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

    PubMed

    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.

  3. 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.

  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. Imaging Active and Relict Seafloor Methane Seep Sites: a Comparison of Seafloor 3D Seismic Reflectivity and Multibeam Sonar Backscatter Intensity at Omakere Ridge, Hikurangi Margin, New Zealand

    NASA Astrophysics Data System (ADS)

    Golding, T. V.; Pecher, I. A.; Crutchley, G. J.; Klaeschen, D.; Papenberg, C. A.; Bialas, J.; Greinert, J.; Townend, J.; SO214 Shipboard Scientific Party

    2011-12-01

    Omakere Ridge is an anticlinal thrust ridge in water depths of 1100-1700 m on the Hikurangi Margin, east of the North Island of New Zealand, and an area of active seafloor methane seepage associated with an extensive gas hydrate province. Methane seep sites on the Hikurangi Margin are characterised by localised build-ups of hard authigenic carbonate and chemosynthetic seep fauna that exist on a seafloor otherwise characterised by soft, muddy sediments. Previous studies have shown that these seep sites appear as areas of high backscatter in sonar images, but backscatter data alone do not provide detailed information on the present level of activity of a seep site, or the thickness of the carbonate build-up. Here we present a comparison of seafloor seismic reflectivity and multibeam sonar backscatter intensity data collected from active and relict methane seep sites on Omakere Ridge. High-resolution P-Cable 3D seismic reflection data and 12 kHz EM120 multibeam sonar data were collected in March 2011 during the RV Sonne cruise SO214. Seafloor seismic amplitude maps have been derived from the shipboard post-stack migrated data cube. A pronounced acquisition artifact is manifest in the seafloor horizon slice as high and low amplitude stripes that alternate periodically in the crossline direction. We have removed this artifact from the seafloor horizon slice using Kx-Ky filtering, followed by direct sampling and deterministic removal of the very-low-frequency components in the spatial domain. The seismic amplitude map has then been transformed into a calibrated seafloor reflection coefficient map. Sonar backscatter mosaics have been created after correcting for instrument response, angular variation in backscatter and bathymetry. Several backscatter mosaics were incorporated into a stacked mosaic over the study area to attenuate random noise. The high sonar backscatter response at the seep sites is generally accompanied by high seismic reflectivity. However, the

  6. 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.

  7. 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.

  8. 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

  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. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. Insights into the activity, formation and origin of seep systems on the seafloor in the SW Barents Sea

    NASA Astrophysics Data System (ADS)

    Mangelsdorf, Kai; Nickel, Julia C.; di Primio, Rolando; Kallmeyer, Jens; Horsfield, Brian; Stoddart, Daniel; Brunstad, Harald

    2014-05-01

    The southwestern Loppa High region, being part of the Barents Sea located in the north of Norway, is a promising area for oil and gas exploration since hydrocarbon discoveries have been made in this area in recent time. Additionally, surface features for hydrocarbon seepage, so called "cold seeps" have been detected on the seafloor, comprising extensive pockmark fields, carbonate crusts bearing areas and fault related gas flares. Leaking hydrocarbons are of specific interest since they are potential indicators for hydrocarbon reservoirs in the subsurface and the emitting hydrocarbons such as the greenhouse gas methane can have significant impact on the evolution of global warming when reaching the atmosphere. In this study cold seep systems like huge pockmark areas and carbonate crust sites from the SW Loppa High region were examined in detail, in order to determine the activity, formation and spatial distribution of the different seepage structures as well as the origin and timing of the seeping hydrocarbon fluids. The sample material comprising sediment cores from pockmarks, reference sites and carbonate crust areas as well as carbonate crust samples have been analyzed applying a combined biogeochemical and microbiological approach. In the carbonate crust area diagnostic biomarkers for the anaerobic oxidation of methane (AOM) were detected in the sediments as well as in the corresponding carbonate crusts. Their depth profiles show a distinct interval of higher concentrations, which points towards a shallow AOM zone in the investigated core. The biomarkers were also characterized by very negative carbon isotope signatures, indicating the involvement of the source microorganisms in the process of AOM. These data and active gas bubbling during sampling indicate the presence of methane at the carbonate crust site. In contrast in the pockmark areas active release of gas from the sediment could not be observed, neither in the gas measurement nor in the biogeochemical

  18. Intense gas bubble emissions in the Kerch seep area - A newly discovered high-flux seep site in the Black Sea

    NASA Astrophysics Data System (ADS)

    Römer, M.; Sahling, H.; Pape, T.; Bahr, A.; Feseker, T.; Wintersteller, P.; Bohrmann, G.

    2012-04-01

    More than 500 bubble-induced hydroacoustic anomalies (flares) were found in the water column above the seafloor in the study area comprising about 430 km2 at the Don-Kuban paleo-fan (Eastern Black Sea) by using ship mounted single beam and multibeam echosounders. Almost all flares originated from the seafloor above the gas hydrate stability zone (GHSZ), which in that region is located below ~700 m water depth. This observation confirms the sealing mechanism of gas hydrate, which impedes migration of free gas through the GHSZ and subsequent bubble emission from the seafloor. However, an intense seep site, called the "Kerch seep area" was discovered as an exception at 890 m water depth well within the GHSZ. In situ temperature measurements in shallow sediments indicate locally elevated temperatures probably caused by enhanced upward fluid flow. The base of the GHSZ in this region is generally situated at about 150 m below the seafloor. However, the local thermal anomalies result in a thinning of the gas hydrate occurrence zone to only a few meters below the seafloor and allow free gas to reach the seafloor. At sites where gas migrated into near-surface deposits, shallow gas hydrate deposits evolved and up-doming of overlying sediments led to the formation of mounds rising several meters from the surrounding seafloor. Further gas bubbles ascending from greater depth are accumulated below the gas hydrate layer at the base of the mound structures and migrate horizontally to their rims. At the mound edges gas bubbles either might form fresh gas hydrates and increase the extent of the mound structures by pushing up overlying sediments or escape at several sites into the water column. Two mounds were mapped in ultra-high resolution during dives with the autonomous underwater vehicle 'AUV MARUM SEAL 5000'. Several individual flares were detected in the Kerch seep area using hydroacoustic systems. Repeated surveys in that area conducted during three cruises within four years

  19. Impact of anaerobic oxidation of methane on the geochemical cycle of redox-sensitive elements at cold-seep sites of the northern South China Sea

    NASA Astrophysics Data System (ADS)

    Hu, Yu; Feng, Dong; Liang, Qianyong; Xia, Zhen; Chen, Linying; Chen, Duofu

    2015-12-01

    Cold hydrocarbon seepage is a frequently observed phenomenon along continental margins worldwide. However, little is known about the impact of seeping fluids on the geochemical cycle of redox-sensitive elements. Pore waters from four gravity cores (D-8, D-5, D-7, and D-F) collected from cold-seep sites of the northern South China Sea were analyzed for SO42-, Mg2+, Ca2+, Sr2+, dissolved inorganic carbon (DIC), δ13CDIC, dissolved Fe, Mn, and trace elements (e.g. Mo, U). The sulfate concentration-depth profiles, δ13CDIC values and (ΔDIC+ΔCa2++ΔMg2+)/ΔSO42- ratios suggest that organoclastic sulfate reduction (OSR) is the dominant process in D-8 core. Besides OSR, anaerobic oxidation of methane (AOM) is partially responsible for depletion of sulfate at D-5 and D-7 cores. The sulfate consumption at D-F core is predominantly caused by AOM. The depth of sulfate-methane interface (SMI) and methane diffusive flux of D-F core are calculated to be ~7 m and 0.035 mol m-2 yr-1, respectively. The relatively shallow SMI and high methane flux at D-F core suggest the activity of gas seepage in this region. The concentrations of dissolved uranium (U) were inferred to decrease significantly within the iron reduction zone. It seems that AOM has limited influence on the U geochemical cycling. In contrast, a good correlation between the consumption of sulfate and the removal of molybdenum (Mo) suggests that AOM has a significantly influence on the geochemical cycle of Mo at cold seeps. Accordingly, cold seep environments may serve as an important potential sink in the marine geochemical cycle of Mo.

  20. Authigenic Mg-calcite at a cold methane seep site in the Laptev Sea

    NASA Astrophysics Data System (ADS)

    Kravchishina, M. D.; Lein, A. Yu.; Savvichev, A. S.; Reykhard, L. E.; Dara, O. M.; Flint, M. V.

    2017-01-01

    Authigenic minerals were studied in Holocene shelf sediments of the Laptev Sea (cold methane seep site, water depth 71 m). The study presents the first finds of large hard carbonate concretions with Mg-calcite cement in recent sediments of the Arctic shelf seas. These concretions differ from previously reported glendonites and concretions from bottom sediments of the White Sea, Kara Sea, Sea of Okhotsk, etc. A study of the morphology, microstructure, and composition of these newly reported concretions revealed the multistage formation of carbonates (structural varieties of Mg-calcite and aragonite). It was shown that organic matter played an important role in the formation of authigenic carbonates, i.e., in the formation of sedimentary-diagenetic Mg-calcite. The role of methane as a possible source for authigenic carbonate formation was estimated. It was found that methane-derived Mg-calcite accounts for 17-35% of concretion materials. Mg-calcite had δ13C-Ccarb values between-24 and-23‰ and δ13C-Corg values between-44.5 and-88.5‰.

  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. Evidence of active methanogen communities in shallow sediments of the sonora margin cold seeps.

    PubMed

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

    2015-05-15

    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.

  4. 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

  5. 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.

  6. 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.

  7. 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

  8. 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

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

    PubMed

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

    2012-12-01

    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.

  10. [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.

  11. 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.

  12. 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.

  13. Active archaeal communities at cold seep sediments populated by Siboglinidae tubeworms from the Storegga Slide.

    PubMed

    Lazar, Cassandre Sara; Dinasquet, Julie; Pignet, Patricia; Prieur, Daniel; Toffin, Laurent

    2010-10-01

    Siboglinid tubeworms in cold seep sediments can locally modify the geochemical gradients of electron acceptors and donors, hence creating potential microhabitats for prokaryotic populations. The archaeal communities associated with sediments populated by Oligobrachia haakonmosbiensis and Sclerolinum contortum Siboglinid tubeworms in the Storegga Slide were examined in this study. Vertical distribution of archaeal communities was investigated using denaturing gradient gel electrophoresis based on 16S rRNA genes. The active fraction of the archaeal community was assessed by using reverse-transcribed rRNA. Archaeal communities associated with sediments colonized by tubeworms were affiliated with uncultivated archaeal lineages of the Crenarchaeota and Euryarchaeota. The composition of the active archaeal populations changed with depth indicating a reorganization of microbial communities. 16S rRNA gene libraries were dominated by sequences affiliated to the Rice Cluster V which are unusual in marine sediment samples. Moreover, this study provides the first evidence of living Crenarchaeota of the Rice Cluster V in cold seep sediments. Furthermore, the Storegga Slide sediments harbored a high diversity of other minor groups of uncultivated lineages including Terrestrial Miscellaneous Euryarchaeotal Group, Marine Benthic Group (MBG)-D, MBG-E, Deep-Sea Hydrothermal Vent Euryarchaeotal Group, Lake Dagow Sediment, Val Kotinen Lake clade III, and Sippenauer Moor 1. Thus, we hypothesize that the vertical geochemical imprint created by the tubeworms could support broad active archaeal populations in the Siboglinidae-populated Storegga Slide sediments.

  14. Spatial Structure and Activity of Sedimentary Microbial Communities Underlying a Beggiatoa spp. Mat in a Gulf of Mexico Hydrocarbon Seep

    PubMed Central

    Lloyd, Karen G.; Albert, Daniel B.; Biddle, Jennifer F.; Chanton, Jeffrey P.; Pizarro, Oscar; Teske, Andreas

    2010-01-01

    Background Subsurface fluids from deep-sea hydrocarbon seeps undergo methane- and sulfur-cycling microbial transformations near the sediment surface. Hydrocarbon seep habitats are naturally patchy, with a mosaic of active seep sediments and non-seep sediments. Microbial community shifts and changing activity patterns on small spatial scales from seep to non-seep sediment remain to be examined in a comprehensive habitat study. Methodology/Principal Findings We conducted a transect of biogeochemical measurements and gene expression related to methane- and sulfur-cycling at different sediment depths across a broad Beggiatoa spp. mat at Mississippi Canyon 118 (MC118) in the Gulf of Mexico. High process rates within the mat (∼400 cm and ∼10 cm from the mat's edge) contrasted with sharply diminished activity at ∼50 cm outside the mat, as shown by sulfate and methane concentration profiles, radiotracer rates of sulfate reduction and methane oxidation, and stable carbon isotopes. Likewise, 16S ribosomal rRNA, dsrAB (dissimilatory sulfite reductase) and mcrA (methyl coenzyme M reductase) mRNA transcripts of sulfate-reducing bacteria (Desulfobacteraceae and Desulfobulbaceae) and methane-cycling archaea (ANME-1 and ANME-2) were prevalent at the sediment surface under the mat and at its edge. Outside the mat at the surface, 16S rRNA sequences indicated mostly aerobes commonly found in seawater. The seep-related communities persisted at 12–20 cm depth inside and outside the mat. 16S rRNA transcripts and V6-tags reveal that bacterial and archaeal diversity underneath the mat are similar to each other, in contrast to oxic or microoxic habitats that have higher bacterial diversity. Conclusions/Significance The visual patchiness of microbial mats reflects sharp discontinuities in microbial community structure and activity over sub-meter spatial scales; these discontinuities have to be taken into account in geochemical and microbiological inventories of seep environments. In

  15. Morphology of Florida escarpment chemosynthetic brine seep community sites: deep-tow, seabeam, and GLORIA surveys

    SciTech Connect

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

    1988-02-01

    The Florida Escarpment near 26/degree/N was surveyed with Deep-Tow, 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/degree/ from 2200 to more than 3250 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-plain 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. Basal talus is uncommon because the abyssal floor is part of the distal Mississippi fan which is rapidly burying the escarpment. However, where talus occurs, it is in tongues of angular megabreccia of meter- and larger-sized blocks which indicate periodic catastrophic collapse. Sidescan images reveal bands of contrast in the reflective texture of the sea floor that extends 10-20 m from the base along more than 10% of the surveyed area. Photographic surveys show that these areas are associated with communities of abundant organisms. 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.

  16. Assessing submarine gas hydrate at active seeps on the Hikurangi Margin, New Zealand, using controlled source electromagnetic data with constraints from seismic, geochemistry, and heatflow data

    NASA Astrophysics Data System (ADS)

    Schwalenberg, K.; Haeckel, M.; Pecher, I. A.; Toulmin, S. J.; Hamdan, L. J.; Netzeband, G.; Wood, W.; Poort, J.; Jegen, M. D.; Coffin, R. B.

    2009-12-01

    Electrical resistivity is one of the key properties useful for evaluating submarine gas hydrate deposits. Gas hydrates are electrically insulating in contrast to the conductive pore fluid. Where they form in sufficient quantities the bulk resistivity of the sub-seafloor is elevated. CSEM data were collected in 2007 as part of the German - International “New Vents” project on R/V Sonne, cruise SO191, at three target areas on the Hikurangi subduction margin, New Zealand. The margin is characterized by widespread bottom simulating reflectors (BSR), seep structures, and active methane and fluid venting indicating the potential for gas hydrate formation. Opouawe Bank is one of the ridge and basin systems on the accretionary wedge and is located off the Wairarapa coast at water depths of 1000-1100 m. The first observed seep sites (North Tower, South Tower, Pukeko, Takahe, and Tui) were identified from individual gas flares in hydro-acoustic data and video observations during voyages on R/V Tangaroa. Seismic reflection data collected during SO191 subsequently identified more than 25 new seep structures. Two intersecting CSEM profiles have been surveyed across North Tower, South Tower, and Takahe. 1-D inversion of the data reveals anomalously high resistivities at North Tower and South Tower, moderately elevated resistivities at Takahe, and normal background resistivities away from the seeps. The high resistivities are attributed to gas hydrate layers at intermediate depths beneath the seeps. At South Tower the hydrate concentration could be possibly as much as 25% of the total sediment volume within a 50m thick layer. This conforms with geochemical pore water analyses which show a trend of increased methane flux towards South Tower. At Takahe, gas pockets and patchy gas hydrate, as well as sediment heterogeneities and carbonates, or temperature driven upward fluid flow indicated by the observed higher heat flow at this site may explain the resistivity pattern

  17. 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.

  18. 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, ...

  19. Importance of seep primary production to Lophelia pertusa and associated fauna in the Gulf of Mexico

    NASA Astrophysics Data System (ADS)

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

    2009-05-01

    To investigate the importance of seep primary production to the nutrition of Lophelia pertusa and associated communities and examine local trophic interactions, we analyzed stable carbon, nitrogen, and sulfur compositions in seven quantitative L. pertusa community collections. A significant seep signature was only detected in one of the 35 species tested ( Provanna sculpta, a common seep gastropod) despite the presence of seep fauna at the three sample sites. A potential predator of L. pertusa was identified ( Coralliophila sp.), and a variety of other trophic interactions among the fauna occupying the coral framework were suggested by the data, including the galatheid crab Munidopsis sp. 2 feeding upon hydroids and the polychaete Eunice sp. feeding upon the sabellid polychaete Euratella sp. Stable carbon abundances were also determined for different sections of L. pertusa skeleton representing different stages in the growth and life of the aggregation. There was no temporal trend detected in the skeleton isotope values, suggesting that L. pertusa settles in these areas only after seepage has largely subsided. Isotope values of individual taxa that were collected from both L. pertusa and vestimentiferan habitats showed decreasing reliance upon seep primary production with average age of the vestimentiferan aggregation, and finally, no seep signature was detected in the coral collections. Together our data suggest that it is the presence of authigenic carbonate substrata, a product of past seep microbial activity, as well as hydrodynamic processes that drive L. pertusa occurrence at seep sites in the Gulf of Mexico, not nutritional dependence upon primary production by seep microbes.

  20. 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

  1. Sources of fluids and gases expelled at cold seeps offshore Georgia, eastern Black Sea

    NASA Astrophysics Data System (ADS)

    Reitz, Anja; Pape, Thomas; Haeckel, Matthias; Schmidt, Mark; Berner, Ulrich; Scholz, Florian; Liebetrau, Volker; Aloisi, Giovanni; Weise, Stephan M.; Wallmann, Klaus

    2011-06-01

    Four seep sites located within an ˜20 km 2 area offshore Georgia (Batumi seep area, Pechori Mound, Iberia Mound, and Colkheti Seep) show characteristic differences with respect to element concentrations, and oxygen, hydrogen, strontium, and chlorine isotope signatures in pore waters, as well as impregnation of sediments with petroleum and hydrocarbon potential. All seep sites have active gas seepage, near surface authigenic carbonates and gas hydrates. Cokheti Seep, Iberia Mound, and Pechori Mound are characterized by oil-stained sediments and gas seepage decoupled from deep fluid advection and bottom water intrusion induced by gas bubble release. Pechori Mound is further characterized by deep fluid advection of lower salinity pore fluids. The Pechori Mound pore fluids are altered by mineral/water reactions at elevated temperatures (between 60 and 110 °C) indicated by heavier oxygen and lighter chlorine isotope values, distinct Li and B enrichment, and K depletion. Strontium isotope ratios indicate that fluids originate from late Oligocene strata. This finding is supported by the occurrence of hydrocarbon impregnations within the sediments. Furthermore, light hydrocarbons and high molecular weight impregnates indicate a predominant thermogenic origin for the gas and oil at Pechori Mound, Iberia Mound, and Colkheti Seep. C 15+ hydrocarbons at the oil seeps are allochtonous, whereas those at the Batumi seep area are autochthonous. The presence of oleanane, an angiosperm biomarker, suggests that the hydrocarbon source rocks belong to the Maikopian Formation. In summary, all investigated seep sites show a high hydrocarbon potential and hydrocarbons of Iberia Mound, Colkheti Seep, and Pechori Mound are predominantly of thermogenic origin. However, only at the latter seep site advection of deep pore fluids is indicated.

  2. 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

  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. Transpressional segment boundaries in strike-slip fault systems offshore southern California: Implications for fluid expulsion and cold seep habitats

    NASA Astrophysics Data System (ADS)

    Maloney, Jillian M.; Grupe, Benjamin M.; Pasulka, Alexis L.; Dawson, Katherine S.; Case, David H.; Frieder, Christina A.; Levin, Lisa A.; Driscoll, Neal W.

    2015-05-01

    The importance of tectonics and fluid flow in controlling cold seep habitats has long been appreciated at convergent margins but remains poorly understood in strike-slip systems. Here we present geophysical, geochemical, and biological data from an active methane seep offshore from Del Mar, California, in the inner California borderlands (ICB). The location of this seep appears controlled by localized transpression associated with a step in the San Diego Trough fault zone and provides an opportunity to examine the interplay between fluid expulsion and restraining step overs along strike-slip fault systems. These segment boundaries may have important controls on seep locations in the ICB and other margins characterized by strike-slip faulting (e.g., Greece, Sea of Marmara, and Caribbean). The strike-slip fault systems offshore southern California appear to have a limited distribution of seep sites compared to a wider distribution at convergent plate boundaries, which may influence seep habitat diversity and connectivity.

  5. 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.

  6. 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.

  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. 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.

  10. 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.

  11. Methane fates in the benthos and water column at cold seep sites along the continental margin of Central and North America

    NASA Astrophysics Data System (ADS)

    Hansman, Roberta L.; Thurber, Andrew R.; Levin, Lisa A.; Aluwihare, Lihini I.

    2017-02-01

    The potential influence of methane seeps on carbon cycling is a key question for global assessments, but the study of carbon cycling in surface sediments and the water column of cold seep environments is complicated by the high temporal and spatial variability of fluid and gas fluxes at these sites. In this study we directly examined carbon sources supporting benthic and planktonic food webs at venting methane seeps using isotopic and molecular approaches that integrate this variability. At four seep environments located along North and Central America, microorganisms from two size fractions were collected over several days from 2800 to 9050 l of seawater to provide a time-integrated measure of key microbial groups and the carbon sources supporting the overall planktonic microbial community. In addition to water column measurements, the extent of seafloor methane release was estimated at two of the sites by examining the stable carbon isotopic signature (δ13C) of benthic metazoan infauna. This signature reveals carbon sources fueling the base of the food chain and thus provides a metric that represents a time-integrated view of the dominant microbial processes within the sediment. The stable carbon isotopic composition of microbial DNA (δ13C-DNA), which had values between -17.0 and -19.5‰, indicated that bulk planktonic microbial production was not ultimately linked to methane or other 13C-depleted seep-derived carbon sources. Instead these data support the importance of organic carbon derived from either photo- or chemoautotrophic CO2 fixation to the planktonic food web. Results of qPCR of microbial DNA sequences coding for a subunit of the particulate methane monooxygenase gene (pmoA) showed that only a small percentage of the planktonic microbial community were potential methane oxidizers possessing pmoA (<5% of 16S rRNA gene copies). There was an overall decrease of 13C-depleted carbon fueling the benthic metazoan community from 3 to 5 cm below the seafloor

  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.

  13. Biogeochemical signatures and microbial activity of different cold-seep habitats along the Gulf of Mexico deep slope

    NASA Astrophysics Data System (ADS)

    Joye, Samantha B.; Bowles, Marshall W.; Samarkin, Vladimir A.; Hunter, Kimberley S.; Niemann, Helge

    2010-11-01

    Microorganisms and the processes they mediate serve as the metabolic foundation of cold seeps. We characterized a suite of biogeochemical constituents and quantified rates of two key microbial processes, Sulfate Reduction (SR) and Anaerobic Oxidation of Methane (AOM), to assess variability between habitats at water depths exceeding 1000 m in the northern Gulf of Mexico. Rates of SR were highest in sediments beneath microbial mats, lower in brine-influenced and oil-influenced sediments, and lowest in animal habitats. Sediments collected near tubeworms had the highest SR rates for animal habitats. Rates of AOM generally were low, but higher rates were associated with brine-influenced, oil-influenced, tubeworm- and urchin-inhabited sediments. Rates of both SR and AOM were orders of magnitude lower at deep-slope sites compared to upper-slope sites examined previously. As observed at upper-slope sites, SR and AOM rates were often loosely coupled. At one site, AOM rates exceeded SR rates, suggesting that an alternate electron acceptor for AOM is possible. Extremely depleted δ13C values in methane illustrated the broad significance of biogenic methane production at deep-slope sites. Brine-influenced habitats were characterized by extremely high concentrations of ammonium and dissolved organic carbon, serving as important focused sources of these chemicals to adjacent environments.

  14. 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.

  15. Patterns of subsurface fluid-flow at cold seeps: the Hikurangi Margin, offshore New Zealand

    NASA Astrophysics Data System (ADS)

    Krabbenhoeft, A.; Bialas, J.; Klaucke, I.; Crutchley, G. J.; Papenberg, C. A.; Netzeband, G. L.

    2012-12-01

    Based on multichannel seismic, geoacoustic, and methane sensor data, four different areas along the Hikurangi Margin show multiple indications for seep activity including bright spots, transparent zones, vertical chimneys, and the occurrence and distribution of bottom simulating reflectors. Locations where these features reach the seafloor are characterised by high backscatter intensity on sidescan sonar images and transparent zones in sediment echosounder profiles, while methane sensors show episodic, elevated methane concentrations near the seep sites. Methane discharge is facilitated by reduced hydrostatic pressure during low tides. The greatest number of seeps at Opouawe Bank correlates with the highest methane activity along the Hikurangi Margin. High heat flow values on flanks of ridges and low heat flow values on anticlines reflect a topographic effect on subsurface temperatures. Elevated heat flow occurs in the vicinity of seeps on Opouawe Bank. We propose that there are two drivers behind methane seepage with respect to the migration pathways of methane through the gas hydrate stability zone (GHSZ) to the seafloor: (1) structurally controlled and (2) stratigraphically controlled. In the structural model, vertical chimneys are the major pathways for methane through the GHSZ. Part of the upwardly migrating methane forms gas hydrate within the chimney. In the stratigraphic model, methane migration is stratigraphically controlled beneath seeps that are located on bathymetric highs and/or where subsurface anticlines occur beneath seeps. The structurally controlled seeps produce higher methane escape at the seafloor than those that are stratigraphically controlled. A combination of both driving mechanisms results in the highest methane seepage rates at the Tui Seep on Opouawe Bank.

  16. 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.

  17. Comparison of the microbial diversity in cold-seep sediments from different depths in the Nankai Trough.

    PubMed

    Arakawa, Shizuka; Sato, Takako; Yoshida, Yasuhiko; Usami, Ron; Kato, Chiaki

    2006-02-01

    We have investigated the molecular phylogeny of cold-seep sediments obtained from the Nankai Trough, at depths of about 600, 2,000, and 3,300 m, and compared the microbial diversity profiles of those sediments samples. The gamma-Proteobacteria that might function as sulfide oxidizers and the symbiotically related delta-Proteobacteria which might function as sulfate reducers were identified amongst the bacteria from all depths of the sediments. However, anoxic methane oxidizing archaea (ANME) and methanogens were only found in the 600 m deep sediments. These results indicated that the cold-seep microbial sulfur circulation system could be functioning in the shallow seep sediment at a depth of 600 m and the microbial activities at these sites might be more dynamic than at other deeper cold-seep sites.

