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Int J Syst Evol Microbiol 57 (2007), 409-413; DOI  10.1099/ijs.0.64375-0
© 2007 International Union of Microbiological Societies

Oceanobacillus profundus sp. nov., isolated from a deep-sea sediment core

Yoon-Gon Kim1, Dong Han Choi1,{dagger}, Sangmin Hyun2 and Byung Cheol Cho1

1 School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, San 56-1 Shillim-dong, Kwanak-gu, Seoul 151-742, Republic of Korea
2 South Sea Institute/Korea Ocean Research and Development Institute (KORDI), 391 Jang mok-ri, Jangmok-myon, Geoje 656-830, Republic of Korea

Correspondence
Byung Cheol Cho
bccho{at}snu.ac.kr


   ABSTRACT
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A halotolerant, facultatively alkaliphilic bacterium, designated CL-MP28T, was isolated from the surface of a sediment core sample collected at a depth of 2247 m in the Ulleung Basin of the East Sea, Korea. Phylogenetic analysis of the 16S rRNA gene sequence of strain CL-MP28T revealed an affiliation with the genus Oceanobacillus. The sequence similarities between the isolate and type strains of members of the genus Oceanobacillus were in the range 95.0–96.0 %, indicating that strain CL-MP28T represented a novel species within the genus. The strain was found to be Gram-positive, rod-shaped and motile by means of peritrichous flagella and was shown to produce ellipsoidal spores. The strain was strictly aerobic and able to grow with NaCl at concentrations in the range 0–14 % (w/v) at pH 7.5. The strain grew at temperatures of 15–42 °C and at pH 6.5–9.5. The major fatty acids were anteiso-C15 : 0 (64.9 %), anteiso-C17 : 0 (11.9 %) and iso-C16 : 0 (7.7 %). The major isoprenoid quinone was MK-7. The DNA G+C content was 40.2 mol%. According to the 16S rRNA gene sequence, DNA–DNA relatedness and physiological data and the fatty acid composition, CL-MP28T could be assigned to the genus Oceanobacillus, but is distinguishable from the recognized species of this genus. Strain CL-MP28T therefore represents a novel species within the genus Oceanobacillus, for which the name Oceanobacillus profundus sp. nov. is proposed. The type strain is CL-MP28T (=KCCM 42318T=DSM 18246T).

The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain CL-MP28T is DQ386635.

Details of the whole-cell fatty acid compositions of strain CL-MP28T and related Oceanobacillus species are available in a supplementary table in IJSEM Online.

{dagger}Present address: Marine Environmental Research Department, KORDI, Ansan 426-744, Republic of Korea Back


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The genus Oceanobacillus was first proposed with the single species Oceanobacillus iheyensis, which was isolated from a deep-sea mud sample collected at a depth of 1050 m on the Iheya Ridge of the Nansei Islands and demonstrated an extremely halotolerant and facultatively alkaliphilic phenotype (Lu et al., 2001Go). The genus description was later emended with the isolation of a halotolerant obligate alkaliphile, Oceanobacillus oncorhynchi, isolated from the skin of a rainbow trout (Oncorhynchus mykiss) (Yumoto et al., 2005Go). Recently, [Virgibacillus] picturae, isolated from deteriorated mural paintings (Heyrman et al. 2003Go), was reclassified as Oceanobacillus picturae (Lee et al., 2006Go). Thus, the genus Oceanobacillus currently comprises three species, comprising motile, Gram-positive rods that produce ellipsoidal endospores within swollen sporangia (Lee et al., 2006Go).

In this study, a novel strain, CL-MP28T, was isolated from the surface of a sediment core sample collected at depth of 2247 m in the Ulleung Basin of the East Sea, Korea. The sediment slurry was spread on a plate containing marine agar 2216 (Difco) and incubated at 20 °C for 2 weeks. Strain CL-MP28T was isolated on the plate and subsequently purified on marine agar 2216 at 30 °C four times. The strain was maintained at –80 °C both on marine agar 2216 at 4 °C and in marine broth 2216 (Difco) supplemented with 30 % (v/v) glycerol.

