Idiomarina gen. nov., comprising novel indigenous deep-sea bacteria from the Pacific Ocean, including descriptions of two species, Idiomarina abyssalis sp. nov. and Idiomarina zobellii sp. nov.

Ivanova, Elena P.; Romanenko, Lyudmila A.; Chun, Jongsik; Matté, Maria Helena; Matté, Glavur Rogério; Mikhailov, Valery V.; Svetashev, Vassilii I.; Huq, A.; Maugel, Timothy K.; Colwell, Rita R.

doi:10.1099/00207713-50-2-901

Cited by 130 publications

(83 citation statements)

References 26 publications

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“…Deep-sea bacteria show limited ability to use carbohydrates as their sole carbon and energy source (19). Indeed, I. loihiensis does not seem to have a functional PEPdependent sugar͞phosphotransferase system or any ABC-type sugar transporters, or the sugar-phosphate permease.…”

Section: Resultsmentioning

confidence: 99%

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Genome sequence of the deep-sea γ-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy

Hou

Saw

Lee

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

122

104

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We report the complete genome sequence of the deep-sea ␥-proteobacterium, Idiomarina loihiensis, isolated recently from a hydrothermal vent at 1,300-m depth on the Lo ihi submarine volcano, Hawaii. The I. loihiensis genome comprises a single chromosome of 2,839,318 base pairs, encoding 2,640 proteins, four rRNA operons, and 56 tRNA genes. A comparison of I. loihiensis to the genomes of other ␥-proteobacteria reveals abundance of amino acid transport and degradation enzymes, but a loss of sugar transport systems and certain enzymes of sugar metabolism. This finding suggests that I. loihiensis relies primarily on amino acid catabolism, rather than on sugar fermentation, for carbon and energy. Enzymes for biosynthesis of purines, pyrimidines, the majority of amino acids, and coenzymes are encoded in the genome, but biosynthetic pathways for Leu, Ile, Val, Thr, and Met are incomplete. Auxotrophy for Val and Thr was confirmed by in vivo experiments. The I. loihiensis genome contains a cluster of 32 genes encoding enzymes for exopolysaccharide and capsular polysaccharide synthesis. It also encodes diverse peptidases, a variety of peptide and amino acid uptake systems, and versatile signal transduction machinery. We propose that the source of amino acids for I. loihiensis growth are the proteinaceous particles present in the deep sea hydrothermal vent waters. I. loihiensis would colonize these particles by using the secreted exopolysaccharide, digest these proteins, and metabolize the resulting peptides and amino acids. In summary, the I. loihiensis genome reveals an integrated mechanism of metabolic adaptation to the constantly changing deep-sea hydrothermal ecosystem.hydrothermal vent

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Section: Resultsmentioning

confidence: 99%

“…Like other deep-sea vent microorganisms, I. loihiensis in vitro produces a highly viscous exopolysaccharide (19,23). It has been suggested that vent microorganisms develop biofilms by using exopolysaccharides to ensure the formation of robust and stable communities (4,23).…”

Section: Resultsmentioning

confidence: 99%

Genome sequence of the deep-sea γ-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy

Hou

Saw

Lee

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

122

104

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“…Members of the family Idiomarinaceae are unique among Alteromonas-like bacteria in possessing a high content of iso-branched fatty acids (Ivanova et al, 2004). The family Idiomarinaceae comprises two recognized genera: Idiomarina (Ivanova et al, 2000) as the type genus and Pseudidiomarina (Jean et al, 2006). Several species of the genus Pseudidiomarina are non-motile, while all species of the genus Idiomarina are motile by means of flagella.…”

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confidence: 99%

Pseudidiomarina aestuarii sp. nov., a marine bacterium isolated from shallow coastal seawater

