Agricultural soil microbiomes differentiate in soil profiles with fertility source, tillage, and cover crops

Soil microbiota are critical to soil health, yet a substantial knowledge gap remains to understand how microbial communities can be interpreted as soil health parameters and, consequently, be informative for sustainable agriculture. This study examined the influence of long-term (over 40 years) agricultural systems (organic and conventional) on the assembly of prokaryotes (bacteria and archaea) and fungi at separate soil depths down 60 cm. These agricultural practices included distinct fertility sources (legume, manure, and synthetic fertilizer), tillage types, and presence or absence of cover crops. A regression model highlighted that prokaryote and fungal richness, but not evenness, differed with agricultural practices and soil depth. Integrated through 60 cm soil depth, prokaryote richness was on average 9 % and 7 % greater with legume fertilizer than with manure or synthetic fertilizer, respectively. The effect of fertility source on soil fungi was mediated by tillage: conventional systems had 4 % lower average richness than organic systems under full tillage and 4 % greater richness under reduced tillage. Indicator taxa analysis revealed that each agricultural practice had a unique set of associated microbial groups. The organically fertilized systems included nitrogen-cycling functional guilds, while two-thirds of indicator groups for the conventional system had suspected parasitic lifestyles. Microbial community composition also changed across systems as determined with permutational multivariate analysis of variance. Prokaryotic communities differed most between legume and manure fertility systems, while fungal communities were most distinct between synthetic fertilizer and either organic system. Overall, this study demonstrates that the effect of fertility source on microbial community diversity is modified by tillage intensity, and to a lesser extent, cover crops and that each interaction is mediated by soil depth. Collectively, these influences may have consequences for microbial functional capacity and the sustainability of agricultural soils.