Bacterial Diversity Profiling around the Orca Seamount in the Bransfield Strait, Antarctica, Based on 16S rRNA Gene Amplicon Sequences

ANNOUNCEMENT

Submerged seamounts in the oceans are generally vestiges of extinct volcanoes; these geological structures are produced by the lava that flows out from the internal part of the earth. The Orca seamount is located in the middle of the Bransfield Strait, a basin that extends along a passage between the South Shetland Island Arc and the Antarctic Peninsula (1). The Orca seamount is at present an inactive volcano; however, recently several studies have been conducted in order to detect some hydrothermal activity inside and around the crater (2). Due to its particular location, bordering a tectonic plate conjunction where trenches and fracture zones occur (3, 4), the Orca seamount may host several unknown deep sea hydrothermal vents. In this context, we report here a high-throughput 16S rRNA gene sequence analysis to study the microbiota in sediment samples collected near the Orca volcano crater.

Seven stations around the Orca seamount in the Bransfield Strait, Antarctica, were visited during the austral summer in February to March 2019 (Table 1). By means of a Van Veen sediment grab sampler, surface sediment samples were collected in 50-ml sterile Falcon tubes and immediately preserved at −20°C for later DNA analysis. DNA was extracted from 250- to 300-mg samples using a Soil DNA Isolation Plus kit (Norgen Biotek, Canada) according to the manufacturer’s protocol. The products of three independent extractions for each sample were pooled, and purified DNA was shipped to Macrogen, Inc. (Seoul, Republic of Korea) for PCR amplification and sequencing. PCR amplification of the V3/V4 hypervariable region was performed according to the Illumina 16S rRNA gene amplicon library method (5). Briefly, Illumina adapters were added to gene-specific primers 341F (CCTACGGGNGGCWGCAG) and 805R (GACTACHVGGGTATCTAATCC), and then a first PCR step was performed under thermocycler conditions according to reference 5. Further, sequencing libraries were constructed by index PCR using the Nextera XT Index kit, and paired-end sequencing was conducted using an Illumina MiSeq instrument. Raw data with paired-end reads (301 bp long) produced by the system are shown in Table 1. Raw sequences were evaluated with the FastQC package v0.11.8 (6). Microbial community analysis was conducted using mothur v1.39.5 (7) as implemented within the Galaxy platform (www.usegalaxy.org). Standard operating procedures, including those for data preparation (demultiplexing/denoising), quality control, chimera filtering, sequence alignments, clustering, and sequence classification steps, were as described by Schloss et al. (7). The SILVA database v128 (8) was used to assign operational taxonomic units (OTUs) at 97% similarity. The VSEARCH tool (9) was used for chimera removal.

Taxonomic classification at the phylum level (Fig. 1) showed that the bacterial taxa were almost the same for all analyzed samples, differing mainly in abundances. The dominant phyla were Proteobacteria (22.7 to 41.8%), Acidobacteria (4.4 to 36.8%), Planctomycetes (8.7 to 32.8%), and Bacteroidetes (3.8 to 18.2%). It is important to remark here that, within the Proteobacteria, members of the classes Epsilonproteobacteria and Zetaproteobacteria were present only at stations E1, E6, and E8. The number of Zetaproteobacteria OTUs was 3-fold higher at station E8. It is noteworthy that the first described and validly named member of the class Zetaproteobacteria, the species Mariprofundus ferrooxydans, was isolated from Fe-rich microbial mats associated with Fe(II)-rich fluids from seamount hydrothermal vents (10).

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FIG 1

Bar chart representing bacterial diversity at seven stations around the Orca seamount volcano, based on 16S rRNA amplicon analysis. Relative abundances at the phylum level are shown.