10.25338/B8N01R
Ettinger, Cassandra
0000-0001-7334-403X
University of California, Davis
Wilkins, Laetitia
0000-0003-3632-2063
University of California, Berkeley
Jospin, Guillaume
University of California, Davis
Eisen, Jonathan
0000-0002-0159-2197
University of California, Davis
Metagenome-assembled genomes provide new insight into the microbial
diversity of two thermal pools in Kamchatka, Russia
Dryad
dataset
2018
Arkashin Shurf
Zavarzin Spring
Uzon Caldera
Kamchatka
Russia
global microbial diversity
Metagenome-assembled genomes (MAG's)
2018-07-27T18:06:35Z
2018-07-27T18:06:35Z
en
https://doi.org/10.1038/s41598-019-39576-6
308477889 bytes
5
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
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.
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.