The 16S rRNA gene was amplified from a single colony by a PCR with Taq DNA polymerase (Bioneer) and primers 27F and 1492R (Lane, 1991Go). The PCR product was purified using an AccuPrep PCR purification kit (Bioneer). Sequencing of the 16S rRNA gene was performed with an Applied Biosystems automatic sequencer (ABI3730XL) at Macrogen Corp. (Seoul, Korea). An almost-complete 16S rRNA gene sequence (1354 bp) of strain CL-MP28T was obtained. This sequence was compared with those available in GenBank by using BLASTN (Altschul et al., 1990Go) searches. The sequence of strain CL-MP28T was manually aligned with those of the type strains of the three Oceanobacillus species and with those of the type species of other genera in the family Bacillaceae, obtained from GenBank and the Ribosomal Database Project (Cole et al., 2003Go) databases using known 16S rRNA secondary structure information. Phylogenetic trees were obtained by using the neighbour-joining (Saitou & Nei, 1987Go), maximum-parsimony (Fitch, 1971Go) and maximum-likelihood (Felsenstein, 1981Go) methods. An evolutionary distance matrix for the neighbour-joining method was generated according to the model of Jukes & Cantor (1969)Go. The robustness of the tree topologies was assessed by using bootstrap analyses based on 1000 replications (for the neighbour-joining and maximum-parsimony methods) or 100 replications (for the maximum-likelihood method). Alignment analyses were carried out using the jPHYDIT program (Jeon et al., 2005Go), and phylogenetic analysis were carried out using MEGA3 (Kumar et al., 2004Go) and PAUP* 4.0 (Swofford, 1998Go). Likelihood parameters were estimated by means of the hierarchical ratio tests in MODELTEST, version 3.04 (Posada & Crandall, 1998Go). The sequence similarities indicated that the closest relatives of strain CL-MP28T were O. iheyensis JCM 11309T (95.96 %) and O. oncorhynchi R-2T (95.48 %). Phylogenetic analyses based on the 16S rRNA gene sequence showed that strain CL-MP28T formed a robust cluster with species of the genus Oceanobacillus (Fig. 1Go). Thus, it is clear that our isolate belongs to the genus Oceanobacillus. However, the low levels of similarity (95.0–96.0 %) between the 16S rRNA gene sequence of the novel isolate and those of previously described species of the genus Oceanobacillus indicated that strain CL-MP28T represents a novel species of the genus (Stackebrandt & Goebel, 1994Go; Rosselló-Mora & Amann, 2001Go). The relatedness of the genomic DNA was determined by means of dot-blot hybridization. Probe DNA labelling was performed using a nick translation kit (Roche), and hybridization and detection were done using the DIG labelling and detection kit (Roche) according to the manufacturer's instruction. The level of DNA–DNA relatedness between strain CL-MP28T and O. iheyensis KCTC 3954T was 24.7 %, while that for O. oncorhynchi R-2T was 17.5 %. These values are below the currently accepted limit for DNA relatedness (70 %) for the phylogenetic definition of a species (Stackebrandt & Goebel, 1994Go) and therefore provide evidence that our isolate (CL-MP28T) represents a novel species of the genus Oceanobacillus. The DNA G+C content was determined by HPLC analysis (Tamaoka & Komagata, 1984Go) at the Korean Culture Center of Microorganisms (Seoul, Korea) and was found to be 40.2 mol%.


Figure 1
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  		Fig. 1. Neighbour-joining phylogenetic tree, based on 16S rRNA gene sequences, showing the position of strain CL-MP28T with respect to Oceanobacillus species and related taxa. Only bootstrap percentages above 60 % are shown (1000 resamplings) at branching points. Filled circles indicate that the corresponding nodes were also recovered in the maximum-likelihood and maximum-parsimony trees. Bar, 0.02 nucleotide substitutions per site.

 
For the phenotypic and chemotaxonomic analyses, strain CL-MP28T was routinely cultivated on PYA medium (1 % peptone, 0.5 % yeast extract, 0.1 % K2HPO4, 0.02 % MgSO4.7H2O, 3 % NaCl, 1.5 % Bacto agar, pH 7.5; Lu et al., 2001Go). Gram-staining was performed as described by Smibert & Krieg (1994)Go. The cell morphology was examined using phase-contrast microscopy and transmission electron microscopy (EX2; JEOL) with cells grown at 30 °C on a PYA agar plate. Electron microscopy showed that the cells were peritrichously flagellated rods (0.2–0.4x0.8–2 µm). Anaerobic growth was checked on PYA using the GasPak anaerobic system (BBL) for 12 days. Hydrolysis of casein, DNA and Tweens 40, 60 and 80 and catalase and oxidase activities were determined according to the protocols described by Barrow & Feltham (1993)Go. Other enzyme activities were also assayed using the API 20NE system (bioMérieux) according to the manufacturer's instruction, except that cell suspensions were prepared using a 3 % (w/v) NaCl solution. Acid production from various carbohydrates was determined by employing the API 50 CH system (bioMérieux) according to the manufacturer's instructions. All suspension media were supplemented with 3 % NaCl (final concentration). For the API 20NE and API 50 CH analyses, O. iheyensis KCTC 3954T was used as a reference strain. The temperature range for growth was determined using PYA broth (the same composition as PYA but without the agar) incubated at various temperatures in the range 5–40 °C (using increments of 5 °C) and at 40–45 °C (using increments of 1 °C). PYA broth and PYA broth containing 100 mM NaHCO3/Na2CO3 were used, respectively, for growth experiments at pH 6.0–8.5 and pH 9.0–10.5. Final pH was adjusted with HCl or NaOH solution. The NaCl concentrations allowing growth of strain CL-MP28T were determined by using PYA broth supplemented with various NaCl concentrations (0, 1, 2, 3, 5, 7, 8, 10, 13, 15, 18, 20, 21, 22 and 25 %, w/v). All media were sterilized with sterile 0.22 µm pore-size syringe filters (Adventec MFS). Growth at different pHs, NaCl concentrations and temperatures was measured by monitoring changes in OD600 over time. All of the experiments were performed under aerobic conditions. The isolate was revealed to be Gram-positive and to produce ellipsoidal spores positioned terminally within swollen sporangia. The acid production from amygdalin demonstrated by strain CL-MP28T differentiates it from the recognized species of the genus Oceanobacillus; furthermore, the species of the genus can be clearly distinguished from each other using a minimal combination of phenotypic characteristics (beta-galactosidase and gelatinase) (Table 1Go). The morphological, physiological and biochemical characteristics of the isolate are given in Table 1Go and in the species description.


