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Article

Characterization of Salinivibrio socompensis sp. nov., A New Halophilic Bacterium Isolated from the High-Altitude Hypersaline Lake Socompa, Argentina

by
Cristina Galisteo
1,
Cristina Sánchez-Porro
1,*,
Rafael R. de la Haba
1,
Clara López-Hermoso
1,
Ana B. Fernández
1,2,
María E. Farias
2 and
Antonio Ventosa
1,*
1
Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
2
Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas, Planta Piloto de Procesos Industriales Microbiológicos, Centro Científico Tecnológico, CONICET Tucumán T4000, Argentina
*
Authors to whom correspondence should be addressed.
Microorganisms 2019, 7(8), 241; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms7080241
Submission received: 30 June 2019 / Revised: 1 August 2019 / Accepted: 2 August 2019 / Published: 5 August 2019
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments)
Browse Figures
Versions Notes

Abstract

:
The genus Salinivibrio belongs to the family Vibrionaceae and includes Gram-stain-negative, motile by a polar flagellum, and facultatively anaerobic curved rods. They are halophilic bacteria commonly found in hypersaline aquatic habitats and salted foods. This genus includes five species and two subspecies. A presumed novel species, strain S35T, was previously isolated from the high-altitude volcanic, alkaline, and saline lake Socompa (Argentinean Andes). In this study we carried out a complete taxonomic characterization of strain S35T, including the 16S rRNA gene sequence and core-genome analysis, the average nucleotide identity (ANIb, ANIm, and orthoANI), and in silico DNA–DNA hybridization (GGDC), as well as the phenotypic and chemotaxonomic characterization. It grew at 3%–20% (w/v) NaCl, pH 6–10, and 10–42 °C, with optimum growth at 7.0%–7.5% (w/v) NaCl, pH 8.0, and 37 °C, respectively. Strain S35T was oxidase- and catalase-positive, able to produce acid from D-glucose and other carbohydrates. Hydrolysis of DNA, methyl red test, and nitrate and nitrite reduction were positive. Its main fatty acids were C16:0, C16:1 ω7c and C16:1 ω6c, and C18:1 ω7c and/or C18:1 ω6c. ANI, GGDC, and core-genome analysis determined that strain S35T constitutes a novel species of the genus Salinivibrio, for which the name Salinivibrio socompensis sp. nov. is proposed. The type strain is S35T (= CECT 9634T = BNM 0535T).

1. Introduction

The two main groups that inhabit hypersaline environments are the extremely halophilic archaea (also called haloarchaea) and the moderately halophilic bacteria [1,2]. The haloarchaea are classified within the class Halobacteria with three orders: Haloferacales, Halobacteriales, and Natrialbales [3]. Regarding moderately halophilic bacteria, they are very heterogeneous and are represented by a large number of species belonging to at least eight phyla of the domain Bacteria: Proteobacteria, Firmicutes, Actinobacteria, Spirochaetes, Bacteroidetes, Thermotoga, Cyanobacteria, and Tenericutes [2].
Halophilic microorganisms have an important biotechnological potential due to their exceptional physiological and biochemical characteristics. Among their most interesting applications are found the production of a novel restriction enzyme [4], agarases, with industrial and medical applications [5], or β-galactosidase, to produce lactose-free dairy products [6]. Other applications include the production of ectoines, polysaccharides, or extracellular enzymes [1].
The genus Salinivibrio belongs to the family Vibrionaceae, order Vibrionales, within the class Gammaproteobacteria in the phylum Proteobacteria [7]. The first strain isolated was named as Vibrio costicola by Smith [8] from bacon rib bones, which was also found lately in aquatic hypersaline environments [9]. V. costicola has the ability to grow over a wide range of salt concentrations, and for this reason it has been used as a model microorganism for studies of osmoregulation and other physiological mechanisms [10,11,12,13]. Relevant phenotypic differences and low phylogenetic relationships with other species of the genus Vibrio, including V. costicola, permitted the reclassification of V. costicola in a separate genus, Salinivibrio [14]. The genus Salinivibrio comprises five species: Salinivibrio costicola, with two subspecies: S. costicola subsp. costicola [8,14,15] and S. costicola subsp. alcaliphilus [16]; S. proteolyticus [17]; S. siamensis [18]; S. sharmensis [19]; and the recently described S. kushneri [20]. S. costicola subsp. vallismortis [15] was also included as a subspecies of S. costicola but according to López-Hermoso et al. [21] it belongs to the species S. proteolyticus. The species of this genus are Gram-stain-negative curved rods (0.5–0.6 x 1.0–3.2 µm), motile by one polar flagellum, and non-endospore forming. They are moderately halophilic, able to grow on a NaCl range from 1% to 20% (w/v), with a temperature range from 5 to 50 °C, and pH range from 5 to 10, with the optimal growth being at 2.5% to 10% (w/v) NaCl, 37 °C, and pH 7.3 to 7.5, respectively. Facultatively anaerobic, catalase, and oxidase positive. The DNA G+C content ranges from 49.3 to 52.5 mol% [7,14,16,17,18,19,20].
In 2017, López-Hermoso et al. [22] carried out an extensive revision of the genus Salinivibrio, studying 70 strains, including new isolates from different solar salterns, where these bacteria are common habitants, as well as the type strains of the species and subspecies of this genus. Initially, their 16S rRNA gene sequences were compared with those of the known species and subspecies of Salinivibrio. A multilocus sequence analysis (MLSA) based on the genes gyrB, recA, rpoA, and rpoD, validated with DNA–DNA hybridization (DDH) studies, allowed the researchers to classify them into four phylogroups and one phylotype. In 2014, Gorriti et al. [23] reported the draft genome of three strains designated as S34, S35, and S10B. Those strains belonged to the genus Salinivibrio; however, in this paper the authors did not perform their systematic characterization, and their taxonomic position was not clarified. These three bacteria were isolated from lake Socompa, at the base of volcano Socompa, located in the Northwestern region of Puna (Argentina) at 3570 m above the sea level. The most relevant features of this lake are high alkalinity (pH 8.5), salinity up to 7% (w/v) NaCl, and extremely high arsenic concentration. It is also remarkable for the presence of actively forming stromatolites [24,25,26], which are considered evidence of early life on Earth [27,28,29]. The aim of this study was to carry out an exhaustive characterization of Salinivibrio sp. strain S35T, selected as representative of these three new isolates due to the unavailability to cultivate the other two strains. We show that strain S35T constitutes a new species for which we propose the designation of Salinivibrio socompensis sp. nov.

