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1 School of Biological Sciences, Seoul National University, 56-1 Shillim-dong, Kwanak-gu, Seoul 151-742, Republic of Korea
2 Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Yusung, PO Box 115, Taejon 305-600, Republic of Korea
Correspondence
Jongsik Chun
jchun{at}snu.ac.kr
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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-Proteobacteria, designated JC2042T and JC2043T, were obtained from a sediment sample of getbol, the Korean tidal flat. Comparative 16S rDNA sequence studies revealed that the test strains were related most closely to the type strains of the genera Alteromonas (93·5–95·5 %) and Glaciecola (91·1–93·3 %). Phylogenetic analyses demonstrated that strains JC2042T and JC2043T formed a distinct monophyletic clade within the family Alteromonadaceae and clustered distantly with the genera Alteromonas and Glaciecola. Physiological, biochemical and chemotaxonomic data also indicated that the two getbol isolates were significantly different from members of these two genera and others with validly published names. Cells were rod-shaped and motile with a polar flagellum. The major isoprenoid quinone was Q8. The predominant cellular fatty acids were C16 : 0, C18 : 1
7c and a mixture of C16 : 17c and iso-C15 : 0 2-OH. DNA G+C contents were 48–54 mol%. On the basis of this polyphasic study, Aestuariibacter gen. nov. is proposed with two novel species, Aestuariibacter salexigens sp. nov. (type strain, JC2042T=IMSNU 14006T=KCTC 12042T=DSM 15300T) and Aestuariibacter halophilus sp. nov. (type strain, JC2043T=IMSNU 14007T=KCTC 12043T=DSM 15266T). Aestuariibacter salexigens is the type species of the genus. In addition, an emended description of Alteromonas macleodii is proposed.
The GenBank/EMBL/DDBJ accession numbers for the 16S rDNA sequences of strains JC2042T and JC2043T are AY207502 and AY207503, respectively.
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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encompasses the genera Alteromonas, Pseudoalteromonas, Idiomarina and Colwellia. The genera Glaciecola Bowman et al. 1998 and Thalassomonas Macián et al. 2001 are phylogenetically closely related to Alteromonas macleodii and also should be regarded as members of this family. All strains of these genera are widespread inhabitants of marine environments and have been isolated from diverse marine sources. In this study, two bacterial strains that were isolated from the sediment of getbol (the Korean tidal flat) were the subject of a taxonomic investigation. On the basis of polyphasic evidence, the test strains formed a novel genus in the family Alteromonadaceae, for which the name Aestuariibacter gen. nov. is proposed. |
METHODS |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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), spread onto a plate that contained marine agar 2216 (MA; Difco) and MR2A [R2A (Difco) supplemented with artificial sea salts (Sigma)] and incubated at 25 °C for 3 weeks. Strains JC2042T and JC2043T were isolated on MA and MR2A, respectively, and were cultured routinely on MA at 30 °C. Alteromonas macleodii LMG 2843T and Glaciecola punicea DSM 14233T were used as reference strains and were grown on MA at 30 and 10 °C, respectively.
Molecular systematics.
Bacterial DNA preparation and PCR amplification and sequencing of 16S rDNA were carried out as described previously (Chun & Goodfellow, 1995). The resultant sequences of strains JC2042T and JC2043T were aligned manually against sequences obtained from GenBank. Phylogenetic trees were inferred by using the Fitch–Margoliash (Fitch & Margoliash, 1967), maximum-likelihood (Felsenstein, 1993), maximum-parsimony (Fitch, 1971) and neighbour-joining (Saitou & Nei, 1987) methods. Evolutionary distance matrices were generated according to Jukes & Cantor (1969). Resultant tree topologies were evaluated by bootstrap analyses (Felsenstein, 1985) based on 1000 resamplings. Alignment and phylogenetic analyses were carried out by using the PHYDIT program (available at http://plaza.snu.ac.kr/
jchun/phydit/) and PAUP 4.0 (Swofford, 1998), as described previously (Chun et al., 2000).
Morphology and physiological properties.
The methods, as well as compositions of media used in this study, have been described previously (Yi et al., 2003). Only additional methods or significant modifications are given below.
