Vibrio aphrogenes sp. nov., in the Rumoiensis clade isolated from a seaweed

Mami Tanaka; Shoko Endo; Fumihito Kotake; Nurhidayu Al-saari; A. K. M. Rohul Amin; Gao Feng; Sayaka Mino; Hidetaka Doi; Yoshitoshi Ogura; Tetsuya Hayashi; Wataru Suda; Masahira Hattori; Isao Yumoto; Toko Sawabe; Tomoo Sawabe; Toshiyoshi Araki

doi:10.1371/journal.pone.0180053

Abstract

A novel strain Vibrio aphrogenes sp. nov. strain CA-1004^T isolated from the surface of seaweed collected on the coast of Mie Prefecture in 1994 [1] was characterized using polyphasic taxonomy including multilocus sequence analysis (MLSA) and a genome based comparison. Both phylogenetic analyses on the basis of 16S rRNA gene sequences and MLSA based on eight protein-coding genes (gapA, gyrB, ftsZ, mreB, pyrH, recA, rpoA, and topA) showed the strain could be placed in the Rumoiensis clade in the genus Vibrio. Sequence similarities of the 16S rRNA gene and the multilocus genes against the Rumoiensis clade members, V. rumoiensis, V. algivorus, V. casei, and V. litoralis, were low enough to propose V. aphrogenes sp. nov. strain CA-1004^T as a separate species. The experimental DNA-DNA hybridization data also revealed that the strain CA-1004^T was separate from four known Rumoiensis clade species. The G+C content of the V. aphrogenes strain was determined as 42.1% based on the genome sequence. Major traits of the strain were non-motile, halophilic, fermentative, alginolytic, and gas production. A total of 27 traits (motility, growth temperature range, amylase, alginase and lipase productions, and assimilation of 19 carbon compounds) distinguished the strain from the other species in the Rumoiensis clade. The name V. aphrogenes sp. nov. is proposed for this species in the Rumoiensis clade, with CA-1004^T as the type strain (JCM 31643^T = DSM 103759^T).

Citation: Tanaka M, Endo S, Kotake F, Al-saari N, Amin AKMR, Feng G, et al. (2017) Vibrio aphrogenes sp. nov., in the Rumoiensis clade isolated from a seaweed. PLoS ONE 12(6): e0180053. https://doi.org/10.1371/journal.pone.0180053

Editor: Cristiane Thompson, UFRJ, BRAZIL

Received: March 20, 2017; Accepted: June 8, 2017; Published: June 29, 2017

Copyright: © 2017 Tanaka et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Data Availability: All relevant data are within the paper and its Supporting Information files sequence data are available public database (accession numbers within the paper).

Funding: This work was supported by Kaken (16H0497606) (TS). This work was also supported by Grant in Aid for Scientific Research on Innovative Area “Genome Science” from Ministry of Education, Culture, Sports, Science, and Technology of Japan (No.221S0002).

Competing interests: Co-author of Ajinomoto Co. Ltd. provided the 8 protein coding gene sequences of V. aphrogenes for the comparison by MLSA. No any financial supports were obtained from this company for this study. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

Introduction

The genus Vibrio, first proposed in 1854, is a large group of bacteria showing Gram negative and with most species requiring salt for growth [2]. Currently 111 Vibrio species have been described (http://www.bacterio.net/) [2]. The genus Vibrio, along with other members of Vibrionaceae, is at the forefront of bacterial taxonomy, having been tested using new methodologies, e.g. amplified fragment length polymorphism (AFLP), multilocus sequence analysis (MLSA), and genome-based sequence comparison [2–6]. Among them, the MLSA has been used as a powerful tool to find “clades” sharing a possible common ancestry among metabolically versatile Vibrionaceae species/strains [3–5]. The 8-gene MLSA defines 23 Vibrio and Photobacterium clades and an Enterovibiro-Grimontia-Salinivibrio super clade, which help us to elucidate the dynamic nature of biodiversity and evolutionary history interacting with the Earth’s ecosystem [5]. Rapid expansion of genome sequencing methodology in bacterial taxonomy also assists and accelerates the accumulation of our knowledge of vibrio biodiversity and has contributed towards the proposals for new clades within the family Vibrionaceae such as Agarivorans [3] and Swingsii [7].

Vibrio rumoiensis was isolated as a strong catalase producer from the drain pool of a fish processing plant that uses H₂O₂ as a bleaching and microbial agent [8]. In one of the first uses of MLSA for Vibrionaceae taxonomy, V. rumoiensis was classified as an orphan clade species [4]. Subsequent MLSA showed that V. litoralis, a tidal flats isolate [9], could share a common ancestry with V. rumoiensis which led to the proposal for the Rumoiensis clade [5]. Currently, there are four species known to be a member of the Rumoiensis clade: V. rumoiensis, V. algivorus [10], V. casei [11], and V. litoralis [9]. V. casei, and V. algivorus were isolated from surface of cheeses and the gut of a turban shell, Turbo cornutus, respectively. All species share an assimilation pattern of carbohydrates such as D-mannose, D-galactose, D-fructose, and D-mannitol, nitrate reduction, and, with the exception of V. casei, non-motility [9–11]. The ecophysiological coherence of Rumoiensis clade species is still unknown.

A vibrio strain phylogenetically related to the Rumoiensis clade was isolated from the surface of seaweed samples collected from the coast of Mie prefecture, Japan in 1994. This bacterium was originally isolated as a κ-carrageenase producer with a cgk gene [1]. Further phylogenetic, genetic and genomic characterizations in this study revealed the novelty of the strain placing it into the Rumoiensis clade. Importantly, the strain is the first microbe to produce hydrogen from alginate. The gas production is supported by having a hyf-type formate hydrogen lyase gene cluster, the discovery of which is the first in the gas producing species in the Rumoiensis clade. The V. aphrogenes sp. nov. CA-1004^T might hold important clues in elucidating the evolutionary history of species in the Rumoiensis clade and a biotechnological novelty in Vibrionaceae.