2. Materials and Methods

2.1. Bacterial Strains

The strain S35T was isolated by M. E. Farias, from Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA-PROIMI), Argentina [23]. The type strains of all species of the genus Salinivibrio, obtained for culture collections, were included as reference: Salinivibrio costicola subsp. costicola CECT 4059T [17], Salinivibrio costicola subsp. alcaliphilus DSM 16359T [19], Salinivibrio proteolyticus DSM 19052T [20], Salinivibrio siamensis JCM 14472T [21], Salinivibrio sharmensis DSM 18182T [22], and Salinivibrio kushneri AL184T [23].

2.2. Culture Media and Growth Conditions

The strains were routinely grown on SW7.5 medium at 37 °C. The composition of this medium was the following (g l−1): NaCl, 58.5; MgCl2·6H2O, 9.75; MgSO4·7H2O, 15.25; CaCl2, 0.25; KCl, 1.5; NaHCO3, 0.05; NaBr, 0.175; and yeast extract, 5.0 [23]. When necessary, the medium was solidified with 2.0% (w/v) agar. The pH was adjusted to 7.5 with 1 M KOH. SW7.5 broth with 20% (v/v) glycerol was used for long-term preservation at −80 °C. For chemotaxonomic characterization, the bacteria were grown for seven days at 37 °C in medium 1, described by Romano et al. [22], containing (g l−1): yeast extract, 10.0; NaCl, 100.0; Na3-citrate, 3.0; Na2CO3, 3.0; KCl, 2.0; MgSO4·7H2O, 1.0; MnCl2·4H2O, 0.00036; and FeSO4, 0.05.

2.3. Taxophylogenomic Characterization

2.3.1. Phylogenetic Analysis Based on 16S rRNA Gene Sequence Comparison

The DNA of strain S35T was obtained using the commercial kit G-spinTM Total DNA Extraction Kit (INtRON Biotechnology), following the instructions of the manufacturer. The 16S rRNA gene was amplified by PCR using the primers 16F27 (5′-AGAGTTTGATCMTGGCTCAG-3′) and 16R1488 (5′-CGGTTACCTTGTTAGGACTTCACC-3′) [30]. The PCR product was purified using the commercial kit MEGAquick-spinTM Plus (INtRON Biotechnology), and sequenced using the Sanger method with oligonucleotides 16F27, 16R1488, 16R343 (5′-ACTGCTGCCTCCCGTA-3′), and 16F530 (5′-GTGCCAGCAGCCGCGG-3′) by StabVida (Oeiras, Portugal). The gene sequences were assembled and edited by ChromasPro software Version 1.5 (Technelysium Pty) and used for initial BLAST, searched against “nt” database in GenBank. To determine the percentages of similarity between strain S35T and the most closely related taxa we used the EzBioCloud.net server [31]. The 16S rRNA gene analysis and phylogenetic trees construction were performed with the ARB software package [32]. Phylogenetic trees were constructed using three different methods: Neighbor-joining [33], maximum parsimony [34], and maximum likelihood [35] algorithms integrated in the ARB software for phylogenetic inference. A bootstrap analysis (1000 replications) was performed to evaluate the robustness of the phylogenetic trees [36]. The 16S rRNA gene sequences of the reference type strains used for the phylogenetic comparison were obtained from GenBank database and their accession numbers are shown in Figure 1.

2.3.2. Phylogenomic Comparative Analysis

For the phylogenomic comparative analysis we used the genomes available from GenBank database that are shown in Table S1. These genomes correspond to the following strains used in this comparative study: Salinivibrio sp. strain 35T, S. costicola subsp. costicola LMG 11651T, S. costicola subsp. alcaliphilus DSM 16359T, S. proteolyticus DSM 19052T, S. siamensis JCM 14472T, S. sharmensis DSM 18182T, and S. kushneri AL184T. The quality of these genome sequences is in accordance with the minimal standards for the use of genome data for the taxonomy of prokaryotes [37].
To determine the core genome, the Enveomics [38] tool was used to perform an all-versus-all BLAST search based on nucleotide gene sequences of strain S35T and type strains of the genus Salinivibrio to identify clusters of orthologous genes (OGs). Those OGs shared among all taxa and present in single copy per genome were selected. They were aligned with Muscle v. 3.8.31 [39] and subsequently concatenated. An approximately maximum-likelihood tree was constructed using FastTree v. 2.1.9 [40] with the JTT replacement matrix [41] under the CAT approximation (single rate for each site) with 20 rate categories. Local support values were estimated with the Shimodaira-Hasegawa test [42].

