Cold Methane Seeps Research Articles

Numerical modeling study of mineralization induced by methane cold seep at the sea bottom

In order to investigate the response of authigenic minerals to gas hydrate geo-systems, the biogeochemical processes and its induced mineralization were predicted by employing the comprehensive reactive transport modeling approach. Based on the available data extracted from the northern continental slope area of the South China Sea, a 1-D vertical column model was developed. Three cases with different upward methane flux rates and three cases with different mineral compositions, i.e., a total of six cases were designed to investigate the effects of variations in the depth of sulfate methane transition zone (SMTZ) and in the mineral composition on the formation of authigenic minerals. The simulation results indicate that the SMTZ depth influenced by both the upward methane flux rate and the initial composition played an important role in the formation of authigenic minerals. The AOM reaction is intensive at the interface, and the precipitation amount of calcite is large, which is mainly controlled by AOM. When the methane leakage rate is 20 times higher than the base case, aragonite starts to precipitate. During the simulation, oligoclase, k-feldspar, smectite-Na, smectite-Ca, chlorite dissolved. Our study specific to this area as a starting point may provide a quantitative approach for investigating carbonate and pyrite formation in hydrate-bearing sediments accounting for methane oxidation and sulfate reduction. The method presented here and the model built in this study can be used for other sites with similar conditions. In addition, this study may serve as an indication for the potential natural gas hydrate reservoir in depth, and is also significant for marine carbon and sulfur cycle.

Methylovulum psychrotolerans sp. nov., a cold-adapted methanotroph from low-temperature terrestrial environments, and emended description of the genus Methylovulum.

Two isolates of aerobic methanotrophic bacteria, strains Sph1T and Sph2, were obtained from cold methane seeps in a floodplain of the river Mukhrinskaya, Irtysh basin, West Siberia. Another morphologically and phenotypically similar methanotroph, strain OZ2, was isolated from a sediment of a subarctic freshwater lake, Archangelsk region, northern Russia. Cells of these three strains were Gram-stain-negative, light-pink-pigmented, non-motile, encapsulated, large cocci that contained an intracytoplasmic membrane system typical of type I methanotrophs. They possessed a particulate methane monooxygenase enzyme and utilized only methane and methanol. Strains Sph1T, Sph2 and OZ2 were able to grow at a pH range of 4.0-8.9 (optimum at pH 6.0-7.0) and at temperatures between 2 and 36 °C. Although their temperature optimum was at 20-25 °C, these methanotrophs grew well at lower temperatures, down to 4 °C. The major cellular fatty acids were C16 : 1ω5c, C16 : 1ω6c, C16 : 1ω7c, C16 : 1ω8c, C16 : 0 and C14 : 0; the DNA G+C content was 51.4-51.9 mol%. Strains Sph1T, Sph2 and OZ2 displayed nearly identical (99.1-99.7 % similarity) 16S rRNA gene sequences and belonged to the family Methylococcaceae of the class Gammaproteobacteria. The most closely related organism was Methylovulum miyakonense HT12T (96.0-96.5 % 16S rRNA gene sequence similarity and 90 % pmoA sequence similarity). The novel isolates, however, differed from Methylovulum miyakonense HT12T by cell morphology, pigmentation, absence of soluble methane monooxygenase, more active growth at low temperatures, growth over a broader pH range and higher DNA G+C content. On the basis of these differences, we propose a novel species, Methylovulum psychrotolerans sp. nov., to accommodate these methanotrophs. Strain Sph1T (=LMG 29227T=VKM B-3018T) is the type strain.

Transformation of Organic Matter by a Microbial Community in Sediments of Lake Baikal under Experimental Thermobaric Conditions of Protocatagenesis

ABSTRACTEarly diagenesis of organic matter in bottom sediments of Lake Baikal is a focus of many geochemical studies, because it is one of the few sites of petroleum formation in a nonmarine environment. Although Baikal is a rift lake and considered one of the prospective fields for deep biosphere investigations, the transformation processes of organic matter by microbial communities from deep bottom sediments and likely entering of the microorganisms from deep sediments into the near-surface sediments were not previously studied in Lake Baikal. The natural microbial community from near-surface sediments of the cold methane seep Goloustnoe (Southern Baikal Basin) was incubated with methane and the diatom Synedra acus at 80°C and 49.5 atm to simulate catagenesis. The 11-month incubation yielded the enrichment culture of viable thermophilic microorganisms. Their presence in low-temperature sediment layers may be indicative of their migration through fault zones together with gas-bearing fluids. After culturing, molecular biological methods allowed for the detection of both widespread microorganisms and unique clones whose phylogenetic status is currently unknown. The sediment after the experiment showed the formation of polycyclic aromatic hydrocarbon, retene. Retene can be either a conifer or algal biomarker, thus, interpretation of paleoclimate data is tenuous.

