Increased microbial carbon use efficiency and metabolic capacity in manure amended soils: A 665-day field experiment

Manure is a valuable agricultural resource, providing essential nutrients for plant growth and soil health improvement, but studies evaluating the consequences of multiple manure applications to the soil microbial community and carbon (C) cycle processes mediated by microbes remains scarce. We compared microbial communities in a 665 days-field study of corn-wheat rotation plots with or without annual composted dairy manure amendments. We found a higher microbial C use efficiency (CUE, p < 0.05) in soils with than without manure. We performed stable isotope probing to identify microbial groups responsible for C incorporation in manure-applied soils. Members of the Actinobacteriota, Bacteroidota, Firmicutes, Gemmatimonadota, Myxococcota, Planctomycetota, and Proteobacteria responded to manure amendments in both summer seasons and increased significantly in abundance and diversity (p < 0.05) over the study period. In contrast, C-incorporators in zero manure soils were of similar abundance in soils with or without manure. Sequencing of soil metagenomes showed an increased relative abundance of functional genes related to C processes in manure-applied soils (+ 18.1%) in comparison to zero manure soils. Those genes were associated with a wide variety of metabolic pathways involved in the processing of C compounds (p < 0.001), indicating a greater metabolic capacity of the soil microbial community with higher CUE in comparison to that observed in zero manure soils. We concluded that multiple manure applications increased soil microbial CUE by selecting a microbial community with an increased capacity for metabolizing C compounds and biomass formation.