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Sample records for active seep sites

  1. Microbial community changes along the active seepage site of one cold seep in the Red Sea

    PubMed Central

    Cao, Huiluo; Zhang, Weipeng; Wang, Yong; Qian, Pei-Yuan

    2015-01-01

    The active seepage of the marine cold seeps could be a critical process for the exchange of energy between the submerged geosphere and the sea floor environment through organic-rich fluids, potentially even affecting surrounding microbial habitats. However, few studies have investigated the associated microbial community changes. In the present study, 16S rRNA genes were pyrosequenced to decipher changes in the microbial communities from the Thuwal seepage point in the Red Sea to nearby marine sediments in the brine pool, normal marine sediments and water, and benthic microbial mats. An unexpected number of reads from unclassified groups were detected in these habitats; however, the ecological functions of these groups remain unresolved. Furthermore, ammonia-oxidizing archaeal community structures were investigated using the ammonia monooxygenase subunit A (amoA) gene. Analysis of amoA showed that planktonic marine habitats, including seeps and marine water, hosted archaeal ammonia oxidizers that differed from those in microbial mats and marine sediments, suggesting modifications of the ammonia oxidizing archaeal (AOA) communities along the environmental gradient from active seepage sites to peripheral areas. Changes in the microbial community structure of AOA in different habitats (water vs. sediment) potentially correlated with changes in salinity and oxygen concentrations. Overall, the present results revealed for the first time unanticipated novel microbial groups and changes in the ammonia-oxidizing archaea in response to environmental gradients near the active seepages of a cold seep. PMID:26284035

  2. Abyssal seep site cementation

    SciTech Connect

    Neumann, A.C.; Paull, C.K.; Commeau, R.; Commeau, J.

    1988-01-01

    The deepest submarine cements known so far occur along the 3,300-m deep base of the Florida escarpment and are associated with methane-bearing brine seeps, which emanate there. These deep Holocene carbonates, which occur as surficial and buried crusts, burrow fillings, and friable horizons, were sampled via ALVIN. The carbonates form irregular halos extending up to 20 m from seeps colonized by chemosynthetic fauna. Mussels, gastropods, and clams, the carbonate components of the community, produce a shell hash that is locally cemented by coarsely crystalline low-Mg calcite. Halos of palisade calcite are reminiscent of ancient examples of marine cements. Also present are carbonate hemipelagics cemented by micrite into crusts and burrow fillings. The degree of cementation varies from pervasive to light. Slabs of cemented crust up to 30 cm thick contrast with typical shallow crusts and exhibit irregular tops and smooth bottoms indicating different chemical gradients and pathways.

  3. Sediment biogeochemistry and microbial activity at natural hydrocarbon seeps and at sites impacted by anthropogenic hydrocarbon discharges

    NASA Astrophysics Data System (ADS)

    Joye, S. B.; Sibert, R.; Battles, J.; Fields, L.; Kleindienst, S.; Crespo-Medina, M.; Hunter, K.; Meile, C. D.; Montoya, J. P.

    2013-12-01

    Natural hydrocarbon seeps occur along the seafloor where geologic faults facilitate transfer of deeply sourced fluids enriched in gas, oil, and dissolved organic matter through shallow sediments and into the water column. At natural seeps, microbial populations specialize in hydrocarbon degradation and rates of microbial activity, including sulfate reduction and anaerobic oxidation of methane, can be extremely high. As a result, the biogeochemical signature of sediments near areas of active natural seepage is distinct: high concentrations of metabolic end products, such as dissolved inorganic carbon and hydrogen sulfide, abound, and often, high dissolved inorganic carbon concentrations result in the precipitation of authigenic carbonate minerals. We examined microbial processes and biogeochemical signatures at two natural seeps, Green Canyon 600 and Mississippi Canyon 118. Higher and more frequent seepage loci at the Green Canyon 600 site led to more widespread hotspots of elevated microbial activity and distinct geochemistry. However, rates of microbial activity were comparable at the two sites in areas of active hydrocarbon seepage. The microbial communities at the two sites were surprisingly different. The second group of sites was impacted by anthropogenic hydrocarbon discharges instead of natural seepage. One site, Oceanus 26, lies near the Deepwater Horizon/Macondo wellhead and was impacted by weathered oil sedimentation during the Macondo discharge. The second set of impacted sites, noted as Taylor Energy, lie near a sunken platform and compromised riser, which have together resulted in persistent hydrocarbon discharge to the adjacent oceanic system for more than 6 years. Rates of microbial activity in the upper sediments at Oceanus 26 were depressed relative to activity in the deeper layers, suggesting inhibition by the presence of weathered oil or an microbial community unable to weather the carbon available in the layer. At the Taylor energy site

  4. SeepC: Preliminary Characterization of Atlantic Margin Seep Ecosystems from Norfolk Canyon to New England Seep Sites.

    NASA Astrophysics Data System (ADS)

    Turner, P. J.; Ball, B.; Cole, E.; LaBella, A.; Wagner, J.; Van Dover, C. L.; Skarke, A. D.; Ruppel, C. D.

    2015-12-01

    Since 2013, more than 500 seep sites have been located along the continental margin of the eastern US using acoustic signals of gas plumes in the water column. During a July 2015 R/V Atlantis expedition, scientists used the submersible Alvin to explore seep sites at depths of 300 to 1500 m. Study sites ranged from Norfolk Canyon north to New England Seep 2 and included Baltimore, Veatch, and Shallop Canyon sites, as well as new unnamed sites between Norfolk and Baltimore Canyons. Mussels dominated the seep sites (cf ''Bathymodiolus'' childressi) but only small populations (<10s of individuals) were observed at seep sites associated with Shallop Canyon. B. heckerae, the dominant mussel at the Blake Ridge and Cape Fear seep sites (sites associated with salt diapirs off the Carolinas), appear to be present at only one of the Atlantic Margin seeps. At the Norfolk Canyon site, dead B. heckerae shells were observed and live individuals may be within the explored area. The abundant vesicomyid clam of Blake Ridge and Cape Fear sites was absent at the continental margin seeps. Apart from B. childressi, the most conspicuous megafaunal invertebrate species at the newly explored seeps was the red crab, Chaceon sp. and the rock crab, Cancer sp. These crabs are not seep endemic but they were especially abundant at the seeps and were observed to feed and mate on the seep grounds. Molecular tools will be used to explore the genetic structure of mussel populations from Norfolk to New England seeps, and stable isotope methods will be used to test for differences among sites in the source of carbon used by mussels. Alvin video transects and photo-mosaics will be used to collect data on macrofauna associated with seeps and to test the hypothesis that shallow seeps (300-500m) support more diverse assemblages than deep sites (1000-1500m).

  5. Abyssal seep site cementation: west Florida escarpment

    SciTech Connect

    Neumann, A.C.; Paull, C.K.; Commeau, R.; Commeau, J.; Chanton, J.; Martens, C.; Gardemal, M.; Trumbull, W.; Showers, W.

    1988-02-01

    The deepest submarine cements known so far occur along the 3300-m deep base of the Florida escarpment and are associated with methane-bearing brine seeps, which emanate there. These deep Holocene carbonates, which occur as surficial and buried crusts, burrow fillings, and friable horizons, were sampled via ALVIN. The carbonates form irregular halos extending up to 20 m from seeps colonized by chemosynthetic fauna. Mussels, gastropods, and clams, the carbonate components of the community, produce a shell hash that is locally cemented by coarsely crystalline low-Mg calcite. Halos of palisade calcite are reminiscent of ancient examples of marine cements. Also present are carbonate hemipelagics cemented by micrite into crusts and burrow fillings. The degree of cementation varies from pervasive to light. Slabs of cemented crust up to 30 cm thick contrast with typical shallow crusts and exhibit irregular tops and smooth bottoms indicating different chemical gradients and pathways. Bulk /delta//sup 13/C values of the carbonates are low, ranging from /minus/ 2.4 to /minus/ 48.5 /per thousand/ (PDB) and implicating as the carbonate source the biogenic methane that occurs in high concentrations at the seeps. The interaction of methane and sulfate in these cement reactions is still unclear. The presence of course mollusk-fragment hardgrounds overlying an eroded limestone and covered by hemipelagics, if encountered elsewhere, could be mistaken for a much shallower setting. The erosion of limestone scarps and the concurrent development of deep hardgrounds containing a fossil chemosynthetic fauna at the unconformity is a scenario that needs to be included in the growing list of limestone facies interpretations.

  6. Rare earth elements of seep carbonates: Indication for redox variations and microbiological processes at modern seep sites

    NASA Astrophysics Data System (ADS)

    Feng, Dong; Lin, Zhijia; Bian, Youyan; Chen, Duofu; Peckmann, Jörn; Bohrmann, Gerhard; Roberts, Harry H.

    2013-03-01

    At marine seeps, methane is microbially oxidized resulting in the precipitation of carbonates close to the seafloor. Methane oxidation leads to sulfate depletion in sediment pore water, which induces a change in redox conditions. Rare earth element (REE) patterns of authigenic carbonate phases collected from modern seeps of the Gulf of Mexico, the Black Sea, and the Congo Fan were analyzed. Different carbonate minerals including aragonite and calcite with different crystal habits have been selected for analysis. Total REE content (ΣREE) of seep carbonates varies widely, from 0.1 ppm to 42.5 ppm, but a common trend is that the ΣREE in microcrystalline phases is higher than that of the associated later phases including micospar, sparite and blocky cement, suggesting that ΣREE may be a function of diagenesis. The shale-normalized REE patterns of the seep carbonates often show different Ce anomalies even in samples from a specific site, suggesting that the formation conditions of seep carbonates are variable and complex. Overall, our results show that apart from anoxic, oxic conditions are at least temporarily common in seep environments.

  7. Chemosynthetic trophic support for the benthic community at an intertidal cold seep site at Mocha Island off central Chile

    NASA Astrophysics Data System (ADS)

    Sellanes, Javier; Zapata-Hernández, Germán; Pantoja, Silvio; Jessen, Gerdhard L.

    2011-12-01

    We analyzed C and N stable isotope ratios of benthic fauna and their potential food sources at an intertidal methane seep site and a control site without emanation at Mocha Island (central Chile). The objective was to trace the origin of the main food sources used by the local heterotrophic fauna, based on the hypothesis that chemosynthetic production could be partially fueling the local food web at the seep site. Food sources sampled at both sites included macroalgae, particulate organic matter and bacteria-like filaments found growing over the red algae Gelidium lingulatum within the areas of active methane release. At the control site, located 11 km away from the gas emanation, fauna exhibited moderate δ 13C values ranging from -16.2‰ (in a nereid polychaete) to -14.8‰ (in a cirolanid isopod), which were consistent with those of the potential photosynthetic food sources sampled at this site (-20.2 to -16.5‰). δ 13C values of the photosynthetic food sources at the seep site similarly ranged between -25.4 and -17.9‰. However, a portion of the animals at this site were consistently more 13C-depleted, with δ 13C values close to that of the seeping methane (-43.8‰) and the bacteria-like filaments (-39.2 ± 2.5‰) also collected at this site. Specific examples were the Marphysa sp. polychaetes (δ 13C = -44.7 ± 0.6‰), the Schistomeringos sp. dorvilleid polychaetes (δ 13C = -42.9‰), and the tanaid crustacean Zeuxo marmoratus (δ 13C = -37.3 ± 0.2‰). The significantly higher δ 13C values of the herbivorous gastropod Tegula atra at the seep site (-29.3 ± 3.1‰) than at the control site (-12.6 ± 0.3‰) also indicated differences among sites of the preferred carbon sources of this species. Mixing model estimates indicate that at the seep site bacteria-like filaments could be contributing up to ˜60% of the assimilated diet of selected invertebrates. Furthermore, several indicators of trophic structure, based in isotopic niche metrics, indicate a

  8. Authigenic carbonates from active methane seeps offshore southwest Africa

    NASA Astrophysics Data System (ADS)

    Pierre, Catherine; Blanc-Valleron, Marie-Madeleine; Demange, Jérôme; Boudouma, Omar; Foucher, Jean-Paul; Pape, Thomas; Himmler, Tobias; Fekete, Noemi; Spiess, Volkhard

    2012-12-01

    The southwest African continental margin is well known for occurrences of active methane-rich fluid seeps associated with seafloor pockmarks at water depths ranging broadly from the shelf to the deep basins, as well as with high gas flares in the water column, gas hydrate accumulations, diagenetic carbonate crusts and highly diverse benthic faunal communities. During the M76/3a expedition of R/V METEOR in 2008, gravity cores recovered abundant authigenic carbonate concretions from three known pockmark sites—Hydrate Hole, Worm Hole, the Regab pockmark—and two sites newly discovered during that cruise, the so-called Deep Hole and Baboon Cluster. The carbonate concretions were commonly associated with seep-benthic macrofauna and occurred within sediments bearing shallow gas hydrates. This study presents selected results from a comprehensive analysis of the mineralogy and isotope geochemistry of diagenetic carbonates sampled at these five pockmark sites. The oxygen isotope stratigraphy obtained from three cores of 2-5 m length indicates a maximum age of about 60,000-80,000 years for these sediments. The authigenic carbonates comprise mostly magnesian calcite and aragonite, associated occasionally with dolomite. Their very low carbon isotopic compositions (-61.0 < δ13C ‰ V-PDB < -40.1) suggest anaerobic oxidation of methane (AOM) as the main process controlling carbonate precipitation. The oxygen isotopic signatures (+2.4 < δ18O ‰ V-PDB < +6.2) lie within the range in equilibrium under present-day/interglacial to glacial conditions of bottom seawater; alternatively, the most positive δ18O values might reflect the contribution of 18O-rich water from gas hydrate decomposition. The frequent occurrence of diagenetic gypsum crystals suggests that reduced sulphur (hydrogen sulphide, pyrite) from sub-seafloor sediments has been oxidized by oxygenated bottom water. The acidity released during this process can potentially induce the dissolution of carbonate, thereby

  9. Application of parasound data for sediment study on methane seep site at Simeulue basin

    SciTech Connect

    Wiguna, Taufan Ardhyastuti, Sri

    2015-09-30

    The Parasound data presents sea depth and sub-bottom profiler. In terms of geological terminology, parasound data represents significant recent surface sedimentary structures that valuable for the selection of subsequent sampling site such as sampling at methane seep site. Therefore, Parasound is used to detailing methane seep at surface sediment following seismic data interpretation. In this study, parasound is used to focus observe area especially for sediment study on methane seep site. The Parasound systems works both as narrow beam sounder use high frequency and as sediment echosounder use low frequency. Parasound acquisition applies parametric effect. It produces additional frequency by nonlinear acoustic interaction of finite amplitude waves. Parasound transducers have 128 elements on 1 m2 and need transmission power up to 70 kW. The results of this study are discovered large seep carbonate with porous surface which means there are gas expulsions passing through that rock.

  10. Application of parasound data for sediment study on methane seep site at Simeulue basin

    NASA Astrophysics Data System (ADS)

    Wiguna, Taufan; Ardhyastuti, Sri

    2015-09-01

    The Parasound data presents sea depth and sub-bottom profiler. In terms of geological terminology, parasound data represents significant recent surface sedimentary structures that valuable for the selection of subsequent sampling site such as sampling at methane seep site. Therefore, Parasound is used to detailing methane seep at surface sediment following seismic data interpretation. In this study, parasound is used to focus observe area especially for sediment study on methane seep site. The Parasound systems works both as narrow beam sounder use high frequency and as sediment echosounder use low frequency. Parasound acquisition applies parametric effect. It produces additional frequency by nonlinear acoustic interaction of finite amplitude waves. Parasound transducers have 128 elements on 1 m2 and need transmission power up to 70 kW. The results of this study are discovered large seep carbonate with porous surface which means there are gas expulsions passing through that rock.

  11. Active seeps, investment climate draw interest to Uganda

    SciTech Connect

    Patton, D.K.; Kashambuzi, R.; Rubondo, E.N.T.

    1995-05-01

    Production has not been established in Uganda, but the hydrocarbon generating capacity of its rift basin is clearly evident. Reports of oil seeps date to 1925 to observations by Wayland; who relates 52 hydrocarbon occurrences in and around Lake Albert. Although not all remain active, nine oil seeps in the rift basin are confirmed active at present. The Albertine graben, a part of the East African rift system, dominates the geology of Uganda. Other, larger basins of similar evolution in Africa include the Sirte basin and the Gulf of Suez basin. These prolific basins account for one third of Africa`s total reserves. The paper describes the geologic setting, reservoirs, source rocks, geologic seals, structures, exploration history, licenses available, and fiscal terms.

  12. Biogeography, biodiversity and fluid dependence of deep-sea cold-seep communities at active and passive margins

    NASA Astrophysics Data System (ADS)

    Sibuet, Myriam; Olu, Karine

    1998-01-01

    To date, several cold-seep areas which fuel chemosynthesis-based benthic communities have been explored, mainly by deployment of manned submersibles. They are located in the Atlantic and in the Eastern and Western Pacific oceans and in the Mediterranean Sea, in depths ranging between 400 and 6000 m in different geological contexts in passive and active margins. Our study is based on a review of the existent literature on 24 deep cold seeps. The geographic distribution of seeps, the variations of origin and composition of fluids, and rates of fluid flow are presented as they are important factors which explain the spatial heterogeneity and the biomass of biological communities. Methane-rich fluid of thermogenic and/or biogenic origin is the principal source of energy for high-productive communities; however, production of sulphide by sulphate reduction in the sediment also has a major role. The dominant seep species are large bivalves belonging to the families Vesicomyidae or Mytilidae. Other symbiont-containing species occur belonging to Solemyidae, Thyasiridae, Lucinidae bivalves, Pogonophora worms, Cladorhizidae and Hymedesmiidae sponges. Most of the symbiont-containing cold-seep species are new to science. Different symbiont-containing species rely on sulphide or methane oxidation, or both, via chemoautotrophic endosymbiotic bacteria. A total of 211 species, from which 64 are symbiont-containing species, have been inventoried. Patterns in biodiversity and biogeography are proposed. A large majority of the species are endemic to a seep area and the symbiont-containing species are mainly endemic to the cold-seep ecosystem. A comparison of species found in other deep chemosynthesis-based ecosystems, hydrothermal vents, whale carcass and shipwreck reduced habitats, reveals from the existing data, that only 13 species, of which five are symbiont-containing species occur, at both seeps and hydrothermal vents. The species richness of cold-seep communities decreases

  13. Morphology of Florida Escarpment chemosynthetic brine seep community sites

    SciTech Connect

    Paull, C.K.; Spiess, F.N.; Curray, J.R.; Twitchell, D.

    1988-01-01

    The Florida Escarpment near 26/sup 0/N was surveyed with Deep-Two, Seabeam, and GLORIA in the area where chemosynthetic communities were discovered via ALVIN in the abyssal Gulf of Mexico. Seabeam bathymetry and GLORIA images indicate that the escarpment is a generally straight cliff with average slopes of about 45/sup 0/ from 2,200 to more than 3,250 m. The escarpment's face is cut by 2-km wide box canyons whose head walls are as steep as the intervening escarpment's face. The shapes of these canyons are difficult to explain with the traditional models of canyon formation. Sidescan sonar images and bottom photographs reveal that the escarpment's face is composed of a series of long, straight bedding-plane terraces which are truncated along nearly vertical orthogonal joints. Exposure of these truncated strata indicate the face of the escarpment is eroded. The contact between the basal escarpment and the flat-lying abyssal hemipelagic sediments is abrupt. Apparently, chemosynthetic communities line extensive sections of the escarpment base where reduced brines seep out into the sea floor. The morphology suggests joints and deep seeps are controlling factors in scarp retreat.

  14. Diversity and Characteristics of Benthic Foraminifera in Cold Seep Areas in the Active Margin of the northeastern South China Sea

    NASA Astrophysics Data System (ADS)

    Chiang, Meng-Ting; Thomas, Ellen; Wei, Kuo-Yen; Lin, Yu-Shih; Lin, Saulwood; Tien-Shun Lin, Andrew

    2015-04-01

    The active continental margin in northeastern South China Sea (SCS) has been considered to have high potential to be a reservoir of gas hydrate, based on geographic features, geophysical evidences, as well as geochemical analyses of samples from the water column, pore water and sediments. Compared to a typical sea floor area, cold seep areas have more food for benthos and more diverse habitats. As a result, we can expect a higher species diversity of benthic organisms in cold seep areas of the SCS. Based on preliminary results of species identification of benthic foraminiferal assemblages in the upper most sediments (0-5 cm) of box cores collected around cold seeps at water depth ~1300m, the species diversity is significantly higher at seep sites (Shannon-Wiener index = 274) than at background sites (Shannon-Wiener index = 3). The faunal assemblages consist of ~68% calcareous benthic foraminifera (CBF) and ~32% agglutinated benthic foraminifera (ABF) at seep sites. On the other hand, faunal assemblages are composed of only ~24% CBF and ~76% ABF at background sites. By staining the sample with rose Bengal-ethanol solution, we were able to recognize in-situ individuals which were alive at the time of collection, and separate them from dead specimens. Among the living individuals, the most abundant CBF species in seep sites is Bulimina aculeata (~51% in the living CBF fauna), followed by the typical 'shelf-species,' Lenticulina inornata, (~10%) and the common 'brackish-species,' Miliolinella subrotunda, (~9%), while the most abundant ABF species is Cribrostomoides subglobosus (~19% in the living ABF fauna). The most common species thus are typical for shallower, more food rich environments.

  15. Three-dimensional structure of fluid conduits sustaining an active deep marine cold seep

    NASA Astrophysics Data System (ADS)

    Hornbach, M. J.; Ruppel, C.; Van Dover, C. L.

    2007-03-01

    Cold seeps in deep marine settings emit fluids to the overlying ocean and are often associated with such seafloor flux indicators as chemosynthetic biota, pockmarks, and authigenic carbonate rocks. Despite evidence for spatiotemporal variability in the rate, locus, and composition of cold seep fluid emissions, the shallow subseafloor plumbing systems have never been clearly imaged in three dimensions. Using a novel, high-resolution approach, we produce the first three-dimensional image of possible fluid conduits beneath a cold seep at a study site within the Blake Ridge gas hydrate province. Complex, dendritic features diverge upward toward the seafloor from feeder conduits at depth and could potentially draw flow laterally by up to 103 m from the known seafloor seep, a pattern similar to that suggested for some hydrothermal vents. The biodiversity, community structure, and succession dynamics of chemosynthetic communities at cold seeps may largely reflect these complexities of subseafloor fluid flow.

  16. Three-dimensional structure of fluid conduits sustaining an active deep marine cold seep

    USGS Publications Warehouse

    Hornbach, M.J.; Ruppel, C.; Van Dover, C.L.

    2007-01-01

    Cold seeps in deep marine settings emit fluids to the overlying ocean and are often associated with such seafloor flux indicators as chemosynthetic biota, pockmarks, and authigenic carbonate rocks. Despite evidence for spatiotemporal variability in the rate, locus, and composition of cold seep fluid emissions, the shallow subseafloor plumbing systems have never been clearly imaged in three dimensions. Using a novel, high-resolution approach, we produce the first three-dimensional image of possible fluid conduits beneath a cold seep at a study site within the Blake Ridge gas hydrate province. Complex, dendritic features diverge upward toward the seafloor from feeder conduits at depth and could potentially draw flow laterally by up to 103 m from the known seafloor seep, a pattern similar to that suggested for some hydrothermal vents. The biodiversity, community structure, and succession dynamics of chemosynthetic communities at cold seeps may largely reflect these complexities of subseafloor fluid flow.

  17. Carbonate-cemented hardgrounds: a subtle indicator for seep activity offshore Humboldt Bay

    NASA Astrophysics Data System (ADS)

    Shapiro, R. S.; Bazard, D.

    2007-12-01

    Active hydrocarbon seeps are common in the accretionary prism of the Cascadia subduction zone. In Humboldt County, California, the prism is exposed at the surface as a series of fault-propagated anticlines trending NW-SE. Offshore of the town of Samoa, a northwest-plunging anticline is breached at approximately 40 meters water depth, allowing hydrocarbons to seep out to the seafloor (40.8° N, 124.25° W). The assumed microbial activity at the seep leads to the production of interstitial carbonate cements forming hardgrounds. Cementation is pervasive and blocks eroded from the seep area of the seabed are transported onshore during storm events. Blocks collected from the beach range from 3--40 centimeters across. The sediments of the blocks are palimpsest transgressive deposits composed mostly of immature fine sand, but ranging from very fine to rounded gravels 4 cm diameter. Cementation is not dependent on grain size as all of the sediment sizes are cemented. In rare void spaces, a concentric banding of cements is obvious. The interstitial cements preserve original sedimentary structures including graded beds and high-angle cross-beds. Centimeter-scale subspherical concretions occur on the undersides of some blocks. There is no disruption of bedding in contrast to other seeps where the expulsion of gas can create pockmarks, brecciation, and other disturbances. Unlike the better studied seeps farther south in the Eel River basin, the Samoa seeps do not seem to host a rich chemosynthetic fauna. Whole and (mostly) fragmented shells preserved by the cemented sands represent a typical benthic inner shelf community including Dendraster, Macoma, and Olivella. Burrows preserved in the sands are largely horizontal and 1--2 mm diameter. Seep carbonate-cemented hardgrounds are less well studied then the more obvious meter-scale 'chemoherm' deposits. However, they may be more prevalent in the rock record and provide a new proxy for locating ancient seeps and hydrocarbon

  18. The Role of Seep Ecosystems in Distribution Patterns of Deep-Sea Megafauna

    NASA Astrophysics Data System (ADS)

    Wagner, J.; McKelvey, Z.; Jacobson, A.; Hoerauf, E.; Van Dover, C. L.

    2015-12-01

    One of the key questions about methane seeps is the sphere of influence on the surrounding area they provide in terms of habitat structure, food sources, and geochemical environment. Understanding the distribution of megafauna relative to the seep environment is an initial step toward understanding these ecosystem properties. Systematic photo surveys using AUV Sentry were conducted at 4 methane seeps at the Blake Ridge Diapir and a seep at Cape Fear Diapir. Distributions of dominant seep features (bivalves, carbonates, bacterial mats) were used to define the active seep site. Geospatial mapping indicates that non-seep-endemic taxa (those not hosting chemoautotrophic endosymbionts) either avoid (e.g., sea urchins, certain sea cucumbers), are attracted to (e.g., squat lobsters, cake urchins) or show no distributional bias to (e.g., sea stars, certain fish) the presence of a seep. Further investigation into these faunal relationships may improve understanding of services that seeps provide to the larger ocean ecosystem.

  19. Escarpment seeps at Shiprock, New Mexico. [Risk posed by seep water to human health and the environment

    SciTech Connect

    Not Available

    1991-10-01

    The purpose of this report is to characterize the seeps identified at the Shiprock UMTRA Project site during the prelicensing custodial care inspection conducted in December of 1990, to evaluate the relationship between the seeps and uranium processing activities or tailings disposal, and to evaluate the risk posed by the seep water to human health and the environment. The report provides a brief description of the geology, groundwater hydrology, and surface water hydrology. The locations of the seeps and monitor wells are identified, and the water quality of the seeps and groundwater is discussed in the context of past activities at the site. The water quality records for the site are presented in tables and appendices; this information was used in the risk assessment of seep water.

  20. Active oil seep at Nevada gold mine holds intrigue for more exploration

    SciTech Connect

    Pinnell, M.L.; Blake, J.G. ); Hulen, J.B. )

    1991-07-15

    This paper reports on an active oil seep has been discovered in one of Nevada's famous Carlin-type low grade disseminated gold deposits. This unique seep, at the Yankee gold mine in White Pine County, may have important implications for both oil and gas and gold exploration in the Basin and Range province of the western U.S. The open pit Yankee mine, near the western margin of Long Valley, exploits one of numerous Carlin-type gold ore bodies in the alligator Ridge mining district; all are currently owned and operated by USMX Corp.

  1. Estimation of past intermittent methane seep activity using radiocarbon dating of Calyptogena shells in the eastern Nankai subduction zone

    NASA Astrophysics Data System (ADS)

    Yagasaki, K.; Ashi, J.; Yokoyama, Y.; Miyairi, Y.; Kuramoto, S.

    2013-12-01

    Radioisotope carbon dating samples from the deep ocean has always been a difficult phenomenon due to the carbon offset present. This research presents a way of utilizing such method to date shell samples in order to study past fault activities. The research presented will be based on the preliminary data collected thus far. The Nankai and the Tokai regions are common areas for cold seeps, where seepage of hydrogen sulfide and methane rich fluid occurs. These various substances encourage the growth of Calyptogena colonies to flourish at these sites. Cold seeps generally occur at tectonically active continental margins and are mostly ephemeral. This suggests that the cold seep events are possibly influenced by the tectonic activity during the plate divergence. In 1997, a submersible dive by Shinkai 2000 discovered an unusually large Calyptogena colony ranging over 200 m2 off Daini Tenryu Knoll. Majority of the shells were fossilized with few live shells remaining. It is assumed that past tectonic events in the region may have caused a high flux of methane fluid or gas to be released, making it possible to support such a vast scale colony to survive until their eventual death. Previous attempt to reconstruct the cold seep activity history through amino acid racemisation dating revealed two different age grouped shells. Further data using a different method is required to prove its reliability, as acid racemization dating technique can easily be affected by seawater temperature changes and microbial activity. This consequently alters the protein structure of the sample and its overall age. As 14C radioisotope dating is not affected by temperature change, it will provide additional information to the accuracy of the acid racemisation dating of the shell. However, the possibility of contamination is likely due to the shells incorporating older carbon from the sediments during their early stages of growth. The old carbon value can be calculated by subtracting the formerly

  2. Evidence of Active Methanogen Communities in Shallow Sediments of the Sonora Margin Cold Seeps

    PubMed Central

    L'Haridon, Stéphane; Godfroy, Anne; Roussel, Erwan G.; Cragg, Barry A.; Parkes, R. John; Toffin, Laurent

    2015-01-01

    In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic Archaea were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic Methanococcoides burtonii relatives and several new autotrophic Methanogenium lineages, confirming the cooccurrence of Methanosarcinales and Methanomicrobiales methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps. PMID:25769831

  3. Characterisation of the Nematode Community of a Low-Activity Cold Seep in the Recently Ice-Shelf Free Larsen B Area, Eastern Antarctic Peninsula

    PubMed Central

    Hauquier, Freija; Ingels, Jeroen; Gutt, Julian; Raes, Maarten; Vanreusel, Ann

    2011-01-01

    Background Recent climate-induced ice-shelf disintegration in the Larsen A (1995) and B (2002) areas along the Eastern Antarctic Peninsula formed a unique opportunity to assess sub-ice-shelf benthic community structure and led to the discovery of unexplored habitats, including a low-activity methane seep beneath the former Larsen B ice shelf. Since both limited particle sedimentation under previously permanent ice coverage and reduced cold-seep activity are likely to influence benthic meiofauna communities, we characterised the nematode assemblage of this low-activity cold seep and compared it with other, now seasonally ice-free, Larsen A and B stations and other Antarctic shelf areas (Weddell Sea and Drake Passage), as well as cold-seep ecosystems world-wide. Principal Findings The nematode community at the Larsen B seep site differed significantly from other Antarctic sites in terms of dominant genera, diversity and abundance. Densities in the seep samples were high (>2000 individuals per 10 cm2) and showed below-surface maxima at a sediment depth of 2–3 cm in three out of four replicates. All samples were dominated by one species of the family Monhysteridae, which was identified as a Halomonhystera species that comprised between 80 and 86% of the total community. The combination of high densities, deeper density maxima and dominance of one species is shared by many cold-seep ecosystems world-wide and suggested a possible dependence upon a chemosynthetic food source. Yet stable 13C isotopic signals (ranging between −21.97±0.86‰ and −24.85±1.89‰) were indicative of a phytoplankton-derived food source. Conclusion The recent ice-shelf collapse and enhanced food input from surface phytoplankton blooms were responsible for the shift from oligotrophic pre-collapse conditions to a phytodetritus-based community with high densities and low diversity. The parthenogenetic reproduction of the highly dominant Halomonhystera species is rather unusual for marine

  4. Marine oil seeps

    SciTech Connect

    Meyer, R.F. )

    1991-03-01

    Petroleum hydrocarbons of both biogenic and thermogenic origin are common constituents of the marine water column and sediment of the continental shelves. Approximately 0.25 million metric tons of oil per year, constituting about 8% of the oil input into the sea, is derived from natural seeps, the rest being anthropogenic. Seepage has occurred world-wide for millions of years and must have been many times greater in the past, when enormous oil deposits, such as the Orinoco Oil Belt, were first exposed to erosion. Although the amount varies from site to site with time, seepage is pervasive in polar and temperate seas. Marine-seep oil is intensely weathered and thus can be distinguished chemically from recent biogenic or undegraded crude oil. The degraded oil from seeps appears to have little deleterious effect on many marine organisms, which ingest and discharge the oil mostly unmetabolized. Chemical analyses suggest that a very large oil-rich layer in the Sargasso Sea originated from a large and as yet undetected seep. Oil seeps have long been used as guides for oil exploration onshore but have been underutilized for this purpose offshore because of oil-plume drift from the site of the seep and because natural oil slicks may be masked by spilled oil. At least one marine seep, in the Santa Barbara Channel, California, is producing oil and natural gas into two hollow steel pyramids from which the oil is collected by work boats and the natural gas is transported to shore by pipeline. This facility effectively reduces atmospheric pollution, controls marine oil pollution from the largest seep in the area, provides emission credits, and yields a modest economic benefit, but the seep is not known to have been used directly in oil exploration.

  5. Cold seep epifaunal communities on the Hikurangi margin, New Zealand: composition, succession, and vulnerability to human activities.

    PubMed

    Bowden, David A; Rowden, Ashley A; Thurber, Andrew R; Baco, Amy R; Levin, Lisa A; Smith, Craig R

    2013-01-01

    Cold seep communities with distinctive chemoautotrophic fauna occur where hydrocarbon-rich fluids escape from the seabed. We describe community composition, population densities, spatial extent, and within-region variability of epifaunal communities at methane-rich cold seep sites on the Hikurangi Margin, New Zealand. Using data from towed camera transects, we match observations to information about the probable life-history characteristics of the principal fauna to develop a hypothetical succession sequence for the Hikurangi seep communities, from the onset of fluid flux to senescence. New Zealand seep communities exhibit taxa characteristic of seeps in other regions, including predominance of large siboglinid tubeworms, vesicomyid clams, and bathymodiolin mussels. Some aspects appear to be novel; however, particularly the association of dense populations of ampharetid polychaetes with high-sulphide, high-methane flux, soft-sediment microhabitats. The common occurrence of these ampharetids suggests they play a role in conditioning sulphide-rich sediments at the sediment-water interface, thus facilitating settlement of clam and tubeworm taxa which dominate space during later successional stages. The seep sites are subject to disturbance from bottom trawling at present and potentially from gas hydrate extraction in future. The likely life-history characteristics of the dominant megafauna suggest that while ampharetids, clams, and mussels exploit ephemeral resources through rapid growth and reproduction, lamellibrachid tubeworm populations may persist potentially for centuries. The potential consequences of gas hydrate extraction cannot be fully assessed until extraction methods and target localities are defined but any long-term modification of fluid flow to seep sites would have consequences for all chemoautotrophic fauna. PMID:24204691

  6. Cold Seep Epifaunal Communities on the Hikurangi Margin, New Zealand: Composition, Succession, and Vulnerability to Human Activities

    PubMed Central

    Bowden, David A.; Rowden, Ashley A.; Thurber, Andrew R.; Baco, Amy R.; Levin, Lisa A.; Smith, Craig R.

    2013-01-01

    Cold seep communities with distinctive chemoautotrophic fauna occur where hydrocarbon-rich fluids escape from the seabed. We describe community composition, population densities, spatial extent, and within-region variability of epifaunal communities at methane-rich cold seep sites on the Hikurangi Margin, New Zealand. Using data from towed camera transects, we match observations to information about the probable life-history characteristics of the principal fauna to develop a hypothetical succession sequence for the Hikurangi seep communities, from the onset of fluid flux to senescence. New Zealand seep communities exhibit taxa characteristic of seeps in other regions, including predominance of large siboglinid tubeworms, vesicomyid clams, and bathymodiolin mussels. Some aspects appear to be novel; however, particularly the association of dense populations of ampharetid polychaetes with high-sulphide, high-methane flux, soft-sediment microhabitats. The common occurrence of these ampharetids suggests they play a role in conditioning sulphide-rich sediments at the sediment-water interface, thus facilitating settlement of clam and tubeworm taxa which dominate space during later successional stages. The seep sites are subject to disturbance from bottom trawling at present and potentially from gas hydrate extraction in future. The likely life-history characteristics of the dominant megafauna suggest that while ampharetids, clams, and mussels exploit ephemeral resources through rapid growth and reproduction, lamellibrachid tubeworm populations may persist potentially for centuries. The potential consequences of gas hydrate extraction cannot be fully assessed until extraction methods and target localities are defined but any long-term modification of fluid flow to seep sites would have consequences for all chemoautotrophic fauna. PMID:24204691

  7. Two-Dimensional Heat Transfer Modeling of the Formosa Ridge Offshore SW Taiwan: Implication for Fluid Migrating Paths of a Cold Seep Site

    NASA Astrophysics Data System (ADS)

    Tsai, Y.; Chi, W.; Liu, C.; Shyu, C.

    2011-12-01

    The Formosa Ridge, a small ridge located on the passive China continental slope offshore southwestern Taiwan, is an active cold seep site. Large and dense chemosynthetic communities were found there by the ROV Hyper-Dolphin during the 2007 NT0705 cruise. A vertical blank zone is clearly observed on all the seismic profiles across the cold seep site. This narrow zone is interpreted to be the fluid conduit of the seep site. Previous studies suggest that cold sea water carrying large amount of sulfate could flow into the fluid system from flanks of the ridge, and forms a very effective fluid circulation system that emits both methane and hydrogen sulfide to feed the unusual chemosynthetic communities observed at the Formosa Ridge cold seep site. Here we use thermal signals to study possible fluid flow migration paths. In 2008 and 2010, we have collected vdense thermal probe data at this site. We also study the temperatures at Bottom-Simulating Reflectors (BSRs) based on methane hydrate phase diagram. We perform 2D finite element thermal conductive simulations to study the effects of bathymetry on the temperature field in the ridge, and compare the simulation result with thermal probe and BSR-derived datasets. The boundary conditions include insulated boundaries on both sides, and we assign a fix temperature at the bottom of the model using an average regional geothermal gradient. Sensitivity tests and thermal probe data from a nearby region give a regional background geothermal gradient of 0.04 to 0.05 °C/m. The outputs of the simulation runs include geothermal gradient and temperature at different parts of the model. The model can fit the geothermal gradient at a distance away from the ridge where there is less geophysics evidence of fluid flow. However our model over-predicts the geothermal gradient by 50% at the ridge top. We also compare simulated temperature field and found that under the flanks of the ridge the temperature is cooled by 2 °C compared with the

  8. Evidence and biogeochemical implications for glacially-derived sediments in an active margin cold seep

    USGS Publications Warehouse

    Pohlman, John W.; Riedel, Michael; Novosel, Ivana; Bauer, James E.; Canuel, Elizabeth A.; Paull, Charles K.; Coffin, Richard B.; Grabowski, Kenneth S.; Knies, David L.; Hyndman, Roy D.; Spence, George D.

    2011-01-01

    Delineating sediment organic matter origins and sediment accumulation rates at gas hydratebearing and hydrocarbon seeps is complicated by the microbial transfer of 13C-depleted and 14Cdepleted methane carbon into sedimentary pools. Sediment 13C and 14C measurements from four cores recovered at Bullseye vent on the northern Cascadia margin are used to identify methane carbon assimilation into different carbon pools. While the total organic carbon (TOC) is mostly unaltered and primarily terrigenous in origin, planktonic foraminifera and the bulk carbonate display evidence of methane overprinting. Mass balance models are applied to determine the extent to which methane overprinting increased the radiocarbon ages of the biogenic foraminifera. The corrected and calibrated foraminifera ages between sediment depths of 70 and 573 cm are from 14.9 to 15.9 ka BP, which coincides with the retreat of the late Quaternary Cordilleran Ice Sheet from Vancouver Island. Uniform TOC _13C values of -24.5 ± 0.5‰ from the upper 8 meters of sediment at Bullseye vent suggest all cored material is Pleistocene-derived glacimarine material deposited as the ice edge retreated landward. Bullseye vent is located within an uplifted sediment block isolated from turbidite deposition and has been a site of non-deposition since the ice sheet retreated from the shelf. Biogeochemical implications of seep sediments being dominated by aged, organic-poor (<0.4 wt% TOC) material are that methane is the primary energy source, and microbes directly and indirectly associated with the anaerobic oxidation of methane (AOM) will dominate the seep microbial community.

  9. Methanotrophic Bacteria Maintaining and Coexisting With a Methanogenic Consortium in Soils at Man-Made Natural gas Seeps at Petroleum Well Sites in Western Canada

    NASA Astrophysics Data System (ADS)

    Arkadakskiy, S.; Muehlenbachs, K.

    2007-12-01

    Unwanted leakage of natural gas (>90% vol. CH4) in soil is ubiquitous at petroleum well sites in western Canada. Long term monitoring at several of those man-made seeps demonstrates that aerobic methanotrophy is the most important microbially mediated process in the soil. Bacterial oxidation of methane is severely impeded by soil freezing in winter and also in soils contaminated with liquid hydrocarbons. Soil gas compositions and carbon stable isotope data demonstrate that bacterial methanogenesis also occurs in deeper sections of the soil column at a number of the seeps. While methanogenic activity is common in soil contaminated with liquid hydrocarbons, it is also detected in soils where no evidence of oil contamination has been found (i.e., in "clean" soils). Methanogenic activity in "clean" soils occurs in the summer when soil temperature and moisture are comparatively high. Results also demonstrate that at this time of the year metanotrophic bacteria move upwards in the soil column whereby consuming nearly all available oxygen methanotrops are, thus, providing a habitat for the methane producing microorganisms. The concentrations of electron acceptors other than CO2 (HCO2) in soil moisture are very low or below detection, hence, indicating that methanogenesis is the energetically favorable terminal electron acceptor process in this environment. Conspicuous lack of soil biomass of methanotrophic origin evident from the low concentrations of soil organic matter (SOM) and the comparatively high carbon stable isotope composition of SOM, suggests that fermenting bacteria from the methanogenic consortium metabolize lysed cells and polysaccharide film left over from the demise of methanotrophic bacteria in winter, therefore practically feeding of the latter. Methane generated by the methanogens mixes with leaking gas and it is, sometimes, completely consumed by the methanotrophs. The seasonal interplay of methanogenic and methanotrophic bacteria at the man

  10. Differential methane oxidation activity and microbial community composition at cold seeps in the Arctic off western Svalbard

    NASA Astrophysics Data System (ADS)

    Gründger, Friederike; Svenning, Mette M.; Niemann, Helge; Silyakova, Anna; Serov, Pavel; Li Hong, Wei; Wegener, Gunter; Panieri, Giuliana; Carroll, JoLynn

    2016-04-01

    Most models considering climate change related bottom water warming suggest that gas hydrates may become destabilized, leading to the mobilization of methane into seabed and water column ecosystems, and, eventually, into the atmosphere. However, the capacity of methanotrophic microbes retaining methane in sediments and the hydrosphere is not well constrained. Here, we investigate the microbial utilization of methane in sediments and the water column, focusing on cold seeps discovered at the arctic continental margin of western Svalbard. We measured ex situ rates of methane oxidation and sulfate reduction in two active gas flare sites with different geological settings at the Vestnesa Ridge (1204 m water depth) and within a pingolike feature area southwest off Svalbard (PLF; 380 m water depth). Our results show contrarily situations at our two sampling sites: At Vestnesa Ridge we find high methane oxidation rates with values up to 2055 nmol cm-3 d-1 at the sediment surface where the sediments are oversaturated with methane. Whereas, methane concentration and oxidation rates are low in the overlying water column (2 pmol cm-3 d-1). In contrast, at the sediment surface at PLF methane concentration and oxidation rates are considerably lower (up to 1.8 nmol cm-3 d-1). While the overlying bottom water contains high concentration of methane and shows oxidation rates with values of up to 3.8 nmol cm-3 d-1. The data on methane oxidation and sulfate reduction activity are compared to the sediment geochemistry and to data from metagenomic analysis identifying the methanotrophic community composition. These results provide unique insight into the dynamic responses of the seabed biological filter at cold seeps in the Arctic off western Svalbard. This study is part of the Centre for Arctic Gas Hydrate, Environment and Climate and was supported by the Research Council of Norway through its Centres of Excellence funding scheme grant No. 223259.

  11. Diversity of symbioses between chemosynthetic bacteria and metazoans at the Guiness cold seep site (Gulf of Guinea, West Africa)

    PubMed Central

    Duperron, Sébastien; Rodrigues, Clara F; Léger, Nelly; Szafranski, Kamil; Decker, Carole; Olu, Karine; Gaudron, Sylvie M

    2012-01-01

    Fauna from deep-sea cold seeps worldwide is dominated by chemosymbiotic metazoans. Recently, investigation of new sites in the Gulf of Guinea yielded numerous new species for which symbiosis was strongly suspected. In this study, symbioses are characterized in five seep-specialist metazoans recently collected from the Guiness site located at ∼600 m depth. Four bivalve and one annelid species belonging to families previously documented to harbor chemosynthetic bacteria were investigated using bacterial marker gene sequencing, fluorescence in situ hybridization, and stable isotope analyses. Results support that all five species display chemosynthetic, sulfur-oxidizing γ-proteobacteria. Bacteria are abundant in the gills of bivalves, and in the trophosome of the siboglinid annelid. As observed for their relatives occurring at deeper sites, chemoautotrophy is a major source of carbon for animal nutrition. Although symbionts found in each host species are related to symbionts found in other metazoans from the same families, several incongruencies are observed among phylogenetic trees obtained from the different bacterial genes, suggesting a certain level of heterogeneity in symbiont strains present. Results provide new insights into the diversity, biogeography, and role of symbiotic bacteria in metazoans from the Gulf of Guinea, at a site located at an intermediate depth between the continental shelf and the deep sea. PMID:23233246

  12. [Detection of methane in the water column at gas and oil seep sites in central and southern Lake Baikal].

    PubMed

    Zakharenko, A S; Pimenov, N V; Ivanov, V G; Zemskaia, T I

    2015-01-01

    Microbiological and biogeochemical investigation of the water column of oligotrophic Lake Baikal at the sites of the K2 and Bolshoy mud volcanoes and the Gorevoy Utes oil seep was carried out in July 2013. Total microbial numbers (TMN), cell numbers of type I and type II methanotrophs, and methane concentrations were measured; the rate of methane oxidation was determined. Methane concentrations in Lake Baikal water column varied from 0.09 to 1 μL/L, while methane oxidation rates varied from 0.007 to 0.9 nL/(L day). The highest rates of methane oxidation were revealed in the near-bottom water horizons at the sites of the Bolshoy mud volcano and the Gorevoy Utes oil seep. These were the sites where the most pronounced anomalies in methane concentration were also detected. TMN varied from 0.123 x 10(6) to 1.64 x 10(6) cells/mL. Methanotrophic bacteria were revealed in the water column at all sites, their abundance did not always correlate with methane concentrationsand the rates of methane oxidation. Methanotrophs constituted not more than 1.63% of the total microbial number, with their highest abundance in the upper 200 m of the water column. PMID:25916152

  13. [Detection of methane in the water column at gas and oil seep sites in central and southern Lake Baikal].

    PubMed

    Zakharenko, A S; Pimenov, N V; Ivanov, V G; Zemskaia, T I

    2015-01-01

    Microbiological and biogeochemical investigation of the water column of oligotrophic Lake Baikal at the sites of the K2 and Bolshoy mud volcanoes and the Gorevoy Utes oil seep was carried out in July 2013. Total microbial numbers (TMN), cell numbers of type I and type II methanotrophs, and methane concentrations were measured; the rate of methane oxidation was determined. Methane concentrations in Lake Baikal water column varied from 0.09 to 1 μL/L, while methane oxidation rates varied from 0.007 to 0.9 nL/(L day). The highest rates of methane oxidation were revealed in the near-bottom water horizons at the sites of the Bolshoy mud volcano and the Gorevoy Utes oil seep. These were the sites where the most pronounced anomalies in methane concentration were also detected. TMN varied from 0.123 x 10(6) to 1.64 x 10(6) cells/mL. Methanotrophic bacteria were revealed in the water column at all sites, their abundance did not always correlate with methane concentrationsand the rates of methane oxidation. Methanotrophs constituted not more than 1.63% of the total microbial number, with their highest abundance in the upper 200 m of the water column.

  14. Evidence for microbial methane oxidation at cold seeps along the main active fault in the Marmara Sea

    NASA Astrophysics Data System (ADS)

    Chevalier, Nicolas; Birgel, Daniel; Lopez-Garcia, Purificacion; Taphanel, Marie-Helene; Bouloubassi, Ioanna

    2010-05-01

    The North Anatolian Fault in the Marmara Sea is a spectacular example of a seismically active fault where, in recent years, numerous sites of active fluid venting have been discovered and explored. During the MARNAUT cruise (2007), multidisciplinary sampling was carried out with the Nautile submersible in order to investigate biogeochemical and hydrogeological processes taking place at these newly discovered cold seeps. We have studied short sediment cores (< 20 cm) and authigenic carbonate crusts retrieved with the Nautile submersible from sub-basins of the Marmara Sea, aiming at gaining insight into microbial processes and assemblages in this recently discovered methane-rich setting and at comparing it with previously studied cold seeps. To do so, we investigated diagnostic microbial lipids and their carbon isotope composition, and, in selected sediment samples, we carried out cloning and sequencing of 16S rRNA genes. The sediment core retrieved from the southern slope of the Çinarcik Basin, in an area of black patches, bacterial mats and polychaetes, contained abundant and strongly 13C-depleted archaeal and bacterial lipids. Archaeal lipids consisted mainly of archaeol, sn-2-hydroxyarchaeol, crocetane, and unsaturated PMIs, and showed δ13C values as low as -125 per mille. Concurrently, bacterial lipids (e.g. cyclopropyl-C17:0, C16:1?5, i-/ai-C15:0, and non-isoprenoidal glycerol monoethers), previously assigned to sulphate reducing bacteria (SRB), were identified with low δ13C values (-55 to -115 per mille). The structural and isotopic features of microbial lipids provided compelling evidence for anaerobic oxidation of methane (AOM) taking place within the upper 17 cm of the sediment core, mediated by methanotrophic archaea (ANME) and sulphate reducing bacteria. No biomarker evidence for aerobic oxidation of methane was found. Depth profiles of microbial lipids revealed the vertical zonation of AOM and associated microbial biomass, and implied that AOM is

  15. Resistivity image beneath an area of active methane seeps in the west Svalbard continental slope

    NASA Astrophysics Data System (ADS)

    Goswami, Bedanta K.; Weitemeyer, Karen A.; Minshull, Timothy A.; Sinha, Martin C.; Westbrook, Graham K.; Marín-Moreno, Héctor

    2016-11-01

    The Arctic continental margin contains large amounts of methane in the form of methane hydrates. The west Svalbard continental slope is an area where active methane seeps have been reported near the landward limit of the hydrate stability zone. The presence of bottom simulating reflectors (BSRs) on seismic reflection data in water depths greater than 600 m suggests the presence of free gas beneath gas hydrates in the area. Resistivity obtained from marine controlled source electromagnetic (CSEM) data provides a useful complement to seismic methods for detecting shallow hydrate and gas as they are more resistive than surrounding water saturated sediments. We acquired two CSEM lines in the west Svalbard continental slope, extending from the edge of the continental shelf (250 m water depth) to water depths of around 800 m. High resistivities (5-12 Ωm) observed above the BSR support the presence of gas hydrate in water depths greater than 600 m. High resistivities (3-4 Ωm) at 390-600 m water depth also suggest possible hydrate occurrence within the gas hydrate stability zone (GHSZ) of the continental slope. In addition, high resistivities (4-8 Ωm) landward of the GHSZ are coincident with high-amplitude reflectors and low velocities reported in seismic data that indicate the likely presence of free gas. Pore space saturation estimates using a connectivity equation suggest 20-50 per cent hydrate within the lower slope sediments and less than 12 per cent within the upper slope sediments. A free gas zone beneath the GHSZ (10-20 per cent gas saturation) is connected to the high free gas saturated (10-45 per cent) area at the edge of the continental shelf, where most of the seeps are observed. This evidence supports the presence of lateral free gas migration beneath the GHSZ towards the continental shelf.

  16. Analysis of past recurrent methane seep activity using radiocarbon dating of Calyptogena spp. shells in the eastern Nankai subduction zone, Japan

    NASA Astrophysics Data System (ADS)

    Yagasaki, Kazuhiro; Ashi, Juichiro; Yokoyama, Yusuke; Miyairi, Yosuke; Kuramoto, Shin'ichi

    2016-04-01

    Fault activity around subduction zones have been widely studied and monitored through drilling of oceanic plates, studying piston cores, use of monitoring equipment or through visual analysis using submersible vehicles. Yet the understanding of how small scale faults near shallow regions of the seabed behave in relation to cold seep vent activity is still vague, especially determining when they were active in the past. In tectonically active margins such as the Nankai and Tokai regions off Japan, dense methane hydrate reservoirs have been identified. Cold seeps releasing methane rich hydrocarbon fluids are common here, supporting a wide variety of biological species that hold a symbiotic relationship with the chemosynthetic bacteria. In 1998 a large dead Calyptogena spp. bivalve colony (over 400m2 in size) was discovered off Tokai, Japan. It is unusual for a bivalve colony this size to mostly be dead, raising questions as to what caused their death. In this study we document the radiocarbon 14C age of these bivalve shells to attempt analysing the possible methane seep bahaviour in the past. The measured 14C age ranged in three age groups of 1396±36-1448±34, 1912±31-1938±35 and 5975±34. The 14C age of shells that were alive upon collection and the dissolved inorganic carbon (DIC) in seawater show little difference (˜100 14C age) indicating that shells are not heavily affected by the dead carbon effect from cold seeps that is of biogenic or thermogenic origin, which can make the age to become considerably older than the actual age. Thus the novel calibration model used was based on the seawater DIC collected above the Calyptogena spp. colony site (1133±31), which resulted in the dead shells to be clustered around 1900 Cal AD. This proves to be interesting as the predicted epicenter of the Ansei-Tokai earthquake (M 8.4) in 1854 is extremely close to the bibalve colony site. Using geological data obtained using visual analysis and sub-seafloor structural

  17. SHEEP CREEK SEEP CHARACTERIZATION

    EPA Science Inventory

    The materials presented represent an assessment of site conditions related to the LaCrone property seep, located in the NW 1/4 of Section 34, Township 7E, Range 2N, near Harden City, OK. The primary objective of the study was to identify possible source(s) for the saline water, ...

  18. Methane release from sediment seeps to the atmosphere is counteracted by highly active Methylococcaceae in the water column of deep oligotrophic Lake Constance.

    PubMed

    Bornemann, Maren; Bussmann, Ingeborg; Tichy, Lucas; Deutzmann, Jörg; Schink, Bernhard; Pester, Michael

    2016-08-01

    Methane emissions from freshwater environments contribute substantially to global warming but are under strong control of aerobic methane-oxidizing bacteria. Recently discovered methane seeps (pockmarks) in freshwater lake sediments have the potential to bypass this control by their strong outgassing activity. Whether this is counteracted by pelagic methanotrophs is not well understood yet. We used a (3)H-CH4-radiotracer technique and pmoA-based molecular approaches to assess the activity, abundance and community structure of pelagic methanotrophs above active pockmarks in deep oligotrophic Lake Constance. Above profundal pockmarks, methane oxidation rates (up to 458 nmol CH4 l(-1) d(-1)) exceeded those of the surrounding water column by two orders of magnitude and coincided with maximum methanotroph abundances of 0.6% of the microbial community. Phylogenetic analysis indicated a dominance of members of the Methylococcaceae in the water column of both, pockmark and reference sites, with most of the retrieved sequences being associated with a water-column specific clade. Communities at pockmark and reference locations also differed in parts, which was likely caused by entrainment of sediment-hosted methanotrophs at pockmark sites. Our results show that the release of seep-derived methane to the atmosphere is counteracted by a distinct methanotrophic community with a pronounced activity throughout bottom waters. PMID:27267930

  19. Methane release from sediment seeps to the atmosphere is counteracted by highly active Methylococcaceae in the water column of deep oligotrophic Lake Constance.

    PubMed

    Bornemann, Maren; Bussmann, Ingeborg; Tichy, Lucas; Deutzmann, Jörg; Schink, Bernhard; Pester, Michael

    2016-08-01

    Methane emissions from freshwater environments contribute substantially to global warming but are under strong control of aerobic methane-oxidizing bacteria. Recently discovered methane seeps (pockmarks) in freshwater lake sediments have the potential to bypass this control by their strong outgassing activity. Whether this is counteracted by pelagic methanotrophs is not well understood yet. We used a (3)H-CH4-radiotracer technique and pmoA-based molecular approaches to assess the activity, abundance and community structure of pelagic methanotrophs above active pockmarks in deep oligotrophic Lake Constance. Above profundal pockmarks, methane oxidation rates (up to 458 nmol CH4 l(-1) d(-1)) exceeded those of the surrounding water column by two orders of magnitude and coincided with maximum methanotroph abundances of 0.6% of the microbial community. Phylogenetic analysis indicated a dominance of members of the Methylococcaceae in the water column of both, pockmark and reference sites, with most of the retrieved sequences being associated with a water-column specific clade. Communities at pockmark and reference locations also differed in parts, which was likely caused by entrainment of sediment-hosted methanotrophs at pockmark sites. Our results show that the release of seep-derived methane to the atmosphere is counteracted by a distinct methanotrophic community with a pronounced activity throughout bottom waters.

  20. Investigating Microbial Activity in Diazotrophic Methane Seep Sediment via Transcript Analysis and Single-Cell FISH-NanoSIMS

    NASA Astrophysics Data System (ADS)

    Dekas, A. E.; Connon, S. A.; Chadwick, G.; Orphan, V. J.

    2012-12-01

    Methane seep microbial ecosystems are phylogenetically diverse and physiologically complex, and require culture-independent techniques to accurately investigate metabolic activity. In the present study we combine an RNA analysis of four key microbial genes with FISH-NanoSIMS analysis of single cells to determine the diversity of nitrogen fixing microorganisms (diazotrophs) present at a deep-sea methane-seeping site, as well as investigate the methane-dependency of a variety of community members. Recently, methane-dependent nitrogen fixation was observed in Mound 12 Costa Rica sediments, and was spatially correlated with the abundance of aggregates of anaerobic methanotrophic archaea (ANME) and sulfate reducing bacterial symbionts (SRB). Combined with the detection of 15N uptake from 15N2 in these aggregates, this suggested that the ANME-SRB aggregates are the primary diazotrophs in seep sediment. However, the diversity of dinitrogenase reductase (nifH) sequences recovered from several deep-sea locales, including Mound 12, suggests a greater diversity of diazotrophs in marine sediment. To investigate the activity of these potential diazotrophs in Mound 12 sediment, we investigated a suite of RNA transcripts in 15N2 incubations in both the presence and absence of methane: nifH, bacterial 16S rRNA, methyl coenzyme M reductase A (mcrA), and adenosine-5'-phosposulfate reductase alpha subunit (aprA). No nifH transcripts were recovered in incubations without methane, consistent with previous measurements lacking 15N2 uptake in the same sediments. The activity of the bacterial community in general, assessed by variable transcription, was also greatly affected by the presence or absence of methane. Single-cell fluorescence in situ hybridization coupled to nanoscale secondary ion mass spectrometry (FISH-NanoSIMS) was employed to confirm diazotrophic activity (15N2 uptake) and protein synthesis (15NH4+ uptake) of particular species implicated as ecologically important by the

  1. Air-sea flux of methane from selected marine hydrate/seep sites in the northern Gulf of Mexico during HYFLUX

    NASA Astrophysics Data System (ADS)

    Hu, L.; Yvon-Lewis, S. A.; Kessler, J. D.; MacDonald, I.

    2009-12-01

    Methane is one of the most important greenhouse gases, playing a significant role in global climate change and atmospheric chemistry. In spite of tremendous efforts made to constrain the strength of its sources and sinks, large uncertainties remain for some individual sources. Based on the previous observations and modeling studies, the flux of CH4 from marine hydrates and seeps to the atmosphere comprises a significant fraction of the entire methane flux from the global ocean. However, most of the estimates are based on the seafloor methane flux or discrete water column concentrations of methane and the averaged atmospheric methane ratios. In this study, we investigated three marine hydrate/seep sites in northern Gulf of Mexico in July of 2009 during the HYFLUX cruise. Continuous saturation-anomaly (deviation from equilibrium) measurements of methane, ethane and propane were made by alternately sampling the air or the headspace of Weiss-type equilibrator and analyzing it in a GC-FID system. Some 13CH4 measurements were also made continuously using a cavity ring-down spectrometer (CRDS). During this cruise, the maximum concentrations observed at the 3 marine hydrate/seep sites MC118, GC600, and GC185 were 14.5, 5.1, and 2.2 nmol/L, respectively. The air-sea fluxes, calculated from saturation anomalies, are used to create extremely high resolution flux maps for the three marine hydrate/seeps sites.

  2. Authigenic minerals related to carbon and sulfur biogeochemical cycling from deep-sea active methane seeps offshore South-West Africa

    NASA Astrophysics Data System (ADS)

    Pierre, C.; Blanc-Valleron, M.; Demange, J.; Boudouma, O.; Pape, T.; Himmler, T.; Fekete, N.; Spiess, V.

    2011-12-01

    The South-West African continental margin is well known for occurrences of active methane-rich fluid seeps that are associated with seafloor pockmarks in a broad range of water depths, from the shelf to the deep basins. High gas flares in the water column, luxurious oases of benthic fauna, gas hydrate accumulations and diagenetic carbonate crusts have been observed at these seeps. During the M76/3a expedition of R/V METEOR (summer 2008) gravity cores recovered abundant authigenic carbonate concretions from five pockmarks of the South-West African margin including previously studied sites (Hydrate Hole, Worm Hole, Regab Pockmark) and two sites (Deep Hole, Baboon Cluster) newly discovered during the cruise. Carbonate concretions were mostly associated to sediments settled by seep-associated benthic macrofauna and bearing shallow gas hydrates. We present new results of the comprehensive analysis of the mineralogy and isotope geochemistry of the diagenetic carbonates sampled in the five pockmarks. The mineralogy of authigenic carbonates is dominated by magnesian calcite and aragonite, associated occasionally with dolomite. The oxygen and carbon isotopic compositions of authigenic carbonates (+2.4 < δ18O % V-PDB < +6.2 ; -61.0 < δ13C % V-PDB < -40.1) indicate that microbial anaerobic oxidation of methane (AOM) was the main process controling carbonate precipitation within sub-seafloor sediments deposited from the glacial-time up to the present. The frequent occurrence of diagenetic gypsum crystals within the sediments demonstrates that bio-irrigation with oxygenated bottom water by the burrowing activity of benthic fauna caused the secondary oxidation of reduced sulfur (hydrogen sulfide and pyrite) that was produced by sulfate reducting bacteria as a by-product of AOM; during the sulfide oxidation process, the released acidity induced the partial dissolution of carbonates. Our results demonstrate also the strong link that existed between the carbon and sulfur cycles

  3. Identification, visualization, and sorting of translationally active microbial consortia from deep-sea methane seeps

    NASA Astrophysics Data System (ADS)

    Hatzenpichler, R.; Connon, S. A.; Goudeau, D.; Malmstrom, R.; Woyke, T.; Orphan, V. J.

    2015-12-01

    Within the past few years, great progress has been made in tapping the genomes of individual cells separated from environmental samples. Unfortunately, however, most often these efforts have been target blind, as they did not pre-select for taxa of interest or focus on metabolically active cells that could be considered key species of the system at the time. This problem is particularly pronounced in low-turnover systems such as deep sea sediments. In an effort to tap the genetic potential hidden within functionally active cells, we have recently developed an approach for the in situ fluorescent tracking of protein synthesis in uncultured cells via bioorthogonal non-canonical amino acid-tagging (BONCAT). This technique depends on the incorporation of synthetic amino acids that carry chemically modifiable tags into newly made proteins, which later can be visualized via click chemistry-mediated fluorescence-labeling. BONCAT is thus able to specifically target proteins that have been expressed in reaction to an experimental condition. We are particularly interested in using BONCAT to understand the functional potential of slow-growing syntrophic consortia of anaerobic methanotrophic archaea and sulfate-reducing bacteria which together catalyze the anaerobic oxidation of methane (AOM) in marine methane seeps. In order to specifically target consortia that are active under varying environmental regimes, we are studying different subpopulations of these inter-domain consortia via a combination of BONCAT with rRNA-targeted FISH. We then couple the BONCAT-enabled staining of active consortia with their separation from inactive members of the community via fluorescence-activated cell-sorting (FACS) and metagenomic sequencing of individual consortia. Using this approach, we were able to identify previously unrecognized AOM-partnerships. By comparing the mini-metagenomes obtained from individual consortia with each other we are starting to gain a more hollistic understanding

  4. Biogeochemistry of a low-activity cold seep in the Larsen B area, western Weddell Sea, Antarctica

    NASA Astrophysics Data System (ADS)

    Niemann, H.; Fischer, D.; Graffe, D.; Knittel, K.; Montiel, A.; Heilmayer, O.; Nöthen, K.; Pape, T.; Kasten, S.; Bohrmann, G.; Boetius, A.; Gutt, J.

    2009-06-01

    First videographic indication of an Antarctic cold seep ecosystem was recently obtained from the collapsed Larsen B ice shelf, western Weddell Sea (Domack et al., 2005). Within the framework of the R/V Polarstern expedition ANTXXIII-8, we revisited this area for geochemical, microbiological and further videographical examinations. During two dives with ROV Cherokee (MARUM, Bremen), several bivalve shell agglomerations of the seep-associated, chemo syntheticclam Calyptogena sp. were found in the trough of the Crane and Evans glacier. The absence of living clam specimens indicates that the flux of sulphide and hence the seepage activity is diminished at present. This impression was further substantiated by our geochemical observations. Concentrations of thermogenic methane were moderately elevated with 2 μM in surface sediments of a clam patch, increasing up to 9 μM at a sediment depth of about 1 m in the bottom sections of the sediment cores. This correlated with a moderate decrease in sulphate from 28 mM at the surface down to 23.4 mM, an increase in sulphide to up to 1.43 mM and elevated rates of the anaerobic oxidation of methane (AOM) of up to 600 pmol cm-3 d-1 at about 1 m below the seafloor. Molecular analyses indicate that methanotrophic archaea related to ANME-3 are the most likely candidates mediating AOM in sediments of the Larsen B seep (Domack et al., 2005; EOS 86, 269-276).

  5. Biogeochemistry of a low-activity cold seep in the Larsen B area, western Weddell Sea, Antarctica

    NASA Astrophysics Data System (ADS)

    Niemann, H.; Fischer, D.; Graffe, D.; Knittel, K.; Montiel, A.; Heilmayer, O.; Nöthen, K.; Pape, T.; Kasten, S.; Bohrmann, G.; Boetius, A.; Gutt, J.

    2009-11-01

    First videographic indication of an Antarctic cold seep ecosystem was recently obtained from the collapsed Larsen B ice shelf, western Weddell Sea (Domack et al., 2005). Within the framework of the R/V Polarstern expedition ANTXXIII-8, we revisited this area for geochemical, microbiological and further videographical examinations. During two dives with ROV Cherokee (MARUM, Bremen), several bivalve shell agglomerations of the seep-associated, chemosynthetic clam Calyptogena sp. were found in the trough of the Crane and Evans glacier. The absence of living clam specimens indicates that the flux of sulphide and hence the seepage activity is diminished at present. This impression was further substantiated by our geochemical observations. Concentrations of thermogenic methane were moderately elevated with 2 μM in surface sediments of a clam patch, increasing up to 9 μM at a sediment depth of about 1 m in the bottom sections of the sediment cores. This correlated with a moderate decrease in sulphate from about 28 mM at the surface down to 23.4 mM, an increase in sulphide to up to 1.43 mM and elevated rates of the anaerobic oxidation of methane (AOM) of up to 600 pmol cm-3 d-1 at about 1 m below the seafloor. Molecular analyses indicate that methanotrophic archaea related to ANME-3 are the most likely candidates mediating AOM in sediments of the Larsen B seep.

  6. Molecular evidence that phylogenetically diverged ciliates are active in microbial mats of deep-sea cold-seep sediment.

    PubMed

    Takishita, Kiyotaka; Kakizoe, Natsuki; Yoshida, Takao; Maruyama, Tadashi

    2010-01-01

    Cold seeps are areas of the seafloor where hydrogen sulfide- and methane-rich fluid seepage occurs, often sustaining chemosynthetic ecosystems. It is well known that both archaea and bacteria oxidize sulfides and methane to produce chemical energy and that several endemic animals use this energy to thrive in cold seeps. On the other hand, there is little knowledge regarding diversity and ecology of microbial eukaryotes in this ecosystem. In this study we isolated environmental RNA and DNA from microbial mats of cold-seep sediment in Sagami Bay, Japan, and retrieved eukaryotic small-subunit ribosomal RNA sequences with polymerase chain reaction methods followed by clone library construction. Most RNA-derived clones obtained were from ciliates, although DNA-derived clones were mainly from the fungus Cryptococcus curvatus, suggesting that ciliates are active in the environment. The ciliate sequences were phylogenetically diverse, and represented eight known class lineages as well as undesignated lineages. Because most ciliates are bacterivorous, it is highly likely that the ciliates for which sequences were recovered play a role in the food web of this ecosystem as grazers of microbial mats. In addition, given that the environment studied is under highly reduced (anoxic) conditions, based on the prokaryotic community structure deduced from T-RFLP profiles, the ciliates detected may be obligatory or facultative anaerobes.

  7. Activity and interactions of methane seep microorganisms assessed by parallel transcription and FISH-NanoSIMS analyses

    PubMed Central

    Dekas, Anne E; Connon, Stephanie A; Chadwick, Grayson L; Trembath-Reichert, Elizabeth; Orphan, Victoria J

    2016-01-01

    To characterize the activity and interactions of methanotrophic archaea (ANME) and Deltaproteobacteria at a methane-seeping mud volcano, we used two complimentary measures of microbial activity: a community-level analysis of the transcription of four genes (16S rRNA, methyl coenzyme M reductase A (mcrA), adenosine-5′-phosphosulfate reductase α-subunit (aprA), dinitrogenase reductase (nifH)), and a single-cell-level analysis of anabolic activity using fluorescence in situ hybridization coupled to nanoscale secondary ion mass spectrometry (FISH-NanoSIMS). Transcript analysis revealed that members of the deltaproteobacterial groups Desulfosarcina/Desulfococcus (DSS) and Desulfobulbaceae (DSB) exhibit increased rRNA expression in incubations with methane, suggestive of ANME-coupled activity. Direct analysis of anabolic activity in DSS cells in consortia with ANME by FISH-NanoSIMS confirmed their dependence on methanotrophy, with no 15NH4+ assimilation detected without methane. In contrast, DSS and DSB cells found physically independent of ANME (i.e., single cells) were anabolically active in incubations both with and without methane. These single cells therefore comprise an active ‘free-living' population, and are not dependent on methane or ANME activity. We investigated the possibility of N2 fixation by seep Deltaproteobacteria and detected nifH transcripts closely related to those of cultured diazotrophic Deltaproteobacteria. However, nifH expression was methane-dependent. 15N2 incorporation was not observed in single DSS cells, but was detected in single DSB cells. Interestingly, 15N2 incorporation in single DSB cells was methane-dependent, raising the possibility that DSB cells acquired reduced 15N products from diazotrophic ANME while spatially coupled, and then subsequently dissociated. With this combined data set we address several outstanding questions in methane seep microbial ecosystems and highlight the benefit of measuring microbial activity in the

  8. Activity and interactions of methane seep microorganisms assessed by parallel transcription and FISH-NanoSIMS analyses.

    PubMed

    Dekas, Anne E; Connon, Stephanie A; Chadwick, Grayson L; Trembath-Reichert, Elizabeth; Orphan, Victoria J

    2016-03-01

    To characterize the activity and interactions of methanotrophic archaea (ANME) and Deltaproteobacteria at a methane-seeping mud volcano, we used two complimentary measures of microbial activity: a community-level analysis of the transcription of four genes (16S rRNA, methyl coenzyme M reductase A (mcrA), adenosine-5'-phosphosulfate reductase α-subunit (aprA), dinitrogenase reductase (nifH)), and a single-cell-level analysis of anabolic activity using fluorescence in situ hybridization coupled to nanoscale secondary ion mass spectrometry (FISH-NanoSIMS). Transcript analysis revealed that members of the deltaproteobacterial groups Desulfosarcina/Desulfococcus (DSS) and Desulfobulbaceae (DSB) exhibit increased rRNA expression in incubations with methane, suggestive of ANME-coupled activity. Direct analysis of anabolic activity in DSS cells in consortia with ANME by FISH-NanoSIMS confirmed their dependence on methanotrophy, with no (15)NH4(+) assimilation detected without methane. In contrast, DSS and DSB cells found physically independent of ANME (i.e., single cells) were anabolically active in incubations both with and without methane. These single cells therefore comprise an active 'free-living' population, and are not dependent on methane or ANME activity. We investigated the possibility of N2 fixation by seep Deltaproteobacteria and detected nifH transcripts closely related to those of cultured diazotrophic Deltaproteobacteria. However, nifH expression was methane-dependent. (15)N2 incorporation was not observed in single DSS cells, but was detected in single DSB cells. Interestingly, (15)N2 incorporation in single DSB cells was methane-dependent, raising the possibility that DSB cells acquired reduced (15)N products from diazotrophic ANME while spatially coupled, and then subsequently dissociated. With this combined data set we address several outstanding questions in methane seep microbial ecosystems and highlight the benefit of measuring microbial activity in

  9. Origin and transport of pore fluids in the Nankai accretionary prism inferred from chemical and isotopic compositions of pore water at cold seep sites off Kumano

    NASA Astrophysics Data System (ADS)

    Toki, Tomohiro; Higa, Ryosaku; Ijiri, Akira; Tsunogai, Urumu; Ashi, Juichiro

    2014-12-01

    We used push corers during manned submersible dives to obtain sediment samples of up to 30 cm from the subseafloor at the Oomine Ridge. The concentrations of B in pore water extracted from the sediment samples from cold seep sites were higher than could be explained by organic matter decomposition, suggesting that the seepage fluid at the site was influenced by B derived from smectite-illite alteration, which occurs between 50°C and 160°C. Although the negative δ18OH2O and δDH2O values of the pore fluids cannot be explained by freshwater derived from clay mineral dehydration (CMD), we considered the contribution of pore fluids in the shallow sediments of the accretionary prism, which showed negative δ18OH2O and δDH2O values according to the results obtained during Integrated Ocean Drilling Program (IODP) Expeditions 315 and 316. We calculated the mixing ratios based on a four-end-member mixing model including freshwater derived from CMD, pore fluids in the shallow (SPF) accretionary prism sediment, seawater (SW), and freshwater derived from methane hydrate (MH) dissociation. However, the Oomine seep fluids were unable to be explained without four end members, suggesting that deep-sourced fluids in the accretionary prism influenced the seeping fluids from this area. This finding presents the first evidence of deep-sourced fluids at cold seep sites in the Oomine Ridge, indicating that a megasplay fault is a potential pathway for the deep-sourced fluids.

  10. Trace Elemental Geochemistry of Pacific Margin Seep and Non-seep Benthic Foraminifera

    NASA Astrophysics Data System (ADS)

    Burkett, A. M.; Rathburn, A. E.; De Deckker, P.; Perez, M. E.

    2015-12-01

    As part of a continued effort to evaluate factors that influence carbonate biogeochemistry of living foraminifera, stable isotopic and trace elemental analyses of epibenthic and infaunal species of benthic foraminifera collected from the Pacific margin revealed clues for assessment of the presence, history and origin of cold and hydrothermal methane seepage sites. Hydrothermal seeps have only recently been discovered, prioritizing their recognition and assessments of the origins/sources of these anomalously warm environments. Trace elements were analyzed with a laser ablation ICP-MS at the Australian National University, avoiding contamination and allowing measurements of recently generated chambers. Living Cibicidoides wuellerstorfi and Uvigerina peregrina collected from active methane seeps on the east Pacific margin (Costa Rica, Alaska and Hydrate Ridge) have a wider range in both stable isotopic signals and some trace elemental values (e.g., Mg/Ca) compared to nearby inactive areas. Comparisons of additional trace elemental values (e.g., Li/Ca, Cd/Ca, B/Ca, and Ba/Ca) from living Cibicidoides wuellerstorfi and Uvigerina peregrina from these unique seafloor environments provide additional information in the geochemical influences of cold and hydrothermal seepage on foraminiferal calcite geochemistry. Seep environments are often the result of complex tectonic processes, have implications in past rapid climatic shifts and in future climate change predictions and models, and can influence modern ecosystems and biogeochemical cycles in ways which are not fully understood. Benthic foraminiferal geochemistry provides a potential means to identify seep fluid origins, elucidate seep fluid records and recognize hydrothermal seeps and their spatial and temporal history.

  11. Resistivity structure of the Del Mar methane seep.

    NASA Astrophysics Data System (ADS)

    Kannberg, P. K.; Constable, S.

    2015-12-01

    In March of 2015 we mapped the resistivity structure of the Del Mar methane seep in the inner California borderlands using a deep towed electromagnetic (EM) source and receiver array. Located in the San Diego trough at a depth of 1km, the seep site is on the flank of a mound associated with a transpressive step in the San Diego trough fault. The seep site has previously been associated with seafloor pockmarks, acoustic wipeouts, chemosynthetic communities, and active methane bubble venting. Controlled source electromagnetic (CSEM) surveys are performed by deep-towing an EM source that is transmitting a known signal; this signal is detected by towed receivers. This transmitted signal is altered by the electrical properties of the surrounding environment. Compared to seismic methods, EM methods are largely insensitive to free gas, making it an especially useful tool for detecting electrically resistive methane hydrate in areas of active gas venting. We used a 50m dipole transmitting 100A, with 3-axis electric field receivers spaced at 130m, 230m, 330m, and 430m behind the transmitter dipole center. The receiver data are inverted using MARE2DEM, a finite element 2D inversion routine. The inversion results show the background resistivity of the trough sediments to be about 1-2 ohmm, and are largely featureless outside of the seep site. However at the seep site we see a decanter-shaped 100 ohmm resistor whose base is 100m below the seafloor, and 1km wide at its widest. This feature narrows at the top to form a pipe structure about 200m wide that extends to the seafloor. These resistive structures are interpreted to be methane hydrate resulting from methane rich fluid flow along faults associated with the transpressional system that brackets the seep site.

  12. Biosynthesis of selenium rich exopolysaccharide (Se-EPS) by Pseudomonas PT-8 and characterization of its antioxidant activities.

    PubMed

    Ye, Shuhong; Zhang, Jiajia; Liu, Zhaofang; Zhang, Yu; Li, Jiang; Li, Yao Olive

    2016-05-20

    Biosynthesis of organo-selenium is achieved by submerged fermentation of selenium-tolerant Pseudomonas PT-8. The end product of metabolic process is selenium-bearing exopolysaccharide (Se-EPS), which contains a higher content of uronic acid than the exopolysaccharide (EPS) by the strain without selenium in the culture medium. Selenium content in Se-EPS reached a maximum yield of 256.7 mg/kg when using an optimized culture condition. Crude Se-EPS was purified into two fractions-a pH neutral Se-EPS-1 and an acidic Se-EPS-2. Structure and chemical composition of Se-EPS-2 were investigated by chromatographic analyses. Results showed that Se-EPS-2 was a homogenous polysaccharide with molecular weight of 7.3 kDa, consisting of monosaccharides, rhamnose, arabinose, xylose, mannose, glucose and galactose with a molar ratio of 19.58:19.28:5.97:18.99:23.70:12.48, respectively. Compared to the EPS, the content of rhamnose in Se-EPS increased and molecular weight decreased. The Se-EPS had strong scavenging actions on DPPH•, •OH and •O2(-), which is much higher than the EPS. PMID:26917395

  13. Methanotrophic gastropods from a bathyal hydrocarbon seep, Gulf of Mexico

    SciTech Connect

    Anderson, L.C.; Aharon, P.; Gupta, S. )

    1992-01-01

    Two gastropods, Neritina sp. and Truncatella sp., collected live from a Gulf of Mexico active gas seep with the submersible Johnson Sea Link in September 1991, apparently incorporate methane-derived carbon in their soft tissues. Flesh of an individual Neritina sp. had a delta C-13 of [minus]50.92 per mil PDB, and that of two coexisting individuals of Truncatella sp. had values of [minus]45.11 and [minus]49.27 per mil. These isotope values are comparable to those reported for the methanotrophic mytilid bivalve Bathymodiolus sp. from other hydrocarbon seeps on the Gulf of Mexico, and are lighter than published isotopic values of chemosynthetic organisms with sulfur-oxidizing symbionts. The anomalously light carbon-isotopic values of Neritina sp. and Truncatella sp. may steam from one of three causes: (1) these gastropods host symbiotic methanotrophic bacteria, (2) their chief food is methane-oxidizing bacteria present at the seep, or (3) they incorporate some carbon from the periostracum of mussels on which they may graze. The presence of abundant juveniles of Bathymodiolus, reported to settle preferentially in areas of active seepage and high methane release, indicates that methane was abundant and supported a community with multiple trophic levels. Generally, studies of hydrocarbon-seep communities have focused on larger community members, especially bivalves and tube worms. The presence of living Neritina and Truncatella at the authors sampling site, however, draws attention to the fact that these gastropods are integral and significant parts of hydrocarbon-seep communities. Both gastropod species are members of genera that characteristically inhabit shallow marine, intertidal, and semiterrestrial environments. The presence of these genera in bathyal hydrocarbon seeps indicates that they have very broad environmental ranges, thus limiting their utility in paleoecologic reconstructions.