A unique isotopic fingerprint of sulfate-driven anaerobic oxidation of methane

Research Article| July 01, 2015 A unique isotopic fingerprint of sulfate-driven anaerobic oxidation of methane Gilad Antler; Gilad Antler 1Department of Earth Sciences, University of Cambridge, Cambridge CB2 3EQ, UK Search for other works by this author on: GSW Google Scholar Alexandra V. Turchyn; Alexandra V. Turchyn 1Department of Earth Sciences, University of Cambridge, Cambridge CB2 3EQ, UK Search for other works by this author on: GSW Google Scholar Barak Herut; Barak Herut 2Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa 31080, Israel Search for other works by this author on: GSW Google Scholar Orit Sivan Orit Sivan 3Department of Geological and Environmental Sciences, Ben Gurion University of the Negev, Beer-Sheva 84105, Israel Search for other works by this author on: GSW Google Scholar Geology (2015) 43 (7): 619–622. https://doi.org/10.1130/G36688.1 Article history received: 08 Feb 2015 rev-recd: 29 Apr 2015 accepted: 29 Apr 2015 first online: 09 Mar 2017 Cite View This Citation Add to Citation Manager Share Icon Share Facebook Twitter LinkedIn MailTo Tools Icon Tools Get Permissions Search Site Citation Gilad Antler, Alexandra V. Turchyn, Barak Herut, Orit Sivan; A unique isotopic fingerprint of sulfate-driven anaerobic oxidation of methane. Geology 2015;; 43 (7): 619–622. doi: https://doi.org/10.1130/G36688.1 Download citation file: Ris (Zotero) Refmanager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentBy SocietyGeology Search Advanced Search Abstract The largest reservoir of the powerful greenhouse gas methane is in marine sediments, and catastrophic release of this methane has been invoked to explain climate perturbations throughout Earth history. Marine methane oxidation is mainly coupled anaerobically to microbial sulfate reduction, which both limits and controls the release of methane from this sedimentary reservoir to the rest of Earth’s surface. Methane can be transported within the pore space of marine sediments either via diffusion or as bubbles. When methane travels in bubbles, these bubbles often are not completely oxidized and reach the overlying water where the methane emerges from the sediment in cold seeps. Although paleo–cold seeps can be identified by geological features such as carbonate mounds, a geochemical signature for cold seeps remains elusive. We demonstrate, using the sulfur and oxygen isotope composition of sulfate, that a unique isotopic signature emerges during microbial sulfate reduction coupled to methane oxidation in bubbling cold seeps. This isotope signature differs from that when sulfate is reduced by either organic matter oxidation or by the slower, diffusive flux of methane within marine sediments. We also show, through a comparison with the literature, that this unique isotope fingerprint is preserved in the rock record in authigenic buildups of barite associated with methane cold seeps. You do not have access to this content, please speak to your institutional administrator if you feel you should have access.

A carbonate platform associated with shallow cold methane seeps in Golfo Dulce, Pacific Costa Rica

A carbonate platform associated with shallow cold methane seeps in Golfo Dulce, Pacific Costa Rica

