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Announcement
10 August 2017

Draft Genome Sequence of Magnetospirillum sp. Strain 15-1, a Denitrifying Toluene Degrader Isolated from a Planted Fixed-Bed Reactor

ABSTRACT

Here, we report the draft genome sequence of Magnetospirillum sp. 15-1. This strain was isolated from a planted fixed-bed reactor based on its ability to degrade toluene under anaerobic conditions. The genome assembly consists of 5.4 Mb in 28 contigs and 5,095 coding sequences containing the genes involved in anaerobic toluene degradation.

GENOME ANNOUNCEMENT

Anaerobic degradation of toluene has been investigated most intensively among Betaproteobacteria strains, represented by Thauera aromatica and Azoarcus sp. (13). Within the Alphaproteobacteria group, there are three strains that have been identified as toluene degraders, Blastochloris sulfoviridis (4), Magnetospirillum sp. TS-6 (5), and Magnetospirillum sp. 15-1 (6).
Here, we present the draft genome sequence of Magnetospirillum sp.15-1, a nonmagnetic strain isolated from a planted fixed-bed reactor (PFR) continuously fed with toluene (6). Sequencing was carried out using the 454-GS Junior system (Roche Applied Science) and MiSeq instrument (Illumina). Illumina libraries were paired-end sequenced with a maximum 300-bp read length (MiSeq reagent kit version 3, 600 cycles, Illumina). Together, sequencing resulted in 1,674,000 reads. De novo assembly was conducted with the A5-miseq pipeline (7) and Geneious assembler (http://www.geneious.com) (8), generating 527 contigs initially. Contigs shorter than 400 bp with a coverage percentage below 20, an aberrant GC content below 50%, and a low Q score (9) were not considered further. The relative proportion of omitted nucleotides was 1.2%. Five gaps were closed by PCR, resulting in 28 final contigs. The draft genome sequence of Magnetospirillum sp. 15-1 consists of 5,422,505 bp with an average G+C content of 65.6%. The genome contains 6 rRNAs, 49 tRNAs, and 5,095 coding sequences (CDSs) (coding percentage 98.82%). The assembled sequences were functionally annotated using the RAST online service (10) and IMG (11). Of 5,095 CDSs, 62.61% were assigned to at least one COG group.
Magnetic strains of Magnetospirillum contain a large magnetosome genomic island that harbors a high concentration of insertion sequences and is flanked by repetitive elements (12, 13). This island is absent in strain 15-1. Phylogenetic analyses based on comparisons of average nucleotide identities and 16S rRNA gene alignment showed that strain 15-1 is related more closely to the magnetosome-producing strains M. magneticum AMB-1 (87%) (14), M. magnetotacticum MS-1 (86%) (15), Magnetospirillum sp. XM-1 (16) (88%), Magnetospirillum sp. SO-1 (89%) (17), and M. gryphiswaldense sp. MSR-1 (76%) (18) than to the nonmagnetic M. bellicus VDY (77%) (19) and Magnetospirillum sp. WD (77%) (20). This finding suggests that the absence of the magnetosome island in the Magnetospirillum sp. 15-1 genome is due to a secondary loss of function.
The genes for degradation of toluene under anaerobic conditions were found to be organized in three operons on the chromosome (bss, bbs, and bam), as observed for Thauera aromatica K172 (21). Homology searches of the bss operon of strain 15-1 against other anaerobic toluene degraders were performed through BLAST (https://blast.ncbi.nlm.nih.gov/Blast.cgi). Results showed similarities of 99% to Magnetospirillum sp. TS-6 and 80% to both T. aromatica K172 (22) and Azoarcus sp. (23). Analysis of xenobiotic degradation pathways through the KEGG pipeline to sequenced Magnetospirillum strains (excluding strain 15-1) showed that none of these strains contain genes related to aromatic compound degradation pathways.

Accession number(s).

This whole-genome shotgun project has been deposited in the European Nucleotide Archive (ENA) under the accession no. FXXN01000001to FXXN01000028. The versions described in this paper are the first versions.

ACKNOWLEDGMENTS

This work was funded by CONICYT (grant no. 72140034), Chile, and by the Helmholtz Centre for Environmental Research–UFZ, Leipzig, Germany.

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Genome Announcements cover image
Genome Announcements
Volume 5Number 3210 August 2017
eLocator: e00764-17
PubMed: 28798176

History

Received: 20 June 2017
Accepted: 7 July 2017
Published online: 10 August 2017

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Contributors

Authors

Ingrid Meyer-Cifuentes
Helmholtz Centre for Environmental Research–UFZ, Department of Environmental Biotechnology, Leipzig, Germany
Stefan Fiedler
Robert Koch Institute, Division of Nosocomial Pathogens and Antibiotic Resistances, National Reference Centre for Staphylococci and Enterococci, Department of Infectious Diseases, Wernigerode, Germany
Jochen A. Müller
Helmholtz Centre for Environmental Research–UFZ, Department of Environmental Biotechnology, Leipzig, Germany
Uwe Kappelmeyer
Helmholtz Centre for Environmental Research–UFZ, Department of Environmental Biotechnology, Leipzig, Germany
Ines Mäusezahl
Helmholtz Centre for Environmental Research–UFZ, Department of Environmental Biotechnology, Leipzig, Germany
Helmholtz Centre for Environmental Research–UFZ, Department of Environmental Biotechnology, Leipzig, Germany

Notes

Address correspondence to Hermann J. Heipieper, [email protected].

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