Genome Sequences of Vibrio maerlii sp. nov. and Vibrio rhodolitus sp. nov., Isolated from Rhodoliths.

We report here the genome sequences of the novel isolates G62T and G98T from rhodoliths. The nearly complete genomes consisted of 4.7 Mbp (4,233 coding sequences [CDS]) for G62T and 4.5 Mbp (4,085 CDS) for G98T. Genomic taxonomy places these new genomes into 2 new species.

ANNOUNCEMENT

The genus Vibrio and 6 other genera (Aliivibrio, Echinimonas, Enterovibrio, Grimontia, Photobacterium, and Salinivibrio) form the family Vibrionaceae (1). These bacteria are Gram-negative fermentative, halophilic, mesophilic, chemoorganotrophic, and ubiquitous in the marine environment (2).

The aim of the present study was to determine the genome sequences of the novel isolates G62T and G98T. These isolates were obtained from rhodoliths at a 43-m depth (sinkhole, Abrolhos Bank, Brazil, 17.81399°S, 38.24306°W and 17.81330°S, 38.23744°W) in 2010. Samples were cultured in marine agar and incubated at 30°C for 48 h. Genomic DNA was extracted with the NucleoSpin tissue kit (Macherey-Nagel GmbH & Co. KG) and used for 300-bp paired-end library preparation with the Nextera XT DNA sample preparation kit and sequencing on the MiSeq platform (Illumina, San Diego, CA, USA) (3). The sequences obtained were preprocessed with PRINSEQ software to remove reads smaller than 35 bp and low-score sequences (Phred < 30) (4). Sequence reads were assembled with A5-miseq software v. 20160825 (5). A second assembly was performed with CAP3 software (6). The gene prediction and functional annotation were performed with the Rapid Annotation using Subsystem Technology program (7).

The reads from G62T were assembled in 49 contigs (N50, 382,658 bp). The estimated genome size is 4,758,035 bp (G+C content, 44.5%) with a coverage of 108-fold. In total, 4,233 coding sequences (CDS), 143 RNAs, 106 tRNAs, and 26 rRNAs were identified. G98T reads were assembled in 62 contigs (N50, 161,850 bp). The estimated genome size is 4,559,723 bp (G+C content, 45.2%) with a coverage of 94-fold. In total, 4,085 CDS, 143 RNAs, 108 tRNAs, and 24 rRNAs were identified.

The novel isolates G62T and G98T had less than a 95% average amino acid identity/average nucleotide identity (AAI/ANI) and less than a 70% genome-to-genome distance (GGDH) from their closest neighbors (V. atypicus and V. tubiashii and V. ponticus and V. furnissii, respectively). The cutoffs used for the delimitation of Vibrio species are more than 95% AAI and more than 70% GGDH, and so we conclude that the 2 novel isolates belong to novel species of the genus (8–11), designated V. maerlii G62T sp. nov. and V. rhodolitus G98T sp. nov. Their cells are motile, and growth occurs between 12 and 35°C in the presence of 1.0 to 3.0% NaCl. Optimum bacterial growth occurs between 27 and 30°C in the presence of 3.0% NaCl. Colonies are cream colored and circular with the entire margin on marine agar. Useful in silico phenotypic features to differentiate the novel species from their closest neighbors include sucrose, indole, d-mannitol, cellobiose, and d-mannose (Table 1).

TABLE 1

In silico phenotypic characterization distinguishing Vibrio maerlii sp. nov. strain G62T and Vibrio rhodolitus sp. nov. strain G98T from closely related Vibrio species

Property	V. maerlii G62T	V. rhodolitus G98T	V. fluvialis ATCC 33809T	V. furnissiiNCTC 11218T	V. parahemolyticusRIMD 2210633T	V. ponticus CECT 5869T	V. scophthalmiVS-12	V. tasmaniensisLGP32	V. tubiashii ATCC 19109T	V. xuii DSM 17185T
l-Arabinose	−	−	+	+	+	−	−	−	−	−
Sucrose	+	−	+	+	−	−	−	−	+	−
Ornithine	−	−	−	−	+	−	−	−	−	−
Vogues	−	−	−	−	−	−	−	−	−	−
Galactose	−	−	+	±	+	−	−	−	−	−
Cellobiose	−	+	±	−	−	+	+	−	−	+
d-Mannitol	+	−	−	+	+	+	+	−	+	+
Arginine	−	−	+	+	−	−	−	+	−	+
Trehalose	−	−	+	+	+	−	−	+	−	+
d-Sorbitol	−	−	−	−	−	−	−	−	−	−
Indole	+	+	±	−	+	+	+	+	+	+
m-Inositol	−	−	−	−	−	−	−	−	−	−
d-Mannose	−	+	±	+	+	+	+	+	−	+

Closely related Vibrio species (RefSeq assembly accession number) include the following: V. fluvialis ATCC 33809T (GCF_001558415), V. furnissii NCTC 11218T (GCF_000176175), V. parahaemolyticus RIMD 2210633T (GCF_000196095), V. ponticus CECT 5869T (GCF_001939685), V. scophthalmi VS-12 (GCF_001685465), V. tasmaniensis LGP32 (GCF_000091465), V. tubiashii ATCC 19109T (GCF_000772105), and V. xuii DSM 17185T (GCF_001274855). +, present; −, absent; ±, variable.

Description of Vibrio maerlii sp. nov.

Vibrio maerlii (ma.er′.li.i. L. n. maerlii, referring to the Breton word “maërl” = rhodolith). The estimated genome size is 4.7 Mbp, and it has a G+C content of 45.2%. G62T is positive for sucrose, indole, and d-mannitol based on an in silico phenotype (12).

Description of Vibrio rhodolitus sp. nov.

Vibrio rhodolitus (rhod.o.li′.tus. L. masc. rhodoliths, referring to the isolation source, the rhodolith structures dominated by free-living coralline algae). The estimated genome size is 4.5 Mbp, and it has a G+C content of 44.5%. G98T is positive for cellobiose, indole, and d-mannose based on an in silico phenotype (12).

Data availability.

V. maerlii G62T and V. rhodoliths G98T are deposited in the Bacteria Collection of Environmental and Health (CBAS) at the Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ) in Rio de Janeiro, Brazil (http://cbas.fiocruz.br/), under the accession numbers CBAS 711T and CBAS 710T, and in the Collection of Aquatic Microorganisms (CAIM) in Mazatlán, Sinaloa, Mexico (http://www.ciad.mx/caim/CAIM.html), under the accession numbers CAIM 1940T and CAIM 1941T, respectively.

The whole-genome shotgun projects for V. maerlii G62T (= CBAS 711T = CAIM 1940T) and V. rhodoliths G98T (= CBAS 710T = CAIM 1941T) have been deposited in DDBJ/EMBL/GenBank under accession numbers QRHC00000000 and QLYZ00000000, respectively. The BioProject accession numbers are PRJNA476538 and PRJNA476543, respectively.