Effects of carbon sources on soil bacterial community dynamics during anaerobic soil disinfestation in an organic tomato production system

Anaerobic soil disinfestation (ASD) is a biologically-based agricultural practice used to manage soilborne pests and pathogens and enhance soil fertility. Successful implementation of ASD requires the use of distinct soil organic amendments as a source of carbon (C) and nitrogen (N), which dynamically affect the microbial-mediated processes of organic C breakdown and stabilization. Here, we established a field experiment to test the effects of different soil organic amendments – including cover crops characterized by different C:N ratios and an agricultural by-product (i.e., wheat middlings) – on the temporal dynamics of soil bacterial communities and their implications for ASD efficacy and subsequent tomato crop performance. We used a combination of time-series analyses to investigate variation in the soil bacterial community and soil chemical properties (e.g., pH, electrical conductivity (EC), cumulative redox potential (ΣEh), ammonium, and nitrate content) over 21 days of ASD treatment and following tomato planting. Our results revealed that the organic amendments used to apply ASD caused a shift in soil bacterial communities driven primarily by changes in pH and EC. However, post-tomato planting, soil bacterial communities exhibited resilience to ASD treatment and were compositionally similar to the pre-ASD bacterial communities. Beneficial taxa were differentially enriched during ASD treatment and the tomato crop cycle. Taxa enriched during ASD treatment included Candidatus Udaeobacter, Gaiella, Pseudomonas, Rhizobium, Klebsiella, Paenibacillus, and Bacillus. Likewise, taxa enriched during tomato production included Nitrospira, Geobacter, and Haliangium. Additionally, the amendment with wheat middlings caused faster shifts in soil bacterial communities 2 days after the ASD treatment, while crimson clover residues were associated with greater tomato crop yield by increasing soil ammonium and nitrate contents. Collectively, this study demonstrates that ASD application using C sources with C:N ratios < 20:1 and rapid decomposability effectively improves soil nutrient status and crop performance.