Materials and methods

Bacterial strains and phenotypic characterization

V. aphrogenes strain CA-1004^T isolated from seaweed surface in 1994 collected at Mie Prefecture in Japan [1] was characterized. For phenotypic characterization, all type strains belonging to the Rumoiensis clade were cultured on ZoBell 2216E agar medium and the phenotypic characteristics were determined according to previously described methods [3].

Phylogenetic analysis based on a 16S rRNA gene

A 1400 bp of 16S rRNA gene sequence of the strain CA-1004^T was obtained according to Al-saari et al. [3], using the amplification primers (24F and 1509R) corresponding to positions 25 to 1521 in the Escherichia coli sequence. The other Vibrionaceae sequences used to reconstruct a broad phylogenetic tree shown in S1 Fig were retrieved from the GenBank/DDBJ/EMBL database and analyzed using ClustalX version 2.1 [12] and MEGA version 7.0.16 programs [13]. In the final tree (Fig 1), the 16S rRNA gene sequences of A. fischeri NCIMB 1281^T (X70640), A. logei NCIMB 2252^T (AJ437616), V. algivorus NBRC 111146^T (SA2^T) (LC060680), V. casei DSM 22364^T (NR_116870), V. litoralis DSM 17657^T (DQ097523), and V. rumoiensis FERM P-14531^T (S-1^T) (AB013297) were used to reconstruct the tree using the MEGA program with three different methods; neighbor-joining (NJ), maximum parsimony (MP), and maximum likelihood (ML). The robustness of each topology was checked using the NJ method with 500 bootstrap replications. Evolutionary distances of the NJ method were corrected using the Jukes-Cantor method.

Download:

Fig 1. A rooted phylogenetic tree on the basis of 16S rRNA gene sequences.

This figure combines the results of three analyses, i.e. neighbor-joining (NJ), maximum-parsimony, and maximum-likelihood. The topology shown was obtained by NJ with 500 bootstrap replications. The bootstrap value was only indicated on branches supported by three methods.

https://doi.org/10.1371/journal.pone.0180053.g001

Genome sequencing

Draft genome sequences of strain CA-1004^T, V. algivorus NBRC 111146^T, V. casei DSM 22364^T, and V. rumoiensis FERM P-14531^T were obtained using the MiSeq platform. For CA-1004^T only, a paired-end library and an 8 kb mate-pair library were constructed using the Nextera XT DNA Library Preparation Kit and the Nextera Mate Pair Sample Preparation Kit, respectively. Genome sequences of the other strains were obtained from a paired-end library preparing using the Nextera XT DNA Library Preparation Kit for V. aphrogenes and TruSeq PCR-Free kit for V. algivorus, V. casei and V. rumoiensis. The genome sequence was assembled using Platanus [14]. The sequence was deposited in the DDBJ/GenBank/EMBL database under accession numbers described below.

Multilocus sequence analysis (MLSA)

Sequences of eight protein-coding genes (ftsZ, gapA, gyrB, mreB, pyrH, recA, rpoA, and topA) of CA-1004^T were retrieved from the genome sequences. MLSA was conducted in the same manner as previously described [4–5]. The sequences were aligned using ClustalX 2.1 [12]. The domains used to construct the tree shown in Fig 2 were regions of the ftsZ, gapA, gyrB, mreB, pyrH, recA, rpoA, and topA genes; positions 196–630, 226–861, 442–1026, 391–895, 175–543, 430–915, 385–762, and 571–990 (V. cholerae O1 Eltor N16961 (AE003852) numbering), respectively. The MEGA program was used to calculate the sequence similarity. Split decomposition analysis (SDA) was performed using SplitsTree version 4.14.3 with a neighbor net drawing and a Jukes-Cantor correction [15–16]. Each aligned set was concatenated and used to reconstruct the network.

Download:

Fig 2. Concatenated split network tree based on eight gene loci.

The gapA, gyrB, ftsZ, mreB, pyrH, recA, rpoA, and topA gene sequences were concatenated including the representative of the Vibrio aphrogenes sp. nov. strain CA-1004^T. Phylogenetic tree was generated using the SplitsTree4 program.

https://doi.org/10.1371/journal.pone.0180053.g002

DNA-DNA hybridizations

Strains used for DNA-DNA hybridization were CA-1004^T, V. algivorus NBRC 111146^T, V. casei DSM 22364^T, V. litoralis DSM 17657^T, and V. rumoiensis FERM P-14531^T. DNAs of the strains were prepared accordingly to Marmur [17] with minor modifications. DNA-DNA hybridization experiments were performed using the fluorometric direct binding method in microdilution wells described previously [3]. In brief, the DNAs of CA-1004^T were labeled with photobiotin (Vector Laboratories, Inc., Burlingame, CA). After immobilization of unlabeled single stranded DNA of CA-1004^T in microdilution wells (Immuron 200, FIA/LIA plate, black type, Greiner labotechnik, Germany), hybridization was performed under optimal conditions using the CA-1004^T labeled DNA as a probe following pre-hybridization [3]. Detection of the hybridized probe was performed using fluorometry (Infinite 200, Tecan, Switzerland) after binding streptavidin-β-galactosidase to the probe DNA. 4-Methylumbelliferyl-β-d-galactopyranoside (6 x 10⁻⁴ M; Wako, Osaka, Japan) was used for a fluorogenic substrate for β-galactosidase. DNA-DNA homology was calculated according to the previous report [3] based on an average value measured from three wells.