2.3.3. Average Nucleotide Identity (ANI) and n-silico DNA–DNA Hybridization (DDH)

The average nucleotide identity (ANI) among Salinivibrio sp. strain 35T and S. costicola subsp. costicola LMG 11651T, S. costicola subsp. alcaliphilus DSM 16359T, S. proteolyticus DSM 19052T, S. siamensis JCM 14472T, S. sharmensis DSM 18182T, and S. kushneri AL184T was calculated using three different methods: The percentages of ANIb based on BLAST+ and ANIm based on MUMmer were performed with JSpeciesWS [43], and the orthoANI was calculated with ChunLab’s Orthologous Average Nucleotide Identity Tool (OAT) [44], available on the EzBioCloud server. In-silico DDH was calculated by the bioinformatic tool Genome-to-Genome Distance Calculator (GGDC version 2.1) available from the Leibniz Institute DSMZ [45].

2.4. Phenotypic Characterization

2.4.1. Morphology and Motility

Morphology and pigmentation of colonies were observed on SW7.5 solid medium at pH 7.5 after 24 h at 37 °C. Cell morphology and motility were examined by phase-contrast microscopy (Olympus CX41 with DP70 digital camera).

2.4.2. Physiological Characteristics

The range and optimal conditions of salinity for growth were determined by using SW liquid medium at pH 7.5 supplemented with 3%, 6%, 7%, 7.5%, 8%, 9%, 10%, 15%, and 20% (w/v) total salts respectively. In order to determine the optimal (and range) growth at different pH values of strain S35T, the isolate was cultured under the optimal salt concentration conditions, adjusting the medium to pH 5, 6, 7, 7.5, 8, 9, and 10, respectively, with appropriate buffers. The optimal and range of temperature were determined by incubating strain S35T under the optimal salt concentration and pH conditions, at temperatures of 4, 10, 15, 28, 37, 40, 42, 45, and 48 °C, respectively. Growth rates were determined by monitoring the increase in the optical density (O.D.) at 600 nm (ThermoSpectronics Spectronic 20D+).

2.4.3. Biochemical Characteristics

Catalase activity was determined by adding 3% (w/v) H2O2 solution to colonies and observing bubble presence [46]. Oxidase activity was examined using 1% (v/v) tetramethyl-p-phenylenendiamine [47]. Hydrolysis of gelatin, starch, Tween 80, DNA, casein, and aesculin; production of indole, methyl red, and Voges–Proskauer tests; Simmon’s citrate, nitrate, and nitrite reduction; H2S production; ornithine, arginine, and lysine decarboxylases; urease; and phenylalanine deaminase were determined as described by Cowan and Steel [46], with the addition of 7.5% (w/v) total salts to the medium [9]. Acid production from carbohydrates was determined using a modified phenol red base medium prepared with SW7.5 supplemented with 1% (w/v) carbohydrate [9,46]. The carbohydrates studied were: D-arabinose, D-fructose, D-galactose, glycerol, D-glucose, lactose, maltose, mannitol, D-sucrose, D-trehalose, and D-xylose.

2.4.4. Nutritional Characteristics

The medium described by Koser [48], as modified by Ventosa et al. [9], was used for the determination of the growth using different carbohydrates, alcohols, organic acids, and amino acids as carbon and energy or carbon, nitrogen, and energy sources. Substrates were added as filter-sterilized solutions to give a final concentration of 1 g L−1 for all substrates except for carbohydrates, whose final concentration was 2 g L−1. The studied substrates were: amygdalin, D-arabinose, cellobiose, D-fructose, D-galactose, D-glucose, lactose, maltose, mannose, melibiose, melezitose, raffinose, sucrose, starch, D-trehalose, D-xylose, butanol, dulcitol, ethanol, glycerol, mannitol, methanol, propranolol, sorbitol, xylitol, acetate, benzoate, butyrate, citrate, fumarate, hypurate, propionate, succinate, valerate, alanine, arginine, aspartic acid, cysteine, L-phenylalanine, glutamine, lysine, methionine, ornithine, and serine.

2.4.5. Chemotaxonomic Characterization

The strain S35T was grown on medium 1 at 37 °C for 48 h and the fatty acids composition was determined following the protocol recommended by MIDI Microbial Identification System [49]. The fatty acids were determined by gas chromatography at the Spanish Type Culture Collection (CECT), Valencia, Spain.

3. Results and Discussion

3.1. Phylogenetic Analysis Based on 16S rRNA Gene Sequence Comparison

The 16S rRNA gene sequence comparative analysis of strain S35T with respect to the type strains of S. costicola subsp. costicola CECT 4059T, S. costicola subsp. alcaliphilus DSM 16359T, S. proteolyticus DSM 19052T, S. siamensis JCM 14472T, S. sharmensis DSM 18182T, and S. kushneri AL184T showed percentages of similarity of 99.2%, 99.4%, 97.7%, 97.7%, 97.9%, and 98.9%, respectively. These high percentages indicate that strain S35T is a member of the genus Salinivibrio, but they are not conclusive to determinate if strain S35T may constitute a novel species. The phylogenetic tree (Figure 1) based on the 16S rRNA gene sequences, constructed by the neighbor-joining algorithm, showed that strain S35T clustered with the other species of the genus Salinivibrio. Topologies of phylogenetic trees inferred using the maximum likelihood and maximum parsimony were very similar to those of this tree.

3.2. Phylogenomic Comparative Analysis

Since the comparison of the 16S rRNA gene sequence does not allow us to determine in depth the phylogenetic relationships within the genus Salinivibrio [22], and in order to increase the resolution, we carried out a phylogenomic analysis based on the gene sequences obtained from the available genomes, whose characteristics are shown in Table S1, of strain S35T, Salinivibrio costicola subsp. costicola LMG 11651T, Salinivibrio costicola subsp. alcaliphilus DSM 16359T, Salinivibrio proteolyticus DSM 19052T, Salinivibrio siamensis JCM 14472T, Salinivibrio sharmensis DSM 18182T, and Salinivibrio kushneri AL184T.
The core genome tree was based on 1265 common genes of the seven studied Salinivibrio strains. Figure 2 shows that strain S35T constitutes a phylogroup different enough from the other type strains of Salinivibrio as to be considered as a new species. As shown in Figure 2, strain S35T did not cluster together with any of the species and subspecies of Salinivibrio, being separated from all of them. Thus, we concluded that strain S35T constitutes a new species of this genus.

