Soil enzyme activities and abundance of microbial functional genes involved in nitrogen transformations in an organic farming system

Organic farming systems receive organic amendments to maintain soil fertility and supply nutrients for plant growth. This study investigated the effect of organic fertilizers (no amendment as control, compost, and manure), and their interaction with cover crops (millet, buckwheat, and black turtle bean) on soil enzyme activities, N transformation rates, and functional gene abundances under an organic production system. Organic N fertilizers had a stronger effect than cover crop type on soil function and functional gene abundances. Soil enzyme activities were increased by both compost and manure, but there were few differences between these treatments. Nitrification potential, nitrite oxidation potential, and denitrification potential were significantly higher in manure-treated than in control and compost-treated soils, indicating application of manure had a higher N loss potential than compost application in this organic farming system. Organic N fertilizers significantly increased the abundance of some genes involved in N mineralization, ammonification, and nitrification (sub, ureC, bacterial amoA and nxrB). The activity of ammonia-oxidizing bacteria and archaea were both increased by organic N fertilizers, and their activities were higher in manure-treated than in compost-treated soils. Overall, the abundance of functional genes was significantly correlated with their corresponding enzyme activity. However, functional gene abundance was less important than soil chemical and microbiological properties in explaining the variation in the corresponding enzyme activity.