  14. Timing of active methane seep events in the eastern margin of the Japan Sea based on benthic foraminifera

    NASA Astrophysics Data System (ADS)

    Oi, T.

    2015-12-01

    We study the late Quaternary assemblages and stable isotope analyses of benthic foraminifera from the marine core sediments around three methane seep area in the eastern margin of the Japan Sea. Study samples are collected on the Umitaka Spur (MD179-3304), a west part of the Oki Trough (UT14-PC1303&PC1305), and a north part of the Mogami Trough (HR14-RC1408). Each sedimentation rate is calculated by the ages of 14C, tephra, oxygen isotope events, and bottoms of the thin laminated layer.Obvious occurrences of the methane related foraminifera, Rutherfordoides sp., are found from three all core sediments, and these sedimentation ages range to 28-25ka, early part of the MIS 2. However, we never find the unique occurrences from RC1408 sections except of MIS 2 even if another low stand stage of MIS 6. Above Rutherfordoides distributions, rare benthic foraminiferal number shows an anoxic bottom condition where most benthic foraminifera couldn't live during the LGM (Oba et al., 1991), nonetheless, Rutherfordoides sp. lived continuously until the LGM. From the surface sediments, Rutherfordoides cornuta, lives on plural area from the northwest Pacific but not from the Japan Sea (Matoba and Nakagawa, 2009) is related to high methane gas content of the sediments in the Sagami Bay (Akimoto et al., 1996). Nakagawa et al. (2009) reported that distributions of Rutherfordoides rotundata (closely related R. cornuta) indicate that an expulsion of a large amount of methane occurred on the Umitaka Spur during the LGM due to a massive dissociation of subsurface methane hydrate. And, the negative carbon isotope peak signal of Rutherfordoides sp. from RC1408 in the Mogami Trough, also indicate to dissociations of methane hydrate and active methane seeps by the lowest sea level same as Umitaka Spur (Takeuchi et al., 2007). Acknowledgement This research was a part of METI's project entitled "FY2014 Promoting research and development on methane hydrate" .

  15. Investigation of shallow gas hydrate occurrence and gas seep activity on the Sakhalin continental slope, Russia

    NASA Astrophysics Data System (ADS)

    Jin, Young Keun; Baranov, Boris; Obzhirov, Anatoly; Salomatin, Alexander; Derkachev, Alexander; Hachikubo, Akihiro; Minami, Hrotsugu; Kuk Hong, Jong

    2016-04-01

    The Sakhalin continental slope has been a well-known gas hydrate area since the first finding of gas hydrate in 1980's. This area belongs to the southernmost glacial sea in the northern hemisphere where most of the area sea is covered by sea ice the winter season. Very high organic carbon content in the sediment, cold sea environment, and active tectonic regime in the Sakhalin slope provide a very favorable condition for occurring shallow gas hydrate accumulation and gas emission phenomena. Research expeditions under the framework of a Korean-Russian-Japanese long-term international collaboration projects (CHAOS, SSGH-I, SSGH-II projects) have been conducted to investigate gas hydrate occurrence and gas seepage activities on the Sakhalin continental slope, Russia from 2003 to 2015. During the expeditions, near-surface gas hydrate samples at more than 30 sites have been retrieved and hundreds of active gas seepage structures on the seafloor were newly registered by multidisciplinary surveys. The gas hydrates occurrence at the various water depths from about 300 m to 1000 m in the study area were accompanied by active gas seepage-related phenomena in the sub-bottom, on the seafloor, and in the water column: well-defined upward gas migration structures (gas chimney) imaged by high-resolution seismic, hydroacoustic anomalies of gas emissions (gas flares) detected by echosounders, seafloor high backscatter intensities (seepage structures) imaged by side-scan sonar and bathymetric structures (pockmarks and mounds) mapped by single/multi-beam surveys, and very shallow SMTZ (sulphate-methane transition zone) depths, strong microbial activities and high methane concentrations measured in sediment/seawater samples. The highlights of the expeditions are shallow gas hydrate occurrences around 300 m in the water depth which is nearly closed to the upper boundary of gas hydrate stability zone in the area and a 2,000 m-high gas flare emitted from the deep seafloor.

  16. Tracking Dissolved Methane Concentrations near Active Seeps and Gas Hydrates: Sea of Japan.

    NASA Astrophysics Data System (ADS)

    Snyder, G. T.; Aoki, S.; Matsumoto, R.; Tomaru, H.; Owari, S.; Nakajima, R.; Doolittle, D. F.; Brant, B.

    2015-12-01

    A number of regions in the Sea of Japan are known for active gas venting and for gas hydrate exposures on the sea floor. In this investigation we employed several gas sensors mounted on a ROV in order to determine the concentrations of dissolved methane in the water near these sites. Methane concentrations were determined during two-second intervals throughout each ROV deployment during the cruise. The methane sensor deployments were coupled with seawater sampling using Niskin bottles. Dissolved gas concentrations were later measured using gas chromatography in order to compare with the sensor results taken at the same time. The observed maximum dissolved methane concentrations were much lower than saturation values, even when the ROV manipulators were in contact with gas hydrate. Nonetheless, dissolved concentrations did reach several thousands of nmol/L near gas hydrate exposures and gas bubbles, more than two orders of magnitude over the instrumental detection limits. Most of the sensors tested were able to detect dissolved methane concentrations as low as 10 nmol/L which permitted detection when the ROV approached methane plume sites, even from several tens of meters above the sea floor. Despite the low detection limits, the methane sensors showed variable response times when returning to low-background seawater (~5nM). For some of the sensors, the response time necessary to return to background values occurred in a matter of minutes, while for others it took several hours. Response time, as well as detection limit, should be an important consideration when selecting methane sensors for ROV or AUV investigations. This research was made possible, in part, through funding provided by the Japanese Ministry of Economy, Trade and Industry (METI).

  17. Ecology of Two Terrestrial Serpentinizing Fluid Seeps Offers a Glimpse of the Deep Biosphere

    NASA Astrophysics Data System (ADS)

    Woycheese, K. M.; Meyer-Dombard, D. R.; Cardace, D.; Gulecal, Y.; Arcilla, C. A.

    2013-12-01

    biofilms. Despite the variations in taxonomic diversity at both sites, functional diversity inferred from sequencing data is similar. The presence of Thaumarchaeota taxa at both locations suggests ammonia oxidation. Methanogenic archaeal taxa may indicate methanogenesis, but it is possible that these archaea are using methanogenesis pathways in reverse (methanotrophy). Clostridia and Bacteriodetes were present at both seep sources, which suggests anaerobic fermentation is a viable metabolism. The ability of Clostridia to form spores may be advantageous at the ephemeral Yanartas seep. The contrast between anaerobic taxa abundances at both locations may be due to the difference in surface mixing at the seeps' surface expressions. Sequencing reads from both localities revealed a preponderance of methanogens, fermenters, and nitrifiers that may be remnants of a deep subsurface population exposed abruptly to atmospheric conditions. Further work is necessary to determine which metabolisms are most active within the microbial community, and to ascertain the biogenecity of the methane at both seeps.

  18. Biogeochemical processes and microbial diversity of the Gullfaks and Tommeliten methane seeps (Northern North Sea)

    NASA Astrophysics Data System (ADS)

    Wegener, G.; Shovitri, M.; Knittel, K.; Niemann, H.; Hovland, M.; Boetius, A.

    2008-02-01

    Fluid-flow related seafloor structures and gas seeps were detected in the North Sea in the 1970s and 1980s by acoustic sub-bottom profiling and oil rig surveys. A variety of features like pockmarks, gas vents and authigenic carbonate cements were found to be associated with sites of oil and gas exploration, indicating a link between these surface structures and underlying deep hydrocarbon reservoirs. In this study we performed acoustic surveys and videographic observation at Gullfaks, Holene Trench, Tommeliten, Witch's Hole and the giant pockmarks of the UK Block 15/25, to investigate the occurrence and distribution of cold seep ecosystems in the Northern North Sea. The most active gas seep sites, i.e. Gullfaks and Tommeliten, were investigated in detail: at both sites gas bubbles escaped continuously from small holes in the seabed to the water column, reaching the upper mixed surface layer as indicated by acoustic images of the gas flares. At Gullfaks a 0.1 km2 large gas emission site was detected on a flat sandy seabed, covered by filamentous sulfide-oxidizing bacteria. At Tommeliten we found a patchy distribution of small bacterial mats indicating sites of gas seepage. Here the seafloor consists of layers of sand and stiff clay, and gas emission was observed from small cracks in the seafloor. At both sites the anaerobic oxidation of methane (AOM) coupled to sulfate reduction is the major source of sulfide. Molecular analyses targeting specific lipid biomarkers and 16 S rRNA gene sequences identified an active microbial community dominated by sulfide-oxidizing and sulfate-reducing bacteria (SRB) as well as methanotrophic bacteria and archaea. Carbon isotope values of specific microbial fatty acids and alcohols were highly depleted, indicating that the microbial community at both gas seeps incorporates methane or its metabolites. The microbial community composition of both shallow seeps show high similarities to the deep water seeps associated with gas hydrates

  19. Enumeration of viruses and prokaryotes in deep-sea sediments and cold seeps of the Gulf of Mexico

    USGS Publications Warehouse

    Kellogg, Christina A.

    2010-01-01

    Little is known about the distribution and abundance of viruses in deep-sea cold-seep environments. Like hydrothermal vents, seeps support communities of macrofauna that are sustained by chemosynthetic bacteria. Sediments close to these communities are hypothesized to be more microbiologically active and therefore to host higher numbers of viruses than non-seep areas. Push cores were taken at five types of Gulf of Mexico habitats at water depths below 1000 m using a remotely operated vehicle (ROV). The habitats included non-seep reference sediment, brine seeps, a microbial mat, an urchin field, and a pogonophoran worm community. Samples were processed immediately for enumeration of viruses and prokaryotes without the addition of a preservative. Prokaryote counts were an order of magnitude lower in sediments directly in contact with macrofauna (urchins, pogonophorans) compared to all other samples (107 vs. 108 cells g-1 dry weight) and were highest in areas of elevated salinity (brine seeps). Viral-Like Particle (VLP) counts were lowest in the reference sediments and pogonophoran cores (108 VLP g-1 dry wt), higher in brine seeps (109 VLP g-1 dry wt), and highest in the microbial mats (1010 VLP g-1 dry wt). Virus-prokaryote ratios (VPR) ranged from <5 in the reference sediment to >30 in the microbial mats and >60 in the urchin field. VLP counts and VPR were all significantly greater than those reported from sediments in the deep Mediterranean Sea and in most cases were higher than recent data from a cold-seep site near Japan. The high VPR suggest that greater microbial activity in or near cold-seep environments results in greater viral production and therefore higher numbers of viruses.

  20. Enumeration of viruses and prokaryotes in deep-sea sediments and cold seeps of the Gulf of Mexico

    NASA Astrophysics Data System (ADS)

    Kellogg, Christina A.

    2010-11-01

    Little is known about the distribution and abundance of viruses in deep-sea cold-seep environments. Like hydrothermal vents, seeps support communities of macrofauna that are sustained by chemosynthetic bacteria. Sediments close to these communities are hypothesized to be more microbiologically active and therefore to host higher numbers of viruses than non-seep areas. Push cores were taken at five types of Gulf of Mexico habitats at water depths below 1000 m using a remotely operated vehicle (ROV). The habitats included non-seep reference sediment, brine seeps, a microbial mat, an urchin field, and a pogonophoran worm community. Samples were processed immediately for enumeration of viruses and prokaryotes without the addition of a preservative. Prokaryote counts were an order of magnitude lower in sediments directly in contact with macrofauna (urchins, pogonophorans) compared to all other samples (107 vs. 108 cells g-1 dry weight) and were highest in areas of elevated salinity (brine seeps). Viral-Like Particle (VLP) counts were lowest in the reference sediments and pogonophoran cores (108 VLP g-1 dry wt), higher in brine seeps (109 VLP g-1 dry wt), and highest in the microbial mats (1010 VLP g-1 dry wt). Virus-prokaryote ratios (VPR) ranged from <5 in the reference sediment to >30 in the microbial mats and >60 in the urchin field. VLP counts and VPR were all significantly greater than those reported from sediments in the deep Mediterranean Sea and in most cases were higher than recent data from a cold-seep site near Japan. The high VPR suggest that greater microbial activity in or near cold-seep environments results in greater viral production and therefore higher numbers of viruses.

  1. Hydrocarbon seep-carbonates of a Miocene forearc (East Coast Basin), North Island, New Zealand

    NASA Astrophysics Data System (ADS)

    Campbell, Kathleen A.; Francis, David A.; Collins, Mike; Gregory, Murray R.; Nelson, Campbell S.; Greinert, Jens; Aharon, Paul

    2008-02-01

    An ancient hydrocarbon seep province of 14 isolated, authigenic carbonate deposits has been identified in fine-grained, deep-marine siliciclastic strata of the Miocene East Coast Basin, North Island, New Zealand. These forearc sediments have been uplifted and complexly deformed into accretionary ridges, adjacent to the still-active Hikurangi convergent margin. Older active and passive margin strata (mid-Cretaceous to Oligocene in age) underlie the Neogene sequence, and contain oil- and gas-prone source rocks. Older Mesozoic meta-sedimentary rocks constitute the backstop against which the current phase of subduction-related sedimentation has accumulated (~ 24 Ma-present). The seep-carbonates (up to 10 m thick, 200 m across) archive methane signatures in their depleted carbon isotopes (to δ13C -51.7‰ PDB), and contain chemosynthesis-based paleocommunities (e.g. worm tubes, bathymodioline mussels, and vesicomyid, lucinid and thyasirid bivalves) typical of other Cenozoic and modern seeps. Northern and southern sites are geographically separated, and exhibit distinct lithological and faunal differences. Structural settings are variable. Seep-associated lithologies also are varied, and suggest carbonate development in sub-seafloor, seafloor and physically reworked (diapiric expansion, gas explosion, gravity slide or debris flow) settings, similar to Italian Apennine seep deposits of overlapping ages. Peculiar attributes of the New Zealand Miocene seep deposits are several, including digitate thrombolites of clotted microbial micrite encased in thick, isopachous horizons and botryoids of aragonite. Seep plumbing features are also well-exposed at some sites, displaying probable gas-explosion breccias filled with aragonite, tubular concretions (fluid conduits), and carbonate-cemented, thin sandstone beds and burrows within otherwise impermeable mudstones. A few seeps were large enough to develop talus-debris piles on their flanks, which were populated by lucinid bivalves

  2. An overview of the latest results of cold seep research along the Hikurangi Margin, New Zealand

    NASA Astrophysics Data System (ADS)

    Greinert, J.; Faure, K.; Bialas, J.; Linke, P.; Pecher, I.; Rowden, A.

    2008-12-01

    Prior to 2006, the knowledge about cold seeps around New Zealand was based mainly on accidental recovery of seep fauna or methane-derived carbonates by fishermen and flares in echo sounders. Lewis and Marshall (1996) compiled these findings, providing the first details on 13 seep sites. Four of those are located at the Hikurangi Margin along the east coast of New Zealand's North Island. Since then, three international cruises in 2006 and 2007 enhanced our knowledge considerably about methane seepage along the Hikurangi Margin, an area which has in places very strong BSRs. Two cruises on RV TANGAROA in 2006 focused on extensive reconnaissance work as well as fauna sampling, geochemical pore water analyses and CTD casts including water sampling for methane analyses. Several new seep sites were discovered during these cruises. Using these data, very detailed investigations in four main working areas could be performed during a 10-weeks expedition with RV SONNE (SO191). All research topics currently discussed in the scientific community were addressed using state-of-the-art equipment (e.g. deep- tow side-scan and ROV-deployments). Fourteen institutes from seven countries were involved. Echosounder and sidescan surveys unmistakably revealed active seep sites by detecting bubbles in the water column and carbonate precipitation at the seafloor forming massive chemoherm complexes. These complexes are associated with typical seep fauna like tube worms, bivalve mollusk species (Calyptogena, Bathymodiolus),and bacterial mats. At the fringe of these chemoherms dark sediment patches were observed which exihibit a novel seep habitat dominated by dense beds of two new species of heterotrophic ampharetid polychaetes. Bubble release was visually observed at several sites and recorded in the backscatter of various acoustic devices. At one site (680m water depth) very strong, pulsing outbursts could be observed repeatedly with methane fluxes of 20 to 25 l/min (60 to 74 mol

  3. Atmospheric methane emissions coupled to a CO2-sink at an Arctic shelf seep area offshore NW Svalbard: Introducing the "Seep-Fertilization Hypothesis"

    NASA Astrophysics Data System (ADS)

    Greinert, Jens; Pohlman, John; Silyakova, Anna; Mienert, Jürgen; Ruppel, Carolyn; Casso, Michael

    2015-04-01

    Documented warming of intermediate waters by ~1C over the past 30 years along the western Svalbard margin has been suggested as a driver of climate-change induced dissociation of marine methane hydrate. However, recent evidence suggests methane release has been occurring for thousands of years near the upper limit of methane hydrate stability zone and that seasonal changes in bottom water temperature may be more important than longer-term warming of intermediate waters. However, the existence of hydrates at the upper limit of the gas hydrate zone has been based on modeling results only and gas hydrates have not been sampled successfully. Yearly studies, undertaken during RV Helmer Hanssen cruises as part of CAGE have shown that no significant amount of methane reaches the upper water column and is being released towards the atmosphere from this ca. 400m deep sites. The same is true for a very active seep area at the shelf break in 240m water depth where detailed hydroacoustic studies show fluctuating fluxes between 71 and 114 T/yr in total. Here we focus on studies conducted with the USGS Gas Analysis System (USGS-GAS). Continuous surface water methane and carbon dioxide concentrations and associated data are used to calculate sea-air fluxes with this cavity ring-down spectrometer-based analytical system. Only the shallow seep site (~90 m water depth) had appreciable methane in surface waters. We conducted an exhaustive survey of this site, mapping the full extent of the surface methane plume. To provide three-dimensional constraints, we acquired 65 vertical dissolved methane profiles to delineate the vertical and horizontal extent of the subsurface methane plume. The USGS-GAS data show that methane beyond the 'normal' background fluxes of ~1 µmol m-2 d-1 is elevated at the intensively bubbling shallow seep site (max. 35 µmol m-2 d-1) and near the shallow coastal zone where the fluxes over a large area reach 25 µmol m-2 d-1. Comparing coastal and seep fluxes on

  4. Submeter Mapping Of Methane Seeps By ROV Observations And Measurements At The Hikurangi Margin, New Zeeland

    NASA Astrophysics Data System (ADS)

    Naudts, L.; Greinert, J.; Poort, J.; Belza, J.; Vangampelaere, E.; Boone, D.; Linke, P.; Henriet, J.; de Batist, M.

    2008-12-01

    During R.V. Sonne cruise SO191-3, part of the "New (Zealand Cold) Vents" expedition, RCMG deployed their CHEROKEE ROV "Genesis" on the Hikurangi Margin. This accretionary margin, on the east coast of New Zealand, is related to the subduction of the Pacific Plate under the Australian Plate. Several cold seep locations as well as an extensive BSR, indicating the presence of gas hydrates, have been found at this margin. The aims of the ROV-work were to precisely localize active methane seeps, to conduct detailed visual observations of the seep structures and activity, and to perform measurements of physical properties and collect samples at and around the seep locations. The ROV allowed first ever visual observations of bubble- releasing seeps at the Hikurangi Margin. Seeps were observed at Faure Site and LM-3 in the Rock Garden area, at a flat to moderately undulating sea floor where soft sediments alternate with carbonate platforms. Bubble-releasing activity was very variable in time, with periods of almost non-activity (5 bubbles/second) alternating with periods of violent outbursts (190 bubbles/second). Bubbles sizes ranged from less than 5 mm to more than 20 mm. At Faure Site, bubble release was monitored over a period of 20 minutes, resulting in the observation of 6 outbursts, each lasting 1 minute at a 3 minute interval. These violent outbursts were accompanied by the displacement and resuspension of sediment grains and the formation of small depressions showing what is possibly an initial stage of pockmark formation. At the LM-3 site only some small bubbling seeps were observed near a large carbonate platform covered by Bathymodiolus mussels, Calyptogena shells and tube worms. Sediment-temperature measurements, in both areas, were largely comparable with the bottom-water temperature except at LM-3, at a site densely populated by polychaetes, where anomalous low sediment-temperature was measured. Overall, both seep areas are very confined in space and bottom

  5. Influence of seep emission on the non-symbiont-bearing fauna and vagrant species at an active giant pockmark in the Gulf of Guinea (Congo-Angola margin)

    NASA Astrophysics Data System (ADS)

    Olu, K.; Caprais, J. C.; Galéron, J.; Causse, R.; von Cosel, R.; Budzinski, H.; Ménach, K. Le; Roux, C. Le; Levaché, D.; Khripounoff, A.; Sibuet, M.

    2009-12-01

    Detailed surveying with an ROV found that a dense and diverse cold-seep community colonises a giant pockmark located at 3200 m depth, 8 km north from the deep Congo channel. Several types of assemblages, either dominated by Mytilidae and Vesicomyidae bivalves or Siboglinidae polychaetes, are distributed on the 800-m diameter active area. The site is characterised by a most active central zone in a depression with abundant carbonate concretions and high methane fluxes where high-density clusters of mussels and siboglinids dominate. In contrast, the peripheral zones display large fields of dead and live vesicomyids on soft sediment, with a lower mean density and lower methane concentration in seawater. The associated megafauna includes Alvinocarididae shrimps, echinoids, holothurians of the family Synaptidae, several species of gastropods, two species of galatheids, and Zoarcidae and Ophidiidae fishes. Multivariate analyses of video transect data show that the distribution of these major megafauna species at the pockmark scale is influenced by the habitat heterogeneity due to fluid or gas emission, occurrence of hydrates, substratum variability and by the presence of large symbiont-bearing species. Several assemblages dominated either by mytilids, vesicomyids, or siboglinids have been sampled for megafauna densities and biomass estimations and stable isotope measurements ( δ13C and δ15N) of dominant species and food sources. The highest estimates of megafauna densities have been obtained in mytilid beds. According to their stable isotopes values, non-symbiont-bearing species mainly rely on chemosynthesis-originated carbon, either as primary consumers of chemoautotrophic microorganisms, or at higher trophic level recycling organic matter, or relying on bivalve and tubeworm production. Most of them likely feed on different sources like shrimps, but differences according to habitat have been evidenced. Carbon and nitrogen isotope ratios of galatheids and benthic or

  6. Investigating Hydrocarbon Seep Environments with High-Resolution, Three-Dimensional Geographic Visualizations.

    NASA Astrophysics Data System (ADS)

    Doolittle, D. F.; Gharib, J. J.; Mitchell, G. A.

    2015-12-01

    Detailed photographic imagery and bathymetric maps of the seafloor acquired by deep submergence vehicles such as Autonomous Underwater Vehicles (AUV) and Remotely Operated Vehicles (ROV) are expanding how scientists and the public view and ultimately understand the seafloor and the processes that modify it. Several recently acquired optical and acoustic datasets, collected during ECOGIG (Ecosystem Impacts of Oil and Gas Inputs to the Gulf) and other Gulf of Mexico expeditions using the National Institute for Undersea Science Technology (NIUST) Eagle Ray, and Mola Mola AUVs, have been fused with lower resolution data to create unique three-dimensional geovisualizations. Included in these data are multi-scale and multi-resolution visualizations over hydrocarbon seeps and seep related features. Resolution of the data range from 10s of mm to 10s of m. When multi-resolution data is integrated into a single three-dimensional visual environment, new insights into seafloor and seep processes can be obtained from the intuitive nature of three-dimensional data exploration. We provide examples and demonstrate how integration of multibeam bathymetry, seafloor backscatter data, sub-bottom profiler data, textured photomosaics, and hull-mounted multibeam acoustic midwater imagery are made into a series a three-dimensional geovisualizations of actively seeping sites and associated chemosynthetic communities. From these combined and merged datasets, insights on seep community structure, morphology, ecology, fluid migration dynamics, and process geomorphology can be investigated from new spatial perspectives. Such datasets also promote valuable inter-comparisons of sensor resolution and performance.

  7. Multiscale Image of a Seep Structure - Takahe, Offshore New Zealand

    NASA Astrophysics Data System (ADS)

    Koch, S.; Dumke, I.; Bialas, J.; Crutchley, G.; Greinert, J.; Klaschen, D.; Klaucke, I.; Papenberg, C.

    2012-04-01

    We present a multi-scale geophysical study of a methane seep site "Takahe" on the southern Hikurangi Margin offshore New Zealand's North Island. Seismic, Parasound, sidescan sonar and subbottom profiler data were combined to image the spatial structure of the seep and its expression at the seafloor. The data were acquired in March of 2011 during the cruise SO214 with the German research vessel R/V Sonne. The aim of the project was to investigate cold seep structures within the gas hydrate stability zone (GHSZ). 2.5D seismic reflection data reveal the sub-seafloor structure of gas migration pathways beneath Takahe, which can be traced to a source that is at least as deep as the base of the GHSZ. The structure can be divided into three parts: i) a broad feeding base that narrows into an inverted bathtub-shaped funnel, ii) a narrow, vertical conduit extending upwards from the funnel to approximately 50 m beneath the seafloor and iii) a second bathtub-shaped expression fanning out from the top of the narrow conduit to the seafloor. Multiple Parasound transects acquired over Takahe reveal the shallow structure of the upper 50 m of the gas conduit in very high detail. The conduit penetrates a strong reflection representing an unconformity between less-consolidated sediments above and well-indurated "hard" sediments below. Shallow amplitude anomalies within the conduit are interpreted as free gas close to the seafloor. The high-frequency component of the Parasound system was used to image numerous flares in the water column, revealing that gas is actively venting from the seafloor at this site. Active venting is also suggested by several flares imaged in the water-column of the unprocessed sidescan sonar data. Takahe site is marked by slightly elevated backscatter over a 0.059 km2 large, oval-shaped area. Authigenic carbonates are not present on the seafloor, which distinguishes Takahe from the majority of seeps on Opouawe Bank. Takahe possibly is a relatively young seep

  8. Biogeochemical processes and microbial diversity of the Gullfaks and Tommeliten methane seeps (Northern North Sea)

    NASA Astrophysics Data System (ADS)

    Wegener, G.; Shovitri, M.; Knittel, K.; Niemann, H.; Hovland, M.; Boetius, A.

    2008-08-01

    Fluid flow related seafloor structures and gas seeps were detected in the North Sea in the 1970s and 1980s by acoustic sub-bottom profiling and oil rig surveys. A variety of features like pockmarks, gas vents and authigenic carbonate cements were found to be associated with sites of oil and gas exploration, indicating a link between these surface structures and the underlying, deep hydrocarbon reservoirs. In this study we performed acoustic surveys and videographic observation at Gullfaks, Holene Trench, Tommeliten, Witch's Hole and the giant pockmarks of the UK Block 15/25, to investigate the occurrence and distribution of cold seep ecosystems in the Northern North Sea. The most active gas seep sites, i.e. Gullfaks and Tommeliten, were investigated in detail. At both sites, gas bubbles escaped continuously from small holes in the seabed to the water column, reaching the upper mixed surface layer. At Gullfaks a gas emitting, flat area of 0.1 km2 of sandy seabed covered by filamentous sulfur-oxidizing bacteria was detected. At Tommeliten, we found a patchy distribution of small bacterial mats indicating sites of gas seepage. Below the patches the seafloor consisted of sand from which gas emissions were observed. At both sites, the anaerobic oxidation of methane (AOM) coupled to sulfate reduction (SR) was the major source of sulfide. Molecular analyses targeting specific lipid biomarkers and 16S rRNA gene sequences identified an active microbial community dominated by sulfur-oxidizing and sulfate-reducing bacteria (SRB) as well as methanotrophic bacteria and archaea. Stable carbon isotope values of specific, microbial fatty acids and alcohols from both sites were highly depleted in the heavy isotope 13C, indicating that the microbial community incorporates methane or its metabolites. The microbial community composition of both shallow seeps shows high similarities to the deep water seeps associated with gas hydrates such as Hydrate Ridge or the Eel River basin.

  9. Hydrothermal vents and methane seeps: Rethinking the sphere of influence

    USGS Publications Warehouse

    Levin, Lisa A.; Baco, Amy; Bowden, David; Colaco, Ana; Cordes, Erik E.; Cunha, Marina; Demopoulos, Amanda; Gobin, Judith; Grupe, Ben; Le, Jennifer; Metaxas, Anna; Netburn, Amanda; Rouse, Greg; Thurber, Andrew; Tunnicliffe, Verena; Van Dover, Cindy L.; Vanreusel, Ann; Watling, Les

    2016-01-01

    Although initially viewed as oases within a barren deep ocean, hydrothermal vent and methane seep communities are now recognized to interact with surrounding ecosystems on the sea floor and in the water column, and to affect global geochemical cycles. The importance of understanding these interactions is growing as the potential rises for disturbance from oil and gas extraction, seabed mining and bottom trawling. Here we synthesize current knowledge of the nature, extent and time and space scales of vent and seep interactions with background systems. We document an expanded footprint beyond the site of local venting or seepage with respect to elemental cycling and energy flux, habitat use, trophic interactions, and connectivity. Heat and energy are released, global biogeochemical and elemental cycles are modified, and particulates are transported widely in plumes. Hard and biotic substrates produced at vents and seeps are used by “benthic background” fauna for attachment substrata, shelter, and access to food via grazing or through position in the current, while particulates and fluid fluxes modify planktonic microbial communities. Chemosynthetic production provides nutrition to a host of benthic and planktonic heterotrophic background species through multiple horizontal and vertical transfer pathways assisted by flow, gamete release, animal movements, and succession, but these pathways remain poorly known. Shared species, genera and families indicate that ecological and evolutionary connectivity exists among vents, seeps, organic falls and background communities in the deep sea; the genetic linkages with inactive vents and seeps and background assemblages however, are practically unstudied. The waning of venting or seepage activity generates major transitions in space and time that create links to surrounding ecosystems, often with identifiable ecotones or successional stages. The nature of all these interactions is dependent on water depth, as well as

  10. Gas flux and carbonate occurrence at a shallow seep of thermogenic natural gas

    NASA Astrophysics Data System (ADS)

    Kinnaman, Franklin S.; Kimball, Justine B.; Busso, Luis; Birgel, Daniel; Ding, Haibing; Hinrichs, Kai-Uwe; Valentine, David L.

    2010-06-01

    The Coal Oil Point seep field located offshore Santa Barbara, CA, consists of dozens of named seeps, including a peripheral ˜200 m2 area known as Brian Seep, located in 10 m water depth. A single comprehensive survey of gas flux at Brian Seep yielded a methane release rate of ˜450 moles of CH4 per day, originating from 68 persistent gas vents and 23 intermittent vents, with gas flux among persistent vents displaying a log normal frequency distribution. A subsequent series of 33 repeat surveys conducted over a period of 6 months tracked eight persistent vents, and revealed substantial temporal variability in gas venting, with flux from each individual vent varying by more than a factor of 4. During wintertime surveys sediment was largely absent from the site, and carbonate concretions were exposed at the seafloor. The presence of the carbonates was unexpected, as the thermogenic seep gas contains 6.7% CO2, which should act to dissolve carbonates. The average δ13C of the carbonates was -29.2 ± 2.8‰ VPDB, compared to a range of -1.0 to +7.8‰ for CO2 in the seep gas, indicating that CO2 from the seep gas is quantitatively not as important as 13C-depleted bicarbonate derived from methane oxidation. Methane, with a δ13C of approximately -43‰, is oxidized and the resulting inorganic carbon precipitates as high-magnesium calcite and other carbonate minerals. This finding is supported by 13C-depleted biomarkers typically associated with anaerobic methanotrophic archaea and their bacterial syntrophic partners in the carbonates (lipid biomarker δ13C ranged from -84 to -25‰). The inconsistency in δ13C between the carbonates and the seeping CO2 was resolved by discovering pockets of gas trapped near the base of the sediment column with δ13C-CO2 values ranging from -26.9 to -11.6‰. A mechanism of carbonate formation is proposed in which carbonates form near the sediment-bedrock interface during times of sufficient sediment coverage, in which anaerobic oxidation

  11. Paleozoic Hydrocarbon-Seep Limestones

    NASA Astrophysics Data System (ADS)

    Peckmann, J.

    2007-12-01

    To date, five Paleozoic hydrocarbon-seep limestones have been recognized based on carbonate fabrics, associated fauna, and stable carbon isotopes. These are the Middle Devonian Hollard Mound from the Antiatlas of Morocco [1], Late Devonian limestone lenses with the dimerelloid brachiopod Dzieduszyckia from the Western Meseta of Morocco [2], Middle Mississippian limestones with the dimerelloid brachiopod Ibergirhynchia from the Harz Mountains of Germany [3], Early Pennsylvanian limestones from the Tantes Mound in the High Pyrenees of France [4], and Late Pennsylvanian limestone lenses from the Ganigobis Shale Member of southern Namibia [5]. Among these examples, the composition of seepage fluids varied substantially as inferred from delta C-13 values of early diagenetic carbonate phases. Delta C-13 values as low as -50 per mil from the Tantes Mound and -51 per mil from the Ganigobis limestones reveal seepage of biogenic methane, whereas values of -12 per mil from limestones with Dzieduszyckia associated with abundant pyrobitumen agree with oil seepage. Intermediate delta C-13 values of carbonate cements from the Hollard Mound and Ibergirhynchia deposits probably reflect seepage of thermogenic methane. It is presently very difficult to assess the faunal evolution at seeps in the Paleozoic based on the limited number of examples. Two of the known seeps were typified by extremely abundant rhynchonellide brachiopods of the superfamily Dimerelloidea. Bivalve mollusks and tubeworms were abundant at two of the known Paleozoic seep sites; one was dominated by bivalve mollusks (Hollard Mound, Middle Devonian), another was dominated by tubeworms (Ganigobis Shale Member, Late Pennsylvanian). The tubeworms from these two deposits are interpreted to represent vestimentiferan worms, based on studies of the taphonomy of modern vestimentiferans. However, this interpretation is in conflict with the estimated evolutionary age of vestimentiferans based on molecular clock methods

  12. Environmental effects of submarine seeping natural gas

    NASA Astrophysics Data System (ADS)

    Dando, P. R.; Hovland, M.

    1992-10-01

    It is suspected that most shallow reservoirs of natural gas vent to the surface to some degree. This seeping may be through diffusion of dissolved gas or by a flow of gas bubbles which entrain interstitial water during the rise through the sediments to the surface. Methane bubbles dissolved other gases, notably hydrogen sulphide and carbon dioxide, during their ascent. Under suitable temperature-pressure conditions gas hydrates may be formed close to or at the seabed Black suphide-rich sediments and mats of sulphur oxidizing bacteria are frequently observed close to the sediments surface at seep sites, including a sharp oxic/anoxic boundary. Animal species associated with these gas seeps include both species which obtain nutrition from symbiotic methane-oxidizing bacteria and species with symbolic sulphur-oxidizing bacteria. It is suspected that at some microseepage an enhanced biomass of meiofauna and macrofauna is supported by a food chain based on free-living and symbiotic sulphur-oxidizing and methane-oxidizing bacteria. The most common seep-related features of sea floor topography are local depressions including pockmark craters. Winnowing of the sediment during their creation leads to an accumulation of larger detritis in the depressions. Where the deprssions overlies salt diapirs they may be filled with hypersaline solutions. In some areas dome-shaped features are associated with seepage and these may be colonized by coral reefs. Other reefs, "hard-grounds", columnar and disc-shaped protrusions, all formed of carbonate-cemented sediments, are common on the sea floor in seep areas. Much of the carbonate appears to be derived from carbon dioxide formed as a result of methane oxidation. The resulting hard-bottoms on the sea floor are often colonized by species not found on the neighboring soft-bottoms. As a result seep areas may be characterized by the presence of a rich epifauna.

  13. Microbial eukaryotic distributions and diversity patterns in a deep-sea methane seep ecosystem.

    PubMed

    Pasulka, Alexis L; Levin, Lisa A; Steele, Josh A; Case, David H; Landry, Michael R; Orphan, Victoria J

    2016-09-01

    Although chemosynthetic ecosystems are known to support diverse assemblages of microorganisms, the ecological and environmental factors that structure microbial eukaryotes (heterotrophic protists and fungi) are poorly characterized. In this study, we examined the geographic, geochemical and ecological factors that influence microbial eukaryotic composition and distribution patterns within Hydrate Ridge, a methane seep ecosystem off the coast of Oregon using a combination of high-throughput 18S rRNA tag sequencing, terminal restriction fragment length polymorphism fingerprinting, and cloning and sequencing of full-length 18S rRNA genes. Microbial eukaryotic composition and diversity varied as a function of substrate (carbonate versus sediment), activity (low activity versus active seep sites), sulfide concentration, and region (North versus South Hydrate Ridge). Sulfide concentration was correlated with changes in microbial eukaryotic composition and richness. This work also revealed the influence of oxygen content in the overlying water column and water depth on microbial eukaryotic composition and diversity, and identified distinct patterns from those previously observed for bacteria, archaea and macrofauna in methane seep ecosystems. Characterizing the structure of microbial eukaryotic communities in response to environmental variability is a key step towards understanding if and how microbial eukaryotes influence seep ecosystem structure and function.

  14. An overview of gas hydrate and cold seep research along the Hikurangi Margin, New Zealand (2006 & 2007)

    NASA Astrophysics Data System (ADS)

    Greinert, J.; Faure, K.; Naudts, L.; de Batist, M.; Bialas, J.; Linke, P.; Pecher, I.; Rowden, R.

    2009-04-01

    Prior to 2006, the knowledge about cold seeps around New Zealand was based mainly on accidental recovery of seep fauna or methane-derived carbonates by fishermen and the detection of flares in fish-finding sonars. Lewis and Marshall (1996; NZJGG) compiled these findings, providing the first details on 13 seep sites. Four of those are located at the Hikurangi Margin along the east coast of New Zealand's North Island. Since then, three international cruises in 2006 and 2007 enhanced our knowledge considerably about methane seepage along the Hikurangi Margin, an area which has widely distributed and in places very strong BSR. Two cruises on the RV TANGAROA (led by GNS Science and NIWA, NZ) in 2006 focused on extensive reconnaissance work (multibeam mapping, seismic surveys, flare imaging, visual observations) as well as fauna sampling, geochemical pore water analyses and CTD casts including water sampling for methane analyses. Several new seep sites were discovered during these cruises. Using these data, very detailed investigations in four main working areas could be performed during a 10-week expedition with RV SONNE (SO191, led by IFM-GEOMAR, Germany). All research topics currently discussed in the scientific community were addressed using state-of-the-art equipment (e.g. deep-tow side-scan, TV-guided sampling, lander and ROV-deployments). Fourteen institutes from seven countries were involved (Australia, Belgium, Germany, New Zealand, United Kingdom, United States, Switzerland). Echosounder and sidescan surveys unmistakably revealed active seep sites by detecting bubbles in the water column and carbonate precipitation at the seafloor forming massive chemoherm complexes. These complexes are associated with typical seep fauna like tube worms, bivalve mollusk species (Calyptogena, Bathymodiolus),and bacterial mats. At the fringe of these chemoherms dark sediment patches were observed which exihibit a novel seep habitat dominated by dense beds of two new species of

  15. Use of LANDSAT-1 data for the detection and mapping of saline seeps in Montana

    NASA Technical Reports Server (NTRS)

    May, G. A. (Principal Investigator); Petersen, G. W.

    1976-01-01

    The author has identified the following significant results. April, May, and August are the best times to detect saline seeps. Specific times within these months would be dependent upon weather, phenology, and growth conditions. Saline seeps can be efficiently and accurately mapped, within resolution capabilities, from merged May and August LANDSAT 1 data. Seeps were mapped by detecting salt crusts in the spring and indicator plants in the fall. These indicator plants were kochia, inkweed, and foxtail barley. The total hectares of the mapped saline seeps were calculated and tabulated. Saline seeps less than two hectares in size or that have linear configurations less than 200 meters in width were not mapped using the LANDSAT 1 data. Saline seep signatures developed in the Coffee Creek test site were extended to map saline seeps located outside this area.

  16. Methane seeps along boundaries of receding glaciers in Alaska and Greenland

    NASA Astrophysics Data System (ADS)

    Walter Anthony, K. M.; Anthony, P. M.; Grosse, G.; Chanton, J.

    2012-12-01

    Glaciers, ice sheets, and permafrost form a 'cryosphere cap' that traps methane formed in the subsurface, restricting its flow to the Earth's surface and atmosphere. Despite model predictions that glacier melt and degradation of permafrost open conduits for methane's escape, there has been a paucity of field evidence for 'subcap' methane seepage to the atmosphere as a direct result of cryosphere disintegration in the terrestrial Arctic. Here, we document for the first time the release of sub-cryosphere methane to lakes, rivers, shallow marine fjords and the atmosphere from abundant gas seeps concentrated along boundaries of receding glaciers and permafrost thaw in Alaska and Greenland. Through aerial and ground surveys of 6,700 lakes and fjords in Alaska we mapped >150,000 gas seeps identified as bubbling-induced open holes in seasonal ice. Using gas flow rates, stable isotopes, and radiocarbon dating, we distinguished recent ecological methane from subcap, geologic methane. Subcap seeps had anomalously high bubbling rates, 14C-depletion, and stable isotope values matching microbial sources associated with sedimentary deposits and coal beds as well as thermogenic methane accumulations in Alaska. Since differential ice loading can overpressurize fluid reservoirs and cause sediment fracturing beneath ice sheets, and since the loss of glacial ice reduces normal stress on ground, opens joints, and activates faults and fissures, thereby increasing permeability of the crust to fluid flow, we hypothesized that in the previously glaciated region of Southcentral Alaska, where glacial wastage continues presently, subcap seeps should be disproportionately associated with neotectonic faults. Geospatial analysis confirmed that subcap seep sites were associated with faults within a 7 km belt from the modern glacial extent. The majority of seeps were located in areas affected by seismicity from isostatic rebound associated with deglaciation following the Little Ice Age (LIA; ca

  17. Adaptation to deep-sea methane seeps from Cretaceous shallow-water black shale environments?

    NASA Astrophysics Data System (ADS)

    Kiel, Steffen; Wiese, Frank; Titus, Alan

    2013-04-01

    Sulfide-enriched environments in shallow water were considered as sites where animals acquire pre-adaptations enabling them to colonize deep-sea hydrothermal vents and seeps or where they survived extinction events in their deep-sea habitats. Here we present upper Cenomanian (early Late Cretaceous) shallow-water seep communities from the Tropic Shale in the Western Interior Seaway, USA, that lived during a time of extremely warm deep-water temperatures, which supposedly facilitates adaptations to the deep sea, and time-equivalent with a period of widespread oceanic and photic zone anoxia (OAE 2) that supposedly extinguished deep-water vent and seep faunas. Contrary to the expectation, the taxa inhabiting the Tropic Shale seeps were not found at any coeval or younger deep-water seep or vent deposit. This suggests that (i) pre-adaptations for living at deep-sea vents and seeps do not evolve at shallow-water methane seeps, and probably also not in sulfide-rich shallow-water environments in general; (ii) a low temperature gradient from shallow to deep water does not facilitate onshore-offshore adaptations to deep-sea vents and seeps; and (iii) shallow-water seeps did not act as refuges for deep-sea vent and seep animals. We hypothesize that the vast majority of adaptations to successfully colonize deep-sea vents and seeps are acquired below the photic zone.

  18. Sulfur isotope and porewater geochemistry of Florida escarpment seep sediments

    USGS Publications Warehouse

    Chanton, J.P.; Martens, C.S.; Paull, C.K.; Coston, J.A.

    1993-01-01

    Distributions of porewater constituents, SO4=, NH4+, Cl-, ???CO2, and H2S, solid phase iron, and sulfur concentrations, and the sulfur isotopic composition of dissolved and solid phases were investigated in sediments from abyssal seeps at the base of the Florida escarpment. Despite the apparent similarity of seep sediment porewater chemistry to that of typical marine sediments undergoing early diagenesis, relationships between chemical distributions and isotopic measurements revealed that the distribution of pore fluid constituents was dominated by processes occurring within the platform rather than by in situ microbial processes. Ammonium and sulfate concentrations were linearly correlated with chloride concentrations, indicating that variations in porewater chemistry were controlled by the admixture of seawater and a sulfate depleted brine with a chlorinity of 27.5 ?? 1.9%. and 2.2 ?? 1.3 mM ammonium concentration. At sites dominated by seepage, dissolved sulfate isotopic composition remained near seawater values despite depletion in porewater concentrations. Porewater ???CO2 concentrations were found to be elevated relative to seawater, but not to the extent predicted from the observed sulfate depletion. Sediment solid phase sulfur was predominantly pyrite, at concentrations as high as 20% S by weight. In contrast to typical marine deposits, pyrite concentrations were not related to the quantity of sedimentary organic matter. Pyrite ??34S values ranged from -29%. to + 21%. (CDT). However, only positive ??34S values were observed at sites associated with high pyrite concentrations. Isotopically heavy pyrite was observed at sites with porewater sulfate of seawater-like isotopic composition. Isotopically light pyrite was associated with sites where porewater sulfate exhibited ??34S values greater than those in seawater, indicating the activity of in situ microbial sulfate reduction. Thus, dual sulfide sources are suggested to explain the range in sediment pyrite

  19. Transcription, Signaling Receptor Activity, Oxidative Phosphorylation, and Fatty Acid Metabolism Mediate the Presence of Closely Related Species in Distinct Intertidal and Cold-Seep Habitats.

    PubMed

    Van Campenhout, Jelle; Vanreusel, Ann; Van Belleghem, Steven; Derycke, Sofie

    2016-01-01

    Bathyal cold seeps are isolated extreme deep-sea environments characterized by low species diversity while biomass can be high. The Håkon Mosby mud volcano (Barents Sea, 1,280 m) is a rather stable chemosynthetic driven habitat characterized by prominent surface bacterial mats with high sulfide concentrations and low oxygen levels. Here, the nematode Halomonhystera hermesi thrives in high abundances (11,000 individuals 10 cm(-2)). Halomonhystera hermesi is a member of the intertidal Halomonhystera disjuncta species complex that includes five cryptic species (GD1-5). GD1-5's common habitat is characterized by strong environmental fluctuations. Here, we compared the transcriptomes of H. hermesi and GD1, H. hermesi's closest relative. Genes encoding proteins involved in oxidative phosphorylation are more strongly expressed in H. hermesi than in GD1, and many genes were only observed in H. hermesi while being completely absent in GD1. Both observations could in part be attributed to high sulfide concentrations and low oxygen levels. Additionally, fatty acid elongation was also prominent in H. hermesi confirming the importance of highly unsaturated fatty acids in this species. Significant higher amounts of transcription factors and genes involved in signaling receptor activity were observed in GD1 (many of which were completely absent in H. hermesi), allowing fast signaling and transcriptional reprogramming which can mediate survival in dynamic intertidal environments. GC content was approximately 8% higher in H. hermesi coding unigenes resulting in differential codon usage between both species and a higher proportion of amino acids with GC-rich codons in H. hermesi. In general our results showed that most pathways were active in both environments and that only three genes are under natural selection. This indicates that also plasticity should be taken in consideration in the evolutionary history of Halomonhystera species. Such plasticity, as well as possible

  20. Transcription, Signaling Receptor Activity, Oxidative Phosphorylation, and Fatty Acid Metabolism Mediate the Presence of Closely Related Species in Distinct Intertidal and Cold-Seep Habitats

    PubMed Central

    Van Campenhout, Jelle; Vanreusel, Ann; Van Belleghem, Steven; Derycke, Sofie

    2016-01-01

    Bathyal cold seeps are isolated extreme deep-sea environments characterized by low species diversity while biomass can be high. The Håkon Mosby mud volcano (Barents Sea, 1,280 m) is a rather stable chemosynthetic driven habitat characterized by prominent surface bacterial mats with high sulfide concentrations and low oxygen levels. Here, the nematode Halomonhystera hermesi thrives in high abundances (11,000 individuals 10 cm−2). Halomonhystera hermesi is a member of the intertidal Halomonhystera disjuncta species complex that includes five cryptic species (GD1-5). GD1-5’s common habitat is characterized by strong environmental fluctuations. Here, we compared the transcriptomes of H. hermesi and GD1, H. hermesi’s closest relative. Genes encoding proteins involved in oxidative phosphorylation are more strongly expressed in H. hermesi than in GD1, and many genes were only observed in H. hermesi while being completely absent in GD1. Both observations could in part be attributed to high sulfide concentrations and low oxygen levels. Additionally, fatty acid elongation was also prominent in H. hermesi confirming the importance of highly unsaturated fatty acids in this species. Significant higher amounts of transcription factors and genes involved in signaling receptor activity were observed in GD1 (many of which were completely absent in H. hermesi), allowing fast signaling and transcriptional reprogramming which can mediate survival in dynamic intertidal environments. GC content was approximately 8% higher in H. hermesi coding unigenes resulting in differential codon usage between both species and a higher proportion of amino acids with GC-rich codons in H. hermesi. In general our results showed that most pathways were active in both environments and that only three genes are under natural selection. This indicates that also plasticity should be taken in consideration in the evolutionary history of Halomonhystera species. Such plasticity, as well as possible

  1. Methane Seep Carbonates Host Distinct, Diverse, and Dynamic Microbial Assemblages

    PubMed Central

    Pasulka, Alexis L.; Marlow, Jeffrey J.; Grupe, Benjamin M.; Levin, Lisa A.

    2015-01-01

    ABSTRACT Marine methane seeps are globally distributed geologic features in which reduced fluids, including methane, are advected upward from the subsurface. As a result of alkalinity generation during sulfate-coupled methane oxidation, authigenic carbonates form slabs, nodules, and extensive pavements. These carbonates shape the landscape within methane seeps, persist long after methane flux is diminished, and in some cases are incorporated into the geologic record. In this study, microbial assemblages from 134 native and experimental samples across 5,500 km, representing a range of habitat substrates (carbonate nodules and slabs, sediment, bottom water, and wood) and seepage conditions (active and low activity), were analyzed to address two fundamental questions of seep microbial ecology: (i) whether carbonates host distinct microbial assemblages and (ii) how sensitive microbial assemblages are to habitat substrate type and temporal shifts in methane seepage flux. Through massively parallel 16S rRNA gene sequencing and statistical analysis, native carbonates are shown to be reservoirs of distinct and highly diverse seep microbial assemblages. Unique coupled transplantation and colonization experiments on the seafloor demonstrated that carbonate-associated microbial assemblages are resilient to seep quiescence and reactive to seep activation over 13 months. Various rates of response to simulated seep quiescence and activation are observed among similar phylogenies (e.g., Chloroflexi operational taxonomic units) and similar metabolisms (e.g., putative S oxidizers), demonstrating the wide range of microbial sensitivity to changes in seepage flux. These results imply that carbonates do not passively record a time-integrated history of seep microorganisms but rather host distinct, diverse, and dynamic microbial assemblages. PMID:26695630

  2. Spatial scales of bacterial community diversity at cold seeps (Eastern Mediterranean Sea)

    PubMed Central

    Pop Ristova, Petra; Wenzhöfer, Frank; Ramette, Alban; Felden, Janine; Boetius, Antje

    2015-01-01

    Cold seeps are highly productive, fragmented marine ecosystems that form at the seafloor around hydrocarbon emission pathways. The products of microbial utilization of methane and other hydrocarbons fuel rich chemosynthetic communities at these sites, with much higher respiration rates compared with the surrounding deep-sea floor. Yet little is known as to the richness, composition and spatial scaling of bacterial communities of cold seeps compared with non-seep communities. Here we assessed the bacterial diversity across nine different cold seeps in the Eastern Mediterranean deep-sea and surrounding seafloor areas. Community similarity analyses were carried out based on automated ribosomal intergenic spacer analysis (ARISA) fingerprinting and high-throughput 454 tag sequencing and were combined with in situ and ex situ geochemical analyses across spatial scales of a few tens of meters to hundreds of kilometers. Seep communities were dominated by Deltaproteobacteria, Epsilonproteobacteria and Gammaproteobacteria and shared, on average, 36% of bacterial types (ARISA OTUs (operational taxonomic units)) with communities from nearby non-seep deep-sea sediments. Bacterial communities of seeps were significantly different from those of non-seep sediments. Within cold seep regions on spatial scales of only tens to hundreds of meters, the bacterial communities differed considerably, sharing <50% of types at the ARISA OTU level. Their variations reflected differences in porewater sulfide concentrations from anaerobic degradation of hydrocarbons. This study shows that cold seep ecosystems contribute substantially to the microbial diversity of the deep-sea. PMID:25500510

  3. Remote detection of hydrocarbon seeps

    SciTech Connect

    Barringer, A. R.

    1985-05-14

    A method of detecting hydrocarbon seeps in a sea or in earth is disclosed. The method involves interrogating aerosols formed above the sea or earth surface with an intense beam of primary light radiation generated aboard an aircraft or other vehicle. The spectral composition of the beam is selected to induce secondary light radiation in certain hydrocarbon materials contained in aerosols generated by hydrocarbon seeps rising to the sea or earth surface. The secondary light radiation is detected aboard the aircraft and subjected to spectral analysis to determine whether the composition of the aerosols is characteristic of aerosols generated by hydrocarbon seeps. Apparatus for implementing the method is also disclosed.

  4. Anaerobic oxidation of methane in the Concepción Methane Seep Area, Chilean continental margin

    NASA Astrophysics Data System (ADS)

    Steeb, P.; Linke, P.; Scholz, F.; Schmidt, M.; Liebetrau, V.; Treude, T.

    2012-04-01

    Within subduction zones of active continental margins, large amounts of methane can be mobilized by dewatering processes and transported to the seafloor along migration pathways. A recently discovered seep area located off Concepción (Chile) at water depth between 600 to 1100 mbsl is characterized by active methane vent sites as well as massive carbonates boulders and plates which probably are related to methane seepage in the past. During the SO210 research expedition "Chiflux" (Sept-Oct 2010), sediment from the Concepción Methane Seep Area (CSMA) at the fore arc of the Chilean margin was sampled to study microbial activity related to methane seepage. We sampled surface sediments (0-30cm) from sulfur bacteria mats, as well as clam, pogonophoran, and tubeworm fields with push cores and a TV-guided multicorer system. Anaerobic oxidation of methane (AOM) and sulfate reduction rates were determined using ex-situ radioisotope tracer techniques. Additionally, porewater chemistry of retrieved cores as well as isotopic composition and age record of surrounding authigenic carbonates were analyzed. The shallowest sulfate-methane-transition zone (SMTZ) was identified at 4 cm sediment depth hinting to locally strong fluid fluxes. However, a lack of Cl- anomalies in porewater profiles indicates a shallow source of these fluids, which is supported by the biogenic origin of the methane (δ13C -70‰ PDB). Sulfide and alkalinity was relatively high (up to 20 mM and 40 mEq, respectively). Rates of AOM and sulfate reduction within this area reached magnitudes typical for seeps with variation between different habitat types, indicating a diverse methane supply, which is affecting the depths of the SMTZ. Rates were highest at sulfur a bacteria mats (20 mmol m-2 d-1) followed by a large field of dead clams, a pogonophoran field, a black sediment spot, and a carbonate rich clam field. Lowest rates (0.2 mmol m-2 d-1) were measured in close vicinity to these hot spots. Abundant massive

  5. Distribution and in situ abundance of sulfate-reducing bacteria in diverse marine hydrocarbon seep sediments.

    PubMed

    Kleindienst, Sara; Ramette, Alban; Amann, Rudolf; Knittel, Katrin

    2012-10-01

    Marine gas and hydrocarbon seeps are hot spots of sulfate reduction which is fuelled by methane, other short-chain alkanes or a complex mixture of hydrocarbons. In this study, we investigated the global distribution and abundance of sulfate-reducing bacteria (SRB) in eight gas and hydrocarbon seeps by catalysed reporter deposition fluorescence in situ hybridization (CARD-FISH). The majority of Deltaproteobacteria were assigned to specific SRB groups, i.e. 83 ± 14% at gas seeps and 61 ± 35% at hydrocarbon seeps, indicating that the probe set used was sufficient for classification of marine SRB. Statistical analysis showed that SRB abundance and distribution were significantly influenced by habitat type and sediment depth. Members of the Desulfosarcina/Desulfococcus (DSS) clade strongly dominated all sites. Our data indicated the presence of many diverse and highly specialized DSS species of low abundance rather than a single abundant subgroup. In addition, SEEP-SRB2, an uncultured deep-branching deltaproteobacterial group, was ubiquitously found in high abundances at all sites. SEEP-SRB2 members occurred either in a novel association with methanotrophic archaea in shell-type ANME-2/SEEP-SRB2 consortia, in association with ANME-1 archaea in Black Sea microbial mats or as single cells. Two other uncultured groups, SEEP-SRB3 and SEEP-SRB4, were preferentially detected in surface sediments from mud volcanoes.

  6. Late Pleistocene to Holocene sedimentation and hydrocarbon seeps on the continental shelf of a steep, tectonically active margin, southern California, USA

    USGS Publications Warehouse

    Draut, Amy E.; Hart, Patrick E.; Lorenson, T.D.; Ryan, Holly F.; Wong, Florence L.; Sliter, Ray W.; Conrad, James E.

    2009-01-01

    Small, steep, uplifting coastal watersheds are prolific sediment producers that contribute significantly to the global marine sediment budget. This study illustrates how sedimentation evolves in one such system where the continental shelf is largely sediment-starved, with most terrestrial sediment bypassing the shelf in favor of deposition in deeper basins. The Santa Barbara-Ventura coast of southern California, USA, is considered a classic area for the study of active tectonics and of Tertiary and Quaternary climatic evolution, interpretations of which depend upon an understanding of sedimentation patterns. High-resolution seismic-reflection data over >570 km2 of this shelf show that sediment production is concentrated in a few drainage basins, with the Ventura and Santa Clara River deltas containing most of the upper Pleistocene to Holocene sediment on the shelf. Away from those deltas, the major factor controlling shelf sedimentation is the interaction of wave energy with coastline geometry. Depocenters containing sediment 5-20 m thick exist opposite broad coastal embayments, whereas relict material (bedrock below a regional unconformity) is exposed at the sea floor in areas of the shelf opposite coastal headlands. Locally, natural hydrocarbon seeps interact with sediment deposition either to produce elevated tar-and-sediment mounds or as gas plumes that hinder sediment settling. As much as 80% of fluvial sediment delivered by the Ventura and Santa Clara Rivers is transported off the shelf (some into the Santa Barbara Basin and some into the Santa Monica Basin via Hueneme Canyon), leaving a shelf with relatively little recent sediment accumulation. Understanding factors that control large-scale sediment dispersal along a rapidly uplifting coast that produces substantial quantities of sediment has implications for interpreting the ancient stratigraphic record of active and transform continental margins, and for inferring the distribution of hydrocarbon resources

  7. Biodiversity on the Rocks: Macrofauna Inhabiting Authigenic Carbonate at Costa Rica Methane Seeps.

    PubMed

    Levin, Lisa A; Mendoza, Guillermo F; Grupe, Benjamin M; Gonzalez, Jennifer P; Jellison, Brittany; Rouse, Greg; Thurber, Andrew R; Waren, Anders

    2015-01-01

    Carbonate communities: The activity of anaerobic methane oxidizing microbes facilitates precipitation of vast quantities of authigenic carbonate at methane seeps. Here we demonstrate the significant role of carbonate rocks in promoting diversity by providing unique habitat and food resources for macrofaunal assemblages at seeps on the Costa Rica margin (400-1850 m). The attendant fauna is surprisingly similar to that in rocky intertidal shores, with numerous grazing gastropods (limpets and snails) as dominant taxa. However, the community feeds upon seep-associated microbes. Macrofaunal density, composition, and diversity on carbonates vary as a function of seepage activity, biogenic habitat and location. The macrofaunal community of carbonates at non-seeping (inactive) sites is strongly related to the hydrography (depth, temperature, O2) of overlying water, whereas the fauna at sites of active seepage is not. Densities are highest on active rocks from tubeworm bushes and mussel beds, particularly at the Mound 12 location (1000 m). Species diversity is higher on rocks exposed to active seepage, with multiple species of gastropods and polychaetes dominant, while crustaceans, cnidarians, and ophiuroids were better represented on rocks at inactive sites. Macro-infauna (larger than 0.3 mm) from tube cores taken in nearby seep sediments at comparable depths exhibited densities similar to those on carbonate rocks, but had lower diversity and different taxonomic composition. Seep sediments had higher densities of ampharetid, dorvilleid, hesionid, cirratulid and lacydoniid polychaetes, whereas carbonates had more gastropods, as well as syllid, chrysopetalid and polynoid polychaetes. Stable isotope signatures and metrics: The stable isotope signatures of carbonates were heterogeneous, as were the food sources and nutrition used by the animals. Carbonate δ13Cinorg values (mean = -26.98‰) ranged from -53.3‰ to +10.0‰, and were significantly heavier than carbonate δ13

  8. Biodiversity on the Rocks: Macrofauna Inhabiting Authigenic Carbonate at Costa Rica Methane Seeps.

    PubMed

    Levin, Lisa A; Mendoza, Guillermo F; Grupe, Benjamin M; Gonzalez, Jennifer P; Jellison, Brittany; Rouse, Greg; Thurber, Andrew R; Waren, Anders

    2015-01-01

    Carbonate communities: The activity of anaerobic methane oxidizing microbes facilitates precipitation of vast quantities of authigenic carbonate at methane seeps. Here we demonstrate the significant role of carbonate rocks in promoting diversity by providing unique habitat and food resources for macrofaunal assemblages at seeps on the Costa Rica margin (400-1850 m). The attendant fauna is surprisingly similar to that in rocky intertidal shores, with numerous grazing gastropods (limpets and snails) as dominant taxa. However, the community feeds upon seep-associated microbes. Macrofaunal density, composition, and diversity on carbonates vary as a function of seepage activity, biogenic habitat and location. The macrofaunal community of carbonates at non-seeping (inactive) sites is strongly related to the hydrography (depth, temperature, O2) of overlying water, whereas the fauna at sites of active seepage is not. Densities are highest on active rocks from tubeworm bushes and mussel beds, particularly at the Mound 12 location (1000 m). Species diversity is higher on rocks exposed to active seepage, with multiple species of gastropods and polychaetes dominant, while crustaceans, cnidarians, and ophiuroids were better represented on rocks at inactive sites. Macro-infauna (larger than 0.3 mm) from tube cores taken in nearby seep sediments at comparable depths exhibited densities similar to those on carbonate rocks, but had lower diversity and different taxonomic composition. Seep sediments had higher densities of ampharetid, dorvilleid, hesionid, cirratulid and lacydoniid polychaetes, whereas carbonates had more gastropods, as well as syllid, chrysopetalid and polynoid polychaetes. Stable isotope signatures and metrics: The stable isotope signatures of carbonates were heterogeneous, as were the food sources and nutrition used by the animals. Carbonate δ13Cinorg values (mean = -26.98‰) ranged from -53.3‰ to +10.0‰, and were significantly heavier than carbonate δ13

  9. Biodiversity on the Rocks: Macrofauna Inhabiting Authigenic Carbonate at Costa Rica Methane Seeps

    PubMed Central

    Levin, Lisa A.; Mendoza, Guillermo F.; Grupe, Benjamin M.; Gonzalez, Jennifer P.; Jellison, Brittany; Rouse, Greg; Thurber, Andrew R.; Waren, Anders

    2015-01-01

    Carbonate communities: The activity of anaerobic methane oxidizing microbes facilitates precipitation of vast quantities of authigenic carbonate at methane seeps. Here we demonstrate the significant role of carbonate rocks in promoting diversity by providing unique habitat and food resources for macrofaunal assemblages at seeps on the Costa Rica margin (400–1850 m). The attendant fauna is surprisingly similar to that in rocky intertidal shores, with numerous grazing gastropods (limpets and snails) as dominant taxa. However, the community feeds upon seep-associated microbes. Macrofaunal density, composition, and diversity on carbonates vary as a function of seepage activity, biogenic habitat and location. The macrofaunal community of carbonates at non-seeping (inactive) sites is strongly related to the hydrography (depth, temperature, O2) of overlying water, whereas the fauna at sites of active seepage is not. Densities are highest on active rocks from tubeworm bushes and mussel beds, particularly at the Mound 12 location (1000 m). Species diversity is higher on rocks exposed to active seepage, with multiple species of gastropods and polychaetes dominant, while crustaceans, cnidarians, and ophiuroids were better represented on rocks at inactive sites. Macro-infauna (larger than 0.3 mm) from tube cores taken in nearby seep sediments at comparable depths exhibited densities similar to those on carbonate rocks, but had lower diversity and different taxonomic composition. Seep sediments had higher densities of ampharetid, dorvilleid, hesionid, cirratulid and lacydoniid polychaetes, whereas carbonates had more gastropods, as well as syllid, chrysopetalid and polynoid polychaetes. Stable isotope signatures and metrics: The stable isotope signatures of carbonates were heterogeneous, as were the food sources and nutrition used by the animals. Carbonate δ13Cinorg values (mean = -26.98‰) ranged from -53.3‰ to +10.0‰, and were significantly heavier than carbonate δ13

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

    PubMed Central

    Siegert, Michael; Krüger, Martin; Teichert, Barbara; Wiedicke, Michael; Schippers, Axel

    2011-01-01

    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. PMID:22207865

  11. HYFLUX: Satellite Exploration of Natural Hydrocarbon Seeps and Discovery of a Methane Hydrate Mound at GC600

    NASA Astrophysics Data System (ADS)

    Garcia-Pineda, O. G.; MacDonald, I. R.; Shedd, W.; Zimmer, B.

    2009-12-01

    Analysis of natural hydrocarbon seeps is important to improve our understanding of methane flux from deeper sediments to the water column. In order to quantify natural hydrocarbon seep formations in the Northern Gulf of Mexico, a set of 686 Synthetic Aperture Radar (SAR) images was analyzed using the Texture Classifying Neural Network Algorithm (TCNNA), which processes SAR data to delineate oil slicks. This analysis resulted in a characterization of 396 natural seep sites distributed in the northern GOM. Within these sites, a maximum of 1248 individual vents where identified. Oil reaching the sea-surface is deflected from its source during transit through the water column. This presentation describes a method for estimating locations of active oil vents based on repeated slick detection in SAR. One of the most active seep formations was detected in MMS lease block GC600. A total of 82 SAR scenes (collected by RADARSAT-1 from 1995 to 2007) was processed covering this region. Using TCNNA the area covered by each slick was computed and Oil Slicks Origins (OSO) were selected as single points within detected oil slicks. At this site, oil slick signatures had lengths up to 74 km and up to 27 km^2 of area. Using SAR and TCNNA, four active vents were identified in this seep formation. The geostatistical mean centroid among all detections indicated a location along a ridge-line at ~1200m. Sea truth observations with an ROV, confirmed that the estimated location of vents had a maximum offset of ~30 m from their actual locations on the seafloor. At the largest vent, a 3-m high, 12-m long mound of oil-saturated gas hydrate was observed. The outcrop contained thousands of ice worms and numerous semi-rigid chimneys from where oily bubbles were escaping in a continuous stream. Three additional vents were found along the ridge; these had lower apparent flow, but were also plugged with gas hydrate mounds. These results support use of SAR data for precise delineation of active seep

  12. Imaging hydrological processes in headwater riparian seeps with time-lapse electrical resistivity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The activation of subsurface seepage in response to precipitation events represents a potentially important pathway of nitrogen (N) delivery to streams in agricultural catchments. We used electrical resistivity imaging (ERI) and shallow piezometers to elucidate how seep and non-seep areas within the...

  13. Comparative Composition, Diversity and Trophic Ecology of Sediment Macrofauna at Vents, Seeps and Organic Falls

    PubMed Central

    Bernardino, Angelo F.; Levin, Lisa A.; Thurber, Andrew R.; Smith, Craig R.

    2012-01-01

    Sediments associated with hydrothermal venting, methane seepage and large organic falls such as whale, wood and plant detritus create deep-sea networks of soft-sediment habitats fueled, at least in part, by the oxidation of reduced chemicals. Biological studies at deep-sea vents, seeps and organic falls have looked at macrofaunal taxa, but there has yet to be a systematic comparison of the community-level attributes of sediment macrobenthos in various reducing ecosystems. Here we review key similarities and differences in the sediment-dwelling assemblages of each system with the goals of (1) generating a predictive framework for the exploration and study of newly identified reducing habitats, and (2) identifying taxa and communities that overlap across ecosystems. We show that deep-sea seep, vent and organic-fall sediments are highly heterogeneous. They sustain different geochemical and microbial processes that are reflected in a complex mosaic of habitats inhabited by a mixture of specialist (heterotrophic and symbiont-associated) and background fauna. Community-level comparisons reveal that vent, seep and organic-fall macrofauna are very distinct in terms of composition at the family level, although they share many dominant taxa among these highly sulphidic habitats. Stress gradients are good predictors of macrofaunal diversity at some sites, but habitat heterogeneity and facilitation often modify community structure. The biogeochemical differences across ecosystems and within habitats result in wide differences in organic utilization (i.e., food sources) and in the prevalence of chemosynthesis-derived nutrition. In the Pacific, vents, seeps and organic-falls exhibit distinct macrofaunal assemblages at broad-scales contributing to ß diversity. This has important implications for the conservation of reducing ecosystems, which face growing threats from human activities. PMID:22496753

  14. Recognition of fossil prokaryotes in Cretaceous methane seep carbonates: relevance to astrobiology.

    PubMed

    Shapiro, Russell Scott

    2004-01-01

    Recovery of prokaryotic body fossils from methane seep carbonates such as those of the Cretaceous Tepee Buttes of Colorado serves as a model for sampling in future astrobiological missions. The fossils, found primarily at the interface between paragenetic fabrics, suggest a sharp physicochemical gradient. Evidence of these microbial fossils occurs at a variety of scales. In the field, microbialite is found as meter-scale thrombolitic zones and centimeterscale stromatolitic crusts lining voids inferred to be the sites of ancient methane seepage. Petrographic fabrics suggestive of microbialite include indistinct peloids (0.1-1 mm in diameter) and crusts of authigenic micrite. Primary evidence obtained from scanning electron microscopy coupled with energy-dispersive x-ray spectroscopy analysis comprises pinnate bacteria (0.3 microm in diameter and 1-1.5 microm long), sheaths (2-4 microm in diameter), coccoids (0.5-1 microm in diameter, up to 40 per cluster), and the presence of framboidal pyrite (6-8 microm in diameter). These results are in agreement with studies of other ancient and modern seeps and suggest a morphological conservatism of microbial form that can be incorporated into studies of extraterrestrial environments where it is presumed that reduced gases drive the metabolic activity of prokaryote-like organisms. Target areas that could serve as conduits for reduced gas seeps include tectonic or impact-driven faulting, zones of cryosphere melting, or other disruptions in crustal coherence. Ancient seeps, preserved as localized anomalous evaporite deposits in the sedimentary cover, could be detected by remote sensing.

  15. Comparative composition, diversity and trophic ecology of sediment macrofauna at vents, seeps and organic falls.

    PubMed

    Bernardino, Angelo F; Levin, Lisa A; Thurber, Andrew R; Smith, Craig R

    2012-01-01

    Sediments associated with hydrothermal venting, methane seepage and large organic falls such as whale, wood and plant detritus create deep-sea networks of soft-sediment habitats fueled, at least in part, by the oxidation of reduced chemicals. Biological studies at deep-sea vents, seeps and organic falls have looked at macrofaunal taxa, but there has yet to be a systematic comparison of the community-level attributes of sediment macrobenthos in various reducing ecosystems. Here we review key similarities and differences in the sediment-dwelling assemblages of each system with the goals of (1) generating a predictive framework for the exploration and study of newly identified reducing habitats, and (2) identifying taxa and communities that overlap across ecosystems. We show that deep-sea seep, vent and organic-fall sediments are highly heterogeneous. They sustain different geochemical and microbial processes that are reflected in a complex mosaic of habitats inhabited by a mixture of specialist (heterotrophic and symbiont-associated) and background fauna. Community-level comparisons reveal that vent, seep and organic-fall macrofauna are very distinct in terms of composition at the family level, although they share many dominant taxa among these highly sulphidic habitats. Stress gradients are good predictors of macrofaunal diversity at some sites, but habitat heterogeneity and facilitation often modify community structure. The biogeochemical differences across ecosystems and within habitats result in wide differences in organic utilization (i.e., food sources) and in the prevalence of chemosynthesis-derived nutrition. In the Pacific, vents, seeps and organic-falls exhibit distinct macrofaunal assemblages at broad-scales contributing to ß diversity. This has important implications for the conservation of reducing ecosystems, which face growing threats from human activities. PMID:22496753

  16. Aragonite precipitation induced by anaerobic oxidation of methane in shallow-water seeps, Tyrrhenian Sea, Italy

    NASA Astrophysics Data System (ADS)

    Wiedling, Johanna; Kuhfuß, Hanna; Lott, Christian; Böttcher, Michael E.; Lichtschlag, Anna; Wegener, Gunter; Deusner, Christian; Bach, Wolfgang; Weber, Miriam

    2014-05-01

    flow path. The Elba aragonites, showed a carbon isotope signature of -14.9o vs. VPDB, mirroring the isotopic signature of the pore-water DIC at this sediment depth. Similar δ13C-compositions of -15.3o were obtained for the discharging methane, giving room for discussion about the origin of the gas. We suppose that AOM is the main driver for aragonite precipitation in the permeable sands at the shallow-water seeps because of (1) very low organic carbon contents (0.5 mg/g) in the sediment, (2) 13C enrichment in the methane gas, (3) elevated DIC concentrations in the pore-water, and (4) AOM in vitro activity. Thus, aragonite precipitates of the seep site near Elba may represent a unique system to study ongoing abiogenic seep carbonate formation at shallow depth as a modern analogue for seep carbonates occurring in the geological record.

  17. Methane from shallow seep areas of the NW Svalbard Arctic margin does not reach the sea surface

    NASA Astrophysics Data System (ADS)

    Silyakova, Anna; Greinert, Jens; Jansson, Pär; Ferré, Bénédicte

    2015-04-01

    Methane, an important greenhouse gas, leaks from large areas of the Arctic Ocean floor. One overall question is how much methane passes from the seabed through the water column, potentially reaching the atmosphere. Transport of methane from the ocean floor into and through the water column depends on many factors such as distribution of gas seeps, microbial methane oxidation, and ambient oceanographic conditions, which may trigger a change in seep activity. From June-July 2014 we investigated dissolved methane in the water column emanating from the "Prins Karls Forland seeps" area offshore the NW Svalbard Arctic margin. Measurements of the spatial variability of dissolved methane in the water column included 65 CTD stations located in a grid covering an area of 30 by 15 km. We repeated an oceanographic transect twice in a week for time lapse studies, thus documenting significant temporal variability in dissolved methane above one shallow seep site (~100 m water depth). Analysis of both nutrient concentrations and dissolved methane in water samples from the same transect, reveal striking similarities in spatial patterns of both dissolved methane and nutrients indicating that microbial community is involved in methane cycling above the gas seepage. Our preliminary results suggest that although methane release can increase in a week's time, providing twice as much dissolved gas to the water column, no methane from a seep reaches the sea surface. Instead it spreads horizontally under the pycnocline. Yet microbial communities react rapidly to the methane supply above gas seepage areas and may also have an important role as an effective filter, hindering methane release from the ocean to the atmosphere during rapid methane ebullition. This study is funded by CAGE (Centre for Arctic Gas Hydrate, Environment and Climate), Norwegian Research Council grant no. 223259.

  18. Control of Quaternary sea-level changes on gas seeps

    NASA Astrophysics Data System (ADS)

    Riboulot, Vincent; Thomas, Yannick; Berné, Serge; Jouet, Gwénaël.; Cattaneo, Antonio

    2014-07-01

    Gas seeping to the seafloor through structures such as pockmarks may contribute significantly to the enrichment of atmospheric greenhouse gases and global warming. Gas seeps in the Gulf of Lions, Western Mediterranean, are cyclical, and pockmark "life" is governed both by sediment accumulation on the continental margin and Quaternary climate changes. Three-dimensional seismic data, correlated to multi-proxy analysis of a deep borehole, have shown that these pockmarks are associated with oblique chimneys. The prograding chimney geometry demonstrates the syn-sedimentary and long-lasting functioning of the gas seeps. Gas chimneys have reworked chronologically constrained stratigraphic units and have functioned episodically, with maximum activity around sea level lowstands. Therefore, we argue that one of the main driving mechanisms responsible for their formation is the variation in hydrostatic pressure driven by relative sea level changes.

  19. Salt site performance assessment activities

    SciTech Connect

    Kircher, J.F.; Gupta, S.K.

    1983-01-01

    During this year the first selection of the tools (codes) for performance assessments of potential salt sites have been tentatively selected and documented; the emphasis has shifted from code development to applications. During this period prior to detailed characterization of a salt site, the focus is on bounding calculations, sensitivity and with the data available. The development and application of improved methods for sensitivity and uncertainty analysis is a focus for the coming years activities and the subject of a following paper in these proceedings. Although the assessments to date are preliminary and based on admittedly scant data, the results indicate that suitable salt sites can be identified and repository subsystems designed which will meet the established criteria for protecting the health and safety of the public. 36 references, 5 figures, 2 tables.

  20. Natural gas seeps in the French Alps: Sources and pathways

    NASA Astrophysics Data System (ADS)

    Kloppmann, Wolfram; Blessing, Michaela; Proust, Eric; Gal, Frédéric; Bentivegna, Gaetan; Henry, Benoit; Defossez, Pierrick; Catherine, Lerouge; Humez, Pauline; Mayer, Bernhard; Millot, Romain; Gaucher, Eric

    2016-04-01

    Natural gas emanations are part of the geochemical baseline to take into account when assessing global greenhouse gas emissions and potential impacts of conventional and unconventional gas exploration and exploitation on groundwater. Examples of such natural gas macro-seeps are known in several parts of the world (Etiope et al., 2009). Only a limited number of them have been characterized for their gas and isotopic compositions. Such analyses can provide essential information for baseline studies, providing insight in the sources (biogenic vs. thermogenic or modified thermogenic) and pathways of such seeps and may allow for distinction of natural seeps from stray gas leakage associated with human activities. Here, we report gas concentrations and multi-isotope data (δ13C and δ2H of methane and ethane, δ13C and δ18O of CO2, 3He/4He ratio) of two gas seeps in the French subalpine chains, both in a similar geological and structural position within Middle Jurassic claystones along the eastern border of the large synclinal structures of the Vercors and the Chartreuse massifs (Moss, 1992). The "ardent fountain" (fontaine ardente) of Le Gua, 30 km south of Grenoble has most likely the longest continuous written record of existence of any individual natural gas seep, mentioned explicitly as early as the first quarter of the 5th century (Augustin of Hippo (St. Augustin), approx. 426) This natural seep was described in the past as a "wet seep" associated with a spring, whereas the second investigated seep, Rochasson near Meylan north of Grenoble, is a dry seep. Both seeps contain methane and ethane with thermogenic C and H isotope signatures, comparable with a seep in the Northern Swiss Alps at Giswil (Etiope et al., 2010) but with a higher dryness (C1/(C2+C3)>1000) for the Le Gua seep, possibly due to molecular fractionation upon advective fluid+gas migration (Etiope et al., 2009). Maturity (R0) of the reservoir rocks deduced from δ13C(CH4), δ13C(C2H6) is similar to

  1. Does the "sleeping Dragon" Really Sleep?: the Case for Continuous Long-Term Monitoring at a Gulf of Mexico Cold Seep Site

    NASA Astrophysics Data System (ADS)

    Wilson, R. M.; Lapham, L.; Farr, N.; Lutken, C.; MacDonald, I. R.; Macelloni, L.; Riedel, M.; Sleeper, K.; Chanton, J.

    2011-12-01

    Continuous porewater monitoring indicates that the methane flux away from exposed hydrate mounds can vary considerably over time. Recently, we retrieved a Pore Fluid Array instrument pack from a hydrate outcrop adjacent to a NEPTUNE Canada observatory node. The sampler was designed to continuously collect and store sediment pore fluids over the course of 9 months. On analysis, we observed a 35mM variation in methane concentrations corresponding with an abrupt shift in current direction at the site. Video and resistivity data have led to previous speculation that hydrate growth and dissolution/dissociation may be seasonally variable. Cumulatively, these findings suggest that the persistence of hydrate outcrops may be extremely dynamic, driven by fluctuations in physical conditions on short time scales. Short-term monitoring in the Gulf of Mexico within Mississippi Canyon lease block 118 (MC118), a known hydrate-bearing site, indicates that physical conditions even at these depths (~540-890m) may be highly variable. Pressure can vary within hours, and recorded temperature changes of ~1.5°C have been associated with passing storms. Moreover, increased particle abundance was observed at the site in 2007 suggesting that organic matter flux to the sediments may vary on the scale of months to years. These inputs have the potential to alter the chemical environment surrounding the hydrate, thereby affecting dissolution rates. Continuous, long-term observations of physical conditions at MC118 could provide information about the potential for natural perturbations to impact hydrate dynamics on the scale of weeks or even days necessary for assessing the long-term persistence of hydrate outcrops. Sleeping Dragon is a massive hydrate outcrop at MC118 that has been monitored since 2006. Three years ago, researchers returning to the site found it visibly diminished relative to previous observations. This apparent shift toward net dissolution of the mound may have been

  2. The potential of near-surface geophysical methods in a hierarchical monitoring approach for the detection of shallow CO2 seeps at geological storage sites

    NASA Astrophysics Data System (ADS)

    Sauer, U.; Schuetze, C.; Dietrich, P.

