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National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama-City, Kanagawa 236-8648, Japan
Correspondence
Masataka Satomi
msatomi{at}affrc.go.jp
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ABSTRACT |
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Published online ahead of print on 23 August 2002 as DOI 10.1099/ijs.0.02392-0.
The GenBank/EMBL/DDBJ accession numbers for the 16S rDNA and gyrB sequences determined in this study are AB081757–AB081768, as detailed in Fig. 1
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A list of characters that gave the same result for all six novel isolates is available as supplementary material in IJSEM Online (http://ijs.sgmjournals.org).
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MAIN TEXT |
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; Myers & Nealson, 1988; Stenström & Molin, 1990; Simidu et al., 1990; Nealson et al., 1991; Bowman et al., 1997; Makemson et al., 1997; Nogi et al., 1998; Venkateswaran et al., 1998b, 1999; Leonardo et al., 1999; Ivanova et al., 2001; Bozal et al., 2002). Originally, the genus was established for Alteromonas putrefaciens, isolated from butter and clinical samples (MacDonell & Colwell, 1985). However, advanced taxonomic techniques such as PCR technology have contributed to an increase in the number of described Shewanella species; a recent list (http://www.bacterio.cict.fr/s/shewanella.html) includes 17 species. The genus Shewanella is divided roughly into two groups based on phylogenetic and physiological characteristics such as growth temperature, requirement for sodium ions for growth, fatty acid composition and so on; members of one group, represented by Shewanella putrefaciens, are non-halophilic and most of them are mesophilic and lack the ability to produce eicosapentaenoic acid (EPA). The other group is represented by Shewanella benthica, which was isolated from the deep sea and is psychrophilic and halophilic and can produce large amounts of EPA (Russell & Nichols, 1999). All of the psychrophilic and halophilic species have been isolated from marine environments.
For a long time, prokaryotes were considered unable to produce polyunsaturated fatty acids (PUFA), including EPA, docosahexaenoic acid and arachidonic acid, until the isolation of EPA-producing bacteria from the marine environment (Johns & Perry, 1977). Further investigations found that PUFA-producing bacteria are distributed in cold or deep-sea environments (DeLong & Yayanos, 1985; Wilkinson, 1988; Yazawa et al., 1988; Yano et al., 1994, 1997; Yazawa, 1996; Bowman et al., 1997, 1998; Ivanova et al., 2001), although species that can produce PUFA are taxonomically limited (Russell & Nichols, 1999). In order to understand the distribution of PUFA-producing bacteria, we have tried to isolate PUFA producers from various sea-animal intestines and then to identify them by phylogenetic analysis of 16S rRNA gene sequences. In this study, we have examined three novel Shewanella species that contain EPA at about 20 % of the total cellular fatty acids and have identified their taxonomic positions based on polyphasic analyses.
Bacterial strains
A total of six strains (IK-1T, 2T11, HZ17, HRKA1T, HRKC24 and SM2-1T) were isolated from various sea animals in Japan (Table 1) by using standard microbiological methods (Baumann et al., 1972). The isolates have been deposited in the Japan Collection of Microorganisms (JCM) and BCCM/LMG Bacteria Collection, Laboratorium voor Microbiologie, University of Ghent, Belgium (LMG). The strains were maintained as stab cultures in Marine broth 2216 (MB; Difco) with 0·5 % agar at 4 °C or frozen in MB supplemented with 15 % glycerol at -80 °C. Incubations were carried out for 2 days at 20 °C.
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Unless indicated otherwise, the inocula used for tests were prepared from cells in the exponential growth stage in MB at 20 °C. In all of the phenotypic tests, Shewanella pealeana ANG-SQ1T and ANG-SQ2 were used as reference strains.
