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Sample records for abyssal sediment communities

  1. Temporal and depth-related differences in prokaryotic communities in abyssal sediments associated with particulate organic carbon flux

    Moeseneder, M. M.; Smith, K. L.; Ruhl, H. A.; Jones, D. O. B.; Witte, U.; Prosser, J. I.

    2012-12-01

    Particulate organic carbon (POC) flux is hypothesized to be the most important parameter influencing activity and biomass of prokaryotic and faunal communities in the abyssal seafloor, but there is little evidence of POC-related changes in community composition of prokaryotes. This hypothesis was tested by 16S rRNA-gene-based analysis of prokaryotic DNA and RNA extracted from abyssal seafloor sediments during periods of low and high POC flux. Fingerprint analysis of prokaryotic communities indicated that approximately 50% of the phylotypes were identical at each sediment horizon, regardless of the temporal variations in POC flux. However, phylotypes were also detected that represented a relatively dynamic component of these communities and were probably strongly influenced by the prevalent POC flux regime. These patterns were also detected in deeper sediment horizons. DNA- and RNA-based community profiles differed, although both approaches had similar community dynamics. Crenarchaeota showed the strongest shift in community composition in response to availability of labile POC, indicating that POC flux may have a more pronounced impact on crenarchaeal communities than on bacterial communities. The high number of phylotypes common to each sample time suggests that both standing stock and active prokaryotic communities are stable.

  2. Glacial magnetite dissolution in abyssal NW Pacific sediments - evidence for carbon trapping?

    Korff, Lucia; von Dobeneck, Tilo; Frederichs, Thomas; Kasten, Sabine; Kuhn, Gerhard; Gersonde, Rainer; Diekmann, Bernhard

    2016-04-01

    The abyssal North Pacific Ocean's large volume, depth, and terminal position on the deep oceanic conveyor make it a candidate site for deep carbon trapping as postulated by climate theory to explain the massive glacial drawdown of atmospheric CO2. As the major basins of the North Pacific have depths of 5500-6500m, far below the modern and glacial Calcite Compensation Depths (CCD), these abyssal sediments are carbonate-free and therefore not suitable for carbonate-based paleoceanographic proxy reconstructions. Instead, paleo-, rock and environmental magnetic methods are generally well applicable to hololytic abyssal muds and clays. In 2009, the international paleoceanographic research cruise SO 202 INOPEX ('Innovative North Pacific Experiment') of the German RV SONNE collected two ocean-spanning EW sediment core transects of the North Pacific and Bering Sea recovering a total of 50 piston and gravity cores from 45 sites. Out of seven here considered abyssal Northwest Pacific piston cores collected at water depths of 5100 to 5700m with mostly coherent shipboard susceptibility logs, the 20.23m long SO202-39-3, retrieved from 5102 m water depth east of northern Shatsky Rise (38°00.70'N, 164°26.78'E), was rated as the stratigraphically most promising record of the entire core transect and selected for detailed paleo- and environmental magnetic, geochemical and sedimentological investigations. This core was dated by correlating its RPI and Ba/Ti records to well-dated reference records and obviously provides a continuous sequence of the past 940 kyrs. The most striking orck magnetic features are coherent magnetite-depleted zones corresponding to glacial periods. In the interglacial sections, detrital, volcanic and even submicron bacterial magnetite fractions are excellently preserved. These alternating magnetite preservation states seem to reflect dramatic oxygenation changes in the deep North Pacific Ocean and hint at large-scale benthic glacial carbon trapping

  3. Abyssal Scavenging Communities attracted to Sargassum and fish in the Sargasso Sea

    Fleury, Aharon G.; Drazen, Jeffrey C.

    2013-02-01

    Deep-sea communities rely on epipelagic surface production as a primary source of energy and food. The flux of phytodetritus drives many abyssal ecological processes but the flux of large particles such as nekton carcasses, macroalgae, and wood may also be important. Recent baited camera experiments noted that some abyssal fish consumed spinach and phytoplankton placed on the seafloor. To evaluate if fish or other scavengers would consume natural plant or macroalgal material falling to the deep-sea floor we conducted camera experiments using Sargassum or mackerel bait in the Sargasso Sea. A benthic community of invertebrates was attracted to Sargassum, which naturally falls to the seafloor in this area. In five instances it was observed that an isopod Bathyopsurus sp. removed a piece of Sargassum from the main clump and left the field of view with it. An ophiuroid is also observed handling a piece of Sargassum. The group of scavengers attracted to mackerel bait was very different and was dominated by large ophidiid fish. In contrast to studies elsewhere in the abyssal North Atlantic, only a small number of rattails are observed, which could be related to water depth or an ichthyofaunal zonal change between oligotrophic and eutrophic regions.

  4. Geochemistry of the near surface sediments of the Nares Abyssal Plain

    The geochemistry of a suite of box and 2m gravity cores from the Nares Abyssal Plain has been characterised by means of pore water analyses, XRF determination of major and trace element concentrations, mineralogy and 230Thsub(excess) dating. The interstitial fluid environment of those deep-sea clays is mildly reducing, although one site exhibits manganese remobilisation and precipitation. Despite their marked colour differences, there is a similarity in clay mineralogy between the grey silt/clay turbidites and the brown clays found in the area. Sediment accumulation rates of pelagic brown clays range between 0.5 and 1.0 cm/103 yr. These pelagic brown clays are metal-rich relative to the grey clays, and a model is used to estimate the hydrogenous metal fluxes on the assumption that they are constant over the Plain. This model gives values of approx. 1300 μg/cm2/103 yr for Mn, approx. 2600 μg/cm2/103 yr for Fe and Co, Ni, Cu, V and Zn in the range 6 to 26 μg/cm2/103 yr. An associated model-derived estimate of the detrital contents of the same elements agrees well with the mean values of the grey clays and of average shale. Metal-poor brown clays and assorted minor lithologies are intermediate in composition between these two end-members. (author)

  5. Cyclic magnetite dissolution in Pleistocene sediments of the abyssal northwest Pacific Ocean: Evidence for glacial oxygen depletion and carbon trapping

    Korff, Lucia; Dobeneck, Tilo; Frederichs, Thomas; Kasten, Sabine; Kuhn, Gerhard; Gersonde, Rainer; Diekmann, Bernhard

    2016-05-01

    The carbonate-free abyss of the North Pacific defies most paleoceanographic proxy methods and hence remains a "blank spot" in ocean and climate history. Paleomagnetic and rock magnetic, geochemical, and sedimentological methods were combined to date and analyze seven middle to late Pleistocene northwest Pacific sediment cores from water depths of 5100 to 5700 m. Besides largely coherent tephra layers, the most striking features of these records are nearly magnetite-free zones corresponding to glacial marine isotope stages (MISs) 22, 12, 10, 8, 6, and 2. Magnetite depletion is correlated with organic carbon and quartz content and anticorrelated with biogenic barite and opal content. Within interglacial sections and mid-Pleistocene transition glacial stages MIS 20, 18, 16, and 14, magnetite fractions of detrital, volcanic, and bacterial origin are all well preserved. Such alternating successions of magnetic iron mineral preservation and depletion are known from sapropel-marl cycles, which accumulated under periodically changing bottom water oxygen and redox conditions. In the open central northwest Pacific Ocean, the only conceivable mechanism to cause such abrupt change is a modified glacial bottom water circulation. During all major glaciations since MIS 12, oxygen-depleted Antarctic Bottom Water (AABW)-sourced bottom water seems to have crept into the abyssal northwest Pacific below ~5000 m depth, thereby changing redox conditions in the sediment, trapping and preserving dissolved and particulate organic matter and, in consequence, reducing and dissolving both, biogenic and detrital magnetite. At deglaciation, a downward progressing oxidation front apparently remineralized and released these sedimentary carbon reservoirs without replenishing the magnetite losses.

  6. Fate of corrosion products released from stainless steel in marine sediments and seawater. Part 4: Hatteras abyssal red clay

    A study in which neutron-activated 347 stainless steel was exposed to surficial sediment from a site in the Hatteras Abyssal Plain of the Northwest Atlantic Ocean is described. This sediment consists of approx. 20% CaCO3, which could lead to the formation of calcareous scale on the metal surface and reduce the corrosion rate. The distribution of indigenous metals among different chemical fractions shows that extractable Cr, Mn, Fe, Co, and Zn were associated with amorphous Mn and Fe oxides. Most of the remaining extractable Cr, and about a third of the extractable Cu appear to have been weakly complexed. Major fractions (25 to 36%) of extractable Mn, Co and Ni were present as adsorbed cations. Organic complexation appears to account for a large amount of extractable Fe, Ni, Cu and Zn. Neutron-activated 347 stainless steel specimens were exposed to sediment slurry under aerobic and non-oxygenated conditions for a period of 94 days. The redox potential measurements for air-sparged and N2, CO2-sparged sediment slurries were +410 and +60 mv, respectively. The presence of 02 produced increased amounts of corrosion products. Chemical extraction showed that relatively labile substances constituted about 84% of the 60Co activity released in aerated sediment. Relatively labile substances constitute about 82% of the total 60Co activity released under non-oxygenated conditions. A large fraction of 60Co which was in the soluble or easily dissolved forms under non-oxygenated conditions appears to have been more strongly adsorbed to the sediment under aerated conditions

  7. Mineralogical and rock magnetic provenance variation in Alaskan Abyssal Plain sediments, Gulf of Alaska

    Ullrich, A. D.; Jaeger, J. M.

    2009-12-01

    The interplay between regional tectonic activity and climate is a fundamental issue in ocean and earth sciences. These interactions are greatest in areas of high topographic relief coupled with aggressive erosional agents. Focused erosion in uplifting glaciated regions generates a positive feedback loop, accelerating uplift (Tompkin, 2007) and depositing erosional products into adjacent basins. Gulf of Alaska (GoA) strata offer insight into erosional responses to shifts in climate, such as the intensification of Cordilleran glaciation at 2.6 Ma. This coincides with increased accumulation of terrigenous sediment and appearance of ice rafted debris in the adjacent mud-rich Surveyor Fan (SF). It is hypothesized that this change in sediment accumulation and lithology at 2.6 Ma between the Lower Fan Sequence (LFS) and Upper Fan Sequence (UFS) may represent intensification of glacial erosion along the windward side of coastal mountains in southern Alaska. Establishing a provenance record of the UFS and LFS would provide insight into the history of glaciation and subsequent erosion of this region. Determining provenance of fine-grained sediments of the SF requires tracers that not only uniquely differentiate the adjacent Chugach and Yakutat geologic terranes, but are also preserved in offshore muds. Preliminary quantitative powder XRD mineralogy suggests that muds from onshore terranes and UFS sediments can be largely characterized by their distribution as resolved clusters on cross-plots of quartz, feldspar, clinochlore, and muscovite abundance. Within these plots, UFS sediments predominantly occupy the same region as Yakutat-derived samples, suggesting the mineralogy of UFS fine-grained sediments reflects that of the Yakutat Terrane. Distinctive groupings of on- and offshore sediments can also be observed on a Day plot of coercivity of remnance (Hcr/Hc) versus magnetic grain size (Mr/Ms), where Chugach and Yakutat samples group into separate clusters in the multi

  8. Demographic indicators of change in a deposit-feeding abyssal holothurian community (Station M, 4000 m)

    Huffard, Christine L.; Kuhnz, Linda A.; Lemon, Larissa; Sherman, Alana D.; Smith, Kenneth L.

    2016-03-01

    Holothurians are among the most abundant benthic megafauna at abyssal depths, and important consumers and bioturbators of organic carbon on the sea floor. Significant fluctuations in abyssal holothurian density are often attributed to species-specific responses to variable particulate organic carbon flux (food supply) stemming from surface ocean events. We report changes in densities of 19 holothurian species at the abyssal monitoring site Station M in the northeast Pacific, recorded during 11 remotely operated vehicle surveys between Dec 2006 and Oct 2014. Body size demographics are presented for Abyssocucumis abyssorum, Synallactidae sp. 1, Paelopatides confundens, Elpidia sp. A, Peniagone gracilis, Peniagone papillata, Peniagone vitrea, Peniagone sp. A, Peniagone sp. 1, and Scotoplanes globosa. Densities were lower and species evenness was higher from 2006-2009 compared to 2011-2014. Food supply of freshly-settled phytodetritus was exceptionally high during this latter period. Based on relationships between median body length and density, numerous immigration and juvenile recruitment events of multiple species appeared to take place between 2011 and 2014. These patterns were dominated by elpidiids (Holothuroidea: Elasipodida: Elpidiidae), which consistently increased in density during a period of high food availability, while other groups showed inconsistent responses. We considered minimum body length to be a proxy for size at juvenile recruitment. Patterns in density clustered by this measure, which was a stronger predictor of maximum density than median and mean body length.

  9. In situ experimental evidence of the fate of a phytodetritus pulse at the abyssal sea floor

    Witte, U.; Wenzhofer, F.; Sommer, S.; Boetius, A.; Heinz, P.; Aberle, N.; Sand, M.; Cremer, A.; Abraham, WR; Jørgensen, BB; Pfannkuche, O.

    2003-01-01

    quantified (over a period of 2.5 to 23 days) the response of an abyssal benthic community to a phytodetritus pulse, on the basis of 11 in situ experiments. Here we report that, in contrast to previous hypotheses(5-11), the sediment community oxygen consumption doubled immediately, and that macrofauna were...

  10. Bioturbation, geochemistry and geotechnics of sediments affected by the oxygen minimum zone on the Oman continental slope and abyssal plain, Arabian Sea

    Meadows, Azra; Meadows, Peter S.; West, Fraser J. C.; Murray, John M. H.

    2000-01-01

    We investigate the way the oxygen minimum zone (OMZ) alters interactions between bioturbation and sediment geochemistry, and geotechnical properties. Sediments are compared within and below the OMZ on the Oman continental slope and adjacent abyssal plain during the post monsoonal autumn season. Quantitative measurements were made of Eh and pH, of total organic matter (TOM) and carbonate, of water content and shear strength, and of bioturbation structures in vertical profiles of subcores taken from spade-box core samples. The OMZ stations had distinctively low redox conditions and high carbonate content, and different geotechnical properties and different bioturbation structures than stations below the OMZ on the abyssal plain. These differences are related to the degree of anoxia and to water depth. Within the OMZ, Eh, pH and carbonate increased with water depth, and TOM and water content decreased. We also noted the presence of subsurface sediment heterogeneity on the continental slope within the OMZ. In the OMZ, Eh, water content and bioturbation decreased with increasing sediment depth. There was a slight decrease in pH in the top 5 cm at all stations. Shear strength nearly always increased with increasing sediment depth. At each water depth correlations show down-core trends in these parameters, while across all water depths correlations were significant at deeper sediment depths (20-30 cm). An Eh-pH diagram identified two water-depth groupings: 391-1008 and 1265-3396 m. Cluster analysis showed the upper and lower sediment depths form separate clusters, the break occurring at 4-7.5 cm; while there are also distinct clusters related to water depth. We relate our results to bottom-water oxygen concentrations reported by other investigators, and to regional-scale geochemical processes.

  11. Inter-annual dynamics of abyssal polychaete communities in the North East Pacific and North East Atlantic—A family-level study

    Laguionie-Marchais, C.; Billett, D. S. M.; Paterson, G. L. D.; Ruhl, H. A.; Soto, E. H.; Smith, K. L., Jr.; Thatje, S.

    2013-05-01

    Characterising how deep-sea communities change on contemporary time-scales and understanding underlying ecosystem processes has become important under changing climate and the rise in the exploitation of deep-sea resources. However, little is known about these dynamics and processes. Long-term observations from which inter-annual variations can be detected are scarce in the deep sea. This study examines inter-annual changes in density, family richness and evenness, family and functional group rank abundance distributions of infaunal polychaetes at two abyssal stations in the North East Pacific (Station M, 1991 to 2005) and in the North East Atlantic (Porcupine Abyssal Plain, 1991 to 1999). The two long-term data sets were used to investigate not only if polychaete community structure and composition varied at inter-annual scales in terms of diversity and rank abundance distributions but also if any changes were related to previous observations in megafauna and environmental factors at each locality. The polychaete community structure at each locality was analysed using univariate statistics as well as multivariate ordination techniques based on Bray-Curtis similarity of the yearly family density. Sub-surface deposit feeders, such as Paraonidae, dominated the North East Pacific, whereas surface deposit feeders, such as Cirratulidae, dominated the North East Atlantic. Both stations showed inter-annual variations in density, family evenness and rank abundance distributions. The greatest changes occurred in 1998 in both time series when polychaete densities peaked, and switches in the rank abundance of the most abundant families and functional groups took place. Inter-annual variations in the polychaete community were correlated with a limited number of holothurian species changes, but no correlation was found with particulate organic matter flux or climate indices. Ecological and environmental factors behind the family-level changes remain elusive. Overall, changes in

  12. Unexpectedly higher metazoan meiofauna abundances in the Kuril-Kamchatka Trench compared to the adjacent abyssal plains

    Schmidt, Christina; Martínez Arbizu, Pedro

    2015-01-01

    We studied meiofauna standing stocks and community structure in the Kuril-Kamchatka Trench and its adjacent abyssal plains in the northwestern Pacific Ocean. In general, the Nematoda were dominant (93%) followed by the Copepoda (4%). Nematode abundances ranged from 87% to 96%; those of copepods from 2% to 7%. The most diverse deployment yielded 17 taxa: Acari, Amphipoda, Annelida, Bivalvia, Coelenterata, Copepoda, Cumacea, Gastrotricha, Isopoda, Kinorhyncha, Loricifera, Nematoda, Ostracoda, Priapulida, Tanaidacea, Tantulocarida, and Tardigrada. Nauplii were also present. Generally, the trench slope and the southernmost deployments had the highest abundances (850-1392 individuals/cm2). The results of non-metric multidimensional scaling indicated that these deployments were similar to each other in meiofauna community structure. The southernmost deployments were located in a zone of higher particulate organic carbon (POC) flux (g Corg m-2 yr-1), whereas the trench slope should have low POC flux due to depth attenuation. Also, POC and abundance were significantly correlated in the abyssal plains. This correlation may explain the higher abundances at the southernmost deployments. Lateral transport was also assumed to explain high meiofauna abundances on the trench slope. Abundances were generally higher than expected from model results. ANOSIM revealed significant differences between the trench slope and the northern abyssal plains, between the central abyssal plains and the trench slope, between the trench slope and the southern abyssal plains, between the central and the southern abyssal plains, and between the central and northern deployments. The northern and southern abyssal plains did not differ significantly. In addition, a U-test revealed highly significant differences between the trench-slope and abyssal deployments. The taxa inhabited mostly the upper 0-3 cm of the sediment layer (Nematoda 80-90%; Copepoda 88-100%). The trench-slope and abyssal did not differ

  13. Abyssal hills - hidden source of increased habitat heterogeneity, benthic megafaunal biomass and diversity in the deep sea

    Durden, Jennifer M.; Bett, Brian J.; Jones, Daniel O. B.; Huvenne, Veerle A. I.; Ruhl, Henry A.

    2015-09-01

    Abyssal hills are the most abundant landform on Earth, yet the ecological impact of the resulting habitat heterogeneity on the wider abyss is largely unexplored. Topographic features are known to influence food availability and the sedimentary environment in other deep-sea habitats, in turn affecting the species assemblage and biomass. To assess this spatial variation, benthic assemblages and environmental conditions were compared at four hill and four plain sites at the Porcupine Abyssal Plain. Here we show that differences in megabenthic communities on abyssal hills and the adjacent plain are related to environmental conditions, which may be caused by local topography and hydrodynamics. Although these hills may receive similar particulate organic carbon flux (food supply from the surface ocean) to the adjacent plain, they differ significantly in depth, slope, and sediment particle size distribution. We found that megafaunal biomass was significantly greater on the hills (mean 13.45 g m-2, 95% confidence interval 9.25-19.36 g m-2) than the plain (4.34 g m-2, 95% CI 2.08-8.27 g m-2; ANOVA F(1, 6) = 23.8, p local sedimentary environment may be the mechanism driving these assemblage differences. Since the ecological heterogeneity provided by hills in the abyss has been underappreciated, regional assessments of abyssal biological heterogeneity and diversity may be considerably higher than previously thought.

  14. Functional diversity patterns of abyssal nematodes in the Eastern Mediterranean: A comparison between cold seeps and typical deep sea sediments

    Kalogeropoulou, V.; Keklikoglou, K.; Lampadariou, N.

    2015-04-01

    Spatial patterns in deep sea nematode biological trait composition and functional diversity were investigated between chemosynthetic and typical deep sea ecosystems as well as between different microhabitats within the chemosynthetic ecosystems, in the Eastern Mediterranean. The chemosynthetic ecosystems chosen were two mud volcanoes, Napoli at 1950 m depth and Amsterdam at 2040 m depth which are cold seeps characterized by high chemosynthetic activity and spatial heterogeneity. Typical deep sea ecosystems consisted of fine-grained silt-clay sediments which were collected from three areas located in the south Ionian Sea at 2765 to 2840 m depth, the southern Cretan margin at 1089 to 1998 m depth and the Levantine Sea at 3055 to 3870 m depth. A range of biological traits (9 traits; 31 categories) related to buccal morphology, tail shape, body size, body shape, life history strategy, sediment position, cuticle morphology, amphid shape and presence of somatic setae were combined to identify patterns in the functional composition of nematode assemblages between the two habitats, the two mud volcanoes (macroscale) and between the microhabitats within the mud volcanoes (microscale). Data on trait correspondence was provided by biological information on species and genera. A total of 170 nematode species were allocated in 67 different trait combinations, i.e. functional groups, based on taxonomic, morphological and behavioral characteristics. The Biological Trait Analysis (BTA) revealed significant differences between the mud volcanoes and the typical deep sea sediments indicating the presence of different biological functions in ecologically very different environments. Moreover, chemosynthetic activity and habitat heterogeneity within mud volcanoes enhance the presence of different biological and ecological functions in nematode assemblages of different microhabitats. Functional diversity and species richness patterns varied significantly across the different

  15. Mass accumulation rates and fallout radionuclides 210Pb, 137Cs and 241Am inventories determined in radiometrically dated abyssal sediments of the Black Sea

    Five abyssal (deep-sea) sediment cores collected during the two international cruises on R/V 'Professor Vodyanitskiy' (RADEUX-1998 and RADEUX-2000) in the framework of the Regional Technical Co-operation Project RER/2/003 'Marine Environmental Assessment in the Black Sea Region' were subjected to detailed radiometric analysis. The sediments were dated using the radionuclides 210Pb, 137Cs and 241Am and the results used to calculate a number of key parameters, e.g. radionuclide inventories, fluxes and sediment accumulation rates. The sediment cores were collected using a MARK II-400 multi-corer (Bowers and Connelly) in both Western and Eastern sub-basins of the Black Sea. The cores were sliced on board with a resolution of 0.2-0.4 cm for the top 5 cm and 1-5 cm downward using an extruder that was specially designed to prevent loss of the uppermost fluff-layer, possible down-smearing and interlayer cross-contamination of the sediment. Dry bulk density (DBD) and cumulative dry mass (CDM) were calculated on a salt-free basis using direct determination of the salt contribution to the dry mass of the sediment. Calculations showed that in the near surface sediments, and particularly in the top fluff-layer, the salt dissolved in pore-water contributed up to 30-60% of the mass of dried sediments. Neglecting this correction could cause an erroneous interpretation of the 210Pb activity profile, resulting in overestimation of both the average sedimentation rate and its recent temporal changes. Sediment samples were analysed for 210Pb, 226Ra, 137Cs and 241Am by direct gamma assay in UHMI after 3 weeks equilibration in hermetically sealed plastic holders, using an EG and G Ortec (Ametek) HPGe GWL series well-type coaxial low background intrinsic germanium detector. Correction was made for the effect of self-absorption of low energy γ-rays within the sample using attenuation parameters determined in. Chronostratigraphical analysis of the data and sediment age calculation have

  16. Nematode communities in contaminated river sediments

    Nematode communities of eight sites from three river catchments were investigated in terms of the genera composition, feeding types, and life-history strategists. The sampling sites showed a gradient of anthropogenic contamination with heavy metals and organic pollutants being important factors in differentiating the sites. Nematode community structure was related to sediment pollution and the hydro-morphological structure of the sampling sites. Heavily contaminated sites were characterized by communities with high relative abundances of omnivorous and predacious nematodes (Tobrilus, c-p 3; Mononchus, c-p 4), while sites with low to medium contamination were dominated by bacterivorous nematodes (Monhystera, Daptonema; c-p 2) or suction feeders (Dorylaimus, c-p 4). The relatively high Maturity Index values in the heavily polluted sites were surprising. Nematodes turned out to be a suitable organism group for monitoring sediment quality, with generic composition being the most accurate indicator for assessing differences in nematode community structure. - Nematode community structure of river sediments is related to pollution and site structure

  17. Nematode communities in contaminated river sediments

    Heininger, Peter [Federal Institute of Hydrology (BfG), Am Mainzer Tor 1, 56068 Koblenz (Germany); Hoess, Sebastian [Ecossa - Ecological Sediment and Soil Assessment, Thierschstr. 43, 80538 Munich (Germany); Claus, Evelyn [Federal Institute of Hydrology (BfG), Am Mainzer Tor 1, 56068 Koblenz (Germany); Pelzer, Juergen [Federal Institute of Hydrology (BfG), Am Mainzer Tor 1, 56068 Koblenz (Germany); Traunspurger, Walter [University of Bielefeld, Department of Animal Ecology, Morgenbreede 45, 33615 Bielefeld (Germany)]. E-mail: traunspurger@uni-bielefeld.de

    2007-03-15

    Nematode communities of eight sites from three river catchments were investigated in terms of the genera composition, feeding types, and life-history strategists. The sampling sites showed a gradient of anthropogenic contamination with heavy metals and organic pollutants being important factors in differentiating the sites. Nematode community structure was related to sediment pollution and the hydro-morphological structure of the sampling sites. Heavily contaminated sites were characterized by communities with high relative abundances of omnivorous and predacious nematodes (Tobrilus, c-p 3; Mononchus, c-p 4), while sites with low to medium contamination were dominated by bacterivorous nematodes (Monhystera, Daptonema; c-p 2) or suction feeders (Dorylaimus, c-p 4). The relatively high Maturity Index values in the heavily polluted sites were surprising. Nematodes turned out to be a suitable organism group for monitoring sediment quality, with generic composition being the most accurate indicator for assessing differences in nematode community structure. - Nematode community structure of river sediments is related to pollution and site structure.

  18. Endolithic Microbial Communities in Fractures: Insights Gleaned from Mineralized Filaments in Cretaceous-age Calcite Veins in Serpentinized Peridotites, Iberia Abyssal Plain

    Milliken, K. L.

    2001-03-01

    The occurrence of diverse mineralized microbial features in calcitized fractures in serpentinized peridotite, Iberia Abyssal Plain, suggests that mineralized fractures are of particular interest in the search for fossil or extant life on Mars.

  19. Geology and geochemistry of abyssal plains

    Weaver, P.P.E.; Thomson, J. (eds.)

    1987-01-01

    In this publication is assembled a set of 14 papers from the presentations at a meeting of the Marine Studies Group of the Geological Society, held on the 29th and 30th January 1986. The papers cover various aspects of the geophysics, sedimentology, geochemistry and geotechnics of abyssal-plain sediments. During the late 1970s an international research program began to examine selected areas of the N Atlantic and Pacific Ocean sea beds to assess the feasibility of disposal of radioactive wastes in deep-sea sediments. The considerations of sea-floor properties required for such studies had the results that some of the N Atlantic study areas were in abyssal plains. The availability of new geological information from this program provided the impetus for convening this meeting, but the papers are not restricted to those deriving from such studies. All papers have been abstracted separately for inclusion on the Energy Data Base.

  20. Biogeochemical, Isotopic and Bacterial Distributions Trace Oceanic Abyssal Circulation.

    Rubino, Angelo; Bensi, Manuel; Hainbucher, Dagmar; Zanchettin, Davide; Mapelli, Francesca; Ogrinc, Nives; Marchetto, Davide; Borin, Sara; Cardin, Vanessa; Fajon, Vesna; Horvat, Milena; Taricco, Carla; Baldi, Franco

    2016-01-01

    We explore the possibility of tracing routes of dense waters toward and within the ocean abyss by the use of an extended set of observed physical and biochemical parameters. To this purpose, we employ mercury, isotopic oxygen, biopolymeric carbon and its constituents, together with indicators of microbial activity and bacterial diversity found in bottom waters of the Eastern Mediterranean. In this basin, which has been considered as a miniature global ocean, two competing sources of bottom water (one in the Adriatic and one in the Aegean seas) contribute to the ventilation of the local abyss. However, due to a recent substantial reduction of the differences in the physical characteristics of these two water masses it has become increasingly complex a water classification using the traditional approach with temperature, salinity and dissolved oxygen alone. Here, we show that an extended set of observed physical and biochemical parameters allows recognizing the existence of two different abyssal routes from the Adriatic source and one abyssal route from the Aegean source despite temperature and salinity of such two competing sources of abyssal water being virtually indistinguishable. Moreover, as the near-bottom development of exogenous bacterial communities transported by convectively-generated water masses in the abyss can provide a persistent trace of episodic events, intermittent flows like those generating abyssal waters in the Eastern Mediterranean basin may become detectable beyond the availability of concomitant measurements. PMID:26761666

  1. Biogeochemical, Isotopic and Bacterial Distributions Trace Oceanic Abyssal Circulation

    Rubino, Angelo; Bensi, Manuel; Hainbucher, Dagmar; Zanchettin, Davide; Mapelli, Francesca; Ogrinc, Nives; Marchetto, Davide; Borin, Sara; Cardin, Vanessa; Fajon, Vesna; Horvat, Milena; Taricco, Carla; Baldi, Franco

    2016-01-01

    We explore the possibility of tracing routes of dense waters toward and within the ocean abyss by the use of an extended set of observed physical and biochemical parameters. To this purpose, we employ mercury, isotopic oxygen, biopolymeric carbon and its constituents, together with indicators of microbial activity and bacterial diversity found in bottom waters of the Eastern Mediterranean. In this basin, which has been considered as a miniature global ocean, two competing sources of bottom water (one in the Adriatic and one in the Aegean seas) contribute to the ventilation of the local abyss. However, due to a recent substantial reduction of the differences in the physical characteristics of these two water masses it has become increasingly complex a water classification using the traditional approach with temperature, salinity and dissolved oxygen alone. Here, we show that an extended set of observed physical and biochemical parameters allows recognizing the existence of two different abyssal routes from the Adriatic source and one abyssal route from the Aegean source despite temperature and salinity of such two competing sources of abyssal water being virtually indistinguishable. Moreover, as the near-bottom development of exogenous bacterial communities transported by convectively-generated water masses in the abyss can provide a persistent trace of episodic events, intermittent flows like those generating abyssal waters in the Eastern Mediterranean basin may become detectable beyond the availability of concomitant measurements. PMID:26761666

  2. Changes in abundance and community structure of nematodes from the abyssal polymetallic nodule field, Tropical Northeast Pacific

    Miljutin, Dmitry; Miljutina, Maria; Messié, Monique

    2015-12-01

    Deep-sea fields of polymetallic nodules in the Clarion-Clipperton Zone (CCFZ, tropical NE Pacific) are currently being investigated to assess their potential for commercial mining. During such mining, benthic communities will be inevitably disturbed or destroyed. Therefore, assessments of their standing stock and composition may be helpful for the future evaluation of possible impacts of commercial nodule exploitation. Analysis of nematode communities (at genus level) inhabiting the French license area of the CCFZ were studied based on data from the cruises NODINAUT (2004) and BIONOD (2012). The total nematode density was ca. 1.5-fold higher in 2012 as compared with 2004. This reflected a 2-2.5 times higher density of non-selective deposit-feeders (i.e. possessing a small buccal cavity without armature) in 2012 compared with 2004, whereas no significant differences between sampling periods were observed in the density of the other feeding groups. Consequently, whilst the list of the most abundant genera was identical, their relative abundances changed significantly. The relative abundance of the genus Thalassomonhystera was two times greater in 2012 than in 2004, whereas the relative abundances of the genera Acantholaimus and Theristus were significantly lower in 2012 (10% and 4%, respectively) than in 2004 (28% and 9%). Nematode diversity (including values of diversity indices and total number of recorded genera) was significantly lower in 2012 in comparison with 2004. Although our data do not take into account seasonal and shorter temporal scales of variability in nematode assemblages, we report here that a certain fraction of variations observed between the two sampling periods could be associated with differences in primary production. Future studies should aim to better characterise temporal variability in nematode communities of the CCFZ at seasonal and interannual scales.

  3. A comparison of benthic infaunal abundance on two abyssal plains in the northeast Pacific Ocean

    Carey, Andrew G.

    1981-05-01

    Benthic macro-infauna were sampled in the northeast Pacific Ocean at 12 stations on an east-west transect across Cascadia and Eastern Tufts abyssal plains to determine ecological effects of continental influences and depth on those communities. The two plains, separated by the East Pacific Rise, differ in depth and distance from the continental margin. Tufts Plain lies to the west; primary production in the overlying water and the amount of organic carbon in the surface sediments are lower than for the Cascadia Plain region. Five benthic ecological zones were distinguished: (1) Cascadia Plain Slope-Base; (2) Eastern Cascadia Plain; (3) Cascadia Deep-Sea Channel; (4) Western Cascadia Plain; and (5) Eastern Tufts Plain. These differ in faunal biomass, numerical density, gross composition of the fauna by phyla, and composition of sediment. Comparatively, the slope-base environment supports the most abundant fauna. The numerical density of infauna on Eastern Tufts Plain is similar to that on Eastern and Western Cascadia Plain; however, the biomass tends to be lower in the deeper, more distant environment. It is concluded that these differences in the benthic fauna are probably caused by varying levels of input from primary production in overlying waters and differences in the transport of organic-rich particles off the continental shelf. Distance-related environmental characteristics are shown to be critical in the deep sea for controlling benthic community structure. On Cascadia Abyssal Plain, a plateau-like feature, the gross structure of communities changes with increasing distance from the continent but at constant depth. Faunal densities, biomass, and composition by phyla lie within the range of values normally associated with upper abyssal environments.

  4. Mangrove succession enriches the sediment microbial community in South China.

    Chen, Quan; Zhao, Qian; Li, Jing; Jian, Shuguang; Ren, Hai

    2016-01-01

    Sediment microorganisms help create and maintain mangrove ecosystems. Although the changes in vegetation during mangrove forest succession have been well studied, the changes in the sediment microbial community during mangrove succession are poorly understood. To investigate the changes in the sediment microbial community during succession of mangroves at Zhanjiang, South China, we used phospholipid fatty acid (PLFA) analysis and the following chronosequence from primary to climax community: unvegetated shoal; Avicennia marina community; Aegiceras corniculatum community; and Bruguiera gymnorrhiza + Rhizophora stylosa community. The PLFA concentrations of all sediment microbial groups (total microorganisms, fungi, gram-positive bacteria, gram-negative bacteria, and actinomycetes) increased significantly with each stage of mangrove succession. Microbial PLFA concentrations in the sediment were significantly lower in the wet season than in the dry season. Regression and ordination analyses indicated that the changes in the microbial community with mangrove succession were mainly associated with properties of the aboveground vegetation (mainly plant height) and the sediment (mainly sediment organic matter and total nitrogen). The changes in the sediment microbial community can probably be explained by increases in nutrients and microhabitat heterogeneity during mangrove succession. PMID:27265262

  5. Microbial community transitions across the deep sediment-basement interface

    Labonté, J.; Lever, M. A.; Orcutt, B.

    2015-12-01

    Previous studies of microbial abundance and geochemistry in deep marine sediments indicate a stimulation of microbial activity near the sediment-basement interface; yet, the extent to which microbial communities in bottom sediments and underlying crustal habitats interact is unclear. We conducted tag pyrosequencing on DNA extracted from a spectrum of deep sediment-basement samples to try to identify patterns in microbial community shifts across sediment-basement interfaces, focusing on samples from the subsurface of the Juan de Fuca Ridge flank (IODP Expedition 327). Our results demonstrate that sediment and the basaltic crust harbor microbial communities that are phylogenetically connected, but the eveness is characteristic of the environment. We will discuss the microbial community transitions that occur horizontally along fluid flow pathways and vertically across the sediment basement interface, as well as the possible implications regarding the controls of microbial community composition along deep sediment-basement interfaces in hydrothermal systems. We will also highlight efforts to overcome sample contamination in crustal subsurface samples.

  6. Impact of oil on bacterial community structure in bioturbated sediments

    Stauffert, Magali; Cravo-Laureau, Cristiana; Jezequel, Ronan; Barantal, Sandra; Cuny, Philippe; Gilbert, Franck; Cagnon, Christine; Militon, Cécile; Amouroux, David; Mahdaoui, Fatima; Bouyssiere, Brice; Stora, Georges; Merlin, François-Xavier; Duran, Robert

    2013-01-01

    Oil spills threaten coastlines where biological processes supply essential ecosystem services. Therefore, it is crucial to understand how oil influences the microbial communities in sediments that play key roles in ecosystem functioning. Ecosystems such as sediments are characterized by intensive bioturbation due to burrowing macrofauna that may modify the microbial metabolisms. It is thus essential to consider the bioturbation when determining the impact of oil on microbial communities. In t...

  7. Hydrocarbon pollutants shape bacterial community assembly of harbor sediments

    Barbato, Marta

    2016-02-02

    Petroleum pollution results in co-contamination by different classes of molecules, entailing the occurrence of marine sediments difficult to remediate, as in the case of the Ancona harbor (Mediterranean Sea, Italy). Autochthonous bioaugmentation (ABA), by exploiting the indigenous microbes of the environment to be treated, could represent a successful bioremediation strategy. In this perspective we aimed to i) identify the main drivers of the bacterial communities\\' richness in the sediments, ii) establish enrichment cultures with different hydrocarbon pollutants evaluating their effects on the bacterial communities\\' composition, and iii) obtain a collection of hydrocarbon degrading bacteria potentially exploitable in ABA. The correlation between the selection of different specialized bacterial populations and the type of pollutants was demonstrated by culture-independent analyses, and by establishing a collection of bacteria with different hydrocarbon degradation traits. Our observations indicate that pollution dictates the diversity of sediment bacterial communities and shapes the ABA potential in harbor sediments.

  8. Hydrocarbon pollutants shape bacterial community assembly of harbor sediments.

    Barbato, Marta; Mapelli, Francesca; Magagnini, Mirko; Chouaia, Bessem; Armeni, Monica; Marasco, Ramona; Crotti, Elena; Daffonchio, Daniele; Borin, Sara

    2016-03-15

    Petroleum pollution results in co-contamination by different classes of molecules, entailing the occurrence of marine sediments difficult to remediate, as in the case of the Ancona harbor (Mediterranean Sea, Italy). Autochthonous bioaugmentation (ABA), by exploiting the indigenous microbes of the environment to be treated, could represent a successful bioremediation strategy. In this perspective we aimed to i) identify the main drivers of the bacterial communities' richness in the sediments, ii) establish enrichment cultures with different hydrocarbon pollutants evaluating their effects on the bacterial communities' composition, and iii) obtain a collection of hydrocarbon degrading bacteria potentially exploitable in ABA. The correlation between the selection of different specialized bacterial populations and the type of pollutants was demonstrated by culture-independent analyses, and by establishing a collection of bacteria with different hydrocarbon degradation traits. Our observations indicate that pollution dictates the diversity of sediment bacterial communities and shapes the ABA potential in harbor sediments. PMID:26849913

  9. Comparing actinomycete and bacterial soil and sediment communities for metagenomics

    Hill, P.; Krištůfek, Václav; Feijoo, A. M.; Caballero, S.; van Elsas, D.

    Praha: Výzkumný ústav rostlinné výroby, Praha, 2005. s. 10. [Život v pode /6./. 01.02.2005-02.02.2005, Praha] Institutional research plan: CEZ:AV0Z60660521 Keywords : actinomycete * bacterial soil and sediment communities * metagenomics Subject RIV: EH - Ecology, Behaviour

  10. Changes in northern Gulf of Mexico sediment bacterial and archaeal communities exposed to hypoxia

    Biogeochemical changes in marine sediments during coastal water hypoxia are well described, but less is known about underlying changes in microbial communities. Bacterial and archaeal communities in Louisiana continental shelf (LCS) hypoxic zone sediments were characterized by py...

  11. Bacterial community survey of sediments at Naracoorte Caves, Australia

    Ball Andrew S.

    2012-07-01

    Full Text Available Bacterial diversity in sediments at UNESCO World Heritage listed Naracoorte Caves was surveyed as part of an investigation carried out in a larger study on assessing microbial communities in caves. Cave selection was based on tourist accessibility; Stick Tomato and Alexandra Cave (> 15000 annual visits and Strawhaven Cave was used as control (no tourist access. Microbial analysis showed that Bacillus was the most commonly detected microbial genus by culture dependent and independent survey of tourist accessible and inaccessible areas of show (tourist accessible and control caves. Other detected sediment bacterial groups were assigned to the Firmicutes, Actinobacteria and Proteobacteria. The survey also showed differences in bacterial diversity in caves with human access compared to the control cave with the control cave having unique microbial sequences (Acinetobacter, Agromyces, Micrococcus and Streptomyces. The show caves had higher bacterial counts, different 16S rDNA based DGGE cluster patterns and principal component groupings compared to Strawhaven. Different factors such as human access, cave use and configurations could have been responsible for the differences observed in the bacterial community cluster patterns (tourist accessible and inaccessible areas of these caves. Cave sediments can therefore act as reservoirs of microorganisms. This might have some implications on cave conservation activities especially if these sediments harbor rock art degrading microorganisms in caves with rock art.

  12. Bacterial community survey of sediments at Naracoorte Caves, Australia

    Ball Andrew S.; Kirby Greg; Bourne Steven; Cao Xiangsheng; Mazaheri Nezhad Fard Ramin; Adetutu Eric M.; Shahsavari Esamaeil; Thorpe Krystal

    2012-01-01

    Bacterial diversity in sediments at UNESCO World Heritage listed Naracoorte Caves was surveyed as part of an investigation carried out in a larger study on assessing microbial communities in caves. Cave selection was based on tourist accessibility; Stick Tomato and Alexandra Cave (> 15000 annual visits) and Strawhaven Cave was used as control (no tourist access). Microbial analysis showed that Bacillus was the most commonly detected microbial genus by culture dependent and independent survey ...

  13. Phytopigments as biomarkers of selectivity in abyssal holothurians; interspecific differences in response to a changing food supply

    FitzGeorge-Balfour, Tania; Billett, David S.M.; Wolff, George A.; Thompson, Anu; Tyler, Paul A.

    2010-01-01

    Holothurians dominate the abyssal megabenthos. They are key consumers and bioturbators of surficial sediment. Compounds essential for holothurian reproduction, such as carotenoids, are in short supply in the deep ocean. Holothurians cannot synthesise carotenoids de novo; the compounds are supplied with the flux of phytodetritus. Therefore, the supply of these compounds may play an important role in regulating processes on the seafloor. This study examines the link between the diet of abyssal ...

  14. Impact of oil on bacterial community structure in bioturbated sediments.

    Magalie Stauffert

    Full Text Available Oil spills threaten coastlines where biological processes supply essential ecosystem services. Therefore, it is crucial to understand how oil influences the microbial communities in sediments that play key roles in ecosystem functioning. Ecosystems such as sediments are characterized by intensive bioturbation due to burrowing macrofauna that may modify the microbial metabolisms. It is thus essential to consider the bioturbation when determining the impact of oil on microbial communities. In this study, an experimental laboratory device maintaining pristine collected mudflat sediments in microcosms closer to true environmental conditions--with tidal cycles and natural seawater--was used to simulate an oil spill under bioturbation conditions. Different conditions were applied to the microcosms including an addition of: standardized oil (Blend Arabian Light crude oil, 25.6 mg.g⁻¹ wet sediment, the common burrowing organism Hediste (Nereis diversicolor and both the oil and H. diversicolor. The addition of H. diversicolor and its associated bioturbation did not affect the removal of petroleum hydrocarbons. After 270 days, 60% of hydrocarbons had been removed in all microcosms irrespective of the H. diversicolor addition. However, 16S-rRNA gene and 16S-cDNA T-RFLP and RT-PCR-amplicon libraries analysis showed an effect of the condition on the bacterial community structure, composition, and dynamics, supported by PerMANOVA analysis. The 16S-cDNA libraries from microcosms where H. diversicolor was added (oiled and un-oiled showed a marked dominance of sequences related to Gammaproteobacteria. However, in the oiled-library sequences associated to Deltaproteobacteria and Bacteroidetes were also highly represented. The 16S-cDNA libraries from oiled-microcosms (with and without H. diversicolor addition revealed two distinct microbial communities characterized by different phylotypes associated to known hydrocarbonoclastic bacteria and dominated by

  15. Impact of oil on bacterial community structure in bioturbated sediments.

    Stauffert, Magalie; Cravo-Laureau, Cristiana; Jézéquel, Ronan; Barantal, Sandra; Cuny, Philippe; Gilbert, Franck; Cagnon, Christine; Militon, Cécile; Amouroux, David; Mahdaoui, Fatima; Bouyssiere, Brice; Stora, Georges; Merlin, François-Xavier; Duran, Robert

    2013-01-01

    Oil spills threaten coastlines where biological processes supply essential ecosystem services. Therefore, it is crucial to understand how oil influences the microbial communities in sediments that play key roles in ecosystem functioning. Ecosystems such as sediments are characterized by intensive bioturbation due to burrowing macrofauna that may modify the microbial metabolisms. It is thus essential to consider the bioturbation when determining the impact of oil on microbial communities. In this study, an experimental laboratory device maintaining pristine collected mudflat sediments in microcosms closer to true environmental conditions--with tidal cycles and natural seawater--was used to simulate an oil spill under bioturbation conditions. Different conditions were applied to the microcosms including an addition of: standardized oil (Blend Arabian Light crude oil, 25.6 mg.g⁻¹ wet sediment), the common burrowing organism Hediste (Nereis) diversicolor and both the oil and H. diversicolor. The addition of H. diversicolor and its associated bioturbation did not affect the removal of petroleum hydrocarbons. After 270 days, 60% of hydrocarbons had been removed in all microcosms irrespective of the H. diversicolor addition. However, 16S-rRNA gene and 16S-cDNA T-RFLP and RT-PCR-amplicon libraries analysis showed an effect of the condition on the bacterial community structure, composition, and dynamics, supported by PerMANOVA analysis. The 16S-cDNA libraries from microcosms where H. diversicolor was added (oiled and un-oiled) showed a marked dominance of sequences related to Gammaproteobacteria. However, in the oiled-library sequences associated to Deltaproteobacteria and Bacteroidetes were also highly represented. The 16S-cDNA libraries from oiled-microcosms (with and without H. diversicolor addition) revealed two distinct microbial communities characterized by different phylotypes associated to known hydrocarbonoclastic bacteria and dominated by Gammaproteobacteria

  16. Bioturbating shrimp alter the structure and diversity of bacterial communities in coastal marine sediments.

    Laverock, Bonnie; Smith, Cindy J; Tait, Karen; Osborn, A Mark; Widdicombe, Steve; Gilbert, Jack A

    2010-12-01

    Bioturbation is a key process in coastal sediments, influencing microbially driven cycling of nutrients as well as the physical characteristics of the sediment. However, little is known about the distribution, diversity and function of the microbial communities that inhabit the burrows of infaunal macroorganisms. In this study, terminal-restriction fragment length polymorphism analysis was used to investigate variation in the structure of bacterial communities in sediment bioturbated by the burrowing shrimp Upogebia deltaura or Callianassa subterranea. Analyses of 229 sediment samples revealed significant differences between bacterial communities inhabiting shrimp burrows and those inhabiting ambient surface and subsurface sediments. Bacterial communities in burrows from both shrimp species were more similar to those in surface-ambient than subsurface-ambient sediment (R=0.258, P<0.001). The presence of shrimp was also associated with changes in bacterial community structure in surrounding surface sediment, when compared with sediments uninhabited by shrimp. Bacterial community structure varied with burrow depth, and also between individual burrows, suggesting that the shrimp's burrow construction, irrigation and maintenance behaviour affect the distribution of bacteria within shrimp burrows. Subsequent sequence analysis of bacterial 16S rRNA genes from surface sediments revealed differences in the relative abundance of bacterial taxa between shrimp-inhabited and uninhabited sediments; shrimp-inhabited sediment contained a higher proportion of proteobacterial sequences, including in particular a twofold increase in Gammaproteobacteria. Chao1 and ACE diversity estimates showed that taxon richness within surface bacterial communities in shrimp-inhabited sediment was at least threefold higher than that in uninhabited sediment. This study shows that bioturbation can result in significant structural and compositional changes in sediment bacterial communities, increasing

  17. Phylogenetic analysis of the bacterial communities in marine sediments.

    Gray, J P; Herwig, R P

    1996-01-01

    For the phylogenetic analysis of microbial communities present in environmental samples microbial DNA can be extracted from the sample, 16S rDNA can be amplified with suitable primers and the PCR, and clonal libraries can be constructed. We report a protocol that can be used for efficient cell lysis and recovery of DNA from marine sediments. Key steps in this procedure include the use of a bead mill homogenizer for matrix disruption and uniform cell lysis and then purification of the released...

  18. Bidecadal Thermal Changes in the Abyssal Ocean

    Wunsch, Carl; Heimbach, Patrick

    2014-01-01

    A dynamically consistent state estimate is used for the period 1992–2011 to describe the changes in oceanic temperatures and heat content, with an emphasis on determining the noise background in the abyssal (below 2000 m) depths. Interpretation requires close attention to the long memory of the deep ocean, implying that meteorological forcing of decades to thousands of years ago should still be producing trendlike changes in abyssal heat content. Much of the deep-ocean volume remained unobser...

  19. Organic carbon cycling in abyssal benthic food chains: numerical simulations of bioenhancement by sewage sludge

    Rowe, Gilbert T.

    1998-05-01

    The hypothetical bioenhancement of the endemic benthic biota on an oligotrophic abyssal plain by organic carbon has been investigated with mathematical simulation experiments. First, the responses of the biomass and respiration to seasonal variations in the rain of organic carbon (POC) have been simulated in a simplified benthic assemblage (sediment organic carbon, sediment-dwelling heterotrophs (bacteria, meiofauna, macrofauna and detritus feeding megafauna) and predatory megafauna), with no added organic matter. These calculations were based on measured standing stocks and respiration in the central North Pacific (5.8 km depth, 31°N Lat.×159°W Long.). The dynamic relationships in this natural "oligotrophic" food chain were then subjected to added inputs of organic carbon presumed to be in sewage sludge. Two examples are presented: a modest but continuous input of organic carbon (100 mg C m -2 d -1) and a year-long pulse of the same intensity. The continuous input forced the biomass and community respiration to steadily increase until they reached steady state in 15 years at values similar to those found on a typical continental shelf. The pulse exhibited the same pattern, but biomass and respiration returned to levels found under natural oligotrophic conditions several years after cessation of intensified carbon loading. The responses of the sediment community to added organic matter were validated using information from a deep-ocean sewage disposal site (DWD106) off the coast of New Jersey. The models are also used to illustrate an approach for estimating possible transfers of potentially toxic contaminants, such as total polycyclic aromatic hydrocarbons (tPAHs), in lipid-rich eggs. In the future it will be necessary to validate model results with deep-ocean in situ experiments.

  20. Linking geology and microbiology: inactive pockmarks affect sediment microbial community structure.

    Haverkamp, Thomas H A; Hammer, Øyvind; Jakobsen, Kjetill S

    2014-01-01

    Pockmarks are geological features that are found on the bottom of lakes and oceans all over the globe. Some are active, seeping oil or methane, while others are inactive. Active pockmarks are well studied since they harbor specialized microbial communities that proliferate on the seeping compounds. Such communities are not found in inactive pockmarks. Interestingly, inactive pockmarks are known to have different macrofaunal communities compared to the surrounding sediments. It is undetermined what the microbial composition of inactive pockmarks is and if it shows a similar pattern as the macrofauna. The Norwegian Oslofjord contains many inactive pockmarks and they are well suited to study the influence of these geological features on the microbial community in the sediment. Here we present a detailed analysis of the microbial communities found in three inactive pockmarks and two control samples at two core depth intervals. The communities were analyzed using high-throughput amplicon sequencing of the 16S rRNA V3 region. Microbial communities of surface pockmark sediments were indistinguishable from communities found in the surrounding seabed. In contrast, pockmark communities at 40 cm sediment depth had a significantly different community structure from normal sediments at the same depth. Statistical analysis of chemical variables indicated significant differences in the concentrations of total carbon and non-particulate organic carbon between 40 cm pockmarks and reference sample sediments. We discuss these results in comparison with the taxonomic classification of the OTUs identified in our samples. Our results indicate that microbial communities at the sediment surface are affected by the water column, while the deeper (40 cm) sediment communities are affected by local conditions within the sediment. PMID:24475066

  1. Linking geology and microbiology: inactive pockmarks affect sediment microbial community structure.

    Thomas H A Haverkamp

    Full Text Available Pockmarks are geological features that are found on the bottom of lakes and oceans all over the globe. Some are active, seeping oil or methane, while others are inactive. Active pockmarks are well studied since they harbor specialized microbial communities that proliferate on the seeping compounds. Such communities are not found in inactive pockmarks. Interestingly, inactive pockmarks are known to have different macrofaunal communities compared to the surrounding sediments. It is undetermined what the microbial composition of inactive pockmarks is and if it shows a similar pattern as the macrofauna. The Norwegian Oslofjord contains many inactive pockmarks and they are well suited to study the influence of these geological features on the microbial community in the sediment. Here we present a detailed analysis of the microbial communities found in three inactive pockmarks and two control samples at two core depth intervals. The communities were analyzed using high-throughput amplicon sequencing of the 16S rRNA V3 region. Microbial communities of surface pockmark sediments were indistinguishable from communities found in the surrounding seabed. In contrast, pockmark communities at 40 cm sediment depth had a significantly different community structure from normal sediments at the same depth. Statistical analysis of chemical variables indicated significant differences in the concentrations of total carbon and non-particulate organic carbon between 40 cm pockmarks and reference sample sediments. We discuss these results in comparison with the taxonomic classification of the OTUs identified in our samples. Our results indicate that microbial communities at the sediment surface are affected by the water column, while the deeper (40 cm sediment communities are affected by local conditions within the sediment.

  2. Direct observation of episodic growth in an abyssal xenophyophore (Protista)

    Gooday, A. J.; Bett, B. J.; Pratt, D. N.

    1993-11-01

    Three specimens of the xenophyophore Reticulammina labyrinthica were photographed on the Madeira Abyssal Plain (31°6.1'N, 21°10.9'W; 4944 m) using the Bathysnap time-lapse camera system. During the 8 month observation period, the specimens underwent an estimated 3-10 fold increase in volume. Growth occurred episodically in several distinct phases, each lasting 2-3 days, during which sediment was collected and incorporated into the test. These phases were separated by fairly regular periods of about 2 months when the organisms showed little obvious activity. The growth phases were approximately synchronous between specimens. However, it is not clear whether the periodicity and apparent synchronization of these events resulted from an external (environmental) cue or whether growth is internally controlled and the synchronization arose by chance. These unique observations, which represent the first direct measurement of growth in any abyssal organism living outside a hydrothermal vent field, suggest that xenophyophores combine test growth with deposit feeding. The tests appear to grow more quickly, and to be more active, dynamic structures, than previously believed.

  3. Sediment quality in the Douro river estuary based on trace metal contents, macrobenthic community and elutriate sediment toxicity test (ESTT).