Genome analysis and in silico DNA-DNA similarity calculation

General genome features including DNA G+C content were determined using the Rapid Annotations Using Subsystems Technology (The RAST server version 4.0) [18]. In silico DDH values from Genome-to-Genome Distance Calculator (GGDC 2) [19–20] and Average Nucleotide Identity (ANI) values of CA-1004^T against V. algivorus NBRC 111146^T, V. casei DSM 22364^T, V. litoralis DSM 17657^T, and V. rumoiensis FERM P-14531^T were estimated using Orthologous Average Nucleotide Identity Tool version 0.93 [21]. Comparison of genes encoding the hyf-type formate hydrogen lyase complex and the flanking region was performed using GenomeTraveler (In Silico Biology, Inc., Yokohama, Japan).

Hydrogen production from alginate

Strain CA-1004 was cultured at 25°C in a 100 mL marine broth (0.5% (w/v) polypeptone, 0.1% (w/v) yeast extract) containing 100 mM MES (Dojindo, Kumamoto, Japan), supplemented with 1.0% (w/v) sodium alginate. A 3.0% (w/v) mannitol supplemented marine broth was used as a positive control. The pH of the medium was maintained at 6.0 using a pH controller (DT-1023P, ABLE, Tokyo, Japan) equipped with an autoclavable electrode (FermProbe pH electrodes, Broadley-James Corp., Branford, USA) by adding 5 N NaOH or HCl. Biogas was captured in an aluminium bag, and the H₂ gas production was determined using gas chromatography (GC2014 Shimadzu, Kyoto, Japan) with a thermal conductivity detector and a ShinCarbon ST column (Shinwa Chemical Industries Ltd., Kyoto, Japan).

Nucleotide sequence accession number

The genome sequence data for CA-1004^T, V. algivorus NBRC 111146^T, V. casei DSM 22364^T, and V. rumoiensis FERM P-14531^T were deposited at DDBJ/EMBL/GenBank under the accession number BDGR01000001-BDGR01000024, BDSC01000001-BDSC01000008, BDSD01000001-BDSD01000055, and BDSE01000001-BDSE01000047, respectively. The 16S rRNA gene sequence of CA-1004^T was deposited in GenBank under KX713151.

Results and discussion

The phylogenic analysis based on 16S rRNA gene sequences showed the strain CA-1004^T is a member of the genus Vibrio (S1 Fig): more precisely, the strain was closely related to members of the Rumoiensis clade with a high bootstrap support [4–5] (Fig 1). Sequence similarities of the 16S rRNA gene against those of Rumoiensis clade species, V. algivorus NBRC 111146^T, V. rumoiensis FERM P-14531^T, V. casei DSM 22364^T, and V. litoralis DSM 17657^T were 98.4%, 98.0%, 97.9%, and 96.8%, respectively. These levels of similarity are below or in the proposed threshold range for the species boundary, 98.2–99.0% [22,23,24]. To further confirm the genetic coherence, DNA-DNA similarity of CA-1004^T against Rumoiensis clade species was experimentally measured. Using CA-1004^T as a labelled strain, DDH values against V. algivorus NBRC 111146^T, V. casei DSM 22364^T, V. litoralis DSM 17657^T, and V. rumoiensis FERM P-14531^T were 15.4%, 12.0%, 4.9%, and 5.6%, respectively. These DDH values were sufficiently below the species boundary (<70%) to propose CA-1004^T as a new species in the Rumoiensis clade. MLSA using eight protein-coding genes also showed the clear separation of the Rumoiensis clade containing the CA-1004^T from the other clades of Vibrionaceae species, which suggests a common ancestry of the CA-1004^T and the other Rumioensis clade species (Fig 2, S2 Fig).

In silico genome comparison with CA-1004^T was also performed using the draft genomes of V. algivorus NBRC 111146^T, V. casei DSM 22364^T, V. litoralis DSM 17657^T, and V. rumoiensis FERM P-14531^T. The in silico DDH values (Formula 2, recommended) of CA-1004^T against V. algivorus NBRC 111146^T, V. casei DSM 22364^T, V. litoralis DSM 17657^T, and V. rumoiensis FERM P-14531^T were 19.5%, 20.9%, 20.2%, and 20.5%, respectively, further distinguishing CA-1004^T from these species. Average nucleotide identity (ANI) was also calculated using the draft genome sequences, and the ANI values of CA-1004^T against V. algivorus NBRC 111146^T, V. casei DSM 22364^T, V. litoralis DSM 17657^T and V. rumoiensis FERM P-14531^T were 78.2%, 76.4%, 78.0%, and 78.0%, respectively (Fig 3), much below the species threshold of 95–96% for species circumscription [6,21,25–26]. These values of experimental DDH, in silico DDH, and ANI, along with phylogenic analyses, showed that CA-1004^T should be considered as a new species, indicating less genetic cohesion of CA-1004^T to the other Rumoiensis clade species.