  18. A biogeographic network reveals evolutionary links between deep-sea hydrothermal vent and methane seep faunas.

    PubMed

    Kiel, Steffen

    2016-12-14

    Deep-sea hydrothermal vents and methane seeps are inhabited by members of the same higher taxa but share few species, thus scientists have long sought habitats or regions of intermediate character that would facilitate connectivity among these habitats. Here, a network analysis of 79 vent, seep, and whale-fall communities with 121 genus-level taxa identified sedimented vents as a main intermediate link between the two types of ecosystems. Sedimented vents share hot, metal-rich fluids with mid-ocean ridge-type vents and soft sediment with seeps. Such sites are common along the active continental margins of the Pacific Ocean, facilitating connectivity among vent/seep faunas in this region. By contrast, sedimented vents are rare in the Atlantic Ocean, offering an explanation for the greater distinction between its vent and seep faunas compared with those of the Pacific Ocean. The distribution of subduction zones and associated back-arc basins, where sedimented vents are common, likely plays a major role in the evolutionary and biogeographic connectivity of vent and seep faunas. The hypothesis that decaying whale carcasses are dispersal stepping stones linking these environments is not supported.

  19. Sidescan backscatter variations of cold seeps on the Hikurangi Margin (New Zealand): indications for different stages in seep development

    NASA Astrophysics Data System (ADS)

    Dumke, Ines; Klaucke, Ingo; Berndt, Christian; Bialas, Jörg

    2014-06-01

    Cold seeps on the Hikurangi Margin off New Zealand exhibit various seabed morphologies producing different intensity patterns in sidescan backscatter images. Acoustic backscatter characteristics of 25 investigated seep sites fall into four distinct types characterised by variations in backscatter intensity, distribution and inferred structural heights. The types reflect different carbonate morphologies including up to 20-m-high structures (type 1), low-relief crusts (type 2), scattered blocks (type 3) and carbonate-free sites (type 4). Each seep corresponds to a single type; intermediates were not observed. This correlates well with published data on seep fauna at each site, with the four types representing three different faunal habitats of successive stages of seep development. Backscatter signatures in sidescan sonar images of cold seeps may therefore serve as a convenient proxy for variations in faunal habitats.

  20. 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.

  1. 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).

  2. 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.

  3. 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

  4. 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

  5. List 9 - Active CERCLIS Sites:

    EPA Pesticide Factsheets

    The List 9 displays the sequence of activities undertaken at active CERCLIS sites. An active site is one at which site assessment, removal, remedial, enforcement, cost recovery, or oversight activities are being planned or conducted.

  6. Sidescan sonar imagery of widespread fossil and active cold seeps along the central Chilean continental margin

    NASA Astrophysics Data System (ADS)

    Klaucke, Ingo; Weinrebe, Wilhelm; Linke, Peter; Kläschen, Dirk; Bialas, Jörg

    2012-12-01

    The central Chilean subduction zone between 35°S and 37°S was investigated in order to identify, document and possibly understand fluid flow and fluid venting within the forearc region. Several areas were mapped using multibeam bathymetry and backscatter, high-resolution sidescan sonar, chirp subbottom profiling and reflection seismic data. On a subsequent cruise ground-truthing observations were made using a video sled. In general, this dataset shows surprisingly little evidence of fluid venting along the mid-slope region, in contrast to other subduction zones such as Central America and New Zealand. There were abundant indications of active and predominantly fossil fluid venting along the upper slope between 36.5°S and 36.8°S at the seaward margin of an intraslope basin. Here, backscatter anomalies suggest widespread authigenic carbonate deposits, likely the result of methane-rich fluid expulsion. There is unpublished evidence that these fluids are of biogenic origin and generated within the slope sediments, similar to other accretionary margins but in contrast to the erosional margin off Central America, where fluids have geochemical signals indicating an origin from the subducting plate.

  7. 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.

  8. 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

  9. Authigenic carbonates from an active cold seep of the northern South China Sea: New insights into fluid sources and past seepage activity

    NASA Astrophysics Data System (ADS)

    Feng, Dong; Chen, Duofu

    2015-12-01

    Site F (also named Formosa ridge) represents the most vigorous cold seep on the northern South China Sea continental slope. In order to constrain the fluid sources and intensities of seepage, we investigated the petrography, mineralogy, stable carbon and oxygen isotopic compositions, element geochemistry and radiocarbon dating of authigenic carbonate rocks retrieved from the seafloor. Carbonate rocks mainly occurred as crusts, nodules, and nodular masses incorporated in carbonate breccias. The carbonates were comprised mainly of high-Mg calcite and aragonite. The δ13C of authigenic carbonate varied from -55.3‰ to -34.3‰ (mean: -48.5‰; n=47) vs. V-PDB, suggesting biogenic methane is the dominant carbon source fuelling the system. The δ18OCarbonate values were from +3.6‰ to +4.8‰ (mean: +3.9‰; n=47). The observed 18O-enrichement in relation to calculated equilibrium values in the carbonates probably reflects dissolution of gas hydrates. Combination of seafloor observations and the obtained AMS 14C ages suggest that (1) initiation of methane seepage from at least 10.6 ka ago; (2) environmental conditions may have been favorable for enhanced fluid seepage around 6 ka BP and (3) relatively low intensity of seepage from 2 ka BP till today.

  10. Cold seep status archived in authigenic carbonates: Mineralogical and isotopic evidence from Northern South China Sea

    NASA Astrophysics Data System (ADS)

    Lu, Yang; Sun, Xiaoming; Lin, Zhiyong; Xu, Li; Gong, Junli; Lu, Hongfeng

    2015-12-01

    Cold-seep carbonates are precipitated under high alkalinity conditions created by the anaerobic oxidation of methane in cold-seep sites. Multiple Ca-Mg-carbonate phases are identified, including aragonite, low-Mg calcite (LMC), high-Mg calcite (HMC), protodolomite, and dolomite. These phases result from different conditions that are related with cold-seep activities. Here, we report on the relationship between the Ca-Mg-carbonate phases and the cold-seep status. Authigenic carbonates were sampled from northern slope of South China Sea. Carbon isotopic compositions of samples from Shenhu area are lower than -40‰, indicating methane-derived carbon. The δ13C values of samples from Southwest (SW) Taiwan area range from ~-30‰ to ~-20‰, which is the result of the mixture of methane carbon and seawater carbon. Carbonate phases were identified according to the composition and structure results. Samples from Shenhu area are composed of protodolomite and HMC. Three zones were discovered from the center to the rim of the cross-section of the tube-like sample from SW Taiwan area. From the external to the internal zones, the carbonate phases are HMC; LMC and protodolomite; HMC, respectively. The intensity of superstructure reflections of the protodolomite from Shenhu area is stronger than that from SW Taiwan area, indicating higher MgCO3 content. Based on the formation conditions of Ca-Mg-carbonates from LMC to dolomite, those with higher MgCO3 content are formed in more active cold-seep environment. According to the distribution of carbonate phases in each sample, the cold seep flux was high in Shenhu area and was sustained for a long time. By contrast, the flux in SW Taiwan area was relatively low and not stable. It once became higher, but finally returned to low.

  11. 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.

  12. 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

  13. 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.

  14. 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

    2015-12-03

    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

  15. 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

  16. 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.

  17. Efficiency and adaptability of the benthic methane filter at Quepos Slide cold seeps, offshore Costa Rica

    NASA Astrophysics Data System (ADS)

    Steeb, P.; Krause, S.; Linke, P.; Hensen, C.; Dale, A. W.; Nuzzo, M.; Treude, T.

    2014-11-01

    Large amounts of methane are delivered by fluids through the erosive forearc of the convergent margin offshore Costa Rica and lead to the formation of cold seeps at the sediment surface. Besides mud extrusion, numerous cold seeps are created by landslides induced by seamount subduction or fluid migration along major faults. Most of the dissolved methane reaching the seafloor at cold seeps is oxidized within the benthic microbial methane filter by anaerobic oxidation of methane (AOM). Measurements of AOM and sulfate reduction as well as numerical modeling of porewater profiles revealed a highly active and efficient benthic methane filter at Quepos Slide site; a landslide on the continental slope between the Nicoya and Osa Peninsula. Integrated areal rates of AOM ranged from 12.9 ± 6.0 to 45.2 ± 11.5 mmol m-2 d-1, with only 1 to 2.5% of the upward methane flux being released into the water column. Additionally, two parallel sediment cores from Quepos Slide were used for in vitro experiments in a recently developed Sediment-F low-Through (SLOT) system to simulate an increased fluid and methane flux from the bottom of the sediment core. The benthic methane filter revealed a high adaptability whereby the methane oxidation efficiency responded to the increased fluid flow within 150-170 days. To our knowledge, this study provides the first estimation of the natural biogeochemical response of seep sediments to changes in fluid flow.

  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. Management of dryland saline seeps

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Discussed is the identification, diagnosis, control, and reclamation of dryland saline seep problems as found in the North American Great Plains. Saline seeps develop because of geologic stratifications within the soil profile and insufficient use of precipitation by crops used in dryland farming s...

  20. First records of Lithodes longispina Sakai, 1971 (Crustacea: Decapoda: Anomura: Lithodidae) from southwestern Taiwan, including a site in the vicinity of a cold seep.

    PubMed

    Wang, Teng-Wei; Ahyong, Shane T; Chan, Tin-Yam

    2016-01-14

    Lithodid crabs (Lithodidae Samouelle, 1819), commonly known as king crabs, are frequent targets of commercial fishing worldwide with most of them living in deep water (Sakai 1971; Ahyong et al. 2010). Lithodes Latreille, 1806, is the second largest genus of lithodid crabs, currently including 29 species worldwide (Ahyong 2010). In Taiwanese waters, however, only two species, L. turritus Ortmann, 1892, and L. formosae Ahyong & Chan, 2010, have been reported (Wu et al. 1998; Ahyong & Chan 2010; Ahyong et al. 2010). We report herein the discovery of L. longispina Sakai, 1971, previously known reliably only from Japan (Sakai 1971; Ikeda 1998; Ahyong 2010), from off southwestern Taiwan, including a specimen collected in the vicinity of a cold seep.

  1. 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

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

    PubMed

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

    2015-06-01

    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.

  3. 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

  4. 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

  5. Hydrocarbon Seeps Formations: a Study Using 3-D Seismic Attributes in Combination with Satellite Data

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

    Analyzing the magnitude of oil discharges from natural hydrocarbon seeps is important in improving our understanding of carbon contribution as oil migrates from deeper sediments to the water column, and then eventually to the atmosphere. Liquid hydrocarbon seepage in the deep water of the Gulf of Mexico (GOM) is associated with deep cutting faults, associated with vertical salt movement, that provide conduits for the upward migration of oil and gas. Seeps transform surface geology and generate prominent geophysical targets that can be identified on 3-D seismic data as seafloor amplitude anomalies maps that correlate with the underlying deep fault systems. Using 3D seismic data, detailed mapping of the northern GOM has identified more than 21,000 geophysical anomalies across the basin. In addition to seismic data, Synthetic Aperture Radar (SAR) images have proven to be a reliable tool for localizing natural seepage of oil. We used a Texture Classifier Neural Network Algorithm (TCNNA) to process more than 1200 SAR images collected over the GOM. We quantified more than 900 individual seep formations distributed along the continental shelf and in deep water. Comparison of the geophysical anomalies with the SAR oil slick targets shows good general agreement between the distributions of the two indicators. However, there are far fewer active oil slicks than geophysical anomalies, most of which are probably associated with gas seepage. By examining several sites where the location of active venting can be determined by submersibles observations, we found that the active oily vents are often spatially offset from the most intense geophysical targets (i.e. GC600, GC767, GC204, etc). In addition to the displacement of the oil by deep sea currents, we propose that during the 100K years of activity, the location of the vents on the seafloor probably migrate as carbonate cementation reduces the permeability of the upper sediment. Many of the geophysical targets may represent

  6. 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

  7. Identification of members of the metabolically active microbial populations associated with Beggiatoa species mat communities from Gulf of Mexico cold-seep sediments.

    PubMed

    Mills, Heath J; Martinez, Robert J; Story, Sandra; Sobecky, Patricia A

    2004-09-01

    In this study, the composition of the metabolically active fraction of the microbial community occurring in Gulf of Mexico marine sediments (water depth, 550 to 575 m) with overlying filamentous bacterial mats was determined. The mats were mainly composed of either orange- or white-pigmented Beggiatoa spp. Complementary 16S ribosomal DNA (crDNA) was obtained from rRNA extracted from three different sediment depths (0 to 2, 6 to 8, and 10 to 12 cm) that had been subjected to reverse transcription-PCR amplification. Domain-specific 16S PCR primers were used to construct 12 different 16S crDNA libraries containing 333 Archaea and 329 Bacteria clones. Analysis of the Archaea clones indicated that all sediment depths associated with overlying orange- and white-pigmented microbial mats were almost exclusively dominated by ANME-2 (95% of total Archaea clones), a lineage related to the methanogenic order Methanosarcinales. In contrast, bacterial diversity was considerably higher, with the dominant phylotype varying by sediment depth. An equivalent number of clones detected at 0 to 2 cm, representing a total of 93%, were related to the gamma and delta classes of Proteobacteria, whereas clones related to delta-Proteobacteria dominated the metabolically active fraction of the bacterial community occurring at 6 to 8 cm (79%) and 10 to 12 cm (85%). This is the first phylogenetics-based evaluation of the presumptive metabolically active fraction of the Bacteria and Archaea community structure investigated along a sediment depth profile in the northern Gulf of Mexico, a hydrocarbon-rich cold-seep region.

  8. Macro-ecology of Gulf of Mexico cold seeps.

    PubMed

    Cordes, Erik E; Bergquist, Derk C; Fisher, Charles R

    2009-01-01

    Shortly after the discovery of chemosynthetic ecosystems at deep-sea hydrothermal vents, similar ecosystems were found at cold seeps in the Gulf of Mexico. Over the past two decades, these sites have become model systems for understanding the physiology of the symbiont-containing megafauna and the ecology of seep communities worldwide. Symbiont-containing bi-valves and siboglinid polychaetes dominate the communities, including five bathymodiolin mussel species and six vestimentiferan (siboglinid polychaete) species in the Gulf of Mexico. The mussels include the first described examples of methanotrophic symbiosis and dual methanotrophic/thiotrophic symbiosis. Studies with the vestimentiferans have demonstrated their potential for extreme longevity and their ability to use posterior structures for subsurface exchange of dissolved metabolites. Ecological investigations have demonstrated that the vestimentiferans function as ecosystem engineers and identified a community succession sequence from a specialized high-biomass endemic community to a low-biomass community of background fauna over the life of a hydrocarbon seep site.

  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. 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

  11. 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

  12. Petrology of a Jurassic cold seep carbonate mound, Great Valley Group, northern California

    SciTech Connect

    Campbell, K.A.; Bottjer, D.J. . Dept. of Geological Sciences)

    1992-01-01

    Ancient sites of chemosynthetic marine invertebrate communities have been increasingly described from the stratigraphic record. Fossil cold seeps are best identified by the stratigraphically restricted co-occurrence of anomalous carbonates and fossils of organisms that in modern environments are chemosymbiotic. A Late Jurassic (Tithonian) age fossil seep site is preserved in deep-water turbidites of the Stony Creek Formation (Great Valley Group). Two low-relief carbonate mounds contain an abundant and diverse fossil macrofauna including taxa whose modern counterparts are chemosymbiotic, as well as several associate taxa. Two broad carbonate fabric types are present: a bioturbated, peloidal, fossiliferous micrite with abundant flecks of organic matter and several wavy laminated marine cements. The micrite and cements are either irregularly interlayered on distinctly separated by corrosion surfaces coated with iron oxides that may mark pulses of H[sub 2]S-rich fluids to the seep. Petrographic observations indicate the following idealized paragenetic sequence: deposition of micrite, with contemporaneous biotic activity; corrosion event, with preferential preservation of some peloids; precipitation of pyrite on some corrosion surfaces and concentration of insoluble siltstone linings where corrosion has opened vugs; precipitation of blocky yellow calcite cement with organic-rich inclusions in void spaces and around peloids; growth of clear to gray, botryoidal to fibrous cement; and precipitation of late, clear calcite spar. Similar fabrics and abundant tube-like structures are present in another Great Valley carbonate lens of Early Cretaceous (Albian-Aptian) age exposed on the Cold Fork of Cottonwood Creek near Red Bluff, California. Detailed integration of petrological studies of these fabrics with stable isotope studies and fossil faunal distributions provide a powerful approach for understanding the history of development and individual fossil seeps.

  13. Turbine tent measurements of marine hydrocarbon seeps on subhourly timescales

    NASA Astrophysics Data System (ADS)

    Leifer, Ira; Boles, Jim

    2005-01-01

    Three turbine seep-tents simultaneously measured marine seep gas fluxes with high time resolution (0.2 s) at multiple locations. Tents were inverted polyvinyl cones, 2-m diameter, 1-m tall, and weighted on their lower skirt edges. Rising gas bubbles induce vertical fluid motions, which were measured by laboratory-calibrated turbines in chimneys on top of the tents. Initial deployment was at an active seep area in the Coal Oil Point seep field, in the Santa Barbara Channel, California. The three tents simultaneously collected data for continuous time periods of 2 hours in both the morning and afternoon. Seabed temperature and pressure were acquired every 3 s over the same time periods as the flux measurements from a conductivity temperature depth, CTD, mounted on one tent. Results strongly suggest that oceanic swell had a significant forcing effect on the flux at a subhourly timescale. There was an inverse relationship between effect of swell height on the flux and flux. Swells from 1 to 4 m height and periodicities of 7 and 12 s caused variations of ˜1% to 4% from the average flux. Proposed mechanisms to explain the observations are diffusion with surrounding sediments, termed gas charging, swell induced changes in fracture size, termed fracture forcing, and swell induced vent activation/deactivation, termed pore activation. On the basis of the seep frequency response, we propose pore activation was dominant.

  14. Efficiency and adaptability of the benthic methane filter at Quepos Slide cold seeps, offshore of Costa Rica

    NASA Astrophysics Data System (ADS)

    Steeb, P.; Krause, S.; Linke, P.; Hensen, C.; Dale, A. W.; Nuzzo, M.; Treude, T.

    2015-11-01

    Large amounts of methane are delivered by fluids through the erosive forearc of the convergent margin offshore of Costa Rica and lead to the formation of cold seeps at the sediment surface. Besides mud extrusion, numerous cold seeps are created by landslides induced by seamount subduction or fluid migration along major faults. Most of the dissolved methane migrating through the sediments of cold seeps is oxidized within the benthic microbial methane filter by anaerobic oxidation of methane (AOM). Measurements of AOM and sulfate reduction as well as numerical modeling of porewater profiles revealed a highly active and efficient benthic methane filter at the Quepos Slide site, a landslide on the continental slope between the Nicoya and Osa Peninsula. Integrated areal rates of AOM ranged from 12.9 ± 6.0 to 45.2 ± 11.5 mmol m-2 d-1, with only 1 to 2.5 % of the upward methane flux being released into the water column. Additionally, two parallel sediment cores from Quepos Slide were used for in vitro experiments in a recently developed sediment-flow-through (SLOT) system to simulate an increased fluid and methane flux from the bottom of the sediment core. The benthic methane filter revealed a high adaptability whereby the methane oxidation efficiency responded to the increased fluid flow within ca. 170 d. To our knowledge, this study provides the first estimation of the natural biogeochemical response of seep sediments to changes in fluid flow.

  15. Application of Satellite SAR for Discovery and Quantification of Natural Marine Oil Seeps

    NASA Astrophysics Data System (ADS)

    Amos, J.; Lai, R.; Zimmer, B.; Leiva, A.; MacDonald, I.

    2006-12-01

    Natural marine oil seeps discharge gassy drops from the seafloor. Oil drops and gas bubbles reach the surface from water depths as great as 3000m. The oil spreads rapidly, forming an invisible layer that drifts down-wind and down-current in long, linear streaks called slicks. Oil slicks are visible in SAR data because the surfactant dampens capillary waves and reduces backscatter. Application of SAR as an exploration tool in energy prospecting is well-established. We have applied this technique for discovering the chemosynthetic communities that colonize the seafloor in the vicinity of deep-water seeps on the continental margin of the Gulf of Mexico. The management goal for this effort is to prevent harmful impact to these communities resulting from exploration or production activities. The scientific goals are to delineate the zoogeography of the chemosynthetic fauna, which is widespread on continental margins, and to establish study sites where their life history can be investigated. In the course of an ongoing, multidisciplinary study in the spring and summer of 2006, we explored 20 possible sites where SAR and geophysical data indicated seeps might occur. SAR was only partly diagnostic: all sites with SAR-detected slicks were found to have biologic communities, but communities were also found at geophysical anomalies that did not produce slicks. We acquired over 60 RADARSAT SAR images from the northern Gulf of Mexico in cooperation with the Alaska Satellite Facility. The ship RV ATLANTIS was at sea during the acquisition and collected synoptic weather and oceanographic data. To automate interpretation of large image dataset we have employed texture recognition with use of a library of textons applied iteratively to the images. This treatment shows promise in distinguishing floating oil from false targets generated by rain fronts and other phenomena. One goal of the analysis is to delineate bounding boxes to quantify the ocean area covered by the thin oil layer

  16. 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

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

    PubMed

    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 (13)C-depleted isotopic signatures of dissolved inorganic carbon. The anaerobic conversion of methane to CO(2) was confirmed in a (13)C-labeling experiment. Methane fueled a vital microbial community with cell numbers of up to 4 × 10(9) 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.

  18. 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

  19. 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...

  20. 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

  1. 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.

  2. 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.

  3. Recognition of Fossil Prokaryotes in Cretaceous Methane Seep Carbonates: Relevance to Astrobiology

    NASA Astrophysics Data System (ADS)

    Shapiro, Russell Scott

    2004-12-01

    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 µm in diameter and 1-1.5 µm long), sheaths (2-4 µm in diameter), coccoids (0.5-1 µm in diameter, up to 40 per cluster), and the presence of framboidal pyrite (6-8 µm 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. Astrobiology 4, 438-449.

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. 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

  9. Anaerobic oxidation of methane in hypersaline cold seep sediments.

    PubMed

    Maignien, Loïs; Parkes, R John; Cragg, Barry; Niemann, Helge; Knittel, Katrin; Coulon, Stephanie; Akhmetzhanov, Andrey; Boon, Nico

    2013-01-01

    Life in hypersaline environments is typically limited by bioenergetic constraints. Microbial activity at the thermodynamic edge, such as the anaerobic oxidation of methane (AOM) coupled to sulphate reduction (SR), is thus unlikely to thrive in these environments. In this study, carbon and sulphur cycling was investigated in the extremely hypersaline cold seep sediments of Mercator mud volcano. AOM activity was partially inhibited but still present at salinity levels of 292 g L(-1) (c. eightfold sea water concentration) with rates of 2.3 nmol cm(-3) day(-1) and was even detectable under saturated conditions. Methane and evaporite-derived sulphate comigrated in the ascending geofluids, which, in combination with a partial activity inhibition, resulted in AOM activity being spread over unusually wide depth intervals. Up to 79% of total cells in the AOM zone were identified by fluorescence in situ hybridization (FISH) as anaerobic methanotrophs of the ANME-1. Most ANME-1 cells formed monospecific chains without any attached partner. At all sites, AOM activity co-occurred with SR activity and sometimes significantly exceeded it. Possible causes of these unexpected results are discussed. This study demonstrates that in spite of a very low energy yield of AOM, microorganisms carrying this reaction can thrive in salinity up to halite saturation.

  10. 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

  11. 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.

  12. A kinetic model for the methane hydrate precipitated from venting gas at cold seep sites at Hydrate Ridge, Cascadia margin, Oregon

    NASA Astrophysics Data System (ADS)

    Cao, Yuncheng; Chen, Duofu; Cathles, Lawrence M.

    2013-09-01

    develop a kinetic model for hydrate crystallization from methane gas venting through shallow sediments at Hydrate Ridge on the Cascadia margin of Oregon that predicts how pore water chlorinity, temperature, and crystallized hydrate evolve after the onset of steady venting. Predictions are compared to observations at Ocean Drilling Program Site 1249. In the preferred model, calculated gas hydrate saturation and chloride concentrations reach those observed at depths less than 20 m below seafloor (bsf) under the southern summit of Hydrate Ridge in ~650 years, and the vertical water flux must be less than 50 kg/m2/yr. Hydrate accumulates more slowly between 20 m bsf and the base of the hydrate stability zone where there is no free gas, accumulating to observed levels of a few volume percent of hydrate in 105 to 106 years, depending on the water flux that is assumed through this zone. This dichotomy means that the presently observed gas venting must have been diverted to this area ~650 years ago, or be episodic and infrequent. If the gas venting for the last 650 years has been as observed today, the latent heat of hydrate precipitation in the upper 20 m of sediments would have caused the temperature to increase ~0.8°C at ~20 m bsf and ~0.2°C at ~100 m bsf. This would have caused a ~5 m rise in the elevation of the base of hydrate stability zone, and decreased the rate of hydrate crystallization from 1.5 kg CH4/m2/yr 650 years ago to 0.7 kg CH4/m2/yr today.

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. 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

  18. 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.

  19. Thermal Imagery of Groundwater Seeps: Possibilities and Limitations.

    PubMed

    Mundy, Erin; Gleeson, Tom; Roberts, Mark; Baraer, Michel; McKenzie, Jeffrey M

    2017-03-01

    Quantifying groundwater flow at seepage faces is crucial because seepage faces influence the hydroecology and water budgets of watersheds, lakes, rivers and oceans, and because measuring groundwater fluxes directly in aquifers is extremely difficult. Seepage faces provide a direct and measurable groundwater flux but there is no existing method to quantitatively image groundwater processes at this boundary. Our objective is to determine the possibilities and limitations of thermal imagery in quantifying groundwater discharge from discrete seeps. We developed a conceptual model of temperature below discrete seeps, observed 20 seeps spectacularly exposed in three dimensions at an unused limestone quarry and conducted field experiments to examine the role of diurnal changes and rock face heterogeneity on thermal imagery. The conceptual model suggests that convective air-water heat exchange driven by temperature differences is the dominant heat transfer mechanism. Thermal imagery is effective at locating and characterizing the flux of groundwater seeps. Areas of active groundwater flow and ice growth can be identified from thermal images in the winter, and seepage rates can be differentiated in the summer. However, the application of thermal imagery is limited by diverse factors including technical issues of image acquisition, diurnal changes in radiation and temperature, and rock face heterogeneity. Groundwater discharge rates could not be directly quantified from thermal imagery using our observations but our conceptual model and experiments suggest that thermal imagery could quantify groundwater discharge when there are large temperature differences, simple cliff faces, non-freezing conditions, and no solar radiation.

  20. 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.

  1. Automated Characterization and Quantification of Hydrocarbon Seeps Based on Frontal Illuminated Video Observations

    NASA Astrophysics Data System (ADS)

    Boelmann, J.; Zielinski, O.

    2015-04-01

    Hydrocarbon releases, either natural or due to anthropogenic activities, are of major relevance for the marine environment. In this work we specify our approach to quantify these seeps by subsea imaging utilizing camera systems and frontal illumination setups on board remotely operated vehicles. This work showcases, based on a campaign in the region west of Svalbard, improved methodological guidelines for the seep quantification operation together with a novel automated post-mission evaluation. The comparison of automated quantification with manual information extraction illustrates the efficiency of this new method while processing comparable estimates of seep characteristics.

  2. Normal Modes Expose Active Sites in Enzymes

    PubMed Central

    Glantz-Gashai, Yitav; Samson, Abraham O.

    2016-01-01

    Accurate prediction of active sites is an important tool in bioinformatics. Here we present an improved structure based technique to expose active sites that is based on large changes of solvent accessibility accompanying normal mode dynamics. The technique which detects EXPOsure of active SITes through normal modEs is named EXPOSITE. The technique is trained using a small 133 enzyme dataset and tested using a large 845 enzyme dataset, both with known active site residues. EXPOSITE is also tested in a benchmark protein ligand dataset (PLD) comprising 48 proteins with and without bound ligands. EXPOSITE is shown to successfully locate the active site in most instances, and is found to be more accurate than other structure-based techniques. Interestingly, in several instances, the active site does not correspond to the largest pocket. EXPOSITE is advantageous due to its high precision and paves the way for structure based prediction of active site in enzymes. PMID:28002427

  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.

