Soil microbes govern fundamental ecosystem processes such as nutrient cycling dynamics through decomposition, maintenance of soil stability and carbon storage, and interact directly with plants along a mutualistic-parasitic continuum. Agricultural practices represent compounding disturbances on ecosystems, and shifting global agriculture toward lower-input systems is imperative to reconcile productivity and conservation goals. The objective of this research is to better understand how specific agricultural practices affect bacterial and fungal community assembly patterns in agricultural soils, with a particular focus on arbuscular mycorrhizal (AM) fungi. In Oregon, viticulture provides an ideal system to elucidate community responses to agricultural disturbances as cultivation of wine grapes provokes unique incentives for sustainability and there exists a variety of management intensities throughout Oregon vineyards. Here, we used high-throughput sequencing of soil microbial communities present in vineyard soils to answer the following questions: (1) how do specific agricultural practices affect soil microbial community assembly patterns; (2) how do geography and soil type influence shifts in microbial composition; and (3) do these patterns persist across space and time? We characterized microbial composition using 16S (bacteria) ITS (fungi) and SSU (AM fungi) amplicon sequencing of >2500 DNA extracts from Oregon vineyard soils collected in the Winter, Summer and Fall of 2018.
Results/Conclusions
We show that geographic region, climate variables and agricultural management hierarchically structure fungal and bacterial communities in Oregon vineyard soils. Extreme gradient-boosted machine learning algorithms predicted agricultural management categories and presence/absence of specific practices with ≥65% accuracy based off of fungal and bacterial composition alone. Microbial composition also varied significantly with growing region across all seasons, and differences in soil fertility management and tillage practices specifically influenced shifts in fungal saprotroph and arbuscular mycorrhizal composition and abundance, respectively (PERMANOVA p ≤ 0.001). Shannon and Simpson estimates of bacterial and fungal alpha diversity revealed distinct patterns across soil fertility management, with a marked decrease in fungal species richness associated with chemical inputs in conventional vineyards (p < 0.05). We also found significant differences in fungal functional group composition and pathogen richness in response to climate variables such as annual precipitation. Arbuscular mycorrhizal fungal communities were also significantly structured by region, management and grape variety (ANOSIM p < 0.05). These results have implications for soil management practices and their relation to sustaining agroecosystem resiliency to a changing environment.