Download:

Fig 3. Heatmap generated with OrthoANI values calculated from Orthologous Average Nucleotide Identity Tool version 0.93 [21].

https://doi.org/10.1371/journal.pone.0180053.g003

On the basis of concatenated sequences of eight MLSA protein-coding genes, CA-1004^T is likely to share a common ancestry with members of the Rumoiensis clade. This was confirmed by comparative analysis of phenotypic and biochemical features of CA100-4^T with other members of the Rumoiensis clade (Table 1), showing some degree of phenotypic coherence between the different species. They grow at temperatures between 4 and 30°C, require salt for growth, and tested positive for nitrate reduction, oxidase, catalase, DNase, and alginase production. They were negative for growth on TCBS agar, lysine and ornithine decarboxylation, acetoin production, and indole production. On the other hand, CA-1004^T was distinguished from the close neighbors by several traits, such as showing positive results for gas production from D-glucose and arginine dihydrolase. Apparent κ-carrageenase activity reported by Araki et al. [1] was detected in the type strain proposed, but no any κ-carrageenase activities or cgk genes were retained in the draft genome sequence. The genes may have been lost during the long term serial transfers. The five species belonged into the Rumoiensis clade can grow wide range of NaCl concentration (Table 1).

Download:

Table 1. Phenotypic characteristics for distinguishing Vibrio aphrogenes sp. nov. and their closely related species.

Taxa are indicated as: (1) V. aphrogenes CA-1004^T, (2) V. algivorus NBRC 111146^T, (3) V. casei DSM 22364^T, (4) V. liotralis DSM 17657^T, (5) V. rumoiensis DSM 19141^T.

https://doi.org/10.1371/journal.pone.0180053.t001

Interestingly, the strain CA-1004^T possessed an entire gene set responsible for a hyf-type formate hydrogen lyase complex [27] (Fig 4A). The gene cluster consisted of genes for a major part of FHL (a hydrogenase complex and a formate dehydrogenase), and the flhA activator gene, which corresponds to the FHL-Hyp gene cluster of V. tritonius AM2^T [27]. The presence of the gene cluster supports the gas production phenotype of the strain. In addition to the gene cluster, a possible nickel transporter gene, hupE, was located between the formate dehydrogenase gene and the hyp gene cluster (Fig 4A). The V. aphogenes-type of FHL gene cluster involving the hupE gene is also found in Gazogenes clade species including V. gazogenes (Fig 4A) but the hydrogen productions by these strains are rather low (unpublished data). The biochemistry and molecular biology of HupE in the V. aphrogenes CA-1004^T have not been investigated yet, but the function of the R. leguminosarum HupE is recently identified as an energy-independent and specific diffusion facilitator for nickel transport for hydrogenase synthesis, on the basis of the kinetics using inhibitors and uncouplers such azide, arsenate, CCCP, and DCCD in the Rhizobium hydrogen uptake system [28–29]. Mutant assays also revealed good correlation between the nickel transport and the hydrogenase activity in R. leguminosarum [29]. The hydrogenase of V. aphrogenes is predicted as a [NiFe] hydrogenase on the basis of the primary structure comparison possessing CxxC motif required for [NiFe] center construction [27], the nickel transport via the HupE could have a strong link to the hydrogenase activity. Further genome comparison with other members of Rumoiensis clade revealed no any FHL-fdhF-hyp gene cluster. Other members of Rumoiensis possessed regions containing serine/threonine protein kinase, RIO1 family protein gene, replacing 66-kb genome region with FHL-fdhF-hyp gene cluster in V. aphrogenes (Fig 4B). As the gas production is an atypical phenotype not only in the genus Vibrio but also in the family Vibrionaceae [2,4–5,30], this might give important clues in revealing the evolutionary history of hyf-type gene cluster present in vibrios.

Download:

Fig 4. Comparison of hyf type formate hydrogen lyase (FHL) complex gene cluster.

(A) Comparison of the FHL gene cluster of Vibrio aphrogenes sp. nov strain CA-1004 and those from Escherichia coli K-12, Vibrio furnissii NCTC 11218, Vibrio tritonius AM2^T, and Vibrio gazogenes ATCC 29988^T (B) Comparison of the FHL gene cluster and the flanking region of Vibrio aphrogenes CA-1004^T to those of V. algivorus NBRC 111146^T, V. casei DSM 22364^T, Vibrio litoralis DSM 17657^T, and V. rumoiensis FERM P-14531^T. FHL complex gene cluster and RIO1 genes are shown in green and black, respectively. Genes shared among all genomes are represented in red. Genes shown in gray are unique genes in each strain.

https://doi.org/10.1371/journal.pone.0180053.g004

More interestingly, we found a direct hydrogen production (2.9 mL H₂ gas at 25°C at 48 hours) by the V. aphrogenes strain CA-1004^T from alginate, which is major polysaccharide in brown seaweed. As alginate is known as one of the most oxidized polysaccharides, reduced fermentation products such as ethanol and lactate are unlikely to be produced from such substrate during the fermentation of bacteria due to the redox imbalance [31–32]. Since H₂ is also known to be a reduced fermentation gaseous product, no bacteria possessing direct alginate-H₂ conversion metabolisms have been reported until now. The new findings of the V. aphrogenes sp. nov. could illuminate the future metabolic pathway designs in H₂ production even when using redox imbalanced substrates. We need further characterization to show how direct H₂ production from alginate is controlled genetically and/or biochemically in this unique Vibrio species for future applications of V. aphorogenes.

In conclusion, polyphasic taxonomy with a genome-based strategy indicated V. aphrogenes as a new species in the genus Vibrio. Both 16S rRNA gene sequences phylogeny and MLSA based on eight protein-coding gene sequences placed the stain CA-1004^T into the Rumoiensis clade. Comparison of phenotypic features also places V. aphrogenes CA-1004^T in the genus Vibrio, while supporting its novelty (Table 1). The name V. aphrogenes is proposed to show its gas-producing features. Unfortunately we have only one strain of V. aphrogenes today, further ecological study is necessary for understanding the biodiversity and ecophysiological roles of the V. aphrogenes strains.

Description of Vibrio aphrogenes sp. nov.