    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

  4. Microbial characterization of a subzero, hypersaline methane seep in the Canadian High Arctic.

    PubMed

    Niederberger, Thomas D; Perreault, Nancy N; Tille, Stephanie; Lollar, Barbara Sherwood; Lacrampe-Couloume, Georges; Andersen, Dale; Greer, Charles W; Pollard, Wayne; Whyte, Lyle G

    2010-10-01

    We report the first microbiological characterization of a terrestrial methane seep in a cryo-environment in the form of an Arctic hypersaline (∼24% salinity), subzero (-5 °C), perennial spring, arising through thick permafrost in an area with an average annual air temperature of -15 °C. Bacterial and archaeal 16S rRNA gene clone libraries indicated a relatively low diversity of phylotypes within the spring sediment (Shannon index values of 1.65 and 1.39, respectively). Bacterial phylotypes were related to microorganisms such as Loktanella, Gillisia, Halomonas and Marinobacter spp. previously recovered from cold, saline habitats. A proportion of the bacterial phylotypes were cultured, including Marinobacter and Halomonas, with all isolates capable of growth at the in situ temperature (-5 °C). Archaeal phylotypes were related to signatures from hypersaline deep-sea methane-seep sediments and were dominated by the anaerobic methane group 1a (ANME-1a) clade of anaerobic methane oxidizing archaea. CARD-FISH analyses indicated that cells within the spring sediment consisted of ∼84.0% bacterial and 3.8% archaeal cells with ANME-1 cells accounting for most of the archaeal cells. The major gas discharging from the spring was methane (∼50%) with the low CH(4)/C(2+) ratio and hydrogen and carbon isotope signatures consistent with a thermogenic origin of the methane. Overall, this hypersaline, subzero environment supports a viable microbial community capable of activity at in situ temperature and where methane may behave as an energy and carbon source for sustaining anaerobic oxidation of methane-based microbial metabolism. This site also provides a model of how a methane seep can form in a cryo-environment as well as a mechanism for the hypothesized Martian methane plumes.

  5. 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.

  6. Stimulated Emission of Energetic Particles (SEEP).

    DTIC Science & Technology

    1987-11-30

    a.... W W w w w w w I I li IJr Ir % i "f J2 I l AD-A 188 724 MLMSCD068456 For Period Ending 30 September 1987 CD Contract N00014-79-C4824 0 IC FILE...CLASSIFICATION 0 -UNCLASSIFIED/UNLIMITED [ SAME AS RPT C:" DTIC USERS UNCLASSIFIED 22a NAME OF RESPONSIBLE INDIVIDUAL 22b TELEPHONE (Include Area Code) 22c O...34---" ,. LMSC/D068456 . 0 SEEP FINAL REPORT I. OBJECTIVES OF THE SEEP PROGRAM The SEEP (Stimulated Emission of Energetic Particles) program had important

  7. 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.

  8. 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.

  9. Imaging Hydrological Processes in Headwater Riparian Seeps with Time-Lapse Electrical Resistivity.

    PubMed

    Williams, Mark R; Buda, Anthony R; Singha, Kamini; Folmar, Gordon J; Elliott, Herschel A; Schmidt, John P

    2017-01-01

    Delineating hydrologic and pedogenic factors influencing groundwater flow in riparian zones is central in understanding pathways of water and nutrient transport. In this study, we combined two-dimensional time-lapse electrical resistivity imaging (ERI) (depth of investigation approximately 2 m) with hydrometric monitoring to examine hydrological processes in the riparian area of FD-36, a small (0.4 km(2) ) agricultural headwater basin in the Valley and Ridge region of east-central Pennsylvania. We selected two contrasting study sites, including a seep with groundwater discharge and an adjacent area lacking such seepage. Both sites were underlain by a fragipan at 0.6 m. We then monitored changes in electrical resistivity, shallow groundwater, and nitrate-N concentrations as a series of storms transitioned the landscape from dry to wet conditions. Time-lapse ERI revealed different resistivity patterns between seep and non-seep areas during the study period. Notably, the seep displayed strong resistivity reductions (∼60%) along a vertically aligned region of the soil profile, which coincided with strong upward hydraulic gradients recorded in a grid of nested piezometers (0.2- and 0.6-m depth). These patterns suggested a hydraulic connection between the seep and the nitrate-rich shallow groundwater system below the fragipan, which enabled groundwater and associated nitrate-N to discharge through the fragipan to the surface. In contrast, time-lapse ERI indicated no such connections in the non-seep area, with infiltrated rainwater presumably perched above the fragipan. Results highlight the value of pairing time-lapse ERI with hydrometric and water quality monitoring to illuminate possible groundwater and nutrient flow pathways to seeps in headwater riparian areas.

  10. 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

  11. 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.

  12. Validated ligand mapping of ACE active site

    NASA Astrophysics Data System (ADS)

    Kuster, Daniel J.; Marshall, Garland R.

    2005-08-01

    Crystal structures of angiotensin-converting enzyme (ACE) complexed with three inhibitors (lisinopril, captopril, enalapril) provided experimental data for testing the validity of a prior active site model predicting the bound conformation of the inhibitors. The ACE active site model - predicted over 18 years ago using a series of potent ACE inhibitors of diverse chemical structure - was recreated using published data and commercial software. Comparison between the predicted structures of the three inhibitors bound to the active site of ACE and those determined experimentally yielded root mean square deviation (RMSD) values of 0.43-0.81 Å, among the distances defining the active site map. The bound conformations of the chemically relevant atoms were accurately deduced from the geometry of ligands, applying the assumption that the geometry of the active site groups responsible for binding and catalysis of amide hydrolysis was constrained. The mapping of bound inhibitors at the ACE active site was validated for known experimental compounds, so that the constrained conformational search methodology may be applied with confidence when no experimentally determined structure of the enzyme yet exists, but potent, diverse inhibitors are available.

  13. 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

  14. 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

  15. Advances in Optical Characterization of Methane Seeps and Bubble Plumes

    NASA Astrophysics Data System (ADS)

    Pizarro, O.; Farr, N.; Camilli, R.; Whelan, J.; Martens, C.; Goudreau, J.; Mendlovitz, H.; Camilli, L.

    2005-12-01

    Methane seeps are potentially a key contributor to the atmospheric methane reservoir and to the global greenhouse gas budget. Improved estimates of methane flux from ocean floor seeps are required to understand the magnitude and characteristics of this potential source. At less active, deep water seeps a large portion of the migrating gas is dissolved and oxidized before reaching the surface. However, in high-intensity, shallow water methane seeps the bubble density, speed and size are such that a significant fraction of the gas may reach the atmosphere. New types of in-situ chemical sensors are now available to quickly and reliably quantify dissolved methane throughout the water column. However, quantifying methane within the water column in the free gas phase (i.e., in bubbles) remains a challenging problem. Current approaches rely either on indirect acoustic methods or direct collection of bubbles. Acoustic methods have the disadvantage of requiring extensive calibration, and can fail to distinguish the bubble signal from other sources of acoustic noise. Gas-capture techniques are mechanically complex, have a surface expression that introduces some noise, and can potentially alias episodic events. In both cases the fine scale structure such as heterogeneity of the rising bubbling plume is lost. We describe a vision-based system to characterize bubble plumes and the seep features from which they emanate. Video-rate optical imagery from 3 cameras is used to generate precise measurements of the motion of bubbles. Lighting is provided by a distributed array of LED modules synchronized to the cameras. In order to conserve power and extend deployment times the system can be configured to be dormant until triggered by chemical sensors indicating high concentrations of methane. Plume characterization is based on the identification of the individual bubbles (and rejection of other particles). Additional image processing steps are then used to estimate each bubble

  16. 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.

  17. 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.

  18. 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.

  19. Paleo-environmental controls on cold seep carbonate authigenesis in the Sea of Marmara

    NASA Astrophysics Data System (ADS)

    Crémière, Antoine; Bayon, Germain; Ponzevera, Emmanuel; Pierre, Catherine

    2013-08-01

    studied sites (average 9.4±1.8 ka, n=16) and the regional anoxic sapropel event support the idea that the drop in bottom water dissolved oxygen content was probably a key factor to enhance microbial activity and associated carbonate precipitation at that time. Overall, these results provide straightforward evidence that fluid emission dynamics and hydrocarbon oxidation at cold seeps can be directly related to changing environmental conditions through time.

  20. 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.

  1. 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.

  2. 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

  3. 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

  4. A Peek at Fluid Flow in Monterey bay Cold Seeps Using Peepers

    NASA Astrophysics Data System (ADS)

    Plant, J. N.; Wheat, C. G.; Jannasch, H.

    2001-12-01

    The egress of pore water from the oceanic crust along plate boundaries includes pore water and bound volatiles from sediment as well as seawater that have interacted with basement rock. The chemical composition of these fluids is governed by complex water-rock interactions that are also a function of temperature and pressure. Several such sites of fluid seepage were located in Monterey Bay (USA), which has active strike-slip faulting and evidence for compression in the northern portion of the bay. Fluid and chemical fluxes were determined from these seeps to provide insights to the mechanisms for fluid release and the chemical conditions under which this fluid was altered. Systematic variations in pore water chemical and thermal data provide a measure of the composition of the fluid at depth, an estimate of the speed of upwelling, and an assessment of chemical reactions that alter the fluid as it ascends to the seafloor. Pore water chemical data, which were collected from in-situ extractors ("peepers") that provide for a contamination-free sample, and thermal data indicate maximum upwelling speeds of 1-5 cm/yr at most seeps, with the exception of Extrovert Cliff where upwelling speeds are as high as hundreds of m/yr. These fluids are the most altered fluids in the bay (units mmol/kg: S 12; SO4 0; Ca 16.4; Mg 28.4; K 6.0; Sr 0.35; Li 0.038; Alk 15; Cl 560). Elucidating environmental conditions under which fluids from each of the sites formed may ultimately permit us to constrain some of the variables controlling tectonic phenomena in Monterey Bay and along plate margins in general.

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. Seeps regulate stream nitrate concentration in a forested Appalachian catchment.

    PubMed

    O'Driscoll, Michael A; DeWalle, David R

    2010-01-01

    Surface seeps can be defined as locations where upwelling ground water saturates the surface for most of the year and excess ground water can be delivered to the stream channel via surface flowpaths. If a stream is predominantly fed by seeps, then ground water added to the stream via these surface flowpaths may result in reduced interactions with the subsurface riparian zone. It is generally believed that seep ground water that upwells and then flows along surface flowpaths can be subject to diminished denitrification and biologic uptake processes. Seep effects on stream nitrate (NO(3)) concentration were studied in Baldwin Creek (5.35 km(2)), southwestern Pennsylvania. Nitrate retention within seep zones was evaluated over a 1-yr period (May 2002-2003) using a monthly, nested (top and bottom of seep) sampling approach along 15 individual seeps. Seep samples were analyzed for NO(3)-N, NH(3)-N, and dissolved organic carbon, along with stream waters and streamflow measurements at seven stream stations. Seeps were generally NO(3) sinks with concentrations decreasing downseep: 31% median annual reduction and 73% maximum monthly reduction. During cold and wet periods, seeps frequently behaved as NO(3) sources to the stream (NO(3) concentrations increased or remained constant downseep). Seep temperature and discharge were related to seasonal variability in seep NO(3) retention. Seasonal variations in stream NO(3) concentration have been attributed to upland soil and vegetation processes in numerous watersheds. At Baldwin Creek, seep NO(3) processing regulated the seasonal variability of stream NO(3) concentrations. These results suggest that seeps provide important water quality functions and can modulate the effects of elevated regional N deposition in Appalachian catchments.

  10. Circulation and exchange at the continental shelf and slope, SEEP-II

    SciTech Connect

    Houghton, R.W.; Ou, Hsien-Wang.

    1990-01-01

    This project is a component of the SEEP-2 program to study shelf-slope exchange in the southern Middle Atlantic bight (MBA). It represents the physical oceanographic portion of the SEEP-2 research at Lamont-Doherty Geological Observatory (L-DGO). Since the work consists of two parts: data analysis and theoretical modeling, this report will be divided into two parts to describe the progress of each activity. It covers work performed during the time interval March to December 1990 and is a sequel to the report submitted in February 1990. 25 figs.

  11. 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

  12. Corrosion Research And Web Site Activities

    NASA Technical Reports Server (NTRS)

    Heidersbach, Robert H.

    2001-01-01

    This report covers corrosion-related activities at the NASA Kennedy Space Center during the summer of 2000. The NASA Kennedy Space Center's corrosion web site, corrosion.ksc.nasa.gov, was updated with new information based on feedback over the past two years. The methodology for a two-year atmospheric exposure testing program to study the effectiveness of commercial chemicals sold for rinsing aircraft and other equipment was developed and some preliminary laboratory chemical analyses are presented.

  13. Corrosion Research and Web Site Activities

    NASA Technical Reports Server (NTRS)

    Heidersbach, Robert H.

    2002-01-01

    This report covers corrosion-related activities at the NASA Kennedy Space Center during the summer of 2000. The NASA Kennedy Space Center's corrosion web site, corrosion.ksc.nasa.gov, was updated with new information based on feedback over the past two years. The methodology for a two-year atmospheric exposure testing program to study the effectiveness of commercial chemicals sold for rinsing aircraft and other equipment was developed and some preliminary laboratory chemical analyses are presented.

  14. 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

    2014-01-08

    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.

  15. 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.

  16. 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.

  17. More than three thousand years of microbial methane consumption at cold seeps offshore Svalbard

    NASA Astrophysics Data System (ADS)

    Steinle, Lea; Vögtli, Irina; Liebetrau, Volker; Krause, Stefan; Treude, Tina; Lehmann, Moritz; Niemann, Helge

    2014-05-01

    Microbial consumption retains a significant fraction of methane in marine sediments. Under anoxic conditions, the anaerobic oxidation of methane (AOM) is mediated by archaea with sulfate as the terminal electron acceptor, whereas the aerobic oxidation of methane (MOx) is mediated by bacteria. MOx is typically less important in marine systems because oxygen availability in sediments is very low and methane is consumed in deeper sediments through AOM. At cold seeps, however, the methane flux can be high enough to bypass the AOM filter so that methane and oxygen overlap in surface sediments. The role of MOx thus becomes more significant at highly active cold seeps. To further test this hypothesis, and the applicability of MOx-signatures as a tracer for paleo seep activity, we investigated lipid biomarkers of methanotrophic communities in modern sediments and compared them to fossilised lipids in more than 3000 years old authigenic carbonate accretions. Sediments and carbonates were recovered in the direct vicinity of bubble release sites at cold seeps offshore Svalbard, systems that have been active for at least 3000 years (Berndt et al., 2014). Samples were recovered with the submersible JAGO during an expedition with R/V M.S. Merian (MSM 21/4) in 2012. The composition of lipid biomarkers and their associated stable carbon isotope signatures provide evidence for distinctly different methanotrophic communities in modern sediments and the old carbonates. In deeper sediments, where AOM rate measurements were maximal (~500 nmol ml-1 d-1 at ~5 cm sediment depth), the dominance of the 13C-depleted archaeal biomarker archaeol and the absence of sn2-hydroxyarchaeol and crocetane point to an AOM community dominated by ANME1-archaea. At the surface of the sediment core, we found 13C-depleted 4α-methylsteroids and diploptene, lipid biomarkers originating from MOx communities. The biomarker profiles are consistent with our visual observations. During sampling, methane bubbles

  18. Mercury concentrations, speciation, and isotopic composition in sediment from a cold seep in the northern Gulf of Mexico.

    PubMed

    Brown, Garry; Sleeper, Kenneth; Johnson, Marcus W; Blum, Joel D; Cizdziel, James V

    2013-12-15

    Total-Hg, monomethylmercury (MMHg), and mercury isotopic composition was determined in sediment from a cold seep and background sites in the northern Gulf of Mexico (nGoM). Total-Hg averaged 50 ng/g (n=28), ranged from 31 to 67 ng/g, and decreased with depth (0-15 cm). MMHg averaged 0.91 ng/g (n=18), and ranged from 0.2 to 1.9 ng/g. There was no significant difference for total-Hg or MMHg between cold seep and background sites. δ(202)Hg ranged from -0.5 to -0.8‰ and becomes more negative with depth (r=0.989). Mass independent fractionation (Δ(199)Hg) was small but consistently positive (0.04-0.12‰); there was no difference between cold seeps (Δ(199)Hg = +0.09±0.03; n=7, 1SD) and background sites (Δ(199)Hg=+0.07±0.02; n=5, 1SD). This suggests that releases of hydrocarbons at the cold seep do not significantly alter Hg levels, and that cold seeps are likely not major sources of MMHg to nGoM waters.

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

    PubMed Central

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

    2014-01-01

    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. PMID:25246590

  20. Landsat detection of oil from natural seeps

    USGS Publications Warehouse

    Deutsch, M.; Estes, J.E.

    1980-01-01

    Oil on the ocean surface from the natural seeps in the Santa Barbara Channel, California, could not be detected on frames of any of the four bands of standard Landsat positive or negative film transparencies, nor could the slicks be detected using digital scaling, density slicing, or ratioing techniques. Digital contrast-stretch enhancement, however, showed the distribution of oil on the surface. - from Authors

  1. 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...

  2. 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.

  3. 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.

  4. Deep-sea methane seep sediments in the Okhotsk Sea sustain diverse and abundant anammox bacteria.

    PubMed

    Shao, Sudong; Luan, Xiwu; Dang, Hongyue; Zhou, Haixia; Zhao, Yakun; Liu, Haitao; Zhang, Yunbo; Dai, Lingqing; Ye, Ying; Klotz, Martin G

    2014-02-01

    Marginal sea methane seep sediments sustain highly productive chemosynthetic ecosystems and are hotspots of intense biogeochemical cycling. Rich methane supply stimulates rapid microbial consumption of oxygen; these systems are thus usually hypoxic to anoxic. This and reported evidence for resident nitrogen fixation suggest the presence of an anaerobic ammonium-oxidizing (anammox) bacterial community in methane seep sediments. To test this hypothesis, we employed detection of genes encoding 16S rRNA gene and hydrazine dehydrogenase (hzo) to investigate the structure, abundance and distribution of the anammox bacterial community in the methane seep sediments of the Okhotsk Sea. Diverse complements of Candidatus Scalindua-related 16S rRNA and hzo gene sequences were obtained. Most of the deep-sea sites harbored abundant hzo genes with copy numbers as high as 10(7)  g(-1) sediment. In general, anammox bacterial signatures were significantly more abundant in the deep-water sediments. Sediment porewater NO3-, NOx- (i.e. NO3- + NO2-), NOx-/NH4+ and sediment silt content correlated with in situ distribution patterns of anammox bacterial marker genes, likely because they determine anammox substrate availability and sediment geochemistry, respectively. The abundance and distribution of anammox bacterial gene markers indicate a potentially significant contribution of anammox bacteria to the marine N cycle in the deep-sea methane seep sediments.

  5. 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.

  6. 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

  7. 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 D.; 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

  8. Molecular phylogenetic and chemical analyses of the microbial mats in deep-sea cold seep sediments at the northeastern Japan Sea.

    PubMed

    Arakawa, Shizuka; Sato, Takako; Sato, Rumi; Zhang, Jing; Gamo, Toshitaka; Tsunogai, Urumu; Hirota, Akinari; Yoshida, Yasuhiko; Usami, Ron; Inagaki, Fumio; Kato, Chiaki

    2006-08-01

    Microbial communities inhabiting deep-sea cold seep sediments at the northeastern Japan Sea were characterized by molecular phylogenetic and chemical analyses. White patchy microbial mats were observed along the fault offshore the Hokkaido Island and sediment samples were collected from two stations at the southern foot of the Shiribeshi seamount (M1 site at a depth of 2,961 m on the active fault) and off the Motta Cape site (M2 site at a depth of 3,064 m off the active fault). The phylogenetic and terminal-restriction fragment polymorphism analyses of PCR-amplified 16S rRNA genes revealed that microbial community structures were different between two sampling stations. The members of ANME-2 archaea and diverse bacterial components including sulfate reducers within Deltaproteobacteria were detected from M1 site, indicating the occurrence of biologically mediated anaerobic oxidation of methane, while microbial community at M2 site was predominantly composed of members of Marine Crenarchaeota group I, sulfate reducers of Deltaproteobacteria, and sulfur oxidizers of Epsilonproteobacteria. Chemical analyses of seawater above microbial mats suggested that concentrations of sulfate and methane at M1 site were largely decreased relative to those at M2 site and carbon isotopic composition of methane at M1 site shifted heavier ((13)C-enriched), the results of which are consistent with molecular analyses. These results suggest that the mat microbial communities in deep-sea cold seep sediments at the northeastern Japan Sea are significantly responsible for sulfur and carbon circulations and the geological activity associated with plate movements serves unique microbial habitats in deep-sea environments.

  9. 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

  10. Physiological and ecological performance differs in four coral taxa at a volcanic carbon dioxide seep.

    PubMed

    Strahl, J; Stolz, I; Uthicke, S; Vogel, N; Noonan, S H C; Fabricius, K E

    2015-06-01

    Around volcanic carbon dioxide (CO2) seeps in Papua New Guinea, partial pressures of CO2 (pCO2) approximate those as predicted for the end of this century, and coral communities have low diversity and low structural complexity. To assess the mechanisms for such community shifts in response to ocean acidification, we examined the physiological performance of two hard corals that occur with increased or unaltered abundance at a seep site (mean pHTotal=7.8, pCO2=862 μatm) compared to a control site (mean pHTotal=8.1, pCO2=323 μatm), namely massive Porites spp. and Pocillopora damicornis, and two species with reduced abundance, Acropora millepora and Seriatopora hystrix. Oxygen fluxes, calcification, and skeletal densities were analyzed in corals originating from the seep and control site. Net photosynthesis rates increased considerably in Porites spp. and A. millepora and slightly in P. damicornis at increased pCO2, but remained unaltered in S. hystrix. Dark respiration rates remained constant in all corals investigated from both sites. Rates of light calcification declined in S. hystrix at high pCO2, but were unaffected by pCO2 in the other three coral taxa. Dark and net calcification rates remained unchanged in massive Porites and P. damicornis, but were drastically reduced at high pCO2 in A. millepora and S. hystrix. However, skeletal densities were similar at both seep and control sites in all coral taxa investigated. Our data suggest that the pCO2-tolerant corals were characterized by an increased ability to acclimatize to ocean acidification, e.g. by maintaining net calcification. Thus, robust corals, such as Porites spp. and P. damicornis, are more likely to persist for longer in a future high pCO2 world than those unable to acclimatize.

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. [Structural regularities in activated cleavage sites of thrombin receptors].

    PubMed

    Mikhaĭlik, I V; Verevka, S V

    1999-01-01

    Comparison of thrombin receptors activation splitting sites sequences testifies to their similarity both in activation splitting sites of protein precursors and protein proteinase inhibitors reactive sites. In all these sites corresponded to effectory sites P2'-positions are placed by hydrophobic amino-acids only. The regularity defined conforms with previous thesis about the role of effectory S2'-site in regulation of the processes mediated by serine proteinases.

  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. [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.

  19. 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.

  20. 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

  1. 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

  2. Deep sequencing of Myxilla (Ectyomyxilla) methanophila, an epibiotic sponge on cold-seep tubeworms, reveals methylotrophic, thiotrophic, and putative hydrocarbon-degrading microbial associations.

    PubMed

    Arellano, Shawn M; Lee, On On; Lafi, Feras F; Yang, Jiangke; Wang, Yong; Young, Craig M; Qian, Pei-Yuan

    2013-02-01

    The encrusting sponge Myxilla (Ectyomyxilla) methanophila (Poecilosclerida: Myxillidae) is an epibiont on vestimentiferan tubeworms at hydrocarbon seeps on the upper Louisiana slope of the Gulf of Mexico. It has long been suggested that this sponge harbors methylotrophic bacteria due to its low δ(13)C value and high methanol dehydrogenase activity, yet the full community of microbial associations in M. methanophila remained uncharacterized. In this study, we sequenced 16S rRNA genes representing the microbial community in M. methanophila collected from two hydrocarbon-seep sites (GC234 and Bush Hill) using both Sanger sequencing and next-generation 454 pyrosequencing technologies. Additionally, we compared the microbial community in M. methanophila to that of the biofilm collected from the associated tubeworm. Our results revealed that the microbial diversity in the sponges from both sites was low but the community structure was largely similar, showing a high proportion of methylotrophic bacteria of the genus Methylohalomonas and polycyclic aromatic hydrocarbon (PAH)-degrading bacteria of the genera Cycloclasticus and Neptunomonas. Furthermore, the sponge microbial clone library revealed the dominance of thioautotrophic gammaproteobacterial symbionts in M. methanophila. In contrast, the biofilm communities on the tubeworms were more diverse and dominated by the chemoorganotrophic Moritella at GC234 and methylotrophic Methylomonas and Methylohalomonas at Bush Hill. Overall, our study provides evidence to support previous suggestion that M. methanophila harbors methylotrophic symbionts and also reveals the association of PAH-degrading and thioautotrophic microbes in the sponge.

  3. 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.

  4. 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

  5. Biogenic methane from abyssal brine seeps at the base of the Florida escarpment

    SciTech Connect

    Martens, C.S.; Chanton, J.P.; Paull, C.K. )

    1991-08-01

    Dissolved methane is present at concentrations exceeding 10mM in the pore waters of sulfidic, salt-brine-enriched sediments underlying chemosynthetic communities at the base of the Florida escarpment. Light hydrocarbon samples were obtained from brine seep sediments by means of an in situ probe and push cores deployed by the deep submersible Alvin. Pore-water methane had a {delta}{sup 13}C value of {minus}83.3 {plus minus}7.0 (Peedee belemnite, N = 17), contained < 1.3% modern carbon, and was enriched over ethane concentrations by 10{sup 3} to 10{sup 5}; these results all indicate a fossil, biogenic carbon source within the Florida platform. Methane-rich brine fluids arriving at seep sites are depleted in dissolved sulfate, although they have been diluted twenty-fold with sulfate-rich seawater during transit. It appears that sulfate reduction and methano-genesis are important processes within the platform.

  6. MYST protein acetyltransferase activity requires active site lysine autoacetylation.

    PubMed

    Yuan, Hua; Rossetto, Dorine; Mellert, Hestia; Dang, Weiwei; Srinivasan, Madhusudan; Johnson, Jamel; Hodawadekar, Santosh; Ding, Emily C; Speicher, Kaye; Abshiru, Nebiyu; Perry, Rocco; Wu, Jiang; Yang, Chao; Zheng, Y George; Speicher, David W; Thibault, Pierre; Verreault, Alain; Johnson, F Bradley; Berger, Shelley L; Sternglanz, Rolf; McMahon, Steven B; Côté, Jacques; Marmorstein, Ronen

    2012-01-04

    The MYST protein lysine acetyltransferases are evolutionarily conserved throughout eukaryotes and acetylate proteins to regulate diverse biological processes including gene regulation, DNA repair, cell-cycle regulation, stem cell homeostasis and development. Here, we demonstrate that MYST protein acetyltransferase activity requires active site lysine autoacetylation. The X-ray crystal structures of yeast Esa1 (yEsa1/KAT5) bound to a bisubstrate H4K16CoA inhibitor and human MOF (hMOF/KAT8/MYST1) reveal that they are autoacetylated at a strictly conserved lysine residue in MYST proteins (yEsa1-K262 and hMOF-K274) in the enzyme active site. The structure of hMOF also shows partial occupancy of K274 in the unacetylated form, revealing that the side chain reorients to a position that engages the catalytic glutamate residue and would block cognate protein substrate binding. Consistent with the structural findings, we present mass spectrometry data and biochemical experiments to demonstrate that this lysine autoacetylation on yEsa1, hMOF and its yeast orthologue, ySas2 (KAT8) occurs in solution and is required for acetylation and protein substrate binding in vitro. We also show that this autoacetylation occurs in vivo and is required for the cellular functions of these MYST proteins. These findings provide an avenue for the autoposttranslational regulation of MYST proteins that is distinct from other acetyltransferases but draws similarities to the phosphoregulation of protein kinases.