Morphology and growth characteristics
The cellular morphology and motility of the novel isolates were observed by phase-contrast microscopy. Flagella formation was observed microscopically with a flagella staining kit (Shionogi). Gram stain was performed by using the modified Hucker method (Conn et al., 1957). Cells of the novel isolates were Gram-negative rods, motile by means of polar flagella. Poly-
-hydroxybutyrate accumulation and spore formation were negative. Cells of the novel isolates under optimum conditions were 0·5–0·8 µm in diameter and 2–3 µm long. Colonies were entire, smooth, opaque, ivory, non-luminescent and 2–3 mm in diameter on plates of Marine agar 2216 (MA; Difco) incubated at 20 °C for 2 days. Ranges of NaCl concentration for growth were determined on LB plates (1 % tryptone, 0·5 % yeast extract, 1·5 % agar, pH 7·2) supplemented with NaCl at 0–10 %. All of the novel isolates were able to grow at 1–5 % NaCl but not in the absence of NaCl, and the optimal concentration for growth was 2–3 %. Temperature ranges for growth (0, 4, 5, 10, 20, 25, 27, 30, 32 and 35 °C) were determined on LB plates supplemented with 2·5 % NaCl for 3 weeks. All strains were able to grow at 4–27 °C; optimum growth occurred at 20–25 °C. Strains HRKA1T and HRKC24 were able to grow at 32 °C, but the remaining strains did not. The ability to grow at pH 4·0–11·0 was tested in LB broth adjusted to various pH values with 0·1 M NaOH and supplemented with 2·5 % NaCl; all grew at pH 5·0–10·0, with optimum growth at pH 7·0–8·0. Anaerobic growth with trimethylamine oxide (TMAO) reduction was tested according to the method of Bowman et al. (1997). Oxygen requirement for growth were determined by comparison of growth on MA plates in an anaerobic jar and under aerobic conditions. All strains tested required aerobic conditions for growth without TMAO, but almost all strains (except SM2-1T) were able to grow under anaerobic conditions with TMAO.
Phenotypic characteristics
Routine biochemical tests were carried out using API kits (API 20NE, API ZYM and API 50CH), which were prepared according to the instruction manual except that cells were suspended in a solution adjusted to a final concentration of 2·5 % NaCl. Further utilization tests, mainly amino acids, were performed by adding energy sources (0·1 % final concentration) to minimal medium (Baumann et al., 1972) solidified with agar noble (Difco). Observations of utilization tests were continued for 3 weeks. H2S production was determined with triple-sugar iron (TSI) agar (Eiken). Haemolytic activity was determined on trypticase soy agar (BBL) supplemented with 2·5 % NaCl and 5 % defibrinated sheep blood. Casein hydrolysis, production of DNase, RNase, lipase (hydrolysis of Tween 40 or 80) and phenylalanine deaminase, hydrolysis of hippurate and O/129 antibacterial susceptibility were tested as described by Smibert & Krieg (1994). Chitin and alginate hydrolysis were tested as described by West & Colwell (1984). A summary of the phenotypic characteristics used to differentiate between the novel isolates and other Shewanella species is shown in Table 2. The following morphological and physiological characteristics indicated that the novel isolates were members of the genus Shewanella: negative Gram reaction, presence of rod-shaped cells, motile by means of a polar flagellum, production of oxidase, catalase and H2S and reduction of nitrate to nitrite. The novel isolates were able to grow at more than 25 °C, were halophilic and did not produce acid from glucose, suggesting that they are similar to S. pealeana, Shewanella colwelliana, Shewanella hanedai and Shewanella woodyi, although some characteristics, such as production of luminescence or pigment, differ from those found for the novel isolates (Weiner et al., 1988, Gauthier & Breittmayer, 1992; Holt et al., 1994; Gauthier et al., 1995; Bowman et al., 1997; Makemson et al., 1997; Leonardo et al., 1999; Venkateswaran et al., 1998b, 1999; Nogi et al., 1998). S. pealeana did not show significant differences from the novel isolates. Detailed phenotypic characteristics, enzyme profiles and metabolic features indicated that the novel isolates were distinguished from S. pealeana and were divided into three groups; one consisting of IK-1T, HZ17 and 2T11, the second containing HRKA1T and HRKC24 and the third containing SM2-1T.
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-glucosaminidase (negative for SM2-1T), acid phosphatase (negative for HRKA1T and HRKC24), aesculin hydrolysis, growth at 32 °C and utilization of acetate, L-arginine, L-histidine and L-leucine. Strain HRKC24 did not hydrolyse casein. The following characteristics of S. pealeana differed from those given in the original description by Leonardo et al. (1999): gelatinase, lipase, citrate utilization and acetate utilization. This seems to have been caused by the use of different methods from those used in the original report; for example, gelatinase and citrate utilization were determined using API kits and lipase was detected by observation of hydrolysis of Tween 40 or 80 in this study.
Isoprenoid quinone composition
The isoprenoid quinone type and isoprenoid length were analysed by using the method described by Akagawa-Matsushita et al. (1992). Total acetone-soluble extracts of whole cells were separated by one-dimensional cellulose TLC (Merck) with benzene as eluant. Isoprenoid length was analysed by HPLC using a reverse-phase column (Cosmosil C18 column; Nacalai Tesque). All of the novel isolates had ubiquinones that consisted of mainly Q-7 and Q-8. Menaquinone and methylmenaquinone were not detected.
