Continuous monoculture shapes root and rhizosphere fungal communities of corn and soybean in soybean cyst nematode-infested soil

The rhizosphere effect shapes microbial communities around and within plant roots and may lead to the enrichment of fungi involved in both positive and negative plant-soil feedbacks. We used internal transcribed spacer 1 amplicon sequencing to investigate how continuous monoculture affects the fungal communities in the corn and soybean rhizosphere, rhizoplane, and root endosphere in a long-term crop rotation experiment where soils were infested with a major soybean pathogen, the soybean cyst nematode (SCN, Heterodera glycines). Community-level statistical analyses showed evidence of selective filtering and enrichment of fungi in and around corn and soybean roots and in SCN cysts. Patterns of relatedness between fungal communities in various agroecosystem compartments suggested that SCN cysts are colonized by soybean root endophytic fungi and that colonization of roots and cysts may aid proliferation of these fungi in the bulk soil agroecosystem compartment over time. Natural antagonists of the SCN such as nematode-trapping fungi and nematode endoparasites increased in relative abundance in the rhizosphere and root endosphere, respectively, over continuous soybean monoculture. In contrast, arbuscular mycorrhizal and plant-pathogenic fungi, several of which were negatively correlated with corn yield, increased in relative abundance over continuous corn monoculture. These results suggest the possibility of positive plant-soil feedbacks involving nematophagous fungi over continuous soybean monoculture and negative plant-soil feedbacks involving plant pathogens and some nonbeneficial arbuscular mycorrhizal fungi over continuous corn monoculture.