Geodermatophilaceae and in OTUs related to Flavobacterium, Pseudomonas, and Bradyrhizobiaceae. Co-occurrence networks among communities from bulk soil and earthworm casts collected from agricultural fields were strikingly different than those from prairie soils and formed only two modules of co-occurring taxa, compared to 8–9 modules in the prairie soils, indicating a greater complexity of interactions. Networks from agricultural fields tended to have lower ratios of positive to negative edges (interactions) compared to prairie soils, suggesting more competition and antagonism among bacteria. Thus, the specific co-occurring taxa, as well as the aggregate structure of ecological interactions, are largely distinct between Palouse prairie soil communities versus those of earthworm casts in agricultural settings.