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1 National Research Institute of Fisheries Science, Fisheries Research Agency, 2-12-4 Fukuura, Kanazawa-ku, Yokohama 236-8648, Japan
2 Danish Institute for Fisheries Research, Department of Seafood Research, Søltofts Plads, c/o Technical University of Denmark, Bldg 221, DK-2800 Kgs Lyngby, Denmark
3 California Institute of Technology, Jet Propulsion Laboratory, Biotechnology and Planetary Protection Group, 89-2 Oak Grove Drive, Pasadena, CA 91109, USA
Correspondence
Masataka Satomi
msatomi{at}affrc.go.jp
| ABSTRACT |
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85 %) and the results of DNA hybridization (
28 %) indicated that the new isolates represented a novel species. Furthermore, when compared to each other, the type strains of S. colwelliana and S. affinis had almost identical gyrB sequences and significantly high DNA reassociation values (7683 %), indicating that they belonged to the same species. Based on the conclusions of this study, we propose the novel species Shewanella glacialipiscicola sp. nov. (type strain T147T=LMG 23744T=NBRC 102030T) for group 1 strains and Shewanella algidipiscicola sp. nov. (type strain S13T=LMG 23746T=NBRC 102032T) for group 2 strains, and we propose that Shewanella affinis as a later heterotypic synonym of Shewanella colwelliana.
The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene and gyrB sequences of six of the new isolates are AB205568AB205571, AB205574 and AB205577 (16S rRNA gene) and AB266200AB266205 (gyrB), as indicated in Figs 1 and 2![]()
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Details of strains and DNADNA hybridization results are available as supplementary material in IJSEM Online.
| MAIN TEXT |
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A total of 40 strains of novel H2S-producing bacteria were isolated from cod and plaice caught between August 1995 and September 2001 from the Baltic Sea off Denmark. Bacterial isolation was carried out as reported by Vogel et al. (2005)
. Briefly, tissue samples were taken from the belly flap area of iced fish, homogenized, serially diluted in sterile peptone saline and pour-plated in iron agar (Oxoid CM964). Plates were then incubated at 25 °C for 3 days and black colonies, indicative of H2S-producing bacteria, were picked, purified and stored for further characterization. Of 40 strains tested for phenotypic analysis, representative strains were selected for molecular taxonomy to determine their phylogenetic affiliation. The bacterial strains analysed in detail in this study are shown in Supplementary Table S1, available in IJSEM Online. In addition to these newly described strains, type strains of closely related species were purchased from several established culture collections and were used as reference strains. All isolates were maintained in trypticase soy agar (TSA; Becton Dickinson) stabs at room temperature for short-term analysis and in a medium containing skimmed-milk powder and glycerol at 80 °C for long-term storage. Liquid cultures were grown in trypticase soy broth (TSB; Becton Dickinson) incubated at 25 °C for 27 days. Representative strains have been deposited in the BCCM/LMG Bacteria Collection, Laboratorium voor Microbiologie, University of Ghent, Ghent, Belgium (LMG), and the National Institute of Technology and Evaluation, Biological Resource Center (NBRC), Japan (Supplementary Table S1).
All strains were tested at 25 °C for the following key characteristics: Gram reaction (Gregerson, 1978
), motility and cell shape [phase-contrast microscopy after growth in veal infusion broth (Difco), for 24 h], cytochrome oxidase (BBL DrySlide oxidase; Becton Dickinson), catalase reaction (3 % H2O2), reduction of TMAO in TMAO medium (Gram et al., 1987
) and production of H2S from thiosulfate (Gram et al., 1987
). Fermentation of glucose was tested in O-F medium (Merck) at 25 °C. Growth at various temperatures (4, 37 and 42 °C) and in 6 % NaCl (Vogel et al., 1997
) and assimilation of several carbon and energy sources, citrate, gluconate, glucose, lactate and sucrose (Ziemke et al., 1998
), were used to differentiate the Shewanella isolates further. API 20NE kits (bioMérieux) were also employed for assimilation tests according to the manufacturer's instructions. Type strains of S. putrefaciens, Shewanella affinis, S. baltica, Shewanella colwelliana, Shewanella hafniensis and Shewanella morhuae were included in each trial and served as controls. The genomic G+C content was determined by HPLC (Vogel et al., 1997
). The ability to degrade gelatin (Frazier, 1926
), DNA (Difco DNase test agar with methyl green) and ornithine (Difco) was also tested.