Cryptic species ofArchinome(Annelida: Amphinomida) from vents and seeps

Since its description from the Galapagos Rift in the mid-1980s, Archinome rosacea has been recorded at hydrothermal vents in the Pacific, Atlantic and Indian Oceans. Only recently was a second species described from the Pacific Antarctic Ridge. We inferred the identities and evolutionary relationships of Archinome representatives sampled from across the hydrothermal vent range of the genus, which is now extended to cold methane seeps. Species delimitation using mitochondrial cytochrome c oxidase subunit I (COI) recovered up to six lineages, whereas concatenated datasets (COI, 16S, 28S and ITS1) supported only four or five of these as clades. Morphological approaches alone were inconclusive to verify the identities of species owing to the lack of discrete diagnostic characters. We recognize five Archinome species, with three that are new to science. The new species, designated based on molecular evidence alone, include: Archinome levinae n. sp., which occurs at both vents and seeps in the east Pacific, Archinome tethyana n. sp., which inhabits Atlantic vents and Archinome jasoni n. sp., also present in the Atlantic, and whose distribution extends to the Indian and southwest Pacific Oceans. Biogeographic connections between vents and seeps are highlighted, as are potential evolutionary links among populations from vent fields located in the east Pacific and Atlantic Oceans, and Atlantic and Indian Oceans; the latter presented for the first time.

Effects of the oophagous bivalve Acesta oophaga on the morphology and fecundity of its deep‐sea tubeworm host, Lamellibrachia luymesi

AbstractThe deep‐sea bivalve Acesta oophaga lives attached to the anterior end of the vestimentiferan tubeworm, Lamellibrachia luymesi, at cold methane seeps. The bivalve is found almost exclusively on female tubeworms, where it consumes the lipid‐rich eggs of L. luymesi that are spawned year round (Biological Bulletin, 209, 2005, 87). It is apparent that A. oophaga benefits directly from this close association, but the consequences for the tubeworm host may be more complicated than just a simple predator–prey interaction. Since A. oophaga completely surrounds the tube opening and plume of the worm, it is likely that its presence would limit oxygen uptake by L. luymesi, thereby inhibiting worm growth and reproduction. We hypothesized that occupied tubeworms would compensate for this by growing larger plumes for oxygen uptake. To explore the effects of bivalve presence/absence on female tubeworms, several morphological features, including body size, plume length, tube diameter, and tube segment length, as well as instantaneous fecundity, were compared. Results suggest that the mere presence of A. oophaga has a significant impact on the morphology of its host worm, as all measures of worm size, except for tube segment length, were significantly greater with clams present. Additionally, instantaneous fecundity was 3.5 times higher in occupied worms, implying that tubeworms are not oxygen‐deprived or energy limited as a result of bivalve presence. Our findings suggest that the association between these two deep‐sea organisms may be a more complex form of symbiosis than the simple predator–prey relationship, as previously thought.

A New Species ofHoploscaphites(Ammonoidea: Ancyloceratina) from Cold Methane Seeps in the Upper Cretaceous of the U.S. Western Interior

We describe Hoploscaphites gilberti, n. sp. (Ammonoidea: Ancyloceratina), from the Upper Cretaceous (middle-upper Campanian) Pierre Shale spanning the zones of Baculites scotti and Didymoceras nebrascense in Colorado, Wyoming, Montana, and South Dakota. This species is strongly dimorphic and is characterized by a compressed whorl section, with a rounded to elongate outline in lateral view. The apertural angle is approximately 50° in macroconchs. The body chamber is ornamented with fine flexuous ribs, umbilicolateral bullae, and ventrolateral tubercles. Hoploscaphites gilberti, n. sp., most closely resembles H. gilli Cobban and Jeletzky, 1965, but differs from this species in several important features: (1) the flanks of the body chamber are nearly subparallel rather than steeply convergent toward the venter, (2) the ventrolateral tubercles are larger and more numerous, and (3) the ribs are more widely spaced. Hoploscaphites gilberti, n. sp., is abundant at “tepee buttes” in the Pierre Shale, which are now interpreted as cold methane seeps.

Molecular evidence that deep‐branching fungi are major fungal components in deep‐sea methane cold‐seep sediments

The motile cells of chytrids were once believed to be relics from the time before the colonization of land by fungi. However, the majority of chytrids had not been found in marine but freshwater environments. We investigated fungal diversity by a fungal-specific PCR-based analysis of environmental DNA in deep-sea methane cold-seep sediments, identifying a total of 35 phylotypes, 12 of which were early diverging fungi (basal fungi, ex 'lower fungi'). The basal fungi occupied a major portion of fungal clones. These were phylogenetically placed into a deep-branching clade of fungi and the LKM11 clade that was a divergent group comprised of only environmental clones from aquatic environments. As suggested by Lara and colleagues, species of the endoparasitic genus Rozella, being recently considered of the earliest branching taxa of fungi, were nested within the LKM11 clade. In the remaining 23 phylotypes identified as the Dikarya, the majority of which were similar to those which appeared in previously deep-sea studies, but also highly novel lineages associated with Soil Clone Group I (SCGI), Entorrhiza sp. and the agaricomycetous fungi were recorded. The fungi of the Dikarya may play a role in the biodegradation of lignin and lignin-derived materials in deep-sea, because the characterized fungal species related to the frequent phylotypes within the Dikarya have been reported to possess an ability to degrade lignin.

