Sea‐floor fissures, biological communities and sediment fatty acids of the Northern Okushiri Ridge, Japan Sea: Implications for possible methane seepage

Naganuma, Takeshi; Meisel, C. Julius; Wada, Hideki; Kato, Y.; Takeuchi, Akira; Fujikura, Katsunori; Naka, Jiro; Fujioka, Kantaro

doi:10.1046/j.1440-1738.1999.00234.x

Cited by 10 publications

(6 citation statements)

References 20 publications

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“…The anoxic nature of these habitats may account for the divergence of the genes for anaerobic RuBisCO form II (15,45).…”

Section: Resultsmentioning

confidence: 99%

“…Reducing sediments were collected from the known and presumed seeps: (i) a bathyal methane seep (1,199 m deep) at Sagami Trough, central Japan, collected by the DSV Shinkai 2000 (JAMSTEC); (ii) a hadal seep (7,434 m deep) in the Japan Trench, collected by the ROV Kaiko (JAMSTEC); and (iii) a presumed seep (1,709 m deep) at Northern Okushiri Ridge, northern Japan, collected by the DSV Shinkai 2000. This presumed seep was suggested on the basis of observation of bacterial mats and unidentified isopods and gastropods in association with fissures at this site, which was the epicenter of the Hokkaido Nanseioki earthquake in July 1993 (45). All the sediment samples were taken by push-core samplers, and the microbiological samples were scooped from inside of the cores about 1 to 5 cm below the top.…”

Section: Methodsmentioning

confidence: 92%

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Phylogenetic Diversity of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Large-Subunit Genes from Deep-Sea Microorganisms

Elsaied

Naganuma

2001

Appl Environ Microbiol

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The phylogenetic diversity of the ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO, E.C. 4.1.1.39) large-subunit genes of deep-sea microorganisms was analyzed. Bulk genomic DNA was isolated from seven samples, including samples from the Mid-Atlantic Ridge and various deep-sea habitats around Japan. The kinds of samples were hydrothermal vent water and chimney fragment; reducing sediments from a bathyal seep, a hadal seep, and a presumed seep; and symbiont-bearing tissues of the vent mussel, Bathymodiolus sp., and the seep vestimentiferan tubeworm, Lamellibrachia sp. The RuBisCO genes that encode both form I and form II large subunits (cbbL and cbbM) were amplified by PCR from the seven deep-sea sample DNA populations, cloned, and sequenced. From each sample, 50 cbbL clones and 50 cbbM clones, if amplified, were recovered and sequenced to group them into operational taxonomic units (OTUs). A total of 29 OTUs were recorded from the 300 total cbbL clones, and a total of 24 OTUs were recorded from the 250 total cbbM clones. All the current OTUs have the characteristic RuBisCO amino acid motif sequences that exist in other RuBisCOs. The recorded OTUs were related to different RuBisCO groups of proteobacteria, cyanobacteria, and eukarya. The diversity of the RuBisCO genes may be correlated with certain characteristics of the microbial habitats. The RuBisCO sequences from the symbiont-bearing tissues showed a phylogenetic relationship with those from the ambient bacteria. Also, the RuBisCO sequences of known species of thiobacilli and those from widely distributed marine habitats were closely related to each other. This suggests that the Thiobacillus-related RuBisCO may be distributed globally and contribute to the primary production in the deep sea.Phylogenetic information on deep-sea microorganisms that has been accumulated relates mainly to the 16S ribosomal DNA (rDNA) sequences (9,33,53). In understanding the microbial contribution to deep-sea primary production, the 16S rDNA-based phylogeny will be better complemented by knowledge of the genes encoding the enzymes relevant to carbon fixation. The genes encoding ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) represent such an enzyme that is involved in autotrophy. RuBisCO is the most abundant enzyme on the globe and has attracted much phylogenetic attention (5). RuBisCO catalyzes the assimilation of carbon dioxide to organic carbon via the Calvin-Benson cycle. The enzyme consists of large and small subunits (42). The site responsible for carbon fixation is in the large subunit (42). More than 20% of the amino acid residues in the large subunit are conserved among the higher plants (32). Generally, RuBisCO has two forms. Form I consists of large and small subunits (L n S n , typically L 8 S 8 ), and form II contains only large subunits (L n ) with 25 to 30% amino acid sequence identity with those of form I (32). The large subunits of form I and form II are coded by genes designated cbbL and cbbM, respectively (37). Some organisms have two genes en...