All of the new isolates were Gram-negative, motile rods, with positive oxidase and catalase reactions. They were unable to ferment glucose or produce indole but reduced nitrate and TMAO and produced H2S. Based on these traits, the strains were tentatively classified as members of the genus Shewanella according to established procedures (Stenstrom & Molin, 1990
). However, these characteristics were not sufficient to allow for a complete identification at the species level among the psychrotolerant shewanellae (Ziemke et al., 1997
). Under optimum conditions, cells of these new isolates were 0.50.7 µm in diameter and 1.01.2 µm long. Colonies were round, undulate, beige and non-luminescent and had irregular margins on TSA plates incubated at 25 °C for 1 day. All strains were able to grow between 4 and 30 °C.
The first group (group 1; group C5 of Vogel et al., 2005
) was composed of seven strains, including strain T147T, and showed similar phenotypic traits to psychrotolerant S. morhuae strains, but differed from S. morhuae in that they assimilated lactate (Table 1
). These strains were also distinguished from S. putrefaciens, S. baltica and S. hafniensis by their carbohydrate assimilation patterns, ability to grow at 37 °C and production of gelatinase. Furthermore, the G+C content of these strains was 44 mol%, which differs from that of S. putrefaciens, S. baltica and S. hafniensis. These results suggest that group 1 was phenotypically similar to, but nevertheless distinguishable from, known authentic Shewanella species. A second group (group 2; groups C1 and C2 of Vogel et al., 2005
) encompassing 33 strains and represented by strain S13T grew well at 4 °C, but assimilated only three of the carbohydrates tested (Table 1
). This group was phenotypically different from S. colwelliana ATCC 39565T and S. affinis ATCC BAA-642T, which were phylogenetically closest to the new isolates based on 16S rRNA gene sequence analysis (Vogel et al., 2005
). Strains of group 2 grew in 6 % NaCl but did not degrade DNA or ornithine. The G+C content was 47 mol%, indicating that they were different from S. colwelliana (46 mol%) and S. affinis (45 mol%). Although the phenotypic traits of group 2 strains were somewhat similar to those of S. putrefaciens, they showed a number of phenotypic differences (Table 1
): they liquefied gelatin and grew in 6 % NaCl, arabinose was not utilized as a sole carbon source and they did not produce DNase or ornithine decarboxylase.
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Approximately 1.4 kbp nucleotide sequences of 16S rRNA genes and 1.1 kbp nucleotide sequences of the gyrB genes were used for phylogenetic analyses. A phylogenetic tree based on the 16S rRNA gene (Fig. 1
) indicated that the new isolates clustered with members of the genus Shewanella. Based on 16S rRNA gene sequences, the nearest neighbour of the group 1 (T147T) strains was S. morhuae ATCC BAA-1205T, with sequence similarity of 99.9 %. The sequences of the group 2 (S13T) strains shared more than 99 % similarity with S. colwelliana ATCC 39565T (99.4 %) and S. affinis ATCC BAA-642T (99.6 %). In the case of the genus Shewanella, Venkateswaran et al. (1999)
and Satomi et al. (2003)
have reported that analysis of gyrB sequences is useful, since the resolution of the 16S rRNA gene sequence is insufficient to evaluate their phylogenetic position. Fig. 2
shows the phylogenetic tree constructed based on gyrB sequences. The group 1 strains clustered with S. morhuae, sharing 95.6 % sequence similarity, and the group 2 strains were positioned monophyletically, apart from both S. affinis (85.6 %) and S. colwelliana (85.6 %), clearly delineating them as a distinct species. The gyrB sequences of S. affinis and S. colwelliana were almost identical; there is only one base difference, and the deduced amino acid sequences were identical between the two type strains, indicating that they were probably members of the same species. The taxonomic status of the group 1 strains was still unresolved, since they shared 99.2 and 95.6 % similarity with S. morhuae based on 16S rRNA gene and gyrB sequences, respectively. Such similarity values are not sufficient to distinguish closely related species according to established procedures (Stackebrandt & Goebel, 1994
; Satomi et al., 2003
; Venkateswaran et al., 1999
). Therefore, DNADNA hybridization was carried out to confirm the novelty of these isolates.
