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Sequencing Study Finds Microbial Changes in Japan's Soil Following Tsunami

NEW YORK (GenomeWeb) – Researchers from the University of Tokyo have genomically characterized the microbial make-up of soil impacted by the 2011 tsunami that occurred off Japan's Pacific coast.

In work published last week in BMC Genomics, the investigators found that microbes impacted by the tsunami and resulting floods had adapted to an environment high in iron and salt, and that soil samples contained marine-living microbes.

First, the researchers used 16S RNA sequencing of samples from tsunami-affected and nonimpacted sites and identified four strains from the Arthobacter genus that could grow in both conditions. Then they sequenced the whole genomes of the four strains — two on the Pacific Biosciences RS II platform and two on Roche's GS FLX+ and Thermo Fisher Scientific's Ion Torrent PGM — compared the genomes to 21 publicly available Arthobacter genomes, and constructed a phylogenetic tree.

Notably, the team found that the genomes from affected soil samples had all independently lost the siderophore synthesis gene, which harvests iron from the environment to make it available to the microbe. Iron is an essential mineral for most bacteria and the gene is commonly found in species living in a low-iron environment. The researchers confirmed that the tsunami-affected soil samples had around 13 times more iron than soil from a nearby region.

"The independent losses of the siderophore-synthesis genes are not likely to have occurred by chance but likely because of natural selection," the researchers wrote.

The researchers also performed metagenomic shotgun sequencing on affected and unaffected soil samples. In both samples, the most abundant genus was Burkholderi, which made up about 4.85 percent of the total in the affected sample and 7.2 percent in the unaffected sample, followed by Bradyrhizobium, Rhodopseudomonas, and Pseudomonas. The finding was not too surprising, the authors wrote, since the two soil samples had similar overall chemical characteristics.

Next, they looked at the genera whose abundance differed greatly between the two samples. Arthobacter was the only genus that was abundant in both types of samples, but nonetheless also "differed substantially between the two samples," the authors wrote, reflecting its "greater potential for adaptation to tsunami-affected soils."

The bacteria Erysipelothrix, which causes bacterial skin infection in animals, was also more abundant in the tsunami-affected soil.

Finally, the team looked at the abundance of genes related to nitrogen fixation, since the chemical analysis of the soil found differences in the amount of nitrogen compounds, with the tsunami-affected sample containing much less nitrate. They found that genes involved in denitrification and nitrogren fixation were more abundant in the tsunami-affected sample, while genes related to nitrite reduction were more abundant in the unaffected sample. The "dominance of denitrification-related genes" may also be a cause of the small amounts of nitrate observed in the tsunami-affected soil sample and could also indirectly impact terrestrial vegetation, the authors wrote.

The authors added that their results should be confirmed. "We envision that further comprehensive analyses on microbial ecology and evolution after a tsunami will be necessary to develop a deeper understanding of the recovery processes of terrestrial microbial ecosystems," the researchers wrote.