V. aphrogenes sp. nov. (aph.ro'ge.nes. Gr. n. aphros, foam; Gr. suff. -genes, producing; N.L. adj. aphrogenes, foam-producing, referring to gas formation of the strain)

Gram-negative, facultative anaerobic, non-motile rods isolated from surface of seaweed collected in Mie Prefecture in Japan. Colonies on ZoBell 2216E agar medium were cream or transparent white, round, and smooth on the edge. No flagellum was observed. Sodium ion is essential for growth. Growth occurs at NaCl concentrations of 1.0 to 10.0% and at temperatures between 4 and 40°C. V. aphrogenes tested positive for production of alginase, lipase and DNase, oxidase, catalase, gas production from D-glucose, arginine dihydrolase, and is able to assimilate D-glucose, D-mannitol, D-mannose, D-galactose, maltose, D-gluconate, fumarate, glycerol, acetate, D-glucosamine, pyruvate, L-proline, D-ribose, L-alanine, L-asparagine, and L-serine. The bacteria tested negative for indole production, acetoin production, lysine decarboxylase, ornithine decarboxylase, amylase, agarose, gelatinase and κ-carrageenase productions, and is incapable of assimilating D-fructose, sucrose, melibiose, lactose, N-acetylglucosamine, succinate, citrate, aconitate, meso-erythritol, γ-aminobutyrate, L-tyrosine, D-sorbitol, DL-malate, α-ketoglutarate, trehalose, gluconate, δ-aminovalate, cellobiose, L-glutamate, putrescine, propionate, amygdalin, arabinose, D-galacturonate, glycerate, D-raffinose, rhamnose, salicine, DL-lactate, L-arginine, L-citrulline, glycine, histidine, and L-ornithine. The G+C content of DNA is 42.1%. Estimated genome size is 3.4 Mb on the basis of genome sequencing.

Supporting information

S1 Fig. A broad NJ tree on the basis of 16S rRNA gene sequences.

https://doi.org/10.1371/journal.pone.0180053.s001

(PDF)

S2 Fig. A broad Split network tree based on concatenated sequences of eight gene loci (gapA, gyrB, ftsZ, mreB, pyrH, recA, rpoA, and topA).

https://doi.org/10.1371/journal.pone.0180053.s002

(PDF)

Acknowledgments

This work was supported by Kaken (16H0497606) (TS). This work was also supported by Grant in Aid for Scientific Research on Innovative Area “Genome Science” from Ministry of Education, Culture, Sports, Science, and Technology of Japan (No.221S0002).

Author Contributions

Conceptualization: Tomoo S.
Data curation: MT SM Tomoo S.
Formal analysis: MT SE FK NA AKMRA GF YO WS.
Funding acquisition: TH Tomoo S.
Investigation: MT SE FK NA SM HD YO TH WS MH IY Toko S. TA.
Methodology: HD YO TH WS MH IY SM Tomoo S.
Project administration: Tomoo S. TA.
Resources: HD IY TA.
Supervision: Tomoo S.
Validation: SM Tomoo S.
Writing – original draft: MT Tomoo S.
Writing – review & editing: SE FK NA AKMRA GF SM HD YO TH WS MH IY Toko S. TA.

