Arable soil microbial communities are affected by plant community and agricultural management

Abstract

Plants shape soil microbiomes, yet this interaction is underexplored in the cultivated farmlands of the boreal region. We assessed the soil microbiome of seven differently managed major crop types in the region (pasture, ley, oat, rye, faba bean, oilseed, and cabbage), alongside a long-term environmental fallow, in 73 fields in Southern Finland. Microbial data were cross-analyzed with plant community data, which combined the cultivated and other vascular plants observed in the fields. Amplicon sequence analysis indicated that crop type, plant richness, plant coverage, and agricultural management affect the soil microbiome’s taxonomic and predicted functional composition. The most dissimilar microbial communities were under fallow and cabbage, which represented the management and plant diversity extremes. Plant richness influenced the community composition and predicted functional potential of bacteria and fungi. Microbial diversity was a poor indicator of the putative beneficial fungal functional group, arbuscular mycorrhizal fungi (AMF), and of bacterial predicted genes related to soil ecosystem functions, inorganic-phosphorus (Pi) solubilizing and nitrogen-fixing genes. Fallow with lowered microbial diversity had the highest proportions of nitrogen-fixing and Pi solubilizing genes, and AMF. Similarly, organic production method with lowered fungal richness in perennial crop types (pasture and ley) had high proportion of AMF and nitrogen-fixing genes across crop types. Tillage intensity was positively associated with the proportion of bacterial beta-glucosidase genes involved in carbon cycling. We show that in the boreal region, crop type and plant community (especially richness), and agricultural management all affect soil microbial communities, with potential implications for microbial-mediated soil functions.