Effect of soil disinfection with chemical and biological methods on bacterial communities. soil metagenome

Little is known about the effect of soil disinfection on bacterial communities. Four chemical and biological materials were used against natural farm soil. Soil was treated with wheat bran and ethanol for soil reduction, chloropicrin for chemical fumigation, and mustard greens (Brassica juncea) for soil reduction plus biofumigation. Tomato seedlings were planted after disinfection treatment. Total organic carbon, which somehow reflects the microbial biomass, was significantly low in chloropicrin-applied soils. Bacterial communities were analyzed with PCR-DGGE and amplicon pyrosequencing using 16S rRNA gene partial sequences. The overall bacterial community structures were similar based on DGGE analyses among soils except chloropicrin-applied soils. Several chloropicrin-treated specific bands were observed. Bacterial species richness in chloropicrin-applied soils was about one-half of those in other soils and recovered to some extent after planting tomato. The two most abundant phyla were Acidobacteria and Proteobacteria in the farm soil. Soil reduction with ethanol, wheat bran, and mustard greens did not change the phylum structure very much. However, chemical fumigation with chloropicrin made the phylum Firmicutes dominant by occupying more than 80%. After planting tomato, the proportion of Firmicutes was reduced to the basal level and the phyla Bacteroidetes and Proteobacteria became dominant. A taxonomic classification on family level supported this observation. Beta diversity analyzed by Principal Coordinate Analysis showed that bacterial communities in the soils except chloropicrin-applied soils formed a cluster. A community of chloropicrin-applied soil was quite different from those of other soils and also distinct from that of soil after planting tomato, assuming that the bacterial community structure was dramatically altered by chemical fumigation with chloropicrin and shifted over time, while it did not go back to the original state.