Fatty acid analysis
Bacterial lipids were extracted by using the method of Folch et al. (1957). For analysis of the fatty acid composition, total lipids were converted to fatty acid methyl esters (FAMEs) with 2·5 % HCl in methanol at 85 °C for 2·5 h. FAMEs were analysed by GC (Hitachi G-500) equipped with a flame-ionization detector and a capillary column. Helium was used as the carrier gas. Details of the analytical conditions of GC and identification of the fatty acids by GC-MS were described previously (Yano et al., 1997). The fatty acid compositions of the novel isolates are shown in Table 3. All of the novel isolates produced EPA at 15·2–18·6 % of the total fatty acids. The other major fatty acids were iso-15 : 0, 16 : 0, 16 : 1
7 and 18 : 17, which together accounted for 80 % or more of the total fatty acids. The fatty acid compositions of the novel isolates and Shewanella gelidimarina were similar, though their proportions were slightly different. All of the novel strains and the two strains of S. pealeana used as references produced large amounts of EPA although, in the original description of the fatty acid composition of S. pealeana reported by Leonardo et al. (1999), EPA was not recorded in its lipids. In this study, the strains analysed were cultivated aerobically at 20 °C, but Leonardo et al. (1999) employed a high growth temperature, 28 °C. Russell & Nichols (1999) also reported that S. pealeana contains EPA. Generally, unsaturated fatty acid molecules of bacteria are easily induced by low growth temperatures (a process known as homeoviscous adaptation), so this difference may have been caused by the growth temperature.
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).
DNA base compositions (G+C content) were determined by the HPLC method of Tamaoka & Komagata (1984). The G+C contents of strains HRKA1T and HRKC24 were 45 mol% and that of the rest of the novel isolates was 43 mol%. Strains HRKA1T and HRKC24 seem to represent a different species from the other novel isolates. The DNA base compositions of the novel isolates and other Shewanella species are shown in Table 2.
16S rDNA and gyrB were amplified by using the PCR method. For amplification of 16S rDNA, universal primers were used, corresponding to positions 8–27 as the forward primer and 1492–1510 as the reverse primer (Escherichia coli numbering system; Weisburg et al., 1991). Amplicons of 1·2 kbp from the gyrB gene (covering positions 274–1525; E. coli numbering) were amplified by using PCR with universal primer sets; the PCR conditions were as described by Yamamoto & Harayama (1995). The PCR products were visualized by electrophoresis in 1·5 % (w/v) agarose gels (Nippon Gene) stained with ethidium bromide. Direct sequencing of the amplified DNA fragments was performed as described previously (Satomi et al., 1997). The accession numbers of the sequences generated in this study are listed in Fig. 1.
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). Multiple alignment, calculation of nucleotide substitution rates (Knuc values; Kimura, 1980) and construction of phylogenetic trees by the neighbour-joining (NJ) method (Saitou & Nei, 1987) and maximum-likelihood of method were performed by using the CLUSTAL W program (Thompson et al., 1994) and the PHYLIP program (Felsenstein, 1995). Alignment gaps, primer regions for PCR amplification and unidentified base positions were not taken into consideration for the calculations. The robustness of the topology in the phylogenetic trees was evaluated by a bootstrap analysis through 1000 replications.