  7. MYST protein acetyltransferase activity requires active site lysine autoacetylation

    PubMed Central

    Yuan, Hua; Rossetto, Dorine; Mellert, Hestia; Dang, Weiwei; Srinivasan, Madhusudan; Johnson, Jamel; Hodawadekar, Santosh; Ding, Emily C; Speicher, Kaye; Abshiru, Nebiyu; Perry, Rocco; Wu, Jiang; Yang, Chao; Zheng, Y George; Speicher, David W; Thibault, Pierre; Verreault, Alain; Johnson, F Bradley; Berger, Shelley L; Sternglanz, Rolf; McMahon, Steven B; Côté, Jacques; Marmorstein, Ronen

    2012-01-01

    The MYST protein lysine acetyltransferases are evolutionarily conserved throughout eukaryotes and acetylate proteins to regulate diverse biological processes including gene regulation, DNA repair, cell-cycle regulation, stem cell homeostasis and development. Here, we demonstrate that MYST protein acetyltransferase activity requires active site lysine autoacetylation. The X-ray crystal structures of yeast Esa1 (yEsa1/KAT5) bound to a bisubstrate H4K16CoA inhibitor and human MOF (hMOF/KAT8/MYST1) reveal that they are autoacetylated at a strictly conserved lysine residue in MYST proteins (yEsa1-K262 and hMOF-K274) in the enzyme active site. The structure of hMOF also shows partial occupancy of K274 in the unacetylated form, revealing that the side chain reorients to a position that engages the catalytic glutamate residue and would block cognate protein substrate binding. Consistent with the structural findings, we present mass spectrometry data and biochemical experiments to demonstrate that this lysine autoacetylation on yEsa1, hMOF and its yeast orthologue, ySas2 (KAT8) occurs in solution and is required for acetylation and protein substrate binding in vitro. We also show that this autoacetylation occurs in vivo and is required for the cellular functions of these MYST proteins. These findings provide an avenue for the autoposttranslational regulation of MYST proteins that is distinct from other acetyltransferases but draws similarities to the phosphoregulation of protein kinases. PMID:22020126

  8. A paradox resolved: sulfide acquisition by roots of seep tubeworms sustains net chemoautotrophy.

    PubMed

    Freytag, J K; Girguis, P R; Bergquist, D C; Andras, J P; Childress, J J; Fisher, C R

    2001-11-06

    Vestimentiferan tubeworms, symbiotic with sulfur-oxidizing chemoautotrophic bacteria, dominate many cold-seep sites in the Gulf of Mexico. The most abundant vestimentiferan species at these sites, Lamellibrachia cf. luymesi, grows quite slowly to lengths exceeding 2 meters and lives in excess of 170-250 years. L. cf. luymesi can grow a posterior extension of its tube and tissue, termed a "root," down into sulfidic sediments below its point of original attachment. This extension can be longer than the anterior portion of the animal. Here we show, using methods optimized for detection of hydrogen sulfide down to 0.1 microM in seawater, that hydrogen sulfide was never detected around the plumes of large cold-seep vestimentiferans and rarely detectable only around the bases of mature aggregations. Respiration experiments, which exposed the root portions of L. cf. luymesi to sulfide concentrations between 51-561 microM, demonstrate that L. cf. luymesi use their roots as a respiratory surface to acquire sulfide at an average rate of 4.1 micromol x g(-1) x h(-1). Net dissolved inorganic carbon uptake across the plume of the tubeworms was shown to occur in response to exposure of the posterior (root) portion of the worms to sulfide, demonstrating that sulfide acquisition by roots of the seep vestimentiferan L. cf. luymesi can be sufficient to fuel net autotrophic total dissolved inorganic carbon uptake.

  9. Diversity and distribution of methanotrophic archaea at cold seeps.

    PubMed

    Knittel, Katrin; Lösekann, Tina; Boetius, Antje; Kort, Renate; Amann, Rudolf

    2005-01-01

    In this study we investigated by using 16S rRNA-based methods the distribution and biomass of archaea in samples from (i) sediments above outcropping methane hydrate at Hydrate Ridge (Cascadia margin off Oregon) and (ii) massive microbial mats enclosing carbonate reefs (Crimea area, Black Sea). The archaeal diversity was low in both locations; there were only four (Hydrate Ridge) and five (Black Sea) different phylogenetic clusters of sequences, most of which belonged to the methanotrophic archaea (ANME). ANME group 2 (ANME-2) sequences were the most abundant and diverse sequences at Hydrate Ridge, whereas ANME-1 sequences dominated the Black Sea mats. Other seep-specific sequences belonged to the newly defined group ANME-3 (related to Methanococcoides spp.) and to the Crenarchaeota of marine benthic group B. Quantitative analysis of the samples by fluorescence in situ hybridization (FISH) showed that ANME-1 and ANME-2 co-occurred at the cold seep sites investigated. At Hydrate Ridge the surface sediments were dominated by aggregates consisting of ANME-2 and members of the Desulfosarcina-Desulfococcus branch (DSS) (ANME-2/DSS aggregates), which accounted for >90% of the total cell biomass. The numbers of ANME-1 cells increased strongly with depth; these cells accounted 1% of all single cells at the surface and more than 30% of all single cells (5% of the total cells) in 7- to 10-cm sediment horizons that were directly above layers of gas hydrate. In the Black Sea microbial mats ANME-1 accounted for about 50% of all cells. ANME-2/DSS aggregates occurred in microenvironments within the mat but accounted for only 1% of the total cells. FISH probes for the ANME-2a and ANME-2c subclusters were designed based on a comparative 16S rRNA analysis. In Hydrate Ridge sediments ANME-2a/DSS and ANME-2c/DSS aggregates differed significantly in morphology and abundance. The relative abundance values for these subgroups were remarkably different at Beggiatoa sites (80% ANME-2a, 20

  10. The vesicomyid bivalve habitat at cold seeps supports heterogeneous and dynamic macrofaunal assemblages

    NASA Astrophysics Data System (ADS)

    Guillon, Erwan; Menot, Lénaïck; Decker, Carole; Krylova, Elena; Olu, Karine

    2017-02-01

    The high biodiversity found at cold seeps, despite elevated concentrations of methane and hydrogen sulfide, is attributed to multiple sources of habitat heterogeneity. In addition to geological and geochemical processes, biogenic habitats formed by large symbiont-bearing taxa, such as bivalves and siboglinid tubeworms, or by microbial mats drive the biodiversity of small-sized fauna. However, because these habitat-forming species also depend on geochemical gradients, the respective influence of abiotic and biotic factors in structuring associated macrofaunal communities is often unresolved. The giant pockmark Regab located at 3200 m depth on the Congo margin is characterized by different fluid-flow regimes, providing a mosaic of the most common biogenic habitats encountered at seeps: microbial mats, mussel beds, and vesicomyid clam beds; the latter being distributed along a gradient of environmental conditions from the center to the periphery of the pockmark. Here, we examined the structure of macrofaunal communities in biogenic habitats formed in soft sediment to (1) determine the influence of the habitats on the associated macrofaunal communities (inter-habitat comparison), (2) describe how macrofaunal communities vary among vesicomyid clam beds (intra-habitat comparison) and (3) assess the inter-annual variation in vesicomyid beds based on repeated sampling at a three-year interval. The highest densities were found in the microbial mat communities in intermediate fluid-flow areas, but they had low diversity - also observed in the sediment close to mussel beds. In contrast, vesicomyid beds harbored the highest diversity. The vesicomyid beds did not show a homogeneous macrofaunal community across sampled areas; instead, density and composition of macrofauna varied according to the location of the beds inside the pockmark. The clam bed sampled in the most active, central part of the pockmark resembled bacterial mat communities by the presence of highly sulfide

  11. 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.

  12. 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

  13. 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

  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. SEEP 2 zooplankton data report: Winter, spring and summer collections at mooring 3 during 1988

    SciTech Connect

    Lane, P.V.Z.; Smith, S.L.; Flagg, C.N.; Schwarting, E.M.

    1991-03-01

    The second Shelf Edge Exchange Processes (SEEP II) experiment was designed as an extension of SEEP I work and was a multidisciplinary effort to describe the transport of carbon along and across the shelf and slope of the middle Atlantic Bight. A significant portion of the zooplankton work conducted during this project was devoted to repeated net sampling in close proximity to a moored acoustic Doppler current profiler (ADCP) in order to establish the calibration of the backscatter amplitude with respect to biomass in the water column. The Brookhaven ADCP was deployed at mooring site M-3 of the SEEP II study region. We used a multiple opening/closing net and environmental sensing system to collect stratified samples of zooplankton as close to the ADCP as towing conditions would allow. In addition, when MOCNESS tows were not feasible due to time constraints, Bongo nets were towed vertically in close proximity to the ADCP. The data in this report are the quantitative taxonomic analyses of the samples collected for ADCP calibration in 1988. 3 refs., 1 fig.

  16. 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.

  17. 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.

  18. 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.

  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. 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

  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. 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.

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

    PubMed

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

    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

  4. 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

  5. Soda ash treatment of a strontium-90-contaminated groundwater seep

    SciTech Connect

    Spalding, B.P.; Munro, I.I.

    1983-01-01

    A /sup 90/Sr-contaminated groundwater seep on the perimeter of a low-level radioactive solid waste disposal area at the Oak Ridge National Laboratory (ORNL) was treated by burying 315 kg of soda ash in the groundwater flow path leading to the seep, and placing 45 kg of soda ash on the surface of the seep. The concentration of /sup 90/Sr in the seep water fell from an average of 7000 Bq L/sup -1/ to 900 Bq L/sup -1/ for the 90 d after burial, followed by a period of gradual rise back to pretreatment levels over the next 100 d. The electrical conductivity and pH of the seep water increased following soda ash burial, while water hardness fell. Hardness was highly correlated (r = 0.84) with /sup 90/Sr concentrations over the entire 2-year observation period, indicating the similar behavior of /sup 90/Sr and soluble Ca and Mg. This in situ softening of, and /sup 90/Sr precipitation from, the seep water was achieved by coprecipitation of /sup 90/Sr with Ca(Mg)CO/sub 3/ until the buried soda ash was depleted by dissolution in the groundwater. The soda ash treatment of groundwater seeps appears to be most practical as an interim technique for those situations requiring an immediate, but temporary, corrective action. During this limited but effective period, more permanent corrective actions could be planned at the source of contamination. The electrical conductivity, pH, and hardness of the larger surface stream, into which this seep discharges, were not affected by the soda ash burial, most likely due to the approximately 2000-fold dilution effected by this stream.

  6. Development of saline seeps in Southwestern United States

    USGS Publications Warehouse

    Johnson, Kenneth S.; ,

    1994-01-01

    Saline seeps are an increasingly serious problem in semi-arid regions of the southwestern United States. They result when excessive recharge of the shallow ground water in soils raises the water table locally to within one meter of the land surface, and the salinity of the shallow water is increased through evaporation. In this connection, a comprehensive study is being undertaken in Oklahoma and Texas to determine the geologic setting, hydrology, soils, land use, and history of saline-seep development.

  7. 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.

  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. 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.

  10. 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.

  11. 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.

  12. 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.

  13. Controlled Orientation of Active Sites in a Nanostructured Multienzyme Complex

    PubMed Central

    Lim, Sung In; Yang, Byungseop; Jung, Younghan; Cha, Jaehyun; Cho, Jinhwan; Choi, Eun-Sil; Kim, Yong Hwan; Kwon, Inchan

    2016-01-01

    Multistep cascade reactions in nature maximize reaction efficiency by co-assembling related enzymes. Such organization facilitates the processing of intermediates by downstream enzymes. Previously, the studies on multienzyme nanocomplexes assembled on DNA scaffolds demonstrated that closer interenzyme distance enhances the overall reaction efficiency. However, it remains unknown how the active site orientation controlled at nanoscale can have an effect on multienzyme reaction. Here, we show that controlled alignment of active sites promotes the multienzyme reaction efficiency. By genetic incorporation of a non-natural amino acid and two compatible bioorthogonal chemistries, we conjugated mannitol dehydrogenase to formate dehydrogenase with the defined active site arrangement with the residue-level accuracy. The study revealed that the multienzyme complex with the active sites directed towards each other exhibits four-fold higher relative efficiency enhancement in the cascade reaction and produces 60% more D-mannitol than the other complex with active sites directed away from each other. PMID:28004799

  14. Multiple archaeal groups mediate methane oxidation in anoxic cold seep sediments.

    PubMed

    Orphan, Victoria J; House, Christopher H; Hinrichs, Kai-Uwe; McKeegan, Kevin D; DeLong, Edward F

    2002-05-28

    No microorganism capable of anaerobic growth on methane as the sole carbon source has yet been cultivated. Consequently, information about these microbes has been inferred from geochemical and microbiological observations of field samples. Stable isotope analysis of lipid biomarkers and rRNA gene surveys have implicated specific microbes in the anaerobic oxidation of methane (AOM). Here we use combined fluorescent in situ hybridization and secondary ion mass spectrometry analyses, to identify anaerobic methanotrophs in marine methane-seep sediments. The results provide direct evidence for the involvement of at least two distinct archaeal groups (ANME-1 and ANME-2) in AOM at methane seeps. Although both archaeal groups often occurred in direct physical association with bacteria, they also were observed as monospecific aggregations and as single cells. The ANME-1 archaeal group more frequently existed in monospecific aggregations or as single filaments, apparently without a bacterial partner. Bacteria associated with both archaeal groups included, but were not limited to, close relatives of Desulfosarcina species. Isotopic analyses suggest that monospecific archaeal cells and cell aggregates were active in anaerobic methanotrophy, as were multispecies consortia. In total, the data indicate that the microbial species and biotic interactions mediating anaerobic methanotrophy are diverse and complex. The data also clearly show that highly structured ANME-2/Desulfosarcina consortia are not the sole entities responsible for AOM at marine methane seeps. Other microbial groups, including ANME-1 archaea, are capable of anaerobic methane consumption either as single cells, in monospecific aggregates, or in multispecies consortia.

  15. Perspective: On the active site model in computational catalyst screening

    NASA Astrophysics Data System (ADS)

    Reuter, Karsten; Plaisance, Craig P.; Oberhofer, Harald; Andersen, Mie

    2017-01-01

    First-principles screening approaches exploiting energy trends in surface adsorption represent an unparalleled success story in recent computational catalysis research. Here we argue that our still limited understanding of the structure of active sites is one of the major bottlenecks towards an ever extended and reliable use of such computational screening for catalyst discovery. For low-index transition metal surfaces, the prevalently chosen high-symmetry (terrace and step) sites offered by the nominal bulk-truncated crystal lattice might be justified. For more complex surfaces and composite catalyst materials, computational screening studies will need to actively embrace a considerable uncertainty with respect to what truly are the active sites. By systematically exploring the space of possible active site motifs, such studies might eventually contribute towards a targeted design of optimized sites in future catalysts.

  16. Diffusional correlations among multiple active sites in a single enzyme.

    PubMed

    Echeverria, Carlos; Kapral, Raymond

    2014-04-07

    Simulations of the enzymatic dynamics of a model enzyme containing multiple substrate binding sites indicate the existence of diffusional correlations in the chemical reactivity of the active sites. A coarse-grain, particle-based, mesoscopic description of the system, comprising the enzyme, the substrate, the product and solvent, is constructed to study these effects. The reactive and non-reactive dynamics is followed using a hybrid scheme that combines molecular dynamics for the enzyme, substrate and product molecules with multiparticle collision dynamics for the solvent. It is found that the reactivity of an individual active site in the multiple-active-site enzyme is reduced substantially, and this effect is analyzed and attributed to diffusive competition for the substrate among the different active sites in the enzyme.

  17. Robotics at Savannah River site: activity report

    SciTech Connect

    Byrd, J.S.

    1984-09-01

    The objectives of the Robotics Technology Group at the Savannah River Laboratory are to employ modern industrial robots and to develop unique automation and robotic systems to enhance process operations at the Savannah River site (SRP and SRL). The incentives are to improve safety, reduce personnel radiation exposure, improve product quality and productivity, and to reduce operating costs. During the past year robotic systems have been installed to fill chemical dilution vials in a SRP laboratory at 772-F and remove radioactive waste materials in the SRL Californium Production Facility at 773-A. A robotic system to lubricate an extrusion press has been developed and demonstrated in the SRL robotics laboratory and is scheduled for installation at the 321-M fuel fabrication area. A mobile robot was employed by SRP for a radiation monitoring task at a waste tank top in H-Area. Several other robots are installed in the SRL robotics laboratories and application development programs are underway. The status of these applications is presented in this report.

  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. Active sites of thioredoxin reductases: why selenoproteins?

    PubMed

    Gromer, Stephan; Johansson, Linda; Bauer, Holger; Arscott, L David; Rauch, Susanne; Ballou, David P; Williams, Charles H; Schirmer, R Heiner; Arnér, Elias S J

    2003-10-28

    Selenium, an essential trace element for mammals, is incorporated into a selected class of selenoproteins as selenocysteine. All known isoenzymes of mammalian thioredoxin (Trx) reductases (TrxRs) employ selenium in the C-terminal redox center -Gly-Cys-Sec-Gly-COOH for reduction of Trx and other substrates, whereas the corresponding sequence in Drosophila melanogaster TrxR is -Ser-Cys-Cys-Ser-COOH. Surprisingly, the catalytic competence of these orthologous enzymes is similar, whereas direct Sec-to-Cys substitution of mammalian TrxR, or other selenoenzymes, yields almost inactive enzyme. TrxRs are therefore ideal for studying the biology of selenocysteine by comparative enzymology. Here we show that the serine residues flanking the C-terminal Cys residues of Drosophila TrxRs are responsible for activating the cysteines to match the catalytic efficiency of a selenocysteine-cysteine pair as in mammalian TrxR, obviating the need for selenium. This finding suggests that the occurrence of selenoenzymes, which implies that the organism is selenium-dependent, is not necessarily associated with improved enzyme efficiency. Our data suggest that the selective advantage of selenoenzymes is a broader range of substrates and a broader range of microenvironmental conditions in which enzyme activity is possible.

  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. Altererythrobacter epoxidivorans gen. nov., sp. nov., an epoxide hydrolase-active, mesophilic marine bacterium isolated from cold-seep sediment, and reclassification of Erythrobacter luteolus Yoon et al. 2005 as Altererythrobacter luteolus comb. nov.

    PubMed

    Kwon, Kae Kyoung; Woo, Jung-Hee; Yang, Sung-Hyun; Kang, Ji-Hyun; Kang, Sung Gyun; Kim, Sang-Jin; Sato, Takako; Kato, Chiaki

    2007-10-01

    A novel marine bacterium, strain JCS350(T), was isolated from marine sediment samples collected from a cold-seep area. The 16S rRNA gene sequence of the isolate showed high similarity to that of Erythrobacter luteolus SW-109(T) (95.9 % sequence similarity). Lower 16S rRNA gene sequence similarities were shown to other members of the genus Erythrobacter (94.6-95.4 %) and members of the genus Porphyrobacter (94.5-95.2 %). Phylogenetic analysis with all members of the family Erythrobacteraceae and several members of the family Sphingomonadaceae revealed that the isolate formed a phyletic line with [Erythrobacter] luteolus that was distinct from other members of the family Erythrobacteraceae. The dominant fatty acids of strain JCS350(T) were 18 : 1omega7c, 16 : 1omega7c and cyclopropane 17 : 0. The major respiratory quinone was ubiquinone 10. The DNA G+C content was 54.5 mol%. The isolate did not contain bacteriochlorophyll a. Optimal growth required the presence of 2 % (w/v) NaCl with either 0.18 % CaCl(2) or 0.59 % MgCl(2), at pH 6.5 and at 35 degrees C. On the basis of the evidence of this polyphasic taxonomic study, strain JCS350(T) should be classified in a novel genus and species in the family Erythrobacteraceae, for which the name Altererythrobacter epoxidivorans gen. nov., sp. nov. is proposed. The misclassified species [Erythrobacter] luteolus is transferred to the new genus as Altererythrobacter luteolus comb. nov. The type strain of Altererythrobacter epoxidivorans is JCS350(T) (=KCCM 42314(T) =JCM 13815(T)) and the type strain of Altererythrobacter luteolus is SW-109(T) (=KCTC 12311(T) =JCM 12599(T)).

  2. 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.

  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.

  4. Community Update on Site Activities, July 19, 2013

    EPA Pesticide Factsheets

    In an effort to engage and inform community members interested in the New Bedford Harbor Superfund Site cleanup, EPA will be issuing periodic topic-based fact sheets that will provide background information and updates about ongoing activities.

  5. Active seepage and water infiltration in Lake Baikal sediments: new thermal data from TTR-Baikal 2014 (Class@Baikal)

    NASA Astrophysics Data System (ADS)

    Poort, Jeffrey; Khlystov, Oleg M.; Akhmanov, Grigorii G.; Khabuev, Andrei V.; Belousov, Oleg V.

    2015-04-01

    New thermal data from the sediments of Lake Baikal were collected in July 2014 during the first Training-Through-Research cruise on Lake Baikal (Class@Baikal) organized by MGU and LIN. TTR-Baikal is a comprehensive multidisciplinary program to train students on the field on pertinent scientific topics. The cruise program focused on seafloor sampling, acoustic investigations and heat flow measurements of gas seeps, flares, mud volcanoes, slumps and debris flows, canyons and channels in the coastal proximity. The thermal data were acquired using autonomous temperature sensors on a 3 meter long gravity corer that allowed analysis at the same spot of sediments, pore fluids, hydrates and microbiology. A total of eight thermal measurements were performed in five structures located on the lake floor of the Central Baikal Basin at 333-1530 meter water depths: 3 mud volcanoes (Novosibirsk, Unshuy and Krest), 1 seep site (Seep 13), and one fault outcrop in the Selenga transfer zone. All studied structures show signals of active seepage, water infiltration and/or hydrate dynamics. The strongest thermal gradient has been measured in Seep 13, suggesting a strong upflow of warm fluids similar to the Gorevoy Utes seep. At the three mud volcanoes, hydrate presence have been evidenced and both enhanced and reduced thermal gradients have been observed. This is similar to the hydrate-bearing K-2 mud volcano in Baikal (Poort et al., 2012). A strongly reduced thermal gradient was observed in the Krest mud volcano where the presence of oxidized channels at 30-40 cm under the sediment surface indicate an infiltration of cold lake water. The water infiltration process at hydrate bearing seep sites will be discussed and compared with other seep areas in the world.

  6. 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

  7. Seep-carbonate lamination controlled by cyclic particle flux

    NASA Astrophysics Data System (ADS)

    Himmler, Tobias; Bayon, Germain; Wangner, David; Enzmann, Frieder; Peckmann, Jörn; Bohrmann, Gerhard

    2016-11-01

    Authigenic carbonate build-ups develop at seafloor methane-seeps, where microbially mediated sulphate-dependent anaerobic oxidation of methane facilitates carbonate precipitation. Despite being valuable recorders of past methane seepage events, their role as archives of atmospheric processes has not been examined. Here we show that cyclic sedimentation pulses related to the Indian monsoon in concert with authigenic precipitation of methane-derived aragonite gave rise to a well-laminated carbonate build-up within the oxygen minimum zone off Pakistan (northern Arabian Sea). U–Th dating indicates that the build-up grew during past ~1,130 years, creating an exceptional high-resolution archive of the Indian monsoon system. Monsoon-controlled formation of seep-carbonates extends the known environmental processes recorded by seep-carbonates, revealing a new relationship between atmospheric and seafloor processes.

  8. Seep-carbonate lamination controlled by cyclic particle flux

    PubMed Central

    Himmler, Tobias; Bayon, Germain; Wangner, David; Enzmann, Frieder; Peckmann, Jörn; Bohrmann, Gerhard

    2016-01-01

    Authigenic carbonate build-ups develop at seafloor methane-seeps, where microbially mediated sulphate-dependent anaerobic oxidation of methane facilitates carbonate precipitation. Despite being valuable recorders of past methane seepage events, their role as archives of atmospheric processes has not been examined. Here we show that cyclic sedimentation pulses related to the Indian monsoon in concert with authigenic precipitation of methane-derived aragonite gave rise to a well-laminated carbonate build-up within the oxygen minimum zone off Pakistan (northern Arabian Sea). U–Th dating indicates that the build-up grew during past ~1,130 years, creating an exceptional high-resolution archive of the Indian monsoon system. Monsoon-controlled formation of seep-carbonates extends the known environmental processes recorded by seep-carbonates, revealing a new relationship between atmospheric and seafloor processes. PMID:27876764

  9. Seep-carbonate lamination controlled by cyclic particle flux.

    PubMed

    Himmler, Tobias; Bayon, Germain; Wangner, David; Enzmann, Frieder; Peckmann, Jörn; Bohrmann, Gerhard

    2016-11-23

    Authigenic carbonate build-ups develop at seafloor methane-seeps, where microbially mediated sulphate-dependent anaerobic oxidation of methane facilitates carbonate precipitation. Despite being valuable recorders of past methane seepage events, their role as archives of atmospheric processes has not been examined. Here we show that cyclic sedimentation pulses related to the Indian monsoon in concert with authigenic precipitation of methane-derived aragonite gave rise to a well-laminated carbonate build-up within the oxygen minimum zone off Pakistan (northern Arabian Sea). U-Th dating indicates that the build-up grew during past ~1,130 years, creating an exceptional high-resolution archive of the Indian monsoon system. Monsoon-controlled formation of seep-carbonates extends the known environmental processes recorded by seep-carbonates, revealing a new relationship between atmospheric and seafloor processes.

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

    PubMed Central

    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

  11. 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

  12. 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

  13. 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.

  14. 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

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

    PubMed

    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

    2014-06-15

    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.

  16. 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.

  17. Ethane and propane emissions to the ocean and atmosphere from 550-1200 m seeps in the Gulf of Mexico

    NASA Astrophysics Data System (ADS)

    Solomon, E. A.; Kastner, M.; Leifer, I.