    Mucha, Ana P; Bordalo, Adriano A; Vasconcelos, M Teresa S D

    2004-07-01

    The aim of this study was to evaluate the sediment quality in the mesotidal Douro River estuarine environment, in order to identify areas where sediment contamination could cause ecosystem degradation. Samples were obtained in five locations and sediment characterised for grain size, total organic matter, total-recoverable metals (Al, Fe, Cu, Pb, Cr, Ni, Cd, Zn and Mn), as well as acid volatile sulfide (AVS) and simultaneously extracted metals (SEM). In situ effects were evaluated by examining the macrobenthic community structure. An elutriate sediment toxicity test (ESTT) was used to estimate the amount of metals and nutrients that could be exchanged with the water column through resuspension, and its positive or negative effects on the growth of the micro-alga Emiliania huxleyi in a 10 day test. Anthropogenic metal contamination was identified at the north bank of the Douro estuary, with deleterious effects on the macrobenthic community, namely decrease in number of species and diversity. This contamination could possibly also be toxic for water column organisms, in case of resuspension, as shown by the ESTT. Sediments from the salt marsh at the south bank showed an impoverished macrobenthic community and elutriate toxicity, which appeared to be due to anaerobic conditions. This study clearly shows the usefulness of the ESST approach to assess the biological effect of resuspension of estuarine sediments. PMID:15237288

  4. Temporal dynamics of sediment bacterial communities in monospecific stands of Juncus maritimus and Spartina maritima.

    Cleary, D F R; Polónia, A R M; Sousa, A I; Lillebø, A I; Queiroga, H; Gomes, N C M

    2016-09-01

    In the present study, we used 16S rRNA barcoded pyrosequencing to investigate to what extent monospecific stands of different salt marsh plant species (Juncus maritimus and Spartina maritima), sampling site and temporal variation affect sediment bacterial communities. We also used a bioinformatics tool, PICRUSt, to predict metagenome gene functional content. Our results showed that bacterial community composition from monospecific stands of both plant species varied temporally, but both host plant species maintained compositionally distinct communities of bacteria. Juncus sediment was characterised by higher abundances of Alphaproteobacteria, Myxococcales, Rhodospirillales, NB1-j and Ignavibacteriales, while Spartina sediment was characterised by higher abundances of Anaerolineae, Synechococcophycidae, Desulfobacterales, SHA-20 and Rhodobacterales. The differences in composition and higher taxon abundance between the sediment bacterial communities of stands of both plant species may be expected to affect overall metabolic diversity. In line with this expectation, there were also differences in the predicted enrichment of selected metabolic pathways. In particular, bacterial communities of Juncus sediment were predicted to be enriched for pathways related to the degradation of various (xenobiotic) compounds. Bacterial communities of Spartina sediment in turn were predicted to be enriched for pathways related to the biosynthesis of various bioactive compounds. Our study highlights the differences in composition and predicted functions of sediment-associated bacterial communities from two different salt marsh plant species. Loss of salt marsh habitat may thus be expected to both adversely affect microbial diversity and ecosystem functioning and have consequences for environmental processes such as nutrient cycling and pollutant remediation. PMID:27061465

  5. Links between surface productivity and deep ocean particle flux at the Porcupine Abyssal Plain (PAP) sustained observatory

    Frigstad, H.; Henson, S. A.; Hartman, S. E.; Omar, A. M.; Jeansson, E.; Cole, H.; Pebody, C.; Lampitt, R. S.

    2015-04-01

    In this study we present hydrography, biogeochemistry and sediment trap observations between 2003 and 2012 at Porcupine Abyssal Plain (PAP) sustained observatory in the northeast Atlantic. The time series is valuable as it allows for investigation of the link between surface productivity and deep ocean carbon flux. The region is a perennial sink for CO2, with an average uptake of around 1.5 mmol m-2 d-1. The average monthly drawdowns of inorganic carbon and nitrogen were used to quantify the net community production (NCP) and new production, respectively. Seasonal NCP and new production were found to be 4.57 ± 0.27 mol C m-2 and 0.37 ± 0.14 mol N m-2. The Redfield ratio was high (12), and the production calculated from carbon was higher than production calculated from nitrogen, which is indicative of carbon overconsumption. The export ratio and transfer efficiency were 16 and 4%, respectively, and the site thereby showed high flux attenuation. Particle tracking was used to examine the source region of material in the sediment trap, and there was large variation in source regions, both between and within years. There were higher correlations between surface productivity and export flux when using the particle-tracking approach, than by comparing with the mean productivity in a 100 km box around the PAP site. However, the differences in correlation coefficients were not significant, and a longer time series is needed to draw conclusions on applying particle tracking in sediment trap analyses.

  6. Links between surface productivity and deep ocean particle flux at the Porcupine Abyssal Plain sustained observatory

    Frigstad, H.; Henson, S. A.; Hartman, S. E.; Omar, A. M.; Jeansson, E.; Cole, H.; Pebody, C.; Lampitt, R. S.

    2015-10-01

    In this study we present hydrography, biogeochemistry and sediment trap observations between 2003 and 2012 at Porcupine Abyssal Plain (PAP) sustained observatory in the Northeast Atlantic. The time series is valuable as it allows for investigation of the link between surface productivity and deep ocean carbon flux. The region is a perennial sink for CO2, with an average uptake of around 1.5 mmol m-2 day-1. The average monthly drawdowns of inorganic carbon and nitrogen were used to quantify the net community production (NCP) and new production. Seasonal NCP and new production were found to be 4.57 ± 0.85 mol C m-2 and 0.37 ± 0.14 mol N m-2, respectively. The C : N ratio was high (12) compared to the Redfield ratio (6.6), and the production calculated from carbon was higher than production calculated from nitrogen, which is indicative of carbon overconsumption. The export ratio and transfer efficiency were 16 and 4 %, respectively, and the site thereby showed high flux attenuation. Particle tracking was used to examine the source region of material in the sediment trap, and there was large variation in source regions, both between and within years. There were higher correlations between surface productivity and export flux when using the particle-tracking approach, than by comparing with the mean productivity in a 100 km box around the PAP site. However, the differences in correlation coefficients were not significant, and a longer time series is needed to draw conclusions on applying particle tracking in sediment trap analyses.

  7. Polychaete burrows harbour distinct microbial communities in oil-contaminated coastal sediments.

    Taylor, Joe D; Cunliffe, Michael

    2015-08-01

    Previous studies have shown that the bioturbating polychaete Hediste (Nereis) diversicolor can affect the composition of bacterial communities in oil-contaminated sediments, but have not considered diversity specifically within bioturbator burrows or the impact on microbial eukaryotes. We tested the hypothesis that H. diversicolor burrows harbour different eukaryotic and bacterial communities compared with un-bioturbated sediment, and that bioturbation stimulates oil degradation. Oil-contaminated sediment was incubated with or without H. diversicolor for 30 days, after which sediment un-affected by H. diversicolor and burrow DNA/RNA samples were analysed using quantitative reverse transcription PCR (Q-RT-PCR) and high-throughput sequencing. Fungi dominated both burrow and un-bioturbated sediment sequence libraries; however, there was significant enrichment of bacterivorous protists and nematodes in the burrows. There were also significant differences between the bacterial communities in burrows compared with un-bioturbated sediment. Increased activity and relative abundance of aerobic hydrocarbon-degrading bacteria in the burrows coincided with the significant reduction in hydrocarbon concentration in the bioturbated sediment. This study represents the first detailed assessment of the effect of bioturbation on total microbial communities in oil-contaminated sediments. In addition, it further shows that bioturbation is a significant factor in determining microbial diversity within polluted sediments and plays an important role in stimulating bioremediation. PMID:25858418

  8. Links between surface productivity and deep ocean particle flux at the Porcupine Abyssal Plain sustained observatory

    Frigstad, H.; Henson, S. A.; Hartman, S. E.; A. M. Omar; E. Jeansson; Cole, H.; Pebody, C.; Lampitt, R. S.

    2015-01-01

    In this study we present hydrography, biogeochemistry and sediment trap observations between 2003 and 2012 at Porcupine Abyssal Plain (PAP) sustained observatory in the Northeast Atlantic. The time series is valuable as it allows for investigation of the link between surface productivity and deep ocean carbon flux. The region is a perennial sink for CO2, with an average uptake of around 1.5 mmol m−2 day−1. The average monthly drawdowns of inorganic carbon and nitrogen were used to...

  9. Macrofaunal Impact on the Denitrifying Bacterial Community in Freshwater Sediment

    Poulsen, Morten; Stief, Peter; Schramm, Andreas

    Sediment-dwelling macroinvertebrates alter their habitat by transporting oxic water into the sediment and enriching it for organic matter, thereby affecting microbial processes in the sediment. Here we report that burrowing macroinvertebrates can also have a pronounced effect on microbial diversity......, with nitrate-reducing and denitrifying bacteria as examples. The diversity of these functional groups was compared in sediment microcosms with and without Chironomus plumosus larvae, using the genes encoding nitrate reductase (narG) and nitrous oxide reductase (nosZ) as functional markers. The...... estimated phylotype richness of narG increased from 68 in sediment without larvae to 170 in sediment with larvae. Part of this increase in narG diversity could be explained by metabolic activation of certain nitrate-reducing bacteria in the gut of C. plumosus, since 18.3 % of the additional phylotypes were...

  10. Immobilisation of manganese, cobalt and nickel by deep-sea-sediment microbial communities

    Sujith, P.P.; Das, A.; Mourya, B.S.; LokaBharathi, P.A.

    Box core samples BC26 and BC36 from geologically different settings were examined to test the hypothesis that autochthonous microbial communities from polymetallic-nodule-rich Central Indian Basin sediments actively participate in immobilising metal...

  11. Effects of hydraulic shellfish harvesting on benthic communities and sediment chemistry 2009-2013

    National Oceanic and Atmospheric Administration, Department of Commerce — The effects of hydraulic shellfish harvesting on the ecology of biological communities and chemistry of benthic sediments were investigated through a series of...

  12. Phenotypic and genotypic adaptation of aerobic heterotrophic sediment bacterial communities to mercury stress.

    Barkay, T; Olson, B. H.

    1986-01-01

    The effects of mercury contamination of lake sediments on the phenotypic and genotypic mercury resistance of the indigenous heterotrophic aerobic bacterial communities were investigated. Strong positive correlations between mercury sediment concentration and the frequency of the gene coding for mercury volatilization (mer) (r = 0.96) or the phenotypic mercury resistance (r = 0.86) of the studied communities suggested that the inheritance via selection or genetic exchange of the mer gene had p...

  13. Microbial communities of urban stormwater sediments: the phylogenetic structure of bacterial communities varies with porosity.

    Badin, Anne-Laure; Mustafa, Tarfa; Bertrand, Cédric; Monier, Armelle; Delolme, Cécile; Geremia, Roberto A; Bedell, Jean-Philippe

    2012-08-01

    This study focuses on the distribution of bacterial and fungal communities within the microstructure of a multi-contaminated sedimentary layer resulting from urban stormwater infiltration. Fractionation was performed on the basis of differential porosity and aggregate grain size, resulting in five fractions: leachable fitting macroporosity, 1000 μm. Amounts of both bacterial and fungal biomasses are greater in the < 10 μm and leachable fractions. The aggregates contain numerous bacteria but very low amounts of fungal biomass. Single-strand conformational polymorphism molecular profiles highlighted the differences between bacterial and fungal communities of the leachable fraction and those of the aggregates. Random Sanger sequencing of ssu clones revealed that these differences were mainly because of the presence of Epsilonproteobacteria and Firmicutes in the leachable fractions, while the aggregates contained more Cyanobacteria. The Cyanobacteria phylotypes in the aggregates were dominated by the sequences related to Microcoleus vaginatus while the leachable fractions presented the sequences of chloroplastic origin. Therefore, more than 50% of the phylotypes observed were related to Proteobacteria while 40% were related to Cyanobacteria and Bacteroidetes. Preferential distribution of clades in almost all the phyla or classes detected was observed. This study provides insight into the identities of dominant members of the bacterial communities of urban sediments. Microcoleus vaginatus appeared to predominate in pioneer soils. PMID:22404135

  14. Analysis of effect of nicotine on microbial community structure in sediment using PCR-DGGE fingerprinting

    Ai-dong Ruan

    2015-10-01

    Full Text Available Solid or liquid waste containing a high concentration of nicotine can pollute sediment in rivers and lakes, and may destroy the ecological balance if it is directly discharged into the environment without any treatment. In this study, the polymerase chain reaction (PCR and denaturing gradient gel electrophoresis (DGGE method was used to analyze the variation of the microbial community structure in the control and nicotine-contaminated sediment samples with nicotine concentration and time of exposure. The results demonstrated that the growth of some bacterial species in the nicotine-contaminated sediment samples was inhibited during the exposure. Some bacteria decreased in species diversity and in quantity with the increase of nicotine concentration or time of exposure, while other bacteria were enriched under the effect of nicotine, and their DGGE bands changed from undertones to deep colors. The microbial community structure, however, showed a wide variation in the nicotine-contaminated sediment samples, especially in the sediment samples treated with high-concentration nicotine. The Jaccard index was only 35.1% between the initial sediment sample and the sediment sample with a nicotine concentration of 0.030 μg/g after 28 d of exposure. Diversity indices showed that the contaminated groups had a similar trend over time. The diversity indices of contaminated groups all decreased in the first 7 d after exposure, then increased until day 42. It has been found that nicotine decreased the diversity of the microbial community in the sediment.

  15. Phylogenetic analysis of bacterial community in deep-sea sediment from the western Pacific "warm pool"

    2005-01-01

    A depth profile of bacterial community structure in one deep-sea sediment core of the western Pacific "warm pool" (WP) was investigated and compared with that in a sediment sample from the eastern Pacific (EP) by phylogenetic analysis of 16S rDNA fragments.Five bacterial 16S rDNA clone libraries were constructed, and t33 clones with different restriction fragment length polymorphism(RFLP) patterns were sequenced. A phylogenetic analysis of these sequences revealed that the bacterial diversity in a sample from the WP was more abundant than that in the EP sample. The bacterial population in the sediment core of WP was composed of eight major lineages of the domain bacteria. Among them the γ-Proteobacteria was the predominant and most diverse group in each section of WP sediment core, followed by the α-Proteobacteria. The genus Colwellia belonging to γ-Proteobacteria was predominant in this sample.The shift of bacterial communities among different sections of the WP sediment core was δ-, ε-Proteobacteria, and Cytopahga-Flexibacteria-Bacteroides (CFB) group. The ratios between them in the bacterial communities all showed inversely proportional to the depth of sediment. The sequences related to sulphate reducing bacteria (SRB) were detected in every section. The bacterial community structure in this sediment core might be related to the environmental characteristics of the surface seawater of the western Pacific WP.

  16. Effects of pesticides on community composition and activity of sediment microbes - responses at various levels of microbial community organization

    Widenfalk, Anneli [Department of Environmental Assessment, Swedish University of Agricultural Sciences, P.O. Box 7050, SE-750 07 Uppsala (Sweden)], E-mail: anneli.widenfalk@kemi.se; Bertilsson, Stefan [Limnology/Department of Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Norbyvaegen 20, SE-752 36 Uppsala (Sweden); Sundh, Ingvar [Department of Microbiology, Swedish University of Agricultural Sciences, P.O. Box 7025, SE-750 07 Uppsala (Sweden); Goedkoop, Willem [Department of Environmental Assessment, Swedish University of Agricultural Sciences, P.O. Box 7050, SE-750 07 Uppsala (Sweden)

    2008-04-15

    A freshwater sediment was exposed to the pesticides captan, glyphosate, isoproturon, and pirimicarb at environmentally relevant and high concentrations. Effects on sediment microorganisms were studied by measuring bacterial activity, fungal and total microbial biomass as community-level endpoints. At the sub-community level, microbial community structure was analysed (PLFA composition and bacterial 16S rRNA genotyping, T-RFLP). Community-level endpoints were not affected by pesticide exposure. At lower levels of microbial community organization, however, molecular methods revealed treatment-induced changes in community composition. Captan and glyphosate exposure caused significant shifts in bacterial community composition (as T-RFLP) at environmentally relevant concentrations. Furthermore, differences in microbial community composition among pesticide treatments were found, indicating that test compounds and exposure concentrations induced multidirectional shifts. Our study showed that community-level end points failed to detect these changes, underpinning the need for application of molecular techniques in aquatic ecotoxicology. - Molecular techniques revealed pesticide-induced changes at lower levels of microbial community organization that were not detected by community-level end points.

  17. Effects of pesticides on community composition and activity of sediment microbes - responses at various levels of microbial community organization

    A freshwater sediment was exposed to the pesticides captan, glyphosate, isoproturon, and pirimicarb at environmentally relevant and high concentrations. Effects on sediment microorganisms were studied by measuring bacterial activity, fungal and total microbial biomass as community-level endpoints. At the sub-community level, microbial community structure was analysed (PLFA composition and bacterial 16S rRNA genotyping, T-RFLP). Community-level endpoints were not affected by pesticide exposure. At lower levels of microbial community organization, however, molecular methods revealed treatment-induced changes in community composition. Captan and glyphosate exposure caused significant shifts in bacterial community composition (as T-RFLP) at environmentally relevant concentrations. Furthermore, differences in microbial community composition among pesticide treatments were found, indicating that test compounds and exposure concentrations induced multidirectional shifts. Our study showed that community-level end points failed to detect these changes, underpinning the need for application of molecular techniques in aquatic ecotoxicology. - Molecular techniques revealed pesticide-induced changes at lower levels of microbial community organization that were not detected by community-level end points

  18. Global variations in abyssal peridotite compositions

    Warren, Jessica M.

    2016-04-01

    Abyssal peridotites are ultramafic rocks collected from mid-ocean ridges that are the residues of adiabatic decompression melting. Their compositions provide information on the degree of melting and melt-rock interaction involved in the formation of oceanic lithosphere, as well as providing constraints on pre-existing mantle heterogeneities. This review presents a compilation of abyssal peridotite geochemical data (modes, mineral major elements, and clinopyroxene trace elements) for > 1200 samples from 53 localities on 6 major ridge systems. On the basis of composition and petrography, peridotites are classified into one of five lithological groups: (1) residual peridotite, (2) dunite, (3) gabbro-veined and/or plagioclase-bearing peridotite, (4) pyroxenite-veined peridotite, and (5) other types of melt-added peridotite. Almost a third of abyssal peridotites are veined, indicating that the oceanic lithospheric mantle is more fertile, on average, than estimates based on residual peridotites alone imply. All veins appear to have formed recently during melt transport beneath the ridge, though some pyroxenites may be derived from melting of recycled oceanic crust. A limited number of samples are available at intermediate and fast spreading rates, with samples from the East Pacific Rise indicating high degrees of melting. At slow and ultra-slow spreading rates, residual abyssal peridotites define a large (0-15% modal clinopyroxene and spinel Cr# = 0.1-0.6) compositional range. These variations do not match the prediction for how degree of melting should vary as a function of spreading rate. Instead, the compositional ranges of residual peridotites are derived from a combination of melting, melt-rock interaction and pre-existing compositional variability, where melt-rock interaction is used here as a general term to refer to the wide range of processes that can occur during melt transport in the mantle. Globally, ~ 10% of abyssal peridotites are refractory (0

  19. Effects of benthic macrofauna bioturbation on the bacterial community composition in lake sediments.

    Zeng, Jin; Zhao, Da-Yong; Liu, Peng; Yu, Zhong-Bo; Huang, Rui; Wu, Qinglong L

    2014-08-01

    Benthic macrofauna are considered to be an important part of the lacustrine ecosystem, and bioturbation may greatly affect the biogeochemical processes and microbial activities in sediments. In the present study, the bacterial community composition in sediments inhabited by 3 different types of benthic macrofauna (Corbicula fluminea, Chironomidae larvae, and tubificid worms) in the shallow and eutrophic Lake Taihu was studied to investigate the different effects of bioturbation on the composition of these communities. Microcosms were constructed, and culture-independent methods, including terminal restriction fragment length polymorphism (T-RFLP) and clone library analysis, were performed to evaluate the bacterial communities. Analysis of similarities (ANOSIM) and multidimensional scaling (MDS) analysis of T-RFLP patterns demonstrated that differences in the bacterial community composition between the control and the macrofauna-inhabited sediments were not as great as expected, although the chemical properties of the sediments changed remarkably. Nevertheless, the dominant bacterial group in each type of macrofauna-inhabited sediment was different. Acidobacteria, Betaproteobacteria, and Deltaproteobacteria were the dominant bacterial groups in sediments inhabited by C. fluminea, tubificid worms, and Chironomidae larvae, respectively. The data obtained in this study are helpful for understanding the effects of bioturbation in a shallow, eutrophic lake. PMID:25070418

  20. Influence of Wastewater Discharge on the Metabolic Potential of the Microbial Community in River Sediments

    Li, Dong

    2015-09-24

    To reveal the variation of microbial community functions during water filtration process in river sediments, which has been utilized widely in natural water treatment systems, this study investigates the influence of municipal wastewater discharge to streams on the phylotype and metabolic potential of the microbiome in upstream and particularly various depths of downstream river sediments. Cluster analyses based on both microbial phylogenetic and functional data collectively revealed that shallow upstream sediments grouped with those from deeper subsurface downstream regions. These sediment samples were distinct from those found in shallow downstream sediments. Functional genes associated with carbohydrate, xenobiotic, and certain amino acid metabolisms were overrepresented in upstream and deep downstream samples. In contrast, the more immediate contact with wastewater discharge in shallow downstream samples resulted in an increase in the relative abundance of genes associated with nitrogen, sulfur, purine and pyrimidine metabolisms, as well as restriction–modification systems. More diverse bacterial phyla were associated with upstream and deep downstream sediments, mainly including Actinobacteria, Planctomycetes, and Firmicutes. In contrast, in shallow downstream sediments, genera affiliated with Betaproteobacteria and Gammaproteobacteria were enriched with putative functions that included ammonia and sulfur oxidation, polyphosphate accumulation, and methylotrophic bacteria. Collectively, these results highlight the enhanced capabilities of microbial communities residing in deeper stream sediments for the transformation of water contaminants and thus provide a foundation for better design of natural water treatment systems to further improve the removal of contaminants. © 2015, Springer Science+Business Media New York.

  1. Using in situ bacterial communities to monitor contaminants in river sediments.

    Xie, Yuwei; Wang, Jizhong; Wu, Yaketon; Ren, Chen; Song, Chao; Yang, Jianghua; Yu, Hongxia; Giesy, John P; Zhang, Xiaowei

    2016-05-01

    Bacterial communities in sediments of human-impacted rivers are exposed to multiple anthropogenic contaminants and eventually lead to biodiversity lost and ecological functions disable. Nanfei River of Anhui province has been contaminated by pollutants from industrial and/or agricultural sources. This study was conducted to investigate the structure of in situ sediment bacterial communities in Nanfei River and to examine the correlation between the different taxonomic components and contaminant concentrations. The bacterial communities were dominated by Proteobacteria, Bacteroidetes and Chloroflexi. Both the profiles of environmental predictors and the composition of microbial communities differed among agriculture, industrial and confluence regions. There were significant associations between bacterial community phylogenies and the measured contaminants in the sediments. Nutrients (TN and TP) and two metals (Cd and Zn) were negatively correlated with the essential "core" of the bacterial interaction network (Betaproteobacteria and Deltaproteobacteria). Metals (Fe, Ni and Zn) and nutrients (TN and TP) had higher impact on bacterial community compositions than PAHs, OPs and PRTs according to the correlation and network analyses. Furthermore, several sensitive candidate genera were identified as potential bioindicators to monitor key contaminants by species contaminant correlation analysis. Overall, in situ bacterial communities could provide a useful tool for monitoring and assessing ecological stressors in freshwater sediments. PMID:26866572

  2. Prokaryotic community composition involved production of nitrogen in sediments of Mejillones Bay

    Conventional denitrification and anaerobic ammonium oxidation (anammox) contributes to nitrogen loss in oxygen-deficient systems, thereby influencing many aspects of ecosystem function and global biogeochemistry. Mejillones Bay, northern Chile, presents ideal conditions to study nitrogen removal processes, because it is inserted in a coastal upwelling system, its sediments have anoxia and hypoxia conditions and under the influence of the Oxygen Minimum Zone (OMZ), unknown processes that occur there and what are the microbial communities responsible for their removal. Microbial communities associated with coastal sediments of Mejillones Bay were studied by denaturing gel electrophoresis (DGGE) and fluorescence in situ hybridization (FISH), by incubation experiments with 15N isotope tracers were studied nitrogen loss processes operating in these sediments. DGGE analysis showed high bacterial diversity, certain redundant phylotypes and differences in community structure given by the depth; this reflects the microbial community adaptations to environmental conditions. A large fraction (up to 70%) of DAPI-stained cells hybridized with the bacterial probes. Nearly 52-90% of the cell could be further identified to know phyla. Members of the Cytophaga-Flavobacterium cluster were most abundant in the sediments (13-26%), followed by Proteobacteria. Isotopic tracer experiments for the sediments studied indicated that nitrogen loss processes that predominated were performed by denitrifying communities (43.31-111.20 μMd-1) was not possible to detect anammox in the area and not anammox bacteria were detected

  3. Infaunal macrobenthic community of soft bottom sediment in a tropical shelf

    Jayaraj, K.A.; Jacob, J.; DineshKumar, P.K.

    as food in the sandy environment. During postmonsoon in the three clusters obtained, shallow depth cluster Prionospio pinnata–Lumbrineries in the fine sediment texture changed to the molluscan assemblage of the Tellina– Mactra community as depth increased... feeders in the fine sediment was due to the available food in the form of OM. The fine fraction indicates the depository environment with reduced current activities that bring food particles to deposit feeders. The filter feeders or animals that obtain...

  4. Comparative geoscience studies of the Madeira and Southern Nares Abyssal Plains: NEA/SWG preference location document

    Auffret, G.A.; Buckley, D.E.; Schuttenhelm, R.T.E.; Searle, R.C.; Shephard, L.E.; Cranston, R.E.

    1986-01-01

    This document summarizes the status of geoscience investigations in the two primary North Atlantic study locations Great Meteor East (GME) in the Madeira Abyssal Plain, and the Southern Nares Abyssal Plain (SNAP), and assesses the characteristics of these locations relative to the guidelines considered desirable and necessary for a potential subseabed high-level waste repository. These characteristics will be continually reevaluated as additional data become available and as our understanding of deep-sea sediment processes within abyssal plain environments improves. Initially, a number of areas of minimum size were identified in the ocean basins that appeared to comply with most of the stability and barrier guidelines. However, detailed studies in both GME and SNAP demonstrate that as our level of knowledge improves, and the degree of resolution increases, the number of 100 km/sup 2/ areas complying with these guidelines becomes much more limited. This observation may be characteristic of abyssal plain and abyssal hill environments in both the North Atlantic and North Pacific basins. Marked differences in geoscience characteristics exist between the Great Meteor East and the Southern Nares Abyssal Plain study locations. The significance of these differences, as they impact the selection of a single preferred site for a potential subseabed repository, can only be determined by using an integrated systems risk assessment modeling approach. The known geoscience characteristics can, however, be used in conjunction with the site assessment guidelines to draw conclusions concerning the geoscience suitability of these two locations. These conclusions will be modified as specific types of data from future expeditions become available.

  5. Drivers of abundance and community composition of benthic macroinvertebrates in Ottawa River sediment near Chalk River Laboratories

    The Ottawa River has received effluent from Chalk River Laboratories (CRL) for more than 60 years. Some radionuclides and contaminants released in effluents are bound rapidly to particles and deposited in bottom sediments where they may be biologically available to benthic invertebrates and other aquatic biota. As part of a larger ecological assessment, we assess the potential impact of contaminated sediments in the vicinity of CRL on local benthic community structure. Using bivariate and multivariate approaches, we demonstrate that CRL operations have had little impact on the local benthic community. Despite elevated anthropogenic radionuclide activity concentrations in sediment near CRL's process outfall, the benthic community is no less abundant or diverse than what is observed upstream at background levels. The Ottawa River benthic invertebrate community is structured predominantly by natural physical and biological conditions in the sediment, specifically sediment water content and organic content. These natural habitat conditions have a stronger influence on macroinvertebrate communities than sediment contamination. (author)

  6. Drivers of abundance and community composition of benthic macroinvertebrates in Ottawa River sediment near Chalk River Laboratories

    Bond, M.J.; Rowan, D.; Silke, R.; Carr, J., E-mail: bondm@aecl.ca [Atomic Energy of Canada Limited, Chalk River, Ontario (Canada)

    2013-12-15

    The Ottawa River has received effluent from Chalk River Laboratories (CRL) for more than 60 years. Some radionuclides and contaminants released in effluents are bound rapidly to particles and deposited in bottom sediments where they may be biologically available to benthic invertebrates and other aquatic biota. As part of a larger ecological assessment, we assess the potential impact of contaminated sediments in the vicinity of CRL on local benthic community structure. Using bivariate and multivariate approaches, we demonstrate that CRL operations have had little impact on the local benthic community. Despite elevated anthropogenic radionuclide activity concentrations in sediment near CRL's process outfall, the benthic community is no less abundant or diverse than what is observed upstream at background levels. The Ottawa River benthic invertebrate community is structured predominantly by natural physical and biological conditions in the sediment, specifically sediment water content and organic content. These natural habitat conditions have a stronger influence on macroinvertebrate communities than sediment contamination. (author)

  7. Remnants of marine bacterial communities can be retrieved from deep sediments in lakes of marine origin.

    Langenheder, Silke; Comte, Jérôme; Zha, Yinghua; Samad, Md Sainur; Sinclair, Lucas; Eiler, Alexander; Lindström, Eva S

    2016-08-01

    Some bacteria can be preserved over time in deep sediments where they persist either in dormant or slow-growing vegetative stages. Here, we hypothesized that such cells can be revived when exposed to environmental conditions similar to those before they were buried in the sediments. To test this hypothesis, we collected bacteria from sediment samples of different ages (140-8500 calibrated years before present, cal BP) from three lakes that differed in the timing of their physical isolation from the Baltic Sea following postglacial uplift. After these bacterial communities were grown in sterile water from the Baltic Sea, we determined the proportion of 16S rRNA sequence reads associated with marine habitats by extracting the environment descriptive terms of homologous sequences retrieved from public databases. We found that the proportion of reads associated with marine descriptive term was significantly higher in cultures inoculated with sediment layers formed under Baltic conditions and where salinities were expected to be similar to current levels. Moreover, a similar pattern was found in the original sediment layers. Our study, therefore, suggests that remnants of marine bacterial communities can be preserved in sediments over thousands of years and can be revived from deep sediments in lakes of marine origin. PMID:26929161

  8. Response of the methanogenic microbial communities in Amazonian oxbow lake sediments to desiccation stress.

    Conrad, Ralf; Ji, Yang; Noll, Matthias; Klose, Melanie; Claus, Peter; Enrich-Prast, Alex

    2014-06-01

    Methanogenic microbial communities in soil and sediment function only when the environment is inundated and anoxic. In contrast to submerged soils, desiccation of lake sediments happens only rarely. However, some predictions suggest that extreme events of drying will become more common in the Amazon region, and this will promote an increase in sediments drying and exposure. We asked whether and how such methanogenic communities can withstand desiccation stress. Therefore, we determined the rates and pathways of CH(4) production (analysis of CH(4) and δ(13) C of CH(4), CO(2) and acetate), the copy numbers of bacterial and archaeal 16S rRNA genes and mcrA genes (quantitative PCR), and the community composition of Archaea and Bacteria (T-RFLP and pyrosequencing) in oxbow lake sediments of rivers in the Brazilian Amazon region. The rivers were of white water, black water and clear water type. The measurements were done with sediment in fresh state and after drying and rewetting. After desiccation and rewetting the composition of both, the archaeal and bacterial community changed. Since lake sediments from white water rivers exhibited only negligible methanogenic activity, probably because of relatively high iron and low organic matter content, they were not further analysed. The other sediments produced CH(4), with hydrogenotrophic methanogenesis usually accounting for > 50% of total activity. After desiccation and rewetting, archaeal and bacterial gene copy numbers decreased. The bacterial community showed a remarkable increase of Clostridiales from about 10% to > 30% of all Bacteria, partially caused by proliferation of specific taxa as the numbers of OTU shared with fresh sediment decreased from about 9% to 3%. Among the Archaea, desiccation specifically enhanced the relative abundance of either Methanocellales (black water) and/or Methanosarcinaceae (clear water). Despite the changes in gene copy numbers and composition of the microbial community, rates of CH

  9. Heat flow measurements in Great Meteor East, Madeira Abyssal Plain, during Discovery Cruise 144

    This report describes 21 closely spaced heat flow measurements which were made along two survey lines in an area of faulted sediments east of Great Meteor Seamount in the Madeira Abyssal Plain. The heat flow was found to be correlated with basement topography as mapped by seismic reflection profiling. Data modelling suggests that this is due both to the thermal conductivity contrast between sediments and basement rocks and to the presence of hydrothermal circulation within basement highs. The existence of non-linear temperature profiles in sediments covering basement highs suggests that the underlying circulation is causing an upward movement of porewater. There is no firm evidence to show that the sediment faults act as preferred pathways for porewater advection. (author)

  10. A STUDY ON THE BAROCLINIC STRUCTURE OF THE ABYSSAL CIRCULATION

    2001-01-01

    In this paper, the linear continuously stratified model of the abyssal circulation proposed by Pedlosky (1992) was extended to include the second order term -(γθzzz) in the vertical turbulent mixing parameterization of -(w′θ′)z=kυθzz-γθzzz, in which kυ is a vertical diffusion coefficient, and γ is the second order coefficient of turbulent mixing (or simply called γ-term and γ<0 is only allowed). The influence of the γ-term on the baroclinic structure of the abyssal circulation driven by upwelling out of the abyss was investigated. It was found that the γ-term has a noticeable influence on the baroclinic structure of the upwelling driven abyssal circulation. For uniform upwelling, it favors the baroclinic layering of the abyssal circulation in the eastern part of the basin, but prevents the layering in the west. In addition, this parameter was found to decrease the vertically averaging meridional velocity of the abyssal circulation from the west to the east on the southern boundary. For upwelling localized near the eastern boundary, the γ-term favors baroclinic layering of the abyssal circulation in the whole basin. Especially, on the southern boundary the γ-term could strengthen the vertically averaging meridional velocity in the west, but greatly weaken it in the east. The model presented here might be considered as an extension of the Pedlosky baroclinic model of the abyssal circulation.

  11. A study on the baroclinic structure of the abyssal circulation

    Luo, De-Hai; Huang, Fei

    2001-03-01

    In this paper, the linear continuously tratified model of the abyssal circulation proposed by Pedlosky (1992) was extended to include the second order term -(γθ zzz ) in the vertical turbulent mixing parameterization of - overline {(w' θ ' )} _z = k_u θ _{zz} - γ θ _{zzz} , in which k v is a vertical diffusion coefficient, and γ is the second order coefficient of turbulent mixing (or simply called γ-term and γ<0 is only allowed). The influence of the γ-term on the baroclinic structure of the abyssal circulation driven by upwelling out of the abyss was investigated. It was found that the γ-term has a noticeable influence on the baroclinic structure of the upwelling driven abyssal circulation. For uniform upwelling, it favors the baroclinic layering of the abyssal circulation in the eastern part of the basin, but prevents the layering in the west. In addition, this parameter was found to decrease the vertically averaging meridional velocity of the abyssal circulation from the west to the east on the southern boundary. For upwelling localized near the eastern boundary, the γ-term favors baroclinic layering of the abyssal circulation in the whole basin. Especially, on the southern boundary the γ-term could strengthen the vertically averaging meridional velocity in the west, but greatly weaken it in the east. The model presented here might be considered as an extension of the Pedlosky baroclinic model of the abyssal circulation.

  12. Bacterial community response to petroleum contamination and nutrient addition in sediments from a temperate salt marsh.

    Ribeiro, Hugo; Mucha, Ana P; Almeida, C Marisa R; Bordalo, Adriano A

    2013-08-01

    Microbial communities play an important role in the biodegradation of organic pollutants in sediments, including hydrocarbons. The aim of this study was to evaluate the response of temperate salt marsh microbial communities to petroleum contamination, in terms of community structure, abundance and capacity to degrade hydrocarbons. Sediments un-colonized and colonized (rhizosediments) by Juncus maritimus, Phragmites australis and Triglochin striata were collected in a temperate estuary (Lima, NW Portugal), spiked with petroleum under variable nutritional conditions, and incubated for 15 days. Results showed that plant speciation emerged as the major factor for shaping the rhizosphere community structure, overriding the petroleum influence. Moreover, when exposed to petroleum contamination, the distinct salt marsh microbial communities responded similarly with (i) increased abundance, (ii) changes in structure, and (iii) decreased diversity. Communities, particularly those associated to J. maritimus and P. australis roots displayed a potential to degrade petroleum hydrocarbons, with degradation percentages between 15% and 41%, depending on sediment type and nutritional conditions. In conclusion, distinct salt marsh microbial communities responded similarly to petroleum contamination, but presented different pace, nutritional requirements, and potential for its biodegradation, which should be taken into account when developing bioremediation strategies. PMID:23707865

  13. Microbial Community Composition and Extracellular Enzyme Activities Associated with Juncus roemerianus and Spartina alterniflora Vegetated Sediments in Louisiana Saltmarshes.

    Rietl, Anthony J; Overlander, Megan E; Nyman, Andrew J; Jackson, Colin R

    2016-02-01

    Saltmarshes are typically dominated by perennial grasses with large underground rhizome systems that can change local sediment conditions and be important in shaping the sediment microbial community. Factors such as salinity that control plant zonation in saltmarshes are also likely to influence the microbial community, but little is known as to whether microbial communities share distribution patterns with plants in these systems. To determine the extent to which microbial assemblages are influenced by saltmarsh plant communities, as well as to examine patterns in microbial community structure at local and regional scales, we sampled sediments at three saltmarshes in Louisiana, USA. All three systems exhibit a patchy distribution of Juncus roemerianus stands within a Spartina alterniflora marsh. Sediment samples were collected from the interior of several J. roemerianus stands as well as from the S. alterniflora matrix. Samples were assayed for extracellular enzyme activity and DNA extracted to determine microbial community composition. Denaturing gradient gel electrophoresis of rRNA gene fragments was used to determine regional patterns in bacterial, archaeal, and fungal assemblages, while Illumina sequencing was used to examine local, vegetation-driven, patterns in community structure at one site. Both enzyme activity and microbial community structure were primarily influenced by regional site. Within individual saltmarshes, bacterial and archaeal communities differed between J. roemerianus and S. alterniflora vegetated sediments, while fungal communities did not. These results highlight the importance of the plant community in shaping the sediment microbial community in saltmarshes but also demonstrate that regional scale factors are at least as important. PMID:26271740

  14. Effect of organic carbon and metal accumulation on the bacterial communities in sulphidogenic sediments.

    Bueche, Matthieu; Junier, Pilar

    2016-06-01

    A unique geochemical setting in Lake Cadagno, Switzerland, has led to the accumulation of insoluble metal sulphides in the sedimentary record as the result of past airborne pollution. This offers an exceptional opportunity to study the effect of these metals on the bacterial communities in sediments, and in particular to investigate further the link between metal contamination and an increase in the populations of endospore-forming bacteria observed previously in other metal-contaminated sediments. A decrease in organic carbon and total bacterial counts was correlated with an increase in the numbers of endospores in the oldest sediment samples, showing the first environmental evidence of a decrease in nutrient availability as a trigger of sporulation. Proteobacteria and Firmicutes were the two dominant bacterial phyla throughout the sediment, the former in an area with high sulphidogenic activity, and the latter in the oldest samples. Even though the dominant Firmicutes taxa were stable along the sediment core and did not vary with changes in metal contamination, the prevalence of some molecular species like Clostridium sp. was positively correlated with metal sulphide concentration. However, this cannot be generalized to all endospore-forming species. Overall, the community composition supports the hypothesis of sporulation as the main mechanism explaining the dominance of endospore formers in the deepest part of the sediment core, while metal contamination in the form of insoluble metal sulphide deposits appears not to be linked with sporulation as a mechanism of metal tolerance in this sulphidogenic ecosystem. PMID:26780045

  15. Links between surface productivity and deep ocean particle flux at the Porcupine Abyssal Plain (PAP sustained observatory

    H. Frigstad

    2015-04-01

    Full Text Available In this study we present hydrography, biogeochemistry and sediment trap observations between 2003 and 2012 at Porcupine Abyssal Plain (PAP sustained observatory in the northeast Atlantic. The time series is valuable as it allows for investigation of the link between surface productivity and deep ocean carbon flux. The region is a perennial sink for CO2, with an average uptake of around 1.5 mmol m−2 d−1. The average monthly drawdowns of inorganic carbon and nitrogen were used to quantify the net community production (NCP and new production, respectively. Seasonal NCP and new production were found to be 4.57 ± 0.27 mol C m−2 and 0.37 ± 0.14 mol N m−2. The Redfield ratio was high (12, and the production calculated from carbon was higher than production calculated from nitrogen, which is indicative of carbon overconsumption. The export ratio and transfer efficiency were 16 and 4%, respectively, and the site thereby showed high flux attenuation. Particle tracking was used to examine the source region of material in the sediment trap, and there was large variation in source regions, both between and within years. There were higher correlations between surface productivity and export flux when using the particle-tracking approach, than by comparing with the mean productivity in a 100 km box around the PAP site. However, the differences in correlation coefficients were not significant, and a longer time series is needed to draw conclusions on applying particle tracking in sediment trap analyses.

  16. Stratified active archaeal communities in the sediments of Jiulong River Estuary, China

    Qianqian eLi

    2012-08-01

    Full Text Available Here the composition of total and active archaeal communities in a sediment core of Jiulong River estuary at Fujian Province, Southern China was reported. Profiles of CH4 and SO42- concentrations from the sediment core indicated the existence of a sulfate-methane transition zone (SMTZ in which sulfate reduction-coupled anaerobic oxidation of methane occurs. Accordingly, three sediment layers (16-18.5 cm, 71-73.5 cm, 161-163.5 cm from the 1.2 m sediment core were sectioned and named top, middle and bottom, respectively. Total DNA and RNA of each layer were extracted and used for clone libraries and sequence analysis of 16S rRNA genes, the reverse transcription (RT-PCR products of 16S rRNA and methyl CoM reductase alpha subunit (mcrA genes. Phylogenetic analysis indicated that archaeal communities of the three layers were dominated by the Miscellaneous Crenarchaeotal Group (MCG whose ecological functions were still unknown. The MCG could be further divided into seven subgroups, named MCG-A, B, C, D, E, F and G. MCG-A and MCG-G were the most active groups in the estuarine sediments. Known anaerobic methanotrophic archaea (ANMEs were only found as minor components in these estuarine archaeal communities. This study, together with the studies of deep subsurface sediments, would be a very good start point to target and compare the specific active archaeal groups and their roles in the dark, deep subsurface sediment environments.

  17. Links between surface productivity and deep ocean particle flux at the Porcupine Abyssal Plain (PAP) sustained observatory

    Frigstad, H.; Henson, S. A.; Hartman, S. E.; A. M. Omar; E. Jeansson; Cole, H.; Pebody, C.; Lampitt, R. S.

    2015-01-01

    In this study we present hydrography, biogeochemistry and sediment trap observations between 2003 and 2012 at Porcupine Abyssal Plain (PAP) sustained observatory in the northeast Atlantic. The time series is valuable as it allows for investigation of the link between surface productivity and deep ocean carbon flux. The region is a perennial sink for CO2, with an average uptake of around 1.5 mmol m−2 d−1. The average monthly drawdowns of inorganic carbon and ...

  18. Diversity and distribution of fungal communities in the marine sediments of Kongsfjorden, Svalbard (High Arctic)

    Zhang, Tao; Fei Wang, Neng; Qin Zhang, Yu; Yu Liu, Hong; Yan Yu, Li

    2015-10-01

    This study assessed the diversity and distribution of fungal communities in eight marine sediments of Kongsfjorden (Svalbard, High Arctic) using 454 pyrosequencing with fungal-specific primers targeting the internal transcribed spacer (ITS) region of the ribosomal rRNA gene. Sedimentary fungal communities showed high diversity with 42,219 reads belonging to 113 operational taxonomic units (OTUs). Of these OTUs, 62 belonged to the Ascomycota, 26 to Basidiomycota, 2 to Chytridiomycota, 1 to Zygomycota, 1 to Glomeromycota, and 21 to unknown fungi. The major known orders included Hypocreales and Saccharomycetales. The common fungal genera were Pichia, Fusarium, Alternaria, and Malassezia. Interestingly, most fungi occurring in these Arctic sediments may originate from the terrestrial habitats and different basins in Kongsfjorden (i.e., inner basin, central basin, and outer basin) harbor different sedimentary fungal communities. These results suggest the existence of diverse fungal communities in the Arctic marine sediments, which may serve as a useful community model for further ecological and evolutionary study of fungi in the Arctic.

  19. Bacterial communities in the sediments of Dianchi Lake, a partitioned eutrophic waterbody in China.

    Yaohui Bai

    Full Text Available Bacteria play an important role in the decomposition and cycling of a variety of compounds in freshwater aquatic environments, particularly nutrient-rich eutrophic lakes. A unique Chinese eutrophic lake--Dianchi--was selected for study because it has two separate and distinct basins, Caohai with higher organic carbon levels and Waihai with lower organic carbon levels. Sediment bacterial communities were studied in the two basins using samples collected in each season from June 2010 to March 2011. Barcoded pyrosequencing based on the 16 S rRNA gene found that certain common phyla, Proteobacteria, Bacteroidetes, Firmicutes and Chloroflexi, were dominant in the sediments from both basins. However, from the class to genus level, the dominant bacterial groups found in the sediments were distinct between the two basins. Correlation analysis revealed that, among the environmental parameters examined, total organic carbon (TOC accounted for the greatest proportion of variability in bacterial community. Interestingly, study results suggest that increasing allochthonous organic carbon could enhance bacterial diversity and biomass in the sediment. In addition, analysis of function genes (amoA and nosZ demonstrated that ammonia-oxidizing bacteria (AOB were dominant in sediments, with 99% belonging to Nitrosomonas. Denitrifying bacteria were comparatively diverse and were associated with some cultivatable bacteria.

  20. Metal concentrations in stream biofilm and sediments and their potential to explain biofilm microbial community structure

    Concentrations of metals associated with sediments have traditionally been analysed to assess the extent of heavy metal contamination in freshwater environments. Stream biofilms present an alternative medium for this assessment which may be more relevant to the risk incurred by stream ecosystems as they are intensively grazed by aquatic organisms at a higher trophic level. Therefore, we investigated zinc, copper and lead concentrations in biofilms and sediments of 23 stream sites variously impacted by urbanisation. Simultaneously, biofilm bacterial and ciliate protozoan community structure was analysed by Automated Ribosomal Intergenic Spacer Analysis and Terminal Restriction Fragment Length Polymorphism, respectively. Statistical analysis revealed that biofilm associated metals explained a greater proportion of the variations observed in bacterial and ciliate communities than did sediment associated-metals. This study suggests that the analysis of metal concentrations in biofilms provide a good assessment of detrimental effects of metal contaminants on aquatic biota. - Highlights: ► Zn, Cu and Pb concentrations in biofilm and sediments from 23 streams were assessed. ► Bacteria and ciliate protozoa were simultaneously used as biological indicators. ► Zn and Cu were generally enriched in biofilm compared to sediments. ► Metals in biofilm provide a useful assessment of freshwater ecosystem contamination. ► Results highlight the likely ecological importance of biofilm associated metals. - Metal concentrations in stream biofilms provide a good assessment of the effects of trace metal contaminants on freshwater ecosystems.

  1. Bacterial community composition and extracellular enzyme activity in temperate streambed sediment during drying and rewetting.

    Elisabeth Pohlon

    Full Text Available Droughts are among the most important disturbance events for stream ecosystems; they not only affect stream hydrology but also the stream biota. Although desiccation of streams is common in Mediterranean regions, phases of dryness in headwaters have been observed more often and for longer periods in extended temperate regions, including Central Europe, reflecting global climate change and enhanced water withdrawal. The effects of desiccation and rewetting on the bacterial community composition and extracellular enzyme activity, a key process in the carbon flow of streams and rivers, were investigated in a typical Central European stream, the Breitenbach (Hesse, Germany. Wet streambed sediment is an important habitat in streams. It was sampled and exposed in the laboratory to different drying scenarios (fast, intermediate, slow for 13 weeks, followed by rewetting of the sediment from the fast drying scenario via a sediment core perfusion technique for 2 weeks. Bacterial community structure was analyzed using CARD-FISH and TGGE, and extracellular enzyme activity was assessed using fluorogenic model substrates. During desiccation the bacterial community composition shifted toward composition in soil, exhibiting increasing proportions of Actinobacteria and Alphaproteobacteria and decreasing proportions of Bacteroidetes and Betaproteobacteria. Simultaneously the activities of extracellular enzymes decreased, most pronounced with aminopeptidases and less pronounced with enzymes involved in the degradation of polymeric carbohydrates. After rewetting, the general ecosystem functioning, with respect to extracellular enzyme activity, recovered after 10 to 14 days. However, the bacterial community composition had not yet achieved its original composition as in unaffected sediments within this time. Thus, whether the bacterial community eventually recovers completely after these events remains unknown. Perhaps this community undergoes permanent changes

  2. Bacterial community in deep subseafloor sediments from the western Pacific "warm pool"

    2008-01-01

    The bacterial community in deep subseafloor sediments at a depth of 230 cm from the western Pacific "warm pool" is studied by construction of 16S rDNA clone library and PCR-RFLP (Restriction Fragment Length Polymorphism) analysis. The results indicate that the bacterial community in these sediments is mainly composed of five groups: α-Proteobacteria, β-Proteobacteria, CFB group (Cytophaga / Flexi-bacteria / Bacteroides), Acidobacteria and gram positive bacteria, with a few genera detected in each group. The most abundant bacteria group is α-Proteobacteria, and the next is β-Proteobacteria. The dominant species in α-and β-Proteobacteria are Sphingomonas paucimobilis and Pseudomonas alca-ligenes respectively. The CFB group is simply composed of members belonging to Flavobacterium. The gram positive bacteria are rich, and mainly consists of the genus Geobacillus. The analysis of bacterial community indicates that organic matter is still abundant in the subseafloor sediments at the depth of 230 cm in the western Pacific "warm pool" . These bacteria in this deep biosphere may play an impor-tant role in the nitrogen cycle of deep sea sediments at "warm pool" .

  3. Bacterial community in deep subseafloor sediments from the western Pacific "warm pool"

    ZHAO Jing; ZENG RunYing

    2008-01-01

    The bacterial community in deep subseafloor sediments at a depth of 230 cm from the western Pacific "warm pool" is studied by construction of 16S rDNA clone library and PCR-RFLP (Restriction Fragment Length Polymorphism) analysis. The results indicate that the bacterial community in these sediments is mainly composed of five groups: α-Proteobacteria, β-Proteobacteria, CFB group (Cytophaga / Flexibacteria / Bacteroides), Acidobacteria and gram positive bacteria, with a few genera detected in each group. The most abundant bacteria group is α-Proteobacteria, and the next is β-Proteobacteria. The dominant species in α-and β-Proteobacteria are Sphingomonas paucimobilis and Pseudomonas alcaligenes respectively. The CFB group is simply composed of members belonging to Flavobacterium. The gram positive bacteria are rich, and mainly consists of the genus Geobacillus. The analysis of bacterial community indicates that organic matter is still abundant in the subseafloor sediments at the depth of 230 cm in the western Pacific "warm pool". These bacteria in this deep biosphere may play an important role in the nitrogen cycle of deep sea sediments at "warm pool".

  4. Microbial communities in methane- and short chain alkane-rich hydrothermal sediments of Guaymas Basin

    Frederick eDowell

    2016-01-01

    Full Text Available The hydrothermal sediments of Guaymas Basin, an active spreading center in the Gulf of California (Mexico, are rich in porewater methane, short-chain alkanes, sulfate and sulfide, and provide a model system to explore habitat preferences of microorganisms, including sulfate-dependent, methane- and short chain alkane-oxidizing microbial communities. In this study, sediments (above 60˚C covered with sulfur-oxidizing microbial mats surrounding a hydrothermal mound (termed Mat Mound were characterized by porewater geochemistry of methane, C2-C6 short-chain alkanes, sulfate, sulfide, sulfate reduction rate measurements, in-situ temperature gradients, bacterial and archaeal 16S rRNA gene clone libraries and V6 tag pyrosequencing. The most abundantly detected groups in the Mat mound sediments include anaerobic methane-oxidizing archaea of the ANME-1 lineage and its sister clade ANME-1Guaymas, the uncultured bacterial groups SEEP-SRB2 within the Deltaproteobacteria and the separately branching HotSeep-1 Group; these uncultured bacteria are candidates for sulfate-reducing alkane oxidation and for sulfate-reducing syntrophy with ANME archaea. The archaeal dataset indicates distinct habitat preferences for ANME-1, ANME-1-Guaymas and ANME-2 archaea in Guaymas Basin hydrothermal sediments. The bacterial groups SEEP-SRB2 and HotSeep-1 co-occur with ANME-1 and ANME-1Guaymas in hydrothermally active sediments underneath microbial mats in Guaymas Basin. We propose the working hypothesis that this mixed bacterial and archaeal community catalyzes the oxidation of both methane and short-chain alkanes, and constitutes a microbial community signature that is characteristic for hydrothermal and/or cold seep sediments containing both substrates.

  5. Structural iron (II of basaltic glass as an energy source for Zetaproteobacteria in an abyssal plain environment, off the Mid Atlantic Ridge

    Pauline Audrey Henri

    2016-01-01

    Full Text Available To explore the capability of basaltic glass to support the growth of chemosynthetic microorganisms, complementary in situ and in vitro colonization experiments were performed. Microbial colonizers containing synthetic tholeitic basaltic glasses, either enriched in reduced or oxidized iron, were deployed off-axis from the Mid Atlantic Ridge on surface sediments of the abyssal plain (35°N; 29°W. In situ microbial colonization was assessed by sequencing of the 16S rRNA gene and basaltic glass alteration was characterized using Scanning Electron Microscopy, micro-X-ray Absorption Near Edge Structure at the Fe-K-edge and Raman microspectroscopy. The colonized surface of the reduced basaltic glass was covered by a rind of alteration made of iron-oxides trapped in a palagonite-like structure with thicknesses up to 150 µm. The relative abundance of the associated microbial community was dominated (39% of all reads by a single operational taxonomic unit (OTU that shared 92% identity with the iron-oxidizer Mariprofundus ferrooxydans PV-1. Conversely, the oxidized basaltic glass showed the absence of iron-oxides enriched surface deposits and correspondingly there was a lack of known iron-oxidizing bacteria in the inventoried diversity. In vitro, a similar reduced basaltic glass was incubated in artificial seawater with a pure culture of the iron-oxidizing M. ferrooxydans DIS-1 for 2 weeks, without any additional nutrients or minerals. Confocal Laser Scanning Microscopy revealed that the glass surface was covered by twisted stalks characteristic of this iron-oxidizing Zetaproteobacteria. This result supported findings of the in situ experiments indicating that the Fe(II present in the basalt was the energy source for the growth of representatives of Zetaproteobacteria in both the abyssal plain and the in vitro experiment. In accordance, the surface alteration rind observed on the reduced basaltic glass incubated in situ could at least partly result from

  6. Prokaryotic Community in Lacustrine Sediments of Byers Peninsula (Livingston Island, Maritime Antarctica).

    Gugliandolo, Concetta; Michaud, Luigi; Lo Giudice, Angelina; Lentini, Valeria; Rochera, Carlos; Camacho, Antonio; Maugeri, Teresa Luciana

    2016-02-01

    . Ilumatobacter (Actinobacteria), Gp16 (Acidobacteria), and Gemmatimonas (Gemmatimonadetes) were recovered as dominant genera in both inland and coastal lakes, but not in the estuarine sample, indicating that they may be useful markers of Antarctic lakes. The proximity to the sea, the different lake depths and the external or internal origin of the nutrient sources shape the bacterial communities composition in lacustrine sediments of Byers Peninsula. PMID:26337826

  7. Active bacterial community structure along vertical redox gradients in Baltic Sea sediment

    Jansson, Janet; Edlund, Anna; Hardeman, Fredrik; Jansson, Janet K.; Sjoling, Sara

    2008-05-15

    Community structures of active bacterial populations were investigated along a vertical redox profile in coastal Baltic Sea sediments by terminal-restriction fragment length polymorphism (T-RFLP) and clone library analysis. According to correspondence analysis of T-RFLP results and sequencing of cloned 16S rRNA genes, the microbial community structures at three redox depths (179 mV, -64 mV and -337 mV) differed significantly. The bacterial communities in the community DNA differed from those in bromodeoxyuridine (BrdU)-labeled DNA, indicating that the growing members of the community that incorporated BrdU were not necessarily the most dominant members. The structures of the actively growing bacterial communities were most strongly correlated to organic carbon followed by total nitrogen and redox potentials. Bacterial identification by sequencing of 16S rRNA genes from clones of BrdU-labeled DNA and DNA from reverse transcription PCR (rt-PCR) showed that bacterial taxa involved in nitrogen and sulfur cycling were metabolically active along the redox profiles. Several sequences had low similarities to previously detected sequences indicating that novel lineages of bacteria are present in Baltic Sea sediments. Also, a high number of different 16S rRNA gene sequences representing different phyla were detected at all sampling depths.

  8. Effects of zinc pyrithione and copper pyrithione on microbial community function and structure in sediments

    Petersen, DG; Dahllof, I.; Nielsen, LP

    2004-01-01

    incorporation) were used, whereas molecular fingerprinting methods (polymerase chain reaction/ denaturing gradient gel electrophoresis) were used to describe the bacterial community structure. The lowest-observed-effect concentration (LOEC) for ZPT was 0.001 nmol/g dry sediment for the phosphate flux and total...... DNA content, whereas the LOEC for CPT was 0.1 nmol/g dry sediment for the nitrate flux and total DNA content. Nitrate fluxes increased significantly following additions of both ZPT and CPT, whereas ammonium fluxes decreased significantly after ZPT addition, suggesting changes in the nitrification and...... denitrification processes. The total DNA content decreased significantly following addition of both ZPT and CPT, but at the highest addition of ZPT (10 nmol ZPT/g dry sediment), an increase in total DNA content was found. Increased protein synthesis and bacterial diversity were also observed at this concentration...

