Effects of Cover Crop and Fertilizer Incorporation on the Structure and Function of Microbial Communities in Soils Under Long-Term Organic Management.

Incorporation of organic materials, including cover crop residues and biological fertilizers, is an important element of organic farming practices. These amendments can alter the composition of soil microbial communities that carry out nutrient cycling and perform other functions crucial to crop health and growth. These changes may be detectable through use of 16S rDNA profiling of soil bacterial community composition. We conducted a field experiment at three southern Minnesota sites under long-term organic management to determine the effects of cover crop and organic fertilizer treatments on soil bacterial community structure, nutrient cycling functions, and physicochemical properties. Illumina sequencing of 16S rDNA revealed diverse communities encompassing 45 bacterial phyla in bulk and rhizosphere soil. Soil functional profiles were more strongly predicted by location than by treatment, and location differences were largely explained by soil physicochemical parameters. Treatment and location effects on bacterial community structure and soil function were largely mediated by soil physicochemical properties including pH, moisture, soil organic matter, and nutrient levels. We observed treatment effects on several soil functions, including respiration and enzyme activities. However, these effects were not consistent across locations and sampling time points. Differences in soil function were better explained by using both soil physicochemical test values and community structure data than using soil physicochemical tests alone. We also observed correlations between nutrient cycling functions and bacterial family abundances, although Bayesian analysis showed no inferred regulation of specific functional activities by particular bacterial families or physicochemical parameters. These results indicate that cover crop and fertilizer application practices are capable of affecting the microbial environment encountered by subsequent crops. Our results also support the use of sequencing-based microbial community profiling as an important tool for increasing our understanding of community structure-function relationships, with the goal of improving our ability to predict the effects of agricultural management practices on important soil functions.