    2009-12-01

    Ethane (C2) and propane (C3) are highly reactive trace gases in the atmosphere that are important precursors of organic aerosols and contribute to ozone formation. The global flux of C2 and C3 based on tropospheric removal are 13-15.5 and 12 Tg/yr, respectively. Current emission inventories that include fossil fuel, biomass burning, biofuels, and waste treatment underestimate the global flux by ~2-5 Tg/yr. Previous studies have indicated that the open ocean contributes only marginally to global C2 and C3 budgets, but very few studies have investigated the natural emissions from marine seeps and their potential significance to global C2 and C3 fluxes. During a recent study at 3 seeps at depths from 550-600 m in the Gulf of Mexico (GOM), a submersible was used to collect water column samples immediately adjacent to 5 bubble plumes from the seafloor vents to the sea surface. Bottom water C2 and C3 concentrations above the seeps ranged from 24.3-2220 and 15.8-385 nM, respectively. Ethane and propane concentrations decrease by ~50-95% in the bottom 200 m. Mixed layer C2 and C3 concentrations were extremely high ranging from 6.3-147 and 4.0-110 nM. These mixed layer C2 and C3 concentrations are up to 1×105 and 5×105 times saturation with respect to atmospheric equilibrium. In general, C1/C2 and C2/C3 ratios decrease from the seafloor to the mixed layer with surface ratios lower than previously reported from marine seeps and the ocean, indicating preferential loss of light hydrocarbons from the plumes during water column transit. Preliminary results from numerical bubble models show the importance of bubble plume-driven upwelling flows, bubble size, and pressure effects for enhancing hydrocarbon transfer to the mixed layer. Based on contemporaneous wind speeds at the study sites, preliminary estimates for the diffusive C2 and C3 fluxes to the atmosphere above the seeps range from 10-400 μmol/m2d; 2-4 orders of magnitude greater than estimates from the open ocean

  18. Identification of putative active site residues of ACAT enzymes.

    PubMed

    Das, Akash; Davis, Matthew A; Rudel, Lawrence L

    2008-08-01

    In this report, we sought to determine the putative active site residues of ACAT enzymes. For experimental purposes, a particular region of the C-terminal end of the ACAT protein was selected as the putative active site domain due to its high degree of sequence conservation from yeast to humans. Because ACAT enzymes have an intrinsic thioesterase activity, we hypothesized that by analogy with the thioesterase domain of fatty acid synthase, the active site of ACAT enzymes may comprise a catalytic triad of ser-his-asp (S-H-D) amino acid residues. Mutagenesis studies revealed that in ACAT1, S456, H460, and D400 were essential for activity. In ACAT2, H438 was required for enzymatic activity. However, mutation of D378 destabilized the enzyme. Surprisingly, we were unable to identify any S mutations of ACAT2 that abolished catalytic activity. Moreover, ACAT2 was insensitive to serine-modifying reagents, whereas ACAT1 was not. Further studies indicated that tyrosine residues may be important for ACAT activity. Mutational analysis showed that the tyrosine residue of the highly conserved FYXDWWN motif was important for ACAT activity. Furthermore, Y518 was necessary for ACAT1 activity, whereas the analogous residue in ACAT2, Y496, was not. The available data suggest that the amino acid requirement for ACAT activity may be different for the two ACAT isozymes.

  19. 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

  20. 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.

  1. Methane in shallow cold seeps at Mocha Island off central Chile

    NASA Astrophysics Data System (ADS)

    Jessen, Gerdhard L.; Pantoja, Silvio; Gutiérrez, Marcelo A.; Quiñones, Renato A.; González, Rodrigo R.; Sellanes, Javier; Kellermann, Matthias Y.; Hinrichs, Kai-Uwe

    2011-04-01

    We studied for the first time the intertidal and subtidal gas seepage system in Mocha Island off Central Chile. Four main seepage sites were investigated (of which one site included about 150 bubbling points) that release from 150 to 240 tonnes CH 4 into the atmosphere per year. The total amount of methane emitted into the atmosphere is estimated in the order of 800 tonnes per year. The gases emanated from the seeps contain 70% methane, and the stable carbon isotopic composition of methane, δ 13C-CH 4 averaged -44.4±1.4‰ which indicates a major contribution of thermogenic gas. Adjacent to one of the subtidal seeps, rocky substrates support a diverse community of microbial filaments, macroalgae, and benthic organisms. While stable carbon isotopic compositions of marine benthic organisms indicate a dominant photosynthesis-based food web, those of some hard-substrate invertebrates were in the range -48.8‰ to -36.8‰, suggesting assimilation of methane-derived carbon by some selected taxa. This work highlights the potential subsidy of the trophic web by CH 4-C, and that its emission to the atmosphere justifies the need of evaluating the use of methane to support the energy requirements of the local community.

  2. Detection of low-chloride fluids beneath a cold seep field on the Nankai accretionary wedge off Kumano, south of Japan

    NASA Astrophysics Data System (ADS)

    Toki, T.; Tsunogai, U.; Gamo, T.; Kuramoto, S.; Ashi, J.

    2004-11-01

    Chemical and isotopic characteristics were determined for interstitial waters extracted from surface sediments in and around dense biological communities on the seafloor of the Nankai accretionary prism off Kumano, south of Japan. We found the following unique features when compared with usual interstitial water samples of normal seafloor in those of samples from bacterial mats on the Oomine Ridge, one of the outer ridge in the Nankai accretionary prism: (1) significant depletion of chloride concentration (maximum 10% depletion from bottom seawater), (2) high concentrations of CH4 and ΣCO2 (more than 660 μmol/kg and 60 mmol/kg, respectively), (3) sulfate depletion (more than 90% depletion compared to bottom seawater), and (4) δDH2O and δ18OH2O depletion [more than 4‰ and 0.7‰ depletion, respectively, compared to standard mean ocean water (SMOW)]. The highest CH4 value among these samples was comparable to the highest value so far reported at one of the most active seep areas in the Nankai Trough, suggesting that these sites should also be regarded as one of the most active seep sites in the Nankai Trough. The chemical compositions of the samples taken from the Oomine Ridge strongly suggest that the fluid originates not from normal sediment-seawater interaction at the sediment surface of hemipelagic environments, but from active seepage of fluids that are rich in CH4 and ΣCO2, depleted in Cl- and SO42-, and low in δDH2O and δ18OH2O compared to normal seawater. Values for the carbon isotopic composition (δ13CCH4) of the dissolved methane in the interstitial fluid [less than -70‰ PeeDee Belemnite (PDB)] and for the C2H6/CH4 ratio (less than 10-3) suggest that the methane originates from microbial production in a relatively shallow layer of sediment, not from the deep sedimentary layer of higher temperature than 60 °C at the depth of more than 300 m below the seafloor. The Cl-=0 mmol/kg extrapolated end-member δDH2O and δ18OH2O values of low

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

    PubMed

    Kiel, Steffen; Little, Crispin T S

    2006-09-08

    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.

  4. Promoter-proximal polyadenylation sites reduce transcription activity

    PubMed Central

    Andersen, Pia K.; Lykke-Andersen, Søren; Jensen, Torben Heick

    2012-01-01

    Gene expression relies on the functional communication between mRNA processing and transcription. We previously described the negative impact of a point-mutated splice donor (SD) site on transcription. Here we demonstrate that this mutation activates an upstream cryptic polyadenylation (CpA) site, which in turn causes reduced transcription. Functional depletion of U1 snRNP in the context of the wild-type SD triggers the same CpA event accompanied by decreased RNA levels. Thus, in accordance with recent findings, U1 snRNP can shield premature pA sites. The negative impact of unshielded pA sites on transcription requires promoter proximity, as demonstrated using artificial constructs and supported by a genome-wide data set. Importantly, transcription down-regulation can be recapitulated in a gene context devoid of splice sites by placing a functional bona fide pA site/transcription terminator within ∼500 base pairs of the promoter. In contrast, promoter-proximal positioning of a pA site-independent histone gene terminator supports high transcription levels. We propose that optimal communication between a pA site-dependent gene terminator and its promoter critically depends on gene length and that short RNA polymerase II-transcribed genes use specialized termination mechanisms to maintain high transcription levels. PMID:23028143

  5. 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.

  6. 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.

  7. 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

  8. Active and regulatory sites of cytosolic 5'-nucleotidase.

    PubMed

    Pesi, Rossana; Allegrini, Simone; Careddu, Maria Giovanna; Filoni, Daniela Nicole; Camici, Marcella; Tozzi, Maria Grazia

    2010-12-01

    Cytosolic 5'-nucleotidase (cN-II), which acts preferentially on 6-hydroxypurine nucleotides, is essential for the survival of several cell types. cN-II catalyses both the hydrolysis of nucleotides and transfer of their phosphate moiety to a nucleoside acceptor through formation of a covalent phospho-intermediate. Both activities are regulated by a number of phosphorylated compounds, such as diadenosine tetraphosphate (Ap₄A), ADP, ATP, 2,3-bisphosphoglycerate (BPG) and phosphate. On the basis of a partial crystal structure of cN-II, we mutated two residues located in the active site, Y55 and T56. We ascertained that the ability to catalyse the transfer of phosphate depends on the presence of a bulky residue in the active site very close to the aspartate residue that forms the covalent phospho-intermediate. The molecular model indicates two possible sites at which adenylic compounds may interact. We mutated three residues that mediate interaction in the first activation site (R144, N154, I152) and three in the second (F127, M436 and H428), and found that Ap₄A and ADP interact with the same site, but the sites for ATP and BPG remain uncertain. The structural model indicates that cN-II is a homotetrameric protein that results from interaction through a specific interface B of two identical dimers that have arisen from interaction of two identical subunits through interface A. Point mutations in the two interfaces and gel-filtration experiments indicated that the dimer is the smallest active oligomerization state. Finally, gel-filtration and light-scattering experiments demonstrated that the native enzyme exists as a tetramer, and no further oligomerization is required for enzyme activation.

  9. 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

  10. 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

    2016-07-22

    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.

  11. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-08-01

    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.

  13. 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.

  14. BAX Activation is Initiated at a Novel Interaction Site

    PubMed Central

    Gavathiotis, Evripidis; Suzuki, Motoshi; Davis, Marguerite L.; Pitter, Kenneth; Bird, Gregory H.; Katz, Samuel G.; Tu, Ho-Chou; Kim, Hyungjin; Cheng, Emily H.-Y.; Tjandra, Nico; Walensky, Loren D.

    2008-01-01

    BAX is a pro-apoptotic protein of the BCL-2 family stationed in the cytosol until activated by a diversity of stress stimuli to induce cell death. Anti-apoptotic proteins such as BCL-2 counteract BAX-mediated cell death. Although an interaction site that confers survival functionality has been defined for anti-apoptotic proteins, an activation site has not been identified for BAX, rendering its explicit trigger mechanism unknown. We previously developed Stabilized Alpha-Helix of BCL-2 domains (SAHBs) that directly initiate BAX-mediated mitochondrial apoptosis. Here we demonstrate by NMR analysis that BIM SAHB binds BAX at an interaction site that is distinct from the canonical binding groove characterized for anti-apoptotic proteins. The specificity of the BIM SAHB-BAX interaction is highlighted by point mutagenesis that abrogates functional activity, confirming that BAX activation is initiated at this novel structural location. Thus, we have now defined a BAX interaction site for direct activation, establishing a new target for therapeutic modulation of apoptosis. PMID:18948948

  15. Involvement of novel autophosphorylation sites in ATM activation.

    PubMed

    Kozlov, Sergei V; Graham, Mark E; Peng, Cheng; Chen, Philip; Robinson, Phillip J; Lavin, Martin F

    2006-08-09

    ATM kinase plays a central role in signaling DNA double-strand breaks to cell cycle checkpoints and to the DNA repair machinery. Although the exact mechanism of ATM activation remains unknown, efficient activation requires the Mre11 complex, autophosphorylation on S1981 and the involvement of protein phosphatases and acetylases. We report here the identification of several additional phosphorylation sites on ATM in response to DNA damage, including autophosphorylation on pS367 and pS1893. ATM autophosphorylates all these sites in vitro in response to DNA damage. Antibodies against phosphoserine 1893 revealed rapid and persistent phosphorylation at this site after in vivo activation of ATM kinase by ionizing radiation, paralleling that observed for S1981 phosphorylation. Phosphorylation was dependent on functional ATM and on the Mre11 complex. All three autophosphorylation sites are physiologically important parts of the DNA damage response, as phosphorylation site mutants (S367A, S1893A and S1981A) were each defective in ATM signaling in vivo and each failed to correct radiosensitivity, genome instability and cell cycle checkpoint defects in ataxia-telangiectasia cells. We conclude that there are at least three functionally important radiation-induced autophosphorylation events in ATM.

  16. 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.

  17. 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

  18. Sperm storage, internal fertilization, and embryonic dispersal in vent and seep tubeworms (Polychaeta: Siboglinidae: Vestimentifera).

    PubMed

    Hilário, Ana; Young, Craig M; Tyler, Paul A

    2005-02-01

    Vestimentiferan tubeworms are ecologically important members of deep-sea chemosynthetic communities, including hydrothermal vents and cold seeps. Some are community dominants and others are primary colonists of new vent sites; they include some of the longest living and fastest growing marine invertebrates. Their mechanisms of propagation, dispersal, and genetic exchange have been widely discussed. Direct sperm transfer from males to females has been documented in one species, Ridgeia piscesae, but others are known to discharge what are apparently primary oocytes. Brooding of embryos has never been observed in any vestimentiferan. These observations have led to the supposition that fertilization might be external in most species. Here we report sperm storage at the posterior end of the oviduct in five species, including tubeworms from both vents and seeps. We show experimentally that most eggs are inseminated internally, that fertilization rate is typically lower than 100%, that meiosis is completed after eggs are released from the female, and that the dispersal phase includes the entire embryonic period.

  19. 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…

  20. Spectroscopic studies of the active site of galactose oxidase

    SciTech Connect

    Knowles, P.F.; Brown, R.D. III; Koenig, S.H.

    1995-07-19

    X-ray absorption and EPR spectroscopy have been used to probe the copper site structure in galactose oxidase at pH 4.5 and 7.0. the results suggest that there are no major differences in the structure of the tetragonal Cu(II) site at these pH values. Analysis of the extended X-ray absorption fine structure (EXAFS) indicates that four N,O scatterers are present at approximately 2 {Angstrom}; these are presumably the equatorial ligands. In addition, the EXAFS data establish that oxidative activation to produce the active-site tyrosine radical does not cause major changes in the copper coordination environment. Therefore results obtained on the one-electron reduced enzyme, containing Cu(II) but not the tyrosine radical, probably also apply to the catalytically active Cu(II)/tyrosine radical state. Solvent water exchange, inhibitor binding, and substrate binding have been probed via nuclear magnetic relaxation dispersion (NMRD) measurements. The NMRD profile of galactose oxidase is quantitatively consistent with the rapid exchange of a single, equatorial water ligand with a Cu(II)-O separation of about 2.4 {Angstrom}. Azide and cyanide displace this coordinated water. The binding of azide and the substrate dihydroxyacetone produce very similar effects on the NMRD profile of galactose oxidase, indicating that substrates also bind to the active site Cu(II) in an equatorial position.

  1. 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.

  2. Characterization of the acidic cold seep emplaced jarositic Golden Deposit, NWT, Canada, as an analogue for jarosite deposition on Mars

    NASA Astrophysics Data System (ADS)

    Battler, Melissa M.; Osinski, Gordon R.; Lim, Darlene S. S.; Davila, Alfonso F.; Michel, Frederick A.; Craig, Michael A.; Izawa, Matthew R. M.; Leoni, Lisa; Slater, Gregory F.; Fairén, Alberto G.; Preston, Louisa J.; Banerjee, Neil R.

    2013-06-01

    Surficial deposits of the OH-bearing iron sulfate mineral jarosite have been observed in several places on Mars, such as Meridiani Planum and Mawrth Vallis. The specific depositional conditions and mechanisms are not known, but by comparing martian sites to analogous locations on Earth, the conditions of formation and, thus, the martian depositional paleoenvironments may be postulated. Located in a cold semi-arid desert ˜100 km east of Norman Wells, Northwest Territories, Canada, the Golden Deposit (GD) is visible from the air as a brilliant golden-yellow patch of unvegetated soil, approximately 140 m × 50 m. The GD is underlain by permafrost and consists of yellow sediment, which is precipitating from seeps of acidic, iron-bearing groundwater. On the surface, the GD appears as a patchwork of raised polygons, with acidic waters flowing from seeps in troughs between polygonal islands. Although UV-Vis-NIR spectral analysis detects only jarosite, mineralogy, as determined by X-ray diffraction and inductively coupled plasma emission spectrometry, is predominantly natrojarosite and jarosite, with hydronium jarosite, goethite, quartz, clays, and small amounts of hematite. Water pH varies significantly over short distances depending on proximity to acid seeps, from 2.3 directly above seeps, to 5.7 several m downstream from seeps within the deposit, and up to 6.5 in ponds proximal to the deposit. Visual observations of microbial filament communities and phospholipid fatty acid analyses confirm that the GD is capable of supporting life for at least part of the year. Jarosite-bearing sediments extend beneath vegetation up to 70 m out from the deposit and are mixed with plant debris and minerals presumably weathered from bedrock and glacial till. This site is of particular interest because mineralogy (natrojarosite, jarosite, hematite, and goethite) and environmental conditions (permafrost and arid conditions) at the time of deposition are conceivably analogous to jarosite

  3. 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.

  4. 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

  5. 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

    2016-09-06

    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.

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

    PubMed Central

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

    2016-01-01

    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

  7. 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

  8. Probing the promiscuous active site of myo-inositol dehydrogenase using synthetic substrates, homology modeling, and active site modification.

    PubMed

    Daniellou, Richard; Zheng, Hongyan; Langill, David M; Sanders, David A R; Palmer, David R J

    2007-06-26

    The active site of myo-inositol dehydrogenase (IDH, EC 1.1.1.18) from Bacillus subtilis recognizes a variety of mono- and disaccharides, as well as 1l-4-O-substituted inositol derivatives. It catalyzes the NAD+-dependent oxidation of the axial alcohol of these substrates with comparable kinetic constants. We have found that 4-O-p-toluenesulfonyl-myo-inositol does not act as a substrate for IDH, in contrast to structurally similar compounds such as those bearing substituted benzyl substituents in the same position. X-ray crystallographic analysis of 4-O-p-toluenesulfonyl-myo-inositol and 4-O-(2-naphthyl)methyl-myo-inositol, which is a substrate for IDH, shows a distinct difference in the preferred conformation of the aryl substituent. Conformational analysis of known substrates of IDH suggests that this conformational difference may account for the difference in reactivity of 4-O-p-toluenesulfonyl-myo-inositol in the presence of IDH. A sequence alignment of IDH with the homologous glucose-fructose oxidoreductase allowed the construction of an homology model of inositol dehydrogenase, to which NADH and 4-O-benzyl-scyllo-inosose were docked and the active site energy minimized. The active site model is consistent with all experimental results and suggests that a conserved tyrosine-glycine-tyrosine motif forms the hydrophobic pocket adjoining the site of inositol recognition. Y233F and Y235F retain activity, while Y233R and Y235R do not. A histidine-aspartate pair, H176 and D172, are proposed to act as a dyad in which H176 is the active site acid/base. The enzyme is inactivated by diethyl pyrocarbonate, and the mutants H176A and D172N show a marked loss of activity. Kinetic isotope effect experiments with D172N indicate that chemistry is rate-determining for this mutant.

  9. The active site structure and mechanism of phosphoenolpyruvate utilizing enzymes

    SciTech Connect

    Cheng, K.C.

    1989-01-01

    Arginine specific reagents showed irreversible inhibition of avian liver mitochondrial phosphoenolpyruvate carboxykinase. Potent protection against modification was elicited by CO{sub 2} or CO{sub 2} in the presence of other substrates. Labeling of enzyme with (7-{sup 14}C) phenylglyoxal showed that 1 or 2 arginines are involved in CO{sub 2} binding and activation. Peptide map studies showed this active site arginine residues is located at position 289. Histidine specific reagents showed pseudo first order inhibition of avian mitochondrial phosphoenolpyruvate carboxykinase activity. The best protection against modification was elicited by IDP or IDP and Mn{sup +2}. One histidine residue is at or near the phosphoenolpyruvate binding site as demonstrated in the increased absorbance at 240 nm and proton relaxation rate studies. Circular dichroism studies reveal that enzyme structure was perturbed by diethylpyrocarbonate modification. Metal binding studies suggest that this enzyme has only one metal binding site. The putative binding sites from several GTP and phosphoenolpyruvate utilizing enzymes are observed in P-enolpyruvate carboxykinase from different species.

  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. 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

  12. Identification of Ice Nucleation Active Sites on Silicate Dust Particles

    NASA Astrophysics Data System (ADS)

    Zolles, Tobias; Burkart, Julia; Häusler, Thomas; Pummer, Bernhard; Hitzenberger, Regina; Grothe, Hinrich

    2015-04-01

    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 [1-3]. Nevertheless, among those structures K-feldspar showed by far the highest ice nucleation activity. In this study, the reasons for its activity and the difference in the activity of the different feldspars were investigated in closer details. Conclusions are drawn from scanning electron microscopy, X-ray powder diffraction, infrared spectroscopy, and oil-immersion freezing experiments. We give a potential explanation of the increased ice nucleation activity of K-feldspar. The ice nucleating sites are very much dependent on the alkali ion present by altering the water structure and the feldspar surface. The higher activity of K-feldspar can be attributed to the presence of potassium ions on the surface and surface bilayer. The alkali-ions have different hydration shells and thus an influence on the ice nucleation activity of feldspar. Chaotropic behavior of Calcium and Sodium ions are lowering the ice nucleation potential of the other feldspars, while kosmotropic Potassium has a neutral or even positive effect. Furthermore we investigated the influence of milling onto the ice nucleation of quartz particles. The ice nucleation activity can be increased by mechanical milling, by introducing more molecular, nucleation active defects to the particle surface. This effect is larger than expected by plane surface increase. [1] Atkinson et al. The Importance of Feldspar for Ice Nucleation by Mineral Dust in Mixed-Phase Clouds. Nature 2013, 498, 355-358. [2] Yakobi-Hancock et al.. Feldspar Minerals as Efficient Deposition Ice Nuclei. Atmos. Chem. Phys. 2013, 13, 11175-11185. [3] Zolles et al. Identification of Ice Nucleation Active Sites on Feldspar Dust Particles. J. Phys. Chem. A 2015 accepted.

  13. 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

    2013-11-07

    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.

  14. 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

  15. Face the Edges: Catalytic Active Sites of Nanomaterials

    PubMed Central

    Ni, Bing

    2015-01-01

    Edges are special sites in nanomaterials. The atoms residing on the edges have different environments compared to those in other parts of a nanomaterial and, therefore, they may have different properties. Here, recent progress in nanomaterial fields is summarized from the viewpoint of the edges. Typically, edge sites in MoS2 or metals, other than surface atoms, can perform as active centers for catalytic reactions, so the method to enhance performance lies in the optimization of the edge structures. The edges of multicomponent interfaces present even more possibilities to enhance the activities of nanomaterials. Nanoframes and ultrathin nanowires have similarities to conventional edges of nanoparticles, the application of which as catalysts can help to reduce the use of costly materials. Looking beyond this, the edge structures of graphene are also essential for their properties. In short, the edge structure can influence many properties of materials. PMID:27980960

  16. 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

  17. 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.

  18. 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

  19. 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.

  20. 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.

  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.

  2. 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.

  3. Nest predation increases with parental activity: separating nest site and parental activity effects.

    PubMed Central

    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. PMID:11413645

  4. Active site amino acid sequence of human factor D.

    PubMed

    Davis, A E

    1980-08-01

    Factor D was isolated from human plasma by chromatography on CM-Sephadex C50, Sephadex G-75, and hydroxylapatite. Digestion of reduced, S-carboxymethylated factor D with cyanogen bromide resulted in three peptides which were isolated by chromatography on Sephadex G-75 (superfine) equilibrated in 20% formic acid. NH2-Terminal sequences were determined by automated Edman degradation with a Beckman 890C sequencer using a 0.1 M Quadrol program. The smallest peptide (CNBr III) consisted of the NH2-terminal 14 amino acids. The other two peptides had molecular weights of 17,000 (CNBr I) and 7000 (CNBr II). Overlap of the NH2-terminal sequence of factor D with the NH2-terminal sequence of CNBr I established the order of the peptides. The NH2-terminal 53 residues of factor D are somewhat more homologous with the group-specific protease of rat intestine than with other serine proteases. The NH2-terminal sequence of CNBr II revealed the active site serine of factor D. The typical serine protease active site sequence (Gly-Asp-Ser-Gly-Gly-Pro was found at residues 12-17. The region surrounding the active site serine does not appear to be more highly homologous with any one of the other serine proteases. The structural data obtained point out the similarities between factor D and the other proteases. However, complete definition of the degree of relationship between factor D and other proteases will require determination of the remainder of the primary structure.

  5. 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.

  6. [Mechanism of arginine deiminase activity by site-directed mutagenesis].

    PubMed

    Li, Lifeng; Ni, Ye; Sun, Zhihao

    2012-04-01

    Arginine deiminase (ADI) has been studied as a potential anti-cancer agent for inhibiting arginine-auxotrophic tumors (such as melanomas and hepatocellular carcinomas) in phase III clinical trials. In this work, we studied the molecular mechanism of arginine deiminase activity by site-directed mutagenesis. Three mutation sites, A128, H404 and 1410, were introduced into wild-type ADI gene by QuikChange site-directed mutagenesis method, and four ADI mutants M1 (A128T), M2 (H404R), M3 (I410L), and M4 (A128T, H404R) were obtained. The ADI mutants were individually expressed in Escherichia coli BL21 (DE3), and the enzymatic properties of the purified mutant proteins were determined. The results show that both A128T and H404R had enhanced optimum pH, higher activity and stability of ADI under physiological condition (pH 7.4), as well as reduced K(m) value. This study provides an insight into the molecular mechanism of the ADI activity, and also the experimental evidence for the rational protein evolution in the future.

  7. Potential sites of CFTR activation by tyrosine kinases

    PubMed Central

    Billet, Arnaud; Jia, Yanlin; Jensen, Timothy J.; Hou, Yue-Xian; Chang, Xiu-Bao; Riordan, John R.; Hanrahan, John W.

    2016-01-01

    ABSTRACT The CFTR chloride channel is tightly regulated by phosphorylation at multiple serine residues. Recently it has been proposed that its activity is also regulated by tyrosine kinases, however the tyrosine phosphorylation sites remain to be identified. In this study we examined 2 candidate tyrosine residues near the boundary between the first nucleotide binding domain and the R domain, a region which is important for channel function but devoid of PKA consensus sequences. Mutating tyrosines at positions 625 and 627 dramatically reduced responses to Src or Pyk2 without altering the activation by PKA, suggesting they may contribute to CFTR regulation. PMID:26645934

  8. 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

  9. MSK1 activity is controlled by multiple phosphorylation sites

    PubMed Central

    McCOY, Claire E.; Campbell, David G.; Deak, Maria; Bloomberg, Graham B.; Arthur, J. Simon C.

    2004-01-01

    MSK1 (mitogen- and stress-activated protein kinase) is a kinase activated in cells downstream of both the ERK1/2 (extracellular-signal-regulated kinase) and p38 MAPK (mitogen-activated protein kinase) cascades. In the present study, we show that, in addition to being phosphorylated on Thr-581 and Ser-360 by ERK1/2 or p38, MSK1 can autophosphorylate on at least six sites: Ser-212, Ser-376, Ser-381, Ser-750, Ser-752 and Ser-758. Of these sites, the N-terminal T-loop residue Ser-212 and the ‘hydrophobic motif’ Ser-376 are phosphorylated by the C-terminal kinase domain of MSK1, and their phosphorylation is essential for the catalytic activity of the N-terminal kinase domain of MSK1 and therefore for the phosphorylation of MSK1 substrates in vitro. Ser-381 is also phosphorylated by the C-terminal kinase domain, and mutation of Ser-381 decreases MSK1 activity, probably through the inhibition of Ser-376 phosphorylation. Ser-750, Ser-752 and Ser-758 are phosphorylated by the N-terminal kinase domain; however, their function is not known. The activation of MSK1 in cells therefore requires the activation of the ERK1/2 or p38 MAPK cascades and does not appear to require additional signalling inputs. This is in contrast with the closely related RSK (p90 ribosomal S6 kinase) proteins, whose activity requires phosphorylation by PDK1 (3-phosphoinositide-dependent protein kinase 1) in addition to phosphorylation by ERK1/2. PMID:15568999

  10. Increased methane emissions from deep osmotic and buoyant convection beneath submarine seeps as climate warms.

    PubMed

    Cardoso, Silvana S S; Cartwright, Julyan H E

    2016-10-27

    High speeds have been measured at seep and mud-volcano sites expelling methane-rich fluids from the seabed. Thermal or solute-driven convection alone cannot explain such high velocities in low-permeability sediments. Here we demonstrate that in addition to buoyancy, osmotic effects generated by the adsorption of methane onto the sediments can create large overpressures, capable of recirculating seawater from the seafloor to depth in the sediment layer, then expelling it upwards at rates of up to a few hundreds of metres per year. In the presence of global warming, such deep recirculation of seawater can accelerate the melting of methane hydrates at depth from timescales of millennia to just decades, and can drastically increase the rate of release of methane into the hydrosphere and perhaps the atmosphere.