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  		Table 1. Differential phenotypic characteristics of strain CL-MP28T and related Oceanobacillus species

Strains: 1, CL-MP28T (this study); 2, O. iheyensis KCTC 3954T (unless indicated, data from Lu et al., 2001Go); 3, O. oncorhynchi R-2T (Yumoto et al., 2005Go); 4, O. picturae KCTC 3821T (Heyrman et al., 2003Go). +, Positive; –, negative; W, weakly positive; VW, very weakly positive; ND, not determined; All strains are motile, Gram-positive, oxidase- and catalase-positive and produce ellipsoid spores and are negative for indole production. None of the strains produced acid from D-arabinose, L-rhamnose, myo-inositol, L-fucose or 5-keto-D-gluconate.

 
Isoprenoid quinones were isolated according to Minnikin et al. (1984)Go and analysed by HPLC as described by Collins (1985)Go. The major isoprenoid quinone in CL-MP28T is MK-7. The fatty acid methyl esters present in whole cells grown on PYA at 27 °C for 48 h were analysed by gas chromatography according to the instructions of the Microbial Identification System (MIDI) at the Korean Culture Center of Microorganisms. The fatty acid profile of CL-MP28T was dominated by branched fatty acids: anteiso-C15 : 0 (64.9 %), anteiso-C17 : 0 (11.9 %), iso-C16 : 0 (7.7 %), iso-C14 : 0 (5.6 %) and iso-C15 : 0 (3.8 %) (see Supplementary Table S1 available in IJSEM Online). The relative proportions of the predominant fatty acids in CL-MP28T were different from those of O. iheyensis KCTC 3954T and O. oncorhynchi R-2T, but were relatively similar to those of O. picturae KCTC 3821T. However, the absence of summed feature 7 (C18 : 1{omega}7c, C18 : 1{omega}9t and/or C18 : 1{omega}12t), the relatively low optimal NaCl concentration for growth and the lack of growth at temperatures below 15 °C of strain CL-MP28T differentiate it from O. picturae KCTC 3821T.

Some phenotypic characteristics of strain CL-MP28T, e.g. acid production from amygdalin and a relatively low optimal NaCl concentration for growth, clearly distinguish the novel isolate from previously described species of the genus Oceanobacillus. Furthermore, the DNA–DNA relatedness data supported our suggestion that strain CL-MP28T should be classified within a novel species within the genus Oceanobacillus (Stackebrandt & Goebel, 1994Go). In conclusion, phylogenetic analyses based on 16S rRNA gene sequences, DNA–DNA relatedness and physiological and chemotaxonomic features suggest that strain CL-MP28T represents a novel species of the genus Oceanobacillus, for which the name Oceanobacillus profundus sp. nov. is proposed.

Description of Oceanobacillus profundus sp. nov.
Oceanobacillus profundus (pro.fun'dus. L. masc. adj. profundus from the deep).

Cells are Gram-positive, peritrichously flagellated, straight rods that are approximately 0.2–0.4x0.8–2 µm in size and produce ellipsoidal spores terminally positioned within swollen sporangia. Colonies are circular and creamy white in colour. Obligately aerobic or facultatively alkaliphilic. Grows at 15–42 °C (optimum 35 °C) and pH 6.5–9.5 (optimum pH 7.5–8.5). Catalase- and oxidase-positive. The NaCl range for growth is 0–14 % (w/v) at pH 7.5 (optimum 1–3 %). Nitrate reductase, beta-galactosidase (ONPG) and DNase activities are present and hydrolysis of gelatin, aesculin, casein and Tweens 40 and 60 is demonstrated. Indole production, urease and hydrolysis of Tween 80 are absent. Acids are produced from glycerol, D-xylose, D-glucose, D-fructose, D-mannose, mannitol, N-acetylglucosamine, amygdalin, maltose, lactose, D-trehalose and D-turanose, but not from D-arabinose, galactose, L-rhamnose, myo-inositol, D-melibiose, glycogen or L-fucose. The DNA G+C content is 40.2 mol%. The major fatty acids are anteiso-C15 : 0 (64.9 %), anteiso-C17 : 0 (11.9 %), iso-C16 : 0 (7.7 %), iso-C14 : 0 (5.6 %), iso-C15 : 0 (3.8 %) and C16 : 0 (2.5 %). The major isoprenoid quinone is MK-7.

The type strain, CL-MP28T (=KCCM 42318T=DSM 18246T), was isolated from the surface of a sediment core sample collected at a depth of 2247 m in the Ulleung Basin of the East Sea, Korea.


   ACKNOWLEDGEMENTS
 
This work was supported, in part, by the BK21 project of the Korean Government and a KORDI project (PG43802).


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