    2013-12-01

    The MONACO project (Monitoring approach for geological CO2 storage sites using a hierarchic observation concept) aims to find reliable monitoring tools that work on different spatial and temporal scales at geological CO2 storage sites. This integrative hierarchical monitoring approach based on different levels of coverage and resolutions is proposed as a means of reliably detecting CO2 degassing areas at ground surface level and for identifying CO2 leakages from storage formations into the shallow subsurface, as well as CO2 releases into the atmosphere. As part of this integrative hierarchical monitoring concept, several methods and technologies from ground-based remote sensing (Open-path Fourier-transform infrared (OP-FTIR) spectroscopy), regional measurements (near-surface geophysics, chamber-based soil CO2 flux measurement) and local in-situ measurements (using shallow boreholes) will either be combined or used complementary to one another. The proposed combination is a suitable concept for investigating CO2 release sites. This also presents the possibility of adopting a modular monitoring concept whereby our monitoring approach can be expanded to incorporate other methods in various coverage scales at any temporal resolution. The link between information obtained from large-scale surveys and local in-situ monitoring can be realized by sufficient geophysical techniques for meso-scale monitoring, such as geoelectrical and self-potential (SP) surveys. These methods are useful for characterizing fluid flow and transport processes in permeable near-surface sedimentary layers and can yield important information concerning CO2-affected subsurface structures. Results of measurements carried out a natural analogue site in the Czech Republic indicate that the hierarchical monitoring approach represents a successful multidisciplinary modular concept that can be used to monitor both physical and chemical processes taking place during CO2 migration and seepage. The

  3. High pH microbial ecosystems in a newly discovered, ephemeral, serpentinizing fluid seep at Yanartaş (Chimera), Turkey

    PubMed Central

    Meyer-Dombard, D'Arcy R.; Woycheese, Kristin M.; Yargıçoğlu, Erin N.; Cardace, Dawn; Shock, Everett L.; Güleçal-Pektas, Yasemin; Temel, Mustafa

    2015-01-01

    Gas seeps emanating from Yanartaş (Chimera), Turkey, have been documented for thousands of years. Active serpentinization produces hydrogen and a range of carbon gases that may provide fuel for life. Here we report a newly discovered, ephemeral fluid seep emanating from a small gas vent at Yanartaş. Fluids and biofilms were sampled at the source and points downstream. We describe site conditions, and provide microbiological data in the form of enrichment cultures, Scanning electron microscopy (SEM), carbon and nitrogen isotopic composition of solids, and PCR screens of nitrogen cycle genes. Source fluids are pH 11.95, with a Ca:Mg of ~200, and sediments under the ignited gas seep measure 60°C. Collectively, these data suggest the fluid is the product of active serpentinization at depth. Source sediments are primarily calcite and alteration products (chlorite and montmorillonite). Downstream, biofilms are mixed with montmorillonite. SEM shows biofilms distributed homogeneously with carbonates. Organic carbon accounts for 60% of the total carbon at the source, decreasing downstream to <15% as inorganic carbon precipitates. δ13C ratios of the organic carbon fraction of solids are depleted (−25 to −28‰) relative to the carbonates (−11 to −20‰). We conclude that heterotrophic processes are dominant throughout the surface ecosystem, and carbon fixation may be key down channel. δ15N ratios ~3‰, and absence of nifH in extracted DNA suggest that nitrogen fixation is not occurring in sediments. However, the presence of narG and nirS at most locations and in enrichments indicates genomic potential for nitrate and nitrite reduction. This small seep with shallow run-off is likely ephemeral, but abundant preserved microterracettes in the outflow and the surrounding area suggest it has been present for some time. This site and others like it present an opportunity for investigations of preserved deep biosphere signatures, and subsurface-surface interactions

  4. High pH microbial ecosystems in a newly discovered, ephemeral, serpentinizing fluid seep at Yanartaş (Chimera), Turkey.

    PubMed

    Meyer-Dombard, D'Arcy R; Woycheese, Kristin M; Yargıçoğlu, Erin N; Cardace, Dawn; Shock, Everett L; Güleçal-Pektas, Yasemin; Temel, Mustafa

    2014-01-01

    Gas seeps emanating from Yanartaş (Chimera), Turkey, have been documented for thousands of years. Active serpentinization produces hydrogen and a range of carbon gases that may provide fuel for life. Here we report a newly discovered, ephemeral fluid seep emanating from a small gas vent at Yanartaş. Fluids and biofilms were sampled at the source and points downstream. We describe site conditions, and provide microbiological data in the form of enrichment cultures, Scanning electron microscopy (SEM), carbon and nitrogen isotopic composition of solids, and PCR screens of nitrogen cycle genes. Source fluids are pH 11.95, with a Ca:Mg of ~200, and sediments under the ignited gas seep measure 60°C. Collectively, these data suggest the fluid is the product of active serpentinization at depth. Source sediments are primarily calcite and alteration products (chlorite and montmorillonite). Downstream, biofilms are mixed with montmorillonite. SEM shows biofilms distributed homogeneously with carbonates. Organic carbon accounts for 60% of the total carbon at the source, decreasing downstream to <15% as inorganic carbon precipitates. δ(13)C ratios of the organic carbon fraction of solids are depleted (-25 to -28‰) relative to the carbonates (-11 to -20‰). We conclude that heterotrophic processes are dominant throughout the surface ecosystem, and carbon fixation may be key down channel. δ(15)N ratios ~3‰, and absence of nifH in extracted DNA suggest that nitrogen fixation is not occurring in sediments. However, the presence of narG and nirS at most locations and in enrichments indicates genomic potential for nitrate and nitrite reduction. This small seep with shallow run-off is likely ephemeral, but abundant preserved microterracettes in the outflow and the surrounding area suggest it has been present for some time. This site and others like it present an opportunity for investigations of preserved deep biosphere signatures, and subsurface-surface interactions. PMID

  5. Elevated surface chlorophyll associated with natural oil seeps in the Gulf of Mexico

    NASA Astrophysics Data System (ADS)

    D'Souza, N. A.; Subramaniam, A.; Juhl, A. R.; Hafez, M.; Chekalyuk, A.; Phan, S.; Yan, B.; MacDonald, I. R.; Weber, S. C.; Montoya, J. P.

    2016-03-01

    Natural hydrocarbon seeps occur on the sea floor along continental margins, and account for up to 47% of the oil released into the oceans. Hydrocarbon seeps are known to support local benthic productivity, but little is known about their impact on photosynthetic organisms in the overlying water column. Here we present observations with high temporal and spatial resolution of chlorophyll concentrations in the northern Gulf of Mexico using in situ and shipboard flow-through fluorescence measurements from May to July 2012, as well as an analysis of ocean-colour satellite images from 1997 to 2007. All three methods reveal elevated chlorophyll concentrations in waters influenced by natural hydrocarbon seeps. Temperature and nutrient profiles above seep sites suggest that nutrient-rich water upwells from depth, which may facilitate phytoplankton growth and thus support the higher chlorophyll concentrations observed. Because upwelling occurs at natural seep locations around the world, we conclude that offshore hydrocarbon seeps, and perhaps other types of deep ocean vents and seeps at depths exceeding 1,000 m, may influence biogeochemistry and productivity of the overlying water column.

  6. Pockmarks: self-scouring seep features?

    USGS Publications Warehouse

    Brothers, Laura L.; Kelley, Joseph T.; Belknap, Daniel F.; Barnhardt, Walter A.; Koons, Peter O.

    2011-01-01

    Pockmarks, or seafloor craters, occur worldwide in a variety of geologic settings and are often associated with fluid discharge. The mechanisms responsible for pockmark preservation, and pockmarks? relation to active methane venting are not well constrained. Simple numerical simulations run in 2-and 3-dimensions, and corroborated by flume tank experiments, indicate turbulence may play a role in pockmark maintenance, and, potentially, in pockmark excavation. Morphological analysis of the pockmarks indicates an abundance of flat-bottomed and/or elongated pockmarks. Pockmarks transition into furrows as the bay narrows and tidal flow is enhanced, providing unmistakable evidence of post-formation evolution. We hypothesize that some pockmarks formed from seafloor perturbations (e.g., gas or methane discharge), are1 maintained and gradually modified by vortical flow. This hypothesis provides a mechanism for pockmark preservation and enlargement without active fluid venting, which has implications for the interpretation of seafloor seep features in gas hydrates areas.

  7. Phosphogenesis at a Cretaceous methane seep from New Zealand

    NASA Astrophysics Data System (ADS)

    Zwicker, Jennifer; Steindl, Florian; Smrzka, Daniel; Böttcher, Michael; Gier, Susanne; Kiel, Steffen; Peckmann, Jörn

    2016-04-01

    Phosphate-rich deposits have been a topic of intense research for decades. The process of phosphogenesis is mainly observed in marine sediments of coastal upwelling zones, where organic matter delivers sufficient phosphorus (P) to enable the formation of phosphorites. As P may be cycled within marine sediments on short timescales, only specific geochemical conditions allow for the precipitation and preservation of phosphate minerals. The processes that enable phosphogenesis are still a matter of debate, and not all mechanisms involved are fully understood. We expand the scope of known phosphorous-rich deposits further, with evidence of phosphogenesis at methane seeps. Cretaceous methane-seep limestones from Waipiro Bay, New Zealand, exhibit (1) a matrix composed of cryptocrystalline fluorapatite in between micritic spheroids and coated calcite grains, and (2) phosphatic spheroids within a micritic matrix. Due to the abundant spherical morphologies of phosphate and carbonate grains, and the exceptionally well preserved phosphate matrix, we suggest that their formation was associated with microbial activity. Methane seeps provide ideal conditions for chemosynthetic communities to thrive, and for the growth of bacterial mats at the sediment water interface. To understand these unique deposits, we derive a formation scenario for apatite and spheroidal carbonate, using detailed petrographical observations, X-ray diffraction, scanning electron microscopy, and electron microprobe analyses. Furthermore, it is shown that phase-specific stable carbon and oxygen isotopes confirm that both phosphate and carbonate formation occurred at a methane seep.

  8. Cold seep carbonates along the Norwegian margin, insights into U-Th geochronology and S geochemistry

    NASA Astrophysics Data System (ADS)

    Cremiere, A.; Lepland, A.; Wing, B. A.; Sahy, D.; Condon, D. J.; Chand, S.; Noble, S. R.; Bui, T. H.; Thorsnes, T.; Brunstad, H.

    2015-12-01

    Cold seep carbonates along the Norwegian margin, insights into U-Th geochronology and S geochemistryAuthigenic carbonate crusts form in shallow subsurface of marine sediments due to the microbial anaerobic oxidation of methane (AOM). As a result they are unique archives of the locus and intensity of past methane seepage that can be dated by using U-daughter decay affording the unique opportunity to constrain the absolute timing of methane release events. Because AOM is mainly driven by the microbial reduction of seawater sulfate, multiple sulfur isotope compositions of paired carbonate-associated sulfate (CAS) and pyrite in seep carbonates taken as proxies for porewater sulfate and sulfide, respectively, have the potential to reconstruct the biogeochemical conditions under which seep carbonates precipitate. Methane-derived carbonate crusts were collected from several seepage sites on the Norwegian continental shelf, including sites in the North Sea, the Norwegian Sea and the Barents Sea. The U-Th dating results constrain the main episode of carbonate crust formation in the Barents and Norwegian seas during the time interval between 14 and 7 ka. Such ages suggest that the methane seepage along the northern Norwegian margin was most active after the collapse of the Scandinavian ice sheet and deglaciation of the area that took place at about 15 ka. The methane flux for the carbonate crust formation was likely provided by the dissociation of methane hydrates that extensively formed in underlying sediments during the last glacial period, but became unstable due to depressuring effects of retreating ice sheet. The precipitation of studied North Sea carbonate crusts occurred more recently, from 6 to 1 ka, suggesting that their formation is unrelated to the glacial history of the area. The paired sulfur stable isotope compositions of pyrite-CAS record a large range of fractionation factors (from 30 to 70 ‰) reflecting change of sulfate-reduction rates possibly controlled

  9. Assessing the health risks of natural CO2 seeps in Italy

    SciTech Connect

    Roberts, J.J.; Wood, R.A.; Haszeldine, R.S.

    2011-10-04

    Industrialized societies which continue to use fossil fuel energy sources are considering adoption of Carbon Capture and Storage (CCS) technology to meet carbon emission reduction targets. Deep geological storage of CO2 onshore faces opposition regarding potential health effects of CO2 leakage from storage sites. There is no experience of commercial scale CCS with which to verify predicted risks of engineered storage failure. Studying risk from natural CO2 seeps can guide assessment of potential health risks from leaking onshore CO2 stores. Italy and Sicily are regions of intense natural CO2 degassing from surface seeps. These seeps exhibit a variety of expressions, characteristics (e.g., temperature/ flux), and location environments. Here we quantify historical fatalities from CO2 poisoning using a database of 286 natural CO2 seeps in Italy and Sicily. We find that risk of human death is strongly influenced by seep surface expression, local conditions (e.g., topography and wind speed), CO2 flux, and human behavior. Risk of accidental human death from these CO2 seeps is calculated to be 10-8 year-1 to the exposed population. This value is significantly lower than that of many socially accepted risks. Seepage from future storage sites is modeled to be less than Italian natural flux rates. With appropriate hazard management, health risks from unplanned seepage at onshore storage sites can be adequately minimized.

  10. Assessing the health risks of natural CO2 seeps in Italy.

    PubMed

    Roberts, Jennifer J; Wood, Rachel A; Haszeldine, R Stuart

    2011-10-01

    Industrialized societies which continue to use fossil fuel energy sources are considering adoption of Carbon Capture and Storage (CCS) technology to meet carbon emission reduction targets. Deep geological storage of CO(2) onshore faces opposition regarding potential health effects of CO(2) leakage from storage sites. There is no experience of commercial scale CCS with which to verify predicted risks of engineered storage failure. Studying risk from natural CO(2) seeps can guide assessment of potential health risks from leaking onshore CO(2) stores. Italy and Sicily are regions of intense natural CO(2) degassing from surface seeps. These seeps exhibit a variety of expressions, characteristics (e.g., temperature/flux), and location environments. Here we quantify historical fatalities from CO(2) poisoning using a database of 286 natural CO(2) seeps in Italy and Sicily. We find that risk of human death is strongly influenced by seep surface expression, local conditions (e.g., topography and wind speed), CO(2) flux, and human behavior. Risk of accidental human death from these CO(2) seeps is calculated to be 10-8 year-1 to the exposed population. This value is significantly lower than that of many socially accepted risks. Seepage from future storage sites is modeled to be less that Italian natural flux rates. With appropriate hazard management, health risks from unplanned seepage at onshore storage sites can be adequately minimized. PMID:21911398

  11. Assessing the health risks of natural CO2 seeps in Italy

    NASA Astrophysics Data System (ADS)

    Roberts, Jennifer J.; Wood, Rachel A.; Haszeldine, R. Stuart

    2011-10-01

    Industrialized societies which continue to use fossil fuel energy sources are considering adoption of Carbon Capture and Storage (CCS) technology to meet carbon emission reduction targets. Deep geological storage of CO2 onshore faces opposition regarding potential health effects of CO2 leakage from storage sites. There is no experience of commercial scale CCS with which to verify predicted risks of engineered storage failure. Studying risk from natural CO2 seeps can guide assessment of potential health risks from leaking onshore CO2 stores. Italy and Sicily are regions of intense natural CO2 degassing from surface seeps. These seeps exhibit a variety of expressions, characteristics (e.g., temperature/flux), and location environments. Here we quantify historical fatalities from CO2 poisoning using a database of 286 natural CO2 seeps in Italy and Sicily. We find that risk of human death is strongly influenced by seep surface expression, local conditions (e.g., topography and wind speed), CO2 flux, and human behavior. Risk of accidental human death from these CO2 seeps is calculated to be 10-8 year-1 to the exposed population. This value is significantly lower than that of many socially accepted risks. Seepage from future storage sites is modeled to be less that Italian natural flux rates. With appropriate hazard management, health risks from unplanned seepage at onshore storage sites can be adequately minimized.

  12. Assessing the health risks of natural CO2 seeps in Italy

    PubMed Central

    Roberts, Jennifer J.; Wood, Rachel A.; Haszeldine, R. Stuart

    2011-01-01

    Industrialized societies which continue to use fossil fuel energy sources are considering adoption of Carbon Capture and Storage (CCS) technology to meet carbon emission reduction targets. Deep geological storage of CO2 onshore faces opposition regarding potential health effects of CO2 leakage from storage sites. There is no experience of commercial scale CCS with which to verify predicted risks of engineered storage failure. Studying risk from natural CO2 seeps can guide assessment of potential health risks from leaking onshore CO2 stores. Italy and Sicily are regions of intense natural CO2 degassing from surface seeps. These seeps exhibit a variety of expressions, characteristics (e.g., temperature/flux), and location environments. Here we quantify historical fatalities from CO2 poisoning using a database of 286 natural CO2 seeps in Italy and Sicily. We find that risk of human death is strongly influenced by seep surface expression, local conditions (e.g., topography and wind speed), CO2 flux, and human behavior. Risk of accidental human death from these CO2 seeps is calculated to be 10-8 year-1 to the exposed population. This value is significantly lower than that of many socially accepted risks. Seepage from future storage sites is modeled to be less that Italian natural flux rates. With appropriate hazard management, health risks from unplanned seepage at onshore storage sites can be adequately minimized. PMID:21911398

  13. Geochemical zonation and characteristics of cold seeps along the Makran continental margin off Pakistan

    NASA Astrophysics Data System (ADS)

    Fischer, D.; Bohrmann, G.; Zabel, M.; Kasten, S.

    2009-04-01

    Several highly dynamic and spatially extended cold seeps were found and analyzed on the Makran accretionary wedge off Pakistan during R/V Meteor cruise M74-3 in 2007. In water depths of 550m to 2870m along the continental slope nine different gas escape structures were examined some of which are situated within a stable oxygen minimum zone (OMZ) between 150m and 1100m water depth (von Rad et al., 1996, 2000). Echosounder data indicate several gas bubble streams in the water column. The gas seepage presumably originates from squeezing of massive sediment packages being compressed by subduction at the continental margin off Pakistan. Gas- and fluid venting and associated surface-near anaerobic oxidation of methane (AOM) feed several cold seepage systems in the seabed. The seep sites show strong inter- and intraspecific variability of benthic chemosynthetic microhabitats. Singular seeps are often colonized by different chemosynthetic organisms in a concentric fashion. The seep-center, where active bubble ebullition occurs, is often colonized by large hydrogen sulfide-oxidizing bacteria, which are surrounded by a rim inhabited by small chemosynthetic clams and tube worms. These different habitats and the associated sediments show distinct geochemical zonations and gradients. Geochemical analyses of pore water and sediment samples obtained via ROV (push corer) show that concentrations of hydrogen sulfide and alkalinity rapidly increase to >15 mmol/l and >35 mmol/l respectively several cm below the seafloor in the center of the cold seep. In places, sulfate is depleted to concentrations below detection limit at the same depth (ROV push core GeoB 12313-6). Ammonium concentrations in this core on the other hand show a different pattern: In the center of the cold seep, which is colonized by bacterial assemblages, ammonium concentrations fluctuate around 100 µmol/l and peak with 274.4 µmol/l just above the aforementioned sulfide maximum values at 5 cm followed by a rapid

  14. Groundwater seeps facilitate exposure to Burkholderia pseudomallei.

    PubMed

    Baker, Anthony; Tahani, Donald; Gardiner, Christopher; Bristow, Keith L; Greenhill, Andrew R; Warner, Jeffrey

    2011-10-01

    Burkholderia pseudomallei is a saprophytic bacterium which is the causative agent of melioidosis, a common cause of fatal bacterial pneumonia and sepsis in the tropics. The incidence of melioidosis is clustered spatially and temporally and is heavily linked to rainfall and extreme weather events. Clinical case clustering has recently been reported in Townsville, Australia, and has implicated Castle Hill, a granite monolith in the city center, as a potential reservoir of infection. Topsoil and water from seasonal groundwater seeps were collected around the base of Castle Hill and analyzed by quantitative real-time PCR targeting the type III secretion system genes for the presence of B. pseudomallei. The organism was identified in 65% (95% confidence interval [CI], 49.5 to 80.4) of soil samples (n = 40) and 92.5% (95% CI, 83.9 to 100) of seasonal groundwater samples (n = 40). Further sampling of water collected from roads and gutters in nearby residential areas after an intense rainfall event found that 88.2% (95% CI, 72.9 to 100) of samples (n = 16) contained viable B. pseudomallei at concentrations up to 113 CFU/ml. Comparison of isolates using multilocus sequence typing demonstrated clinical matches and close associations between environmental isolates and isolates derived from clinical samples from patients in Townsville. This study demonstrated that waterborne B. pseudomallei from groundwater seeps around Castle Hill may facilitate exposure to B. pseudomallei and contribute to the clinical clustering at this site. Access to this type of information will advise the development and implementation of public health measures to reduce the incidence of melioidosis.

  15. Subseafloor to Sea-Air Interface Characterization of Methane Dynamics in the northern US Atlantic Margin Seep Province

    NASA Astrophysics Data System (ADS)

    Ruppel, C. D.; Kluesner, J.; Danforth, W. W.; Casso, M.; Pohlman, J.

    2015-12-01

    Since the discovery of hundreds of northern US Atlantic margin (USAM) cold seeps in 2012 and 2013, the USGS Gas Hydrates Project has undertaken intensive studies of the along-margin gas hydrate/free gas distribution, the plumbing systems sustaining seeps, seafloor gas emissions, and sea-air methane flux. Interest in the USAM is motivated both by climate change (i.e., documented ocean warming may contribute to seepage) and energy resource (i.e., the amount of gas-in-place in hydrates on the USAM is about the same as that in the northern Gulf of Mexico) issues. USGS-led field efforts have included an April 2015 study to acquire high-resolution multichannel seismic data, coincident split-beam water column methane plume imaging data, and real-time sea-air methane flux measurements between Wilmington and Norfolk Canyons and a September 2015 cruise (with OSU, UCLA, and Geomar) to collect piston cores, multicores, heat flow data, subbottom imagery, CTDs, and coincident water column imagery from Block Canyon to the Currituck Slide. In April 2015, we discovered methane seeps not included in the previously-published database, but found that some known seeps were not active. New high-resolution multi-channel seismic data revealed clear differences between the deep gas distribution in mid-Atlantic upper slope zones that are replete with (up to 240 sites) and lacking in seeps. Based on sea-air flux measurements, even shallow-water outer shelf (~125 m water depth) seeps and a 900-m-high methane plume originating on the mid-slope do not contribute methane to the atmosphere. Using thermistors placed on piston core outriggers, we will in September 2015 acquire thermal data to identify zones of high fluid advection and to constrain background geotherms in areas where heat flow has never been measured. During that same cruise, we will collect a series of piston cores across the no-hydrate/hydrate transition on the upper slope to constrain fluid and gas dynamics in this zone.

  16. Methane emission and consumption at a North Sea gas seep (Tommeliten area)

    NASA Astrophysics Data System (ADS)

    Niemann, H.; Elvert, M.; Hovland, M.; Orcutt, B.; Judd, A.; Suck, I.; Gutt, J.; Joye, S.; Damm, E.; Finster, K.; Boetius, A.

    2005-11-01

    The North Sea hosts large coal, oil and gas reservoirs of commercial value. Natural leakage pathways of subsurface gas to the hydrosphere have been recognized during geological surveys (Hovland and Judd, 1988). The Tommeliten seepage area is part of the Greater Ekofisk area, which is situated above the Tommeliten Delta salt diapir in the central North Sea. In this study, we report of an active seep site (56°29.90'N, 2°59.80'E) located in the Tommeliten area, Norwegian Block 1/9, at 75 m water depth. Here, cracks in a buried marl horizon allow methane to migrate into overlying clay-silt and sandy sediments. Hydroacoustic sediment echosounding showed several venting spots coinciding with the apex of marl domes where methane is released into the water column and potentially to the atmosphere during deep mixing situations. In the vicinity of the gas seeps, sea floor observations showed small mats of giant sulphide-oxidizing bacteria above patches of black sediments and carbonate crusts, which are exposed 10 to 50 cm above seafloor forming small reefs. These Methane-Derived Authigenic Carbonates (MDACs) contain 13C-depleted, archaeal lipids indicating previous gas seepage and AOM activity. High amounts of sn2-hydroxyarchaeol relative to archaeol and low abundances of biphytanes in the crusts give evidence that ANaerobic MEthane-oxidising archaea (ANME) of the phylogenetic cluster ANME-2 were the potential mediators of Anaerobic Oxidation of Methane (AOM) at the time of carbonate formation. Small pieces of MDACs were also found subsurface at about 1.7 m sediment depth, associated with the Sulphate-Methane Transition Zone (SMTZ). The SMTZ of Tommeliten is characterized by elevated AOM and Sulphate Reduction (SR) rates, increased concentrations of 13C-depleted tetraether derived biphytanes, and specific bacterial Fatty Acids (FA). Further biomarker and 16S rDNA based analyses give evidence that AOM at the Tommeliten SMTZ is mediated by archaea belonging to the ANME-1b

  17. Bacterioplankton growth and production at the Louisiana hydrocarbon seeps

    NASA Astrophysics Data System (ADS)

    Larock, P. A.; Hyun, J.-H.; Bennison, B. W.

    1994-06-01

    The growth rate and potential production of bacterioplankton in cold hydrocarbon seeps located along the Louisiana coast were determined using a pulse-labeling technique. Surprisingly, community doubling times are on the order of 1.1 h, which compares to laboratory-grown cultures. We also found that there are differences in growth rates on relatively small geographic scales, suggesting the influence of site-specific geological features (e.g., gas hydrate mounds). Proceeding downslope to deeper waters, methane-oxidizing bacteria appeared to play a more significant role in community productivity. These preliminary experiments indicated, quite unexpectedly, that water column microbes are growing at a more rapid rate than in any other marine system so far studied and that methane may serve as a primary nutrient (carbon) source in these seep-associated microbial assemblages.

  18. Gas seep induced interstitial water circulation: observations and environmental implications

    NASA Astrophysics Data System (ADS)

    O'Hara, S. C. M.; Dando, P. R.; Schuster, U.; Bennis, A.; Boyle, J. D.; Chui, F. T. W.; Hatherell, T. V. J.; Niven, S. J.; Taylor, L. J.

    1995-07-01

    An interstitial water circulation, generated by gas flow through a permeable sediment, was observed at an intertidal site on the Kattegat coast of Denmark. Concentrations of methane dissolved in the interstitial water of the near-surface sediment decreased sharply only centimetres away from gas seeps venting almost pure methane (≈99% methane). Water was driven out of the sediment by the rising bubbles of gas at the seep and was replaced by an equivalent draw-down of overlying, oxygenated water into the surrounding sediment. This process steepened the chemical gradients close to the gas flow channel, with the effects progressively diminishing with increasing distance from the seep. The position of the redox potential discontinuity (RPD) moved by as much as 7 cm deeper into the sediment close to the seep: this effect was less marked, but still detectable, 50 cm away. The degree of displacement from the "normal" sediment profiles depended on the magnitude of the interstitial flow rate. The distribution of pore water pH and sulphate: sodium ratios were also dependent on the flow rate of the circulating water. The concentrations of sulphide, thiosulphate and sulphite in the interstitial water from the top 10 cm of sediment, were high at a seep, decreased to a minimum at 20-30 cm distance, then increased again at 40-50 cm distance. Laboratory experiments confirmed that gas bubbling through a fluid filled permeable matrix generated a flow, out of the sediment at the gas exit and into the sediment over the peripheral surfaces surrounding the outlet. Experimentally determined rates of dispersion, for gas flow rates of 3-20 ml min -1, for a 40 g l -1 sodium chloride solution, were 62.5 × 10 -9 to 540 × 10 -9 m 2 s -1, 40-400 times the molecular diffusion coefficient. Linear interstitial fluid velocities of 3-12 mm min -1, were recorded at 14-3 cm from the seep axis respectively, with a gas flow rate of 5 ml min -1. Two-dimensional modelling of the experimental system

  19. Water Column Methanotrophy Fueled by Methane from the Hudson Canyon Seep Field, US Atlantic Margin

    NASA Astrophysics Data System (ADS)

    Redmond, M. C.; Chan, E. W.; Kellermann, M. Y.; Arrington, E.; Valentine, D. L.; Kessler, J. D.

    2014-12-01

    Several areas of methane seepage have recently been discovered along the US Atlantic margin, including parts of Hudson Canyon, offshore New York and New Jersey. However, little is known about the magnitude of seepage, the fate of this methane once it enters the water column, or the bacteria that may consume it. In July 2014, water column methane concentrations were measured throughout Hudson Canyon and methane oxidation tracked using a 13C-methane tracer. Samples for microbial community composition analysis were collected throughout the water column in areas with and without active seepage. 16S rRNA gene sequencing will be used to compare microbial communities from different depths, locations, and in samples with low and high methane concentrations and oxidation rates. DNA stable isotope probing experiments with 13C-labeled methane were also conducted and will be used to detect active water column methanotrophs from seep and non-seep sites. In addition, mesocosm experiments were used for high resolution measurements of methane oxidation, with samples for microbial community composition taken at several time points. 16S rRNA gene sequencing will be used to track changes in methanotrophic bacteria and the overall microbial community as methane was consumed.

  20. Preliminary Engineering Report contaminated groundwater seeps 317/319/ENE area

    SciTech Connect

    1996-10-01

    When the Resource Conservation and Recovery Act Facility Investigation (RFI) in the 317/319/ENE Area of Argonne National Laboratory-East (ANL-E) was being completed, groundwater was discovered moving to the surface through a series of seeps. The seeps are located approximately 600 ft south of the ANL fence line in Waterfall Glen Forest Preserve. Samples of this water were collected and analyzed for selected parameters. Two of five seeps sampled were found to contain detectable levels of organic contaminants. Three chemical species were identified: chloroform (14-25 {mu}g/L), carbon tetrachloride (56-340 {mu}g/L), and tetrachloroethylene (3-6 {mu}g/L). The other seeps did not contain detectable levels of volatile organic compounds (VOCs). The water issuing from these two contaminated seeps flows into a narrow ravine, where it is visible as a trickle of water flowing through sand and gravel deposits on the floor of the ravine. Approximately 100-ft downstream of the seep area, the contaminated water is no longer visible, having drained back into the soil in the bed of the ravine. Figure 1 shows the location of the 317/319/ENE Area in relation to the ANL-E site and the Waterfall Glen Forest Preserve.

  1. Reverse transcriptase directs viral evolution in a deep ocean methane seep

    NASA Astrophysics Data System (ADS)

    Paul, B. G.; Bagby, S. C.

    2013-12-01

    Deep ocean methane seeps are sites of intense microbial activity, with complex communities fueled by aerobic and anaerobic methanotrophy. Methane consumption in these communities has a substantial impact on the global carbon cycle, yet little is known about their evolutionary history or their likely evolutionary trajectories in a warming ocean. As in other marine systems, viral predation and virally mediated horizontal gene transfer are expected to be major drivers of evolutionary change in these communities; however, the host cells' resistance to cultivation has impeded direct study of the viral population. We conducted a metagenomic study of viruses in the anoxic sediments of a deep methane seep in the Santa Monica Basin in the Southern California Bight. We retrieved 1660 partial viral genomes, tentatively assigning 1232 to bacterial hosts and 428 to archaea. One abundant viral genome, likely hosted by Clostridia species present in the sediment, was found to encode a diversity-generating retroelement (DGR), a module for reverse transcriptase-mediated directed mutagenesis of a distal tail fiber protein. While DGRs have previously been described in the viruses of human pathogens, where diversification of viral tail fibers permits infection of a range of host cell types, to our knowledge this is the first description of such an element in a marine virus. By providing a mechanism for massively broadening potential host range, the presence of DGRs in these systems may have a major impact on the prevalence of virally mediated horizontal gene transfer, and even on the phylogenetic distances across which genes are moved.

  2. Evidences of the Presence of Methane Seeps in the Colombian Caribbean Sea

    NASA Astrophysics Data System (ADS)

    Gracia, Adriana; Rangel-Buitrago, Nelson; Sellanes, Javier

    2010-05-01

    For the first time in the southern Caribbean Sea Margin of Colombia (between 450 - 700 m deep) we confirm the presence of methane seep communities near the deltas of the Magdalena and Sinu rivers. Some evidences of the occurrence of those communities include: i) bivalves constituents of marine chemosynthesis-based communities, which are indicators of reducing environments as vesicomyid and lucinid bivalves (Vesicomya caribbea, Calyptogena ponderosa, Ectenagena modioliforma, Lucinoma spp. and Graecina colombiensis), together with the rare solemyid clam Acharax caribbaea, ii) other seep-associated fauna such as the trochid snail Cataegis meroglypta, iii) the first report of vestimentiferan tubeworms for the area and, iv) the presence of authigenic carbonates; these constructions form hard substrates colonized by sessile fauna. Additionally, more than 20 species of benthic non-seep fauna were found associated in the area. The collected fauna exhibits an elevated taxonomic similarity to other modern and fossil seep communities from the Caribbean (Barbados Prism, Gulf of Mexico, Cenozoic seep taxa from Barbados, Trinidad and Venezuela). The presence of these chemosymbiotic species seems to be related to mud diapirism activity in the South West of the Colombian coast, this geologic characteristic indicates tectonic and depositional processes associated with the aforementioned deltas. Further research is necessary to establish biological and geological interactions, geochemical and geophysical controls, and organization of cold seeps communities in this unexplored area of the Caribbean. Keywords: Methane, Chemosynthesis-based communities,Bivalves, Mud diapirs, Colombian Caribbean Sea

  3. Active Venting Sites On The Gas-Hydrate-Bearing Hikurangi Margin, Off New Zealand: ROV Measurements And Observations

    NASA Astrophysics Data System (ADS)

    Naudts, L.; Poort, J.; Boone, D.; Linke, P.; Greinert, J.; de Batist, M.; Henriet, J.

    2007-12-01

    During R.V. Sonne cruise SO191-3, part of the "New (Zealand Cold) Vents" expedition, RCMG deployed a CHEROKEE ROV "Genesis" on the Hikurangi Margin. This accretionary margin, on the east coast of New Zealand, is related to the subduction of the Pacific Plate under the Australian Plate. Several cold vent locations as well as an extensive BSR, indicating the presence of gas hydrates, have been found at this margin. The aims of the ROV-work were to precisely localize active methane vents, to conduct detailed visual observations of the vent structures and activity, and to perform measurements of physical properties and collect samples at and around the vent locations. The three investigated areas generally have a flat to moderate undulating sea floor with soft sediments alternating with carbonate platforms. The different sites were sometimes covered with dense fields of live clams or shell debris, often in association with tube worms, sponges and/or soft tissue corals. Active bubble- releasing seeps were observed at Faure's site and LM-3 site. Bubble-releasing activity was very variable in time, with periods of almost non-activity alternating with periods of violent outbursts. Bubble release occurred mainly from prominent depressions in soft-sediment sea floor. Bottom-water sampling revealed sometimes high concentrations of methane. Sediment-temperature measurements were largely comparable with the bottom- water temperature except for a "raindrop site" (with dense populations of polychaetes), where anomalous low sediment-temperature was measured. Further analysis of the ROV data together with the integration of other datasets will enable us to produce a model characterizing seep structure and environment.

  4. Physical basis of coastal productivity: The SEEP and MASAR experiments

    NASA Astrophysics Data System (ADS)

    Csanady, G. T.

    Two major cooperative experiments, code-named Shelf Edge Exchange Processes (SEEP) I and II, were carried out on the northeast U.S. continental shelf and slope by an interdisciplinary group of scientists in the past decade. The work, supported by the Department of Energy, Office of Health and Environmental Research, had the broad aim of determining whether or to what extent energy-related human activities interfere with the high biological productivity of coastal waters. Much of SEEP I work was reported in a dedicated issue of Continental Shelf Research, including a summary article on the experiment as a whole [Walsh et al., 1988[. A parallel experiment, supported by the Minerals Management Service and code-named Mid Atlantic Slope and Rise (MASAR), had the objective of exploring physical processes over the continental slope and rise, including especially currents in the upper part of the water column. A good deal of MASAR work was also reported in the SEEP issue just mentioned, mainly in an article by Csanady and Hamilton (1988). There have been other papers and publications on these experiments, and more are forthcoming. While many questions remain, our horizons have broadened considerably after a decade of work on this problem, as if our aeroplane had just emerged from clouds to expose an interesting landscape. In this article I shall try to describe the physical (-oceanographic) features of that landscape, not in the chronological order in which we have espied them, but as the logic of the subject dictates.

  5. Significance of aragonite cements around Cretaceous marine methane seeps

    SciTech Connect

    Savard, M.M.; Beauchamp, B.; Veizer, J.

    1996-05-01

    Detailed petrography and geochemistry of carbonate precipitates in Cretaceous cold seep mounds from the Canadian Arctic show spectacular early diagenetic products: some still-preserved splays and isopachous layers of fine, acicular aragonite, and large botryoids and crusts of low-magnesium calcite showing unusual entanglement of former fibrous calcite and aragonite. The latter mineralogy is suggested by clear, flat-terminated cathodoluminescence patterns interpreted as ancient crystal growth steps, and the former by rhombohedral terminations. The early cement phases very likely precipitated in cold Arctic water dominated by bicarbonates derived from bacterially oxidized methane: these cements have {delta}{sup 13}C values around {minus}44.0% and {delta}{sup 18}O values of 1.8 to 0.1% PDB. Coexistence of calcite and aragonite early cements in the Cretaceous seep mounds is unusual, because precipitation occurred in high-latitude, cold-water settings, and during a so-called calcite sea mode. As in modern marine hydrocarbon seeps, the chemistry of the Cretaceous system was apparently controlled by chemosynthetic bacterial activity, resulting in high a{sub HCO{sub 3}{sup {minus}}} that promoted precipitation of carbonates. The authors suggest that, locally, fluctuations in a{sub HCO{sub 3}{sup {minus}}}/a{sub SO{sub 4}{sup 2{minus}}} resulted in oscillating aragonite or calcite supersaturation, and hence, controlled the mineralogy of the early precipitates.

  6. Seep Carbonates From Tubeworm- and Mussel-Associated Environments at Atwater Valley, Northern Gulf of Mexico

    NASA Astrophysics Data System (ADS)

    Feng, D.; Roberts, H. H.; Chen, D.

    2008-12-01

    During 2006 and 2007, MMS and NOAA jointly supported cruises where fifteen hydrocarbon seep sites at greater than 1000 m water depth on the lower Louisiana slope in the Gulf of Mexico (GOM) were explored. These sites contain numerous authigenic carbonates as well as high-density communities of tubeworms and mussels. However, the integrated petrographic and geochemical characterization of the tubeworm- and mussel-associated carbonates remains poorly known. Here, a comparative study of petrographic and geochemical features of the carbonate samples from tubeworm- and mussel- associated environments was approached for an active and complex seep site at Atwater Valley lease block 340 (AT 340) at 2200 m water depth in the GOM. The carbonate morphologies include concretion, blocky and massive carbonates up to several meters in size, and irregularly shaped carbonates, some of them are displaying high porosity. Some are highly brecciaed with aragonite layers of varying thicknesses lining fractures and voids. Lithologically, the carbonates are microcrystalline Mg-calcite, calcite and aragonite containing peloids, clasts and shell fragments. The carbon isotopic composition of carbonates varies narrowly, ranging from -46.45 ‰ to - 60.81 ‰, indicating 13C-depleted carbon source probably methane of microbial origin. But the common trend is that the tubeworm-associated carbonates have more depleted δ13C values when compared to mussel-associated carbonates. A similarly small variability of δ18O values (+3.12 ‰ to +5.09 ‰) demonstrates the temperature and/or fluid composition did not change greatly during carbonate. The total content of rare earth elements (REE) of the 5% HNO3-treated solution of the carbonates is from 6.54 ppm to 29.41 ppm. The shale-normalized REE patterns show slightly positive Ce anomalies, suggests that the carbonates precipitated under anoxic conditions. The possible factors (i.e. habitat of chemosynthetic animals, depth of carbonate precipitation

  7. Catalysis: Elusive active site in focus

    NASA Astrophysics Data System (ADS)

    Labinger, Jay A.

    2016-08-01

    The identification of the active site of an iron-containing catalyst raises hopes of designing practically useful catalysts for the room-temperature conversion of methane to methanol, a potential fuel for vehicles. See Letter p.317

  8. Biogeography and Potential Exchanges Among the Atlantic Equatorial Belt Cold-Seep Faunas

    PubMed Central

    Olu, Karine; Cordes, Erik E.; Fisher, Charles R.; Brooks, James M.; Sibuet, Myriam; Desbruyères, Daniel

    2010-01-01

    Like hydrothermal vents along oceanic ridges, cold seeps are patchy and isolated ecosystems along continental margins, extending from bathyal to abyssal depths. The Atlantic Equatorial Belt (AEB), from the Gulf of Mexico to the Gulf of Guinea, was one focus of the Census of Marine Life ChEss (Chemosynthetic Ecosystems) program to study biogeography of seep and vent fauna. We present a review and analysis of collections from five seep regions along the AEB: the Gulf of Mexico where extensive faunal sampling has been conducted from 400 to 3300m, the Barbados accretionary prism, the Blake ridge diapir, and in the Eastern Atlantic from the Congo and Gabon margins and the recently explored Nigeria margin. Of the 72 taxa identified at the species level, a total of 9 species or species complexes are identified as amphi-Atlantic. Similarity analyses based on both Bray Curtis and Hellinger distances among 9 faunal collections, and principal component analysis based on presence/absence of megafauna species at these sites, suggest that within the AEB seep megafauna community structure is influenced primarily by depth rather than by geographic distance. Depth segregation is observed between 1000 and 2000m, with the middle slope sites either grouped with those deeper than 2000m or with the shallower sites. The highest level of community similarity was found between the seeps of the Florida escarpment and Congo margin. In the western Atlantic, the highest degree of similarity is observed between the shallowest sites of the Barbados prism and of the Louisiana slope. The high number of amphi-atlantic cold-seep species that do not cluster according to biogeographic regions, and the importance of depth in structuring AEB cold-seep communities are the major conclusions of this study. The hydrothermal vent sites along the Mid Atlantic Ridge (MAR) did not appear as “stepping stones” for dispersal of the AEB seep fauna, however, the south MAR and off axis regions should be further

  9. Biogeography and potential exchanges among the atlantic Equatorial belt cold-seep faunas.

    PubMed

    Olu, Karine; Cordes, Erik E; Fisher, Charles R; Brooks, James M; Sibuet, Myriam; Desbruyères, Daniel

    2010-08-05

    Like hydrothermal vents along oceanic ridges, cold seeps are patchy and isolated ecosystems along continental margins, extending from bathyal to abyssal depths. The Atlantic Equatorial Belt (AEB), from the Gulf of Mexico to the Gulf of Guinea, was one focus of the Census of Marine Life ChEss (Chemosynthetic Ecosystems) program to study biogeography of seep and vent fauna. We present a review and analysis of collections from five seep regions along the AEB: the Gulf of Mexico where extensive faunal sampling has been conducted from 400 to 3300 m, the Barbados accretionary prism, the Blake ridge diapir, and in the Eastern Atlantic from the Congo and Gabon margins and the recently explored Nigeria margin. Of the 72 taxa identified at the species level, a total of 9 species or species complexes are identified as amphi-Atlantic. Similarity analyses based on both Bray Curtis and Hellinger distances among 9 faunal collections, and principal component analysis based on presence/absence of megafauna species at these sites, suggest that within the AEB seep megafauna community structure is influenced primarily by depth rather than by geographic distance. Depth segregation is observed between 1000 and 2000 m, with the middle slope sites either grouped with those deeper than 2000 m or with the shallower sites. The highest level of community similarity was found between the seeps of the Florida escarpment and Congo margin. In the western Atlantic, the highest degree of similarity is observed between the shallowest sites of the Barbados prism and of the Louisiana slope. The high number of amphi-atlantic cold-seep species that do not cluster according to biogeographic regions, and the importance of depth in structuring AEB cold-seep communities are the major conclusions of this study. The hydrothermal vent sites along the Mid Atlantic Ridge (MAR) did not appear as "stepping stones" for dispersal of the AEB seep fauna, however, the south MAR and off axis regions should be further

  10. Detection of Natural Oil Seeps in the Atlantic Ocean Using MODIS

    NASA Technical Reports Server (NTRS)

    Reahard, Ross; Jones, Jason B.; Mitchell, Mark

    2010-01-01

    Natural oil seepage is the release of crude oil into the ocean from fissures in the seabed. Oil seepage is a major contributor to the total amount of oil entering the world s oceans. According to a 2003 study by the National Academy of Sciences (NAS), 47 percent of oil entering the world s oceans is from natural seeps, and 53 percent is from human sources (extraction, transportation, and consumption). Oil seeps cause smooth oil slicks to form on the water s surface. Oil seeps can indicate the location of stores of fossil fuel beneath the ocean floor. Knowledge of the effect of oil seepage on marine life and marine ecosystems remains limited. In the past, remote sensing has been used to detect oil seeps in the Gulf of Mexico and off of the coast of southern California. This project utilized sun glint MODIS imagery to locate oil slicks off of the Atlantic coast, an area that had not previously been surveyed for natural oil seeps using remote sensing. Since 1982, the Atlantic Ocean has been closed to any oil and gas drilling. Recently, however, the U.S. Minerals Management Services (MMS) has proposed a lease for oil and gas drilling off the coasts of Virginia and North Carolina. Determining the location of seepage sites in the Atlantic Ocean will help MMS locate potential deposits of oil and natural gas, thereby reducing the risk of leasing areas for petroleum extraction that do not contain these natural resources.

  11. Hydrocarbon geochemistry of cold seeps in the Monterey Bay National Marine Sanctuary

    USGS Publications Warehouse

    Lorenson, T.D.; Kvenvolden, K.A.; Hostettler, F.D.; Rosenbauer, R.J.; Orange, D.L.; Martin, J.B.

    2002-01-01

    Samples from four geographically and tectonically discrete cold seeps named Clam Flat, Clamfield, Horseshoe Scarp South, and Tubeworm City, within the Monterey Bay National Marine Sanctuary were analyzed for their hydrocarbon content. The sediment contains gaseous hydrocarbons and CO2, as well as high molecular weight aliphatic and aromatic hydrocarbons with various combinations of thermogenic and biogenic contributions from petroleum, marine, and terrigenous sources. Of particular interest is the cold seep site at Clamfield which is characterized by the presence of thermogenic hydrocarbons including oil that can likely be correlated with oil-saturated strata at Majors Creek near Davenport, CA, USA. At Clam Flat, the evidence for thermogenic hydrocarbons is equivocal. At Horseshoe Scarp South and Tubeworm City, hydrocarbon gases, mainly methane, are likely microbial in origin. These varied sources of hydrocarbon gases highlight the diverse chemical systems that appear at cold seep communities. ?? 2002 Elsevier Science B.V. All rights reserved.

  12. Diverse sulfate-reducing bacteria of the Desulfosarcina/Desulfococcus clade are the key alkane degraders at marine seeps.

    PubMed

    Kleindienst, Sara; Herbst, Florian-Alexander; Stagars, Marion; von Netzer, Frederick; von Bergen, Martin; Seifert, Jana; Peplies, Jörg; Amann, Rudolf; Musat, Florin; Lueders, Tillmann; Knittel, Katrin

    2014-10-01

    Biogeochemical and microbiological data indicate that the anaerobic oxidation of non-methane hydrocarbons by sulfate-reducing bacteria (SRB) has an important role in carbon and sulfur cycling at marine seeps. Yet, little is known about the bacterial hydrocarbon degraders active in situ. Here, we provide the link between previous biogeochemical measurements and the cultivation of degraders by direct identification of SRB responsible for butane and dodecane degradation in complex on-site microbiota. Two contrasting seep sediments from Mediterranean Amon mud volcano and Guaymas Basin (Gulf of California) were incubated with (13)C-labeled butane or dodecane under sulfate-reducing conditions and analyzed via complementary stable isotope probing (SIP) techniques. Using DNA- and rRNA-SIP, we identified four specialized clades of alkane oxidizers within Desulfobacteraceae to be distinctively active in oxidation of short- and long-chain alkanes. All clades belong to the Desulfosarcina/Desulfococcus (DSS) clade, substantiating the crucial role of these bacteria in anaerobic hydrocarbon degradation at marine seeps. The identification of key enzymes of anaerobic alkane degradation, subsequent β-oxidation and the reverse Wood-Ljungdahl pathway for complete substrate oxidation by protein-SIP further corroborated the importance of the DSS clade and indicated that biochemical pathways, analog to those discovered in the laboratory, are of great relevance for natural settings. The high diversity within identified subclades together with their capability to initiate alkane degradation and growth within days to weeks after substrate amendment suggest an overlooked potential of marine benthic microbiota to react to natural changes in seepage, as well as to massive hydrocarbon input, for example, as encountered during anthropogenic oil spills.

  13. Diverse sulfate-reducing bacteria of the Desulfosarcina/Desulfococcus clade are the key alkane degraders at marine seeps

    PubMed Central

    Kleindienst, Sara; Herbst, Florian-Alexander; Stagars, Marion; von Netzer, Frederick; von Bergen, Martin; Seifert, Jana; Peplies, Jörg; Amann, Rudolf; Musat, Florin; Lueders, Tillmann; Knittel, Katrin

    2014-01-01

    Biogeochemical and microbiological data indicate that the anaerobic oxidation of non-methane hydrocarbons by sulfate-reducing bacteria (SRB) has an important role in carbon and sulfur cycling at marine seeps. Yet, little is known about the bacterial hydrocarbon degraders active in situ. Here, we provide the link between previous biogeochemical measurements and the cultivation of degraders by direct identification of SRB responsible for butane and dodecane degradation in complex on-site microbiota. Two contrasting seep sediments from Mediterranean Amon mud volcano and Guaymas Basin (Gulf of California) were incubated with 13C-labeled butane or dodecane under sulfate-reducing conditions and analyzed via complementary stable isotope probing (SIP) techniques. Using DNA- and rRNA-SIP, we identified four specialized clades of alkane oxidizers within Desulfobacteraceae to be distinctively active in oxidation of short- and long-chain alkanes. All clades belong to the Desulfosarcina/Desulfococcus (DSS) clade, substantiating the crucial role of these bacteria in anaerobic hydrocarbon degradation at marine seeps. The identification of key enzymes of anaerobic alkane degradation, subsequent β-oxidation and the reverse Wood–Ljungdahl pathway for complete substrate oxidation by protein-SIP further corroborated the importance of the DSS clade and indicated that biochemical pathways, analog to those discovered in the laboratory, are of great relevance for natural settings. The high diversity within identified subclades together with their capability to initiate alkane degradation and growth within days to weeks after substrate amendment suggest an overlooked potential of marine benthic microbiota to react to natural changes in seepage, as well as to massive hydrocarbon input, for example, as encountered during anthropogenic oil spills. PMID:24722631

  14. Marine cold seeps and their manifestations: geological control, biogeochemical criteria and environmental conditions

    NASA Astrophysics Data System (ADS)

    Suess, Erwin

    2014-10-01

    Characteristics of cold seeps at different geologic settings are the subject of this review primarily based on results of the Research Consortium SFB 574. Criteria are drawn from examples on the erosive convergent margin off Costa Rica, the accretionary margin off Chile supplemented by examples from the transform margin of the Golf of Cadiz and the convergent Hikurangi margin off New Zealand. Others are from well-studied passive margins of the Black Sea, the Golf of Mexico, the eastern Mediterranean Sea and the South China Sea. Seeps at all settings transport water and dissolved compounds to the ocean through the seafloor by different forcing mechanism and from different depths of the submerged geosphere (10s of meters to 10s of km). The compounds sustain oasis-type ecosystems by providing bioactive reductants sulfide, methane and hydrogen. Hereby, the interaction between fluid composition, flux rates and biota results in a diagnostic hydrocarbon-metazoan-microbe-carbonate association; currently, well over 100 active sites are known. The single most important reaction is microbially mediated anaerobic oxidation of methane with secondary reactions involving S-biogeochemistry and carbonate mineral precipitation. Seep fluids and their seafloor manifestations provide clues as to source depth, fluid-sediment/rock interaction during ascent, lifetime and cyclicity of seepage events but less so on the magnitude of return flow. At erosive margins, Cl-depleted and B-enriched fluids from clay dehydration provide criteria for source depth and temperature. The upward material flow generates mud volcanoes at the seafloor above the projected location of dehydration at depth. At accretionary margins, fluids are derived from more shallow depths by compaction of sediments as they ride on the incoming oceanic plate; they are emitted through thrust faults. At highly sedimented margins, organic-rich and evaporite-containing strata (when present) determine the final fluid composition

  15. Comparison of Two Techniques to Calculate Methane Oxidation rates in Samples Obtained From the Hudson Canyon Seep Field in the North Atlantic

    NASA Astrophysics Data System (ADS)

    Leonte, M.; Kessler, J. D.; Chepigin, A.; Kellermann, M. Y.; Arrington, E.; Valentine, D. L.; Sylva, S.

    2014-12-01

    Aerobic methane oxidation, or methanotrophy, is the dominant process by which methane is removed from the water column in oceanic environments. Therefore, accurately quantifying methane oxidation rates is crucial when constructing methane budgets on a local or global scale. Here we present a comparison of two techniques used to determine methane oxidation rates based on samples obtained over the Hudson Canyon seep field in the North Atlantic. Traditional methane oxidation rate measurements require inoculation of water samples with isotopically labeled methane and tracking the changes to methane concentrations and isotopes as the samples are incubated. However, the addition of methane above background levels is thought to increase the potential for methane oxidation in the sample. A new technique to calculate methane oxidation rates is based on kinetic isotope models and incorporates direct measurements of methane concentrations, methane 13C isotopes, and water current velocity. Acoustic instrumentation (ADCP) aboard the R/V Endeavor was used to obtain water current velocity data while water samples were collected for methane concentration and isotopic ratio analysis. Methane δ13C measurements allow us to attribute changes in methane concentration to either water dispersion or bacterial methane oxidation. The data obtained from this cruise will tell us a comprehensive story of methane removal processes from this active seep field. The kinetic isotope models will allow us to estimate the total flux of methane from the seep site and calculate methane oxidation rates at different depths and locations away from seafloor plumes.

  16. Seeps and springs sampling and analysis plant for the Environmental Monitoring Plan at Waste Area Grouping 6, Oak Ridge National Laboratory, Oak Ridge, Tennessee

    SciTech Connect

    1995-09-01

    This Sampling and Analysis Plan addresses the monitoring, sampling, and analysis activities that will be conducted at seeps and springs and at two french drain outlets in support of the Environmental Monitoring Plan for Waste Area Grouping (WAG) 6. WAG 6 is a shallow-land-burial disposal facility for low-level radioactive waste at Oak Ridge National Laboratory, a research facility owned by the U.S. Department of Energy and operated by Lockheed Martin Energy System, Inc. Initially, sampling will be conducted at as many as 15 locations within WAG 6 (as many as 13 seeps and 2 french drain outlets). After evaluating the results obtained and reviewing the observations made by field personnel during the first round of sampling, several seeps and springs will be chosen as permanent monitoring points, together with the two french drain outlets. Baseline sampling of these points will then be conducted quarterly for 1 year (i.e., four rounds of sampling after the initial round). The samples will be analyzed for various geochemical, organic, inorganic, and radiological parameters. Permanent sampling points having suitable flow rates and conditions may be outfitted with automatic flow-monitoring equipment. The results of the sampling and flow-monitoring efforts will help to quantify flux moving across the ungauged perimeter of the site and will help to identify changes in releases from the contaminant sources.

  17. Seeps and springs sampling and analysis plan for the environmental monitoring plan for Waste Area Grouping 6 at Oak Ridge National Laboratory, Oak Ridge, Tennessee

    SciTech Connect

    Not Available

    1994-08-01

    This Sampling and Analysis Plan addresses the monitoring, sampling, and analysis activities that will be conducted at seeps and springs and at two french drain outlets in support of the Environmental Monitoring Plan for Waste Area Grouping (WAG) 6. WAG 6 is a shallow-land-burial disposal facility for low-level radioactive waste at Oak Ridge National Laboratory, a research facility owned by the US Department of Energy and operated by Martin Marietta Energy Systems, Inc. Initially, sampling will be conducted at as many as 15 locations within WAG 6 (as many as 13 seeps and 2 french drain outlets). After evaluating the results obtained and reviewing the observations made by field personnel during the first round of sampling, several seeps and springs will be chosen as permanent monitoring points, together with the two french drain outlets. Baseline sampling of these points will then be conducted quarterly for 1 year (i.e., four rounds of sampling after the initial round). The samples will be analyzed for various geochemical, organic, inorganic, and radiological parameters. Permanent sampling points having suitable flow rates and conditions may be outfitted with automatic flow-monitoring equipment. The results of the sampling and flow-monitoring efforts will help to quantify flux moving across the ungauged perimeter of the site and will help to identify changes in releases from the contaminant sources.

  18. Influence of parasitism in controlling the health, reproduction and PAH body burden of petroleum seep mussels

    NASA Astrophysics Data System (ADS)

    Powell, Eric N.; Barber, Robert D.; Kennicutt, Mahlon C., II; Ford, Susan E.

    1999-12-01

    Petroleum seep mussels are often exposed to high hydrocarbon concentrations in their natural habitat and, thus, offer the opportunity to examine the relationship between parasitism, disease and contaminant exposure under natural conditions. This is the first report on the histopathology of cold-seep mussels. Seep mussels were collected by submersible from four primary sites in the Gulf of Mexico, lease blocks Green Canyon (GC) 184, GC-234, GC-233, and Garden Banks 425 in 550-650 m water depth. Five types of parasites were identified in section: (1) gill "rosettes" of unknown affinity associated with the gill bacteriocytes, (2) gill "inclusions" similar to chlamydia/rickettsia inclusions, (3) extracellular gill ciliates, (4) body "inclusions" that also resemble chlamydial/rickettsial inclusions, and (5) Bucephalus-like trematodes. Comparison to shallow-water mytilids demonstrates that: (1) both have similar parasite faunas; (2) seep mytilids are relatively heavily parasitized; and (3) infection intensities are extremely high in comparison to shallow-water mytilids for Bucephalus and chlamydia/rickettsia. In this study, the lowest prevalence for chlamydia/rickettsia was 67%. Prevalences of 100% were recorded from three populations. Bucephalus prevalence was ⩾70% in three of 10 populations. The parasite fauna was highly variable between populations. Some important parasites were not observed in some primary sites. Even within primary sites, some important parasites were not observed in some populations. Bucephalus may exert a significant influence on seep mussel population dynamics. Forty percent of the populations in this study are severely reproductively compromised by Bucephalus infection. Only a fraction of petroleum seep mussel populations are maintaining the entire beta-level population structure of this species. Variation in two parasites, gill ciliates and Bucephalus, explained most of the variation in PAH body burden between mussel populations. PAHs are

  19. Low dielectric response in enzyme active site

    PubMed Central

    Mertz, Edward L.; Krishtalik, Lev I.

    2000-01-01

    The kinetics of charge transfer depend crucially on the dielectric reorganization of the medium. In enzymatic reactions that involve charge transfer, atomic dielectric response of the active site and of its surroundings determines the efficiency of the protein as a catalyst. We report direct spectroscopic measurements of the reorganization energy associated with the dielectric response in the active site of α-chymotrypsin. A chromophoric inhibitor of the enzyme is used as a spectroscopic probe. We find that water strongly affects the dielectric reorganization in the active site of the enzyme in solution. The reorganization energy of the protein matrix in the vicinity of the active site is similar to that of low-polarity solvents. Surprisingly, water exhibits an anomalously high dielectric response that cannot be described in terms of the dielectric continuum theory. As a result, sequestering the active site from the aqueous environment inside low-dielectric enzyme body dramatically reduces the dielectric reorganization. This reduction is particularly important for controlling the rate of enzymatic reactions. PMID:10681440

  20. Field Exploration of Methane Seep Near Atqasuk

    SciTech Connect

    Katey Walter, Dennis Witmer, Gwen Holdmann

    2008-12-31

    Methane (CH{sub 4}) in natural gas is a major energy source in the U.S., and is used extensively on Alaska's North Slope, including the oilfields in Prudhoe Bay, the community of Barrow, and the National Petroleum Reserve, Alaska (NPRA). Smaller villages, however, are dependent on imported diesel fuel for both power and heating, resulting in some of the highest energy costs in the U.S. and crippling local economies. Numerous CH{sub 4} gas seeps have been observed on wetlands near Atqasuk, Alaska (in the NPRA), and initial measurements have indicated flow rates of 3,000-5,000 ft{sup 3} day{sup -1} (60-100 kg CH{sub 4} day{sup -1}). Gas samples collected in 1996 indicated biogenic origin, although more recent sampling indicated a mixture of biogenic and thermogenic gas. In this study, we (1) quantified the amount of CH{sub 4} generated by several seeps and evaluated their potential use as an unconventional gas source for the village of Atqasuk; (2) collected gas and analyzed its composition from multiple seeps several miles apart to see if the source is the same, or if gas is being generated locally from isolated biogenic sources; and (3) assessed the potential magnitude of natural CH{sub 4} gas seeps for future use in climate change modeling.

  1. Infaunal and megafaunal benthic community structure associated with cold seeps at the Vestnesa Ridge (79 N°)

    NASA Astrophysics Data System (ADS)

    Åström, Emmelie K. L.; Carroll, Michael L.; Sen, Arunima; Ambrose, William G., Jr.; Silyakova, Anna; Carroll, JoLynn

    2016-04-01

    Cold seeps are locations where hydrocarbons, sulfide or reduced compounds emanate from the seafloor, which may fuel chemoautotrophic production and form additional hard bottom substrate through carbonate precipitation. Chemosynthetic symbiosis, trophic interactions, and additional bottom substrate types can provide a heterogeneous environment for deep-sea organisms supporting macrofaunal communities including increased biodiversity and biomass. We combined quantitative benthic faunal samples with sea floor photographs from an active, methane seeping pockmark at Vestnesa Ridge (1200 meters depth) to examine community structure and biodiversity in a high Arctic deep cold seep. Quantitative data were compared with samples from the nearby inactive Svyatogor Ridge (1577-1706 meters depth). We measured highly elevated methane concentrations (up to 100x background levels) in the sediment at Vestnesa Ridge. Faunal abundance, species richness and biomass were significantly higher at the Vestnesa pockmark compared to inactive Svyatogor Ridge. Seabed photos from Vestnesa Ridge reveal high megafaunal diversity and biomass and cold seep features including carbonate crust and microbial mats. Our observations indicate that chemoautotrophic production enhances deep-sea biomass and diversity at Vestnesa Ridge. The focused methane emissions create a heterogeneous deep-sea habitat for chemo-associated organisms coexisting with heterotrophic conventional fauna in a high Arctic seep. Keywords: Arctic, benthic ecology, biodiversity, chemosynthesis, methane

  2. Colonization of over a thousand Cibicidoides wuellerstorfi (foraminifera: Schwager, 1866) on artificial substrates in seep and adjacent off-seep locations in dysoxic, deep-sea environments

    NASA Astrophysics Data System (ADS)

    Burkett, Ashley M.; Rathburn, Anthony E.; Elena Pérez, M.; Levin, Lisa A.; Martin, Jonathan B.

    2016-11-01

    After ~1 yr on the seafloor at water depths of ~700 m on Hydrate Ridge in the Pacific, eight colonization experiments composed primarily of a plastic mesh cube (from here on refered to as SEA3, for Seafloor Epibenthic Attachment Cubes) were colonized by 1076 Cibicidoides wuellerstorfi on ~1841 cm2 of experimental substrate. This species is typically considered an indicator of well-oxygenated conditions, and recruitment of such large numbers in bottom waters with low dissolved oxygen availability (0.24-0.37 mL/L) indicate that this taxon may not be as limited by oxygen as previously thought. Clues about substrate preferences were evident from the distribution, or lack thereof, of individuals among plastic mesh, coated steel frame, wooden dowels and reflective tape. Abundance, individual size distributions within cage populations and isotopic biogeochemistry of living foraminifera colonizing experimental substrates were compared between active seep and adjacent off-seep experiment locations, revealing potential differences between these environments. Few studies have examined foraminiferal colonization of hard substrates in the deep-sea and to our knowledge no previous study has compared foraminiferal colonization of active seep and off-seep substrates from the same region. This study provides initial results of recruitment, colonization, geochemical and morphological aspects of the paleoceanographically significant species, C. wuellerstorfi, from dynamic deep-sea environments. Further experimental deployments of SEA3s will provide a means to assess relatively unknown ecologic dynamics of important foraminiferal deep-sea species.

  3. Waste Area Grouping 2 Remedial Investigation Phase 1 Seep Task data report: Contaminant source area assessment

    SciTech Connect

    Hicks, D.S.

    1996-03-01

    This report presents the findings of the Waste Area Grouping (WAG) 2, Phase 1 Remedial Investigation (RI) Seep Task efforts during 1993 and 1994 at Oak Ridge National Laboratory (ORNL). The results presented here follow results form the first year of sampling, 1992, which are contained in the Phase 1 RI report for WAG 2 (DOE 1995a). The WAG 2 Seep Task efforts focused on contaminants in seeps, tributaries, and main streams within the White Oak Creek (WOC) watershed. This report is designed primarily as a reference for contaminants and a resource for guiding remedial decisions. Additional in-depth assessments of the Seep Task data may provide clearer understandings of contaminant transport from the different source areas in the WOC watershed. WAG 2 consists of WOC and its tributaries downstream of the ORNL main plant area, White Oak Lake, the White Oak Creek Embayment of the Clinch River, and the associated flood plains and subsurface environment. The WOC watershed encompasses ORNL and associated WAGs. WAG 2 acts as an integrator for contaminant releases from the contaminated sites at ORNL and as the conduit transporting contaminants to the Clinch River. The main objectives of the Seep Task were to identify and characterize seeps, tributaries and source areas that are responsible for the contaminant releases to the main streams in WAG 2 and to quantify their input to the total contaminant release from the watershed at White Oak Dam (WOD). Efforts focused on {sup 90}Sr, {sup 3}H, and {sup 137}Cs because these contaminants pose the greatest potential human health risk from water ingestion at WOD. Bimonthly sampling was conducted throughout the WOC watershed beginning in March 1993 and ending in August 1994. Samples were also collected for metals, anions, alkalinity, organics, and other radionuclides.

  4. Laboratory investigation of a passive acoustic method for measurement of underwater gas seep ebullition.

    PubMed

    Greene, Chad A; Wilson, Preston S

    2012-01-01

    Passive acoustic techniques are of interest as a low-power means of quantifying underwater point-source gas ebullition. Toward the development of systems for logging natural seep activity, laboratory experiments were performed that exploited the bubble's Minnaert natural frequency for the measurement of gas flow from a model seep. Results show agreement among acoustic, optical, and gas trap ebullition measurements over the range of emission rates from 0 to 10 bubbles per second. A mathematical model is proposed to account for the real gas behavior of bubbles which cannot be approximated as ideal, such as methane at marine depths exceeding 30 m.

  5. Laboratory investigation of a passive acoustic method for measurement of underwater gas seep ebullition.

    PubMed

    Greene, Chad A; Wilson, Preston S

    2012-01-01

    Passive acoustic techniques are of interest as a low-power means of quantifying underwater point-source gas ebullition. Toward the development of systems for logging natural seep activity, laboratory experiments were performed that exploited the bubble's Minnaert natural frequency for the measurement of gas flow from a model seep. Results show agreement among acoustic, optical, and gas trap ebullition measurements over the range of emission rates from 0 to 10 bubbles per second. A mathematical model is proposed to account for the real gas behavior of bubbles which cannot be approximated as ideal, such as methane at marine depths exceeding 30 m. PMID:22280731

  6. Benthic Community Structure and Sediment Geochemical Properties at Hydrocarbon Seeps Along the Continental Slope of the Western North Atlantic

    NASA Astrophysics Data System (ADS)

    Demopoulos, A. W.; Bourque, J. R.; Brooke, S.

    2015-12-01

    Hydrocarbon seeps support distinct benthic communities capable of utilizing reduced chemical compounds for nutrition. In recent years, methane seepage has been increasingly documented along the continental slope of the U.S. Atlantic margin. In 2012 and 2013, two seeps were investigated in this region: a shallow site near Baltimore Canyon (410-450 m) and a deep site near Norfolk Canyon (1600 m). Both sites contain extensive mussel beds and microbial mats. Sediment cores and grab samples were collected to quantify the abundance, diversity, and community structure of benthic macrofauna (>300 mm) in relationship to the associated sediment environment (organic carbon and nitrogen, stable isotopes 13C and 15N, grain size, and depth) of mussel beds, mats, and slope habitats. Macrofaunal densities in microbial mats were four times greater than those present in mussel beds and slope sediments. Macrofaunal communities were distinctly different both between depths and among habitat types. Specifically, microbial mat sediments were dominated by the annelid families Dorvilleidae, Capitellidae, and Tubificidae, while mussel habitats had higher proportions of crustaceans. Diversity was lower in Baltimore microbial mat habitats, but higher in mussel and slope sediments compared to Norfolk seep habitats found at deeper depths. Multivariate statistical analysis identified sediment carbon:nitrogen (C:N) ratios and 13C values as important variables for structuring the macrofaunal communities. Higher C:N ratios were present within microbial mat habitats and depleted 13C values occurred in sediments adjacent to mussel beds found in Norfolk Canyon seeps. Differences in the quality and source of organic matter present in the seep habitats are known to be important drivers in macrofaunal community structure and associated food webs. The multivariate analysis provides new insight into the relative importance of the seep sediment quality in supporting dense macrofaunal communities compared

  7. Mapping cold seeps with high-resolution deep water multibeam echosounders in the Black Sea

    NASA Astrophysics Data System (ADS)

    Wintersteller, P.; dos Santos Ferreira, C.; Klaucke, I.; Ivanov, M.; Sahling, H.; Bohrmann, G.

    2011-12-01

    Cold seeps are locations at the seafloor where gas and/or fluids are emitting. In contrast to mud volcanoes, which distinctly change the seafloor morphology, cold seeps often lack significant relief. However, in comparison with surrounding sediments seep locations on the sea floor are often characterized by high acoustic backscatter intensity. This was documented during several investigations with deep towed side-scan sonar (SSS) systems in recent years. Authigenic carbonates, free gas and gas hydrates, as evidenced by ground truthing, are responsible for the high backscatter values. Last year's upgrade of the 1°x2° KONGSBERG deep water echosounder EM120 to EM122 on RV Meteor enhanced the system to almost 4 times the previous resolution due to multi-ping and high density signal processing. Based on the physics of sound propagation in the water column, multibeam echosounders (MBES) for deep water use relatively low frequencies of about 12-15 kHz. Apparently highly water-saturated sediments are penetrated by these signals and can cause artificial offsets in bottom detection in comparison to high-frequency echosounders. Nevertheless the effect of the slightly penetrating signal has a useful side effect on the backscatter. Investigations on several seep sites in the Black Sea, carried out with both EM122 and EM710 during Meteror cruise M84-2, resulted in maps of remarkable bathymetric resolution but also showed multibeam backscatter information of a 12 kHz signal to be an excellent tool to map seep-influenced seafloor areas. New seep locations have been mapped in regions of the western Turkish continental margin close to Eregli and of the eastern Turkish margin off Samsun. In both areas high backscatter patches were mapped with nearly comparable resolution as achieved by deep-tow SSS systems. At Eregli the new data is compared with data from a deep-towed EdgeTech SSS system recorded with a frequency of 75 kHz. At Samsun the results are compared with data from a MAK-1

  8. Population structure of two deep sea tubeworms, Lamellibrachia luymesi and Seepiophila jonesi, from the hydrocarbon seeps of the Gulf of Mexico

    NASA Astrophysics Data System (ADS)

    McMullin, Erin R.; Nelson, Kimberlyn; Fisher, Charles R.; Schaeffer, Stephen W.

    2010-11-01

    Vestimentiferan tubeworms are a group of large sessile marine polychaete annelids (family Siboglinidae) found in the regions of hydrothermal venting or seepage of the reduced chemical hydrogen sulfide. Hydrocarbon seeps on the Louisiana Slope of the Gulf of Mexico support large communities of the co-occurring vestimentiferan species Lamellibrachia luymesi and Seepiophila jonesi. These sessile species have the opportunity to disperse between the patchy sites of active seepage on the seafloor during a planktonic larval stage. However, it is unclear whether dispersal occurs at a local or global scale. Four ( L. luymesi) and seven ( S. jonesi) microsatellite loci were used to test for population substructure among ten hydrocarbon seep sites on the Louisiana Slope. Both species showed high levels of allelic diversity, averaging 18.5 ( L. luymesi) and 22 ( S. jonesi) alleles/locus, respectively, and high observed heterozygosity at all microsatellite loci (0.71-0.9 in L. luymesi, 0.27-0.84 in S. jonesi). The two species showed a significant deficiency in heterozygotes compared to that predicted under the Hardy-Weinberg equilibrium. L. luymesi showed a small but significant amount of population structure, with a positive correlation between genetic and geographic distance among the sample sites spanning 540 km. S. jonesi, in contrast, showed no evidence for isolation by distance, but did show a significant genetic difference between aggregations of different ages. These results suggest that these two species differ in how larvae are able to colonize new seep sites through space ( L. luymesi) and though time ( S. jonesi).

  9. Methane oxidation in permeable sediments at hydrocarbon seeps in the Santa Barbara Channel, California

    NASA Astrophysics Data System (ADS)

    Treude, T.; Ziebis, W.

    2010-03-01

    A shallow-water area in the Santa Barbara Channel (California), known collectively as the Coal Oil Point seep field, is one the largest natural submarine oil and gas emission areas in the world. Both gas and oil are seeping constantly through a predominantly sandy seabed into the ocean. This study focused on the methanotrophic activity within the surface sediments (0-15 cm) of the permeable seabed in the so-called Brian Seep area at a water depth ~10 m. Detailed investigations of biogeochemical parameters in the sediment surrounding active gas vents indicated that methane seepage through the permeable seabed induces a convective transport of fluids within the surface sediment layer, which results in a deeper penetration of oxidants (oxygen, sulfate) into the sediment, as well as in a faster removal of potentially inhibiting reduced end products (e.g. hydrogen sulfide). Methanotrophic activity was often found close to the sediment-water interface, indicating the involvement of aerobic bacteria. However, biogeochemical data suggests that the majority of methane is consumed by anaerobic oxidation of methane (AOM) coupled to sulfate reduction below the surface layer (>15 cm), where sulfate is still available in high concentrations. This subsurface maximum of AOM activity in permeable sands is in contrast to known deep-sea seep habitats, where upward fluid advection through more fine-grained sediments leads to an accumulation of AOM activity within the top 10 cm of the sediments, because sulfate is rapidly depleted.

  10. Establishing criteria to distinguish oil- from methane-seep carbonates

    NASA Astrophysics Data System (ADS)

    Smrzka, Daniel; Zwicker, Jennifer; Bach, Wolfgang; Bohrmann, Gerhard; Peckmann, Jörn

    2016-04-01

    Hydrocarbon seeps harbor biota depending on chemosynthesis that is preserved in the fossil record as part of authigenic carbonate deposits. Seep environments are characterized by emanation of methane-rich fluids, yet an increasing number of seeps have been discovered in recent years that are typified by seepage of crude oil. Fluid composition is an important factor governing the composition and diversity of seep-dwelling fauna at modern seeps, as different species have differing tolerances and requirements with regard to the emitted compounds. In this regard, oil seepage has a profound influence on the diversity and distribution of seep-endemic macrofauna and microbial communities. Despite current efforts to better understand oil seeps and their ecology, the confident identification of oil seeps in the geologic record still poses fundamental problems. We present new geochemical data that allow for a more reliable identification of oil seepage during the Phanerozoic. Clear, fibrous aragonite cements of modern and putative ancient oil- and methane-seep deposits were analyzed for their rare earth element (REE) content. This cement is common in seep limestones and represents a product of the anaerobic oxidation of methane and higher hydrocarbons. Clear aragonite is particularly pure and virtually free of detrital inclusions, making it an ideal mineral for comparative geochemical analyses. Its REE composition reveals that oil-seep deposits are significantly enriched in REEs compared to methane- seep deposits. Furthermore, bulk total organic carbon (TOC) measurements suggest that modern and putative ancient oil seep carbonates are enriched in organic carbon. The combined data serve as a promising tool for identifying oil seepage in the fossil record. Our results provide the foundation for an improved understanding of the adaptation of chemosynthesis-based life to oil as an energy source.

  11. Gulf of Mexico hydrocarbon seep communities. V. Biofacies and shell orientation of autochthonous shell beds below storm wave base

    SciTech Connect

    Callender, W.R.; Staff, G.M.; Powell, E.N.; MacDonald, I.R. )

    1990-02-01

    Clam and mussel assemblages associated with petroleum seepage on the Louisiana continental slope form the only substantial shell accumulations below storm wave base on the northwestern Gulf of Mexico shelf and slope. Four distinct biofacies are present at the seeps, dominated respectively by mussels, lucinid clams, vesicomyid clams and tubeworms. Each primary seep site is typically composed of a series of not necessarily contiguous, autochthonous beds dominated by one biofacies. Mussels and tubeworms often co-occur, but neither normally co-occur with lucinid or vesicomyid clams. Lucinid and vesicomyid clam beds have the best chance of preservation. Despite essentially undisturbed accumulation in quiet water below storm wave base, concavity ratios rarely differ from 1:1 and frequency of articulation may be low. Dominantly concave-up valves previously reported in quiet water may result from man's fishing activities. Significant variability in shell orientation, frequency of articulation and concavity ratio between adjacent samples indicates that many individual stratigraphically-equivalent samples should be used in any taphofacies analysis of assemblages formed in low-energy environments. Lucinid beds which form below the sediment surface and vesicomyid beds which form on the sediment surface differed significantly in shell orientation and articulation frequency. Assemblages forming below storm wave base in low-energy environments may comprise a wide variety of taphofacies depending upon whether formation occurs primarily beneath the sediment surface or on the sediment surface, despite contemporaneous formation under similar environmental conditions.

  12. Iron oxides stimulate sulfate-driven anaerobic methane oxidation in seeps

    NASA Astrophysics Data System (ADS)

    Sivan, Orit; Antler, Gilad; Turchyn, Alexandra V.; Marlow, Jeffrey J.; Orphan, Victoria J.

    2014-10-01

    Seep sediments are dominated by intensive microbial sulfate reduction coupled to the anaerobic oxidation of methane (AOM). Through geochemical measurements of incubation experiments with methane seep sediments collected from Hydrate Ridge, we provide insight into the role of iron oxides in sulfate-driven AOM. Seep sediments incubated with 13C-labeled methane showed co-occurring sulfate reduction, AOM, and methanogenesis. The isotope fractionation factors for sulfur and oxygen isotopes in sulfate were about 40‰ and 22‰, respectively, reinforcing the difference between microbial sulfate reduction in methane seeps versus other sedimentary environments (for example, sulfur isotope fractionation above 60‰ in sulfate reduction coupled to organic carbon oxidation or in diffusive sedimentary sulfate-methane transition zone). The addition of hematite to these microcosm experiments resulted in significant microbial iron reduction as well as enhancing sulfate-driven AOM. The magnitude of the isotope fractionation of sulfur and oxygen isotopes in sulfate from these incubations was lowered by about 50%, indicating the involvement of iron oxides during sulfate reduction in methane seeps. The similar relative change between the oxygen versus sulfur isotopes of sulfate in all experiments (with and without hematite addition) suggests that oxidized forms of iron, naturally present in the sediment incubations, were involved in sulfate reduction, with hematite addition increasing the sulfate recycling or the activity of sulfur-cycling microorganisms by about 40%. These results highlight a role for natural iron oxides during bacterial sulfate reduction in methane seeps not only as nutrient but also as stimulator of sulfur recycling.

  13. Detection of natural oil seeps as a guide to petroleum exploration using new generation remote sensor data

    SciTech Connect

    Baker, R.N.

    1989-03-01

    The remote-sensing literature gives ample reference to oil-seep related anomalies and their use as exploration guides. Little technical evidence has been published examining the cause-and-effect relationship between surface signature and petroleum traps. An attempt was made to detect spectral signatures (tonal and textural) related to known natural oil seeps to establish criteria for remote detection of additional seeps in frontier areas. Sites included a variety of physical settings where surface expression of geologic structure, topography, vegetation, and degree of field development were varied to determine the hypothetical potential for discovery by remote-sensing techniques. Test sites included known shallow fields in Indonesia, oil sands in northern Alberta, and giant fields in the Middle East and western US. Results indicated tonal data recorded by Landsat helped discriminate possible unique (i.e. seep-related) but site-dependent signatures. SPOT 10-m resolution panchromatic data were most useful for detecting subtle textural signatures that are possibly seep related. Additional information is being analyzed, and intersite correlations between surface and sensor are being examined.