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24 and
28 % DNA relatedness with S. affinis ATCC BAA-642T and S. colwelliana ATCC 39565T, respectively. The DNADNA hybridization results strongly support the claim that isolates of group 1 (T147T) and group 2 (S13T) represent novel species within the genus Shewanella (Wayne et al., 1987
Interestingly, S. affinis ATCC BAA-642T and S. colwelliana ATCC 39565T had a DNADNA hybridization value of 7683 %. This supported the results of gyrB and 16S rRNA gene sequence analysis, though some phenotypic differences exist between the two strains, such as growth at 4 °C and in 6 % NaCl and gluconate assimilation (Table 1
). However, Ivanova et al. (2004)
reported that DNA relatedness values were only 4552 % between S. affinis ATCC BAA-642T and S. colwelliana ATCC 39565T. The gyrB and 16S rRNA gene sequence analyses and DNADNA hybridization newly performed in this study show no evidence to separate the two species genetically. Based on these results, S. affinis ATCC BAA-642T and S. colwelliana ATCC 39565T received from the ATCC in March 2005 should be considered members of the same species.
Based on the findings of the polyphasic taxonomic study, it was determined that some of the strains isolated from marine fish from the Danish Baltic Sea represent two novel species within the genus Shewanella, Shewanella glacialipiscicola sp. nov. (represented by strain T147T) and Shewanella algidipiscicola sp. nov. (represented by strain S13T). In addition, Shewanella affinis Ivanova et al. 2004
should be considered as a later heterotypic synonym of Shewanella colwelliana (Weiner et al. 1988
) Coyne et al. 1990.
Description of Shewanella glacialipiscicola sp. nov.
Shewanella glacialipiscicola (gla'ci.a.li.pis'ci.co'la. L. adj. glacialis icy; L. n. piscis fish; L. suff. -cola dweller; N.L. n. glacialipiscicola iced fish dweller).
Mesophilic, aerobic and chemoheterotrophic. Cells are Gram-negative rods, 0.50.7 µm in diameter and 1.01.2 µm long, motile by means of polar flagella. None of the strains are capable of growing at concentrations of 6 % (w/v) NaCl. The temperature range for growth is 430 °C, with 25 °C being optimal. Growth does not occur at temperatures above 37 °C. Colonies are round, undulate, whitedull and non-luminescent and have irregular margins on marine agar plates incubated at 25 °C for 24 h. Cells are positive for oxidase and catalase reactions. They are unable to ferment glucose but reduce TMAO and produce H2S. Cells hydrolyse gelatin and aesculin, reduce nitrate and are positive for the production of DNase and ornithine decarboxylase, but do not produce acetoin, arginine dihydrolase, indole, urease or
-galactosidase. Cells utilize lactate, gluconate, N-acetylglucosamine and malate readily as energy sources. D-Glucose, citrate, sucrose, mannose, mannitol, adipic acid and phenylacetate are not utilized as sole carbon sources, but more than half of the strains tested assimilate arabinose. Cells do not grow on minimal media, indicating the presence of a required growth factor. The DNA G+C content is 44 mol%.
The type strain is T147T (=LMG 23744T=NBRC 102030T), isolated from cod from Danish waters of the Baltic Sea. Strain U718 (=LMG 23745=NBRC 102031) is a reference strain.
Description of Shewanella algidipiscicola sp. nov.
Shewanella algidipiscicola (al.gi'di.pis'ci.co'la. L. adj. algidus cold; L. n. piscis fish; L. suff. -cola dweller; N.L. n. algidipiscicola cold-fish dweller).
Mesophilic, aerobic and chemoheterotrophic. Cells are Gram-negative rods, 0.50.7 µm in diameter and 1.01.2 µm long, motile by means of polar flagella. Capable of growing at 6 % (w/v) NaCl. The temperature range for growth is 437 °C, with 25 °C being optimal. Growth does not occur at temperatures above 42 °C. Colonies are round, undulate, whitedull and non-luminescent and have irregular margins on TSA plates incubated at 25 °C for 24 h. Cells are positive for oxidase and catalase reactions. They are unable to ferment glucose or hydrolyse gelatin, but reduce TMAO and produce H2S. Cells reduce nitrate and are positive for the production of DNase and ornithine decarboxylase, but do not produce acetoin, arginine dihydrolase, indole, urease or
-galactosidase. Cells are unable to use most of the carbon substrates tested, although lactate, N-acetylglucosamine and malate are readily utilized as energy sources. D-Glucose, gluconate, maltose, citrate, sucrose, mannose, mannitol, adipic acid and phenylacetate are not utilized as sole carbon sources, but several strains assimilate arabinose and capric acid. Cells do not grow on minimal media, indicating the presence of a required growth factor. The DNA G+C content is 47 mol%.
The type strain is S13T (=LMG 23746T=NBRC 102032T), isolated from plaice from Danish waters of the Baltic Sea. Strains Q14 (=LMG 23477=NBRC 102033), Q213 and W01 are reference strains.
| ACKNOWLEDGEMENTS |
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