3.3. ANI Values and In-Silico DNA–DNA Hybridization (GGDC)

Table 1 shows the ANIb, ANIm, and orthoANI percentages of strain S35T with respect to the other species and subspecies of Salinivibrio. The current threshold value for delineating to bacterial species using the aforementioned indexes is 95%, meaning that if a result is above or equal to this value then the strains belong to the same species, but they constitute different species when this value is below 95% [44]. All ANI values obtained using the three different methods were below 95% between strain S35T and the type strains of the species and subspecies of the genus Salinivibrio. Regarding GGCD, strain S35T is beneath 70% threshold with respect to the type strains of the species of the genus Salinivibrio (Table 1). According to Kim et al. [50], GGDC percentages above or equal to 70% indicate that the strains can be assigned to the same species, and values under 70% indicate that the strains belong to different species.

3.4. Phenotypic Characterization

Colonies of strain S35T showed cream-pink pigmentation and spherical shape, with a diameter lower than 3 mm. Cells were motile, Gram-stain-negative, curved rods, similar to those reported for other Salinivibrio species [14,15,16,17,18,19,20,21]. Strain S35T was able to grow in a range of 3%–20% (w/v) NaCl, with an optimum at 7.0%–7.5% (w/v) NaCl (Figure S1). Strain S35T can be considered as a moderately halophilic bacterium, as are the other species of Salinivibrio (Table 2). The pH allowing growth ranged from 6 to 10, with an optimum at pH 8.0 (Figure S2). These values are similar to those described for other Salinivibrio strains, except for S. costicola subsp. alcaliphilus and S. sharmensis, that had optimum pH at 9.0. The temperature range for growth was 10–42 °C with an optimal growth at 37 °C. Biochemical and nutritional characteristics of strain S35T with respect to those of the species and subspecies of the genus Salinivibrio are given in Table 2. It is noticeable that strain S35T is not able to hydrolyze any of the substrates tested, with the exception of DNA and gelatin. On the other hand, in contrast with the other species of Salinivibrio, strain S35T is the only one that showed a positive result for the methyl red test. Finally, strain S35T has predominance for the utilization of sugars instead of alcohols or organic acids as sole source of carbon and energy (Table 2).

3.5. Chemotaxonomic Characterization

The percentage of the major fatty acids composition, determined by gas chromatography, is shown in Table S2. Fatty acids C16:0 (20.8%), C16:1 ω7c, and C16:1 ω6c (summed feature 3; 26.2%), and C18:1 ω7c and/or C18:1 ω6c (summed feature 8; 14.4%) were predominant in strain S35T, similarly to other species of the genus Salinivibrio, or even of the genus Vibrio, both genera included in the family Vibrionaceae [51,52].

4. Conclusions

On the basis of the results of the polyphasic taxonomic analysis, it is concluded that strain S35T should be considered as a novel species of the genus Salinivibrio, for which the name Salinivibrio socompensis sp. nov. is proposed. We enclose the taxonomic description of this new species.
Description of Salinivibrio socompensis sp. nov.
Salinivibrio socompensis (so.com.pen’sis L. masc. adj. socompensis, belonging to lake Socompa, Argentina).
Cells are Gram-stain-negative, motile, non-endospore-forming, curved rods. Colonies on SW7.5 medium are circular, with entire edges, convex, 2–3 mm diameter, and cream-pink-pigmented. Moderately halophilic, able to grow at 3%–20% (w/v) NaCl (optimally at 7.0–7.5% [w/v] NaCl); pH 6.0–10.0 (with an optimum at 8.0); and 10–42 °C (optimally at 37 °C). Facultatively anaerobic. Positive for catalase, oxidase, hydrolysis of gelatin and DNA, methyl red test, and nitrate and nitrite reduction. Negative for the hydrolysis of starch, casein, aesculin, and Tween 80; production of indole; Simmon’s citrate; Voges–Proskauer; H2S production; ornithine, arginine, and lysine decarboxylases; urease; and phenylalanine deaminase. Acid is produced from D-fructose, D-galactose, glycerol, D-glucose, lactose, D-trehalose, and sucrose, but not from D-arabinose, maltose, mannitol, or D-xylose. Amygdalin, cellobiose, D-glucose, maltose, raffinose, sucrose, dulcitol, glycerol, starch, citrate, propionate, succinate, or valerate are used as sole carbon and energy source, but not D-arabinose, D- fructose, D-galactose, lactose, D-mannose, melezitose, melibiose, D-trehalose, butanol, ethanol, mannitol, methanol, propranolol, sorbitol, xylitol, acetate, benzoate, butyrate, fumarate, or hypurate. The amino acids alanine, arginine, and ornithine are used as sole carbon, nitrogen, and energy source, but not aspartic acid, cysteine, glutamine, L-phenylalanine, lysine, methionine, or serine. The major fatty acids are C16:0, C16:1 ω7c, and C16:1 ω6c, and C18:1 ω7c and/or C18:1 ω6c. The DNA G + C content is 49.5 mol% (genome).
The type strain is S35T (= CECT 9634T = BNM 0535T), isolated from the volcanic saline lake Socompa, Argentina.
The GenBank/EMBL/DDBJ accession numbers of the 16S rRNA gene sequence and complete genome sequence of the type strain S35T are HF953987 and AQOD00000000, respectively.

