Metagenomic analysis of bacterial communities on Dokdo Island

Abstract

Dokdo, located east of the mainland of South Korea, is a volcanic island designated as a natural monument of South Korea due to its ecological value. Dokdo is divided into Dongdo and Seodo, islands with geological differences. The soil bacterial communities on Dokdo (Dongdo and Seodo) were analyzed using the pyrosequencing method. There were 1,693 and 1,408 operational taxonomic units (OTU) from Dongdo and Seodo, respectively. The statistical analyses (rarefaction curves as well as Chao1, Shannon, and Simpson indices) showed that bacterial diversity was slightly higher in Dongdo than Seodo. From results of a BLASTN search against the EzTaxon-e database, the validated reads (obtained after sequence preprocessing) were almost all classified at the phylum level. From the phylum level down to the species level, the number of classified reads considerably decreased due to the absence of information concerning unculturable or unidentified bacteria to date. Among the 36 phyla identified, three phyla (Proteobacteria, Actinobacteria and Acidobacteria) accounted for around 74.64%. The taxonomic composition was similar at the higher ranks (family and above) between Dongdo and Seodo, but a little different at the genus level. There were also various differences in the relative abundance of taxonomic ranks between Dongdo and Seodo. In particular, the proportion of the genus Acidobacterium (of the phylum Acidobacteria) was about six times higher in Seodo than Dongdo. In addition, the percentage of the genus Mycobacterium (of the phylum Actinobacteria) was nearly three times higher in Seodo than Dongdo, and the proportion of the genus Gaiella was about 3.7 times higher in Dongdo than Seodo. Overall, through the metagenomic analysis, the number of species identified in Dongdo and Seodo was 1,239 and 1,055, respectively. This information on the numerous culturable and unculturable bacteria is expected to help in the screening of new species in Dokdo.

Actinobacterial Diversity in Volcanic Caves and Associated Geomicrobiological Interactions

“…All but one of the sequences were singletons. Gaiellaceae , another recently described family, was originally found in a water borehole, and sequences from this family have subsequently been found in soil, volcanic soil, thermal springs and marine ascidians (Albuquerque et al, 2011 ; Kim et al, 2014 ; Rozanov et al, 2014 ; Steinert et al, 2015 ). Rubrobacterales occurred in the New Mexico and Hawai'i samples.…”

The Effect of Root Exudate 7,4′-Dihydroxyflavone and Naringenin on Soil Bacterial Community Structure

“…This genus and the order Gaiellales currently have only a single described species, which was isolated from water from a deep aquifer [ 64 ]. Gaiella 16S rRNA sequences have been found in sediments from a thermal spring [ 65 ], in high abundance in soil [ 66 ], and in rhizosphere and root samples of rice [ 67 ]. Their presence in the rhizosphere soil and root tissues shows that some members of this genus interact with plants.…”

Isolation and Identification of Alkali-tolerant Bacteria from Near-Shore Soils in Dokdo Island

“…While the flora and fauna of Dokdo have been frequently studied, its microbial flora has been under research only recently. According to metagenomics analyses of Dokdo soils by Kim et al [31], three phyla (Proteobacteria, Actinobacteria, and Acidobacteria) among the 36 phyla identified in Dokdo soils accounted for approximately 74.64% of the total community with average relative abundances of 34.3%, 23.9%, and 16.1%, respectively. In a culture dependent study, Gamma-Proteobacteria (53.8%) and Firmicutes (30.8%) dominated the halotolerant isolates from rhizosphere soil of coastal plants in Dokdo Island [32].…”