Soil microbial biomass, functional microbial diversity, and nematode community structure as affected by cover crops and compost in an organic vegetable production system

Soil microorganisms play a crucial role in mineralization and breakdown of complex organic compounds in soil. Microbial populations and functional diversity are greatly influenced by quantity and quality of crop residue and other incorporate organic amendments. This study investigated the effect of cover crops (rye or a mixture of rye-vetch) and compost on soil microflora and microfauna under an organic tomato production system. Each cover crop treatment was used in conjunction with or without compost in a split-plot experimental design. Data on soil respiration, microbial biomass, metabolic quotient, and nematode populations were measured at the end of the growing season. Metabolic characteristics of the soil microbial community were determined using 31 C substrates on Biolog-EcoPlate™. Community level physiological profile (CLPP) was assessed by calculating average well color development (AWCD), richness (S), Shannon–Wiener diversity index (H), and evenness (E). Effect of compost was more pronounced on soil respiration than cover crop treatment. Highest microbial biomass was found in the soils amended with rye and compost (195–210 μg g dry soil−1). Regression analysis between microbial biomass and soil organic matter (SOM) showed strong correlation (R2 value of 0.68–0.56) in two out of the three growing seasons. Calcium, magnesium, and potassium concentrations in soil also positively correlated with microbial biomass. There were significant differences among soils in numbers of plant parasitic, bacterial, and fungal feeding nematodes during the initial years of the study but the differences were not evident later. Shannon–Wiener diversity index was significantly affected by cover crop treatment with rye treatments generally exhibiting higher degree of soil microbial functional diversity. Biolog-EcoPlate™ assay was sensitive to changes in the short-term. Principal component analysis of the Biolog data allowed differentiation of treatments but distribution patterns varied from year to year. We conclude that both rye and rye-vetch mixture can affect the functional diversity of soil microbial community but differences between them are marginal when compared to compost and no-compost treatments. Microbial communities were more responsive to compost applications than cover crop effects.