  11. Increased methane emissions from deep osmotic and buoyant convection beneath submarine seeps as climate warms

    NASA Astrophysics Data System (ADS)

    Cardoso, Silvana S. S.; Cartwright, Julyan H. E.

    2016-10-01

    High speeds have been measured at seep and mud-volcano sites expelling methane-rich fluids from the seabed. Thermal or solute-driven convection alone cannot explain such high velocities in low-permeability sediments. Here we demonstrate that in addition to buoyancy, osmotic effects generated by the adsorption of methane onto the sediments can create large overpressures, capable of recirculating seawater from the seafloor to depth in the sediment layer, then expelling it upwards at rates of up to a few hundreds of metres per year. In the presence of global warming, such deep recirculation of seawater can accelerate the melting of methane hydrates at depth from timescales of millennia to just decades, and can drastically increase the rate of release of methane into the hydrosphere and perhaps the atmosphere.

  12. Increased methane emissions from deep osmotic and buoyant convection beneath submarine seeps as climate warms

    PubMed Central

    Cardoso, Silvana S. S.; Cartwright, Julyan H. E.

    2016-01-01

    High speeds have been measured at seep and mud-volcano sites expelling methane-rich fluids from the seabed. Thermal or solute-driven convection alone cannot explain such high velocities in low-permeability sediments. Here we demonstrate that in addition to buoyancy, osmotic effects generated by the adsorption of methane onto the sediments can create large overpressures, capable of recirculating seawater from the seafloor to depth in the sediment layer, then expelling it upwards at rates of up to a few hundreds of metres per year. In the presence of global warming, such deep recirculation of seawater can accelerate the melting of methane hydrates at depth from timescales of millennia to just decades, and can drastically increase the rate of release of methane into the hydrosphere and perhaps the atmosphere. PMID:27807343

  13. 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.

  14. Evolution and biogeography of deep-sea vent and seep invertebrates.

    PubMed

    Van Dover, C L; German, C R; Speer, K G; Parson, L M; Vrijenhoek, R C

    2002-02-15

    Deep-sea hydrothermal vents and cold seeps are submarine springs where nutrient-rich fluids emanate from the sea floor. Vent and seep ecosystems occur in a variety of geological settings throughout the global ocean and support food webs based on chemoautotrophic primary production. Most vent and seep invertebrates arrive at suitable habitats as larvae dispersed by deep-ocean currents. The recent evolution of many vent and seep invertebrate species (<100 million years ago) suggests that Cenozoic tectonic history and oceanic circulation patterns have been important in defining contemporary biogeographic patterns.

  15. 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

  16. Species distribution and population connectivity of deep-sea mussels at hydrocarbon seeps in the Gulf of Mexico.

    PubMed

    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.

  17. 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

  18. 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.

  19. 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.

  20. Vitamin K epoxide reductase: homology, active site and catalytic mechanism.

    PubMed

    Goodstadt, Leo; Ponting, Chris P

    2004-06-01

    Vitamin K epoxide reductase (VKOR) recycles reduced vitamin K, which is used subsequently as a co-factor in the gamma-carboxylation of glutamic acid residues in blood coagulation enzymes. VKORC1, a subunit of the VKOR complex, has recently been shown to possess this activity. Here, we show that VKORC1 is a member of a large family of predicted enzymes that are present in vertebrates, Drosophila, plants, bacteria and archaea. Four cysteine residues and one residue, which is either serine or threonine, are identified as likely active-site residues. In some plant and bacterial homologues the VKORC1 homologous domain is fused with domains of the thioredoxin family of oxidoreductases. These might reduce disulfide bonds of VKORC1-like enzymes as a prerequisite for their catalytic activities.

  1. 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

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

    PubMed

    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.

  3. 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.

  4. 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.

  5. Identification of covalent active site inhibitors of dengue virus protease

    PubMed Central

    Koh-Stenta, Xiaoying; Joy, Joma; Wang, Si Fang; Kwek, Perlyn Zekui; Wee, John Liang Kuan; Wan, Kah Fei; Gayen, Shovanlal; Chen, Angela Shuyi; Kang, CongBao; Lee, May Ann; Poulsen, Anders; Vasudevan, Subhash G; Hill, Jeffrey; Nacro, Kassoum

    2015-01-01

    Dengue virus (DENV) protease is an attractive target for drug development; however, no compounds have reached clinical development to date. In this study, we utilized a potent West Nile virus protease inhibitor of the pyrazole ester derivative class as a chemical starting point for DENV protease drug development. Compound potency and selectivity for DENV protease were improved through structure-guided small molecule optimization, and protease-inhibitor binding interactions were validated biophysically using nuclear magnetic resonance. Our work strongly suggests that this class of compounds inhibits flavivirus protease through targeted covalent modification of active site serine, contrary to an allosteric binding mechanism as previously described. PMID:26677315

  6. Target-classification approach applied to active UXO sites

    NASA Astrophysics Data System (ADS)

    Shubitidze, F.; Fernández, J. P.; Shamatava, Irma; Barrowes, B. E.; O'Neill, K.

    2013-06-01

    This study is designed to illustrate the discrimination performance at two UXO active sites (Oklahoma's Fort Sill and the Massachusetts Military Reservation) of a set of advanced electromagnetic induction (EMI) inversion/discrimination models which include the orthonormalized volume magnetic source (ONVMS), joint diagonalization (JD), and differential evolution (DE) approaches and whose power and flexibility greatly exceed those of the simple dipole model. The Fort Sill site is highly contaminated by a mix of the following types of munitions: 37-mm target practice tracers, 60-mm illumination mortars, 75-mm and 4.5'' projectiles, 3.5'', 2.36'', and LAAW rockets, antitank mine fuzes with and without hex nuts, practice MK2 and M67 grenades, 2.5'' ballistic windshields, M2A1-mines with/without bases, M19-14 time fuzes, and 40-mm practice grenades with/without cartridges. The site at the MMR site contains targets of yet different sizes. In this work we apply our models to EMI data collected using the MetalMapper (MM) and 2 × 2 TEMTADS sensors. The data for each anomaly are inverted to extract estimates of the extrinsic and intrinsic parameters associated with each buried target. (The latter include the total volume magnetic source or NVMS, which relates to size, shape, and material properties; the former includes location, depth, and orientation). The estimated intrinsic parameters are then used for classification performed via library matching and the use of statistical classification algorithms; this process yielded prioritized dig-lists that were submitted to the Institute for Defense Analyses (IDA) for independent scoring. The models' classification performance is illustrated and assessed based on these independent evaluations.

  7. Restriction to large-scale gene flow vs. regional panmixia among cold seep Escarpia spp. (Polychaeta, Siboglinidae).

    PubMed

    Cowart, Dominique A; Huang, Chunya; Arnaud-Haond, Sophie; Carney, Susan L; Fisher, Charles R; Schaeffer, Stephen W

    2013-08-01

    The history of colonization and dispersal in fauna distributed among deep-sea chemosynthetic ecosystems remains enigmatic and poorly understood because of an inability to mark and track individuals. A combination of molecular, morphological and environmental data improves understanding of spatial and temporal scales at which panmixia, disruption of gene flow or even speciation may occur. Vestimentiferan tubeworms of the genus Escarpia are important components of deep -sea cold seep ecosystems, as they provide long-term habitat for many other taxa. Three species of Escarpia, Escarpia spicata [Gulf of California (GoC)], Escarpia laminata [Gulf of Mexico (GoM)] and Escarpia southwardae (West African Cold Seeps), have been described based on morphology, but are not discriminated through the use of mitochondrial markers (cytochrome oxidase subunit 1; large ribosomal subunit rDNA, 16S; cytochrome b). Here, we also sequenced the exon-primed intron-crossing Haemoglobin subunit B2 intron and genotyped 28 microsatellites to (i) determine the level of genetic differentiation, if any, among the three geographically separated entities and (ii) identify possible population structure at the regional scale within the GoM and West Africa. Results at the global scale support the occurrence of three genetically distinct groups. At the regional scale among eight sampling sites of E. laminata (n = 129) and among three sampling sites of E. southwardae (n = 80), no population structure was detected. These findings suggest that despite the patchiness and isolation of seep habitats, connectivity is high on regional scales.

  8. 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.

  9. 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.

  10. 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

  11. Identification of Phosphorylation Sites Altering Pollen Soluble Inorganic Pyrophosphatase Activity.

    PubMed

    Eaves, Deborah J; Haque, Tamanna; Tudor, Richard L; Barron, Yoshimi; Zampronio, Cleidiane G; Cotton, Nicholas P J; de Graaf, Barend H J; White, Scott A; Cooper, Helen J; Franklin, F Christopher H; Harper, Jeffery F; Franklin-Tong, Vernonica E

    2017-03-01

    Protein phosphorylation regulates numerous cellular processes. Identifying the substrates and protein kinases involved is vital to understand how these important posttranslational modifications modulate biological function in eukaryotic cells. Pyrophosphatases catalyze the hydrolysis of inorganic phosphate (PPi) to inorganic phosphate Pi, driving biosynthetic reactions; they are essential for low cytosolic inorganic phosphate. It was suggested recently that posttranslational regulation of Family I soluble inorganic pyrophosphatases (sPPases) may affect their activity. We previously demonstrated that two pollen-expressed sPPases, Pr-p26.1a and Pr-p26.1b, from the flowering plant Papaver rhoeas were inhibited by phosphorylation. Despite the potential significance, there is a paucity of data on sPPase phosphorylation and regulation. Here, we used liquid chromatographic tandem mass spectrometry to map phosphorylation sites to the otherwise divergent amino-terminal extensions on these pollen sPPases. Despite the absence of reports in the literature on mapping phosphorylation sites on sPPases, a database survey of various proteomes identified a number of examples, suggesting that phosphorylation may be a more widely used mechanism to regulate these enzymes. Phosphomimetic mutants of Pr-p26.1a/b significantly and differentially reduced PPase activities by up to 2.5-fold at pH 6.8 and 52% in the presence of Ca(2+) and hydrogen peroxide over unmodified proteins. This indicates that phosphoregulation of key sites can inhibit the catalytic responsiveness of these proteins in concert with key intracellular events. As sPPases are essential for many metabolic pathways in eukaryotic cells, our findings identify the phosphorylation of sPPases as a potential master regulatory mechanism that could be used to attenuate metabolism.

  12. Evidence for segmental mobility in the active site of pepsin

    SciTech Connect

    Pohl, J.; Strop, P.; Senn, H.; Foundling, S.; Kostka, V.

    1986-05-01

    The low hydrolytic activity (k/sub cat/ < 0.001 s/sup -1/) of chicken pepsin (CP) towards tri- and tetrapeptides is enhanced at least 100 times by modification of its single sulfhydryl group of Cys-115, with little effect on K/sub m/-values. Modification thus simulates the effect of secondary substrate binding on pepsin catalysis. The rate of Cys-115 modification is substantially decreased in the presence of some competitive inhibitors, suggesting its active site location. Experiments with CP alkylated at Cys-115 with Acrylodan as a fluorescent probe or with N-iodoacetyl-(4-fluoro)-aniline as a /sup 19/F-nmr probe suggest conformation change around Cys-115 to occur on substrate or substrate analog binding. The difference /sup 1/H-nmr spectra (500 MHz) of unmodified free and inhibitor-complexed CP reveal chemical shifts almost exclusively in the aromatic region. The effects of Cu/sup + +/ on /sup 19/F- and /sup 1/H-nmr spectra have been studied. Examination of a computer graphics model of CP based on E. parasitica pepsin-inhibitor complex X-ray coordinates suggests that Cys-115 is located near the S/sub 3//S/sub 5/ binding site. The results are interpreted in favor of segmental mobility of this region important for pepsin substrate binding and catalysis.

  13. First Principles Computational Study of the Active Site of Arginase

    SciTech Connect

    Ivanov, Ivaylo; Klien, Micheal

    2004-01-14

    Ab initio density functional theory (DFT) methods were used to investigate the structural features of the active site of the binuclear enzyme rat liver arginase. Special emphasis was placed on the crucial role of the second shell ligand interactions. These interactions were systematically studied by performing calculations on models of varying size. It was determined that a water molecule, and not hydroxide, is the bridging exogenous ligand. The carboxylate ligands facilitate the close approach of the Mn (II) ions by attenuating the metal-metal electrostatic repulsion. Of the two metals, MnA was shown to carry a larger positive charge. Analysis of the electronic properties of the active site revealed that orbitals involving the terminal Asp234 residue, as well as the flexible -1,1 bridging Asp232, lie at high energies, suggesting weaker coordination. This is reflected in certain structural variability present in our models and is also consistent with recent experimental findings. Finally, implications of our findings for the biological function of the enzyme are delineated.

  14. 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.

  15. Seep and stream nitrogen dynamics in two adjacent mixed land use watersheds

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In many headwater catchments, stream flow originates from surface seeps and springs. The objective of this study was to determine the influence of seeps on nitrogen (N) dynamics within the stream and at the outlet of two adjacent mixed land use watersheds. Nitrogen concentrations in stream water wer...

  16. Seep and stream nitrogen dynamics in two adjacent mixed land use watersheds

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In many headwater catchments, streamflow originates from surface seeps and springs. The objective of this study was to determine the influence of seeps on nitrogen (N) dynamics within the stream and at the outlet of two adjacent mixed land use watersheds. Nitrogen concentrations in stream water were...

  17. 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.

  18. C-H Activation on Co,O Sites: Isolated Surface Sites versus Molecular Analogs.

    PubMed

    Estes, Deven P; Siddiqi, Georges; Allouche, Florian; Kovtunov, Kirill V; Safonova, Olga V; Trigub, Alexander L; Koptyug, Igor V; Copéret, Christophe

    2016-11-16

    The activation and conversion of hydrocarbons is one of the most important challenges in chemistry. Transition-metal ions (V, Cr, Fe, Co, etc.) isolated on silica surfaces are known to catalyze such processes. The mechanisms of these processes are currently unknown but are thought to involve C-H activation as the rate-determining step. Here, we synthesize well-defined Co(II) ions on a silica surface using a metal siloxide precursor followed by thermal treatment under vacuum at 500 °C. We show that these isolated Co(II) sites are catalysts for a number of hydrocarbon conversion reactions, such as the dehydrogenation of propane, the hydrogenation of propene, and the trimerization of terminal alkynes. We then investigate the mechanisms of these processes using kinetics, kinetic isotope effects, isotopic labeling experiments, parahydrogen induced polarization (PHIP) NMR, and comparison with a molecular analog. The data are consistent with all of these reactions occurring by a common mechanism, involving heterolytic C-H or H-H activation via a 1,2 addition across a Co-O bond.

  19. 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

  20. 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.

  1. 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

  2. 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.

  3. 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.

  4. An active site water network in the plasminogen activator pla from Yersinia pestis.

    PubMed

    Eren, Elif; Murphy, Megan; Goguen, Jon; van den Berg, Bert

    2010-07-14

    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 A. 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.

  5. 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

  6. Constraining spatial variability of methane ebullition seeps in thermokarst lakes using point process models

    NASA Astrophysics Data System (ADS)

    Walter Anthony, Katey M.; Anthony, Peter

    2013-07-01

    is an important but highly heterogeneous mode of methane emission in lakes. Variability in both spatial distribution and temporal flux creates difficulty in constraining uncertainties in whole lake emission estimates. Analysis of short- and long-term flux measurements on 162 ebullition seeps in 24 panarctic lakes confirmed that seep classes, identified a priori according to bubble patterns in winter lake ice, have distinct associated fluxes irrespective of lake or region. To understand the drivers of ebullition's spatial variability and uncover ways to better quantify ebullition in field work, we combined point-process modeling with field measurements of 2679 GPS-marked and classified ebullition seeps in three Alaskan thermokarst (thaw) lakes that varied by region, permafrost type, and seep distribution. Spatial analysis of field data revealed that seeps cluster above thawed permafrost soil mounds in lake bottoms. Seep density and clustering, determined from field observations, were used as parameters in a Poisson cluster process model to simulate seeps across entire lake surfaces. Sampling results indicated that (1) applying seep-class mean flux values to unmeasured seeps counted on ice-bubble surveys does not compromise accuracy of whole lake flux estimates; (2) three distributed 50 m2 ice-bubble survey transects more accurately estimate mean lake ebullition than 17 dispersed 0.2 m2 bubble traps; and (3) the uncertainty associated with whole lake mean ebullition estimated by lake-ice survey transects is inversely related to seep density. Findings suggest that transect field data collected on a large number of widely distributed lakes can be combined to provide a well-constrained, bottom-up estimate of regional lake ebullition.

  7. Diversity and functional analysis of bacterial communities associated with natural hydrocarbon seeps in acidic soils at Rainbow Springs, Yellowstone National Park.

    PubMed

    Hamamura, Natsuko; Olson, Sarah H; Ward, David M; Inskeep, William P

    2005-10-01

    In this paper we describe the bacterial communities associated with natural hydrocarbon seeps in nonthermal soils at Rainbow Springs, Yellowstone National Park. Soil chemical analysis revealed high sulfate concentrations and low pH values (pH 2.8 to 3.8), which are characteristic of acid-sulfate geothermal activity. The hydrocarbon composition of the seep soils consisted almost entirely of saturated, acyclic alkanes (e.g., n-alkanes with chain lengths of C15 to C30, as well as branched alkanes, predominately pristane and phytane). Bacterial populations present in the seep soils were phylogenetically characterized by 16S rRNA gene clone library analysis. The majority of the sequences recovered (>75%) were related to sequences of heterotrophic acidophilic bacteria, including Acidisphaera spp. and Acidiphilium spp. of the alpha-Proteobacteria. Clones related to the iron- and sulfur-oxidizing chemolithotroph Acidithiobacillus spp. were also recovered from one of the seep soils. Hydrocarbon-amended soil-sand mixtures were established to examine [14C]hexadecane mineralization and corresponding changes in the bacterial populations using denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments. Approximately 50% of the [14C]hexadecane added was recovered as 14CO2 during an 80-day incubation, and this was accompanied by detection of heterotrophic acidophile-related sequences as dominant DGGE bands. An alkane-degrading isolate was cultivated, whose 16S rRNA gene sequence was identical to the sequence of a dominant DGGE band in the soil-sand mixture, as well as the clone sequence recovered most frequently from the original soil. This and the presence of an alkB gene homolog in this isolate confirmed the alkane degradation capability of one population indigenous to acidic hydrocarbon seep soils.

  8. 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

  9. Characterization of the active site of ADP-ribosyl cyclase.

    PubMed

    Munshi, C; Thiel, D J; Mathews, I I; Aarhus, R; Walseth, T F; Lee, H C

    1999-10-22

    ADP-ribosyl cyclase synthesizes two Ca(2+) messengers by cyclizing NAD to produce cyclic ADP-ribose and exchanging nicotinic acid with the nicotinamide group of NADP to produce nicotinic acid adenine dinucleotide phosphate. Recombinant Aplysia cyclase was expressed in yeast and co-crystallized with a substrate, nicotinamide. x-ray crystallography showed that the nicotinamide was bound in a pocket formed in part by a conserved segment and was near the central cleft of the cyclase. Glu(98), Asn(107) and Trp(140) were within 3.5 A of the bound nicotinamide and appeared to coordinate it. Substituting Glu(98) with either Gln, Gly, Leu, or Asn reduced the cyclase activity by 16-222-fold, depending on the substitution. The mutant N107G exhibited only a 2-fold decrease in activity, while the activity of W140G was essentially eliminated. The base exchange activity of all mutants followed a similar pattern of reduction, suggesting that both reactions occur at the same active site. In addition to NAD, the wild-type cyclase also cyclizes nicotinamide guanine dinucleotide to cyclic GDP-ribose. All mutant enzymes had at least half of the GDP-ribosyl cyclase activity of the wild type, some even 2-3-fold higher, indicating that the three coordinating amino acids are responsible for positioning of the substrate but not absolutely critical for catalysis. To search for the catalytic residues, other amino acids in the binding pocket were mutagenized. E179G was totally devoid of GDP-ribosyl cyclase activity, and both its ADP-ribosyl cyclase and the base exchange activities were reduced by 10,000- and 18,000-fold, respectively. Substituting Glu(179) with either Asn, Leu, Asp, or Gln produced similar inactive enzymes, and so was the conversion of Trp(77) to Gly. However, both E179G and the double mutant E179G/W77G retained NAD-binding ability as shown by photoaffinity labeling with [(32)P]8-azido-NAD. These results indicate that both Glu(179) and Trp(77) are crucial for catalysis and

  10. Mutations inducing an active-site aperture in Rhizobium sp. sucrose isomerase confer hydrolytic activity.

    PubMed

    Lipski, Alexandra; Watzlawick, Hildegard; Ravaud, Stéphanie; Robert, Xavier; Rhimi, Moez; Haser, Richard; Mattes, Ralf; Aghajari, Nushin

    2013-02-01

    Sucrose isomerase is an enzyme that catalyzes the production of sucrose isomers of high biotechnological and pharmaceutical interest. Owing to the complexity of the chemical synthesis of these isomers, isomaltulose and trehalulose, enzymatic conversion remains the preferred method for obtaining these products. Depending on the microbial source, the ratio of the sucrose-isomer products varies significantly. In studies aimed at understanding and explaining the underlying molecular mechanisms of these reactions, mutations obtained using a random-mutagenesis approach displayed a major hydrolytic activity. Two of these variants, R284C and F164L, of sucrose isomerase from Rhizobium sp. were therefore crystallized and their crystal structures were determined. The three-dimensional structures of these mutants allowed the identification of the molecular determinants that favour hydrolytic activity compared with transferase activity. Substantial conformational changes resulting in an active-site opening were observed, as were changes in the pattern of water molecules bordering the active-site region.

  11. Site-specific PEGylation of lidamycin and its antitumor activity

    PubMed Central

    Li, Liang; Shang, Boyang; Hu, Lei; Shao, Rongguang; Zhen, Yongsu

    2015-01-01

    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 (Mw 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

  12. 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.

  13. Allosteric site-mediated active site inhibition of PBP2a using Quercetin 3-O-rutinoside and its combination.

    PubMed

    Rani, Nidhi; Vijayakumar, Saravanan; P T V, Lakshmi; Arunachalam, Annamalai

    2016-08-01

    Recent crystallographic study revealed the involvement of allosteric site in active site inhibition of penicillin binding protein (PBP2a), where one molecule of Ceftaroline (Cef) binds to the allosteric site of PBP2a and paved way for the other molecule (Cef) to bind at the active site. Though Cef has the potency to inhibit the PBP2a, its adverse side effects are of major concern. Previous studies have reported the antibacterial property of Quercetin derivatives, a group of natural compounds. Hence, the present study aims to evaluate the effect of Quercetin 3-o-rutinoside (Rut) in allosteric site-mediated active site inhibition of PBP2a. The molecular docking studies between allosteric site and ligands (Rut, Que, and Cef) revealed a better binding efficiency (G-score) of Rut (-7.790318) and Cef (-6.194946) with respect to Que (-5.079284). Molecular dynamic (MD) simulation studies showed significant changes at the active site in the presence of ligands (Rut and Cef) at allosteric site. Four different combinations of Rut and Cef were docked and their G-scores ranged between -6.320 and -8.623. MD studies revealed the stability of the key residue (Ser403) with Rut being at both sites, compared to other complexes. Morphological analysis through electron microscopy confirmed that combination of Rut and Cefixime was able to disturb the bacterial cell membrane in a similar fashion to that of Rut and Cefixime alone. The results of this study indicate that the affinity of Rut at both sites were equally good, with further validations Rut could be considered as an alternative for inhibiting MRSA growth.

  14. Extensive site-directed mutagenesis reveals interconnected functional units in the alkaline phosphatase active site

    PubMed Central

    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. DOI: http://dx.doi.org/10.7554/eLife.06181.001 PMID:25902402

  15. A split active site couples cap recognition by Dcp2 to activation

    PubMed Central

    Floor, Stephen N.; Jones, Brittnee N.; Hernandez, Gail A.; Gross, John D.

    2010-01-01

    Decapping by Dcp2 is an essential step in 5′-3′ mRNA decay. In yeast, decapping requires an open-to-closed transition in Dcp2, though the link between closure and catalysis remains elusive. Here we show using NMR that cap binds conserved residues on both the catalytic and regulatory domains of Dcp2. Lesions in the cap-binding site on the regulatory domain reduce the catalytic step two orders of magnitude and block formation of the closed state whereas Dcp1 enhances the catalytic step by a factor of ten and promotes closure. We conclude that closure occurs during the rate-limiting catalytic step of decapping, juxtaposing the cap-binding region of each domain to form a composite active site. This work suggests a model for regulation of decapping, where coactivators trigger decapping by stabilizing a labile composite active site. PMID:20711189

  16. Epizooic metazoan meiobenthos associated with tubeworm and mussel aggregations from cold seeps of the northern Gulf of Mexico.

    PubMed

    Bright, M; Plum, C; Riavitz, L A; Nikolov, N; Martinez Arbizu, P; Cordes, E E; Gollner, S

    2010-11-01

    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.

  17. 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

  18. 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

  19. 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.

  20. 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

  1. 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.

  2. Characterization of Active Site Residues of Nitroalkane Oxidase†

    PubMed Central

    Valley, Michael P.; Fenny, Nana S.; Ali, Shah R.; Fitzpatrick, Paul F.

    2010-01-01

    The flavoenzyme nitroalkane oxidase catalyzes the oxidation of primary and secondary nitrolkanes to the corresponding aldehydes and ketones plus nitrite. The structure of the enzyme shows that Serl71 forms a hydrogen bond to the flavin N5, suggesting that it plays a role in catalysis. Cys397 and Tyr398 were previously identified by chemical modification as potential active site residues. To more directly probe the roles of these residues, the S171A, S171V, S171T, C397S, and Y398F enzymes have been characterized with nitroethane as substrate. The C397S and Y398 enzymes were less stable than the wild-type enzyme, and the C397S enzyme routinely contained a substoichiometric amount of FAD. Analysis of the steady-state kinetic parameters for the mutant enzymes, including deuterium isotope effects, establishes that all of the mutations result in decreases in the rate constants for removal of the substrate proton by ~5-fold and decreases in the rate constant for product release of ~2-fold. Only the S171V and S171T mutations alter the rate constant for flavin oxidation. These results establish that these residues are not involved in catalysis, but rather are required for maintaining the protein structure. PMID:20056514

  3. 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.

  4. 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.

  5. 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.