The phylogenetic trees constructed by using the NJ method based on 16S rRNA and gyrB genes are shown in Fig. 1. For the 16S rRNA genes, the number of nucleotide substitutions in the sequences of the novel isolates varied from two to eight, with a mean of more than 99·5 % sequence similarity between the novel isolates. BLAST searches showed that the novel isolates were positioned in the S. pealeana/S. gelidimarina cluster, and the closest species to the novel isolates was S. pealeana, with 97·0 % sequence similarity. However, Venkateswaran et al. (1999) have pointed out that the threshold of 16S rRNA similarity for members of the same known Shewanella species is more than 97·7 %. Moreover, some previous workers have reported that the resolution of the 16S rRNA gene is not sufficient to determine the precise phylogenetic positions for some bacteria such as Bacillus, Pseudomonas and Vibrio (Fox et al., 1992; Stackebrandt & Goebel, 1994; Takewaki et al., 1994; Viale et al., 1994; Yamamoto & Harayama, 1995, 1996, 1998; Morse et al., 1996; Edgell et al., 1997). For instance, Vibrio parahaemolyticus and Vibrio alginolyticus have almost completely identical 16S rRNA sequences, but the phylogenetic distances between their gyrB genes were magnified to allow them to be recognized as different species (Venkateswaran et al., 1998a). On the basis on the 16S rRNA gene data alone, it is unclear whether the phylogenetic relationships among the strains of the S. pealeana/S. gelidimarina cluster, including the novel isolates, are sufficient to allow differentiation of the species. We therefore used the gyrB sequence data to analyse the phylogenetic positions of the novel isolates. Sequence analysis of gyrB indicated that the novel isolates were clearly separated into three groups, which is the same grouping as that based on phenotypic characteristics, and were distinguished from S. pealeana and S. gelidimarina. Sequence diversity within strains of the same group was less than 3 %; hence, there is 10 % sequence diversity among each group, indicating that each group of the novel isolates satisfied the threshold criterion (10 % nucleotide substitution rate; Venkateswaran et al., 1999) of sequence diversity as distinct species.
DNA–DNA hybridization
DNA–DNA relatedness was studied by the microplate hybridization method (Ezaki et al., 1989) with photobiotin labelling and colorimetric detection as described previously (Satomi et al., 1997). DNA–DNA hybridization experiments indicated that the novel isolates were divided into three groups (Table 4), the same grouping as revealed by the phenotypic characteristics, with >90 % DNA relatedness within strains of each group, and each group was clearly separated as a distinct species (significantly less than 70 % relatedness) according to the recommended criteria for different species in bacterial taxonomy (Wayne et al., 1987).
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) or general characteristics (Table 2). Recently, two novel species, Shewanella japonica and Shewanella livingstonensis, were respectively reported by Ivanova et al. (2001) and Bozal et al. (2002). S. japonica produces EPA in the cell membrane, but its growth temperature (it can grow at 37 °C) and phylogenetic position are different from those of our novel isolates. Although S. livingstonensis is a psychrophile, it does not produce EPA and its phylogenetic position is close to Shewanella frigidimarina. Therefore, we conclude that the novel isolates should be classified as novel species of the genus Shewanella and propose the names Shewanella marinintestina sp. nov., Shewanella schlegeliana sp. nov. and Shewanella sairae sp. nov.
Description of Shewanella marinintestina sp. nov.
Shewanella marinintestina (ma.rin.in.tes'ti.na. L. adj. marinus of the sea; L. adj. intestinus of the intestine; N.L. fem. adj. marinintestina of the intestine from the sea, referring to the isolation of strains from the intestines of sea animals).
Cells are Gram-negative rods, 2·0–3·0 µm long, motile by means of polar flagella. Circular, opaque, ivory colonies are formed after 2 days on MA at 20 °C. Facultatively anaerobic chemoheterotroph. Anaerobic growth occurs by anaerobic respiration with TMAO as electron acceptor. Psychrophilic. Growth occurs at temperatures from 4 to 30 °C, with an optimum of 20–25 °C. The pH range for growth is 6·0–10·0, with an optimum of pH 7·0–8·0. Requires NaCl for growth; growth occurs at concentrations of 1–5 % (w/v) and is optimal at 2·0–3·0 %. Catalase, oxidase, lipase, gelatinase, phosphatase, N-acetyl--glucosaminidase, DNase and RNase are positive. Hydrolysis of casein, hippurate and ONPG are also positive. H2S production and reduction of nitrate to nitrite occur. Amylase, chitinase, alginase, agarase and urease are negative. Haemolytic activity for sheep blood is negative. Decarboxylation of ornithine, arginine and lysine is negative. Acid is formed oxidatively from D-ribose, D-glucosamine and N-acetylglucosamine. D-Ribose is fermented. No acid is produced from D-glucose, L-arabinose, D-fructose, D-galactose, D-xylose, lactose, melibiose, rhamnose, sucrose, maltose, inositol, D-mannitol, sorbitol or amygdalin. The following energy sources are utilized: D-glucose, acetate, pyruvate, propionate, D-glucosamine, N-acetylglucosamine, D-ribose, valerate, L-alanine, L-arginine, L-asparagine, L-glutamine, L-glutamate, L-histidine, L-isoleucine, L-leucine, L-serine and L-threonine. Produces EPA. Major isoprenoid quinones are Q-7 and Q-8. The G+C content of the DNA is 43 mol% (as determined by HPLC). The type strain is IK-1T (=JCM 11558T =LMG 21403T), which was isolated from the intestine of a squid.
