Open access
Announcement
10 January 2019

Genome Sequence of Arenibacter algicola Strain SMS7, Found in Association with the Marine Diatom Skeletonema marinoi

ABSTRACT

Arenibacter algicola strain SMS7 was isolated from a culture of the marine diatom Skeletonema marinoi strain ST54, sampled from top-layer sediments in Kosterfjord, Sweden. Here, we present its 5,857,781-bp genome, consisting of a circular chromosome and one circular plasmid, in all containing 4,932 coding sequences.

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).
TABLE 1
TABLE 1 Summary of assembly and annotation statistics for Arenibacter algicola strain SMS7
 Value for:
StatisticTotal assemblyChromosomepSMS7
Assembly
    No. of reads98,352  
    No. of bases1,266,330,556  
    Final assembly size (bp)5,857,7815,793,05364,728
    G+C content (%)39.839.843.8
    Avg read coverage (×)173.06  
Annotation (no.)
    CDSs4,9324,85280
    Pseudogenes17170
    tRNAs47470
    rRNAs990
    ncRNAs22220
    tmRNAs110
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 TG409T. 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 TG409T 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 TG409T (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 TG409T 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).
We thank the Linnéus Center for Marine Evolutionary Biology (CeMEB; http://cemeb.science.gu.se/) for support. All bioinformatics analyses were run on the Albiorix computer cluster (http://albiorix.bioenv.gu.se/) at the Department of Marine Sciences, University of Gothenburg.

REFERENCES

1.
Gordon D, Huddleston J, Chaisson MJ, Hill CM, Kronenberg ZN, Munson KM, Malig M, Raja A, Fiddes I, Hillier LW, Dunn C, Baker C, Armstrong J, Diekhans M, Paten B, Shendure J, Wilson RK, Haussler D, Chin C-S, Eichler EE. 2016. Long-read sequence assembly of the gorilla genome. Science 352:aae0344.
2.
Chin C-S, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10:563–569.
3.
Seemann T. 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069.
4.
Segata N, Börnigen D, Morgan XC, Huttenhower C. 2013. PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nat Commun 4:2304.
5.
Gutierrez T, Whitman WB, Huntemann M, Copeland A, Chen A, Kyrpides N, Markowitz V, Pillay M, Ivanova N, Mikhailova N, Ovchinnikova G, Andersen E, Pati A, Stamatis D, Reddy TBK, Ngan CY, Chovatia M, Daum C, Shapiro N, Cantor MN, Woyke T. 2016. Genome sequence of Arenibacter algicola strain TG409, a hydrocarbon-degrading bacterium associated with marine eukaryotic phytoplankton. Genome Announc 4:e00765-16.
6.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215:403–410.
7.
Gutierrez T, Rhodes G, Mishamandani S, Berry D, Whitman WB, Nichols PD, Semple KT, Aitken MD. 2014. Polycyclic aromatic hydrocarbon degradation of phytoplankton-associated Arenibacter spp. and description of Arenibacter algicola sp. nov., an aromatic hydrocarbon-degrading bacterium. Appl Environ Microbiol 80:618–628.

Information & Contributors

Information

Published In

cover image Microbiology Resource Announcements
Microbiology Resource Announcements
Volume 8Number 210 January 2019
eLocator: 10.1128/mra.01461-18
Editor: Julie C. Dunning Hotopp, University of Maryland School of Medicine
PubMed: 30643889

History

Received: 23 October 2018
Accepted: 16 November 2018
Published online: 10 January 2019

Contributors

Authors

Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
Matthew I. M. Pinder
Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
Oskar N. Johansson
Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
Olga Kourtchenko
Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
Anna Godhe
Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
Adrian K. Clarke
Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden

Editor

Julie C. Dunning Hotopp
Editor
University of Maryland School of Medicine

Notes

Address correspondence to Mats Töpel, [email protected].
M.T. and M.I.M.P. contributed equally to this work.

Metrics & Citations

Metrics

Note:

  • For recently published articles, the TOTAL download count will appear as zero until a new month starts.
  • There is a 3- to 4-day delay in article usage, so article usage will not appear immediately after publication.
  • Citation counts come from the Crossref Cited by service.

Citations

If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. For an editable text file, please select Medlars format which will download as a .txt file. Simply select your manager software from the list below and click Download.

View Options

Figures

Tables

Media

Share

Share

Share the article link

Share with email

Email a colleague

Share on social media

American Society for Microbiology ("ASM") is committed to maintaining your confidence and trust with respect to the information we collect from you on websites owned and operated by ASM ("ASM Web Sites") and other sources. This Privacy Policy sets forth the information we collect about you, how we use this information and the choices you have about how we use such information.
FIND OUT MORE about the privacy policy