  6. A molecular gut content study of Themisto abyssorum (Amphipoda) from Arctic hydrothermal vent and cold seep systems.

    PubMed

    Olsen, Bernt Rydland; Troedsson, Christofer; Hadziavdic, Kenan; Pedersen, Rolf B; Rapp, Hans Tore

    2014-08-01

    The use of DNA as a marker for prey inside the gut of predators has been instrumental in further understanding of known and unknown interactions. Molecular approaches are in particular useful in unavailable environments like the deep sea. Trophic interactions in the deep sea are difficult to observe in situ, correct deep-sea experimental laboratory conditions are difficult to obtain, animals rarely survive the sampling, or the study organisms feed during the sampling due to long hauls. Preliminary studies of vent and seep systems in the Nordic Seas have identified the temperate-cold-water pelagic amphipod Themisto abyssorum as a potentially important predator in these chemosynthetic habitats. However, the prey of this deep-sea predator is poorly known, and we applied denaturing high performance liquid chromatography (DHPLC) to investigate the predator-prey interactions of T. abyssorum in deep-water vent and seep systems. Two deep-water hydrothermally active localities (The Jan Mayen and Loki's Castle vent fields) and one cold seep locality (The Håkon Mosby mud volcano) in the Nordic Seas were sampled, genomic DNA of the stomachs of T. abyssorum was extracted, and 18S rDNA gene was amplified and used to map the stomach content. We found a wide range of organisms including micro-eukaryotes, metazoans and detritus. Themisto abyssorum specimens from Loki's Castle had the highest diversity of prey. The wide range of prey items found suggests that T. abyssorum might be involved in more than one trophic level and should be regarded as an omnivore and not a strict carnivore as have previously been suggested.

  7. 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.

  8. 40 CFR 61.154 - Standard for active waste disposal sites.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 9 2012-07-01 2012-07-01 false Standard for active waste disposal... for Asbestos § 61.154 Standard for active waste disposal sites. Each owner or operator of an active... visible emissions to the outside air from any active waste disposal site where asbestos-containing...

  9. 40 CFR 61.154 - Standard for active waste disposal sites.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 9 2014-07-01 2014-07-01 false Standard for active waste disposal... for Asbestos § 61.154 Standard for active waste disposal sites. Each owner or operator of an active... visible emissions to the outside air from any active waste disposal site where asbestos-containing...

  10. 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...

  11. 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...

  12. 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...

  13. 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...

  14. 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...

  15. 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.

  16. 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.

  17. Microbial diversity of cold-seep sediments in Sagami Bay, Japan, as determined by 16S rRNA gene and lipid analyses.

    PubMed

    Fang, Jiasong; Shizuka, Arakawa; Kato, Chiaki; Schouten, Stefan

    2006-09-01

    Microbial communities in Calyptogena sediment and microbial mats of Sagami Bay, Japan, were characterized using 16S rRNA gene sequencing and lipid biomarker analysis. Characterization of 16S rRNA gene isolated from these samples suggested a predominance of bacterial phylotypes related to Gammaproteobacteria (57-64%) and Deltaproteobacteria (27-29%). The Epsilonproteobacteria commonly found in cold seeps and hydrothermal vents were only detected in the microbial mat sample. Significantly different archaeal phylotypes were found in Calyptogena sediment and microbial mats; the former contained only Crenarchaeota clones (100% of the total archaeal clones) and the latter exclusively Euryarchaeota clones, including the anaerobic oxidation of methane archaeal groups ANME-2a and ANME-2c. Many of these lineages are as yet uncultured and undescribed groups of bacteria and archaea. Phospholipid fatty acid analysis suggested the presence of sulphate-reducing and sulphur-oxidizing bacteria. Results of intact glyceryl dialkyl glyceryl tetraether lipid analysis indicated the presence of nonthermophilic marine planktonic archaea. These results suggest that the microbial community in the Sagami Bay seep site is distinct from previously characterized cold-seep environments.

  18. Microbial Diversity of Cold-Seep Sediments in Sagami Bay, Japan as Determined by 16S rDNA and Lipid Analyses

    NASA Astrophysics Data System (ADS)

    Fang, J.; Arakawa, S.; Kato, C.; Schouten, S.

    2006-12-01

    Microbial communities in Calyptogena sediment and microbial mats of Sagami Bay, Japan were characterized by using 16S rDNA sequencing and lipid biomarker analysis. Characterization of 16S rDNA isolated from these samples suggested a predominance of bacterial phylotypes related to γ- (57-64%) and δ-subclasses (27-29%) of the Proteobacteria. The ɛ-subclass of the Proteobacteria commonly found in cold seeps and hydrothermal vents were only detected in the microbial mat sample. There are significantly different archaeal phylotypes between Calyptogena sediment and microbial mat; the former contains only Crenarchaeota clones (100% of the total archaeal clones) and the latter exclusively Euryarchaeota clones including the ANME-2a and ANME-2c archaeal groups. Many of these lineages are as yet uncultured and undescribed groups of bacteria and archaea. Phospholipid fatty acid analysis suggests the presence of sulfate-reducing and sulfur-oxidizing bacteria. Results of intact glyceryl dialkyl glyceryl tetraether (GDGT) lipid analysis indicate the presence of nonthermophilic marine planktonic archaea. These results suggest that the microbial community in the Sagami Bay seep site is distinct from previously characterized cold seep environments.

  19. Lidar research activities and observations at NARL site, Gadanki, India

    NASA Astrophysics Data System (ADS)

    Yellapragada, Bhavani Kumar

    2016-05-01

    The National Atmospheric Research Laboratory (NARL), a unit of Department of Space (DOS), located at Gadanki village (13.5°N, 79.2°E, 370 m AMSL) in India, is involved in the development of lidar remote sensing technologies for atmospheric research. Several advanced lidar technologies employing micropulse, polarization, Raman and scanning have been developed at this site and demonstrated for atmospheric studies during the period between 2008 and 2015. The technology of micropulse lidar, operates at 532 nm wavelength, was successfully transferred to an industry and the commercial version has been identified for Indian Lidar network (I-LINK) programme. Under this lidar network activity, several lidar units were installed at different locations in India to study tropospheric aerosols and clouds. The polarization sensitive lidar technology was realized using a set of mini photomultiplier tube (PMT) units and has the capability to operate during day and night without a pause. The lidar technology uses a compact flashlamp pumped Qswitched laser and employs biaxial configuration between the transmitter and receiver units. The lidar technology has been utilized for understanding the polarization characteristics of boundary layer aerosols during the mixed layer development. The demonstrated Raman lidar technology, uses the third harmonic wavelength of Nd:YAG laser, provides the altitude profiles of aerosol backscattering, extinction and water vapor covering the boundary layer range and allows operation during nocturnal periods. The Raman lidar derived height profiles of aerosol backscattering and extinction coefficient, lidar ratio, and watervapor mixing ratio inform the tropical boundary layer aerosol characteristics. The scanning lidar technology uses a near infrared laser wavelength for probing the lower atmosphere and has been utilized for high resolution cloud profiling during convective periods. The lidar technology is also used for rain rate measurement during

  20. 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.

  1. 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.

  2. Active-site zinc ligands and activated H2O of zinc enzymes.

    PubMed Central

    Vallee, B L; Auld, D S

    1990-01-01

    The x-ray crystallographic structures of 12 zinc enzymes have been chosen as standards of reference to identify the ligands to the catalytic and structural zinc atoms of other members of their respective enzyme families. Universally, H2O is a ligand and critical component of the catalytically active zinc sites. In addition, three protein side chains bind to the catalytic zinc atom, whereas four protein ligands bind to the structural zinc atom. The geometry and coordination number of zinc can vary greatly to accommodate particular ligands. Zinc forms complexes with nitrogen and oxygen just as readily as with sulfur, and this is reflected in catalytic zinc sites having a binding frequency of His much greater than Glu greater than Asp = Cys, three of which bind to the metal atom. The systematic spacing between the ligands is striking. For all catalytic zinc sites except the coenzyme-dependent alcohol dehydrogenase, the first two ligands are separated by a "short-spacer" consisting of 1 to 3 amino acids. These ligands are separated from the third ligand by a "long spacer" of approximately 20 to approximately 120 amino acids. The spacer enables formation of a primary bidentate zinc complex, whereas the long spacer contributes flexibility to the coordination sphere, which can poise the zinc for catalysis as well as bring other catalytic and substrate binding groups into apposition with the active site. The H2O is activated by ionization, polarization, or poised for displacement. Collectively, the data imply that the preferred mechanistic pathway for activating the water--e.g., zinc hydroxide or Lewis acid catalysis--will be determined by the identity of the other three ligands and their spacing. Images PMID:2104979

  3. 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.

  4. 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.

  5. Dynamics of cell proliferation and apoptosis reflect different life strategies in hydrothermal vent and cold seep vestimentiferan tubeworms.

    PubMed

    Pflugfelder, Bettina; Cary, S Craig; Bright, Monika

    2009-07-01

    Deep-sea vestimentiferan tubeworms, which live in symbiosis with bacteria, exhibit different life strategies according to their habitat. At unstable and relatively short-lived hydrothermal vents, they grow extremely fast, whereas their close relatives at stable and long-persisting cold seeps grow slowly and live up to 300 years. Growth and age differences are thought to occur because of ecological and physiological adaptations. However, the underlying mechanisms of cell proliferation and death, which are closely linked to homeostasis, growth, and longevity, are unknown. Here, we show by immunohistochemical and ultrastructural cell cycle analyses that cell proliferation activities of the two species studied are higher than in any other characterized invertebrate, being only comparable with tumor and wound-healing processes. The slow growth in Lamellibrachia luymesi from cold seeps results from balanced activities of proliferation and apoptosis in the epidermis. In contrast, Riftia pachyptila from hydrothermal vents grows fast because apoptosis is down-regulated in this tissue. The symbiont-housing organ, the trophosome, exhibits a complex cell cycle and terminal differentiation pattern in both species, and growth is regulated by proliferation. These mechanisms have similarities to the up- and down-regulation of proliferation or apoptosis in various types of tumor, although they occur in healthy animals in this study, thus providing significant insights into the underlying mechanisms of growth and longevity.

  6. 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

  7. The yeast regulator of transcription protein Rtr1 lacks an active site and phosphatase activity.

    PubMed

    Xiang, Kehui; Manley, James L; Tong, Liang

    2012-07-10

    The activity of RNA polymerase II (Pol II) is controlled in part by the phosphorylation state of the C-terminal domain (CTD) of its largest subunit. Recent reports have suggested that yeast regulator of transcription protein, Rtr1, and its human homologue RPAP2, possess Pol II CTD Ser5 phosphatase activity. Here we report the crystal structure of Kluyveromyces lactis Rtr1, which reveals a new type of zinc finger protein and does not have any close structural homologues. Importantly, the structure does not show evidence of an active site, and extensive experiments to demonstrate its CTD phosphatase activity have been unsuccessful, suggesting that Rtr1 has a non-catalytic role in CTD dephosphorylation.

  8. Saline-seep development in the Hailstone Basin, northern Stillwater County, Montana

    USGS Publications Warehouse

    Lewis, Barney D.; Custer, Stephen G.; Miller, Marvin R.

    1979-01-01

    As a result of an increase in saline seep occurrence in Montana, a study was begun in 1974 to determine the hydrogeology of saline seeps in the Hailstone basin. The aquifer is composed of colluvium of Holocene age. The impermeable Cretaceous Niobrara Formation underlies the saturated zone basinwide. The ground-water system is shallow, unconfined, and locally recharged. Ground-water levels and size of the saline seeps respond rapidly to precipitation in the basin. The appearance and growth of saline seeps are related to precipitation patterns; the agricultural practice of summer follow; topography; the presence of a shallow, unconfined, and locally recharged ground-water system; and a soluble salt source. Continuous cropping could reduce the amount of water percolating beneath local recharge areas, and thus minimize the water available for seep formation and growth. The lateral variation in chemical quality of water from wells suggests a shallow flow system. The field specific conductance of 29 ground-water samples collected in 1976 ranged from 2,160 to 14,000 micromhos per centimeter and averaged 6,660 micromhos per centimeter. Water from saline seeps in the study area contains principally sodium, magnesium, calcium, and sulfate. Nitrate is present in the ground water in concentrations of as much as 855 milligrams per liter. The high nitrate concentrations are interpreted to originate primarily from oxidation of organic material once native sod is broken by cultivation. (USGS).

  9. 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.

  10. 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.

  11. 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

  12. Metatranscriptomic analysis of diminutive Thiomargarita-like bacteria ("Candidatus Thiopilula" spp.) from abyssal cold seeps of the Barbados Accretionary Prism.

    PubMed

    Jones, Daniel S; Flood, Beverly E; Bailey, Jake V

    2015-05-01

    Large sulfur-oxidizing bacteria in the family Beggiatoaceae are important players in the global sulfur cycle. This group contains members of the well-known genera Beggiatoa, Thioploca, and Thiomargarita but also recently identified and relatively unknown candidate taxa, including "Candidatus Thiopilula" spp. and "Ca. Thiophysa" spp. We discovered a population of "Ca. Thiopilula" spp. colonizing cold seeps near Barbados at a ∼4.7-km water depth. The Barbados population consists of spherical cells that are morphologically similar to Thiomargarita spp., with elemental sulfur inclusions and a central vacuole, but have much smaller cell diameters (5 to 40 μm). Metatranscriptomic analysis revealed that when exposed to anoxic sulfidic conditions, Barbados "Ca. Thiopilula" organisms expressed genes for the oxidation of elemental sulfur and the reduction of nitrogenous compounds, consistent with their vacuolated morphology and intracellular sulfur storage capability. Metatranscriptomic analysis further revealed that anaerobic methane-oxidizing and sulfate-reducing organisms were active in the sediment, which likely provided reduced sulfur substrates for "Ca. Thiopilula" and other sulfur-oxidizing microorganisms in the community. The novel observations of "Ca. Thiopilula" and associated organisms reported here expand our knowledge of the globally distributed and ecologically successful Beggiatoaceae group and thus offer insight into the composition and ecology of deep cold seep microbial communities.

  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. Revealing the nature of the active site on the carbon catalyst for C-H bond activation.

    PubMed

    Sun, XiaoYing; Li, Bo; Su, Dangsheng

    2014-09-28

    A reactivity descriptor for the C-H bond activation on the nanostructured carbon catalyst is proposed. Furthermore the calculations reveal that the single ketone group can be an active site in ODH reaction.

  16. Cellular Active N-Hydroxyurea FEN1 Inhibitors Block Substrate Entry to the Active Site

    PubMed Central

    Exell, Jack C.; Thompson, Mark J.; Finger, L. David; Shaw, Steven J.; Debreczeni, Judit; Ward, Thomas A.; McWhirter, Claire; Siöberg, Catrine L. B.; Martinez Molina, Daniel; Mark Abbott, W.; Jones, Clifford D.; Nissink, J. Willem M.; Durant, Stephen T.; Grasby, Jane A.

    2016-01-01

    The structure-specific nuclease human flap endonuclease-1 (hFEN1) plays a key role in DNA replication and repair and may be of interest as an oncology target. We present the first crystal structure of inhibitor-bound hFEN1 and show a cyclic N-hydroxyurea bound in the active site coordinated to two magnesium ions. Three such compounds had similar IC50 values but differed subtly in mode of action. One had comparable affinity for protein and protein–substrate complex and prevented reaction by binding to active site catalytic metal ions, blocking the unpairing of substrate DNA necessary for reaction. Other compounds were more competitive with substrate. Cellular thermal shift data showed engagement of both inhibitor types with hFEN1 in cells with activation of the DNA damage response evident upon treatment. However, cellular EC50s were significantly higher than in vitro inhibition constants and the implications of this for exploitation of hFEN1 as a drug target are discussed. PMID:27526030

  17. 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.

  18. 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

  19. Are nest sites actively chosen? Testing a common assumption for three non-resource limited birds

    NASA Astrophysics Data System (ADS)

    Goodenough, A. E.; Elliot, S. L.; Hart, A. G.

    2009-09-01

    Many widely-accepted ecological concepts are simplified assumptions about complex situations that remain largely untested. One example is the assumption that nest-building species choose nest sites actively when they are not resource limited. This assumption has seen little direct empirical testing: most studies on nest-site selection simply assume that sites are chosen actively (and seek explanations for such behaviour) without considering that sites may be selected randomly. We used 15 years of data from a nestbox scheme in the UK to test the assumption of active nest-site choice in three cavity-nesting bird species that differ in breeding and migratory strategy: blue tit ( Cyanistes caeruleus), great tit ( Parus major) and pied flycatcher ( Ficedula hypoleuca). Nest-site selection was non-random (implying active nest-site choice) for blue and great tits, but not for pied flycatchers. We also considered the relative importance of year-specific and site-specific factors in determining occupation of nest sites. Site-specific factors were more important than year-specific factors for the tit species, while the reverse was true for pied flycatchers. Our results show that nest-site selection, in birds at least, is not always the result of active choice, such that choice should not be assumed automatically in studies of nesting behaviour. We use this example to highlight the need to test key ecological assumptions empirically, and the importance of doing so across taxa rather than for single "model" species.

  20. Trace elements in seep waters along Whitewood Creek, South Dakota, and their toxicity to fathead minnows

    USGS Publications Warehouse

    Hamilton, S.J.; Buhl, K.J.

    2000-01-01

    Whitewood Creek, located in the Black Hills of southwestern South Dakota, has a long history of contamination from mining activity. Gold exploration began in the 1870s, and has continued since that time. Whitewood Creek received direct releases of tailings from 1870 to 1977 from Gold Run Creek in Lead, SD. It has been estimated that approximately 100 million to 1 billion tons of mining, milling, and ore processing wastes have been released by mining activity in the last century in to Whitewood Creek, the Belle Fourche river, and the Cheyenne River (Fox Consultants, Inc. 1984). Tailings deposition has altered the geomorphology of Whitewood Creek, and deposits up to 4.6 m. deep, have become stabilized by vegetation. Several other streams in the Black Hills also have been adversely affected by mining operations (Rahn 1996).As water leaches through rock strata that are disturbed by surface and subsurface mining, it dissolves inorganic elements and carries them to the groundwater.  Groundwater movement through the extensive tailings deposits in the Whitewood Creek valley enter the creek at various seeps along its downstream course to the Belle Fourche river, and the Belle Fourche River itself, which empties into the Cheyenne River and eventually into Lake Oahe.

  1. 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.

  2. Structural characterization of single nucleotide variants at ligand binding sites and enzyme active sites of human proteins

    PubMed Central

    Yamada, Kazunori D.; Nishi, Hafumi; Nakata, Junichi; Kinoshita, Kengo

    2016-01-01

    Functional sites on proteins play an important role in various molecular interactions and reactions between proteins and other molecules. Thus, mutations in functional sites can severely affect the overall phenotype. Progress of genome sequencing projects has yielded a wealth of information on single nucleotide variants (SNVs), especially those with less than 1% minor allele frequency (rare variants). To understand the functional influence of genetic variants at a protein level, we investigated the relationship between SNVs and protein functional sites in terms of minor allele frequency and the structural position of variants. As a result, we observed that SNVs were less abundant at ligand binding sites, which is consistent with a previous study on SNVs and protein interaction sites. Additionally, we found that non-rare variants tended to be located slightly apart from enzyme active sites. Examination of non-rare variants revealed that most of the mutations resulted in moderate changes of the physico-chemical properties of amino acids, suggesting the existence of functional constraints. In conclusion, this study shows that the mapping of genetic variants on protein structures could be a powerful approach to evaluate the functional impact of rare genetic variations. PMID:27924270

  3. Lamellipodial actin mechanically links myosin activity with adhesion site formation

    PubMed Central

    Giannone, Gregory; Dubin-Thaler, Benjamin; Rossier, Olivier; Cai, Yunfei; Chaga, Oleg; Jiang, Guoying; Beaver, William; Döbereiner, Hans-Günther; Freund, Yoav; Borisy, Gary; Sheetz, Michael P.

    2013-01-01

    Summary Cell motility proceeds by cycles of edge protrusion, adhesion and retraction. Whether these functions are coordinated by biochemical or biomechanical processes is unknown. We find that myosin II pulls the rear of the lamellipodial actin network, causing upward bending, edge retraction and initiation of new adhesion sites. The network then separates from the edge and condenses over the myosin. Protrusion resumes as lamellipodial actin regenerates from the front and extends rearward until it reaches newly assembled myosin, initiating the next cycle. Upward bending, observed by evanescence and electron microscopy, results in ruffle formation when adhesion strength is low. Correlative fluorescence and electron microscopy shows that the regenerating lamellipodium forms a cohesive, separable layer of actin above the lamellum. Thus, actin polymerization periodically builds a mechanical link, the lamellipodium, connecting myosin motors with the initiation of adhesion sites, suggesting that the major functions driving motility are coordinated by a biomechanical process. PMID:17289574

  4. In Situ Stable Isotopic Detection of Anaerobic Oxidation of Methane in Monterey Bay Cold Seeps Via Off-Axis Integrated Cavity Output Spectroscopy

    NASA Astrophysics Data System (ADS)

    Wankel, S. D.; Gupta, M.; Leen, J.; Provencal, R. A.; Parsotam, V.; Girguis, P. R.

    2010-12-01

    Anaerobic methane oxidation (AOM) plays an important role in global climate change by governing the release of methane from anoxic sediments into the global ocean and ultimately the atmosphere. Thus, gaining an accurate understanding of both the distribution of methane sources and the occurrence of AOM as well as the spatial and temporal variability of cycling pathways is critical. Environmental analyses of methane stable isotopic composition (δ13C-CH4) provide just such an indicator of methane source, whether biogenic or thermogenic, as well as a spatial and temporal integrator of microbial cycling pathways, such as AOM. Here we present results from several deployments of a newly developed in situ methane stable isotope analyzer capable of measuring δ13C-CH4 to full ocean depths. The instrument consisted of a miniaturized Off-Axis Integrated Cavity Output Spectroscopy (Off-Axis ICOS) analyzer housed in a cylindrical titanium pressure vessel for deep sea deployment. Dissolved gas was extracted from seawater using a Teflon AF diffusion membrane inlet. The instrument had an operating wavelength of 1647 nm and used chemometric spectral decomposition to determine the relative concentrations of 13CH4 and 12CH4 with a sensitivity of ± 0.2‰. Deployments to cold seep environments revealed a distinct separation in carbon isotopic composition between methane in advecting fluids as compared with methane from sediment pore fluids. During multiple visits to two different sites at Extrovert Cliff in Monterey Bay (960m), methane in advecting fluids ranged from -70.2‰ to -63.8‰. In contrast, methane-rich fluids sampled directly from pushcore holes taken through seep sediments contained methane with substantially higher δ13C values ranging from -64.2‰ to -50.2‰. These data implicate the influence of anaerobic oxidation of methane within these seep sediments. While the advective flux of methane to the seafloor from the central orifice of the seep is substantial, using

  5. 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.

  6. 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.

  7. 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

  8. Structural mechanism of RuBisCO activation by carbamylation of the active site lysine.

    PubMed

    Stec, Boguslaw

    2012-11-13

    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 CO(2). We report two crystal structures of nitrosylated RuBisCO from the red algae Galdieria sulphuraria with O(2) and CO(2) bound at the active site. G. sulphuraria RuBisCO is inhibited by cysteine nitrosylation that results in trapping of these gaseous ligands. The structure with CO(2) defines an elusive, preactivation complex that contains a metal cation Mg(2+) surrounded by three H(2)O/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.

  9. Silver-Coated Nylon Dressing Plus Active DC Microcurrent for Healing of Autogenous Skin Donor Sites

    DTIC Science & Technology

    2013-08-01

    Silver-Coated Nylon Dressing Plus Active DC Microcurrent for Healing of Autogenous Skin Donor Sites Edward W. Malin, MD, Chaya M. Galin, BSN, RN... microcurrent in comparison to silver-coated dressing with sham microcurrent on wound-closure time for autogenous skin donor sites. Methods: Four...hundred five patients were screened for treatment of their donor sites using a silver-coated nylon dressing with either sham or active microcurrent

  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. 76 FR 30696 - Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-26

    ... Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites AGENCY: Department of... eligible active uranium and thorium processing site licensees for reimbursement under Title X of the Energy... requires DOE to reimburse eligible uranium and thorium licensees for certain costs of...

  12. 76 FR 24871 - Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-03

    ... Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites AGENCY: Department of... from eligible active uranium and thorium processing site licensees for reimbursement under Title X of...). Title X requires DOE to reimburse eligible uranium and thorium licensees for certain costs...

  13. A model of the rabies virus glycoprotein active site.

    PubMed

    Rustici, M; Bracci, L; Lozzi, L; Neri, P; Santucci, A; Soldani, P; Spreafico, A; Niccolai, N

    1993-06-01

    The glycoprotein from the neurotropic rabies virus shows a significant homology with the alpha neurotoxin that binds to the nicotinic acetylcholine receptor. The crystal structure of the alpha neurotoxins suggests that the Arg 37 guanidinium group and the Asp 31 side-chain carboxylate of the erabutoxin have stereochemical features resembling those of acetylcholine. Conformational studies on the Asn194-Ser195-Arg196-Gly197 tetrapeptide, an essential part of the binding site of the rabies virus glycoprotein, indicate that the side chains of Asn and Arg could also mimic the acetylcholine structure. This observation is consistent with the recently proposed mechanism of the viral infection.

  14. 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

  15. Active Site Hydrophobicity and the Convergent Evolution of Paraoxonase Activity in Structurally Divergent Enzymes: The Case of Serum Paraoxonase 1

    PubMed Central

    2016-01-01

    Serum paraoxonase 1 (PON1) is a native lactonase capable of promiscuously hydrolyzing a broad range of substrates, including organophosphates, esters, and carbonates. Structurally, PON1 is a six-bladed β-propeller with a flexible loop (residues 70–81) covering the active site. This loop contains a functionally critical Tyr at position 71. We have performed detailed experimental and computational analyses of the role of selected Y71 variants in the active site stability and catalytic activity in order to probe the role of Y71 in PON1’s lactonase and organophosphatase activities. We demonstrate that the impact of Y71 substitutions on PON1’s lactonase activity is minimal, whereas the kcat for the paraoxonase activity is negatively perturbed by up to 100-fold, suggesting greater mutational robustness of the native activity. Additionally, while these substitutions modulate PON1’s active site shape, volume, and loop flexibility, their largest effect is in altering the solvent accessibility of the active site by expanding the active site volume, allowing additional water molecules to enter. This effect is markedly more pronounced in the organophosphatase activity than the lactonase activity. Finally, a detailed comparison of PON1 to other organophosphatases demonstrates that either a similar “gating loop” or a highly buried solvent-excluding active site is a common feature of these enzymes. We therefore posit that modulating the active site hydrophobicity is a key element in facilitating the evolution of organophosphatase activity. This provides a concrete feature that can be utilized in the rational design of next-generation organophosphate hydrolases that are capable of selecting a specific reaction from a pool of viable substrates. PMID:28026940

  16. Larvae from deep-sea methane seeps disperse in surface waters.

    PubMed

    Arellano, Shawn M; Van Gaest, Ahna L; Johnson, Shannon B; Vrijenhoek, Robert C; Young, Craig M

    2014-07-07

    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.

  17. 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.

  18. Hydrologic investigation and remediation of a post-remining acidic seep

    SciTech Connect

    Aljoe, W.W.; Linberg, N.A.

    1996-12-31

    Surface remining of coal pillars in abandoned underground workings in the Pittsburgh seam in southwestern Pennsylvania has often resulted in post-remining discharges whose water quality is the same or better than the pre-existing discharges. However, at one such operation in Washington County, PA, an increase in contaminant loading occurred at an outcrop seep after remining. This problem was believed to be at least partly related to a small unstrapped area of the old deep mine workings immediately upgradient from the seep. A hydrologic investigation that included a chemical tracer test, slug tests in the remined spoil, and water quality monitoring indicated that the mine pool in the old workings discharged through the seep. However, the water in the mine pool and much of the remined spoil was consistently alkaline; this suggested that the acidic water may have originated in other areas of the spoil and old workings, and passed rapidly to the seep through a highly transmissive portion of the spoil. Acting on this assumption, the mine operator successfully implemented a remediation scheme in which the spoil was excavated to intercept the acidic spoil water. The excavation was then re-emplaced with an anoxic limestone drain at its base. The drain now serves both to add alkalinity to the water and to divert the seep to an area where metals can be removed easily via precipitation in wetlands.