  14. SURVEY OF LOW FLOW DRAINAGES AND SEEPS IN COLORADO TO ASSESS IMPLEMENTABILITY OF PASSIVE TREATMENT OPTIONS

    EPA Science Inventory

    Low flow drainages and seeps are typically not evaluated for mitigation due to the perceived low impact on the watershed. However, localized metals concentrations and acidity can be at levels of concern. Future passage of a “Good Samaritan Act” should increase activity at curren...

  15. Active Sites Environmental Monitoring Program: Action levels

    SciTech Connect

    Ashwood, J.S.; Ashwood, T.L.

    1991-10-01

    The Active Sites Environmental Monitoring Program (ASEMP) was established at Oak Ridge National Laboratory to provide for early leak detection and to monitor performance of the active low-level waste disposal facilities in Solid Waste Storage Area (SWSA) 6 and the transuranic waste storage areas in SWSA 5 North. Early leak detection is accomplished by sampling runoff, groundwater, and perched water in burial trenches. Sample results are compared to action levels that represent background contamination by naturally occurring and fallout-derived radionuclides. 15 refs., 3 figs., 12 tabs.

  16. Food-web structure of seep sediment macrobenthos from the Gulf of Mexico

    NASA Astrophysics Data System (ADS)

    Demopoulos, Amanda W. J.; Gualtieri, Daniel; Kovacs, Kaitlin

    2010-11-01

    The slope environment of the Gulf of Mexico (GOM) supports dense communities of seep megafaunal invertebrates that rely on endosymbiotic bacteria for nutrition. Seep sediments also contain smaller macrofaunal invertebrates whose nutritional pathways are not well understood. Using stable-isotope analysis, we investigate the utilization of chemosynthetically fixed and methane-derived organic matter by macrofauna. Biological sampling was conducted in three lower-slope GOM seep environs: Green Canyon (GC852, 1428 m), Atwater Valley (AT340, 2230 m), and Alaminos Canyon (AC601, 2384 m). Infaunal δ13C and δ15N exhibited a broad range of values; most infauna appeared to be heterotrophic, although several taxa had very light δ15N and δ13C values, indicating possible reliance on chemoautotrophic symbioses. The lightest δ13C and δ15N values were observed in nematodes (δ13C=-54.6±0.1‰, δ15N=-6.1±0.2‰) and one gastropod (δ13C=-54.1‰, δ15N=-1.1‰) from Green Canyon. Mixing-model results indicated that sulfur-oxidizing Beggiatoa may be an important food source for seep infauna; the rate of utilization ranged from 60% to 100% at Green Canyon and Atwater Valley. The overall range in isotope values was similar across the three sites, suggesting that biogeochemical processes may be very similar in these geographically distinct areas.

  17. Food-web structure of seep sediment macrobenthos from the Gulf of Mexico

    USGS Publications Warehouse

    Demopoulos, Amanda W.J.; Gualtieri, Daniel; Kovacs, Kaitlin

    2010-01-01

    The slope environment of the Gulf of Mexico (GOM) supports dense communities of seep megafaunal invertebrates that rely on endosymbiotic bacteria for nutrition. Seep sediments also contain smaller macrofaunal invertebrates whose nutritional pathways are not well understood. Using stable-isotope analysis, we investigate the utilization of chemosynthetically fixed and methane-derived organic matter by macrofauna. Biological sampling was conducted in three lower-slope GOM seep environs: Green Canyon (GC852, 1428 m), Atwater Valley (AT340, 2230 m), and Alaminos Canyon (AC601, 2384 m). Infaunal delta13C and delta15N exhibited a broad range of values; most infauna appeared to be heterotrophic, although several taxa had very light delta15N and delta13C values, indicating possible reliance on chemoautotrophic symbioses. The lightest delta13C and delta15N values were observed in nematodes (delta13C=-54.6 + or - 0.1 per mil, delta15N=-6.1 + or - 0.2 per mil) and one gastropod (delta13C=-54.1 per mil, delta15N=-1.1 per mil) from Green Canyon. Mixing-model results indicated that sulfur-oxidizing Beggiatoa may be an important food source for seep infauna; the rate of utilization ranged from 60% to 100% at Green Canyon and Atwater Valley. The overall range in isotope values was similar across the three sites, suggesting that biogeochemical processes may be very similar in these geographically distinct areas.

  18. Shell growth and environmental control of methanophyllic Thyasirid bivalves from Svalbard cold seeps

    NASA Astrophysics Data System (ADS)

    Carroll, Michael; Åström, Emmelie; Ambrose, William; Locke, William; Oliver, Graham; Hong, Wei-Li; Carroll, JoLynn

    2016-04-01

    The analysis of molluscan shell material (sclerochronology) can provide information about an organism's age, growth history, and environmental conditions during its lifetime. Bivalve molluscs are common members of hydrothermal vents and methane cold seeps communities where, supported by chemosynthetic symbionts, they can reach high density and biomass. But little is known about methane-associated bivalve populations inhabiting high-Arctic cold seeps, and sclerochronological analysis of methane-influenced bivalves is rare. We measured growth rates and elemental and isotopic shell signatures in a newly discovered species of bivalve (Thyasiridae) from cold seeps at 350-390m depth southwest of Svalbard. First discovered in 2014, recently described shells of Thyasira capitanea sp.nov. were found at 2 independent seep systems in Storfjordrenna. Mean shell carbon isotopic ratios from inorganic δ13C (mean = -4.8‰) and organic δ13C (mean = -26.9‰) fractions clearly indicate a methane influenced habitat and food source for these organisms. Shell mineral ratios (Li/Ca, Mg/Ca, Mn/Ca, Fe/Ca, Sr/Ca, Ba/Ca, Pb/Ca) sampled along the axis of growth with laser-ablated ICP-MS exhibit variability through time and between sites, suggesting that concentrations of these elements that may be affected by methane emissions. The mineralogical data also elucidates the internal pattern of shell deposition and growth checks, and combined with the isotopic and growth rate data, enables us to interpret the temporal history of methane release from these locations.

  19. Insights into methane dynamics from analysis of authigenic carbonates and chemosynthetic mussels at newly-discovered Atlantic Margin seeps

    NASA Astrophysics Data System (ADS)

    Prouty, N. G.; Sahy, D.; Ruppel, C. D.; Roark, E. B.; Condon, D.; Brooke, S.; Ross, S. W.; Demopoulos, A. W. J.

    2016-09-01

    The recent discovery of active methane venting along the US northern and mid-Atlantic margin represents a new source of global methane not previously accounted for in carbon budgets from this region. However, uncertainty remains as to the origin and history of methane seepage along this tectonically inactive passive margin. Here we present the first isotopic analyses of authigenic carbonates and methanotrophic deep-sea mussels, Bathymodiolus sp., and the first direct constraints on the timing of past methane emission, based on samples collected at the upper slope Baltimore Canyon (∼385 m water depth) and deepwater Norfolk (∼1600 m) seep fields within the area of newly-discovered venting. The authigenic carbonates at both sites were dominated by aragonite, with an average δ13C signature of - 47 ‰, a value consistent with microbially driven anaerobic oxidation of methane-rich fluids occurring at or near the sediment-water interface. Authigenic carbonate U and Sr isotope data further support the inference of carbonate precipitation from seawater-derived fluids rather than from formation fluids from deep aquifers. Carbonate stable and radiocarbon (δ13C and Δ13C) isotope values from living Bathymodiolus sp. specimens are lighter than those of seawater dissolved inorganic carbon, highlighting the influence of fossil carbon from methane on carbonate precipitation. U-Th dates on authigenic carbonates suggest seepage at Baltimore Canyon between 14.7 ± 0.6 ka to 15.7 ± 1.6 ka, and at the Norfolk seep field between 1.0 ± 0.7 ka to 3.3 ± 1.3 ka, providing constraint on the longevity of methane efflux at these sites. The age of the brecciated authigenic carbonates and the occurrence of pockmarks at the Baltimore Canyon upper slope could suggest a link between sediment delivery during Pleistocene sea-level lowstand, accumulation of pore fluid overpressure from sediment compaction, and release of overpressure through subsequent venting. Calculations show that the

  20. Insights into methane dynamics from analysis of authigenic carbonates and chemosynthetic mussels at newly-discovered Atlantic Margin seeps

    USGS Publications Warehouse

    Prouty, Nancy G.; Sahy, Diana; Ruppel, Carolyn; Roark, E. Brendan; Condon, Dan; Brooke, Sandra; Ross, Steve W.; Demopoulos, Amanda

    2016-01-01

    The recent discovery of active methane venting along the US northern and mid-Atlantic margin represents a new source of global methane not previously accounted for in carbon budgets from this region. However, uncertainty remains as to the origin and history of methane seepage along this tectonically inactive passive margin. Here we present the first isotopic analyses of authigenic carbonates and methanotrophic deep-sea mussels, Bathymodiolus   sp., and the first direct constraints on the timing of past methane emission, based on samples collected at the upper slope Baltimore Canyon (∼385 m water depth) and deepwater Norfolk (∼1600 m) seep fields within the area of newly-discovered venting. The authigenic carbonates at both sites were dominated by aragonite, with an average  signature of −47‰, a value consistent with microbially driven anaerobic oxidation of methane-rich fluids occurring at or near the sediment–water interface. Authigenic carbonate U and Sr isotope data further support the inference of carbonate precipitation from seawater-derived fluids rather than from formation fluids from deep aquifers. Carbonate stable and radiocarbon ( and ) isotope values from living Bathymodiolus   sp. specimens are lighter than those of seawater dissolved inorganic carbon, highlighting the influence of fossil carbon from methane on carbonate precipitation. U–Th dates on authigenic carbonates suggest seepage at Baltimore Canyon between 14.7±0.6 ka to 15.7±1.6 ka, and at the Norfolk seep field between 1.0±0.7 ka to 3.3±1.3 ka, providing constraint on the longevity of methane efflux at these sites. The age of the brecciated authigenic carbonates and the occurrence of pockmarks at the Baltimore Canyon upper slope could suggest a link between sediment delivery during Pleistocene sea-level lowstand, accumulation of pore fluid overpressure from sediment compaction, and release of overpressure through subsequent venting. Calculations show that

  1. Insights into methane dynamics from analysis of authigenic carbonates and chemosynthetic mussels at newly-discovered Atlantic Margin seeps

    NASA Astrophysics Data System (ADS)

    Prouty, N. G.; Sahy, D.; Ruppel, C. D.; Roark, E. B.; Condon, D.; Brooke, S.; Ross, S. W.; Demopoulos, A. W. J.

    2016-09-01

    The recent discovery of active methane venting along the US northern and mid-Atlantic margin represents a new source of global methane not previously accounted for in carbon budgets from this region. However, uncertainty remains as to the origin and history of methane seepage along this tectonically inactive passive margin. Here we present the first isotopic analyses of authigenic carbonates and methanotrophic deep-sea mussels, Bathymodiolus sp., and the first direct constraints on the timing of past methane emission, based on samples collected at the upper slope Baltimore Canyon (∼385 m water depth) and deepwater Norfolk (∼1600 m) seep fields within the area of newly-discovered venting. The authigenic carbonates at both sites were dominated by aragonite, with an average δ13C signature of - 47 ‰, a value consistent with microbially driven anaerobic oxidation of methane-rich fluids occurring at or near the sediment-water interface. Authigenic carbonate U and Sr isotope data further support the inference of carbonate precipitation from seawater-derived fluids rather than from formation fluids from deep aquifers. Carbonate stable and radiocarbon (δ13C and Δ13C) isotope values from living Bathymodiolus sp. specimens are lighter than those of seawater dissolved inorganic carbon, highlighting the influence of fossil carbon from methane on carbonate precipitation. U-Th dates on authigenic carbonates suggest seepage at Baltimore Canyon between 14.7 ± 0.6 ka to 15.7 ± 1.6 ka, and at the Norfolk seep field between 1.0 ± 0.7 ka to 3.3 ± 1.3 ka, providing constraint on the longevity of methane efflux at these sites. The age of the brecciated authigenic carbonates and the occurrence of pockmarks at the Baltimore Canyon upper slope could suggest a link between sediment delivery during Pleistocene sea-level lowstand, accumulation of pore fluid overpressure from sediment compaction, and release of overpressure through subsequent venting. Calculations show that the

  2. Characterization of active sites in zeolite catalysts

    SciTech Connect

    Eckert, J.; Bug, A.; Nicol, J.M.

    1997-11-01

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). Atomic-level details of the interaction of adsorbed molecules with active sites in catalysts are urgently needed to facilitate development of more effective and/or environmentally benign catalysts. To this end the authors have carried out neutron scattering studies combined with theoretical calculations of the dynamics of small molecules inside the cavities of zeolite catalysts. The authors have developed the use of H{sub 2} as a probe of adsorption sites by observing the hindered rotations of the adsorbed H{sub 2} molecule, and they were able to show that an area near the four-rings is the most likely adsorption site for H{sub 2} in zeolite A while adsorption of H{sub 2} near cations located on six-ring sites decreases in strength as Ni {approximately} Co > Ca > Zn {approximately} Na. Vibrational and rotational motions of ethylene and cyclopropane adsorption complexes were used as a measure for zeolite-adsorbate interactions. Preliminary studies of the binding of water, ammonia, and methylamines were carried out in a number of related guest-host materials.

  3. Combined carbonate carbon isotopic and cellular ultrastructural studies of individual benthic foraminifera: 2. Toward an understanding of apparent disequilibrium in hydrocarbon seeps

    NASA Astrophysics Data System (ADS)

    Bernhard, Joan M.; Martin, Jonathan B.; Rathburn, Anthony E.

    2010-10-01

    Numerous previous studies show disequilibrium between stable carbon isotope ratios of foraminiferal calcite and pore water dissolved inorganic carbon in hydrocarbon seeps, calling into question the utility of this widely used paleoceanographic tracer as a proxy. We use a recently developed method to compare stable carbon isotope ratios of foraminiferal carbonate with cell ultrastructural observations from individual benthic foraminifera from seep (under chemosynthetic bivalves) and nonseep habitats in Monterey Bay, California, to better understand control(s) of benthic foraminiferal carbon isotope ratios. Two attributes previously proposed to cause the isotopic offsets are diet and symbionts. Ultrastructural analysis shows that positive staining with Rose Bengal indicates presence of foraminiferal cytoplasm, bacterial biomass, or a combination of both and, thus, is not an unequivocal indicator of viability. We also show for the first time that some living seep foraminifera have endobionts. Results from our unique, yet limited, data set are consistent with suggestions that, in our sites, several foraminiferal species collected from seep clam beds may not survive there, diet and symbiont presence do not appear to be major contributors to disequilibrium, little calcification of seep-tolerant foraminiferal species occurs while seep conditions prevail, and microscale variability in habitats could influence δ13C of benthic foraminiferal carbonate. Results further suggest that our knowledge of benthic foraminiferal ecology and biomineralization, especially in extreme habitats such as seeps, must be bolstered before we fully understand the fidelity of paleoenvironmental records derived from benthic foraminiferal test δ13C data.

  4. Tectono-Stratigraphy of the Seeps on the Guaymas Basin at the Sonora Margin, Gulf of California, Mexico

    NASA Astrophysics Data System (ADS)

    Figueroa Albornoz, L. J.; Mortera-Gutierrez, C. A.; Bandy, W. L.; Escobar-Briones, E. G.; Godfroy, A.; Fouquet, Y.

    2013-05-01

    Recently several hydrothermal and gas seeps systems has been located precisely at the Sonora margin within the Guaymas Basin (GB), Gulf of California. Since late 1970's , several marine studies had reported two main hydrothermal systems in the Guaymas Rift (one at the Northern Rift, and other at the Southern Rift) and a cold seeps system at the Satellite Basin in the Sonora-margin lower edge. During the campaign BIG10, onboard the IFREMER vessel, NO L'Atalante, the EM122 echo-sounder log more than 30,000 water column acoustic images, which allows us to create a data base of the bubble plumes active systems on the northern part of the GB and the Sonora Margin. These plumes are the expression on the water column of an active seeps site during the cruise time. These images document the presence of the cold seep activity around the scarp of the Guaymas Transform Fault (GTF), and within the Satellite Basin. Few active plumes are first located off-axis, on both sides of the Northern Rift. Although it is not observed any plume within NR. Sub-bottom profiles and bathymetric data logged during the campaign GUAYRIV10, onboard the UNAM vessel, BO EL PUMA, are analyzed to determine the shallow tectonic-stratigraphy of GB near the Sonora Margin. We analyze 17 high-resolution seismic profiles (13 with NE-SW strike and 3 with NW-SE strike). From this data set, the continental shelf stratigraphy at the Sonora Margin tilts toward the slope, showing 3 low angle unconformities due to tectonics and slope angle changes. The strata slope changes angle up to 60°. However, the constant trans-tension shear along the GTF causes gravitation instability on the slope, generating a few submarine landslides close to the Northern Rift, and the rotation of blocks, tilting toward the shelf. To the north, the GTF splits in two fault escarpments, forming a narrow pull-apart basin, known as Satellite Basin. The submarine canyon from the Sonora River flows through the Satellite Basin into the GB

  5. Sulfur biogeochemistry of cold seeps in the Green Canyon region of the Gulf of Mexico

    NASA Astrophysics Data System (ADS)

    Formolo, Michael J.; Lyons, Timothy W.

    2013-10-01

    Cold seeps in the Gulf of Mexico provide a natural laboratory to study biogeochemical cycling of sulfur, carbon, and oxygen at hydrate- and hydrocarbon-rich deep marine settings with obvious additional relevance to studies of diverse modern and ancient seeps. Of particular interest are the sulfur isotope signatures of microbial sulfate reduction coupled to anaerobic oxidation of methane and other non-methane liquid and gaseous hydrocarbons. Whereas most of the published sulfur isotope data from cold seep systems pertain to pore-water species, our study integrates both solid and dissolved sulfur: acid-volatile sulfides (SAVS), pyrite (Spy), elemental sulfur (S°), dissolved sulfate and ΣH2S. Modeled and 35SO42- reduction rates and δ13C and δ18O data for authigenic carbonates are integrated within this sulfur framework. Our results indicate extreme variability over narrow spatial and temporal scales within short distances (meters) from active seeps. High rates of microbial sulfate reduction can lead to complete consumption of the sulfate within the upper few centimeters of burial, while meters away the sulfate profile shows little depletion. Such small-scale variability must reflect the structure and temporal dynamics of hydrocarbon migration in the presence of low amounts of background organic matter. Our past work demonstrated that electron donors other than methane drive significant levels of microbial activity at these seeps, and very recent work has demonstrated that oxidation of higher chain volatile hydrocarbons can contribute to the high levels of microbial activity. These findings are consistent with our new results. Elevated concentrations of pyrite and diagenetic carbonate relative to background sediments are diagnostic of active seepage, yet the S isotopes tell more complex stories. Low levels of the transient, 'instantaneous' products of S cycling-AVS and S°-show high δ34S values that increase with depth. Most of the pyrite formation, however, seems

  6. Seep Mapping: Using NOAA Ship Okeanos Explorer Data to Visualize the Physical Environments of Seeps in the Gulf of Mexico

    NASA Astrophysics Data System (ADS)

    Auner, L.; McKenna, L.; Lobecker, E.; Sowers, D.

    2014-12-01

    More than 550 possible gaseous seeps were previously identified along the continental margin in the northwestern Gulf of Mexico using water-column acoustic backscatter data collected on the NOAA Ship Okeanos Explorer in the spring of 2014. Although the presence of macro-seeps can only be verified through visual confirmation, several studies suggest that gaseous bubbles emitted by seeps are uniquely detected in sonar water-column backscatter returns (Judd and Hovland, 1992; Nikolovska et al., 2008; Weber et al., 2012). In this study, more than 200 seeps were independently identified from a subset of water-column backscatter data collected in March and April, 2014. Additional data collected aboard the Okeanos Explorer includes bathymetry, seafloor backscatter, sub-bottom seismic reflection profiles, and ROV video footage. These datasets, along with calculated geomorphic parameters such as slope, were used to develop specialized mapping products to display physical characteristics of the seafloor and subsurface surrounding a number of gaseous seeps. Preliminary results indicate that seeps occur in a wide variety of geomorphic settings, including the edges of salt domes, and at depths ranging from approximately 300 meters to 1,100 meters. Study results could be used to make predictions about where seeps are most likely to be detected along the continental margin of the northwestern Gulf of Mexico. These predictions could inform future efforts to study seeps and their associated biological communities within the study area or aid in the development of larger scale seep characterization and predictive modeling.

  7. Global dispersion and local diversification of the methane seep microbiome

    PubMed Central

    Ruff, S. Emil; Biddle, Jennifer F.; Teske, Andreas P.; Knittel, Katrin; Boetius, Antje

    2015-01-01

    Methane seeps are widespread seafloor ecosystems shaped by the emission of gas from seabed reservoirs. The microorganisms inhabiting methane seeps transform the chemical energy in methane to products that sustain rich benthic communities around the gas leaks. Despite the biogeochemical relevance of microbial methane removal at seeps, the global diversity and dispersion of seep microbiota remain unknown. Here we determined the microbial diversity and community structure of 23 globally distributed methane seeps and compared these to the microbial communities of 54 other seafloor ecosystems, including sulfate–methane transition zones, hydrothermal vents, coastal sediments, and deep-sea surface and subsurface sediments. We found that methane seep communities show moderate levels of microbial richness compared with other seafloor ecosystems and harbor distinct bacterial and archaeal taxa with cosmopolitan distribution and key biogeochemical functions. The high relative sequence abundance of ANME (anaerobic methanotrophic archaea), as well as aerobic Methylococcales, sulfate-reducing Desulfobacterales, and sulfide-oxidizing Thiotrichales, matches the most favorable microbial metabolisms at methane seeps in terms of substrate supply and distinguishes the seep microbiome from other seafloor microbiomes. The key functional taxa varied in relative sequence abundance between different seeps due to the environmental factors, sediment depth and seafloor temperature. The degree of endemism of the methane seep microbiome suggests a high local diversification in these heterogeneous but long-lived ecosystems. Our results indicate that the seep microbiome is structured according to metacommunity processes and that few cosmopolitan microbial taxa mediate the bulk of methane oxidation, with global relevance to methane emission in the ocean. PMID:25775520

  8. Global dispersion and local diversification of the methane seep microbiome.

    PubMed

    Ruff, S Emil; Biddle, Jennifer F; Teske, Andreas P; Knittel, Katrin; Boetius, Antje; Ramette, Alban

    2015-03-31

    Methane seeps are widespread seafloor ecosystems shaped by the emission of gas from seabed reservoirs. The microorganisms inhabiting methane seeps transform the chemical energy in methane to products that sustain rich benthic communities around the gas leaks. Despite the biogeochemical relevance of microbial methane removal at seeps, the global diversity and dispersion of seep microbiota remain unknown. Here we determined the microbial diversity and community structure of 23 globally distributed methane seeps and compared these to the microbial communities of 54 other seafloor ecosystems, including sulfate-methane transition zones, hydrothermal vents, coastal sediments, and deep-sea surface and subsurface sediments. We found that methane seep communities show moderate levels of microbial richness compared with other seafloor ecosystems and harbor distinct bacterial and archaeal taxa with cosmopolitan distribution and key biogeochemical functions. The high relative sequence abundance of ANME (anaerobic methanotrophic archaea), as well as aerobic Methylococcales, sulfate-reducing Desulfobacterales, and sulfide-oxidizing Thiotrichales, matches the most favorable microbial metabolisms at methane seeps in terms of substrate supply and distinguishes the seep microbiome from other seafloor microbiomes. The key functional taxa varied in relative sequence abundance between different seeps due to the environmental factors, sediment depth and seafloor temperature. The degree of endemism of the methane seep microbiome suggests a high local diversification in these heterogeneous but long-lived ecosystems. Our results indicate that the seep microbiome is structured according to metacommunity processes and that few cosmopolitan microbial taxa mediate the bulk of methane oxidation, with global relevance to methane emission in the ocean.

  9. Microbial Sulfate Reduction at Cold Seeps Based on Analysis of Carbonate Associated Sulfate

    NASA Astrophysics Data System (ADS)

    Feng, D.; Peng, Y.

    2014-12-01

    Microbial sulfate reduction and coupled anaerobic oxidation of methane (AOM) are the dominant biogeochemical processes occurring at cold seeps in marine settings. These processes not only support the growth of chemosynthetic communities but also promote the precipitation of authigenic carbonates. However, investigations of microbial sulfate reduction have been conducted only using porewaters or seep-related barites. The fact is that many seeps are either inactive or do not precipitate any barite minerals. Thus, little is known about the microbial sulfate reduction at these seep environments. The occurrence of authigenic carbonate has been documented at almost all cold seep sites, which provide a unique opportunity to investigate the microbial sulfate reduction using such carbonate. The presentation is focused on the concentrations and isotopic signatures of carbonate associated sulfate (CAS). The aim of the project is to determine the role of sulfate and sulfate reduction during carbonate precipitation at cold seeps. The CAS concentrations are 67-537 ppm in high-Mg calcite, 51-181 ppm in low-Mg calcite, and 116-565 in aragonite. The δ34SCAS and δ18OCAS also vary considerably, ranging from 21.9‰ to 56.2‰ (V-CDT) and from 10.1‰ to 24.8‰ (V-SMOW), respectively. On δ34SCAS versus δ18OCAS plots, both aragonite and calcite show linear trends that project down toward those of open seawater sulfate. The trends suggest that sulfate has been isotopically modified to various degrees in pore fluids before being incorporated into carbonate lattice. The much narrower δ34SCAS and δ18OCAS ranges for aragonite than for calcite suggests a much "pickier" condition for aragonite formation during early diagenesis. Our results suggest that concentration and isotopic composition of CAS in seep carbonates may be controlled by the supply of pore-water sulfate during carbonate precipitation. The reliability of CAS in carbonate of early diagenetic origin as a proxy of

  10. Gammaproteobacterial methanotrophs dominate cold methane seeps in floodplains of West Siberian rivers.

    PubMed

    Oshkin, Igor Y; Wegner, Carl-Eric; Lüke, Claudia; Glagolev, Mikhail V; Filippov, Illiya V; Pimenov, Nikolay V; Liesack, Werner; Dedysh, Svetlana N

    2014-10-01

    A complex system of muddy fluid-discharging and methane (CH4)-releasing seeps was discovered in a valley of the river Mukhrinskaya, one of the small rivers of the Irtysh Basin, West Siberia. CH4 flux from most (90%) of these gas ebullition sites did not exceed 1.45 g CH4 h(-1), while some seeps emitted up to 5.54 g CH4 h(-1). The δ(13)C value of methane released from these seeps varied between -71.1 and -71.3‰, suggesting its biogenic origin. Although the seeps were characterized by low in situ temperatures (3.5 to 5°C), relatively high rates of methane oxidation (15.5 to 15.9 nmol CH4 ml(-1) day(-1)) were measured in mud samples. Fluorescence in situ hybridization detected 10(7) methanotrophic bacteria (MB) per g of mud (dry weight), which accounted for up to 20.5% of total bacterial cell counts. Most (95.8 to 99.3%) methanotroph cells were type I (gammaproteobacterial) MB. The diversity of methanotrophs in this habitat was further assessed by pyrosequencing of pmoA genes, encoding particulate methane monooxygenase. A total of 53,828 pmoA gene sequences of seep-inhabiting methanotrophs were retrieved and analyzed. Nearly all of these sequences affiliated with type I MB, including the Methylobacter-Methylovulum-Methylosoma group, lake cluster 2, and several as-yet-uncharacterized methanotroph clades. Apparently, microbial communities attenuating methane fluxes from these local but strong CH4 sources in floodplains of high-latitude rivers have a large proportion of potentially novel, psychrotolerant methanotrophs, thereby providing a challenge for future isolation studies.

  11. Gammaproteobacterial Methanotrophs Dominate Cold Methane Seeps in Floodplains of West Siberian Rivers

    PubMed Central

    Oshkin, Igor Y.; Wegner, Carl-Eric; Lüke, Claudia; Glagolev, Mikhail V.; Filippov, Illiya V.; Pimenov, Nikolay V.; Liesack, Werner

    2014-01-01

    A complex system of muddy fluid-discharging and methane (CH4)-releasing seeps was discovered in a valley of the river Mukhrinskaya, one of the small rivers of the Irtysh Basin, West Siberia. CH4 flux from most (90%) of these gas ebullition sites did not exceed 1.45 g CH4 h−1, while some seeps emitted up to 5.54 g CH4 h−1. The δ13C value of methane released from these seeps varied between −71.1 and −71.3‰, suggesting its biogenic origin. Although the seeps were characterized by low in situ temperatures (3.5 to 5°C), relatively high rates of methane oxidation (15.5 to 15.9 nmol CH4 ml−1 day−1) were measured in mud samples. Fluorescence in situ hybridization detected 107 methanotrophic bacteria (MB) per g of mud (dry weight), which accounted for up to 20.5% of total bacterial cell counts. Most (95.8 to 99.3%) methanotroph cells were type I (gammaproteobacterial) MB. The diversity of methanotrophs in this habitat was further assessed by pyrosequencing of pmoA genes, encoding particulate methane monooxygenase. A total of 53,828 pmoA gene sequences of seep-inhabiting methanotrophs were retrieved and analyzed. Nearly all of these sequences affiliated with type I MB, including the Methylobacter-Methylovulum-Methylosoma group, lake cluster 2, and several as-yet-uncharacterized methanotroph clades. Apparently, microbial communities attenuating methane fluxes from these local but strong CH4 sources in floodplains of high-latitude rivers have a large proportion of potentially novel, psychrotolerant methanotrophs, thereby providing a challenge for future isolation studies. PMID:25063667

  12. Gammaproteobacterial methanotrophs dominate cold methane seeps in floodplains of West Siberian rivers.

    PubMed

    Oshkin, Igor Y; Wegner, Carl-Eric; Lüke, Claudia; Glagolev, Mikhail V; Filippov, Illiya V; Pimenov, Nikolay V; Liesack, Werner; Dedysh, Svetlana N

    2014-10-01

    A complex system of muddy fluid-discharging and methane (CH4)-releasing seeps was discovered in a valley of the river Mukhrinskaya, one of the small rivers of the Irtysh Basin, West Siberia. CH4 flux from most (90%) of these gas ebullition sites did not exceed 1.45 g CH4 h(-1), while some seeps emitted up to 5.54 g CH4 h(-1). The δ(13)C value of methane released from these seeps varied between -71.1 and -71.3‰, suggesting its biogenic origin. Although the seeps were characterized by low in situ temperatures (3.5 to 5°C), relatively high rates of methane oxidation (15.5 to 15.9 nmol CH4 ml(-1) day(-1)) were measured in mud samples. Fluorescence in situ hybridization detected 10(7) methanotrophic bacteria (MB) per g of mud (dry weight), which accounted for up to 20.5% of total bacterial cell counts. Most (95.8 to 99.3%) methanotroph cells were type I (gammaproteobacterial) MB. The diversity of methanotrophs in this habitat was further assessed by pyrosequencing of pmoA genes, encoding particulate methane monooxygenase. A total of 53,828 pmoA gene sequences of seep-inhabiting methanotrophs were retrieved and analyzed. Nearly all of these sequences affiliated with type I MB, including the Methylobacter-Methylovulum-Methylosoma group, lake cluster 2, and several as-yet-uncharacterized methanotroph clades. Apparently, microbial communities attenuating methane fluxes from these local but strong CH4 sources in floodplains of high-latitude rivers have a large proportion of potentially novel, psychrotolerant methanotrophs, thereby providing a challenge for future isolation studies. PMID:25063667

  13. Active site of ribulosebisphosphate carboxylase/oxygenase

    SciTech Connect

    Hartman, F.C.; Stringer, C.D.; Milanez, S.; Lee, E.H.

    1985-01-01

    Previous affinity labeling studies and comparative sequence analyses have identified two different lysines at the active site of ribulosebisphosphate carboxylase/oxygenase and have suggested their essentiality to function. The essential lysines occupy positions 166 and 329 in the Rhodospirillum rubrum enzyme and positions 175 and 334 in the spinach enzyme. Based on the pH-dependencies of inactivations of the two enzymes by trinitrobenzene sulfonate, Lys-166 (R. rubrum enzyme) exhibits a pK/sub a/ of 7.9 and Lys-334 (spinach enzyme) exhibits a pK/sub a/ of 9.0. These low pK/sub a/ values as well as the enhanced nucleophilicities of the lysyl residues argue that both are important to catalysis rather than to substrate binding. Lys-166 may correspond to the essential base that initiates catalysis and that displays a pK/sub a/ of 7.5 in the pH-curve for V/sub max//K/sub m/. Cross-linking experiments with 4,4'-diisothiocyano-2,2'-disulfonate stilbene demonstrate that the two active-site lysines are within 12 A. 50 refs., 7 figs., 1 tab.

  14. [Methanotrophic bacteria in cold seeps of the floodplains of northern rivers].

    PubMed

    Belova, S É; Oshkin, I Iu; Glagolev, M V; Lapshina, E D; Maksiutov, Sh Sh; Dedysh, S N

    2013-01-01

    Small mud volcanoes (cold seeps), which are common in the floodplains of northern rivers, are a potentially important, although poorly studied sources of atmospheric methane. Field research on the cold seeps of the Mukhrina River (Khanty-Mansiysk Autonomous okrug, Russia) revealed methane fluxes from these structures to be orders of magnitude higher than from equivalent areas of the mid-taiga bogs. Microbial communities developing around the seeps were formed under conditions of high methane concentrations, low temperatures (3-5 degrees C), and near-neutral pH. Molecular identification of methane-oxidizing bacteria from this community by analysis of the pmoA gene encoding particulate methane monooxygenase revealed both type I and type II methanotrophs (classes Gammaproteobacteria and Alphaproteobacteria, respectively), with predomination of type I methanotrophs. Among the latter, microorganisms related to Methylobacterpsychrophilus and Methylobacter tundripaludum, Crenothrix polyspora (a stagnant water dweller), and a number of methanotrophs belonging to unknown taxa were detected. Growth characteristics of two isolates were determined. Methylobactersp. CMS7 exhibited active growth at 4-10 degrees C, while Methylocystis sp. SB12 grew better at 20 degrees C. Experimental results confirmed the major role ofmethanotrophic gammaproteobacteria in controlling the methane emission from cold river seeps.

  15. [Methanotrophic bacteria in cold seeps of the floodplains of northern rivers].

    PubMed

    Belova, S É; Oshkin, I Iu; Glagolev, M V; Lapshina, E D; Maksiutov, Sh Sh; Dedysh, S N

    2013-01-01

    Small mud volcanoes (cold seeps), which are common in the floodplains of northern rivers, are a potentially important, although poorly studied sources of atmospheric methane. Field research on the cold seeps of the Mukhrina River (Khanty-Mansiysk Autonomous okrug, Russia) revealed methane fluxes from these structures to be orders of magnitude higher than from equivalent areas of the mid-taiga bogs. Microbial communities developing around the seeps were formed under conditions of high methane concentrations, low temperatures (3-5 degrees C), and near-neutral pH. Molecular identification of methane-oxidizing bacteria from this community by analysis of the pmoA gene encoding particulate methane monooxygenase revealed both type I and type II methanotrophs (classes Gammaproteobacteria and Alphaproteobacteria, respectively), with predomination of type I methanotrophs. Among the latter, microorganisms related to Methylobacterpsychrophilus and Methylobacter tundripaludum, Crenothrix polyspora (a stagnant water dweller), and a number of methanotrophs belonging to unknown taxa were detected. Growth characteristics of two isolates were determined. Methylobactersp. CMS7 exhibited active growth at 4-10 degrees C, while Methylocystis sp. SB12 grew better at 20 degrees C. Experimental results confirmed the major role ofmethanotrophic gammaproteobacteria in controlling the methane emission from cold river seeps. PMID:25509412

  16. A microbiological and biogeochemical investigation of the cold seep tubeworm Escarpia southwardae (Annelida: Siboglinidae): Symbiosis and trace element composition of the tube

    NASA Astrophysics Data System (ADS)

    Duperron, Sébastien; Gaudron, Sylvie M.; Lemaitre, Nolwenn; Bayon, Germain

    2014-08-01

    Tubeworms within the annelid family Siboglinidae rely on sulfur-oxidizing autotrophic bacterial symbionts for their nutrition, and are among the dominant metazoans occurring at deep-sea hydrocarbon seeps. Contrary to their relatives from hydrothermal vents, sulfide uptake for symbionts occurs within the anoxic subsurface sediment, in the posterior ‘root' region of the animal. This study reports on an integrated microbiological and geochemical investigation of the cold seep tubeworm Escarpia southwardae collected at the Regab pockmark (Gulf of Guinea). Our aim was to further constrain the links between the animal and its symbiotic bacteria, and their environment. We show that E. southwardae harbors abundant sulfur-oxidizing bacterial symbionts in its trophosome. Symbionts are able to fix inorganic carbon using the Calvin-Benson cycle, as reported in most other Siboglinidae, but can also use the reverse Tricarboxilic Acid Cycle. Surprisingly, the observed bacteria appear to be more closely related to symbionts of Escarpia and Lamellibrachia species from very distant sites located in the Gulf of Mexico and eastern Pacific, than to symbionts of a siboglinid occurring at a nearby methane seep site, only a few hundred km away from Regab. Then, by combining scanning electron microscopy and trace element (Mn, Fe, Sr, Zr) analyses of E. southwardae tube, we also show that two distinct oxidation fronts occur along the tube. The first one, near the posterior end of the tube, corresponds to the interface between oxic bottom waters and the underlying anoxic sediment. In contrast, the second redox front is located in the most anterior part of the tube, and could result from active oxygen uptake by the plume of the tubeworm. We speculate that intense oxygen consumption in this region could create favorable conditions for sulfate reduction by specialized bacteria associated with the plume, possibly leading to an additional source of dissolved sulfide that would further enhance

  17. The Microbial Ferrous Wheel in a Neutral pH Groundwater Seep

    PubMed Central

    Roden, Eric E.; McBeth, Joyce M.; Blöthe, Marco; Percak-Dennett, Elizabeth M.; Fleming, Emily J.; Holyoke, Rebecca R.; Luther, George W.; Emerson, David; Schieber, Juergen

    2012-01-01

    Evidence for microbial Fe redox cycling was documented in a circumneutral pH groundwater seep near Bloomington, Indiana. Geochemical and microbiological analyses were conducted at two sites, a semi-consolidated microbial mat and a floating puffball structure. In situ voltammetric microelectrode measurements revealed steep opposing gradients of O2 and Fe(II) at both sites, similar to other groundwater seep and sedimentary environments known to support microbial Fe redox cycling. The puffball structure showed an abrupt increase in dissolved Fe(II) just at its surface (∼5 cm depth), suggesting an internal Fe(II) source coupled to active Fe(III) reduction. Most probable number enumerations detected microaerophilic Fe(II)-oxidizing bacteria (FeOB) and dissimilatory Fe(III)-reducing bacteria (FeRB) at densities of 102 to 105 cells mL−1 in samples from both sites. In vitro Fe(III) reduction experiments revealed the potential for immediate reduction (no lag period) of native Fe(III) oxides. Conventional full-length 16S rRNA gene clone libraries were compared with high throughput barcode sequencing of the V1, V4, or V6 variable regions of 16S rRNA genes in order to evaluate the extent to which new sequencing approaches could provide enhanced insight into the composition of Fe redox cycling microbial community structure. The composition of the clone libraries suggested a lithotroph-dominated microbial community centered around taxa related to known FeOB (e.g., Gallionella, Sideroxydans, Aquabacterium). Sequences related to recognized FeRB (e.g., Rhodoferax, Aeromonas, Geobacter, Desulfovibrio) were also well-represented. Overall, sequences related to known FeOB and FeRB accounted for 88 and 59% of total clone sequences in the mat and puffball libraries, respectively. Taxa identified in the barcode libraries showed partial overlap with the clone libraries, but were not always consistent across different variable regions and sequencing platforms. However, the barcode

  18. Ocean Bottom Gamma-Ray Anomaly Around Methane Seeps Related to Gas Hydrate- Bearing Zone in The Eastern Margin of Japan Sea and Off Southwest Taiwan

    NASA Astrophysics Data System (ADS)

    Machiyama, H.; Kinoshita, M.; Lin, S.; Matsumoto, R.; Soh, W.

    2008-12-01

    JAMSTEC has conducted the ocean bottom gamma-ray measurement using ROVs and Submersibles since 1997. Gamma-ray spectrometer utilizes 3-inch spherical NaI(Tl) scintillator and the signal processor including DA converter in a pressure case. After processing data, we get total count rate (intensity value: count per second (cps)) of gamma ray and contents of K, U-, and Th-series radionuclides. The sensor was equipped to the side of the sample basket or foot of ROVs and submersibles, and always touches the seafloor when ROVs completely landed. Their results are posted on JAMSTEC website as a database. On the basis of past achievements, we present the results of the ocean bottom gamma-ray measurement at the methane seep sites related to gas hydrate off Joetsu in the eastern margin of Japan Sea and off southwest Taiwan. Off Joetsu: A number of mounds, large pockmarks (20 - 50 m deep and 200 - 500 m across), gas plumes, and gas hydrate are found at water depth of 900 - 1000 m in the Umitaka Spur and the Joetsu Knoll. Gamma-ray intensity values are 50 - 70 cps in normal muddy seafloor. On the other hand, the intensity values are 100 - 200 cps around methane venting sites, bacteria mats, and 'collapsed hydrate zone' which has an undulating, rugged seafloor with carbonate nodules and gravels. Contents of each radionuclide are also high. Low U/Th ratio suggests that there is less contribution of Rn accompanied with a recent fault activity. Off southwest Taiwan: Large, dense chemosynthetic communities, associated with carbonate pavements, were discovered at water depth of about 1100 - 1200 m on the top of the Formosa Ridge. Gamma-ray intensity values in normal muddy seafloor (120 - 150 cps) are higher than those around Japan. Since Th-series radionuclide easily absorbs other particles, it is commonly included in surface sediments. This may cause higher content of Th-series radionuclide in normal muddy seafloor. On the other hand, anomaly of gamma-ray intensity (200 - 300 cps

  19. Active Sites Environmental Monitoring Program: Program plan

    SciTech Connect

    Ashwood, T.L.; Wickliff, D.S.; Morrissey, C.M.

    1992-02-01

    The Active Sites Environmental Monitoring Program (ASEMP), initiated in 1989, provides early detection and performance monitoring of transuranic (TRU) waste and active low-level waste (LLW) facilities at Oak Ridge National Laboratory (ORNL) in accordance with US Department of Energy (DOE) Order 5820.2A. Active LLW facilities in Solid Waste Storage Area (SWSA) 6 include Tumulus I and Tumulus II, the Interim Waste Management Facility (IWMF), LLW silos, high-range wells, asbestos silos, and fissile wells. The tumulus pads and IWMF are aboveground, high-strength concrete pads on which concrete vaults containing metal boxes of LLW are placed; the void space between the boxes and vaults is filled with grout. Eventually, these pads and vaults will be covered by an engineered multilayered cap. All other LLW facilities in SWSA 6 are below ground. In addition, this plan includes monitoring of the Hillcut Disposal Test Facility (HDTF) in SWSA 6, even though this facility was completed prior to the data of the DOE order. In SWSA 5 North, the TRU facilities include below-grade engineered caves, high-range wells, and unlined trenches. All samples from SWSA 6 are screened for alpha and beta activity, counted for gamma-emitting isotopes, and analyzed for tritium. In addition to these analytes, samples from SWSA 5 North are analyzed for specific transuranic elements.

  20. Oil and gas seeps within Absaroka volcanics of northwestern Wyoming

    SciTech Connect

    Sundell, K.A.; Love, J.D.

    1986-08-01

    Three new occurrences of asphaltic, liquid, and gaseous hydrocarbons have been discovered in the southeastern Absaroka Range. These petroleum seeps are 40 to 110 mi southeast of previously known seeps within Eocene volcaniclastic rocks at Calcite Springs, Tower Junction, and Sweetwater Mineral Springs, Wyoming. The Middle Fork seep and Castle Rocks seep are near the headwaters of the Middle and North Forks of Owl Creek, respectively. The Chimney Rock asphalt locality is along the South Fork of the Wood River. Water samples from the Middle Fork seep fluoresce greenish-orange and contain 6 to 8 mg/L of extractable bituminous hydrocarbons. An iridescent oily film forms on the water surface and on abundant gas bubbles trapped within moss. The Castle Rocks seep, in Quaternary gravels along the bed of the North Fork of Owl Creek, shows iridescent oily bubbles in emerging spring water and black, sooty lenses of carbon-coated gravels in overlying dry deposits. The Middle Fork and Castle Rocks seeps rise through thin Quaternary deposits overlying the Aycross Formation (Eocene). The Chimney Rock asphalt locality is in a northwest-trending paleovalley fill consisting of highly deformed masses of volcanic strata in the Tepee Trail and Wiggins Formations. Thin (< 1 in. thick), discontinuous, subvertical veins of asphaltum cut through these rocks. These petroleum seeps demonstrate migration of hydrocarbons after the volcaniclastic strata were emplaced and suggest that significant petroleum resources may occur elsewhere within Eocene volcaniclastic rocks and/or within Mesozoic and Paleozoic reservoirs beneath the volcanics.

  1. Cenozoic Methane-Seep Faunas of the Caribbean Region.

    PubMed

    Kiel, Steffen; Hansen, Bent T

    2015-01-01

    We report new examples of Cenozoic cold-seep communities from Colombia, Cuba, the Dominican Republic, Trinidad, and Venezuela, and attempt to improve the stratigraphic dating of Cenozoic Caribbean seep communities using strontium isotope stratigraphy. Two seep faunas are distinguished in Barbados: the late Eocene mudstone-hosted 'Joes River fauna' consists mainly of large lucinid bivalves and tall abyssochrysoid gastropods, and the early Miocene carbonate-hosted 'Bath Cliffs fauna' containing the vesicomyid Pleurophopsis, the mytilid Bathymodiolus and small gastropods. Two new Oligocene seep communities from the Sinú River basin in Colombia consist of lucinid bivalves including Elongatolucina, thyasirid and solemyid bivalves, and Pleurophopsis. A new early Miocene seep community from Cuba includes Pleurophopsis and the large lucinid Meganodontia. Strontium isotope stratigraphy suggests an Eocene age for the Cuban Elmira asphalt mine seep community, making it the oldest in the Caribbean region. A new basal Pliocene seep fauna from the Dominican Republic is characterized by the large lucinid Anodontia (Pegophysema). In Trinidad we distinguish two types of seep faunas: the mudstone-hosted Godineau River fauna consisting mainly of lucinid bivalves, and the limestone-hosted Freeman's Bay fauna consisting chiefly of Pleurophopsis, Bathymodiolus, and small gastropods; they are all dated as late Miocene. Four new seep communities of Oligocene to Miocene age are reported from Venezuela. They consist mainly of large globular lucinid bivalves including Meganodontia, and moderately sized vesicomyid bivalves. After the late Miocene many large and typical 'Cenozoic' lucinid genera disappeared from the Caribbean seeps and are today known only from the central Indo-Pacific Ocean. We speculate that the increasingly oligotrophic conditions in the Caribbean Sea after the closure of the Isthmus of Panama in the Pliocene may have been unfavorable for such large lucinids because they

  2. Cenozoic Methane-Seep Faunas of the Caribbean Region.

    PubMed

    Kiel, Steffen; Hansen, Bent T

    2015-01-01

    We report new examples of Cenozoic cold-seep communities from Colombia, Cuba, the Dominican Republic, Trinidad, and Venezuela, and attempt to improve the stratigraphic dating of Cenozoic Caribbean seep communities using strontium isotope stratigraphy. Two seep faunas are distinguished in Barbados: the late Eocene mudstone-hosted 'Joes River fauna' consists mainly of large lucinid bivalves and tall abyssochrysoid gastropods, and the early Miocene carbonate-hosted 'Bath Cliffs fauna' containing the vesicomyid Pleurophopsis, the mytilid Bathymodiolus and small gastropods. Two new Oligocene seep communities from the Sinú River basin in Colombia consist of lucinid bivalves including Elongatolucina, thyasirid and solemyid bivalves, and Pleurophopsis. A new early Miocene seep community from Cuba includes Pleurophopsis and the large lucinid Meganodontia. Strontium isotope stratigraphy suggests an Eocene age for the Cuban Elmira asphalt mine seep community, making it the oldest in the Caribbean region. A new basal Pliocene seep fauna from the Dominican Republic is characterized by the large lucinid Anodontia (Pegophysema). In Trinidad we distinguish two types of seep faunas: the mudstone-hosted Godineau River fauna consisting mainly of lucinid bivalves, and the limestone-hosted Freeman's Bay fauna consisting chiefly of Pleurophopsis, Bathymodiolus, and small gastropods; they are all dated as late Miocene. Four new seep communities of Oligocene to Miocene age are reported from Venezuela. They consist mainly of large globular lucinid bivalves including Meganodontia, and moderately sized vesicomyid bivalves. After the late Miocene many large and typical 'Cenozoic' lucinid genera disappeared from the Caribbean seeps and are today known only from the central Indo-Pacific Ocean. We speculate that the increasingly oligotrophic conditions in the Caribbean Sea after the closure of the Isthmus of Panama in the Pliocene may have been unfavorable for such large lucinids because they

  3. Cenozoic Methane-Seep Faunas of the Caribbean Region

    PubMed Central

    Kiel, Steffen; Hansen, Bent T.

    2015-01-01

    We report new examples of Cenozoic cold-seep communities from Colombia, Cuba, the Dominican Republic, Trinidad, and Venezuela, and attempt to improve the stratigraphic dating of Cenozoic Caribbean seep communities using strontium isotope stratigraphy. Two seep faunas are distinguished in Barbados: the late Eocene mudstone-hosted ‘Joes River fauna’ consists mainly of large lucinid bivalves and tall abyssochrysoid gastropods, and the early Miocene carbonate-hosted ‘Bath Cliffs fauna’ containing the vesicomyid Pleurophopsis, the mytilid Bathymodiolus and small gastropods. Two new Oligocene seep communities from the Sinú River basin in Colombia consist of lucinid bivalves including Elongatolucina, thyasirid and solemyid bivalves, and Pleurophopsis. A new early Miocene seep community from Cuba includes Pleurophopsis and the large lucinid Meganodontia. Strontium isotope stratigraphy suggests an Eocene age for the Cuban Elmira asphalt mine seep community, making it the oldest in the Caribbean region. A new basal Pliocene seep fauna from the Dominican Republic is characterized by the large lucinid Anodontia (Pegophysema). In Trinidad we distinguish two types of seep faunas: the mudstone-hosted Godineau River fauna consisting mainly of lucinid bivalves, and the limestone-hosted Freeman’s Bay fauna consisting chiefly of Pleurophopsis, Bathymodiolus, and small gastropods; they are all dated as late Miocene. Four new seep communities of Oligocene to Miocene age are reported from Venezuela. They consist mainly of large globular lucinid bivalves including Meganodontia, and moderately sized vesicomyid bivalves. After the late Miocene many large and typical ‘Cenozoic’ lucinid genera disappeared from the Caribbean seeps and are today known only from the central Indo-Pacific Ocean. We speculate that the increasingly oligotrophic conditions in the Caribbean Sea after the closure of the Isthmus of Panama in the Pliocene may have been unfavorable for such large lucinids

  4. Constraints on Methane and Methane Hydrate Distribution at a Gulf of Mexico Seep Using Waveform Inversion of Seismic Data

    NASA Astrophysics Data System (ADS)

    Wood, W.; Knapp, C. C.; Knapp, J. H.

    2010-12-01

    The seafloor mound at the Gulf of Mexico lease block MC (Mississippi Canyon) 118 is a known active seep lying directly above a salt dome. The site lies at 850-900 m water depth - within the methane hydrate stability zone, but there is no obvious BSR or other indicator of large quantities of gas or gas hydrate. Air-gun seismic data acquired with a 4180 cu in source and 7200 m, 288-channel hydrophone array, exhibit several bright, but laterally-limited reflections in the ~500 m sediment column above the salt. The bright spots are largely conformable with the strata, and there is no apparent pull-up or push-down associated with the bright spots, suggesting they are thin. There are also no significant frequency changes below the bright spots. We interpret the bright spots to be caused by gas, gas hydrate, or carbonate, or combinations of the three. The long offsets used to acquire these data allow for the analysis of refracted arrivals that not only provide accurate P-wave velocities, but also provide a background velocity profile for full waveform inversion. Preliminary results from the waveform inversion confirm at least some of the bright spots are free gas, constraining the position of the gas hydrate stability zone, but very thin (sub-wavelength) layers of carbonate and hydrate may also be present. Knowing the exact composition of the material responsible for the bright spots will better constrain the linkage between the salt tectonics (with implied fault activity) and seep activity, as well as the longevity of the hydrate system at MC 118.

  5. Methane-Stimulated Benthic Marine Nitrogen Fixation at Deep-Sea Methane Seeps

    NASA Astrophysics Data System (ADS)

    Dekas, A. E.; Orphan, V.

    2011-12-01

    Biological nitrogen fixation (the conversion of N2 to NH3) is a critical process in the oceans, counteracting the production of N2 gas by dissimilatory bacterial metabolisms and providing a source of bioavailable nitrogen to many nitrogen-limited ecosystems. Although current measurements of N2 production and consumption in the oceans indicate that the nitrogen cycle is not balanced, recent findings on the limits of nitrogen fixation suggest that the perceived imbalance is an artifact of an incomplete assessment of marine diazotrophy. One currently poorly studied and potentially underappreciated habitat for diazotrophic organisms is the sediments of the deep-sea. In the present study we investigate the distribution and magnitude of benthic marine diazotrophy at several active deep-sea methane seeps (Mound 12, Costa Rica; Eel River Basin, CA, USA; Hydrate Ridge, OR, USA; and Monterey Canyon, CA, USA). Using 15N2 and 15NH4 sediment incubation experiments followed by single-cell (FISH-NanoSIMS) and bulk isotopic analysis (EA-IRMS), we observed total protein synthesis (15N uptake from 15NH4) and nitrogen fixation (15N update from 15N2). The highest rates of nitrogen fixation observed in the methane seep sediment incubation experiments were over an order of magnitude greater than those previously published from non-seep deep-sea sediments (Hartwig and Stanley, Deep-Sea Research, 1978, 25:411-417). However, methane seep diazotrophy appears to be highly spatially variable, with sediments exhibiting no nitrogen fixation originating only centimeters away from sediments actively incorporating 15N from 15N2. The greatest spatial variability in diazotrophy was observed with depth in the sediment, and corresponded to steep gradients in sulfate and methane. The maximum rates of nitrogen fixation were observed within the methane-sulfate transition zone, where organisms mediating the anaerobic oxidation of methane are typically in high abundance. Additionally, incubation

  6. Disentangling oil weathering at a marine seep using GC x GC: broad metabolic specificity accompanies subsurface petroleum biodegradation.

    PubMed

    Wardlaw, George D; Arey, J Samuel; Reddy, Christopher M; Nelson, Robert K; Ventura, G Todd; Valentine, David L

    2008-10-01

    Natural seeps contribute nearly half of the oil entering the coastal ocean. However, environmental fate studies generally monitor fewer than 5% of these petroleum compounds. Hence, the rates and relevance of physical, chemical, and biological weathering processes are unknown for the large majority of hydrocarbons, both released from natural seeps and also from human activities. To investigate the specific compositional changes occurring in petroleum during subsurface degradation and submarine seepage, we studied the natural oil seeps offshore Santa Barbara, California with comprehensive, two-dimensional gas chromatography (GC x GC). With this technique, we quantified changes in the molecular diversity and abundance of hydrocarbons between subsurface reservoirs, a proximal sea floor seep, and the sea surface overlying the seep. We also developed methods to apportion hydrocarbon mass losses due to biodegradation, dissolution, and evaporation, for hundreds of tracked compounds that ascended from the subsurface to the sea floor to the sea surface. The results provide the first quantitative evidence of broad metabolic specificity for anaerobic hydrocarbon degradation in the subsurface and reveal new trends of rapid hydrocarbon evaporation at the sea surface. This study establishes GC x GC as a powerful technique for differentiating biological and physical weathering processes of complex mixtures at a molecular level.

  7. Discovery of "Hydrothermal" Chemosynthetic Community in a Cold Seep Environment, Formosa Ridge: Seafloor Observation Results from First ROV Cruise, off Southwestern Taiwan

    NASA Astrophysics Data System (ADS)

    Machiyama, H.; Lin, S.; Fujikura, K.; Huang, C.; Ku, C.; Lin, L.; Liu, C.; Morita, S.; Nunoura, T.; Soh, W.; Toki, T.; Yang, T. F.

    2007-12-01

    First ROV diving survey has been conducted around the selected three sites (Formosa Ridge, Sites C and G) in offshore SW Taiwan, where gas hydrate broadly occurs within the thick Quaternary marine sediments. The Formosa Ridge and Site G are located in the South China Sea Continental Slope, whereas Site C is located in the frontal portion of a fault-bend fold in the accretionary wedge off SW Taiwan. Large, dense chemosynthetic communities were discovered at water depth of about 1120 - 1140 m on the top of the Formosa Ridge by direct observation using ROV Hyper-Dolphin of JAMSTEC. Colonies are distributed in depressions or fissures of large, carbon-depleted authigenic carbonates. The community is dominated by deep- sea mussel, Bathymodiolus platifrons, and galatheid crab, Shinkaia crosnieri. Most of species corresponds to those of hydrothermal vent fields in the Okinawa Trough, such as the Hatoma Knoll and the Iheya Ridge. Methane gas bubbles were found within the colony, and methane hydrate was also found beneath the aggregation of B. platifrons, which is harboured endosymbiont methanotroph in their gill in the Okinawa Trough. On the other hand, S. crosnieri from the Okinawa Trough culture numerous epibiont sulfur-oxidizing bacteria on their carapace. Therefore, they require high concentration of H2S from the subseafloor fluids. Single channel seismic profiles show the presence of clear BSR underneath the Formosa Ridge, and suggest the possible upward migration of gassy fluids beneath the top of the ridge. Therefore, the 'hydrothermal' chemosynthetic communities are supported by unusual high concentrations of methane and H2S fluids from the subseafloor. This is first discovery of "hydrothermal" chemosynthetic communities in cold seep environments of the world. No active seeps and the related phenomena are found around the Site G. Large seep carbonates around the summit are often covered by mud veneer and organisms. Therefore, this mud volcano is inferred to be

  8. Control of active sites in flocculation: Concept of equivalent active sites''

    SciTech Connect

    Behl, S.; Moudgil, B.M. . Dept. of Materials Science and Engineering)

    1993-12-01

    Flocculation and dispersion of solids are strong functions of the amount and conformation of the adsorbed polymer. Regions of dispersion and flocculation of solids with particular polymer molecules may be deduced from saturation adsorption data. The concept of equivalent active sites'' is proposed to explain flocculation and dispersion behavior irrespective of the amount or conformation of the adsorbed polymer. The concept has been further extended to study the selective flocculation process.

  9. Source and fate of methane seeping from continental margin sediments offshore Svalbard

    NASA Astrophysics Data System (ADS)

    Graves, C. A.; Stott, A.; Steinle, L.; Niemann, H.; Treude, T.; Berndt, C.; Wright, I. C.; Connelly, D.; James, R. H.

    2013-12-01

    A significant proportion of the world's organic carbon is currently trapped in and beneath submarine methane hydrates (e.g. Milkov, 2004). As ocean bottom waters warm, the gas hydrate stability zone (GHSZ) contracts, releasing gaseous methane into the sediments and potentially into the overlying water column and the atmosphere. In 2008, more than 250 plumes of methane gas were discovered rising from the seabed offshore Svalbard immediately upslope of the current GHSZ. As recent increases in ocean bottom water temperature may have destabilized hydrate in sediments beneath the plume locations, gas seepage has been hypothesized to be the result of this process (Westbrook et al., 2009). The implications of methane seepage offshore Svalbard in the context of changing global climate depend on the source and fate of the methane in these bubble plumes. To provide support for, or evidence contrary to, a gas-hydrate dissociation mechanism for methane release and to constrain potential atmospheric emission signatures we have characterized the chemical and isotopic signatures of: (i) hydrate recovered from within the GHSZ, (ii) shallow gas in sediments near the seep sites, (iii) plume gas bubbles, and (iv) dissolved gas in the water column. The absence of significant proportions of higher hydrocarbons in all samples suggests that the methane has a biogenic source, while methane carbon isotopic signatures point to a mixed biogenic and thermogenic origin. The chemical and isotopic composition of the hydrate-bound methane is consistent with that of the free gas in sediments below the seafloor seeps as well as the gas that escapes into the overlying water column. Away from bubble plume inputs (δ13C-CH4 -51 to -57 ‰) dissolved methane concentrations decrease while δ13C-CH4 values increase, indicating active aerobic oxidation of methane in the water column and implying surface seawater δ13C-CH4 values of < -20 ‰. Despite widespread methane supersaturated surface waters

  10. Community composition and temporal change at deep Gulf of Mexico cold seeps

    NASA Astrophysics Data System (ADS)

    Lessard-Pilon, Stephanie; Porter, Matthew D.; Cordes, Erik E.; MacDonald, Ian; Fisher, Charles R.

    2010-11-01

    Specialized cold-seep communities have been known to exist in the Gulf of Mexico (GOM) since the mid-1980s, but only recently has extensive research been carried out on sites at depths >1000 m. This study uses a combination of imagery and analyses within a Geographic Information Systems (GIS) framework to examine the composition of mussel and tubeworm communities at depths between 2200 and 2800 m in the Gulf of Mexico, spatial relations among the fauna, and changes in these communities over time. Photomosaics at three discrete seep communities were obtained in 2006 and a video mosaic of another community was obtained in 1992. Each of these communities was re-imaged in 2007. In addition, quantitative physical collections were made within two of the photomosaic sites and used to confirm the identification of megafauna, quantify the occurrence of smaller and cryptic macrofauna, and allow first-order calculations of biomass within the sites. Substrate type had a significant effect on community composition. Significant associations were identified between live mussels with anemones, shrimp, and sea cucumbers, and between tubeworm aggregations and Munidopsis sp. crabs and encrusting fauna, indicating differences in the composition of megafauna associated with adjacent mussel and tubeworm aggregations. Little change was seen in the total area colonized by foundation fauna (tubeworms and mussels) between years at any site. However, significant changes occurred in the positions of mussels, even over periods of a single year, at all sites, and evidence for the establishment of new tubeworm aggregations between 1992 and 2007 was noted at one site. These photomosaics provide data suggesting that environmental conditions can change over small spatial and temporal scales and mussels move in response to these changes. The successional trends are examined and compared to the patterns that have been documented in shallow (<1000-m depth) Gulf of Mexico seep communities.

  11. Cold-seep carbonates of the middle and lower continental slope, northern Gulf of Mexico

    NASA Astrophysics Data System (ADS)

    Roberts, Harry H.; Feng, Dong; Joye, Samantha B.

    2010-11-01

    Authigenic carbonates from cold seeps on the middle and lower continental slope of the northern Gulf of Mexico (GOM) exhibit a wide range of mineralogical and stable isotopic compositions. These carbonates consist of concretions and nodules in surface sediments, hardgrounds of crusts and isolated slabs, and mounded buildups of blocks and slabs of up to over 10 meters in relief above the surrounding seafloor. Mineralogically, the carbonates are dominated by high-Mg calcite (HMC) and aragonite. However, low levels (<5 wt%) of dolomite are present in most samples. Petrographically, Mg-calcite peloidal matrix and acicular to botryoidal aragonitic void-filling cements are the most frequent associations. The carbon isotopic compositions of the carbonates range from -60.8 to 14.0‰ PDB, indicating complex carbon sources that include 13C-depleted biogenic and thermogenic methane, biodegraded crude oil, seawater CO2, and 13C-enriched residual CO2 from methanogenesis. A similarly large variability in δ18O values (2.5 to 6.7‰ PDB) demonstrates the geochemical complexity of the slope, with some samples pointing toward an 18O-enriched oxygen source that is possibly related to advection of 18O-enriched formation water and/or to the decomposition of gas hydrate. A considerable range of mineralogical and isotopic variations in cold-seep carbonate composition was noted even within individual study sites. However, common trends occur across multiple geographic areas. This situation suggests that local controls on fluid and gas flux, types of seep hydrocarbons, the presence or absence of gas hydrate in the near-surface sediment, and chemosynthetic communities, as well as the temporal evolution of the local hydrocarbon reservoir, all may play a part in determining carbonate mineralogy and isotope geochemistry. The carbon isotope data clearly indicate that between-site variation is greater than within-site variation. Seep carbonates formed on the middle and lower continental slope

  12. Formation of modern and Paleozoic stratiform barite at cold methane seeps on continental margins

    USGS Publications Warehouse

    Torres, M.E.; Bohrmann, G.; Dube, T.E.; Poole, F.G.

    2003-01-01

    Stratiform (bedded) Paleozoic barite occurs as large conformable beds within organic- and chert-rich sediments; the beds lack major sulfide minerals and are the largest and most economically significant barite deposits in the geologic record. Existing models for the origin of bedded barite fail to explain all their characteristics: the deposits display properties consistent with an exhalative origin involving fluid ascent to the seafloor, but they lack appreciable polymetallic sulfide minerals and the corresponding strontium isotopic composition to support a hydrothermal vent source. A new mechanism of barite formation, along structurally controlled sites of cold fluid seepage in continental margins, involves barite remobilization in organic-rich, highly reducing sediments, transport of barium-rich fluids, and barite precipitation at cold methane seeps. The lithologic and depositional framework of Paleozoic and cold seep barite, as well as morphological, textural, and chemical characteristics of the deposits, and associations with chemosymbiotic fauna, all support a cold seep origin for stratiform Paleozoic barite. This understanding is highly relevant to paleoceanographic and paleotectonic studies, as well as to economic geology.

  13. High-throughput transcriptome sequencing of the cold seep mussel Bathymodiolus platifrons.

    PubMed

    Wong, Yue Him; Sun, Jin; He, Li Sheng; Chen, Lian Guo; Qiu, Jian-Wen; Qian, Pei-Yuan

    2015-01-01

    Bathymodiolid mussels dominate hydrothermal vents, cold methane/sulfide-hydrocarbon seeps, and other sites of organic enrichment. Here, we aimed to explore the innate immune system and detoxification mechanism of the deep sea mussel Bathymodiolus platifrons collected from a methane seep in the South China Sea. We sequenced the transcriptome of the mussels' gill, foot and mantle tissues and generated a transcriptomic database containing 96,683 transcript sequences. Based on GO and KEGG annotations, we reported transcripts that were related to the innate immune system, heavy metal detoxification and sulfide metabolic genes. Our in-depth analysis on the isoforms of peptidoglycan recognition protein (PGRP) that have different cellular location and potentially differential selectivity towards peptidoglycan (PGN) from gram-positive and gram-negative bacteria were differentially expressed in different tissues. We also reported a potentially novel form of metallothionein and the production of phytochelatin in B. platifrons, which has not been reported in any of its coastal relative Mytilus mussel species. Overall, the present study provided new insights into heavy metal and sulfide metabolism in B. platifrons and can be served as the basis for future molecular studies on host-symbiont interactions in cold seep mussels. PMID:26593439

  14. High-throughput transcriptome sequencing of the cold seep mussel Bathymodiolus platifrons

    PubMed Central

    Wong, Yue Him; Sun, Jin; He, Li Sheng; Chen, Lian Guo; Qiu, Jian-Wen; Qian, Pei-Yuan

    2015-01-01

    Bathymodiolid mussels dominate hydrothermal vents, cold methane/sulfide-hydrocarbon seeps, and other sites of organic enrichment. Here, we aimed to explore the innate immune system and detoxification mechanism of the deep sea mussel Bathymodiolus platifrons collected from a methane seep in the South China Sea. We sequenced the transcriptome of the mussels’ gill, foot and mantle tissues and generated a transcriptomic database containing 96,683 transcript sequences. Based on GO and KEGG annotations, we reported transcripts that were related to the innate immune system, heavy metal detoxification and sulfide metabolic genes. Our in-depth analysis on the isoforms of peptidoglycan recognition protein (PGRP) that have different cellular location and potentially differential selectivity towards peptidoglycan (PGN) from gram-positive and gram-negative bacteria were differentially expressed in different tissues. We also reported a potentially novel form of metallothionein and the production of phytochelatin in B. platifrons, which has not been reported in any of its coastal relative Mytilus mussel species. Overall, the present study provided new insights into heavy metal and sulfide metabolism in B. platifrons and can be served as the basis for future molecular studies on host-symbiont interactions in cold seep mussels. PMID:26593439

  15. High-throughput transcriptome sequencing of the cold seep mussel Bathymodiolus platifrons.

    PubMed

    Wong, Yue Him; Sun, Jin; He, Li Sheng; Chen, Lian Guo; Qiu, Jian-Wen; Qian, Pei-Yuan

    2015-11-23

    Bathymodiolid mussels dominate hydrothermal vents, cold methane/sulfide-hydrocarbon seeps, and other sites of organic enrichment. Here, we aimed to explore the innate immune system and detoxification mechanism of the deep sea mussel Bathymodiolus platifrons collected from a methane seep in the South China Sea. We sequenced the transcriptome of the mussels' gill, foot and mantle tissues and generated a transcriptomic database containing 96,683 transcript sequences. Based on GO and KEGG annotations, we reported transcripts that were related to the innate immune system, heavy metal detoxification and sulfide metabolic genes. Our in-depth analysis on the isoforms of peptidoglycan recognition protein (PGRP) that have different cellular location and potentially differential selectivity towards peptidoglycan (PGN) from gram-positive and gram-negative bacteria were differentially expressed in different tissues. We also reported a potentially novel form of metallothionein and the production of phytochelatin in B. platifrons, which has not been reported in any of its coastal relative Mytilus mussel species. Overall, the present study provided new insights into heavy metal and sulfide metabolism in B. platifrons and can be served as the basis for future molecular studies on host-symbiont interactions in cold seep mussels.

  16. Deep-water hydrocarbon seeps in Guaymas Basin, Gulf of California

    USGS Publications Warehouse

    Simoneit, B.R.T.; Lonsdale, P.F.; Edmond, J.M.; Shanks, Wayne C.

    1990-01-01

    Acoustically discovered hydrocarbon seeps along a transform fault zone on the Sonoran margin of Guaymas Basin and in the Southern Trough of Guaymas Basin were examined and sampled during dives of DSV Alvin. Seepage of methane and heavier hydrocarbons occurs through shallow pockmarks along the eroding crest of a steep anticline, 1600 m below sea level. Extensive ledges of aragonite crop out around the rims of the pockmarks; isotopic analysis indicates that carbonate precipitation is a result of methane oxidation. Seepage zones within the pockmarks support dense communities of Calyptogena, half buried in the mud; tubeworms (Lamellibracheae sp.) have colonized many of the aragonite outcrops. Though the margin site is only a few kilometers from a high-temperature sulfide-precipitating and petroleum-discharging vent system at a nearby center, its structural setting is more akin to pockmarks described from continental shelves, and its chemosynthetic fauna is more like that around low temperature seeps on other continental slopes and margins (e.g. Oregon, U.S.A., and Japan). The seep in the Southern Trough is a condensate-type petroleum (C1-C40) and rises as a plume from a young vent-mound system about 2000 m below sea level. ?? 1990.

  17. Food-Web Complexity in Guaymas Basin Hydrothermal Vents and Cold Seeps

    PubMed Central

    Olu, Karine; Dubois, Stanislas F.; Escobar-Briones, Elva; Gelinas, Yves; Menot, Lénaick; Sarrazin, Jozée

    2016-01-01

    In the Guaymas Basin, the presence of cold seeps and hydrothermal vents in close proximity, similar sedimentary settings and comparable depths offers a unique opportunity to assess and compare the functioning of these deep-sea chemosynthetic ecosystems. The food webs of five seep and four vent assemblages were studied using stable carbon and nitrogen isotope analyses. Although the two ecosystems shared similar potential basal sources, their food webs differed: seeps relied predominantly on methanotrophy and thiotrophy via the Calvin-Benson-Bassham (CBB) cycle and vents on petroleum-derived organic matter and thiotrophy via the CBB and reductive tricarboxylic acid (rTCA) cycles. In contrast to symbiotic species, the heterotrophic fauna exhibited high trophic flexibility among assemblages, suggesting weak trophic links to the metabolic diversity of chemosynthetic primary producers. At both ecosystems, food webs did not appear to be organised through predator-prey links but rather through weak trophic relationships among co-occurring species. Examples of trophic or spatial niche differentiation highlighted the importance of species-sorting processes within chemosynthetic ecosystems. Variability in food web structure, addressed through Bayesian metrics, revealed consistent trends across ecosystems. Food-web complexity significantly decreased with increasing methane concentrations, a common proxy for the intensity of seep and vent fluid fluxes. Although high fluid-fluxes have the potential to enhance primary productivity, they generate environmental constraints that may limit microbial diversity, colonisation of consumers and the structuring role of competitive interactions, leading to an overall reduction of food-web complexity and an increase in trophic redundancy. Heterogeneity provided by foundation species was identified as an additional structuring factor. According to their biological activities, foundation species may have the potential to partly release the

  18. The effect of pulse venting on anaerobic oxidation of methane and pyrite formation in the cold seep environment, offshore SW Taiwan

    NASA Astrophysics Data System (ADS)

    Cheng, Wan-Yen; Lin, Saulwood; Tseng, Yi-Ting; Chen, NeiChen; Hsieh, I.-Chih

    2016-04-01

    AOM (Anaerobic oxidation of methane) is a key process in seep environment. Sulfate was consumed during oxidation of methane or organic matter with pyrite as a major end product in the anoxic marine environment. Typical changes observed in the pore water include an increase of methane with depth beneath the SMTZ (sulfate methane transition zone), as a result of diffusion and/or advection, and appearances of a dissolved sulfide maximum underneath a dissolved iron peak with depth. A number of other related biogeochemical processes and end products may register their respective changes in sediments as a result of AOM and related reactions. However, flux, time and duration of gas migration may have changed by either long term processes, e.g., tectonic activities and/or climatic induced sea level changes, or short term, e.g., tidal variations. There is relatively little study addressing termination of gas migrations and subsequent changes in the seep environments. In this study, we will present our study on a seep environment where pulses of gas migration may have occurred with a number of chemical anomalies in sediments. We have collected pore water and sediments for their chemical compositions of sulfate, dissolved sulfide, chloride, organic carbon, carbonate carbon and pyrite as well as echo sounding for flares, and towcam for sea surface topography and benthic community. Our results show that methane gas may have migrated in sediments in carrying out AOM reaction and pyrite formation, however, gas migration may have been relatively short and in pulses. Pulses of gas migration resulted in little or even no sulfate reduction in pore water, but with appearance of dissolved sulfide as well as very high concentrations of pyrite in sediments. Flares were observed but not constantly at the site where chemical anomalies were observed. Pulses of gas migration may come from solid gas hydrate formation and dissociation as evidence from pore water chloride enrichment and

  19. High Diversity of Anaerobic Alkane-Degrading Microbial Communities in Marine Seep Sediments Based on (1-methylalkyl)succinate Synthase Genes

    PubMed Central

    Stagars, Marion H.; Ruff, S. Emil; Amann, Rudolf; Knittel, Katrin

    2016-01-01

    Alkanes comprise a substantial fraction of crude oil and are prevalent at marine seeps. These environments are typically anoxic and host diverse microbial communities that grow on alkanes. The most widely distributed mechanism of anaerobic alkane activation is the addition of alkanes to fumarate by (1-methylalkyl)succinate synthase (Mas). Here we studied the diversity of MasD, the catalytic subunit of the enzyme, in 12 marine sediments sampled at seven seeps. We aimed to identify cosmopolitan species as well as to identify factors structuring the alkane-degrading community. Using next generation sequencing we obtained a total of 420 MasD species-level operational taxonomic units (OTU0.96) at 96% amino acid identity. Diversity analysis shows a high richness and evenness of alkane-degrading bacteria. Sites with similar hydrocarbon composition harbored similar alkane-degrading communities based on MasD genes; the MasD community structure is clearly driven by the hydrocarbon source available at the various seeps. Two of the detected OTU0.96 were cosmopolitan and abundant while 75% were locally restricted, suggesting the presence of few abundant and globally distributed alkane degraders as well as specialized variants that have developed under specific conditions at the diverse seep environments. Of the three MasD clades identified, the most diverse was affiliated with Deltaproteobacteria. A second clade was affiliated with both Deltaproteobacteria and Firmicutes likely indicating lateral gene transfer events. The third clade was only distantly related to known alkane-degrading organisms and comprises new divergent lineages of MasD homologs, which might belong to an overlooked phylum of alkane-degrading bacteria. In addition, masD geneFISH allowed for the in situ identification and quantification of the target guild in alkane-degrading enrichment cultures. Altogether, these findings suggest an unexpectedly high number of yet unknown groups of anaerobic alkane degraders

  20. Natural volcanic CO2 seeps reveal future trajectories for host-microbial associations in corals and sponges.

    PubMed

    Morrow, Kathleen M; Bourne, David G; Humphrey, Craig; Botté, Emmanuelle S; Laffy, Patrick; Zaneveld, Jesse; Uthicke, Sven; Fabricius, Katharina E; Webster, Nicole S

    2015-03-17

    Atmospheric carbon dioxide (CO2) levels are rapidly rising causing an increase in the partial pressure of CO2 (pCO2) in the ocean and a reduction in pH known as ocean acidification (OA). Natural volcanic seeps in Papua New Guinea expel 99% pure CO2 and thereby offer a unique opportunity to explore the effects of OA in situ. The corals Acropora millepora and Porites cylindrica were less abundant and hosted significantly different microbial communities at the CO2 seep than at nearby control sites <500 m away. A primary driver of microbial differences in A. millepora was a 50% reduction of symbiotic Endozoicomonas. This loss of symbiotic taxa from corals at the CO2 seep highlights a potential hurdle for corals to overcome if they are to adapt to and survive OA. In contrast, the two sponges Coelocarteria singaporensis and Cinachyra sp. were ∼ 40-fold more abundant at the seep and hosted a significantly higher relative abundance of Synechococcus than sponges at control sites. The increase in photosynthetic microbes at the seep potentially provides these species with a nutritional benefit and enhanced scope for growth under future climate scenarios (thus, flexibility in symbiosis may lead to a larger niche breadth). The microbial community in the apparently pCO2-sensitive sponge species S. massa was not significantly different between sites. These data show that responses to elevated pCO2 are species-specific and that the stability and flexibility of microbial partnerships may have an important role in shaping and contributing to the fitness and success of some hosts.

  1. Natural volcanic CO2 seeps reveal future trajectories for host–microbial associations in corals and sponges

    PubMed Central

    Morrow, Kathleen M; Bourne, David G; Humphrey, Craig; Botté, Emmanuelle S; Laffy, Patrick; Zaneveld, Jesse; Uthicke, Sven; Fabricius, Katharina E; Webster, Nicole S

    2015-01-01

    Atmospheric carbon dioxide (CO2) levels are rapidly rising causing an increase in the partial pressure of CO2 (pCO2) in the ocean and a reduction in pH known as ocean acidification (OA). Natural volcanic seeps in Papua New Guinea expel 99% pure CO2 and thereby offer a unique opportunity to explore the effects of OA in situ. The corals Acropora millepora and Porites cylindrica were less abundant and hosted significantly different microbial communities at the CO2 seep than at nearby control sites <500 m away. A primary driver of microbial differences in A. millepora was a 50% reduction of symbiotic Endozoicomonas. This loss of symbiotic taxa from corals at the CO2 seep highlights a potential hurdle for corals to overcome if they are to adapt to and survive OA. In contrast, the two sponges Coelocarteria singaporensis and Cinachyra sp. were ∼40-fold more abundant at the seep and hosted a significantly higher relative abundance of Synechococcus than sponges at control sites. The increase in photosynthetic microbes at the seep potentially provides these species with a nutritional benefit and enhanced scope for growth under future climate scenarios (thus, flexibility in symbiosis may lead to a larger niche breadth). The microbial community in the apparently pCO2-sensitive sponge species S. massa was not significantly different between sites. These data show that responses to elevated pCO2 are species-specific and that the stability and flexibility of microbial partnerships may have an important role in shaping and contributing to the fitness and success of some hosts. PMID:25325380

  2. New Isotopic Constraints on the Sources of Methane at Sites of Active Continental Serpentinization

    NASA Astrophysics Data System (ADS)

    Wang, D. T.; Gruen, D.; Morrill, P. L.; Rietze, A.; Nealson, K. H.; Kubo, M. D.; Cardace, D.; Schrenk, M. O.; Hoehler, T. M.; McCollom, T. M.; Etiope, G.; Hosgormez, H.; Schoell, M.; Ono, S.

