Metagenomic data on prokaryotic diversity of Kunashir island geothermal spring.

This is data on the microbial diversity of a geothermal spring located on the banks of the acidic creek of Kunashir Island. Data was obtained using 16s rRNA amplicon directed metagenomic sequencing on Illumina MiSeq. The raw sequence data used for analysis is available in NCBI under the Sequence Read Archive (SRA) with the BioProject No. PRJNA637298, PRJNA637447 and SRA accession number SRP265942, SRP266050. The data sequences of the 16s rRNA gene are presented at the accession numbers MT604934-MT604967, MT604911-MT604921 in NCBI GenBank database.

Specifications Table

Data Description

A description of the sampling points is given in Table 1. Photographs of the sampling sites are shown in Fig. 1.

Table 1

Description of the sampling points

Point No.	рН	t,°C	Description
8	2.0	38	The nameless creek originating from a hot spring with a temperature of 73°C and pH 2.0 and flowing into the Kislyi stream. A green bloom and sediment underneath were selected. Coordinates: 43.998029N, 145.767768E
10	3.0	18	The sour Kislyi stream. Orange-red bottom sediments selected. Coordinates: 43.997836N, 145.767671E

Fig. 1

Sampling locations: A - point No. 8, backwater of a hot spring; B - view of the Kislyi stream at the sampling site.

The raw sequencing data contain 19,213 paired-end sequences with a length of 301 bp totalling 11.6 M base pairs for a sample No. 10. Whereas for sample No. 8, 40.380 paired-end sequences with a length of 301 bp totalling 24.3 M base pairs were obtained.

A total of 52 OTUs including 10631 sequences were obtained for the two communities. For community No. 8 from the geothermal stream, 44 OTU and 11 for the microbial community from the bottom sediments of Kislyi Stream. The distribution of the types and classes of received OTUs is shown in Fig. 2.

Fig. 2

Charts of the taxonomic composition of communities: A - point No. 8; B - point No. 10.

In community No. 8, about 38% are occupied by archaea, the rest are bacteria, while in community No. 10 only bacteria are present. The following types (or classes in the case of proteobacteria) occupy more than 1% in community No. 8: Thermi, Euryarchaeota, Actinobacteria, Crenarchaeota, Parvarchaeota, Alphaproteobacteria, Firmicutes, Betaproteobacteria, Nitrospirae. In community No. 8, the following types (or classes in the case of proteobacteria) occupy more than 1%: Betaproteobacteria, Bacteroidetes, Alphaproteobacteria, Gammaproteobacteria, Actinobacteria. The studied communities turned out to be completely dissimilar, which is probably associated with various conditions, primarily with the temperature of the media.

Experimental Design, Materials and Methods

Sample collection and DNA extraction

Bottom sediments were taken from the Kislyi stream and the nameless creek flowing into it, originating from a hot spring with a temperature of 73°C and pH 2.0. The samples was taken in sterile 50 ml Falcon tubes and was stored in alcohol at -70°C. Total DNA was isolated from the samples (0,3 g) using the Genomic DNA from soil NucleoSpin® Soil kit (Macherey-Nagel) according to the manufacturer's protocol.

Library preparation and next-generation DNA sequencing

To obtain the target fragment comprising the V3-V4 region 16s rRNA, degenerate primers U343F (5′-CCTACGGGRSGCAGCAG-3 ') and U806R (5′-GGACTACNVGGGTWTCTAAT-3′) were used, which allow the amplification of the 16s rRNA gene of a wide range of microorganisms. Previously, these primers showed wide coverage in terms of amplification of various types of microorganisms. [1]. The regime of first amplification: 96°C - 2’; 25*(96°C-8”; 54°C-20”; 68°C-30”). Purified PCR product was used for a second PCR reaction which attached Illumina sequencing adapters and dual-index barcodes to the amplicon target. The regime of second amplification: 96°C - 2’; 5*(96°C-8”; 54°C-20”; 68°C-30”); 20*(96°C-8”; 60°C-20”; 68°C-30”). Fusion polymerase Q5 (NewEnglandBiolabs) and low primer annealing temperature were used to obtain gene libraries with the smallest number shift. Sequencing was performed at the Genomics Laboratory of the IMKB SB RAS using an Illumina MiSeq instrument using the TG MiSeq Reagent Kit v3 (600 cycle) kit. Sequenced reads were automatically divided by barcodes.

Taxonomic analysis

Paired reads obtained during sequencing of 16S rRNA libraries were processed using QIIME2 v.2020.2 platform [2]. Noise removal, integration of paired reads, and construction of OTUs were performed using the DADA2 algorithm. For taxonomic classification of OTUs, the scikit-learn classifier was used, trained on fragments of 16S rRNA of the Greengenes v.13_8 database, limited by the primers used.

Ethics Statement

In the work were not involve the use of human subjects, animals, cell lines and endangered species of wild fauna and flora.

Declaration of Competing Interest

The authors declare that they have no known competing financial interests or personal relationships which have, or could be perceived to have, influenced the work reported in this article.

Subject	Biochemistry, Genetics and Molecular Biology (General)
Specific subject area	Geothermal Metagenomics
Type of data	Figures and 16S rRNA amplicon sequencing data
How data were acquired	Illumina MiSeq platform, QIIME2 v.2020.2
Data format	Raw and analyzed
Parameters for data collection	Metagenomic RNA isolated from sediment samples were prepared by amplifying the V3-V4 region of the 16S rRNA gene paired-end sequenced on an Illumina MiSeq platform.
Description of data collection	Metagenomic DNA extraction, amplicon sequencing of V3-V4 region of 16S rRNA gene and paired reads processing using QIIME2 v.2020.2 platform
Data source location	Kunashir island, Russia: 43.997242N, 145.767607E
Data accessibility	Raw sequencing data:Repository name: NCBI SRAData identification number: SRP266050 (point #10) and SRP265942 (point #8)Direct URL to data: https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP266050 (point #10) and https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP265942 (point #8)