Supplementary Materials

The following are available online at https://0-www-mdpi-com.brum.beds.ac.uk/2076-2607/7/8/241/s1. Table S1. Genomes of the type strains of species of the genus Salinivibrio available in GenBank database used in this study, including their basic statistical information. Table S2. Cellular fatty acids composition (%) of strain S35T and the type strain of species and subspecies of the genus Salinivibrio. Figure S1. Growth curve for strain S35T at different salt concentrations. Culture media had the same composition than the medium used for routinely growth at 3, 6, 7, 7.5, 8, 9, 10, 15 and 20% (w/v) total salt, respectively. Figure S2. Growth curve for strain S35T at different pH values. Culture media had the same composition than the medium used for routinely growth and the pH was adjusted to 5, 6, 7, 7.5, 8, 9 and 10, respectively.

Author Contributions

M.E.F. performed the isolation of strain S35T. C.G. and C.L.-H. performed the phenotypic characterization. R.R.d.l.H., C.G., A.B.F., and C.S.-P. carried out the phylogenetic and genomic analyses. C.G. prepared the manuscript and the tables and figures. C.S.-P. and A.V. designed the experiments and edited the manuscript. All authors revised and contributed to the preparation of the manuscript.

Funding

This study was supported by the Spanish Ministry of Economy and Competitiveness (MINECO) through project CGL2017-83385-P, which included European (FEDER) funds, the Junta de Andalucía (Spain), and the Argentinean Ministry of Science and Technology, project PICT1707.

Acknowledgments

We thank A. Oren for his help on the nomenclature of the new species. C. Galisteo was recipient of a predoctoral fellowship from the Spanish Ministerio de Ciencia, Innovación y Universidades.

Conflicts of Interest

The authors declare that there are no conflicts of interest.