    2014-12-01

    At continental sites of serpentinization, high concentrations of reduced gases (e.g., H2, CH4) are frequently found in association with highly-alkaline groundwater. Identification of the process(es) responsible for the generation of methane—as well as the source(s) of C & H—in these environments has been challenging. The difficulty is due to both the wide range of processes (microbial, thermal, abiotic) that could be involved, and the limited number of parameters that are accessible to currently-available analytical technologies (e.g., δ13C, δD). The recent development of a new technique based on tunable infrared laser spectroscopy [1] has enabled the fully-resolved quantification of four isotopologues of methane: 12CH4, 13CH4, 12CH3D, and 13CH3D, a doubly-substituted ("clumped") isotopologue. We used this technique to measure 13CH3D in gases sampled from continental sites of serpentinization, in order to provide independent constraints on C-H bond-forming processes involved in the generation of the methane found in these systems. Our study sites are hosted in ultramafic units that are presently undergoing serpentinization. These include The Cedars peridotite body (Calif., USA) [2], the Coast Range Ophiolite Microbial Observatory (Calif., USA) [3], and the Chimaera seep (Tekirova Ophiolite, Turkey) [4]. Preliminary measurements indicate that Δ13CH3D (the deviation of the abundance of 13CH3D from the stochastic distribution) in methane sampled from these sites spans nearly the entire range of thermodynamically-predicted values, from >+5‰ (13CH3D-based apparent equilibrium temperature < 45 °C) to ~0‰ (Tapparent → ∞). The new 13CH3D data is complemented by conventional geochemical analyses (e.g., dissolved ions/organics, δ13C, δD) on samples collected during the same field campaigns. Our study demonstrates that the measurement of 13CH3D provides a new dimension of isotopic constraints for unraveling the complex processes controlling the distribution

  3. Dissecting the active site of a photoreceptor protein

    NASA Astrophysics Data System (ADS)

    Hoff, Wouter; Hara, Miwa; Ren, Jie; Moghadam, Farzaneh; Xie, Aihua; Kumauchi, Masato

    While enzymes are quite large molecules, functionally important chemical events are often limited to a small region of the protein: the active site. The physical and chemical properties of residues at such active sites are often strongly altered compared to the same groups dissolved in water. Understanding such effects is important for unraveling the mechanisms underlying protein function and for protein engineering, but has proven challenging. Here we report on our ongoing efforts on using photoactive yellow protein (PYP), a bacterial photoreceptor, as a model system for such effects. We will report on the following questions: How many residues affect active site properties? Are these residues in direct physical contact with the active site? Can functionally important residues be recognized in the crystal structure of a protein? What structural resolution is needed to understand active sites? What spectroscopic techniques are most informative? Which weak interactions dominate active site properties?

  4. Phylogenetic placement of Cibicidoides wuellerstorfi (Schwager, 1866) from methane seeps and non-seep habitats on the Pacific margin.

    PubMed

    Burkett, A M; Rathburn, A E; Pérez, M E; Levin, L A; Cha, H; Rouse, G W

    2015-01-01

    Benthic foraminifera are among the most abundant groups found in deep-sea habitats, including methane seep environments. Unlike many groups, no endemic foraminiferal species have been reported from methane seeps, and to our knowledge, genetic data are currently sparse for Pacific deep-sea foraminifera. In an effort to understand the relationships between seep and non-seep populations of the deep-sea foraminifera Cibicidoides wuellerstorfi, a common paleo-indicator species, specimens from methane seeps in the Pacific were analyzed and compared to one another for genetic similarities of small subunit rDNA (SSU rDNA) sequences. Pacific Ocean C. wuellerstorfi were also compared to those collected from other localities around the world (based on 18S gene available on Genbank, e.g., Schweizer et al., 2009). Results from this study revealed that C. wuellerstorfi living in seeps near Costa Rica and Hydrate Ridge are genetically similar to one another at the species level. Individuals collected from the same location that display opposite coiling directions (dextral and sinstral) had no species level genetic differences. Comparisons of specimens with genetic information available from Genbank (SSU rDNA) showed that Pacific individuals, collected for this study, are genetically similar to those previously analyzed from the North Atlantic and Antarctic. These observations provide strong evidence for the true cosmopolitan nature of C. wuellerstorfi and highlight the importance of understanding how these microscopic organisms are able to maintain sufficient genetic exchange to remain within the same species between seep and non-seep habitats and over global distances.

  5. Mars Surveyor Project Landing Site Activities

    NASA Technical Reports Server (NTRS)

    Gulick, Virginia C.; Briggs, Geoffrey; Saunders, R. Stephen; Gilmore, Martha; Soderblom, Larry

    1999-01-01

    The Mars Surveyor Program --now a cooperative program led by NASA and CNES along with other international partners -- is underway. It has the primary science objective of furthering our understanding of the biological potential and possible biological history of Mars and has the complementary objective of improving our understanding of martian climate evolution and planetary history The missions will develop technology and acquire data necessary for eventual human Exploration. Launches of orbiters, landers and rovers will take place in 2001 and in 2003; in 2005 a complete system will be launched capable of returning samples to Earth by 2008. A key aspect of the program is the selection of landing sites. This abstract 1) reports on the status of the landing site selection process that begins with the 2001 lander mission and 2) outlines be opportunities for the Mars community to provide input into the landing site selection process.

  6. Mars Surveyor Project Landing Site Activities

    NASA Technical Reports Server (NTRS)

    Gulick, V. C.; Briggs, Geoffrey; Saunders, R. Stephen; Gilmore, Martha; Soderblom, Larry

    1999-01-01

    The Mars Surveyor Program -- now a cooperative program led by NASA and CNES along with other international partners -- is underway. It has the primary science objective of furthering our understanding of the biological potential and possible biological history of Mars and has the complementary objective of improving our understanding of martian climate evolution and planetary history. The missions will develop technology and acquire data necessary for eventual human exploration. Launches of orbiters, landers and rovers will take place in 2001 and in 2003; in 2005 a complete system will be launched capable of returning samples to Earth by 2008. A key aspect of the program is the selection of landing sites. This abstract 1) reports on the status of the landing site selection process that begins with the 2001 lander mission and 2) outlines the opportunities for the Mars community to provide input into the landing site selection process.

  7. Use of remote sensing techniques and aeromagnetic data to study episodic oil seep discharges along the Gulf of Suez in Egypt.

    PubMed

    Kaiser, M F; Aziz, A M; Ghieth, B M

    2013-07-15

    Four successive oil discharges were observed during the last 2 years following the recording of the earthquake events. Oil slicks were clearly observed in the thermal band of the Enhanced Thematic Mapper images acquired during the discharge events. Lineaments were extracted from the ETM+ image data and SRTM (DEM). The seismic activity is conformable in time and spatially related to active major faults and structural lineaments. The concerned site was subjected to a numerous earthquakes with magnitudes ranging from 3 to 5.4 Mb. Aeromagnetic field data analyses indicated the existence of deep major faults crossing the Gebel El-Zeit and the Mellaha basins (oil reservoirs). The magnetic field survey showed major distinctive fault striking NE-SW at 7000 m depth. Occurrence of these faults at great depth enables the crude oil to migrate upward and appear at the surfaces as oil seeps onshore and as offshore slicks in the Gemsa-Hurghada coastal zone. PMID:23688834

  8. Use of remote sensing techniques and aeromagnetic data to study episodic oil seep discharges along the Gulf of Suez in Egypt.

    PubMed

    Kaiser, M F; Aziz, A M; Ghieth, B M

    2013-07-15

    Four successive oil discharges were observed during the last 2 years following the recording of the earthquake events. Oil slicks were clearly observed in the thermal band of the Enhanced Thematic Mapper images acquired during the discharge events. Lineaments were extracted from the ETM+ image data and SRTM (DEM). The seismic activity is conformable in time and spatially related to active major faults and structural lineaments. The concerned site was subjected to a numerous earthquakes with magnitudes ranging from 3 to 5.4 Mb. Aeromagnetic field data analyses indicated the existence of deep major faults crossing the Gebel El-Zeit and the Mellaha basins (oil reservoirs). The magnetic field survey showed major distinctive fault striking NE-SW at 7000 m depth. Occurrence of these faults at great depth enables the crude oil to migrate upward and appear at the surfaces as oil seeps onshore and as offshore slicks in the Gemsa-Hurghada coastal zone.

  9. Activation of Inhibitors by Sortase Triggers Irreversible Modification of the Active Site*S

    PubMed Central

    Maresso, Anthony W.; Wu, Ruiying; Kern, Justin W.; Zhang, Rongguang; Janik, Dorota; Missiakas, Dominique M.; Duban, Mark-Eugene; Joachimiak, Andrzej; Schneewind, Olaf

    2011-01-01

    Sortases anchor surface proteins to the cell wall of Gram-positive pathogens through recognition of specific motif sequences. Loss of sortase leads to large reductions in virulence, which identifies sortase as a target for the development of antibacterials. By screening 135,625 small molecules for inhibition, we report here that aryl (β-amino)ethyl ketones inhibit sortase enzymes from staphylococci and bacilli. Inhibition of sortases occurs through an irreversible, covalent modification of their active site cysteine. Sortases specifically activate this class of molecules via β-elimination, generating a reactive olefin intermediate that covalently modifies the cysteine thiol. Analysis of the three-dimensional structure of Bacillus anthracis sortase B with and without inhibitor provides insights into the mechanism of inhibition and reveals binding pockets that can be exploited for drug discovery. PMID:17545669

  10. The bifunctional active site of s-adenosylmethionine synthetase. Roles of the active site aspartates.

    PubMed

    Taylor, J C; Markham, G D

    1999-11-12

    S-Adenosylmethionine (AdoMet) synthetase catalyzes the biosynthesis of AdoMet in a unique enzymatic reaction. Initially the sulfur of methionine displaces the intact tripolyphosphate chain (PPP(i)) from ATP, and subsequently PPP(i) is hydrolyzed to PP(i) and P(i) before product release. The crystal structure of Escherichia coli AdoMet synthetase shows that the active site contains four aspartate residues. Aspartate residues Asp-16* and Asp-271 individually provide the sole protein ligand to one of the two required Mg(2+) ions (* denotes a residue from a second subunit); aspartates Asp-118 and Asp-238* are proposed to interact with methionine. Each aspartate has been changed to an uncharged asparagine, and the metal binding residues were also changed to alanine, to assess the roles of charge and ligation ability on catalytic efficiency. The resultant enzyme variants all structurally resemble the wild type enzyme as indicated by circular dichroism spectra and are tetramers. However, all have k(cat) reductions of approximately 10(3)-fold in AdoMet synthesis, whereas the MgATP and methionine K(m) values change by less than 3- and 8-fold, respectively. In the partial reaction of PPP(i) hydrolysis, mutants of the Mg(2+) binding residues have >700-fold reduced catalytic efficiency (k(cat)/K(m)), whereas the D118N and D238*N mutants are impaired less than 35-fold. The catalytic efficiency for PPP(i) hydrolysis by Mg(2+) site mutants is improved by AdoMet, like the wild type enzyme. In contrast AdoMet reduces the catalytic efficiency for PPP(i) hydrolysis by the D118N and D238*N mutants, indicating that the events involved in AdoMet activation are hindered in these methionyl binding site mutants. Ca(2+) uniquely activates the D271A mutant enzyme to 15% of the level of Mg(2+), in contrast to the approximately 1% Ca(2+) activation of the wild type enzyme. This indicates that the Asp-271 side chain size is a discriminator between the activating ability of Ca(2+) and the

  11. Methane-derived carbonates form at the sediment-bedrock interface in a shallow marine gas seep.

    NASA Astrophysics Data System (ADS)

    Kimball, J.; Ding, H.; Valentine, D. L.

    2006-12-01

    Hydrocarbon seeps occur world-wide, and release large quantities of oil and natural gas to the ocean and atmosphere. One of the world's most prolific hydrocarbon seep fields is located just offshore from Goleta, CA, and serves as the study site for this investigation. In the course of investigating gas fluxes from a 10 m deep coastal seep, samples of seafloor bedrock were collected by scuba diving during a time of low sediment burden. These samples were found to be concretions composed primarily of carbonate-cemented sand. The delta13C values of the carbonate range from -25 to -32 per mille, and indicate a role for methane oxidation in the formation of the carbonates. Long chain fatty acids were extracted from the concretions and were quantified, identified, and analyzed for their 13C composition. Fatty acids typical of sulfate reducing bacteria were observed, and interpreted as a signature of anoxia. Further mineralogical and isotopic studies are planned. From these observations we interpret a shallow water origin for these concretions, whereby the seasonal migration of sand to the seep environment drives anoxia and anaerobic methane oxidation at the sediment-bedrock interface. The alkalinity generated from sulfate reduction causes the precipitation of methane-derived carbonate- which forms a concretion with sand.

  12. The active site of ribulose-bisphosphate carboxylase/oxygenase

    SciTech Connect

    Hartman, F.C.

    1991-01-01

    The active site of ribulose-bisphosphate carboxylase/oxygenase requires interacting domains of adjacent, identical subunits. Most active-site residues are located within the loop regions of an eight-stranded {beta}/{alpha}-barrel which constitutes the larger C-terminal domain; additional key residues are located within a segment of the smaller N-terminal domain which partially covers the mouth of the barrel. Site-directed mutagenesis of the gene encoding the enzyme from Rhodospirillum rubrum has been used to delineate functions of active-site residues. 6 refs., 2 figs.

  13. Savannah River Site prioritization of transition activities

    SciTech Connect

    Finley, R.H.

    1993-11-01

    Effective management of SRS conversion from primarily a production facility to other missions (or Decontamination and Decommissioning (D&D)) requires a systematic and consistent method of prioritizing the transition activities. This report discusses the design of a prioritizing method developed to achieve systematic and consistent methods of prioritizing these activities.

  14. DOE site performance assessment activities. Radioactive Waste Technical Support Program

    SciTech Connect

    Not Available

    1990-07-01

    Information on performance assessment capabilities and activities was collected from eight DOE sites. All eight sites either currently dispose of low-level radioactive waste (LLW) or plan to dispose of LLW in the near future. A survey questionnaire was developed and sent to key individuals involved in DOE Order 5820.2A performance assessment activities at each site. The sites surveyed included: Hanford Site (Hanford), Idaho National Engineering Laboratory (INEL), Los Alamos National Laboratory (LANL), Nevada Test Site (NTS), Oak Ridge National Laboratory (ORNL), Paducah Gaseous Diffusion Plant (Paducah), Portsmouth Gaseous Diffusion Plant (Portsmouth), and Savannah River Site (SRS). The questionnaire addressed all aspects of the performance assessment process; from waste source term to dose conversion factors. This report presents the information developed from the site questionnaire and provides a comparison of site-specific performance assessment approaches, data needs, and ongoing and planned activities. All sites are engaged in completing the radioactive waste disposal facility performance assessment required by DOE Order 5820.2A. Each site has achieved various degrees of progress and have identified a set of critical needs. Within several areas, however, the sites identified common needs and questions.

  15. Safety Oversight of Decommissioning Activities at DOE Nuclear Sites

    SciTech Connect

    Zull, Lawrence M.; Yeniscavich, William

    2008-01-15

    The Defense Nuclear Facilities Safety Board (Board) is an independent federal agency established by Congress in 1988 to provide nuclear safety oversight of activities at U.S. Department of Energy (DOE) defense nuclear facilities. The activities under the Board's jurisdiction include the design, construction, startup, operation, and decommissioning of defense nuclear facilities at DOE sites. This paper reviews the Board's safety oversight of decommissioning activities at DOE sites, identifies the safety problems observed, and discusses Board initiatives to improve the safety of decommissioning activities at DOE sites. The decommissioning of former defense nuclear facilities has reduced the risk of radioactive material contamination and exposure to the public and site workers. In general, efforts to perform decommissioning work at DOE defense nuclear sites have been successful, and contractors performing decommissioning work have a good safety record. Decommissioning activities have recently been completed at sites identified for closure, including the Rocky Flats Environmental Technology Site, the Fernald Closure Project, and the Miamisburg Closure Project (the Mound site). The Rocky Flats and Fernald sites, which produced plutonium parts and uranium materials for defense needs (respectively), have been turned into wildlife refuges. The Mound site, which performed R and D activities on nuclear materials, has been converted into an industrial and technology park called the Mound Advanced Technology Center. The DOE Office of Legacy Management is responsible for the long term stewardship of these former EM sites. The Board has reviewed many decommissioning activities, and noted that there are valuable lessons learned that can benefit both DOE and the contractor. As part of its ongoing safety oversight responsibilities, the Board and its staff will continue to review the safety of DOE and contractor decommissioning activities at DOE defense nuclear sites.

  16. Mutations of fumarase that distinguish between the active site and a nearby dicarboxylic acid binding site.

    PubMed Central

    Weaver, T.; Lees, M.; Banaszak, L.

    1997-01-01

    Two mutant forms of fumarase C from E. coli have been made using PCR and recombinant DNA. The recombinant form of the protein included a histidine arm on the C-terminal facilitating purification. Based on earlier studies, two different carboxylic acid binding sites, labeled A- and B-, were observed in crystal structures of the wild type and inhibited forms of the enzyme. A histidine at each of the sites was mutated to an asparagine. H188N at the A-site resulted in a large decrease in specific activity, while the H129N mutation at the B-site had essentially no effect. From the results, we conclude that the A-site is indeed the active site, and a dual role for H188 as a potential catalytic base is proposed. Crystal structures of the two mutant proteins produced some unexpected results. Both mutations reduced the affinity for the carboxylic acids at their respective sites. The H129N mutant should be particularly useful in future kinetic studies because it sterically blocks the B-site with the carboxyamide of asparagine assuming the position of the ligand's carboxylate. In the H188N mutation at the active site, the new asparagine side chain still interacts with an active site water that appears to have moved slightly as a result of the mutation. PMID:9098893

  17. Ionizable Side Chains at Catalytic Active Sites of Enzymes

    PubMed Central

    Jimenez-Morales, David; Liang, Jie

    2012-01-01

    Catalytic active sites of enzymes of known structure can be well defined by a modern program of computational geometry. The CASTp program was used to define and measure the volume of the catalytic active sites of 573 enzymes in the Catalytic Site Atlas database. The active sites are identified as catalytic because the amino acids they contain are known to participate in the chemical reaction catalyzed by the enzyme. Acid and base side chains are reliable markers of catalytic active sites. The catalytic active sites have 4 acid and 5 base side chains, in an average volume of 1072 Å3. The number density of acid side chains is 8.3 M (in chemical units); the number density of basic side chains is 10.6 M. The catalytic active site of these enzymes is an unusual electrostatic and steric environment in which side chains and reactants are crowded together in a mixture more like an ionic liquid than an ideal infinitely dilute solution. The electrostatics and crowding of reactants and side chains seems likely to be important for catalytic function. In three types of analogous ion channels, simulation of crowded charges accounts for the main properties of selectivity measured in a wide range of solutions and concentrations. It seems wise to use mathematics designed to study interacting complex fluids when making models of the catalytic active sites of enzymes. PMID:22484856

  18. Constraining silica diagenesis in methane-seep deposits

    NASA Astrophysics Data System (ADS)

    Smrzka, Daniel; Kraemer, Stephan; Zwicker, Jennifer; Birgel, Daniel; Fischer, David; Kasten, Sabine; Goedert, James; Peckmann, Jörn

    2015-04-01

    Silicified fossils and silicified early diagenetic carbonate minerals as well as authigenic silica phases are common in ancient seep limestones. Silicification of calcareous fossils facilitates the preservation of even fine details and is therefore of great interest to paleontologists, permitting a reliable taxonomic identification of the chemosynthesis-based taxa that lived at ancient hydrocarbon seeps. Four methane-seep limestones of Paleozoic, Mesozoic, and Cenozoic age with abundant silica phases are compared in this study; one, an Eocene seep deposit on the north shore of the Columbia River at Knappton, western Washington State, USA, is described for the first time. Its lithology and fabrics, negative δ13Ccarbonate values as low as -27.6‰, and 13C-depleted biomarkers of archaea involved in the anaerobic oxidation of methane (AOM) reveal that the carbonate rock formed at a methane seep. The background sediments of the studied Phanerozoic seep limestones contain abundant siliceous microfossils, radiolarian tests in case of the Late Carboniferous Dwyka Group deposits from Namibia and the Late Triassic Graylock Butte deposits from eastern Oregon (USA), diatom frustules in case of the Eocene Knappton limestone and an Oligocene seep deposit from the Lincoln Creek Formation (western Washington State, USA). These microfossils are regarded as the source of dissolved silica, causing silicification and silica precipitation. All seep limestones used in this study are characterized by very similar paragenetic sequences. Silicified fossils include brachiopods and worm tubes, silica cements include microquartz, fibrous microcrystalline silica, and megaquartz. The silica cements formed after the AOM-derived cements ceased to precipitate but before equant calcite spar formed. Numerical experiments using the computer code PHREEQC were conducted to test the hypothesis that (1) AOM increases the pH of pore waters and that (2) this pH increase subsequently mobilizes biogenic

  19. Relationships between the distribution and stable isotopic composition of living benthic foraminifera and cold methane seep biogeochemistry in Monterey Bay, California

    NASA Astrophysics Data System (ADS)

    Rathburn, Anthony E.; PéRez, M. Elena; Martin, Jonathan B.; Day, Shelley A.; Mahn, Chris; Gieskes, Joris; Ziebis, Wiebke; Williams, David; Bahls, Amanda

    2003-12-01

    As part of an ongoing effort to explore the use of foraminifera as a means to assess modern and ancient methane release, we compared ambient pore water chemistry with the distribution and stable isotopic composition of living (rose Bengal stained) foraminifera in MBARI ROV Ventana tube cores taken from modern seepage areas (about 1000 m water depth) in Monterey Bay, California. Benthic foraminiferal isotopic differences between sites clearly indicate that methane-influenced pore waters affect foraminiferal distributions and carbonate isotope geochemistry. Carbon isotope signatures of living benthic foraminifera did not conform to the very negative (-30 to -48‰), methane-influenced carbon isotope values of the pore waters they live in. Instead, the influence of methane seep pore waters was reflected in the greater range and carbon isotopic variability of living seep foraminifera compared with published δ13C values of foraminifera living in nonseep habitats. It is not clear what relative influences biological, ecological, and physical factors have on the carbon isotopic signatures observed in seep foraminifera. Substantial carbon isotope differences can exist between individuals of the same seep species. For instance, δ13C values of living Globobulimina pacifica varied by as much as 2.9‰ between seeps within 8 km of each other, whereas δ13C values of living Uvigerina peregrina varied by as much as 1.95‰ within the same seep. Provided there is no diagenetic alteration of the test carbonate, isotopic results of individual seep foraminifera support the hypothesis that foraminifera can be used to assess past and present methane seepage.

  20. Cruise summary for P-1-02-SC: acoustic imaging of natural oil and gas seeps and measurement of dissolved methane concentration in coastal waters near Pt. Conception, California

    USGS Publications Warehouse

    Lorenson, T.D.; Dougherty, Jennifer A.; Ussler, William; Paull, Charles K.

    2003-01-01

    Water-column acoustic anomalies and methane concentrations were documented in coastal waters surrounding Pt. Conception, California, in March 2002. The purpose of this survey, supported by the Minerals Management Service, was to locate active oil and gas seeps in the area as a background for further studies to determine hydrocarbon flux, mainly oil, into the environment. Objectives in reaching this goal are to (1) document the locations and geochemically fingerprint natural seeps within the offshore southern Santa Maria Basin; (2) geochemically fingerprint coastal tar residues and potential sources, both onshore and offshore, in this region; (3) establish chemical correlations between offshore active seeps and coastal residues thus linking seep sources to oil residues; (4) measure the rate of natural seepage of individual seeps and attempt to assess regional natural oil and gas seepage rates; (5) attempt to predict transport pathways of oil from seep sources to the coastline and; (6) interpret the petroleum system history for the natural seeps. This survey, addressing objective 1, focused on the area from offshore Surf Beach to the north and Gaviota to the south in water depths ranging from 20 to 500m. In addition, nine stations were sampled outside this area to provide a regional context. Water-column methane concentrations were measured in water samples collected from the R/V Point Sur with Niskin bottles from various depths. A total of 724 water samples from 94 stations were collected.

  1. Cold seeps associated with a submarine debris avalanche deposit at Kick'em Jenny volcano, Grenada (Lesser Antilles)

    NASA Astrophysics Data System (ADS)

    Carey, Steven; Ballard, Robert; Bell, Katherine L. C.; Bell, Richard J.; Connally, Patrick; Dondin, Frederic; Fuller, Sarah; Gobin, Judith; Miloslavich, Patricia; Phillips, Brennan; Roman, Chris; Seibel, Brad; Siu, Nam; Smart, Clara

    2014-11-01

    Remotely operated vehicle (ROV) exploration at the distal margins of a debris avalanche deposit from Kick'em Jenny submarine volcano in Grenada has revealed areas of cold seeps with chemosynthetic-based ecosystems. The seeps occur on steep slopes of deformed, unconsolidated hemipelagic sediments in water depths between 1952 and 2042 m. Two main areas consist of anastomosing systems of fluid flow that have incised local sediments by several tens of centimeters. No temperature anomalies were observed in the vent areas and no active flow was visually observed, suggesting that the venting may be waning. An Eh sensor deployed on a miniature autonomous plume recorder (MAPR) recorded a positive signal and the presence of live organisms indicates at least some venting is still occurring. The chemosynthetic-based ecosystem included giant mussels (Bathymodiolus sp.) with commensal polychaetes (Branchipolynoe sp.) and cocculinid epibionts, other bivalves, Siboglinida (vestimentiferan) tubeworms, other polychaetes, and shrimp, as well as associated heterotrophs, including gastropods, anemones, crabs, fish, octopods, brittle stars, and holothurians. The origin of the seeps may be related to fluid overpressure generated during the collapse of an ancestral Kick'em Jenny volcano. We suggest that deformation and burial of hemipelagic sediment at the front and base of the advancing debris avalanche led to fluid venting at the distal margin. Such deformation may be a common feature of marine avalanches in a variety of geological environments especially along continental margins, raising the possibility of creating large numbers of ephemeral seep-based ecosystems.

  2. How oil seeps, discoveries relate in deepwater Gulf of Mexico

    SciTech Connect

    Sassen, R.; Brooks, J.M.; Kennicutt, M.C. II; MacDonald, I.R.; Guinasso, N.L. Jr. )

    1993-04-19

    Biomarker compounds of crude oils from deep-water Gulf of Mexico seeps are consistent with an origin from deeply-buried Mesozoic carbonate source rocks. The known oil reserves, however, are trapped in shallow Miocene to Pleistocene sands. Several kilometers of vertical migration must be invoked to explain the presence of crude oil from deep sources in shallow reservoir sands. Salt-related fractures and faults serve as efficient conduits for vertical migration through the thick sedimentary section. Thermal history models suggest that oil migration off Louisiana started during the Miocene and continues at present in some areas. The paper describes visual inspection of seeps; gives an overview of the deep Gulf; and discusses seeps and fields, case histories, and frontier basins.

  3. First respiration estimates of cold-seep vesicomyid bivalves from in situ total oxygen uptake measurements.

    PubMed

    Decker, Carole; Caprais, Jean-Claude; Khripounoff, Alexis; Olu, Karine

    2012-04-01

    Vesicomyid bivalves are one of the most abundant symbiont-bearing species inhabiting deep-sea reducing ecosystems. Nevertheless, except for the hydrothermal vent clam Calyptogena magnifica, their metabolic rates have not been documented, and only assessed with ex situ experiments. In this study, gathering benthic chamber measurements and biomass estimation, we give the first in situ assessment of the respiration rate of these bivalves. The giant pockmark Regab, located at 3160m depth along the Congo-Angola margin, is a cold-seep site characterised by dense assemblages of two species of vesicomyids: Christineconcha regab and Laubiericoncha chuni with high dominance of C. regab. Two sites with dense aggregates of vesicomyids were selected to measure total oxygen uptake (TOU), and methane fluxes using IFREMER's benthic chamber CALMAR deployed by the ROV Quest 4000 (MARUM). Photographs were taken and bivalves were sampled using blade corers to estimate density and biomass. Total oxygen uptake was higher at Site 2 compared to Site 1 (respectively 492 mmol.m(-2).d(-1) and 332 mmol.m(-2).d(-1)). However, given vesicomyid densities and biomass, mean oxygen consumption rates were similar at both sites (1.9 to 2.5 μmol.g total dry mass(-1).h(-1) at the Site 1 and 1.8 to 2.3 μmol.g total dry mass(-1).h(-1) at Site 2). These respiration rates are higher than published ex situ estimates for cold-seep or hydrothermal vent bivalves. Although methane fluxes at the base of sulphide production were clearly higher at Site 2 (14.6 mmol.m(-2).d(-1)) than at Site 1 (0.3 mmol.m(-2).d(-1)), they do not seem to influence the respiration rates of these bivalves associated to sulphide-oxidizing symbionts. PMID:22578572

  4. First respiration estimates of cold-seep vesicomyid bivalves from in situ total oxygen uptake measurements.

    PubMed

    Decker, Carole; Caprais, Jean-Claude; Khripounoff, Alexis; Olu, Karine

    2012-04-01

    Vesicomyid bivalves are one of the most abundant symbiont-bearing species inhabiting deep-sea reducing ecosystems. Nevertheless, except for the hydrothermal vent clam Calyptogena magnifica, their metabolic rates have not been documented, and only assessed with ex situ experiments. In this study, gathering benthic chamber measurements and biomass estimation, we give the first in situ assessment of the respiration rate of these bivalves. The giant pockmark Regab, located at 3160m depth along the Congo-Angola margin, is a cold-seep site characterised by dense assemblages of two species of vesicomyids: Christineconcha regab and Laubiericoncha chuni with high dominance of C. regab. Two sites with dense aggregates of vesicomyids were selected to measure total oxygen uptake (TOU), and methane fluxes using IFREMER's benthic chamber CALMAR deployed by the ROV Quest 4000 (MARUM). Photographs were taken and bivalves were sampled using blade corers to estimate density and biomass. Total oxygen uptake was higher at Site 2 compared to Site 1 (respectively 492 mmol.m(-2).d(-1) and 332 mmol.m(-2).d(-1)). However, given vesicomyid densities and biomass, mean oxygen consumption rates were similar at both sites (1.9 to 2.5 μmol.g total dry mass(-1).h(-1) at the Site 1 and 1.8 to 2.3 μmol.g total dry mass(-1).h(-1) at Site 2). These respiration rates are higher than published ex situ estimates for cold-seep or hydrothermal vent bivalves. Although methane fluxes at the base of sulphide production were clearly higher at Site 2 (14.6 mmol.m(-2).d(-1)) than at Site 1 (0.3 mmol.m(-2).d(-1)), they do not seem to influence the respiration rates of these bivalves associated to sulphide-oxidizing symbionts.

  5. Trace element behaviour at cold seeps and the potential export of dissolved iron to the ocean

    NASA Astrophysics Data System (ADS)

    Lemaitre, Nolwenn; Bayon, Germain; Ondréas, Hélène; Caprais, Jean-Claude; Freslon, Nicolas; Bollinger, Claire; Rouget, Marie-Laure; de Prunelé, Alexis; Ruffine, Livio; Olu-Le Roy, Karine; Sarthou, Géraldine

    2014-10-01

    Seawater samples were collected by submersible above methane seeps in the Gulf of Guinea (Regab and Baboon pockmarks) in order to investigate the behaviour of iron (Fe), manganese (Mn) and rare earth elements (REE) during fluid seepage. Our aim was to determine whether cold seeps may represent potential sources of dissolved chemical species to the ocean. Dissolved (<0.45 μm filtered samples) and total dissolvable (unfiltered samples) concentrations were determined over ∼50 m long vertical transects above the seafloor and at various discrete locations within the pockmarks. We show that substantial amounts of Fe and Mn are released into seawater during seepage of methane-rich fluids. Mn is exported almost quantitatively in the dissolved form (more than 90% of total Mn; mean MnDISS∼12±11 nmol/kg). Although a significant fraction of Fe is bound to particulate phases, the dissolved iron pool still accounts on average for approximately 20 percent of total iron flux at vent sites (mean FeDISS∼22±11 nmol/kg). This dissolved Fe fraction also appears to remain stable in the water column. In contrast, there was no evidence for any significant benthic fluxes of pore water REE associated with fluid seepage at the studied sites. Overall, our results point towards distinct trace element behaviour during fluid seepage, with potential implications for the marine geochemical budget. The absence of any dissolved REE enrichments in bottom waters clearly indicates effective removal in sub-surface sediments. Most likely, precipitation of authigenic mineral phases at cold seeps (i.e. carbonates) represents a net sink for these elements. While Mn appears to behave near-conservatively during fluid seepage, the observed relative stability of dissolved Fe in the water column above seepage sites could be explained by complexation with strong organic ligands and/or the presence of Fe-bearing sulfide nanoparticles, as reported previously for submarine hydrothermal systems. Considering

  6. In situ environment rather than substrate type dictates microbial community structure of biofilms in a cold seep system.

    PubMed

    Lee, On On; Wang, Yong; Tian, Renmao; Zhang, Weipeng; Shek, Chun Shum; Bougouffa, Salim; Al-Suwailem, Abdulaziz; Batang, Zenon B; Xu, Wei; Wang, Guang Chao; Zhang, Xixiang; Lafi, Feras F; Bajic, Vladmir B; Qian, Pei-Yuan

    2014-01-01

    Using microscopic and molecular techniques combined with computational analysis, this study examined the structure and composition of microbial communities in biofilms that formed on different artificial substrates in a brine pool and on a seep vent of a cold seep in the Red Sea to test our hypothesis that initiation of the biofilm formation and spreading mode of microbial structures differs between the cold seep and the other aquatic environments. Biofilms on different substrates at two deployment sites differed morphologically, with the vent biofilms having higher microbial abundance and better structural features than the pool biofilms. Microbes in the pool biofilms were more taxonomically diverse and mainly composed of various sulfate-reducing bacteria whereas the vent biofilms were exclusively dominated by sulfur-oxidizing Thiomicrospira. These results suggest that the redox environments at the deployment sites might have exerted a strong selection on microbes in the biofilms at two sites whereas the types of substrates had limited effects on the biofilm development. PMID:24399144

  7. Methane Seep in Shallow-Water Permeable Sediment Harbors High Diversity of Anaerobic Methanotrophic Communities, Elba, Italy.

    PubMed

    Ruff, S Emil; Kuhfuss, Hanna; Wegener, Gunter; Lott, Christian; Ramette, Alban; Wiedling, Johanna; Knittel, Katrin; Weber, Miriam

    2016-01-01

    The anaerobic oxidation of methane (AOM) is a key biogeochemical process regulating methane emission from marine sediments into the hydrosphere. AOM is largely mediated by consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB), and has mainly been investigated in deep-sea sediments. Here we studied methane seepage at four spots located at 12 m water depth in coastal, organic carbon depleted permeable sands off the Island of Elba (Italy). We combined biogeochemical measurements, sequencing-based community analyses and in situ hybridization to investigate the microbial communities of this environment. Increased alkalinity, formation of free sulfide and nearly stoichiometric methane oxidation and sulfate reduction rates up to 200 nmol g(-1) day(-1) indicated the predominance of sulfate-coupled AOM. With up to 40 cm thickness the zones of AOM activity were unusually large and occurred in deeper sediment horizons (20-50 cm below seafloor) as compared to diffusion-dominated deep-sea seeps, which is likely caused by advective flow of pore water due to the shallow water depth and permeability of the sands. Hydrodynamic forces also may be responsible for the substantial phylogenetic and unprecedented morphological diversity of AOM consortia inhabiting these sands, including the clades ANME-1a/b, ANME-2a/b/c, ANME-3, and their partner bacteria SEEP-SRB1a and SEEP-SRB2. High microbial dispersal, the availability of diverse energy sources and high habitat heterogeneity might explain that the emission spots shared few microbial taxa, despite their physical proximity. Although the biogeochemistry of this shallow methane seep was very different to that of deep-sea seeps, their key functional taxa were very closely related, which supports the global dispersal of key taxa and underlines strong selection by methane as the predominant energy source. Mesophilic, methane-fueled ecosystems in shallow-water permeable sediments may comprise distinct

  8. Methane Seep in Shallow-Water Permeable Sediment Harbors High Diversity of Anaerobic Methanotrophic Communities, Elba, Italy.

    PubMed

    Ruff, S Emil; Kuhfuss, Hanna; Wegener, Gunter; Lott, Christian; Ramette, Alban; Wiedling, Johanna; Knittel, Katrin; Weber, Miriam

    2016-01-01

    The anaerobic oxidation of methane (AOM) is a key biogeochemical process regulating methane emission from marine sediments into the hydrosphere. AOM is largely mediated by consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB), and has mainly been investigated in deep-sea sediments. Here we studied methane seepage at four spots located at 12 m water depth in coastal, organic carbon depleted permeable sands off the Island of Elba (Italy). We combined biogeochemical measurements, sequencing-based community analyses and in situ hybridization to investigate the microbial communities of this environment. Increased alkalinity, formation of free sulfide and nearly stoichiometric methane oxidation and sulfate reduction rates up to 200 nmol g(-1) day(-1) indicated the predominance of sulfate-coupled AOM. With up to 40 cm thickness the zones of AOM activity were unusually large and occurred in deeper sediment horizons (20-50 cm below seafloor) as compared to diffusion-dominated deep-sea seeps, which is likely caused by advective flow of pore water due to the shallow water depth and permeability of the sands. Hydrodynamic forces also may be responsible for the substantial phylogenetic and unprecedented morphological diversity of AOM consortia inhabiting these sands, including the clades ANME-1a/b, ANME-2a/b/c, ANME-3, and their partner bacteria SEEP-SRB1a and SEEP-SRB2. High microbial dispersal, the availability of diverse energy sources and high habitat heterogeneity might explain that the emission spots shared few microbial taxa, despite their physical proximity. Although the biogeochemistry of this shallow methane seep was very different to that of deep-sea seeps, their key functional taxa were very closely related, which supports the global dispersal of key taxa and underlines strong selection by methane as the predominant energy source. Mesophilic, methane-fueled ecosystems in shallow-water permeable sediments may comprise distinct

  9. Methane Seep in Shallow-Water Permeable Sediment Harbors High Diversity of Anaerobic Methanotrophic Communities, Elba, Italy

    PubMed Central

    Ruff, S. Emil; Kuhfuss, Hanna; Wegener, Gunter; Lott, Christian; Ramette, Alban; Wiedling, Johanna; Knittel, Katrin; Weber, Miriam

    2016-01-01

    The anaerobic oxidation of methane (AOM) is a key biogeochemical process regulating methane emission from marine sediments into the hydrosphere. AOM is largely mediated by consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB), and has mainly been investigated in deep-sea sediments. Here we studied methane seepage at four spots located at 12 m water depth in coastal, organic carbon depleted permeable sands off the Island of Elba (Italy). We combined biogeochemical measurements, sequencing-based community analyses and in situ hybridization to investigate the microbial communities of this environment. Increased alkalinity, formation of free sulfide and nearly stoichiometric methane oxidation and sulfate reduction rates up to 200 nmol g-1 day-1 indicated the predominance of sulfate-coupled AOM. With up to 40 cm thickness the zones of AOM activity were unusually large and occurred in deeper sediment horizons (20–50 cm below seafloor) as compared to diffusion-dominated deep-sea seeps, which is likely caused by advective flow of pore water due to the shallow water depth and permeability of the sands. Hydrodynamic forces also may be responsible for the substantial phylogenetic and unprecedented morphological diversity of AOM consortia inhabiting these sands, including the clades ANME-1a/b, ANME-2a/b/c, ANME-3, and their partner bacteria SEEP-SRB1a and SEEP-SRB2. High microbial dispersal, the availability of diverse energy sources and high habitat heterogeneity might explain that the emission spots shared few microbial taxa, despite their physical proximity. Although the biogeochemistry of this shallow methane seep was very different to that of deep-sea seeps, their key functional taxa were very closely related, which supports the global dispersal of key taxa and underlines strong selection by methane as the predominant energy source. Mesophilic, methane-fueled ecosystems in shallow-water permeable sediments may comprise distinct

  10. Active site - a site of binding of affinity inhibitors in baker's yeast inorganic pyrophosphatase

    SciTech Connect

    Svyato, I.E.; Sklyankina, V.A.; Avaeva, S.M.

    1986-03-20

    The interaction of the enzyme-substrate complex with methyl phosphate, O-phosphoethanolamine, O-phosphopropanolamine, N-acetylphosphoserine, and phosphoglyolic acid, as well as pyrophosphatase, modified by monoesters of phosphoric acid, with pyrophosphate and tripolyphosphate, was investigated. It was shown that the enzyme containing the substrate in the active site does not react with monophosphates, but modified pyrophosphatase entirely retains the ability to bind polyanions to the regulatory site. It is concluded that the inactivation of baker's yeast inorganic pyrophosphatase by monoesters of phosphoric acid, which are affinity inhibitors of it, is the result of modification of the active site of the enzyme.

  11. Observation of alive benthos under a sharp hypoxia and high H2S concentrations inside the microbial mats (methane seeps in the shallows of Black Sea)

    NASA Astrophysics Data System (ADS)

    Gulin, M.

    2009-04-01

    In 2008 experimental as well as in situ investigations were implemented for studying of vitality and locomotion activity of the micro- and meiobenthos associated with the gas seeps. Research area: near-shore shallow field with the gas seeps, southern sector of Tarkhankut Cape, NW Crimea Peninsula, Black Sea. Cuvette LDO-oxymeter coupled with other sensors and also life-time diagnostics of the organisms including microscopic video filming were used for this case. Concentrations of dissolved methane in the pore space of microbial mats were varied from 27 to 1076 µL/cm3 (220 on average). Content of organic matter of the uppermost seep mats was approximately in 50 times higher than at the background stations. Probably, such enrichments is attractive for benthic organisms. At the same time, H2S-pollution of seep microbiotope environment is detected as critical (Eh = -400/-460 mV). Near to the gas seeps alive and active Polychaeta, Nematoda, Harpacticoida and Ciliata were found. It is important, that anoxia-adapted organisms of the last two groups were quickly died at contact with air.

  12. Metagenomic analysis of microbial consortium from natural crude oil that seeps into the marine ecosystem offshore Southern California

    PubMed Central

    Hawley, Erik R.; Piao, Hailan; Scott, Nicole M.; Malfatti, Stephanie; Pagani, Ioanna; Huntemann, Marcel; Chen, Amy; Glavina del Rio, Tijana; Foster, Brian; Copeland, Alex; Jansson, Janet; Pati, Amrita; Tringe, Susannah; Gilbert, Jack A.; Lorenson, Thomas D.; Hess, Matthias

    2014-01-01

    Crude oils can be major contaminants of the marine ecosystem and microorganisms play a significant role in the degradation of its main constituents. To increase our understanding of the microbial hydrocarbon degradation process in the marine ecosystem, we collected crude oil from an active seep area located in the Santa Barbara Channel (SBC) and generated a total of about 52 Gb of raw metagenomic sequence data. The assembled data comprised ~500 Mb, representing ~1.1 million genes derived primarily from chemolithoautotrophic bacteria. Members of Oceanospirillales, a bacterial order belonging to the Deltaproteobacteria, recruited less than 2% of the assembled genes within the SBC metagenome. In contrast, the microbial community associated with the oil plume that developed in the aftermath of the Deepwater Horizon (DWH) blowout in 2010, was dominated by Oceanospirillales, which comprised more than 60% of the metagenomic data generated from the DWH oil plume. This suggests that Oceanospirillales might play a less significant role in the microbially mediated hydrocarbon conversion within the SBC seep oil compared to the DWH plume oil. We hypothesize that this difference results from the SBC oil seep being mostly anaerobic, while the DWH oil plume is aerobic. Within the Archaea, the phylum Euryarchaeota, recruited more than 95% of the assembled archaeal sequences from the SBC oil seep metagenome, with more than 50% of the sequences assigned to members of the orders Methanomicrobiales and Methanosarcinales. These orders contain organisms capable of anaerobic methanogenesis and methane oxidation (AOM) and we hypothesize that these orders – and their metabolic capabilities – may be fundamental to the ecology of the SBC oil seep. PMID:25197496

  13. Metagenomic analysis of microbial consortium from natural crude oil that seeps into the marine ecosystem offshore Southern California

    SciTech Connect

    Hawley, Erik R.; Piao, Hailan; Scott, Nicole M.; Malfatti, Stephanie; Pagani, Ioanna; Huntemann, Marcel; Chen, Amy; del Rio, Tijana G.; Foster, Brian; Copeland, A.; Jansson, Janet K.; Pati, Amrita; Gilbert, Jack A.; Tringe, Susannah G.; Lorenson, Thomas D.; Hess, Matthias

    2014-01-02

    Crude oils can be major contaminants of the marine ecosystem and microorganisms play a significant role in the degradation of the main constituents of crude oil. To increase our understanding of the microbial hydrocarbon degradation process in the marine ecosystem, we collected crude oil from an active seep area located in the Santa Barbara Channel (SBC) and generated a total of about 52 Gb of raw metagenomic sequence data. The assembled data comprised ~500 Mb, representing ~1.1 million genes derived primarily from chemolithoautotrophic bacteria. Members of Oceanospirillales, a bacterial order belonging to the Deltaproteobacteria, recruited less than 2% of the assembled genes within the SBC metagenome. In contrast, the microbial community associated with the oil plume that developed in the aftermath of the Deepwater Horizon (DWH) blowout in 2010, was dominated by Oceanospirillales, which comprised more than 60% of the metagenomic data generated from the DWH oil plume. This suggests that Oceanospirillales might play a less significant role in the microbially mediated hydrocarbon conversion within the SBC seep oil compared to the DWH plume oil. We hypothesize that this difference results from the SBC oil seep being mostly anaerobic, while the DWH oil plume is aerobic. Within the Archaea, the phylum Euryarchaeota, recruited more than 95% of the assembled archaeal sequences from the SBC oil seep metagenome, with more than 50% of the sequences assigned to members of the orders Methanomicrobiales and Methanosarcinales. These orders contain organisms capable of anaerobic methanogenesis and methane oxidation (AOM) and we hypothesize that these orders and their metabolic capabilities may be fundamental to the ecology of the SBC oil seep.

  14. A novel approach to predict active sites of enzyme molecules.

    PubMed

    Chou, Kuo-Chen; Cai, Yu-dong

    2004-04-01

    Enzymes are critical in many cellular signaling cascades. With many enzyme structures being solved, there is an increasing need to develop an automated method for identifying their active sites. However, given the atomic coordinates of an enzyme molecule, how can we predict its active site? This is a vitally important problem because the core of an enzyme molecule is its active site from the viewpoints of both pure scientific research and industrial application. In this article, a topological entity was introduced to characterize the enzymatic active site. Based on such a concept, the covariant discriminant algorithm was formulated for identifying the active site. As a paradigm, the serine hydrolase family was demonstrated. The overall success rate by jackknife test for a data set of 88 enzyme molecules was 99.92%, and that for a data set of 50 independent enzyme molecules was 99.91%. Meanwhile, it was shown through an example that the prediction algorithm can also be used to find any typographic error of a PDB file in annotating the constituent amino acids of catalytic triad and to suggest a possible correction. The very high success rates are due to the introduction of a covariance matrix in the prediction algorithm that makes allowance for taking into account the coupling effects among the key constituent atoms of active site. It is anticipated that the novel approach is quite promising and may become a useful high throughput tool in enzymology, proteomics, and structural bioinformatics. PMID:14997541

  15. Growth exponents in surface models with non-active sites

    NASA Astrophysics Data System (ADS)

    Santos, M.; Figueiredo, W.; Aarão Reis, F. D. A.

    2006-11-01

    In this work, we studied the role played by the inactive sites present on the substrate of a growing surface. In our model, one particle sticks at the surface if the site where it falls is an active site. However, we allow the deposited particle to diffuse along the surface in accordance with some mechanism previously defined. Using Monte Carlo simulations, and some analytical results, we have investigated the model in (1+1) and (2+1) dimensions considering different relaxation mechanisms. We show that the consideration of non-active sites is a crucial point in the model. In fact, we have seen that the saturation regime is not observed for any value of the density of inactive sites. Besides, the growth exponent β turns to be one, at long times, whatever the mechanism of diffusion we consider in one and two dimensions.

  16. A small ribozyme with dual-site kinase activity

    PubMed Central

    Biondi, Elisa; Maxwell, Adam W.R.; Burke, Donald H.

    2012-01-01

    Phosphoryl transfer onto backbone hydroxyls is a recognized catalytic activity of nucleic acids. We find that kinase ribozyme K28 possesses an unusually complex active site that promotes (thio)phosphorylation of two residues widely separated in primary sequence. After allowing the ribozyme to radiolabel itself by phosphoryl transfer from [γ-32P]GTP, DNAzyme-mediated cleavage yielded two radiolabeled cleavage fragments, indicating phosphorylation sites within each of the two cleavage fragments. These sites were mapped by alkaline digestion and primer extension pausing. Enzymatic digestion and mutational analysis identified nucleotides important for activity and established the active structure as being a constrained pseudoknot with unusual connectivity that may juxtapose the two reactive sites. Nuclease sensitivities for nucleotides near the pseudoknot core were altered in the presence of GTPγS, indicating donor-induced folding. The 5′ target site was more strongly favored in full-length ribozyme K28 (128 nt) than in truncated RNAs (58 nt). Electrophoretic mobilities of self-thiophosphorylated products on organomercurial gels are distinct from the 5′ mono-thiophosphorylated product produced by reaction with polynucleotide kinase, potentially indicating simultaneous labeling of both sites within individual RNA strands. Our evidence supports a single, compact structure with local dynamics, rather than global rearrangement, as being responsible for dual-site phosphorylation. PMID:22618879

  17. Discovery of a natural CO2 seep in the German North Sea: Implications for shallow dissolved gas and seep detection

    NASA Astrophysics Data System (ADS)

    McGinnis, Daniel F.; Schmidt, Mark; Delsontro, Tonya; Themann, SöRen; Rovelli, Lorenzo; Reitz, Anja; Linke, Peter

    2011-03-01

    A natural carbon dioxide (CO2) seep was discovered during an expedition to the southern German North Sea (October 2008). Elevated CO2 levels of ˜10-20 times above background were detected in seawater above a natural salt dome ˜30 km north of the East-Frisian Island Juist. A single elevated value 53 times higher than background was measured, indicating a possible CO2 point source from the seafloor. Measured pH values of around 6.8 support modeled pH values for the observed high CO2 concentration. These results are presented in the context of CO2 seepage detection, in light of proposed subsurface CO2 sequestering and growing concern of ocean acidification. We explore the boundary conditions of CO2 bubble and plume seepage and potential flux paths to the atmosphere. Shallow bubble release experiments conducted in a lake combined with discrete-bubble modeling suggest that shallow CO2 outgassing will be difficult to detect as bubbles dissolve very rapidly (within meters). Bubble-plume modeling further shows that a CO2 plume will lose buoyancy quickly because of rapid bubble dissolution while the newly CO2-enriched water tends to sink toward the seabed. Results suggest that released CO2 will tend to stay near the bottom in shallow systems (<200 m) and will vent to the atmosphere only during deep water convection (water column turnover). While isotope signatures point to a biogenic source, the exact origin is inconclusive because of dilution. This site could serve as a natural laboratory to further study the effects of carbon sequestration below the seafloor.

  18. The origin of gas seeps and shallow gas in northern part of South China Sea

    NASA Astrophysics Data System (ADS)

    Li, M.; Jin, X.

    2003-04-01

    The northern part of South China Sea is of passive continental margin, which geologic units include shelf, slope and deep sea basin. There are rifting basins forming during Paleogene (or Cretaceous ?) to Quaternary developed on shelf and slope, which sediments are dominated by fluvial and lake clastic rock of Paleogene, and marine clastic rock and carbonate of Neogene - Quaternary. The main basins include the Pearl River Mouth Basin, Beibu Gulf basin, Qiongdongnan Basin and Yinggehai basin. They contain rich oil and gas resources, and have become important industrial oil and gas producing region in South China Sea. With the increasing of petroleum exploration actives and marine petroleum engineering, it has been paid more attention to the investigation and research of gas seeps and shallow gas, for they become a potential threaten to the marine engineering while they are regarded as the indicators of industrial oil and gas. By study the distribution and geochemical characteristics of gas seeps in northeast part of Yinggehai basin and shallow gas in sediments on slope, combined with their regional geologic background, this paper deals with the origin, migration pathway and emission mechanism of gas seeps and shallow gas in northern part of South China Sea, for providing a base knowledge for the evaluation of marine engineering geology. In northeast part of Yinggehai basin gas seeps have been found and recorded for near 100 years. During 1990s, as a part of petroleum exploration, the gas seeps in the basin have been investigated and research by oil companies (Baojia Huang et al., 1992; Jiaqiong He et al., 2000). Gas seeps were found in shallow water area along southwest coast of Hainan Island, water depth usually less than 50 m. The occurrence of gas seeps can be divided into two types: (1) gas continuously emission, continuous gas bubbles groups can be detected by sonar underwater and observed on water surface. (2) gas intermittently emission, the time intervals

  19. Cold-seep mollusks are older than the general marine mollusk fauna.

    PubMed

    Kiel, Steffen; Little, Crispin T S

    2006-09-01

    The origin and possible antiquity of faunas at deep-sea hydrothermal vents and seeps have been debated since their discovery. We used the fossil record of seep mollusks to show that the living seep genera have significantly longer geologic ranges than the marine mollusks in general, but have ranges similar to those of deep-sea taxa, suggesting that seep faunas may be shaped by the factors that drive the evolution of life in the deep sea in general. Our data indicate that deep-sea anoxic/dysoxic events did not affect seep faunas, casting doubt on the suggested anoxic nature and/or global extent of these events.

  20. Cold-seep mollusks are older than the general marine mollusk fauna.

    PubMed

    Kiel, Steffen; Little, Crispin T S

    2006-09-01

    The origin and possible antiquity of faunas at deep-sea hydrothermal vents and seeps have been debated since their discovery. We used the fossil record of seep mollusks to show that the living seep genera have significantly longer geologic ranges than the marine mollusks in general, but have ranges similar to those of deep-sea taxa, suggesting that seep faunas may be shaped by the factors that drive the evolution of life in the deep sea in general. Our data indicate that deep-sea anoxic/dysoxic events did not affect seep faunas, casting doubt on the suggested anoxic nature and/or global extent of these events. PMID:16960004

  1. Architecture and active site of particulate methane monooxygenase

    PubMed Central

    Culpepper, Megen A.; Rosenzweig, Amy C.

    2012-01-01

    Particulate methane monooxygenase (pMMO) is an integral membrane metalloenzyme that oxidizes methane to methanol in methanotrophic bacteria, organisms that live on methane gas as their sole carbon source. Understanding pMMO function has important implications for bioremediation applications and for the development of new, environmentally friendly catalysts for the direct conversion of methane to methanol. Crystal structures of pMMOs from three different methanotrophs reveal a trimeric architecture, consisting of three copies each of the pmoB, pmoA, and pmoC subunits. There are three distinct metal centers in each protomer of the trimer, mononuclear and dinuclear copper sites in the periplasmic regions of pmoB and a mononuclear site within the membrane that can be occupied by copper or zinc. Various models for the pMMO active site have been proposed within these structural constraints, including dicopper, tricopper, and diiron centers. Biochemical and spectroscopic data on pMMO and recombinant soluble fragments, denoted spmoB proteins, indicate that the active site involves copper and is located at the site of the dicopper center in the pmoB subunit. Initial spectroscopic evidence for O2 binding at this site has been obtained. Despite these findings, questions remain about the active site identity and nuclearity and will be the focus of future studies. PMID:22725967

  2. Methanopyrus kandleri topoisomerase V contains three distinct AP lyase active sites in addition to the topoisomerase active site.

    PubMed

    Rajan, Rakhi; Osterman, Amy; Mondragón, Alfonso

    2016-04-20

    Topoisomerase V (Topo-V) is the only topoisomerase with both topoisomerase and DNA repair activities. The topoisomerase activity is conferred by a small alpha-helical domain, whereas the AP lyase activity is found in a region formed by 12 tandem helix-hairpin-helix ((HhH)2) domains. Although it was known that Topo-V has multiple repair sites, only one had been mapped. Here, we show that Topo-V has three AP lyase sites. The atomic structure and Small Angle X-ray Scattering studies of a 97 kDa fragment spanning the topoisomerase and 10 (HhH)2 domains reveal that the (HhH)2 domains extend away from the topoisomerase domain. A combination of biochemical and structural observations allow the mapping of the second repair site to the junction of the 9th and 10th (HhH)2 domains. The second site is structurally similar to the first one and to the sites found in other AP lyases. The 3rd AP lyase site is located in the 12th (HhH)2 domain. The results show that Topo-V is an unusual protein: it is the only known protein with more than one (HhH)2 domain, the only known topoisomerase with dual activities and is also unique by having three AP lyase repair sites in the same polypeptide. PMID:26908655

  3. Methanopyrus kandleri topoisomerase V contains three distinct AP lyase active sites in addition to the topoisomerase active site

    PubMed Central

    Rajan, Rakhi; Osterman, Amy; Mondragón, Alfonso

    2016-01-01

    Topoisomerase V (Topo-V) is the only topoisomerase with both topoisomerase and DNA repair activities. The topoisomerase activity is conferred by a small alpha-helical domain, whereas the AP lyase activity is found in a region formed by 12 tandem helix-hairpin-helix ((HhH)2) domains. Although it was known that Topo-V has multiple repair sites, only one had been mapped. Here, we show that Topo-V has three AP lyase sites. The atomic structure and Small Angle X-ray Scattering studies of a 97 kDa fragment spanning the topoisomerase and 10 (HhH)2 domains reveal that the (HhH)2 domains extend away from the topoisomerase domain. A combination of biochemical and structural observations allow the mapping of the second repair site to the junction of the 9th and 10th (HhH)2 domains. The second site is structurally similar to the first one and to the sites found in other AP lyases. The 3rd AP lyase site is located in the 12th (HhH)2 domain. The results show that Topo-V is an unusual protein: it is the only known protein with more than one (HhH)2 domain, the only known topoisomerase with dual activities and is also unique by having three AP lyase repair sites in the same polypeptide. PMID:26908655

  4. Geochemistry of natural gases from mud volcanoes and surface gas seeps in NW-Columbia

    SciTech Connect

    Beeunas, M.A. ); Schoell, M. ); Beroiz, C. )

    1991-03-01

    Mud volcanoes and natural gas seeps are common in the southwest-northeast-trending Sinu Atlantico basin (SAB) and San Jacinto Fold Belt (SJFB) of NW-Colombia. The structural subunits are part of a highly complex active continental margin where the sediments become increasingly younger to the west from Late Cretaceous to Early Tertiary in the SJFB to Late Tertiary in the SAB. Some of the mud volcanoes are permanently active and form huge structures and are often aligned along major faults. Both seep and mud volcano gases are with low C{sub 2}-C{sub 4} and CO{sub 2} contents. Carbon and hydrogen isotope concentrations allow the subdivision into four groups of gas. These gases can be divided into four genetic based on their carbon and hydrocarbon isotope compositions. The isotopic variability of the different groups attests to the fact that very different gas-forming processes are or have been operating in the subsurface ranging from low-temperature thermogenesis. The various groups show, with few exceptions, a distinct regional distribution: Mud volcanoes and seeps with bacterial gases are restricted to the southern part of the SAB where the greatest thickness of young sediments is observed; gases of mixed thermogenic and bacterial origin are found in the coastal areas of the northern SAB; gases of thermogenic origin are predominantly observed in the SJFB; the thermogenic gases of Group 3 are restricted to two locations in the north of the SJFB. This regional association of genetic gas types with specific geotectonic units reflects different thermal histories of the respective tectonic areas and allowed the authors to delineate prospective areas for oil in NW-Colombia.

  5. Constraining Microbial Cycling of Carbon and Sulfur and Relationships to Macrofaunal Ecology in Cretaceous Cold Seeps

    NASA Astrophysics Data System (ADS)

    Lyons, T.; Shapiro, R.; Benjamin, G.; Bates, S.; Anderson, J.; Gilhooly, W.; Parsons-Hubbard, K.

    2007-12-01

    The Pierre Shale in Colorado hosts an extensive fault-controlled network of Late Cretaceous fossil-rich carbonate accumulations expressed topographically as the Teepee Buttes. An ancient methane seep origin for these features is clear from carbonate-carbon isotope values that are as light as -50 per mil and from organic biomakers that point to abundant aerobic and anaerobic methanotrophy. A primary goal is to identify the patterns of sulfate reduction linked to anaerobic oxidation of methane (and other possible hydrocarbons) through a detailed isotopic study of sulfur preserved as carbonate-associated sulfate trapped within authigenic and biogenic phases. We are further constraining these patterns by calibrating them against our studies of modern seeps in the Gulf of Mexico. Delineating micro- and macrofaunal symbiotic linkages driven by chemosynthetic (sulfide-oxidizing) bacterial communities is a related goal. Through ongoing analysis of shell material, we hope to fingerprint thiotrophic activity within specific organisms, including lucinid bivalves. Consistent with the abundant benthic macrofauna, C- S-Fe analysis of the host shales indicates that bottom waters were oxygenated at the time of seep activity. Our work expands on previous studies to include a detailed paragenesis of the carbonate fabrics, which is aided by high-resolution C isotope and trace element analysis. Our results show that early-formed carbonates are characterized by depleted C isotope values, comparatively heavy O, low Fe contents, and high Sr and Mg. Late carbonates show isotope and elemental relationships that are generally opposite those of the early precipitates. Botryoidal cements, pelsparites, and yellow calcite dominate the early diagenetic forms. Blocky white sparry cements formed later, and micrite is mostly a product of later micritization of early fabrics and correspondingly shows broad geochemical properties. The overarching focus of all this work is to understand the timing

  6. From the Belly of the Beast: Biogeochemistry and geomicrobiology of a fluid seep at Chimaera [Yanartas], Turkey

    NASA Astrophysics Data System (ADS)

    Woycheese, K. M.; Yargicoglu, E. N.; Cardace, D.; Meyer-Dombard, D. R.

    2012-12-01

    Serpentinization is proposed to support chemolithotrophic growth of microorganisms in surface and subsurface environments1. Abiotic CH4 production associated with terrestrial ophiolitic outcrops has been reported in southeastern Turkey2. The Yanartas (Chimaera) seep, located within the Tekirova ophiolite in Çirali, Antalya, Turkey, is one of the largest onshore CH4 seeps documented2-5. The seep consists of dozens of flames erupting from fractures within the ophiolite outcrop that burn continuously on CH4 (80-90% of gas composition2) produced by subsurface serpentinization reactions. Previous studies have focused on gas geochemistry from these seeps2, 4, 5. While past reports have not found active fluid seeps at Yanartas2, in February 2012, a fluid seep (possibly ephemeral) originating from a fracture was identified, which supported microbial mats over an outflow channel several m in length. This is the first investigation of the biogeochemical and geomicrobiological properties of this newly-discovered fluid seep. The fluid seep emits from a fracture that is actively burning, and travels down slope along the ophiolite outcrop for ~10 m. Sediment temperatures under the vent source were 50-60°C, while fluid emitting from the fracture was 18.5°C. The pH of the fluid at the vent source was 11.9, indicative of subterranean serpentinization. Approximately 7.3 m downstream, the pH dropped to 9.4, potentially due to meteoric water mixing. Fluid samples were collected along the outflow channel for major ion analysis, trace element analysis, dissolved inorganic carbon (DIC), and dissolved organic carbon (DOC). Biofilm and biomineralized microbial mats were collected for bulk C and N composition, 13C and 15N isotopes, and microscopy. Weight % total C (CT) in solids generally increases with distance from the source, while weight % organic C (Corg) decreases, reflective of a higher degree of carbonate biomineralization downstream. δ13C of solids indicates a general trend of

  7. Methane seep carbonates yield clumped isotope signatures out of equilibrium with formation temperatures

    PubMed Central

    Loyd, S. J.; Sample, J.; Tripati, R. E.; Defliese, W. F.; Brooks, K.; Hovland, M.; Torres, M.; Marlow, J.; Hancock, L. G.; Martin, R.; Lyons, T.; Tripati, A. E.

    2016-01-01

    Methane cold seep systems typically exhibit extensive buildups of authigenic carbonate minerals, resulting from local increases in alkalinity driven by methane oxidation. Here, we demonstrate that modern seep authigenic carbonates exhibit anomalously low clumped isotope values (Δ47), as much as ∼0.2‰ lower than expected values. In modern seeps, this range of disequilibrium translates into apparent temperatures that are always warmer than ambient temperatures, by up to 50 °C. We examine various mechanisms that may induce disequilibrium behaviour in modern seep carbonates, and suggest that the observed values result from several factors including kinetic isotopic effects during methane oxidation, mixing of inorganic carbon pools, pH effects and rapid precipitation. Ancient seep carbonates studied here also exhibit potential disequilibrium signals. Ultimately, these findings indicate the predominance of disequilibrium clumped isotope behaviour in modern cold seep carbonates that must be considered when characterizing environmental conditions in both modern and ancient cold seep settings. PMID:27447820

  8. Methane seep carbonates yield clumped isotope signatures out of equilibrium with formation temperatures

    NASA Astrophysics Data System (ADS)

    Loyd, S. J.; Sample, J.; Tripati, R. E.; Defliese, W. F.; Brooks, K.; Hovland, M.; Torres, M.; Marlow, J.; Hancock, L. G.; Martin, R.; Lyons, T.; Tripati, A. E.

    2016-07-01

    Methane cold seep systems typically exhibit extensive buildups of authigenic carbonate minerals, resulting from local increases in alkalinity driven by methane oxidation. Here, we demonstrate that modern seep authigenic carbonates exhibit anomalously low clumped isotope values (Δ47), as much as ~0.2‰ lower than expected values. In modern seeps, this range of disequilibrium translates into apparent temperatures that are always warmer than ambient temperatures, by up to 50 °C. We examine various mechanisms that may induce disequilibrium behaviour in modern seep carbonates, and suggest that the observed values result from several factors including kinetic isotopic effects during methane oxidation, mixing of inorganic carbon pools, pH effects and rapid precipitation. Ancient seep carbonates studied here also exhibit potential disequilibrium signals. Ultimately, these findings indicate the predominance of disequilibrium clumped isotope behaviour in modern cold seep carbonates that must be considered when characterizing environmental conditions in both modern and ancient cold seep settings.

  9. Methane seep carbonates yield clumped isotope signatures out of equilibrium with formation temperatures.

    PubMed

    Loyd, S J; Sample, J; Tripati, R E; Defliese, W F; Brooks, K; Hovland, M; Torres, M; Marlow, J; Hancock, L G; Martin, R; Lyons, T; Tripati, A E

    2016-01-01

    Methane cold seep systems typically exhibit extensive buildups of authigenic carbonate minerals, resulting from local increases in alkalinity driven by methane oxidation. Here, we demonstrate that modern seep authigenic carbonates exhibit anomalously low clumped isotope values (Δ47), as much as ∼0.2‰ lower than expected values. In modern seeps, this range of disequilibrium translates into apparent temperatures that are always warmer than ambient temperatures, by up to 50 °C. We examine various mechanisms that may induce disequilibrium behaviour in modern seep carbonates, and suggest that the observed values result from several factors including kinetic isotopic effects during methane oxidation, mixing of inorganic carbon pools, pH effects and rapid precipitation. Ancient seep carbonates studied here also exhibit potential disequilibrium signals. Ultimately, these findings indicate the predominance of disequilibrium clumped isotope behaviour in modern cold seep carbonates that must be considered when characterizing environmental conditions in both modern and ancient cold seep settings. PMID:27447820

  10. Cold-seep habitat mapping: high-resolution spatial characterization of the Blake Ridge Diapir seep field

    USGS Publications Warehouse

    Wagner, Jamie K.S.; McEntee, Molly H.; Brothers, Laura L.; German, Christopher R.; Kaiser, Carl L.; Yoerger, Dana R.; Van Dover, Cindy Lee

    2013-01-01

    Relationships among seep community biomass, diversity, and physiographic controls such as underlying geology are not well understood. Previous efforts to constrain these relationships at the Blake Ridge Diapir were limited to observations from piloted deep-submergence vehicles. In August 2012, the autonomous underwater vehicle (AUV) Sentry collected geophysical and photographic data over a 0.131 km2 area at the Blake Ridge Diapir seeps. A nested survey approach was used that began with a regional or reconnaissance-style survey using sub-bottom mapping systems to locate and identify seeps and underlying conduits. This survey was followed by AUV-mounted sidescan sonar and multibeam echosounder systems mapping on a mesoscale to characterize the seabed physiography. At the most detailed survey level, digital photographic imaging was used to resolve sub-meter characteristics of the biology. Four pockmarks (25–70 m diameter) were documented, each supporting chemosynthetic communities. Concentric zonation of mussels and clams suggests the influence of chemical gradients on megafaunal distribution. Data collection and analytical techniques used here yield high-resolution habitat maps that can serve as baselines to constrain temporal evolution of seafloor seeps, and to inform ecological niche modeling and resource management.

  11. Active Sites Environmental Monitoring Program: Mid-FY 1991 report

    SciTech Connect

    Ashwood, T.L.; Wickliff, D.S.; Morrissey, C.M.

    1991-10-01

    This report summarizes the activities of the Active Sites Environmental Monitoring Program (ASEMP) from October 1990 through March 1991. The ASEMP was established in 1989 by Solid Waste Operations and the Environmental Sciences Division to provide early detection and performance monitoring at active low-level radioactive waste (LLW) disposal sites in Solid Waste Storage Area (SWSA) 6 and transuranic (TRU) waste storage sites in SWSA 5 as required by chapters II and III of US Department of Energy Order 5820.2A. Monitoring results continue to demonstrate the no LLW is being leached from the storage vaults on the tumulus pads. Loading of vaults on Tumulus II began during this reporting period and 115 vaults had been loaded by the end of March 1991.

  12. Active chemisorption sites in functionalized ionic liquids for carbon capture.

    PubMed

    Cui, Guokai; Wang, Jianji; Zhang, Suojiang

    2016-07-25

    Development of novel technologies for the efficient and reversible capture of CO2 is highly desired. In the last decade, CO2 capture using ionic liquids has attracted intensive attention from both academia and industry, and has been recognized as a very promising technology. Recently, a new approach has been developed for highly efficient capture of CO2 by site-containing ionic liquids through chemical interaction. This perspective review focuses on the recent advances in the chemical absorption of CO2 using site-containing ionic liquids, such as amino-based ionic liquids, azolate ionic liquids, phenolate ionic liquids, dual-functionalized ionic liquids, pyridine-containing ionic liquids and so on. Other site-containing liquid absorbents such as amine-based solutions, switchable solvents, and functionalized ionic liquid-amine blends are also investigated. Strategies have been discussed for how to activate the existent reactive sites and develop novel reactive sites by physical and chemical methods to enhance CO2 absorption capacity and reduce absorption enthalpy. The carbon capture mechanisms of these site-containing liquid absorbents are also presented. Particular attention has been paid to the latest progress in CO2 capture in multiple-site interactions by amino-free anion-functionalized ionic liquids. In the last section, future directions and prospects for carbon capture by site-containing ionic liquids are outlined.

  13. Active chemisorption sites in functionalized ionic liquids for carbon capture.

    PubMed

    Cui, Guokai; Wang, Jianji; Zhang, Suojiang

    2016-07-25

    Development of novel technologies for the efficient and reversible capture of CO2 is highly desired. In the last decade, CO2 capture using ionic liquids has attracted intensive attention from both academia and industry, and has been recognized as a very promising technology. Recently, a new approach has been developed for highly efficient capture of CO2 by site-containing ionic liquids through chemical interaction. This perspective review focuses on the recent advances in the chemical absorption of CO2 using site-containing ionic liquids, such as amino-based ionic liquids, azolate ionic liquids, phenolate ionic liquids, dual-functionalized ionic liquids, pyridine-containing ionic liquids and so on. Other site-containing liquid absorbents such as amine-based solutions, switchable solvents, and functionalized ionic liquid-amine blends are also investigated. Strategies have been discussed for how to activate the existent reactive sites and develop novel reactive sites by physical and chemical methods to enhance CO2 absorption capacity and reduce absorption enthalpy. The carbon capture mechanisms of these site-containing liquid absorbents are also presented. Particular attention has been paid to the latest progress in CO2 capture in multiple-site interactions by amino-free anion-functionalized ionic liquids. In the last section, future directions and prospects for carbon capture by site-containing ionic liquids are outlined. PMID:27243042

  14. Studies on the active site of pig plasma amine oxidase.

    PubMed Central

    Collison, D; Knowles, P F; Mabbs, F E; Rius, F X; Singh, I; Dooley, D M; Cote, C E; McGuirl, M

    1989-01-01

    Amine oxidase from pig plasma (PPAO) has two bound Cu2+ ions and at least one pyrroloquinoline quinone (PQQ) moiety as cofactors. It is shown that recovery of activity by copper-depleted PPAO is linear with respect to added Cu2+ ions. Recovery of e.s.r. and optical spectral characteristics of active-site copper parallel the recovery of catalytic activity. These results are consistent with both Cu2+ ions contributing to catalysis. Further e.s.r. studies indicate that the two copper sites in PPAO, unlike those in amine oxidases from other sources, are chemically distinct. These comparative studies establish that non-identity of the Cu2+ ions in PPAO is not a requirement for amine oxidase activity. It is shown through the use of a new assay procedure that there are two molecules of PQQ bound per molecule of protein in PPAO; only the more reactive of these PQQ moieties is required for activity. PMID:2559715

  15. In situ Raman-based detections of the hydrothermal vent and cold seep fluids

    NASA Astrophysics Data System (ADS)

    Zhang, Xin; Du, Zengfeng; Zheng, Ronger; Luan, Zhendong; Qi, Fujun; Cheng, Kai; Wang, Bing; Ye, Wangquan; Liu, Xiaorui; Chen, Changan; Guo, Jinjia; Li, Ying; Yan, Jun

    2016-04-01

    Hydrothermal vents and cold seeps, and their associated biological communities play an important role in global carbon and sulphur biogeochemical cycles. Most of the studies of fluid composition geochemistry are based on recovered samples, both with gas-tight samplers and as open specimens, but the in situ conditions are difficult to maintain in recovered samples. Determination in situ of the chemical signals of the emerging fluids are challenging due to the high pressure, often strongly acidic and temperature in which few sensors can survive. Most of those sensors used so far are based on electrochemistry, and can typically detect only a few chemical species. Here we show that direct measurement of critical chemical species of hydrothermal vents and cold seeps can be made rapidly and in situ by means of a new hybrid version of earlier deep-sea pore water Raman probe carried on the ROV (Remote Operated Vehicle) Faxian. The fluid was drawn through the probe by actuating a hydraulic pump on the ROV, and measured at the probe optical cell through a sapphire window. We have observed the concentrations of H2S, HS‑, SO42‑, HSO4‑, CO2, and H2 in hydrothermal vent fluids from the Pacmanus and Desmos vent systems in the Manus back-arc basin, Papua New Guinea. Two black smokers (279° C and 186° C) at the Pacmanus site showed the characteristic loss of SO42‑, and the increase of CO2 and well resolved H2S and HS‑ peaks. At the white smoker of Onsen site the strong HSO4‑peak observed at high temperature quickly dropped with strong accompanying increase of SO42‑and H2 peaks when the sample contained in the Raman sensing cell was removed from the hot fluid due to rapid thermal deprotonation. We report here also the finding of a new lower temperature (88° C) white smoker "Kexue" field at the Desmos site with strong H2S, HS‑ and CO2 signals. We also have detected the concentrations of CH4,H2S, HS‑, SO42‑, and S8 in cold seep fluids and the surrounding

  16. In situ Raman-based detections of the hydrothermal vent and cold seep fluids

    NASA Astrophysics Data System (ADS)

    Zhang, Xin; Du, Zengfeng; Zheng, Ronger; Luan, Zhendong; Qi, Fujun; Cheng, Kai; Wang, Bing; Ye, Wangquan; Liu, Xiaorui; Chen, Changan; Guo, Jinjia; Li, Ying; Yan, Jun

    2016-04-01

    Hydrothermal vents and cold seeps, and their associated biological communities play an important role in global carbon and sulphur biogeochemical cycles. Most of the studies of fluid composition geochemistry are based on recovered samples, both with gas-tight samplers and as open specimens, but the in situ conditions are difficult to maintain in recovered samples. Determination in situ of the chemical signals of the emerging fluids are challenging due to the high pressure, often strongly acidic and temperature in which few sensors can survive. Most of those sensors used so far are based on electrochemistry, and can typically detect only a few chemical species. Here we show that direct measurement of critical chemical species of hydrothermal vents and cold seeps can be made rapidly and in situ by means of a new hybrid version of earlier deep-sea pore water Raman probe carried on the ROV (Remote Operated Vehicle) Faxian. The fluid was drawn through the probe by actuating a hydraulic pump on the ROV, and measured at the probe optical cell through a sapphire window. We have observed the concentrations of H2S, HS-, SO42-, HSO4-, CO2, and H2 in hydrothermal vent fluids from the Pacmanus and Desmos vent systems in the Manus back-arc basin, Papua New Guinea. Two black smokers (279° C and 186° C) at the Pacmanus site showed the characteristic loss of SO42-, and the increase of CO2 and well resolved H2S and HS- peaks. At the white smoker of Onsen site the strong HSO4-peak observed at high temperature quickly dropped with strong accompanying increase of SO42-and H2 peaks when the sample contained in the Raman sensing cell was removed from the hot fluid due to rapid thermal deprotonation. We report here also the finding of a new lower temperature (88° C) white smoker "Kexue" field at the Desmos site with strong H2S, HS- and CO2 signals. We also have detected the concentrations of CH4,H2S, HS-, SO42-, and S8 in cold seep fluids and the surrounding sediment pore water from

  17. Computer simulation of the active site of human serum cholinesterase

    SciTech Connect

    Kefang Jiao; Song Li; Zhengzheng Lu

    1996-12-31

    The first 3D-structure of acetylchelinesterase from Torpedo California electric organ (T.AChE) was published by JL. Sussman in 1991. We have simulated 3D-structure of human serum cholinesterase (H.BuChE) and the active site of H.BuChE. It is discovered by experiment that the residue of H.BuChE is still active site after a part of H.BuChE is cut. For example, the part of 21KD + 20KD is active site of H.BuChE. The 20KD as it is. Studies on these peptides by Hemelogy indicate that two active peptides have same negative electrostatic potential maps diagram. These negative electrostatic areas attached by acetyl choline with positive electrostatic potency. We predict that 147...236 peptide of AChE could be active site because it was as 20KD as with negative electrostatic potential maps. We look forward to proving from other ones.

  18. Identification of Methane, Ethane, and Propane Oxidizing Bacteria at Marine Hydrocarbon Seeps by Stable Isotope Probing

    NASA Astrophysics Data System (ADS)

    Redmond, M.; Ding, H.; Friedrich, M. W.; Valentine, D. L.

    2008-12-01

    Hydrocarbon seeps emit substantial amounts of oil and natural gas into the marine environment, where they can be oxidized by microorganisms in the sediment and water column. Here, we used stable isotope probing of DNA and lipid biomarkers to identify the microorganisms actively consuming 13C-labeled natural gas compounds in seep sediment samples. Surface sediment was collected from the Coal Oil Point seep field (offshore Santa Barbara, California, USA) and incubated under aerobic conditions with 13C labeled methane, ethane, or propane for up to 37 days, with sediment sub-samples taken at 3-4 intermediate time points. DNA was extracted from sediment and separated by CsCl density gradient centrifugation. The microbial community in each fraction was profiled using T-RFLP, and bacterial 16S rRNA gene clone libraries were constructed from un-incubated hydrocarbon seep sediment and selected isotopically 'heavy' (13C) and 'light' (12C) gradient fractions from ethane incubations. All clone libraries were dominated by sequences from members of the family Rhodobacteraceae (>25% of sequences) and a diverse group of Gammaproteobacteria, including sequences related to those of methylotrophs and to those of bacteria known to consume the longer-chain alkanes present in crude oil. After 14 days of incubation, the relative abundance of Rhodobacteraceae was higher in 'heavy' fractions from the 13C-ethane incubation than in 'light' fractions, suggesting incorporation of 13C label. The Rhodobacteraceae are very diverse metabolically, but have often been observed in abundance in oil contaminated seawater. Several members of this group have been shown to oxidize longer chain alkanes (C10 or higher), but none have been previously linked to the consumption of the gaseous alkanes ethane, propane, and butane. For the final time point, 13C content of phospholipid fatty acids (PLFA) were also analyzed, showing substantial incorporation of 13C over 37 days. In the methane incubation

  19. Short-chain alkane cycling in deep Gulf of Mexico cold-seep sediments

    NASA Astrophysics Data System (ADS)

    Sibert, R.; Joye, S. B.; Hunter, K.