New species of the genus Isorropodon (Bivalvia: Vesicomyidae: Pliocardiinae) from cold methane seeps at Nyegga (Norwegian Sea, Vøring Plateau, Storrega Slide)

A new species of vesicomyid bivalve (Isorropodon nyeggaensis sp. nov.) is described based on shell morphology, from the Nyegga cold methane seep area on the Norwegian continental margin. This is the first description of vesicomyids from the Norwegian Sea and the northernmost record of recent representatives of the family Vesicomyidae. A dispersion of the genus into the Norwegian Sea basin from the north-eastern Atlantic is suggested. A brief description of other macrofauna from methane seep sites at Nyegga is also given.

Anaerobic Oxidation of Methane at a Marine Methane Seep in a Forearc Sediment Basin off Sumatra, Indian Ocean

A cold methane seep was discovered in a forearc sediment basin off the island Sumatra, exhibiting a methane-seep adapted microbial community. A defined seep center of activity, like in mud volcanoes, was not discovered. The seep area was rather characterized by a patchy distribution of active spots. The relevance of anaerobic oxidation of methane (AOM) was reflected by 13C-depleted isotopic signatures of dissolved inorganic carbon. The anaerobic conversion of methane to CO2 was confirmed in a 13C-labeling experiment. Methane fueled a vital microbial community with cell numbers of up to 4 × 109 cells cm−3 sediment. The microbial community was analyzed by total cell counting, catalyzed reporter deposition–fluorescence in situ hybridization (CARD–FISH), quantitative real-time PCR (qPCR), and denaturing gradient gel electrophoresis (DGGE). CARD–FISH cell counts and qPCR measurements showed the presence of Bacteria and Archaea, but only small numbers of Eukarya. The archaeal community comprised largely members of ANME-1 and ANME-2. Furthermore, members of the Crenarchaeota were frequently detected in the DGGE analysis. Three major bacterial phylogenetic groups (δ-Proteobacteria, candidate division OP9, and Anaerolineaceae) were abundant across the study area. Several of these sequences were closely related to the genus Desulfococcus of the family Desulfobacteraceae, which is in good agreement with previously described AOM sites. In conclusion, the majority of the microbial community at the seep consisted of AOM-related microorganisms, while the relevance of higher hydrocarbons as microbial substrates was negligible.

An Ordovician “Lost City” — venting serpentinite and life oases on Iapetus seafloor

Highly brecciated carbonate-rich serpentinites (or ophicalcites) of Early Ordovician age in the Dunnage Zone of Quebec are host to fracture-fill, high-temperature (80–230 °C) carbonate cements. Away from, or crosscut by the fractures, centimetre- to decimetre-thick crusts made up of massive to laminated micrite, peloidal layers and threads are associated with low-temperature botryoidal calcite cements. The peloidal masses are characterized by a clotted texture that is reminiscent of interpreted fossilized Ordovician microbial communities. The ophicalcite contains carbonate botryoids, morphology commonly found at shallow reefal margins but also at modern cold CH4 seeps and recently documented at hot CH4 vents from serpentinite, such as the modern Lost City hydrothermal field in the Atlantic Ocean. The δ18OVPDB ratios of the calcite botryoids and peloidal layers indicate formation and (or) precipitation out of cold Ordovician deep-marine waters. To the contrary of botryoids at cold methane seeps, the botryoids associated with the modern and Ordovician hot vents do not show the negative δ13CVPDB ratios indicative of microbial isotopic fractionation. Therefore, any microbial-derived HCO3– has been overwhelmed by the isotopically heavier marine-derived carbon during the open-system diagenesis. Carbonate-rich serpentinites should be carefully revisited in the search for evidence of microbial life in the Precambrian, as the negative δ13CVPDB ratios used as fingerprints of biological activity are not always reliable.