  9. Abyssalities against the grain: the clown circus without a future

    Ludmila Lima Brandão; Daniel Pellegrim Sanchez

    2015-01-01

    By articulating Boaventura de Sousa Santos’ notion that the Western modern thinking is an abyssal thinking, we examine the functioning of such “abyssalities”, which hierarchize and turn knowledge and practices invisible, as well as operate the transmutation of old colonial domination (or colonialism) into coloniality in the visual arts system. Then we identify – as in the “coloniality of knowledge” – these same devices: the divisions in the reality of artistic production under an abyssal per...

  10. Profiling of Sediment Microbial Community in Dongting Lake before and after Impoundment of the Three Gorges Dam

    Wei Huang

    2016-06-01

    Full Text Available The sediment microbial community in downstream-linked lakes can be affected by the operation of large-scale water conservancy projects. The present study determined Illumina reads (16S rRNA gene amplicons to analyze and compare the bacterial communities from sediments in Dongting Lake (China before and after impoundment of the Three Gorges Dam (TGD, the largest hydroelectric project in the world. Bacterial communities in sediment samples in Dongting Lake before impoundment of the TGD (the high water period had a higher diversity than after impoundment of the TGD (the low water period. The most abundant phylum in the sediment samples was Proteobacteria (36.4%–51.5%, and this result was due to the significant abundance of Betaproteobacteria and Deltaproteobacteria in the sediment samples before impoundment of the TGD and the abundance of Gammaproteobacteria in the sediment samples after impoundment of the TGD. In addition, bacterial sequences of the sediment samples are also affiliated with Acidobacteria (11.0% on average, Chloroflexi (10.9% on average, Bacteroidetes (6.7% on average, and Nitrospirae (5.1% on average. Variations in the composition of the bacterial community within some sediment samples from the river estuary into Dongting Lake were related to the pH values. The bacterial community in the samples from the three lake districts of Dongting Lake before and after impoundment of the TGD was linked to the nutrient concentration.

  11. Profiling of Sediment Microbial Community in Dongting Lake before and after Impoundment of the Three Gorges Dam

    Huang, Wei; Jiang, Xia

    2016-01-01

    The sediment microbial community in downstream-linked lakes can be affected by the operation of large-scale water conservancy projects. The present study determined Illumina reads (16S rRNA gene amplicons) to analyze and compare the bacterial communities from sediments in Dongting Lake (China) before and after impoundment of the Three Gorges Dam (TGD), the largest hydroelectric project in the world. Bacterial communities in sediment samples in Dongting Lake before impoundment of the TGD (the high water period) had a higher diversity than after impoundment of the TGD (the low water period). The most abundant phylum in the sediment samples was Proteobacteria (36.4%–51.5%), and this result was due to the significant abundance of Betaproteobacteria and Deltaproteobacteria in the sediment samples before impoundment of the TGD and the abundance of Gammaproteobacteria in the sediment samples after impoundment of the TGD. In addition, bacterial sequences of the sediment samples are also affiliated with Acidobacteria (11.0% on average), Chloroflexi (10.9% on average), Bacteroidetes (6.7% on average), and Nitrospirae (5.1% on average). Variations in the composition of the bacterial community within some sediment samples from the river estuary into Dongting Lake were related to the pH values. The bacterial community in the samples from the three lake districts of Dongting Lake before and after impoundment of the TGD was linked to the nutrient concentration. PMID:27338434

  12. Biodiversity and community composition of sediment macrofauna associated with deep-sea Lophelia pertusa habitats in the Gulf of Mexico

    Demopoulos, Amanda W.J.; Bourque, Jill R.; Frometa, Janessy

    2014-01-01

    Scleractinian corals create three-dimensional reefs that provide sheltered refuges, facilitate sediment accumulation, and enhance colonization of encrusting fauna. While heterogeneous coral habitats can harbor high levels of biodiversity, their effect on the community composition within nearby sediments remains unclear, particularly in the deep sea. Sediment macrofauna from deep-sea coral habitats (Lophelia pertusa) and non-coral, background sediments were examined at three sites in the northern Gulf of Mexico (VK826, VK906, MC751, 350–500 m depth) to determine whether macrofaunal abundance, diversity, and community composition near corals differed from background soft-sediments. Macrofaunal densities ranged from 26 to 125 individuals 32 cm−2 and were significantly greater near coral versus background sediments only at VK826. Of the 86 benthic invertebrate taxa identified, 16 were exclusive to near-coral habitats, while 14 were found only in background sediments. Diversity (Fisher’s α) and evenness were significantly higher within near-coral sediments only at MC751 while taxon richness was similar among all habitats. Community composition was significantly different both between near-coral and background sediments and among the three primary sites. Polychaetes numerically dominated all samples, accounting for up to 70% of the total individuals near coral, whereas peracarid crustaceans were proportionally more abundant in background sediments (18%) than in those near coral (10%). The reef effect differed among sites, with community patterns potentially influenced by the size of reef habitat. Taxon turnover occurred with distance from the reef, suggesting that reef extent may represent an important factor in structuring sediment communities near L. pertusa. Polychaete communities in both habitats differed from other Gulf of Mexico (GOM) soft sediments based on data from previous studies, and we hypothesize that local environmental conditions found near L

  13. Biodiversity and community composition of sediment macrofauna associated with deep-sea Lophelia pertusa habitats in the Gulf of Mexico

    Demopoulos, Amanda W. J.; Bourque, Jill R.; Frometa, Janessy

    2014-11-01

    Scleractinian corals create three-dimensional reefs that provide sheltered refuges, facilitate sediment accumulation, and enhance colonization of encrusting fauna. While heterogeneous coral habitats can harbor high levels of biodiversity, their effect on the community composition within nearby sediments remains unclear, particularly in the deep sea. Sediment macrofauna from deep-sea coral habitats (Lophelia pertusa) and non-coral, background sediments were examined at three sites in the northern Gulf of Mexico (VK826, VK906, MC751, 350-500 m depth) to determine whether macrofaunal abundance, diversity, and community composition near corals differed from background soft-sediments. Macrofaunal densities ranged from 26 to 125 individuals 32 cm-2 and were significantly greater near coral versus background sediments only at VK826. Of the 86 benthic invertebrate taxa identified, 16 were exclusive to near-coral habitats, while 14 were found only in background sediments. Diversity (Fisher's α) and evenness were significantly higher within near-coral sediments only at MC751 while taxon richness was similar among all habitats. Community composition was significantly different both between near-coral and background sediments and among the three primary sites. Polychaetes numerically dominated all samples, accounting for up to 70% of the total individuals near coral, whereas peracarid crustaceans were proportionally more abundant in background sediments (18%) than in those near coral (10%). The reef effect differed among sites, with community patterns potentially influenced by the size of reef habitat. Taxon turnover occurred with distance from the reef, suggesting that reef extent may represent an important factor in structuring sediment communities near L. pertusa. Polychaete communities in both habitats differed from other Gulf of Mexico (GOM) soft sediments based on data from previous studies, and we hypothesize that local environmental conditions found near L. pertusa

  14. High levels of sediment contamination have little influence on estuarine beach fish communities.

    Andrew C McKinley

    Full Text Available While contaminants are predicted to have measurable impacts on fish assemblages, studies have rarely assessed this potential in the context of natural variability in physico-chemical conditions within and between estuaries. We investigated links between the distribution of sediment contamination (metals and PAHs, physico-chemical variables (pH, salinity, temperature, turbidity and beach fish assemblages in estuarine environments. Fish communities were sampled using a beach seine within the inner and outer zones of six estuaries that were either heavily modified or relatively unmodified by urbanization and industrial activity. All sampling was replicated over two years with two periods sampled each year. Shannon diversity, biomass and abundance were all significantly higher in the inner zone of estuaries while fish were larger on average in the outer zone. Strong differences in community composition were also detected between the inner and outer zones. Few differences were detected between fish assemblages in heavily modified versus relatively unmodified estuaries despite high concentrations of sediment contaminants in the inner zones of modified estuaries that exceeded recognized sediment quality guidelines. Trends in species distributions, community composition, abundance, Shannon diversity, and average fish weight were strongly correlated to physico-chemical variables and showed a weaker relationship to sediment metal contamination. Sediment PAH concentrations were not significantly related to the fish assemblage. These findings suggest that variation in some physico-chemical factors (salinity, temperature, pH or variables that co-vary with these factors (e.g., wave activity or grain size have a much greater influence on this fish assemblage than anthropogenic stressors such as contamination.

  15. Petroleum-influenced beach sediments of the campeche bank, Mexico: Diversity and bacterial community structure assessment

    In Mexican, either spilled or seeped out petroleum impacts nearly 300 km of the beach between Dos Bocas (Tabasco State) to Champoton town (Campeche State), where between 9 to exceptionally 9 to exceptionally 300 tonnes of oil as tar balls have been measured. This study was focused to explore, for the first time, the bacterial diversity and community structure (α-diversity)- in a kilometric scale on petroleum influenced sediments of 100 km of sandy beach. (Author)

  16. Petroleum-influenced beach sediments of the campeche bank, Mexico: Diversity and bacterial community structure assessment

    Rosano-Hernandez, M. C.; Ramirez-Saad, H.; Fernandez-Linares, L.; Xoconostle, B.

    2009-07-01

    In Mexican, either spilled or seeped out petroleum impacts nearly 300 km of the beach between Dos Bocas (Tabasco State) to Champoton town (Campeche State), where between 9 to exceptionally 9 to exceptionally 300 tonnes of oil as tar balls have been measured. This study was focused to explore, for the first time, the bacterial diversity and community structure ({alpha}-diversity)- in a kilometric scale on petroleum influenced sediments of 100 km of sandy beach. (Author)

  17. Metal-macrofauna interactions determine microbial community structure and function in copper contaminated sediments.

    Daniel J Mayor

    Full Text Available Copper is essential for healthy cellular functioning, but this heavy metal quickly becomes toxic when supply exceeds demand. Marine sediments receive widespread and increasing levels of copper contamination from antifouling paints owing to the 2008 global ban of organotin-based products. The toxicity of copper will increase in the coming years as seawater pH decreases and temperature increases. We used a factorial mesocosm experiment to investigate how increasing sediment copper concentrations and the presence of a cosmopolitan bioturbating amphipod, Corophium volutator, affected a range of ecosystem functions in a soft sediment microbial community. The effects of copper on benthic nutrient release, bacterial biomass, microbial community structure and the isotopic composition of individual microbial membrane [phospholipid] fatty acids (PLFAs all differed in the presence of C. volutator. Our data consistently demonstrate that copper contamination of global waterways will have pervasive effects on the metabolic functioning of benthic communities that cannot be predicted from copper concentrations alone; impacts will depend upon the resident macrofauna and their capacity for bioturbation. This finding poses a major challenge for those attempting to manage the impacts of copper contamination on ecosystem services, e.g. carbon and nutrient cycling, across different habitats. Our work also highlights the paucity of information on the processes that result in isotopic fractionation in natural marine microbial communities. We conclude that the assimilative capacity of benthic microbes will become progressively impaired as copper concentrations increase. These effects will, to an extent, be mitigated by the presence of bioturbating animals and possibly other processes that increase the influx of oxygenated seawater into the sediments. Our findings support the move towards an ecosystem approach for environmental management.

  18. Macrophytes in Phytoremediation of Heavy Metal Contaminated Water and Sediments in Pariyej Community Reserve, Gujarat, India

    Kumar, J. I. Nirmal; Hiren SONI; Rita N. Kumar; Bhatt, Ira

    2008-01-01

    A phytoremediation study was carried out at Pariyej reservoir, an internationally important wetland listed in Asian Directory of Wetlands, designated as a "Wetland of International Importance" and a proposed community reserve of Gujarat State, India, to ascertain the degree of heavy metal contamination. The study focused on assessment of heavy metal accumulation in certain aquatic macrophytes used as biomonitors, in comparison with water and sediments (abiotic monitors) for phytorem...

  19. Effects of physical disturbance, isolation and key macrozoobenthic species on community development, recolonisation and sedimentation

    Helen Orav-Kotta

    2006-06-01

    Full Text Available The relative effect of physical disturbance, isolation and keymacrozoobenthic species on community development and sedimentationprocesses were studied in an in situ factorial field mesocosmexperiment in the northern Baltic Sea. Differences in abundanceand biomass structure of recolonising invertebrates were dueto exposure and isolation. The initial invertebrate communitieshad a negligible effect on the final communities. However, theorganic matter content of the sediment in isolated cages increasedwith the initial number of invertebrate species. The main conclusionof the study: physically driven fluxes override the effects ofbiological interactions in shallow water systems of the northernBaltic Sea.

  20. Seasonal Effects in a Lake Sediment Archaeal Community of the Brazilian Savanna

    Thiago Rodrigues; Elisa Catão; Mercedes M. C. Bustamante; Quirino, Betania F.; Kruger, Ricardo H; Kyaw, Cynthia M

    2014-01-01

    The Cerrado is a biome that corresponds to 24% of Brazil’s territory. Only recently microbial communities of this biome have been investigated. Here we describe for the first time the diversity of archaeal communities from freshwater lake sediments of the Cerrado in the dry season and in the transition period between the dry and rainy seasons, when the first rains occur. Gene libraries were constructed, using Archaea-specific primers for the 16S rRNA and amoA genes. Analysis revealed marked ...

  1. Community Dynamics and Activity of Ammonia-Oxidizing Prokaryotes in Intertidal Sediments of the Yangtze Estuary

    Zheng, Yanling; Hou, Lijun; Newell, Silvia; LIU Min; Zhou, Junliang; Zhao, Hui; You, Lili; Cheng, Xunliang

    2014-01-01

    Diversity, abundance, and activity of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were investigated using the ammonia monooxygenase α subunit (amoA) in the intertidal sediments of the Yangtze Estuary. Generally, AOB had a lower diversity of amoA genes than did AOA in this study. Clone library analysis revealed great spatial variations in both AOB and AOA communities along the estuary. The UniFrac distance matrix showed that all the AOB communities and 6 out of 7 AOA c...

  2. Multiwall carbon nanotubes increase the microbial community in crude oil contaminated fresh water sediments.

    Abbasian, Firouz; Lockington, Robin; Palanisami, Thavamani; Megharaj, Mallavarapu; Naidu, Ravi

    2016-01-01

    Since crude oil contamination is one of the biggest environmental concerns, its removal from contaminated sites is of interest for both researchers and industries. In situ bioremediation is a promising technique for decreasing or even eliminating crude oil and hydrocarbon contamination. However, since these compounds are potentially toxic for many microorganisms, high loads of contamination can inhibit the microbial community and therefore reduce the removal rate. Therefore, any strategy with the ability to increase the microbial population in such circumstances can be of promise in improving the remediation process. In this study, multiwall carbon nanotubes were employed to support microbial growth in sediments contaminated with crude oil. Following spiking of fresh water sediments with different concentrations of crude oil alone and in a mixture with carbon nanotubes for 30days, the microbial profiles in these sediments were obtained using FLX-pyrosequencing. Next, the ratios of each member of the microbial population in these sediments were compared with those values in the untreated control sediment. This study showed that combination of crude oil and carbon nanotubes can increase the diversity of the total microbial population. Furthermore, these treatments could increase the ratios of several microorganisms that are known to be effective in the degradation of hydrocarbons. PMID:26372939

  3. Meiobenthic and Macrobenthic Community Structure in Carbonate Sediments of Rocas Atoll (North-east, Brazil)

    Netto, S. A.; Warwick, R. M.; Attrill, M. J.

    1999-01-01

    Rocas is the only atoll of the South Atlantic and it is built almost exclusively by coralline red algae, vermetid gastropods and encrusting foraminiferans. Patterns in the community structure of meiofauna and macrofauna, particularly nematodes and polychaetes, at Rocas Atoll, north-east Brazil, are determined and compared for different habitats: sublittoral, tidal flat, reef pools and lagoon. Nematodes and copepods were the most abundant meiofaunal taxa. In all studied habitats at Rocas Atoll, oligochaetes, nematodes and polychaetes numerically dominate the macrofauna. Univariate and multivariate analyses reveal clear differences in community structure between the habitats of the atoll, especially between the sublittoral and the inner habitats. The number of species, total density, diversity (H') and trophic structure vary significantly between the habitats, but the differences are dependent on which faunistic category (meiobenthic or macrobenthic) is analysed. Nematodes belonging to the Epsilonematidae and Draconematidae, together with a diverse community of meiobenthic polychaetes, characterize the sublittoral habitat of Rocas Atoll. Both meiofauna and macrofauna are depressed in the tidal flat, and the local sediment instability particularly affects the polychaete abundance. Reef pools and lagoons support a very dense aggregation of invertebrates, particularly the macrofauna, when compared with other carbonate reef sediments. However, differences in the structure of meiofauna and macrofauna communities between reef pools and lagoons are not significant. Changes in meiobenthic and macrobenthic community structure are related to the gradation in the physical environment of the atoll.

  4. Salinity shapes microbial diversity and community structure in surface sediments of the Qinghai-Tibetan Lakes.

    Yang, Jian; Ma, Li'an; Jiang, Hongchen; Wu, Geng; Dong, Hailiang

    2016-01-01

    Investigating microbial response to environmental variables is of great importance for understanding of microbial acclimatization and evolution in natural environments. However, little is known about how microbial communities responded to environmental factors (e.g. salinity, geographic distance) in lake surface sediments of the Qinghai-Tibetan Plateau (QTP). In this study, microbial diversity and community structure in the surface sediments of nine lakes on the QTP were investigated by using the Illumina Miseq sequencing technique and the resulting microbial data were statistically analyzed in combination with environmental variables. The results showed total microbial community of the studied lakes was significantly correlated (r = 0.631, P < 0.001) with lake salinity instead of geographic distance. This suggests that lake salinity is more important than geographic distance in shaping the microbial diversity and community structure in the studied samples. In addition, the abundant and rare taxa (OTUs with relative abundance higher than 1% and lower than 0.01% within one sample, respectively) were significantly (P < 0.05) correlated (r = 0.427 and 0.783, respectively) with salinity, suggesting rare taxa might be more sensitive to salinity than their abundant counterparts, thus cautions should be taken in future when evaluating microbial response (abundant vs. rare sub-communities) to environmental conditions. PMID:27113678

  5. Water level changes affect carbon turnover and microbial community composition in lake sediments.

    Weise, Lukas; Ulrich, Andreas; Moreano, Matilde; Gessler, Arthur; E Kayler, Zachary; Steger, Kristin; Zeller, Bernd; Rudolph, Kristin; Knezevic-Jaric, Jelena; Premke, Katrin

    2016-05-01

    Due to climate change, many lakes in Europe will be subject to higher variability of hydrological characteristics in their littoral zones. These different hydrological regimes might affect the use of allochthonous and autochthonous carbon sources. We used sandy sediment microcosms to examine the effects of different hydrological regimes (wet, desiccating, and wet-desiccation cycles) on carbon turnover.(13)C-labelled particulate organic carbon was used to trace and estimate carbon uptake into bacterial biomass (via phospholipid fatty acids) and respiration. Microbial community changes were monitored by combining DNA- and RNA-based real-time PCR quantification and terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA. The shifting hydrological regimes in the sediment primarily caused two linked microbial effects: changes in the use of available organic carbon and community composition changes. Drying sediments yielded the highest CO2emission rates, whereas hydrological shifts increased the uptake of allochthonous organic carbon for respiration. T-RFLP patterns demonstrated that only the most extreme hydrological changes induced a significant shift in the active and total bacterial communities. As current scenarios of climate change predict an increase of drought events, frequent variations of the hydrological regimes of many lake littoral zones in central Europe are anticipated. Based on the results of our study, this phenomenon may increase the intensity and amplitude in rates of allochthonous organic carbon uptake and CO2emissions. PMID:26902802

  6. Changes in microbial communities associated with gas hydrates in subseafloor sediments from the Nankai Trough.

    Katayama, Taiki; Yoshioka, Hideyoshi; Takahashi, Hiroshi A; Amo, Miki; Fujii, Tetsuya; Sakata, Susumu

    2016-08-01

    Little is known about the microbial distribution patterns in subseafloor sediments. This study examines microbial diversity and activities in sediments of the Nankai Trough, where biogenic gas hydrates are deposited. Illumina sequencing of 16S rRNA genes revealed that the prokaryotic community structure is correlated with hydrate occurrence and depth but not with the sedimentary facies. The bacterial phyla 'Atribacteria' lineage JS1 and Chloroflexi dominated in all samples, whereas lower taxonomic units of Chloroflexi accounted for community variation related to hydrate saturation. In archaeal communities, 'Bathyarchaeota' was significantly abundant in the hydrate-containing samples, whereas Marine Benthic Group-B dominated in the upper sediments without hydrates. mcrA gene sequences assigned to deeply branching groups and ANME-1 were detected only in hydrate-containing samples. A predominance of hydrogenotrophic methanogens, Methanomicrobiales and Methanobacteriales, over acetoclastic methanogens was found throughout the depth. Incubation tests on hydrate-containing samples with a stable isotope tracer showed anaerobic methane oxidation activities under both low- and seawater-like salinity conditions. These results indicate that the distribution patterns of microorganisms involved in carbon cycling changed with gas hydrate occurrence, possibly because of the previous hydrate dissociation followed by pore water salinity decrease in situ, as previously proposed by a geochemical study at the study site. PMID:27170363

  7. Diversity and Composition of Bacterial Community in Soils and Lake Sediments from an Arctic Lake Area

    Wang, Neng Fei; Zhang, Tao; Yang, Xiao; Wang, Shuang; Yu, Yong; Dong, Long Long; Guo, Yu Dong; Ma, Yong Xing; Zang, Jia Ye

    2016-01-01

    This study assessed the diversity and composition of bacterial communities within soils and lake sediments from an Arctic lake area (London Island, Svalbard). A total of 2,987 operational taxonomic units were identified by high-throughput sequencing, targeting bacterial 16S rRNA gene. The samples from four sites (three samples in each site) were significantly different in geochemical properties and bacterial community composition. Proteobacteria and Acidobacteria were abundant phyla in the nine soil samples, whereas Proteobacteria and Bacteroidetes were abundant phyla in the three sediment samples. Furthermore, Actinobacteria, Chlorobi, Chloroflexi, Elusimicrobia, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, Proteobacteria significantly varied in their abundance among the four sampling sites. Additionally, members of the dominant genera, such as Clostridium, Luteolibacter, Methylibium, Rhodococcus, and Rhodoplanes, were significantly different in their abundance among the four sampling sites. Besides, distance-based redundancy analysis revealed that pH (p soils and sediments from a lake area in the Arctic harbor a high diversity of bacterial communities, which are influenced by many geochemical factors of Arctic environments.

  8. Water level changes affect carbon turnover and microbial community composition in lake sediments

    Weise, Lukas; Ulrich, Andreas; Moreano, Matilde; Gessler, Arthur; E. Kayler, Zachary; Steger, Kristin; Zeller, Bernd; Rudolph, Kristin; Knezevic-Jaric, Jelena; Premke, Katrin

    2016-01-01

    Due to climate change, many lakes in Europe will be subject to higher variability of hydrological characteristics in their littoral zones. These different hydrological regimes might affect the use of allochthonous and autochthonous carbon sources. We used sandy sediment microcosms to examine the effects of different hydrological regimes (wet, desiccating, and wet-desiccation cycles) on carbon turnover. 13C-labelled particulate organic carbon was used to trace and estimate carbon uptake into bacterial biomass (via phospholipid fatty acids) and respiration. Microbial community changes were monitored by combining DNA- and RNA-based real-time PCR quantification and terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA. The shifting hydrological regimes in the sediment primarily caused two linked microbial effects: changes in the use of available organic carbon and community composition changes. Drying sediments yielded the highest CO2 emission rates, whereas hydrological shifts increased the uptake of allochthonous organic carbon for respiration. T-RFLP patterns demonstrated that only the most extreme hydrological changes induced a significant shift in the active and total bacterial communities. As current scenarios of climate change predict an increase of drought events, frequent variations of the hydrological regimes of many lake littoral zones in central Europe are anticipated. Based on the results of our study, this phenomenon may increase the intensity and amplitude in rates of allochthonous organic carbon uptake and CO2 emissions. PMID:26902802

  9. Variations of Bacterial Community Structure and Composition in Mangrove Sediment at Different Depths in Southeastern Brazil

    Lucas William Mendes

    2014-12-01

    Full Text Available Tropical mangroves are considered one of the most productive ecosystems of the world, being characterized as nurseries and food sources for fish and other animals. Microorganisms play important roles in these environments, and the study of bacterial communities is of paramount importance for a better comprehension of mangrove dynamics. This study focused on the structure and composition of bacterial communities in mangrove sediments at different depths and points, located in Southeastern Brazil. Terminal Restriction Fragment Length Polymorphism (T-RFLP was used to determine the community structure, and 16S rRNA gene pyrosequencing was used to characterize the community composition. Redundancy analysis of T-RFLP patterns revealed differences in bacterial community structure according to soil attributes and depth. The parameters K and depth presented significant correlation with general community structure. Most sequences were classified into the phylum Proteobacteria (88%, which presented differences according to the depth, where the classes Betaproteobacteria (21% and Deltaproteobacteria (16% were abundant at 10 cm and Epsilonproteobacteria (35% was abundant at 40 cm depth. Clear differences were observed in community composition as shown by the differential distribution of the phyla Firmicutes (1.13% and 3.8%, for 10 cm and 40 cm respectively, Chloroflexi (2.8% and 0.75%, and Acidobacteria (2.75% and 0.57% according to the depth. Bacterial diversity measurements indicated higher diversity in shallow samples. Taken together, our findings indicate that mangrove holds a diverse bacterial community, which is shaped by the variations found in the ecosystem, such as sediment properties and depth.

  10. Comparison of Aerobic Methanotrophic Communities in Littoral and Profundal Sediments of Lake Constance by a Molecular Approach▿

    Rahalkar, Monali; Schink, Bernhard

    2007-01-01

    Analysis of pmoA and 16S rRNA gene clone libraries of methanotrophic bacteria in Lake Constance revealed an overall dominance of type I methanotrophs in both littoral and profundal sediments. The sediments exhibited minor differences in their methanotrophic community structures. Type X methanotrophs made up a significant part of the clone libraries only in the profundal sediment and were also found only there as a prominent peak by T-RFLP analyses.

  11. LC/IRMS analysis: A powerful technique to trace carbon flow in microphytobenthic communities in intertidal sediments

    T.C.W. Moerdijk-Poortvliet; L.J. Stal; H.T.S. Boschker

    2014-01-01

    Microphytobenthic communities are important for primary production in intertidal marine sediments. Extracellular polymeric substances (EPS), comprising polysaccharides and proteins, play a key role in the structure and functioning of microphytobenthic biofilms and allow interactions between the bent

  12. Dynamics of microalgal communities in the water-column/sediment interface of the inner shelf off Parana State, Southern Brazil

    Ricardo Luiz Queiroz; Frederico Pereira Brandini; Franciane Maria Pellizzari

    2004-01-01

    The composition and biomass of the microalgal community at the water-column/sediment interface on the continental shelf off Parana State (Brazil) were studied every 2 months during 1999. Samples for cell identification and determination of chlorophyll a were taken from the interface layer and at discrete depths up to 4 m above the sediment. Results showed a community mainly formed by benthic and planktonic diatoms >30 µm, benthic diatoms 30 µm, which accounted for most of the pigment biomass,...

  13. Linking microbial community structure to biogeochemical function in coastal marine sediments: Stable isotope probing combined with magnetic bead capture

    Stal, L.J.; Boschker, H.T.S.; Miyatake, T.

    2011-01-01

    Microbial community structure and its biogeochemical functions in marine sediments can be successfully linked by using the improved Mag-SIP method in combination with other approaches. In this thesis, we were able to provide detailed information on the microorganisms responsible for the utilization of major substrates in marine sediments. It was shown that a number of important groups in the microbial community played a broader role than expected. Some surprising results are that oxygenic pho...

  14. Polychlorinated biphenyl (PCB) anaerobic degradation in marine sediments: microcosm study and role of autochthonous microbial communities.

    Matturro, Bruna; Ubaldi, Carla; Grenni, Paola; Caracciolo, Anna Barra; Rossetti, Simona

    2016-07-01

    Polychlorobiphenyl (PCB) biodegradation was followed for 1 year in microcosms containing marine sediments collected from Mar Piccolo (Taranto, Italy) chronically contaminated by this class of hazardous compounds. The microcosms were performed under strictly anaerobic conditions with or without the addition of Dehalococcoides mccartyi, the main microorganism known to degrade PCBs through the anaerobic reductive dechlorination process. Thirty PCB congeners were monitored during the experiments revealing that the biodegradation occurred in all microcosms with a decrease in hepta-, hexa-, and penta-chlorobiphenyls (CBs) and a parallel increase in low chlorinated PCBs (tri-CBs and tetra-CBs). The concentrations of the most representative congeners detected in the original sediment, such as 245-245-CB and 2345-245-CB, and of the mixture 2356-34-CB+234-245-CB, decreased by 32.5, 23.8, and 46.7 %, respectively, after only 70 days of anaerobic incubation without any bioaugmentation treatment. Additionally, the structure and population dynamics of the microbial key players involved in the biodegradative process and of the entire mixed microbial community were accurately defined by Catalyzed Reporter Deposition Fluorescence In Situ Hybridization (CARD-FISH) in both the original sediment and during the operation of the microcosm. The reductive dehalogenase genes of D. mccartyi, specifically involved in PCB dechlorination, were also quantified using real-time PCR (qPCR). Our results demonstrated that the autochthonous microbial community living in the marine sediment, including D. mccartyi (6.32E+06 16S rRNA gene copy numbers g(-1) sediment), was able to efficiently sustain the biodegradation of PCBs when controlled anaerobic conditions were imposed. PMID:26162439

  15. Marine microbial community response to inorganic and organic sediment amendments in laboratory mesocosms.

    Kan, Jinjun; Wang, Yanbing; Obraztsova, Anna; Rosen, Gunther; Leather, James; Scheckel, Kirk G; Nealson, Kenneth H; Arias-Thode, Y Meriah

    2011-10-01

    Sediment amendments provide promising strategies of enhancing sequestration of heavy metals and degradation of organic contaminants. The impacts of sediment amendments for metal and organic remediation including apatite, organoclay (and apatite and organoclay in geotextile mats), acetate, and chitin on environmental microbial communities in overlying water and sediment profiles are reported here. These experiments were performed concurrent with an ecotoxicity evaluation (data submitted in companion paper) and X-ray absorption spectroscopy of zinc speciation post apatite amendments. X-ray absorption spectra showed that a modest modification of zinc speciation occurred in amended treatments. Significant changes in both bacterial cell densities and populations were observed in response to amendments of apatite+organoclay, chitin, and acetate. The enriched bacteria and breakdown of these amendments were likely attributed to water quality degradation (e.g. ammonia and dissolved oxygen). Molecular fingerprints of bacterial communities by denaturant gradient gel electrophoresis (DGGE) showed that distinct bacterial populations occurred in overlying waters from different amendments: apatite+organoclay led to the dominance of Gammaproteobacteria, acetate enriched Alphaproteobacteria, and chitin treatment led to a dominance of Bacteroidetes and Alphaproteobacteria. In amended sediments, Firmicutes, Bacteroidetes, and Deltaproteobacteria (Desulfovibrio) were commonly found with chitin and apatite+chitin treatments. Finally, sulfate-reducing bacteria (e.g. Desulfovibrio) and metal-reducing bacteria were also recovered with most probable number (MPN) analyses in treatments with acetate, chitin, and apatite+chitin. These geochemically important bacteria were stimulated by amendments and may play critical functional roles in the metal and organic contaminant remediation process for future investigations of contaminated sediments. PMID:21784523

  16. Source-To-Sink Perspectives On The Mississippi River System, Miocene To Present, Mountain To Abyss

    Bentley, S. J.; Blum, M. D.

    2013-12-01

    . The objective of this study is to present a synthesis of the Mississippi River source-to-sink system, from montane source to abyssal sink, to elucidate specific geomorphic components and boundaries in the system, controls on mass transfer, and resultant geomorphic and statigraphic development. The Mississippi River source-to-sink system constitutes one of the largest sources, conduits, and depocenters of sediment on Earth, extending from elevations of 3.7 km in the Rocky Mountains to the Gulf of Mexico abyssal plain. Despite being one of the most intensely studied fluvial-marine systems in the world, comprehensive understanding and management of the system's resources remain a challenge. The system is valuable in many ways: it provides navigation and water to the heart of North America, and sustains extensive marine fisheries. The river has built a delta that is home to millions of people and yet is subsiding rapidly. Ancestral Mississippi fluvial-marine deposits continue to yield high-value petroleum resources to exploration. To address the range of temporal and spatial scales over which the system has developed and continues to evolve, we will focus on three geological time spans that display contrasting geologic forcing and response: Miocene, Pleistocene, and late Holocene. The present configuration of source, conduit, and sink were established during the Miocene epoch, when tectonics (via the uplifting southern Rockies, and later the rejuvenated Appalachians) and climate (wet in the east and dry in the west) provided abundant water and sediment to prograde the shelf margin and initiate deep-sea fan growth. Pleistocene continental glaciation, eustasy, and catastrophic drainage events further sculpted the alluvial valley, and extended the shelf margin, and fan. Studies of Modern processes and Holocene delta development have provided keys to both the delta's past and future evolution, in terms of cyclic autogenic lobe-switching, mass-transport events, storm

  17. Seasonal Effects in a Lake Sediment Archaeal Community of the Brazilian Savanna

    Thiago Rodrigues

    2014-01-01

    Full Text Available The Cerrado is a biome that corresponds to 24% of Brazil’s territory. Only recently microbial communities of this biome have been investigated. Here we describe for the first time the diversity of archaeal communities from freshwater lake sediments of the Cerrado in the dry season and in the transition period between the dry and rainy seasons, when the first rains occur. Gene libraries were constructed, using Archaea-specific primers for the 16S rRNA and amoA genes. Analysis revealed marked differences between the archaeal communities found in the two seasons. I.1a and I.1c Thaumarchaeota were found in greater numbers in the transition period, while MCG Archaea was dominant on the dry season. Methanogens were only found in the dry season. Analysis of 16S rRNA sequences revealed lower diversity on the transition period. We detected archaeal amoA sequences in both seasons, but there were more OTUs during the dry season. These sequences were within the same cluster as Nitrosotalea devanaterra’s amoA gene. The principal coordinate analysis (PCoA test revealed significant differences between samples from different seasons. These results provide information on archaeal diversity in freshwater lake sediments of the Cerrado and indicates that rain is likely a factor that impacts these communities.

  18. Response of bacterial community compositions to different sources of pollutants in sediments of a tributary of Taihu Lake, China.

    Wang, Jing; Li, Yi; Wang, Peifang; Niu, Lihua; Zhang, Wenlong; Wang, Chao

    2016-07-01

    Sediment bacterial communities are sensitive to water conditions in river ecosystems. The objective of this study was to compare the influences of different pollution sources, including urban areas, wastewater treatment plants (WWTPs), suburban areas, and agricultural areas, on sediment bacterial communities along a typical tributary of Taihu Lake, China. The dominant composition of the sediment bacterial community was determined using a combination of terminal restriction fragment length polymorphism (T-RFLP) and a 16S rRNA clone library. The results showed that the sediment bacterial communities were distinctly affected by the four pollution sources. Alphaproteobacteria, Betaproteobacteria, and Actinobacteria (>50 % in total) were the predominant bacterial taxa across the sediment samples. Apart from those, the sediment bacterial community composition (BCC) affected by WWTP effluent was subsequently dominated by Nitrospira (12.4 %) and Bacteroidetes (11.5 %), agriculture was dominated by Firmicutes (13.2 %) and Deltaproteobacteria (7.2 %), while urban and suburban were dominated by Bacteroidetes (7.6 and 7.9 %, respectively) and Deltaproteobacteria (7.9 and 7.6 %, respectively). Cluster analysis indicated that the BCC affected by WWTP effluent was distinct from the BCC in urban, suburban, and agricultural areas. In addition, the bacterial community richness and evenness affected by WWTP effluent were much less than those by the other pollution sources. Redundancy analysis (RDA) indicated that the variation in BCC across the sediment samples was significantly associated with ammonium (17 %), organic matter (12 %), and cadmium (3 %) (p < 0.01). Overall, the results indicated that the four different pollution sources (WWTP, urban, suburban, and agriculture) have dissimilar impacts on the sediment BCC in the tributary of Taihu Lake, while WWTPs exhibited the greatest potential to lead to biotic homogenization in river sediments. PMID:27040536

  19. Fringing reefs exposed to different levels of eutrophication and sedimentation can support similar benthic communities

    Highlights: • We assess anthropogenic pressures on coral reef health. • We present a spatio-temporal survey of environmental parameters as bio-indicators. • Poor water quality (e.g. high turbidity and high sediments) was not correlated with lower coral cover. • Phytoplankton community size-composition and habitat stability were important predictors of coral reef health. - Abstract: Benthic communities are sensitive to anthropogenic disturbances which can result in changes in species assemblages. A spatio-temporal survey of environmental parameters was conducted over an 18-month period on four different fringing reefs of Moorea, French Polynesia, with unusual vs. frequent human pressures. This survey included assessment of biological, chemical, and physical parameters. First, the results showed a surprising lack of a seasonal trend, which was likely obscured by short-term variability in lagoons. More frequent sampling periods would likely improve the evaluation of a seasonal effect on biological and ecological processes. Second, the three reef habitats studied that were dominated by corals were highly stable, despite displaying antagonistic environmental conditions through eutrophication and sedimentation gradients, whereas the reef dominated by macroalgae was relatively unstable. Altogether, our data challenge the paradigm of labelling environmental parameters such as turbidity, sedimentation, and nutrient-richness as stress indicators

  20. Bacterial and archaeal community structures in the Arctic deep-sea sediment

    LI Yan; LIU Qun; LI Chaolun; DONG Yi; ZHANG Wenyan; ZHANG Wuchang; XIAO Tian

    2015-01-01

    Microbial community structures in the Arctic deep-sea sedimentary ecosystem are determined by organic matter input, energy availability, and other environmental factors. However, global warming and earlier ice-cover melting are affecting the microbial diversity. To characterize the Arctic deep-sea sediment microbial diversity and its rela-tionship with environmental factors, we applied Roche 454 sequencing of 16S rDNA amplicons from Arctic deep-sea sediment sample. Both bacterial and archaeal communities’ richness, compositions and structures as well as tax-onomic and phylogenetic affiliations of identified clades were characterized. Phylotypes relating to sulfur reduction and chemoorganotrophic lifestyle are major groups in the bacterial groups;while the archaeal community is domi-nated by phylotypes most closely related to the ammonia-oxidizing Thaumarchaeota (96.66%) and methanogenic Euryarchaeota (3.21%). This study describes the microbial diversity in the Arctic deep marine sediment (>3 500 m) near the North Pole and would lay foundation for future functional analysis on microbial metabolic processes and pathways predictions in similar environments.

  1. Seasonality of community structure and carbon flow in Narragansett Bay sediments

    Seasonal patterns of benthic community dynamics and the pathways of detrital decomposition in Narragansett Bay were examined. Benthic meiofauna and macrofauna exhibited a pronounced seasonality, with peak abundances in the late spring and minima in the late summer. This pattern was most pronounced for surface dwelling fauna, particularly harpacticoid copepods. These results were attributed to the seasonality of detrital inputs to the sediment and the fate of these inputs. A six month study in which 14C-sodium bicarbonate was added to a large (13 m3) microcosm enabled the author to observe pathways of carbon flow. Half of the labeled organic carbon that was deposited on the sediment during the winter and spring was found in the sediment in July. At least 20 gC/m2 had accumulated since December. Within the sediment, the existence of two discrete food webs was distinguished by measurement of faunal specific activity. Surface fauna, dominated by the meiofauna, exclusively assimilate fresh (labeled) organics, while subsurface fauna (meiofauna and macrofauna) predominantly assimilated older, non-labeled organics for the duration of the study. Only the subsurface food web had access to the storage of buried detritus. While there was a surplus of detritus for both food webs during the winter and spring, the authors expect that benthic respiration rates exceed organic deposition rates during the summer. Detrital storage may be critical for the survival of the fauna through the summer

  2. [Metagenomic Analysis of Microbial Communities of the Sediments of the Kara Sea Shelf and the Yenisei Bay].

    Mamaeva, E V; Galach'yants, Yu P; Khabudaev, K V; Petrova, D P; Pogodaeva, T V; Khodzher, T B; Zemskaya, T I

    2016-01-01

    Microbial diversity in the sediments of the Kara Sea shelf and the southern Yenisei Bay, differing in pore water mineralization, was studied using massive parallel pyrosequencing according to the 454 (Roche) technology. Members of the same phyla (Cyanobacteria, Verrucomicrobia, Actinobacteria, Proteobacteria, and Bacteroidetes) predominated in bacterial communities of the sediments, while their ratio and taxonomic composition varied within the phyla and depended on pore water mineralization. Increasing salinity gradient was found to coincide with increased share of the γ-Proteobacteria and decreased abundance of α- and β-Proteo- bacteria, as well as of the phyla Verrucomicrobia, Chloroflexi, Chlorobi, and Acidobacteria. Archaeal diversity was lower, with Thaumarchaeota predominant in the sediments with high and low mineralization, while Crenarchaeota predominated in moderately mineralized sediments. Microbial communities of the Kara Sea shelf and Yenisei Gulf sediments were found to contain the organisms capable of utilization of a broad spectrum of carbon sources, including gaseous and petroleum hydrocarbons. PMID:27476207

  3. Variations in community structure and diversity associated with methane-rich sediments offshore southwestern Taiwan

    Lin, L.; Lin, J.; Wu, L.; Wang, P.

    2012-12-01

    Subseafloor sediments have been estimated to harbor more than 50% of the global prokaryotic cells. Such a large quantity of biomass has been considered to play an important role in regulating the elemental cycling between hydrosphere, atmosphere, and geosphere. On the basis of pore water geochemistry and molecular results, numerous studies have demonstrated that sulfate reduction, anaerobic methanotrophy, and methanogenesis appear to be the essential metabolic pathways controlling the organic mineralization and methane cycling in sediments of continental margins. As the extent of microbial community varies from site to site, spatial variations in community structures directly or indirectly catalyzing these metabolic pathways remain to be elucidated. This study aims to uncover community structures along a sediment core collected offshore southwestern Taiwan where the convergence between the Eurasian and Philippine Sea Plates leads to the rapid accumulation of sediments eroded from onshore mountainous regions. The samples were obtained at a 50-cm interval from a gravity core which penetrated to 5 m below seafloor. Crude DNA was extracted and the V4-V6 and V4-V5 regions of 16S rRNA genes in bacteria and archaea were amplified using the barcoded primers, respectively. The amplicons were pooled for sequencing on a Roche GS Junior platform. A total of more than 130,000 bacterial and archaeal reads each were obtained after the processing of raw data for quality check, and chimera, barcode and primer removals. The output reads were clustered into different OTU on the basis of 97% similarity and taxonomically categorized against the Silva database. Despite a significant proportion of sequences whose taxonomical assignments remain to be resolved, sequences affiliated with Firmicutes, Proteobacteria and Chloroflexi within Bacteria, and Thermoplasmata, MBG-B, ANME-1, and MCG within Archaea outnumber the other lineages. The proportions of major OTUs exhibit different trends of

  4. Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill

    Mason, Olivia U.; Scott, Nicole M.; Gonzalez, Antonio;

    2014-01-01

    in surface sediments collected at 64 sites by targeted sequencing of 16S rRNA genes, shotgun metagenomic sequencing of 14 of these samples and mineralization experiments using C-14-labeled model substrates. The 16S rRNA gene data indicated that the most heavily oil-impacted sediments were enriched...... in an uncultured Gammaproteobacterium and a Colwellia species, both of which were highly similar to sequences in the DWH deep-sea hydrocarbon plume. The primary drivers in structuring the microbial community were nitrogen and hydrocarbons. Annotation of unassembled metagenomic data revealed the most abundant......: propylene glycol, dodecane, toluene and phenanthrene. Further, analysis of metagenomic sequence data revealed an increase in abundance of genes involved in denitrification pathways in samples that exceeded the Environmental Protection Agency (EPA)'s benchmarks for polycyclic aromatic hydrocarbons (PAHs...

  5. Internal wave structures in abyssal cataract flows

    Makarenko, Nikolay; Liapidevskii, Valery; Morozov, Eugene; Tarakanov, Roman

    2014-05-01

    We discuss some theoretical approaches, experimental results and field data concerning wave phenomena in ocean near-bottom stratified flows. Such strong flows of cold water form everywhere in the Atlantic abyssal channels, and these currents play significant role in the global water exchange. Most interesting wave structures arise in a powerful cataract flows near orographic obstacles which disturb gravity currents by forced lee waves, attached hydraulic jumps, mixing layers etc. All these effects were observed by the authors in the Romanche and Chain fracture zones of Atlantic Ocean during recent cruises of the R/V Akademik Ioffe and R/V Akademik Sergei Vavilov (Morozov et al., Dokl. Earth Sci., 2012, 446(2)). In a general way, deep-water cataract flows down the slope are similar to the stratified flows examined in laboratory experiments. Strong mixing in the sill region leads to the splitting of the gravity current into the layers having the fluids with different densities. Another peculiarity is the presence of critical layers in shear flows sustained over the sill. In the case under consideration, this critical level separates the flow of near-bottom cold water from opposite overflow. In accordance with known theoretical models and laboratory measurements, the critical layer can absorb and reflect internal waves generated by the topography, so the upward propagation of these perturbations is blocked from above. High velocity gradients were registered downstream in the vicinity of cataract and it indicates the existence of developed wave structures beyond the sill formed by intense internal waves. This work was supported by RFBR (grants No 12-01-00671-a, 12-08-10001-k and 13-08-10001-k).

  6. Brain areas in abyssal demersal fishes.

    Wagner, H J

    2001-06-01

    Four areas of the brain which receive primary projections from chemical senses ([1] olfactory bulb, [2] gustatory area including facial and vagal lobes), the eye ([3] optic tectum), and mechanosensory, and-hair-cell based systems i.e. the lateral line, vestibular and auditory systems ([4] trigeminal and octavolateral regions) have been studied and relative size differences used to make deductions on the sensory preferences of 35 fish species living on or near the bottom of the deep sea. Furthermore the relative volumes of the telencephalon and the corpus cerebelli were determined. Two evaluation modes were applied: (1) the relative mean of each system was calculated and species with above-average areas identified; (2) a cluster analysis established multivariate correlations among the sensory systems. The diversity of sensory brain areas in this population of fish suggests that the benthic and epibenthic environment of the abyss presents a rich sensory environment. Vision seems to be the single most important sense suggesting the presence of relevant bioluminescent stimuli. However, in combination the chemical senses, smell and taste, surpass the visual system; most prominent among them is olfaction. The trigeminal/octavolateral area indicating the role of lateral line input and possibly audition is also well represented, but only in association with other sensory modalities. A large volume telencephalon was often observed in combination with a prominent olfactory system, whereas cerebella of unusually large sizes occurred in species with above-average visual, hair-cell based, but also olfactory systems, confirming their role as multimodal sensorimotor coordination centers. In several species the predictions derived from the volumetric brain analyses were confirmed by earlier observations of stomach content and data obtained by baited cameras. PMID:11713385

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

    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

  8. Active microbial community structure of deep subsurface sediments within Baltic Sea Basin

    Reese, B. K.; Zinke, L.; Carvalho, G.; Lloyd, K. G.; Marshall, I.; Shumaker, A.; Amend, J.

    2014-12-01

    The Baltic Sea Basin (BSB) is a unique depositional setting that has experienced periods of glaciation and deglaciation as a result of climatic fluctuations over past tens of thousands of years. This has resulted in laminated sediments formed during periods with strong permanent salinity stratification. The high sedimentation rates make this an ideal setting to understand the microbial structure of a deep biosphere community in a relatively high carbon, and thus high-energy environment, compared to other deep subsurface sites. Samples were collected through scientific drilling during the International Ocean Discovery Program (IODP) Expedition 347 on board the Greatship Manisha, September-November 2013. We examined the active microbial community structure using the 16S rRNA gene transcript and active functional genes through metatranscriptome sequencing. Major biogeochemical shifts have been observed in response to the depositional history between the limnic, brackish, and marine phases. The active microbial community structure in the BSB is diverse and reflective of the unique changes in the geochemical profile. These data further refine our understanding of the existence life in the deep subsurface and the survival mechanisms required for this extreme environment.

  9. Sedimentological imprint on subseafloor microbial communities in Western Mediterranean Sea Quaternary sediments

    M.-C. Ciobanu

    2012-09-01

    Full Text Available An interdisciplinary study was conducted to evaluate the relationship between geological and paleoenvironmental parameters and the bacterial and archaeal community structure of two contrasting subseafloor sites in the Western Mediterranean Sea (Ligurian Sea and Gulf of Lion. Both depositional environments in this area are well-documented from paleoclimatic and paleooceanographic point of views. Available data sets allowed us to calibrate the investigated cores with reference and dated cores previously collected in the same area, and notably correlated to Quaternary climate variations. DNA-based fingerprints showed that the archaeal diversity was composed by one group, Miscellaneous Crenarchaeotic Group (MCG, within the Gulf of Lion sediments and of nine different lineages (dominated by MCG, South African Gold Mine Euryarchaeotal Group (SAGMEG and Halobacteria within the Ligurian Sea sediments. Bacterial molecular diversity at both sites revealed mostly the presence of the classes Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria within Proteobacteria phylum, and also members of Bacteroidetes phylum. The second most abundant lineages were Actinobacteria and Firmicutes at the Gulf of Lion site and Chloroflexi at the Ligurian Sea site. Various substrates and cultivation conditions allowed us to isolate 75 strains belonging to four lineages: Alpha-, Gammaproteobacteria, Firmicutes and Actinobacteria. In molecular surveys, the Betaproteobacteria group was consistently detected in the Ligurian Sea sediments, characterized by a heterolithic facies with numerous turbidites from a deep-sea levee. Analysis of relative betaproteobacterial abundances and turbidite frequency suggested that the microbial diversity was a result of main climatic changes occurring during the last 20 ka. Statistical direct multivariate canonical correspondence

  10. Fungal Community Successions in Rhizosphere Sediment of Seagrasses Enhalus acoroides under PAHs Stress.

    Ling, Juan; Zhang, Yanying; Wu, Meilin; Wang, Youshao; Dong, Junde; Jiang, Yufeng; Yang, Qingsong; Zeng, Siquan

    2015-01-01

    Seagrass meadows represent one of the highest productive marine ecosystems and are of great ecological and economic values. Recently, they have been confronted with worldwide decline. Fungi play important roles in sustaining the ecosystem health as degraders of polycyclic aromatic hydrocarbons (PAHs), but fewer studies have been conducted in seagrass ecosystems. Hence, we investigated the dynamic variations of the fungal community succession under PAH stress in rhizosphere sediment of seagrasses Enhalus acoroides in this study. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), quantitative PCR (qPCR) and a clone library have been employed to analyze the fungal community's shifts. Sequencing results of DGGE and the clone library showed that the predominant species belong to phyla Ascomycota and Basidiomycota. The abundance of three groups decreased sharply over the incubation period, whereas they demonstrated different fungal diversity patterns. Both the exposure time and the PAH concentrations affected the microbial diversity as assessed by PCR-DGGE analysis. Redundancy analysis (RDA) indicated that significant factors driving community shifts were ammonium and pH (p < 0.05). Significant amounts of the variations (31.1%) were explained by pH and ammonium, illustrating that those two parameters were the most likely ones to influence or be influenced by the fungal communities' changes. Investigation results also indicated that fungal communities in seagrass meadow were very sensitive to PAH-induced stress and may be used as potential indicators for the PAH contamination. PMID:26096007

  11. Changes in sediment bacterial community in response to long-term nutrient enrichment in a subtropical seagrass-dominated estuary.

    Guevara, Rafael; Ikenaga, Makoto; Dean, Amanda L; Pisani, Cristina; Boyer, Joseph N

    2014-10-01

    Florida Bay exhibits a natural gradient of strong P limitation in the east which shifts to weak P or even N limitation at the western boundary. This nutrient gradient greatly affects seagrass abundance and productivity across the bay. We assessed the effects of N and P additions on sediment bacterial community structure in relation to the existing nutrient gradient in Florida Bay. Sediment samples from 24 permanent 0.25 m(2) plots in each of six sites across Florida Bay were fertilized with granular N and P in a factorial design for 26 months. Sediment bacterial community structure was analyzed using PCR-denaturing gradient gel electrophoresis (DGGE) analysis of 16S ribosomal RNA (rRNA) genes and a cloning strategy from DGGE bands. The phylogenetic positions of 16S rRNA sequences mostly fell into common members found in marine sediments such as sulfate-reducing Deltaproteobacteria, Gammaproteobacteria, Spirochaetes, and Bacteriodetes. Twenty-eight common DGGE bands were found in all sediment samples; however, some DGGE bands were only found or were better represented in eastern sites. Bacterial community diversity (Shannon-Weiner index) showed similar values throughout all sediment samples. The N treatment had no effect on the bacterial community structures across the bay. Conversely, the addition of P significantly influenced the bacterial community structure at all but the most western site, where P is least limiting due to inputs from the Gulf of Mexico. P additions enhanced DGGE band sequences related to Cytophagales, Ectothiorhodospiraceae, and Desulfobulbaceae, suggesting a shift toward bacterial communities with increased capability to degrade polymeric organic matter. In addition, a band related to Deferribacteres was enhanced in eastern sites. Thus, indigenous environmental conditions were the primary determining factors controlling the bacterial communities, while the addition of P was a secondary determining factor. This P-induced change in community

  12. Nitrogen cycling processes and microbial community composition in bed sediments in the Yukon River at Pilot Station

    Repert, Deborah A.; Underwood, Jennifer C.; Smith, Richard L.; Song, Bongkeun

    2014-12-01

    Information on the contribution of nitrogen (N)-cycling processes in bed sediments to river nutrient fluxes in large northern latitude river systems is limited. This study examined the relationship between N-cycling processes in bed sediments and N speciation and loading in the Yukon River near its mouth at the Bering Sea. We conducted laboratory bioassays to measure N-cycling processes in sediment samples collected over distinct water cycle seasons. In conjunction, the microbial community composition in the bed sediments using genes involved in N-cycling (narG, napA, nosZ, and amoA) and 16S rRNA gene pyrosequences was examined. Temporal variation was observed in net N mineralization, nitrate uptake, and denitrification rate potentials and correlated strongly with sediment carbon (C) and extractable N content and microbial community composition rather than with river water nutrient concentrations. The C content of the bed sediment was notably impacted by the spring flood, ranging from 1.1% in the midst of an ice-jam to 0.1% immediately after ice-out, suggesting a buildup of organic material (OM) prior to scouring of the bed sediments during ice break up. The dominant members of the microbial community that explained differences in N-processing rates belonged to the genera Crenothrix, Flavobacterium, and the family of Comamonadaceae. Our results suggest that biogeochemical processing rates in the bed sediments appear to be more coupled to hydrology, nutrient availability in the sediments, and microbial community composition rather than river nutrient concentrations at Pilot Station.

  13. Impact of redox-stratification on the diversity and distribution of bacterial communities in sandy reef sediments in a microcosm

    GAO Zheng; WANG Xin; Angelos K. HANNIDES; Francis J. SANSONE; WANG Guangyi

    2011-01-01

    Relationships between microbial communities and geochemical environments are important in marine microbial ecology and biogeochemistry.Although biogeochemical redox stratification has been well documented in marine sediments,its impact on microbial communities remains largely unknown.In this study,we applied denaturing gradient gel electrophoresis (DGGE) and clone library construction to investigate the diversity and stratification of bacterial communities in redox-stratified sandy reef sediments in a microcosm.A total of 88 Operational Taxonomic Units (OTU) were identified from 16S rRNA clone libraries constructed from sandy reef sediments in a laboratory microcosm.They were members of nine phyla and three candidate divisions,including Proteobacteria (Alpha-,Beta-,Gamma-,Delta-,and Epsilonproteobacteria),Actinobacteria,Acidobacteria,Bacteroidetes,Chloroflexi,Cyanobacteria,Firmicutes,Verrucomicrobia,Spirochaetes,and the candidate divisions WS3,SO31 and AO19.The vast majority of these phylotypes are related to clone sequences from other marine sediments,but OTUs of Epsilonproteobacteria and WS3 are reported for the first time from permeable marine sediments.Several other OTUs are potential new bacterial phylotypes because of their low similarity with reference sequences.Results from the 16S rRNA,gene clone sequence analyses suggested that bacterial communities exhibit clear stratification across large redox gradients in these sediments,with the highest diversity found in the anoxic layer (15-25 mm) and the least diversity in the suboxic layer (3-5 mm).Analysis of the nosZ,and amoA gene libraries also indicated the stratification of denitrifiers and nitrifiers,with their highest diversity being in the anoxic and oxic sediment layers,respectively.These results indicated that redox-stratification can affect the distribution of bacterial communities in sandy reef sediments.