Carbon source utilization was tested on basal medium (BM; Baumann et al., 1972) and BM supplemented with 0·01 or 0·1 % yeast extract. Oxidation or fermentation of carbohydrates (D-glucose, N-acetylglucosamine and inulin) was examined by using fermentation media (Baumann et al., 1971) and modified oxidation–fermentation medium (MOF; Leifson, 1963). Strips of the API ZYM and 20NE kits (bioMérieux) were inoculated with cell suspensions in half-strength ASW and incubated at 30 °C, except for G. punicea ACAM 611T, for which tests were done at both 10 and 30 °C. Catalase reaction was determined by 3 % (v/v) hydrogen peroxide. Specific component requirements for ASW (NaCl, 23·5 g; MgCl2, 4·9 g; Na2SO4, 3·9 g; CaCl2.2H2O, 1·1 g; KCl, 0·66 g; NaHCO3, 0·19 g; KBr, 0·096 g; H3BO3, 0·026 g; SrCl2, 0·024 g; NaF, 0·003 g; distilled water, 1 l) were tested by using synthetic MA (10 g Bacto peptone, 2 g yeast extract, 0·2 g ferric citrate and 15 g Bacto agar in 1 l distilled water) supplemented with various combination of artificial sea salts. Growth in synthetic media was determined after 3 days at 30 °C.
Chemotaxonomy.
Chemotaxonomic characteristics were determined from cells grown at 30 °C for 2 days on MA or in marine broth 2216 (MB; Difco). Analysis of fatty acid methyl esters was performed by GLC according to the instructions of the Microbial Identification system (MIDI). Isoprenoid quinones were isolated according to Minnikin et al. (1984) and analysed by HPLC (Waters) as described by Collins (1985). DNA G+C content was determined by HPLC of deoxyribonucleosides as described by Mesbah et al. (1989), using a reverse-phase column (Supelcosil LC-18-S; Supelco).
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RESULTS AND DISCUSSION |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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-Proteobacteria. The newly determined sequences were then aligned manually against representatives of the -Proteobacteria, based on bacterial 16S rRNA secondary structure. Regions available for all sequences were the domains used to construct the phylogenetic tree (positions 35–1459 of the Escherichia coli 16S rDNA sequence), excluding positions that were likely to show ambiguous alignment (positions 75–95, 204–213, 841–846, 1132–1141 and 1448–1454). Sequence similarity between strains JC2042T and JC2043T was 96·6 %, which indicated that these strains belonged to different species (Stackebrandt & Goebel, 1994). The highest similarity values of our isolates to species with validly published names were as follows: Alteromonas marina SW-47T (93·8 %), Alteromonas macleodii DSM 6062T (93·5 %), G. punicea ACAM 611T (93·3 %) and Glaciecola pallidula ACAM 615T (91·1 %) for strain JC2042T, and Alteromonas marina SW-47T (95·5 %), Alteromonas macleodii DSM 6062T (95·3 %), G. pallidula ACAM 615T (92·6 %) and G. punicea ACAM 611T (92·2 %) for strain JC2043T.
This relationship between our isolates and other genera was also highlighted in the phylogenetic trees, as shown in Fig. 1. Strains JC2042T and JC2043T formed a monophyletic clade with a bootstrap value of 77 % that was supported by all tree-making methods employed in this study. The genus Alteromonas also formed a strong monophyletic clade (bootstrap value of 100 %) and was recovered as a sister group to the monophyletic clade that contained the getbol isolates. Members of the genera Alteromonas and Glaciecola and the two test strains were recovered in a significant monophyletic clade with 100 % bootstrap support; the branch pattern within the clade was identical in all phylogenetic trees. On the basis of sequence similarities and phylogenetic analysis, it is clear that our isolates cannot be assigned to either Alteromonas or Glaciecola, and should merit a novel genus in the family Alteromonadaceae.
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) and SMM (Shioi's Marine medium; Shiba, 1981). Both strains grew on MA at pH 6–11; optimal growth occurred at pH 7–8. Strain JC2042T grew at 20–40 °C and the optimum was 35 °C. Strain JC2043T grew at 15–40 °C and the optimum was 40 °C. These two strains were common in strict halophilicity, but exhibited slightly different requirements of sea salts. Strain JC2043T showed growth on 0·5–10 % (w/v) artificial sea salts (Sigma)-based media (the optimum being 2–3 % sea salts) and showed less abundant growth on 1–8 % (w/v) NaCl-containing media (the optimum being 5–6 % NaCl). Similarly, strain JC2042T required 1–10 % (w/v) artificial sea salts-based media for growth (the optimum being 2–6 % sea salts), but completely failed to grow on modified CSY-3 that contained 0–15 % (w/v) NaCl alone. Strain JC2042T showed no growth when NaCl was not added to synthetic MA and very weak growth when any of several sea salts components, namely MgCl2, NaHCO3, H3BO3 and NaF, was omitted. However, growth of strain JC2043T only decreased a little without NaCl, H3BO3 or NaF. No growth was detected under anaerobic conditions, created by a GasPack system (BBL). Strain JC2042T showed a marked loss of viability within 7 days on MA at 30 °C.
Morphological properties
Cellular and colonial morphologies of cells grown on MA at 30 °C for 2 days were observed. Colonies of both strains did not swarm or luminesce on the agar media tested and spore formation was not observed. Cellular and colonial morphologies are given in the species descriptions.