References

1. Araki T, Higashimoto Y, Morishita T. (1999) Purification and characterization of κ-carrageenase from a marine bacterium, Vibrio sp. CA-1004. Fisheries Sci, 65: 937–942.
- View Article
- Google Scholar
2. Gomez-Gil B, Thompson CC, Matsumura Y, Sawabe T, Iida T, Christen R, Thompson F, Sawabe T. (2014) In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F, eds. The Family Vibrionaceae. The Prokaryotes, vol. 9, 4th ed., Springer-Verlag, Berlin Heidelberg, pp. 659–747.
3. Al-saari N, Gao F, Rohul AKM, Sato K, Sato K, Mino S, et al. (2015) Advanced microbial taxonomy combined with genome-based approaches reveals that Vibrio astriarenae sp. nov., an agarolytic marine bacterium, forms a new clade in Vibrionaceae. PLoS ONE 10, e0136279. pmid:26313925
- View Article
- PubMed/NCBI
- Google Scholar
4. Sawabe T, Kita-Tsukamoto K, Thompson FL. (2007) Inferring the evolutionary history of vibrios by means of multilocus sequence analysis. J Bacteriol 189: 7932–7936. pmid:17704223
- View Article
- PubMed/NCBI
- Google Scholar
5. Sawabe T, Ogura Y, Matsumura Y, Feng G, Amin AKMR, Mino S, et al. (2013) Updating the Vibrio clades defined by multilocus sequence phylogeny: proposal of eight new clades, and the description of Vibrio tritonius sp. nov. Front Microbiol 4: 1–14.
- View Article
- Google Scholar
6. Thompson CC, Amaral GR, Campeão M, Edwards RA, Polz MF, Dutilh BE, et al. (2015) Microbial taxonomy in the post-genomic era: rebuilding from scratch? Arch Microbiol 197, 359–370 pmid:25533848
- View Article
- PubMed/NCBI
- Google Scholar
7. Gomez-Gil B, Roque A, Rotllant G, Romalde JL, Doce A, Eggermont M, Defoirdt T. (2016) Photobacterium sanguinicancri sp. nov. isolated from marine animals. Antonie van Leeuwenhoek, 109: 817–825. pmid:27048242
- View Article
- PubMed/NCBI
- Google Scholar
8. Yumoto I, Iwata H, Sawabe T, Ueno K, Ichise N, Matsuyama H, et al. (1999) Characterization of a facultatively psychrophilic bacterium, Vibrio rumoiensis sp. nov., that exhibits high catalase activity. Appl Environ Microbiol 65: 67–72. pmid:9872761
- View Article
- PubMed/NCBI
- Google Scholar
9. Nam YD, Chang HW, Park JR, Kwon HY, Quan ZX, Park YH, et al. (2007) Vibrio litoralis sp. nov., isolated from a Yellow Sea tidal flat in Korea. Int J Syst Evol Microbiol 57: 562–565. pmid:17329785
- View Article
- PubMed/NCBI
- Google Scholar
10. Doi H, Chinen A, Fukuda H, Usuda Y. (2016) Vibrio algivorus sp. nov., an alginate and agarose assimilating bacterium isolated from the gut flora of a turban shell marine snail. Int J Syst Evol Microbiol 66: 3164–3169. pmid:27199227
- View Article
- PubMed/NCBI
- Google Scholar
11. Bleicher A, Neuhaus K, Scherer S. (2010) Vibrio casei sp. nov., isolated from the 275 surfaces of two French red smear soft cheeses. Int J Syst Evol Microbiol 60: 1745–1749. pmid:19749036
- View Article
- PubMed/NCBI
- Google Scholar
12. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, et al. (2007) Clustal W and Clustal X version 2.0. Bioinform 23: 2947–2948.
- View Article
- Google Scholar
13. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. (2013) MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 30: 2725–2729. pmid:24132122
- View Article
- PubMed/NCBI
- Google Scholar
14. Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Ogura Y, Okuno M, et al. (2014) Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. Genome Res 24: 1384–1395. pmid:24755901
- View Article
- PubMed/NCBI
- Google Scholar
15. Bandelt H-J, Dress AWM. (1992) Split decomposition: a new and useful approach to phylogenetic analysis of distance data. Mol Phylogenet Evol 1: 242–252. pmid:1342941
- View Article
- PubMed/NCBI
- Google Scholar
16. Huson DH, Bryant D. (2005) Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23: 254–267. pmid:16221896
- View Article
- PubMed/NCBI
- Google Scholar
17. Marmur J. (1961) A procedure for the isolation of deoxyribonucleic acid from microorganisms. J Mol Biol 3: 208–218.
- View Article
- Google Scholar
18. Aziz RK, Bartels D, Best A, DeJongh M, Disz T, Edwards RA, et al. (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9: 75. pmid:18261238
- View Article
- PubMed/NCBI
- Google Scholar
19. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14: 60. pmid:23432962
- View Article
- PubMed/NCBI
- Google Scholar
20. Nelder JA, Wedderburn RWM. (1972) Generalized Linear Models. J R Stat Soc Ser A 135: 370–384.
- View Article
- Google Scholar
21. Lee I, Kim YO, Park SC, Chun J. (2015) OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66: 1100–1103.
- View Article
- Google Scholar
22. Kim M, Oh H-S, Park S-C, Chun J (2014) Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Micr 64: 346–351.
- View Article
- Google Scholar
23. Meier-Kolthoff JP, Göker M, Spröer C, Klenk H-PP (2013) When should a DDH experiment be mandatory in microbial taxonomy? Arch Microbiol 195: 413–8. pmid:23591456
- View Article
- PubMed/NCBI
- Google Scholar
24. Stackebrandt E, Ebers J (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33: 152–155.
- View Article
- Google Scholar
25. Rosselló-Móra R, Amann R. (2015) Past and future species definitions for Bacteria and Archaea. Syst Appl Microbiol 38: 1–8.
- View Article
- Google Scholar
26. Tindall BJ, Rosselló-Móra R, Busse H-J, Ludwig W, Kämpfer P. (2010) Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 60: 249–266. pmid:19700448
- View Article
- PubMed/NCBI
- Google Scholar
27. Matsumura Y, Al-saari H, Mino S, Nakagawa S, Maruyama F, Ogura Y, et al. (2015) Identification of a gene cluster responsible for hydrogen evolution in Vibrio tritonius strain AM2 with transcriptional analyses. Int J Hydrogen Energy 40: 9137–9146.
- View Article
- Google Scholar
28. Albareda M, Rodrigue A, Brito B, Ruiz-Argüeso T, Imperial J, Mandrand-Berthelot M-A, Palacios J. (2015) Rhizobium leguminosarum HupE is a highly-specific diffusion facilitator for nickel uptake. Metallomics 7: 691. pmid:25652141
- View Article
- PubMed/NCBI
- Google Scholar
29. Brito B, Prieto R-I, Cabrera E, Mandrand-Berthelot M-A, Imperial J, Ruiz-Argüeso T, Palacios J-M. (2010) Rhizobium leguminosarum hupE encodes a nickel transporter required for hydrogenase activity. J Bacteriol 192: 925–935. pmid:20023036
- View Article
- PubMed/NCBI
- Google Scholar
30. Matsumura Y, Sato K, Al-saari N., Nakagawa S, Sawabe T. (2014) Enhanced hydrogen production by a newly described heterotrophic marine bacterium, Vibrio tritonius strain AM2, using seaweed as the feedstock. Int J Hydrogen Energy 39: 7270–7277.
- View Article
- Google Scholar
31. Bruce T, Ferrão-Gonzales AD, Nakashimada Y, Matsumura Y, Thompson F, Sawabe T. (2016) In: Kim S.-K. eds. Biofuel innovation by microbial diversity. Springer Handbook of Marine Biotechnology. Springer, NY. pp.1163–1180.
32. Takeda H, Yoneyama F, Kawai S, Hashimoto W, Murata K. (2011). Bioethanol production from marine biomass alginate by metabolitically engineered bacteria. Energy Environ Sci 4: 2575–2581.
- View Article
- Google Scholar

[ref1] 1. Araki T, Higashimoto Y, Morishita T. (1999) Purification and characterization of κ-carrageenase from a marine bacterium, Vibrio sp. CA-1004. Fisheries Sci, 65: 937–942.
View Article
Google Scholar

[2] View Article

[3] Google Scholar

[ref2] 2. Gomez-Gil B, Thompson CC, Matsumura Y, Sawabe T, Iida T, Christen R, Thompson F, Sawabe T. (2014) In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F, eds. The Family Vibrionaceae. The Prokaryotes, vol. 9, 4th ed., Springer-Verlag, Berlin Heidelberg, pp. 659–747.