  14. Impact of redox-stratification on the diversity and distribution of bacterial communities in sandy reef sediments in a microcosm

    Gao, Zheng; Wang, Xin; Hannides, Angelos K.; Sansone, Francis J.; Wang, Guangyi

    2011-11-01

    Relationships between microbial communities and geochemical environments are important in marine microbial ecology and biogeochemistry. Although biogeochemical redox stratification has been well documented in marine sediments, its impact on microbial communities remains largely unknown. In this study, we applied denaturing gradient gel electrophoresis (DGGE) and clone library construction to investigate the diversity and stratification of bacterial communities in redox-stratified sandy reef sediments in a microcosm. A total of 88 Operational Taxonomic Units (OTU) were identified from 16S rRNA clone libraries constructed from sandy reef sediments in a laboratory microcosm. They were members of nine phyla and three candidate divisions, including Proteobacteria ( Alpha-, Beta-, Gamma-, Delta-, and Epsilonproteobacteria), Actinobacteria, Acidobacteria, Bacteroidetes, Chloroflexi, Cyanobacteria, Firmicutes, Verrucomicrobia, Spirochaetes, and the candidate divisions WS3, SO31 and AO19. The vast majority of these phylotypes are related to clone sequences from other marine sediments, but OTUs of Epsilonproteobacteria and WS3 are reported for the first time from permeable marine sediments. Several other OTUs are potential new bacterial phylotypes because of their low similarity with reference sequences. Results from the 16S rRNA, gene clone sequence analyses suggested that bacterial communities exhibit clear stratification across large redox gradients in these sediments, with the highest diversity found in the anoxic layer (15-25 mm) and the least diversity in the suboxic layer (3-5 mm). Analysis of the nosZ, and amoA gene libraries also indicated the stratification of denitrifiers and nitrifiers, with their highest diversity being in the anoxic and oxic sediment layers, respectively. These results indicated that redox-stratification can affect the distribution of bacterial communities in sandy reef sediments.

  15. Variance and potential niche separation of microbial communities in subseafloor sediments off Shimokita Peninsula, Japan.

    Nunoura, Takuro; Takaki, Yoshihiro; Shimamura, Shigeru; Kakuta, Jungo; Kazama, Hiromi; Hirai, Miho; Masui, Noriaki; Tomaru, Hitoshi; Morono, Yuki; Imachi, Hiroyuki; Inagaki, Fumio; Takai, Ken

    2016-06-01

    Subseafloor pelagic sediments with high concentrations of organic matter form habitats for diverse microorganisms. Here, we determined depth profiles of genes for SSU rRNA, mcrA, dsrA and amoA from just beneath the seafloor to 363.3 m below the seafloor (mbsf) using core samples obtained from the forearc basin off the Shimokita Peninsula. The molecular profiles were combined with data on lithostratigraphy, depositional age, sedimentation rate and pore-water chemistry. The SSU rRNA gene tag structure and diversity changed at around the sulfate-methane transition zone (SMTZ), whereas the profiles varied further with depth below the SMTZ, probably in connection with the variation in pore-water chemistry. The depth profiles of diversity and abundance of dsrA, a key gene for sulfate reduction, suggested the possible niche separations of sulfate-reducing populations, even below the SMTZ. The diversity and abundance patterns of mcrA, a key gene for methanogenesis/anaerobic methanotrophy, suggested a stratified distribution and separation of anaerobic methanotrophy and hydrogenotrophic or methylotrophic methanogensis below the SMTZ. This study provides novel insights into the relationships between the composition and function of microbial communities and the chemical environment in the nutrient-rich continental margin subseafloor sediments, which may result in niche separation and variability in subseafloor microbial populations. PMID:26486095

  16. Constraints on spatial variability in soft-sediment communities affected by contamination from an Antarctic waste disposal site

    A small-scale (<500 m length) transect-based survey was conducted in December 1998 to examine the spatial distribution of soft-sediment communities and of concentrations of heavy metals and hydrocarbons in sediments in Brown Bay, adjacent to an abandoned waste dump, at Casey Station, Antarctica. Samples were taken along three transects at increasing distances (nine stations) from the shore-line waste dump. A gradient of contamination was detected, but concentrations of contaminants were very variable with 'hotspots' or high levels of contaminants at some stations. Multivariate analysis revealed that the distribution of soft-sediment communities was distinctly different between the inner, middle and outer stations. Abundances of most taxa were very variable with few patterns apparent, but some fauna displayed an abundance gradient from the inner to the outer part of the bay. Many taxa had maximum abundances at outer stations and minimum at inner stations. Multivariate correlations between environmental variables and soft-sediment communities indicated that combinations of some metals (Cd, Cu, Sn, Pb) and grain size (mainly finer fractions, fine sands and coarse silts) were the variables that best 'matched' the community patterns within Brown Bay. This study indicated that there were significant correlations between the presence of contaminants and the distribution and composition of soft-sediment communities over very small spatial scales

  17. Quantification of the effects of ocean acidification on sediment microbial communities in the environment: the importance of ecosystem approaches.

    Hassenrück, Christiane; Fink, Artur; Lichtschlag, Anna; Tegetmeyer, Halina E; de Beer, Dirk; Ramette, Alban

    2016-05-01

    To understand how ocean acidification (OA) influences sediment microbial communities, naturally CO2-rich sites are increasingly being used as OA analogues. However, the characterization of these naturally CO2-rich sites is often limited to OA-related variables, neglecting additional environmental variables that may confound OA effects. Here, we used an extensive array of sediment and bottom water parameters to evaluate pH effects on sediment microbial communities at hydrothermal CO2 seeps in Papua New Guinea. The geochemical composition of the sediment pore water showed variations in the hydrothermal signature at seep sites with comparable pH, allowing the identification of sites that may better represent future OA scenarios. At these sites, we detected a 60% shift in the microbial community composition compared with reference sites, mostly related to increases in Chloroflexi sequences. pH was among the factors significantly, yet not mainly, explaining changes in microbial community composition. pH variation may therefore often not be the primary cause of microbial changes when sampling is done along complex environmental gradients. Thus, we recommend an ecosystem approach when assessing OA effects on sediment microbial communities under natural conditions. This will enable a more reliable quantification of OA effects via a reduction of potential confounding effects. PMID:26887661

  18. Characterization of bacterial communities in sediments receiving various wastewater effluents with high-throughput sequencing analysis.

    Lu, Xiao-Ming; Lu, Peng-Zhen

    2014-04-01

    454 Pyrosequencing was applied to examine bacterial communities in sediment samples collected from a river receiving effluent discharge from rural domestic sewage (RDS) and various factories, including a tannery (TNS), clothing plant (CTS), and button factory (BTS), respectively. For each sample, 4,510 effective sequences were selected and utilized to do the bacterial diversity and abundance analysis, respectively. In total, 1,288, 2,036, 1,800, and 2,150 operational taxonomic units were obtained at 3% distance cutoff in TNS, CTS, BTS, and RDS, respectively. Bacterial phylotype richness in RDS was higher than the other samples, and TNS had the least richness. The most predominant class in the TNS, CTS, and BTS samples is Betaproteobacteria. Cyanobacteria (no_rank) is the most predominant one in the RDS sample. Circa 31% sequences in TNS were affiliated with the Rhodocyclales order. In the four samples, Aeromonas, Arcobacter, Clostridium, Legionella, Leptospira, Mycobacterium, Pseudomonas, and Treponema genera containing pathogenic bacteria were detected. Characterization of bacterial communities in sediments from various downstream branches indicated that distinct wastewater effluents have similar potential to reduce the natural variability in river ecosystems and contribute to the river biotic homogenization. PMID:24477925

  19. Potential of the microbial community present in an unimpacted beach sediment to remediate petroleum hydrocarbons.

    Almeida, C Marisa R; Reis, Izabela; Couto, M Nazaré; Bordalo, Adriano A; Mucha, Ana P

    2013-05-01

    The potential of the microbial communities present in the intertidal zone of an unimpacted beach (a beach that did not suffer any significant oil spill) to degrade hydrocarbons was investigated. For that, laboratory-based microcosms (50-ml flasks) were set up with sandy beach sediment spiked with crude oil and incubated with local seawater for 15 days in the dark. Three bioremediation treatments were tested (biostimulation (BS), autochthonous bioaugmentation (AB), and combined treatment of biostimulation + bioaugmentation (BS + AB)) and the results were compared with natural attenuation (NA). Visual inspection showed clearly an oil solubility increase (confirmed by a higher hydrocarbons concentration in supernatant solutions) for all tested treatments when compared to NA. Significant degradation of the oil, shown by different profiles of petroleum hydrocarbons, was also observed for the different treatments particularly for BS + AB. Therefore, the microbial community of this unimpacted beach sediment could respond to an oil spill, degrading hydrocarbons. But to increase the natural attenuation pace, obtained results indicated that BS + AB is an appropriate approach for the bioremediation of beaches recently impacted by an oil spill. The autochthonous microbial cultures can be obtained "before" or "after" the contamination of the target site, being inoculated into the site right after it contamination. PMID:23054799

  20. Sources of organic matter affect depth-related microbial community composition in sediments of Lake Erhai, Southwest China

    Wei Xiong

    2014-02-01

    Full Text Available Sediment cores taken from different areas of the mesotrophic Lake Erhai were analysed to investigate the vertical distribution of bacterial community composition (BCC, as well as physicochemical parameters. PCR-denaturing gradient gel electrophoresis (DGGE, stable carbon isotope (δ13C, C/N atomic ratio and canonical correspondence analysis (CCA were used to explore the relationships between the succession of bacterial communities and environmental variables, emphasising changes in the sources of organic matter (OM. The BCC in natural environments was characterised by DGGE of the 16S rRNA gene with subsequent sequencing of bands of interest. The CCA revealed that the depth-related variation in sediment bacterial communities in different areas of the lake was significantly influenced by varying environmental factors. The OM source, however, played an important role in structuring BCC at all sites. The DGGE banding patterns revealed that the abundance of Deltaproteobacteria decreased with accompanying elevated levels of C4 plant-derived organic carbon. The sequencing of DGGE bands suggested that the majority of the sequences were affiliated with common phylogenetic groups in lake sediments: Chloroflexi, Deltaproteobacteria and Firmicutes. Betaproteobacteria detected in our study appeared as a prominent phylotype in the upper sediment. The Shannon-Wiener diversity index of bacterial communities was directly affected by the OM source. Constant OM sources resulted in a stable higher diversity of bacterial communities and broader enzymatic capabilities to access OM. We conclude that the differences in the diversity of bacterial communities in sediments differing in their sources of OM were related to environmental variables (e.g. water level, river runoff and terrestrial vegetation composition. Our study provided insights into the relationships between natural BCC and OM sources, facilitating a better understanding of microbial community structure in

  1. Long-term natural remediation process in textile dye-polluted river sediment driven by bacterial community changes.

    Ito, Tsukasa; Adachi, Yusuke; Yamanashi, Yu; Shimada, Yosuke

    2016-09-01

    The textile and dyeing industries are major sources of environmental water pollution all over the world. The textile wastewater effluents discharged into rivers often appear dark red-purple in color due to azo dyes, which can be transformed into carcinogenic aromatic amines. The chemicals used in dyeing are not readily degraded in nature and thus precipitate in river sediment. However, little is known about how dyeing chemicals affect river sediment and river water or how long they persist because they are difficult to monitor. To assess undetectable dyes and byproducts in river sediments, we evaluated the potential of river sediment bacteria to degrade dyes and aromatic amines. We describe the natural remediation of river sediment long-contaminated by textile dyeing effluent. After cessation of wastewater discharge, the dye-degradation potential decreased, and the aromatic amine-degradation potential increased initially and then declined over time. The changes in degradation potential were consistent with changes in the sediment bacterial community. The transition occurred on the order of years. Our data strongly suggest that dyes remained in the river sediment and that aromatic amines were produced even in transparent- and no longer colored-river water, but these chemicals were degraded by the changing sediment bacteria. Time-course monitoring of the degradation activities of key bacteria thus enables assessment of the fate of dye pollutants in river sediments. PMID:27232990

  2. Temporal variation of magnetotactic bacterial communities in two freshwater sediment microcosms.

    Lin, Wei; Pan, Yongxin

    2010-01-01

    Magnetotactic bacteria (MTB), which can mineralize nanosized magnetite or greigite crystals within cells, play important roles in biogeochemical processes, for example iron and sulfur cycling, and depositional remanent magnetization acquisitions. Despite decades of research, the knowledge of MTB distribution and ecology is still limited. In the present study, we investigated the temporal variation of MTB communities in freshwater sediment microcosms based on 16S rRNA genes and unifrac analyses. Two microcosms (MY8 and MY11) collected from two separate sites in Lake Miyun (Beijing, China) were analyzed. The majority of retrieved sequences belonged to alphaproteobacterial magnetotactic cocci in both microcosms (representing 64.29% of clones from MY8 and 100% of clones from MY11), whereas so-called 'Magnetobacterium bavaricum'-like MTB affiliated within Nitrospira phylum were exclusively found in microcosm MY8. Over a 3-month period, the temporal variation of MTB communities was evident in both microcosms. In addition, the phylogenetic discrepancy of MTB communities between two microcosms is more prominent than that of the same microcosm at different times, implying adaptation of MTB phylogenetic lineages to specific microenvironments. Among the physical-chemical parameters measured, a strong correlation was shown between nitrate and the main genetic variability of MTB communities, indicating that nitrate may influence the occurrence of MTB phylogenetic lineages in natural environments. PMID:19909346

  3. Nitrogen Cycling and Community Structure of Proteobacterial β-Subgroup Ammonia-Oxidizing Bacteria within Polluted Marine Fish Farm Sediments

    McCaig, Allison E.; Phillips, Carol J.; Stephen, John R.; Kowalchuk, George A.; Harvey, S. Martyn; Herbert, Rodney A.; Embley, T. Martin; Prosser, James I

    1999-01-01

    A multidisciplinary approach was used to study the effects of pollution from a marine fish farm on nitrification rates and on the community structure of ammonia-oxidizing bacteria in the underlying sediment. Organic content, ammonium concentrations, nitrification rates, and ammonia oxidizer most-probable-number counts were determined in samples of sediment collected from beneath a fish cage and on a transect at 20 and 40 m from the cage. The data suggest that nitrogen cycling was significantl...

  4. The Vertical Distribution of Sediment Archaeal Community in the “Black Bloom” Disturbing Zhushan Bay of Lake Taihu

    Fan, Xianfang; Xing, Peng

    2016-01-01

    Using the Illumina sequencing technology, we investigated the vertical distribution of archaeal community in the sediment of Zhushan Bay of Lake Taihu, where the black bloom frequently occurred in summer. Overall, the Miscellaneous Crenarchaeotal Group (MCG), Deep Sea Hydrothermal Vent Group 6 (DHVEG-6), and Methanobacterium dominated the archaeal community. However, we observed significant difference in composition of archaeal community among different depths of the sediment. DHVEG-6 dominated in the surface layer (0–3 cm) sediment. Methanobacterium was the dominating archaeal taxa in the L2 (3–6 cm) and L3 (6–10) sediment. MCG was most abundant in the L4 (10–15 cm) and L5 (15–20 cm) sediment. Besides, DHVEG-6 was significantly affected by the concentration of total phosphorus (TP). And loss on ignition (LOI) was an important environmental factor for Methanobacterium. As the typical archaeal taxa in the surface layer sediment, DHVEG-6 and Methanobacterium might be more adapted to abundant substrate supply from cyanobacterial blooms and take active part in the biomass transformation. We propose that DHVEG-6 and Methanobacterium could be the key archaeal taxa correlated with the “black bloom” formation in Zhushan Bay. PMID:26884723

  5. Microbial community structure in lake and wetland sediments from a high Arctic polar desert revealed by targeted transcriptomics.

    Magdalena K Stoeva

    Full Text Available While microbial communities play a key role in the geochemical cycling of nutrients and contaminants in anaerobic freshwater sediments, their structure and activity in polar desert ecosystems are still poorly understood, both across heterogeneous freshwater environments such as lakes and wetlands, and across sediment depths. To address this question, we performed targeted environmental transcriptomics analyses and characterized microbial diversity across three depths from sediment cores collected in a lake and a wetland, located on Cornwallis Island, NU, Canada. Microbial communities were characterized based on 16S rRNA and two functional gene transcripts: mcrA, involved in archaeal methane cycling and glnA, a bacterial housekeeping gene implicated in nitrogen metabolism. We show that methane cycling and overall bacterial metabolic activity are the highest at the surface of lake sediments but deeper within wetland sediments. Bacterial communities are highly diverse and structured as a function of both environment and depth, being more diverse in the wetland and near the surface. Archaea are mostly methanogens, structured by environment and more diverse in the wetland. McrA transcript analyses show that active methane cycling in the lake and wetland corresponds to distinct communities with a higher potential for methane cycling in the wetland. Methanosarcina spp., Methanosaeta spp. and a group of uncultured Archaea are the dominant methanogens in the wetland while Methanoregula spp. predominate in the lake.

  6. Influence of bioturbation by the polychaete Nereis diversicolor on the structure of bacterial communities in oil contaminated coastal sediments.

    Cuny, Philippe; Miralles, Gilles; Cornet-Barthaux, Véronique; Acquaviva, Monique; Stora, Georges; Grossi, Vincent; Gilbert, Franck

    2007-04-01

    Patterns of change in the structure of bacterial communities monitored by ribosomal intergenic spacer analysis (RISA) in oil contaminated sediments inhabited or not by the marine polychaete Nereis diversicolor were studied during 45 days under laboratory conditions. Results supported by principal component analysis showed a marked response of the bacterial communities to the oil contamination and to the presence of N. diversicolor. Phylogenetic affiliation of specific RISA bands showed that, in the contaminated sediments, the presence of the marine polychaetes favoured the development of bacteria which may play an active role in natural bioremediation processes of oil polluted environments. PMID:17254615

  7. Microbial community responses to organophosphate substrate additions in contaminated subsurface sediments.

    Robert J Martinez

    Full Text Available BACKGROUND: Radionuclide- and heavy metal-contaminated subsurface sediments remain a legacy of Cold War nuclear weapons research and recent nuclear power plant failures. Within such contaminated sediments, remediation activities are necessary to mitigate groundwater contamination. A promising approach makes use of extant microbial communities capable of hydrolyzing organophosphate substrates to promote mineralization of soluble contaminants within deep subsurface environments. METHODOLOGY/PRINCIPAL FINDINGS: Uranium-contaminated sediments from the U.S. Department of Energy Oak Ridge Field Research Center (ORFRC Area 2 site were used in slurry experiments to identify microbial communities involved in hydrolysis of 10 mM organophosphate amendments [i.e., glycerol-2-phosphate (G2P or glycerol-3-phosphate (G3P] in synthetic groundwater at pH 5.5 and pH 6.8. Following 36 day (G2P and 20 day (G3P amended treatments, maximum phosphate (PO4(3- concentrations of 4.8 mM and 8.9 mM were measured, respectively. Use of the PhyloChip 16S rRNA microarray identified 2,120 archaeal and bacterial taxa representing 46 phyla, 66 classes, 110 orders, and 186 families among all treatments. Measures of archaeal and bacterial richness were lowest under G2P (pH 5.5 treatments and greatest with G3P (pH 6.8 treatments. Members of the phyla Crenarchaeota, Euryarchaeota, Bacteroidetes, and Proteobacteria demonstrated the greatest enrichment in response to organophosphate amendments and the OTUs that increased in relative abundance by 2-fold or greater accounted for 9%-50% and 3%-17% of total detected Archaea and Bacteria, respectively. CONCLUSIONS/SIGNIFICANCE: This work provided a characterization of the distinct ORFRC subsurface microbial communities that contributed to increased concentrations of extracellular phosphate via hydrolysis of organophosphate substrate amendments. Within subsurface environments that are not ideal for reductive precipitation of uranium

  8. Fungal Community Successions in Rhizosphere Sediment of Seagrasses Enhalus acoroides under PAHs Stress

    Juan Ling

    2015-06-01

    Full Text Available Seagrass meadows represent one of the highest productive marine ecosystems and are of great ecological and economic values. Recently, they have been confronted with worldwide decline. Fungi play important roles in sustaining the ecosystem health as degraders of polycyclic aromatic hydrocarbons (PAHs, but fewer studies have been conducted in seagrass ecosystems. Hence, we investigated the dynamic variations of the fungal community succession under PAH stress in rhizosphere sediment of seagrasses Enhalus acoroides in this study. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE, quantitative PCR (qPCR and a clone library have been employed to analyze the fungal community’s shifts. Sequencing results of DGGE and the clone library showed that the predominant species belong to phyla Ascomycota and Basidiomycota. The abundance of three groups decreased sharply over the incubation period, whereas they demonstrated different fungal diversity patterns. Both the exposure time and the PAH concentrations affected the microbial diversity as assessed by PCR-DGGE analysis. Redundancy analysis (RDA indicated that significant factors driving community shifts were ammonium and pH (p < 0.05. Significant amounts of the variations (31.1% were explained by pH and ammonium, illustrating that those two parameters were the most likely ones to influence or be influenced by the fungal communities’ changes. Investigation results also indicated that fungal communities in seagrass meadow were very sensitive to PAH-induced stress and may be used as potential indicators for the PAH contamination.

  9. Fungal communities in sediments of subtropical Chinese seas as estimated by DNA metabarcoding.

    Li, Wei; Wang, Meng Meng; Wang, Xi Guang; Cheng, Xiao Li; Guo, Jia Jia; Bian, Xiao Meng; Cai, Lei

    2016-01-01

    Ribosomal RNA internal transcribed spacer-1 (ITS1) metabarcoding was used to investigate the distribution patterns of fungal communities and the factors influencing these patterns in subtropical Chinese seas, including the southern and northern Yellow Sea and the Bohai Sea. These seas were found to harbor high levels of fungal diversity, with 816 operational taxonomic units (OTUs) that span 130 known genera, 36 orders, 14 classes and 5 phyla. Ascomycota was the most abundant phylum, containing 72.18% and 79.61% of all OTUs and sequences, respectively, followed by Basidiomycota (19.98%, 18.64%), Zygomycota (1.10%, 0.11%), Chytridiomycota (0.25%, 0.04%) and Rozellomycota (0.12%, 0.006%). The compositions of fungal communities across these three sea regions were found to be vary, which may be attributed to sediment source, geographical distance, latitude and some environmental factors such as the temperature and salinity of bottom water, water depth, total nitrogen, and the ratio of total organic carbon to nitrogen. Among these environmental factors, the temperature of bottom water is the most important driver that governs the distribution patterns of fungal communities across the sampled seas. Our data also suggest that the cold-water mass of the Yellow Sea likely balances competitive relationships between fungal taxa rather than increasing species richness levels. PMID:27198490

  10. Microbial Communities in Sediments of Lagos Lagoon, Nigeria: Elucidation of Community Structure and Potential Impacts of Contamination by Municipal and Industrial Wastes.

    Obi, Chioma C; Adebusoye, Sunday A; Ugoji, Esther O; Ilori, Mathew O; Amund, Olukayode O; Hickey, William J

    2016-01-01

    Estuarine sediments are significant repositories of anthropogenic contaminants, and thus knowledge of the impacts of pollution upon microbial communities in these environments is important to understand potential effects on estuaries as a whole. The Lagos lagoon (Nigeria) is one of Africa's largest estuarine ecosystems, and is impacted by hydrocarbon pollutants and other industrial and municipal wastes. The goal of this study was to elucidate microbial community structure in Lagos lagoon sediments to identify groups that may be adversely affected by pollution, and those that may serve as degraders of environmental contaminants, especially polycyclic aromatic hydrocarbons (PAHs). Sediment samples were collected from sites that ranged in types and levels of anthropogenic impacts. The sediments were characterized for a range of physicochemical properties, and microbial community structure was determined by Illumina sequencing of the 16S rRNA genes. Microbial diversity (species richness and evenness) in the Apapa and Eledu sediments was reduced compared to that of the Ofin site, and communities of both of the former two were dominated by a single operational taxonomic unit (OTU) assigned to the family Helicobacteraceae (Epsilonproteobacteria). In the Ofin community, Epsilonproteobacteria were minor constituents, while the major groups were Cyanobacteria, Bacteroidetes, and Firmicutes, which were all minor in the Apapa and Eledu sediments. Sediment oxygen demand (SOD), a broad indicator of contamination, was identified by multivariate analyses as strongly correlated with variation in alpha diversity. Environmental variables that explained beta diversity patterns included SOD, as well as levels of naphthalene, acenaphthylene, cobalt, cadmium, total organic matter, or nitrate. Of 582 OTU identified, abundance of 167 was significantly correlated (false discovery rate q≤ 0.05) to environmental variables. The largest group of OTU correlated with PAH levels were PAH

  11. Microbial Communities in Sediments of Lagos Lagoon, Nigeria: Elucidation of Community Structure and Potential Impacts of Contamination by Municipal and Industrial Wastes

    Obi, Chioma C.; Adebusoye, Sunday A.; Ugoji, Esther O.; Ilori, Mathew O.; Amund, Olukayode O.; Hickey, William J.

    2016-01-01

    Estuarine sediments are significant repositories of anthropogenic contaminants, and thus knowledge of the impacts of pollution upon microbial communities in these environments is important to understand potential effects on estuaries as a whole. The Lagos lagoon (Nigeria) is one of Africa’s largest estuarine ecosystems, and is impacted by hydrocarbon pollutants and other industrial and municipal wastes. The goal of this study was to elucidate microbial community structure in Lagos lagoon sediments to identify groups that may be adversely affected by pollution, and those that may serve as degraders of environmental contaminants, especially polycyclic aromatic hydrocarbons (PAHs). Sediment samples were collected from sites that ranged in types and levels of anthropogenic impacts. The sediments were characterized for a range of physicochemical properties, and microbial community structure was determined by Illumina sequencing of the 16S rRNA genes. Microbial diversity (species richness and evenness) in the Apapa and Eledu sediments was reduced compared to that of the Ofin site, and communities of both of the former two were dominated by a single operational taxonomic unit (OTU) assigned to the family Helicobacteraceae (Epsilonproteobacteria). In the Ofin community, Epsilonproteobacteria were minor constituents, while the major groups were Cyanobacteria, Bacteroidetes, and Firmicutes, which were all minor in the Apapa and Eledu sediments. Sediment oxygen demand (SOD), a broad indicator of contamination, was identified by multivariate analyses as strongly correlated with variation in alpha diversity. Environmental variables that explained beta diversity patterns included SOD, as well as levels of naphthalene, acenaphthylene, cobalt, cadmium, total organic matter, or nitrate. Of 582 OTU identified, abundance of 167 was significantly correlated (false discovery rate q≤ 0.05) to environmental variables. The largest group of OTU correlated with PAH levels were PAH

  12. Lead pollution in a large, prairie-pothole lake (Rush Lake, WI, USA): Effects on abundance and community structure of indigenous sediment bacteria

    Rush Lake (WI, USA), the largest prairie-pothole lake east of the Mississippi River, has been contaminated with lead pollution as a result of over 140 years of waterfowl hunting. We examined: (1) the extent of lead pollution in Rush Lake sediments and (2) whether lead pollution in Rush Lake is affecting the abundance and community structure of indigenous sediment bacteria. Sediment lead concentrations did not exceed 59 mg Pb kg-1 dry sediment. No relationship was observed between sediment lead concentration and the abundance of aerobic (P = 0.498) or anaerobic (P = 0.416) heterotrophic bacteria. Similarly, lead did not appear to affect bacterial community structure when considering both culturable and nonculturable community members. In contrast, the culturable fraction of sediment bacteria in samples containing 59 mg Pb kg-1 exhibited a unique community structure. While factors other than lead content likely play roles in determining bacterial community structure in the sediments of Rush Lake, these data suggest that the culturable fraction of sediment bacterial communities is affected by elevated lead levels. - Low levels of lead pollution in Rush Lake are not impinging upon the abundance of indigenous sediment bacteria, but may be affecting the community structure of the culturable fraction of these bacteria

  13. A Microbial Community in Sediments Beneath the Western Antarctic Ice Sheet, Ice Stream C (Kamb)

    Skidmore, M.; Han, S.; Foo, W.; Bui, D.; Lanoil, B.

    2004-12-01

    In 2000, an ice-drilling project focusing on the "sticky spot" of Ice Stream C recovered cores of sub-glacial sediments from beneath the Western Antarctic Ice Sheet. We have characterized several chemical and microbiological parameters of the sole intact sediment core. Pore waters extracted from these sediments were brackish and some were supersaturated with respect to calcite. Ion chromatography demonstrated the presence of several organic acids at low, but detectable, levels in the pore water. DAPI direct cell counts were approximately 107 cells g-1. Aerobic viable plate counts were much lower than direct cell counts; however, they were two orders of magnitude higher on plates incubated at low temperature (4 ° C; 3.63 x 105 CFU ml-1) than at higher temperatures (ca. 22° C; 1.5 x 103 CFU ml-1); no colonies were detected on plates incubated anaerobically at either temperature. 16S rDNA clone library analysis indicates extremely limited bacterial diversity in these samples: six phylogenetic clades were detected. The three dominant bacterial phylogenetic clades in the clone libraries (252 clones total) were most closely related to Thiobacillus thioparus (180 clones), Polaromonas vacuolata (34 clones), and Gallionella ferruginea (35 clones) and their relatives; one clone each represented the other three phylogenetic clades (most closely related to Ralstonia pickettii, Lysobacter antibioticus, and Xylella fastidiosa, respectively). These sequences match closely with sequences previously obtained from other subglacial environments in Alaska, Ellesmere Island, Canada and New Zealand. Implications of this microbial community to subglacial chemistry and microbial biogeography will be discussed.

  14. Sediment denitrifier community composition and nirS gene expression investigated with functional gene microarrays

    Francis, C.A.; Jackson, G.A.; Ward, B.B.; Bülow, Steffen

    2008-01-01

    A functional gene microarray was used to investigate denitrifier community composition and nitrite reductase (nirS) gene expression in sediments along the estuarine gradient in Chesapeake Bay, USA. The nirS oligonucleotide probe set was designed to represent a sequence database containing 539...... Chesapeake Bay clones, as well as sequences from many other environments. Greatest nirS diversity was detected at the freshwater station at the head of the bay and least diversity at the higher salinity station near the mouth of the Bay. The most common OTUs from the sequence database were detected on the......RNA level. These results suggest that the most actively denitrifying groups are responsible for most nirS expression as well Udgivelsesdato: 2008/11...

  15. Community structure of β-Proteobacterial ammonia-oxidizing bacteria in prawn farm sediment

    Ying Ma; Lin Wang; Lumin Qian

    2008-01-01

    To examine the community structure of β-Proteobacterial ammonia-oxidizing bacteria (AOB) in prawn farm sediment, the 16S rRNA gene library was constructed with β-Proteobacterial AOB-specific primers. The library was screened by PCR-restriction fragment length polymorphism (RFLP) analysis and clones with unique RFLP patterns were sequenced. Two groups of β-Proteobacterial AOB, the Nitrosomonas and the Nitrosospira, were detected. The Nitrosomonas occupied an absolute dominant position, accounting for more than 90% of total clones in the clone library, while the Nitrosospira accounting for 5.48%. Nitrosomonas-affiliated clones were grouped into the Nitrosomonas marina and the Nitrosomonas sp. Nm 143 clusters, and Nitrosospira-affiliated clones were grouped into the Nitrosospira cluster 1. No other clusters of β-Proteobacterial AOB were found. The results enriched our knowledge of AOB diversity in the prawn farm sediment and provided important foundational data for further functional studies of these microbes in mariculture environments.

  16. Methane-derived carbon flow through microbial communities in arctic lake sediments.

    He, Ruo; Wooller, Matthew J; Pohlman, John W; Tiedje, James M; Leigh, Mary Beth

    2015-09-01

    Aerobic methane (CH4 ) oxidation mitigates CH4 release and is a significant pathway for carbon and energy flow into aquatic food webs. Arctic lakes are responsible for an increasing proportion of global CH4 emissions, but CH4 assimilation into the aquatic food web in arctic lakes is poorly understood. Using stable isotope probing (SIP) based on phospholipid fatty acids (PLFA-SIP) and DNA (DNA-SIP), we tracked carbon flow quantitatively from CH4 into sediment microorganisms from an arctic lake with an active CH4 seepage. When 0.025 mmol CH4 g(-1) wet sediment was oxidized, approximately 15.8-32.8% of the CH4 -derived carbon had been incorporated into microorganisms. This CH4 -derived carbon equated to up to 5.7% of total primary production estimates for Alaskan arctic lakes. Type I methanotrophs, including Methylomonas, Methylobacter and unclassified Methylococcaceae, were most active at CH4 oxidation in this arctic lake. With increasing distance from the active CH4 seepage, a greater diversity of bacteria incorporated CH4 -derived carbon. Actinomycetes were the most quantitatively important microorganisms involved in secondary feeding on CH4 -derived carbon. These results showed that CH4 flows through methanotrophs into the broader microbial community and that type I methanotrophs, methylotrophs and actinomycetes are important organisms involved in using CH4 -derived carbon in arctic freshwater ecosystems. PMID:25581131

  17. Community characteristics of macrobenthos in the Huanghe (Yellow River) Estuary during water and sediment discharge regulation

    REN Zhonghua; LI Fan; WEI Jiali; LI Shaowen; LV Zhenbo; GAO Yanjie; CONG Xuri

    2016-01-01

    The community characteristics of macrobenthos in the Huanghe (Yellow River) Estuary is influenced by a combination of natural and anthropogenic factors. Here, we investigated short-term changes (1-month) in macrobenthic community structure in response to water and sediment discharge regulation (WSDR) in 2011. Specifically, we sampled the macrobenthos at 18 sampling stations situated at four distances (5, 10, 20, and 40 km) from the mouth of the Huanghe Estuary before (mid-June), during (early-July), and after (mid-July) WSDR. The results showed that a total of 73, 72, and 85 species were collected before, during, and after WSDR, respectively. Then, 13, 1, and 16 dominant species were detected at this three periods. Four phyla were primarily detected at all three periods (Annelida, Mollusca, Arthropoda, and Echinodermata). However, while Mollusca and Annelida were the most important phyla in our study, Echinodermata and Annelida were the most important phyla in 1982, demonstrating major changes to community structure over a 3-decadal period. All stations were of high quality BOPA index before WSDR, whereas two and three stations were of reduced quality BOPA index during and after WSDR, respectively. The results of ABC curves showed that had incurred disturbed conditions after human activities WSDR. Most important of all, multivariate analyses and RDA analysis indicated that the structure of the macrobenthic community was closely linked to environment factors, including that organic content factor caused the distribution of macrobenthic community mostly during WSDR, while water depth after WSDR affected the macro benthos community structure seriously, and during WSDR, the environment factor influencing it was not single, including organic content, sulfide content, Hg and As. These differences may have been due to changes in water transparency negatively impacting the growth and development of macrobenthos, due to specific life-history requirements. Our results

  18. Influence of bioturbation by the polychaete Nereis diversicolor on the structure of bacterial communities in oil contaminated coastal sediments

    Cuny, Philippe; Miralles, Gilles; Cornet-Barthaux, Véronique; Acquaviva, Monique; Stora, Georges; Grossi, Vincent; Gilbert, Franck

    2007-01-01

    Patterns of change in the structure of bacterial communities monitored by ribosomal intergenic spacer analysis (RISA) in oil contaminated sediments inhabited or not by the marine polychaete Nereis diversicolor were studied during 45 days under laboratory conditions. Results supported by principal component analysis showed a marked response of the bacterial communities to the oil contamination and to the presence of N. diversicolor. Phylogenetic affiliation of specific RISA bands showed that, ...

  19. Effects of the antibiotic ciprofloxacin on the bacterial community structure and degradation of pyrene in marine sediment

    The ecological consequences of antibiotics in the aquatic environment have been an issue of concern over the past years due to the potential risk for negative effects on indigenous microorganisms. Microorganisms provide important ecosystem services, such as nutrient recycling, organic matter mineralization and degradation of pollutants. In this study, effects of exposure to the antibiotic ciprofloxacin on the bacterial diversity and pollutant degradation in natural marine sediments were studied using molecular methods (T-RFLP) in combination with radiorespirometry. In a microcosm experiment, sediment spiked with 14C-labelled pyrene was exposed to five concentrations of ciprofloxacin (0, 20, 200, 1000 and 2000 μg L-1) in a single dose to the overlying water. The production of 14CO2 (i.e. complete mineralization of pyrene) was measured during 11 weeks. Sediment samples for bacterial community structure analysis were taken after 7 weeks. Results showed a significant dose-dependent inhibition of pyrene mineralization measured as the total 14CO2 production. The nominal EC50 was calculated to 560 μg L-1, corresponding to 0.4 μg/kg d.w. sediment. The lowest effect concentration on the bacterial community structure was 200 μg L-1, which corresponds to 0.1 μg/kg d.w. sediment. Our results show that antibiotic pollution can be a potential threat to both bacterial diversity and an essential ecosystem service they perform in marine sediment

  20. Environmental Conditions Outweigh Geographical Contiguity in Determining the Similarity of nifH-Harboring Microbial Communities in Sediments of Two Disconnected Marginal Seas.

    Zhou, Haixia; Dang, Hongyue; Klotz, Martin G

    2016-01-01

    Ecological evidence suggests that heterotrophic diazotrophs fueled by organic carbon respiration in sediments play an important role in marine nitrogen fixation. However, fundamental knowledge about the identities, abundance, diversity, biogeography, and controlling environmental factors of nitrogen-fixing communities in open ocean sediments is still elusive. Surprisingly, little is known also about nitrogen-fixing communities in sediments of the more research-accessible marginal seas. Here we report on an investigation of the environmental geochemistry and putative diazotrophic microbiota in the sediments of Bohai Sea, an eutrophic marginal sea of the western Pacific Ocean. Diverse and abundant nifH gene sequences were identified and sulfate-reducing bacteria (SRB) were found to be the dominant putative nitrogen-fixing microbes. Community statistical analyses suggested bottom water temperature, bottom water chlorophyll a content (or the covarying turbidity) and sediment porewater Eh (or the covarying pH) as the most significant environmental factors controlling the structure and spatial distribution of the putative diazotrophic communities, while sediment Hg content, sulfide content, and porewater [Formula: see text]-Si content were identified as the key environmental factors correlated positively with the nifH gene abundance in Bohai Sea sediments. Comparative analyses between the Bohai Sea and the northern South China Sea (nSCS) identified a significant composition difference of the putative diazotrophic communities in sediments between the shallow-water (estuarine and nearshore) and deep-water (offshore and deep-sea) environments, and sediment porewater dissolved oxygen content, water depth and in situ temperature as the key environmental factors tentatively controlling the species composition, community structure, and spatial distribution of the marginal sea sediment nifH-harboring microbiota. This confirms the ecophysiological specialization and niche

  1. Activity, Microenvironments, and Community Structure of Aerobic and Anaerobic Ammonium Oxidizing Prokaryotes in Estuarine Sediment (Randers Fjord, DK)

    Schramm, Andreas; Revsbech, Niels Peter; Dalsgaard, Tage;

    2006-01-01

    ACTIVITY, MICROENVIRONMENTS, AND COMMUNITY STRUCTURE OF AEROBIC AND ANAEROBIC AMMONIUM OXIDIZING PROKARYOTES IN ESTUARINE SEDIMENT (RANDERS FJORD, DK) A. Schramm 1, N.P. Revsbech 1, T. Dalsgaard 2, E. Piña-Ochoa 3, J. de la Torré 4, D.A. Stahl 4, N. Risgaard-Petersen 2 1 Department of Biological...

  2. LC/IRMS analysis: A powerful technique to trace carbon flow in microphytobenthic communities in intertidal sediments

    Moerdijk-Poortvliet, T.C.W.; Stal, L.J.; Boschker, H.T.S.

    2014-01-01

    Microphytobenthic communities are important for primary production in intertidal marine sediments. Extracellular polymeric substances (EPS), comprising polysaccharides and proteins, play a key role in the structure and functioning of microphytobenthic biofilms and allow interactions between the benthic microalgae and the associated heterotrophic bacteria. The use of stable isotopes has provided major insights into the functioning of these microbial ecosystems. Until recently, gas chromatograp...

  3. Linking microbial community structure to biogeochemical function in coastal marine sediments: Stable isotope probing combined with magnetic bead capture

    T. Miyatake

    2011-01-01

    Microbial community structure and its biogeochemical functions in marine sediments can be successfully linked by using the improved Mag-SIP method in combination with other approaches. In this thesis, we were able to provide detailed information on the microorganisms responsible for the utilization

  4. Seasonal patterns of bacterial communities in the coastal brackish sediments of the Gulf of Finland, Baltic Sea

    Vetterli, Adrien; Hyytiäinen, Kirsi; Ahjos, Minttu; Auvinen, Petri; Paulin, Lars; Hietanen, Susanna; Leskinen, Elina

    2015-11-01

    Coastal areas are critical in mitigating the impact of nutrient runoffs and downstream eutrophication of aquatic ecosystems. In the Gulf of Finland, the easternmost sub-basin of the Baltic Sea, seasonal and long-term oxygen depletion at the surface of the sediment feeds back the eutrophication loop by promoting the release of nutrients locked in the sediment matrix. In order to understand how the bacterial community responds to the seasonal variations, we sequenced ribosomal gene fragments from the top sediment layer at two coastal sites in southern Finland in spring, summer and late autumn during two consecutive years. Analysis of the samples collected at a shallow (11 m) and deep site (33 m) revealed that the overall community composition was rather constant over time with an extensive collection of shared operational taxonomic units (OTU) between sites. The dominant taxa were related to organoheterotrophs and sulfate reducers and the variation in community structure was linked to the availability of organic matter in the surface sediment. Proteobacteria formed the most abundant and diverse group. The taxa characteristic of spring samples belonged primarily to Actinobacteria, possibly of fresh water origin and linked to humic carbon. Summer communities were characterized by an increase in the number of reads associated with heterotrophic bacteria such as Bacteroidetes which feed on labile organic matter from spring bloom. Taxa typical of autumn samples were linked to Cyanobacteria and other bloom-forming bacteria from the overlying water and to bacteria feeding on organic matter drifting from the phytal zone.

  5. SEDIMENT TOXICITY AND COMMUNITY COMPOSITION OF BENTHOS AND COLONIZED PERIPHYTON IN THE EVERGLADES - FLORIDA BAY TRANSITIONAL ZONE.

    Lewis, Michael A., Larry R. Goodman, John M. Macauley and James C. Moore. 2004. Sediment Toxicity and Community Composition of Benthos and Colonized Periphyton in the Everglades-Florida Bay Transitional Zone. Ecotoxicology. 13(3):231-244. (ERL,GB 1164). This survey provid...

  6. Evidences of intraplate deformation in the West Madeira Abyssal Plain (eastern North Atlantic) from seismic reflection and multibeam swath bathymetry data

    Roque, C.; Simões, M.; Lourenço, N.; Pinto de Abreu, M.

    2009-04-01

    The West Madeira Abyssal Plain is located in the eastern North Atlantic off Madeira Islands, forming part of the Canary Basin and reaching a mean water depth of 5300 m. This region is also located within Africa plate at about 500 km southwards from the Açores-Gibraltar plate boundary, and for that reason lacks seismic activity. Although this region being located in an intraplate setting, the presence of faulted sediments was reported in several works published during the eighties of last century following a study conducted in late 1970s to evaluate the feasibility of disposal of high-level radioactive wastes in the ocean. According these works, the Madeira Abyssal Plain sediments are cut by many normal growth faults and this deformation is a result of compaction and dewatering of the sediments. Evidences of tectonic deformation of oceanic sediments in intraplate settings are uncommon, but folded sediments and reverse faults extending into the basement, were recognized in the equatorial Indian Ocean and in the West African continental margin. Recently, during 2006 multi-channel seismic reflection and multibeam swath bathymetry surveys were carried out in the West Madeira Abyssal Plain by EMEPC in order to prepare the Portuguese proposal for the extension of the continental shelf. The seismic lines were acquired onboard R/V Akademik Shatskiy using a source of 5720 cu in bolt gun array, cable length of 7950 m and shot interval of 50.00 m. The multibeam swath bathymetry was acquired onboard NRP Gago Coutinho, and allowed a high resolution mapping of the main geomorphological features. The multichannel seismic lines, oriented WNW-ESE, image the Madeira island lower slope located at about 4000 m water depth and the almost flat abyssal plain at about 5300 m water depth. These seismic lines show a thick sedimentary succession that reaches a maximum thickness of about 1.5 sec twt in the deepest parts of the West Madeira Abyssal Plain, overlying an irregular diffractive

  7. Suspended particulate studies over the Madeira Abyssal Plain

    Various aspects relating to suspended matter over the Madeira Abyssal Plain are discussed. Special attention is paid to the nepheloid layer including resuspension and transport processes; time variabilities in particle concentrations and fluxes; particle morphology, microbiology and chemical composition; phase association of metals. Also, tentative predictions of the behaviour of some radionuclides are made based on theory and data on rare earth elements. Instrumentation developed for the project is detailed - the deep water particle sampler. (author)

  8. Structural and functional diversity of microbial communities from a lake sediment contaminated with trenbolone, an endocrine-disrupting chemical

    Effects of trenbolone (TBOH), a hormone used in cattle production, on the structure and function of microbial communities in a fresh water sediment from a lake in Southern Germany were studied in a microcosm experiment. The microbial community structure and the total gene pool of the sediment, assessed by 16S rRNA/rDNA and RAPD fingerprint analysis, respectively, were not significantly affected by TBOH. In contrast, the N-acetyl-glucosaminidase activity was almost 50% lower in TBOH treated samples (P<0.05). Also, the substrate utilization potential, measured using the BIOLOG[reg] system, was reduced after TBOH treatment. Interestingly, this potential did not recover at the end of the experiment, i.e. 19 days after the addition of the chemical. Repeated application of TBOH did not lead to an additional reduction in the substrate utilization potential. Overall results indicate that microbial community function was more sensitive to TBOH treatment than the community structure and the total gene pool. - The steroid hormone trenbolone affects microbial community function in a lake sediment

  9. Chronic Polyaromatic Hydrocarbon (PAH) Contamination Is a Marginal Driver for Community Diversity and Prokaryotic Predicted Functioning in Coastal Sediments.

    Jeanbille, Mathilde; Gury, Jérôme; Duran, Robert; Tronczynski, Jacek; Ghiglione, Jean-François; Agogué, Hélène; Saïd, Olfa Ben; Taïb, Najwa; Debroas, Didier; Garnier, Cédric; Auguet, Jean-Christophe

    2016-01-01

    Benthic microorganisms are key players in the recycling of organic matter and recalcitrant compounds such as polyaromatic hydrocarbons (PAHs) in coastal sediments. Despite their ecological importance, the response of microbial communities to chronic PAH pollution, one of the major threats to coastal ecosystems, has received very little attention. In one of the largest surveys performed so far on coastal sediments, the diversity and composition of microbial communities inhabiting both chronically contaminated and non-contaminated coastal sediments were investigated using high-throughput sequencing on the 18S and 16S rRNA genes. Prokaryotic alpha-diversity showed significant association with salinity, temperature, and organic carbon content. The effect of particle size distribution was strong on eukaryotic diversity. Similarly to alpha-diversity, beta-diversity patterns were strongly influenced by the environmental filter, while PAHs had no influence on the prokaryotic community structure and a weak impact on the eukaryotic community structure at the continental scale. However, at the regional scale, PAHs became the main driver shaping the structure of bacterial and eukaryotic communities. These patterns were not found for PICRUSt predicted prokaryotic functions, thus indicating some degree of functional redundancy. Eukaryotes presented a greater potential for their use as PAH contamination biomarkers, owing to their stronger response at both regional and continental scales. PMID:27594854

  10. Chronic Polyaromatic Hydrocarbon (PAH) Contamination Is a Marginal Driver for Community Diversity and Prokaryotic Predicted Functioning in Coastal Sediments

    Jeanbille, Mathilde; Gury, Jérôme; Duran, Robert; Tronczynski, Jacek; Ghiglione, Jean-François; Agogué, Hélène; Saïd, Olfa Ben; Taïb, Najwa; Debroas, Didier; Garnier, Cédric; Auguet, Jean-Christophe

    2016-01-01

    Benthic microorganisms are key players in the recycling of organic matter and recalcitrant compounds such as polyaromatic hydrocarbons (PAHs) in coastal sediments. Despite their ecological importance, the response of microbial communities to chronic PAH pollution, one of the major threats to coastal ecosystems, has received very little attention. In one of the largest surveys performed so far on coastal sediments, the diversity and composition of microbial communities inhabiting both chronically contaminated and non-contaminated coastal sediments were investigated using high-throughput sequencing on the 18S and 16S rRNA genes. Prokaryotic alpha-diversity showed significant association with salinity, temperature, and organic carbon content. The effect of particle size distribution was strong on eukaryotic diversity. Similarly to alpha-diversity, beta-diversity patterns were strongly influenced by the environmental filter, while PAHs had no influence on the prokaryotic community structure and a weak impact on the eukaryotic community structure at the continental scale. However, at the regional scale, PAHs became the main driver shaping the structure of bacterial and eukaryotic communities. These patterns were not found for PICRUSt predicted prokaryotic functions, thus indicating some degree of functional redundancy. Eukaryotes presented a greater potential for their use as PAH contamination biomarkers, owing to their stronger response at both regional and continental scales.

  11. Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial community

    Handley, KM [University of California, Berkeley; Verberkmoes, Nathan C [ORNL; Steefel, Carl I [Lawrence Berkeley National Laboratory (LBNL); Sharon, I [University of California, Berkeley; Williams, Ken [Lawrence Berkeley National Laboratory (LBNL); Miller, CS [University of California, Berkeley; Frischkorn, Kyle C [University of California, Berkeley; Chourey, Karuna [ORNL; Thomas, Brian [University of California, Berkeley; Shah, Manesh B [ORNL; Long, Phil [Pacific Northwest National Laboratory (PNNL); Hettich, Robert {Bob} L [ORNL; Banfield, Jillian F. [University of California, Berkeley

    2013-01-01

    Stimulation of subsurface microorganisms to induce reductive immobilization of metals is a promising approach for bioremediation, yet the overall microbial community response is typically poorly understood. Here we used community proteogenomics to test the hypothesis that excess input of acetate activates syntrophic interactions among autotrophs and heterotrophs. A flow-through sediment column was incubated in a groundwater well of an acetate-amended aquifer. Genomic sequences from the community recovered during microbial sulfate reduction were used to econstruct, de novo, near-complete genomes for Desulfobacter (Deltaproteobacteria) and relatives of Sulfurovum and Sulfurimonas (Epsilonproteobacteria), and Bacteroidetes. Partial genomes were obtained for Clostridiales (Firmicutes) and Desulfuromonadales-like Deltaproteobacteria. The majority of proteins identified by mass spectrometry corresponded to Desulfobacter-like species, and demonstrate the role of this organism in sulfate reduction (Dsr and APS), nitrogen-fixation (Nif) and acetate oxidation to CO2 during amendment. Results suggest less abundant Desulfuromonadales and Bacteroidetes also actively contributed to CO2 production via the TCA cycle. Proteomic data indicate that sulfide was partially re-oxidized by Epsilonproteobacteria through nitrate-dependent sulfide oxidation (using Nap, Nir, Nos, SQR and Sox), with CO2 fixed using the reverse TCA cycle. Modeling shows that this reaction was thermodynamically possible, and kinetically favorable relative to acetate-dependent denitrification. We conclude that high-levels of carbon amendment aimed to stimulate anaerobic heterotrophy led to carbon fixation in co-dependent chemoautotrophs. These results have implications for understanding complex ecosystem behavior, and show that high levels of organic carbon supplementation can expand the range of microbial functionalities accessible for ecosystem manipulation.

  12. Genetic assessment of meiobenthic community composition and spatial distribution in coastal sediments along northern Gulf of Mexico.

    Brannock, Pamela M; Wang, Lei; Ortmann, Alice C; Waits, Damien S; Halanych, Kenneth M

    2016-08-01

    Meiobenthic (meiofauna and micro-eukaryotes) organisms are important contributors to ecosystem functioning in aquatic environments through their roles in nutrient transport, sediment stability, and food web interactions. Despite their ecological importance, information pertaining to variation of these communities at various spatial and temporal scales is not widely known. Many studies in the Gulf of Mexico (GOM) have focused either on deep sea or continental shelf areas, while little attention has been paid to bays and coastal regions. Herein, we take a holistic approach by using high-throughput sequencing approaches to examine spatial variation in meiobenthic communities within Alabama bays and the coastal northern GOM region. Sediment samples were collected along three transects (Mississippi Sound: MS, FOCAL: FT, and Orange Beach: OB) from September 2010 to April 2012 and community composition was determined by metabarcoding the V9 hypervariable region of the nuclear18S rRNA gene. Results showed that Stramenopiles (diatoms), annelids, arthropods (copepods), and nematodes were the dominate groups within samples, while there was presence of other phyla throughout the dataset. Location played a larger role than time sampled in community composition. However, samples were collected over a short temporal scale. Samples clustered in reference to transect, with the most eastern transect (OB) having a distinct community composition in comparison to the other two transects (MS and FT). Communities also differed in reference to region (Bay versus Shelf). Bulk density and percent inorganic carbon were the only measured environmental factors that were correlated with community composition. PMID:27299291

  13. Heat flow measurements in the vicinity of Great Meteor East, Madeira Abyssal Plain, during Darwin Cruise CD9B

    This report describes 37 new measurements of heat flow in the Madeira Abyssal Plain. These have comprised 22 values in the Great Meteor East Study Area and 15 measurements in the newly defined ''10 km Box'' to the southeast of this region. The aim of the project has been to examine in more detail than hitherto the thermal and fluid processes operating in the oceanic crust. For this purpose, a new thermistor string, with 1/2 m sensor spacing was used. Also, the heat flux data have been compared to the output from a finite element model for heat conduction. No non-linear sediment temperature profiles were discovered indicating that vertical advection of water through the sediment is absent or slow. The results of numerical modelling imply that the variability of measured heat flow cannot be explained entirely on the basis of basement topography. It is necessary to invoke either vertical basement intrusions of differing conductivity or basement hydrothermal circulation. (author)

  14. Microbial community in the potential gas hydrate area Kaoping Canyon bearing sediment at offshore SW Taiwan

    Wu, S. Y.; Hung, C. C.; Lai, S. J.; Ding, J. Y.; Lai, M. C.

    2015-12-01

    The deep sub-seafloor biosphere is among the least-understood habitats on Earth, even though the huge microbial biomass plays a potentially important role in long-term controls of global biogeochemical cycles. The research team from Taiwan, supported by the Central Geological Survey (CGS), has been demonstrated at SW offshore Taiwan that indicated this area is potential gas hydrate region. Therefore, the Gas Hydrate Master Program (GHMP) was brought in the National Energy Program-Phase II (NEP-II) to continue research and development. In this study, the microbial community structure of potential gas hydrate bearing sediments of giant piston core MD-178-10-3291 (KP12N) from the Kaoping Canyon offshore SW of Taiwan were investigated. This core was found many empty spaces and filling huge methane gas (>99.9 %) that might dissociate from solid gas hydrate. 16S rRNA gene clone libraries and phylogenetic analysis showed that the dominant members of Archaea were ANME (13 %), SAGMEG (31 %) and DSAG (20 %), and those of Bacteria were Chloroflexi (13 %), Candidate division JS1 (40 %) and Planctomycetes (15 %). Among them, ANME-3 is only distributed at the sulfate-methane interface (SMI) of 750 cmbsf, and sharing similarity with the Hydrate Ridge clone HydBeg92. ANME-1 and SAGMEG distributed below 750 cmbsf. In addition, DSAG and Candidate division JS1 are most dominant and distributed vertically at all tested depths from 150-3600 cmbsf. Combine the geochemical data and microbial phylotype distribution suggests the potential of gas hydrate bearing sediments at core MD-178-10-3291 (KP12N) from the Kaoping Canyon offshore SW of Taiwan.

  15. Molecular screening of microbial communities for candidate indicators of multiple metal impacts in marine sediments from northern Australia.