Fungal Diversity in Deep-Sea Environments

Fungi are one of the most important components in ecosystems and they occupy a wide variety of environments by virtue of their highly versatile physiology function. Recently, the presence of fungi in one of the extreme environments, deep-sea, has started to be recognized. In this article, recent scientific findings through the investigation of fungal diversity in deep-sea sediments collected from several deep-sea environments, including water depths of 10,000 m and methane cold-seep sites were described. PCR-mediated analysis revealed the presence of diverse highly novel fungal phylotypes, including new taxonomic groups placed in deep branches within the phylum of Chytridiomycota with Rozella spp. as the closest related organisms, which may provide key insights into the early evolution of fungi.

North Pacific Species of the GenusSolemyaLamarck, 1818 (Bivalvia: Solemyidae), with Notes onAcharax johnsoni(Dall, 1891)

North Pacific species of the family Solemyidae — Petrasma pusilla (Gould, 1861); Solemya valvulus Carpenter, 1864; Solemya panamensis Dall, 1908; Petrasma pervernicosa (Kuroda, 1948); Solemya reidi Bernard, 1980; and Solemya tagiri Okutani, Hashimoto & Miura, 2003 — and the type species of subgenera of the genus Solemya Lamarck, 1818, are re-examined. Five species of the genus Solemya are recognized from the North Pacific: Solemya (Solemya) pusilla (Gould, 1861); Solemya (Solemya) valvulus Carpenter, 1864; Solemya (Solemya) tagiri Okutani, Hashimoto & Miura, 2003; Solemya (Petrasma) panamensis Dall, 1908; and Solemya (Petrasma) pervernicosa Kuroda, 1948. The gutless S. reidi from the northeastern Pacific is synonymized with S. pervernicosa from the northwestern Pacific. Solemya pervernicosa was found in the Sea of Okhotsk and in the Sea of Japan near the coast of Sakhalin Island at the 300–800 m depth and was not previously recorded for Russia. A study of the materials of Acharax johnsoni (Dall, 1891) provided additional data on its distribution and ecology in the Pacific Ocean. This species was found in the Sea of Okhotsk (depth 370–1,515 m), as well as in the Monterey Canyon and Peru-Chile Trench (depth 3,040–4,200 m) in cold methane seep areas. The results of a comparative analysis of subgenera and species of the genus Solemya, descriptions of North Pacific species of the genus Solemya, and additional data on the distribution and ecology of A. johnsoni are presented.

Geological, hydrodynamic and biogeochemical variability of a New Zealand deep-water methane cold seep during an integrated three-year time-series study

Cold seeps are widely distributed on active and passive margins and display considerable temporal variability in terms of gas and fluid expulsion rates and volume, over scales of hours to days. To constrain this variability, two cold seeps, the North and South Tower, located at the Wairarapa Seep site on Opouawe Bank, Cook Strait, New Zealand, were monitored in an integrated geological and biogeochemical study during eight surveys between 2005 and 2008. To ensure sampling of the water column within the flare overlying the seeps the vessel was manoeuvred in response to the backscatter data from a hull-mounted 38 kHz single-beam echo-sounder. High methane concentrations (> 100 nmol l − 1 ) were found within 400–450 m-high flares at both sites, and within an 825 m-high flare at a newly identified seep, southeast of Pahaua Bank. Elevated bottom water methane was also found over newly identified mud volcanoes on the Campbell Bank, Cook Strait. The locations of the seeps appear to be structurally controlled with active methane vents occurring on anticlinal ridges and associated with a 30 m-high normal fault scarp on Opouawe Bank. Fluid flow is facilitated by sedimentary layer permeability properties, structural focusing and dilational fracturing on the crest of a large anticlinal ridge, cored by a seaward-verging reverse fault. The South Tower cold seep did not significantly influence bulk sediment and water column particulates and nutrients, although high bacterial biomass, productivity and methane oxidation rates were associated with elevated methane in the flare. The seep flares exhibited depleted δ 13C–CH 4 values (− 63 to − 70‰), characteristic of shallow biogenic gas sources. Incorporation of the δ 13C–CH 4 and CH 4 concentration data in a mixing model, and comparison of the water residence time with methane oxidation rates, indicated that the primary fate of methane in the flare was dilution. The dissolved methane originating from the seeps was retained in the water column at depths > 700 m, with minimal contribution to atmospheric emissions, as confirmed by surface methane mapping. Nevertheless, the South Tower seep was a significant source of methane with a column-integrated burden below 700 m of 5.6 mmol m − 2 , and an estimated annual emission of 0.5–1 × 10 6 mol CH 4. The structural and tectonic setting of the Wairarapa Seep provides a useful analogue model for other convergent margin cold seeps on the Hikurangi Margin and elsewhere. This unique, three-year integrated study provided valuable insights into the linkage between geological structure and overlying water column biogeochemistry, and confirmed the value of this cold seep site for long-term monitoring.

