Idiomarina loihiensis sp. nov., a halophilic  -Proteobacterium from the Lo'ihi submarine volcano, Hawai'i

Donachie, Stuart P.; Hou, Shaobin; Gregory, T.; Malahoff, Alexander; Alam, Maqsudul

doi:10.1099/ijs.0.02701-0

Cited by 74 publications

(45 citation statements)

References 33 publications

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“…The genus Idiomarina has a unique fatty acid composition with a high percentage of iso-branched fatty acids (21). Compared to other Idiomarina spp., I. loihiensis has twice the percentage of saturated fatty acids (6). Indeed, I. loihiensis genome revealed a complete set of enzymes for fatty acid biosynthesis.…”

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%

“…nov. is a ␥-proteobacterium, isolated recently from the hydrothermal vents on the Lo 'ihi Seamount, Hawaii (6). In contrast to obligate anaerobic vent hyperthermophiles Thermotoga spp.…”

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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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“…Of particular importance to diversity studies, 55 cultivated taxa shared o97% identity with published sequences, and 52 of these from seven phyla were absent from the study's clone libraries. The defining phenotypic traits of four new species were not detected by the ribosomal approach (Donachie et al, 2003(Donachie et al, , 2004b(Donachie et al, , 2005(Donachie et al, , 2006. Cultivating so many Bacteria not represented in a clone library demonstrates that a significant fraction of diversity would have been overlooked had only 16S rDNA clone libraries been analyzed.…”

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confidence: 99%

Culture clash: challenging the dogma of microbial diversity

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 loihiensis sp. nov., a halophilic -Proteobacterium from the Lo'ihi submarine volcano, Hawai'i

Cited by 74 publications

References 33 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

Culture clash: challenging the dogma of microbial diversity

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

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