Taxonomic studies of deep-sea barophilic Shewanella strains and description of Shewanella violacea sp. nov.

Abstract Several barophilic Shewanella species have been isolated from deep-sea sediments at depths of 2,485– 6,499 m. From the results of taxonomic studies, all of these isolates have been identified as strains of Shewanella benthica except for strain DSS12. Strain DSS12 is a member of a novel, moderately barophilic Shewanella species isolated from the Ryukyu Trench at a depth of 5,110 m. On Marine Agar 2216 plates, this organism produced a violet pigment, whereas the colonies of other isolates (S. benthica) were rose-colored. Phylogenetic analysis based on 16 S ribosomal RNA gene sequences showed that strain DSS12 represents a separate lineage within the genus Shewanella that is closely related to S. benthica and particularly to the members of the Shewanella barophiles branch. The temperature range for growth and some of the biochemical characteristics indicate that strain DSS12 differs from other Shewanella species. Furthermore, strain DSS12 displayed a low level of DNA similarity to the Shewanella type strains. Based on these differences, it is proposed that strain DSS12 represents a new deep-sea Shewanella species. The name Shewanella violacea (JCM 10179) is proposed.

[1]  C. Collins,et al.  Cowan and Steel's manual for the identification of medical bacteria. 3rd edn , 1993 .

[2]  D. G. Muir,et al.  Reclassification of Alteromonas colwelliana to the Genus Shewanella by DNA-DNA Hybridization, Serology and 5S Ribosomal RNA Sequence Data , 1989 .

[3]  R. Owen,et al.  Base composition, size and sequence similarities of genoma deoxyribonucleic acids from clinical isolates of Pseudomonas putrefaciens. , 1978, Journal of general microbiology.

[4]  T. Ezaki,et al.  Isolation and characterization of Shewanella alga from human clinical specimens and emendation of the description of S. alga Simidu et al., 1990, 335. , 1992, International journal of systematic bacteriology.

[5]  K. Komagata,et al.  Research letterDetermination of DNA base composition by reversed-phase high-performance liquid chromatography , 1984 .

[6]  A. Yayanos,et al.  Isolation of a Deep-Sea Barophilic Bacterium and Some of Its Growth Characteristics , 1979, Science.

[7]  K. Horikoshi,et al.  Extremely Barophilic Bacteria Isolated from the Mariana Trench, Challenger Deep, at a Depth of 11,000 Meters , 1998, Applied and Environmental Microbiology.

[8]  T. McMeekin,et al.  Shewanella gelidimarina sp. nov. and Shewanella frigidimarina sp. nov., novel Antarctic species with the ability to produce eicosapentaenoic acid (20:5 omega 3) and grow anaerobically by dissimilatory Fe(III) reduction. , 1997, International journal of systematic bacteriology.

[9]  J. Deming,et al.  Isolation of an Obligately Barophilic Bacterium and Description of a New Genus, Colwellia gen. nov. , 1988 .

[10]  J. Case,et al.  Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. , 1997, International journal of systematic bacteriology.

[11]  R. Weiner,et al.  Alteromonas colwelliana sp. nov., an Isolate from Oyster Habitats , 1988 .

[12]  K. Horikoshi,et al.  Structure of genes in a pressure-regulated operon and adjacent regions from a barotolerant bacterium strain DSS12 , 1997 .

[13]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[14]  A. Yayanos,et al.  Microbiology to 10,500 meters in the deep sea. , 1995, Annual review of microbiology.

[15]  O. Kandler,et al.  International Committee on Systematic Bacteriology: announcement of the report of the ad hoc Committee on Reconciliation of Approaches to Bacterial Systematics. , 1987, Zentralblatt fur Bakteriologie, Mikrobiologie, und Hygiene. Series A, Medical microbiology, infectious diseases, virology, parasitology.

[16]  M. Nei,et al.  The neighbor-joining method , 1987 .

[17]  K. Horikoshi,et al.  Mechanisms of gene expression controlled by pressure in deep-sea microorganisms , 1998, Extremophiles.

[18]  G. Fox,et al.  The ribonucleotide sequence of 5s rRNA from two strains of deep-sea barophilic bacteria. , 1984, Journal of general microbiology.

[19]  R. Colwell,et al.  Phylogeny of the Vibrionaceae, and recommendation for two new genera, Listonella and Shewanella , 1985 .

[20]  T. Yasumoto,et al.  Taxonomy of four marine bacterial strains that produce tetrodotoxin. , 1990, International journal of systematic bacteriology.

[21]  K. Horikoshi,et al.  Distribution of the pressure-regulated operons in deep-sea bacteria. , 1998, FEMS microbiology letters.

[22]  E. Delong,et al.  Evolutionary relationships of cultivated psychrophilic and barophilic deep-sea bacteria , 1997, Applied and environmental microbiology.

[23]  Takayuki Ezaki,et al.  Fluorometric Deoxyribonucleic Acid-Deoxyribonucleic Acid Hybridization in Microdilution Wells as an Alternative to Membrane Filter Hybridization in which Radioisotopes Are Used To Determine Genetic Relatedness among Bacterial Strains , 1989 .

[24]  K. Horikoshi,et al.  Comparison of the gene expression of aspartate beta-D-semialdehyde dehydrogenase at elevated hydrostatic pressure in deep-sea bacteria. , 1997, Journal of Biochemistry (Tokyo).

[25]  K. Miura,et al.  PREPARATION OF TRANSFORMING DEOXYRIBONUCLEIC ACID BY PHENOL TREATMENT. , 1963, Biochimica et biophysica acta.

[26]  K. Horikoshi,et al.  Properties of obligately barophilic bacteria isolated from a sample of deep-sea sediment from the Izu-Bonin trench , 1996 .

[27]  K. Horikoshi,et al.  Open reading frame 3 of the barotolerant bacterium strain DSS12 is complementary with cydD in Escherichia coli: cydD functions are required for cell stability at high pressure. , 1996, Journal of biochemistry.

[28]  C. Kato,et al.  Photobacterium profundum sp. nov., a new, moderately barophilic bacterial species isolated from a deep-sea sediment , 1998, Extremophiles.

[29]  K. Komagata,et al.  4 Lipid and Cell-Wall Analysis in Bacterial Systematics , 1988 .