Land use and season drive changes in soil microbial communities and related functions in agricultural soils

Abstract Soil microorganisms are important for the maintenance of soil health and related functions. Agricultural management practices such as land use, season, and fertilizer affect soil microbial community structures. However, the effect of these management practices on soil microorganisms and related functions, influenced by regionally different soil types, is still not clear. Hence, the study was conducted in an Andosol (volcanic soil) dominated agricultural region in a cool temperate climate to determine the effect of land use (cropland, grassland), season (spring, summer), and fertilizer (anaerobic digestate—AD) on soil microorganisms and related functions. Soils were sampled from farmers’ fields, deoxyribonucleic acid (DNA) extracted and sequenced targeting 16S rRNA region. As a result, land use had a significant effect on beta diversity and evenness with higher values recorded in cropland than grassland. However, grassland had a higher number of unique operational taxonomic units (OTUs) (10303) compared with cropland (5112). In cropland, season had a significant effect on beta diversity, evenness, OTU numbers, and Shannon index with higher values recorded in summer compared to spring. Based on predicted soil functions, nitrogenase (nifH) had significantly higher values in cropland‐summer while nitrite reductase (nirK) and ammonia monooxygenase (amoA) were significantly higher in cropland‐spring. In grassland, season had a significant effect on beta diversity only. These results indicate that grassland microorganisms were stable and more resistant to seasonal changes than cropland, suggesting that conventional tillage practices have a negative effect on soil microbial stability. Additionally, grassland‐spring (7059) had a higher number of unique OTUs than grassland‐summer (2597). Based on predicted soil functions, nifH was significantly higher in grassland‐spring while nirK and amoA were significantly higher in grassland‐summer. These results indicate that the impact of seasons on soil microorganisms’ distribution and abundance in cropland and grassland may directly affect soil functions.