Soil microbiome response to integrated perennial weed management practices in semi-arid organic cropping systems

Abstract

Creeping perennial weeds are difficult to manage on organic farms in semi-arid regions of the northern Great Plains. Integrated weed management practices that combine biological, cultural, and mechanical controls can improve management of these weeds, but little is known about the soil microbial response to these practices. Our work investigated the soil microbiome response to contrasting, 4-year crop sequences with standard and reduced tillage. The crop sequences included a range of crop competition phases from high (three years of alfalfa, Medicago sativa L.) to low (two years of continuous fallow), within the longer 4-year period, with intermediate levels of crop competition between those two extremes. Soil samples were collected, and bacterial 16S and fungal ITS amplicon sequencing was performed. Differences in alpha diversity were not significant (p > 0.05) between tillage methods. Across all six locations, bacterial alpha diversity was negatively correlated with soil organic matter (R = -0.37, p < 0.001) while fungal alpha diversity was positively correlated (R = 0.17, p = 0.043). Bacterial community composition was not affected by crop sequence or tillage treatment. Fungal community composition was affected by crop sequence (p = 0.00163) and tillage (p = 0.02). The fungal genera Neosetophoma, Boeremia, and Paraphoma were 10 – 35-fold more abundant in continuous alfalfa compared to the mean abundance in the other crop sequences. Reduced tillage led to a 40% reduction in the fungal genus Fusarium, which contains many plant pathogen species. These results suggest that diversified crop sequences and altered tillage methods have minimal impact on bacterial communities, but fungal communities are sensitive to these management changes.