Microbial diversity in the deep-sea sediments of Iheya North and Iheya Ridge, Okinawa Trough

Abstract

In this study, we analyzed the bacterial and archaeal diversities of the deep-sea sediments in Iheya North and Iheya Ridge, Okinawa Trough, using the high-throughput sequencing technology of Illumina MiSeq 2500 platform. Four samples (IN1, IN2, IR1 and IR2) were used in this study, of which IN1 and IN2 were located at regions close to and distant, respectively, from the active hydrothermal vents in Iheya North, while IR1 and IR2 were located at regions close to and distant, respectively, from the active hydrothermal vents in Iheya Ridge. The four samples were rich in different metal elements. Sequence analysis based on the V3-V4 regions of 16S rDNA gene obtained 170,363 taxon tags, including 122,920 bacterial tags and 47,433 archaeal tags, which cover 31 phyla, 50 classes, 59 orders, 87 families, and 138 genera. Overall, the microbial communities in all samples were dominated by bacteria, in which Proteobacteria was the largest phylum, followed by Chloroflexi, Firmicutes, Acidobacteria, Actinobacteria, Gemmatimonadetes, and Nitrospirae, which together accounted for 64.6% of the total taxon tags. In contrast to the high bacterial diversities, the archaeal diversity was low and dominated by Thaumarchaeota, which accounted for 22.9% of the total taxon tags. Comparative analysis showed that (i) IN2 and IR2 exhibited more microbial richness than IN1 and IR1, (ii) IR1 and IR2 exhibited higher microbial diversities than IN1 and IN2, (iii) samples from Iheya Ridge and Iheya North fell into two groups based on principle component analysis. Furthermore, microbes potentially involved in sulfur, nitrogen, and metal metabolism and cycling were detected in all samples. These results provide for the first time a comparative picture of the microbial diversities in the sediments of Iheya North and Iheya Ridge and indicate that geological features and distance from active hydrothermal vents likely play important roles in the shaping of microbial community structure.

A comparative study revealed first insights into the diversity and metabolisms of the microbial communities in the sediments of Pacmanus and Desmos hydrothermal fields

“…Thaumarchaeota was relatively more abundant in the microbial communities of Pacmanus than in the microbial communities of Desmos, suggesting a possibly more important role of these archea in ammonia oxidization in the sediment of Pacmanus hydrothermal field. These results are consistent with the previous reports that Proteobacteria is the dominant community in marine environments and was found in deep-sea sediments and hydrothermal systems [18,37]. Likewise, Thaumarchaeota has been observed in the sediments of Southwest Indian Ridge and Okinwa Trough [18,38,39].…”

“…Gammaproteobacteria has been widely detected in deep-sea environments [18,37,40–43], and Epsilonproteobacteria was reported to occur in the hydrothermal systems of Mid-Atlantic Ridge, Mariana Arc seamounts, and Okinawa Trough [44–46]. In our study, the presence of the genera Sulfurovum , Sulfurimonas , Arcobacter , and Sulfurospirillum within Epsilonproteobacteria suggested that these members potentially participated in sulfur oxidization and reduction as well as nitrate reduction.…”

“…The details of sample processing have been described previously [17,18]. The concentrations of total organic carbon (TOC), total nitrogen (TN) and total sulfur (TS) were determined using an elemental analyzer (Elementar, Germany).…”

“…Details of amplification have been described by Zhang et al [18]. The mixture of purified 16S rRNA gene amplicons was used for library preparation.…”

“…Sequence assembly and quality control processing of the raw reads were done as reported previously [18]. The raw reads without barcodes and 16S rRNA gene primers were assembled to raw tags using FLASH [21].…”