Structure of an F430 Variant from Archaea Associated with Anaerobic Oxidation of Methane

Microbial mats collected at cold methane seeps in the Black Sea carry out anaerobic oxidation of methane (AOM) to carbon dioxide using sulfate as the electron acceptor. These mats, which predominantly consist of sulfate-reducing bacteria and archaea of the ANME-1 and ANME-2 type, contain large amounts of proteins very similar to methyl-coenzyme M reductase from methanogenic archaea. Mass spectrometry of mat samples revealed the presence of two nickel-containing cofactors in comparable amounts, one with the same mass as coenzyme F430 from methanogens (m/z = 905) and one with a mass that is 46 Da higher (m/z = 951). The two cofactors were isolated and purified, and their constitution and absolute configuration were determined. The cofactor with m/z = 905 was proven to be identical to coenzyme F430 from methanogens. For the m/z = 951 species, high resolution ICP-MS pointed to F430 + CH2S as the molecular formula, and LA-ICP-SF MS finally confirmed the presence of one sulfur atom per nickel. Esterification gave two stereoisomeric pentamethyl esters with m/z = 1021, which could be purified by reverse phase HPLC and were subjected to comprehensive NMR analysis, allowing determination of their constitution and configuration as (17(2)S)-17(2)-methylthio-F430 pentamethyl ester and (17(2)R)-17(2)-methylthio-F430 pentamethyl ester. The corresponding diastereoisomeric pentaacids could also be separated by HPLC and were correlated to the esters via mild hydrolysis of the latter. Equilibration of the pentaacids under acid catalysis showed that the (17(2)S) isomer is the naturally occurring albeit thermodynamically less stable one. The more stable (17(2)R) isomer (80% at equilibrium) is an isolation artifact generated under the acidic conditions necessary for the isolation of the cofactors from the calcium carbonate-encrusted mats.

Carbon isotope evidence for widespread methane seeps in the ca. 635 Ma Doushantuo cap carbonate in south China

Distinctive sedimentary structures, textures, and extremely negative δ 13 C carb values from the Ediacaran Doushantuo cap carbonate (ca. 635 Ma) in south China were taken as evidence for a methane hydrate destabilization event, but existing data for a methane-derived δ 13 C carb signature were reported from a single locality in the Yangtze Gorges area. Here we report negative δ 13 C carb values as low as −48‰ (Vienna Peedee belemnite) from two additional sections ~6 km and 55 km from the original locality. These negative δ 13 C carb values were obtained from isopachous cements that fill stromatactis-like cavities, sheet cracks, and fractures, and from partially recrystallized carbonate crusts, consistent with carbonate precipitation at cold methane seeps. The new data support a widespread methane release event following the Nantuo glaciation in south China (ca. 635 Ma), which may have contributed to the origin of unusual sedimentary and isotope features of cap carbonates.

Halobacillus profundi sp. nov. and Halobacillus kuroshimensis sp. nov., moderately halophilic bacteria isolated from a deep-sea methane cold seep