Physiological and biochemical properties
Physiological and biochemical properties of strains JC2042T and JC2043T, as well as some other characteristics, are given in the genus and species descriptions. A summary of the major differential properties between the test strains and phylogenetically related species is given in Table 1.
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, 1984; Gauthier et al., 1995). In contrast to the results described by Gauthier et al. (1995), A. macleodii LMG 2843T showed an obvious catalase-positive reaction. In addition, D-ribose, L-arginine and succinate were utilized as sole carbon sources under the same test conditions as in the previous study (Baumann et al., 1972). Finally, A. macleodii LMG 2843T, together with strain JC2043T, showed slightly fermentative reactions for glucose and N-acetylglucosamine in MOF medium, which may result from residual oxygen in this medium. Based on these differences, an emended description for A. macleodii is given later.
Chemotaxonomic characteristics
Cellular fatty acid profiles of the test strains are given in Table 2. These fatty acid compositions are not only similar to each other, but also to those of the genus Alteromonas. As reported for other members of the family Alteromonadaceae (Ivanova & Mikhailov, 2001), Q8 was the predominant isoprenoid quinone in both strains. The DNA G+C contents of strains JC2042T and JC2043T were 48 and 54 mol%, respectively.
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). Strain JC2043T shows Alteromonas-like phenotypic properties in colonial morphology, lecithinase, acid phosphatase, utilization of D-glucose as sole carbon source and relatively high 16S rDNA sequence similarity to members of the genus Alteromonas (95·1–95·5 %). However, monophyly of the two getbol isolates is not only strongly supported by all tree-inferring methods, but also by several phenotypic characteristics, namely sea salts requirement, nitrate reduction, alginase, 
-galactosidase, valine arylamidase and utilization of D-cellobiose, D-fructose, D-raffinose, D-salicin, D-xylose and lactose (Table 1). It is therefore proposed that the two getbol isolates should be assigned to a novel genus in the family Alteromonadaceae, Aestuariibacter gen. nov., as Aestuariibacter salexigens sp. nov. for strain JC2042T and Aestuariibacter halophilus sp. nov. for strain JC2043T.
Description of Aestuariibacter gen. nov.
Aestuariibacter (Aes.tu.ar.i.i.bac'ter. L. neut. n. aestuarium -i tidal flat; N.L. masc. n. bacter rod; N.L. masc. n. Aestuariibacter rod-shaped bacterium from tidal flat).
Gram-negative and oxidase- and catalase-positive. Strictly aerobic, chemoheterotrophic, halophilic, mesophilic and neutrophilic. Cells are rod-shaped and motile with a polar flagellum. Abundant growth occurs on MA, CSY-3 and SMM media. Spores are not formed. Major isoprenoid quinone is Q8. Predominant cellular fatty acids are C16 : 0, C18 : 17c and a mixture of C16 : 17c and iso-C15 : 0 2-OH. DNA G+C content is 48–54 mol%. Phylogenetically, the genus belongs to the family Alteromonadaceae and currently contains two species. The type species is Aestuariibacter salexigens.
Description of Aestuariibacter salexigens sp. nov.
Aestuariibacter salexigens (sa.lex'i.gens. L. n. sal salis salt, sea water; L. v. exigo to demand; N.L. part. adj. salexigens sea water-demanding).
Cells are approximately 1·0–1·8 µm long and 0·4–0·6 µm wide. Optimal growth is observed at 35 °C, pH 7–8 and 2–6 % artificial sea salts. Colonies are circular, raised, entirely margined, brittle, rough, opaque and white on MA and hard to emulsify. Viability is lost rapidly after 7 days on MA at 30 °C. Reduces nitrate to nitrite. Decomposes DNA, aesculin, gelatin, starch and Tween 80, but not agar, alginate, casein, cellulose, chitin or egg yolk. Does not produce arginine dihydrolase, -galactosidase, fluorescein, H2S, indole, polyhydroxybutyrate or urease. Does not ferment carbohydrates. Produces alkaline phosphatase, esterase (C4), esterase lipase (C8), leucine arylamidase, trypsin and naphthol-AS-BI-phosphohydrolase, but not lipase (C14), valine arylamidase, cystine arylamidase, 
-chymotrypsin, acid phosphatase, -galactosidase, -galactosidase, -glucuronidase, -glucosidase, -glucosidase, N-acetyl--glucosaminidase, -mannosidase or -fucosidase. Utilizes acetate, glycine, inulin, L-arginine, L-ornithine and N-acetylglucosamine as sole carbon sources. D-Galactose, D-ribose, D-sorbitol, ethanol, L-lysine and succinate are utilized weakly. Does not utilize acetamide, adenine, benzoate, citrate, D-cellobiose, D-fructose, D-glucose, D-mannose, D-raffinose, D-salicin, D-xylose, inositol, 2-propanol, lactose, L-cysteine, L-rhamnose, sucrose, salicylate or thiamin. Cellular fatty acid composition is given in Table 2. DNA G+C content is 48 mol%.
