Long-term impacts of organic and conventional farming on the soil microbiome in boreal arable soil

Abstract

Long-term effects of organic and conventional farming systems in parallel on the microbiota of boreal arable soil from forage and cereal crop fields were investigated. Microbial activity was measured as basal respiration and microbial biomass C and N were determined by fumigation extraction. Microbial abundance was determined by gene copy numbers from bacterial and archaeal specific 16S rRNA genes and the fungal ITS2 region with quantitative PCR. Microbial community composition for soil bacteria and fungi, including arbuscular mycorrhiza, were conducted by amplicon sequencing with richness assessed from OTU reads. We detected changes in both bacterial and fungal community composition between the farming systems. Microbial activity and biomass C and N were higher in the organic system for cereal crop rotation compared to the respective conventional system. In the autumn, organic systems had higher microbial richness. As fungi were more abundant in the autumn, they may be responsible for both higher microbial activity and C sequestration in their biomass after harvesting, especially in the organic system for cereal crop rotation. Also, crop type and cow manure explained changes in fungal community composition. The typical bacterial community of the organic system for cereal crop rotation included many soil and plant health promoting bacterial groups. Fungi benefiting from organic farming practices, other than manure, may include endophytic taxa with a variety of functions as well as pathogenic and mycotoxin producing species. Overall, the results suggest that farming practices typical of organic farming, such as use of green manure and continuous plant cover have induced changes in the soil microbiome. • Farming system induced changes in bacterial and fungal community composition in cereal and forage crop rotations. • Organic systems possessed higher microbial richness compared to conventional systems in autumn. • Organic system for cereal crop rotation had higher microbial activity and biomass than in the conventional system . • Organic system for cereal crop rotation had more indicator microbes than the respective conventional system. • Organic system for cereal crop rotation contained many soil and plant health promoting bacteria as indicator species.