Soil microbial communities shift in response to cropping sequence diversification with perennial seed crops

Integrating perennial forage seed crops into annual cropping sequences can diversify the rotations and improve soil health, yet their effects on the soil microbial communities and functions are not yet fully elucidated on the Canadian prairies. Using a 10-year field experiment with eight cropping sequences under varying supplemental nitrogen (N) fertilization levels, we evaluated the impacts of integrating perennial seed crops and annual crops on soil microbial biomass carbon (MBC), the composition and diversity of prokaryotic and fungal communities, and the activities of key enzymes involved in carbon (C), N, phosphorus (P), and sulfur (S) cycling, namely β-glucosidase, N-acetyl-β-glucosaminidase, acid phosphomonoesterase and arylsulfatase. The crop sequences containing intermittent succession of perennial and annual crops had 17% greater soil MBC, higher fungal richness (e.g., Chao1 indices of 92.8 vs. 87.6) and 22% greater β-glucosidase activity than annual-only sequences. The relative abundances of the two most abundant prokaryotic phyla - Actinobacteriota and Proteobacteria - as well as the second most abundant fungal class, Dothideomycetes, followed the same trend. The soils with more frequent recurrence of grassy perennials in the sequences exhibited greater MBC (34%), higher prokaryotic Shannon diversity, greater fungal richness, and higher arylsulfatase activity (68%) than soils with more frequent recurrence of perennial legumes, although the predominant prokaryotic phylum, Actinobacteriota was more abundant in legume-based systems. The cropping sequences dominated by creeping red fescue grass seed crops exhibited the greatest improvement in most of the soil microbial metrics studied. Nitrogen fertilizer increased the relative abundance of the copiotrophic Actinobacteriota but decreased that of the oligotrophic Acidobacteriota. Prokaryotes were associated with C, N, P and S cycling, whereas fungi were primarily linked to C cycling. Overall, diversifying annual grain cropping systems with perennial forage seed crops, particularly creeping red fescue, enhanced key indicators of biological soil health.