Defining anaerobic soil disinfestation through changes in the microbiome

The main driver of anaerobic soil disinfestation (ASD) is manipulation of the microbiome. This is achieved by introducing soil amendments and depleting the soil of oxygen by saturating with water under a plastic tarp. The current standard ASD method in Florida, USA, consists of applying composted poultry litter (13 Mg ha^-1) and feed-grade sugarcane molasses (13,900 L ha^-1), tarping with totally impermeable film (TIF), and saturating the soil with 5 cm water. ASD is applied 3 weeks prior to transplanting. Herein, we report on impacts of modifications of the ASD treatment regarding the soil microbiome. The study was conducted in the greenhouse and field, in which standard ASD, ASD with double application of molasses (ASD2×), and soil covered with TIF (control) were compared. Spatial and temporal soil samples were taken at 0-15 cm and stored at -80°C. Total DNA was extracted and microbial populations were identified using length heterogeneity PCR (LH-PCR) and next-generation sequencing of the 16S ribosomal DNA. Based on the redox potential data, ASD2× was more anaerobic than ASD in the greenhouse, and both were statistically more anaerobic than the control at both locations. Using LH-PCR, shifts in the microbiome were observed, and both ASD-treated soils differed from the control in both the greenhouse and field experiments. Based on 16S rDNA, members of the phyla Firmicutes and Proteobacteria increased compared with the control. From a panel of seven different organic acids, only isobutyric acid was detected in the control samples, while six of the seven acids were detected in the ASD-treated soils. ASD2× had a greater quantity of each organic acid than ASD.