Description of Shewanella schlegeliana sp. nov.
Shewanella schlegeliana (sch.le.gel.i.a'na. N.L. fem. adj. schlegeliana from Acanthopagrus schlegeli, the species name of the black porgy, an oceanic fish, from which the type strain was isolated).
Cells are Gram-negative rods, 2·0–3·0 µm long, motile by means of polar flagella. Circular, opaque, ivory colonies are formed after 2 days on MA at 20 °C. Facultatively anaerobic chemoheterotroph. Anaerobic growth occurs by anaerobic respiration with TMAO as electron acceptor. Psychrophilic. Growth occurs at temperatures from 4 to 32 °C, with an optimum of 20–25 °C. The pH range for growth is 6·0–10·0, with an optimum of pH 7·0–8·0. Requires NaCl for growth; growth occurs at concentrations of 1–5 % (w/v) and is optimal at 2·0–3·0 %. Catalase, oxidase, gelatinase, alkaline phosphatase, N-acetyl--glucosaminidase, urease, DNase and RNase are positive. Hydrolysis of ONPG, aesculin and hippurate is positive. H2S production and reduction of nitrate to nitrite occur. Amylase, lipase, acid phosphatase, chitinase, alginase and agarase are negative. Haemolytic activity for sheep blood is negative. Decarboxylation of ornithine, arginine and lysine is negative. Acid is formed oxidatively from D-ribose, D-glucosamine and N-acetylglucosamine. D-Ribose is fermented. No acid is produced from D-glucose, L-arabinose, D-fructose, D-galactose, D-xylose, lactose, melibiose, rhamnose, sucrose, maltose, inositol, D-mannitol, sorbitol or amygdalin. The following energy sources are utilized: D-glucose, pyruvate, propionate, D-glucosamine, N-acetylglucosamine, D-ribose, valerate, L-alanine, L-asparagine, L-glutamine, L-glutamate, L-isoleucine, L-serine and L-threonine. Produces EPA. Major isoprenoid quinones are Q-7 and Q-8. The G+C content of the DNA is 45 mol% (as determined by HPLC). The type strain is HRKA1T (=JCM 11561T =LMG 21406T), which was isolated from the intestine of a black porgy.
Description of Shewanella sairae sp. nov.
Shewanella sairae (sa.i'rae. N.L. gen. n. sairae from Cololabis saira, the species name of the Pacific saury, an oceanic fish, from which the type strain was isolated).
Cells are Gram-negative rods, 2·0–3·0 µm long, motile by means of polar flagella. Circular, opaque, ivory colonies are formed after 2 days on MA at 20 °C. Aerobic. Psychrophilic. Growth occurs at 4–27 °C, with an optimum at 20–25 °C. The pH range for growth is 6·0–10·0, with an optimum at pH 7·0–8·0. Requires NaCl for growth; growth occurs at concentrations of 1–5 % (w/v) and is optimal at 2·0–3·0 %. Catalase, oxidase, lipase, gelatinase, phosphatase and RNase are positive. Hydrolysis of casein and hippurate is positive. H2S production and reduction of nitrate to nitrite occur. Amylase, chitinase, alginase, agarase, N-acetyl--glucosaminidase, DNase and urease are negative. Hydrolysis of ONPG is negative. Haemolytic activity for sheep blood is negative. Decarboxylation of ornithine, arginine and lysine is negative. Acid is formed oxidatively from D-ribose, D-glucosamine and N-acetyl-D-glucosamine. D-Ribose is fermented. No acid is produced from D-glucose, L-arabinose, D-fructose, D-galactose, D-xylose, lactose, melibiose, rhamnose, sucrose, maltose, inositol, D-mannitol, sorbitol or amygdalin. The following energy sources are utilized: D-glucose, pyruvate, propionate, D-glucosamine, N-acetylglucosamine, D-ribose, valerate, L-alanine, L-arginine, L-asparagine, L-glutamine, L-glutamate, L-isoleucine, L-serine and L-threonine. Produces EPA. Major isoprenoid quinones are Q-7 and Q-8. The G+C content of DNA is 43 mol% (as determined by HPLC). The type strain is SM2-1T (=JCM 11563T =LMG 21408T), which was isolated from the intestine of a Pacific saury.
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ACKNOWLEDGEMENTS |
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