Comparative Analysis of Soil Microbial Communities in High-Tunnel and Field Agricultural Systems

Abstract

High tunnels and open-field systems differ markedly in soil physicochemical properties, yet their effects on belowground microbiomes remain poorly understood. We characterized bacterial and fungal communities in paired high-tunnel and adjacent field soils from 100 small-scale vegetable farms across Minnesota, integrating amplicon sequencing of 16S rRNA and ITS2 regions with soil nutrient data, arbuscular mycorrhizal fungi (AMF) spore counts, and microbial co-occurrence networks. High-tunnel soils had higher pH, organic matter, and multiple macronutrients (notably P, K, and N forms) and lower bulk density than fields, reflecting intensive organic amendments and reduced leaching. Despite these differences, bacterial and fungal alpha diversity did not differ between environments, whereas beta diversity analyses revealed strong shifts in community composition. High tunnels were enriched in salt- and stress-tolerant bacterial phyla (Firmicutes, Deinococcota, Patescibacteria, Halanaerobiaeota, Halobacterota) and saprotrophic fungal groups (Mortierellomycota, Ascomycota, Basidiomycota, Mucoromycota), while several oligotrophic or symbiotic taxa, including Acidobacteriota and Glomeromycota, declined. Glomeromycota relative abundance was negatively correlated with high soil phosphorus, whereas AMF spore densities did not decline, suggesting suppression of active mycorrhizal symbioses rather than propagule loss under high-nutrient conditions. Co-occurrence network analyses showed that bacterial and fungal networks in high tunnels were less dense, more modular, and exhibited higher ratios of positive to negative associations than field networks, consistent with stress-induced shifts toward more facilitative interactions. Collectively, our results indicate that high-tunnel production homogenizes soil microbiomes and selects for stress- and high-nutrient-adapted taxa, with potential consequences for nutrient cycling, AMF function, and long-term agroecosystem outcomes.