Two Gram-positive, rod-shaped, moderately halophilic bacteria were isolated from a deep-sea carbonate rock at a methane cold seep in Kuroshima Knoll, Japan. These bacteria, strains IS-Hb4(T) and IS-Hb7(T), were spore-forming and non-motile. They were able to grow at temperatures as low as 9 degrees C and hydrostatic pressures up to 30 MPa. Based on high sequence similarity of their 16S rRNA genes to those of type strains of the genus Halobacillus, from 96.4 % (strain IS-Hb7(T) to Halobacillus halophilus NCIMB 9251(T)) to 99.4 % (strain IS-Hb4(T) to Halobacillus dabanensis D-8(T)), the strains were shown to belong to this genus. DNA-DNA relatedness values of 49.5 % and 1.0-33.0 %, respectively, were determined between strains IS-Hb4(T) and IS-Hb7(T) and between these strains and other Halobacillus type strains. Both strains showed the major menaquinone MK7 and L-orn-D-Asp cell-wall peptidoglycan type. Straight-chain C(16 : 0), unsaturated C(16 : 1)omega7c alcohol and C(18 : 1)omega7c and cyclopropane C(19 : 0) cyc fatty acids were predominant in both strains. The DNA G+C contents of IS-Hb4(T) and IS-Hb7(T) were respectively 43.3 and 42.1 mol%. Physiological and biochemical analyses combined with DNA-DNA hybridization results allowed us to place strains IS-Hb4(T) (=JCM 14154(T)=DSM 18394(T)) and IS-Hb7(T) (=JCM 14155(T)=DSM 18393(T)) in the genus Halobacillus as the respective type strains of the novel species Halobacillus profundi sp. nov. and Halobacillus kuroshimensis sp. nov.

Diversity of microbial eukaryotes in sediment at a deep-sea methane cold seep: surveys of ribosomal DNA libraries from raw sediment samples and two enrichment cultures

Recent culture-independent surveys of eukaryotic small-subunit ribosomal DNA (SSU rDNA) from many environments have unveiled unexpectedly high diversity of microbial eukaryotes (microeukaryotes) at various taxonomic levels. However, such surveys were most probably biased by various technical difficulties, resulting in underestimation of microeukaryotic diversity. In the present study on oxygen-depleted sediment from a deep-sea methane cold seep of Sagami Bay, Japan, we surveyed the diversity of eukaryotic rDNA in raw sediment samples and in two enrichment cultures. More than half of all clones recovered from the raw sediment samples were of the basidiomycetous fungus Cryptococcus curvatus. Among other clones, phylotypes of eukaryotic parasites, such as Apicomplexa, Ichthyosporea, and Phytomyxea, were identified. On the other hand, we observed a marked difference in phylotype composition in the enrichment samples. Several phylotypes belonging to heterotrophic stramenopiles were frequently found in one enrichment culture, while a phylotype of Excavata previously detected at a deep-sea hydrothermal vent dominated the other. We successfully established a clonal culture of this excavate flagellate. Since these phylotypes were not identified in the raw sediment samples, the approach incorporating a cultivation step successfully found at least a fraction of the "hidden" microeukaryotic diversity in the environment examined.

Spatial patterns of bacterial signature biomarkers in marine sediments of the Gulf of Mexico

Sediment cores near a cold methane seep and gas hydrates in the Gulf of Mexico were analyzed for bacterial membrane phospholipid fatty acids (PLFA) and isoprenoid quinones. Nearby non-seep marine sediments were also analyzed for the purpose of comparison. Our goal was to use these biomarkers as proxies for microbial community structure and redox indicators. Total PLFA varied from core to core and were significantly less abundant in non-seep marine sediments than those near the cold seep or gas hydrates. In general, saturated straight chain, terminal branched and mid-chain branched, and monounsaturated fatty acids contributed > 98% of the total PLFA. The branched fatty acids (i.e., aC15:0, iC15:0, Me10C16:0) could be largely attributed to sulfate-reducing bacteria and the monounsaturated fatty acid (i.e., 16:1ω7c and 18:1ω7c) could be attributed to sulfide-oxidizing bacteria ( Beggiatoa/ Thioploca). Principal component analysis of PLFA data revealed that microbial communities were consistent with the spatial distributions of gas hydrates and Beggiatoa mats and with the variation in geochemical conditions. Isoprenoid quinone profiles indicated that aerobic respiration was the dominant metabolic process in the top-most sediment layers while the anaerobic respiration dominated the deeper intervals in the marine sediments. Significant amount of cyclopropyl fatty acids at all sites indicated the stress adaptation of the bacteria in the extreme environment. The consistency between the distribution of PLFA and respiratory quinones and the variation in geochemical conditions suggested that analyses of PLFA and quinone could help us to locate the existence of the coupled sulfide-oxidization and sulfate-reduction processes.