DOI: 10.25338/b8n01r
title: Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia

description: Culture-independent methods have contributed substantially to our
 understanding of global microbial diversity. Recently developed algorithms
 to construct whole genomes from environmental samples have further
 refined, corrected and revolutionized understanding of the tree of life.
 Here, we assembled draft metagenome-assembled genomes (MAGs) from
 environmental DNA extracted from two hot springs within an active volcanic
 ecosystem on the Kamchatka peninsula, Russia. This hydrothermal system has
 been intensively studied previously with regard to geochemistry,
 chemoautotrophy, microbial isolation, and microbial diversity. We
 assembled genomes of bacteria and archaea using DNA that had previously
 been characterized via 16S rRNA gene clone libraries. We recovered 36
 MAGs, 29 of medium to high quality, and inferred their placement in a
 phylogenetic tree consisting of 3,240 publicly available microbial
 genomes. We highlight MAGs that were taxonomically assigned to groups
 previously underrepresented in available genome data. This includes
 several archaea (Korarchaeota,
 Bathyarchaeota and Aciduliprofundum) and one potentially
 new species within the bacterial genus Sulfurihydrogenibium.
 Putative functions in both pools were compared and are discussed in the
 context of their diverging geochemistry. This study adds comprehensive
 information about phylogenetic diversity and functional potential within
 two hot springs in the caldera of Kamchatka.
description: In this study we focus on two hydrothermal pools, Arkashin Shurf
 and Zavarzin Spring, in Uzon Caldera, Kamchatka, Russia that were
 previously characterized using 16S ribosomal RNA sequencing and
 geochemical analysis undertaken in Burgess et al. 2012 (DOI:
 10.1007/s00248-011-9979-4). First we produced metagenome-assembled genomes
 (MAGs) and then we characterized and compared them between the two pools.
 Raw metagenomic reads were deposited on NCBI’s GenBank under BioProject ID
 PRJNA419931 and BioSample IDs SAMN08105301 and SAMN08105287; i.e., SRA IDs
 SRS2733204 (SRX3442520) and SRS2733205 (SRX3442521). Draft MAG’s were
 deposited in GenBank under accession numbers SAMN08107294 - SAMN08107329
 (BioProject ID PRJNA419931). Here we have included fasta files for all
 binned MAGs and the associated anvi'o files used to generate them. We
 have included all the supplemental tables associated with the analysis
 here as well. Environmental DNA used here is the same
 DNA that was extracted in Burgess et al. (DOI: 10.1007/s00248-011-9979-4).
 In short, Burgess et al. extracted DNA from sediment from Arkashin Schurf,
 collected in the field in 2004 and from sediment from Zavarin Spring
 collected in 2005. Sequencing library preparations for Solexa3 84bp
 paired-end sequencing were performed by the UC Davis Genome Center DNA
 Technologies Core Facility where the samples were sequenced on two lanes.
 Demultiplexed data was quality filtered using bbMap v. 36.99 (https://jgi.doe.gov/data-and-tools/bbtools/) with the following parameters: qtrim = rl, trimq = 10, minlength = 70. Adaptors were removed and reads were assembled into two metagenomes (one for Arkashin Schurf and one for Zavarzin Spring) using SPAdes v. 3.9.0 with default parameters (DOI: 10.1101/gr.213959.116). Metagenomic data was then binned into metagenome-assembled genomes (MAGs) using anvi’o v. 2.4.0 (DOI: 10.7717/peerj.1319). Here we have included fasta files for all generated MAGs and associated anvi'o files.
description: Please see included CSV which includes a key to identify draft
 MAG's as well as a summary of individual MAG assembly statistics,
 quality measurements and taxonomic inferences.