Complete Genome Sequence of Marinobacter sp. Strain JH2, Isolated from Seawater of the Kiel Fjord

Here, we present the genome sequence of the Gram-negative and rod-shaped Marinobacter sp. strain JH2, which was isolated from seawater of the Kiel Fjord in Germany. The draft genome consists of two replicons, including one chromosome (3.6 Mb) and a circular plasmid (36.7 kb). The genome harbors 3,347 protein-coding genes.

M arinobacter sp. strain JH2 is a Gram-negative, moderately halophilic, and rod-shaped bacterium. It was isolated from 200 l seawater of the Kiel Fjord (Germany). Members of the genus Marinobacter are well distributed in aquatic environments all over the world (1)(2)(3)(4). One feature of Marinobacter spp. is their ability to utilize various hydrocarbons (5)(6)(7). The genome sequence of Marinobacter sp. JH2 provided insights into the biocatalytic potential related to hydrocarbon degradation.
Marinobacter sp. JH2 was isolated and grown in Difco marine broth 2216 (BD Biosciences, Heidelberg, Germany) at 28°C. Genomic DNA was extracted using the MasterPure complete DNA purification kit, as recommended by the manufacturer (Epicentre, Illumina, Madison, WI, USA). The isolated DNA was used to generate Illumina shotgun paired-end sequencing libraries. The MiSeq system and the MiSeq reagent kit v3 (600 cycles) were used for sequencing, as recommended by the manufacturer (Illumina, San Diego, CA, USA). Additionally, the 1D genomic DNA sequencing protocol for the MinION device using SQK-LSK109 was conducted (Oxford Nanopore, Oxford, UK). End repair was performed using NEBNext formalin-fixed, paraffin-embedded (FFPE) repair mix (New England Biolabs, Ipswich, MA, USA). The library for Nanopore sequencing was loaded on a SpotON flow cell Mk I (R9.4). Reads were quality filtered using fastp v0.19.4 (8), which resulted in 6,291 long reads (Nanopore) and 2,704,110 short reads (Illumina). The bacterial genome assembler Unicycler v0.4.8-beta (9) was used to perform a de novo hybrid genome assembly, which resulted in a 135-fold coverage. The assembly was validated with Bandage v0.8.1 (10). The complete genome sequence consists of one circular chromosome (3,686,730 bp) and an overall GϩC content of 53.55%. Additionally, one circular plasmid (36,788 bp) with a GϩC content of 50.44% was identified. The genome annotation was performed with the Rapid Prokaryotic Genome Annotation (Prokka) tool v1.13.3 (11). The predicted 3,413 genes included 53 tRNA genes, 12 rRNA genes, 1 transfer-messenger RNA (tmRNA) gene, and 3,347 protein-encoding genes. The relationship to other members of the genus Marinobacter was determined by calculating the average nucleotide identity (ANI) with the Python module for average nucleotide identity analyses (pyANI) v0.2.7 (12). The 35 genome sequences of all species belonging to the genus Marinobacter available at National Center for Biotechnology Information (accessed 12 March 2019) were included in the analysis. The analysis revealed that Marinobacter. sp. JH2 was most closely related to Marinobacter vinifirmus strain Z-F7-3 and Marinobacter litoralis strain Sw-45, with an ANI value of 87.6%. This value indicates that Marinobacter sp. JH2 represents a new species group within the genus Marinobacter.
Data availability. The whole-genome shotgun project of Marinobacter sp. strain JH2 has been deposited at DDBJ/EMBL/GenBank under the accession numbers CP037934 and CP037935, with BioProject accession number PRJNA526490 and SRA accession number SRP199986.

ACKNOWLEDGMENTS
We thank Sarah Teresa Schüßler for technical assistance and Birgit Pfeiffer for providing seawater from the Kiel Fjord.
This study was partly supported by the Deutsche Forschungsgemeinschaft (DFG) as part of the collaborative research center TRR51. The funders had no role in study design, data collection, and interpretation, or the decision to submit the work for publication.