    2015-12-01

    Mixtures of light hydrocarbon gases are common in deep Gulf of Mexico cold-seep sediments, and are typically dissolved in pore fluids, adsorbed to sediment particles, trapped in methane ice, or as free gas. The dominant component in these natural gas mixtures is usually methane (>80% C1), but ethane (C2) and propane (C3) are nearly always present in trace amounts (<1% total). The processes that control the concentration and isotopic signature of these gases in sediments are well explained for methane, but the controls for C2/C3 cycling are still a relative mystery. Methane production proceeds in deep anoxic sediments by either 1) thermocatalytic cracking of fossil organic matter, or 2) as a direct product of microbial metabolism, i.e. methanogenesis. In surface sediments, it appears that both microbial consumption and chemical deposition of methane (i.e. as methane clathrate) ensures that >95% of the methane produced at depth never reaches the water column. Production of C1 and C2 in deep-sea sediments has been historically attributed only to thermocatalytic processes, though limited data suggests production of C2/C3 compounds through the activity of archaea at depth. Furthermore, carbon isotopic data on ethane and propane from deep cores of Gulf of Mexico sediments suggest alkanogenesis at >3 m depth in the sediment column and alkane oxidation in uppermost oxidant-rich sediments. Additional studies have also isolated microorganisms capable of oxidizing ethane and propane in the laboratory, but field studies of microbial-driven dynamics of C2/C3 gases in cold-seep sediments are rare. Here, we present the results of a series of incubation experiments using sediment slurries culled from surface sediments from one of the most prolific natural oil and gas seeps in the Gulf of Mexico. Rates of alkane oxidation were measured under a variety of conditions to assess the surface-driven microbial controls on C2/C3 cycling in cold-seep environments. Such microbial processes

  20. Resonant active sites in catalytic ammonia synthesis: A structural model

    NASA Astrophysics Data System (ADS)

    Cholach, Alexander R.; Bryliakova, Anna A.; Matveev, Andrey V.; Bulgakov, Nikolai N.

    2016-03-01

    Adsorption sites Mn consisted of n adjacent atoms M, each bound to the adsorbed species, are considered within a realistic model. The sum of bonds Σ lost by atoms in a site in comparison with the bulk atoms was used for evaluation of the local surface imperfection, while the reaction enthalpy at that site was used as a measure of activity. The comparative study of Mn sites (n = 1-5) at basal planes of Pt, Rh, Ir, Fe, Re and Ru with respect to heat of N2 dissociative adsorption QN and heat of Nad + Had → NHad reaction QNH was performed using semi-empirical calculations. Linear QN(Σ) increase and QNH(Σ) decrease allowed to specify the resonant Σ for each surface in catalytic ammonia synthesis at equilibrium Nad coverage. Optimal Σ are realizable for Ru2, Re2 and Ir4 only, whereas other centers meet steric inhibition or unreal crystal structure. Relative activity of the most active sites in proportion 5.0 × 10- 5: 4.5 × 10- 3: 1: 2.5: 3.0: 1080: 2270 for a sequence of Pt4, Rh4, Fe4(fcc), Ir4, Fe2-5(bcc), Ru2, Re2, respectively, is in agreement with relevant experimental data. Similar approach can be applied to other adsorption or catalytic processes exhibiting structure sensitivity.

  1. Using Stable Isotope Compositions of Animal Tissues to Infer Trophic Interactions in Gulf of Mexico Lower Slope Seep Communities

    PubMed Central

    Becker, Erin L.; Cordes, Erik E.; Macko, Stephen A.; Lee, Raymond W.; Fisher, Charles R.

    2013-01-01

    We analyzed the tissue carbon, nitrogen, and sulfur stable isotope contents of macrofaunal communities associated with vestimentiferan tubeworms and bathymodiolin mussels from the Gulf of Mexico lower continental slope (970-2800 m). Shrimp in the genus Alvinocaris associated with vestimentiferans from shallow (530 m) and deep (1400-2800 m) sites were used to test the hypothesis that seep animals derive a greater proportion of their nutrition from seeps (i.e. a lower proportion from the surface) at greater depths. To account for spatial variability in the inorganic source pool, we used the differences between the mean tissue δ13C and δ15N of the shrimp in each collection and the mean δ 13C and δ15N values of the vestimentiferans from the same collection, since vestimentiferans are functionally autotrophic and serve as a baseline for environmental isotopic variation. There was a significant negative relationship between this difference and depth for both δ13C and δ15N (p=0.02 and 0.007, respectively), which supports the hypothesis of higher dependence on seep nutrition with depth. The small polychaete worm Protomystides sp. was hypothesized to be a blood parasite of the vestimentiferan Escarpialaminata. There was a highly significant linear relationship between the δ13C values of Protomystides sp. and the E. laminata individuals to which they were attached across all collections (p < 0.001) and within a single collection (p = 0.01), although this relationship was not significant for δ15N and δ34S. We made several other qualitative inferences with respect to the feeding biology of the taxa occurring in these lower slope seeps, some of which have not been described prior to this study. PMID:24324572

  2. Multi-site Phosphorylation Regulates Bim Stability and Apoptotic Activity

    PubMed Central

    Hübner, Anette; Barrett, Tamera; Flavell, Richard A.; Davis, Roger J.

    2008-01-01

    The pro-apoptotic BH3-only protein Bim is established to be an important mediator of signaling pathways that induce cell death. Multi-site phosphorylation of Bim by several members of the MAP kinase group is implicated as a regulatory mechanism that controls the apoptotic activity of Bim. To test the role of Bim phosphorylation in vivo, we constructed mice with a series of mutant alleles that express phosphorylation-defective Bim proteins. We show that mutation of the phosphorylation site Thr-112 causes decreased binding of Bim to the anti-apoptotic protein Bcl2 and can increase cell survival. In contrast, mutation of the phosphorylation sites Ser-55, Ser-65, and Ser-73 can cause increased apoptosis because of reduced proteasomal degradation of Bim. Together, these data indicate that phosphorylation can regulate Bim by multiple mechanisms and that the phosphorylation of Bim on different sites can contribute to the sensitivity of cellular apoptotic responses. PMID:18498746

  3. Hydrocarbon Potential of the Southern Gulf of Mexico. Evidences from Tectonic Features and Oil Seeps

    NASA Astrophysics Data System (ADS)

    Padilla Y Sanch, R.

    2008-05-01

    The Gulf of Mexico has an enormous oil potential, about 104 billion barrels of oil equivalent (BBOE). From these, about 54 BBOE are in Mexican waters. Tectonic features in the sea-floor of the Gulf of Mexico (GOM) are closely related to oil seepage that have been mapped since the early 20 century, and are direct evidences of working petroleum systems, as well as that deep reservoirs are leaking oil to the surface. This could be considered an inconvenience by some, but it is known that the giant field Cantarell was named after a fisherman that reported frequently giant oil seeps offshore northward Ciudad del Carmen. Deep water exploration has become more and more important these days because of the continuously increasing oil prices. The northern half of the Gulf of Mexico today displays an unusual drilling activity, whereas in the southern part drilling activity is too low. In this research work the interest is focused on the satellite detected oil seeps, and ther coincident location with the tectonic structures shown in the new digital tectonic map of mexico.

  4. Water in the Active Site of Ketosteroid Isomerase

    PubMed Central

    Hanoian, Philip; Hammes-Schiffer, Sharon

    2011-01-01

    Classical molecular dynamics simulations were utilized to investigate the structural and dynamical properties of water in the active site of ketosteroid isomerase (KSI) to provide insight into the role of these water molecules in the enzyme-catalyzed reaction. This reaction is thought to proceed via a dienolate intermediate that is stabilized by hydrogen bonding with residues Tyr16 and Asp103. A comparative study was performed for the wild-type (WT) KSI and the Y16F, Y16S, and Y16F/Y32F/Y57F (FFF) mutants. These systems were studied with three different bound ligands: equilenin, which is an intermediate analog, and the intermediate states of two steroid substrates. Several distinct water occupation sites were identified in the active site of KSI for the WT and mutant systems. Three additional sites were identified in the Y16S mutant that were not occupied in WT KSI or the other mutants studied. The number of water molecules directly hydrogen bonded to the ligand oxygen was approximately two waters in the Y16S mutant, one water in the Y16F and FFF mutants, and intermittent hydrogen bonding of one water molecule in WT KSI. The molecular dynamics trajectories of the Y16F and FFF mutants reproduced the small conformational changes of residue 16 observed in the crystal structures of these two mutants. Quantum mechanical/molecular mechanical calculations of 1H NMR chemical shifts of the protons in the active site hydrogen-bonding network suggest that the presence of water in the active site does not prevent the formation of short hydrogen bonds with far-downfield chemical shifts. The molecular dynamics simulations indicate that the active site water molecules exchange much more frequently for WT KSI and the FFF mutant than for the Y16F and Y16S mutants. This difference is most likely due to the hydrogen-bonding interaction between Tyr57 and an active site water molecule that is persistent in the Y16F and Y16S mutants but absent in the FFF mutant and significantly less

  5. Activation of phenylalanine hydroxylase by phenylalanine does not require binding in the active site.

    PubMed

    Roberts, Kenneth M; Khan, Crystal A; Hinck, Cynthia S; Fitzpatrick, Paul F

    2014-12-16

    Phenylalanine hydroxylase (PheH), a liver enzyme that catalyzes the hydroxylation of excess phenylalanine in the diet to tyrosine, is activated by phenylalanine. The lack of activity at low levels of phenylalanine has been attributed to the N-terminus of the protein's regulatory domain acting as an inhibitory peptide by blocking substrate access to the active site. The location of the site at which phenylalanine binds to activate the enzyme is unknown, and both the active site in the catalytic domain and a separate site in the N-terminal regulatory domain have been proposed. Binding of catecholamines to the active-site iron was used to probe the accessibility of the active site. Removal of the regulatory domain increases the rate constants for association of several catecholamines with the wild-type enzyme by ∼2-fold. Binding of phenylalanine in the active site is effectively abolished by mutating the active-site residue Arg270 to lysine. The k(cat)/K(phe) value is down 10⁴ for the mutant enzyme, and the K(m) value for phenylalanine for the mutant enzyme is >0.5 M. Incubation of the R270K enzyme with phenylalanine also results in a 2-fold increase in the rate constants for catecholamine binding. The change in the tryptophan fluorescence emission spectrum seen in the wild-type enzyme upon activation by phenylalanine is also seen with the R270K mutant enzyme in the presence of phenylalanine. Both results establish that activation of PheH by phenylalanine does not require binding of the amino acid in the active site. This is consistent with a separate allosteric site, likely in the regulatory domain.

  6. Chemical Modification of Papain and Subtilisin: An Active Site Comparison

    ERIC Educational Resources Information Center

    St-Vincent, Mireille; Dickman, Michael

    2004-01-01

    An experiment using methyle methanethiosulfonate (MMTS) and phenylmethylsulfonyl flouride (PMSF) to specifically modify the cysteine and serine residues in the active sites of papain and subtilism respectively is demonstrated. The covalent modification of these enzymes and subsequent rescue of papain shows the beginning biochemist that proteins…

  7. Energy transfer at the active sites of heme proteins

    SciTech Connect

    Dlott, D.D.; Hill, J.R.

    1995-12-31

    Experiments using a picosecond pump-probe apparatus at the Picosecond Free-electron Laser Center at Stanford University, were performed to investigate the relaxation of carbon monoxide bound to the active sites of heme proteins. The significance of these experiments is two-fold: (1) they provide detailed information about molecular dynamics occurring at the active sites of proteins; and (2) they provide insight into the nature of vibrational relaxation processes in condensed matter. Molecular engineering is used to construct various molecular systems which are studied with the FEL. We have studied native proteins, mainly myoglobin obtained from different species, mutant proteins produced by genetic engineering using recombinant DNA techniques, and a variety of model systems which mimic the structures of the active sites of native proteins, which are produced using molecular synthesis. Use of these different systems permits us to investigate how specific molecular structural changes affect dynamical processes occurring at the active sites. This research provides insight into the problems of how different species needs are fulfilled by heme proteins which have greatly different functionality, which is induced by rather small structural changes.

  8. Changes in active site histidine hydrogen bonding trigger cryptochrome activation.

    PubMed

    Ganguly, Abir; Manahan, Craig C; Top, Deniz; Yee, Estella F; Lin, Changfan; Young, Michael W; Thiel, Walter; Crane, Brian R

    2016-09-01

    Cryptochrome (CRY) is the principal light sensor of the insect circadian clock. Photoreduction of the Drosophila CRY (dCRY) flavin cofactor to the anionic semiquinone (ASQ) restructures a C-terminal tail helix (CTT) that otherwise inhibits interactions with targets that include the clock protein Timeless (TIM). All-atom molecular dynamics (MD) simulations indicate that flavin reduction destabilizes the CTT, which undergoes large-scale conformational changes (the CTT release) on short (25 ns) timescales. The CTT release correlates with the conformation and protonation state of conserved His378, which resides between the CTT and the flavin cofactor. Poisson-Boltzmann calculations indicate that flavin reduction substantially increases the His378 pKa Consistent with coupling between ASQ formation and His378 protonation, dCRY displays reduced photoreduction rates with increasing pH; however, His378Asn/Arg variants show no such pH dependence. Replica-exchange MD simulations also support CTT release mediated by changes in His378 hydrogen bonding and verify other responsive regions of the protein previously identified by proteolytic sensitivity assays. His378 dCRY variants show varying abilities to light-activate TIM and undergo self-degradation in cellular assays. Surprisingly, His378Arg/Lys variants do not degrade in light despite maintaining reactivity toward TIM, thereby implicating different conformational responses in these two functions. Thus, the dCRY photosensory mechanism involves flavin photoreduction coupled to protonation of His378, whose perturbed hydrogen-bonding pattern alters the CTT and surrounding regions. PMID:27551082

  9. Conformational Transitions in Human AP Endonuclease 1 and Its Active Site Mutant during Abasic Site Repair†

    PubMed Central

    Kanazhevskaya, Lyubov Yu.; Koval, Vladimir V.; Zharkov, Dmitry O.; Strauss, Phyllis R.; Fedorova, Olga S.

    2010-01-01

    AP endonuclease 1 (APE 1) is a crucial enzyme of the base excision repair pathway (BER) in human cells. APE1 recognizes apurinic/apyrimidinic (AP) sites and makes a nick in the phosphodiester backbone 5′ to them. The conformational dynamics and presteady-state kinetics of wild-type APE1 and its active site mutant, Y171F-P173L-N174K, have been studied. To observe conformational transitions occurring in the APE1 molecule during the catalytic cycle, we detected intrinsic tryptophan fluorescence of the enzyme under single turnover conditions. DNA duplexes containing a natural AP site, its tetrahydrofuran analogue, or a 2′-deoxyguanosine residue in the same position were used as specific substrates or ligands. The stopped-flow experiments have revealed high flexibility of the APE1 molecule and the complexity of the catalytic process. The fluorescent traces indicate that wild-type APE1 undergoes at least four conformational transitions during the processing of abasic sites in DNA. In contrast, nonspecific interactions of APE1 with undamaged DNA can be described by a two-step kinetic scheme. Rate and equilibrium constants were extracted from the stopped-flow and fluorescence titration data for all substrates, ligands, and products. A replacement of three residues at the enzymatic active site including the replacement of tyrosine 171 with phenylalanine in the enzyme active site resulted in a 2 × 104-fold decrease in the reaction rate and reduced binding affinity. Our data indicate the important role of conformational changes in APE1 for substrate recognition and catalysis. PMID:20575528

  10. Initial results of comparing cold-seep carbonates from mussel- and tubeworm-associated environments at Atwater Valley lease block 340, northern Gulf of Mexico

    NASA Astrophysics Data System (ADS)

    Feng, Dong; Roberts, Harry H.

    2010-11-01

    Chemosymbiotic macrofauna (such as mussels and tubeworms) and authigenic carbonates are typical of many hydrocarbon seeps. To address whether mussels and tubeworms could impact the sediment geochemistry of their habitat where authigenic carbonates are precipitated, a comparative study of petrographic and geochemical features of the authigenic carbonates from mussel- and tubeworm-associated environments at hydrocarbon seeps in Atwater Valley lease area block 340 (AT340) of the Gulf of Mexico was undertaken. Both mussel- and tubeworm-associated carbonates are dominated by high-magnesium calcite (HMC) and aragonite, and two tubeworm-associated carbonate samples have minor amounts of dolomite. The δ13C values of all carbonates are low, ranging from -60.8‰ to -35.5‰ PDB. Although there is much overlap, surprisingly the δ13C values of mussel-associated carbonates are generally higher than those of tubeworm-associated carbonates (-51.8‰ vs. -54.8‰ for an average of over 60 subsamples). It is suggested that (1) carbon isotopic vital effect of seep mussels and tubeworms, (2) fluid physical pumping of mussels, and (3) release of sulfate by tubeworm roots may be responsible for the relatively lower δ13C values of tubeworm-associated carbonates. It has been suggested that the heterogeneities in mineralogy and stable carbon isotope geochemistry of the seep carbonates may be attributed to the activity of macrofauna (mussels and tubeworms) and associated microbes. Our observations also suggest that at AT340 the geochemical evolution of seep macrofauna is from a mussel-dominated environment to a mixed mussel-tubeworm environment, and finally to a mostly tubeworm-dominated environment. This evolution is controlled mainly by the habitat, e.g., hydrocarbon seep flux.

  11. N-methyl-D-aspartate recognition site ligands modulate activity at the coupled glycine recognition site.

    PubMed

    Hood, W F; Compton, R P; Monahan, J B

    1990-03-01

    In synaptic plasma membranes from rat forebrain, the potencies of glycine recognition site agonists and antagonists for modulating [3H]1-[1-(2-thienyl)cyclohexyl]piperidine ([3H]TCP) binding and for displacing strychnine-insensitive [3H]glycine binding are altered in the presence of N-methyl-D-aspartate (NMDA) recognition site ligands. The NMDA competitive antagonist, cis-4-phosphonomethyl-2-piperidine carboxylate (CGS 19755), reduces [3H]glycine binding, and the reduction can be fully reversed by the NMDA recognition site agonist, L-glutamate. Scatchard analysis of [3H]glycine binding shows that in the presence of CGS 19755 there is no change in Bmax (8.81 vs. 8.79 pmol/mg of protein), but rather a decrease in the affinity of glycine (KD of 0.202 microM vs. 0.129 microM). Similar decreases in affinity are observed for the glycine site agonists, D-serine and 1-aminocyclopropane-1-carboxylate, in the presence of CGS 19755. In contrast, the affinity of glycine antagonists, 1-hydroxy-3-amino-2-pyrrolidone and 1-aminocyclobutane-1-carboxylate, at this [3H]glycine recognition site increases in the presence of CGS 19755. The functional consequence of this change in affinity was addressed using the modulation of [3H]TCP binding. In the presence of L-glutamate, the potency of glycine agonists for the stimulation of [3H]TCP binding increases, whereas the potency of glycine antagonists decreases. These data are consistent with NMDA recognition site ligands, through their interactions at the NMDA recognition site, modulating activity at the associated glycine recognition site.

  12. Out of the dark: transitional subsurface-to-surface microbial diversity in a terrestrial serpentinizing seep (Manleluag, Pangasinan, the Philippines).

    PubMed

    Woycheese, Kristin M; Meyer-Dombard, D'Arcy R; Cardace, Dawn; Argayosa, Anacleto M; Arcilla, Carlo A

    2015-01-01

    In the Zambales ophiolite range, terrestrial serpentinizing fluid seeps host diverse microbial assemblages. The fluids fall within the profile of Ca(2+)-OH(-)-type waters, indicative of active serpentinization, and are low in dissolved inorganic carbon (DIC) (<0.5 ppm). Influx of atmospheric carbon dioxide (CO2) affects the solubility of calcium carbonate as distance from the source increases, triggering the formation of meter-scale travertine terraces. Samples were collected at the source and along the outflow channel to determine subsurface microbial community response to surface exposure. DNA was extracted and submitted for high-throughput 16S rRNA gene sequencing on the Illumina MiSeq platform. Taxonomic assignment of the sequence data indicates that 8.1% of the total sequence reads at the source of the seep affiliate with the genus Methanobacterium. Other major classes detected at the source include anaerobic taxa such as Bacteroidetes (40.7% of total sequence reads) and Firmicutes (19.1% of total reads). Hydrogenophaga spp. increase in relative abundance as redox potential increases. At the carbonate terrace, 45% of sequence reads affiliate with Meiothermus spp. Taxonomic observations and geochemical data suggest that several putative metabolisms may be favorable, including hydrogen oxidation, H2-associated sulfur cycling, methanogenesis, methanotrophy, nitrogen fixation, ammonia oxidation, denitrification, nitrate respiration, methylotrophy, carbon monoxide respiration, and ferrous iron oxidation, based on capabilities of nearest known neighbors. Scanning electron microscopy and energy dispersive X-ray spectroscopy suggest that microbial activity produces chemical and physical traces in the precipitated carbonates forming downstream of the seep's source. These data provide context for future serpentinizing seep ecosystem studies, particularly with regards to tropical biomes. PMID:25745416

  13. Out of the dark: transitional subsurface-to-surface microbial diversity in a terrestrial serpentinizing seep (Manleluag, Pangasinan, the Philippines).

    PubMed

    Woycheese, Kristin M; Meyer-Dombard, D'Arcy R; Cardace, Dawn; Argayosa, Anacleto M; Arcilla, Carlo A

    2015-01-01

    In the Zambales ophiolite range, terrestrial serpentinizing fluid seeps host diverse microbial assemblages. The fluids fall within the profile of Ca(2+)-OH(-)-type waters, indicative of active serpentinization, and are low in dissolved inorganic carbon (DIC) (<0.5 ppm). Influx of atmospheric carbon dioxide (CO2) affects the solubility of calcium carbonate as distance from the source increases, triggering the formation of meter-scale travertine terraces. Samples were collected at the source and along the outflow channel to determine subsurface microbial community response to surface exposure. DNA was extracted and submitted for high-throughput 16S rRNA gene sequencing on the Illumina MiSeq platform. Taxonomic assignment of the sequence data indicates that 8.1% of the total sequence reads at the source of the seep affiliate with the genus Methanobacterium. Other major classes detected at the source include anaerobic taxa such as Bacteroidetes (40.7% of total sequence reads) and Firmicutes (19.1% of total reads). Hydrogenophaga spp. increase in relative abundance as redox potential increases. At the carbonate terrace, 45% of sequence reads affiliate with Meiothermus spp. Taxonomic observations and geochemical data suggest that several putative metabolisms may be favorable, including hydrogen oxidation, H2-associated sulfur cycling, methanogenesis, methanotrophy, nitrogen fixation, ammonia oxidation, denitrification, nitrate respiration, methylotrophy, carbon monoxide respiration, and ferrous iron oxidation, based on capabilities of nearest known neighbors. Scanning electron microscopy and energy dispersive X-ray spectroscopy suggest that microbial activity produces chemical and physical traces in the precipitated carbonates forming downstream of the seep's source. These data provide context for future serpentinizing seep ecosystem studies, particularly with regards to tropical biomes.

  14. Out of the dark: transitional subsurface-to-surface microbial diversity in a terrestrial serpentinizing seep (Manleluag, Pangasinan, the Philippines)

    PubMed Central

    Woycheese, Kristin M.; Meyer-Dombard, D'Arcy R.; Cardace, Dawn; Argayosa, Anacleto M.; Arcilla, Carlo A.

    2015-01-01

    In the Zambales ophiolite range, terrestrial serpentinizing fluid seeps host diverse microbial assemblages. The fluids fall within the profile of Ca2+-OH−-type waters, indicative of active serpentinization, and are low in dissolved inorganic carbon (DIC) (<0.5 ppm). Influx of atmospheric carbon dioxide (CO2) affects the solubility of calcium carbonate as distance from the source increases, triggering the formation of meter-scale travertine terraces. Samples were collected at the source and along the outflow channel to determine subsurface microbial community response to surface exposure. DNA was extracted and submitted for high-throughput 16S rRNA gene sequencing on the Illumina MiSeq platform. Taxonomic assignment of the sequence data indicates that 8.1% of the total sequence reads at the source of the seep affiliate with the genus Methanobacterium. Other major classes detected at the source include anaerobic taxa such as Bacteroidetes (40.7% of total sequence reads) and Firmicutes (19.1% of total reads). Hydrogenophaga spp. increase in relative abundance as redox potential increases. At the carbonate terrace, 45% of sequence reads affiliate with Meiothermus spp. Taxonomic observations and geochemical data suggest that several putative metabolisms may be favorable, including hydrogen oxidation, H2-associated sulfur cycling, methanogenesis, methanotrophy, nitrogen fixation, ammonia oxidation, denitrification, nitrate respiration, methylotrophy, carbon monoxide respiration, and ferrous iron oxidation, based on capabilities of nearest known neighbors. Scanning electron microscopy and energy dispersive X-ray spectroscopy suggest that microbial activity produces chemical and physical traces in the precipitated carbonates forming downstream of the seep's source. These data provide context for future serpentinizing seep ecosystem studies, particularly with regards to tropical biomes. PMID:25745416

  15. Cryptic species of Archinome (Annelida: Amphinomida) from vents and seeps

    PubMed Central

    Borda, Elizabeth; Kudenov, Jerry D.; Chevaldonné, Pierre; Blake, James A.; Desbruyères, Daniel; Fabri, Marie-Claire; Hourdez, Stéphane; Pleijel, Fredrik; Shank, Timothy M.; Wilson, Nerida G.; Schulze, Anja; Rouse, Greg W.

    2013-01-01

    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. PMID:24026823

  16. Anaerobic propane oxidation in marine hydrocarbon seep sediments

    NASA Astrophysics Data System (ADS)

    Quistad, Steven D.; Valentine, David L.

    2011-04-01

    Propane (C 3H 8) is an abundant hydrocarbon in subsurface reservoirs with significance to atmospheric chemistry and to marine biogeochemistry. The anaerobic oxidation of propane coupled to sulfate reduction may prevent sub-seafloor accumulations of propane from entering the ocean and atmosphere. Anaerobic oxidation of propane has recently been demonstrated in cultures of novel sulfate-reducing bacteria, but has not been directly demonstrated or quantified in nature. In this work we describe a method involving incubation with 13C-propane to quantify rates of anaerobic oxidation of propane in anoxic sediment, and we conclusively demonstrate the oxidation of propane under sulfidic conditions in fresh sediments of a marine hydrocarbon seep. Observed rates of anaerobic oxidation of propane adhere to first-order kinetic behavior, enabling the modification of this method for whole core rate determinations. Whole core rates in nine cores from two hydrocarbon seeps measured 0.04-2100 nmoles C 3H 8 cm -3 day -1 by this method. The seep persistently supplied with more propane displayed substantially higher rates of anaerobic oxidation of propane, by 1-2 orders of magnitude when averaged over the top 10-cm, suggesting the development of the microbial community is strongly modulated by the availability of propane. This work is the first to estimate rates for anaerobic oxidation of propane in any environment, and demonstrates the potential importance of the process as a filter for preventing propane from entering the ocean and atmosphere.

  17. Cryptic species of Archinome (Annelida: Amphinomida) from vents and seeps.

    PubMed

    Borda, Elizabeth; Kudenov, Jerry D; Chevaldonné, Pierre; Blake, James A; Desbruyères, Daniel; Fabri, Marie-Claire; Hourdez, Stéphane; Pleijel, Fredrik; Shank, Timothy M; Wilson, Nerida G; Schulze, Anja; Rouse, Greg W

    2013-11-01

    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.

  18. Control of active sites in selective flocculation: I -- Mathematical model

    SciTech Connect

    Behl, S.; Moudgil, B.M.; Prakash, T.S. . Dept. of Materials Science and Engineering)

    1993-12-01

    Heteroflocculation has been determined to be another major reason for loss in selectivity for flocculation process. In a mathematical model developed earlier, conditions for controlling heteroflocculation were discussed. Blocking active sites to control selective adsorption of a flocculant oil a desirable solid surface is discussed. It has been demonstrated that the lower molecular weight fraction of a flocculant which is incapable of flocculating the particles is an efficient site blocking agent. The major application of selective flocculation has been in mineral processing but many potential uses exist in biological and other colloidal systems. These include purification of ceramic powders, separating hazardous solids from chemical waste, and removal of deleterious components from paper pulp.

  19. Short-term monitoring of a gas seep field in the Katakolo bay (Western Greece) using Raman spectra DTS and DAS fibre-optic methods

    NASA Astrophysics Data System (ADS)

    Chalari, A.; Mondanos, M.; Finfer, D.; Christodoulou, D.; Kordella, S.; Papatheodorou, G.; Geraga, M.; Ferentinos, G.

    2012-12-01

    A wide submarine seep of thermogenic gas in the Katakolo bay, Western Greece, was monitored passively using the intelligent Distributed Acoustic Sensor (iDAS) and Ultima Raman spectra Distributed Temperature Sensor (DTS), in order to study the thermal and noise signal of the bubble plumes released from the seafloor. Katakolo is one one of the most prolific thermogenic gas seepage zones in Europe and the biggest methane seep ever reported in Greece. Very detailed repetitive offshore gas surveys, including marine remote sensing (sub-bottom profiling, side scan sonar), underwater exploration by a towed instrumented system (MEDUSA), long-term monitoring benthic station (GMM), compositional and isotopic analyses, and flux measurements of gas, showed that: (a) gas seepage takes place over an extended area in the Katakolo harbour and along two main normal faults off the harbour; (b) at least 823 gas bubble ( 10-20 cm in diameter) plumes escaping over an area of 94,200 m2, at depths ranging from 5.5 to 16 m; (c) the gas consists mainly of methane and has H2S levels of hundreds to thousands ppmv, and shows significant amounts of other light hydrocarbons like ethane, propane, iso-butane and C6 alkanes, (d) offshore and onshore seeps release the same type of thermogenic gas; (e) due to the shallow depth, more than 90 % of CH4 released at the seabed enters the atmosphere, and (f) the gas seeps may produce severe geohazards for people, buildings and construction facilities due to the explosive and toxicological properties of methane and hydrogen sulfide, respectively. For the short-term monitoring, the deployment took place on a site located inside the harbour of Katakolo within a thermogenic gas seepage area where active faults are intersected. The iDAS system makes it possible to observe the acoustical signal along the entire length of an unmodified optical cable without introducing any form of point sensors such as Bragg gratings. When the bubble plumes are released by the

  20. The site of activation of factor X by cancer procoagulant.

    PubMed

    Gordon, S G; Mourad, A M

    1991-12-01

    Cancer procoagulant (CP) is a cysteine proteinase found in a variety of malignant cells and tissues and in human amnion-chorion tissue. It initiates coagulation by activating factor X. However, the amino acid sequence of the substrate protein that determines the cleavage site of cysteine proteinases is different from that of the serine proteinases that normally activate factor X, such as factor IXa, VIIa and Russell's Viper Venom (RVV). Therefore, it was of interest to determine the site of cleavage of human factor X by CP. Purified CP was incubated with purified factor X and the reaction mixture was electrophoresed on a 10% Tris-tricine SDS-PAGE gel. The proteins were electroeluted on to a polyvinylidene difluoride (PVDF) membrane, and stained with Coomassie blue. The heavy chain of activated factor X was cut out of the PVDF membrane and sequenced with an Applied Biosystems 477A with on-line HPLC. The primary cleavage sequence was Asp-Ala-Ala-Asp-Leu-Asp-Pro-; two other secondary sequences Ser-Ile-Thr-Trp-Lys-Pro- and Glu-Asn-Pro-Phe-Asp-Leu were found. The penultimate amino acid on the carbonyl side of the hydrolysed amide bond plays a critical role for the recognition of the cleavage site of cysteine proteinases. These data indicate that the penultimate amino acid for the primary cleavage site of factor X by CP is proline-20 and for the secondary sites, proline-13 and proline-28. This is in contrast to arginine-52 that determines the specificity of the cleavage by normal serine proteinase activation.(ABSTRACT TRUNCATED AT 250 WORDS)

  1. Bacteria associated with iron seeps in a sulfur-rich, neutral pH, freshwater ecosystem.

    PubMed

    Haaijer, Suzanne C M; Harhangi, Harry R; Meijerink, Bas B; Strous, Marc; Pol, Arjan; Smolders, Alfons J P; Verwegen, Karin; Jetten, Mike S M; Op den Camp, Huub J M

    2008-12-01

    The freshwater nature reserve De Bruuk is an iron- and sulfur-rich minerotrophic peatland containing many iron seeps and forms a suitable habitat for iron and sulfur cycle bacteria. Analysis of 16S rRNA gene-based clone libraries showed a striking correlation of the bacterial population of samples from this freshwater ecosystem with the processes of iron reduction (genus Geobacter), iron oxidation (genera Leptothrix and Gallionella) and sulfur oxidation (genus Sulfuricurvum). Results from fluorescence in situ hybridization analyses with a probe specific for the beta-1 subgroup of Proteobacteria, to which the genera Leptothrix and Gallionella belong, and newly developed probes specific for the genera Geobacter and Sulfuricurvum, supported the clone library data. Molecular data suggested members of the epsilonproteobacterial genus Sulfuricurvum as contributors to the oxidation of reduced sulfur compounds in the iron seeps of De Bruuk. In an evaluation of anaerobic dimethyl sulfide (DMS)-degrading activity of sediment, incubations with the electron acceptors sulfate, ferric iron and nitrate were performed. The fastest conversion of DMS was observed with nitrate. Further, a DMS-oxidizing, nitrate-reducing enrichment culture was established with sediment material from De Bruuk. This culture was dominated by dimorphic, prosthecate bacteria, and the 16S rRNA gene sequence obtained from this enrichment was closely affiliated with Hyphomicrobium facile, which indicates that the Hyphomicrobium species are capable of both aerobic and nitrate-driven DMS degradation. PMID:18754044

  2. Parallels between playbacks and Pleistocene tar seeps suggest sociality in an extinct sabretooth cat, Smilodon.

    PubMed

    Carbone, Chris; Maddox, Tom; Funston, Paul J; Mills, Michael G L; Grether, Gregory F; Van Valkenburgh, Blaire

    2009-02-23

    Inferences concerning the lives of extinct animals are difficult to obtain from the fossil record. Here we present a novel approach to the study of extinct carnivores, using a comparison between fossil records (n=3324) found in Late Pleistocene tar seeps at Rancho La Brea in North America and counts (n=4491) from playback experiments used to estimate carnivore abundance in Africa. Playbacks and tar seep deposits represent competitive, potentially dangerous encounters where multiple predators are lured by dying herbivores. Consequently, in both records predatory mammals and birds far outnumber herbivores. In playbacks, two large social species, lions, Panthera leo, and spotted hyenas, Crocuta crocuta, actively moved towards the sounds of distressed prey and made up 84 per cent of individuals attending. Small social species (jackals) were next most common and solitary species of all sizes were rare. In the La Brea record, two species dominated, the presumably social dire wolf Canis dirus (51%), and the sabretooth cat Smilodon fatalis (33%). As in the playbacks, a smaller social canid, the coyote Canis latrans, was third most common (8%), and known solitary species were rare (<4%). The predominance of Smilodon and other striking similarities between playbacks and the fossil record support the conclusion that Smilodon was social. PMID:18957359

  3. Important geological and biological impacts of natural hydrocarbon seeps: Northern Gulf of Mexico continental slope

    SciTech Connect

    Roberts, H.H. )

    1993-11-01

    Large volumes of siliciclastic sediments, input especially during periods of lowered sea level, and compensating salt tectonics have produced a continental slope that is arguably the most complex in today's oceans. Faults associated with deformation of salt and shale provide the primary migration routes for hydrocarbon gases, crude oil, brines, and formation fluids to the modern sea floor. Since the mid 1980s, it has become increasingly clearer that this process has an extremely important impact on the geomorphology, sedimentology, and biology of the modern continental slope. Hydrocarbon source, flux rate, and water depth are important determinants of sea-floor response. Under rapid flux conditions mud volcanoes (to 1 km wide and 50 m high) result, and hydrate hills (rich with authigenic carbonates), carbonate lithoherms, and isolated communities of chemosymbiotic organisms with associated hardgrounds represent much slower flux responses. In numerous moderate- to low-flux cases, cold seep products function to support islands of productivity for communities of chemosymbiotic organisms that contribute both directly (shell material) and through chemical byproducts to the production of massive volumes of calcium-magnesium carbonate in the form of hardgrounds, stacked slabs, and discrete moundlike buildups (commonly >20m). Seep-related carbonates of the Gulf of Mexico continental slope, as well those formed through degassing of accretionary prisms along active margins, are now thought to create hardgrounds and discrete buildups that are excellent analogs for many problematic carbonate buildups in ancient deep-water siliciclastic rocks.

  4. A hydrothermal seep on the Costa Rica margin: middle ground in a continuum of reducing ecosystems

    PubMed Central

    Levin, Lisa A.; Orphan, Victoria J.; Rouse, Greg W.; Rathburn, Anthony E.; Ussler, William; Cook, Geoffrey S.; Goffredi, Shana K.; Perez, Elena M.; Waren, Anders; Grupe, Benjamin M.; Chadwick, Grayson; Strickrott, Bruce

    2012-01-01

    Upon their initial discovery, hydrothermal vents and methane seeps were considered to be related but distinct ecosystems, with different distributions, geomorphology, temperatures, geochemical properties and mostly different species. However, subsequently discovered vents and seep systems have blurred this distinction. Here, we report on a composite, hydrothermal seep ecosystem at a subducting seamount on the convergent Costa Rica margin that represents an intermediate between vent and seep ecosystems. Diffuse flow of shimmering, warm fluids with high methane concentrations supports a mixture of microbes, animal species, assemblages and trophic pathways with vent and seep affinities. Their coexistence reinforces the continuity of reducing environments and exemplifies a setting conducive to interactive evolution of vent and seep biota. PMID:22398162

  5. A hydrothermal seep on the Costa Rica margin: middle ground in a continuum of reducing ecosystems.

    PubMed

    Levin, Lisa A; Orphan, Victoria J; Rouse, Greg W; Rathburn, Anthony E; Ussler, William; Cook, Geoffrey S; Goffredi, Shana K; Perez, Elena M; Waren, Anders; Grupe, Benjamin M; Chadwick, Grayson; Strickrott, Bruce

    2012-07-01

    Upon their initial discovery, hydrothermal vents and methane seeps were considered to be related but distinct ecosystems, with different distributions, geomorphology, temperatures, geochemical properties and mostly different species. However, subsequently discovered vents and seep systems have blurred this distinction. Here, we report on a composite, hydrothermal seep ecosystem at a subducting seamount on the convergent Costa Rica margin that represents an intermediate between vent and seep ecosystems. Diffuse flow of shimmering, warm fluids with high methane concentrations supports a mixture of microbes, animal species, assemblages and trophic pathways with vent and seep affinities. Their coexistence reinforces the continuity of reducing environments and exemplifies a setting conducive to interactive evolution of vent and seep biota. PMID:22398162

  6. Recent MBARI Mapping AUV Surveys of Slumps, Scours, Gas Seeps, and Spreading Centers

    NASA Astrophysics Data System (ADS)

    Caress, D. W.; Thomas, H.; Paull, C. K.; Clague, D. A.; Conlin, D.; Thompson, D.; Lundsten, E.; Anderson, K.; Paduan, J. B.; Martin, J.

    2011-12-01

    The MBARI Mapping AUV D. Allan B. is a Dorado-class autonomous vehicle used for high-resolution, deep-ocean multibeam bathymetry, sidescan, and chirp subbottom profiler surveys. Operational since 2006, the D. Allan B. has been used for more than 125 successful survey missions. In post-processing, the navigation is adjusted to match features in overlapping and crossing swathes. Following navigation adjustment and tide correction, a bathymetric lateral resolution of 1 m and a vertical precision of 0.1 m are achieved from 50 m altitude. We present several examples from 2011 field operations in which a combination of high-resolution seafloor mapping, ROV-based bottom observations and sampling, and other data are used to investigate geological processes. Tubeworm Slump is a crescent shaped, 3.2 km by 1.5 km wide, slide scar with a 200 m high headwall at the top of the Monterey Canyon's north wall. This feature was discovered in 1998 by MBARI through surface multibeam surveys, and subsequently investigated using ROV dives and sampling. The ROV dives revealed patches of chemosynthetic tubeworm communities and surface exposures of authegenic carbonate and barite. The tsunami potential of the feature has been modeled assuming it was created by a single episode of mass wasting. The new high-resolution bathymetry and subbottom profiles reveal that Tubeworm slump has been created by many smaller, individual mass wasting events. During 2009 surveys offshore Cape Mendocino, CA, on R/V Okeonos Explorer, the multibeam water column data revealed several large gas plumes rising from the seafloor in two large depressions. One site coincides with a bend in the Eel Canyon, and the other in a large slump scar a few km to the south. New high-resolution surveys by the Mapping AUV indicate that the gas seep locations coincide with mounds and with rough-textured seafloor typical of other gas seep and shallow methane hydrate exposure sites along continental margins. The Mapping AUV also

  7. Micritic Peloids: Fossil Record of Biofilms Associated With Methane Seeps

    NASA Astrophysics Data System (ADS)

    Shapiro, R. S.

    2006-12-01

    Biofilms of archaea and bacteria are found where reduced hydrocarbons seep upward to the seafloor. The process of oxidizing the methane coupled with the reduction of seawater sulfate increases the alkalinity in the localized area and promotes the precipitation of carbonate minerals. The biofilms and carbonate deposits are ubiquitous in the modern oceans and the geologic record of hydrocarbon seeps goes back well into the Paleozoic. However, the paleontologic record of the microbes responsible for the production of the carbonates is poorly constrained. The few examples comprise casts and molds of filaments and cocci, framboidal pyrite of assumed biological affinity, organic biomarkers (lipids, hopanoids), and microbialite. Volumetrically, these fossils are insignificant compared with the total bulk of seep carbonate. Research into Mesozoic and Cenozoic seep carbonates from California, Oregon, Colorado, and South Dakota has yielded a new recognition for ancient biofilms. Micrite—the most common lithotype of seeps globally—exists as both peloids and groundmass. Common peloids of micrite average 0.5 mm in diameter (range from 0.1 to 0.7 mm), incorporate some siliciclastic material, and have distinct margins. Opaque minerals, likely sulfides, occur throughout the peloids. The matrix surrounding the peloids is a similar micrite, though in some samples, the peloids are surrounded by cement. Diagenesis leads to blurring of the peloid margins until a homogenous micrite groundmass with scattered sulfide and siliciclastic grains results. Use of a white card helps to outline original peloids. Increased levels of diagenesis can lead to crystal coarsening and obliterate original textures. These peloids are likely fecal pellets. A second population of peloids occur that are smaller (0.05 to 0.10 mm), darker in color, and with more diffuse boundaries. There are generally no siliciclastic grains intermixed with these peloids. These peloids occur in millimeter-scale clusters and

  8. Active-Site-Accessible, Porphyrinic Metal;#8722;Organic Framework Materials

    SciTech Connect

    Farha, Omar K.; Shultz, Abraham M.; Sarjeant, Amy A.; Nguyen, SonBinh T.; Hupp, Joseph T.

    2012-02-06

    On account of their structural similarity to cofactors found in many metallo-enzymes, metalloporphyrins are obvious potential building blocks for catalytically active, metal-organic framework (MOF) materials. While numerous porphyrin-based MOFs have already been described, versions featuring highly accessible active sites and permanent microporosity are remarkably scarce. Indeed, of the more than 70 previously reported porphyrinic MOFs, only one has been shown to be both permanently microporous and contain internally accessible active sites for chemical catalysis. Attempts to generalize the design approach used in this single successful case have failed. Reported here, however, is the synthesis of an extended family of MOFs that directly incorporate a variety of metalloporphyrins (specifically Al{sup 3+}, Zn{sup 2+}, Pd{sup 2+}, Mn{sup 3+}, and Fe{sup 3+} complexes). These robust porphyrinic materials (RPMs) feature large channels and readily accessible active sites. As an illustrative example, one of the manganese-containing RPMs is shown to be catalytically competent for the oxidation of alkenes and alkanes.

  9. Functional constituents of the active site of human neutrophil collagenase.

    PubMed

    Mookhtiar, K A; Wang, F; Van Wart, H E

    1986-05-01

    A series of chemical modification reactions has been carried out to identify functional constituents of the active site of human neutrophil collagenase. The enzyme is reversibly inhibited by the transition metal chelating agent 1,10-phenanthroline, and inhibition is fully reversed by zinc. Removal of weakly bound metal ions by gel filtration inactivates collagenase, and activity is fully restored on immediate readdition of calcium. The enzyme is unaffected by reagents that modify serine, cysteine, and arginine residues. However, reaction with the carboxyl reagents cyclohexylmorpholinocarbodiimide and Woodward's Reagent K lowers the activity of the enzyme substantially. Acetylimidazole inactivates the enzyme, but activity is completely restored on addition of hydroxylamine. The enzyme is also inactivated by tetranitromethane, indicating that it contains an essential tyrosine residue. Acylation of collagenase with diethyl pyrocarbonate, diketene, acetic anhydride, or trinitrobenzenesulfonate inactivates the enzyme, and activity is not restored on addition of hydroxylamine, indicating the presence of an essential lysine residue.

  10. Dynamics of hydrothermal seeps from the Salton Sea geothermal system (California, USA) constrained by temperature monitoring and time series analysis

    NASA Astrophysics Data System (ADS)

    Svensen, Henrik; Hammer, Ã.˜Yvind; Mazzini, Adriano; Onderdonk, Nathan; Polteau, Stephane; Planke, Sverre; Podladchikov, Yuri Y.

    2009-09-01

    Water-, mud-, gas-, and petroleum-bearing seeps are part of the Salton Sea geothermal system (SSGS) in southern California. Carbon dioxide is the main component behind the seeps in the Davis-Schrimpf seep field (˜20,000 m2). In order to understand the mechanisms driving the system, we have investigated the seep dynamics of the field by monitoring the temperature of two pools and two gryphons for 2180 h (90.8 days) in the period from December 2006 to March 2007, with a total of 32,700 measurements per station. The time series have been analyzed by statistical methods using cross correlation, autocorrelation and spectral analysis, and autoregressive modeling. The water-rich pools never exceed 34.0°C and are characterized by low-amplitude temperature variations controlled by the diurnal cycles in air temperature. The long-term validity of these results is evident from a second period of temperature monitoring of one of the pools from December 2007 to April 2008 (120 days). In contrast to the pools, the mud-rich gryphons have a strikingly different behavior. The gryphons are hotter (maximum 69.7°C) and have large amplitude variations (standard deviation of 6.4) that overprint any signal from external diurnal forcing. Autoregressive modeling shows the presence of distinct hot and cold pulses in the gryphon temperature time series, with amplitudes up to 3°C. These pulses likely reflect a combination of hydrothermal flux variations from the SSGS and the local temporal changes in bubbling activity within the gryphons.

  11. Nest predation increases with parental activity: Separating nest site and parental activity effects

    USGS Publications Warehouse

    Martin, T.E.; Scott, J.; Menge, C.

    2000-01-01

    Alexander Skutch hypothesized that increased parental activity can increase the risk of nest predation. We tested this hypothesis using ten open-nesting bird species in Arizona, USA. Parental activity was greater during the nestling than incubation stage because parents visited the nest frequently to feed their young during the nestling stage. However, nest predation did not generally increase with parental activity between nesting stages across the ten study species. Previous investigators have found similar results. We tested whether nest site effects might yield higher predation during incubation because the most obvious sites are depredated most rapidly. We conducted experiments using nest sites from the previous year to remove parental activity. Our results showed that nest sites have highly repeatable effects on nest predation risk; poor nest sites incurred rapid predation and caused predation rates to be greater during the incubation than nestling stage. This pattern also was exhibited in a bird species with similar (i.e. controlled) parental activity between nesting stages. Once nest site effects are taken into account, nest predation shows a strong proximate increase with parental activity during the nestling stage within and across species. Parental activity and nest sites exert antagonistic influences on current estimates of nest predation between nesting stages and both must be considered in order to understand current patterns of nest predation, which is an important source of natural selection.

  12. The earliest mollusc dominated seep fauna from the Early Jurassic of Argentina

    NASA Astrophysics Data System (ADS)

    Kaim, Andrzej; Jenkins, Robert; Parent, Horacio; Garrido, Alberto; Moriya, Kazuhiro

    2015-04-01

    The earliest mollusc dominated seep fauna from the Early Jurassic of Argentina Andrzej Kaim, Robert G. Jenkins, Horacio Parent, Alberto C. Garrido The hydrocarbon seep deposits are known from Early Jurassic of Argentina since the report of Gomez-Perez (2003). The latter author identified very negative δ13C values (down to -33) and several fabrics typical for seep carbonates. Nevertheless she identified no macrofaunal assemblages apart from worm tubes. We re-visited the locality of Gomez-Perez (named here La Elina) and we were able to collect several molluscs associated with the seep carbonate. The most common and diversified are molluscs and worm tubes. We identified at least three species of gastropods, including the oldest-known species of neomphalids, lucinid and protobranch bivalves and numerous ammonoids. Unlike another known Early Jurassic seep from Oregon and the only Late Triassic seep (also from Oregon) there are no brachiopods associated with this seep. Therefore we consider the seep at La Elina as the oldest seep of modern aspect where the fauna is dominated by molluscs and not brachiopods.

  13. Species Distribution and Population Connectivity of Deep-Sea Mussels at Hydrocarbon Seeps in the Gulf of Mexico

    PubMed Central

    Faure, Baptiste; Schaeffer, Stephen W.; Fisher, Charles R.

    2015-01-01

    Hydrocarbon seepage is widespread and patchy in the Gulf of Mexico, and six species of symbiont containing bathymodiolin mussels are found on active seeps over wide and overlapping depth and geographic ranges. We use mitochondrial genes to discriminate among the previously known and a newly discovered species and to assess the connectivity among populations of the same species in the northern Gulf of Mexico (GoM). Our results generally validate the morphologically based distribution of the three previously known GoM species of Bathymodiolus, although we found that approximately 10% of the morphologically based identifications were incorrect and this resulted in some inaccuracies with respect to their previously assigned depth and geographical distribution patterns. These data allowed us to confirm that sympatry of two species of Bathymodiolus within a single patch of mussels is common. A new species of bathymodiolin, Bathymodiolus sp. nov., closely related to B. heckerae was also discovered. The two species live at the same depths but have not been found in sympatry and both have small effective population sizes. We found evidence for genetic structure within populations of the three species of Bathymodiolinae for which we had samples from multiple sites and suggest limited connectivity for populations at some sites. Despite relatively small sample sizes, genetic diversity indices suggest the largest population sizes for B. childressi and Tamu fisheri and the smallest for B. heckerae and B. sp. nov. among the GoM bathymodiolins. Moreover, we detected an excess of rare variants indicating recent demographic changes and population expansions for the four species of bathymodiolins from the Gulf of Mexico. PMID:25859657

  14. Active sites in char gasification: Final technical report

    SciTech Connect

    Wojtowicz, M.; Lilly, W.D.; Perkins, M.T.; Hradil, G.; Calo, J.M.; Suuberg, E.M.

    1987-09-01

    Among the key variables in the design of gasifiers and combustors is the reactivity of the chars which must be gasified or combusted. Significant loss of unburned char is unacceptable in virtually any process; the provision of sufficient residence time for complete conversion is essential. A very wide range of reactivities are observed, depending upon the nature of the char in a process. The current work focuses on furthering the understanding of gasification reactivities of chars. It has been well established that the reactivity of char to gasification generally depends upon three principal factors: (1) the concentration of ''active sites'' in the char; (2) mass transfer within the char; and (3) the type and concentration of catalytic impurities in the char. The present study primarily addresses the first factor. The subject of this research is the origin, nature, and fate of active sites in chars derived from parent hydrocarbons with coal-like structure. The nature and number of the active sites and their reactivity towards oxygen are examined in ''model'' chars derived from phenol-formaldehyde type resins. How the active sites are lost by the process of thermal annealing during heat treatment of chars are studied, and actual rate for the annealing process is derived. Since intrinsic char reactivities are of primary interest in the present study, a fair amount of attention was given to the model char synthesis and handling so that the effect of catalytic impurities and oxygen-containing functional groups in the chemical structure of the material were minimized, if not completely eliminated. The project would not be considered complete without comparing characteristic features of synthetic chars with kinetic behavior exhibited by natural chars, including coal chars.

  15. Exploration and Discovery of Hydrocarbon Seeps, Coral Ecosystems, and Shipwrecks in the Deep Gulf of Mexico

    NASA Astrophysics Data System (ADS)

    Shank, T. M.; Hsing, P.; Carney, R. S.; Herrera, S.; Heyl, T.; Munro, C.; Bors, E.; Kiene, W.; Vecchione, M.; Evans, A.; Irion, J.; Warren, D.; Malik, M.; Lobecker, M.; Potter, J.

    2012-12-01

    Between March 20 and April 6, 2012, the NOAA Ship Okeanos Explorer served as a platform for ship-board and shore-side scientists to explore the deep Gulf of Mexico, targeting the northern West Florida Escarpment, DeSoto Canyon, the vicinity (within 11km) of the Deepwater Horizon (DWH) well, and deepwater shipwrecks. We systematically explored and discovered natural hydrocarbon seeps, diverse coral ecosystems, wooden and iron-hulled shipwrecks more than 100 years old colonized by coral communities, and sperm whale habitat between 600 and 1200m. A total of sixteen dives took advantage of new and recent maps to explore and groundtruth both hard and soft-bottom habitats, from cretaceous carbonates to mounds of coral rubble. The final ROV dive successfully groundtruthed expected methane-release areas imaged by the ship's mapping systems up to 1150m above the seafloor. The source of the mapping imagery was a stream of bubbles issuing from beneath thriving seep mussel communities. We visited five sites in the Mississippi Canyon (MC) area (lease blocks MC294, MC297, MC388, MC255, and MC036; the DWH incident took place in MC252). These sites were 11.3 km SW, 6.8 km SW, 7.6 km SW, 25.7 km E, and 27.4 km to the NE of the DWH, respectively. We used high-definition imaging systems on the Little Hercules ROV and Seirios camera platform to document more than 130 coral colonies and over 400 associated individual animals to continue to assessing the impact of the Deepwater Horizon oil spill. All of these efforts were conducted to provide fundamental knowledge of unknown and poorly known regions, ecosystems, and items of historical significance in the deep Gulf of Mexico.

  16. Investigation of Metal Bioavailability and Microbial Metal Utilization in Methane Seep Ecosystems through Integration of Geochemical and Biological Datasets

    NASA Astrophysics Data System (ADS)

    Glass, J. B.; Gadh, V.; Steele, J. A.; Adkins, J. F.; Orphan, V. J.

    2012-12-01

    Methane hydrate seeps are important sources of greenhouse gases and host unique microbial communities that couple anaerobic oxidation of methane and sulfate reduction. Microbial enzymes that catalyze the reactions driving these anaerobic metabolisms require transition metals such as Fe, Ni, Co, Zn, and Mo as essential cofactors. These metals are expected to be drawn down to low concentrations by precipitation as sulfide phases in the highly sulfidic porewaters at methane seep ecosystems. However, in situ concentrations of biologically-important metals in sulfidic methane seep pore fluids and the relative importance of different metals for anaerobic methanotrophic archaea (ANME) vs. sulfate reducing bacteria (SRB) are unknown. We are integrating geochemical and metagenomic datasets with nano-scale maps of cellular metal distributions to gain insights into metal bioavailability and utilization in methane seep ecosystems. We have measured porewater profiles of dissolved metals (V, Ni, Cu, Co, Fe, Mn, Zn, Mo and W) from three habitat types at Hydrate Ridge, offshore Oregon: Calyptogena clam beds, microbial mats and sites with low methane flux. Highly sulfidic sediment porewaters beneath microbial mats contained the lowest metal concentrations, suggesting that microbes inhabiting these environments may be limited by metal scarcity. Cobalt occurred at particularly low abundances (≤5 nM in all cores and frequently at sub-nanomolar levels). We also analyzed the taxonomic distribution of ABC (ATP-binding cassette) metal transporters in metagenomes from environmentally-enriched consortia of ANME-2 and SRB from Eel River Basin methane seeps. Our findings suggest that both ANME and SRB possess genes encoding ABC transporters with high affinity for Fe, Ni, Co, Zn and Mo. Combined with our geochemical data, these results imply that ANME-SRB consortia in highly sulfidic environments have specialized mechanisms that allow them to acquire metal micronutrients

  17. Brownian aggregation rate of colloid particles with several active sites

    SciTech Connect

    Nekrasov, Vyacheslav M.; Yurkin, Maxim A.; Chernyshev, Andrei V.; Polshchitsin, Alexey A.; Yakovleva, Galina E.; Maltsev, Valeri P.

    2014-08-14

    We theoretically analyze the aggregation kinetics of colloid particles with several active sites. Such particles (so-called “patchy particles”) are well known as chemically anisotropic reactants, but the corresponding rate constant of their aggregation has not yet been established in a convenient analytical form. Using kinematic approximation for the diffusion problem, we derived an analytical formula for the diffusion-controlled reaction rate constant between two colloid particles (or clusters) with several small active sites under the following assumptions: the relative translational motion is Brownian diffusion, and the isotropic stochastic reorientation of each particle is Markovian and arbitrarily correlated. This formula was shown to produce accurate results in comparison with more sophisticated approaches. Also, to account for the case of a low number of active sites per particle we used Monte Carlo stochastic algorithm based on Gillespie method. Simulations showed that such discrete model is required when this number is less than 10. Finally, we applied the developed approach to the simulation of immunoagglutination, assuming that the formed clusters have fractal structure.

  18. Active Sites Environmental Monitoring Program: FY 1991 report

    SciTech Connect

    Ashwood, T.L.; Hicks, D.S.; Morrissey, C.M.

    1992-11-01

    This report summarizes the activities of the Active Sites Environmental Monitoring Program (ASEMP) from April 1991 through September 1991. The ASEMP was established in 1989 by Solid Waste Operations (SWO) and the Environmental Sciences Division, both of Oak Ridge National Laboratory, to provide early detection and performance monitoring at active low-level (radioactive) waste (LLW) disposal sites in Solid Waste Storage Area (SWSA) 6 and transuranic (TRU) waste storage sites in SWSA 5 as required by chapters II and III of US Department of Energy Order 5820.2A. A new set of action levels was developed on the basis of a statistical analysis of background contamination. These new action levels have been used to evaluate results in this report. Results of ASEMP monitoring continue to demonstrate that no LLW (except [sup 3]H) is being leached from the storage vaults on the tumulus pads. Loading of vaults on Tumulus II, which began in early FY 1991, was >90% complete at the end of September 1991. Results of sampling of groundwater and surface waters is presented.

  19. Inhibition and active-site modelling of prolidase.

    PubMed

    King, G F; Crossley, M J; Kuchel, P W

    1989-03-15

    Consideration of the active-site model of prolidase led us to examine azetidine, pyrrolidine and piperidine substrate analogs as potential in vivo inhibitors of the enzyme. One of these, N-benzyloxycarbonyl-L-proline, was shown to be a potent competitive inhibitor of porcine kidney prolidase (Ki = 90 microM); its rapid protein-mediated permeation of human and sheep erythrocytes suggests that it may be effective in vivo. The higher homolog, N-benzyloxycarbonyl-L-pipecolic acid, was also a potent inhibitor of the enzyme while the antihypertensive drugs, captopril and enalaprilat, were shown to have mild and no inhibitory effects, respectively. Analysis of inhibitor action and consideration of X-ray crystallographic data of relevant Mn2+ complexes allowed the active-site model of prolidase to be further refined; a new model is presented in which the substrate acts as a bidentate ligand towards the active-site manganous ion. Various aspects of the new model help to explain why Mn2+ has been 'chosen' by the enzyme in preference to other biologically available metal ions. PMID:2924773

  20. Substrate-specific pressure-dependence of microbial sulfate reduction in deep-sea cold seep sediments of the Japan Trench

    PubMed Central

    Vossmeyer, Antje; Deusner, Christian; Kato, Chiaki; Inagaki, Fumio; Ferdelman, Timothy G.

    2012-01-01

    The influence of hydrostatic pressure on microbial sulfate reduction (SR) was studied using sediments obtained at cold seep sites from 5500 to 6200 m water depth of the Japan Trench. Sediment samples were stored under anoxic conditions for 17 months in slurries at 4°C and at in situ pressure (50 MPa), at atmospheric pressure (0.1 MPa), or under methanic conditions with a methane partial pressure of 0.2 MPa. Samples without methane amendment stored at in situ pressure retained higher levels of sulfate reducing activity than samples stored at 0.1 MPa. Piezophilic SR showed distinct substrate specificity after hydrogen and acetate addition. SR activity in samples stored under methanic conditions was one order of magnitude higher than in non-amended samples. Methanic samples stored under low hydrostatic pressure exhibited no increased SR activity at high pressure even with the amendment of methane. These new insights into the effects of pressure on substrate specific sulfate reducing activity in anaerobic environmental samples indicate that hydrostatic pressure must be considered to be a relevant parameter in ecological studies of anaerobic deep-sea microbial processes and long-term storage of environmental samples. PMID:22822404

  1. Carbon isotopes of benthic foraminifera associated with methane seeps in Four-Way Closure Ridge, offshore southwestern Taiwan

    NASA Astrophysics Data System (ADS)

    Wang, W. R.; Wei, K. Y.; Mii, H. S.; Lin, Y. S.; Huang, J. J.; Wang, P. L.; Lin, A. T.

    2015-12-01

    Release of large amounts of methane from marine gas hydrate reservoirs has been considered as a possible trigger of climate change, which can be recorded by the variation of carbon isotopes (δ13C) of the benthic foraminifera. In modern analogs, previous studies have suggested that δ13C becomes more negative when influenced by methane seeps. However, values of δ13C of benthic foraminifera might vary with different species and sedimentary settings in different regions. Seismic profiles in offshore southwestern Taiwan show the existence of Bottom Simulating Reflector (BSR) in the region, indicative of gas hydrate reservoirs. Various methane seepages have been found, and they are suspected to be related to the gas hydrates buried underneath. A better understanding of the δ13C signals of benthic foraminifera near the methane seepages can further clarify the origin of the methane and to evaluate it as a proxy of methane release for the geologic past. We have analyzed δ13C of benthic foraminifera Uvigerina proboscidea (150-250 mm) in the topmost 15 cm sediments in five marine cores (OR1-1092-WFWC-1, OR1-1092-WFWC-4, OR1-1092-WFWC-6, OR3-1806-C5-2 and OR3-1806-C10) collected from the Four-Way Closure Ridge in offshore southwestern Taiwan (water depth from 1330 to 1580 m). Our results show that δ13C values of U. proboscidea range from -0.98‰ to -6.21‰ (VPDB) for core OR3-1806-C5-2, which is considered as a seeps-influenced site. On the other hand, δ13C values of U. proboscidea from the background sites range from -0.40‰ to -1.00‰. The difference between the methane seep-affected and the background sites is in the range of 0.00‰ to 5.01‰, comparable to those documented in previous studies in other areas. The significant negative excursion in carbon isotopes in the seep site foraminifera is likely caused by incorporation of light inorganic carbon generated by methanotrophy in the system.

  2. Overpressure and fluid flow in the new jersey continental slope: implications for slope failure and cold seeps

    PubMed

    Dugan; Flemings

    2000-07-14

    Miocene through Pleistocene sediments on the New Jersey continental slope (Ocean Drilling Program Site 1073) are undercompacted (porosity between 40 and 65%) to 640 meters below the sea floor, and this is interpreted to record fluid pressures that reach 95% of the lithostatic stress. A two-dimensional model, where rapid Pleistocene sedimentation loads permeable sandy silt of Miocene age, successfully predicts the observed pressures. The model describes how lateral pressure equilibration in permeable beds produces fluid pressures that approach the lithostatic stress where overburden is thin. This transfer of pressure may cause slope failure and drive cold seeps on passive margins around the world. PMID:10894774

  3. Methane emission and consumption at a North Sea gas seep (Tommeliten area)

    NASA Astrophysics Data System (ADS)

    Niemann, H.; Elvert, M.; Hovland, M.; Orcutt, B.; Judd, A.; Suck, I.; Gutt, J.; Joye, S.; Damm, E.; Finster, K.; Boetius, A.

    The Tommeliten seepage area is part of the Greater Ekofisk area, which is situated above the Tommeliten Delta salt diapir in the central North Sea (56°29.90' N, 2°59.80' E, Norwegian Block 1/9, 75 m water depth). Here, cracks in a buried marl horizon allow methane to migrate into overlying clay-silt and sandy sediments. Hydroacoustic sediment echosounding showed several venting spots coinciding with the apex of marl domes where methane is released into the water column and potentially to the atmosphere. In the vicinity of the gas seeps, sea floor observations showed small mats of giant sulphide-oxidizing bacteria above patches of black sediments as well as carbonate crusts, which are exposed 10 to 50 cm above seafloor forming small reefs. These Methane-Derived Authigenic Carbonates (MDACs) contain 13C-depleted, archaeal lipids indicating previous gas seepage and AOM activity. High amounts of sn2-hydroxyarchaeol relative to archaeol and low abundances of biphytanes in the crusts give evidence that ANaerobic MEthane-oxidising archaea (ANME) of the phylogenetic cluster ANME-2 were the potential mediators of Anaerobic Oxidation of Methane (AOM) at the time of carbonate formation. Small pieces of MDACs were also found subsurface at about 1.7 m sediment depth, associated with the AOM zone. This zone is characterized by elevated AOM and Sulphate Reduction (SR) rates, increased concentrations of 13C-depleted tetraether derived biphytanes, and specific bacterial Fatty Acids (FA). Further biomarker and 16S rDNA based analyses of this horizon give evidence that AOM is mediated by archaea belonging to the ANME-1b group and Sulphate Reducing Bacteria (SRB) most likely belonging to the Seep-SRB1 cluster. The zone of active methane consumption was restricted to a distinct horizon of about 20 cm. Concentrations of 13C-depleted lipid biomarkers (e.g. 500 ng g-dw-1 biphythanes, 140 ng g-dw-1 fatty acid ai-C15:0), cell numbers (1.5×108 cells cm-3), AOM and SR rates (3 nmol cm-3 d

  4. Development of a passive-flow treatment system for {sup 90}Sr-contaminated seep water at Waste Area Grouping 5 at Oak Ridge National Laboratory

    SciTech Connect

    Taylor, P.A.

    1994-08-01

    Seep C is a free-flowing stream of groundwater (typical flow of 0.2 to 2 L/min) that emerges in a narrow valley below the old low-level waste disposal trenches in Solid Waste Storage Area 5 (SWSA 5), which is part of Waste Area Grouping 5 (WAG 5). The seep water contains high concentrations of Sr-90 (10,000 to 20,000 Bq/L) and contributes about 25% of all the Sr-90 leaving Oak Ridge National Laboratory. Seep C was identified as a primary source of off-site contaminant transport and was designated for an early removal action under the Comprehensive Environmental Response and Liability Act (CERCLA). A passive-flow treatment system was chosen as the most cost-effective method for treating the seep water. The goal of the removal action is to have a system operational by November 1, 1994, that reduces the Sr-90 concentration in the water collected and treated by at least 90%. In order to provide design and operating data for the full-scale system, a pilot-scale system, consisting of a 5-gal bucket with an inlet connection in the lid and a screened outlet on the bottom filled with 16 L of chabazite zeolite, was used to treat the seep water. The test was started on March 17, 1994, and concluded on June 15, 1994. The system treated 63,470 L (3967 bed volumes) of water and 22.7 mCi of Sr-90 from the seep water. The system removed over 99.5% of the Sr-90 from the first 43,000 L of water treated, after which the removal efficiency slowly decreased as the zeolite became loaded until it reached 84% for the final sample. The passive system performed at least as well as comparable pumped zeolite systems in terms of removal efficiency and zeolite utilization. The test was terminated just before the construction crew mobilized at Seep C to build the full-scale system.

  5. Gulf of Mexico hydrocarbon seep communities—I. Regional distribution of hydrocarbon seepage and associated fauna

    NASA Astrophysics Data System (ADS)

    Kennicutt, Mahlon C.; Brooks, James M.; Bidigare, Robert R.; Denoux, Guy J.

    1988-09-01

    A series of otter trawls demonstrate that communities based on chemosynthesis are broadly distributed across the northwestern Gulf of Mexico continental slope in hydrocarbon seep areas. Thirty-nine trawls were taken at 33 locations reported to exhibit transparent or chaotic seismic "wipe-out" zones. The sites, in water depths from 180 to 900 m, span an area from offshore the Mississippi River delta to the upper Texas continental slope. Endosymbiont-containing organisms or their remains (either tube worms, mussels and/or clams) were recovered at 21 sites on the northern Gulf of Mexico slope. Tube worms, clams and mussels known to be associated with symbionts were retreived at 18, 12 and 5 sites, respectively. Carbon isotope analysis of selected animal tissues confirmed the chemosynthetic association. Animals containing isotopically light chemosynthetic carbon were collected at 21 sites. Piston cores at each site were used to determine the presence of mature hydrocarbons. Nine of 30 piston cores were visibly oil-stained. Trawl collections at locations where visibly oil-stained cores were recovered contained at least one species of chemosynthetic-associated organism and generally represented the most abundant catches of endosymbiont-containing animals. The chemical environment (oil and gas seepage) necessary to support chemosynthetic-based ecosystems is widespread on the northern Gulf of Mexico continental slope.

  6. Druggability analysis and classification of protein tyrosine phosphatase active sites

    PubMed Central

    Ghattas, Mohammad A; Raslan, Noor; Sadeq, Asil; Al Sorkhy, Mohammad; Atatreh, Noor

    2016-01-01

    Protein tyrosine phosphatases (PTP) play important roles in the pathogenesis of many diseases. The fact that no PTP inhibitors have reached the market so far has raised many questions about their druggability. In this study, the active sites of 17 PTPs were characterized and assessed for its ability to bind drug-like molecules. Consequently, PTPs were classified according to their druggability scores into four main categories. Only four members showed intermediate to very druggable pocket; interestingly, the rest of them exhibited poor druggability. Particularly focusing on PTP1B, we also demonstrated the influence of several factors on the druggability of PTP active site. For instance, the open conformation showed better druggability than the closed conformation, while the tight-bound water molecules appeared to have minimal effect on the PTP1B druggability. Finally, the allosteric site of PTP1B was found to exhibit superior druggability compared to the catalytic pocket. This analysis can prove useful in the discovery of new PTP inhibitors by assisting researchers in predicting hit rates from high throughput or virtual screening and saving unnecessary cost, time, and efforts via prioritizing PTP targets according to their predicted druggability. PMID:27757011

  7. Current activities handbook: formerly utilized sites remedial action program

    SciTech Connect

    1981-02-27

    This volume is one of a series produced under contract with the DOE, by Politech Corporation to develop a legislative and regulatory data base to assist the FUSRAP management in addressing the institutional and socioeconomic issues involved in carrying out the Formerly Utilized Sites Remedial Action Program. This Information Handbook series contains information about all relevant government agencies at the Federal and state levels, the pertinent programs they administer, each affected state legislature, and current Federal and state legislative and regulatory initiatives. This volume is a compilation of information about the activities each of the thirteen state legislatures potentially affected by the Formerly Utilized Sites Remedial Action Program. It contains a description of the state legislative procedural rules and a schedule of each legislative session; a summary of pending relevant legislation; the name and telephone number of legislative and state agency contacts; and the full text of all bills identified.

  8. Mollusks from late Mesozoic seep deposits, chiefly in California.

    PubMed

    Kaim, Andrzej; Jenkins, Robert G; Tanabe, Kazushige; Kiel, Steffen

    2014-01-01

    Twenty-nine mollusk species from Late Jurassic to Eocene hydrocarbon seep deposits from California (USA), Japan, New Zealand, and Barbados are described and illustrated. Twenty species belong to Gastropoda and nine to Bivalvia. Seven new species, three new genera, and one new family are introduced. The gastropod Hikidea gen. nov. includes smooth-shelled Cantrainea-like colloniins from Cretaceous hydrocarbon seeps and plesiosaur falls. Hikidea osoensis sp. nov. is the oldest species of this genus. Chilodonta? reticulata sp. nov. is a distinctive vetigastropod though its supraspecific position is unclear. Phanerolepida onoensis sp. nov. is the first species of this colloniin genus from a seep deposit. We describe two new genera of Hokkaidoconchidae: Abyssomelania gen. nov. and Ascheria gen. nov.; this family includes now four genera (including Hokkaidoconcha and Humptulipsia) and ranges from the Late Jurassic to the Eocene. Abyssomelania is characterized by a large, high-spired shell and unusual widely-spaced prosocline riblets (here called abyssomelaniid riblets). Abyssomelania is represented by two new species: A. cramptoni sp. nov. from the Late Cretaceous of New Zealand and A. campbellae sp. nov. from the Early Cretaceous of California. Ascheria gen. nov. is characterized by a large high-spired cerithiform shell, a subsutural constriction, and mostly reticulate ornament. Two nominate species are included: Ascheria gigantea (Kiel et al., 2008) and A. eucosmeta (Ascher, 1906), both of Early Cretaceous age. Two further species potentially belonging to Ascheria from the Eocene of Barbados are reported in open nomenclature and are re-illustrated and re-described for comparison. Humtulipsia nobuharai sp. nov. is described based on specimens from the Campanian-Maastrichtian Sada Limestone seep deposit in Japan. The new family Paskentanidae fam. nov. is introduced for the genera Paskentana and Atresius. The species of this family are characterized by thin-shelled, broad

  9. Mollusks from late Mesozoic seep deposits, chiefly in California.

    PubMed

    Kaim, Andrzej; Jenkins, Robert G; Tanabe, Kazushige; Kiel, Steffen

    2014-09-17

    Twenty-nine mollusk species from Late Jurassic to Eocene hydrocarbon seep deposits from California (USA), Japan, New Zealand, and Barbados are described and illustrated. Twenty species belong to Gastropoda and nine to Bivalvia. Seven new species, three new genera, and one new family are introduced. The gastropod Hikidea gen. nov. includes smooth-shelled Cantrainea-like colloniins from Cretaceous hydrocarbon seeps and plesiosaur falls. Hikidea osoensis sp. nov. is the oldest species of this genus. Chilodonta? reticulata sp. nov. is a distinctive vetigastropod though its supraspecific position is unclear. Phanerolepida onoensis sp. nov. is the first species of this colloniin genus from a seep deposit. We describe two new genera of Hokkaidoconchidae: Abyssomelania gen. nov. and Ascheria gen. nov.; this family includes now four genera (including Hokkaidoconcha and Humptulipsia) and ranges from the Late Jurassic to the Eocene. Abyssomelania is characterized by a large, high-spired shell and unusual widely-spaced prosocline riblets (here called abyssomelaniid riblets). Abyssomelania is represented by two new species: A. cramptoni sp. nov. from the Late Cretaceous of New Zealand and A. campbellae sp. nov. from the Early Cretaceous of California. Ascheria gen. nov. is characterized by a large high-spired cerithiform shell, a subsutural constriction, and mostly reticulate ornament. Two nominate species are included: Ascheria gigantea (Kiel et al., 2008) and A. eucosmeta (Ascher, 1906), both of Early Cretaceous age. Two further species potentially belonging to Ascheria from the Eocene of Barbados are reported in open nomenclature and are re-illustrated and re-described for comparison. Humtulipsia nobuharai sp. nov. is described based on specimens from the Campanian-Maastrichtian Sada Limestone seep deposit in Japan. The new family Paskentanidae fam. nov. is introduced for the genera Paskentana and Atresius. The species of this family are characterized by thin-shelled, broad

  10. Families of miocene monterey crude oil, seep, and tarball samples, coastal California

    USGS Publications Warehouse

    Peters, K.E.; Hostettler, F.D.; Lorenson, T.D.; Rosenbauer, R.J.

    2008-01-01

    calcareous-siliceous member (tribe 3) because the latter is thinner and less oil-prone than the overlying members. Tribe 3 occurs mainly north of Point Conception where shallow burial caused preferential generation from the underlying lower calcareous-siliceous member or another unit with similar characteristics. In a test of the decision tree, 10 tarball samples collected from beaches in Monterey and San Mateo counties in early 2007 were found to originate from natural seeps representing different organofacies of Monterey Formation source rock instead from one anthropogenic pollution event. The seeps apparently became more active because of increased storm activity. Copyright ?? 2008. The American Association of Petroleum Geologists. All rights reserved.

  11. A comparison of hydrocarbon gases from springs and seeps of varied geologic provinces of the northwestern US

    SciTech Connect

    Lorenson, T.D.; Kvenvolden, K.A. )

    1993-04-01

    The northwestern US hosts a remarkable quantity and variety of thermal springs and seeps. Although many studies have dealt with the liquids and non-hydrocarbon gases emanating from these sources, few have focused on hydrocarbon gases. methane in particular is now recognized as an important reactive trace gas in the earth's atmosphere. To understand better the magnitude and occurrence of natural sources of hydrocarbons to the atmosphere, the authors have begun a survey of these gases throughout the northwestern US. This area encompasses a number of different tectonic regimes: the Yellowstone Hot Spot, the northern Basin and Range province, the Cascade volcanic arc, and the Cascadia subduction complex. Methane is present in each area at concentration levels ranging from about 2 ppmv (parts per million by volume) to 99.9% (by volume). Hydrothermal activity in the Yellowstone area produces spring gases containing less than 4% methane, with CO[sub 2] as the balance gas. The Teton area has a wide variety of gas compositions with either methane, carbon dioxide, or nitrogen as the primary gas component. In the northern Great Basin, thermal springs and seeps typically occur along fault zones at the base of mountain ranges. Methane concentrations range from 0.2 to 47%, with HMW HC concentrations from 0 to 3,100 ppmv. Areas covered by the Cenozoic Columbia River basalts and the basalts of the Snake River Plain continue to have high heat flow and produce thermal springs and seeps, usually along fault zones. Gases from the southern Cascade volcanic arc (Mt. Shasta and Mt. Lassen) are composed typically of carbon dioxide, with minor amounts of methane (less than 0.2%); however some fumaroles at Mt. Lassen have minor quantities of HMW HC. Along the Pacific coast, melanges of the Cascadia subduction complex host many seeps and springs. In some seeps the gas consists almost exclusively of methane (94.3 to 99.9%) with amounts of HMW HC ranging from about 5 ppmv to 3.5%.

  12. Microsensor studies on Padina from a natural CO2 seep: implications of morphology on acclimation to low pH.

    PubMed

    Hofmann, Laurie C; Fink, Artur; Bischof, Kai; de Beer, Dirk

    2015-12-01

    Low seawater pH can be harmful to many calcifying marine organisms, but the calcifying macroalgae Padina spp. flourish at natural submarine carbon dioxide seeps where seawater pH is low. We show that the microenvironment created by the rolled thallus margin of Padina australis facilitates supersaturation of CaCO3 and calcifi-cation via photosynthesis-induced elevated pH. Using microsensors to investigate oxygen and pH dynamics in the microenvironment of P. australis at a shallow CO2 seep, we found that, under saturating light, the pH inside the microenvironment (pHME ) was higher than the external seawater (pHSW ) at all pHSW levels investigated, and the difference (i.e., pHME - pHSW ) increased with decreasing pHSW (0.9 units at pHSW 7.0). Gross photosynthesis (Pg ) inside the microenvironment increased with decreasing pHSW , but algae from the control site reached a threshold at pH 6.5. Seep algae showed no pH threshold with respect to Pg within the pHSW range investigated. The external carbonic anhydrase (CA) inhibitor, acetazolamide, strongly inhibited Pg of P. australis at pHSW 8.2, but the effect was diminished under low pHSW (6.4-7.5), suggesting a greater dependence on membrane-bound CA for the dehydration of HCO3 (-) ions during dissolved inorganic carbon uptake at the higher pHSW . In comparison, a calcifying green alga, Halimeda cuneata f. digitata, was not inhibited by AZ, suggesting efficient bicarbonate transport. The ability of P. australis to elevate pHME at the site of calcification and its strong dependence on CA may explain why it can thrive at low pHSW . PMID:26987005

  13. Microsensor studies on Padina from a natural CO2 seep: implications of morphology on acclimation to low pH.

    PubMed

    Hofmann, Laurie C; Fink, Artur; Bischof, Kai; de Beer, Dirk

    2015-12-01

    Low seawater pH can be harmful to many calcifying marine organisms, but the calcifying macroalgae Padina spp. flourish at natural submarine carbon dioxide seeps where seawater pH is low. We show that the microenvironment created by the rolled thallus margin of Padina australis facilitates supersaturation of CaCO3 and calcifi-cation via photosynthesis-induced elevated pH. Using microsensors to investigate oxygen and pH dynamics in the microenvironment of P. australis at a shallow CO2 seep, we found that, under saturating light, the pH inside the microenvironment (pHME ) was higher than the external seawater (pHSW ) at all pHSW levels investigated, and the difference (i.e., pHME - pHSW ) increased with decreasing pHSW (0.9 units at pHSW 7.0). Gross photosynthesis (Pg ) inside the microenvironment increased with decreasing pHSW , but algae from the control site reached a threshold at pH 6.5. Seep algae showed no pH threshold with respect to Pg within the pHSW range investigated. The external carbonic anhydrase (CA) inhibitor, acetazolamide, strongly inhibited Pg of P. australis at pHSW 8.2, but the effect was diminished under low pHSW (6.4-7.5), suggesting a greater dependence on membrane-bound CA for the dehydration of HCO3 (-) ions during dissolved inorganic carbon uptake at the higher pHSW . In comparison, a calcifying green alga, Halimeda cuneata f. digitata, was not inhibited by AZ, suggesting efficient bicarbonate transport. The ability of P. australis to elevate pHME at the site of calcification and its strong dependence on CA may explain why it can thrive at low pHSW .

  14. Observations of bubbles in natural seep flares at MC 118 and GC 600 using in situ quantitative imaging

    NASA Astrophysics Data System (ADS)

    Wang, Binbin; Socolofsky, Scott A.; Breier, John A.; Seewald, Jeffrey S.