    Cornall, Alyssa; Rose, Alea; Streten, Claire; McGuinness, Keith; Parry, David; Gibb, Karen

    2016-02-01

    Coastal sediments accumulate metals from anthropogenic sources and as a consequence industry is required to monitor sediment health. The total concentration of a metal does not necessarily reflect its potential toxicity or biological impact, so biological assessment tools are useful for monitoring. Rapid biological assessment tools sensitive enough to detect relatively small increases in metal concentrations would provide early warning of future ecosystem impact. The authors investigated in situ populations of Archaea and Bacteria as potential tools for rapid biological assessment in sediment at 4 northern Australian coastal locations over 2 yr, in both wet and dry seasons. The 1 M HCl-extractable concentrations of metals in sediment were measured, and Archaeal and Bacterial community profiles were obtained by next-generation sequencing of sediment deoxyribonucleic acid (DNA). Species response curves were used to identify several taxonomic groups with potential as biological indicators of metal impact. Spatial variation, sediment grain size, water depth, and dissolved oxygen also correlated with microbial population shifts. Seasonal variation was less important than geographic location. Metal-challenge culture trials supported the identification of metal-resistant and -sensitive taxa. In situ Archaea and Bacteria are potentially sensitive indicators for changes in bioavailable concentrations of metals; however, the complexity of the system suggests it is important to identify metal-specific functional genes that may be informed by these sequencing surveys, and thus provide a useful addition to identity-based assays. Environ Toxicol Chem 2016;35:468-484. © 2015 SETAC. PMID:26274631

  16. Examination of abyssal sea floor and near-bottom water mixing processes using Ra-226 and Rn-222

    Since Broecker's (1965) original work, extensive studies have been made on abyssal near-bottom water-mixing processes using the radioactive parent-daughter pair radium-226 (Ra) - radon-222 (Rn). One assumption critical to all of these studies is that sediments immediately under a given water column are the source of excess radon (=Rn concentration - Ra concentration) found in bottom waters. Since 1965 theoretical works of increasing complexity have tried to explain areal variations of excess radon and radium. However, Key et al. (1979b) have reported the only extensive measurements of radium and radon in bottom water and sediments at the same location. This dissertation is an expansion of that work both in theory and in scope. A diagenetic sediment model based on the work of Schink and Guinasso (1978), Cochran (1979), and Key et al. (1979b) was developed to model Ra-Rn in near-surface abyssal sediments. In order to maximize model application information, the degrees of freedom were minimized by measuring as many of the model parameters as possible. The most glaring discrepancy found was that measured near-surface total radium profiles could not be fit using plutonium-derived bioturbation rates. There is an implication that plutonium profiles modeled with currently accepted bioturbation models do not give a true indication of the real biologically induced mixing process. After adjusting for this problem in the source function, diagenetic theory explains near-surface radon-distributions adequately. Using both the adjusted diagenetic model and the empirical model developed by Key et al. (1979b), reasonable agreement was found between the sedimentary radon deficit and near-bottom water surplus. Inadequacy of present diagenetic theory makes any attempt to differentiate sedimentary radium sources academic

  17. Coral community structure and sedimentation at different distances from the coast of the Abrolhos Bank, Brazil

    Bárbara Segal; Clovis B. Castro

    2011-01-01

    Sedimentation has previously been considered an important source of impact in coral reefs. We compared 3 sites on the Abrolhos Bank, Brazil, regarding sedimentation rates, carbonate sediment composition, coral cover, and colony size for the commonest local coral species (Mussismilia braziliensis, Siderastrea stellata, and Favia gravida). The sites are located at different distances from the mainland: Pedra de Leste (14 km), Pontas Sul (26 km), and Parcel dos Abrolhos (58 km). Sedimentation wa...

  18. Inter-annual species-level variations in an abyssal polychaete assemblage (Sta. M, NE Pacific, 4000 m)

    Laguionie-Marchais, Claire; Paterson, Gordon L. J.; Bett, Brian J.; Smith, Kenneth L.; Ruhl, Henry A.

    2016-01-01

    Understanding the dynamics of abyssal community structure and function has become increasingly important as deep-sea resource exploitation and climate change pressures are expected to ramp up. This time-series study investigates macrofaunal polychaete dynamics at a station in the North East Pacific (Sta. M; 35° N 123° W, 4000 m, 1991-2011). Infaunal polychaete species were identified and their proxy biomass and proxy energy use rate estimated. The assemblage comprised 167 species, having a composition consistent with other abyssal areas globally. Significant changes in univariate and multivariate parameters (rank abundance distribution, Simpson's diversity index, and species and functional group composition) were detected across 1991-2011. However, no change in biomass or energy use rate was apparent through the time-series. The largest changes in the polychaete assemblage coincided with both an increase in sinking particulate organic carbon flux to the seafloor in 2007, and a 40 km relocation of the sampling location to a site 100 m shallower, preventing a conclusive assessment of which might drive the observed variation. Analyses prior to the change of sampling location showed that the polychaete assemblage composition dynamics were primary driven by food supply variation. Changes in several species were also lagged to changes in POC flux by 4-10 months. The polychaete fauna exhibited a significant positive relationship between total density and total energy use rate, suggesting population-level tracking of a common resource (e.g. POC flux food supply). Neither compensatory nor energetic zero-sum dynamics were detected among the polychaete assemblage, but the results suggest that the latter occur in the macrofaunal community as a whole. The results do indicate (a) potential control of species composition, and the density of individual key species, by food supply, when the time-series prior to the sampling location was analysed separately, and (b) generally

  19. Effects of the antibiotic ciprofloxacin on the bacterial community structure and degradation of pyrene in marine sediment

    Naeslund, Johan [Department of Systems Ecology, Stockholm University, 106 91 Stockholm (Sweden)], E-mail: johan@ecology.su.se; Hedman, Jenny E.; Agestrand, Cecilia [Department of Systems Ecology, Stockholm University, 106 91 Stockholm (Sweden)

    2008-11-21

    The ecological consequences of antibiotics in the aquatic environment have been an issue of concern over the past years due to the potential risk for negative effects on indigenous microorganisms. Microorganisms provide important ecosystem services, such as nutrient recycling, organic matter mineralization and degradation of pollutants. In this study, effects of exposure to the antibiotic ciprofloxacin on the bacterial diversity and pollutant degradation in natural marine sediments were studied using molecular methods (T-RFLP) in combination with radiorespirometry. In a microcosm experiment, sediment spiked with {sup 14}C-labelled pyrene was exposed to five concentrations of ciprofloxacin (0, 20, 200, 1000 and 2000 {mu}g L{sup -1}) in a single dose to the overlying water. The production of {sup 14}CO{sub 2} (i.e. complete mineralization of pyrene) was measured during 11 weeks. Sediment samples for bacterial community structure analysis were taken after 7 weeks. Results showed a significant dose-dependent inhibition of pyrene mineralization measured as the total {sup 14}CO{sub 2} production. The nominal EC{sub 50} was calculated to 560 {mu}g L{sup -1}, corresponding to 0.4 {mu}g/kg d.w. sediment. The lowest effect concentration on the bacterial community structure was 200 {mu}g L{sup -1}, which corresponds to 0.1 {mu}g/kg d.w. sediment. Our results show that antibiotic pollution can be a potential threat to both bacterial diversity and an essential ecosystem service they perform in marine sediment.

  20. The effect of human settlement on the abundance and community structure of ammonia oxidizers in tropical stream sediments

    Reis, Mariana P.; Ávila, Marcelo P.; Keijzer, Rosalinde M.; Barbosa, Francisco A. R.; Chartone-Souza, Edmar; Nascimento, Andréa M. A.; Laanbroek, Hendrikus J.

    2015-01-01

    Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are a diverse and functionally important group in the nitrogen cycle. Nevertheless, AOA and AOB communities driving this process remain uncharacterized in tropical freshwater sediment. Here, the effect of human settlement on the AOA and AOB diversity and abundance have been assessed by phylogenetic and quantitative PCR analyses, using archaeal and bacterial amoA and 16S rRNA genes. Overall, each environment contained specific clades of amoA and 16S rRNA genes sequences, suggesting that selective pressures lead to AOA and AOB inhabiting distinct ecological niches. Human settlement activities, as derived from increased metal and mineral nitrogen contents, appear to cause a response among the AOB community, with Nitrosomonas taking advantage over Nitrosospira in impacted environments. We also observed a dominance of AOB over AOA in mining-impacted sediments, suggesting that AOB might be the primary drivers of ammonia oxidation in these sediments. In addition, ammonia concentrations demonstrated to be the driver for the abundance of AOA, with an inversely proportional correlation between them. Our findings also revealed the presence of novel ecotypes of Thaumarchaeota, such as those related to the obligate acidophilic Nitrosotalea devanaterra at ammonia-rich places of circumneutral pH. These data add significant new information regarding AOA and AOB from tropical freshwater sediments, albeit future studies would be required to provide additional insights into the niche differentiation among these microorganisms. PMID:26379659

  1. Human settlement as driver of bacterial, but not of archaeal, ammonia oxidizers abundance and community structure in tropical stream sediments

    Mariana De Paula Reis

    2015-08-01

    Full Text Available Ammonia-oxidizing archaea (AOA and bacteria (AOB are a diverse and functionally important group in the nitrogen cycle. Nevertheless, AOA and AOB communities driving this process remain uncharacterized in tropical freshwater sediment. Here, the effect of human settlement on the AOA and AOB diversity and abundance have been assessed by phylogenetic and quantitative PCR analyses, using archaeal and bacterial amoA and 16S rRNA genes. Overall, each environment contained specific clades of amoA and 16S rRNA genes sequences, suggesting that selective pressures lead to AOA and AOB inhabiting distinct ecological niches. Human settlement activities, as derived from increased metal and mineral nitrogen contents, appear to cause a response among the AOB community, with Nitrosomonas taking advantage over Nitrosospira in impacted environments. We also observed a dominance of AOB over AOA in mining-impacted sediments, suggesting that AOB might be the primary drivers of ammonia oxidation in these sediments. In addition, ammonia concentrations demonstrated to be the driver for the abundance of AOA, with an inversely proportional correlation between them. Our findings also revealed the presence of novel ecotypes of Thaumarchaeota, such as those related to the obligate acidophilic Nitrosotalea devanaterra at ammonia-rich places of circumneutral pH. These data add significant new information regarding AOA and AOB from tropical freshwater sediments, albeit future studies would be required to provide additional insights into the niche differentiation among these microorganisms.

  2. Anaerobic biodegradation of nonylphenol in river sediment under nitrate- or sulfate-reducing conditions and associated bacterial community

    Highlights: • NP biodegradation can occur under both nitrate- and sulfate-reducing conditions. • Anaerobic condition affects sediment bacterial diversity during NP biodegradation. • NP-degrading bacterial community structure varies under different anaerobic conditions. - Abstract: Nonylphenol (NP) is a commonly detected pollutant in aquatic ecosystem and can be harmful to aquatic organisms. Anaerobic degradation is of great importance for the clean-up of NP in sediment. However, information on anaerobic NP biodegradation in the environment is still very limited. The present study investigated the shift in bacterial community structure associated with NP degradation in river sediment microcosms under nitrate- or sulfate-reducing conditions. Nearly 80% of NP (100 mg kg−1) could be removed under these two anaerobic conditions after 90 or 110 days’ incubation. Illumina MiSeq sequencing analysis indicated that Proteobacteria, Firmicutes, Bacteroidetes and Chloroflexi became the dominant phylum groups with NP biodegradation. The proportion of Gammaproteobacteria, Deltaproteobacteria and Choloroflexi showed a marked increase in nitrate-reducing microcosm, while Gammaproteobacteria and Firmicutes in sulfate-reducing microcosm. Moreover, sediment bacterial diversity changed with NP biodegradation, which was dependent on type of electron acceptor

  3. Community Response to a Heavy Precipitation Event in High Temperature, Chemosynthetic Biofilms and Sediments

    Meyer-Dombard, D. R.; Loiacono, S. T.; Shock, E.

    2012-12-01

    Coordinated analysis of the "Bison Pool" (BP) Environmental Genome and a complementary contextual geochemical dataset of ~75 parameters revealed biogeochemical cycling and metabolic and microbial community shifts in a Yellowstone National Park hot spring ecosystem (1). The >22m outflow of BP is a gradient of decreasing temperature, increasing dissolved oxygen, and changing availability of nutrients. Microbial life at BP transitions from a 92°C chemosynthetic community in the BP source pool to a 56°C photosynthetic mat community. Metagenomic data at BP showed the potential for both heterotrophic and autotrophic carbon metabolism (rTCA and acetyl-CoA cycles) in the highest temperature, chemosynthetic regions (1). This region of the outflow is dominated by Aquificales and Pyrococcus relatives, with smaller contributions of heterotrophic Bacteria. Following a 2h heavy precipitation event we observed an influx of exogenous organic material into the source pool supplied from the meadow surrounding the BP area. We sampled biomass and fluid at several locations within the outflow immediately following the event, and on several occasions for the next eight days. Elemental analysis and carbon and nitrogen isotopic analyses were conducted on biomass and sediment, and dissolved organic and inorganic carbon content and δ13C of fluids were analyzed. DNA and RNA were extracted, and following RT-PCR, nitrogen cycle functional gene expression was evaluated. Previous work at BP has shown that chemosynthetic biomass may carry isotopic signatures of fractionation during carbon fixation, via the acetyl-CoA and rTCA cycles (2). However, the addition of exogenous organic carbon during the rain event had an immediate and dramatic effect on the sediments and biofilms in the chemosynthetic zone of the outflow. Dissolved organic carbon was the highest measured in six years. Chemosynthetic biomass responded by incorporating the organic carbon. Carbon isotopic signatures in chemosynthetic

  4. Clay mineral distribution in surface sediments of the South Atlantic: sources, transport, and relation to oceanography

    Petschick, Rainer; Kuhn, Gerhard; Gingele, Franz

    1996-01-01

    Surface samples, mostly from abyssal sediments of the South Atlantic, from parts of the equatorial Atlantic, and of the Antarctic Ocean, were investigated for clay content and clay mineral composition. Maps of relative clay mineral content were compiled, which improve previous maps by showing more details, especially at high latitudes. Large-scale relations regarding the origin and transport paths of detrital clay are revealed. High smectite concentrations are observed in abyssal regions, pri...

  5. Microhabitat use and multivariate pattern of motile epifaunal community in relation to sediment grain size in a tropical seagrass meadow

    PENAGOS GUILLERMO; PALACIO JAIME; AGUIRRE NÉSTOR

    2010-01-01

    The relationship between habitat physical structure and motile epifauna community associated to a Seagrass bed dominated by Thalassia testudinum was study over the isobaths of 1 and 3 m, in terms of species diversity, organisms density, micro habitat use and multivariate species pattern in association with Seagrass biomass, shoot and leaf density, leaves long and wide, epiphytic and rizophytic algae biomass, sponges biomass and sediment grain size. Seagrass features showed significant differ...

  6. Responses of bacterial and archaeal communities to nitrate stimulation after oil pollution in mangrove sediment revealed by Illumina sequencing.

    Wang, Lei; Huang, Xu; Zheng, Tian-Ling

    2016-08-15

    This study aimed to investigate microbial responses to nitrate stimulation in oiled mangrove mesocosm. Both supplementary oil and nitrate changed the water and sediment chemical properties contributing to the shift of microbial communities. Denitrifying genes nirS and nirK were increased several times by the interaction of oil spiking and nitrate addition. Bacterial chao1 was reduced by oil spiking and further by nitrate stimulation, whereas archaeal chao1 was only inhibited by oil pollution on early time. Sampling depth explained most of variation and significantly impacted bacterial and archaeal communities, while oil pollution only significantly impacted bacterial communities (pexplaining less variation, nitrate addition coupled with oil spiking enhanced the growth of hydrocarbon degraders in mangrove. The findings demonstrate the impacts of environmental factors and their interactions in shaping microbial communities during nitrate stimulation. Our study suggests introducing genera Desulfotignum and Marinobacter into oiled mangrove for bioaugmentation. PMID:27262497

  7. Molecular characterization of sulfate-reducing bacteria community in surface sediments from the adjacent area of Changjiang Estuary

    Zhang, Yu; Zhen, Yu; Mi, Tiezhu; He, Hui; Yu, Zhigang

    2016-02-01

    Sulfate-reducing bacteria (SRB), which obtain energy from dissimilatory sulfate reduction, play a vital role in the carbon and sulfur cycles. The dissimilatory sulfite reductase (Dsr), catalyzing the last step in the sulfate reduction pathway, has been found in all known SRB that have been tested so far. In this study, the diversity of SRB was investigated in the surface sediments from the adjacent area of Changjiang Estuary by PCR amplification, cloning and sequencing of the dissimilatory sulfite reductase beta subunit gene ( dsrB). Based on dsrB clone libraries constructed in this study, diversified SRB were found, represented by 173 unique OTUs. Certain cloned sequences were associated with Desulfobacteraceae, Desulfobulbaceae, and a large fraction (60%) of novel sequences that have deeply branched groups in the dsrB tree, indicating that novel SRB inhabit the surface sediments. In addition, correlations of the SRB assemblages with environmental factors were analyzed by the linear model-based redundancy analysis (RDA). The result revealed that temperature, salinity and the content of TOC were most closely correlated with the SRB communities. More information on SRB community was obtained by applying the utility of UniFrac to published dsrB gene sequences from this study and other 9 different kinds of marine environments. The results demonstrated that there were highly similar SRB genotypes in the marine and estuarine sediments, and that geographic positions and environmental factors influenced the SRB community distribution.

  8. Bacterial and archaeal communities in the deep-sea sediments of inactive hydrothermal vents in the Southwest India Ridge.

    Zhang, Likui; Kang, Manyu; Xu, Jiajun; Xu, Jian; Shuai, Yinjie; Zhou, Xiaojian; Yang, Zhihui; Ma, Kesen

    2016-01-01

    Active deep-sea hydrothermal vents harbor abundant thermophilic and hyperthermophilic microorganisms. However, microbial communities in inactive hydrothermal vents have not been well documented. Here, we investigated bacterial and archaeal communities in the two deep-sea sediments (named as TVG4 and TVG11) collected from inactive hydrothermal vents in the Southwest India Ridge using the high-throughput sequencing technology of Illumina MiSeq2500 platform. Based on the V4 region of 16S rRNA gene, sequence analysis showed that bacterial communities in the two samples were dominated by Proteobacteria, followed by Bacteroidetes, Actinobacteria and Firmicutes. Furthermore, archaeal communities in the two samples were dominated by Thaumarchaeota and Euryarchaeota. Comparative analysis showed that (i) TVG4 displayed the higher bacterial richness and lower archaeal richness than TVG11; (ii) the two samples had more divergence in archaeal communities than bacterial communities. Bacteria and archaea that are potentially associated with nitrogen, sulfur metal and methane cycling were detected in the two samples. Overall, we first provided a comparative picture of bacterial and archaeal communities and revealed their potentially ecological roles in the deep-sea environments of inactive hydrothermal vents in the Southwest Indian Ridge, augmenting microbial communities in inactive hydrothermal vents. PMID:27169490

  9. Geothermal heating, diapycnal mixing and the abyssal circulation

    J. Emile-Geay; Madec, G.

    2009-01-01

    The dynamical role of geothermal heating in abyssal circulation is reconsidered using three independent arguments. First, we show that a uniform geothermal heat flux close to the observed average (86.4 mW m−2) supplies as much heat to near-bottom water as a diapycnal mixing rate of ~10−4 m2 s−1 – the canonical value thought to be responsible for the magnitude of the presen...

  10. Arsenic release from shallow aquifers of the Hetao Basin, Inner Mongolia: Evidence from bacterial community in aquifer sediments and groundwater

    Li, Y.; Guo, H.

    2013-12-01

    Indigenous microbes play crucial roles in arsenic mobilization in high arsenic groundwater systems. Databases concerning the presence and the activity of microbial communities are very useful in evaluating the potential of microbe-mediated arsenic mobilization in shallow aquifers hosting high arsenic groundwater. This study characterized microbial communities in groundwaters at different depths with different arsenic concentrations by DGGE and one sediment by 16S rDNA gene clone library, and evaluated arsenic mobilization in microcosm batches with the presence of indigenous bacteria. DGGE fingerprints revealed that the community structure changed substantially with depth at the same location. It indicated that a relatively higher bacterial diversity was present in the groundwater sample with lower arsenic concentration. The clone library of sediment sample 2009M1 and DGGE profiles of microbial community structures of groundwater samples indicated NO3-, Fe(III) and SO42- reducing bacteria are abundant in the As-affected aquifer, which are facultative or anaerobic chemoautotrophic bacteria. Pseudomonas that was rich in both high arsenic groundwater and sediment included a great number of denitrifying bacterium strains that may contribute to the low concentration of nitrate in the groundwater. Fe(III)-reducing bacteria belonging to different species, such as Aquabacterium sp., Thauera sp., Georgfuchsia sp., Methyloversatilis sp., Clostridium sp., were widely found in the community. The genus Desulfosporosinus observed in the sediment sample of 2009M1 was believed to be sulfate reducer. These results offered direct evidences that anaerobic reducing bacteria play a role in the formation of toxic, mobile As(III) in the groundwater of the Hetao basin, especially Fe(III)-reducing bacteria. Incubation of sediments without the addition of organic carbon source showed a significant release of arsenic (predominantly as As(III)). By contrast, sterile incubations and incubations

  11. Community Proteogenomics of a Cold-methane Seep Sediment at Nyegga, Mid-Norwegian Margin

    Stokke, R.; Roalkvam, I.; Lanzen, A.; Chen, Y.; Haflidason, H.; Steen, I.

    2010-12-01

    Anaerobic oxidation of methane (AOM) is limited to anoxic environments and differs in its rates from a few pmol cm-3day-1 in subsurface SMTZ (sulfate-methane transition zone) of deep margins, to a few μmol cm-3 day-1 in surface sediments above gas hydrates [1]. This process is catalyzed by consortia of anaerobic methane oxidizing archaea (ANME) in association with sulfate-reducing bacteria. The Nyegga area is located on the Mid-Norwegian continental slope at the northern flank of the Storegga Slide at 700-800 mbsl. Hundreds of pockmarks are widespread on the seabed in Nyegga and sub-zero temperatures (-0.7 °C), and pingo-structures within the pockmarks are indicators of active fluid flow locations. Preliminary microbial and geochemical profiling of a 22 cm push-core within the G11 pockmark gave strong indications of an ANME-1 dominated community at 14-16 cmbsf. In light of these findings we submitted extracted DNA to 454-pyrosequencing. Sequencing data (829,527 reads) was assembled using the Newbler v2.3, resulting in 13,151 contigs (357,530 reads) over 500 bp with the longest contig being 24,521 bp. MEGAN taxonomic analysis supported the high abundance of Euryarchaea (70%) with 66% of the assembled metagenome belonging to ANME-1. In order to obtain functional information of the ANME-1 community, protein extraction protocols from sediment samples was established. Extracted proteins was separated on a large (18cm) 1D-SDS-PAGE and subsequently cut in 30 gel slices. Peptides extracted after In-gel tryptic digest was injected into an Ultimate 3000 nanoLC system connected to a linear quadropole ion trap-orbitrap (LTQ-Orbitrap XL) mass spectrometer equipped with a nanoelectrospray ion source. A custom database of open reading frames (ORFs) from the metagenome including known contaminants such as trypsin and human keratin was search against using Mascot 2.2. IRMa tool box [2] was used in peptide validation and peptides whose score >= 25.0 (i.e avg identity, pprotein

  12. pmoA-based analysis of methanotrophs in a littoral lake sediment reveals a diverse and stable community in a dynamic environment

    Pester, Michael; Friedrich, Michael W.; Schink, Bernhard; Brune, Andreas

    2004-01-01

    Diversity and community structure of aerobic methane-oxidizing bacteria in the littoral sediment of Lake Constance was investigated by cloning analysis and terminal restriction fragment length polymorphism (T-RFLP) fingerprinting of the pmoA gene. Phylogenetic analysis revealed a high diversity of type I and type II methanotrophs in the oxygenated uppermost centimeter of the sediment. T-RFLP profiles indicated a high similarity between the active methanotrophic community in the oxic layer and...

  13. Chemoautotrophic Carbon Fixation Rates and Active Bacterial Communities in Intertidal Marine Sediments

    Boschker, H.T.S.; Vasquez-Cardenas, D.; Bolhuis, H.; Moerdijk-Poortvliet, T.C.W.; Moodley, L.

    2014-01-01

    Chemoautotrophy has been little studied in typical coastal marine sediments, but may be an important component ofcarbon recycling as intense anaerobic mineralization processes in these sediments lead to accumulation of high amounts ofreduced compounds, such as sulfides and ammonium. We studied chemo

  14. Temperature response of denitrification and anaerobic ammonium oxidation rates and microbial community structure in Arctic fjord sediments.

    Canion, Andy; Overholt, Will A; Kostka, Joel E; Huettel, Markus; Lavik, Gaute; Kuypers, Marcel M M

    2014-10-01

    The temperature dependency of denitrification and anaerobic ammonium oxidation (anammox) rates from Arctic fjord sediments was investigated in a temperature gradient block incubator for temperatures ranging from -1 to 40°C. Community structure in intact sediments and slurry incubations was determined using Illumina SSU rRNA gene sequencing. The optimal temperature (Topt ) for denitrification was 25-27°C, whereas anammox rates were optimal at 12-17°C. Both denitrification and anammox exhibited temperature responses consistent with a psychrophilic community, but anammox bacteria may be more specialized for psychrophilic activity. Long-term (1-2 months) warming experiments indicated that temperature increases of 5-10°C above in situ had little effect on the microbial community structure or the temperature response of denitrification and anammox. Increases of 25°C shifted denitrification temperature responses to mesophilic with concurrent community shifts, and anammox activity was eliminated above 25°C. Additions of low molecular weight organic substrates (acetate and lactate) caused increases in denitrification rates, corroborating the hypothesis that the supply of organic substrates is a more dominant control of respiration rates than low temperature. These results suggest that climate-related changes in sinking particulate flux will likely alter rates of N removal more rapidly than warming. PMID:25115991

  15. Variability of Symbiodinium Communities in Waters, Sediments, and Corals of Thermally Distinct Reef Pools in American Samoa.

    Ross Cunning

    Full Text Available Reef-building corals host assemblages of symbiotic algae (Symbiodinium spp. whose diversity and abundance may fluctuate under different conditions, potentially facilitating acclimatization to environmental change. The composition of free-living Symbiodinium in reef waters and sediments may also be environmentally labile and may influence symbiotic assemblages by mediating supply and dispersal. The magnitude and spatial scales of environmental influence over Symbiodinium composition in different reef habitat compartments are, however, not well understood. We used pyrosequencing to compare Symbiodinium in sediments, water, and ten coral species between two backreef pools in American Samoa with contrasting thermal environments. We found distinct compartmental assemblages of clades A, C, D, F, and/or G Symbiodinium types, with strong differences between pools in water, sediments, and two coral species. In the pool with higher and more variable temperatures, abundance of various clade A and C types differed compared to the other pool, while abundance of D types was lower in sediments but higher in water and in Pavona venosa, revealing an altered habitat distribution and potential linkages among compartments. The lack of between-pool effects in other coral species was due to either low overall variability (in the case of Porites or high within-pool variability. Symbiodinium communities in water and sediment also showed within-pool structure, indicating that environmental influences may operate over multiple, small spatial scales. This work suggests that Symbiodinium composition is highly labile in reef waters, sediments, and some corals, but the underlying drivers and functional consequences of this plasticity require further testing with high spatial resolution biological and environmental sampling.

  16. Variability of Symbiodinium Communities in Waters, Sediments, and Corals of Thermally Distinct Reef Pools in American Samoa

    Cunning, Ross; Yost, Denise M.; Guarinello, Marisa L.; Putnam, Hollie M.; Gates, Ruth D.

    2015-01-01

    Reef-building corals host assemblages of symbiotic algae (Symbiodinium spp.) whose diversity and abundance may fluctuate under different conditions, potentially facilitating acclimatization to environmental change. The composition of free-living Symbiodinium in reef waters and sediments may also be environmentally labile and may influence symbiotic assemblages by mediating supply and dispersal. The magnitude and spatial scales of environmental influence over Symbiodinium composition in different reef habitat compartments are, however, not well understood. We used pyrosequencing to compare Symbiodinium in sediments, water, and ten coral species between two backreef pools in American Samoa with contrasting thermal environments. We found distinct compartmental assemblages of clades A, C, D, F, and/or G Symbiodinium types, with strong differences between pools in water, sediments, and two coral species. In the pool with higher and more variable temperatures, abundance of various clade A and C types differed compared to the other pool, while abundance of D types was lower in sediments but higher in water and in Pavona venosa, revealing an altered habitat distribution and potential linkages among compartments. The lack of between-pool effects in other coral species was due to either low overall variability (in the case of Porites) or high within-pool variability. Symbiodinium communities in water and sediment also showed within-pool structure, indicating that environmental influences may operate over multiple, small spatial scales. This work suggests that Symbiodinium composition is highly labile in reef waters, sediments, and some corals, but the underlying drivers and functional consequences of this plasticity require further testing with high spatial resolution biological and environmental sampling. PMID:26713847

  17. An Integrated Assessment of Geochemical and Community Structure Determinants of Metal Reduction Rates in Subsurface Sediments. Final report

    The objective of this research was to examine the importance of microbial community structure in influencing uranium reduction rates in subsurface sediments. If the redox state alone is the key to metal reduction, then any organisms that can utilize the oxygen and nitrate in the subsurface can change the geochemical conditions so metal reduction becomes an energetically favored reaction. Thus, community structure would not be critical in determining rates or extent of metal reduction unless community structure influenced the rate of change in redox. Alternatively, some microbes may directly catalyze metal reduction (e.g., specifically reduce U). In this case the composition of the community may be more important and specific types of electron donors may promote the production of communities that are more adept at U reduction. Our results helped determine if the type of electron donor or the preexisting community is important in the bioremediation of metal-contaminated environments subjected to biostimulation. In a series of experiments at the DOE FRC site in Oak Ridge we have consistently shown that all substrates promoted nitrate reduction, while glucose, ethanol, and acetate always promoted U reduction. Methanol only occasionally promoted extensive U reduction which is possibly due to community heterogeneity. There appeared to be limitations imposed on the community related to some substrates (e.g. methanol and pyruvate). Membrane lipid analyses (phospholipids and respiratory quinones) indicated different communities depending on electron donor used. Terminal restriction fragment length polymorphism and clone libraries indicated distinct differences among communities even in treatments that promoted U reduction. Thus, there was enough metabolic diversity to accommodate many different electron donors resulting in the U bioimmobilization.

  18. Geochemical characteristics and microbial community composition in toxic metal-rich sediments contaminated with Au-Ag mine tailings.

    Kwon, Man Jae; Yang, Jung-Seok; Lee, Seunghak; Lee, Giehyeon; Ham, Baknoon; Boyanov, Maxim I; Kemner, Kenneth M; O'Loughlin, Edward J

    2015-10-15

    The effects of extreme geochemical conditions on microbial community composition were investigated for two distinct sets of sediment samples collected near weathered mine tailings. One set (SCH) showed extraordinary geochemical characteristics: As (6.7-11.5%), Pb (1.5-2.1%), Zn (0.1-0.2%), and pH (3.1-3.5). The other set (SCL) had As (0.3-1.2%), Pb (0.02-0.22%), and Zn (0.01-0.02%) at pH 2.5-3.1. The bacterial communities in SCL were clearly different from those in SCH, suggesting that extreme geochemical conditions affected microbial community distribution even on a small spatial scale. The clones identified in SCL were closely related to acidophilic bacteria in the taxa Acidobacterium (18%), Acidomicrobineae (14%), and Leptospirillum (10%). Most clones in SCH were closely related to Methylobacterium (79%) and Ralstonia (19%), both well-known metal-resistant bacteria. Although total As was extremely high, over 95% was in the form of scorodite (FeAsO4·2H2O). Acid-extractable As was only ∼118 and ∼14 mg kg(-1) in SCH and SCL, respectively, below the level known to be toxic to bacteria. Meanwhile, acid-extractable Pb and Zn in SCH were above toxic concentrations. Because As was present in an oxidized, stable form, release of Pb and/or Zn (or a combination of toxic metals in the sediment) from the sediment likely accounts for the differences in microbial community structure. The results also suggest that care should be taken when investigating mine tailings, because large differences in chemical/biological properties can occur over small spatial scales. PMID:25917692

  19. Environmental Conditions Outweigh Geographical Contiguity in Determining the Similarity of nifH-Harboring Microbial Communities in Sediments of Two Disconnected Marginal Seas

    Zhou, Haixia; Dang, Hongyue; Klotz, Martin G.

    2016-01-01

    Ecological evidence suggests that heterotrophic diazotrophs fueled by organic carbon respiration in sediments play an important role in marine nitrogen fixation. However, fundamental knowledge about the identities, abundance, diversity, biogeography, and controlling environmental factors of nitrogen-fixing communities in open ocean sediments is still elusive. Surprisingly, little is known also about nitrogen-fixing communities in sediments of the more research-accessible marginal seas. Here we report on an investigation of the environmental geochemistry and putative diazotrophic microbiota in the sediments of Bohai Sea, an eutrophic marginal sea of the western Pacific Ocean. Diverse and abundant nifH gene sequences were identified and sulfate-reducing bacteria (SRB) were found to be the dominant putative nitrogen-fixing microbes. Community statistical analyses suggested bottom water temperature, bottom water chlorophyll a content (or the covarying turbidity) and sediment porewater Eh (or the covarying pH) as the most significant environmental factors controlling the structure and spatial distribution of the putative diazotrophic communities, while sediment Hg content, sulfide content, and porewater SiO32−-Si content were identified as the key environmental factors correlated positively with the nifH gene abundance in Bohai Sea sediments. Comparative analyses between the Bohai Sea and the northern South China Sea (nSCS) identified a significant composition difference of the putative diazotrophic communities in sediments between the shallow-water (estuarine and nearshore) and deep-water (offshore and deep-sea) environments, and sediment porewater dissolved oxygen content, water depth and in situ temperature as the key environmental factors tentatively controlling the species composition, community structure, and spatial distribution of the marginal sea sediment nifH-harboring microbiota. This confirms the ecophysiological specialization and niche differentiation

  20. Seasonal and spatial distribution of ammonia-oxidizing microorganism communities in surface sediments from the East China Sea

    HE Hui; ZHEN Yu; MI Tiezhu; LU Xinglan; YU Zhigang

    2015-01-01

    Ammonia oxidation plays a significant role in the nitrogen cycle in marine sediments. Seasonal and spatial distribution of ammonia-oxidizing archaea (AOA) and betaproteobacteria (β-AOB) in surface sediments from the East China Sea (ECS) were investigated using ammonia monooxygenaseα subunit (amoA) gene. In order to characterize the community of AOA andβ-AOB, real-time quantitative polymerase chain reaction (qPCR) was carried out in this study, along with environmental parameters. The abundance ofβ-AOBamoA gene (2.17×106–4.54×107 copy numbers per gram wet weight sediment) was always greater than that of AOAamoA gene (2.18×105–9.89×106 copy numbers per gram wet weight sediment) in all sampling stations. The qPCR results were correlated with environmental parameters. AOAamoA gene copy numbers in April were positively related to temperature and nitrite concentration (p<0.05).β-AOBamoA gene copy numbers in August correlated negatively with salinity (p<0.01), and correlated positively with ammonium concentration (p<0.05). With the increase of salinity, theamoA gene copy ratio of AOB to AOA had a tendency to decrease, which suggestedβ-AOB dominated in the area of high level ammonium and AOA preferred high salinity area.

  1. Bacterial community composition in the gut content and ambient sediment of sea cucumber Apostichopus japonicus revealed by 16S rRNA gene pyrosequencing.

    Fei Gao

    Full Text Available The composition of the bacterial communities in the contents of the foregut and hindgut of the sea cucumber Apostichopus japonicus and in the ambient surface sediment was surveyed by 16S rRNA gene 454-pyrosequencing. A total of 188,623 optimized reads and 15,527 operational taxonomic units (OTUs were obtained from the ten gut contents samples and four surface sediment samples. The sequences in the sediments, foregut contents, and hindgut contents were assigned to 38.0±4.7, 31.2±6.2 and 27.8±6.5 phyla, respectively. The bacterial richness and Shannon diversity index were both higher in the ambient sediments than in the gut contents. Proteobacteria was the predominant phylum in both the gut contents and sediment samples. The predominant classes in the foregut, hindgut, and ambient sediment were Holophagae and Gammaproteobacteria, Deltaproteobacteria and Gammaproteobacteria, and Gammaproteobacteria and Deltaproteobacteria, respectively. The potential probiotics, including sequences related to Bacillus, lactic acid bacteria (Lactobacillus, Lactococcus, and Streptococcus and Pseudomonas were detected in the gut of A. japonicus. Principle component analysis and heatmap figure showed that the foregut, hindgut, and ambient sediment respectively harbored different characteristic bacterial communities. Selective feeding of A. japonicus may be the primary source of the different bacterial communities between the foregut contents and ambient sediments.

  2. Bacterial Community Composition in the Gut Content and Ambient Sediment of Sea Cucumber Apostichopus japonicus Revealed by 16S rRNA Gene Pyrosequencing

    Gao, Fei; Li, Fenghui; Tan, Jie; Yan, Jingping; Sun, Huiling

    2014-01-01

    The composition of the bacterial communities in the contents of the foregut and hindgut of the sea cucumber Apostichopus japonicus and in the ambient surface sediment was surveyed by 16S rRNA gene 454-pyrosequencing. A total of 188,623 optimized reads and 15,527 operational taxonomic units (OTUs) were obtained from the ten gut contents samples and four surface sediment samples. The sequences in the sediments, foregut contents, and hindgut contents were assigned to 38.0±4.7, 31.2±6.2 and 27.8±6.5 phyla, respectively. The bacterial richness and Shannon diversity index were both higher in the ambient sediments than in the gut contents. Proteobacteria was the predominant phylum in both the gut contents and sediment samples. The predominant classes in the foregut, hindgut, and ambient sediment were Holophagae and Gammaproteobacteria, Deltaproteobacteria and Gammaproteobacteria, and Gammaproteobacteria and Deltaproteobacteria, respectively. The potential probiotics, including sequences related to Bacillus, lactic acid bacteria (Lactobacillus, Lactococcus, and Streptococcus) and Pseudomonas were detected in the gut of A. japonicus. Principle component analysis and heatmap figure showed that the foregut, hindgut, and ambient sediment respectively harbored different characteristic bacterial communities. Selective feeding of A. japonicus may be the primary source of the different bacterial communities between the foregut contents and ambient sediments. PMID:24967593

  3. Ocean abyssal carbon experiments at 0.7 and 4 km depth

    Since 2002, researchers from Japan, the United States and Norway have been collaborating on the Ocean Abyssal Carbon Experiment (OACE) project. This paper presented information on the three year project. It presented a discussion of the high-pressure laboratory work, instrument development and theoretical and numerical modelling associated with field experiments. The purpose of the project is to conduct groundbreaking and challenging experiments to determine of the fate of carbon dioxide (CO2) disposed onto the ocean floor. Several observations from small-scale CO2 experiments at different depths conducted off the coast of California were presented. In the experiments, when the seawater velocity was sufficiently strong, parcels of liquid CO2 were torn off and transported away as discrete units by the turbulent water current. Newly formed frazil hydrate was observed at the interface, occasionally including sediment particles in the deep experiment. In addition, hydrate collected and created a floating consolidated solid consisting of ice in the downstream end of the trough, dissolving slowly from one day to the next. It was concluded that these observations have significant implications for understanding and modelling of larger scale anthropogenic CO2 disposal at the seafloor. 15 refs., 3 figs

  4. MICROHABITAT USE AND MULTIVARIATE PATTERN OF MOTILE EPIFAUNAL COMMUNITY IN RELATION TO SEDIMENT GRAIN SIZE IN A TROPICAL SEAGRASS MEADOW

    PENAGOS GUILLERMO

    2010-05-01

    Full Text Available The relationship between habitat physical structure and motile epifauna community associated to a Seagrass bed dominated by Thalassia testudinum was study over the isobaths of 1 and 3 m, in terms of species diversity, organisms density, micro habitat use and multivariate species pattern in association with Seagrass biomass, shoot and leaf density, leaves long and wide, epiphytic and rizophytic algae biomass, sponges biomass and sediment grain size. Seagrass features showed significant differences between depths, instead epiphytic and rizophytic algae, sponges biomass and sediment grain size did not. Though differences exhibited by Seagrass, epifaunal species diversity and organism density neither were different between depths. In the same way none Seagrass feature showed strong correlations with faunal descriptors, tending even to be negative instead positive.

  5. Variability in the origin of carbon substrates for bacterial communities in mangrove sediments

    BOUILLON, S; Moens, T.; N. Koedam; Dahdouh-Guebas, F.; Baeyens, W.; F. Dehairs

    2004-01-01

    Organic carbon in mangrove sediments originates from both local sources (mangroves, microphytobenthos) and tidal inputs (e.g. phytoplankton, seagrass-derived material). The relative inputs of these sources may vary strongly, both within and between different mangrove sites. We combined elemental (TOC/TN) and bulk d13C analysis on sediment cores from various mangrove sites with d13C data of bacteria-specific phospholipid fatty acids (PLFA) in order to identify the dominant carbon substrates u...

  6. Microbenthic community structure and trophic status of sediments in the Mar Piccolo of Taranto (Mediterranean, Ionian Sea).

    Rubino, F; Cibic, T; Belmonte, M; Rogelja, M

    2016-07-01

    This study aimed to assess the benthic ecosystem trophic status in a heavily polluted marine area and the response of the microbenthic community to multiple and diffuse anthropogenic impacts, integrating information coming from the active and resting (plankton's cysts) components of microbenthos. Two sampling campaigns were carried out in the period 2013-2014 and four sampling sites at different levels of industrial contamination were chosen within the first and second inlet of the Mar Piccolo of Taranto. The chemical contamination affected to a higher extent the active microbenthos than the resting one. In the central part of the first inlet, characterised by more marine features, thrives a very rich and biodiverse microbenthic community. In contrast, at the polluted site near the military navy arsenal, extremely low densities (9576 ± 1732 cells cm(-3)) were observed for active microbenthos, but not for the resting community. Here, the high level of contamination selected for tychopelagic diatom species, i.e., thriving just above the surface sediments, while the other life forms died or moved away. Following the adoption of a 10 μm mesh, for the first time, resting spores produced by small diatoms of the genus Chaetoceros were found. Our results further indicate that although the Mar Piccolo is very shallow, the benthic system is scarcely productive, likely as a consequence of the accumulated contaminants in the surface sediments that probably interfere with the proper functioning of the benthic ecosystem. PMID:26511257

  7. Abyssal θ-S Observations at Hawaii Ocean Time-series Station ALOHA

    Lukas, R.; Santiago-Mandujano, F.; Fumar, C.; McCoy, D.; Deppe, R. W.; Gum, J.; Snyder, J.; Chee, B.; Howe, B. M.; Potemra, J. T.; Duennebier, F. K.

    2014-12-01

    Abyssal θ-S variations observed since June 2011 by the ALOHA Cabled Observatory (ACO) reveal a potential temperature range of 0.025°C, and a salinity range of more than 0.0025 g kg-1. The very large temperature range is associated with episodic cold events (Lukas et al.2001; Alford et al. 2011). The salinity range, while not large in absolute terms, is an order of magnitude larger than the precision of the Sea-Bird Microcat. The absolute salinity is calibrated against simultaneous Hawaii Ocean Time-series (HOT) full-depth CTD profiles that have an accuracy of ~10-3 g kg-1. A slow drift of the SBE-37 conductivity sensor is seen, along with a sudden offset that may have been caused by a nearby glass ball implosion. θ-S variations are dominated by changes in density that are associated with dynamic processes. Large cooling events are associated with increases of salinity ultimately deriving from the neighboring Maui Deep. The slopes of these excursions in θ-S space are consistent with the slopes of HOT CTD depth profiles, suggesting that these are vertical changes due either to gravity currents associated with cold, salty overflow events from the Maui Deep, or to internal seiches within the Kauai Deep. θ-S variations that are nearly isopycnal are also seen during the slow recovery from a major cooling event in 2011. This may be due to diapycnal mixing with fresher waters above the controlling sill depth. It cannot be ruled out that some apparent salinity changes may be associated with sediment resuspension events, with subsequent deviations from the PSS-78 empirical relationship between conductivity, salinity, temperature and pressure. ADCP records show large vacillations of along- and cross-isobath flow. Large vertical current variations are measured that are correlated with horizontal flows, likely due to the bottom slope, even after minimizing correlations to account for the unknown orientation of the ADCP. The primary conclusion is that abyssal dynamics

  8. Molecular detection of Candidatus Scalindua pacifica and environmental responses of sediment anammox bacterial community in the Bohai Sea, China.

    Hongyue Dang

    Full Text Available The Bohai Sea is a large semi-enclosed shallow water basin, which receives extensive river discharges of various terrestrial and anthropogenic materials such as sediments, nutrients and contaminants. How these terrigenous inputs may influence the diversity, community structure, biogeographical distribution, abundance and ecophysiology of the sediment anaerobic ammonium oxidation (anammox bacteria was unknown. To answer this question, an investigation employing both 16S rRNA and hzo gene biomarkers was carried out. Ca. Scalindua bacteria were predominant in the surface sediments of the Bohai Sea, while non-Scalindua anammox bacteria were also detected in the Yellow River estuary and inner part of Liaodong Bay that received strong riverine and anthropogenic impacts. A novel 16S rRNA gene sequence clade was identified, putatively representing an anammox bacterial new candidate species tentatively named "Ca. Scalindua pacifica". Several groups of environmental factors, usually with distinct physicochemical or biogeochemical natures, including general marine and estuarine physicochemical properties, availability of anammox substrates (inorganic N compounds, alternative reductants and oxidants, environmental variations caused by river discharges and associated contaminants such as heavy metals, were identified to likely play important roles in influencing the ecology and biogeochemical functioning of the sediment anammox bacteria. In addition to inorganic N compounds that might play a key role in shaping the anammox microbiota, organic carbon, organic nitrogen, sulfate, sulfide and metals all showed the potentials to participate in the anammox process, releasing the strict dependence of the anammox bacteria upon the direct availability of inorganic N nutrients that might be limiting in certain areas of the Bohai Sea. The importance of inorganic N nutrients and certain other environmental factors to the sediment anammox microbiota suggests that these

  9. Distribution of typical denitrifying functional genes and diversity of the nirS-encoding bacterial community related to environmental characteristics of river sediments

    Huang, S.; Chen, C.; Yang, X.; Wu, Q.; Zhang, R.

    2011-10-01

    Denitrification in river sediments leads to nitrate removal from the aquatic system; therefore, it is necessary to understand functional diversity of denitrifier communities in the system. Sediment samples (0-25 cm depth) were collected from three typical locations along the Pearl River. The real-time PCR approach was used to measure the abundance of nitrate (narG), nitrite (nirS, nirK and nrfA), and nitrous oxide (nosZ) reductase genes from the sediment samples. Assemblages of nirS, nirK and nosZ indicated that complete denitrification occurred in sediment cores, with the greatest number of gene copies from 5-15 cm depth. Dissimilatory nitrate reduction appeared to be important below 15 cm depth, based on increasing gene copies of narG and nrfA with sediment depth. There was a close match (78-94 %) between the nirS sequences recovered from the Pearl River sediment and those detected in estuarine and marine sediments as well as active sludge, suggesting that the nitrogen source in the Pearl River sediment was affected by domestic sewage inputs and irregular tides. Canonical correspondence analysis indicated that the spatial distribution of denitrifying bacteria was highly correlated with dissolved inorganic nitrogen (including NH4+, NO2- and NO3-) concentrations in sediment. It was concluded that the difference in dissolved inorganic nitrogen concentrations along the sediment profile influenced the distribution of denitrifying genes and the nirS-encoding denitrifier community in the river sediment. In addition, a variety of novel denitrifying bacteria were revealed in the river sediment.

  10. Distribution of typical denitrifying functional genes and diversity of the nirS-encoding bacterial community related to environmental characteristics of river sediments

    R. Zhang

    2011-10-01

    Full Text Available Denitrification in river sediments leads to nitrate removal from the aquatic system; therefore, it is necessary to understand functional diversity of denitrifier communities in the system. Sediment samples (0–25 cm depth were collected from three typical locations along the Pearl River. The real-time PCR approach was used to measure the abundance of nitrate (narG, nitrite (nirS, nirK and nrfA, and nitrous oxide (nosZ reductase genes from the sediment samples. Assemblages of nirS, nirK and nosZ indicated that complete denitrification occurred in sediment cores, with the greatest number of gene copies from 5–15 cm depth. Dissimilatory nitrate reduction appeared to be important below 15 cm depth, based on increasing gene copies of narG and nrfA with sediment depth. There was a close match (78–94 % between the nirS sequences recovered from the Pearl River sediment and those detected in estuarine and marine sediments as well as active sludge, suggesting that the nitrogen source in the Pearl River sediment was affected by domestic sewage inputs and irregular tides. Canonical correspondence analysis indicated that the spatial distribution of denitrifying bacteria was highly correlated with dissolved inorganic nitrogen (including NH4+, NO2− and NO3− concentrations in sediment. It was concluded that the difference in dissolved inorganic nitrogen concentrations along the sediment profile influenced the distribution of denitrifying genes and the nirS-encoding denitrifier community in the river sediment. In addition, a variety of novel denitrifying bacteria were revealed in the river sediment.

  11. Methane emission in a specific riparian-zone sediment decreased with bioelectrochemical manipulation and corresponded to the microbial community dynamics

    Elliot S. Friedman

    2016-01-01

    Full Text Available Dissimilatory metal-reducing bacteria are widespread in terrestrial ecosystems, especially in anaerobic soils and sediments. Thermodynamically, dissimilatory metal reduction is more favorable than sulfate reduction and methanogenesis but less favorable than denitrification and aerobic respiration. It is critical to understand the complex relationships, including the absence or presence of terminal electron acceptors, that govern microbial competition and coexistence in anaerobic soils and sediments, because subsurface microbial processes can effect greenhouse gas emissions from soils, possibly resulting in impacts at the global scale. Here, we elucidated the effect of an inexhaustible, ferrous-iron and humic-substance mimicking terminal electron acceptor by deploying potentiostatically poised electrodes in the sediment of a very specific stream riparian zone in Upstate New York state. At two sites within the same stream riparian zone during the course of six weeks in the spring of 2013, we measured CH4 and N2/N2O emissions from soil chambers containing either poised or unpoised electrodes, and we harvested biofilms from the electrodes to quantify microbial community dynamics. At the upstream site, which had a lower vegetation cover and highest soil temperatures, the poised electrodes inhibited CH4 emissions by ~45% (when normalized to remove temporal effects. CH4 emissions were not significantly impacted at the downstream site. N2/N2O emissions were generally low at both sites and were not impacted by poised electrodes. We did not find a direct link between bioelectrochemical treatment and microbial community membership; however, we did find a correspondence between environment/function and microbial community dynamics.

  12. Salt marsh sediment characteristics as key regulators on the efficiency of hydrocarbons bioremediation by Juncus maritimus rhizospheric bacterial community.

    Ribeiro, Hugo; Almeida, C Marisa R; Magalhães, Catarina; Bordalo, Adriano A; Mucha, Ana P

    2015-01-01

    Mitigation of petroleum hydrocarbons was investigated during a 5-month greenhouse experiment, to assess the rhizoremediation (RR) potential in sediments with different characteristics colonized by Juncus maritimus, a salt marsh plant commonly found in temperate estuaries. Furthermore, the efficiency of two bioremediation treatments namely biostimulation (BS) by the addition of nutrients, and bioaugmentation (BA) by addition of indigenous microorganisms, was tested in combination with RR. The effect of the distinct treatments on hydrocarbon degradation, root biomass weight, and bacterial community structure was assessed. Our result showed higher potential for hydrocarbon degradation (evaluated by total petroleum hydrocarbon analysis) in coarse rhizosediments with low organic matter (OM), than rhizosediments with high OM, and small size particles. Moreover, the bacterial community structure was shaped according to the rhizosediment characteristics, highlighting the importance of specific microbe-particle associations to define the structure of rhizospheric bacterial communities, rather than external factors, such as hydrocarbon contamination or the applied treatments. The potential for hydrocarbon RR seems to depend on root system development and bacterial diversity, since biodegradation efficiencies were positively related with these two parameters. Treatments with higher root biomass, and concomitantly with higher bacterial diversity yielded higher hydrocarbon degradation. Moreover, BS and BA did not enhance hydrocarbons RR. In fact, it was observed that higher nutrient availability might interfere with root growth and negatively influence hydrocarbon degradation performance. Therefore, our results suggested that to conduct appropriate hydrocarbon bioremediation strategies, the effect of sediment characteristics on root growth/exploration should be taken into consideration, a feature not explored in previous studies. Furthermore, strategies aiming for the recovery

  13. Microbial community structure and ecology of subglacial sediments in two polythermal Svalbard glaciers characterized by epifluorescence microscopy and PLFA

    Kaštovská, Klára; Stibal, Marek; Šabacká, Marie; Černá, B.; Šantrůčková, H.; Elster, Josef

    2007-01-01

    Roč. 30, č. 3 (2007), s. 277-287. ISSN 0722-4060. [International Conference on Alpine and Polar Microbiology. Innsbruck, 27.3.2006-30.3.2006] R&D Projects: GA AV ČR(CZ) KJB6005409; GA ČR(CZ) GP206/03/P024 Institutional research plan: CEZ:AV0Z60170517; CEZ:AV0Z60050516 Keywords : subglacial sediment * microbial community * PLFA Subject RIV: EH - Ecology, Behaviour Impact factor: 1.734, year: 2007

  14. Lake depth rather than fish planktivory determines cladoceran community structure in Faroese lakes - evidence from contemporary data and sediments

    Amsinck, S.L.; Strzelczak, A.; Bjerring, R.;

    2006-01-01

    richness and community structure of cladocerans were identified from pelagial snapshot samples and from samples of surface sediment (0-1 cm). Multivariate statistical methods were applied to explore cladoceran species distribution relative to measured environmental variables. For Lake Heygsvatn, lake...... maximum lake depth (Zmax) to be the only significant variable in explaining the sedimentary cladoceran species (18 cladoceran taxa, two pelagic, 16 benthic) distribution. Multivariate regression trees revealed benthic taxa to dominate in lakes with Zmax < 4.8 m and pelagic taxa to dominate when Zmax was...

  15. Pore water geochemistry and the oxidation of sedimentary organic matter: Hatteras Abyssal Plain 1981

    This report presents the pore water geochemistry from R/V an Endeavor cruise to an area of the Hatteras Abyssal Plain between 310 45' - 340 00'N and 690 37.5 - 720 07.5'W. The authors report on the down core variations of the products of organic matter oxidation, the stoichiometry of reactions and make a preliminary assessment of the rates of organic matter oxidation at several core locations. The authors found concentrations of total inorganic nitrogen species; nitrate, nitrite and ammonia in pore waters to be less than those predicted from a model of organic matter oxidation (Froelich et al. 1979) in sediments. The observations indicate that nitrogen is depleted over carbon as compared to typical marine organic matter. The down-core nitrate profiles over the study area were used to infer depths at which oxygen is near totally consumed in the sediments and hence to compute rates of oxygen consumption. The authors found oxygen consumption rates to vary by nearly an order of magnitude between core locations (1.7 - >15μmO2 cm-2 yr-1). A simple model which combines the computed rates of oxidant consumption and the stoichiometry of organic matter oxidation was used to make estimates of organic carbon oxidation rates. These latter were found to vary between 1.3 and > 11.5 μm C cm-2 yr-1. Highest carbon oxidation rates were found at the western boundary of the study area, and in all cases oxygen consumption was responsible for >85% of carbon oxidized. 11 references, 5 figures, 4 tables

  16. Last Glacial Maximum and deglacial abyssal seawater oxygen isotopic ratios

    Wunsch, Carl

    2016-06-01

    An earlier analysis of pore-water salinity (chlorinity) in two deep-sea cores, using terminal constraint methods of control theory, concluded that although a salinity amplification in the abyss was possible during the LGM, it was not required by the data. Here the same methodology is applied to δ18Ow in the upper 100 m of four deep-sea cores. An ice volume amplification to the isotopic ratio is, again, consistent with the data but not required by it. In particular, results are very sensitive, with conventional diffusion values, to the assumed initial conditions at -100 ky and a long list of noise (uncertainty) assumptions. If the calcite values of δ18O are fully reliable, then published enriched values of the ratio in seawater are necessary to preclude sub-freezing temperatures, but the seawater δ18O in pore fluids does not independently require the conclusion.

  17. Effects of agricultural tillage and sediment accumulation on emergent plant communities in playa wetlands of the U.S. High Plains.

    O'Connell, Jessica L; Johnson, Lacrecia A; Daniel, Dale W; McMurry, Scott T; Smith, Loren M; Haukos, David A

    2013-05-15

    Identifying community assembly filters is a primary ecological aim. The High Plains, a 30 million ha short-grass eco-region, is intensely cultivated. Cultivation disturbance, including plowing and eroded soil deposition down-slope of plowing, influences plant composition in depressional wetlands, such as playas, within croplands. We evaluated influences of wetland cultivation and sediment deposition on plant composition in playas embedded within croplands (46 plowed and 32 unplowed) and native grasslands (79) across 6 High Plains' states. Sediment accumulation ranged from 7 to 78 cm in cropland and 1 to 35 cm in grassland playas. Deeper sediments and plowing each decreased wetland plant richness, 28% and 70% respectively in cropland wetlands. Sediment depth reduced richness 37% in small grasslands playas while it increased richness 22% in larger ones, suggesting moderate disturbance increased richness when there were nearby propagule sources. Sediment depth was unrelated to species richness in plowed wetlands, probably because plowing was a strong disturbance. Plowing removed perennial plants from vegetation communities. Sediment accumulation also influenced species composition in cropland playas, e.g., probability of Eleocharis atropurpurea increased with sediment depth, while probability of Panicum capillare decreased. In grassland playas, observed lighter sediment depths did not influence species composition after accounting for wetland area. Sediment accumulation and plowing shift wetland plant communities toward annual species and decrease habitat connectivity for wetland-dependent organisms in cropland playas over 39,000 and 23,400 ha respectively. Conservation practices lessening sediment accumulation include short-grass buffer strips surrounding wetlands. Further, wetland tillage, allowed under federal agricultural conservation programs, should be eliminated. PMID:23500104

  18. Community structure, cellular rRNA content, and activity of sulfate-reducing bacteria in marine Arctic sediments

    Ravenschlag, K.; Sahm, K.; Knoblauch, C.;

    2000-01-01

    The community structure of sulfate-reducing bacteria (SRB) of a marine Arctic sediment (Smeerenburg-fjorden, Svalbard) a-as characterized by both fluorescence in situ hybridization (FISH) and rRNA slot blot hybridization by using group- and genus-specific 16S rRNA-targeted oligonucleotide probes......, The SRB community was dominated by members of the Desulfosarcina-Desulfococcus group. This group accounted for up to 73% of the SRB detected and up to 70% of the SRB rRNA detected. The predominance was shown to be a common feature for different stations along the coast of Svalbard, In a top......-Desulfococcus group. A group of clone sequences (group SVAL1) most closely related to Desulfosarcina variabilis (91.2% sequence similarity) was dominant and was shown to be most abundant in situ, accounting for up to 54.8% of the total SRB detected. A comparison of the two methods used for quantification showed...