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“…The anoxic nature of these habitats may account for the divergence of the genes for anaerobic RuBisCO form II (15,45).…”

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 92%

Phylogenetic Diversity of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Large-Subunit Genes from Deep-Sea Microorganisms

Elsaied

Naganuma

2001

Appl Environ Microbiol

Self Cite

126

132

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“…Orange deposits covered approximately 100 m 2 . Naganuma et al (1999) suggested these orange deposits have high bacterial activity, and Tsunogai et al (1996) showed that temperatures are more than 10°C higher below the orange seabed than in ambient water. Black layers in the sediment indicative of a reducing environment were attributed to anaerobic bacterial activity.…”

Section: Survey Fields and Diving Surveysmentioning

confidence: 99%

Estimated Population Densities of Megafauna in Two Chemosynthesisbased Communities: a Cold Seep in Sagami Bay and a Hydrothermal Vent in the Okinawa Trough

2002

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This study investigates the population density characteristics of the megafauna at two previously described chemosynthesis-based communities associated with cold seepage at the Off Hatsushima Island site (OHl) in Sagami Bay and hytlrothermalism at the Minami-Ensei Knoll (MEK) in the Okinawa Trough. Quantitative sampling was conducted using a submersible, ROV and Deep Tow Camera array near each community. A total of 26 and 27 megafaunal species were recorded at OHI and MEK, respectively. The dominant organism with respect to population density was the provannid snail Provanna glabra at OHI. This species also occurred at MEK, but it had a lower density than at OHL Instead, Cantrainea jamsteci was the dominant gastropod species at MEK. The community at MEK was dominated with respect to population density by the symbiont-containing mussel Bathymodiolus japonicus, but this species was not so common at OHI. The mean population densities of almost all megafaunal species, except for a few conspicuously predominant species at OHI and MEK, are similar to those for the dominant species in other deep-sea photosynthesis-based communities. Both sites were characterized by large populations of only a few dominant species (Provanna glabra, Calyptogena okutanii, and C. soyoae at OHI and Bathymodiolus japonicus at MEK). This pattern may be due to the extreme environments that occur near chemosynthesis-based communities.

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“…Ester‐linked phospholipid fatty acids are the major constituents of intact cell membranes of eukarya and bacteria, and, thus, are regarded as biomarkers for live cells (Findlay & Dobbs 1993). The number of PLFA forms is also the measure of microfloral diversity (Naganuma et al . 1999, 2001).…”

Section: Resultsmentioning

confidence: 99%

“…1991), and sea floor fissures with associated bacterial mats were observed in the western slope (Takeuchi et al . 1992; Naganuma et al . 1999).…”

Section: Introductionmentioning

confidence: 99%

Geological and microbial anomalies in the extinct submarine volcano, Shiribeshi Seamount, in the eastern margin of the Japan Sea

Ogawa¹,

Takeuchi²,

Hattori³

et al. 2002

Island Arc

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The manned submersible Shinkai 2000 investigated yellow patches on the near‐summit slope of Shiribeshi Seamount in the Japan Sea. Yellowish patches are often associated with seepage, and the possibility of seepage at Shiribeshi Seamount was tested by the following four lines of observation: (i) high subsurface temperature was measured at a ring‐like patch, although no increase in subsurface temperature was observed at other patches; (ii) high gamma ray (γ‐ray) intensity from the thorium series was recorded in the patch zone; (iii) the yellowish deposit was composed of calcite, quartz and amorphous iron compound, as seen at the yellowish patches in other seeps and volcanoes; (iv) lipid phosphate, a measure of microbial abundance, in sediments of the ring‐like patch was determined, and the recorded microbial abundance was higher inside the patch than outside it. The four lines of observation are explained consistently by postulating that the seepage of warm fluid contained Fe and γ‐ray sources. A hydrothermal origin of the yellow patches is not ruled out for the extinct but young (0.9 Ma) arc volcano.

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Sea‐floor fissures, biological communities and sediment fatty acids of the Northern Okushiri Ridge, Japan Sea: Implications for possible methane seepage

Cited by 10 publications

References 20 publications

Phylogenetic Diversity of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Large-Subunit Genes from Deep-Sea Microorganisms

Phylogenetic Diversity of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Large-Subunit Genes from Deep-Sea Microorganisms

Estimated Population Densities of Megafauna in Two Chemosynthesisbased Communities: a Cold Seep in Sagami Bay and a Hydrothermal Vent in the Okinawa Trough

Geological and microbial anomalies in the extinct submarine volcano, Shiribeshi Seamount, in the eastern margin of the Japan Sea

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