References

  1. Ventosa, A. Unusual micro-organisms from unusual habitats: Hypersaline environments. In Prokaryotic Diversity: Mechanisms and Significance; Cambridge University Press: Cambridge, UK, 2006; pp. 223–254. [Google Scholar]
  2. de la Haba, R.R.; Sánchez-Porro, C.; Márquez, M.C.; Ventosa, V. Taxonomy of halophiles. In Extremophiles Handbook; Springer: Heidelberg, Germany, 2010; pp. 255–309. [Google Scholar]
  3. Amoozegar, M.A.; Siroosi, M.; Atashgahi, S.; Smidt, H.; Ventosa, A. Systematics of haloarchaea and biotechnological potential of their hydrolytic enzymes. Microbiology 2017, 163, 623–645. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  4. Akira Obayashi, U.; Nobutsugu Hiraoka, M.; Keiko Kita, K.; Hiroshi Nakajima, O. Inventors process for producing restriction enzyme. U.S. Patent US 4724209, 9 February 1988. [Google Scholar]
  5. Fu, X.T.; Kim, S.M. Agarase: Review of major sources, categories, purification method, enzyme characteristics and applications. Mar. Drugs 2010, 8, 200–218. [Google Scholar] [CrossRef] [PubMed]
  6. Fernandes, S.; Geueke, B.; Delgado, O.; Coleman, J.; Hatti-Kaul, R. β-galactosidase from a cold-adapted bacterium: Purification, characterization and application for lactose hydrolysis. Appl. Microbiol. Biotechnol. 2002, 58, 313–321. [Google Scholar] [CrossRef] [PubMed]
  7. Ventosa, A. Salinivibrio. In Bergey’s Manual of Systematics of Archaea and Bacteria; Springer: New York, NY, USA, 2005; Volume 2, pp. 552–556. [Google Scholar]
  8. Smith, F.B. An investigation of a taint in rib bones of bacon. The determination of halophilic vibrios (n. spp.). Proc. R. Soc. Qd. 1938, 49, 29–52. [Google Scholar]
  9. Ventosa, A.; Quesada, E.; Rodríguez-Valera, F.; Ruiz-Berraquero, F.; Ramos-Cormenzana, A. Numerical taxonomy of moderately halophilic Gram-negative rods. J. Gen. Microbiol. 1982, 128, 1959–1968. [Google Scholar] [CrossRef]
  10. Kamekura, M.; Wallace, R.; Hipkiss, A.R.; Kushner, D.J. Growth of Vibrio costicola and other moderate halophiles in a chemically defined minimal medium. Can. J. Microbiol. 1985, 31, 870–872. [Google Scholar] [CrossRef] [PubMed]
  11. Oren, A. Diversity of halophilic microorganisms: Environments, phylogeny, physiology, and applications. J. Ind. Microbiol. Biotechnol. 2002, 28, 56–63. [Google Scholar] [CrossRef]
  12. Oren, A. Halophilic Microorganisms and their Environments. In Cellular Origin and Life in Extreme Habitats, vol. 5; Kluwer Academic Press: London, UK, 2002. [Google Scholar]
  13. Ventosa, A.; Nieto, J.J.; Oren, A. Biology of moderately halophilic aerobic bacteria. Microbiol. Mol. Biol. Rev. 1998, 62, 504–544. [Google Scholar]
  14. Mellado, E.; Moore, E.R.B.; Nieto, J.J.; Ventosa, A. Analysis of 16S rRNA gene sequences of Vibrio costicola strains: Description of Salinivibrio costicola gen. nov., comb. nov. Int. J. Syst. Bacteriol. 1996, 46, 817–821. [Google Scholar] [CrossRef]
  15. Huang, C.Y.; García, J.L.; Patel, B.K.C.; Cayol, J.L.; Baresi, L.; Mah, R.A. Salinivibrio costicola subsp. vallismortis subsp. nov., a halotolerant facultative anaerobe from Death Valley, and emended description of Salinivibrio costicola. Int. J. Syst. Evol. Microbiol. 2000, 50, 615–622. [Google Scholar]
  16. Romano, I.; Gambacorta, A.; Lama, L.; Nicolaus, B.; Giordano, A. Salinivibrio costicola subsp. alcaliphilus subsp. nov., a haloalkaliphilic aerobe from Campania Region (Italy). Syst. Appl. Microbiol. 2005, 28, 34–42. [Google Scholar] [PubMed]
  17. Amoozegar, M.A.; Schumann, P.; Hajighasemi, M.; Fatemi, A.Z.; Karbalaei-Heidari, H.R. Salinivibrio proteolyticus sp. nov., a moderately halophilic and proteolytic species from a hypersaline lake in Iran. Int. J. Syst. Evol. Microbiol. 2008, 58, 1159–1163. [Google Scholar] [CrossRef] [PubMed]
  18. Chamroensaksri, N.; Tanasupawat, S.; Akaracharanya, A.; Visessanguan, W.; Kudo, T.; Itoh, T. Salinivibrio siamensis sp. nov., from fermented fish (pla-ra) in Thailand. Int. J. Syst. Evol. Microbiol. 2009, 59, 880–885. [Google Scholar] [CrossRef] [PubMed]
  19. Romano, I.; Orlando, P.; Gambacorta, A.; Nicolaus, B.; Dipasquale, L.; Pascual, J.; Giordano, A.; Lama, L. Salinivibrio sharmensis sp. nov., a novel haloalkaliphilic bacterium from a saline lake in Ras Mohammed Park (Egypt). Extremophiles 2011, 15, 213–220. [Google Scholar] [CrossRef] [PubMed]
  20. López-Hermoso, C.; de la Haba, R.R.; Sánchez-Porro, C.; Ventosa, A. Salinivibrio kushneri sp. nov., a moderately halophilic bacterium isolated from salterns. Syst. Appl. Microbiol. 2018, 41, 159–166. [Google Scholar] [CrossRef]
  21. López-Hermoso, C.; de la Haba, R.R.; Sánchez-Porro, C.; Ventosa, A. Emended description of Salinivibrio proteolyticus, including Salinivibrio costicola subsp. vallismortis and five new isolates. Int. J. Syst. Evol. Microbiol. 2018, 68, 1599–1607. [Google Scholar] [CrossRef]
  22. López-Hermoso, C.; de la Haba, R.R.; Sánchez-Porro, C.; Papke, R.T.; Ventosa, A. Assessment of MultiLocus Sequence Analysis as a valuable tool for the classification of the genus Salinivibrio. Front. Microbiol. 2017, 8, 1107. [Google Scholar]
  23. Gorriti, M.F.; Dias, G.M.; Chimetto, L.A.; Trindade-Silva, A.E.; Silva, B.S.; Mesquita, M.M.; Gregoracci, G.B.; Farias, M.E.; Thompson, C.C.; Thompson, F.L. Genomic and phenotypic attributes of novel salinivibrios from stromatolites, sediment and water from a high altitude lake. BMC Genom. 2014, 15, 473. [Google Scholar] [CrossRef]
  24. Toneatti, D.M.; Albarracín, V.H.; Flores, M.R.; Polerecky, L.; Farías, M.E. Stratified bacterial diversity along physico-chemical gradients in high-altitude modern stromatolites. Front. Microbiol. 2017, 8, 646. [Google Scholar] [CrossRef]