  19. Impacts of Pristine and Transformed Ag and Cu Engineered Nanomaterials on Surficial Sediment Microbial Communities Appear Short-Lived.

    Moore, Joe D; Stegemeier, John P; Bibby, Kyle; Marinakos, Stella M; Lowry, Gregory V; Gregory, Kelvin B

    2016-03-01

    Laboratory-based studies have shown that many soluble metal and metal oxide engineered nanomaterials (ENM) exert strong toxic effects on microorganisms. However, laboratory-based studies lack the complexity of natural systems and often use "as manufactured" ENMs rather than more environmentally relevant transformed ENMs, leaving open the question of whether natural ligands and seasonal variation will mitigate ENM impacts. Because ENMs will accumulate in subaquatic sediments, we examined the effects of pristine and transformed Ag and Cu ENMs on surficial sediment microbial communities in simulated freshwater wetlands. Five identical mesocosms were dosed through the water column with either Ag(0), Ag2S, CuO or CuS ENMs (nominal sizes of 4.67 ± 1.4, 18.1 ± 3.2, 31.1 ± 12, and 12.4 ± 4.1, respectively) or Cu(2+). Microbial communities were examined at 0, 7, 30, 90, 180, and 300 d using qPCR and high-throughput 16S rRNA gene sequencing. Results suggest differential short-term impacts of Ag(0) and Ag2S, similarities between CuO and CuS, and differences between Cu ENMs and Cu(2+). PICRUSt-predicted metagenomes displayed differential effects of Ag treatments on photosynthesis and of Cu treatments on methane metabolism. By 300 d, all metrics pointed to reconvergence of ENM-dosed mesocosm microbial community structure and composition, suggesting that the long-term microbial community impacts from a pulse of Ag or Cu ENMs are limited. PMID:26841726

  20. Ecotoxicity of sediments in rivers: Invertebrate community, toxicity bioassays and the toxic unit approach as complementary assessment tools.

    de Castro-Català, Núria; Kuzmanovic, Maja; Roig, Neus; Sierra, Jordi; Ginebreda, Antoni; Barceló, Damià; Pérez, Sandra; Petrovic, Mira; Picó, Yolanda; Schuhmacher, Marta; Muñoz, Isabel

    2016-01-01

    The determination of the real toxicity of sediments in aquatic ecosystems is challenging and necessary for an appropriate risk assessment. Different approaches have been developed and applied over the last several decades. Currently, the joint implementation of chemical, ecological and toxicological tools is recommended for an appropriate and successful toxicity risk assessment. We chose the combination of the toxic unit approach with acute pore water tests (Vibrio fischeri, Pseudokirchneriella subcapitata and Daphnia magna) and whole-sediment exposure tests (V. fischeri, Chironomus riparius), together with invertebrate community composition (multivariate analyses) to detect short and long-term responses of the organisms in four rivers of the Iberian Peninsula. High toxicity was detected in three sites (the downstream sites of the Llobregat and the Júcar, and the most upstream site of the Ebro). We identified organophosphate insecticides and metals as the main variables responsible for this toxicity, particularly in the whole-sediment tests. In particular, chlorpyrifos was mostly responsible for the toxicity (TUs) of D. magna, coinciding with the C. riparius mortality (long-term toxicity) in the mentioned sites, and copper was the main pollutant responsible for the short-term toxicity of P. subcapitata. The combination of the different approaches allowed us to detect ecotoxicological effects in organisms and identify the main contributors to the toxicity in these multi-stressed rivers. PMID:26118861

  1. Distribution of typical denitrifying functional genes and diversity of the nirS-encoding bacterial community related to environmental characteristics of river sediments

    X. Yang

    2011-05-01

    Full Text Available Denitrification in river sediments leads to nitrate removal from the aquatic system; therefore, it is necessary to understand functional diversity of denitrifier communities in the system. Sediment samples (0–25 cm depth were collected from three typical locations along the Pearl River. The real-time PCR approach was used to measure the abundance of nitrate (narG, nitrite (nirS, nirK and nrfA, and nitrous oxide (nosZ reductase genes from the sediment samples. Assemblages of nirS, nirK and nosZ indicated that complete denitrification occurred in sediment cores, with the greatest number of gene copies from 5–15 cm depth. Dissimilatory nitrate reduction appeared to be important below 15 cm depth, based on increasing gene copies of narG and nrfA with sediment depth. There was a close match (78–94 % between the nirS sequences recovered from Pearl River sediment and those detected in estuarine and marine sediments as well as active sludge, suggesting that domestic sewage inputs and irregular tides. Canonical correspondence analysis indicated that the spatial distribution of denitrifying bacteria was highly correlated with dissolved inorganic N (DIN: NH4+, NO2 and NO3− concentrations in sediment. We conclude that changes in DIN within the sediment profile influences the distribution of denitrifying genes and the nirS-encoding denitrifier community in the river sediment. Our results also reveal a variety of novel denitrifying bacteria in the river sediment.

  2. Prediction of benthic community structure from environmental variables in a soft-sediment tidal basin (North Sea)

    Puls, W.; van Bernem, K.-H.; Eppel, D.; Kapitza, H.; Pleskachevsky, A.; Riethmüller, R.; Vaessen, B.

    2012-09-01

    The relationship between benthos data and environmental data in 308 samples collected from the intertidal zone of the Hörnum tidal basin (German Wadden Sea) was analyzed. The environmental variables were current velocity, wave action, emersion time (all of which were obtained from a 2-year simulation with a numerical model) and four sediment grain-size parameters. A grouping of sample stations into five benthos clusters showed a large-scale (>1 km) zoning of benthic assemblages on the tidal flats. The zoning varied with the distance from the shore. Three sample applications were examined to test the predictability of the benthic community structure based on environmental variables. In each application, the dataset was spatially partitioned into a training set and a test set. Predictions of benthic community structure in the test sets were attempted using a multinomial logistic regression model. Applying hydrodynamic predictors, the model performed significantly better than it did when sediment predictors were applied. The accuracy of model predictions, given by Cohen's kappa, varied between 0.14 and 0.49. The model results were consistent with independently attained evidence of the important role of physical factors in Wadden Sea tidal flat ecology.

  3. Identification and quantification of a novel nitrate-reducing community in sediments of Suquia River basin along a nitrate gradient

    We evaluated the molecular diversity of narG gene from Suquia River sediments to assess the impact of the nitrate concentration and water quality on the composition and structure of the nitrate-reducing bacterial community. To this aim, a library of one of the six monitoring stations corresponding to the highest nitrate concentration was constructed and 118 narG clones were screened. Nucleotide sequences were associated to narG gene from alpha-, beta-, delta-, gammaproteobacteria and Thermus thermophilus. Remarkably, 18% of clones contained narG genes with less than 69% similarity to narG sequences available in databases. Thus, indicating the presence of nitrate-reducing bacteria with novel narG genes, which were quantified by real-time PCR. Results show a variable number of narG copies, ranging from less than 1.0 x 102 to 5.0 x 104 copies per ng of DNA, which were associated with a decreased water quality index monitored along the basin at different times. - A novel narG community present in Suquia River sediments was quantified; values were in line with the water quality index.

  4. The impact of heavy metal pollution gradients in sediments on benthic macrofauna at population and community levels

    Ryu, Jongseong [Office of Policy Research, Korea Ocean Research and Development (KORDI), Ansan, P.O. Box 29, Seoul 425-600 (Korea, Republic of); Khim, Jong Seong, E-mail: jongseongkhim@korea.ac.kr [Division of Environmental Science and Ecological Engineering, Korea University, Seoul 136-713 (Korea, Republic of); Kang, Seong-Gil [Maritime and Ocean Engineering Research Institute (MOERI)/Korea Ocean Research and Development Institute (KORDI), Daejeon 305-600 (Korea, Republic of); Kang, Daeseok [Department of Ecological Engineering, Pukyong National University, Busan 608-737 (Korea, Republic of); Lee, Chang-hee [Department of Environmental Engineering and Biotechnology, Myongji University, Yongin, Gyeonggi-do 449-728 (Korea, Republic of); Koh, Chul-hwan [School of Earth and Environmental Sciences (Oceanography), Seoul National University, Seoul 151-742 (Korea, Republic of)

    2011-10-15

    The effect of sediment pollution on benthos was investigated in the vicinity of a large sewage treatment outflow at Incheon North Harbor, Korea. Animal size, vertical distribution and standard community parameters were analyzed along a 3 km transect line (n = 7). Univariate parameters showed a general trend of increasing species diversity with increasing distance from the pollution source. Multi-dimensional scaling analysis led to the clear separation of 3 locational groups, supporting gradient-dependent faunal composition. The innermost location was dominated by small sub-surface dwellers while the outer locations by large mid to deep burrowers. Looking for the size-frequency distribution, most abundance species (Heteromastus filiformis) showed the presence of larger size animals with increasing proximity to the pollution source. Meanwhile, species-specific vertical distributions, regardless of the pollution gradient, indicated that such shifts were due to species replacement resulting from a higher tolerance to pollutants over some species. - Highlights: > Hypotheses on benthic responses to sediment pollution were tested. > Decrease of species diversity with the proximity to the pollution source. > Shift of vertical distribution along the transect line attributes to species replacement. > Larger-size species occurred distant from the pollution source. > Larger individuals of Heteromastus filiformis occurred closer to the pollution source. - Community and population level response to the polluted environment of the harbor reflected an integration effect, together with biological interactions.

  5. Bacterial communities potentially involved in iron-cycling in Baltic Sea and North Sea sediments revealed by pyrosequencing.

    Reyes, Carolina; Dellwig, Olaf; Dähnke, Kirstin; Gehre, Matthias; Noriega-Ortega, Beatriz E; Böttcher, Michael E; Meister, Patrick; Friedrich, Michael W

    2016-04-01

    To gain insight into the bacterial communities involved in iron-(Fe) cycling under marine conditions, we analysed sediments with Fe-contents (0.5-1.5 wt %) from the suboxic zone at a marine site in the Skagerrak (SK) and a brackish site in the Bothnian Bay (BB) using 16S rRNA gene pyrosequencing. Several bacterial families, including Desulfobulbaceae, Desulfuromonadaceae and Pelobacteraceae and genera, includingDesulfobacterandGeobacter, known to reduce Fe were detected and showed highest abundance near the Fe(III)/Fe(II) redox boundary. Additional genera with microorganisms capable of coupling fermentation to Fe-reduction, includingClostridiumandBacillus, were observed. Also, the Fe-oxidizing families Mariprofundaceae and Gallionellaceae occurred at the SK and BB sites, respectively, supporting Fe-cycling. In contrast, the sulphate (SO4 (2-)) reducing bacteriaDesulfococcusandDesulfobacteriumwere more abundant at greater depths concurring with a decrease in Fe-reducing activity. The communities revealed by pyrosequencing, thus, match the redox stratification indicated by the geochemistry, with the known Fe-reducers coinciding with the zone of Fe-reduction. Not the intensely studied model organisms, such asGeobacterspp., but rather versatile microorganisms, including sulphate reducers and possibly unknown groups appear to be important for Fe-reduction in these marine suboxic sediments. PMID:26960392

  6. The impact of heavy metal pollution gradients in sediments on benthic macrofauna at population and community levels

    The effect of sediment pollution on benthos was investigated in the vicinity of a large sewage treatment outflow at Incheon North Harbor, Korea. Animal size, vertical distribution and standard community parameters were analyzed along a 3 km transect line (n = 7). Univariate parameters showed a general trend of increasing species diversity with increasing distance from the pollution source. Multi-dimensional scaling analysis led to the clear separation of 3 locational groups, supporting gradient-dependent faunal composition. The innermost location was dominated by small sub-surface dwellers while the outer locations by large mid to deep burrowers. Looking for the size-frequency distribution, most abundance species (Heteromastus filiformis) showed the presence of larger size animals with increasing proximity to the pollution source. Meanwhile, species-specific vertical distributions, regardless of the pollution gradient, indicated that such shifts were due to species replacement resulting from a higher tolerance to pollutants over some species. - Highlights: → Hypotheses on benthic responses to sediment pollution were tested. → Decrease of species diversity with the proximity to the pollution source. → Shift of vertical distribution along the transect line attributes to species replacement. → Larger-size species occurred distant from the pollution source. → Larger individuals of Heteromastus filiformis occurred closer to the pollution source. - Community and population level response to the polluted environment of the harbor reflected an integration effect, together with biological interactions.

  7. High resolution study of the spatial distributions of abyssal fishes by autonomous underwater vehicle

    Milligan, R. J.; Morris, K. J.; Bett, B. J.; Durden, J. M.; Jones, D. O. B.; Robert, K; Ruhl, H. A.; Bailey, D. M.

    2016-01-01

    On abyssal plains, demersal fish are believed to play an important role in transferring energy across the seafloor and between the pelagic and benthic realms. However, little is known about their spatial distributions, making it difficult to quantify their ecological significance. To address this, we employed an autonomous underwater vehicle to conduct an exceptionally large photographic survey of fish distributions on the Porcupine Abyssal Plain (NE Atlantic, 4850 m water depth) encompassing...

  8. Long-term change in benthopelagic fish abundance in the abyssal northeast Pacific Ocean

    Bailey, D. M.; Ruhl, H. A.; Smith, K

    2006-01-01

    Food web structure, particularly the relative importance of bottom-up and top-down control of animal abundances, is poorly known for the Earth's largest habitats: the abyssal plains. A unique 15-yr time series of climate, productivity, particulate flux, and abundance of primary consumers (primarily echinoderms) and secondary consumers (fish) was examined to elucidate the response of trophic levels to temporal variation in one another. Towed camera sled deployments in the abyssal northeast Pac...

  9. High resolution study of the spatial distributions of abyssal fishes by autonomous underwater vehicle

    Milligan, R. J.; Morris, K. J.; Bett, B. J.; Durden, J. M.; Jones, D. O. B.; Robert, K; Ruhl, H. A.; Bailey, D. M.

    2016-01-01

    On abyssal plains, demersal fish are believed to play an important role in transferring energy across the seafloor and between the pelagic and benthic realms. However, little is known about their spatial distributions, making it difficult to quantify their ecological significance. To address this, we employed an autonomous underwater vehicle to conduct an exceptionally large photographic survey of fish distributions on the Porcupine Abyssal Plain (NE Atlantic, 4850?m water depth) encompassing...

  10. Epithermal neutron activation analysis investigation of Clarion-Clipperton abyssal plane clay and polymetallic micronodules

    Duliu, O.G. [University of Bucharest, Department of Atomic and Nuclear Physics, P.O. Box MG-11, 077125 Magurele, Ilfov (Romania)], E-mail: duliu@b.astral.ro; Cristache, C.I. [National Institute of Research and Development for Physics and Nuclear Engineering ' Horia-Hulubei' , P.O. Box MG-6, 077125 Magurele, Ilfov (Romania)], E-mail: ocarmen@ifin.nipne.ro; Culicovc, O.A. [Joint Institute of Nuclear Research, 6, Joliot Curie str., 141980 Dubna (Russian Federation)], E-mail: otilia_culicov@yahoo.com; Frontasyeva, M.V. [Joint Institute of Nuclear Research, 6, Joliot Curie str., 141980 Dubna (Russian Federation)], E-mail: marina@nf.jinr.ru; Szobotca, S.A. [National Institute of Geoecology and Marine Geology, 34 Dimitrie Onciul str., 024504 Bucharest (Romania)], E-mail: szobi@geoecomar.ro; Toma, M. [National Institute of Research and Development for Physics and Nuclear Engineering ' Horia-Hulubei' , P.O. Box MG-6, 077125 Magurele, Ilfov (Romania)

    2009-05-15

    The content of seven major (Na, Al, Cl, Mn, K, Ca, Ti, Fe) and 30 trace (Sc, V, Cr, Ni, Co, Zn, Cu, As, Sr, Rb, Zr, Mo, Sn, In, Sb, Ba, Cs, La, Ce, Nd, Eu, Sm, Tb, Dy, Yb, Hf, Ta, W, Th, U) elements determined by INAA in 13 samples of abyssal clay and two samples of micronodules collected from the North pacific Ocean Clarion-Clipperton abyssal plane is presented and discussed with respect to some rocks models.

  11. Effects of Spartina alterniflora invasion on the communities of methanogens and sulfate-reducing bacteria in estuarine marsh sediments

    Jemaneh eZeleke

    2013-08-01

    Full Text Available The effect of plant invasion on the microorganisms of soil sediments is very important for estuary ecology. The community structures of methanogens and sulfate-reducing bacteria (SRB as a function of Spartina alterniflora invasion in Phragmites australis-vegetated sediments of the Dongtan wetland in the Yangtze River estuary, China, were investigated using 454 pyrosequencing and quantitative real-time PCR (qPCR of the methyl coenzyme M reductase A (mcrA and dissimilatory sulfite-reductase (dsrB genes. Sediment samples were collected from two replicate locations, and each location included three sampling stands each covered by monocultures of P. australis, S. alterniflora and both plants (transition stands, respectively. qPCR analysis revealed higher copy numbers of mcrA genes in sediments from S. alterniflora stands than P. australis stands (5- and 7.5-fold more in the spring and summer, respectively, which is consistent with the higher methane flux rates measured in the S. alterniflora stands (up to 8.01 ± 5.61 mg m-2 h-1. Similar trends were observed for SRB, and they were up to two orders of magnitude higher than the methanogens. Diversity indices indicated a lower diversity of methanogens in the S. alterniflora stands than the P. australis stands. In contrast, insignificant variations were observed in the diversity of SRB with the invasion. Although Methanomicrobiales and Methanococcales, the hydrogenotrophic methanogens, dominated in the salt marsh, Methanomicrobiales displayed a slight increase with the invasion and growth of S. alterniflora, whereas the later responded differently. Methanosarcina, the metabolically diverse methanogens, did not vary with the invasion of, but Methanosaeta, the exclusive acetate utilizers, appeared to increase with S. alterniflora invasion. In SRB, sequences closely related to the families Desulfobacteraceae and Desulfobulbaceae dominated in the salt marsh, although they displayed minimal changes with the S

  12. Oxygen dynamics in periphyton communities and associated effects on phosphorus release from lake sediments

    This study used oxygen sensitive microelectrodes with tip diameters of 32P radiotracer and that permitted manipulation of the velocity, flushing rate, and oxygen concentration of overlying water was developed to investigate the role of photosynthetic oxygen production on the phosphorus dynamics in lake sediments colonized by epipelic periphyton

  13. Sediment diatom species and community response to nitrogen addition in Oregon (USA) estuarine tidal wetlands

    Sediment microalgae play an important role in nutrient cycling and are important primary producers in the food web in Pacific Northwest estuaries. This study examines the effects of nitrogen addition to benthic microalgae in tidal wetlands of Yaquina Bay estuary on the Oregon c...

  14. EFFECTS OF DDT SEDIMENT-CONTAMINATION ON MACROFAUNAL COMMUNITY STRUCTURE AND COMPOSITION IN SAN FRANCISCO BAY

    The objectives of this study were to determine the effects of sediment contamination on the benthic macrofauna and to predict macrofaunal changes following remediation at a Superfund (uncontrolled hazardous waste) site in San Francisco Bay, CA, USA. DDT and its metabolites (sumDD...

  15. Bacterial sulfur cycle shapes microbial communities in surface sediments of an ultramafic hydrothermal vent field

    Schauer, Regina; Røy, Hans; Augustin, Nico;

    2011-01-01

    The ultramafic-hosted Logatchev hydrothermal field (LHF) is characterized by vent fluids, which are enriched in dissolved hydrogen and methane compared with fluids from basalt-hosted systems. Thick sediment layers in LHF are partly covered by characteristic white mats. In this study, these...

  16. A novel approach to the assess biotic oxygen consumption in marine sediment communities

    Baranov, Victor; Queiros, Ana; Widdicombe, Stephen; Stephens, Nick; Lessin, Gennadi; Krause, Stefan; Lewandowski, Joerg

    2016-04-01

    Bioturbation , the mixing of the sediment matrix by burrowing animals impacts sediment metabolism, including respiration through redistribution of particulate organics, changes in bacterial biota diversity and acitivity, as well as via burrowing fauna's own metabolism. Bioturbation, reflecting faunal activity, is also a proxy for the general sedimentary ecosystem health, and can be impacted by many of emerging marine environmental issues such as ocean acidification, warming and the occurrence of heat waves. Sedimentary oxygen consumption is often taken as a proxy for the activity of bioturbating fauna, but determining baselines can be difficult because of the confounding effects of other fauna and microbes present in sediments, as well as irnorganic processes that consume oxygen. Limitations therefore exist in current methodologies, and numerous confounding factors are hampering progress in this area. Here, we present novel method for the assessment of sediment respiration which is expected to be affected only by the biogenic oxygen consumption (namely aerobic respiration). As long as tracer reduction "immune" to inorganic oxygen consumption, so that measurements using this method can be used, alongside traditional methods, to decouple biological respiration from inorganic oxygen consumption reactions. The tracer is easily detectable, non-toxic and can be applied in systems with constant oxygen supply. The latter allow for incubation without the need to to work with unsealed experimental units, bringing procedural advantage over traditional methods. Consequently assessed bioturbating fauna is not exposed to hypoxia and additional stress. Here, we had applied system for the first time to investigate impacts of a common North-Atlantic bioturbator, the brittle star Amphiura filiformis, - on respiration of marine sediments. Two series of experiments were conducted with animals and sediment collected from Cawsand Bay, Plymouth, UK Preliminary results show that tracer

  17. Impacts of Alterations of Organic Inputs on the Bacterial Community within the sediments of Wind Cave, South Dakota, USA

    Chelius Marisa K.

    2009-01-01

    Full Text Available Wind Cave (WICA in the Black Hills of South Dakota, like many mostly dry caves in temperate regions is an energy-starved system.The biotic communities that reside in these systems are low in diversity and simple in structure, and sensitive to changes in externalinputs of organic matter. Caves open to tourist traffic offer an opportunity to study the impacts of organic matter amendments in theform of human and rodent hair and dander, clothing lint, material from rodent activity (nesting materials and feces, and algal growthin and around artificial lighting. This study reports on the impacts of carbon amendments from humans and rodents on the bacterialand archaeal communities within the sediments of WICA from annual surveys and from a manipulative study that added lint (‘L’;cellulose plus rodent dander and rodent hair, rodent feces (‘F’, and a combination of both (‘LF’. The survey confirmed that bacterialbiomass was higher in regions of the cave with the highest rates of lint (hair and natural clothing fibers input. The manipulative studyfound that organic amendments in the forms of lint (L and rodent feces (F altered the WICA bacterial community structure in bothabundance and diversity, with the combined lint and feces (LF amendment having the most significant response. The high similarityof the LF and L communities suggests that the cave bacterial community is more carbon than nitrogen limited. The implication ofcave development to management practices is immediate and practical. Even small amounts of lint and organic matter foreign tocave bacteria significantly compromise the integrity of the endemic community resulting in the replacement of undescribed speciesby assemblages with at best, unknown impacts to natural cave features.

  18. A survey of alterations in microbial community diversity in marine sediments in response to oil from the Deepwater Horizon spill: Northern Gulf of Mexico shoreline, Texas to Florida

    Lisle, John T.

    2011-01-01

    Microbial community genomic DNA was extracted from sediment samples collected from the northern Gulf of Mexico (NGOM) coast. These samples had a high probability of being impacted by Macondo-1 (M-1) well oil from the Deepwater Horizon (DWH) drilling site. The hypothesis for this project was that presence of M-1 oil in coastal sediments would significantly alter the diversity within the microbial communities associated with the impacted sediments. To determine if community-level changes did or did not occur following exposure to M-1 oil, microbial community-diversity fingerprints were generated and compared. Specific sequences within the community's genomic DNA were first amplified using the polymerase chain reaction (PCR) using a primer set that provides possible resolution to the species level. A second nested PCR that was performed on the primary PCR products using a primer set on which a GC-clamp was attached to one of the primers. These nested PCR products were separated using denaturing-gradient gel electrophoresis (DGGE) that resolves the nested PCR products based on sequence dissimilarities (or similarities), forming a genomic fingerprint of the microbial diversity within the respective samples. Sediment samples with similar fingerprints were grouped and compared to oil-fingerprint data from Rosenbauer and others (2010). The microbial community fingerprints grouped closely when identifying those sites that had been impacted by M-1 oil (N=12) and/or some mixture of M-1 and other oil (N=4), based upon the oil fingerprints. This report represents some of the first information on naturally occurring microbial communities in sediment from shorelines along the NGOM coast. These communities contain microbes capable of degrading oil and related hydrocarbons, making this information relevant to response and recovery of the NGOM from the DWH incident.

  19. Characterization of Eubacterial and Actinobacterial communities of contrasting terrestrial soils and sediments

    Hill, P.; Krištůfek, Václav; Bolhuis, H.; Martinez, A. F.; Kroetsch, D.; van Elsas, J.D.

    Newcastle upon Tyne: International Commitee, UK body, University of Newcastle upon Tyne, 2007. s. 185. [International Symposium on the Biology of Actinomycetes /14./. 26.08.2007-30.08.2007, The Sage Gateshead] Institutional research plan: CEZ:AV0Z60660521 Keywords : Eubacterial communities * Actinobacterial communities * contrasting terrestrial soils Subject RIV: EH - Ecology, Behaviour

  20. Bacterial Community Composition in the Gut Content and Ambient Sediment of Sea Cucumber Apostichopus japonicus Revealed by 16S rRNA Gene Pyrosequencing

    Fei Gao; Fenghui Li; Jie Tan; Jingping Yan; Huiling Sun

    2014-01-01

    The composition of the bacterial communities in the contents of the foregut and hindgut of the sea cucumber Apostichopus japonicus and in the ambient surface sediment was surveyed by 16S rRNA gene 454-pyrosequencing. A total of 188,623 optimized reads and 15,527 operational taxonomic units (OTUs) were obtained from the ten gut contents samples and four surface sediment samples. The sequences in the sediments, foregut contents, and hindgut contents were assigned to 38.0±4.7, 31.2±6.2 and 27.8±...

  1. Seasonal Variation of the Geochemistry and the Effects on the Composition in Microbial Communities Attached to Fraser River Suspended Sediments

    Bennett, M. C.; Epp, A.; Luymes, R.; DaSilva, J.; Marsh, S. J.; Gillies, S. L.; Peucker-Ehrenbrink, B.; Voss, B.; Coolen, M.

    2013-12-01

    Studies of the temporal dynamics of microbial communities attached to suspended sediments in the Arctic rivers have revealed systematic seasonal changes in microbial community composition, based on 16S ribosomal DNA (rDNA) sequencing (Crump et al., 2007). A time series investigation of the Fraser River system in British Columbia has been conducted with approximately bi-weekly sampling since (2009). The results show significant seasonal variations in many chemical parameters (e.g. nutrient and major element concentrations). An investigation of microbial diversity in the Fraser River is important to understand linkages between microbial diversity and the biogeochemistry of Fraser River water and the particles it transports. The results are the beginning of data analysis to the framework of annual changes that may pose as a threat to biodiversity. Previous studies have shown that decreases in river microbial biodiversity can be linked to decreases in water quality and changes in seasonal water flow (Brown et al., 2007; Vörösmarty et al., 2010). Analysis of microbial DNA (rDNA) attached to the suspended sediment load has not been conducted before on the Fraser River system. The results from this study will therefore establish a bench-mark against which future changes in the Fraser River basin can be compared, it will also serve as an example of seasonal dynamics in microbial community diversity for comparison with other temperate rivers. Such potential changes are of great significance as the Fraser River system is one of the prime salmon spawning river basins in the world. Brown L. E. et al. (2007) Vulnerability of alpine stream biodiversity to shrinking glaciers and snowpacks. Global Change Biology 13, 958-966. Crump B. C. et al. (2007) Biogeography of bacterioplankton in lakes and streams of an arctic tundra catchment. Ecology 88, 1365-1378. Vörösmarty C. J. et al. (2010) Global threats to human water security and river biodiversity. Nature 467, 555-561.

  2. Abyssal Sequestration of Nuclear Waste in Earth's Crust

    Germanovich, L. N.; Garagash, D.; Murdoch, L. C.; Robinowitz, M.

    2013-12-01

    This work outlines a new method for disposing of hazardous (e.g., nuclear) waste. The technique is called Abyssal Sequestration, and it involves placing the waste at extreme depths in Earth's crust where it could achieve the geologically-long period of isolation. Abyssal Sequestration involves storing the waste in hydraulic fractures driven by gravity, a process we term gravity fracturing. In short, we suggest creating a dense fluid (slurry) containing waste, introducing the fluid into a fracture, and extending the fracture downward until it becomes long enough to propagate independently. The fracture will continue to propagate downward to great depth, permanently isolating the waste. Storing solid wastes by mixing them with fluids and injecting them into hydraulic fractures is a well-known technology. The essence of our idea differs from conventional hydraulic fracturing techniques only slightly in that it uses fracturing fluid heavier than the surrounding rock. This difference is fundamental, however, because it allows hydraulic fractures to propagate downward and carry wastes by gravity instead of or in addition to being injected by pumping. An example of similar gravity-driven fractures with positive buoyancy is given by magmatic dikes that may serve as an analog of Abyssal Sequestration occurring in nature. Mechanics of fracture propagation in conditions of positive (diking) and negative (heavy waste slurry) buoyancy is similar and considered in this work for both cases. Analog experiments in gelatin show that fracture breadth (horizontal dimension) remains nearly stationary when fracturing process in the fracture 'head' (where breadth is 'created') is dominated by solid toughness, as opposed to the viscous fluid dissipation dominant in the fracture tail. We model propagation of the resulting 'buoyant' or 'sinking' finger-like fracture of stationary breadth with slowly varying opening along the crack length. The elastic response of the crack to fluid loading

  3. Oxygen dynamics in periphyton communities and associated effects on phosphorus release from lake sediments

    Periphyton is typically a heterogeneous assemblage of filamentous and single celled photoautotrophic and heterotrophic micoorganisms suspended in a mucopolysaccharide matrix which they produce. By definition, the assemblage is attached to a substratum such as rock, sediment, or plant in an aquatic environment. Microtechniques with high spatial and temporal resolution are required to define metabolic interactions among the heterotrophic and autotrophic constituents, and between periphyton and its environment. This study used oxygen sensitive microelectrodes with tip diameters of 32P radiotracer and that permitted manipulation of the velocity, flushing rate, and oxygen concentration of overlying water was developed to investigate the role of photosynthetic oxygen production on the phosphorus dynamics in lake sediments colonized by epipelic periphyton. 89 refs., 20 figs

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

    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

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

    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

  6. Methane seep in shallow-water permeable sediment harbors high diversity of anaerobic methanotrophic communities, Elba, Italy

    S Emil Ruff

    2016-03-01

    Full Text Available 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

  7. Microbial Community Response to Carbon Substrate Amendment in Mercury Impacted Sediments: Implications on Microbial Methylation of Mercury.

    Elias, D. A.; Somenahally, A. C.; Moberly, J. G.; Hurt, R. A., Jr.; Brown, S. D.; Podar, M.; Palumbo, A. V.; Gilmour, C. C.

    2015-12-01

    Methylmercury (MeHg) is a neurotoxic and bio-accumulative product of the microbial methylation of inorganic mercury (Hg(II)). Methylating organisms are now known to exist in almost all anaerobic niches including fermentation, Fe(III)- and sulfate- reduction as well as methanogenesis. The study objective was to determine the effect of different carbon sources on the microbial community and methylating populations in particular along a Hg contaminated creek. Sediment cores from upstream and downstream at the Hg contaminated East Fork Poplar Creek (EFPC), Oak Ridge TN, and a background site were sectioned by depth, and Hg-methylation potential (HgMP) assays were performed using stable isotope spikes. Sediments from the lowest depth possessed the highest in-situ activity. Replicate samples were amended with different carbon substrates (cellulose, acetate, propionate, lactate, ethanol and methanol), spiked with stable isotopes for HgMP assays and incubated for 24hrs. Sequencing of the 16S rRNA gene was performed to determine alterations in Bacterial and Archaeal population dynamics. Additionally, bioinformatics and our new qualitative and quantitative hgcAB primers were utilized to determine microbial community structure alterations and correlate organism and gene abundance with altered MeHg generation. HgMP was significantly reduced in cellulose amended sediments while acetate and propionate slightly decreased HgMP in both sites. Methanol, ethanol and lactate increased the HgMP in EFPC downstream while cellulose amendment significantly decreased the Proteobacteria, and the Firmicutes increased but none are currently known to produce MeHg. Geobacter bemidjiensis in particular significantly decreased in cellulose amended sediments in all three sites from being predominant in-situ. This suggests that in EFPC downstream and background sites, the prevalent Hg-methyaltors might be Deltaprotebacteria, since upstream, cellulose amendment did not reduce HgMP even though

  8. Concretionary methane-seep carbonates and associated microbial communities in Black Sea sediments

    Reitner, J.; Peckmann, J.; M. Blumenberg; W. Michaelis; Reimer, A; V. Thiel

    2005-01-01

    Gas seeps in the euxinic northwestern Black Sea provide an excellent opportunity to study anaerobic, methane-based ecosystems with minimum interference from oxygen-dependent processes. An integrated approach using fluorescence- and electron microscopy, fluorescence in situ hybridization, lipid biomarkers, stable isotopes (δ13C), and petrography revealed insight into the anatomy of concretionary methane-derived carbonates currently forming within the sediment around seeps. Some of the carbonat...

  9. Coral community structure and sedimentation at different distances from the coast of the Abrolhos Bank, Brazil

    Bárbara Segal

    2011-06-01

    Full Text Available Sedimentation has previously been considered an important source of impact in coral reefs. We compared 3 sites on the Abrolhos Bank, Brazil, regarding sedimentation rates, carbonate sediment composition, coral cover, and colony size for the commonest local coral species (Mussismilia braziliensis, Siderastrea stellata, and Favia gravida. The sites are located at different distances from the mainland: Pedra de Leste (14 km, Pontas Sul (26 km, and Parcel dos Abrolhos (58 km. Sedimentation was higher in winter (p A sedimentação tem sido considerada uma importante fonte de impacto nos recifes de coral. Uma comparação entre as taxas de sedimentação, teor de carbonatos nos sedimentos, cobertura coralínea e tamanho de colônias de corais para as espécies mais comuns (Mussismilia braziliensis, Siderastrea stellata, e Favia gravida foi realizada em 3 locais no Banco dos Abrolhos. Os locais representam um gradiente de distância da costa: Pedra de Leste (14 km, Pontas Sul (26 km e Parcel dos Abrolhos (58 km. A sedimentação foi maior no inverno (p <0,05, mas não foi observada diferença entre os locais. O tipo de sedimento diferiu entre locais (P <0,05, sendo que Parcel dos Abrolhos apresentou 90% de carbonatos, Pontas Sul 65% e Pedra de Leste 50%. A cobertura coralínea foi maior no local mais afastado de terra (p <0,01, onde a cobertura de zoantídeos foi menor. Diferenças de tamanho de colônias foram encontradas apenas para M. braziliensis, com menores colônias em Pedra de Leste (p <0,05. A distribuição dos sedimentos terrígenos e a turbidez devem ser os principais fatores controladores do desenvolvimento dos recifes de Abrolhos.

  10. The impacts of thermokarst on sediment, organic matter, and macroinvertebrate community dynamics in arctic headwater streams

    Flinn, M.; Kampman, J.; Larouche, J. R.; Bowden, W. B.

    2010-12-01

    Recent research has documented changes in arctic climate that influence permafrost degradation and the incidence of thermokarst formation. In 2009 and 2010, we examined several thermokarst failures on headwater streams near Toolik Lake, AK, and the Kelly River area of the Noatak National Preserve, AK, USA. We quantified significant differences between reference (upstream) and impacted stream reaches affected by these thermokarst features. Sediment deposition at Toolik in 2009, measured with sediment traps, showed no differences in the organic fractions; however, the inorganic fraction was ~2x higher (PChironomidae) abundance and biomass doubled in the impacted reaches by late summer, mostly due to Dicrotopus, Psudokiefferiella, and Rheotanytarsus. Nemoura (Plecoptera, Nemouridae), a shredding stonefly, abundance and biomass were over 5x higher in the impacted reaches (PChironomidae) showed a 3-fold decrease in the impacted reaches (P<0.05). Results from several years of research indicate that thermokarst failures result in impacts that respond on different temporal scales. High sediment loading during initiation results in negative impacts on primary production and ecosystem function; however, the duration of these effects on primary consumers may diminish relatively quickly downstream and over time. Further research on these failures will help us to determine the trajectory of recovery.

  11. Abyssal fauna of the UK-1 polymetallic nodule exploration claim, Clarion-Clipperton Zone, central Pacific Ocean: Echinodermata

    Glover, Adrian G.; Wiklund,Helena; Rabone, Muriel; Amon, Diva J; Smith, Craig R.; O'Hara,Tim; Mah, Christopher L.; Dahlgren, Thomas G

    2016-01-01

    Abstract We present data from a DNA taxonomy register of the abyssal benthic Echinodermata collected as part of the Abyssal Baseline (ABYSSLINE) environmental survey cruise ‘AB01’ to the UK Seabed Resources Ltd (UKSRL) polymetallic-nodule exploration claim ‘UK-1’ in the eastern Clarion-Clipperton Zone (CCZ), central Pacific Ocean abyssal plain. Morphological and genetic data are presented for 17 species (4 Asteroidea , 4 Crinoidea , 2 Holothuroidea and 7 Ophiuroidea ) identified by a combinat...

  12. Integrated ecotoxicological assessment of marine sediments affected by land-based marine fish farm effluents: physicochemical, acute toxicity and benthic community analyses.

    Silva, C; Yáñez, E; Martín-Díaz, M L; Riba, I; DelValls, T A

    2013-08-01

    An integrated ecotoxicological assessment of marine sediments affected by land-based marine fish farm effluents was developed using physicochemical and benthic community structure analyses and standardised laboratory bioassays with bacteria (Vibrio fischeri), amphipods (Ampelisca brevicornis) and sea urchin larvae (Paracentrotus lividus). Intertidal sediment samples were collected at five sites of the Rio San Pedro (RSP) creek, from the aquaculture effluent to a clean site. The effective concentration (EC50) from bacterial bioluminescence and A. brevicornis survival on whole sediments and P. lividus larval developmental success on sediment elutriates were assessed. Numbers of species, abundance and Shannon diversity were the biodiversity indicators measured in benthic fauna of sediment samples. In parallel, redox potential, pH, organic matter and metal levels (Cd, Cu, Ni, Pb and Zn) in the sediment and dissolved oxygen in the interstitial water were measured in situ. Water and sediment physicochemical analysis revealed the exhibition of a spatial gradient in the RSP, evidenced by hypoxia/anoxia, reduced and acidic conditions, high organic enrichment and metal concentrations at the most contaminated sites. Whereas, the benthic fauna biodiversity decreased the bioassays depicted decreases in EC50, A. brevicornis survival, P. lividus larval success at sampling sites closer to the studied fish farms. This study demonstrates that the sediments polluted by fish farm effluents may lead to alterations of the biodiversity of the exposed organisms. PMID:23681739

  13. Diversity of active microbial communities subjected to long-term exposure to chemical contaminants along a 40-year-old sediment core.

    Kaci, Assia; Petit, Fabienne; Fournier, Matthieu; Cécillon, Sébastien; Boust, Dominique; Lesueur, Patrick; Berthe, Thierry

    2016-03-01

    In estuarine ecosystems, metallic and organic contaminants are mainly associated with fine grain sediments which settle on mudflats. Over time, the layers of sediment accumulate and are then transformed by diagenetic processes mainly controlled by microbial activity, recording the history of the estuary's chemical contamination. In an environment of this specific type, we investigated the evolution of the chemical contamination and the structure of both total and active microbial communities, based on PhyloChip analysis of a 4.6-m core corresponding to a 40-year sedimentary record. While the archaeal abundance remained constant along the core, a decrease by one order of magnitude in the bacterial abundance was observed with depth. Both total and active microbial communities were dominated by Proteobacteria, Actinobacteria, and Firmicutes in all sediment samples. Among Proteobacteria, alpha-Proteobacteria dominated both total (from 37 to 60 %) and metabolically active (from 19.7 to 34.6 %) communities, including the Rhizobiales, Rhodobacter, Caulobacterales, and Sphingomonadales orders. Co-inertia analysis revealed a relationship between polycyclic aromatic hydrocarbons, zinc and some polychlorobiphenyls concentrations, and the structure of total and active microbial communities in the oldest and most contaminated sediments (from 1970 to 1975), suggesting that long-term exposure to chemicals shaped the structure of the microbial community. PMID:25934230

  14. Adaption of the microbial community to continuous exposures of multiple residual antibiotics in sediments from a salt-water aquacultural farm.

    Xi, Xiuping; Wang, Min; Chen, Yongshan; Yu, Shen; Hong, Youwei; Ma, Jun; Wu, Qian; Lin, Qiaoyin; Xu, Xiangrong

    2015-06-15

    Residual antibiotics from aquacultural farming may alter microbial community structure in aquatic environments in ways that may adversely or positively impact microbially-mediated ecological functions. This study investigated 26 ponds (26 composited samples) used to produce fish, razor clam and shrimp (farming and drying) and 2 channels (10 samples) in a saltwater aquacultural farm in southern China to characterize microbial community structure (represented by phospholipid fatty acids) in surface sediments (0-10 cm) with long-term exposure to residual antibiotics. 11 out of 14 widely-used antibiotics were quantifiable at μg kg(-1) levels in sediments but their concentrations did not statistically differ among ponds and channels, except norfloxacin in drying shrimp ponds and thiamphenicol in razor clam ponds. Concentrations of protozoan PLFAs were significantly increased in sediments from razor clam ponds while other microbial groups were similar among ponds and channels. Both canonical-correlation and stepwise-multiple-regression analyses on microbial community and residual antibiotics suggested that roxithromycin residuals were significantly related to shifts in microbial community structure in sediments. This study provided field evidence that multiple residual antibiotics at low environmental levels from aquacultural farming do not produce fundamental shifts in microbial community structure. PMID:25746569

  15. Response of Archaeal Communities in Beach Sediments to Spilled Oil and Bioremediation

    Röling, Wilfred F. M.; Couto de Brito, Ivana R.; Swannell, Richard P. J.; Head, Ian M.

    2004-01-01

    While the contribution of Bacteria to bioremediation of oil-contaminated shorelines is well established, the response of Archaea to spilled oil and bioremediation treatments is unknown. The relationship between archaeal community structure and oil spill bioremediation was examined in laboratory microcosms and in a bioremediation field trial. 16S rRNA gene-based PCR and denaturing gradient gel analysis revealed that the archaeal community in oil-free laboratory microcosms was stable for 26 day...

  16. Effects of acid mine drainage on water, sediment and associated benthic macroinvertebrate communities

    The toxic constituents of abandoned mined land (AML) discharges (acidic pH, heavy metals, total suspended solids) are extremely toxic to aquatic life . Studies were undertaken to ascertain environmental impacts to the upper Powell River, Lee and Wise Counties, Va. These impacts included disruptions in physical water quality, sediment quality, altered benthic macroinvertebrate assemblages, and toxicity of the water column and sediments from short-term impairment bioassays, and the potential to bioaccumulate selected metals (Al, Fe, Mn, P, Zn, Cu, Mg, S, Ni, Cd) by periphyton and resident bivalves. Water chemistry and macroinvertebrate assemblages were collected at upstream control, just below acid mine drainage and other downstream sites. Selected trace metal concentrations (Al, Fe, Mn, P, Zn, Cu, Mg, S, Ni, Cd) were determined for water, sediment and resident bivalves using ICP-AES. Acidic pH ranged from 2.15--3.3 at three AML-influenced seeps and varied from 6.4--8.0 at reference stations. At one AML-influenced creek, acidic pH conditions worsened from summer to fall and eradicated aquatic life throughout a 1.5 km stretch of that creek as it flowed into another creek. An additional dilution of 3.4 km in the second creek was needed to nearly neutralize the acidic pH problem. Conductivity (umhos/cm) ranged from 32--278 at reference sites and from 245--4,180 at AML-impact sites. Benthic macroinvertebrate abundance and taxon richness were essentially eliminated in the seeps or reached numbers of 1 -3 taxa totaling < 10 organisms relative to reference areas where richness values were 12--17 and comprised 300--977 organisms. Concentrations of Fe, Al, Mg and Cu and Zn were highest in the environmentally stressed stations of low pH and high conductivity relative to the reference stations. Iron was, by far, the element in highest concentration followed by Al and Mg

  17. Effect of Wastewater Treatment Plant Effluent on Microbial Function and Community Structure in the Sediment of a Freshwater Stream with Variable Seasonal Flow▿

    Wakelin, Steven A.; Colloff, Matt J.; Kookana, Rai S.

    2008-01-01

    We investigated the effects of wastewater treatment plant (WWTP) discharge on the ecology of bacterial communities in the sediment of a small, low-gradient stream in South Australia. The quantification of genes involved in the biogeochemical cycling of carbon and nitrogen was used to assess potential impacts on ecosystem functions. The effects of disturbance on bacterial community structure were assessed by PCR-denaturing gradient gel electrophoresis of 16S rRNA genes, and clone library analy...

  18. The response of abyssal organisms to low pH conditions during a series of CO2-release experiments simulating deep-sea carbon sequestration

    Barry, J. P.; Buck, K. R.; Lovera, C.; Brewer, P. G.; Seibel, B. A.; Drazen, J. C.; Tamburri, M. N.; Whaling, P. J.; Kuhnz, L.; Pane, E. F.

    2013-08-01

    The effects of low-pH, high-pCO2 conditions on deep-sea organisms were examined during four deep-sea CO2 release experiments simulating deep-ocean C sequestration by the direct injection of CO2 into the deep sea. We examined the survival of common deep-sea, benthic organisms (microbes; macrofauna, dominated by Polychaeta, Nematoda, Crustacea, Mollusca; megafauna, Echinodermata, Mollusca, Pisces) exposed to low-pH waters emanating as a dissolution plume from pools of liquid carbon dioxide released on the seabed during four abyssal CO2-release experiments. Microbial abundance in deep-sea sediments was unchanged in one experiment, but increased under environmental hypercapnia during another, where the microbial assemblage may have benefited indirectly from the negative impact of low-pH conditions on other taxa. Lower abyssal metazoans exhibited low survival rates near CO2 pools. No urchins or holothurians survived during 30-42 days of exposure to episodic, but severe environmental hypercapnia during one experiment (E1; pH reduced by as much as ca. 1.4 units). These large pH reductions also caused 75% mortality for the deep-sea amphipod, Haploops lodo, near CO2 pools. Survival under smaller pH reductions (ΔpH<0.4 units) in other experiments (E2, E3, E5) was higher for all taxa, including echinoderms. Gastropods, cephalopods, and fish were more tolerant than most other taxa. The gastropod Retimohnia sp. and octopus Benthoctopus sp. survived exposure to pH reductions that episodically reached -0.3 pH units. Ninety percent of abyssal zoarcids (Pachycara bulbiceps) survived exposure to pH changes reaching ca. -0.3 pH units during 30-42 day-long experiments.

  19. Nitrobenzene biodegradation ability of microbial communities in water and sediments along Songhua River after a nitrobenzene pollution event

    LI Zonglai; YANG Min; LI Dong; QI Rong; LIU Huijuan; SUN Jingfang; QU Jiuhui

    2008-01-01

    More than 100 t of nitrobenzene (NB) and related compounds were discharged into the Songhua River, the fourth longest river in China, because of the world-shaking explosion of an aniline production factory located in Jilin City on November 13, 2005. As one of the efforts to predict the fate of residual NB in the river, NB biodegradation abilities of the microbes in the water and sediments from different river sections were evaluated systematically. The results indicated that microbial communities from any section of the river, including one section at the upper stream of the NB discharging point, had the ability to biodegrade NB under aerobic (for river water samples) conditions at 22±1℃ or anaerobic (for sediment samples) conditions at 10±1℃. NB degradation rates of microbial communities in the downstream sites were markedly higher than those in the upstream site, indicating that the NB degradation abilities were enhanced because of the pollution of NB. Aerobic degradation got neglected at a temperature of 10℃ or lower. The production of nitrosobenzene and aniline during the aerobic biodegradation suggested the existence of at least two different NB degradation pathways, and the occurrence of the catechol-2,3-dioxygenase (C23O) gene and the significant decrease of dissolved organic carbon (DOC) indicated that NB could be mineralized under aerobic conditions. Although it was a fact that the river have frozen-up during the NB accident, it was speculated that biodegradation was not the major process responsible for the decrease of NB flux in the river.

  20. Evaluating bacterial community structures in oil collected from the sea surface and sediment in the northern Gulf of Mexico after the Deepwater Horizon oil spill.

    Liu, Zhanfei; Liu, Jiqing

    2013-06-01

    Bacterial community structures were evaluated in oil samples using culture-independent pyrosequencing, including oil mousses collected on sea surface and salt marshes during the Deepwater Horizon oil spill, and oil deposited in sediments adjacent to the wellhead 1 year after the spill. Phylogenetic analysis suggested that Erythrobacter, Rhodovulum, Stappia, and Thalassospira of Alphaproteobacteria were the prevailing groups in the oil mousses, which may relate to high temperatures and strong irradiance in surface Gulf waters. In the mousse collected from the leaves of Spartina alterniflora, Vibrio of Gammaproteobacteria represented 57% of the total operational taxonomic units, suggesting that this indigenous genus is particularly responsive to the oil contamination in salt marshes. The bacterial communities in oil-contaminated sediments were highly diversified. The relatively high abundance of the Methylococcus, Methylobacter, Actinobacteria, Firmicutes, and Chlorofexi bacteria resembles those found in certain cold-seep sediments with gas hydrates. Bacterial communities in the overlying water of the oil-contaminated sediment were dominated by Ralstonia of Betaproteobacteria, which can degrade small aromatics, and Saccharophagus degradans of Gammaproteobacteria, a cellulose degrader, suggesting that overlying water was affected by the oil-contaminated sediments, possibly due to the dissolution of small aromatics and biosurfactants produced during biodegradation. Overall, these results provided key information needed to evaluate oil degradation in the region and develop future bioremediation strategies. PMID:23568850

  1. Comparative analysis of bacterial community-metagenomics in coastal Gulf of Mexico sediment microcosms following exposure to Macondo oil (MC252)

    Koo, Hyunmin

    2014-09-10

    The indigenous bacterial communities in sediment microcosms from Dauphin Island (DI), Petit Bois Island (PB) and Perdido Pass (PP) of the coastal Gulf of Mexico were compared following treatment with Macondo oil (MC252) using pyrosequencing and culture-based approaches. After quality-based trimming, 28,991 partial 16S rRNA sequence reads were analyzed by rarefaction, confirming that analyses of bacterial communities were saturated with respect to species diversity. Changes in the relative abundances of Proteobacteria, Bacteroidetes and Firmicutes played an important role in structuring bacterial communities in oil-treated sediments. Proteobacteria were dominant in oil-treated samples, whereas Firmicutes and Bacteroidetes were either the second or the third most abundant taxa. Tenericutes, members of which are known for oil biodegradation, were detected shortly after treatment, and continued to increase in DI and PP sediments. Multivariate statistical analyses (ADONIS) revealed significant dissimilarity of bacterial communities between oil-treated and untreated samples and among locations. In addition, a similarity percentage analysis showed the contribution of each species to the contrast between untreated and oil-treated samples. PCR amplification using DNA from pure cultures of Exiguobacterium,  Pseudoalteromonas,  Halomonas and Dyadobacter, isolated from oil-treated microcosm sediments, produced amplicons similar to polycyclic aromatic hydrocarbon-degrading genes. In the context of the 2010 Macondo blowout, the results from our study demonstrated that the indigenous bacterial communities in coastal Gulf of Mexico sediment microcosms responded to the MC252 oil with altered community structure and species composition. The rapid proliferation of hydrocarbonoclastic bacteria suggests their involvement in the degradation of the spilt oil in the Gulf of Mexico ecosystem.

  2. Abyssal macrofauna of the Kuril-Kamchatka Trench area (Northwest Pacific) collected by means of a camera-epibenthic sledge

    Brandt, A.; Elsner, N. O.; Malyutina, M. V.; Brenke, N.; Golovan, O. A.; Lavrenteva, A. V.; Riehl, T.

    2015-01-01

    Abyssal macrofaunal composition of 21 epibenthic sledge hauls from twelve stations taken in the Kuril-Kamchatka Trench (KKT) and at the adjacent abyssal plain, Northwest Pacific, is presented. Sampling with the fine meshed epibenthic sledge yielded higher abundances and species richness than was reported from previous expeditions from board of RV Vityaz. In total 84,651 invertebrates were sampled with RV Sonne between July and September of 2012 (31,854 invertebrates if standardised for 1000 m2 trawled distances) from 41 taxa of different taxonomic ranks (15 phyla, 28 classes, 7 orders) were sampled from a trawled area of 53,708 m² and have been analyzed. Few taxa were frequent and most taxa were rare in the samples, twelve taxa occurred with more than 1% frequency. Of these, the Polychaeta were most abundant followed by the benthic Copepoda and Isopoda. Total numbers of individuals varied between stations and were highest with 4238 individuals at station 2-10 close to the KKT in 4865 m depth and lowest with 374 individuals at station 6-11 in 5305 m depth. At this station also the lowest number of taxa occurred (18 taxa) while the highest number occurred with 31 taxa at station 3-9 in 4991 m depth. Numbers of individuals decreased with increasing depth between 4830 and 5780 m. Crustaceans of the superorder Peracarida were one of the dominating taxa with four orders occurring frequently in most samples. In total, Isopoda were most important and occurred with 59% of all peracarid orders sampled, followed by Amphipoda with 21%, Tanaidacea with 11%, Cumacea with 9%, and Mysidacea with abyssal area differ in terms of taxon composition from each other. A cluster analysis (nMDS) performed for all sampled stations revealed no clear pattern of community similarity between stations or hauls. All hauls close to the trench (2-9 and 2-10 close to the eastern slope of the KKT; and 3-9 and 4-3 at the western slope) were most different to the other hauls. Hauls 8-9 and 8-12 as

  3. Radiocarbon studies of organic compound classes in plankton and sediment of the northeastern Pacific Ocean

    Wang, XC; Druffel, ERM; Griffin, S.; C. Lee; Kashgarian, M.

    1998-01-01

    Radiocarbon (Δ14C) and stable carbon isotopes (δ13C) were measured in total hydrolyzable amino acid (THAA), total carbohydrate (TCHO), total lipid, and acid-insoluble organic fractions that had been separated from phytoplankton, zooplankton, sediment floc, and sediment samples from an abyssal site in the northeastern Pacific Ocean. THAA, TCHO, and lipid fractions accounted for 91-99% of the total organic carbon (TOC) in phytoplankton and zooplankton, 57% of TOC in sediment floc, and 18-38% of...

