Spatial and temporal changes of soil microbial communities in field tomato production as affected by anaerobic soil disinfestation

Authors: VINCENT, ISAAC - University Of Florida; PAUDEL, BODH - University Of Florida; GUO, HAICHAO - Nobel Foundation; Rosskopf, Erin; DI GIOIA, FRANCESCO - Pennsylvania State University; Hong, Jason; MCNEAR, DAVID - University Of Kentucky; XU, NAN - University Of Florida; ANRECIO, LUCAS - University Of Florida; COLEE, JAMES - University Of Florida; ZHAO, XIN - (NCE, CECR)networks Of Centres Of Exellence Of Canada, Centres Of Excellence For Commercilization A

Submitted to: Frontiers in Sustainable Food Systems
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/17/2022
Publication Date: 7/13/2023
Citation: Vincent, I., Paudel, B., Guo, H., Rosskopf, E.N., Di Gioia, F., Hong, J.C., Mcnear, D., Xu, N., Anrecio, L., Colee, J., Zhao, X. 2023. Spatial and temporal changes of soil microbial communities in field tomato production as affected by anaerobic soil disinfestation. Frontiers in Sustainable Food Systems. https://doi.org/10.3389/fsufs.2022.838635.
DOI: https://doi.org/10.3389/fsufs.2022.838635

Interpretive Summary: Chemical soil fumigants (CSF) are used by many growers to control soilborne pathogens. However, their application is often subject to stringent environmental regulations and lacks adequate pest suppression capabilities. Consequently, there is a critical need for alternative, environmentally sustainable agricultural practices. Anaerobic soil disinfestation (ASD) has been demonstrated as an effective alternative to pre-plant CSF. However, in production systems with low soilborne disease pressure, the ASD effects on spatial and temporal changes in soil microbial communities remain poorly understood. The objective of this study was to assess the influence of ASD treatments on soil microbial community composition at different soil depths during the spring tomato production season in Florida. Two ASD treatments including a high rate of organic amendments and a low rate of organic amendments were compared to the soil fumigant 1,3-dichloropropene combined with chloropicrin. Soil microbial community composition was measured at soil depths of 0-15 cm and 15-30 cm using phospholipid fatty acid analysis (PLFA). Concentrations of total microbial biomass, Gram negative bacteria, and protozoa were significantly increased in both ASD treated soils at 0-15 cm soil depth compared with 15-30 cm, while no significant differences were observed between soil depths of these microbial biomarkers under chemical soil fumigation. Discriminant analysis indicated that soil microbial community composition was distinctly different in CSF compared to ASD treatments. While no separation of community composition was evident within CSF at two soil depths, the impact of soil depth resulted in distinct separation under both ASD treated soils. In general, ASD treatments increased the overall abundance of microbial functional groups compared with fumigation. Thus, ASD shows potential for promoting increased soil microbial activity.

Technical Abstract: Chemical soil fumigants (CSF) are used by many growers to control soilborne pathogens. However, their application is often subject to stringent environmental regulations and lacks adequate pest suppression capabilities. Consequently, there is a critical need for alternative, environmentally sustainable agricultural practices. Anaerobic soil disinfestation (ASD) has been demonstrated as an effective alternative to pre-plant CSF. However, in production systems with low soilborne disease pressure, the ASD effects on spatial and temporal changes in soil microbial communities remain poorly understood. The objective of this study was to assess the influence of ASD treatments on soil microbial community composition at different soil depths during the spring tomato production season in Florida. Soil treatments included ASD using 6.9 m3 ha-1 of molasses with 11 Mg ha-1 of composted poultry litter (CPL) (ASD0.5), ASD with 13.9 m3 ha-1 of molasses and 22 Mg ha-1 CPL (ASD1.0), and conventional soil fumigation using 1,3-dichloropropene (39%) and chloropicrin (59.6%, CSF). Soil microbial community composition was measured at soil depths of 0-15 cm and 15-30 cm using phospholipid fatty acid analysis (PLFA) at 0, 36, 76, and 99 days after treatment (DAT). Fatty acid methyl esters were categorized into biomarker groups including total microbial biomass (TMB), G+ bacteria (G+), G- bacteria (G-), actinomycete (actino), arbuscular mycorrhizal fungi (AMF), protozoa, and general fungi (fungi). Soil concentrations of G+ bacteria, actino, fungi, AMF, and the ratio of F:B were significantly impacted by soil treatment × soil depth × sampling time three-way interaction. Soil concentrations of protozoa and the ratio of G+ bactertia:G- bacteria were significantly impacted by soil treatment × sampling date, while TMB, G- bacteria, G+ bactertia:G- bacteria and protozoa were significantly impacted by soil treatment × sampling depth two-way interactions. Concentrations of TMB, G-, and protozoa were significantly increased in both ASD treated soils at 0-15 cm soil depth compared with 15-30 cm, while no significant differences were observed between soil depths of these microbial biomarkers under CSF. Discriminant analysis indicated that soil microbial community composition was distinctly different in CSF compared to ASD treatments. While no separation of community composition was evident within CSF at two soil depths, the impact of soil depth resulted in distinct separation along Canonical axis 2 under both ASD treated soils. In general, ASD treatments increased the overall abundance of microbial functional groups com¬pared with CSF. Thus, ASD shows potential for promoting increased soil microbial community concentrations compared with CSF at 0-15 cm and 15-30 cm soil depths. Future research may use high-throughput DNA sequencing or other advanced approaches to elucidate soil microbial community composition in response to ASD application.