    2016-04-01

    This paper reports the results of quantitative imaging using a stereoscopic, high-speed camera system at two natural gas seep sites in the northern Gulf of Mexico during the Gulf Integrated Spill Research G07 cruise in July 2014. The cruise was conducted on the E/V Nautilus using the ROV Hercules for in situ observation of the seeps as surrogates for the behavior of hydrocarbon bubbles in subsea blowouts. The seeps originated between 890 and 1190 m depth in Mississippi Canyon block 118 and Green Canyon block 600. The imaging system provided qualitative assessment of bubble behavior (e.g., breakup and coalescence) and verified the formation of clathrate hydrate skins on all bubbles above 1.3 m altitude. Quantitative image analysis yielded the bubble size distributions, rise velocity, total gas flux, and void fraction, with most measurements conducted from the seafloor to an altitude of 200 m. Bubble size distributions fit well to lognormal distributions, with median bubble sizes between 3 and 4.5 mm. Measurements of rise velocity fluctuated between two ranges: fast-rising bubbles following helical-type trajectories and bubbles rising about 40% slower following a zig-zag pattern. Rise speed was uncorrelated with hydrate formation, and bubbles following both speeds were observed at both sites. Ship-mounted multibeam sonar provided the flare rise heights, which corresponded closely with the boundary of the hydrate stability zone for the measured gas compositions. The evolution of bubble size with height agreed well with mass transfer rates predicted by equations for dirty bubbles.

  15. Characterization of Sea-Air Methane Fluxes Around a Seafloor Gas Seep in the Central Laptev Sea

    NASA Astrophysics Data System (ADS)

    Geibel, M. C.; Thornton, B. F.; Prytherch, J.; Brooks, I. M.; Salisbury, D. J.; Tjernstrom, M. K. H.; Semiletov, I. P.; Mörth, C. M.; Humborg, C.; Crill, P. M.

    2015-12-01

    The fate of CH4 released from thawing subsea permafrost on the East Siberian Arctic Shelf (ESAS) is unclear. In recent years, interest has focused on the possibility of large emissions of CH4 directly to the atmosphere from this remote area. It is uncertain how high those emissions are and whether they are primarily of biogenic or thermogenic nature, or some combination of sources. The SWERUS-C3 expedition onboard the Swedish icebreaker Oden during July-August 2014 sought to document possible CH4 release from subsea permafrost, and to understand mechanisms and magnitudes of such CH4 being released to the atmosphere. During the first leg of the expedition continuous high-resolution measurements were made to determine the in situ concentrations of CH4 in both the atmosphere and surface water. During SWERUS-C3, several underwater gas flares were found within the ESAS region showing elevated CH4 concentrations collocated in the surface waters. Here we focus on one seep area, a so-called "mega-flare" site, in the central Laptev Sea. Over individual gas flares of this site the surface water concentration of CH4 reached as high as 200ppm. The atmospheric concentrations of CH4 briefly (< 1 s) reached a maximum of ~3.2 ppm. More typical atmospheric values around the seeps were between 1.9-2.0 ppm (background values were approximately 1.88 ppm). However, such peak concentrations in both air and water were highly localized, returning to background levels within a few hundred meters of the source seeps. Together with continuous high-precision eddy-covariance measurements that were made during the SWERUS-C3 expedition, the combined dataset allows an intensive analysis these highly inhomogeneous gas flares. This gives the opportunity to calculate accurate high-resolution CH4 fluxes and thus give a better insight into the current rates of subsea CH4 outgassing reaching the atmosphere.

  16. Electrostatic fields in the active sites of lysozymes.

    PubMed

    Sun, D P; Liao, D I; Remington, S J

    1989-07-01

    Considerable experimental evidence is in support of several aspects of the mechanism that has been proposed for the catalytic activity of lysozyme. However, the enzymatically catalyzed hydrolysis of polysaccharides proceeds over 5 orders of magnitude faster than that of model compounds that mimic the configuration of the substrate in the active site of the enzyme. Although several possible explanations for this rate enhancement have been discussed elsewhere, a definitive mechanism has not emerged. Here we report striking results obtained by classical electrodynamics, which suggest that bond breakage and the consequent separation of charge in lysozyme is promoted by a large electrostatic field across the active site cleft, produced in part by a very asymmetric distribution of charged residues on the enzyme surface. Lysozymes unrelated in amino acid sequence have similar distributions of charged residues and electric fields. The results reported here suggest that the electrostatic component of the rate enhancement is greater than 9 kcal.mol-1. Thus, electrostatic interactions may play a more important role in the enzymatic mechanism than has generally been appreciated.

  17. Histidine at the active site of Neurospora tyrosinase.

    PubMed

    Pfiffner, E; Lerch, K

    1981-10-13

    The involvement of histidyl residues as potential ligands to the binuclear active-site copper of Neurospora tyrosinase was explored by dye-sensitized photooxidation. The enzymatic activity of the holoenzyme was shown to be unaffected by exposure to light in the presence of methylene blue; however, irradiation of the apoenzyme under the same conditions led to a progressive loss of its ability to be reactivated with Cu2+. This photoinactivation was paralleled by a decrease in the histidine content whereas the number of histidyl residues in the holoenzyme remained constant. Copper measurements of photooxidized, reconstituted apoenzyme demonstrated the loss of binding of one copper atom per mole of enzyme as a consequence of photosensitized oxidation of three out of nine histidine residues. Their sequence positions were determined by a comparison of the relative yields of the histidine containing peptides of photooxidized holo- and apotyrosinases. The data obtained show the preferential modification of histidyl residues 188, 193, and 289 and suggest that they constitute metal ligands to one of the two active-site copper atoms. Substitution of copper by cobalt was found to afford complete protection of the histidyl residues from being modified by dye-sensitized photooxidation. PMID:6458322

  18. Comparative study of vent and seep macrofaunal communities in the Guaymas Basin

    NASA Astrophysics Data System (ADS)

    Portail, M.; Olu, K.; Escobar-Briones, E.; Caprais, J. C.; Menot, L.; Waeles, M.; Cruaud, P.; Sarradin, P. M.; Godfroy, A.; Sarrazin, J.

    2015-09-01

    Understanding the ecological processes and connectivity of chemosynthetic deep-sea ecosystems requires comparative studies. In the Guaymas Basin (Gulf of California, Mexico), the presence of seeps and vents in the absence of a biogeographic barrier, and comparable sedimentary settings and depths offers a unique opportunity to assess the role of ecosystem-specific environmental conditions on macrofaunal communities. Six seep and four vent assemblages were studied, three of which were characterised by common major foundation taxa: vesicomyid bivalves, siboglinid tubeworms and microbial mats. Macrofaunal community structure at the family level showed that density, diversity and composition patterns were primarily shaped by seep- and vent-common abiotic factors including methane and hydrogen sulfide concentrations, whereas vent environmental specificities (higher temperature, higher metal concentrations and lower pH) were not significant. The type of substratum and the heterogeneity provided by foundation species were identified as additional structuring factors and their roles were found to vary according to fluid regimes. At the family level, seep and vent similarity reached at least 58 %. All vent families were found at seeps and each seep-specific family displayed low relative abundances (< 5 %). Moreover, 85 % of the identified species among dominant families were shared between seep and vent ecosystems. This study provides further support to the hypothesis of continuity among deep-sea seep and vent ecosystems.

  19. Northern Gulf of Mexico hydrocarbon seep communities: Implications to the petroleum industry

    SciTech Connect

    Avent, R.M. )

    1990-05-01

    Most animals consume organic food sources based on primary productivity at the base of the food web. Little food reaches deep-sea bottom animals which are usually small, fragile, and sparsely distributed. Recent discoveries of chemosynthetic organisms worldwide have led to investigations into the taxonomy. ecology, biochemistry, and physiology of these forms. The dominant animals in these communities, several large species of vestimentiferan tube worms and bivalve mollusks, energetically use dissolved gases (primarily methane and hydrogen sulfide) issuing from the sea bottom under certain geological conditions. Endosymbiotic bacteria aid metabolic pathways. The large chemosynthetic animals and their dense populations (orders of magnitude over background) are the exceptions that prove the rule that food is an important limiting factor in the deep sea. The discovery of relatively shallow, luxuriant gas-seep communities on the Louisiana upper slope raises concerns on the environmental effects of nearby petroleum operations. To protect these communities, the Minerals Management Service requires photographic bottom surveys in depths from 400 to 900 m if geophysical evidence of seeps (wipeout zones or streams of bubbles) is found. If found near proposed well locations, high-density communities must be avoided thereby preventing physical damage from any structure. Deep-sea community surveys can be expensive and can result in alternative siting plans and development delays. But Minerals Management Service's requirements should conserve these shallow communities that have considerable value as natural laboratories accessible to academic study. We know little about the permanence, dynamics, recruitment recovery potential. and life requirements of chemosynthetic communities. Additional studies, funded by the Minerals Management Service, have been proposed.

  20. Trichodiene synthase. Identification of active site residues by site-directed mutagenesis.

    PubMed

    Cane, D E; Shim, J H; Xue, Q; Fitzsimons, B C; Hohn, T M

    1995-02-28

    Derivatization of 5,5'-dithiobis(2-nitrobenzoic acid)-treated trichodiene synthase with [methyl-14C]methyl methanethiosulfonate and analysis of the derived tryptic peptides suggested the presence of two cysteine residues at the active site. The corresponding C146A and C190A mutants were constructed by site-directed mutagenesis. The C190A mutant displayed partial but significantly reduced activity, with a reduction in kcat/Km of 3000 compared to the wild-type trichodiene synthase, while the C146A mutant was essentially inactive. A hybrid trichodiene synthase, constructed from amino acids 1-309 of the Fusarium sporotrichioides enzyme and amino acids 310-383 of the Gibberella pulicaris cyclase, had steady state kinetic parameters nearly identical to those of the wild-type F. sporotrichioides enzyme. From this parent hybrid, a series of mutants was constructed by site-directed mutagenesis in which the amino acids in the base-rich region, 302-306 (DRRYR), were systematically modified. Three of these mutants were overexpressed and purified to homogeneity. The importance of Arg304 for catalysis was established by the observation that the R304K mutant showed a more than 25-fold increase in Km, as well as a 200-fold reduction in kcat. In addition, analysis of the incubation products of the R304K mutant by gas chromatography-mass spectrometry (GC-MS) indicated that farnesyl diphosphate was converted not only to trichodiene but to at least two additional C15H24 hydrocarbons, mle 204. Replacement of the Tyr305 residue of trichodiene synthase with Phe had little effect on kcat, while increasing the Km by a factor of ca. 7-8.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7873527

  1. The copper active site of CBM33 polysaccharide oxygenases.

    PubMed

    Hemsworth, Glyn R; Taylor, Edward J; Kim, Robbert Q; Gregory, Rebecca C; Lewis, Sally J; Turkenburg, Johan P; Parkin, Alison; Davies, Gideon J; Walton, Paul H

    2013-04-24

    The capacity of metal-dependent fungal and bacterial polysaccharide oxygenases, termed GH61 and CBM33, respectively, to potentiate the enzymatic degradation of cellulose opens new possibilities for the conversion of recalcitrant biomass to biofuels. GH61s have already been shown to be unique metalloenzymes containing an active site with a mononuclear copper ion coordinated by two histidines, one of which is an unusual τ-N-methylated N-terminal histidine. We now report the structural and spectroscopic characterization of the corresponding copper CBM33 enzymes. CBM33 binds copper with high affinity at a mononuclear site, significantly stabilizing the enzyme. X-band EPR spectroscopy of Cu(II)-CBM33 shows a mononuclear type 2 copper site with the copper ion in a distorted axial coordination sphere, into which azide will coordinate as evidenced by the concomitant formation of a new absorption band in the UV/vis spectrum at 390 nm. The enzyme's three-dimensional structure contains copper, which has been photoreduced to Cu(I) by the incident X-rays, confirmed by X-ray absorption/fluorescence studies of both aqueous solution and intact crystals of Cu-CBM33. The single copper(I) ion is ligated in a T-shaped configuration by three nitrogen atoms from two histidine side chains and the amino terminus, similar to the endogenous copper coordination geometry found in fungal GH61. PMID:23540833

  2. Activation of muscarinic acetylcholine receptors via their allosteric binding sites.

    PubMed Central

    Jakubík, J; Bacáková, L; Lisá, V; el-Fakahany, E E; Tucek, S

    1996-01-01

    Ligands that bind to the allosteric-binding sites on muscarinic acetylcholine receptors alter the conformation of the classical-binding sites of these receptors and either diminish or increase their affinity for muscarinic agonists and classical antagonists. It is not known whether the resulting conformational change also affects the interaction between the receptors and the G proteins. We have now found that the muscarinic receptor allosteric modulators alcuronium, gallamine, and strychnine (acting in the absence of an agonist) alter the synthesis of cAMP in Chinese hamster ovary (CHO) cells expressing the M2 or the M4 subtype of muscarinic receptors in the same direction as the agonist carbachol. In addition, most of their effects on the production of inositol phosphates in CHO cells expressing the M1 or the M3 muscarinic receptor subtypes are also similar to (although much weaker than) those of carbachol. The agonist-like effects of the allosteric modulators are not observed in CHO cells that have not been transfected with the gene for any of the subtypes of muscarinic receptors. The effects of alcuronium on the formation of cAMP and inositol phosphates are not prevented by the classical muscarinic antagonist quinuclidinyl benzilate. These observations demonstrate for the first time that the G protein-mediated functional responses of muscarinic receptors can be evoked not only from their classical, but also from their allosteric, binding sites. This represents a new mechanism of receptor activation. PMID:8710935

  3. Risk assessment of seeps from the 317 Area of Argonne National Laboratory

    SciTech Connect

    1996-09-17

    Chlorinated hydrocarbon contaminants have recently been detected in groundwater seeps on forest preserve property south of the 317 Area at ANL. The 317 Area is near ANL`s southern boundary and is considered the source of the contamination. Five seeps are about 200 m south of the ANL property line and about same distance from the nearest developed trails in the forest preserve. Conservative assumptions were used to assess the possibility of adverse health effects associated with forest preserve seeps impacted by the 317 Area. Results indicate that neither cancer risks nor noncarcinogenic effects associated with exposures to seep contaminants are a concern; thus, the area is safe for all visitors. The ecological impact study found that the presence of the three contaminants (CCl{sub 4}, CHCl{sub 3}, tetrachloroethylene) in the seep water does not pose a risk to biota in the area.

  4. Radiation inactivation study of aminopeptidase: probing the active site

    NASA Astrophysics Data System (ADS)

    Jamadar, V. K.; Jamdar, S. N.; Mohan, Hari; Dandekar, S. P.; Harikumar, P.

    2004-04-01

    Ionizing radiation inactivated purified chicken intestinal aminopeptidase in media saturated with gases in the order N 2O>N 2>air. The D 37 values in the above conditions were 281, 210 and 198 Gy, respectively. OH radical scavengers such as t-butanol and isopropanol effectively nullified the radiation-induced damage in N 2O. The radicals (SCN) 2•-, Br 2•- and I 2•- inactivated the enzyme, pointing to the involvement of aromatic amino acids and cysteine in its catalytic activity. The enzyme exhibited fluorescence emission at 340 nm which is characteristic of tryptophan. The radiation-induced loss of activity was accompanied by a decrease in the fluorescence of the enzyme suggesting a predominant influence on tryptophan residues. The enzyme inhibition was associated with a marked increase in the Km and a decrease in the Vmax and kcat values, suggesting an irreversible alteration in the catalytic site. The above observations were confirmed by pulse radiolysis studies.

  5. Mimicking enzymatic active sites on surfaces for energy conversion chemistry.

    PubMed

    Gutzler, Rico; Stepanow, Sebastian; Grumelli, Doris; Lingenfelder, Magalí; Kern, Klaus

    2015-07-21

    Metal-organic supramolecular chemistry on surfaces has matured to a point where its underlying growth mechanisms are well understood and structures of defined coordination environments of metal atoms can be synthesized in a controlled and reproducible procedure. With surface-confined molecular self-assembly, scientists have a tool box at hand which can be used to prepare structures with desired properties, as for example a defined oxidation number and spin state of the transition metal atoms within the organic matrix. From a structural point of view, these coordination sites in the supramolecular structure resemble the catalytically active sites of metallo-enzymes, both characterized by metal centers coordinated to organic ligands. Several chemical reactions take place at these embedded metal ions in enzymes and the question arises whether these reactions also take place using metal-organic networks as catalysts. Mimicking the active site of metal atoms and organic ligands of enzymes in artificial systems is the key to understanding the selectivity and efficiency of enzymatic reactions. Their catalytic activity depends on various parameters including the charge and spin configuration in the metal ion, but also on the organic environment, which can stabilize intermediate reaction products, inhibits catalytic deactivation, and serves mostly as a transport channel for the reactants and products and therefore ensures the selectivity of the enzyme. Charge and spin on the transition metal in enzymes depend on the one hand on the specific metal element, and on the other hand on its organic coordination environment. These two parameters can carefully be adjusted in surface confined metal-organic networks, which can be synthesized by virtue of combinatorial mixing of building synthons. Different organic ligands with varying functional groups can be combined with several transition metals and spontaneously assemble into ordered networks. The catalytically active metal

  6. Polarizability of the active site of cytochrome c reduces the activation barrier for electron transfer

    NASA Astrophysics Data System (ADS)

    Dinpajooh, Mohammadhasan; Martin, Daniel R.; Matyushov, Dmitry V.

    2016-06-01

    Enzymes in biology’s energy chains operate with low energy input distributed through multiple electron transfer steps between protein active sites. The general challenge of biological design is how to lower the activation barrier without sacrificing a large negative reaction free energy. We show that this goal is achieved through a large polarizability of the active site. It is polarized by allowing a large number of excited states, which are populated quantum mechanically by electrostatic fluctuations of the protein and hydration water shells. This perspective is achieved by extensive mixed quantum mechanical/molecular dynamics simulations of the half reaction of reduction of cytochrome c. The barrier for electron transfer is consistently lowered by increasing the number of excited states included in the Hamiltonian of the active site diagonalized along the classical trajectory. We suggest that molecular polarizability, in addition to much studied electrostatics of permanent charges, is a key parameter to consider in order to understand how enzymes work.

  7. Polarizability of the active site of cytochrome c reduces the activation barrier for electron transfer

    PubMed Central

    Dinpajooh, Mohammadhasan; Martin, Daniel R.; Matyushov, Dmitry V.

    2016-01-01

    Enzymes in biology’s energy chains operate with low energy input distributed through multiple electron transfer steps between protein active sites. The general challenge of biological design is how to lower the activation barrier without sacrificing a large negative reaction free energy. We show that this goal is achieved through a large polarizability of the active site. It is polarized by allowing a large number of excited states, which are populated quantum mechanically by electrostatic fluctuations of the protein and hydration water shells. This perspective is achieved by extensive mixed quantum mechanical/molecular dynamics simulations of the half reaction of reduction of cytochrome c. The barrier for electron transfer is consistently lowered by increasing the number of excited states included in the Hamiltonian of the active site diagonalized along the classical trajectory. We suggest that molecular polarizability, in addition to much studied electrostatics of permanent charges, is a key parameter to consider in order to understand how enzymes work. PMID:27306204

  8. Offshore springs and seeps are focus of working group

    NASA Astrophysics Data System (ADS)

    Burnett, Bill

    People have been curious about offshore springs and seeps since at least the days of the Romans. In spite of many centuries of both casual and serious observations, there has been relatively little scientific study concerning the magnitude and effects of groundwater flow into the sea. Rather, studies were performed mostly to address water resource issues. Investigations over the past decade or so have now shown that groundwater discharge, at least in some cases, may be important for geochemical budgets and ecological effects.The Scientific Committee on Oceanic Research (SCOR) and the Land-Ocean Interactions in the Coastal Zone (LOICZ) Project of the International Geosphere-Biosphere Program have recently established a working group of experts to examine questions relating specifically to groundwater discharge in the coastal zone. Direct groundwater flow into the ocean is known to occur as springs and seeps in near-shore areas in many parts of the world. Submarine springs, for example, are well known off both coasts of Florida; Mexico's Yucatan Peninsula; in several areas around the Pacific rim including Chile, Hawaii, Guam, American Samoa, and Australia; in the Persian Gulf near Bahrain; in the Mediterranean Sea off Spain, France, Italy, Greece, Syria, Lebanon, Israel, and Libya; and in many other locations.

  9. Spectroscopic Definition of the Ferroxidase Site in M Ferritin: Comparison of Binuclear Substrate vs. Cofactor Active Sites

    PubMed Central

    Schwartz, Jennifer K.; Liu, Xiaofeng S.; Tosha, Takehiko; Theil, Elizabeth C.; Solomon, Edward I.

    2008-01-01

    Maxi ferritins, 24 subunit protein nanocages, are essential in humans, plants, bacteria, and other animals for the concentration and storage of iron as hydrated ferric oxide, while minimizing free radical generation or use by pathogens. Formation of the precursors to these ferric oxides is catalyzed at a non-heme biferrous substrate site, which has some parallels with the cofactor sites in other biferrous enzymes. A combination of circular dichroism (CD), magnetic circular dichroism (MCD), and variable-temperature, variable-field MCD (VTVH MCD) has been used to probe Fe(II) binding to the substrate active site in frog M ferritin. These data determined that the active site within each subunit consists of two inequivalent five-coordinate (5C) ferrous centers that are weakly anti-ferromagnetically coupled, consistent with a μ-1,3 carboxylate bridge. The active site ligand set is unusual and likely includes a terminal water bound to each Fe(II) center. The Fe(II) ions bind to the active sites in a concerted manner, and cooperativity among the sites in each subunit is observed, potentially providing a mechanism for the control of ferritin iron loading. Differences in geometric and electronic structure – including a weak ligand field, availability of two water ligands at the biferrous substrate site, and the single carboxylate bridge in ferritin – coincide with the divergent reaction pathways observed between this substrate site and the previously studied cofactor active sites. PMID:18576633

  10. An active-site lysine in avian liver phosphoenolpyruvate carboxykinase

    SciTech Connect

    Guidinger, P.F.; Nowak, T. )

    1991-09-10

    The participation of lysine in the catalysis by avian liver phosphoenolpyruvate carboxykinase was studied by chemical modification and by a characterization of the modified enzyme. The rate of inactivation by 2,4-pentanedione is pseudo-first-order and linearly dependent on reagent concentration with a second-order rate constant of 0.36 {plus minus} 0.025 M{sup {minus}1} min{sup {minus}1}. Inactivation by pyridoxal 5{prime}-phosphate of the reversible reaction catalyzed by phosphoenolpyruvate carboxykinase follows bimolecular kinetics with a second-order rate constant of 7,700 {plus minus} 860 m{sup {minus}1} min{sup {minus}1}. Treatment of the enzyme or one lysine residue modified concomitant with 100% loss in activity. A stoichiometry of 1:1 is observed when either the reversible or the irreversible reactions catalyzed by the enzyme are monitored. A study of k{sub obs} vs pH suggests this active-site lysine has a pK{sub a} of 8.1 and a pH-independent rate constant of inactivation of 47,700 m{sup {minus}1} min{sup {minus}1}. Proton relaxation rate measurements suggest that pyridoxal 5{prime}-phosphate modification alters binding of the phosphate-containing substrates. {sup 31}P NMR relaxation rate measurements show altered binding of the substrates in the ternary enzyme {center dot}Mn{sup 2+}{center dot}substrate complex. Circular dichroism studies show little change in secondary structure of pyridoxal 5{prime}-phosphate modified phosphoenolpyruvate carboxykinase. These results indicate that avian liver phosphoenolpyruvate carboxykinase has one reactive lysine at the active site and it is involved in the binding and activation of the phosphate-containing substrates.

  11. Perchlorate Reductase Is Distinguished by Active Site Aromatic Gate Residues.

    PubMed

    Youngblut, Matthew D; Tsai, Chi-Lin; Clark, Iain C; Carlson, Hans K; Maglaqui, Adrian P; Gau-Pan, Phonchien S; Redford, Steven A; Wong, Alan; Tainer, John A; Coates, John D

    2016-04-22

    Perchlorate is an important ion on both Earth and Mars. Perchlorate reductase (PcrAB), a specialized member of the dimethylsulfoxide reductase superfamily, catalyzes the first step of microbial perchlorate respiration, but little is known about the biochemistry, specificity, structure, and mechanism of PcrAB. Here we characterize the biophysics and phylogeny of this enzyme and report the 1.86-Å resolution PcrAB complex crystal structure. Biochemical analysis revealed a relatively high perchlorate affinity (Km = 6 μm) and a characteristic substrate inhibition compared with the highly similar respiratory nitrate reductase NarGHI, which has a relatively much lower affinity for perchlorate (Km = 1.1 mm) and no substrate inhibition. Structural analysis of oxidized and reduced PcrAB with and without the substrate analog SeO3 (2-) bound to the active site identified key residues in the positively charged and funnel-shaped substrate access tunnel that gated substrate entrance and product release while trapping transiently produced chlorate. The structures suggest gating was associated with shifts of a Phe residue between open and closed conformations plus an Asp residue carboxylate shift between monodentate and bidentate coordination to the active site molybdenum atom. Taken together, structural and mutational analyses of gate residues suggest key roles of these gate residues for substrate entrance and product release. Our combined results provide the first detailed structural insight into the mechanism of biological perchlorate reduction, a critical component of the chlorine redox cycle on Earth.

  12. Eel calcitonin binding site distribution and antinociceptive activity in rats

    SciTech Connect

    Guidobono, F.; Netti, C.; Sibilia, V.; Villa, I.; Zamboni, A.; Pecile, A.

    1986-03-01

    The distribution of binding site for (/sup 125/I)-eel-calcitonin (ECT) to rat central nervous system, studied by an autoradiographic technique, showed concentrations of binding in the diencephalon, the brain stem and the spinal cord. Large accumulations of grains were seen in the hypothalamus, the amygdala, in the fasciculus medialis prosencephali, in the fasciculus longitudinalis medialis, in the ventrolateral part of the periventricular gray matter, in the lemniscus medialis and in the raphe nuclei. The density of grains in the reticular formation and in the nucleus tractus spinalis nervi trigemini was more moderate. In the spinal cord, grains were scattered throughout the dorsal horns. Binding of the ligand was displaced equally by cold ECT and by salmon CT(sCT), indicating that both peptides bind to the same receptors. Human CT was much weaker than sCT in displacing (/sup 125/I)-ECT binding. The administration of ECT into the brain ventricles of rats dose-dependently induced a significant and long-lasting enhancement of hot-plate latencies comparable with that obtained with sCT. The antinociceptive activity induced by ECT is compatible with the topographical distribution of binding sites for the peptide and is a further indication that fish CTs are active in the mammalian brain.

  13. Perchlorate Reductase Is Distinguished by Active Site Aromatic Gate Residues.

    PubMed

    Youngblut, Matthew D; Tsai, Chi-Lin; Clark, Iain C; Carlson, Hans K; Maglaqui, Adrian P; Gau-Pan, Phonchien S; Redford, Steven A; Wong, Alan; Tainer, John A; Coates, John D

    2016-04-22

    Perchlorate is an important ion on both Earth and Mars. Perchlorate reductase (PcrAB), a specialized member of the dimethylsulfoxide reductase superfamily, catalyzes the first step of microbial perchlorate respiration, but little is known about the biochemistry, specificity, structure, and mechanism of PcrAB. Here we characterize the biophysics and phylogeny of this enzyme and report the 1.86-Å resolution PcrAB complex crystal structure. Biochemical analysis revealed a relatively high perchlorate affinity (Km = 6 μm) and a characteristic substrate inhibition compared with the highly similar respiratory nitrate reductase NarGHI, which has a relatively much lower affinity for perchlorate (Km = 1.1 mm) and no substrate inhibition. Structural analysis of oxidized and reduced PcrAB with and without the substrate analog SeO3 (2-) bound to the active site identified key residues in the positively charged and funnel-shaped substrate access tunnel that gated substrate entrance and product release while trapping transiently produced chlorate. The structures suggest gating was associated with shifts of a Phe residue between open and closed conformations plus an Asp residue carboxylate shift between monodentate and bidentate coordination to the active site molybdenum atom. Taken together, structural and mutational analyses of gate residues suggest key roles of these gate residues for substrate entrance and product release. Our combined results provide the first detailed structural insight into the mechanism of biological perchlorate reduction, a critical component of the chlorine redox cycle on Earth. PMID:26940877

  14. Preliminary Analysis of Manual and Automated Seep Detection in Multibeam Water-Column Backscatter

    NASA Astrophysics Data System (ADS)

    McKenna, L.; Auner, L.; Weller, E.; Paton, M.; Doucet, M.; Lobecker, E.

    2014-12-01

    Identifying and locating gaseous seafloor seeps using multibeam sonar water-column backscatter is a growing interest in the scientific, energy, and resource management communities. Until recently, seeps were manually detected when viewing water-column backscatter returns in post-processing software. This manual procedure is time consuming and subjective. To examine this subjectivity, the NOAA Office of Exploration and Research conducted a quality control test using data collected during an expedition aboard the NOAA Ship Okeanos Explorer in the Gulf of Mexico from March to April, 2014. Water-column backscatter data was post-processed underway in FMMidwater and seep coordinates were manually geopicked from the beam fan. Ten percent of the original survey lines were independently re-processed using the same manual detection methods but with a different observer. Results show that manual seep selection can be highly variable between two different individuals. To help reduce this subjectivity and time required to manually detect seeps, QPS, Inc. developed a Feature Detection Tool for FMMidwater that uses an algorithm developed by the University of New Hampshire Center for Coastal and Ocean Mapping. To test the tool, the 10% subset of survey lines were run through the Feature Detection Tool using default settings, and the automatically detected seeps were compared with the manual geopicks. Not surprisingly, initial results show there can be variability between manual and algorithm seeps. Scrutiny of the automatic picks shows that the tool identified 60% of the seeps detected, and verified, by the independent manually-detecting observers. 32% of the seeps identified manually were missed by the tool, but 8% additional seeps were identified by the algorithm that had been missed through manual detection. The automatic detection showed several false positives, requiring manual intervention, but at a significantly lower level of effort than manual scrutinization of the raw

  15. An Active Site Water Network in the Plasminogen Activator Pla from Yersinia pestis

    SciTech Connect

    Eren, Elif; Murphy, Megan; Goguen, Jon; van den Berg, Bert

    2010-08-13

    The plasminogen activator Pla from Yersinia pestis is an outer membrane protease (omptin) that is important for the virulence of plague. Here, we present the high-resolution crystal structure of wild-type, enzymatically active Pla at 1.9 {angstrom}. The structure shows a water molecule located between active site residues D84 and H208, which likely corresponds to the nucleophilic water. A number of other water molecules are present in the active site, linking residues important for enzymatic activity. The R211 sidechain in loop L4 is close to the nucleophilic water and possibly involved in the stabilization of the oxyanion intermediate. Subtle conformational changes of H208 result from the binding of lipopolysaccharide to the outside of the barrel, explaining the unusual dependence of omptins on lipopolysaccharide for activity. The Pla structure suggests a model for the interaction with plasminogen substrate and provides a more detailed understanding of the catalytic mechanism of omptin proteases.

  16. Metal active site elasticity linked to activation of homocysteine in methionine synthases

    SciTech Connect

    Koutmos, Markos; Pejchal, Robert; Bomer, Theresa M.; Matthews, Rowena G.; Smith, Janet L.; Ludwig, Martha L.

    2008-04-02

    Enzymes possessing catalytic zinc centers perform a variety of fundamental processes in nature, including methyl transfer to thiols. Cobalamin-independent (MetE) and cobalamin-dependent (MetH) methionine synthases are two such enzyme families. Although they perform the same net reaction, transfer of a methyl group from methyltetrahydrofolate to homocysteine (Hcy) to form methionine, they display markedly different catalytic strategies, modular organization, and active site zinc centers. Here we report crystal structures of zinc-replete MetE and MetH, both in the presence and absence of Hcy. Structural investigation of the catalytic zinc sites of these two methyltransferases reveals an unexpected inversion of zinc geometry upon binding of Hcy and displacement of an endogenous ligand in both enzymes. In both cases a significant movement of the zinc relative to the protein scaffold accompanies inversion. These structures provide new information on the activation of thiols by zinc-containing enzymes and have led us to propose a paradigm for the mechanism of action of the catalytic zinc sites in these and related methyltransferases. Specifically, zinc is mobile in the active sites of MetE and MetH, and its dynamic nature helps facilitate the active site conformational changes necessary for thiol activation and methyl transfer.

  17. Active Sites Environmental Monitoring Program: Program plan. Revision 1

    SciTech Connect

    Ashwood, T.L.; Wickliff, D.S.; Morrissey, C.M.

    1992-02-01

    The Active Sites Environmental Monitoring Program (ASEMP), initiated in 1989, provides early detection and performance monitoring of transuranic (TRU) waste and active low-level waste (LLW) facilities at Oak Ridge National Laboratory (ORNL) in accordance with US Department of Energy (DOE) Order 5820.2A. Active LLW facilities in Solid Waste Storage Area (SWSA) 6 include Tumulus I and Tumulus II, the Interim Waste Management Facility (IWMF), LLW silos, high-range wells, asbestos silos, and fissile wells. The tumulus pads and IWMF are aboveground, high-strength concrete pads on which concrete vaults containing metal boxes of LLW are placed; the void space between the boxes and vaults is filled with grout. Eventually, these pads and vaults will be covered by an engineered multilayered cap. All other LLW facilities in SWSA 6 are below ground. In addition, this plan includes monitoring of the Hillcut Disposal Test Facility (HDTF) in SWSA 6, even though this facility was completed prior to the data of the DOE order. In SWSA 5 North, the TRU facilities include below-grade engineered caves, high-range wells, and unlined trenches. All samples from SWSA 6 are screened for alpha and beta activity, counted for gamma-emitting isotopes, and analyzed for tritium. In addition to these analytes, samples from SWSA 5 North are analyzed for specific transuranic elements.

  18. Active Site and Laminarin Binding in Glycoside Hydrolase Family 55*

    PubMed Central

    Bianchetti, Christopher M.; Takasuka, Taichi E.; Deutsch, Sam; Udell, Hannah S.; Yik, Eric J.; Bergeman, Lai F.; Fox, Brian G.

    2015-01-01

    The Carbohydrate Active Enzyme (CAZy) database indicates that glycoside hydrolase family 55 (GH55) contains both endo- and exo-β-1,3-glucanases. The founding structure in the GH55 is PcLam55A from the white rot fungus Phanerochaete chrysosporium (Ishida, T., Fushinobu, S., Kawai, R., Kitaoka, M., Igarashi, K., and Samejima, M. (2009) Crystal structure of glycoside hydrolase family 55 β-1,3-glucanase from the basidiomycete Phanerochaete chrysosporium. J. Biol. Chem. 284, 10100–10109). Here, we present high resolution crystal structures of bacterial SacteLam55A from the highly cellulolytic Streptomyces sp. SirexAA-E with bound substrates and product. These structures, along with mutagenesis and kinetic studies, implicate Glu-502 as the catalytic acid (as proposed earlier for Glu-663 in PcLam55A) and a proton relay network of four residues in activating water as the nucleophile. Further, a set of conserved aromatic residues that define the active site apparently enforce an exo-glucanase reactivity as demonstrated by exhaustive hydrolysis reactions with purified laminarioligosaccharides. Two additional aromatic residues that line the substrate-binding channel show substrate-dependent conformational flexibility that may promote processive reactivity of the bound oligosaccharide in the bacterial enzymes. Gene synthesis carried out on ∼30% of the GH55 family gave 34 active enzymes (19% functional coverage of the nonredundant members of GH55). These active enzymes reacted with only laminarin from a panel of 10 different soluble and insoluble polysaccharides and displayed a broad range of specific activities and optima for pH and temperature. Application of this experimental method provides a new, systematic way to annotate glycoside hydrolase phylogenetic space for functional properties. PMID:25752603

  19. Active site loop conformation regulates promiscuous activity in a lactonase from Geobacillus kaustophilus HTA426.

    PubMed

    Zhang, Yu; An, Jiao; Yang, Guang-Yu; Bai, Aixi; Zheng, Baisong; Lou, Zhiyong; Wu, Geng; Ye, Wei; Chen, Hai-Feng; Feng, Yan; Manco, Giuseppe

    2015-01-01

    Enzyme promiscuity is a prerequisite for fast divergent evolution of biocatalysts. A phosphotriesterase-like lactonase (PLL) from Geobacillus kaustophilus HTA426 (GkaP) exhibits main lactonase and promiscuous phosphotriesterase activities. To understand its catalytic and evolutionary mechanisms, we investigated a "hot spot" in the active site by saturation mutagenesis as well as X-ray crystallographic analyses. We found that position 99 in the active site was involved in substrate discrimination. One mutant, Y99L, exhibited 11-fold improvement over wild-type in reactivity (kcat/Km) toward the phosphotriesterase substrate ethyl-paraoxon, but showed 15-fold decrease toward the lactonase substrate δ-decanolactone, resulting in a 157-fold inversion of the substrate specificity. Structural analysis of Y99L revealed that the mutation causes a ∼6.6 Å outward shift of adjacent loop 7, which may cause increased flexibility of the active site and facilitate accommodation and/or catalysis of organophosphate substrate. This study provides for the PLL family an example of how the evolutionary route from promiscuity to specificity can derive from very few mutations, which promotes alteration in the conformational adjustment of the active site loops, in turn draws the capacity of substrate binding and activity.

  20. Active Site Loop Conformation Regulates Promiscuous Activity in a Lactonase from Geobacillus kaustophilus HTA426

    PubMed Central

    Zhang, Yu; An, Jiao; Yang, Guang-Yu; Bai, Aixi; Zheng, Baisong; Lou, Zhiyong; Wu, Geng; Ye, Wei; Chen, Hai-Feng; Feng, Yan; Manco, Giuseppe

    2015-01-01

    Enzyme promiscuity is a prerequisite for fast divergent evolution of biocatalysts. A phosphotriesterase-like lactonase (PLL) from Geobacillus kaustophilus HTA426 (GkaP) exhibits main lactonase and promiscuous phosphotriesterase activities. To understand its catalytic and evolutionary mechanisms, we investigated a “hot spot” in the active site by saturation mutagenesis as well as X-ray crystallographic analyses. We found that position 99 in the active site was involved in substrate discrimination. One mutant, Y99L, exhibited 11-fold improvement over wild-type in reactivity (kcat/Km) toward the phosphotriesterase substrate ethyl-paraoxon, but showed 15-fold decrease toward the lactonase substrate δ-decanolactone, resulting in a 157-fold inversion of the substrate specificity. Structural analysis of Y99L revealed that the mutation causes a ∼6.6 Å outward shift of adjacent loop 7, which may cause increased flexibility of the active site and facilitate accommodation and/or catalysis of organophosphate substrate. This study provides for the PLL family an example of how the evolutionary route from promiscuity to specificity can derive from very few mutations, which promotes alteration in the conformational adjustment of the active site loops, in turn draws the capacity of substrate binding and activity. PMID:25706379

  1. Extensive site-directed mutagenesis reveals interconnected functional units in the alkaline phosphatase active site.

    PubMed

    Sunden, Fanny; Peck, Ariana; Salzman, Julia; Ressl, Susanne; Herschlag, Daniel

    2015-01-01

    Enzymes enable life by accelerating reaction rates to biological timescales. Conventional studies have focused on identifying the residues that have a direct involvement in an enzymatic reaction, but these so-called 'catalytic residues' are embedded in extensive interaction networks. Although fundamental to our understanding of enzyme function, evolution, and engineering, the properties of these networks have yet to be quantitatively and systematically explored. We dissected an interaction network of five residues in the active site of Escherichia coli alkaline phosphatase. Analysis of the complex catalytic interdependence of specific residues identified three energetically independent but structurally interconnected functional units with distinct modes of cooperativity. From an evolutionary perspective, this network is orders of magnitude more probable to arise than a fully cooperative network. From a functional perspective, new catalytic insights emerge. Further, such comprehensive energetic characterization will be necessary to benchmark the algorithms required to rationally engineer highly efficient enzymes. PMID:25902402

  2. Extensive site-directed mutagenesis reveals interconnected functional units in the alkaline phosphatase active site.

    PubMed

    Sunden, Fanny; Peck, Ariana; Salzman, Julia; Ressl, Susanne; Herschlag, Daniel

    2015-01-01

    Enzymes enable life by accelerating reaction rates to biological timescales. Conventional studies have focused on identifying the residues that have a direct involvement in an enzymatic reaction, but these so-called 'catalytic residues' are embedded in extensive interaction networks. Although fundamental to our understanding of enzyme function, evolution, and engineering, the properties of these networks have yet to be quantitatively and systematically explored. We dissected an interaction network of five residues in the active site of Escherichia coli alkaline phosphatase. Analysis of the complex catalytic interdependence of specific residues identified three energetically independent but structurally interconnected functional units with distinct modes of cooperativity. From an evolutionary perspective, this network is orders of magnitude more probable to arise than a fully cooperative network. From a functional perspective, new catalytic insights emerge. Further, such comprehensive energetic characterization will be necessary to benchmark the algorithms required to rationally engineer highly efficient enzymes.

  3. Possible roles of uncultured archaea in carbon cycling in methane-seep sediments

    NASA Astrophysics Data System (ADS)

    Yoshinaga, Marcos Y.; Lazar, Cassandre S.; Elvert, Marcus; Lin, Yu-Shih; Zhu, Chun; Heuer, Verena B.; Teske, Andreas; Hinrichs, Kai-Uwe

    2015-09-01

    Studies on microbial carbon cycling uniformly confirm that anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria represent the dominant and most active fraction of the sedimentary microbial community in methane-seep sediments. However, little is known about other frequently observed and abundant microbial taxa, their role in carbon cycling and association with the anaerobic oxidation of methane (AOM). Here, we provide a comprehensive characterization of stable carbon isotopes (δ13C) from several intact polar lipid (IPL) classes and metabolite pools in a downcore profile at a cold seep within the oxygen minimum zone off Pakistan. We aimed to evaluate microbial carbon metabolism using IPLs in relation to redox conditions, metabolites and 16S rRNA gene libraries. The 13C-depleted signature of carbon pools and microbial metabolites in pore waters (e.g., dissolved inorganic carbon, lactate and acetate) demonstrated high accumulation of AOM-associated biomass and subsequent turnover thereof. ANMEs accounted for a small fraction of the archaeal 16S rRNA gene survey, whereas sequences of other uncultured benthic archaea dominated the clone libraries, particularly the Marine Benthic Group D. On the basis of lipid diversity and carbon isotope information, we suggest that structurally diverse phospho- and glycolipids, including the recently identified unsaturated tetraethers that are particularly abundant in this setting, are likely derived from archaea other than ANMEs. Through the evaluation of δ13C values of individual IPL, our results indicate heterotrophy as a possible metabolic pathway of archaea in these AOM-dominated sediments.

  4. Metals in the active site of native protein phosphatase-1.

    PubMed

    Heroes, Ewald; Rip, Jens; Beullens, Monique; Van Meervelt, Luc; De Gendt, Stefan; Bollen, Mathieu

    2015-08-01

    Protein phosphatase-1 (PP1) is a major protein Ser/Thr phosphatase in eukaryotic cells. Its activity depends on two metal ions in the catalytic site, which were identified as manganese in the bacterially expressed phosphatase. However, the identity of the metal ions in native PP1 is unknown. In this study, total reflection X-ray fluorescence (TXRF) was used to detect iron and zinc in PP1 that was purified from rabbit skeletal muscle. Metal exchange experiments confirmed that the distinct substrate specificity of recombinant and native PP1 is determined by the nature of their associated metals. We also found that the iron level associated with native PP1 is decreased by incubation with inhibitor-2, consistent with a function of inhibitor-2 as a PP1 chaperone. PMID:25890482

  5. Metavanadate at the active site of the phosphatase VHZ.

    PubMed

    Kuznetsov, Vyacheslav I; Alexandrova, Anastassia N; Hengge, Alvan C

    2012-09-01

    Vanadate is a potent modulator of a number of biological processes and has been shown by crystal structures and NMR spectroscopy to interact with numerous enzymes. Although these effects often occur under conditions where oligomeric forms dominate, the crystal structures and NMR data suggest that the inhibitory form is usually monomeric orthovanadate, a particularly good inhibitor of phosphatases because of its ability to form stable trigonal-bipyramidal complexes. We performed a computational analysis of a 1.14 Å structure of the phosphatase VHZ in complex with an unusual metavanadate species and compared it with two classical trigonal-bipyramidal vanadate-phosphatase complexes. The results support extensive delocalized bonding to the apical ligands in the classical structures. In contrast, in the VHZ metavanadate complex, the central, planar VO(3)(-) moiety has only one apical ligand, the nucleophilic Cys95, and a gap in electron density between V and S. A computational analysis showed that the V-S interaction is primarily ionic. A mechanism is proposed to explain the formation of metavanadate in the active site from a dimeric vanadate species that previous crystallographic evidence has shown to be able to bind to the active sites of phosphatases related to VHZ. Together, the results show that the interaction of vanadate with biological systems is not solely reliant upon the prior formation of a particular inhibitory form in solution. The catalytic properties of an enzyme may act upon the oligomeric forms primarily present in solution to generate species such as the metavanadate ion observed in the VHZ structure. PMID:22876963

  6. Zymogen Activation and Subcellular Activity of Subtilisin Kexin Isozyme 1/Site 1 Protease*

    PubMed Central

    da Palma, Joel Ramos; Burri, Dominique Julien; Oppliger, Joël; Salamina, Marco; Cendron, Laura; de Laureto, Patrizia Polverino; Seidah, Nabil Georges; Kunz, Stefan; Pasquato, Antonella

    2014-01-01

    The proprotein convertase subtilisin kexin isozyme 1 (SKI-1)/site 1 protease (S1P) plays crucial roles in cellular homeostatic functions and is hijacked by pathogenic viruses for the processing of their envelope glycoproteins. Zymogen activation of SKI-1/S1P involves sequential autocatalytic processing of its N-terminal prodomain at sites B′/B followed by the herein newly identified C′/C sites. We found that SKI-1/S1P autoprocessing results in intermediates whose catalytic domain remains associated with prodomain fragments of different lengths. In contrast to other zymogen proprotein convertases, all incompletely matured intermediates of SKI-1/S1P showed full catalytic activity toward cellular substrates, whereas optimal cleavage of viral glycoproteins depended on B′/B processing. Incompletely matured forms of SKI-1/S1P further process cellular and viral substrates in distinct subcellular compartments. Using a cell-based sensor for SKI-1/S1P activity, we found that 9 amino acid residues at the cleavage site (P1–P8) and P1′ are necessary and sufficient to define the subcellular location of processing and to determine to what extent processing of a substrate depends on SKI-1/S1P maturation. In sum, our study reveals novel and unexpected features of SKI-1/S1P zymogen activation and subcellular specificity of activity toward cellular and pathogen-derived substrates. PMID:25378398

  7. Inspection and monitoring plan, contaminated groundwater seeps 317/319/ENE Area, Argonne National Laboratory

    SciTech Connect

    1996-10-11

    During the course of completing the Resource Conservation and Recovery Act (RCRA) Facility Investigation (RFI) in the 317/319/East-Northeast (ENE) Area of Argonne National Laboratory-East (ANL-E), groundwater was discovered moving to the surface through a series of groundwater seeps. The seeps are located in a ravine approximately 600 ft south of the ANL-E fence line in Waterfall Glen Forest Preserve. Samples of the seep water were collected and analyzed for selected parameters. Two of the five seeps sampled were found to contain detectable levels of organic contaminants. Three chemical species were identified: chloroform (14--25 {micro}g/L), carbon tetrachloride (56--340 {micro}g/L), and tetrachloroethylene (3--6 {micro}g/L). The other seeps did not contain detectable levels of volatile organics. The nature of the contaminants in the seeps will also be monitored on a regular basis. Samples of surface water flowing through the bottom of the ravine and groundwater emanating from the seeps will be collected and analyzed for chemical and radioactive constituents. The results of the routine sampling will be compared with the concentrations used in the risk assessment. If the concentrations exceed those used in the risk assessment, the risk calculations will be revised by using the higher numbers. This revised analysis will determine if additional actions are warranted.

  8. Bivalves from the latest Jurassic-earliest Cretaceous hydrocarbon seep carbonates from central Spitsbergen, Svalbard.

    PubMed

    Hryniewicz, Krzysztof; Little, Crispin T S; Nakrem, Hans Arne

    2014-09-02

    The bivalve fauna from the latest Jurassic-earliest Cretaceous hydrocarbon seep deposits from central Spitsbergen, Svalbard comprises at least 17 species, four of which belong to chemosymbiotic taxa often found at seeps. These are the solemyid Solemya (Petrasma) cf. woodwardiana; Nucinella svalbardensis sp. nov., which belongs to a group of large Nucinella species known from seeps and deep water environments; the lucinid bivalve, Tehamatea rasmusseni sp. nov., included in a genus widely distributed in other Jurassic-Cretaceous seeps; and Cretaxinus hurumi gen. et sp. nov., which is the oldest known thyasirid and is discussed in relation to other large seep-restricted genera in this family. The remaining species in the fauna belong to 'background' genera known from coeval normal marine sediments, mostly from the Boreal area. These include the nuculid Dacromya chetaensis, two new malletiids (Mesosaccella rogovi sp. nov. and M. toddi sp. nov.), the oxytomiid Oxytoma octavia, at least three Buchia species, at least two pectinids, including Camptonectes (Costicamptonectes) aff. milnelandensis and Camptonectes (Camptochlamys) clatrathus, the limid Pseudolimea arctica, the arcticid Pseudotrapezium aff. groenlandicum, and the pholadomyid Goniomya literata. The large number of 'background' species in the bivalve fauna is probably a reflection of the shallow-water setting of the Svalbard seeps. This might also explain the lack of the seep-restricted modiomorphid bivalve Caspiconcha from the fauna. With solemyids, Nucinella, lucinids and thyasirids, the latest Jurassic-earliest Cretaceous bivalve seep fauna of Svalbard contains typical representatives of the Mesozoic bivalve seep faunas, both long established and young evolutionary colonists.

  9. Microbial Communities of Deep-Sea Methane Seeps at Hikurangi Continental Margin (New Zealand)

    PubMed Central

    Ruff, S. Emil; Arnds, Julia; Knittel, Katrin; Amann, Rudolf; Wegener, Gunter; Ramette, Alban; Boetius, Antje

    2013-01-01

    The methane-emitting cold seeps of Hikurangi margin (New Zealand) are among the few deep-sea chemosynthetic ecosystems of the Southern Hemisphere known to date. Here we compared the biogeochemistry and microbial communities of a variety of Hikurangi cold seep ecosystems. These included highly reduced seep habitats dominated by bacterial mats, partially oxidized habitats populated by heterotrophic ampharetid polychaetes and deeply oxidized habitats dominated by chemosynthetic frenulate tubeworms. The ampharetid habitats were characterized by a thick oxic sediment layer that hosted a diverse and biomass-rich community of aerobic methanotrophic Gammaproteobacteria. These bacteria consumed up to 25% of the emanating methane and clustered within three deep-branching groups named Marine Methylotrophic Group (MMG) 1-3. MMG1 and MMG2 methylotrophs belong to the order Methylococcales, whereas MMG3 methylotrophs are related to the Methylophaga. Organisms of the groups MMG1 and MMG3 are close relatives of chemosynthetic endosymbionts of marine invertebrates. The anoxic sediment layers of all investigated seeps were dominated by anaerobic methanotrophic archaea (ANME) of the ANME-2 clade and sulfate-reducing Deltaproteobacteria. Microbial community analysis using Automated Ribosomal Intergenic Spacer Analysis (ARISA) showed that the different seep habitats hosted distinct microbial communities, which were strongly influenced by the seep-associated fauna and the geographic location. Despite outstanding features of Hikurangi seep communities, the organisms responsible for key ecosystem functions were similar to those found at seeps worldwide. This suggests that similar types of biogeochemical settings select for similar community composition regardless of geographic distance. Because ampharetid polychaetes are widespread at cold seeps the role of aerobic methanotrophy may have been underestimated in seafloor methane budgets. PMID:24098632

  10. Microbial communities of deep-sea methane seeps at Hikurangi continental margin (New Zealand).

    PubMed

    Ruff, S Emil; Arnds, Julia; Knittel, Katrin; Amann, Rudolf; Wegener, Gunter; Ramette, Alban; Boetius, Antje

    2013-01-01

    The methane-emitting cold seeps of Hikurangi margin (New Zealand) are among the few deep-sea chemosynthetic ecosystems of the Southern Hemisphere known to date. Here we compared the biogeochemistry and microbial communities of a variety of Hikurangi cold seep ecosystems. These included highly reduced seep habitats dominated by bacterial mats, partially oxidized habitats populated by heterotrophic ampharetid polychaetes and deeply oxidized habitats dominated by chemosynthetic frenulate tubeworms. The ampharetid habitats were characterized by a thick oxic sediment layer that hosted a diverse and biomass-rich community of aerobic methanotrophic Gammaproteobacteria. These bacteria consumed up to 25% of the emanating methane and clustered within three deep-branching groups named Marine Methylotrophic Group (MMG) 1-3. MMG1 and MMG2 methylotrophs belong to the order Methylococcales, whereas MMG3 methylotrophs are related to the Methylophaga. Organisms of the groups MMG1 and MMG3 are close relatives of chemosynthetic endosymbionts of marine invertebrates. The anoxic sediment layers of all investigated seeps were dominated by anaerobic methanotrophic archaea (ANME) of the ANME-2 clade and sulfate-reducing Deltaproteobacteria. Microbial community analysis using Automated Ribosomal Intergenic Spacer Analysis (ARISA) showed that the different seep habitats hosted distinct microbial communities, which were strongly influenced by the seep-associated fauna and the geographic location. Despite outstanding features of Hikurangi seep communities, the organisms responsible for key ecosystem functions were similar to those found at seeps worldwide. This suggests that similar types of biogeochemical settings select for similar community composition regardless of geographic distance. Because ampharetid polychaetes are widespread at cold seeps the role of aerobic methanotrophy may have been underestimated in seafloor methane budgets.

  11. Microbial communities of deep-sea methane seeps at Hikurangi continental margin (New Zealand).

    PubMed

    Ruff, S Emil; Arnds, Julia; Knittel, Katrin; Amann, Rudolf; Wegener, Gunter; Ramette, Alban; Boetius, Antje

    2013-01-01

    The methane-emitting cold seeps of Hikurangi margin (New Zealand) are among the few deep-sea chemosynthetic ecosystems of the Southern Hemisphere known to date. Here we compared the biogeochemistry and microbial communities of a variety of Hikurangi cold seep ecosystems. These included highly reduced seep habitats dominated by bacterial mats, partially oxidized habitats populated by heterotrophic ampharetid polychaetes and deeply oxidized habitats dominated by chemosynthetic frenulate tubeworms. The ampharetid habitats were characterized by a thick oxic sediment layer that hosted a diverse and biomass-rich community of aerobic methanotrophic Gammaproteobacteria. These bacteria consumed up to 25% of the emanating methane and clustered within three deep-branching groups named Marine Methylotrophic Group (MMG) 1-3. MMG1 and MMG2 methylotrophs belong to the order Methylococcales, whereas MMG3 methylotrophs are related to the Methylophaga. Organisms of the groups MMG1 and MMG3 are close relatives of chemosynthetic endosymbionts of marine invertebrates. The anoxic sediment layers of all investigated seeps were dominated by anaerobic methanotrophic archaea (ANME) of the ANME-2 clade and sulfate-reducing Deltaproteobacteria. Microbial community analysis using Automated Ribosomal Intergenic Spacer Analysis (ARISA) showed that the different seep habitats hosted distinct microbial communities, which were strongly influenced by the seep-associated fauna and the geographic location. Despite outstanding features of Hikurangi seep communities, the organisms responsible for key ecosystem functions were similar to those found at seeps worldwide. This suggests that similar types of biogeochemical settings select for similar community composition regardless of geographic distance. Because ampharetid polychaetes are widespread at cold seeps the role of aerobic methanotrophy may have been underestimated in seafloor methane budgets. PMID:24098632

  12. Epizooic metazoan meiobenthos associated with tubeworm and mussel aggregations from cold seeps of the northern Gulf of Mexico

    PubMed Central

    Bright, M.; Plum, C.; Riavitz, L.A.; Nikolov, N.; Martinez Arbizu, P.; Cordes, E.E.; Gollner, S.

    2010-01-01

    The abundance and higher taxonomic composition of epizooic metazoan meiobenthic communities associated with mussel and tubeworm aggregations of hydrocarbon seeps at Green Canyon, Atwater Valley, and Alaminos Canyon in depths between 1400 and 2800 m were studied and compared to the infaunal community of non-seep sediments nearby. Epizooic meiofaunal abundances of associated meiobenthos living in tubeworm bushes and mussel beds at seeps were extremely low (usually <100 ind. 10 cm−2), similar to epizooic meiofauna at deep-sea hydrothermal vents, and the communities were composed primarily of nematodes, copepods, ostracods, and halacarids. In contrast, epizooic meiobenthic abundance is lower than previous studies have reported for infauna from seep sediments. Interestingly, non-seep sediments contained higher abundances and higher taxonomic diversity than epizooic seep communities, although in situ primary production is restricted to seeps. PMID:21264038

  13. Petroleum surface oil seeps from Palaeoproterozoic petrified giant oilfield

    NASA Astrophysics Data System (ADS)

    Melezhik, V.; Fallick, A.; Filippov, M.; Lepland, A.; Rychanchik, D.; Deines, Yu.; Medvedev, P.; Romashkin, A.; Strauss, H.

    2009-04-01

    Evidence of petroleum generation and migration has been previously reported from rocks dating as early as 3.25 Ga. Micron-size carbonaceous streaks and bitumen micronodules were found in abundance in Archaean rocks across the Pilbara craton in Australia suggesting pervasive petroleum generation and migration. However, none of the Archaean petroleum deposits has been reported to be preserved in quantity due to destructive effects of deformation and thermal obliteration during metamorphism. During the Palaeoproterozoic, unprecedented accumulation of Corg-rich rocks worldwide, known as the 2.0 Ga Shunga Event, occurred during the early stage of progressive oxidation of terrestrial environments, and in the aftermath of the Lomagundi-Jatuli isotopic event, which based on the magnitude and duration of positive d13C was the greatest perturbation of the global carbon cycle in Earth history. C. 2.0 Ga Zaonezhskaya Formation (ZF) rocks from the Onega Basin in Russian Fennoscandia contain evidence for substantial accumulation and preservation of organic matter (up to 75 wt.-% total organic carbon) with an estimated original petroleum potential comparable to a modern supergiant oilfield. The basin contains a uniquely preserved petrified oilfield including evidence of oil traps and oil migration pathways. Here, we report the discovery of the surface expression of a migration pathway, along which petroleum was flowing from the sub-surface. This surface oil seep, the first occurrence ever reported from the Palaeoproterozoic, appears as originally bitumen clasts redeposited in Palaeoproterozoic lacustrine turbidites of the Kondopozhskaya Formation. The d13Corg of clastic pyrobitumen ranges between -35.4 and -36.0 per mill (n = 14) which is within the range of interbed- and vein-trapped fossil oil (-46 and -24 per mill), suggesting similar source. Biogenic organic matter, whose isotopic composition was modified during thermal maturation, is the likely source for the migrated

  14. Lipid Biomarkers and Carbon Isotopic Composition from Authigenic Carbonates and Seep Sediments from the US Mid-Atlantic Margin

    NASA Astrophysics Data System (ADS)

    Campbell, P.; Prouty, N.; Demopoulos, A. W.; Roark, B.; Coykendall, K.

    2015-12-01

    Anaerobic oxidation of methane (AOM), mediated by Archaea and sulfate-reducing bacteria, is common in continental margin sediment and can result in authigenic carbonate precipitation. A lipid biomarker study was undertaken in Mid-Atlantic submarine canyons, focusing specifically on Baltimore and Norfolk canyons, to determine biomarker variability of carbonate rock and the associated sediment in cold seep communities dominated by chemosynthetic mussels, Bathymodiolus childressi. Preliminary 16S metagenomic results confirm the presence of free-living sulfur-reducing bacteria and methantrophic endosymbiotic bacteria in the mussels. Depleted d13C values in both the mussel tissue (-63 ‰) and authigenic carbonates (-48 ‰) support methanotrophy as the dominant nutritional pathway and AOM as the main driver of carbonate precipitation. In addition, paired 14C and 230Th dates are highly discordant, reflecting dilution of the 14C pool with fossil hydrocarbon derived carbon. Seep and canyon sediment, as well as authigenic carbonates, were collected and analyzed for a suite of biomarkers, including sterols, alcohols, alkanes and fatty acids, as well as δ13C values of select biomarkers, to elucidate pathways of organic matter cycling. A comparison of terrestrial biomarker signatures (e.g., n-alkane carbon preference index and C23 / (C23 + C29) values, HMW n-alkanes and C29 sterols) suggests that terrestrial inputs dominate the submarine canyon surface sediment, whereas seep sediment is predominantly marine autochthonous (i.e., cholesterol and 5α-cholestanol). Lipid biomarker profiles (e.g., n-alkanes in the C15 to C33 range) from authigenic carbonates mirror those found in the seep sediment, suggesting that the organisms mediating carbonate precipitation on the seafloor are characteristic of the assemblages present in the sediment at these sites. With widespread methane leakage recently discovered along the Atlantic Margin, the presence of AOM-mediated carbonate

  15. Phylogenetic diversity of methanogenic, sulfate-reducing and methanotrophic prokaryotes from deep-sea hydrothermal vents and cold seeps

    NASA Astrophysics Data System (ADS)

    Reed, Andrew J.; Dorn, Ruth; Van Dover, Cindy L.; Lutz, Richard A.; Vetriani, Costantino

    2009-09-01

    Microbial communities of methanogenic, sulfate-reducing and methanotrophic prokaryotes from deep-sea environments were investigated by molecular phylogenetic analysis of the deduced amino acid sequences of the genes encoding for the methyl coenzyme M reductase ( mcrA), dissimilatory sulfite reductase ( dsrAB) and particulate methane monoxygenase ( pmoA), respectively. Clone libraries of PCR amplified genes were constructed using DNA extracted from deep-sea vent chimneys (Rainbow and Logatchev hydrothermal vent fields, Mid-Atlantic Ridge, Atlantic Ocean; 9°N East Pacific Rise, Pacific Ocean) and from vertically subsampled sediment cores from cold-seep areas (Blake Ridge, western Atlantic Ocean; Florida Escarpment, Gulf of Mexico). Recombinant clones were screened by RFLP and representative dsrAB, mcrA and pmoA genes were sequenced. The dsrAB sequences grouped primarily within the orders Desulfobacterales, Syntrophobacterales and the Gram-positive order Clostridales. Cold-seep mcrA sequences were distributed among the ANME-2c, -2d and -2e groups, which were previously shown to be associated with the anaerobic oxidation of methane. This study also reports the first mcrA sequences from a high-temperature, black smoker chimney (Logatchev) to group within the ANME-2e subgroup. The majority of the remaining hydrothermal vent mcrA sequences were primarily related to thermophilic members of the anaerobic, methanogenic order Methanococcales. A shift in the dominant ANME-2 group with depth in the sediment for both Florida Escarpment and Blake Ridge mcrA libraries was detected. ANME-2d related clones were detected in the top zones of both cores, with the frequency of ANME-2e related clones increasing with depth. All pmoA sequences retrieved from the cold-seep sites were found to be related to Type I methanotrophic members of the γ-proteobacteria, and were primarily distributed among three major clusters of sequences. No Type II pmoA sequences related to methanotrophic

  16. Site-specific PEGylation of lidamycin and its antitumor activity.

    PubMed

    Li, Liang; Shang, Boyang; Hu, Lei; Shao, Rongguang; Zhen, Yongsu

    2015-05-01

    In this study, N-terminal site-specific mono-PEGylation of the recombinant lidamycin apoprotein (rLDP) of lidamycin (LDM) was prepared using a polyethyleneglycol (PEG) derivative (M w 20 kDa) through a reactive terminal aldehyde group under weak acidic conditions (pH 5.5). The biochemical properties of mPEG-rLDP-AE, an enediyne-integrated conjugate, were analyzed by SDS-PAGE, RP-HPLC, SEC-HPLC and MALDI-TOF. Meanwhile, in vitro and in vivo antitumor activity of mPEG-rLDP-AE was evaluated by MTT assays and in xenograft model. The results indicated that mPEG-rLDP-AE showed significant antitumor activity both in vitro and in vivo. After PEGylation, mPEG-rLDP still retained the binding capability to the enediyne AE and presented the physicochemical characteristics similar to that of native LDP. It is of interest that the PEGylation did not diminish the antitumor efficacy of LDM, implying the possibility that this derivative may function as a payload to deliver novel tumor-targeted drugs. PMID:26579455

  17. Hybrid [FeFe]-hydrogenases with modified active sites show remarkable residual enzymatic activity.

    PubMed

    Siebel, Judith F; Adamska-Venkatesh, Agnieszka; Weber, Katharina; Rumpel, Sigrun; Reijerse, Edward; Lubitz, Wolfgang

    2015-02-24

    [FeFe]-hydrogenases are to date the only enzymes for which it has been demonstrated that the native inorganic binuclear cofactor of the active site Fe2(adt)(CO)3(CN)2 (adt = azadithiolate = [S-CH2-NH-CH2-S](2-)) can be synthesized on the laboratory bench and subsequently inserted into the unmaturated enzyme to yield fully functional holo-enzyme (Berggren, G. et al. (2013) Nature 499, 66-70; Esselborn, J. et al. (2013) Nat. Chem. Biol. 9, 607-610). In the current study, we exploit this procedure to introduce non-native cofactors into the enzyme. Mimics of the binuclear subcluster with a modified bridging dithiolate ligand (thiodithiolate, N-methylazadithiolate, dimethyl-azadithiolate) and three variants containing only one CN(-) ligand were inserted into the active site of the enzyme. We investigated the activity of these variants for hydrogen oxidation as well as proton reduction and their structural accommodation within the active site was analyzed using Fourier transform infrared spectroscopy. Interestingly, the monocyanide variant with the azadithiolate bridge showed ∼50% of the native enzyme activity. This would suggest that the CN(-) ligands are not essential for catalytic activity, but rather serve to anchor the binuclear subsite inside the protein pocket through hydrogen bonding. The inserted artificial cofactors with a propanedithiolate and an N-methylazadithiolate bridge as well as their monocyanide variants also showed residual activity. However, these activities were less than 1% of the native enzyme. Our findings indicate that even small changes in the dithiolate bridge of the binuclear subsite lead to a rather strong decrease of the catalytic activity. We conclude that both the Brønsted base function and the conformational flexibility of the native azadithiolate amine moiety are essential for the high catalytic activity of the native enzyme. PMID:25633077

  18. Bacterial diversity and biogeochemistry of different chemosynthetic habitats of the REGAB cold seep (West African margin, 3160 m water depth)

    NASA Astrophysics Data System (ADS)

    Pop Ristova, P.; Wenzhöfer, F.; Ramette, A.; Zabel, M.; Fischer, D.; Kasten, S.; Boetius, A.

    2012-07-01

    The giant pockmark REGAB (West African margin, 3160 m water depth) is an active methane-emitting cold seep ecosystem, where the energy derived from microbially mediated oxidation of methane supports high biomass and diversity of chemosynthetic communities. Bare sediments interspersed with heterogeneous chemosynthetic assemblages of mytilid mussels, vesicomyid clams and siboglinid tubeworms form a complex seep ecosystem. To better understand if benthic bacterial communities reflect the patchy distribution of chemosynthetic fauna, all major chemosynthetic habitats at REGAB were investigated using an interdisciplinary approach combining porewater geochemistry, in situ quantification of fluxes and consumption of methane, as well bacterial community fingerprinting. This study revealed that sediments populated by different fauna assemblages show distinct biogeochemical activities and are associated with distinct sediment bacterial communities. The methane consumption and methane effluxes ranged over one to two orders of magnitude across habitats, and reached highest values at the mussel habitat, which hosted a different bacterial community compared to the other habitats. Clam assemblages had a profound impact on the sediment geochemistry, but less so on the bacterial community structure. Moreover, all clam assemblages at REGAB were restricted to sediments characterized by complete methane consumption in the seafloor, and intermediate biogeochemical activity. Overall, variations in the sediment geochemistry were reflected in the distribution of both fauna and microbial communities; and were mostly determined by methane flux.

  19. Bacterial diversity and biogeochemistry of different chemosynthetic habitats of the REGAB cold seep (West African margin, 3160 m water depth)

    NASA Astrophysics Data System (ADS)

    Pop Ristova, P.; Wenzhöfer, F.; Ramette, A.; Zabel, M.; Fischer, D.; Kasten, S.; Boetius, A.

    2012-12-01

    The giant pockmark REGAB (West African margin, 3160 m water depth) is an active methane-emitting cold seep ecosystem, where the energy derived from microbially mediated oxidation of methane supports high biomass and diversity of chemosynthetic communities. Bare sediments interspersed with heterogeneous chemosynthetic assemblages of mytilid mussels, vesicomyid clams and siboglinid tubeworms form a complex seep ecosystem. To better understand if benthic bacterial communities reflect the patchy distribution of chemosynthetic fauna, all major chemosynthetic habitats at REGAB were investigated using an interdisciplinary approach combining pore water geochemistry, in situ quantification of fluxes and consumption of methane, as well as bacterial community fingerprinting. This study revealed that sediments populated by different fauna assemblages show distinct biogeochemical activities and are associated with distinct sediment bacterial communities. The methane consumption rates and methane effluxes ranged over one to two orders of magnitude across habitats, and reached highest values at the mussel habitat, which hosted a different bacterial community compared to the other habitats. Clam assemblages had a profound impact on the sediment geochemistry, but less so on the bacterial community structure. Moreover, all clam assemblages at REGAB were restricted to sediments characterized by complete methane consumption in the seafloor, and intermediate biogeochemical activity. Overall, variations in the sediment geochemistry were reflected in the distribution of both fauna and microbial communities; and were mostly determined by methane flux.

  20. Geochemical analysis of potash mine seep oils, collapsed breccia pipe oil shows and selected crude oils, Eddy County, New Mexico

    USGS Publications Warehouse

    Palacas, J.G.; Snyder, R.P.; Baysinger, J.P.; Threlkeld, C.N.

    1982-01-01

    Oil shows, in the form of oil stains and bleeding oil, in core samples from two breccia pipes, Hills A and C, Eddy County, New Mexico, and seepage oils in a potash mine near Hill C breccia pipe are geochemically similar. The geochemical similarities strongly suggest that they belong to the same family of oils and were derived from similar sources. The oils are relatively high in sulfur (0.89 to 1.23 percent), rich in hydrocarbons (average 82 percent), relatively high in saturated hydrocarbon/aromatic hydrocarbon ratios (average 2.9), and based on analysis of seep oils alone, have a low API gravity (average 19.4?). The oils are for the most part severely biodegraded as attested by the loss of n-paraffin molecules. Geochemical comparison of seven crude oils collected in the vicinity of the breccia pipes indicates that the Yates oils are the likely source of the above family of oils. Six barrels of crude oil that were dumped into a potash exploration borehole near Hill C breccia pipe, to release stuck casing, are considered an unlikely source of the breccia pipe and mine seep oils. Volumetric and hydrodynamic constraints make it highly improbable that such a small volume of 'dumped' oil could migrate over distances ranging from about 600 feet to 2.5 miles to the sites of the oil shows.

  1. Benthic Gouge Marks in the Canadian Beaufort Sea: Associations Between Whales and Methane Seeps?

    NASA Astrophysics Data System (ADS)

    Smalls, P. T.; Paull, C. K.; Dallimore, S.

    2015-12-01

    Numerous distinctive depressions were observed on the seafloor during twenty-eight remotely operated vehicle (ROV) dives conducted on the shelf edge and upper slope of the Canadian Beaufort Sea. Surface ship and autonomous underwater vehicle (AUV) multibeam bathymetric maps were used to identify potential methane seepage sites, such as areas with persistent water column acoustic anomalies and the tops of mud volcanoes. ROV dives were conducted at these sites and at background sites for stratigraphic sampling. The high abundance of these distinctive depressions stimulated an analysis of the video observations made on these ROV dives. Depressions were analyzed to document their characteristics, to help determine their origin, and to establish whether their frequency varies with bottom type. One hundred fifty-two of the depressions observed had shared characteristics consisting of an "oval-shaped" depression with raised ridged edges that extended laterally along the flanks, and traces of uplifted sediment either in or around the depression. Similar depressions have been called "gouge marks" and attributed to bottom feeding beaked whales in previous studies. The size and water depth of the measured depressions matched well with beak sizes and feeding depths of beaked whale species known to exist in this area. This supports the conclusion that beaked whales created the depressions. The occurrence of these gouge marks and the estimates of the total area observed on these ROV dives (~45,000 m2), suggests they are common (e.g., ~4,000 per km2) features on the seafloor in this area of the Arctic. Gouges were also found 2.25 times more often at suspected methane seep-sites when normalized for depth and area. This suggests that the whales are preferentially attracted to seepage sites. While the reason for this possible preferential feeding behavior is unknown, it provides an intriguing avenue for further research.

  2. Characterization of the active site of chloroperoxidase using physical techniques

    SciTech Connect

    Hall, K.S.

    1986-01-01

    Chloroperoxidase (CPO) and Cytochrome P-450, two very different hemeproteins, have been shown to have similar active sites by several techniques. Recent work has demonstrated thiolate ligation from a cysteine residue to the iron in P-450. A major portion of this research has been devoted to obtaining direct evidence that CPO also has a thiolate 5th ligand from a cysteine residue. This information will provide the framework for a detailed analysis of the structure-function relationships between peroxidases, catalase and cytochrome P-450 hemeproteins. To determine whether the 5th ligand is a cysteine, methionine or a unique amino acid, specific isotope enrichment experiments were used. Preliminary /sup 1/H-NMR studies show that the carbon monoxide-CPO complex has a peak in the upfield region corresponding to alpha-protons of a thiolate amino acid. C. fumago was grown on 95% D/sub 2/O media with a small amount of /sup 1/H-cysteine added. Under these conditions C. fumago slows down the biosynthesis of cysteine by at least 50% and utilizes the exogenous cysteine in the media. GC-MS was able to show that the methylene protons next to the sulfur atom in cysteine are 80-90% protonated while these positions in methionine are approximately 73% deuterated. Comparison of the /sup 1/H-NMR spectra of CO-CPO and CO-CPO indicate the presence of a cysteine ligand in chloroperoxidase.

  3. N6-Methyldeoxyadenosine Marks Active Transcription Start Sites in Chlamydomonas

    PubMed Central

    Chen, Kai; Deng, Xin; Yu, Miao; Han, Dali; Hao, Ziyang; Liu, Jianzhao; Lu, Xingyu; Dore, Louis C; Weng, Xiaocheng; Ji, Quanjiang; Mets, Laurens; He, Chuan

    2015-01-01

    SUMMARY N6-methyldeoxyadenosine (6mA or m6A) is a DNA modification preserved in prokaryotes to eukaryotes. It is widespread in bacteria, and functions in DNA mismatch repair, chromosome segregation, and virulence regulation. In contrast, the distribution and function of 6mA in eukaryotes have been unclear. Here we present a comprehensive analysis of the 6mA landscape in the genome of Chlamydomonas using new sequencing approaches. We identified the 6mA modification in 84% of genes in Chlamydomonas. We found that 6mA mainly locates at ApT dinucleotides around transcription start sites (TSS) with a bimodal distribution, and appears to mark active genes. A periodic pattern of 6mA deposition was also observed at base resolution, which is associated with nucleosome distribution near the TSS, suggesting a possible role in nucleosome positioning. The new genome-wide mapping of 6mA and its unique distribution in the Chlamydomonas genome suggest potential regulatory roles of 6mA in gene expression in eukaryotic organisms. PMID:25936837

  4. Detection limit for activation measurements in ultralow background sites

    NASA Astrophysics Data System (ADS)

    Trache, Livius; Chesneanu, D.; Margineanu, R.; Pantelica, A.; Ghita, D. G.; Burducea, I.; Straticiuc, M.; Tang, X. D.

    2014-09-01

    We used 12C +13C fusion at the beam energies E = 6, 7 and 8 MeV to determine the sensitivity and the limits of activation method measurements in ultralow background sites. A 13C beam of 0.5 μA from the 3 MV Tandem accelerator of the Horia Hulubei National Institute of Physics and Nuclear Engineering - IFIN HH impinged on thick graphite targets. After about 24 hrs of irradiation targets were measured in two different laboratories: one with a heavy shielded Ge detector in the institute (at the surface) and one located underground in the microBequerel laboratory, in the salt mine of Slanic-Prahova, Romania. The 1369- and 2754 keV peaks from 24Na deactivation were clearly observed in the γ-ray spectra obtained for acquisitions lasting a few hours, or a few days. Determination of the detection limit in evaluating the cross sections for the target irradiated at Ec . m = 3 MeV indicates the fact that it is possible to measure gamma spectrum in underground laboratory down to Ec . m = 2 . 6 MeV. Cleaning the spectra with beta-gamma coincidences and increasing beam intensity 20 times will take as further down. The measurements are motivated by the study of the 12 C +12 C reaction at astrophysical energies.

  5. Disturbance opens recruitment sites for bacterial colonization in activated sludge.

    PubMed

    Vuono, David C; Munakata-Marr, Junko; Spear, John R; Drewes, Jörg E

    2016-01-01

    Little is known about the role of immigration in shaping bacterial communities or the factors that may dictate success or failure of colonization by bacteria from regional species pools. To address these knowledge gaps, the influence of bacterial colonization into an ecosystem (activated sludge bioreactor) was measured through a disturbance gradient (successive decreases in the parameter solids retention time) relative to stable operational conditions. Through a DNA sequencing approach, we show that the most abundant bacteria within the immigrant community have a greater probability of colonizing the receiving ecosystem, but mostly as low abundance community members. Only during the disturbance do some of these bacterial populations significantly increase in abundance beyond background levels and in few cases become dominant community members post-disturbance. Two mechanisms facilitate the enhanced enrichment of immigrant populations during disturbance: (i) the availability of resources left unconsumed by established species and (ii) the increased availability of niche space for colonizers to establish and displace resident populations. Thus, as a disturbance decreases local diversity, recruitment sites become available to promote colonization. This work advances our understanding of microbial resource management and diversity maintenance in complex ecosystems. PMID:25727891

  6. Active Site Characterization of Proteases Sequences from Different Species of Aspergillus.

    PubMed

    Morya, V K; Yadav, Virendra K; Yadav, Sangeeta; Yadav, Dinesh

    2016-09-01

    A total of 129 proteases sequences comprising 43 serine proteases, 36 aspartic proteases, 24 cysteine protease, 21 metalloproteases, and 05 neutral proteases from different Aspergillus species were analyzed for the catalytically active site residues using MEROPS database and various bioinformatics tools. Different proteases have predominance of variable active site residues. In case of 24 cysteine proteases of Aspergilli, the predominant active site residues observed were Gln193, Cys199, His364, Asn384 while for 43 serine proteases, the active site residues namely Asp164, His193, Asn284, Ser349 and Asp325, His357, Asn454, Ser519 were frequently observed. The analysis of 21 metalloproteases of Aspergilli revealed Glu298 and Glu388, Tyr476 as predominant active site residues. In general, Aspergilli species-specific active site residues were observed for different types of protease sequences analyzed. The phylogenetic analysis of these 129 proteases sequences revealed 14 different clans representing different types of proteases with diverse active site residues.

  7. A proposed definition of the 'activity' of surface sites on lactose carriers for dry powder inhalation.

    PubMed

    Grasmeijer, Floris; Frijlink, Henderik W; de Boer, Anne H

    2014-06-01

    A new definition of the activity of surface sites on lactose carriers for dry powder inhalation is proposed which relates to drug detachment during dispersion. The new definition is expected to improve the understanding of 'carrier surface site activity', which stimulates the unambiguous communication about this subject and may aid in the rational design and interpretation of future formulation studies. In contrast to the currently prevailing view on carrier surface site activity, it follows from the newly proposed definition that carrier surface site activity depends on more variables than just the physicochemical properties of the carrier surface. Because the term 'active sites' is ambiguous, it is recommended to use the term 'highly active sites' instead to denote carrier surface sites with a relatively high activity. PMID:24613490

  8. SEEP II, Shelf Edge Exchange Processes-II: Chlorophyll a fluorescence, temperature, and beam attenuation measurements from moored fluorometers

    SciTech Connect

    Medeiros, W.H.; Wirick, C.D.

    1992-02-01

    The Shelf Edge Exchange Processes (SEEP) program sponsored by the United States Department of Energy is a multi-institutional effort designed to investigate the flux of suspended material from the continental shelf to the waters of the upper slope, and then possibly into the slope sediments. The first SEEP experiment (SEEP I) was across the outer continental shelf of New England during 1983--1984 and consisted of a series of nine cruises and a mooring array. The second experiment (SEEP II) focused specifically of the shelf/slope frontal region of the mid-Atlantic Bight off the Delmarva peninsula. This report presents data collected during SEEP II. The SEEP II experiment consisted of a series of ten cruises and mooring arrays as well as over-flights by NASA aircraft. The cruises were consecutively designated SEEP2-01 to SEEP2-10. Hydrographic data were collected on all cruises except SEEP2-04 and SEEP2-07 during which benthic processes were investigated. Mooring arrays were deployed during three cruises in the Spring, Summer and Winter of 1988. Brookhaven National Laboratory deployed sixteen fluorometer instrument packages on their moorings with sensors to measure: the in vivo fluorescence of phytoplankton, temperature, subsurface light, dissolved oxygen, and water transparency. Data from the fluorometer, temperature, and transmissometer sensors are reported herein.

