Organic cropping systems alter metabolic potential and carbon, nitrogen and phosphorus cycling capacity of soil microbial communities

Intensive agriculture can impair soil quality and threaten the provision of critical soil ecosystem services. Organic cropping systems aim to ensure sustainable production by promoting soil biodiversity to enhance soil functioning and regulate nutrient cycling through microbial processes. While taxonomic changes in microbial community composition in response to agricultural management are well described, there is still a fundamental knowledge gap when it comes to the impact of cropping system on soil functional diversity. Therefore, we revisited the 42-year-old DOK field experiment and used shotgun metagenomics to assess the metabolic potential and nutrient cycling capacities in organic and conventionally managed soils. The functional annotation of 11.4 billion reads to universal (EC, SEED), as well as carbon (CAZy), nitrogen (NCycDB) and phosphorus (PCycDB) cycling gene ontologies showed that manure fertilization was the main factor altering soil metabolic potential. But also, organic management practices, such as omission of synthetic pesticides and mineral fertilization induced changes in soil metabolic potential e.g. by enriching functional genes involved in organic phosphorus acquisition, nitrate transformation, organic degradation and non-hydrolytic carbohydrate cleavage. Conventional systems, receiving mineral fertilization and chemical plant protection, enriched genes associated with inorganic nutrient acquisition and transcriptional activity. The results of this study demonstrate that cropping systems influence the functional potential of soils, affecting fundamental mechanisms of nutrient cycling and thus soil regulating capacity. Consequently, cropping systems can be utilized to steer the regulating potential of agricultural soils and to lower the environmental impact of food systems. • Long-term soil management affects soil functional capacity to regulate nutrients. • Organic amendments enhance soil capacity for organic matter degradation. • Organic cropping fosters the capacity for mineralization of organic compounds as well as phosphate and nitrate acquisition. • Conventional cropping enhances cellular processes and biosynthesis.