Strong agricultural management effects on soil microbial community in a non-experimental agroecosystem

Soil microbial communities are indicators of soil health and are affected by factors such as agricultural management, plant selection and soil compartment. It remains unclear how these factors interact and affect microbial community structure and function in non-experimental agroecosystems. In this study, we take a holistic approach to investigate the composition and function of the bacterial and fungal communities associated with different agricultural management systems (organic/conventional) of two crop species (cabbage/lettuce) in two soil compartments (rhizosphere/bulk) using Illumina sequencing. Microbial alpha diversity indices were higher in soils from the organic compared to conventional system. Microbial beta diversities were significantly affected by both individual [agricultural management (M) and plant selection (P)] and interactive (M × P) effects. Bacterial and fungal community composition were more strongly influenced by agricultural management (explained 26.0% and 18.0%, respectively) compared to plant selection (8.5% and 12.0%), soil compartment (2.4% and 1.1%) and interactions between factors (0.1–2.4%). Soils from the organic system had higher pH, organic matter concentration and available phosphorus, and pH was identified as having the largest influence on bacterial and fungal communities. Taxonomic and functional analyses identified potential benefits of soils from the organic system, such as having higher levels of plant disease suppression (Streptomyces) and nutrient cycling (enriched metabolism, higher proportion of taxa in order Rhizobiales). Network analyses inferred that bacterial and fungal networks in soils from the organic system compared to the conventional system are more connected and centralized. Our findings suggest that organic management practices have a large effect increasing diversity, promoting healthier soils via beneficial microbial taxa and functions and supporting more complex bacterial networks.