[ref3] 3. Al-saari N, Gao F, Rohul AKM, Sato K, Sato K, Mino S, et al. (2015) Advanced microbial taxonomy combined with genome-based approaches reveals that Vibrio astriarenae sp. nov., an agarolytic marine bacterium, forms a new clade in Vibrionaceae. PLoS ONE 10, e0136279. pmid:26313925
View Article
PubMed/NCBI
Google Scholar

[6] View Article

[7] PubMed/NCBI

[8] Google Scholar

[ref4] 4. Sawabe T, Kita-Tsukamoto K, Thompson FL. (2007) Inferring the evolutionary history of vibrios by means of multilocus sequence analysis. J Bacteriol 189: 7932–7936. pmid:17704223
View Article
PubMed/NCBI
Google Scholar

[10] View Article

[11] PubMed/NCBI

[12] Google Scholar

[ref5] 5. Sawabe T, Ogura Y, Matsumura Y, Feng G, Amin AKMR, Mino S, et al. (2013) Updating the Vibrio clades defined by multilocus sequence phylogeny: proposal of eight new clades, and the description of Vibrio tritonius sp. nov. Front Microbiol 4: 1–14.
View Article
Google Scholar

[14] View Article

[15] Google Scholar

[ref6] 6. Thompson CC, Amaral GR, Campeão M, Edwards RA, Polz MF, Dutilh BE, et al. (2015) Microbial taxonomy in the post-genomic era: rebuilding from scratch? Arch Microbiol 197, 359–370 pmid:25533848
View Article
PubMed/NCBI
Google Scholar

[17] View Article

[18] PubMed/NCBI

[19] Google Scholar

[ref7] 7. Gomez-Gil B, Roque A, Rotllant G, Romalde JL, Doce A, Eggermont M, Defoirdt T. (2016) Photobacterium sanguinicancri sp. nov. isolated from marine animals. Antonie van Leeuwenhoek, 109: 817–825. pmid:27048242
View Article
PubMed/NCBI
Google Scholar

[21] View Article

[22] PubMed/NCBI

[23] Google Scholar

[ref8] 8. Yumoto I, Iwata H, Sawabe T, Ueno K, Ichise N, Matsuyama H, et al. (1999) Characterization of a facultatively psychrophilic bacterium, Vibrio rumoiensis sp. nov., that exhibits high catalase activity. Appl Environ Microbiol 65: 67–72. pmid:9872761
View Article
PubMed/NCBI
Google Scholar

[25] View Article

[26] PubMed/NCBI

[27] Google Scholar

[ref9] 9. Nam YD, Chang HW, Park JR, Kwon HY, Quan ZX, Park YH, et al. (2007) Vibrio litoralis sp. nov., isolated from a Yellow Sea tidal flat in Korea. Int J Syst Evol Microbiol 57: 562–565. pmid:17329785
View Article
PubMed/NCBI
Google Scholar

[29] View Article

[30] PubMed/NCBI

[31] Google Scholar

[ref10] 10. Doi H, Chinen A, Fukuda H, Usuda Y. (2016) Vibrio algivorus sp. nov., an alginate and agarose assimilating bacterium isolated from the gut flora of a turban shell marine snail. Int J Syst Evol Microbiol 66: 3164–3169. pmid:27199227
View Article
PubMed/NCBI
Google Scholar

[33] View Article

[34] PubMed/NCBI

[35] Google Scholar

[ref11] 11. Bleicher A, Neuhaus K, Scherer S. (2010) Vibrio casei sp. nov., isolated from the 275 surfaces of two French red smear soft cheeses. Int J Syst Evol Microbiol 60: 1745–1749. pmid:19749036
View Article
PubMed/NCBI
Google Scholar

[37] View Article

[38] PubMed/NCBI

[39] Google Scholar

[ref12] 12. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, et al. (2007) Clustal W and Clustal X version 2.0. Bioinform 23: 2947–2948.
View Article
Google Scholar

[41] View Article

[42] Google Scholar

[ref13] 13. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. (2013) MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 30: 2725–2729. pmid:24132122
View Article
PubMed/NCBI
Google Scholar

[44] View Article

[45] PubMed/NCBI

[46] Google Scholar

[ref14] 14. Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Ogura Y, Okuno M, et al. (2014) Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. Genome Res 24: 1384–1395. pmid:24755901
View Article
PubMed/NCBI
Google Scholar

[48] View Article

[49] PubMed/NCBI

[50] Google Scholar

[ref15] 15. Bandelt H-J, Dress AWM. (1992) Split decomposition: a new and useful approach to phylogenetic analysis of distance data. Mol Phylogenet Evol 1: 242–252. pmid:1342941
View Article
PubMed/NCBI
Google Scholar

[52] View Article

[53] PubMed/NCBI

[54] Google Scholar

[ref16] 16. Huson DH, Bryant D. (2005) Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23: 254–267. pmid:16221896
View Article
PubMed/NCBI
Google Scholar