  25. Kurth, D.; Amadio, A.; Ordoñez, O.F.; Albarracín, V.H.; Gärtnerm, W.; Farías, M.E. Arsenic metabolism in high altitude modern stromatolites revealed by metagenomic analysis. Sci. Rep. 2017, 7, 1024. [Google Scholar] [CrossRef]
  26. Farias, M.E.; Rascovan, N.; Toneatti, D.M.; Albarracin, V.H.; Flores, M.R.; Poiré, D.G.; Collavino, M.M.; Aguilar, A.M.; Vazquez, M.P.; Polerecky, L. The discovery of stromatolites developing at 3570 m above sea level in a high-altitude volcanic lake Socompa, Argentinean Andes. PLoS ONE 2013, 8, e53497. [Google Scholar] [CrossRef] [PubMed]
  27. Allwood, A.C.; Walter, M.R.; Kamber, B.S.; Marshall, C.P.; Burch, I.W. Stromatolite reef from the early Archaean era of Australia. Nature 2006, 441, 714–718. [Google Scholar] [CrossRef] [PubMed]
  28. Burne, R.V.; Moore, L.S. Microbialites; organosedimentary deposits of benthic microbial communities. Palaios 1987, 2, 241–254. [Google Scholar] [CrossRef]
  29. Schopf, J.W. Fossil evidence of Archaean life. Philos. Trans. R. Soc. Lond. B Biol. Sci. 2006, 361, 869–885. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  30. Sambrook, J.; Russell, D.W. Molecular Cloning: A Laboratory Manual; Laboratory Press: Cold Spring Harbor, NY, USA, 2001. [Google Scholar]
  31. Yoon, S.H.; Ha, S.M.; Kwon, S.; Lim, J.; Kim, Y.; Seo, H.; Chun, J. Introducing EzBioCloud: A taxonomically united database of 16S rRNA and whole genome assemblies. Int. J. Syst. Evol. Microbiol. 2017, 67, 1613–1617. [Google Scholar] [PubMed]
  32. Ludwig, W.; Strunk, O.; Westram, R.; Richter, L.; Meier, H.; Yadhukumar; Buchner, A.; Lai, T.; Steppi, S.; Jobb, G.; et al. ARB: A software environment for sequence data. Nucleic Acids Res. 2004, 32, 1363–1371. [Google Scholar] [CrossRef] [PubMed]
  33. Saitou, N.; Nei, M. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 1987, 4, 406–425. [Google Scholar] [PubMed]
  34. Fitch, W.M. Toward defining the course of evolution: Minimum change for a specific tree topology. Syst. Biol. 1971, 20, 406–416. [Google Scholar] [CrossRef]
  35. Felsenstein, J. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 1981, 17, 368–376. [Google Scholar] [CrossRef]
  36. Felsenstein, J. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 1985, 39, 783–791. [Google Scholar] [CrossRef]
  37. Chun, J.; Oren, A.; Ventosa, A.; Christensen, H.; Arahal, D.R.; da Costa, M.S.; Rooney, A.P.; Yi, H.; Xu, X.W.; De Meyer, S.; et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int. J. Syst. Evol. Microbiol. 2018, 68, 461–466. [Google Scholar] [CrossRef] [PubMed]
  38. Rodríguez-R, L.M.; Konstantinidis, K.T. The enveomics collection: A toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ. Prepr. 2016, 4, e1900v1. [Google Scholar]
  39. Edgar, R.C. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2002, 32, 1792–1797. [Google Scholar] [CrossRef] [PubMed]
  40. Price, M.N.; Dehal, P.S.; Arkin, A.P. FastTree 2–Approximately maximum-likelihood trees for large alignments. PLoS ONE 2010, 5, e9490. [Google Scholar] [CrossRef] [PubMed]
  41. Jones, D.T.; Taylor, W.R.; Thornton, J.M. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 1992, 8, 275–282. [Google Scholar] [CrossRef] [PubMed]
  42. Shimodaira, H.; Hasegawa, M. Multiple comparisons of loglikelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 1999, 16, 1114–1116. [Google Scholar] [CrossRef]
  43. Richter, M.; Rosselló-Móra, R.; Glöckner, F.O.; Peplies, J. JSpeciesWS: A web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016, 32, 929–931. [Google Scholar] [CrossRef]
  44. Lee, I.; Kim, Y.O.; Park, S.C.; Chun, J. OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int. J. Syst. Evol. Microbiol. 2015, 66, 1100–1103. [Google Scholar] [CrossRef] [PubMed]
  45. Meier-Kolthoff, J.P.; Auch, A.F.; Klenk, H.-P.; Göker, M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform. 2013, 14, 60. [Google Scholar] [CrossRef] [PubMed]
  46. Cowan, S.T.; Steel, K.J. Manual for the Identification of Medical Bacteria, 3rd ed.; Cambridge University Press: London, UK, 1965. [Google Scholar]
  47. Kovacs, N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956, 178, 703. [Google Scholar] [CrossRef] [PubMed]
  48. Koser, S.A. Utilization of the salts of organic acids by the colon-aerogenes group. J. Bacteriol. 1923, 8, 493–523. [Google Scholar] [PubMed]
  49. Sasser, M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids; MIDI Technical Note 101; MIDI Inc.: Newark, DE, USA, May 1990. [Google Scholar]
  50. Kim, M.; Oh, H.S.; Park, S.C.; Chun, J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int. J. Syst. Evol. Microbiol. 2014, 64, 346. [Google Scholar] [CrossRef] [PubMed]
  51. Doi, H.; Osawa, I.; Adachi, H.; Kawada, M. Vibrio japonicus sp. nov., a novel member of the Nereis clade in the genus Vibrio isolated from the coast of Japan. PLoS ONE 2017, 12, e0172164. [Google Scholar] [CrossRef] [PubMed]
  52. Paek, J.; Shin, J.H.; Shin, Y.; Park, I.S.; Kim, H.; Kook, J.K.; Kang, S.S.; Kim, D.S.; Park, K.H.; Chang, Y.H. Vibrio injenensis sp. nov., isolated from human clinical specimens. Antonie Van Leeuwenhoek 2017, 110, 145–152. [Google Scholar] [CrossRef] [PubMed]
Microorganisms 07 00241 g001 550
Figure 1. Neighbor-joining phylogenetic tree based on the 16S rRNA gene sequence comparison, showing the relationships between strain S35T and other members of the genus Salinivibrio and the family Vibrionaceae. Filled circles indicate nodes that were also obtained in trees based on maximum parsimony and maximum likelihood algorithms. Bootstrap values over 70% are shown at the nodes. The accession numbers are shown in parenthesis. Bar, 0.01 substitutions per nucleotide position.
