Genomic and metagenomic analysis of microbes in a soil environment affected by the 2011 Great East Japan Earthquake tsunami

BMC Genomics
Satoshi HiraokaWataru Iwasaki

Abstract

The Great East Japan Earthquake of 2011 triggered large tsunami waves, which flooded broad areas of land along the Pacific coast of eastern Japan and changed the soil environment drastically. However, the microbial characteristics of tsunami-affected soil at the genomic level remain largely unknown. In this study, we isolated microbes from a soil sample using general low-nutrient and seawater-based media to investigate microbial characteristics in tsunami-affected soil. As expected, a greater proportion of strains isolated from the tsunami-affected soil than the unaffected soil grew in the seawater-based medium. Cultivable strains in both the general low-nutrient and seawater-based media were distributed in the genus Arthrobacter. Most importantly, whole-genome sequencing of four of the isolated Arthrobacter strains revealed independent losses of siderophore-synthesis genes from their genomes. Siderophores are low-molecular-weight, iron-chelating compounds that are secreted for iron uptake; thus, the loss of siderophore-synthesis genes indicates that these strains have adapted to environments with high-iron concentrations. Indeed, chemical analysis confirmed the investigated soil samples to be rich in iron, and culture experime...Continue Reading

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Citations

Mar 26, 2016·Frontiers in Plant Science·Kareem A MosaOm Parkash Dhankher
Apr 17, 2019·The Cleft Palate-craniofacial Journal : Official Publication of the American Cleft Palate-Craniofacial Association·Yoshimichi ImaiMasahiro Tachi
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Dec 23, 2017·Frontiers in Microbiology·Sital UpretyThanh H Nguyen

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Datasets Mentioned

BETA
SAMD00023516

Methods Mentioned

BETA
amplicon sequencing
amplicon-sequencing

Software Mentioned

RDP
Newbler assembler
Prodigal
MEGA
MUSCLE
blastp searches
SortMeRNA
PhyloPhlAn
MetaMetaDB
RNAmmer

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