Impacts of anaerobic soil disinfestation and chemical fumigation on soil microbial communities in field tomato production system

Anaerobic soil disinfestation (ASD), a potential alternative to pre-plant chemical fumigation for controlling soilborne pathogens, has been demonstrated in several agricultural production systems. The effect of ASD on the soil microbial community is considered one of the major factors responsible for pathogen suppression. However, rather limited information is available regarding the response of the soil microbial community to ASD throughout the cropping season, particularly in sandy soils. A field experiment was conducted to optimize the ASD technique for tomato production in Florida, utilizing two rates of molasses and composted poultry litter (CPL), and a pre-emergent herbicide application. The pre-plant soil treatments included ASD with 6.9 m3 ha−1 of molasses and 11 Mg ha−1 of CPL (ASD0.5), ASD with 13.9 m3 ha−1 of molasses and 22 Mg ha−1 of CPL (ASD1.0), and chemical soil fumigation control (CSF). The herbicide treatments included with and without halosulfuron application. Soil microbial community composition was monitored using phospholipid fatty acid (PLFA) analysis during the fall 2015 tomato production season. Halosulfuron application did not result in changes in the soil microbial community during the season. CSF led to significantly lower levels of bulk soil total microbial biomass, Gram negative bacteria, Gram positive bacteria and actinomycetes, compared to the ASD treatments. However, the rhizosphere effect of plants under CSF alleviated the microbial suppression and stimulated the growth of Gram negative bacteria and protozoa to reach similar levels to that of rhizosphere soils under the ASD treatments. Compared to 0 day after transplanting (DAT), Gram positive bacteria in bulk soils under the three pre-plant soil treatments significantly decreased while the fungi:bacteria ratio in bulk soils under CSF significantly increased at 36 DAT, and then remained stable throughout the season. Despite the similar microbial composition in bulk and rhizosphere soils between the two ASD treatments, the dynamic changes of some biomarker groups in bulk soils during 0-99 DAT showed distinct patterns particularly for total microbial biomass, Gram negative bacteria, actinomycetes, and fungi. Compared to 0 DAT, bulk soil microbial community composition shifted after 36 DAT under all soil treatments and remained stable until the end of the season. The changes in soil microbial community composition over time were related to changes in soil nutrient availability.