  4. Dynamics of microalgal communities in the water-column/sediment interface of the inner shelf off Parana State, Southern Brazil

    Ricardo Luiz Queiroz

    2004-12-01

    Full Text Available The composition and biomass of the microalgal community at the water-column/sediment interface on the continental shelf off Parana State (Brazil were studied every 2 months during 1999. Samples for cell identification and determination of chlorophyll a were taken from the interface layer and at discrete depths up to 4 m above the sediment. Results showed a community mainly formed by benthic and planktonic diatoms >30 µm, benthic diatoms 30 µm, which accounted for most of the pigment biomass, were resuspended from the interface after turbulent periods, and may take advantage of calm periods to stay and grow at the interface. Small benthic diatoms were more susceptible to wind-induced turbulence occurring in higher densities in the water column just above the water-sediment interface. A cyanobacterial bloom (Trichodesmiun was observed at these bottom layers in the spring-summer periods.A composição geral e a biomassa da comunidade microalgal da interface sedimento/água da plataforma do Estado do Paraná (Brasil foram estudadas em 1999 em relação ao regime de ventos. A cada dois meses foram coletadas amostras para a identificação de organismos e determinação de clorofila a, na interface água-sedimento e em profundidades discretas, ao longo da coluna d'água, até 4m acima do sedimento. Os resultados obtidos revelaram uma comunidade constituída principalmente por diatomáceas planctônicas e bentônicas maiores que 30 µm, diatomáceas bentônicas menores que 30 µm, e cianobactérias coloniais. As densidades celulares foram geralmente mais altas na interface. Eventos de mistura e sedimentação parecem ser determinantes na regulação da composição e biomassa de tais comunidades. Formas menores, mais susceptíveis à turbulência, dominaram a comunidade de água de fundo na maioria das ocasiões, e foram as mais abundantes na interface apenas em períodos de extrema estabilidade. Células maiores, aparentemente contendo a maior parte

  5. Assessment of sediment metal contamination in the Mar Menor coastal lagoon (SE Spain: Metal distribution, toxicity, bioaccumulation and benthic community structure

    2005-01-01

    Full Text Available The Mar Menor coastal lagoon is one of the largest of the Mediterranean Sea. Ancient mining activities in the mountains near its southern basin have resulted in metal contamination in the sediment. The metal bioavailability of these sediments was determined through laboratory toxicity bioassays using three Mediterranean sea urchin species and two amphipod species, and by means of field bioaccumulation measurements involving the seagrass Cymodocea nodosa. The effect of sediment metal contamination on benthic communities was assessed through benthic infaunal analyses, applying classical descriptive parameters and multivariate techniques. The sediments affected by the mining activities presented high levels of toxicity and metals were also accumulated in the seagrass tissues, pointing to metal bioavailability. Although the classical benthic indices were not clear indicators of disturbance, the multivariate techniques applied provided more consistent conclusions.

  6. Sub-fossils of cladocerans in the surface sediment of 135 lakes as proxies for community structure of zooplankton, fish abundance and lake temperature

    Jeppesen, E.; Jensen, J. P.; Lauridsen, T. L.;

    2003-01-01

    pelagic zone. However, in most lakes the abundance of Ceriodaphnia was higher in the sediment than in the water, which may be attributed to the overall preference by this genus for the littoral habitat. Using contemporary data from 27 Danish lakes sampled fortnightly during summer for 10 years, we found......To elucidate the possibilities of using zooplankton remains in the surface sediment to describe present-days community structure and population dynamics of zooplankton, fish abundance and temperature, we compared contemporary data sampled in the pelagial during summer with the sediment record from...... the upper 1 cm of the sediment in 135 lakes covering a latitude gradient from Greenland in the north to New Zealand in the south. The abundance of three genera Bosmina, Daphnia and Ceriodaphnia of the total pool of ephippia was significantly related to the total abundance of the same taxa in the...

  7. Spatial and temporal variability of bacterial communities in high alpine water spring sediments.

    Esposito, Alfonso; Engel, Michael; Ciccazzo, Sonia; Daprà, Luca; Penna, Daniele; Comiti, Francesco; Zerbe, Stefan; Brusetti, Lorenzo

    2016-05-01

    Water springs are complex, fragile and taxa-rich environments, especially in highly dynamic ecosystems such as glacier forefields experiencing glacier retreat. Bacterial communities are important actors in alpine water body metabolism, and have shown both high seasonal and spatial variations. Seven springs from a high alpine valley (Matsch Valley, South Tyrol, Italy) were examined via a multidisciplinary approach using both hydrochemical and microbiological techniques. Amplified ribosomal intergenic spacer analysis (ARISA) and electric conductivity (EC) measurements, as well as elemental composition and water stable isotopic analyses, were performed. Our target was to elucidate whether and how bacterial community structure is influenced by water chemistry, and to determine the origin and extent of variation in space and time. There existed variations in both space and time for all variables measured. Diversity values more markedly differed at the beginning of summer and then at the end; the extent of variation in space was prevalent over the time scale. Bacterial community structural variation responded to hydrochemical parameter changes; moreover, the stability of the hydrochemical parameters played an important role in shaping distinctive bacterial communities. PMID:26776565

  8. High resolution study of the spatial distributions of abyssal fishes by autonomous underwater vehicle.

    Milligan, R J; Morris, K J; Bett, B J; Durden, J M; Jones, D O B; Robert, K; Ruhl, H A; Bailey, D M

    2016-01-01

    On abyssal plains, demersal fish are believed to play an important role in transferring energy across the seafloor and between the pelagic and benthic realms. However, little is known about their spatial distributions, making it difficult to quantify their ecological significance. To address this, we employed an autonomous underwater vehicle to conduct an exceptionally large photographic survey of fish distributions on the Porcupine Abyssal Plain (NE Atlantic, 4850 m water depth) encompassing two spatial scales (1-10 km(2)) on and adjacent to a small abyssal hill (240 m elevation). The spatial distributions of the total fish fauna and that of the two dominant morphotypes (Coryphaenoides sp. 1 and C. profundicolus) appeared to be random, a result contrary to common expectation but consistent with previous predictions for these fishes. We estimated total fish density on the abyssal plain to be 723 individuals km(-2) (95% CI: 601-844). This estimate is higher, and likely more precise, than prior estimates from trawl catch and baited camera techniques (152 and 188 individuals km(-2) respectively). We detected no significant difference in fish density between abyssal hill and plain, nor did we detect any evidence for the existence of fish aggregations at any spatial scale assessed. PMID:27180728

  9. High resolution study of the spatial distributions of abyssal fishes by autonomous underwater vehicle

    Milligan, R. J.; Morris, K. J.; Bett, B. J.; Durden, J. M.; Jones, D. O. B.; Robert, K.; Ruhl, H. A.; Bailey, D. M.

    2016-05-01

    On abyssal plains, demersal fish are believed to play an important role in transferring energy across the seafloor and between the pelagic and benthic realms. However, little is known about their spatial distributions, making it difficult to quantify their ecological significance. To address this, we employed an autonomous underwater vehicle to conduct an exceptionally large photographic survey of fish distributions on the Porcupine Abyssal Plain (NE Atlantic, 4850 m water depth) encompassing two spatial scales (1–10 km2) on and adjacent to a small abyssal hill (240 m elevation). The spatial distributions of the total fish fauna and that of the two dominant morphotypes (Coryphaenoides sp. 1 and C. profundicolus) appeared to be random, a result contrary to common expectation but consistent with previous predictions for these fishes. We estimated total fish density on the abyssal plain to be 723 individuals km‑2 (95% CI: 601–844). This estimate is higher, and likely more precise, than prior estimates from trawl catch and baited camera techniques (152 and 188 individuals km‑2 respectively). We detected no significant difference in fish density between abyssal hill and plain, nor did we detect any evidence for the existence of fish aggregations at any spatial scale assessed.

  10. Modern and fossilized biological communities from sediments of Bolshoy Harbei lake (Bolshezemelskaya tundra, Russia) and their response to climate change

    Tumanov, Oleg; Nazarova, Larisa; Fefilova, Elena; Baturina, Maria; Loskutova, Olga; Frolova, Larisa; Palagushkina, Olga

    2013-04-01

    High-altitude regions are subjected to the threats of global warming. During the last decade the depth of seasonal melting of permafrost in Northern Russia, significantly increased. Investigation of lake sediments from polar regions has an extreme importance for understanding of the modern environmental processes and their influence on northern ecosystems and biological diversity of these regions. Invertebrate communities are used for diagnostic of lake ecosystems because they have a great sensitivity to climatic changes (Andronnikova, 1996; Lazareva, 2008; O'Brien et al., 2005). The data can be used as well as a basis for inference models for reconstruction of the paleoclimatic conditions. Chironomid-based, Cladocera-based and diatom models have successfully been developed (Nazarova et al., 2008, 2011; Self et al., 2011) and can be used for precise paleotemperature reconstructions (Kienast et al., 2011). In summer 2012, we investigated complex of Kharbei lakes, located in the interfluve of Korotaiha and Bolshaya Rogovaya rivers in the east side of Bolshezemelskaya tundra, Russia (67°33'22″ N, 62°53'23″ E). Six different lakes were investigated using modern hydrobiological and palaeoecological methods. In total 9 cores were obtained, cut, dated and further investigated using sedimenthological, geochemical, and paleobiological methods. The standard hydrobiological methods have shown that the modern zooplankton communities did not change significantly during the last 40 years. Taxonomic composition and structure of planktonic communities didn't change, except for appearance of crustaceans Polyarthra euryptera and Daphnia cucullata. In planktonic communities of Bolshoy Harbei lake we revealed 39 species and forms of Rotifera, 19 - Cladocera and 11 - Copepoda. In zoobenthic communities we registered 24 taxonomical groups characteristic for large tundra lakes of the North East of Russia. Chironomids and Oligochaeta are dominant groups of invertebrates. 103 taxa of

  11. The Ability of Microbial Community of Lake Baikal Bottom Sediments Associated with Gas Discharge to Carry Out the Transformation of Organic Matter under Thermobaric Conditions

    Bukin, Sergei V.; Pavlova, Olga N.; Manakov, Andrei Y.; Kostyreva, Elena A.; Chernitsyna, Svetlana M.; Mamaeva, Elena V.; Pogodaeva, Tatyana V.; Zemskaya, Tamara I.

    2016-01-01

    The ability to compare the composition and metabolic potential of microbial communities inhabiting the subsurface sediment in geographically distinct locations is one of the keys to understanding the evolution and function of the subsurface biosphere. Prospective areas for study of the subsurface biosphere are the sites of hydrocarbon discharges on the bottom of the Lake Baikal rift, where ascending fluxes of gas-saturated fluids and oil from deep layers of bottom sediments seep into near-surface sediment. The samples of surface sediments collected in the area of the Posolskaya Bank methane seep were cultured for 17 months under thermobaric conditions (80°C, 5 MPa) with the addition of complementary organic substrate, and a different composition for the gas phase. After incubation, the presence of intact cells of microorganisms, organic matter transformation and the formation of oil biomarkers was confirmed in the samples, with the addition of Baikal diatom alga Synedra acus detritus, and gas mixture CH4:H2:CO2. Taxonomic assignment of the 16S rRNA sequence data indicates that the predominant sequences in the enrichment were Sphingomonas (55.3%), Solirubrobacter (27.5%) and Arthrobacter (16.6%). At the same time, in heat-killed sediment and in sediment without any additional substrates, which were cultivated in a CH4 atmosphere, no geochemical changes were detected, nor the presence of intact cells and 16S rRNA sequences of Bacteria and Archaea. This data may suggest that the decomposition of organic matter under culturing conditions could be performed by microorganisms from low-temperature sediment layers. One possible explanation of this phenomenon is migration of the representatives of the deep thermophilic community through fault zones in the near surface sediment layers, together with gas-bearing fluids. PMID:27242716

  12. Effect of Lake Trophic Status and Rooted Macrophytes on Community Composition and Abundance of Ammonia-oxidizing Prokaryotes in Freshwater Sediments

    Herrmann, Martina; Saunders, Aaron Marc; Schramm, Andreas

    2009-01-01

    and acidic heathland pools. Archaeal and bacterial ammonia monooxygenase alpha-subunit (amoA) gene diversity increased from oligotrophic to mesotrophic sites; the number of detected operational taxonomic units was positively correlated to ammonia availability and pH and negatively correlated to sediment C....../N ratios. AOA communities could be grouped according to lake trophic status and pH; plant species-specific communities were not detected, and no grouping was apparent for AOB communities. Relative abundance, determined by quantitative PCR targeting amoA, was always low for AOB (

  13. Succession of Phenotypic, Genotypic, and Metabolic Community Characteristics during In Vitro Bioslurry Treatment of Polycyclic Aromatic Hydrocarbon-Contaminated Sediments

    Ringelberg, David B.; Talley, Jeffrey W.; Perkins, Edward J.; Tucker, Samuel G.; Luthy, Richard G.; Bouwer, Edward J.; Fredrickson, Herbert L.

    2001-01-01

    Dredged harbor sediment contaminated with polycyclic aromatic hydrocarbons (PAHs) was removed from the Milwaukee Confined Disposal Facility and examined for in situ biodegradative capacity. Molecular techniques were used to determine the successional characteristics of the indigenous microbiota during a 4-month bioslurry evaluation. Ester-linked phospholipid fatty acids (PLFA), multiplex PCR of targeted genes, and radiorespirometry techniques were used to define in situ microbial phenotypic, genotypic, and metabolic responses, respectively. Soxhlet extractions revealed a loss in total PAH concentrations of 52%. Individual PAHs showed reductions as great as 75% (i.e., acenapthene and fluorene). Rates of 14C-PAH mineralization (percent/day) were greatest for phenanthrene, followed by pyrene and then chrysene. There was no mineralization capacity for benzo[a]pyrene. Ester-linked phospholipid fatty acid analysis revealed a threefold increase in total microbial biomass and a dynamic microbial community composition that showed a strong correlation with observed changes in the PAH chemistry (canonical r2 of 0.999). Nucleic acid analyses showed copies of genes encoding PAH-degrading enzymes (extradiol dioxygenases, hydroxylases, and meta-cleavage enzymes) to increase by as much as 4 orders of magnitude. Shifts in gene copy numbers showed strong correlations with shifts in specific subsets of the extant microbial community. Specifically, declines in the concentrations of three-ring PAH moieties (i.e., phenanthrene) correlated with PLFA indicative of certain gram-negative bacteria (i.e., Rhodococcus spp. and/or actinomycetes) and genes encoding for naphthalene-, biphenyl-, and catechol-2,3-dioxygenase degradative enzymes. The results of this study suggest that the intrinsic biodegradative potential of an environmental site can be derived from the polyphasic characterization of the in situ microbial community. PMID:11282603

  14. Anatomy of methane-derived carbonate concretions and associated microbial communities in Black Sea sediments

    Reitner, J.; Peckmann, J.; Reimer, A.; Schumann, G.; Blumenberg, M.; Thiel, V.

    2003-04-01

    Methane seeps on the northwestern shelf and slope of the Black Sea were investigated during the GHOSTDABS expedition with RV "Professor Logachev" and the research submersible "Jago" in July/August 2001. Seep areas close to the Dniepr Canyon are sites of intense carbonate formation. In anoxic waters, at depths between 200 and 400m, we found different modes of carbonate precipitation, such as cavernous chimney-like buildups projecting up to 4 m into the anoxic water column (Michaelis et al., Science 297, 813-815) and, lenticular concretions abundantly forming within the sediment. Isotope analyses of the concretionary Mg-calcite yielded δ13C values as low as -31 ppm PDB, suggesting that the carbonate predominantly derives from the anaerobic oxidation of methane (AOM). The concretions are surrounded by grey, pink, or orange colored microbial mats. These mats apparently mediate the formation of ca. 100 μm sized aggregates of fibrous calcite that fuse together to form the concretions. Surrounding sediment and concretional carbonates are clearly distinguishable by a strong UV-epifluorescence induced by large amounts of organic matter enclosed in the calcite aggregates. The conspicious angular arrangement of the crystallites appears to be controlled by the spatial organization of extracellular polymeric substances (EPS). Fluorescence in situ hybridization, TEM, and field emission electron microscopy reveal that the microbial mats harbour numerous types of microorganisms. Prominent members are large colonies of sulfate reducing bacteria (DSS 658 probe, Desulfosarcina group), surrounded by sheeted, rod-shaped archaea (ANME-1 probe, Methanosaeta group) and further ones. Three different types of AOM consortia are distinguishable. The metabolism of sulfate reducing bacteria apparently accounts for the observed, significant enrichment of the concretions in framboidal Fe-sulfides. In organic extracts from mat samples and concretional carbonate, we found distinctive, isoprene

  15. Use of LH-PCR as a DNA fingerprint technique to trace sediment-associated microbial communities from various land uses

    Joe-Strack, J. A.; Petticrew, E. L.

    2012-04-01

    The search for new techniques to effectively and efficiently trace sediment from its source along catchment pathways continues, with a range of new methods being developed and tested annually. A relatively recent approach marries genetic techniques to sediment analysis in order to characterize and differentiate the bacterial populations associated with soil and/or sediment originating from specific locations. Here we present the preliminary results of DNA fingerprint profiles of soil and sediment-associated bacterial communities in and around two different industrial land uses in the central interior of British Columbia, a feedlot and a copper/gold mining site. We assessed the naturally varying 16S rDNA gene using amplicon length heterogeneity-polymerase chain reaction (LH-PCR). Statistical differences between bacterial community profiles were investigated using a suite of methods of which non-metric multidimensional scaling (NMS) and indicator species analysis (ISA) were the most useful. Stronger statistical results were observed for the feedlot data set with spatial differences observed from the source location and within the adjacent creek. Results from the mine site were more difficult to assess although responses were detected in downstream waterways. While bacterial DNA fingerprinting of soil and sediment appears to be a promising tracing technique issues of scale and transferability may limit its use. Lessons learned from this preliminary study will be presented.

  16. Biogeochemical and microbial variation across 5500 km of Antarctic surface sediment implicates organic matter as a driver of benthic community structure

    Deric R Learman

    2016-03-01

    Full Text Available Western Antarctica, one of the fastest warming locations on Earth, is a unique environment that is underexplored with regards to biodiversity. Although pelagic microbial communities in the Southern Ocean and coastal Antarctic waters have been well studied, there are fewer investigations of benthic communities and most have a focused geographic range. We sampled surface sediment from 24 sites across a 5,500 km region of Western Antarctica (covering the Ross Sea to the Weddell Sea to examine relationships between microbial communities and sediment geochemistry. Sequencing of the 16S and 18S rRNA genes showed microbial communities in sediments from the Antarctic Peninsula (AP and Western Antarctica (WA, including the Ross, Amundsen, and Bellingshausen Seas, could be distinguished by correlations with organic matter concentrations and stable isotope fractionation (total organic carbon; TOC, nitrogen, and δ13C. Overall, samples from the AP were higher in nutrient content (TOC, nitrogen, and NH4+ and communities in these samples had higher relative abundances of operational taxonomic units (OTUs classified as the diatom, Chaetoceros, a marine cercozoan and four OTUs classified as Cytophaga or Flavobacteria. As these OTUs were strongly correlated with TOC, the data suggests the diatoms could be a source of organic matter and the Bacteroidetes and cercozoan are grazers that consume the organic matter. Additionally, samples from WA have lower nutrients and were dominated by Thaumarchaeota, which could be related to their known ability to thrive as lithotrophs. This study documents the largest analysis of benthic microbial communities to date in the Southern Ocean, representing almost half the continental shoreline of Antarctica, and documents trophic interactions and coupling of pelagic and benthic communities. Our results indicate potential modifications in carbon sequestration processes related to change in community composition, identifying a

  17. Structural stability, microbial biomass and community composition of sediments affected by the hydric dynamics of an urban stormwater infiltration basin. Dynamics of physical and microbial characteristics of stormwater sediment.

    Badin, Anne Laure; Monier, Armelle; Volatier, Laurence; Geremia, Roberto A; Delolme, Cécile; Bedell, Jean-Philippe

    2011-05-01

    The sedimentary layer deposited at the surface of stormwater infiltration basins is highly organic and multicontaminated. It undergoes considerable moisture content fluctuations due to the drying and inundation cycles (called hydric dynamics) of these basins. Little is known about the microflora of the sediments and its dynamics; hence, the purpose of this study is to describe the physicochemical and biological characteristics of the sediments at different hydric statuses of the infiltration basin. Sediments were sampled at five time points following rain events and dry periods. They were characterized by physical (aggregation), chemical (nutrients and heavy metals), and biological (total, bacterial and fungal biomasses, and genotypic fingerprints of total bacterial and fungal communities) parameters. Data were processed using statistical analyses which indicated that heavy metal (1,841 μg/g dry weight (DW)) and organic matter (11%) remained stable through time. By contrast, aggregation, nutrient content (NH₄⁺, 53-717 μg/g DW), pH (6.9-7.4), and biological parameters were shown to vary with sediment water content and sediment biomass, and were higher consecutive to stormwater flows into the basin (up to 7 mg C/g DW) than during dry periods (0.6 mg C/g DW). Coinertia analysis revealed that the structure of the bacterial communities is driven by the hydric dynamics of the infiltration basin, although no such trend was found for fungal communities. Hydric dynamics more than rain events appear to be more relevant for explaining variations of aggregation, microbial biomass, and shift in the microbial community composition. We concluded that the hydric dynamics of stormwater infiltration basins greatly affects the structural stability of the sedimentary layer, the biomass of the microbial community living in it and its dynamics. The decrease in aggregation consecutive to rewetting probably enhances access to organic matter (OM), explaining the consecutive release

  18. Epithermal neutron activation analysis investigation of Clarion-Clipperton abyssal plane clay and polymetallic micronodules.

    Duliu, O G; Cristache, C I; Culicovc, O A; Frontasyeva, M V; Szobotca, S A; Toma, M

    2009-05-01

    The content of seven major (Na, Al, Cl, Mn, K, Ca, Ti, Fe) and 30 trace (Sc, V, Cr, Ni, Co, Zn, Cu, As, Sr, Rb, Zr, Mo, Sn, In, Sb, Ba, Cs, La, Ce, Nd, Eu, Sm, Tb, Dy, Yb, Hf, Ta, W, Th, U) elements determined by INAA in 13 samples of abyssal clay and two samples of micronodules collected from the North pacific Ocean Clarion-Clipperton abyssal plane is presented and discussed with respect to some rocks models. PMID:19230682

  19. Bacterial community shift in the coastal Gulf of Mexico salt-marsh sediment microcosm in vitro following exposure to the Mississippi Canyon Block 252 oil (MC252)

    Koo, Hyunmin

    2014-07-10

    In this study, we examined the responses by the indigenous bacterial communities in salt-marsh sediment microcosms in vitro following treatment with Mississippi Canyon Block 252 oil (MC252). Microcosms were constructed of sediment and seawater collected from Bayou La Batre located in coastal Alabama on the Gulf of Mexico. We used an amplicon pyrosequencing approach on microcosm sediment metagenome targeting the V3–V5 region of the 16S rRNA gene. Overall, we identified a shift in the bacterial community in three distinct groups. The first group was the early responders (orders Pseudomonadales and Oceanospirillales within class Gammaproteobacteria), which increased their relative abundance within 2 weeks and were maintained 3 weeks after oil treatment. The second group was identified as early, but transient responders (order Rhodobacterales within class Alphaproteobacteria; class Epsilonproteobacteria), which increased their population by 2 weeks, but returned to the basal level 3 weeks after oil treatment. The third group was the late responders (order Clostridiales within phylum Firmicutes; order Methylococcales within class Gammaproteobacteria; and phylum Tenericutes), which only increased 3 weeks after oil treatment. Furthermore, we identified oil-sensitive bacterial taxa (order Chromatiales within class Gammaproteobacteria; order Syntrophobacterales within class Deltaproteobacteria), which decreased in their population after 2 weeks of oil treatment. Detection of alkane (alkB), catechol (C2,3DO) and biphenyl (bph) biodegradation genes by PCR, particularly in oil-treated sediment metacommunity DNA, delineates proliferation of the hydrocarbon degrading bacterial community. Overall, the indigenous bacterial communities in our salt-marsh sediment in vitro microcosm study responded rapidly and shifted towards members of the taxonomic groups that are capable of surviving in an MC252 oil-contaminated environment.

  20. Abyssal Hill Segmentation: Quantitative analysis of the East Pacific Rise flanks 7°S-9°S

    Goff, John A.; Malinverno, Alberto; Fornari, Daniel J.; Cochran, James R.

    1993-08-01

    The recent R/V Maurice Ewing EW9105 Hydrosweep survey of the East Pacific Rise (EPR) and adjacent flanks between 7°S and 9°S provides an excellent opportunity to explore the causal relationship between the ridge and the abyssal hills which form on its flanks. These data cover 100% of the flanking abyssal hills to 115 km on either side of the axis. We apply the methodology of Goff and Jordan (1988) for estimating statistical characteristics of abyssal hill morphology (rms height, characteristic lengths and widths, plan view aspect ratio, azimuthal orientation, and fractal dimension). Principal observations include the following: (1) the rms height of abyssal hill morphology is negatively correlated with the width of the 5- to 20-km-wide crestal high, consistent with the observations of Goff (1991) for northern EPR abyssal hill morphology; (2) the characteristic abyssal hill width displays no systematic variation with position relative to ridge segmentation within the EW9105 survey area, in contrast with observations of Goff (1991) for northern EPR abyssal hill morphology in which characteristic widths tend to be smallest at segment ends and largest toward the middle of segments; (3) abyssal hill rms heights and characteristic widths are very large just north of a counterclockwise rotating "nannoplate", suggesting that the overlap region is being pushed northward in response to microplate-style tectonics; and (4) within the 7°12'S-8°38'S segment, abyssal hill lineaments are generally parallel to the ridge axis, while south of this area, abyssal hill lineaments rotate with a larger "radius of curvature" than does the EPR axis approaching the EPR-Wilkes ridge-transform intersection.

  1. Vadose zone microbial community structure and activity in metal/radionuclide contaminated sediments. Final technical report

    Balkwill, David L.

    2002-08-17

    This final technical report describes the research carried out during the final two months of the no-cost extension ending 11/14/01. The primary goals of the project were (1) to determine the potential for transformation of Cr(VI) (oxidized, mobile) to Cr(III) (reduced, immobile) under unsaturated conditions as a function of different levels and combinations of (a) chromium, (b) nitrate (co-disposed with Cr), and (c) molasses (inexpensive bioremediation substrate), and (2) to determine population structure and activity in experimental treatments by characterization of the microbial community by signature biomarker analysis and by RT-PCR and terminal restriction fragment length polymorphism (T-RFLP) and 16S ribosomal RNA genes. It was determined early in the one-year no-cost extension period that the T-RFLP approach was problematic in regard to providing information on the identities of microorganisms in the samples examined. As a result, it could not provide the detailed information on microbial community structure that was needed to assess the effects of treatments with chromium, nitrate, and/or molasses. Therefore, we decided to obtain the desired information by amplifying (using TR-PCR, with the same primers used for T-RFLP) and cloning 16S rRNA gene sequences from the same RNA extracts that were used for T-RFLP analysis. We also decided to use a restriction enzyme digest procedure (fingerprinting procedure) to place the clones into types. The primary focus of the research carried out during this report period was twofold: (a) to complete the sequencing of the clones, and (b) to analyze the clone sequences phylogenetically in order to determine the relatedness of the bacteria detected in the samples to each other and to previously described genera and species.

  2. Differences in nutrient concentrations and resources between seagrass communities on carbonate and terrigenous sediments in South Sulawesi, Indonesia

    Erftemeijer, P.L.A.

    1994-01-01

    Water column, sediment and plant parameters were studied in six tropical seagrass beds in South Sulawesi, Indonesia, to evaluate the relation between seagrass bed nutrient concentrations and sediment type. Coastal seagrass beds on terrigenous sediments had considerably higher biomass of phytoplankto

  3. A survey of microbial community diversity in marine sediments impacted by petroleum hydrocarbons from the Gulf of Mexico and Atlantic shorelines, Texas to Florida

    Lisle, John T.; Stellick, Sarah H.

    2011-01-01

    Microbial community genomic DNA was extracted from sediment samples collected along the Gulf of Mexico and Atlantic coasts from Texas to Florida. Sample sites were identified as being ecologically sensitive and (or) as having high potential of being impacted by Macondo-1 (M-1) well oil from the Deepwater Horizon blowout. The diversity within the microbial communities associated with the collected sediments provides a baseline dataset to which microbial community-diversity data from impacted sites could be compared. To determine the microbial community diversity in the samples, genetic fingerprints were generated and compared. Specific sequences within the community genomic DNA were first amplified using the polymerase chain reaction (PCR) with a primer set that provides possible resolution to the species level. A second nested PCR was performed on the primary PCR products using a primer set on which a GC-clamp was attached to one of the primers. The nested PCR products were separated using denaturing-gradient gel electrophoresis (DGGE) that resolves the nested PCR products based on sequence dissimilarities (or similarities), forming a genomic fingerprint of the microbial diversity within the respective samples. Samples with similar fingerprints were grouped and compared to oil-fingerprint data from the same sites (Rosenbauer and others, 2011). The microbial community fingerprints were generally grouped into sites that had been shown to contain background concentrations of non-Deepwater Horizon oil. However, these groupings also included sites where no oil signature was detected. This report represents some of the first information on naturally occurring microbial communities in sediment from shorelines along the Gulf of Mexico and Atlantic coasts from Texas to Florida.

  4. Fine-scale community structure analysis of ANME in Nyegga sediments with high and low methane flux

    Irene eRoalkvam

    2012-06-01

    Full Text Available To obtain knowledge on how regional variations in methane seepage rates influence the stratification, abundance and diversity of anaerobic methanotrophs (ANME we analyzed the vertical microbial stratification in a gravity core from a methane micro-seeping area at Nyegga by using 454-pyrosequencing of 16S rRNA gene tagged amplicons and quantitative PCR. The results were compared with previously obtained data from the more active G11 pockmark, characterized by higher methane flux. A downcore stratification and high relative abundance of ANME was observed in both cores, with transition from an ANME-2a/b dominated community in low-sulfide and low-methane horizons to ANME-1 dominance in horizons near the sulfate methane transition zone (SMTZ. The stratification was over a wider spatial region and at greater depth in the core with lower methane flux, and the total 16S rRNA copy numbers were two orders of magnitude lower than in the sediments at G11 pockmark. A fine-scale view into the ANME communities at each location was achieved through OTU clustering of ANME-affiliated sequences. The majority of ANME-1 sequences from both sampling sites clustered within one OTU, while ANME-2a/b sequences were represented in unique OTUs. We suggest that free living ANME-1 is the most abundant taxon in Nyegga cold seeps, and also the main consumer of methane. The specific ANME-2a/b ecotypes could reflect adaptations to the geochemical composition at each location, with different affinities to methane. Given that the ANME-2a/b population could be sustained in less active seepage areas, this subgroup could be potential seed populations in newly developed methane-enriched environments.

  5. New occurrence of Youngest Toba Tuff in abyssal sediments of the Central Indian Ocean

    Pattan, J.N.; Shane, P.; Banakar, V.K.

    in Malaysia, India (Shane et al., 1995) and the northern Indian Ocean (Dehn et al., 1991) (Fig. 2B). Glass from the CIB can be distinguished from other Toba eruptives, namely the Middle (ca. 500 ka) and Oldest (ca. 840 ka) Toba Tuff correlatives found in core.... Recalculated to 100% on a volatile-free basis. H 2 O by difference. Total Fe expressed as FeO. Youngest Toba analyses from distal fallout sites in India and Malaysia (Shane et al., 1995). J.N. Pattan et al. / Marine Geology 155 (1999) 243–248 247 Fig. 2. (A...

  6. Abyssal sediment erosion from the Central Indian Basin: Evidence from radiochemical and radiolarian studies

    Banakar, V.K.; Gupta, S.M.; Padmavati, V.K.

    -16. Levitus, S., 1982. Climatological Atlas of the World Oceans. Natl. Oceanic Atmos. Admin. Prof. Pap., 13: 172 pp. Mangini, A. and Kuhnel, U., 1987. Depositional history in the Clarion-Clipperton zone during the last 250,000 years - 23°Th and 23tpa...

  7. Effects of microbially induced transformations and shift in bacterial community on arsenic mobility in arsenic-rich deep aquifer sediments.

    Das, Suvendu; Liu, Chia-Chuan; Jean, Jiin-Shuh; Lee, Chuan-Chun; Yang, Huai-Jen

    2016-06-01

    Elevated concentration of arsenic (As) prevailed in deep aquifers of Chianan Plain, Taiwan. Arsenic release in relation to microbially induced transformations and shift in bacterial communities in deep aquifer sediments of Budai, southwestern Taiwan were investigated using microcosm experiments and substrate amendments over 90 days of anaerobic incubation. The results revealed that As reduction was independent of Fe reduction and a modest rate of sedimentary As release into aqueous phase occurred at the expense of the native organic carbon. Addition of lactate resulted in a parallel increase in As(III) (3.7-fold), Fe(II) (6.2-fold) and Mn (3.5 fold) in aqueous phase compared to un-amended slurries and the enrichment of sequences related to mostly Bacillus, Flavisolibacter, and Geobacter spp, suggesting the important role of these bacteria in As enrichment through reductive dissolution of As-bearing Fe and Mn minerals. The increase in phosphate-extractable As in solid phase with concomitant rise in As in aqueous phase over the course of incubation further attested to the importance of reductive dissolution in promoting As release. Furthermore, the increase in arrA gene abundance with addition of labile carbon suggests that dissimilatory As reduction also may contribute to As enrichment in the water of the deep aquifer of Budai. PMID:26897570

  8. LC/IRMS analysis: A powerful technique to trace carbon flow in microphytobenthic communities in intertidal sediments

    Moerdijk-Poortvliet, Tanja C. W.; Stal, Lucas J.; Boschker, Henricus T. S.

    2014-09-01

    Microphytobenthic communities are important for primary production in intertidal marine sediments. Extracellular polymeric substances (EPS), comprising polysaccharides and proteins, play a key role in the structure and functioning of microphytobenthic biofilms and allow interactions between the benthic microalgae and the associated heterotrophic bacteria. The use of stable isotopes has provided major insights into the functioning of these microbial ecosystems. Until recently, gas chromatography-isotope ratio mass spectrometry (GC/IRMS) was the principal method for compound specific stable isotope analysis in these studies. Liquid chromatography linked to IRMS (LC/IRMS) is a more recently developed technique that broadens the range of compounds that can be targeted, in particular enabling the analysis of 13C in non-volatile, aqueous soluble organic compounds, such as carbohydrates and amino acids. In this paper we present an overview of the possibilities and limitations of the LC/IRMS technique to study metabolic processes in microphytobenthic biofilms consisting of mainly diatoms. With a preliminary in-situ labeling experiment, we show that the biosynthesis of carbohydrates and amino acids in EPS and total carbohydrate and amino acid pools can be determined by LC/IRMS. Water extractable EPS were composed predominantly of carbohydrates, whereas amino acids played a minor role, both in terms of content and production. By using LC/IRMS, we will be able to quantify the biosynthesis of metabolites and, hence, to unravel in detail the metabolic pathways of the transfer of carbon from the diatoms via EPS to the bacteria.

  9. Submarine ridges do not prevent large-scale dispersal of abyssal fauna: A case study of Mesocletodes (Crustacea, Copepoda, Harpacticoida)

    Menzel, Lena; George, Kai Horst; Arbizu, Pedro Martínez

    2011-08-01

    We examined the large-scale distribution of deep-sea harpacticoid copepods at the species level, in order to clarify the underlying processes of copepod dispersal. The study was based on samples collected from 12 regions and a total of 113 stations: 57 stations at depths between 1107 and 5655 m on abyssal plains in the South and North Atlantic, Southern Ocean, southern Indian Ocean, and the Pacific Ocean, and 56 stations above 900 m in the North Atlantic and eastern Mediterranean Sea. We chose the genus Mesocletodes Sars, 1909 as an ideal group to study the large-scale distribution of harpacticoid copepods in the deep oceans. Clear apomorphies and a comparatively large body size of about 1 mm allow rapid recognition of allied species in meiofauna samples. In addition, Mesocletodes represents more than 50% of the family Argestidae Por, 1986, one of the most abundant harpacticoid families in the deep sea. The geographical distributions of 793 adult females of Mesocletodes belonging to 61 species throughout the South and North Atlantic, Southern Ocean, southern Indian Ocean, Pacific Ocean, and eastern Mediterranean Sea indicated that most species are cosmopolitan. Neither the topography of the sea bottom nor long distances seem to prevent species from dispersing. Passive transport by bottom currents after resuspension is likely the propulsive factor for the dispersal of Harpacticoida, while plate tectonics and movement of individuals in the sediment may play relatively minor roles.

  10. Temperature response of denitrification and anammox reveals the adaptation of microbial communities to in situ temperatures in permeable marine sediments that span 50° in latitude

    A. Canion

    2013-09-01

    Full Text Available Despite decades of research on the physiology and biochemistry of nitrate/nitrite-respiring microorganisms, little is known regarding their metabolic response to temperature, especially under in situ conditions. The temperature regulation of microbial communities that mediate anammox and denitrification was investigated in near shore permeable sediments at polar, temperate, and subtropical sites with annual mean temperatures ranging from −5 to 23 °C. Total N2 production rates were determined using the isotope pairing technique in intact core incubations under diffusive and simulated advection conditions and ranged from 2 to 359 μmol N m−2 d−1. For the majority of sites studied, N2 removal was 2 to 7 times more rapid under advective flow conditions. Anammox comprised 6 to 14% of total N2 production at temperate and polar sites and was not detected at the subtropical site. Potential rates of denitrification and anammox were determined in anaerobic slurries in a temperature gradient block incubator across a temperature range of −1 to 42 °C. The highest optimum temperature (Topt for denitrification was 36 °C and was observed in subtropical sediments, while the lowest Topt of 21 °C was observed at the polar site. Seasonal variation in the Topt was observed at the temperate site with values of 26 and 34 °C in winter and summer, respectively. The Topt values for anammox were 9 and 26 °C at the polar and temperate sites, respectively. The results demonstrate adaptation of denitrifying communities to in situ temperatures in permeable marine sediments across a wide range of temperatures, whereas marine anammox bacteria may be predominately psychrophilic to psychrotolerant. To our knowledge, we provide the first rates of denitrification and anammox from permeable sediments of a polar permanently cold ecosystem. The adaptation of microbial communities to in situ temperatures suggests that the relationship between temperature and rates of N

  11. Community composition and distribution of sulfate- and sulfite-reducing prokaryotes in sediments from the Changjiang estuary and adjacent East China Sea

    He, Hui; Zhen, Yu; Mi, Tiezhu; Xu, Bochao; Wang, Guoshan; Zhang, Yu; Yu, Zhigang

    2015-11-01

    Sulfate- and sulfite-reducing prokaryotes (SSRP) communities play a vital role in both sulfur and carbon cycles. Community composition and abundance of SSRP were investigated using dissimilatory sulfite reductase β subunit (dsrB) gene sequencing in sediments from the Changjiang estuary and its adjacent area in the East China Sea (ECS). Clone libraries were constructed and real-time fluorescence quantitative polymerase chain reaction (qPCR) was applied to understand the community information of SSRP. In addition to sequences affiliated to sulfate-reducing prokaryotes (SRP), those affiliated with sulfite-reducing prokaryotes (SiRP) were also observed. Four phylotypes of SRP in this study showed genetic similarity to Desulfobulbaceae, Syntrophobacteraceae, Desulfobacteraceae and Peptococcaceae, and an unknown group that could not be clearly affiliated with known lineages was found. Salinity, temperature and contents of total organic carbon (TOC) were most closely correlated with the SSRP communities by canonical correspondence analysis (CCA). 210Pb activities demonstrated the sedimentary environment at S33 was more stable than that at S31. Intense resuspension and reconstruction of sediments made the vertical abundance profile of SSRP fluctuate violently. For surface sediments, the dsrB gene copy numbers near the Changjiang estuary were higher than those in the mouth of Hangzhou Bay and the mud deposits along the Zhejiang coast, and contents of TOC were positively related to the copy numbers of dsrB gene. Our data provided valuable information to achieve a better understanding of the potential role of SSRP in sediments from the Changjiang estuary and adjacent East China Sea.

  12. A comparative study of microbial diversity and community structure in marine sediments using poly(A) tailing and reverse transcription-PCR

    Hoshino, Tatsuhiko; Inagaki, Fumio

    2013-01-01

    To obtain a better understanding of metabolically active microbial communities, we tested a molecular ecological approach using poly(A) tailing of environmental 16S rRNA, followed by full-length complementary DNA (cDNA) synthesis and sequencing to eliminate potential biases caused by mismatching of polymerase chain reaction (PCR) primer sequences. The RNA pool tested was extracted from marine sediments of the Yonaguni Knoll IV hydrothermal field in the southern Okinawa Trough. The sequences o...

  13. A comparative study of microbial diversity and community structure in marine sediments using poly(A) tailing and reverse transcription PCR

    Tatsuhiko eHoshino; Fumio eInagaki

    2013-01-01

    To obtain a better understanding of metabolically active microbial communities, we tested a molecular ecological approach using poly(A) tailing of environmental 16S rRNA, followed by full-length complementary DNA (cDNA) synthesis and sequencing to eliminate potential biases caused by mismatching of PCR primer sequences. The RNA pool tested was extracted from marine sediments of the Yonaguni Knoll IV hydrothermal field in the southern Okinawa Trough. The sequences obtained using the ploy(A) ta...

  14. Evaluating bacterial community structures in oil collected from the sea surface and sediment in the northern Gulf of Mexico after the Deepwater Horizon oil spill

    Liu, Zhanfei; Liu, Jiqing

    2013-01-01

    Bacterial community structures were evaluated in oil samples using culture-independent pyrosequencing, including oil mousses collected on sea surface and salt marshes during the Deepwater Horizon oil spill, and oil deposited in sediments adjacent to the wellhead 1 year after the spill. Phylogenetic analysis suggested that Erythrobacter, Rhodovulum, Stappia, and Thalassospira of Alphaproteobacteria were the prevailing groups in the oil mousses, which may relate to high temperatures and strong ...

  15. Insights into the abundance and diversity of abyssal megafauna in a polymetallic-nodule region in the eastern Clarion-Clipperton Zone

    Amon, Diva J.; Ziegler, Amanda F.; Dahlgren, Thomas G.; Glover, Adrian G.; Goineau, Aurélie; Gooday, Andrew J.; Wiklund, Helena; Smith, Craig R.

    2016-01-01

    There is growing interest in mining polymetallic nodules in the abyssal Clarion-Clipperton Zone (CCZ) in the Pacific. Nonetheless, benthic communities in this region remain poorly known. The ABYSSLINE Project is conducting benthic biological baseline surveys for the UK Seabed Resources Ltd. exploration contract area (UK-1) in the CCZ. Using a Remotely Operated Vehicle, we surveyed megafauna at four sites within a 900 km2 stratum in the UK-1 contract area, and at a site ~250 km east of the UK-1 area, allowing us to make the first estimates of abundance and diversity. We distinguished 170 morphotypes within the UK-1 contract area but species-richness estimators suggest this could be as high as 229. Megafaunal abundance averaged 1.48 ind. m−2. Seven of 12 collected metazoan species were new to science, and four belonged to new genera. Approximately half of the morphotypes occurred only on polymetallic nodules. There were weak, but statistically significant, positive correlations between megafaunal and nodule abundance. Eastern-CCZ megafaunal diversity is high relative to two abyssal datasets from other regions, however comparisons with CCZ and DISCOL datasets are problematic given the lack of standardised methods and taxonomy. We postulate that CCZ megafaunal diversity is driven in part by habitat heterogeneity. PMID:27470484

  16. Insights into the abundance and diversity of abyssal megafauna in a polymetallic-nodule region in the eastern Clarion-Clipperton Zone

    Amon, Diva J.; Ziegler, Amanda F.; Dahlgren, Thomas G.; Glover, Adrian G.; Goineau, Aurélie; Gooday, Andrew J.; Wiklund, Helena; Smith, Craig R.

    2016-07-01

    There is growing interest in mining polymetallic nodules in the abyssal Clarion-Clipperton Zone (CCZ) in the Pacific. Nonetheless, benthic communities in this region remain poorly known. The ABYSSLINE Project is conducting benthic biological baseline surveys for the UK Seabed Resources Ltd. exploration contract area (UK-1) in the CCZ. Using a Remotely Operated Vehicle, we surveyed megafauna at four sites within a 900 km2 stratum in the UK-1 contract area, and at a site ~250 km east of the UK-1 area, allowing us to make the first estimates of abundance and diversity. We distinguished 170 morphotypes within the UK-1 contract area but species-richness estimators suggest this could be as high as 229. Megafaunal abundance averaged 1.48 ind. m‑2. Seven of 12 collected metazoan species were new to science, and four belonged to new genera. Approximately half of the morphotypes occurred only on polymetallic nodules. There were weak, but statistically significant, positive correlations between megafaunal and nodule abundance. Eastern-CCZ megafaunal diversity is high relative to two abyssal datasets from other regions, however comparisons with CCZ and DISCOL datasets are problematic given the lack of standardised methods and taxonomy. We postulate that CCZ megafaunal diversity is driven in part by habitat heterogeneity.

  17. Distributions and assemblages of microbial communities along a sediment core retrieved from a potential hydrate-bearing region offshore southwestern Taiwan

    Lin, Li-Hung; Wu, Li-Wei; Cheng, Ting-Wen; Tu, Wei-Xain; Lin, Ji-Rong; Yang, Tsanyao F.; Chen, Po-Chun; Wang, Yunshuen; Wang, Pei-Ling

    2014-10-01

    Assessing the impacts of methane released from hydrate-bearing environments on global carbon cycling would require detailed insights into the distributions and capacities of microbial communities at different horizons of sediment column. In this study, we conducted geochemical, gene abundance and diversity analyses for a sediment core retrieved from a potential hydrate-bearing region off southwestern Taiwan. Geochemical profiles were characterized by a sulfate-to-methane transition with decreasing total organic carbon and nitrogen in sediments, and increasing dissolved inorganic carbon, ammonium and total sulfur in sediments. Bacterial and archaeal 16S rRNA and amoA gene abundances decreased with depth. In contrast, ANME-1 and -2 16S rRNA gene abundances increased significantly across the sulfate-to-methane transition and peaked at different horizons below this interface. A total of 124,379 bacterial and 130,351 archaeal reads were recovered through tag-pyrosequencing of 16S rRNA genes and categorized into 9014 bacterial and 6394 archaeal operational taxonomic units on the basis of 97% sequence similarity, respectively. Major bacterial phyla/divisions and archaeal groups (>5% of the total reads) detected included Chloroflexi, Planctomycetes, OP9, Deltaproteobacteria, BHI80-139, MBG-B, Halobacteria, MCG, Thermoplasmata, ANME-1 and MG-I. The abundance variations of most major OTUs (>0.5% of the total reads) were statistically correlated with those of geochemical parameters. These lines of evidence suggest that the populations represented by the major OTUs or detected by group-specific primers were compartmentalized into different horizons and involved directly or indirectly in the cycling of methane, sulfate, organic carbon and nitrogen. Overall, this study demonstrates that the deep sequencing coverage combined with the quantification of gene abundance and geochemical characterization would enable to uncover the detailed distributions and potential metabolic

  18. DOE ER63951-3 Final Report: An Integrated Assessment of Geochemical and Community Structure Determinants of Metal Reduction Rates in Subsurface Sediments

    Susan Pfiffner

    2010-06-28

    The objective of this research was to examine the importance of microbial community structure in influencing uranium reduction rates in subsurface sediments. If the redox state alone is the key to metal reduction, then any organisms that can utilize the oxygen and nitrate in the subsurface can change the geochemical conditions so metal reduction becomes an energetically favored reaction. Thus, community structure would not be critical in determining rates or extent of metal reduction unless community structure influenced the rate of change in redox. Alternatively, some microbes may directly catalyze metal reduction (e.g., specifically reduce U). In this case the composition of the community may be more important and specific types of electron donors may promote the production of communities that are more adept at U reduction. Our results helped determine if the type of electron donor or the preexisting community is important in the bioremediation of metal-contaminated environments subjected to biostimulation. In a series of experiments at the DOE FRC site in Oak Ridge we have consistently shown that all substrates promoted nitrate reduction, while glucose, ethanol, and acetate always promoted U reduction. Methanol only occasionally promoted extensive U reduction which is possibly due to community heterogeneity. There appeared to be limitations imposed on the community related to some substrates (e.g. methanol and pyruvate). Membrane lipid analyses (phospholipids and respiratory quinones) indicated different communities depending on electron donor used. Terminal restriction fragment length polymorphism and clone libraries indicated distinct differences among communities even in treatments that promoted U reduction. Thus, there was enough metabolic diversity to accommodate many different electron donors resulting in the U bioimmobilization.

  19. New insights into the abyssal sponge fauna of the Kurile-Kamchatka plain and Trench region (Northwest Pacific)

    Downey, Rachel V.; Janussen, Dorte

    2015-01-01

    The under-explored abyssal depths of the Kurile-Kamchatka region have been re-examined during the KuramBio (Kurile-Kamchatka Biodiversity Study) expedition. Combining new KuramBio data with previous expedition data in this region has enhanced our understanding abyssal sponge fauna, in particular, the patchiness, rarity, and exceptional richness of the Cladorhizidae family. In total, 14 sponge species, from 7 genera, in 5 families, within two classes (Demospongiae and Hexactinellida) were collected. Of the 14 species, 29% (4 spp.) have been found previously in this region, 36% (5 spp.) were new to the regional abyssal fauna, and 21% (3 spp.) were new to science. The number of abyssal species in this region has now been increased by 26% (8 spp.) and genera by nearly 15% (2 genera). Rarity is a prominent feature of this abyssal fauna, with more than half of species only found at one station, and 83% (19 spp.) of species found previously in this region were not re-found during KuramBio. Cladorhizid sponges dominate demosponge species and genera richness in the abyssal Kurile-Kamchatka region; accounting for 87% (20 spp.) of all demosponge species, and accounting for over 60% (5 genera) of all demosponge genera. Sponge richness in this region is potentially aided by the productivity of the ocean waters, the geological age of the Pacific Ocean, low population densities, and the varied topographic features (ridges, trenches, and seamounts) found in this region. Unusually, the dominance of demosponges in the Kurile-Kamchatka sponge faunal composition is not replicated in other well-sampled abyssal regions, which tend to be richer in deep-sea hexactinellid fauna. Broad depth, latitudinal and longitudinal ranges in Kurile-Kamchatka abyssal fauna are a key characteristic of this faunal assemblage. Strong abyssal faunal connectivity is found between the Kurile-Kamchatka region and North Pacific abyssal fauna, with weaker faunal connections found with the adjacent semi

  20. RRS Discovery Cruise 377 & 378, 05 - 27 Jul 2012, Southampton to Southampton. Autonomous ecological surveying of the abyss: understanding mesoscale spatical heterogeneity at the Porcupine Abyssal Plain

    Ruhl, H.A.; et al, .

    2013-01-01

    Determining the distribution and abundance of life is challenging, especially in the deep sea where high pressure and other logistical challenges limit data availability to a tiny fraction of what is available for other systems. Most of Earth’s surface is nonetheless covered by water > 2000 m deep. Life in these abyssal regions influences the burial of carbon and nutrient cycling. Long-term research has now shown that even larger animals in the deep sea can vary in density by orders of magnit...

  1. Temperature response of denitrification and anammox reveals the adaptation of microbial communities to in situ temperatures in permeable marine sediments that span 50° in latitude

    Canion, A.; Kostka, J. E.; Gihring, T. M.; Huettel, M.; van Beusekom, J. E. E.; Gao, H.; Lavik, G.; Kuypers, M. M. M.

    2014-01-01

    Despite decades of research on the physiology and biochemistry of nitrate/nitrite-respiring microorganisms, little is known regarding their metabolic response to temperature, especially under in situ conditions. The temperature regulation of microbial communities that mediate anammox and denitrification was investigated in near shore permeable sediments at polar, temperate, and subtropical sites with annual mean temperatures ranging from -5 to 23 °C. Total N2 production rates were determined using the isotope pairing technique in intact core incubations under diffusive and simulated advection conditions and ranged from 2 to 359 μmol N m-2 d-1. For the majority of sites studied, N2 removal was 2-7 times more rapid under simulated advective flow conditions. Anammox comprised 6-14% of total N2 production at temperate and polar sites and was not detected at the subtropical site. Potential rates of denitrification and anammox were determined in anaerobic slurries in a temperature gradient block incubator across a temperature range of -1 °C to 42 °C. The highest optimum temperature (Topt) for denitrification was 36 °C and was observed in subtropical sediments, while the lowest Topt of 21 °C was observed at the polar site. Seasonal variation in the Topt was observed at the temperate site with values of 26 and 34 °C in winter and summer, respectively. The Topt values for anammox were 9 and 26 °C at the polar and temperate sites, respectively. The results demonstrate adaptation of denitrifying communities to in situ temperatures in permeable marine sediments across a wide range of temperatures, whereas marine anammox bacteria may be predominately psychrophilic to psychrotolerant. The adaptation of microbial communities to in situ temperatures suggests that the relationship between temperature and rates of N removal is highly dependent on community structure.

  2. Unique 16S rRNA sequences of Eurythenes gryllus (Crustacea: Amphipoda: Lysianassidae) from the Gulf of Mexico abyssal plain

    Elva Escobar-Briones; Eduardo Nájera-Hillman; Fernando Álvarez

    2010-01-01

    Amphipods of the species Eurythenes gryllus were collected at 2 locations on the abyssal plain (~3 400 m) of the Gulf of Mexico in order to test whether or not these scavenger amphipods are isolated in this peripheral sea or show connectivity by their predominant swimming behavior, moving horizontally along the abyssal water masses in the region. Partial sequences of the mitochondrial 16S rRNA gene from 2 individuals of E. gryllus were determined and showed small differences when compared to ...

  3. RRS James Cook Cruise 62, 24 Jul-29 Aug 2011. Porcupine Abyssal Plain – sustained observatory research

    Ruhl, H.A.; et al

    2012-01-01

    Science rationale for the activities comes from the fact that during the EU Framework programme IV project BENGAL (1996 to 1999) radical changes were noted in fauna living on the abyssal seafloor (Progress in Oceanography, Billett 2001). The changes appeared to be related to changes in upper ocean productivity and the flux of organic matter to the abyss (Wigham et al., 2003). Various hypotheses have been created concerning the effect of total organic carbon input, shown by Lampitt et al (2010...

  4. Encountering the Abyss: Deconstructing the Political Philosophy of Leo Strauss and the Straussian Interventions Relating to the Invasion of Iraq

    Hirst, Agnes

    2010-01-01

    This thesis focuses on the figure of an abyss residing at the heart of metaphysics, and argues that thinking in light of its destabilising connotations opens up the possibility of attempting to take responsibility for the violence immanent to any and all politico-philosophical positions. It argues that this abyss represents a void or lack always already underpinning the attempt to posit universal or essential premises, and that it is precisely this lack which may be mobilised to unsettle the ...

  5. Meiofauna communities, nematode diversity and C degradation rates in seagrass (Posidonia oceanica L.) and unvegetated sediments invaded by the algae Caulerpa cylindracea (Sonder).

    Pusceddu, Antonio; Fraschetti, Simona; Scopa, Mariaspina; Rizzo, Lucia; Danovaro, Roberto

    2016-08-01

    We investigated meiofauna and sedimentary C cycling in seagrass (Posidonia oceanica) and unvegetated sediments invaded and not invaded by the non-indigenous tropical algae Caulerpa cylindracea. In both habitats, invaded sediments were characterized by higher organic matter contents. No effect was observed for prokaryotes and C degradation rates. In seagrass sediments, C turnover in invaded beds was about half that in not invaded ones. Meiofaunal communities varied significantly among invaded and not invaded grounds only in bare sediments. In both habitats, nematode species richness and assemblage composition were not affected by the algae. The effect of C. cylindracea on the turnover and nestedness components of the Jaccard dissimilarity varied between the two habitats. We show that the presence of C. cylindracea gives rise to variable consequences on meiofauna biodiversity and C cycling in different habitats. We conclude that further studies across different habitats and ecological components are needed to ultimately understand and predict the consequences of C. cylindracea invasion in shallow Mediterranean ecosystems. PMID:27258353

  6. Towing large nets by single warp at abyssal depths I: methods

    In December, 1981, members of the School of Oceanography at Oregon State University towed a midwater rope trawl of about 107 m2 mouth area at abyssal and bathyal depths about 290 km west of Cape Mendocino, California. This was the first attempt to fish commercial-size nets at depths below 3000 meters. A total of 11 good otter trawl tows were obtained from 4300 m and 4 midwater trawl tows were made at depths from 2000-3100 m. The equipment and techniques required to tow commercial-size nets at bathyal and abyssal depths are described. The nets, doors and bridles of otter trawl and the midwater trawl are described. Depth monitors used are also described. The wire and winches used are also described, along with the difficulties encountered with gear failure. 7 references

  7. Threatened by mining, polymetallic nodules are required to preserve abyssal epifauna

    Vanreusel, Ann; Hilario, Ana; Ribeiro, Pedro A.; Menot, Lenaick; Arbizu, Pedro Martínez

    2016-01-01

    Polymetallic nodule mining at abyssal depths in the Clarion Clipperton Fracture Zone (Eastern Central Pacific) will impact one of the most remote and least known environments on Earth. Since vast areas are being targeted by concession holders for future mining, large-scale effects of these activities are expected. Hence, insight into the fauna associated with nodules is crucial to support effective environmental management. In this study video surveys were used to compare the epifauna from si...

  8. The absence of sharks from abyssal regions of the world's oceans.

    Priede, I. G.; Froese, Rainer; Bailey, D. M.; Berkstad, O.A.; Collins, M A; Dyb, J.E.; Henriques, C.; Jones, E G; King, N.

    2006-01-01

    The oceanic abyss (depths greater than 3000 m), one of the largest environments on the planet, is characterized by absence of solar light, high pressures and remoteness from surface food supply necessitating special molecular, physiological, behavioural and ecological adaptations of organisms that live there. Sampling by trawl, baited hooks and cameras we show that the Chondrichthyes (sharks, rays and chimaeras) are absent from, or very rare in this region. Analysis of a global data set shows...

  9. On a simple empirical parameterization of topography-catalyzed diapycnal mixing in the abyssal ocean

    Decloedt, T.; Luther, D.S.

