Soil prokaryotes are associated with decreasing Fusarium oxysporum density during anaerobic soil disinfestation in the tomato field

Anaerobic soil disinfestation (ASD) is a chemical-independent method that can reduce pathogens, such as Fusarium oxysporum. Although soil microbes play essential roles in ASD, the relationship between the microbial community structure and disinfestation efficiency remains unclear. Thus for improving our understanding of this relationship, we investigated the changes in the microbial community and pathogen density during an ASD period for 14 days in a greenhouse using three different substrates, as wheat bran, sugar-contained diatoms, and dried molasses. Soil samples were collected at 0, 3, 7, and 14 days after ASD treatment. The pathogen densities were analyzed by real-time polymerase chain reactions. Furthermore, prokaryotic community analysis was conducted by using an Illumina Miseq sequencer, and the factors related to pathogen density were statistically analyzed. The pathogen density rapidly decreased by >90% at 3 days after treatment and then slowly decreased until day 14; however the rate of decrease differed among the substrates. On the other hand, the microbial communities were altered after 3 days but recovered to their original state on day 14. The iron reduction level, microbial diversity, richness, and community structure did not correlate with pathogen density. The operational taxonomic units that drastically negatively correlated with pathogen density were Clostridia and Bacilli, both belonging to Firmicutes. This study showed that the changes in the prokaryotic community as a whole did not correlate to ASD efficiency, whereas changes in the abundance of specific microbes in the community were likely related to disinfestation efficiency. •The pathogen was rapidly decreased until 3 days after anaerobic soil disinfestation.•The microbial communities were affected by substrates and the disinfestation period.•The changes in microbial community were not correlated with disinfestation efficiency.•Clostridia and Bacilli were negatively correlated with disinfestation efficiency.