Figure 1. Neighbor-joining phylogenetic tree based on the 16S rRNA gene sequence comparison, showing the relationships between strain S35T and other members of the genus Salinivibrio and the family Vibrionaceae. Filled circles indicate nodes that were also obtained in trees based on maximum parsimony and maximum likelihood algorithms. Bootstrap values over 70% are shown at the nodes. The accession numbers are shown in parenthesis. Bar, 0.01 substitutions per nucleotide position.
Microorganisms 07 00241 g001
Microorganisms 07 00241 g002 550
Figure 2. Approximately maximum likelihood tree based on the nucleotide sequences of the core genome (1265 genes) of strain S35T and the type strains of the genus Salinivibrio. Bootstrap values over 70% are shown at the nodes. Bar, 0.02 substitutions per nucleotide position.
Figure 2. Approximately maximum likelihood tree based on the nucleotide sequences of the core genome (1265 genes) of strain S35T and the type strains of the genus Salinivibrio. Bootstrap values over 70% are shown at the nodes. Bar, 0.02 substitutions per nucleotide position.
Microorganisms 07 00241 g002
Table
Table 1. Average nucleotide identity (ANI), calculated using three different methods (ANIb, ANIm, and orthoANI) and in silico DNA–DNA hybridization (GDDC) values (%) for strain S35T and the type strains of the species and subspecies of the genus Salinivibrio.
Table 1. Average nucleotide identity (ANI), calculated using three different methods (ANIb, ANIm, and orthoANI) and in silico DNA–DNA hybridization (GDDC) values (%) for strain S35T and the type strains of the species and subspecies of the genus Salinivibrio.
ANIbANImorthoANIGGDC
StrainsStrain S35T
S. costicola subsp. costicola LMG 11651T87.888.988.135
S. costicola subsp. alcaliphilus DSM 16359T87.988.688.235
S. proteolyticus DSM 19052T78.184.678.622
S. sharmensis DSM 18182T80.484.580.823
S. siamensis JCM 14472T80.684.680.924
S. kushneri AL184T80.684.781.024
Table
Table 2. Differential characteristics between strain S35T and the type strains of the closely related species and subspecies of the genus Salinivibrio.
Table 2. Differential characteristics between strain S35T and the type strains of the closely related species and subspecies of the genus Salinivibrio.
Characteristic1234567
NaCl range (% w/v)3–200.5–20 a2–25 b1–17 c1–22 d6–16 e2–20 f
NaCl optimum (% w/v)7–7.510 a10 b5 c10 d10 e7.5 f
pH range6–105–10 a7–10.5 b5–9.5 c5–9 d6–10 e5–10 f
pH optimum87.5 a9 b8 c8 d9 e7.2–7.4 f
Temperature range (°C) 10–425–45 a10–40 b10–45 c10–47 d25–40 e17–49 f
Temperature optimum (°C)3737 a30 b35 c37 d35 e37 f
Hydrolysis of starch−+−++++
Hydrolysis of Tween 80−+−+−−−
Hydrolysis of casein−−+−−+−
Hydrolysis of aesculin−++−−+−
Production of indole−−−−+−−
Methyl red test+−−−−−−
Nitrate and nitrite reduction+++−+++
Arginine decarboxylase−++−++−
Acid production from carbohydrates:
  D-fructose+++−+++
  D-galactose+−+−−−−
  Lactose+−+−−−−
  Maltose−−++++−
  Mannitol−+++++−
  Sucrose+++++−+
  D-xylose−++−−−−
Utilization as sole carbon and energy source of the:
  Amygdalin+−−+++−
  D-arabinose−−−++−−
  Cellobiose+−−+++−
  D-fructose−−−−++−
  D-glucose+−−++++
  Maltose+−−++++
  D-mannose−++++++
  Melibiose−−+−−−−
  Sucrose+−−++++
  Starch+−−+++−
  D-trehalose−−−++−−
  D-xylose+−−+++−
  Butanol−++−−−−
  Ethanol−−+++++
  Glycerol+−−++++
  Mannitol−++++++
  Methanol−−+−+−+
  Propranolol−−+−+++
  Sorbitol−−−+−−−
  Xylitol−−−−++−
  Benzoate−+−+++−
  Butyrate−−−++++
  Citrate+−−+−+−
  Fumarate−−−+++−
  Hypurate−−−++++
  Succinate+−−++−+
  Valerate+---+++
Utilization as sole carbon, nitrogen and energy source of:
  Alanine+--++++
  Arginine+--++++
  Aspartic acid---++-+
  Cysteine---++-+
  Glutamine---++--
  L-phenylalanine---++++
  Ornithine+--++++
  Serine----+--
1. Strain S35T; 2. S. costicola subsp. costicola DSM 11403T; 3. S. costicola subsp. alcaliphilus DSM 16359T; 4. S. proteolyticus DSM 19052T; 5. S. siamensis JCM 14472T; 6. S. sharmensis DSM 18182T; 7. S. kushneri AL184T. All strains were positive for catalase, oxidase, and hydrolysis of DNA and gelatine, and negative for Voges–Proskauer, Simmon’s citrate, H2S production, ornithine decarboxylase, lysine decarboxylase, urease, and phenylalanine deaminase. Acid was produced from glycerol, D-glucose, and D-trehalose but not from D-arabinose. All strains were positive for raffinose, dulcitol, and propionate as sole carbon and energy source, and negative for D-galactose, lactose, melezitose, and acetate, along with lysine and methionine as sole carbon, nitrogen, and energy source. a Mellado et al. [14]. b Romano et al. [16]. c Amoozegar et al. [17]. d Chamroensaksri et al. [18]. e Romano et al. [19]. f López-Hermoso et al. [20].

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Galisteo, C.; Sánchez-Porro, C.; de la Haba, R.R.; López-Hermoso, C.; Fernández, A.B.; Farias, M.E.; Ventosa, A. Characterization of Salinivibrio socompensis sp. nov., A New Halophilic Bacterium Isolated from the High-Altitude Hypersaline Lake Socompa, Argentina. Microorganisms 2019, 7, 241. https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms7080241

AMA Style

Galisteo C, Sánchez-Porro C, de la Haba RR, López-Hermoso C, Fernández AB, Farias ME, Ventosa A. Characterization of Salinivibrio socompensis sp. nov., A New Halophilic Bacterium Isolated from the High-Altitude Hypersaline Lake Socompa, Argentina. Microorganisms. 2019; 7(8):241. https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms7080241

Chicago/Turabian Style

Galisteo, Cristina, Cristina Sánchez-Porro, Rafael R. de la Haba, Clara López-Hermoso, Ana B. Fernández, María E. Farias, and Antonio Ventosa. 2019. "Characterization of Salinivibrio socompensis sp. nov., A New Halophilic Bacterium Isolated from the High-Altitude Hypersaline Lake Socompa, Argentina" Microorganisms 7, no. 8: 241. https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms7080241

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