The type strain is JC2042T (=IMSNU 14006T=KCTC 12042T=DSM 15300T). Isolated from the sediment of getbol, the Korean tidal flat.
Description of Aestuariibacter halophilus sp. nov.
Aestuariibacter halophilus (ha.lo'phi.lus. Gr. n. hals halos salt; Gr. adj. philos loving; N.L. masc. adj. halophilus salt-loving).
Cells are approximately 1·2–1·8 µm long and 0·5–0·6 µm wide. Optimal growth is observed at 40 °C, pH 7–8 and 2–3 % artificial sea salts. Colonies are circular, convex, entirely margined, butyraceous, glistening, opaque and white on MA. Reduces nitrate to nitrite. Decomposes casein, DNA, egg yolk, aesculin, gelatin, starch and Tween 80, but not agar, alginate, cellulose or chitin. Does not produce arginine dihydrolase, -galactosidase, fluorescein, H2S, indole, polyhydroxybutyrate or urease. Does not ferment carbohydrates. Produces alkaline phosphatase, esterase (C4), esterase lipase (C8), leucine arylamidase, trypsin, acid phosphatase, naphthol-AS-BI-phosphohydrolase and -glucosidase, but not lipase (C14), valine arylamidase, cystine arylamidase, -chymotrypsin, -galactosidase, -galactosidase, -glucuronidase, -glucosidase, N-acetyl--glucosaminidase, -mannosidase or -fucosidase. Utilizes acetate, D-glucose, D-ribose, L-arginine, N-acetylglucosamine and sucrose as sole carbon sources. Does not utilize acetamide, adenine, benzoate, citrate, D-cellobiose, D-fructose, D-galactose, D-mannose, D-raffinose, D-salicin, D-sorbitol, D-xylose, ethanol, glycine, inositol, inulin, 2-propanol, lactose, L-cysteine, L-lysine, L-ornithine, L-rhamnose, salicylate, succinate or thiamin. Cellular fatty acid composition is given in Table 2. DNA G+C content is 54 mol%.
The type strain is JC2043T (=IMSNU 14007T=KCTC 12043T=DSM 15266T). Isolated from the sediment of getbol, the Korean tidal flat.
Emended description of Alteromonas macleodii
The description remains as those given by Baumann et al. (1972, 1984) and Gauthier et al. (1995), with the following modification: positive for catalase reaction. The following is added to the descriptions of Baumann et al. (1972, 1984) and Gauthier et al. (1995). Major isoprenoid quinone is ubiquinone-8. Positive for -galactosidase, aesculinase and lecithinase. Negative for urease, caseinase and cellulase. Does not produce indole. Utilizes D-raffinose, D-ribose, L-arginine and succinate as sole carbon sources, but not D-sorbitol or thiamin. Produces alkaline phosphatase, esterase (C4), esterase lipase (C8), leucine arylamidase, valine arylamidase, acid phosphatase and naphthol-AS-BI-phosphohydrolase, but not lipase (C14), cystine arylamidase, trypsin, -chymotrypsin, -galactosidase, -galactosidase, -glucuronidase, -glucosidase, -glucosidase, N-acetyl--glucosaminidase, -mannosidase or -fucosidase.
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ACKNOWLEDGEMENTS |
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REFERENCES |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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Baumann, L., Baumann, P., Mandel, M. & Allen, R. D. (1972). Taxonomy of aerobic marine eubacteria. J Bacteriol 110, 402–429.
Baumann, P., Baumann, L., Bowditch, R. D. & Beaman, B. (1984). Taxonomy of Alteromonas: A. nigrifaciens sp. nov., nom. rev.; A. macleodii; and A. haloplanktis. Int J Syst Bacteriol 34, 145–149.
Bowman, J. P., McCammon, S. A., Brown, J. L. & McMeekin, T. A. (1998). Glaciecola punicea gen. nov., sp. nov. and Glaciecola pallidula gen. nov., sp. nov.: psychrophilic bacteria from Antarctic sea-ice habitats. Int J Syst Bacteriol 48, 1213–1222.
Chun, J. & Goodfellow, M. (1995). A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int J Syst Bacteriol 45, 240–245.
Chun, J., Bae, K. S., Moon, E. Y., Jung, S.-O., Lee, H. K. & Kim, S.-J. (2000). Nocardiopsis kunsanensis sp. nov., a moderately halophilic actinomycete isolated from a saltern. Int J Syst Evol Microbiol 50, 1909–1913.[Abstract]
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1 % of the total fatty acids of at least one of the strains are shown.