ANNOUNCEMENT
In an ongoing study of the microbiome of the chain-forming diatom Skeletonema marinoi strain ST54, we isolated and sequenced the associated bacterial strain SMS7.
The ST54 culture was established from a revived resting cell taken from top-layer sediment in Kosterfjord, Sweden (58
°51.0′N, 10
°45.7′E; 102 m depth) in May 2009. This bacterial strain was sampled from a colony formed after multiple-dilution streaking on marine agar. Genomic DNA was extracted using Plant DNAzol reagent (Invitrogen Life Technologies, USA) from pure cultures grown from a single bacterial colony, according to the manufacturer’s instructions. Genome sequencing was performed with the PacBio RS II platform (Pacific Biosciences, Menlo Park, CA, USA) on a single-molecule real-time (SMRT) cell. The sequencing produced 98,352 uncorrected reads totaling 1.3 Gbp, which were assembled using Falcon version 1.7.5 (
https://github.com/PacificBiosciences/FALCON [
1]; seed read length, 17,000 bp). To ensure that the contigs were circular, the corresponding contig ends were joined, and the SMRT Portal version 2.3.0 RS_Resequencing.1 protocol (Pacific Biosciences [
2]) was used to remap the reads to the contigs; this included a correction step using Quiver (
2). The assembly contains two circular contigs, a chromosome of 5,793,053 bp (G+C content, 39.8%) and a plasmid of 64,728 bp (G+C content, 43.8%), with an average assembly read coverage of 173.06× (statistics are summarized in
Table 1).
The assembly was annotated with Prokka version 1.12beta (
3); this inferred 4,932 coding sequences (CDSs; of which 4,061 have a predicted function), 17 pseudogenes, 47 tRNAs, 9 rRNAs, 22 noncoding RNAs (ncRNAs), and one transfer-messenger RNA (tmRNA) (statistics are summarized in
Table 1). Strain SMS7’s chromosome contains three identical 16S rRNA sequences, which share 99.9% identity with the three found in the
Arenibacter algicola type strain TG409 (NCBI RefSeq accession number
NZ_JPOO00000000). In addition, the housekeeping genes
gyrB and
rpoB show 99.1% and 99.0% sequence similarity, respectively, between strain SMS7 and
A. algicola strain TG409
T. Given this similarity, strain SMS7 was compared to all whole-genome-sequenced
Flavobacteriaceae species available in RefSeq (
ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/) using the phylotaxonomic analysis software PhyloPhlAn version 0.99 (
4). This showed strain SMS7 as sister to the clade of
A. algicola TG409
T and
Arenibacter sp. strain C-21, with 100% bootstrap support. Taking the above-described analyses together, we place strain SMS7 in the taxon
Arenibacter algicola. In addition, colonies of strain SMS7 showed the characteristic orange pigmentation of
A. algicola, attributed to its pigment absorbing at 450/470/476 nm.
Arenibacter algicola strain SMS7 contains a plasmid, pSMS7 (with 80 predicted CDSs), a feature not reported for strain TG409
T (
5). This plasmid was compared to the type strain assembly and SMS7 chromosome using BLASTn (
6), and the result implies that pSMS7 is a unique replicon, as no sizable equivalent appears in the strain TG409
T assembly or the SMS7 chromosome.
The
A. algicola type strain TG409 was originally isolated from the
Skeletonema type species,
S. costatum (
7). Our identification of another
A. algicola strain associated with
S. marinoi provides further evidence of functional links between the two organisms. One suggested link is the diatoms’ ability to accumulate polycyclic aromatic hydrocarbons (PAHs) on their silica frustules, which associated
A. algicola bacteria can use as a carbon source (
7).
Data availability.
This whole-genome project has been deposited in GenBank under the accession numbers
CP022515 and
CP022516 as part of BioProject number
PRJNA380207.
ACKNOWLEDGMENTS
This work was supported by the Gordon and Betty Moore Foundation (to A.K.C., M.T., and A.G., grant 4967), the Swedish Research Council VR (to A.K.C., grant 2015-04286), and the Swedish Research Council Formas (to M.T. and A.G., grant 2017-00466; and to A.G., grant 219-2012-2070).