COS 116-6 - 100 Years of Disturbance: Long-term Impacts of Agriculture Practices on the Soil Microbiome

Abstract: Industrial agricultural practices characteristic of the 21^st century have relied on maximizing crop yield at the cost of important biological complexity that underlies ecosystem health. To wholistically improve agriculture, we need to understand the complex and long-term interactions between plants, management practices, and the soil microbiota. To address this gap in knowledge, we characterized the soil microbiome from the University of Illinois Morrow Plots over the course of 100 years of farming. The Morrow Plots represent one of the most ambitious and long-lasting experiments to comprehend how agricultural management practices alter soil fertility. Using a soil archive from this experiment, we were able to measure how crop rotation and fertilizer inputs shaped the soil microbiome from the early 1900s to the 2020s. To determine how microbiome diversity and function changed across time and treatments we carried out shotgun metagenomics and enzyme assays. We found the microbiome composition dramatically changed over time with our oldest samples having high concentrations of endospore-forming bacteria (namely Prietia megaterium) (perMANOVA R²=0.19, p< 0.001). Furthermore, we found impacts of crop rotation, and fertility on the composition of the microbiome both independent and dependent of time (Rotation: R²=0.04, Rotation*Time: R²=0.03 | Fertilizer: R²=0.15, Fertilizer *Time: R²=0.04). To elucidate how diversity within a species was transformed by agriculture treatments across the chronosequence, we carried out a co-assembly across all samples and found 850 high-quality MAGs. Using Prietia megaterium as a model species, we wanted to explore how long-term fertilization and crop rotation treatments shaped the Prietia pangenome. To do this, we mapped reads from individual samples to the Prietia MAG to determine the prevalence of specific genes across time and treatment. From this analysis, we found that agricultural treatments resulted in the loss of novel genes within the Prietia pangenome and a change in the organism’s nutrient cycling genes. These results were validated with an assembly-independent approach (HUMANN3). Overall, these results show that long-term industrial agriculture practices have shaped the ecology and evolution of these microorganisms, and potentially transformed how they move nutrients within ecosystems. Grasping how long-term agriculture drives microbiome erosion and alleviating it is imperative to creating regenerative sustainable food-producing systems.