A study of Glycine max (soybean) fungal communities under different agricultural practices

Both Glycine max (soybean) and Thlaspi arvense (pennycress) are valuable resources for renewable biofuels and industrial products. Pennycress, a member of the Brassicaceae, can be grown over the winter months providing soil cover and thus reducing erosion. In addition, pennycress does not compete with food production making it an appealing option for biofuels. The objective of this study was to determine the effect of different agricultural practices on fungal communities associated with soybean roots and their interactions with an emerging crop/cover crop, pennycress. We examined roots collected in the summer of 2013 and 2014 from three treatment plots (organic, conventional soybeans, and conventional soybean with pennycress as a cover crop). Root DNA was amplified using fungal primers followed by 454 pyrosequencing. A total of 560,948 sequences were obtained with Ascomycota as the dominant fungal phylum in all plot treatments. Soybean roots in all treatments were dominated by the order Hypocreales with Fusarium as the most abundant genus. Fungal community structure was affected by host and farming practice. The magnitude of the effect was determined by sampling year. The cover crop, pennycress, had a distinct fungal assembly from soybean and did not affect the structure of fungal communities in soybean when used as a cover crop. The organic soybean fungal community was significantly different and contained lower diversity than the conventional soybean, with the greatest differences observed in 2014. This study shows that the structure of fungal communities associated with plants in agroecosystems are regulated by a complex number of abiotic and biotic factors including weather conditions, farming practice, and host.