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

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.