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

Authors: ONO-RAPHEL, JOE - Pennsylvania State University; CUSTER, GORDON - Pennsylvania State University; ARRINGTON, KATHLEEN - Pennsylvania State University; MORRISON, BEN - Pennsylvania State University; KAYE, JASON - Pennsylvania State University; Rosskopf, Erin; DIN-ANDREOTE, FRANCISCO - Pennsylvania State University; DI GIOIA, FRANCESCO - Pennsylvania State University

Submitted to: Agriculture Ecosystems and the Environment
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/16/2024
Publication Date: 12/20/2024
Citation: Ono-Raphel, J., Custer, G., Arrington, K., Morrison, B., Kaye, J., Rosskopf, E.N., Din-Andreote, F., Di Gioia, F. Effects of carbon sources on soil bacterial community dynamics during anaerobic soil disinfestation in an organic tomato production system. Agriculture Ecosystems and the Environment. 381:109448. 2024. https://doi.org/10.1016/j.agee.2024.109448.
DOI: https://doi.org/10.1016/j.agee.2024.109448

Interpretive Summary: Environmental and applicator safety concerns related to soil fumigation have increased interest in non-fumigant soil treatments. Anaerobic soil disinfestation (ASD) is a biologically based agricultural practice used to manage soilborne pests and pathogens and enhance soil fertility. ASD can be used in an organic production system and 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 carbon breakdown and stabilization. A field experiment was established to test the effects of different soil organic amendments, including cover crops characterized by different C:N ratios and an agricultural by-product, wheat middlings, on the temporal dynamics of soil bacterial communities and their implications for ASD efficacy and subsequent tomato crop performance. 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. The addition of wheat middlings also accelerated the shift in soil bacterial communities 2 days after the ASD treatment, while crimson clover residues improved tomato crop yield by increasing soil ammonium and nitrate contents. Collectively, this study demonstrates that ASD applied with C sources possessing optimal C:N ratios (<20:1) and rapid decomposability effectively improve soil health and crop performance.

Technical Abstract: 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 carbon breakdown and stabilization. A field experiment was established to test the effects of different soil organic amendments, including cover crops characterized by different C:N ratios and an agricultural by-product like wheat middlings, on the temporal dynamics of soil bacterial communities and their implications for ASD efficacy and subsequent tomato crop performance. A combination of time-series analyses was used to understand variation in the soil bacterial community and soil chemical properties (e.g., pH, electrical conductivity (EC), ammonium, and nitrate content) over 21 days of ASD treatment and following tomato planting. 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. Meanwhile, taxa enriched during tomato production included Nitrospira, Geobacter, and Haliangium. Additionally, the addition of wheat middlings also accelerated the shift in soil bacterial communities 2 days after the ASD treatment, while crimson clover residues improved tomato crop yield by increasing soil ammonium and nitrate contents. Collectively, this study demonstrates that ASD applied with C sources possessing optimal C:N ratios (<20:1) and rapid decomposability effectively improve soil health and crop performance.