[56] View Article

[57] PubMed/NCBI

[58] Google Scholar

[ref17] 17. Marmur J. (1961) A procedure for the isolation of deoxyribonucleic acid from microorganisms. J Mol Biol 3: 208–218.
View Article
Google Scholar

[60] View Article

[61] Google Scholar

[ref18] 18. Aziz RK, Bartels D, Best A, DeJongh M, Disz T, Edwards RA, et al. (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9: 75. pmid:18261238
View Article
PubMed/NCBI
Google Scholar

[63] View Article

[64] PubMed/NCBI

[65] Google Scholar

[ref19] 19. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14: 60. pmid:23432962
View Article
PubMed/NCBI
Google Scholar

[67] View Article

[68] PubMed/NCBI

[69] Google Scholar

[ref20] 20. Nelder JA, Wedderburn RWM. (1972) Generalized Linear Models. J R Stat Soc Ser A 135: 370–384.
View Article
Google Scholar

[71] View Article

[72] Google Scholar

[ref21] 21. Lee I, Kim YO, Park SC, Chun J. (2015) OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66: 1100–1103.
View Article
Google Scholar

[74] View Article

[75] Google Scholar

[ref22] 22. Kim M, Oh H-S, Park S-C, Chun J (2014) Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Micr 64: 346–351.
View Article
Google Scholar

[77] View Article

[78] Google Scholar

[ref23] 23. Meier-Kolthoff JP, Göker M, Spröer C, Klenk H-PP (2013) When should a DDH experiment be mandatory in microbial taxonomy? Arch Microbiol 195: 413–8. pmid:23591456
View Article
PubMed/NCBI
Google Scholar

[80] View Article

[81] PubMed/NCBI

[82] Google Scholar

[ref24] 24. Stackebrandt E, Ebers J (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33: 152–155.
View Article
Google Scholar

[84] View Article

[85] Google Scholar

[ref25] 25. Rosselló-Móra R, Amann R. (2015) Past and future species definitions for Bacteria and Archaea. Syst Appl Microbiol 38: 1–8.
View Article
Google Scholar

[87] View Article

[88] Google Scholar

[ref26] 26. Tindall BJ, Rosselló-Móra R, Busse H-J, Ludwig W, Kämpfer P. (2010) Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 60: 249–266. pmid:19700448
View Article
PubMed/NCBI
Google Scholar

[90] View Article

[91] PubMed/NCBI

[92] Google Scholar

[ref27] 27. Matsumura Y, Al-saari H, Mino S, Nakagawa S, Maruyama F, Ogura Y, et al. (2015) Identification of a gene cluster responsible for hydrogen evolution in Vibrio tritonius strain AM2 with transcriptional analyses. Int J Hydrogen Energy 40: 9137–9146.
View Article
Google Scholar

[94] View Article

[95] Google Scholar

[ref28] 28. Albareda M, Rodrigue A, Brito B, Ruiz-Argüeso T, Imperial J, Mandrand-Berthelot M-A, Palacios J. (2015) Rhizobium leguminosarum HupE is a highly-specific diffusion facilitator for nickel uptake. Metallomics 7: 691. pmid:25652141
View Article
PubMed/NCBI
Google Scholar

[97] View Article

[98] PubMed/NCBI

[99] Google Scholar

[ref29] 29. Brito B, Prieto R-I, Cabrera E, Mandrand-Berthelot M-A, Imperial J, Ruiz-Argüeso T, Palacios J-M. (2010) Rhizobium leguminosarum hupE encodes a nickel transporter required for hydrogenase activity. J Bacteriol 192: 925–935. pmid:20023036
View Article
PubMed/NCBI
Google Scholar

[101] View Article

[102] PubMed/NCBI

[103] Google Scholar

[ref30] 30. Matsumura Y, Sato K, Al-saari N., Nakagawa S, Sawabe T. (2014) Enhanced hydrogen production by a newly described heterotrophic marine bacterium, Vibrio tritonius strain AM2, using seaweed as the feedstock. Int J Hydrogen Energy 39: 7270–7277.
View Article
Google Scholar

[105] View Article

[106] Google Scholar

[ref31] 31. Bruce T, Ferrão-Gonzales AD, Nakashimada Y, Matsumura Y, Thompson F, Sawabe T. (2016) In: Kim S.-K. eds. Biofuel innovation by microbial diversity. Springer Handbook of Marine Biotechnology. Springer, NY. pp.1163–1180.

[ref32] 32. Takeda H, Yoneyama F, Kawai S, Hashimoto W, Murata K. (2011). Bioethanol production from marine biomass alginate by metabolitically engineered bacteria. Energy Environ Sci 4: 2575–2581.
View Article
Google Scholar

[109] View Article

[110] Google Scholar

Vibrio aphrogenes sp. nov., in the Rumoiensis clade isolated from a seaweed

Vibrio aphrogenes sp. nov., in the Rumoiensis clade isolated from a seaweed

Correction

Figures

Abstract

Introduction

Materials and methods

Bacterial strains and phenotypic characterization

Phylogenetic analysis based on a 16S rRNA gene

Genome sequencing

Multilocus sequence analysis (MLSA)

DNA-DNA hybridizations

Genome analysis and in silico DNA-DNA similarity calculation

Hydrogen production from alginate

Nucleotide sequence accession number

Results and discussion

Description of Vibrio aphrogenes sp. nov.

Supporting information

S1 Fig. A broad NJ tree on the basis of 16S rRNA gene sequences.

S2 Fig. A broad Split network tree based on concatenated sequences of eight gene loci (gapA, gyrB, ftsZ, mreB, pyrH, recA, rpoA, and topA).

Acknowledgments

Author Contributions

References