  9. Metagenomes from two microbial consortia associated with Santa Barbara seep oil.

    PubMed

    Hawley, Erik R; Malfatti, Stephanie A; Pagani, Ioanna; Huntemann, Marcel; Chen, Amy; Foster, Brian; Copeland, Alexander; del Rio, Tijana Glavina; Pati, Amrita; Jansson, Janet R; Gilbert, Jack A; Tringe, Susannah Green; Lorenson, Thomas D; Hess, Matthias

    2014-12-01

    The metagenomes from two microbial consortia associated with natural oils seeping into the Pacific Ocean offshore the coast of Santa Barbara (California, USA) were determined to complement already existing metagenomes generated from microbial communities associated with hydrocarbons that pollute the marine ecosystem. This genomics resource article is the first of two publications reporting a total of four new metagenomes from oils that seep into the Santa Barbara Channel. PMID:24958360

  10. Behavioural impairment in reef fishes caused by ocean acidification at CO2 seeps

    NASA Astrophysics Data System (ADS)

    Munday, Philip L.; Cheal, Alistair J.; Dixson, Danielle L.; Rummer, Jodie L.; Fabricius, Katharina E.

    2014-06-01

    Experiments have shown that the behaviour of reef fishes can be seriously affected by projected future carbon dioxide (CO2) concentrations in the ocean. However, whether fish can acclimate to elevated CO2 over the longer term, and the consequences of altered behaviour on the structure of fish communities, are unknown. We used marine CO2 seeps in Papua New Guinea as a natural laboratory to test these questions. Here we show that juvenile reef fishes at CO2 seeps exhibit behavioural abnormalities similar to those seen in laboratory experiments. Fish from CO2 seeps were attracted to predator odour, did not distinguish between odours of different habitats, and exhibited bolder behaviour than fish from control reefs. High CO2 did not, however, have any effect on metabolic rate or aerobic performance. Contrary to expectations, fish diversity and community structure differed little between CO2 seeps and nearby control reefs. Differences in abundances of some fishes could be driven by the different coral community at CO2 seeps rather than by the direct effects of high CO2. Our results suggest that recruitment of juvenile fish from outside the seeps, along with fewer predators within the seeps, is currently sufficient to offset any negative effects of high CO2 within the seeps. However, continuous exposure does not reduce the effect of high CO2 on behaviour in natural reef habitat, and this could be a serious problem for fish communities in the future when ocean acidification becomes widespread as a result of continued uptake of anthropogenic CO2 emissions.

  11. 10 CFR 63.16 - Review of site characterization activities. 2

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of... conduct of site characterization activities at the Yucca Mountain site, DOE shall report the nature and... activities at the Yucca Mountain site, NRC staff shall be permitted to visit and inspect the locations...

  12. 10 CFR 63.16 - Review of site characterization activities. 2

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of... conduct of site characterization activities at the Yucca Mountain site, DOE shall report the nature and... activities at the Yucca Mountain site, NRC staff shall be permitted to visit and inspect the locations...

  13. 10 CFR 63.16 - Review of site characterization activities. 2

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of... conduct of site characterization activities at the Yucca Mountain site, DOE shall report the nature and... activities at the Yucca Mountain site, NRC staff shall be permitted to visit and inspect the locations...

  14. 10 CFR 63.16 - Review of site characterization activities. 2

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of... conduct of site characterization activities at the Yucca Mountain site, DOE shall report the nature and... activities at the Yucca Mountain site, NRC staff shall be permitted to visit and inspect the locations...

  15. 10 CFR 63.16 - Review of site characterization activities. 2

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of... conduct of site characterization activities at the Yucca Mountain site, DOE shall report the nature and... activities at the Yucca Mountain site, NRC staff shall be permitted to visit and inspect the locations...

  16. Shelf Edge Exchange Processes, II: SEEP2-08, R/V ENDEAVOR cruise 188

    SciTech Connect

    Wilson, C.; Behrens, W.J.; Flagg, C.N.; Wallace, D.W.R.; Wilke, R.J.; Wyman, K.D.

    1989-12-01

    The Shelf Edge Exchange Processes (SEEP) program sponsored by the United States Department of Energy is a multi-institutional effort designed to investigate the flux of suspended material from the continental shelf to the waters of the upper slope, and then possibly into the slope sediments. Phase I of SEEP consisted of a series of nine cruises and a mooring array across the outer continental shelf of New England during 1983--1984 (Behrens and Flagg, 1986). Phase II focused specifically on the shelf/slope frontal region of the mid-Atlantic bight off the Delmarva Peninsula. This project consisted of a series of ten cruises, a mooring array, and a series of over-flights by NASA aircraft. Hydrographic data were collected on eight of the cruises, six of which were primarily mooring deployment or recovery cruises. The cruises were consecutively designated SEEP2-01 to SEEP2-10. Two cruises (SEEP2-04 and SEEP2-07) were dedicated to investigating benthic processes and hydrographic data were not collected.

  17. Processes controlling water and hydrocarbon composition in seeps from the Salton Sea geothermal system, California, USA

    NASA Astrophysics Data System (ADS)

    Svensen, Henrik; Karlsen, Dag A.; Sturz, Anne; Backer-Owe, Kristian; Banks, David A.; Planke, Sverre

    2007-01-01

    Water-, mud-, gas-, and petroleum-bearing seeps are part of the Salton Sea geothermal system (SSGS) in Southern California. Seeps in the Davis-Schrimpf seep field (˜14,000 m2) show considerable variations in water temperature, pH, density, and solute content. Water-rich springs have low densities (<1.4 g/cm3), Cl contents as high as 45,000 ppm, and temperatures between 15 and 34 °C. Gryphons expel denser water-mud mixtures (to 1.7 g/cm3), have low salinities (3600 5200 ppm Cl), and have temperatures between 23 and 63 °C. The main driver for the seep system is CO2 (>98 vol%). Halogen geochemistry of the waters indicates that mixing of deep and shallow waters occurs and that near-surface dissolution of halite may overprint the original fluid compositions. Carbon isotopic analyses suggest that hydrocarbon seep gases have a thermogenic origin. This hypothesis is supported by the presence of petroleum in a water-dominated spring, composed of 53% saturated compounds, 35% aromatics, and 12% polar compounds. The abundance of polyaromatic hydrocarbons and immature biomarkers suggests a hydrothermal formation of the petroleum, making the SSGS a relevant analogue to less accessible hydrothermal seep systems, e.g., the Guaymas Basin in the Gulf of California.

  18. Association of oil seeps and chemosynthetic communities with oil discoveries, upper continental slope, Gulf of Mexico

    SciTech Connect

    Sassen, R.; Brooks, J.M.; MacDonald, I.R.; Kennicutt, M.C. II; Guinasso, N.L. Jr. )

    1993-09-01

    A belt of sea-floor oil seeps and chemosynthetic communities has been mapped across the upper continental slope, offshore Louisiana, at depths ranging from 2000 to 1000 m. Visibly oil-stained sediments and thelmogenic gas hydrates have been recovered using piston cores and research submarines. Biomarker fingerprinting of seep oils suggests an origin from deeply buried Cretaceous or Jurassic source rocks characterized by marine kerogen. The abundance of seeps provides a unique opportunity to define their relationship to oil discoveries including Auger, Cooper, Jolliet, Marquette, Vancouver, Popeye, and Mars. Seeps are preferentially distributed over shallow salt ridges that rim intrasalt basin cooking pots, over salt diapirs, and along shallow fault traces near discoveries. Diagnostic seep-related features on the sea floor include gas hydrate mounds and outcrops, pockmarks and craters, mud volcanoes, and carbonate buildups. Many of the 50 chemosynthetic communities including tube worms, mussels, or clams thus far documented in the gulf occur near discoveries. Recent imagery from orbital platforms, including the space shuttle, shows that natural oil slicks are common on the sea surface in this area. Additional mapping of seep distributions should contribute to better defining of the limits of the deep Gulf play fairway.

  19. GAS HYDRATES AT TWO SITES OF AN ACTIVE CONTINENTAL MARGIN.

    USGS Publications Warehouse

    Kvenvolden, K.A.

    1985-01-01

    Sediment containing gas hydrates from two distant Deep Sea Drilling Project sites (565 and 568), located about 670 km apart on the landward flank of the Middle America Trench, was studied to determine the geochemical conditions that characterize the occurrence of gas hydrates. Site 565 was located in the Pacific Ocean offshore the Nicoya Peninsula of Costa Rica in 3,111 m of water. The depth of the hole at this site was 328 m, and gas hydrates were recovered from 285 and 319 m. Site 568 was located about 670 km to the northwest offshore Guatemala in 2,031 m of water. At this site the hole penetrated to 418 m, and gas hydrates were encountered at 404 m.

  20. Control of active sites in selective flocculation: III -- Mechanism of site blocking

    SciTech Connect

    Behl, S.; Moudgil, B.M. . Dept. of Materials Science and Engineering)

    1993-12-01

    It has been shown in Parts I and II of this paper that heteroflocculation can be controlled by poisoning the sites for flocculant adsorption using a site blocking agent (SBA). An efficient SBA was determined to be the lower molecular weight fraction of the flocculant. In this paper, the underlying mechanism of SBA action is described. Also, the mathematical model detailed in Part I is used to determine the effect of different SBAs on apatite-dolomite separation efficiency. It has been demonstrated that the depression in flocculation is directly related to the site blocking parameter ([bar [Phi

  1. A Long-Term Cultivation of an Anaerobic Methane-Oxidizing Microbial Community from Deep-Sea Methane-Seep Sediment Using a Continuous-Flow Bioreactor

    PubMed Central

    Aoki, Masataka; Ehara, Masayuki; Saito, Yumi; Yoshioka, Hideyoshi; Miyazaki, Masayuki; Saito, Yayoi; Miyashita, Ai; Kawakami, Shuji; Yamaguchi, Takashi; Ohashi, Akiyoshi; Nunoura, Takuro; Takai, Ken; Imachi, Hiroyuki

    2014-01-01

    Anaerobic oxidation of methane (AOM) in marine sediments is an important global methane sink, but the physiological characteristics of AOM-associated microorganisms remain poorly understood. Here we report the cultivation of an AOM microbial community from deep-sea methane-seep sediment using a continuous-flow bioreactor with polyurethane sponges, called the down-flow hanging sponge (DHS) bioreactor. We anaerobically incubated deep-sea methane-seep sediment collected from the Nankai Trough, Japan, for 2,013 days in the bioreactor at 10°C. Following incubation, an active AOM activity was confirmed by a tracer experiment using 13C-labeled methane. Phylogenetic analyses demonstrated that phylogenetically diverse Archaea and Bacteria grew in the bioreactor. After 2,013 days of incubation, the predominant archaeal components were anaerobic methanotroph (ANME)-2a, Deep-Sea Archaeal Group, and Marine Benthic Group-D, and Gammaproteobacteria was the dominant bacterial lineage. Fluorescence in situ hybridization analysis showed that ANME-1 and -2a, and most ANME-2c cells occurred without close physical interaction with potential bacterial partners. Our data demonstrate that the DHS bioreactor system is a useful system for cultivating fastidious methane-seep-associated sedimentary microorganisms. PMID:25141130

  2. Dynamically achieved active site precision in enzyme catalysis.

    PubMed

    Klinman, Judith P

    2015-02-17

    CONSPECTUS: The grand challenge in enzymology is to define and understand all of the parameters that contribute to enzymes' enormous rate accelerations. The property of hydrogen tunneling in enzyme reactions has moved the focus of research away from an exclusive focus on transition state stabilization toward the importance of the motions of the heavy atoms of the protein, a role for reduced barrier width in catalysis, and the sampling of a protein conformational landscape to achieve a family of protein substates that optimize enzyme-substrate interactions and beyond. This Account focuses on a thermophilic alcohol dehydrogenase for which the chemical step of hydride transfer is rate determining across a wide range of experimental conditions. The properties of the chemical coordinate have been probed using kinetic isotope effects, indicating a transition in behavior below 30 °C that distinguishes nonoptimal from optimal C-H activation. Further, the introduction of single site mutants has the impact of either enhancing or eliminating the temperature dependent transition in catalysis. Biophysical probes, which include time dependent hydrogen/deuterium exchange and fluorescent lifetimes and Stokes shifts, have also been pursued. These studies allow the correlation of spatially resolved transitions in protein motions with catalysis. It is now possible to define a long-range network of protein motions in ht-ADH that extends from a dimer interface to the substrate binding domain across to the cofactor binding domain, over a distance of ca. 30 Å. The ongoing challenge to obtaining spatial and temporal resolution of catalysis-linked protein motions is discussed.

  3. Coupled LBM-DEM Three-phase Simulation on Gas Flux Seeping from Marine Sediment

    NASA Astrophysics Data System (ADS)

    Kano, Y.; Sato, T.

    2014-12-01

    One of the main issues of the geological storage of CO2 under the seabed is a risk of CO2 leakage. Once CO2seeps into the ocean, it rises in water column dissolving into seawater, which results in the acidification of seawater and/or returning to the air. Its behaviour significantly depends on flow rate and bubble size (Kano et al., 2009; Dewar et al., 2013). As for porous media, bubble size is generally predicted through simple force balance based on flow rate, surface tension and channel size which is estimated by porosity and grain size. However, in shallow marine sediments, grains could be mobilised and displaced by buoyant gas flow, which causes distinctive phenomena such as blow-out or formation of gas flow conduit. As a result, effective gas flux into seawater can be intermissive, and/or concentrated in narrow area (QICS, 2012; Kawada, 2013). Bubble size is also affected by these phenomena. To predict effective gas flux and bubble size into seawater, three-phase behaviour of gas-water-sediment grains should be revealed. In this presentation, we will report the results of gas-liquid-solid three-phase simulations and their comparisons with experimental and observation data. Size of solid particles is based on grain size composing marine sediments at some CCS project sites. Fluid-particle interactions are solved using the lattice Boltzmann method (LBM), while the particle-particle interactions are treated by coupling with the Discrete Element method (DEM). References: Dewar, M., Wei, W., McNeil, D., Chen, B., 2013. Small-scale modelling of the physiochemical impacts of CO2leaked from sub-seabed reservoirs or pipelines within the North Sea and surrounding waters. Marine Pollution Bulletin 73(2), 504-515. Kano, Y., Sato, T., Kita, J., Hirabayashi, S., Tabeta, S., 2009. Model prediction on the rise of pCO2 in uniform flows by leakage of CO2purposefully stored under the seabed. Int. J. Greenhouse Gas Control, Vol. 3(5), 617-625. Kawada, R. 2014. A study on the

  4. Lethal Factor Active-Site Mutations Affect Catalytic Activity In Vitro

    PubMed Central

    Hammond, S. E.; Hanna, P. C.

    1998-01-01

    The lethal factor (LF) protein of Bacillus anthracis lethal toxin contains the thermolysin-like active-site and zinc-binding consensus motif HEXXH (K. R. Klimpel, N. Arora, and S. H. Leppla, Mol. Microbiol. 13:1093–1100, 1994). LF is hypothesized to act as a Zn2+ metalloprotease in the cytoplasm of macrophages, but no proteolytic activities have been previously shown on any target substrate. Here, synthetic peptides are hydrolyzed by LF in vitro. Mass spectroscopy and peptide sequencing of isolated cleavage products separated by reverse-phase high-pressure liquid chromatography indicate that LF seems to prefer proline-containing substrates. Substitution mutations within the consensus active-site residues completely abolish all in vitro catalytic functions, as does addition of 1,10-phenanthroline, EDTA, and certain amino acid hydroxamates, including the novel zinc metalloprotease inhibitor ZINCOV. In contrast, the protease inhibitors bestatin and lysine CMK, previously shown to block LF activity on macrophages, did not block LF activity in vitro. These data provide the first direct evidence that LF may act as an endopeptidase. PMID:9573135

  5. Monoclonal antibody against the active site of caeruloplasmin and the ELISA system detecting active caeruloplasmin.

    PubMed

    Hiyamuta, S; Ito, K

    1994-04-01

    Serum caeruloplasmin deficiency is a characteristic biochemical abnormality found in patients with Wilson's disease, but the mechanism of this disease is unknown. Although the phenylenediamine oxidase activity of serum caeruloplasmin is markedly low in patients with Wilson's disease, mRNA of caeruloplasmin exists to some extent. To investigate the deficiency of caeruloplasmin oxidase activity in Wilson's disease, we generated 14 monoclonal antibodies (MAbs) and selected ID1, which had the strongest reactivity, and ID2, which had neutralizing ability. We also established a system to measure active caeruloplasmin specifically using these MAbs. These MAbs and the system will be useful tools in analyzing the active site of caeruloplasmin in patients with Wilson's disease.

  6. Robotics and Automation Activities at the Savannah River Site: A Site Report for SUBWOG 39F

    SciTech Connect

    Teese, G.D.

    1995-09-28

    The Savannah River Site has successfully used robots, teleoperators, and remote video to reduce exposure to ionizing radiation, improve worker safety, and improve the quality of operations. Previous reports have described the use of mobile teleoperators in coping with a high level liquid waste spill, the removal of highly contaminated equipment, and the inspection of nuclear reactor vessels. This report will cover recent applications at the Savannah River, as well as systems which SRS has delivered to other DOE site customers.

  7. Control of active sites in selective flocculation: II -- Role of site blocking agents

    SciTech Connect

    Behl, S.; Moudgil, B.M. . Dept. of Materials Science and Engineering)

    1993-12-01

    Control of heteroflocculation using a lower molecular weight fraction of the flocculant as a site blocking agent is demonstrated in the apatite-dolomite-polyethylene oxide system. The most effective SBA (site blocking agent) was determined to be the highest molecular weight fraction of the flocculant itself which was not capable of flocculating any of the components of the mixture. In the presence of the SBA, flocculant adsorption decreased significantly on apatite particles, thereby inhibiting coflocculation.

  8. Mutation at a Strictly Conserved, Active Site Tyrosine in the Copper Amine Oxidase Leads to Uncontrolled Oxygenase Activity

    SciTech Connect

    Chen, Zhi-wei; Datta, Saumen; DuBois, Jennifer L.; Klinman, Judith P.; Mathews, F. Scott

    2010-09-07

    The copper amine oxidases carry out two copper-dependent processes: production of their own redox-active cofactor (2,4,5-trihydroxyphenylalanine quinone, TPQ) and the subsequent oxidative deamination of substrate amines. Because the same active site pocket must facilitate both reactions, individual active site residues may serve multiple roles. We have examined the roles of a strictly conserved active site tyrosine Y305 in the copper amine oxidase from Hansenula polymorpha kinetically, spetroscopically (Dubois and Klinman (2006) Biochemistry 45, 3178), and, in the present work, structurally. While the Y305A enzyme is almost identical to the wild type, a novel, highly oxygenated species replaces TPQ in the Y305F active sites. This new structure not only provides the first direct detection of peroxy intermediates in cofactor biogenesis but also indicates the critical control of oxidation chemistry that can be conferred by a single active site residue.

  9. Linking nitrogen management, seep chemistry, and stream water quality in two agricultural headwater watersheds.

    PubMed

    Williams, Mark R; Buda, Anthony R; Elliott, Herschel A; Collick, Amy S; Dell, Curtis; Kleinman, Peter J A

    2015-05-01

    Riparian seepage zones in headwater agricultural watersheds represent important sources of nitrate-nitrogen (NO-N) to surface waters, often connecting N-rich groundwater systems to streams. In this study, we examined how NO-N concentrations in seep and stream water were affected by NO-N processing along seep surface flow paths and by upslope applications of N from fertilizers and manures. The research was conducted in two headwater agricultural watersheds, FD36 (40 ha) and RS (45 ha), which are fed, in part, by a shallow fractured aquifer system possessing high (3-16 mg L) NO-N concentrations. Data from in-seep monitoring showed that NO-N concentrations generally decreased downseep (top to bottom), indicating that most seeps retained or removed a fraction of delivered NO-N (16% in FD36 and 1% in RS). Annual mean N applications in upslope fields (as determined by yearly farmer surveys) were highly correlated with seep NO-N concentrations in both watersheds (slope: 0.06; = 0.79; < 0.001). Strong positive relationships also existed between seep and stream NO-N concentrations in FD36 (slope: 1.01; = 0.79; < 0.001) and in RS (slope: 0.64; = 0.80; < 0.001), further indicating that N applications control NO-N concentrations at the watershed scale. Our findings clearly point to NO-N leaching from upslope agricultural fields as the primary driver of NO-N losses from seeps to streams in these watersheds and therefore suggest that appropriate management strategies (cover crops, limiting fall/winter nutrient applications, decision support tools) be targeted in these zones. PMID:26024271

  10. Identification of promiscuous ene-reductase activity by mining structural databases using active site constellations

    PubMed Central

    Steinkellner, Georg; Gruber, Christian C.; Pavkov-Keller, Tea; Binter, Alexandra; Steiner, Kerstin; Winkler, Christoph; Łyskowski, Andrzej; Schwamberger, Orsolya; Oberer, Monika; Schwab, Helmut; Faber, Kurt; Macheroux, Peter; Gruber, Karl

    2014-01-01

    The exploitation of catalytic promiscuity and the application of de novo design have recently opened the access to novel, non-natural enzymatic activities. Here we describe a structural bioinformatic method for predicting catalytic activities of enzymes based on three-dimensional constellations of functional groups in active sites (‘catalophores’). As a proof-of-concept we identify two enzymes with predicted promiscuous ene-reductase activity (reduction of activated C–C double bonds) and compare them with known ene-reductases, that is, members of the Old Yellow Enzyme family. Despite completely different amino acid sequences, overall structures and protein folds, high-resolution crystal structures reveal equivalent binding modes of typical Old Yellow Enzyme substrates and ligands. Biochemical and biocatalytic data show that the two enzymes indeed possess ene-reductase activity and reveal an inverted stereopreference compared with Old Yellow Enzymes for some substrates. This method could thus be a tool for the identification of viable starting points for the development and engineering of novel biocatalysts. PMID:24954722

  11. Characteristics of vesicomyid clams and their environment at the Blake Ridge cold seep, South Carolina, USA

    USGS Publications Warehouse

    Heyl, Taylor P.; Gilhooly, William P.; Chambers, Randolph M.; Gilchrist, George W.; Macko, Stephen A.; Ruppel, Carolyn D.; Van Dover, Cindy L.

    2007-01-01

    Spatial distributions and patchiness of dominant megafaunal invertebrates in deep-sea seep environments may indicate heterogeneities in the flux of reduced chemical compounds. At the Blake Ridge seep off South Carolina, USA, the invertebrate assemblage includes dense populations of live vesicomyid clams (an undescribed species) as well as extensive clam shell beds (i.e. dead clams). In the present study, we characterized clam parameters (density, size-frequency distribution, reproductive condition) in relation to sulfur chemistry (sulfide and sulfate concentrations and isotopic compositions, pyrite and elemental sulfur concentrations) and other sedimentary metrics (grain size, organic content). For clams >5 mm, clam density was highest where the total dissolved sulfide concentration at 10 cm depth (ΣH2S10cm) was 0.4 to 1.1 mmol l–1; juvenile clams (2S10cm was lowest. Clams were reproductively capable across a broad range of ΣH2S10cm (0.1 to 6.4 mmol l–1), and females in the sampled populations displayed asynchronous gametogenesis. Sulfide concentrations in porewaters at the shell–sediment interface of cores from shell beds were high, 3.3 to 12.1 mmol l–1, compared to –1 sulfide concentrations at the clam–sediment interface in live clam beds. Concentration profiles for sulfide and sulfate in shell beds were typical of those expected where there is active microbial sulfate reduction. In clam beds, profiles of sulfide and sulfate concentrations were also consistent with rapid uptake of sulfide by the clams. Sulfate in shell beds was systematically enriched in 34S relative to that in clam beds due to microbial fractionation during sulfate reduction, but in clam beds, sulfate δ34S matched that of seawater (~20‰). Residual sulfide values in clam and shell beds were correspondingly depleted in 34S. Based on porewater sulfide concentrations in shell beds at the time of sampling, we suggest that clam mortality may have been due to an abrupt increase in

  12. An ionizable active-site tryptophan imparts catalase activity to a peroxidase core.

    PubMed

    Loewen, Peter C; Carpena, Xavi; Vidossich, Pietro; Fita, Ignacio; Rovira, Carme

    2014-05-21

    Catalase peroxidases (KatG's) are bifunctional heme proteins that can disproportionate hydrogen peroxide (catalatic reaction) despite their structural dissimilarity with monofunctional catalases. Using X-ray crystallography and QM/MM calculations, we demonstrate that the catalatic reaction of KatG's involves deprotonation of the active-site Trp, which plays a role similar to that of the distal His in monofunctional catalases. The interaction of a nearby mobile arginine with the distal Met-Tyr-Trp essential adduct (in/out) acts as an electronic switch, triggering deprotonation of the adduct Trp.

  13. Nuclear Site Security in the Event of Terrorist Activity

    SciTech Connect

    Thomson, M.L.; Sims, J.

    2008-07-01

    This paper, presented as a poster, identifies why ballistic protection should now be considered at nuclear sites to counter terrorist threats. A proven and flexible form of multi purpose protection is described in detail with identification of trial results that show its suitability for this role. (authors)

  14. Preliminary siting activities for new waste handling facilities at the Idaho National Engineering Laboratory

    SciTech Connect

    Taylor, D.D.; Hoskinson, R.L.; Kingsford, C.O.; Ball, L.W.

    1994-09-01

    The Idaho Waste Processing Facility, the Mixed and Low-Level Waste Treatment Facility, and the Mixed and Low-Level Waste Disposal Facility are new waste treatment, storage, and disposal facilities that have been proposed at the Idaho National Engineering Laboratory (INEL). A prime consideration in planning for such facilities is the selection of a site. Since spring of 1992, waste management personnel at the INEL have been involved in activities directed to this end. These activities have resulted in the (a) identification of generic siting criteria, considered applicable to either treatment or disposal facilities for the purpose of preliminary site evaluations and comparisons, (b) selection of six candidate locations for siting,and (c) site-specific characterization of candidate sites relative to selected siting criteria. This report describes the information gathered in the above three categories for the six candidate sites. However, a single, preferred site has not yet been identified. Such a determination requires an overall, composite ranking of the candidate sites, which accounts for the fact that the sites under consideration have different advantages and disadvantages, that no single site is superior to all the others in all the siting criteria, and that the criteria should be assigned different weighing factors depending on whether a site is to host a treatment or a disposal facility. Stakeholder input should now be solicited to help guide the final selection. This input will include (a) siting issues not already identified in the siting, work to date, and (b) relative importances of the individual siting criteria. Final site selection will not be completed until stakeholder input (from the State of Idaho, regulatory agencies, the public, etc.) in the above areas has been obtained and a strategy has been developed to make a composite ranking of all candidate sites that accounts for all the siting criteria.

  15. Active Layer and Moisture Measurements for Intensive Site 0 and 1, Barrow, Alaska

    DOE Data Explorer

    John Peterson

    2015-04-17

    These are measurements of Active Layer Thickness collected along several lines beginning in September, 2011 to the present. The data were collected at several time periods along the Site0 L2 Line, the Site1 AB Line, and an ERT Monitoring Line near Area A in Site1.

  16. Structural mechanism of RuBisCO activation by carbamylation of the active site lysine

    PubMed Central

    Stec, Boguslaw

    2012-01-01

    Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is a crucial enzyme in carbon fixation and the most abundant protein on earth. It has been studied extensively by biochemical and structural methods; however, the most essential activation step has not yet been described. Here, we describe the mechanistic details of Lys carbamylation that leads to RuBisCO activation by atmospheric CO2. We report two crystal structures of nitrosylated RuBisCO from the red algae Galdieria sulphuraria with O2 and CO2 bound at the active site. G. sulphuraria RuBisCO is inhibited by cysteine nitrosylation that results in trapping of these gaseous ligands. The structure with CO2 defines an elusive, preactivation complex that contains a metal cation Mg2+ surrounded by three H2O/OH molecules. Both structures suggest the mechanism for discriminating gaseous ligands by their quadrupole electric moments. We describe conformational changes that allow for intermittent binding of the metal ion required for activation. On the basis of these structures we propose the individual steps of the activation mechanism. Knowledge of all these elements is indispensable for engineering RuBisCO into a more efficient enzyme for crop enhancement or as a remedy to global warming. PMID:23112176

  17. Groundwater seeps in Taylor Valley Antarctica: an example of a subsurface melt event

    NASA Astrophysics Data System (ADS)

    Lyons, W. Berry; Welch, Kathleen A.; Carey, Anne E.; Doran, Peter T.; Wall, Diana H.; Virginia, Ross A.; Fountain, Andrew G.; Csathó, Bea M.; Tremper, Catherine M.

    The 2001/02 austral summer was the warmest summer on record in Taylor Valley, Antarctica, (˜78° S) since continuous records of temperature began in 1985. The highest stream-flows ever recorded in the Onyx River, Wright Valley, were also recorded that year (the record goes back to the 1969/70 austral summer). In early January 2002, a groundwater seep was observed flowing in the southwest portion of Taylor Valley. This flow has been named 'Wormherder Creek' (WHC) and represents an unusual event, probably occurring on a decadal time-scale. The physical characteristics of this feature suggest that it may have flowed at other times in the past. Other groundwater seeps, emanating from the north-facing slope of Taylor Valley, were also observed. Little work has been done previously on these very ephemeral seeps, and the source of water is unknown. These features, resembling recently described features on Mars, represent the melting of subsurface ice. The Martian features have been interpreted as groundwater seeps. In this paper we compare the chemistry of the WHC groundwater seep to that of the surrounding streams that flow every austral summer. The total dissolved solids content of WHC was ˜6 times greater than that of some nearby streams. The Na : Cl and SO4 : Cl ratios of the seep waters are higher than those of the streams, but the Mg : Cl and HCO3 : Cl ratios are lower, indicating different sources of solutes to the seeps compared to the streams. The enrichment of Na and SO4 relative to Cl may suggest significant dissolution of mirabilite within the previously unwetted soil. The proposed occurrence of abundant mirabilite in higher-elevation soils of the dry valley region agrees with geochemical models developed, but not tested, in the late 1970s. The geochemical data demonstrate that these seeps could be important in 'rinsing' the soils by dissolving and redistributing the long-term accumulation of salts, and perhaps improving habitat suitability for soil biota

  18. Using catalytic atom maps to predict the catalytic functions present in enzyme active sites.

    PubMed

    Nosrati, Geoffrey R; Houk, K N

    2012-09-18

    Catalytic atom maps (CAMs) are minimal models of enzyme active sites. The structures in the Protein Data Bank (PDB) were examined to determine if proteins with CAM-like geometries in their active sites all share the same catalytic function. We combined the CAM-based search protocol with a filter based on the weighted contact number (WCN) of the catalytic residues, a measure of the "crowdedness" of the microenvironment around a protein residue. Using this technique, a CAM based on the Ser-His-Asp catalytic triad of trypsin was able to correctly identify catalytic triads in other enzymes within 0.5 Å rmsd of the CAM with 96% accuracy. A CAM based on the Cys-Arg-(Asp/Glu) active site residues from the tyrosine phosphatase active site achieved 89% accuracy in identifying this type of catalytic functionality. Both of these CAMs were able to identify active sites across different fold types. Finally, the PDB was searched to locate proteins with catalytic functionality similar to that present in the active site of orotidine 5'-monophosphate decarboxylase (ODCase), whose mechanism is not known with certainty. A CAM, based on the conserved Lys-Asp-Lys-Asp tetrad in the ODCase active site, was used to search the PDB for enzymes with similar active sites. The ODCase active site has a geometry similar to that of Schiff base-forming Class I aldolases, with lowest aldolase rmsd to the ODCase CAM at 0.48 Å. The similarity between this CAM and the aldolase active site suggests that ODCase has the correct catalytic functionality present in its active site for the generation of a nucleophilic lysine. PMID:22909276

  19. Using Catalytic Atom Maps to Predict the Catalytic Functions Present in Enzyme Active Sites

    PubMed Central

    Nosrati, Geoffrey R.; Houk, K. N.

    2012-01-01

    Catalytic Atom Maps (CAMs) are minimal models of enzyme active sites. The structures in the Protein Data Bank (PDB) were examined to determine if proteins with CAM-like geometries in their active sites all share the same catalytic function. We combined the CAM-based search protocol with a filter based on the weighted contact number (WCN) of the catalytic residues, a measure of the “crowdedness” of the microenvironment around a protein residue. Using this technique, a CAM based on the Ser-His-Asp catalytic triad of trypsin was able to correctly identify catalytic triads in other enzymes within 0.5 Å RMSD of the Catalytic Atom Map with 96% accuracy. A CAM based on the Cys-Arg-(Asp/Glu) active site residues from the tyrosine phosphatase active site achieved 89% accuracy in identifying this type of catalytic functionality. Both of these Catalytic Atom Maps were able to identify active sites across different fold types. Finally, the PDB was searched to locate proteins with catalytic functionality similar to that present in the active site of orotidine 5′-monophosphate decarboxylase (ODCase), whose mechanism is not known with certainty. A CAM, based on the conserved Lys-Asp-Lys-Asp tetrad in the ODCase active site, was used to search the PDB for enzymes with similar active sites. The ODCase active site has a geometry similar to that of Schiff base-forming Class I aldolases, with lowest aldolase RMSD to the ODCase CAM at 0.48 Å. The similarity between this CAM and the aldolase active site suggests that ODCase has the correct catalytic functionality present in its active site for the generation of a nucleophilic lysine. PMID:22909276

  20. Larvae from deep-sea methane seeps disperse in surface waters

    PubMed Central

    Arellano, Shawn M.; Van Gaest, Ahna L.; Johnson, Shannon B.; Vrijenhoek, Robert C.; Young, Craig M.

    2014-01-01

    Many species endemic to deep-sea methane seeps have broad geographical distributions, suggesting that they produce larvae with at least episodic long-distance dispersal. Cold-seep communities on both sides of the Atlantic share species or species complexes, yet larval dispersal across the Atlantic is expected to take prohibitively long at adult depths. Here, we provide direct evidence that the long-lived larvae of two cold-seep molluscs migrate hundreds of metres above the ocean floor, allowing them to take advantage of faster surface currents that may facilitate long-distance dispersal. We collected larvae of the ubiquitous seep mussel “Bathymodiolus” childressi and an associated gastropod, Bathynerita naticoidea, using remote-control plankton nets towed in the euphotic zone of the Gulf of Mexico. The timing of collections suggested that the larvae might disperse in the water column for more than a year, where they feed and grow to more than triple their original sizes. Ontogenetic vertical migration during a long larval life suggests teleplanic dispersal, a plausible explanation for the amphi-Atlantic distribution of “B.” mauritanicus and the broad western Atlantic distribution of B. naticoidea. These are the first empirical data to demonstrate a biological mechanism that might explain the genetic similarities between eastern and western Atlantic seep fauna. PMID:24827437

  1. Comparative study of vent and seep macrofaunal communities in the Guaymas Basin

    NASA Astrophysics Data System (ADS)

    Portail, M.; Olu, K.; Escobar-Briones, E.; Caprais, J. C.; Menot, L.; Waeles, M.; Cruaud, P.; Sarradin, P. M.; Godfroy, A.; Sarrazin, J.

    2015-06-01

    Understanding the ecological processes and connectivity of chemosynthetic deep-sea ecosystems requires comparative studies. In the Guaymas Basin (Gulf of California, Mexico), the presence of seeps and vents in the absence of biogeographic barrier, comparable sedimentary settings and depths offers a unique opportunity to assess the role of ecosystem specific environmental conditions on macrofaunal communities. Six seep and four vent assemblages were studied, three of which were characterised by common major foundation taxa: vesicomyid bivalves, siboglinid tubeworms and microbial mats. Macrofaunal community structure at the family level showed that density, diversity and composition patterns were primarily shaped by seep and vent common abiotic factors including methane and hydrogen sulphide concentrations. The type of substratum and the heterogeneity provided by foundation species were identified as additional structuring factors and their roles were found to vary according to fluid regimes. Surprisingly, the presence of vent environmental specificities, with higher temperature, higher metal concentrations and lower pH was not significant in explaining community patterns. Moreover, Guaymas seep and vent shared an important number of common species suggesting frequent connections between the two ecosystems. Finally, this study provides further support for the hypothesis of continuity among deep-sea seep and vent ecosystems.

  2. Identification of Methanotrophic Biomarker Lipids in the Symbiont-Containing Gills of Seep Mussels

    NASA Technical Reports Server (NTRS)

    Jahnke, L. L.; Zahiralis, K. D.; Klein, H. P.; Morrison, David (Technical Monitor)

    1994-01-01

    Mussels collected from hydrocarbon seeps in the Gulf of Mexico grow with methane as sole carbon and energy source due to a symbiotic association with methane-oxidizing bacteria. Transmission electron micrographs of mussel gills show cells with stacked intracytoplasmic membranes similar to type I methanotrophic bacteria. Methanotrophs are known to synthesize several types of cyclic triterpenes, hopanoids and methyl sterols, as well as unique monounsaturated fatty acid, double bond positional isomers that serve as biomarkers for this group. Lipid analysis of dissected mussels demonstrated the presence of these biomarkers predominantly in the gill tissue with much smaller amounts in mantle and remaining body tissues. Gill tissue contained 1150 micrograms/g dry wt. of hopanepolyol derivatives and diplopterol while the mantle tissue contained only 17 micrograms/g. The C16 monounsaturated fatty acids (16:1) characteristic of type I methanotrophic membranes dominated the gill tissue making up 53% of the total while only 5% 16:1 was present in the mantle tissue. The methyl sterol distribution was more dispersed. The predominant sterol in all tissues was cholesterol with lesser amounts of other desmethyl and 4-methyl sterols. The gill and mantle tissues contained 3461 micrograms (17% methyl) and 2750 micrograms (5% methyl) sterol per gm dry wt., respectively. Methyl sterol accounted for 44% of the sterol esters isolated from the gill, suggesting active demethylation of the methanotrophic sterols in this tissue. The use of lipid biomarkers could provide an effective means for identifying host-symbiont relationships.

  3. Identification of Methanogens and Controls on Methane Production in Incubations of Natural Methane Seep Sediments

    NASA Astrophysics Data System (ADS)

    Kevorkian, R.; Lloyd, K. G.

    2014-12-01

    Methane, the most abundant hydrocarbon in Earth's atmosphere, is produced in large quantities in sediments underlying the world's oceans. Very little of this methane makes it to surface sediments as it is consumed by Anaerobic Methanotrophs (ANME's) in consortia with Sulfate Reducing Bacteria (SRB). Less is known about which organisms are responsible for methane production in marine sediments, and whether that production is under thermodynamic control based on hydrogen concentrations. Although ANMEs have been found to be active in methanogenic sediments and incubations, it is currently unknown whether they are able to grow in methanogenic conditions. We demonstrated with bottle incubations of methane seep sediment taken from Cape Lookout Bight, NC, that hydrogen controls methane production. While sulfate was present the hydrogen concentration was maintained at below 2 nM. Only after the depletion of sulfate allowed hydrogen concentrations to rise above 5 nM did we see production of methane. The same sediments when spiked with methane gas demonstrated its complete removal while sulfate reduction occurred. Quantitative PCR shows that ANME-2 and ANME-1 increase in 16S copy number as methane increases. Total direct cell counts demonstrate a decline in cells with the decrease of sulfate until a recovery corresponding with production of methane. Our results strongly suggest that hydrogen concentrations influence what metabolic processes can occur in marine sediments, and that ANME-1 and ANME-2 are able to grow on the energy provided from methane production.

  4. Active-Site Hydration and Water Diffusion in Cytochrome P450cam: A Highly Dynamic Process

    SciTech Connect

    Miao, Yinglong; Baudry, Jerome Y

    2011-01-01

    Long-timescale molecular dynamics simulations (300 ns) are performed on both the apo- (i.e., camphor-free) and camphor-bound cytochrome P450cam (CYP101). Water diffusion into and out of the protein active site is observed without biased sampling methods. During the course of the molecular dynamics simulation, an average of 6.4 water molecules is observed in the camphor-binding site of the apo form, compared to zero water molecules in the binding site of the substrate-bound form, in agreement with the number of water molecules observed in crystal structures of the same species. However, as many as 12 water molecules can be present at a given time in the camphor-binding region of the active site in the case of apo-P450cam, revealing a highly dynamic process for hydration of the protein active site, with water molecules exchanging rapidly with the bulk solvent. Water molecules are also found to exchange locations frequently inside the active site, preferentially clustering in regions surrounding the water molecules observed in the crystal structure. Potential-of-mean-force calculations identify thermodynamically favored trans-protein pathways for the diffusion of water molecules between the protein active site and the bulk solvent. Binding of camphor in the active site modifies the free-energy landscape of P450cam channels toward favoring the diffusion of water molecules out of the protein active site.

  5. Parameterization of an Active Thermal Erosion Site, Caribou Creek, Alaska

    NASA Astrophysics Data System (ADS)

    Busey, R.; Bolton, W. R.; Cherry, J. E.; Hinzman, L. D.

    2012-12-01

    Thermokarst features are thought to be an important mechanism for landscape change in permafrost-dominated cold regions, but few such features have been incorporated into full featured landscape models. The root of this shortcoming is that historic observations are not detailed enough to parameterize a model, and the models typically do not include the relevant processes for thermal erosion. A new, dynamic thermokarst feature has been identified at the Caribou-Poker Creek Research Watershed (CPCRW) in the boreal forest of Interior Alaska. Located adjacent to a traditional use trail, this feature terminates directly in Caribou Creek. Erosion within the feature is driven predominantly by fluvial interflow. CPCRW is a Long-Term Ecological Research site underlain by varying degrees of relatively warm, discontinuous permafrost. This poster will describe the suite of measurements that have been undertaken to parameterize the ERODE model for this site, including thorough surveys, time lapse- and aerial photography, and 3-D structure from motion algorithms.

  6. Blogs and Social Network Sites as Activity Systems: Exploring Adult Informal Learning Process through Activity Theory Framework

    ERIC Educational Resources Information Center

    Heo, Gyeong Mi; Lee, Romee

    2013-01-01

    This paper uses an Activity Theory framework to explore adult user activities and informal learning processes as reflected in their blogs and social network sites (SNS). Using the assumption that a web-based space is an activity system in which learning occurs, typical features of the components were investigated and each activity system then…

  7. Early Site Permit Demonstration Program: Recommendations for communication activities and public participation in the Early Site Permit Demonstration Program

    SciTech Connect

    Not Available

    1993-01-27

    On October 24, 1992, President Bush signed into law the National Energy Policy Act of 1992. The bill is a sweeping, comprehensive overhaul of the Nation`s energy laws, the first in more than a decade. Among other provisions, the National Energy Policy Act reforms the licensing process for new nuclear power plants by adopting a new approach developed by the US Nuclear Regulatory Commission (NRC) in 1989, and upheld in court in 1992. The NRC 10 CFR Part 52 rule is a three-step process that guarantees public participation at each step. The steps are: early site permit approval; standard design certifications; and, combined construction/operating licenses for nuclear power reactors. Licensing reform increases an organization`s ability to respond to future baseload electricity generation needs with less financial risk for ratepayers and the organization. Costly delays can be avoided because design, safety and siting issues will be resolved before a company starts to build a plant. Specifically, early site permit approval allows for site suitability and acceptability issues to be addressed prior to an organization`s commitment to build a plant. Responsibility for site-specific activities, including communications and public participation, rests with those organizations selected to try out early site approval. This plan has been prepared to assist those companies (referred to as sponsoring organizations) in planning their communications and public involvement programs. It provides research findings, information and recommendations to be used by organizations as a resource and starting point in developing their own plans.

  8. Active Site Structure and Peroxidase Activity of Oxidatively Modified Cytochrome c Species in Complexes with Cardiolipin.

    PubMed

    Capdevila, Daiana A; Oviedo Rouco, Santiago; Tomasina, Florencia; Tortora, Verónica; Demicheli, Verónica; Radi, Rafael; Murgida, Daniel H

    2015-12-29

    We report a resonance Raman and UV-vis characterization of the active site structure of oxidatively modified forms of cytochrome c (Cyt-c) free in solution and in complexes with cardiolipin (CL). The studied post-translational modifications of Cyt-c include methionine sulfoxidation and tyrosine nitration, which lead to altered heme axial ligation and increased peroxidase activity with respect to those of the wild-type protein. In spite of the structural and activity differences between the protein variants free in solution, binding to CL liposomes induces in all cases the formation of a spectroscopically identical bis-His axial coordination conformer that more efficiently promotes lipid peroxidation. The spectroscopic results indicate that the bis-His form is in equilibrium with small amounts of high-spin species, thus suggesting a labile distal His ligand as the basis for the CL-induced increase in enzymatic activity observed for all protein variants. For Cyt-c nitrated at Tyr74 and sulfoxidized at Met80, the measured apparent binding affinities for CL are ∼4 times larger than for wild-type Cyt-c. On the basis of these results, we propose that these post-translational modifications may amplify the pro-apoptotic signal of Cyt-c under oxidative stress conditions at CL concentrations lower than for the unmodified protein.

  9. Identification of ice nucleation active sites on feldspar dust particles.

    PubMed

    Zolles, Tobias; Burkart, Julia; Häusler, Thomas; Pummer, Bernhard; Hitzenberger, Regina; Grothe, Hinrich

    2015-03-19

    Mineral dusts originating from Earth's crust are known to be important atmospheric ice nuclei. In agreement with earlier studies, feldspar was found as the most active of the tested natural mineral dusts. Here we investigated in closer detail the reasons for its activity and the difference in the activity of the different feldspars. Conclusions are drawn from scanning electron microscopy, X-ray powder diffraction, infrared spectroscopy, and oil-immersion freezing experiments. K-feldspar showed by far the highest ice nucleation activity. Finally, we give a potential explanation of this effect, finding alkali-metal ions having different hydration shells and thus an influence on the ice nucleation activity of feldspar surfaces. PMID:25584435

  10. Identification of Ice Nucleation Active Sites on Feldspar Dust Particles

    PubMed Central

    2015-01-01

    Mineral dusts originating from Earth’s crust are known to be important atmospheric ice nuclei. In agreement with earlier studies, feldspar was found as the most active of the tested natural mineral dusts. Here we investigated in closer detail the reasons for its activity and the difference in the activity of the different feldspars. Conclusions are drawn from scanning electron microscopy, X-ray powder diffraction, infrared spectroscopy, and oil-immersion freezing experiments. K-feldspar showed by far the highest ice nucleation activity. Finally, we give a potential explanation of this effect, finding alkali-metal ions having different hydration shells and thus an influence on the ice nucleation activity of feldspar surfaces. PMID:25584435

  11. Stereospecific suppression of active site mutants by methylphosphonate substituted substrates reveals the stereochemical course of site-specific DNA recombination.

    PubMed

    Rowley, Paul A; Kachroo, Aashiq H; Ma, Chien-Hui; Maciaszek, Anna D; Guga, Piotr; Jayaram, Makkuni

    2015-07-13

    Tyrosine site-specific recombinases, which promote one class of biologically important phosphoryl transfer reactions in DNA, exemplify active site mechanisms for stabilizing the phosphate transition state. A highly conserved arginine duo (Arg-I; Arg-II) of the recombinase active site plays a crucial role in this function. Cre and Flp recombinase mutants lacking either arginine can be rescued by compensatory charge neutralization of the scissile phosphate via methylphosphonate (MeP) modification. The chemical chirality of MeP, in conjunction with mutant recombinases, reveals the stereochemical contributions of Arg-I and Arg-II. The SP preference of the native reaction is specified primarily by Arg-I. MeP reaction supported by Arg-II is nearly bias-free or RP-biased, depending on the Arg-I substituent. Positional conservation of the arginines does not translate into strict functional conservation. Charge reversal by glutamic acid substitution at Arg-I or Arg-II has opposite effects on Cre and Flp in MeP reactions. In Flp, the base immediately 5' to the scissile MeP strongly influences the choice between the catalytic tyrosine and water as the nucleophile for strand scission, thus between productive recombination and futile hydrolysis. The recombinase active site embodies the evolutionary optimization of interactions that not only favor the normal reaction but also proscribe antithetical side reactions. PMID:25999343

  12. Stereospecific suppression of active site mutants by methylphosphonate substituted substrates reveals the stereochemical course of site-specific DNA recombination.

    PubMed

    Rowley, Paul A; Kachroo, Aashiq H; Ma, Chien-Hui; Maciaszek, Anna D; Guga, Piotr; Jayaram, Makkuni

    2015-07-13

    Tyrosine site-specific recombinases, which promote one class of biologically important phosphoryl transfer reactions in DNA, exemplify active site mechanisms for stabilizing the phosphate transition state. A highly conserved arginine duo (Arg-I; Arg-II) of the recombinase active site plays a crucial role in this function. Cre and Flp recombinase mutants lacking either arginine can be rescued by compensatory charge neutralization of the scissile phosphate via methylphosphonate (MeP) modification. The chemical chirality of MeP, in conjunction with mutant recombinases, reveals the stereochemical contributions of Arg-I and Arg-II. The SP preference of the native reaction is specified primarily by Arg-I. MeP reaction supported by Arg-II is nearly bias-free or RP-biased, depending on the Arg-I substituent. Positional conservation of the arginines does not translate into strict functional conservation. Charge reversal by glutamic acid substitution at Arg-I or Arg-II has opposite effects on Cre and Flp in MeP reactions. In Flp, the base immediately 5' to the scissile MeP strongly influences the choice between the catalytic tyrosine and water as the nucleophile for strand scission, thus between productive recombination and futile hydrolysis. The recombinase active site embodies the evolutionary optimization of interactions that not only favor the normal reaction but also proscribe antithetical side reactions.

  13. Active site densities, oxygen activation and adsorbed reactive oxygen in alcohol activation on npAu catalysts.

    PubMed

    Wang, Lu-Cun; Friend, C M; Fushimi, Rebecca; Madix, Robert J

    2016-07-01

    The activation of molecular O2 as well as the reactivity of adsorbed oxygen species is of central importance in aerobic selective oxidation chemistry on Au-based catalysts. Herein, we address the issue of O2 activation on unsupported nanoporous gold (npAu) catalysts by applying a transient pressure technique, a temporal analysis of products (TAP) reactor, to measure the saturation coverage of atomic oxygen, its collisional dissociation probability, the activation barrier for O2 dissociation, and the facility with which adsorbed O species activate methanol, the initial step in the catalytic cycle of esterification. The results from these experiments indicate that molecular O2 dissociation is associated with surface silver, that the density of reactive sites is quite low, that adsorbed oxygen atoms do not spill over from the sites of activation onto the surrounding surface, and that methanol reacts quite facilely with the adsorbed oxygen atoms. In addition, the O species from O2 dissociation exhibits reactivity for the selective oxidation of methanol but not for CO. The TAP experiments also revealed that the surface of the npAu catalyst is saturated with adsorbed O under steady state reaction conditions, at least for the pulse reaction. PMID:27376884

  14. Circulation and exchange at the continental shelf and slope SEEP-2

    SciTech Connect

    Houghton, R.W.; Ou, Hsien-Wang.

    1991-01-01

    This project was a component of the SEEP-II program. It contributed to the instrumentation of the SEEP-II moored array to the processing and analysis of the time-series data of water temperature and currents, and to a theoretical modeling study of the circulation on the continental margin. We are responsible for nearly half of the current meters and thermistor chains that were deployed in the SEEP-II moored array on the continental margin off the Delmarva peninsula. Data tapes derived from three deployments of the instruments in this array were processed. A second component of this project was a theoretical study of the interaction of the Gulf Stream with the continental margin north of Cape Hatteras. The model shows how the topographic influence on the local vorticity balance leads to back-folding filaments of Gulf Stream water and to the Slope Sea gyre circulation.

  15. Transport and transfer rates in the waters of the continental shelf and slope: SEEP

    SciTech Connect

    Biscaye, P.E.; Anderson, R.F.

    1990-12-01

    At this writing we are in the midst of the first year of the present funding period. This period was approved as a three year grant, but, with the planned restructuring of the DOE regional programs, it will undoubtedly be less than that. With the exception of some relatively minor participation in connection with the French ECOMARGE programme and finishing of some work on SEEP-1 samples, all of our efforts in the current year have been in the preparation and analysis of samples and data obtained during the SEEP-2 field experiment in 1988--1989. We review briefly the progress on these sediment trap samples and transmissometer data at present and the status anticipated at the end of the current funding year with respect to the several kinds of analyses planned for them. We also briefly review the status of the last of the work on SEEP-1 samples and data, and of our participation in other collaborative projects. 14 refs.

  16. Possible active site of the sweet-tasting protein thaumatin.

    PubMed

    Slootstra, J W; De Geus, P; Haas, H; Verrips, C T; Meloen, R H

    1995-10-01

    Epitopes on thaumatin and monellin were studied using the PEPSCAN-technology. The antibodies used were raised against thaumatin. Only antibodies that, in an ELISA, both recognized thaumatin and monellin were used in the PEPSCAN-analyses. On thaumatin two major overlapping epitopes were identified. On monellin no epitopes could be identified. The identified epitope region on thaumatin shares structural features with various peptide and protein sweeteners. It contains an aspartame-like site which is formed by Asp21 and Phe80, tips of the two extruding loops KGDAALDAGGR19-29 and CKRFGRPP77-84, which are spatially positioned next to each other. Furthermore, sub-sequences of the KGDAALDAGGR19-29 loop are similar to peptide-sweeteners such as L-Asp-D-Ala-L-Ala-methyl ester and L-Asp-D-Ala-Gly-methyl ester. Since the aspartame-like Asp21-Phe80 site and the peptide-sweetener-like sequences are also not present in non-sweet thaumatin-like proteins it is postulated that the KGDAALDAGGR19-29- and CKRFGRPP77-84 loop contain important sweet-taste determinants. This region has previously not been implicated as a sweet-taste determinant of thaumatin.

  17. Barite encrustation of benthic sulfur-oxidizing bacteria at a marine cold seep.

    PubMed

    Stevens, E W N; Bailey, J V; Flood, B E; Jones, D S; Gilhooly, W P; Joye, S B; Teske, A; Mason, O U

    2015-11-01

    Crusts and chimneys composed of authigenic barite are found at methane seeps and hydrothermal vents that expel fluids rich in barium. Microbial processes have not previously been associated with barite precipitation in marine cold seep settings. Here, we report on the precipitation of barite on filaments of sulfide-oxidizing bacteria at a brine seep in the Gulf of Mexico. Barite-mineralized bacterial filaments in the interiors of authigenic barite crusts resemble filamentous sulfide-oxidizing bacteria of the genus Beggiatoa. Clone library and iTag amplicon sequencing of the 16S rRNA gene show that the barite crusts that host these filaments also preserve DNA of Candidatus Maribeggiatoa, as well as sulfate-reducing bacteria. Isotopic analyses show that the sulfur and oxygen isotope compositions of barite have lower δ(34)S and δ(18)O values than many other marine barite crusts, which is consistent with barite precipitation in an environment in which sulfide oxidation was occurring. Laboratory experiments employing isolates of sulfide-oxidizing bacteria from Gulf of Mexico seep sediments showed that under low sulfate conditions, such as those encountered in brine fluids, sulfate generated by sulfide-oxidizing bacteria fosters rapid barite precipitation localized on cell biomass, leading to the encrustation of bacteria in a manner reminiscent of our observations of barite-mineralized Beggiatoa in the Gulf of Mexico. The precipitation of barite directly on filaments of sulfide-oxidizing bacteria, and not on other benthic substrates, suggests that sulfide oxidation plays a role in barite formation at certain marine brine seeps where sulfide is oxidized to sulfate in contact with barium-rich fluids, either prior to, or during, the mixing of those fluids with sulfate-containing seawater in the vicinity of the sediment/water interface. As with many other geochemical interfaces that foster mineral precipitation, both biological and abiological processes likely contribute

  18. Chemical and thermal variations in seeps discharged from a burning coal refuse pile

    NASA Astrophysics Data System (ADS)

    Lopez, D. L.; Doe, C. F.; Stuart, B. J.; Stoertz, M. W.

    2002-12-01

    Acid mine drainage generated by coal refuse piles is affecting the Moxahala watershed in Southeastern Ohio. The major contributor of acidity to this watershed is the Misco refuse pile. This pile was formed during the exploitation of the Misco Mine in Perry County, Ohio, in the early 1950's. In addition to the generation of acid mine drainage, the Misco Pile is burning. There is an impounded pond on the southwest end of the west gob pile, which was created when the valley was filled with refuse. The water from this pond flows into and throughout the gob pile and discharges on the northeast end into Bennet Run. At an elevation close to the elevation of the pond, two seeps are discharged. Temperature, specific conductivity, and pH was monitored in these seeps and correlated to rainfall. A lack of response of water temperature to small rainfall events was observed. This behavior suggest channeling of water inside the pile from the source pond to the main seep, and probably evaporation effects. In comparison, during high rainfall events, transfer of heat from the burning spots to the infiltrating water occurred and an increase in seep temperature was observed. A decrease in conductivity and an increase in pH was observed during the studied period as a dilution effect produced by an increased water storage within the pond and pile. Diurnal effects were stronger in the smaller seep, probably due to lower water velocities and greater residence time at the air-pile interface. From the location of the burning spots and seeps, a water velocity of 1 to 5 feet/s (0.3 to 1.7 m/s) was estimated. The pile can be viewed as a dual-porosity system of continuous conduits and matrix porosity. Only flow with sufficient head can penetrate and transfer heat from the hot areas in the matrix.

  19. Barite encrustation of benthic sulfur-oxidizing bacteria at a marine cold seep.

    PubMed

    Stevens, E W N; Bailey, J V; Flood, B E; Jones, D S; Gilhooly, W P; Joye, S B; Teske, A; Mason, O U

    2015-11-01

    Crusts and chimneys composed of authigenic barite are found at methane seeps and hydrothermal vents that expel fluids rich in barium. Microbial processes have not previously been associated with barite precipitation in marine cold seep settings. Here, we report on the precipitation of barite on filaments of sulfide-oxidizing bacteria at a brine seep in the Gulf of Mexico. Barite-mineralized bacterial filaments in the interiors of authigenic barite crusts resemble filamentous sulfide-oxidizing bacteria of the genus Beggiatoa. Clone library and iTag amplicon sequencing of the 16S rRNA gene show that the barite crusts that host these filaments also preserve DNA of Candidatus Maribeggiatoa, as well as sulfate-reducing bacteria. Isotopic analyses show that the sulfur and oxygen isotope compositions of barite have lower δ(34)S and δ(18)O values than many other marine barite crusts, which is consistent with barite precipitation in an environment in which sulfide oxidation was occurring. Laboratory experiments employing isolates of sulfide-oxidizing bacteria from Gulf of Mexico seep sediments showed that under low sulfate conditions, such as those encountered in brine fluids, sulfate generated by sulfide-oxidizing bacteria fosters rapid barite precipitation localized on cell biomass, leading to the encrustation of bacteria in a manner reminiscent of our observations of barite-mineralized Beggiatoa in the Gulf of Mexico. The precipitation of barite directly on filaments of sulfide-oxidizing bacteria, and not on other benthic substrates, suggests that sulfide oxidation plays a role in barite formation at certain marine brine seeps where sulfide is oxidized to sulfate in contact with barium-rich fluids, either prior to, or during, the mixing of those fluids with sulfate-containing seawater in the vicinity of the sediment/water interface. As with many other geochemical interfaces that foster mineral precipitation, both biological and abiological processes likely contribute

  20. Assessment of activation products in the Savannah River Site environment

    SciTech Connect

    Carlton, W.H.; Denham, M.

    1996-07-01

    This document assesses the impact of radioactive activation products released from SRS facilities since the first reactor became operational late in 1953. The isotopes reported here are those whose release resulted in the highest dose to people living near SRS: {sup 32}P, {sup 51}Cr, {sup 60}C, and {sup 65}Zn. Release pathways, emission control features, and annual releases to the aqueous and atmospheric environments are discussed. No single incident has resulted in a major acute release of activation products to the environment. The releases were the result of normal operations of the reactors and separations facilities. Releases declined over the years as better controls were established and production was reduced. The overall radiological impact of SRS activation product atmospheric releases from 1954 through 1994 on the offsite maximally exposed individual can be characterized by a total dose of 0.76 mrem. During the same period, such an individual received a total dose of 14,400 mrem from non-SRS sources of ionizing radiation present in the environment. SRS activation product aqueous releases between 1954 and 1994 resulted in a total dose of 54 mrem to the offsite maximally exposed individual. The impact of SRS activation product releases on offsite populations also has been evaluated.

  1. Quantifying the density and utilization of active sites in non-precious metal oxygen electroreduction catalysts

    PubMed Central

    Sahraie, Nastaran Ranjbar; Kramm, Ulrike I.; Steinberg, Julian; Zhang, Yuanjian; Thomas, Arne; Reier, Tobias; Paraknowitsch, Jens-Peter; Strasser, Peter

    2015-01-01

    Carbon materials doped with transition metal and nitrogen are highly active, non-precious metal catalysts for the electrochemical conversion of molecular oxygen in fuel cells, metal air batteries, and electrolytic processes. However, accurate measurement of their intrinsic turn-over frequency and active-site density based on metal centres in bulk and surface has remained difficult to date, which has hampered a more rational catalyst design. Here we report a successful quantification of bulk and surface-based active-site density and associated turn-over frequency values of mono- and bimetallic Fe/N-doped carbons using a combination of chemisorption, desorption and 57Fe Mössbauer spectroscopy techniques. Our general approach yields an experimental descriptor for the intrinsic activity and the active-site utilization, aiding in the catalyst development process and enabling a previously unachieved level of understanding of reactivity trends owing to a deconvolution of site density and intrinsic activity. PMID:26486465

  2. Shelf edge exchange processes-II SEEP2-06, R/V Endeavor cruise 186

    SciTech Connect

    Wilson, C.; Behrens, W.J.; Flagg, C.N.; Wallace, D.W.R.; Wilke, R.J.; Wyman, K.D.

    1989-12-01

    The Shelf Edge Exchange Processes (SEEP) program sponsored by the United States Department of Energy is a multi-institutional effort designed to investigate the flux of suspended material from the continental shelf to the waters of the upper slope, and then possibly into the slope sediments. Phase I of SEEP consisted of a series of nine cruises and a mooring array across the outer continental shelf of New England during 1983--1984. Phase II focused specifically on the shelf/slope frontal region of the mid-Atlantic bight off the Delmarva Peninsula. Hydrographic data were collected on eight of the six cruises.

  3. The Importance of Chemosynthetic Communities and 'Seep-Hunting' to Deepwater Oil and Gas Exploration

    NASA Astrophysics Data System (ADS)

    McConnell, D.; Gharib, J. J.; Orange, D.; Henderson, J.; Danque, H.; Digby, A.

    2007-12-01

    Seafloor surveying techniques have often evolved as the industry's needs have evolved. Oil and gas exploration costs have escalated over the last several years, both as a result of increasing offshore overhead costs as well as the increased demand being met by offshore service-related companies. Consequently, more companies are prospecting using inexpensive techniques that rely on scientific expertise, such as seep-hunting, as a means of identifying reservoirs, and the past few years have seen several large-scale industrial deepwater surveys with locating hydrocarbon seeps as a primary goal. The identification of seeps is also a necessity for many pre-drilling operations, as many potential developers must conform to local regulations protecting chemosynthetic communities (eg MMS NTL 2000-G20 for Gulf of Mexico development). In addition to identifying chemosynthetic communities for permitting issues, as prospecting has moved into deeper water the ability to identify seep-related drilling hazards, such as hardgrounds or shallow gas (and hydrates) has also increased in importance. The specialized field of identifying seeps, and related chemosynthetics, hardgrounds, etc., is rapidly growing, aided by advances in mapping technology, such as multibeam backscatter and interferometry, among others. Today all of the geophysical data can be brought into a common interpretation environment providing multiple perspectives, different data overlays, and/or 3D visualizations. Using these techniques, high resolution multibeam and/or side-scan surveys rapidly cover large swaths of seafloor and identify potential seeps in real- time. These targets can then be examined geochemically with a coring program, potentially working simultaneously with the multibeam program. Modern USBL navigation can position a deepwater core in <10m diameter targets. Much of the geochemistry can be analyzed in near-real time at sea (eg headspace/interstitial gas, trace/minor/major ions in porefluids, etc

  4. Characterization of an Active Thermal Erosion Site, Caribou Creek, Alaska

    NASA Astrophysics Data System (ADS)

    Busey, R.; Bolton, W. R.; Cherry, J. E.; Hinzman, L. D.

    2013-12-01

    The goal of this project is to estimate volume loss of soil over time from this site, provide parameterizations on erodibility of ice rich permafrost and serve as a baseline for future landscape evolution simulations. Located in the zone of discontinuous permafrost, the interior region of Alaska (USA) is home to a large quantity of warm, unstable permafrost that is both high in ice content and has soil temperatures near the freezing point. Much of this permafrost maintains a frozen state despite the general warming air temperature trend in the region due to the presence of a thick insulating organic mat and a dense root network in the upper sub-surface of the soil column. At a rapidly evolving thermo-erosion site, located within the Caribou-Poker Creeks Research Watershed (part of the Bonanza Creek LTER) near Chatanika, Alaska (N65.140, W147.570), the protective organic layer and associated plants were disturbed by an adjacent traditional use trail and the shifting of a groundwater spring. These triggers have led to rapid geomorphological change on the landscape as the soil thaws and sediment is transported into the creek at the valley bottom. Since 2006 (approximately the time of initiation), the thermal erosion has grown to 170 meters length, 3 meters max depth, and 15 meters maximum width. This research combines several data sets: DGPS survey, imagery from an extremely low altitude pole-based remote sensing (3 to 5 meters above ground level), and imagery from an Unmanned Aerial System (UAS) at about 60m altitude.

  5. Molecular Basis for Enzymatic Sulfite Oxidation -- HOW THREE CONSERVED ACTIVE SITE RESIDUES SHAPE ENZYME ACTIVITY

    SciTech Connect

    Bailey, Susan; Rapson, Trevor; Johnson-Winters, Kayunta; Astashkin, Andrei; Enemark, John; Kappler, Ulrike

    2008-11-10

    Sulfite dehydrogenases (SDHs) catalyze the oxidation and detoxification of sulfite to sulfate, a reaction critical to all forms of life. Sulfite-oxidizing enzymes contain three conserved active site amino acids (Arg-55, His-57, and Tyr-236) that are crucial for catalytic competency. Here we have studied the kinetic and structural effects of two novel and one previously reported substitution (R55M, H57A, Y236F) in these residues on SDH catalysis. Both Arg-55 and His-57 were found to have key roles in substrate binding. An R55M substitution increased Km(sulfite)(app) by 2-3 orders of magnitude, whereas His-57 was required for maintaining a high substrate affinity at low pH when the imidazole ring is fully protonated. This effect may be mediated by interactions of His-57 with Arg-55 that stabilize the position of the Arg-55 side chain or, alternatively, may reflect changes in the protonation state of sulfite. Unlike what is seen for SDHWT and SDHY236F, the catalytic turnover rates of SDHR55M and SDHH57A are relatively insensitive to pH (~;;60 and 200 s-1, respectively). On the structural level, striking kinetic effects appeared to correlate with disorder (in SDHH57A and SDHY236F) or absence of Arg-55 (SDHR55M), suggesting that Arg-55 and the hydrogen bonding interactions it engages in are crucial for substrate binding and catalysis. The structure of SDHR55M has sulfate bound at the active site, a fact that coincides with a significant increase in the inhibitory effect of sulfate in SDHR55M. Thus, Arg-55 also appears to be involved in enabling discrimination between the substrate and product in SDH.

  6. Active Site Metal Occupancy and Cyclic Di-GMP Phosphodiesterase Activity of Thermotoga maritima HD-GYP.

    PubMed

    Miner, Kyle D; Kurtz, Donald M

    2016-02-16

    HD-GYPs make up a subclass of the metal-dependent HD phosphohydrolase superfamily and catalyze conversion of cyclic di(3',5')-guanosine monophosphate (c-di-GMP) to 5'-phosphoguanylyl-(3'→5')-guanosine (pGpG) and GMP. Until now, the only reported crystal structure of an HD-GYP that also exhibits c-di-GMP phosphodiesterase activity contains a His/carboxylate ligated triiron active site. However, other structural and phylogenetic correlations indicate that some HD-GYPs contain dimetal active sites. Here we provide evidence that an HD-GYP c-di-GMP phosphodiesterase, TM0186, from Thermotoga maritima can accommodate both di- and trimetal active sites. We show that an as-isolated iron-containing TM0186 has an oxo/carboxylato-bridged diferric site, and that the reduced (diferrous) form is necessary and sufficient to catalyze conversion of c-di-GMP to pGpG, but that conversion of pGpG to GMP requires more than two metals per active site. Similar c-di-GMP phosphodiesterase activities were obtained with divalent iron or manganese. On the basis of activity correlations with several putative metal ligand residue variants and molecular dynamics simulations, we propose that TM0186 can accommodate both di- and trimetal active sites. Our results also suggest that a Glu residue conserved in a subset of HD-GYPs is required for formation of the trimetal site and can also serve as a labile ligand to the dimetal site. Given the anaerobic growth requirement of T. maritima, we suggest that this HD-GYP can function in vivo with either divalent iron or manganese occupying di- and trimetal sites.

  7. A rapid and direct method for the determination of active site accessibility in proteins based on ESI-MS and active site titrations.

    PubMed

    O'Farrell, Norah; Kreiner, Michaela; Moore, Barry D; Parker, Marie-Claire

    2006-11-01

    We have developed an electrospray ionisation mass spectrometry (ESI-MS) technique that can be applied to rapidly determine the number of intact active sites in proteins. The methodology relies on inhibiting the protein with an active-site irreversible inhibitor and then using ESI-MS to determine the extent of inhibition. We have applied this methodology to a test system: a serine protease, subtilisin Carlsberg, and monitored the extent of inhibition by phenylmethylsulfonyl fluoride (PMSF), an irreversible serine hydrolase inhibitor as a function of the changes in immobilisation and hydration conditions. Two types of enzyme preparation were investigated, lyophilised enzymes and protein-coated microcrystals (PCMC).

  8. Cyanide does more to inhibit heme enzymes, than merely serving as an active-site ligand.

    PubMed

    Parashar, Abhinav; Venkatachalam, Avanthika; Gideon, Daniel Andrew; Manoj, Kelath Murali

    2014-12-12

    The toxicity of cyanide is hitherto attributed to its ability to bind to heme proteins' active site and thereby inhibit their activity. It is shown herein that the long-held interpretation is inadequate to explain several observations in heme-enzyme reaction systems. Generation of cyanide-based diffusible radicals in heme-enzyme reaction milieu could shunt electron transfers (by non-active site processes), and thus be detrimental to the efficiency of oxidative outcomes.

  9. Bacterial Biomass, Metabolic State, and Activity in Stream Sediments: Relation to Environmental Variables and Multiple Assay Comparisons

    PubMed Central

    Bott, T. L.; Kaplan, L. A.

    1985-01-01

    Bacterial biomass, metabolic condition, and activity were measured over a 16-month period in the surface sediments of the following four field sites with differing dissolved organic matter regimes: a woodlot spring seep, a meadow spring seep, a second-order stream, and a third-order stream. Total bacterial biomass was measured by lipid phosphate and epifluorescence microscopic counts (EMC), and viable biomass was measured by 14C most probable number, EMC with 2-(p-iodophenyl)-3-(p-nitrophenyl)-5-phenyl tetrazolium chloride reduction, and ATP. Bacterial metabolic condition was determined from the percentage of respiring cells, poly-β-hydroxybutyrate concentrations, and adenylate energy charge. Activity measures included 14C-lipid synthesis, 32P-phospholipid synthesis, the rate of uptake of algal lysate dissolved organic carbon, and respiration, from which biosynthesis was calculated (dissolved organic carbon uptake corrected for respiration). Total bacterial biomass (from EMC) ranged from 0.012 to 0.354 μg of C/mg of dry sediment and was usually lowest in the third-order stream. The percentage of cells respiring was less than 25% at all sites, indicating that most bacteria were dormant or dead. Adenylate energy charge was measured only in the third-order stream and was uniformly low. Poly-β-hydroxybutyrate concentrations were greater in the woodlot spring seep than in the second- and third-order streams. Uptake of algal lysate dissolved organic carbon ranged from undetectable levels to 166 mg of C · m−2 · h−1. Little community respiration could be attributed to algal lysate metabolism. Phospholipid synthesis ranged from 0.006 to 0.354 pmol · mg of dry sediment−1 · h−1. Phospholipid synthesis rates were used to estimate bacterial turnover at the study sites. An estimated 375 bacterial generations per year were produced in the woodlot spring seep, and 67 per year were produced in the third-order stream. PMID:16346867

  10. Bacterial biomass, metabolic state, and activity in stream sediments: relation to environmental variables and multiple assay comparisons.

    PubMed

    Bott, T L; Kaplan, L A

    1985-08-01

    Bacterial biomass, metabolic condition, and activity were measured over a 16-month period in the surface sediments of the following four field sites with differing dissolved organic matter regimes: a woodlot spring seep, a meadow spring seep, a second-order stream, and a third-order stream. Total bacterial biomass was measured by lipid phosphate and epifluorescence microscopic counts (EMC), and viable biomass was measured by C most probable number, EMC with 2-(p-iodophenyl)-3-(p-nitrophenyl)-5-phenyl tetrazolium chloride reduction, and ATP. Bacterial metabolic condition was determined from the percentage of respiring cells, poly-beta-hydroxybutyrate concentrations, and adenylate energy charge. Activity measures included C-lipid synthesis, P-phospholipid synthesis, the rate of uptake of algal lysate dissolved organic carbon, and respiration, from which biosynthesis was calculated (dissolved organic carbon uptake corrected for respiration). Total bacterial biomass (from EMC) ranged from 0.012 to 0.354 mug of C/mg of dry sediment and was usually lowest in the third-order stream. The percentage of cells respiring was less than 25% at all sites, indicating that most bacteria were dormant or dead. Adenylate energy charge was measured only in the third-order stream and was uniformly low. Poly-beta-hydroxybutyrate concentrations were greater in the woodlot spring seep than in the second- and third-order streams. Uptake of algal lysate dissolved organic carbon ranged from undetectable levels to 166 mg of C . m . h. Little community respiration could be attributed to algal lysate metabolism. Phospholipid synthesis ranged from 0.006 to 0.354 pmol . mg of dry sediment . h. Phospholipid synthesis rates were used to estimate bacterial turnover at the study sites. An estimated 375 bacterial generations per year were produced in the woodlot spring seep, and 67 per year were produced in the third-order stream.

  11. Marine Biology Field Trip Sites. Ocean Related Curriculum Activities.

    ERIC Educational Resources Information Center

    Pauls, John

    The ocean affects all of our lives. Therefore, awareness of and information about the interconnections between humans and oceans are prerequisites to making sound decisions for the future. Project ORCA (Ocean Related Curriculum Activities) has developed interdisciplinary curriculum materials designed to meet the needs of students and teachers…

  12. Endolysosomes Are the Principal Intracellular Sites of Acid Hydrolase Activity.

    PubMed

    Bright, Nicholas A; Davis, Luther J; Luzio, J Paul

    2016-09-12

    The endocytic delivery of macromolecules from the mammalian cell surface for degradation by lysosomal acid hydrolases requires traffic through early endosomes to late endosomes followed by transient (kissing) or complete fusions between late endosomes and lysosomes. Transient or complete fusion results in the formation of endolysosomes, which are hybrid organelles from which lysosomes are re-formed. We have used synthetic membrane-permeable cathepsin substrates, which liberate fluorescent reporters upon proteolytic cleavage, as well as acid phosphatase cytochemistry to identify which endocytic compartments are acid hydrolase active. We found that endolysosomes are the principal organelles in which acid hydrolase substrates are cleaved. Endolysosomes also accumulated acidotropic probes and could be distinguished from terminal storage lysosomes, which were acid hydrolase inactive and did not accumulate acidotropic probes. Using live-cell microscopy, we have demonstrated that fusion events, which form endolysosomes, precede the onset of acid hydrolase activity. By means of sucrose and invertase uptake experiments, we have also shown that acid-hydrolase-active endolysosomes and acid-hydrolase-inactive, terminal storage lysosomes exist in dynamic equilibrium. We conclude that the terminal endocytic compartment is composed of acid-hydrolase-active, acidic endolysosomes and acid hydrolase-inactive, non-acidic, terminal storage lysosomes, which are linked and function in a lysosome regeneration cycle. PMID:27498570

  13. Quantification of gas bubble emissions from submarine hydrocarbon seeps at the Makran continental margin (offshore Pakistan)

    NASA Astrophysics Data System (ADS)

    RöMer, Miriam; Sahling, Heiko; Pape, Thomas; Bohrmann, Gerhard; Spieß, Volkhard

    2012-10-01

    Evidence for twelve sites with gas bubble emissions causing hydroacoustic anomalies in 18 kHz echosounder records (`flares') was obtained at the convergent Makran continental margin. The hydroacoustic anomalies originating from hydrocarbon seeps at water depths between 575 and 2870 m disappeared after rising up to 2000 m in the water column. Dives with the remotely operated vehicle `Quest 4000 m' revealed that several individual bubble vents contributed to one hydroacoustic anomaly. Analyzed gas samples suggest that bubbles were mainly composed of methane of microbial origin. Bubble size distributions and rise velocities were determined and the volume flux was estimated by counting the emitted bubbles and using their average volume. We found that a low volume flux (Flare 1 at 575 mbsl: 90 ml/min) caused a weak hydroacoustic signal in echograms whereas high volume fluxes (Flare 2 at 1027 mbsl: 1590 ml/min; Flare 5 C at 2870 mbsl: 760 ml/min) caused strong anomalies. The total methane bubble flux in the study area was estimated by multiplying the average methane flux causing a strong hydroacoustic anomaly in the echosounder record with the total number of equivalent anomalies. An order-of-magnitude estimate further considers the temporal variability of some of the flares, assuming a constant flux over time, and allows a large range of uncertainty inherent to the method. Our results on the fate of bubbles and the order-of-magnitude estimate suggest that all of the ˜40 ± 32 × 106 mol methane emitted per year within the gas hydrate stability zone remain in the deep ocean.

  14. Outside-binding site mutations modify the active site's shapes in neuraminidase from influenza A H1N1.

    PubMed

    Tolentino-Lopez, Luis; Segura-Cabrera, Aldo; Reyes-Loyola, Paola; Zimic, Mirko; Quiliano, Miguel; Briz, Veronica; Muñoz-Fernández, Angeles; Rodríguez-Pérez, Mario; Ilizaliturri-Flores, Ian; Correa-Basurto, Jose

    2013-01-01

    The recent occurrence of 2009 influenza A (H1N1) pandemic as well as others has raised concern of a far more dangerous outcome should this virus becomes resistant to current drug therapies. The number of clinical cases that are resistant to oseltamivir (Tamiflu®) is larger than the limited number of neuraminidase (NA) mutations (H275Y, N295S, and I223R) that have been identified at the active site and that are associated to oseltamivir resistance. In this study, we have performed a comparative analysis between a set of NAs that have the most representative mutations located outside the active site. The recently crystallized NA-oseltamivir complex (PDB ID: 3NSS) was used as a wild-type structure. After selecting the target NA sequences, their three-dimensional (3D) structure was built using 3NSS as a template by homology modeling. The 3D NA models were refined by molecular dynamics (MD) simulations. The refined models were used to perform a docking study, using oseltamivir as a ligand. Furthermore, the docking results were refined by free-energy analysis using the MM-PBSA method. The analysis of the MD simulation results showed that the NA models reached convergence during the first 10 ns. Visual inspection and structural measures showed that the mutated NA active sites show structural variations. The docking and MM-PBSA results from the complexes showed different binding modes and free energy values. These results suggest that distant mutations located outside the active site of NA affect its structure and could be considered to be a new source of resistance to oseltamivir, which agrees with reports in the clinical literature.

  15. Active site proton delivery and the lyase activity of human CYP17A1

    SciTech Connect

    Khatri, Yogan; Gregory, Michael C.; Grinkova, Yelena V.; Denisov, Ilia G.; Sligar, Stephen G.

    2014-01-03

    equivalents and protons are funneled into non-productive pathways. This is similar to previous work with other P450 catalyzed hydroxylation. However, catalysis of carbon–carbon bond scission by the T306A mutant was largely unimpeded by disruption of the CYP17A1 acid-alcohol pair. The unique response of CYP17A1 lyase activity to mutation of Thr306 is consistent with a reactive intermediate formed independently of proton delivery in the active site, and supports involvement of a nucleophilic peroxo-anion rather than the traditional Compound I in catalysis.

  16. Identification of inhibitors against the potential ligandable sites in the active cholera toxin.

    PubMed

    Gangopadhyay, Aditi; Datta, Abhijit

    2015-04-01

    The active cholera toxin responsible for the massive loss of water and ions in cholera patients via its ADP ribosylation activity is a heterodimer of the A1 subunit of the bacterial holotoxin and the human cytosolic ARF6 (ADP Ribosylation Factor 6). The active toxin is a potential target for the design of inhibitors against cholera. In this study we identified the potential ligandable sites of the active cholera toxin which can serve as binding sites for drug-like molecules. By employing an energy-based approach to identify ligand binding sites, and comparison with the results of computational solvent mapping, we identified two potential ligandable sites in the active toxin which can be targeted during structure-based drug design against cholera. Based on the probe affinities of the identified ligandable regions, docking-based virtual screening was employed to identify probable inhibitors against these sites. Several indole-based alkaloids and phosphates showed strong interactions to the important residues of the ligandable region at the A1 active site. On the other hand, 26 top