Bacterial and fungal co-occurrence patterns in agricultural soils amended with compost and bokashi

Abstract

The living soil harbors a significant number and diversity of bacteria and fungi, which are essential in sustaining soil ecosystem functions. Most studies focus on soil bacteria or fungi, ignoring potential interrelationships between kingdoms that coevolve and synergistically provide ecosystem functions. In a seven-year agricultural field, we explored the effects of organic amendments (OAs; i.e., compost and bokashi) on intra- and inter-kingdom co-occurrence networks of soil bacterial and fungal communities. We observed that OAs changed the co-occurrence patterns of bacteria and fungi. Distinct network modules were observed in the unamended and amended soils, and the physicochemical properties of the soil could partially explain the formation of these modules. We also found that compost and bokashi increased the proportion of positive correlations, and this could reduce competition among microorganisms for soil resources. Our study reveals that soil management with OAs affects relationships between bacterial and fungal subpopulations that physically co-exist, cooperate, and compete in non-random structured networks. It highlights that ecosystem functions may depend on inter-kingdom interactions shaped by different amendments and their applied dose.