Deep-Sea Microbiology

Jannasch, Holger W.; Taylor, Craig D.

doi:10.1146/annurev.mi.38.100184.002415

Cited by 234 publications

(84 citation statements)

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“…I. loihiensis maintains several diverged copies of genes for fatty acid synthesis. Given that the composition and modification of fatty acids plays a crucial role in maintaining cell membrane integrity in deep-sea microorganisms (22), and further analysis of these genes could help understand the regulation of membrane fluidity under constantly changing pressure and temperature.…”

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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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%

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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“…Menzies et al 1967;Schoener and Rowe 1970;Wiebe et al, 1976;Suchanek et al 1985;Wolff 1979) and pelagic animals (e.g. Jannasch 1978;Cacchione et al 1978), have been observed on the deep sea floor and are also passively transported through the water column. These larger parcels are generally not sampled by sediment traps (McCave 1975).…”

Section: Discussionmentioning

confidence: 99%

Food energy supply and demand: A discrepancy between particulate organic carbon flux and sediment community oxygen consumption in the deep ocean1

Smith¹

1987

Limnology & Oceanography

184

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Sediment community oxygen consumption (SCOC) and particulate organic carbon (POC) flux to the benthic boundary layer were concurrently measured at five deep-sea stations on a transect across the eastern and central North Pacific at various times of year. A free vehicle grab respirometer and Alvin-manipulated grab respirometer were used to measure SCOC. Paired particle interceptor traps (PITS) were used to collect sedimenting small POC at 100 and 600 m above the bottom. SCOC decreased across the transect from the eutrophic coastal areas off southern California to the oligotrophic central Pacific gyre. These rates were generally highest in June and lowest between fall and early spring across the transect with a recurrent pattern in the magnitude of rates measured during the same months but different years. Flux of POC into the benthic boundary layer decreased across the transect from the eutrophic eastern to the oligotrophic central Pacific. No consistent temporal trends were evident in POC flux across the transect, possibly because of small sample sizes, high intra-station variability, and short-term deployments (57 d). Comparison of concurrently measured supply of POC with organic carbon demand of the sediment community as estimated from SCOC reveals a supply deficit across the transect for all seasons measured. For one nearly synoptic sampling period across the transect in June 1982, the supply-to-demand ratio is lowest at the two nearshore stations where current speeds are highest. A predictive equation for SCOC with a least-squares regression analysis and log-transformed data revealed that POC flux as the independent variable accounted for only 59% of the variability in SCOC. Direct coupling between SCOC and POC flux is not confirmed by these results, which may be attributed to the limitations of the measurements or other organic carbon sources.Sediment community oxygen consumption (SCOC) has been measured at various times of year at five deep sea stations on a transect across the eastern and central North Pacific (CNP-ENP transect) over the past 8 yr. Initial results indicated spatial variability in SCOC which increased along a gradient of increasing surface water primary productivity from the oligotrophic central gyre to the more eutrophic coastal upwelling areas off southern California . Temporal variability was also identified in SCOC at two of the transect stations and appeared related to the seasonal productivity of the overlying water (Smith and Baldwin 1984a). This result is not surprising given recent reports of seasonal fluctuations in the fluxes of small organic particles to abyssal depths (Deuser and Ross 1980; l This research was supported by NSF grants OCE 81-17661, OCE 84-09075, and OCE 84-17913 and a contract from Sandia Laboratories. Deuser et al. 198 1;Honjo 1982;Billett et al. 1983;Cole et al. 1985)-a source of food supply for deep sea benthos. The next logical step is to explore the possible coupling between this food supply from the overlying water column and the food demand of...

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“…nov. is proposed. The type strain is M41 T (5DSM 18887 T 5LMG 24143 T ).The deep sea is an extreme habitat in which organisms need to adapt to such factors as high pressure, low nutrient concentrations, low temperatures, darkness and irregular food availability (Jannasch & Taylor, 1984). At deep-sea hydrothermal vent fields, organisms also have to deal with steep physico-chemical gradients such as extremely large ranges in temperature, heavy-metal concentrations, oxygen supply and pH (Kelley et al, 2002).…”

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confidence: 99%

Amphritea atlantica gen. nov., sp. nov., a gammaproteobacterium from the Logatchev hydrothermal vent field

Gärtner

Wiese

Imhoff

2008

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLO

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A novel Gram-negative, motile, aerobic rod-shaped bacterium was isolated from a Bathymodiolus sp. specimen collected from the Logatchev hydrothermal vent field at the Mid-Atlantic Ridge. The novel strain, M41 T , was catalase-and oxidase-positive and metabolised various carbohydrates and amino acids. It grew well in marine broth with an optimal growth temperature of 31 6C to 34 6C (range 4-40 6C) and salinity requirement of 3 % (range 0.3-9 %). The pH range for growth was pH 4.6 to 9.5, with an optimum at pH 8.0. The predominant fatty acids were C 16 : 1 v7c, C 16 : 0 and C 18 : 1 v7c. The DNA G+C content of strain M41 T was 52.2 mol%. The 16S rRNA gene sequence was 94 % similar to that of the type strain of Oceanospirillum beijerinckii, the closest cultivated relative. Other related type strains were Oceanospirillum multiglobuliferum (93 % gene sequence similarity), Neptunomonas naphthovorans (92%) and Marinobacterium jannaschii (92 %). According to phylogenetic analysis and physiological characteristics, it is suggested that strain M41 T represents a new genus and novel species for which the name Amphritea atlantica gen. nov., sp. nov. is proposed. The type strain is M41 T (5DSM 18887 T 5LMG 24143 T ).The deep sea is an extreme habitat in which organisms need to adapt to such factors as high pressure, low nutrient concentrations, low temperatures, darkness and irregular food availability (Jannasch & Taylor, 1984). At deep-sea hydrothermal vent fields, organisms also have to deal with steep physico-chemical gradients such as extremely large ranges in temperature, heavy-metal concentrations, oxygen supply and pH (Kelley et al., 2002). Along these gradients, many microhabitats are formed and a high diversity of micro-organisms can develop. Even though an increasing number of bacterial clone sequences in the databases originate from deep-sea habitats and also from deep-sea hydrothermal fields ( Phylogenetic information derived from 16S rRNA gene sequences does not provide ecological or physiological information that could support the functional characterization of these extreme habitats. Hence, cultivation approaches are necessary and need to be applied. Moreover, micro-organisms from extreme marine environments are considered as a rich source for the detection of new secondary metabolites, new metabolic pathways and new enzymes and therefore have become a special focus of research in recent years (Faulkner, 2000;Haefner, 2003;Jensen & Fenical, 1994;Kelecom, 2002).As part of a study of the microbial biodiversity of hydrothermal vents in the Mid-Atlantic Ridge, we have isolated numerous bacteria living in habitats influenced by hydrothermal activity. Among these, a novel Gramnegative, mesophilic, rod-shaped gammaproteobacterium, strain M41 T , showed less than 94 % 16S rRNA gene sequence similarity to any other recognized bacterium. In this study, the novel isolate was characterized by phenotypic and phylogenetic analyses and is proposed to be a member of a new genus and novel species.Strain M41 T was isolated by t...

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Deep-Sea Microbiology

Cited by 234 publications

References 0 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

Food energy supply and demand: A discrepancy between particulate organic carbon flux and sediment community oxygen consumption in the deep ocean1

Amphritea atlantica gen. nov., sp. nov., a gammaproteobacterium from the Logatchev hydrothermal vent field

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