Park

Lim

Baik

et al. 2010

International Journal of Systematic and Evolutionary Microbiology

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A non-motile, rod-shaped and aerobic marine bacterium, designated strain KYW314 T , was isolated from seawater collected from the South Sea, Republic of Korea. Cells were Gramnegative, catalase-and oxidase-positive and had proteolytic activity. The major fatty acids were iso-C 15 : 0 (17.2 %), C 16 : 0 (11.1 %), iso-C 17 : 0 (10.5 %) and C 18 : 1 v7c (10.0 %). The DNA G+C content was 56.4 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain KYW314 T formed a lineage within the genus Pseudidiomarina (95.4-97.3 % sequence similarity) and a distinct branch within the clade containing Pseudidiomarina taiwanensis PIT1 T and Pseudidiomarina sediminum c121 T . Phenotypic characteristics could distinguish strain KYW314 T from members of the genus Pseudidiomarina. On the basis of the data presented, strain KYW314 T represents a novel species, for which the name Pseudidiomarina aestuarii sp. nov. is proposed. The type strain is KYW314 T (5KCTC 22740 T 5JCM 16344 T ).A study of Alteromonas-like bacteria by Ivanova et al. (2004) resulted in the proposal of the family Idiomarinaceae, on the basis of phylogeny and signature nucleotide positions in the 16S rRNA gene. Members of the family Idiomarinaceae are unique among Alteromonas-like bacteria in possessing a high content of iso-branched fatty acids (Ivanova et al., 2004). The family Idiomarinaceae comprises two recognized genera: Idiomarina (Ivanova et al., 2000) as the type genus and Pseudidiomarina (Jean et al., 2006). Several species of the genus Pseudidiomarina are non-motile, while all species of the genus Idiomarina are motile by means of flagella.At the time of writing, the genus Pseudidiomarina comprises eight species, with Pseudidiomarina taiwanensis as the type species (Jean et al., 2006(Jean et al., , 2009Hu & Li, 2007;Wu et al., 2009). Members of the genus Pseudidiomarina have been isolated from saline habitats with a wide range of salinities such as coastal and oceanic waters, seashore sands, coastal sediment and solar salterns (Jean et al., 2006(Jean et al., , 2009Kwon et al., 2006;Yoon et al., 2007;Hu & Li, 2007;Wu et al., 2009). During a survey of the diversity of heterotrophic marine bacteria, a bacterial strain, KYW314 T , was recovered from seawater samples collected from the shallow coastal region of Gwangyang Bay in the south of the Republic of Korea (34 u 519 N 128 u 479 E) in July 2008. Strain KYW314 T was isolated from seawater using the standard dilution-plating technique. Isolation was achieved using marine agar 2216 (MA; BD) (Yang et al., 2006) at 30 u C for 7 days. The isolate was routinely cultured on MA and maintained at -80 u C as a suspension in marine broth (MB; BD) containing glycerol (20 %, w/v).DNA preparation and PCR amplification and sequencing of the 16S rRNA gene were carried out as described by Chun & Goodfellow (1995). Identification of phylogenetic neighbours and calculation of pairwise 16S rRNA gene sequence similarities were achieved using the EzTaxon server (http:// www.eztaxon.org/; Chun et al., 2007). ...

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“…However, the species of Pseudidiomarina were recently reassigned to the genus Idiomarina (Taborda et al, 2009) because of the difficulty in differentiating the two genera by phenotypic characteristics. At the time of writing, the genus Idiomarina accommodated 16 species, Idiomarina abyssalis (Ivanova et al, 2000), I. baltica (Brettar et al, 2003), I. fontislapidosi (Martínez-Cánovas et al, 2004), I. loihiensis (Donachie et al, 2003), I. ramblicola (Martínez-Cánovas et al, 2004), I. seosinensis (Choi & Cho, 2005), I. zobellii (Ivanova et al, 2000), I. insulisalsae, I. taiwanensis, I. homiensis, I. marina, I. salinarum, I. sediminum and I. tainanensis (Taborda et al, 2009), and I. donghaiensis and I. maritima (Wu et al (2009); the latter eight formerly belonged to the genus Pseudidiomarina. Members of the genus Idiomarina have been isolated from saline habitats with a wide range of salinity, such as coastal and oceanic waters, coastal sediments, inland hypersaline wetlands, solar salterns and submarine hydrothermal fluids.…”

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confidence: 99%

Aliidiomarina taiwanensis gen. nov., sp. nov., isolated from shallow coastal water

Huang

Chang

Chen

et al. 2012

International Journal of Systematic and Evolutionary Microbiology

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A Gram-negative, heterotrophic, aerobic, marine bacterium, designated AIT1T, was isolated from a seawater sample collected in the shallow coastal region of Bitou Harbour, New Taipei City, Taiwan. Cells grown in broth cultures were straight or slightly curved rods that were motile by means of a single polar flagellum. Strain AIT1T required NaCl for growth, grew optimally at 30–40 °C and with 1.5–5.0 % NaCl, and was incapable of anaerobic growth by fermentation of glucose or other carbohydrates. The isoprenoid quinones consisted of Q-8 (95.2 %) and Q-9 (4.8 %). The major polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The cellular fatty acids were predominantly iso-branched and included iso-C17 : 0 (26.5 %), summed feature 9 (comprising iso-C17 : 1ω9c and/or 10-methyl C16 : 0; 25.9 %) and iso-C15 : 0 (20.5 %). The DNA G+C content was 51.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain AIT1T formed a distinct lineage within the class Gammaproteobacteria and was most closely related to members of the genus Idiomarina in the family Idiomarinaceae (91.5–93.9 % 16S rRNA gene sequence similarity). The phylogenetic data, together with chemotaxonomic, physiological and morphological data, revealed that the isolate should be classified as a representative of a novel species in a new genus in the family Idiomarinaceae, for which the name Aliidiomarina taiwanensis gen. nov., sp. nov. is proposed. The type strain is AIT1T ( = JCM 16052T = BCRC 80035T = NCCB 100321T).

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Idiomarina gen. nov., comprising novel indigenous deep-sea bacteria from the Pacific Ocean, including descriptions of two species, Idiomarina abyssalis sp. nov. and Idiomarina zobellii sp. nov.

Cited by 130 publications

References 26 publications

Genome sequence of the deep-sea γ-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy

Genome sequence of the deep-sea γ-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy

Pseudidiomarina aestuarii sp. nov., a marine bacterium isolated from shallow coastal seawater

Aliidiomarina taiwanensis gen. nov., sp. nov., isolated from shallow coastal water

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