Hoidal, N. | bioRxiv Science

bioRxiv2026

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

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.

microbiology↗

bioRxiv2026

Managing soil sustainably on small-scale vegetable farms: Lessons learned from high tunnel and open field vegetable production

Small-scale vegetable farms are increasingly important to local food systems, but the soils on these farms are not well understood, particularly in high tunnel production environments. Therefore, this study aimed to 1. Compare soil nutrients and soil health metrics in high tunnels and nearby open fields. 2. Document soil nutrient accumulation on diversified vegetable farms and assess loss potential. 3. Explore the impacts of specific management practices (input use, cover crops, tillage, and soil testing) and farm demographics on a variety of soil health and soil nutrient metrics. Just under half of the high tunnels in this study had soluble salt accumulation, which was associated with higher soil nitrate concentrations. The pH of many high tunnel soils was above the optimal range for crop production, which was correlated with irrigation water alkalinity. Some high tunnel soils had rapid water infiltration rates, with implications for irrigation water management. Both high tunnel and open field soil were rich in nutrients compared with other Minnesota farms. Preliminary assessments suggested risks to surface and groundwater from nutrient runoff and leaching. While farmer experience and more years in vegetable production were negatively associated with soil health metrics, management practices including reduced tillage, organic management, and application of plant-based compost were positively associated with soil health. Cation exchange capacity and permanganate oxidizable carbon did not provide significantly more insight than simply measuring organic matter. Arbuscular mycorrhizal fungal spore counts were inconclusive, but aggregate stability and bulk density were responsive to farmer reported soil management activities. Core ideasO_LIHigh tunnel soil tends to be rich in nutrients and organic matter. They also accumulate soluble salts, likely from excess inputs C_LIO_LIIrrigation water routinely tested high in pH and alkalinity. These factors may explain high soil pH in high tunnels. C_LIO_LISmall-scale vegetable farms often have high concentrations of soil nutrients in both high tunnels and open fields, with potential to cause environmental contamination through leaching and runoff C_LIO_LIVegetable production may be inherently hard on soil health, but conservation practices including reduced tillage, organic management, and use of plant-based composts can improve soil health in these production systems C_LI

ecology↗