  19. Proteome-wide analysis of nonsynonymous single-nucleotide variations in active sites of human proteins.

    PubMed

    Dingerdissen, Hayley; Motwani, Mona; Karagiannis, Konstantinos; Simonyan, Vahan; Mazumder, Raja

    2013-03-01

    An enzyme's active site is essential to normal protein activity such that any disruptions at this site may lead to dysfunction and disease. Nonsynonymous single-nucleotide variations (nsSNVs), which alter the amino acid sequence, are one type of disruption that can alter the active site. When this occurs, it is assumed that enzyme activity will vary because of the criticality of the site to normal protein function. We integrate nsSNV data and active site annotations from curated resources to identify all active-site-impacting nsSNVs in the human genome and search for all pathways observed to be associated with this data set to assess the likely consequences. We find that there are 934 unique nsSNVs that occur at the active sites of 559 proteins. Analysis of the nsSNV data shows an over-representation of arginine and an under-representation of cysteine, phenylalanine and tyrosine when comparing the list of nsSNV-impacted active site residues with the list of all possible proteomic active site residues, implying a potential bias for or against variation of these residues at the active site. Clustering analysis shows an abundance of hydrolases and transferases. Pathway and functional analysis shows several pathways over- or under-represented in the data set, with the most significantly affected pathways involved in carbohydrate metabolism. We provide a table of 32 variation-substrate/product pairs that can be used in targeted metabolomics experiments to assay the effects of specific variations. In addition, we report the significant prevalence of aspartic acid to histidine variation in eight proteins associated with nine diseases including glycogen storage diseases, lacrimo-auriculo-dento-digital syndrome, Parkinson's disease and several cancers.

  20. 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.

  1. 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.

  2. 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.

  3. All the catalytic active sites of MoS2 for hydrogen evolution

    DOE PAGES

    Li, Guoqing; Zhang, Du; Qiao, Qiao; ...

    2016-11-29

    MoS2 presents a promising low-cost catalyst for the hydrogen evolution reaction (HER), but the understanding about its active sites has remained limited. Here we present an unambiguous study of the catalytic activities of all possible reaction sites of MoS2, including edge sites, sulfur vacancies, and grain boundaries. We demonstrate that, in addition to the well-known catalytically active edge sites, sulfur vacancies provide another major active site for the HER, while the catalytic activity of grain boundaries is much weaker. Here, the intrinsic turnover frequencies (Tafel slopes) of the edge sites, sulfur vacancies, and grain boundaries are estimated to be 7.5more » s–1 (65–75 mV/dec), 3.2 s–1 (65–85 mV/dec), and 0.1 s–1 (120–160 mV/dec), respectively. We also demonstrate that the catalytic activity of sulfur vacancies strongly depends on the density of the vacancies and the local crystalline structure in proximity to the vacancies. Unlike edge sites, whose catalytic activity linearly depends on the length, sulfur vacancies show optimal catalytic activities when the vacancy density is in the range of 7–10%, and the number of sulfur vacancies in high crystalline quality MoS2 is higher than that in low crystalline quality MoS2, which may be related with the proximity of different local crystalline structures to the vacancies.« less

  4. 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

  5. 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…

  6. An active site mutation increases the polymerase activity of the guinea pig-lethal Marburg virus.

    PubMed

    Koehler, Alexander; Kolesnikova, Larissa; Becker, Stephan

    2016-10-01

    Marburg virus (MARV) causes severe, often fatal, disease in humans and transient illness in rodents. Sequential passaging of MARV in guinea pigs resulted in selection of a lethal virus containing 4 aa changes. A D184N mutation in VP40 (VP40D184N), which leads to a species-specific gain of viral fitness, and three mutations in the active site of viral RNA-dependent RNA polymerase L, which were investigated in the present study for functional significance in human and guinea pig cells. The transcription/replication activity of L mutants was strongly enhanced by a substitution at position 741 (S741C), and inhibited by other substitutions (D758A and A759D) in both species. The polymerase activity of L carrying the S741C substitution was eightfold higher in guinea pig cells than in human cells upon co-expression with VP40D184N, suggesting that the additive effect of the two mutations provides MARV a replicative advantage in the new host.

  7. Encroachment of Human Activity on Sea Turtle Nesting Sites

    NASA Astrophysics Data System (ADS)

    Ziskin, D.; Aubrecht, C.; Elvidge, C.; Tuttle, B.; Baugh, K.; Ghosh, T.

    2008-12-01

    The encroachment of anthropogenic lighting on sea turtle nesting sites poses a serious threat to the survival of these animals [Nicholas, 2001]. This danger is quantified by combining two established data sets. The first is the Nighttime Lights data produced by the NOAA National Geophysical Data Center [Elvidge et al., 1997]. The second is the Marine Turtle Database produced by the World Conservation Monitoring Centre (WCMC). The technique used to quantify the threat of encroachment is an adaptation of the method described in Aubrecht et al. [2008], which analyzes the stress on coral reef systems by proximity to nighttime lights near the shore. Nighttime lights near beaches have both a direct impact on turtle reproductive success since they disorient hatchlings when they mistake land-based lights for the sky-lit surf [Lorne and Salmon, 2007] and the lights are also a proxy for other anthropogenic threats. The identification of turtle nesting sites with high rates of encroachment will hopefully steer conservation efforts to mitigate their effects [Witherington, 1999]. Aubrecht, C, CD Elvidge, T Longcore, C Rich, J Safran, A Strong, M Eakin, KE Baugh, BT Tuttle, AT Howard, EH Erwin, 2008, A global inventory of coral reef stressors based on satellite observed nighttime lights, Geocarto International, London, England: Taylor and Francis. In press. Elvidge, CD, KE Baugh, EA Kihn, HW Kroehl, ER Davis, 1997, Mapping City Lights with Nighttime Data from the DMSP Operational Linescan System, Photogrammatic Engineering and Remote Sensing, 63:6, pp. 727-734. Lorne, JK, M Salmon, 2007, Effects of exposure to artificial lighting on orientation of hatchling sea turtles on the beach and in the ocean, Endangered Species Research, Vol. 3: 23-30. Nicholas, M, 2001, Light Pollution and Marine Turtle Hatchlings: The Straw that Breaks the Camel's Back?, George Wright Forum, 18:4, p77-82. Witherington, BE, 1999, Reducing Threats To Nesting Habitat, Research and Management Techniques for

  8. 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.

  9. Dimorphism in methane seep-dwelling ecotypes of the largest known bacteria

    PubMed Central

    Bailey, Jake V; Salman, Verena; Rouse, Gregory W; Schulz-Vogt, Heide N; Levin, Lisa A; Orphan, Victoria J

    2011-01-01

    We present evidence for a dimorphic life cycle in the vacuolate sulfide-oxidizing bacteria that appears to involve the attachment of a spherical Thiomargarita-like cell to the exteriors of invertebrate integuments and other benthic substrates at methane seeps. The attached cell elongates to produce a stalk-like form before budding off spherical daughter cells resembling free-living Thiomargarita that are abundant in surrounding sulfidic seep sediments. The relationship between the attached parent cell and free-living daughter cell is reminiscent of the dimorphic life modes of the prosthecate Alphaproteobacteria, but on a grand scale, with individual elongate cells reaching nearly a millimeter in length. Abundant growth of attached Thiomargarita-like bacteria on the integuments of gastropods and other seep fauna provides not only a novel ecological niche for these giant bacteria, but also for animals that may benefit from epibiont colonization. PMID:21697959

  10. 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.

  11. 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 scoring hits were identified against the ligandable region at the A1 ARF6 interface which showed strong hydrogen bonding interactions, including guanidines, phosphates, Leucopterin and Aristolochic acid VIa. This study has important implications in the application of hybrid structure-based and ligand-based methods against the identified ligandable sites using the identified inhibitors as reference ligands, for drug design against the active cholera toxin.

  12. Barium ions selectively activate BK channels via the Ca2+-bowl site.

    PubMed

    Zhou, Yu; Zeng, Xu-Hui; Lingle, Christopher J

    2012-07-10

    Activation of Ca(2+)-dependent BK channels is increased via binding of micromolar Ca(2+) to two distinct high-affinity sites per BK α-subunit. One site, termed the Ca(2+) bowl, is embedded within the second RCK domain (RCK2; regulator of conductance for potassium) of each α-subunit, while oxygen-containing residues in the first RCK domain (RCK1) have been linked to a separate Ca(2+) ligation site. Although both sites are activated by Ca(2+) and Sr(2+), Cd(2+) selectively favors activation via the RCK1 site. Divalent cations of larger ionic radius than Sr(2+) are thought to be ineffective at activating BK channels. Here we show that Ba(2+), better known as a blocker of K(+) channels, activates BK channels and that this effect arises exclusively from binding at the Ca(2+)-bowl site. Compared with previous estimates for Ca(2+) bowl-mediated activation by Ca(2+), the affinity of Ba(2+) to the Ca(2+) bowl is reduced about fivefold, and coupling of binding to activation is reduced from ∼3.6 for Ca(2+) to about ∼2.8 for Ba(2+). These results support the idea that ionic radius is an important determinant of selectivity differences among different divalent cations observed for each Ca(2+)-binding site.

  13. Activation of brown adipose tissue mitochondrial GDP binding sites

    SciTech Connect

    Swick, A.G.

    1987-01-01

    The primary function of brown adipose tissue (BAT) is heat production. This ability is attributed to the existence of a unique inner mitochondrial membrane protein termed the uncoupling protein or thermogenin. This protein is permeable to H+ and thus allows respiration (and therefore thermogenesis) to proceed at a rapid rate, independent of ADP phosphorylation. Proton conductance can be inhibited by the binding of purine nucleotides to the uncoupling protein. The binding of (/sup 3/H)-GDP to BAT mitochondria is frequently used as a measure of BAT thermogenic activity. Rats fed a diet that was low but adequate in protein exhibited a decrease in feed efficiency. In addition, BAT thermogenesis was activated as indicated by an elevation in the level of GDP binding to BAT mitochondria. This phenomena occurred in older rats and persisted over time.

  14. Structure and Reactivity of the Phosphotriesterase Active Site

    DTIC Science & Technology

    2002-01-01

    characterize different catalytic conformations for chorismate mutase . Preliminary evidence for water binding in phosphotriesterase suggests that activity in...MD/QM study of the chorismate mutase catalyzed Claisen rearrangement reaction. 2001.subm. J.Phys.Chem.B 22.Day, P.N.J., J.H.; Gordon,M.S.; Webb,S.P...Claisen rearrangement of an unusual substrate in chorismate mutase . 2001.subm. J.Phys.Chem.B 38.Stevens, W.J., Basch,H., Krauss,M., Compact effective

  15. 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.

  16. 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

  17. 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.

  18. Pathways of H2 toward the Active Site of [NiFe]-Hydrogenase

    PubMed Central

    Teixeira, Vitor H.; Baptista, António M.; Soares, Cláudio M.

    2006-01-01

    Hydrogenases catalyze the reversible oxidation of molecular hydrogen (H2), but little is known about the diffusion of H2 toward the active site. Here we analyze pathways for H2 permeation using molecular dynamics (MD) simulations in explicit solvent. Various MD simulation replicates were done, to improve the sampling of the system states. H2 easily permeates hydrogenase in every simulation and it moves preferentially in channels. All H2 molecules that reach the active site made their approach from the side of the Ni ion. H2 is able to reach distances of <4 Å from the active site, although after 6 Å permeation is difficult. In this region we mutated Val-67 into alanine and perform new MD simulations. These simulations show an increase of H2 inside the protein and at lower distances from the active site. This valine can be a control point in the H2 access to the active center. PMID:16731562

  19. 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

  20. Maintenance of plastid RNA editing activities independently of their target sites.

    PubMed

    Tillich, Michael; Poltnigg, Peter; Kushnir, Sergei; Schmitz-Linneweber, Christian

    2006-03-01

    RNA editing in plant organelles is mediated by site-specific, nuclear-encoded factors. Previous data suggested that the maintenance of these factors depends on the presence of their rapidly evolving cognate sites. The surprising ability of allotetraploid Nicotiana tabacum (tobacco) to edit a foreign site in the chloroplast ndhA messenger RNA was thought to be inherited from its diploid male ancestor, Nicotiana tomentosiformis. Here, we show that the same ndhA editing activity is also present in Nicotiana sylvestris, which is the female diploid progenitor of tobacco and which lacks the ndhA site. Hence, heterologous editing is not simply a result of tobacco's allopolyploid genome organization. Analyses of other editing sites after sexual or somatic transfer between land plants showed that heterologous editing occurs at a surprisingly high frequency. This suggests that the corresponding editing activities are conserved despite the absence of their target sites, potentially because they serve other functions in the plant cell.

  1. 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.

  2. A Processive Carbohydrate Polymerase That Mediates Bifunctional Catalysis Using a Single Active Site

    PubMed Central

    May, John F.; Levengood, Matthew R.; Splain, Rebecca A.; Brown, Christopher D.; Kiessling, Laura L.

    2012-01-01

    Even in the absence of a template, glycosyltransferases can catalyze the synthesis of carbohydrate polymers of specific sequence. The paradigm has been that one enzyme catalyzes the formation of one type of glycosidic linkage, yet certain glycosyltransferases generate polysaccharide sequences composed of two distinct linkage types. In principle, bifunctional glycosyltransferases can possess separate active sites for each catalytic activity or one active site with dual activities. We encountered the fundamental question of one or two distinct active sites in our investigation of the galactosyltransferase GlfT2. GlfT2 catalyzes the formation of mycobacterial galactan, a critical cell-wall polymer composed of galactofuranose residues connected with alternating, regioisomeric linkages. We found that GlfT2 mediates galactan polymerization using only one active site that manifests dual regioselectivity. Structural modeling of the bifunctional glycosyltransferases hyaluronan synthase and cellulose synthase suggests that these enzymes also generate multiple glycosidic linkages using a single active site. These results highlight the versatility of glycosyltransferases for generating polysaccharides of specific sequence. We postulate that a hallmark of processive elongation of a carbohydrate polymer by a bifunctional enzyme is that one active site can give rise to two separate types of glycosidic bonds. PMID:22217153

  3. 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.

  4. An Accessory Agonist Binding Site Promotes Activation of α4β2* Nicotinic Acetylcholine Receptors*

    PubMed Central

    Wang, Jingyi; Kuryatov, Alexander; Sriram, Aarati; Jin, Zhuang; Kamenecka, Theodore M.; Kenny, Paul J.; Lindstrom, Jon

    2015-01-01

    Neuronal nicotinic acetylcholine receptors containing α4, β2, and sometimes other subunits (α4β2* nAChRs) regulate addictive and other behavioral effects of nicotine. These nAChRs exist in several stoichiometries, typically with two high affinity acetylcholine (ACh) binding sites at the interface of α4 and β2 subunits and a fifth accessory subunit. A third low affinity ACh binding site is formed when this accessory subunit is α4 but not if it is β2. Agonists selective for the accessory ACh site, such as 3-[3-(3-pyridyl)-1,2,4-oxadiazol-5-yl]benzonitrile (NS9283), cannot alone activate a nAChR but can facilitate more efficient activation in combination with agonists at the canonical α4β2 sites. We therefore suggest categorizing agonists according to their site selectivity. NS9283 binds to the accessory ACh binding site; thus it is termed an accessory site-selective agonist. We expressed (α4β2)2 concatamers in Xenopus oocytes with free accessory subunits to obtain defined nAChR stoichiometries and α4/accessory subunit interfaces. We show that α2, α3, α4, and α6 accessory subunits can form binding sites for ACh and NS9283 at interfaces with α4 subunits, but β2 and β4 accessory subunits cannot. To permit selective blockage of the accessory site, α4 threonine 126 located on the minus side of α4 that contributes to the accessory site, but not the α4β2 sites, was mutated to cysteine. Alkylation of this cysteine with a thioreactive reagent blocked activity of ACh and NS9283 at the accessory site. Accessory agonist binding sites are promising drug targets. PMID:25869137

  5. Stable isotope trophic patterns in echinoderm megafauna in close proximity to and remote from Gulf of Mexico lower slope hydrocarbon seeps

    NASA Astrophysics Data System (ADS)

    Carney, Robert Spencer

    2010-11-01

    Hydrocarbon-seep communities in the Gulf of Mexico have a high biomass that is exploited as a food source to varying degrees by the photosynthesis-dependent fauna inhabiting the surrounding mud bottom. A decline concurrent with ocean depth in detritus influx to that background habitat results in a much lower background biomass. The biomass contrast between population-rich seeps and depauperate mud bottom leads to the prediction that seep utilization by the background fauna should be extensive at all depths and should increase with depth. Species depth zonation makes like-species comparisons over the full depth of the Gulf of Mexico impossible. Seeps and normal bottom above 1000 m have different fauna from those below 1000 m. Lower slope seeps are surrounded by a fauna rich in echinoderm species, especially asteroids, ophiuroids, and holothuroids. All three taxa have species that are abundant within seeps and are probably endemic to them. They also contain species found only in mud background or within mud and seeps backgrounds. Tissue analyses of δ13C and δ15N of echinoderms collected by ROV within seeps and trawling away from seeps indicate a pattern of utilization similar to that found in upper slope seeps exploited by different taxa. Seastar and ophiuroid species abundant in or endemic to seeps have tissue isotope values reflecting seep chemosynthetic input via a free-living microbial detritus or predation. A single seep-endemic deposit-feeding holothuroid showed distinct seep tissue values. Background deposit-feeding holothuroids collected within seeps showed either no or only minor incorporation of seep carbon, indicating either a lack of access to seep detritus or short feeding times within the seep. A predicted extensive utilization of seep productivity at the deeper seeps was not found. Seeps may be relatively closed systems that require special adaptations of species in order for them to enter, exploit, and survive. Alternately, the surrounding deep

  6. Extending the Diffuse Layer Model of Surface Acidity Behavior: III. Estimating Bound Site Activity Coefficients

    EPA Science Inventory

    Although detailed thermodynamic analyses of the 2-pK diffuse layer surface complexation model generally specify bound site activity coefficients for the purpose of accounting for those non-ideal excess free energies contributing to bound site electrochemical potentials, in applic...

  7. 75 FR 71677 - Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-11-24

    ... Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites AGENCY: Department of... uranium and thorium processing site licensees for reimbursement under Title X of the Energy Policy Act of... requires DOE to reimburse eligible uranium and thorium licensees for certain costs of...

  8. 40 CFR 61.154 - Standard for active waste disposal sites.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...). (e) For all asbestos-containing waste material received, the owner or operator of the active waste... 40 Protection of Environment 9 2013-07-01 2013-07-01 false Standard for active waste disposal... for Asbestos § 61.154 Standard for active waste disposal sites. Each owner or operator of an...

  9. Unmasking tandem site interaction in human acetylcholinesterase. Substrate activation with a cationic acetanilide substrate.

    PubMed

    Johnson, Joseph L; Cusack, Bernadette; Davies, Matthew P; Fauq, Abdul; Rosenberry, Terrone L

    2003-05-13

    Acetylcholinesterase (AChE) contains a narrow and deep active site gorge with two sites of ligand binding, an acylation site (or A-site) at the base of the gorge, and a peripheral site (or P-site) near the gorge entrance. The P-site contributes to catalytic efficiency by transiently binding substrates on their way to the acylation site, where a short-lived acyl enzyme intermediate is produced. A conformational interaction between the A- and P-sites has recently been found to modulate ligand affinities. We now demonstrate that this interaction is of functional importance by showing that the acetylation rate constant of a substrate bound to the A-site is increased by a factor a when a second molecule of substrate binds to the P-site. This demonstration became feasible through the introduction of a new acetanilide substrate analogue of acetylcholine, 3-(acetamido)-N,N,N-trimethylanilinium (ATMA), for which a = 4. This substrate has a low acetylation rate constant and equilibrates with the catalytic site, allowing a tractable algebraic solution to the rate equation for substrate hydrolysis. ATMA affinities for the A- and P-sites deduced from the kinetic analysis were confirmed by fluorescence titration with thioflavin T as a reporter ligand. Values of a >1 give rise to a hydrolysis profile called substrate activation, and the AChE site-specific mutant W86F, and to a lesser extent wild-type human AChE itself, showed substrate activation with acetylthiocholine as the substrate. Substrate activation was incorporated into a previous catalytic scheme for AChE in which a bound P-site ligand can also block product dissociation from the A-site, and two additional features of the AChE catalytic pathway were revealed. First, the ability of a bound P-site ligand to increase the substrate acetylation rate constant varied with the structure of the ligand: thioflavin T accelerated ATMA acetylation by a factor a(2) of 1.3, while propidium failed to accelerate. Second, catalytic rate

  10. Structure and nuclearity of active sites in Fe-zeolites: comparison with iron sites in enzymes and homogeneous catalysts.

    PubMed

    Zecchina, Adriano; Rivallan, Mickaël; Berlier, Gloria; Lamberti, Carlo; Ricchiardi, Gabriele

    2007-07-21

    Fe-ZSM-5 and Fe-silicalite zeolites efficiently catalyse several oxidation reactions which find close analogues in the oxidation reactions catalyzed by homogeneous and enzymatic compounds. The iron centres are highly dispersed in the crystalline matrix and on highly diluted samples, mononuclear and dinuclear structures are expected to become predominant. The crystalline and robust character of the MFI framework has allowed to hypothesize that the catalytic sites are located in well defined crystallographic positions. For this reason these catalysts have been considered as the closest and best defined heterogeneous counterparts of heme and non heme iron complexes and of Fenton type Fe(2+) homogeneous counterparts. On this basis, an analogy with the methane monooxygenase has been advanced several times. In this review we have examined the abundant literature on the subject and summarized the most widely accepted views on the structure, nuclearity and catalytic activity of the iron species. By comparing the results obtained with the various characterization techniques, we conclude that Fe-ZSM-5 and Fe-silicalite are not the ideal samples conceived before and that many types of species are present, some active and some other silent from adsorptive and catalytic point of view. The relative concentration of these species changes with thermal treatments, preparation procedures and loading. Only at lowest loadings the catalytically active species become the dominant fraction of the iron species. On the basis of the spectroscopic titration of the active sites by using NO as a probe, we conclude that the active species on very diluted samples are isolated and highly coordinatively unsaturated Fe(2+) grafted to the crystalline matrix. Indication of the constant presence of a smaller fraction of Fe(2+) presumably located on small clusters is also obtained. The nitrosyl species formed upon dosing NO from the gas phase on activated Fe-ZSM-5 and Fe-silicalite, have been analyzed

  11. Monocopper active site for partial methane oxidation in Cu-exchanged 8MR zeolites

    SciTech Connect

    Kulkarni, Ambarish R.; Zhao, Zhi -Jian; Siahrostami, Samira; Nørskov, Jens K.; Studt, Felix

    2016-08-17

    Direct conversion of methane to methanol using oxygen is experiencing renewed interest owing to the availability of new natural gas resources. Copper-exchanged zeolites such as mordenite and ZSM-5 have shown encouraging results, and di- and tri-copper species have been suggested as active sites. Recently, small eight-membered ring (8MR) zeolites including SSZ-13, -16, and -39 have been shown to be active for methane oxidation, but the active sites and reaction mechanisms in these 8MR zeolites are not known. In this work, we use density functional theory (DFT) calculations to systematically evaluate monocopper species as active sites for the partial methane oxidation reaction in Cu-exchanged SSZ-13. On the basis of kinetic and thermodynamic arguments, we suggest that [CuIIOH]+ species in the 8MR are responsible for the experimentally observed activity. Furthermore, our results successfully explain the available spectroscopic data and experimental observations including (i) the necessity of water for methanol extraction and (ii) the effect of Si/Al ratio on the catalyst activity. Monocopper species have not yet been suggested as an active site for the partial methane oxidation reaction, and our results suggest that [CuIIOH]+ active site may provide complementary routes for methane activation in zeolites in addition to the known [Cu–O–Cu]2+ and Cu3O3 motifs.

  12. Monocopper active site for partial methane oxidation in Cu-exchanged 8MR zeolites

    DOE PAGES

    Kulkarni, Ambarish R.; Zhao, Zhi -Jian; Siahrostami, Samira; ...

    2016-08-17

    Direct conversion of methane to methanol using oxygen is experiencing renewed interest owing to the availability of new natural gas resources. Copper-exchanged zeolites such as mordenite and ZSM-5 have shown encouraging results, and di- and tri-copper species have been suggested as active sites. Recently, small eight-membered ring (8MR) zeolites including SSZ-13, -16, and -39 have been shown to be active for methane oxidation, but the active sites and reaction mechanisms in these 8MR zeolites are not known. In this work, we use density functional theory (DFT) calculations to systematically evaluate monocopper species as active sites for the partial methane oxidationmore » reaction in Cu-exchanged SSZ-13. On the basis of kinetic and thermodynamic arguments, we suggest that [CuIIOH]+ species in the 8MR are responsible for the experimentally observed activity. Furthermore, our results successfully explain the available spectroscopic data and experimental observations including (i) the necessity of water for methanol extraction and (ii) the effect of Si/Al ratio on the catalyst activity. Monocopper species have not yet been suggested as an active site for the partial methane oxidation reaction, and our results suggest that [CuIIOH]+ active site may provide complementary routes for methane activation in zeolites in addition to the known [Cu–O–Cu]2+ and Cu3O3 motifs.« less

  13. 1993 annual report of hazardous waste activities for the Oak Ridge K-25 site

    SciTech Connect

    Not Available

    1994-02-01

    This report is a detailed listing of all of the Hazardous Waste activities occurring at Martin Marietta`s K-25 site. Contained herein are hazardous waste notification forms, waste stream reports, generator fee forms and various TSDR reports.

  14. The surface chemistry of heterogeneous catalysis: mechanisms, selectivity, and active sites.

    PubMed

    Zaera, Francisco

    2005-01-01

    The role of chemical kinetics in defining the requirements for the active sites of heterogeneous catalysts is discussed. A personal view is presented, with specific examples from our laboratory to illustrate the role of the chemical composition, structure, and electronic properties of specific surface sites in determining reaction activity and selectivity. Manipulation of catalytic behavior via the addition of chemical modifiers and by tuning of the reaction conditions is also introduced.

  15. Nuclear waste: Status of DOE`s nuclear waste site characterization activities

    SciTech Connect

    1987-12-31

    Three potential nuclear waste repository sites have been selected to carry out characterization activities-the detailed geological testing to determine the suitability of each site as a repository. The sites are Hanford in south-central Washington State, Yucca Mountain in southern Nevada, and Deaf Smith in the Texas Panhandle. Two key issues affecting the total program are the estimations of the site characterization completion data and costs and DOE`s relationship with the Nuclear Regulatory Commission which has been limited and its relations with affected states and Indian tribes which continue to be difficult.

  16. Number and locations of agonist binding sites required to activate homomeric Cys-loop receptors.

    PubMed

    Rayes, Diego; De Rosa, María José; Sine, Steven M; Bouzat, Cecilia

    2009-05-06

    Homo-pentameric Cys-loop receptors contain five identical agonist binding sites, each formed at a subunit interface. To determine the number and locations of binding sites required to generate a stable active state, we constructed a receptor subunit with a mutation that disables the agonist binding site and a reporter mutation that alters unitary conductance and coexpressed mutant and nonmutant subunits. Although receptors with a range of different subunit compositions are produced, patch-clamp recordings reveal that the amplitude of each single-channel opening event reports the number and, for certain subunit combinations, the locations of subunits with intact binding