Fungal communities of soybean cyst nematode-infested fields under corn and soybean monoculture and crop rotation

Abstract

Understanding how continuous monoculture impacts fungal communities of corn and soybean is essential for developing agricultural practices that minimize yield losses and protect plants from disease. In continuous crop monoculture, negative plant-soil feedbacks involving a build-up of detrimental fungi are thought to be involved in yield declines. However, positive plant-soil feedbacks involving a build-up of microbial antagonists to specific plant pathogens may also occur over long-term monoculture. Changes in soil properties and depletion of key nutrients may also negatively impact yields under crop monoculture. In my dissertation, I investigate soil and root-associated fungal communities under long-term corn-soybean monoculture and crop rotation. I focus on relationships between the mycobiota in different agroecosystem compartments (bulk soil, rhizosphere, rhizoplane, and root endosphere) and on shifts in fungal communities in relation to soil properties, pathogen density, and yield. In chapters 1 and 2, I explore fungal communities in bulk soils, rhizosphere soils, and root endospheres of corn and soybean using a high throughput amplicon sequencing approach and ask whether variation in communities is related to continuous monoculture, soil properties, or the density of a major soybean pathogen, the soybean cyst nematode (Heterodera glycines, SCN). Long-term monoculture of both crops resulted in dramatically different soil and root-associated mycobiota compared to annual crop rotation. Nematophagous fungi increased in abundance and diversity over continuous soybean monoculture, while arbuscular mycorrhizal fungi (AMF) increased in abundance and diversity over continuous corn monoculture. In chapter 1, positive relationships between soil P and Mortierellales, an order containing phosphate-solubilizing fungi, and negative relationships between soil P and AMF suggest biological causes for the observed shifts in available soil P under continuous soybean and corn monoculture. However, structural equation modeling did not show that changes in soil P had a direct effect on yield in either crop and identified soil N and crop host-specific pathogens (fungal pathogens of corn and the SCN) as the most important factors in monoculture yield decline. In chapter 2, I found evidence of selective filtering and enrichment of nematophagous taxa in soybean root-associated compartments due to the "rhizosphere effect" and overlap between fungal communities in soybean roots and SCN cysts, suggesting that the soybean root promotes the growth of fungi that ultimately colonize the SCN cysts. In chapter 3, I used a culture-based approach to characterize the root endophytic mycobiota of corn and soybean and investigated the potential for soybean and corn root endophytes to produce substances that are toxic to the SCN. This project resulted in the first reported isolation of the nematode biocontrol fungus Hirsutella rhossiliensis from a soybean root and showed that the diversity of soybean fungal endophyte communities was correlated with the density of the SCN. Several corn and soybean endophytes produced nematicidal metabolites, in vitro. These projects open the door to future research investigating the utilization of fungi for improved P uptake by plants and the use of root endophytes in the biocontrol of the SCN.