    2010-01-01

    The global spatial distribution of the turbulent diapycnal diffusivity in the abyssal ocean is reexamined in light of the growing body of microstructure data revealing bottom-intensified turbulent mixing in regions of rough topography. A direct and nontrivial implication of the observed intensification is that the diapycnal diffusivity Kr, is depth dependent and patchily distributed horizontally across the world’s oceans. Theoretical and observational studies show that bottom-intensified mixi...

  10. Comparison and relationship between functional changes of macroinvertebrates and microbial communities in response to resuspension of contaminated sediment

    Colas, F.; Devin, S.; Archaimbault, V.

    2010-01-01

    In the European water Framework directive context, long term management and prevention of damages on aquatic ecosystems is needed. Among pressures, historical contamination of sediments from surrounding industry and urbanization pose a serious ecological threat. Therefore, water storages within dams represent a critical system, retaining runoff and particulate-bound contaminants and thereby exposes organisms to elevated concentrations of contaminants. Moreover, when sediment is disturbed ( i....

  11. Three manganese oxide-rich marine sediments harbor similar communities of acetate-oxidizing manganese-reducing bacteria

    Vandieken, Verona; Pester, Michael; Finke, Niko; Hyun, Jung-Ho; Friedrich, Michael W.; Loy, Alexander; Thamdrup, Bo

    2012-01-01

    Dissimilatory manganese reduction dominates anaerobic carbon oxidation in marine sediments with high manganese oxide concentrations, but the microorganisms responsible for this process are largely unknown. In this study, the acetate-utilizing manganese-reducing microbiota in geographically well-separated, manganese oxide-rich sediments from Gullmar Fjord (Sweden), Skagerrak (Norway) and Ulleung Basin (Korea) were analyzed by 16S rRNA-stable isotope probing (SIP). Manganese reduction was the p...

  12. Morphological, histochemical and immunohistochemical study of the gill epithelium in the abyssal teleost fish Coelorhynchus coelorhynchus.

    Calabrò, Concetta; Albanese, Maria Pia; Lauriano, Eugenia Rita; Martella, Silvestro; Licata, Aurelio

    2005-01-01

    Histochemical and immunohistochemical study was carried out on nitrinergic innervation and neuroendocrine system in the gill epithelium of the abyssal fish Coelorhynchus coelorhynchus. The results showed that nNOS-positive nerve fibers, originating from the branchial arch were present in the subepithelial tissue of branchial primary filament. nNOS-positive neuroendocrine cells were also present in the primary filaments and secondary lamellae. Numerous mucous cells in the gill epithelium were AB/PAS-positive, while sialic acid was absent as confirmed by neuraminidase reaction and WGA lectin histochemistry. The mucus compounds in abyssal teleost fish are different from those found in pelagic species, being related to their living conditions. In abyssal species, greater numbers of chloride and neuroendocrine cells are involved in the movement of water and electrolytes. Neuroendocrine cells possess oxygen receptors which mediate the cardiovascular and ventilatory response to oxygen deficiency, as reported in teleost species. Besides, NO contributes through nervous stimulation to the regulation of vascular tone and blood circulation in the gill. PMID:15871563

  13. Ocean floor sediment as a repository barrier: comparative diffusion data for selected radionuclides in sediments from the Atlantic and Pacific Oceans

    Schreiner, F.; Sabau, C.; Friedman, A.; Fried, S.

    1985-01-01

    Effective diffusion coefficients for selected radionuclides have been measured in ocean floor sediments to provide data for the assessment of barrier effectiveness in subseabed repositories for nuclear waste. The sediments tested include illite-rich and smectite-rich red clays from the mid-plate gyre region of the Pacific Ocean, reducing sediment from the continental shelf of the northwest coast of North America, and Atlantic Ocean sediments from the Southern Nares Abyssal Plain and the Great Meteor East region. Results show extremely small effective diffusion coefficients with values less than 10/sup -14/ m/sup 2/s/sup -1/ for plutonium, americium, curium, thorium, and tin. Radionuclides with high diffusion coefficients of approximately 10/sup -10/ m/sup 2/s/sup -1/ include the anionic species pertechnetate, TcO/sub 4//sup -/, iodide, I/sup -/, and selenite, SeO/sub 3//sup -2/. Uranyl(VI) and neptunyl(V) ions, which are stable in solution, have diffusion coefficients around 10/sup -12/ m/sup 2/s/sup -1/. The diffusion behavior of most radionuclides is similar in the oxygenated Pacific sediments and in the anoxic sediments from the Atlantic. An exception is neptunium, which is immobilized by Great Meteor East sediment, but has high mobility in Southern Nares Abyssal Plain sediment. Under stagnant conditions a 30 m thick sediment layer forms an effective geologic barrier isolating radionuclides in a subseabed repository from the biosphere. 13 refs., 5 figs., 1 tab.

  14. Ocean floor sediment as a repository barrier: comparative diffusion data for selected radionuclides in sediments from the Atlantic and Pacific Oceans

    Effective diffusion coefficients for selected radionuclides have been measured in ocean floor sediments to provide data for the assessment of barrier effectiveness in subseabed repositories for nuclear waste. The sediments tested include illite-rich and smectite-rich red clays from the mid plate gyre region of the Pacific Ocean, reducing sediment from the continental shelf of the northwest coast of North America, and Atlantic Ocean sediments from the Southern Nares Abyssal Plain and the Great Meteor East region. Results show extremely small effective diffusion coefficients with values less than 10-14 m2s-1 for plutonium, americium, curium, thorium, and tin. Radionuclides with high diffusion coefficients of approximately 10-10 m2s- include the anionic species pertechnetate, TcO4-, iodide, I-, and selenite, SO3-2. Uranyl(VI) and neptunyl(V) ions, which are stable in solution, have diffusion coefficients around 10-12m2s-1. The diffusion behavior of most radionuclides is similar in the oxygenated Pacific sediments and in the anoxic sediments from the Atlantic. An exception is neptunium, which is immobilized by Great Meteor East sediment, but has high mobility in Southern Nares Abyssal Plain sediment. Under stagnant conditions a 30 m thick sediment layer forms an effective geologic barrier isolating radionuclides in a subseabed repository from the biosphere

  15. Controls on melting at spreading ridges from correlated abyssal peridotite - mid-ocean ridge basalt compositions

    Regelous, Marcel; Weinzierl, Christoph G.; Haase, Karsten M.

    2016-09-01

    Variations in the volume and major element composition of basalt erupted along the global mid-ocean ridge system have been attributed to differences in mantle potential temperature, mantle composition, or plate spreading rate and lithosphere thickness. Abyssal peridotites, the residues of mantle melting beneath mid-ocean ridges, provide additional information on the melting process, which could be used to test these hypotheses. We compiled a global database of abyssal peridotite compositions averaged over the same ridge segments defined by Gale et al. (2013). In addition, we calculated the distance of each ridge segment to the nearest hotspots. We show that Cr# in spinel in abyssal peridotites is negatively correlated with Na90 in basalts from the same ridge segments on a global scale. Ridge segments that erupt basalts apparently produced by larger degrees of mantle melting are thus underlain by peridotites from which large amounts of melt have been extracted. We find that near-ridge hotspots have a more widespread influence on mid-ocean ridge basalt (MORB) composition and ridge depth than previously thought. However, when these hotspot-influenced ridge segments are excluded, the remaining segments show clear relationships between MORB composition, peridotite composition, and ridge depth with spreading rate. Very slow-spreading ridges (<20 mm/yr) are deeper, erupt basalts with higher Na90, Al90, K90/Ti90, and lower Fe90, Ca90/Al90, and expose peridotites with lower Cr# than intermediate and fast-spreading ridges. We show that away from hotspots, the spreading-rate dependence of the maximum degree of mantle melting inferred from Cr# in peridotites (FM) and the bulk degree of melting inferred from Na90 in basalts (FB) from the same ridge segments is unlikely to be due to variations in mantle composition. Nor can the effects of dynamic mantle upwelling or incomplete melt extraction at low spreading rates satisfactorily explain the observed compositions of abyssal

  16. Preliminary Insights Into the Interplay Among Oxygen, Organic Carbon, and Microbial Metabolism in North Atlantic Subseafloor Sediment Communities

    Amenabar, M. J.; Dore, J. E.; Spivack, A. J.; Murray, R. W.; D'Hondt, S.; Boyd, E. S.

    2015-12-01

    Deep marine sediments harbor abundant microbial cells that, if active, are likely to exert a strong influence on element biogeochemical cycling. However, our understanding of the fraction of cells that are active in situ and the metabolic processes that sustain them remain underexplored. Here we describe recent results of our studies aimed at unraveling the links between geochemical heterogeneity, cellular viability and synthesis, and metabolism along a vertical depth profile in sediment from four deep sites (>5 km beneath ocean surface) cored by R/V KNORR Expedition KN-223 in the North Atlantic (2014). These sediment columns exhibit varying levels of organic carbon and different vertical extents of oxygen (O2) penetration, which we hypothesize is due to variation in the extent of heterotrophic metabolism. We prepared most probable number (MPN) assays with acetate or peptone as electron donor and carbon source, and five different terminal electron acceptors (O2, NO3, SO4, MnO2, and ferrihydrite) with sediments from 4 to 5 depths in each of the four cores MPNs were similar for acetate- and peptone-amended cultures, regardless of electron acceptor, and generally decreased with depth in the sediment column. MPNs amended with O2 as electron acceptor were greater than MPNs amended with NO3, SO4, MnO2, and ferrihydrite in samples from all depths. Moreover, MPNs were higher for assays amended with O2 from cores where the depth of O2 penetration was shallow when compared to cores where O2 is predicted to penetrate to basement rock. These results are consistent with aerobic heterotrophs limiting the penetration of O2 in deep marine sediments, and thereby provide a mechanism to explain the relationship between low O2 penetrations in sediment cores with elevated organic carbon contents. We will also present results of our ongoing isotopic labeling experiments aimed at determining rates of DNA and protein synthesis as proxies for cell replication and productivity, respectively

  17. High activity and low temperature optima of extracellular enzymes in Arctic sediments: implications for carbon cycling by heterotrophic microbial communities

    Arnosti, C.; Jørgensen, BB

    2003-01-01

    The rate of the initial step in microbial remineralization of organic carbon, extracellular enzymatic hydrolysis, was investigated as a function of temperature in permanently cold sediments from 2 fjords on the west coast of Svalbard (Arctic Ocean). We used 4 structurally distinct polysaccharides...... hydrolysis in order to determine the relative temperature responses of the initial and terminal steps in microbial remineralization of carbon. The temperature optimum of sulfate reduction, 21degreesC, was considerably lower than previous reports of sulfate reduction in marine sediments, but is consistent...... with recent studies of psychrophilic sulfate reducers isolated from Svalbard sediments. A calculation of potential carbon flow into the microbial food chain demonstrated that the activity of just one type of polysaccharide-hydrolyzing enzyme could in theory supply 21 to 100% of the carbon consumed via...

  18. Spatio-temporal changes in the distribution of phytopigments and phytoplanktonic groups at the Porcupine Abyssal Plain (PAP) site

    Smythe-Wright, Denise; Boswell, Stephen; Kim, Young-Nam; Kemp, Alan

    2010-08-01

    We have made a comprehensive study of pigment distributions and microscopically determined phytoplankton abundances within the Porcupine Abyssal Plain (PAP) location in the North Atlantic to better understand phytoplankton variability, and make some suggestions regarding the composition of the material falling to the sea bed and its impacts on benthic organisms such as Amperima rosea. The area has been the focus of many studies of ocean fluxes and benthic communities over recent years, but little attention has been given to the spatio-temporal variability in the surface waters. Dawn casts over a 12-day period at the PAP mooring site (48.83°N 16.5°W) revealed the presence of only one species, the diatom Actinocyclus exiguus, at bloom concentrations for just 5 days. Smaller populations of other diatoms and the dinoflagellates Gymnodinium and Gyrodinium were also present at this time. Following this 5-day interval, a mixed population of small-sized dinoflagellates, prymnesiophytes, prasinophytes, chrysophytes and cyanobacteria occurred. It is clear from concomitant CTD/bottle surveys that rapid changes in phytoplankton community structure at a fixed time series position do not necessarily reflect a degradation or manifestation of one particular species but rather represent the movement of eddies and other water masses within very short timescales. These cause substantial variability in the species class and size fraction that may explain the variability in carbon export that has been seen at the PAP site. We also make some suggestions on the variable composition of the material falling to the seabed and its impact on benthic organisms such as Amperima rosea.

  19. Sewage impact on metal accumulation in sediments and fish (Clarias gariepinus from the University of Cape Coast community and its environs

    Sarfo D.K

    2013-07-01

    Full Text Available The objectives of this study was to measure the concentration levels of the heavy metals As, Co, Cr, Cu, Fe and Hg upon samples of mudfish(Clarias gariepinus and sediments in wastewater discharge from the University of Cape Coast community and environs. This measurement was done using Instrumental Neutron Activation Analysis. The average concentration of elements (in mg/kg in the fish samples, in decreasing order of magnitude were: Fe (130.63 > Cu (3.77 > Cr(0.16 > Co(0.04 and Fe(209.67 > Cu(2.74 > Cr(0.57 > Co(0.09 from piont A and point B respectively. Arsenic and Hg concentrations were below detection limits of INAA in samples from both point A and point B. The chronic daily intake (CDI obtained for each of the metals in the fish sample shows that the population is not prone to adverse health effects (i.e CDI>>1 due to the concentrations of the metals. From the sediments, Fe recorded the highest concentration of 9808 mg/kg whilst Hg was below the detection limits of INAA. The metals As, Cu, Cr and Co recorded concentrations in mg/kg of 2.04, 4.82, 0.21 and 3.73 respectively in the sediments.

  20. Fungal community analysis in the deep-sea sediments of the Pacific Ocean assessed by comparison of ITS, 18S and 28S ribosomal DNA regions

    Xu, Wei; Luo, Zhu-Hua; Guo, Shuangshuang; Pang, Ka-Lai

    2016-03-01

    We investigated the diversity of fungal communities in 6 different deep-sea sediment samples of the Pacific Ocean based on three different types of clone libraries, including internal transcribed spacer (ITS), 18S rDNA, and 28S rDNA regions. A total of 1978 clones were generated from 18 environmental clone libraries, resulting in 140 fungal operational taxonomic units (OTUs), including 18 OTUs from ITS, 44 OTUs from 18S rDNA, and 78 OTUs from 28S rDNA gene primer sets. The majority of the recovered sequences belonged to diverse phylotypes of the Ascomycota and Basidiomycota. Additionally, our study revealed a total of 46 novel fungal phylotypes, which showed low similarities (<97%) with available fungal sequences in the GenBank, including a novel Zygomycete lineage, suggesting possible new fungal taxa occurring in the deep-sea sediments. The results suggested that 28S rDNA is an efficient target gene to describe fungal community in deep-sea environment.

  1. Benthic community structure in the Gorgan Bay (Southeast of the Caspian Sea, Iran: Correlation to water physiochemical factors and heavy metal concentration of sediment

    Mahmood Saghali

    2013-11-01

    Full Text Available Macrobentos frequency and biomass was investigated in the Gorgan Bay in 2011. Five sampling sites were chosen to collect benthos and sediment from the Bay using a Van Veen grab sampler. Samples were collected seasonally. Macrobenthos were indentified and their biomass was recorded. Sediment heavy metals concentration were measured using Atomic Absorption Spectroscopy. A total of 11 families belonging to three phyla of invertebrates were found. The phyla were Annelids (Nereidae, Naididae, Ampharetidae, Lumbriculidae, Tubificidae and Amphiporidae, Arthropods (Pontogammaridae, Balanidae and Chironomidae and Mollusks (Cardiidae and Scrobicularidae. Lumbriculidae (413 individuals m-2, corresponding to 18.7% and Cardiidae (55.2 g m-2, corresponding to 82.4% had the highest frequency and biomass, respectively. Annelids with an average of 1557 individuals m-2 was the most frequent groups, while, mollusks with the average of 141 g per m2 had the highest biomass. Results showed that macrobenthos frequency in summer was significantly higher than those of the other seasons, however, in the case of biomass, there was a significantly higher biomass in the spring than the other seasons. The maximum metal concentration was related to Zn and Pb, whereas, Cr and Cd had the lowest values. There was no significant difference in Zn and Cr concentrations among the sampling seasons. Pb concentration in winter was significantly lower than the other seasons, whereas, Cd concentrations in the spring and summer were significantly lower than the autumn and winter. There were some correlations between benthos frequency and water physiochemical characteristics and sediment heavy metal levels. This study indicated that benthic fauna of the Gorgan Bay and the Caspian Sea are not similar. Also, results showed that benthic fauna communities are affected by sediment heavy metal concentrations and water physiochemical characteristics, however, different benthos groups show

  2. Quantitative determination of microbial activity and community nutritional status in estuarine sediments: evidence for a disturbance artifact

    Findlay, R. H.; Pollard, P. C.; Moriarty, D. J.; White, D. C.

    1985-01-01

    In estuarine sediments with a high degree of vertical heterogeneity in reduced substrate and terminal electron acceptor concentrations, the method of exposure of the microbiota to labeled substrates can introduce a "disturbance artifact" into measures of metabolic activity. The detection of this artifact is based on quantitative measurement of the relative rates of incorporation of [14C]acetate into phospholipid fatty acids (PLFA) and endogenous storage lipid, poly-beta-hydroxyalkanoate (PHA). Previous studies have shown that PLFA synthesis measures cellular growth and that PHA synthesis measures carbon accumulation (unbalanced growth). The "disturbance artifact" of exposure to [14C]acetate was demonstrated by comparing injection of a core with the usual or pore-water replacement or slurry techniques. Only injection of labeled substrate allowed detection of preassay disturbance of the sediment with a garden rake. The raking increased PLFA synthesis with little effect to differences in concentration or distribution of [14C]acetate in the 10-min incubation. Bioturbation induced by sand dollar feeding in estuarine sediment could be detected in an increased PLFA/PHA ratio which was due to decreased PHA synthesis if the addition of labeled substrate was by the injection technique. Addition of labeled precursors to sediment by slurry or pore-water replacement induces greater disturbance artifacts than injection techniques.

  3. Long-term maintenance and public exhibition of deep-sea hydrothermal fauna: The AbyssBox project

    Shillito, Bruce; Ravaux, Juliette; Sarrazin, Jozée; Zbinden, Magali; Sarradin, Pierre-Marie; Barthelemy, Dominique

    2015-11-01

    The AbyssBox project aims to provide the first permanent public exhibition of live deep-sea hydrothermal fauna maintained at in situ pressure. AbyssBox is a pressurized aquarium designed to function permanently. Here we present details of the project after the public exhibition functioned for more than three years at Océanopolis aquarium in Brest, France. We also describe the AbyssBox pressure aquarium, and provide data and observations on vent shrimp (Mirocaris fortunata) and crabs (Segonzacia mesatlantica) that were sampled from 1700 m depth at the Lucky Strike vent field (Mid-Atlantic Ridge) during different cruises. While mortalities exceeded 50% during the first days following sampling, the remaining animals appeared to acclimate fairly well. Some crabs have now been kept for more than 2 years, and some shrimp have spent more than 3 years in captivity. Primarily designed for a public exhibition, the AbyssBox is already used for scientific purposes, since it provides one of the most effective tools for long-term rearing of deep-sea fauna. AbyssBox is a first step towards maintaining a variety of deep-sea fauna year-round at in situ pressure, which will serve both scientific and public interests.

  4. Oil spill effects on macrofaunal communities and bioturbation of pristine marine sediments (Caleta Valdés, Patagonia, Argentina): experimental evidence of low resistance capacities of benthic systems without history of pollution

    Ferrando, Agustina; Gonzalez, Emilia; Franco, Marcos; Commendatore, Marta; Nievas, Marina; Militon, Cécile; Stora, Georges; Gilbert, Franck; Esteves, José Luis; Cuny, Philippe

    2015-01-01

    The Patagonian coast is characterized by the existence of pristine ecosystems which may be particularly sensitive to oil contamination. In this study, a simulated oil spill at acute and chronic input levels was carried out to assess the effects of contamination on the macrobenthic community structure and the bioturbation activity of sediments sampled in Caleta Valdés creek. Superficial sediments were either noncontaminated or contaminated by Escalante crude oil and incubated in the laboratory...

  5. Tipping into the abyss: with more than a virtual parachute?

    Chris Tompsett

    2007-12-01

    Full Text Available Any application of information and communication technology in education (ICTE sits, at times uncomfortably, at the intersection of three key disciplines: technology, education and sociology (including reflexivity. To confuse matters, any specific study may need to take account of specific knowledge within subdisciplines, such as organisational management and technology transfer, and of knowledge within the domain of application (e.g. nursing, social work, fashion, etc.. Researchers must build a consistent model of knowledge that can integrate disparate methodologies, research goals and even conflicting interpretations of the same terminology. Without this, the ICTE research field will be dominated by what is simply novel, irrespective of the relevance of particular changes to educational practice. If existing models in this field are as limited as suggested by Moule, when should lecturers and teachers, with no motivation to use technology for its own sake and no additional financial support, review progress in this field for effective examples of innovative practice, let alone wide-scale change? On most of the criteria that could be introduced to compare two papers, the views of Moule and Salmon appear almost diametrically opposed and a detailed comparison would seem of limited value. Instead, this paper asks a more fundamental question: what could be the basis within this research community for establishing coherence within the field and ensuring that research can justify actual changes in educational practice?

  6. Moored observations of episodic abyssal flow and mixing at station ALOHA

    Alford, M. H.; Lukas, Roger; Howe, Bruce; Pickering, Andy; Santiago-Mandujano, Fernando

    2011-08-01

    Moored measurements of abyssal velocity and temperature are presented with a focus on episodic cold overflow events first observed by Lukas et al. (2001) in the Hawaii Ocean Time-series (HOT), a 23-year-long time series of ≈ monthly CTD profiles at station ALOHA (22.75°N, 158°W). Three major cold events were observed in our 2.5-year record, of which we present one in detail. The event appeared in two pulses spaced by about two weeks, wherein potential temperature anomaly was <-0.015°C over the bottom 600 m. Flow was about 10 cms-1 to the southwest, confirming earlier interpretations of the events as overflows from the Maui deep to the east. Between the two pulses, flow veered to the northwest, possibly associated with seiching. Speed decreased rapidly below the sill depth (≈4625) m, suggesting sheltering by the basin walls. The associated shear, even smoothed over 200 m and not including internal waves, was nearly unstable to Kelvin-Helmholtz instability. During this period, a large mixed region was observed wherein the lower 240 m was homogenized, remaining so for 14 hours (1.2 buoyancy periods). From Thorpe scale analysis, the implied diffusivity of the event was (0.5-4.5) × 10-1m2s-1. No other overturning events greater than 50 m high were observed in the record, suggesting that abyssal mixing is strongly intermittent. We suggest that such intermittency in abyssal mixing and flow is likely the rule rather than the exception, calling for more highly temporally resolved observations.

  7. Polychaete community structure and biodiversity change in space and time at the abyssal seafloor

    Laguionie-Marchais, Claire

    2015-01-01

    The deep sea is a dynamic environment over various spatio-temporal scales. But, the characteristics of deep-sea natural variations and underlying processes remain poorly understood, which prevents contextualising any anthropogenic impact on this environment. Long-term observations, from which inter-annual variations can be detected, as well as detailed broad-scale spatial observations, are scarce in the deep sea. In this thesis, I examined changes in both spatial (~ 0.1-10s km scale) and temp...

  8. Seawater-derived rare earth element addition to abyssal peridotites during serpentinization

    Frisby, Carl; Bizimis, Michael; Mallick, Soumen

    2016-04-01

    Serpentinized abyssal peridotites are evidence for active communication between the Earth's hydrosphere and the upper mantle, where exchange and retention of both major and trace elements occur. Bulk rock Nd isotopes in serpentinized abyssal peridotites imply interaction of seawater with the peridotite. In contrast, the Nd isotopes of clinopyroxenes from serpentinized abyssal peridotites retain their primary magmatic signature. It is currently unclear if, how and where seawater-derived Nd and other REE are being added or exchanged with the mantle peridotite minerals during serpentinization. To remedy this knowledge gap, we present in situ trace and major element concentrations, bulk rock and sequential leaching experiment trace element concentrations as well as Nd, Sr isotope data on refertilized and depleted serpentinized abyssal peridotites from the Southwest Indian Ridge. The secondary serpentine matrix and magnetite veins in these peridotites have elevated LREE concentrations, with variable negative Ce anomalies and large Rb, Sr, Pb and U enrichments that resemble seawater trace element patterns. The LREE concentrations in the serpentine phase are higher than those expected for the primary mantle mineralogy (olivine, orthopyroxene) based on data from relic clinopyroxenes and equilibrium partition coefficients. These data are consistent with seawater-derived REE addition to the peridotite during serpentinization. The bulk rocks have more radiogenic Sr and more unradiogenic Nd isotopes than their clinopyroxene (up to 8 εNd units lower than clinopyroxene). Sequential leaching experiments designed to mobilize secondary carbonates and Fe-oxides show even more unradiogenic Nd isotope ratios in the leachates than the bulk rock and clinopyroxene, approaching seawater compositions (up to 15 εNd units lower than clinopyroxene). Mass balance calculations using trace elements or Nd isotopes suggest that up to 30% of the bulk peridotite Nd budget is of seawater origin and

  9. Ecotoxicity of sediments in rivers: Invertebrate community, toxicity bioassays and the toxic unit approach as complementary assessment tools

    Castro-Català, Núria de; Kuzmanović, Maja; Roig, Neus; Sierra, Jordi; Ginebreda, Antoni; Barceló i Cullerés, Damià; Pérez, Sandra; Petrović, Mira; Picó, Yolanda; Schuhmacher, Marta; Muñoz, Isabel

    2016-01-01

    The determination of the real toxicity of sediments in aquatic ecosystems is challenging and necessary for an appropriate risk assessment. Different approaches have been developed and applied over the last several decades. Currently, the joint implementation of chemical, ecological and toxicological tools is recommended for an appropriate and successful toxicity risk assessment. We chose the combination of the toxic unit approach with acute pore water tests (Vibrio fischeri, Pseudokirchneriel...

  10. The Significance of Myriophyllum elatinoides for Swine Wastewater Treatment: Abundance and Community Structure of Ammonia-Oxidizing Microorganisms in Sediments

    Xi Li; Miaomiao Zhang; Feng Liu(Central China Normal University); Yong Li; Yang He; Shunan Zhang; Jinshui Wu

    2015-01-01

    Myriophyllum elatinoides was reported to effectively treat wastewater by removing nitrogen (N) and phosphorus (P). However, little is known about the abundance and community structure of ammonia-oxidizing microorganisms associated with M. elatinoides purification systems. The objective of this research was to characterize the abundance and community structure of ammonia-oxidizing microorganisms in swine wastewater and determine the main nitrogen removal pathways. In this study, five different...

  11. Enhanced bioreduction of iron and arsenic in sediment by biochar amendment influencing microbial community composition and dissolved organic matter content and composition.

    Chen, Zheng; Wang, Yuanpeng; Xia, Dong; Jiang, Xiuli; Fu, Dun; Shen, Liang; Wang, Haitao; Li, Qing Biao

    2016-07-01

    Biochar derived from the pyrolysis at 500 °C with fresh biogas slurry and residue, was conducted to investigate its potential role in mediating the speciation and mobilization of As(V) and Fe(III) from arsenic-contaminated tailing mine sediment, with consideration of the changes in microbial populations and dissolved organic matter (DOM). The reduction of As(V) (10-13%) and Fe(III) (12-17%) were partly in response to biochar abiotically causing desorption and reduction effect, but were predominantly (87-90% and 83-88% for As(V) and Fe(III)) attributed to biochar stimulating biological reduction. The level of As(III) released from sediment upon biochar amendment (656.35±89.25 μg L(-1)) was significantly higher than the level released without biochar amendment (98.06±19.38 μg L(-1)) after 49 days incubation. Although a low level of Fe(II) (0.81±0.07 mg L(-1)) was determined in the solution when amending with biochar, most of released Fe(II) (166.25±40.25 mg L(-1)) was formed as biochar-Fe(II)minerals composite. More importantly, biochar stimulated the DOM bioavailability in association with bacterial activities mediating As(V) and Fe(III) reduction. High-throughput sequencing results indicated biochar application shifted the soil microbial community and increased the relative abundance of As(V)-/Fe(III)-reducing bacteria, mostly Geobacter, Anaeromyxobacter, Desulfosporosinus and Pedobacter. The discovery of biochar-bacteria-DOM consortium may broaden new understanding into speciation and mobilization of metals, which arouses attention to exploit feasible bioremediation for metal-contaminated sediment. PMID:26954472

  12. Effects of invasive fish and quality of water and sediment on macrophytes biomass, and their consequences for the waterbird community of a Mediterranean floodplain.

    Laguna, Celia; López-Perea, Jhon J; Viñuela, Javier; Florín, Máximo; Feliu, Jordi; Chicote, Álvaro; Cirujano, Santos; Mateo, Rafael

    2016-05-01

    Floodplains are among the most threatened ecosystems world-wide because of multiple stressors, i.e., invasive species, pollution and aquifer overexploitation; the Tablas de Daimiel National Park (Spain) is a clear example of these kinds of impact. This work aims to test whether invasive fish and/or the water and sediment quality are significant drivers of the decline of stonewort (Chara spp.) meadows in the Tablas de Daimiel, investigating how this could explain changes observed in the waterbird community. Bird surveys performed monthly between June 2010 and April 2014 have shown that herbivorous species like the red-crested pochard (Netta rufina) reached historical records between September 2010 and June 2011, but have decreased since then. Piscivorous waterbirds like the great cormorant (Phalacrocorax carbo) and herons increased in population after 2011, however. These changes may be due to the decline of Chara spp. meadows, connected to overexploitation by herbivores, or to changes in water and sediment quality. To test this hypothesis, we studied the growth of Chara spp. biomass in ten sites of the Tablas de Daimiel, where experimental exclosures were set up to exclude herbivory by birds, and bioturbation and herbivory by fish. Our results have shown that the absence of Chara spp. in the Tablas de Daimiel is mostly explained by presence of invasive fish (i.e. common carp). Moreover, the physicochemical characteristics of the water (lower values of conductivity and higher values of inorganic carbon and organic nitrogen), as well as of the sediment (lower values of inorganic and organic phosphorus), favour the increase of Chara spp., in the absence of the fish effect. These results led the National Park managers to begin the control of invasive fish as an urgent measure to assure the ecological conservation of this Mediterranean wetland. PMID:26896580

  13. Iodine diagenesis in non-pelagic deep sea sediments

    Measurements of sediment geochemistry and porewater speciation have been made using light cores containing turbidite sections from the Madeira and Nares Abyssal Plains. The results have been used to evaluate how the diagenetic chemistry of iodine in these sediments compares with that in sediments undergoing steady-state diagenesis. The behaviour of iodine is related to the development of a redox front within the turbidite, between the organic-rich unoxidised sediment and its oxidised cap, and its downward migration through the turbidite with time. Comparison with Mn data demonstrates that the I enrichment above the redox front is supplied by upward diffusion from the oxidising turbidite, the increasing I content with depth being accounted for by progressive diagenetic enrichment with time. (author)

  14. Class 1 Integrons Potentially Predating the Association with Tn402-Like Transposition Genes Are Present in a Sediment Microbial Community

    Stokes, Harold W.; Nesbø, Camilla L.; Holley, Marita;

    2006-01-01

    Integrons are genetic elements that contribute to lateral gene transfer in bacteria as a consequence of possessing a site-specific recombination system. This system facilitates the spread of genes when they are part of mobile cassettes. Most integrons are contained within chromosomes and are...... for bacteria, especially pathogens, which harbor class 1 integrons and their associated antibiotic resistance genes. Here, we have isolated bacteria from soil and sediment in the absence of antibiotic selection. Class 1 integrons were recovered from four different bacterial species not known to be...

  15. Model Behavior and Sensitivity in an Application of the Cohesive Bed Component of the Community Sediment Transport Modeling System for the York River Estuary, VA, USA

    Kelsey A. Fall

    2014-05-01

    Full Text Available The Community Sediment Transport Modeling System (CSTMS cohesive bed sub-model that accounts for erosion, deposition, consolidation, and swelling was implemented in a three-dimensional domain to represent the York River estuary, Virginia. The objectives of this paper are to (1 describe the application of the three-dimensional hydrodynamic York Cohesive Bed Model, (2 compare calculations to observations, and (3 investigate sensitivities of the cohesive bed sub-model to user-defined parameters. Model results for summer 2007 showed good agreement with tidal-phase averaged estimates of sediment concentration, bed stress, and current velocity derived from Acoustic Doppler Velocimeter (ADV field measurements. An important step in implementing the cohesive bed model was specification of both the initial and equilibrium critical shear stress profiles, in addition to choosing other parameters like the consolidation and swelling timescales. This model promises to be a useful tool for investigating the fundamental controls on bed erodibility and settling velocity in the York River, a classical muddy estuary, provided that appropriate data exists to inform the choice of model parameters.

  16. The absence of sharks from abyssal regions of the world's oceans.

    Priede, Imants G; Froese, Rainer; Bailey, David M; Bergstad, Odd Aksel; Collins, Martin A; Dyb, Jan Erik; Henriques, Camila; Jones, Emma G; King, Nicola

    2006-06-01

    The oceanic abyss (depths greater than 3000 m), one of the largest environments on the planet, is characterized by absence of solar light, high pressures and remoteness from surface food supply necessitating special molecular, physiological, behavioural and ecological adaptations of organisms that live there. Sampling by trawl, baited hooks and cameras we show that the Chondrichthyes (sharks, rays and chimaeras) are absent from, or very rare in this region. Analysis of a global data set shows a trend of rapid disappearance of chondrichthyan species with depth when compared with bony fishes. Sharks, apparently well adapted to life at high pressures are conspicuous on slopes down to 2000 m including scavenging at food falls such as dead whales. We propose that they are excluded from the abyss by high-energy demand, including an oil-rich liver for buoyancy, which cannot be sustained in extreme oligotrophic conditions. Sharks are apparently confined to ca 30% of the total ocean and distribution of many species is fragmented around sea mounts, ocean ridges and ocean margins. All populations are therefore within reach of human fisheries, and there is no hidden reserve of chondrichthyan biomass or biodiversity in the deep sea. Sharks may be more vulnerable to over-exploitation than previously thought. PMID:16777734

  17. Long-term change in benthopelagic fish abundance in the abyssal northeast Pacific Ocean.

    Bailey, D M; Ruhl, H A; Smith, K L

    2006-03-01

    Food web structure, particularly the relative importance of bottom-up and top-down control of animal abundances, is poorly known for the Earth's largest habitats: the abyssal plains. A unique 15-yr time series of climate, productivity, particulate flux, and abundance of primary consumers (primarily echinoderms) and secondary consumers (fish) was examined to elucidate the response of trophic levels to temporal variation in one another. Towed camera sled deployments in the abyssal northeast Pacific (4100 m water depth) showed that annual mean numbers of the dominant fish genus (Coryphaenoides spp.) more than doubled over the period 1989-2004. Coryphaenoides spp. abundance was significantly correlated with total abundance of mobile epibenthic megafauna (echinoderms), with changes in fish abundance lagging behind changes in the echinoderms. Direct correlations between surface climate and fish abundances, and particulate organic carbon (POC) flux and fish abundances, were insignificant, which may be related to the varied response of the potential prey taxa to climate and POC flux. This study provides a rare opportunity to study the long-term dynamics of an unexploited marine fish population and suggests a dominant role for bottom-up control in this system. PMID:16602284

  18. Threatened by mining, polymetallic nodules are required to preserve abyssal epifauna

    Vanreusel, Ann; Hilario, Ana; Ribeiro, Pedro A.; Menot, Lenaick; Arbizu, Pedro Martínez

    2016-06-01

    Polymetallic nodule mining at abyssal depths in the Clarion Clipperton Fracture Zone (Eastern Central Pacific) will impact one of the most remote and least known environments on Earth. Since vast areas are being targeted by concession holders for future mining, large-scale effects of these activities are expected. Hence, insight into the fauna associated with nodules is crucial to support effective environmental management. In this study video surveys were used to compare the epifauna from sites with contrasting nodule coverage in four license areas. Results showed that epifaunal densities are more than two times higher at dense nodule coverage (>25 versus ≤10 individuals per 100 m2), and that taxa such as alcyonacean and antipatharian corals are virtually absent from nodule-free areas. Furthermore, surveys conducted along tracks from trawling or experimental mining simulations up to 37 years old, suggest that the removal of epifauna is almost complete and that its full recovery is slow. By highlighting the importance of nodules for the epifaunal biodiversity of this abyssal area, we urge for cautious consideration of the criteria for determining future preservation zones.

  19. Evidence for deep-water deposition of abyssal Mediterranean evaporites during the Messinian salinity crisis

    Christeleit, Elizabeth C.; Brandon, Mark T.; Zhuang, Guangsheng

    2015-10-01

    Scientific drilling of the abyssal evaporites beneath the deepest parts of the Mediterranean basin gave rise to the idea that the Mediterranean sea completely evaporated at the end of the Messinian. Herein, we show, using new organic geochemical data, that those evaporites were deposited beneath a deep-water saline basin, not in a subaerial saltpan, as originally proposed. Abundant fossil organic lipids were extracted from evaporites in Mediterranean Deep Sea Drilling Project cores. The archaeal lipid distribution and new analyses, using the ACE salinity proxy and TEX86 temperature proxy, indicate that surface waters at the time of evaporite deposition had normal marine salinity, ranging from ∼26 to 34 practical salinity units, and temperatures of 25-28 °C. These conditions require a deep-water setting, with a mixed layer with normal marine salinity and an underlying brine layer at gypsum and halite saturation. After correction for isostatic rebound, our results indicate maximum drawdown of ∼2000 m and ∼2900 m relative to modern sea level in the western and eastern Mediterranean basins, respectively. Our results are consistent with previously proposed scenarios for sea level drawdown based on both subaerial and submarine incision and backfilling of the Rhone and Nile rivers, which require Messinian sea level drops of ∼1300 m and ∼200 m, respectively. This study provides new evidence for an old debate and also demonstrates the importance of further scientific drilling and sampling of deeper part of the abyssal Messinian units.

  20. Moored current meter data from the Madeira Abyssal Plain (GME). 1. deployment (1984)

    Near bottom current have been measured at three closely spaced sites in the N.E. Atlantic for 13 months. Locations were selected in the Great Meteor East study site area, near 310 30'N 250W, one on the abyssal plain, one on top of a small abyssal hill about 400 m high and one on its flank just above the plain. Current meters were moored 10, 100, and 1000 m above the local bottom (5438 m, 5398 m and 4999 m) in January 1984 and recovered in February 1985. This report displays the characteristics of the currents in numerous tables and figures. In the mean they ar found to be very weak and though adjacent moorings are separated by only 12 km and 27 km the year-long current directions differ radically. Current variations are principally due to semi-diurnal tides, inertial oscillations and eddies the latter of which migrate over the moorings. The tidal energy meets expectations as does the eddy energy with magnitude 2-3 cm2 s-2. Horizontal (isopycnal) diffusivity is estimated as about 2x102 m2 s-1. Currents 10 m above the bottom exceed 10 cm/s least frequently on the plain and most frequently at the hill-foot. The influence of the hill is surprisingly large. At all three sites the strongest currents are found near the sea bed. Speeds also show a Weibull distribution and rough 50 year return currents are inferred. (author)

  1. Moored current meter data from the Madeira Abyssal Plain (GME). 2. deployment (1984)

    Near bottom currents have been measured at three closely spaced sites in the N.E. Atlantic for 22 months. This report describes the results for the period 13-22 months and closely follows the pattern used in describing the first 13 months of data (IOS Report No. 221, 1986). The three locations were in the Great Meteor East study site area, near 310 30'N 250W, one on the abyssal plain, one on top of a small abyssal hill about 400 m high and one on its eastern flank. For the period of this report current meters were moored 10,100 and 1000 m above the local bottom (5438 m, 5433 m and 4989 m) between February and November 1985. The characteristics of the currents are displayed in numerous tables and figures: the mean currents for the 9 months are strikingly similar to those measured for the first 13 months. The variations in current strengths are also similar and yield eddy energies of between 2 and 3 cm2 s-2 and horizontal (isopycnal) diffusivity of 2x102 m2 s-1. Currents in excess of 10 cm/s were considerably less frequent than found for the earlier data set. (author)

  2. A comparative study of microbial diversity and community structure in marine sediments using poly(A tailing and reverse transcription PCR

    Tatsuhiko eHoshino

    2013-06-01

    Full Text Available To obtain a better understanding of metabolically active microbial communities, we tested a molecular ecological approach using poly(A tailing of environmental 16S rRNA, followed by full-length complementary DNA (cDNA synthesis and sequencing to eliminate potential biases caused by mismatching of PCR primer sequences. The RNA pool tested was extracted from marine sediments of the Yonaguni Knoll IV hydrothermal field in the southern Okinawa Trough. The sequences obtained using the ploy(A tailing method were compared statistically and phylogenetically with those obtained using conventional reverse transcription-polymerase chain reaction (RT-PCR with published domain-specific primers. Both methods indicated that Deltaproteobacteria are predominant in sediment (>85% of the total sequence read. The poly(A tailing method indicated that Desulfobacterales were the predominant deltaproteobacteria, while most of the sequences in libraries constructed using RT-PCR were derived from Desulfuromonadales. This discrepancy may have been due to low coverage of Desulfobacterales by the primers used. A comparison of library diversity indices indicated that the poly(A tailing method retrieves more phylogenetically diverse sequences from the environment. The four archaeal 16S rRNA sequences that were obtained using the poly(A tailing method formed deeply branching lineages that were related to Candidatus Parvarchaeum and the Ancient Archaeal Group. These results clearly demonstrate that poly(A tailing followed by cDNA sequencing is a powerful and less biased molecular ecological approach for the study of metabolically active microbial communities.

  3. Major Elements Budget Between Abyssal Peridotite And Seawater During The Serpentinization

    Yu, X.; Dong, Y.; Li, X.; Chu, F.

    2012-12-01

    Water-Rock Interaction is one of the most hot-debated issues among geologists, geophysicists, as well as geochemists. Abyssal peridotites recovered from the seafloor are often greatly affected or alterated by seawater in the form of serpentinization. The alteration to the peridotites makes it difficult to do the straightforward analysis for its primary composition as it was settled in the upper mantle, which confine the usage of these rare direct samples from the mantle in the scientific study, such as mantle dynamics, mantle composition and crust-mantle interaction. Besides, It was revealed recently that the serpentinization of abyssal peridotites may give birth to the hydrothermal activity. The elements migration during the serpentinization may perform a great role on the chemical composition of the hydrothermal fluid, which can support a hidden chemosynthetic ecosystem in the abyssal seabed. The research work focused on the major elements behavior during the serpentinization by studying the partially serpentinized samples of abyssal peridotite from Southwest Indian Ridge. The primary mineral assemblage of peridotite is olivine (Mg2SiO4), orthopyroxene (Mg2Si2O6), clinopyroxene (CaMgSi2O6) and spinel ((Mg,Fe)(Al,Cr)2O4). The major chemical composition are usually as SiO2 (30~45wt.%), MgO (20~45 wt.%), FeO and Fe2O3 (total 5~15 wt.%). Besides there are very few MnO, CaO, Al2O3, Cr2O3, NiO, Na2O, K2O and H2O. While on the other hand the serpentinized peridotite shows a more complicated mineral assemblage, besides the primary minerals there are more alteration minerals, such as serpentine (Mg3[Si2O5](OH)4), magnetite (Fe3O4), talc (Mg3[Si4O10](OH)2), brucite (Mg(OH)2), tremolite (Ca2Mg5[Si8O22](OH)2), chromite (FeCr2O4), chlorite ((Mg,Fe)6[(Si,Al)4O10](OH)8), and other accessary minerals like native metals, sulfides, clay minerals and hornblende. According to the EMPA analysis, the serpentinized sample shows the chemical composition as SiO2(~40 wt.%), MgO(~30 wt

  4. Do abyssal scavengers use phytodetritus as a food resource? Video and biochemical evidence from the Atlantic and Mediterranean

    Jeffreys, Rachel M.; Lavaleye, Marc S. S.; Bergman, Magda J. N.; Duineveld, Gerard C. A.; Witbaard, Rob

    2011-04-01

    Deep-sea benthic communities derive their energetic requirements from overlying surface water production, which is deposited at the seafloor as phytodetritus. Benthic invertebrates are the primary consumers of this food source, with deep-sea fish at the top of the trophic hierarchy. Recently, we demonstrated with the use of baited cameras that macrourid fish rapidly respond to and feed vigorously on large plant food falls mimicked by spinach ( Jeffreys et al., 2010). Since higher plant remains are scarce in the deep-sea, with the exception of canyons, where terrestrial material has been observed, these results led us to ask if a more commonly documented plant material i.e. phytodetritus might form a food source for deep-sea fish and mobile scavenging megafauna. We simulated a phytodetritus dump at the seafloor in two contrasting environments (1) the NE Atlantic where carpets of phytodetritus have been previously observed and (2) the oligotrophic western Mediterranean, where the deposition of phytodetritus at the seafloor is a rare occurrence. We recorded the response of the scavenging fauna using an in situ benthic lander equipped with baited time-lapse cameras. In the NE Atlantic at 3000 m, abyssal macrourids and cusk-eels were observed ingesting the phytodetritus. The phytodetrital patch was significantly diminished within 2 h. Abundance estimates calculated from first arrival times of macrourids at the phytodetrital patch in the Atlantic corresponded with abundance estimates from video-transect indicating that fish were attracted to the scent of phytodetrital bait. In contrast to this, in the western Mediterranean at 2800 m a single macrourid was observed investigating the phytodetrital patch but did not feed from it. The phytodetrital patch was significantly diminished within 6.5 h as a result of mainly invertebrate activity. At 1900 m, Lepidion lepidion was observed near the lander and the bait, but did not feed. The phytodetrital patch remained intact until

  5. Keep your Sox on: Community genomics-directed isolation and microscopic characterization of the dominant subsurface sulfur-oxidizing bacterium in a sediment aquifer

    Mullin, S. W.; Wrighton, K. C.; Luef, B.; Wilkins, M. J.; Handley, K. M.; Williams, K. H.; Banfield, J. F.

    2012-12-01

    Community genomics and proteomics (proteogenomics) can be used to predict the metabolic potential of complex microbial communities and provide insight into microbial activity and nutrient cycling in situ. Inferences regarding the physiology of specific organisms then can guide isolation efforts, which, if successful, can yield strains that can be metabolically and structurally characterized to further test metagenomic predictions. Here we used proteogenomic data from an acetate-stimulated, sulfidic sediment column deployed in a groundwater well in Rifle, CO to direct laboratory amendment experiments to isolate a bacterial strain potentially involved in sulfur oxidation for physiological and microscopic characterization (Handley et al, submitted 2012). Field strains of Sulfurovum (genome r9c2) were predicted to be capable of CO2 fixation via the reverse TCA cycle and sulfur oxidation (Sox and SQR) coupled to either nitrate reduction (Nap, Nir, Nos) in anaerobic environments or oxygen reduction in microaerobic (cbb3 and bd oxidases) environments; however, key genes for sulfur oxidation (soxXAB) were not identified. Sulfidic groundwater and sediment from the Rifle site were used to inoculate cultures that contained various sulfur species, with and without nitrate and oxygen. We isolated a bacterium, Sulfurovum sp. OBA, whose 16S rRNA gene shares 99.8 % identity to the gene of the dominant genomically characterized strain (genome r9c2) in the Rifle sediment column. The 16S rRNA gene of the isolate most closely matches (95 % sequence identity) the gene of Sulfurovum sp. NBC37-1, a genome-sequenced deep-sea sulfur oxidizer. Strain OBA grew via polysulfide, colloidal sulfur, and tetrathionate oxidation coupled to nitrate reduction under autotrophic and mixotrophic conditions. Strain OBA also grew heterotrophically, oxidizing glucose, fructose, mannose, and maltose with nitrate as an electron acceptor. Over the range of oxygen concentrations tested, strain OBA was not

  6. Recoding of the stop codon UGA to glycine by a BD1-5/SN-2 bacterium and niche partitioning between Alpha- and Gammaproteobacteria in a tidal sediment microbial community naturally selected in a laboratory chemostat

    MarcStrous

    2014-05-01

    Full Text Available Sandy coastal sediments are global hotspots for microbial mineralization of organic matter and denitrification. These sediments are characterized by advective porewater flow, tidal cycling and an active and complex microbial community. Metagenomic sequencing of microbial communities sampled from such sediments showed that potential sulfur oxidizing Gammaproteobacteria and members of the enigmatic BD1-5/SN-2 candidate phylum were abundant in situ (>10% and ~2% respectively. By mimicking the dynamic oxic/anoxic environmental conditions of the sediment in a laboratory chemostat, a simplified microbial community was selected from the more complex inoculum. Metagenomics, proteomics and fluorescence in situ hybridization showed that this simplified community contained both a potential sulfur oxidizing Gammaproteobacterium (at 24±2% abundance and a member of the BD1-5/SN-2 candidate phylum (at 7±6% abundance. Despite the abundant supply of organic substrates to the chemostat, proteomic analysis suggested that the selected gammaproteobacterium grew partially autotrophically and performed hydrogen/formate oxidation. The enrichment of a member of the BD1-5/SN-2 candidate phylum enabled, for the first time, direct microscopic observation by fluorescent in situ hybridization and the experimental validation of the previously predicted translation of the stop codon UGA into glycine.

  7. Hydrogeological Importance of Bedrock Sediments to the Community and Growth of Sugar Cane in Fadama Rake Area of Madagali, Northeast Nigeria

    Gaiya Stephen

    2014-04-01

    Full Text Available Thirty Vertical Electrical Sounding (VES points were sited on the alluvial plain of Madagali fadama area. This was aimed at establishing the lithological character of the drainage plain and its contributions to the growth of sugar cane. 1X1D shareware package was used to interpret the curves. Over the floodplain, potential recharge water into the subsurface units probably takes place through migration routes of coarse-grained colluvial deposits which act as effective soak away for surface runoff. The nature of the basin and/or the transporting routes conditioned the thickness of the surface layer. Effects of near surface bedrock or buried granite boulders disengaged from nearby hills are demonstrated by sandwiching of the bedrock in place in the second resistivity layer. Closely spaced iso-ohmic contour values suggest presence of different types of sediments within the medium of deposition. The high thickness associated with this horizon suggests that the basin was large enough to contain the sediments. Clay materials in the third resistivity layer occur as lens bodies within sandy material. Clay free sand and gravel constitute a great proportion of the stratigraphy. Parts of the bedrock’s summits that approached the surface at two separate places are resistant to weathering. Thicker sediments were available where sandy and gravelly materials prevailed. Gradual increases in thickness of the sediments suggest a gentle sloping depositional basin. Sharp gradation of the grain size from clay to bedrock within the fourth resistivity layer depicts a basin that did not permit transportation of the material far from its source. Three zones of groundwater potentials were identified from the total longitudinal conductance and the porosity maps of the area. These were based on the weathered products that constitute the aquifer zone where thick saturated sand and gravel are associated to deep aquifer development and thin saturated sand and gravel to

  8. Community structure and activity of sulfate-reducing bacteria in an intertidal surface sediment: a multi-method approach

    Llobet-Brossa, Enrique; Rabus, Ralf; Böttcher, Michael E.;

    2002-01-01

    The community structure of sulfate-reducing bacteria (SRB) in an intertidal mud flat of the German Wadden Sea (Site Dangast, Jade Bay) was studied and related to sedimentary biogeochemical gradients and processes. Below the penetration depths of oxygen (~3 mm) and nitrate (~4 mm), the presence of...

  9. Three new species of deep-sea Gromia (Protista, Rhizaria) from the bathyal and abyssal Weddell Sea, Antarctica

    Rothe, Nina; Gooday, Andrew J.; Cedhagen, Tomas; Fahrni, José; Hughes, J. Alan; Page, Anton; Pearce, Richard B.; Pawlowski, Jan

    2009-01-01

    We describe three new species of the genus Gromia from bathyal and abyssal depths in the Weddell Sea. The new species are characterized by a combination of morphological and molecular criteria. All three species possess a distinct oral capsule and a layer of ‘honeycomb membranes’, which form the ...

  10. Chlor-alkali plant contamination of Aussa River sediments induced a large Hg-resistant bacterial community

    Baldi, Franco; Marchetto, Davide; Gallo, Michele; Fani, Renato; Maida, Isabel; Covelli, Stefano; Fajon, Vesna; Zizek, Suzana; Hines, Mark; Horvat, Milena

    2012-11-01

    A closed chlor-alkali plant (CAP) discharged Hg for decades into the Aussa River, which flows into Marano Lagoon, resulting in the large-scale pollution of the lagoon. In order to get information on the role of bacteria as mercury detoxifying agents, analyses of anions in the superficial part (0-1 cm) of sediments were conducted at four stations in the Aussa River. In addition, measurements of biopolymeric carbon (BPC) as a sum of the carbon equivalent of proteins (PRT), lipids (LIP), and carbohydrates (CHO) were performed to correlate with bacterial biomass such as the number of aerobic heterotrophic cultivable bacteria and their percentage of Hg-resistant bacteria. All these parameters were used to assess the bioavailable Hg fraction in sediments and the potential detoxification activity of bacteria. In addition, fifteen isolates were characterized by a combination of molecular techniques, which permitted their assignment into six different genera. Four out of fifteen were Gram negative with two strains of Stenotrophomonas maltophilia, one Enterobacter sp., and one strain of Brevibacterium frigoritolerans. The remaining strains (11) were Gram positive belonging to the genera Bacillus and Staphylococcus. We found merA genes in only a few isolates. Mercury volatilization from added HgCl2 and the presence of plasmids with the merA gene were also used to confirm Hg reductase activity. We found the highest number of aerobic heterotrophic Hg-resistant bacteria (one order magnitude higher) and the highest number of Hg-resistant species (11 species out of 15) at the confluence of the River Aussa and Banduzzi's channel, which transport Hg from the CAP, suggesting that Hg is strongly detoxified [reduced to Hg(0)] at this location.

  11. Fungal community analysis in the deep-sea sediments of the central Indian Basin by culture-independent approach

    Singh, P.; Raghukumar, C.; Verma, P.; Shouche, Y.

    ecosystem may have enormous potential in the development of new products such as pharmaceuticals, molecular probes, enzymes, cosmetics, nutritional supplements and agrichemicals [35]. A recently described antibiotic–resistance enzyme from the deep... vents oases for parasitic protists? Trends Parasitol 19: 556–558 26. O’Brien H, Parrent JL, Jackson JA, Moncalvo J, Vilgalys R (2005) Fungal community analysis by large-scale sequencing of environmental samples. Appl Environ Microbiol 71: 5544...

  12. Impacts of Alterations of Organic Inputs on the Bacterial Community within the sediments of Wind Cave, South Dakota, USA

    Chelius Marisa K.; Beresford Guy; Horton Howard; Quirk Megan; Selby Greg; Simpson Rodney T.; Horrocks Rodney; Moore John C.

    2009-01-01

    Wind Cave (WICA) in the Black Hills of South Dakota, like many mostly dry caves in temperate regions is an energy-starved system.The biotic communities that reside in these systems are low in diversity and simple in structure, and sensitive to changes in externalinputs of organic matter. Caves open to tourist traffic offer an opportunity to study the impacts of organic matter amendments in theform of human and rodent hair and dander, clothing lint, material from rodent activity (nesting mater...

  13. Rich and rare—First insights into species diversity and abundance of Antarctic abyssal Gastropoda (Mollusca)

    Schwabe, Enrico; Michael Bohn, Jens; Engl, Winfried; Linse, Katrin; Schrödl, Michael

    2007-08-01

    The abyssal depths of the polar oceans are thought to be low in diversity compared with the shallower polar shelves and temperate and tropical deep-sea basins. Our recent study on the gastropod fauna of the deep Southern Ocean gives evidence of the existence of a rich gastropod assemblage at abyssal depths. During the ANDEEP I and II expeditions to the southern Drake Passage, Northwestern Weddell Sea, and South Sandwich Trench, gastropods were collected by bottom and Agassiz trawls, epibenthic sledge, and multicorer, at 40 stations in depths between 127 and 5194 m. On the whole, 473 specimens, corresponding to 93 species of 36 families, were obtained. Of those, 414 specimens were caught below 750 m depth and refer to 84 (90%) benthic species of 32 (89%) families. Most families were represented by a single species only. The numerically dominant families were Skeneidae and Buccinidae (with 10 and 11 species, respectively), Eulimidae and Trochidae (with 9 species each), and Turridae (6 species). Thirty-Seven benthic deep-sea species (44%) were represented by a single specimen, and another 20 species (24%) were found at a single station, suggesting that more than two thirds of Antarctic deep-sea gastropod species are very rare or have a very scattered distribution. Of the 27 species occurring at two or more deep-sea stations, 14 were collected with different gear. Approximately half of the deep-water species are new to science or have been recently described. The present investigation increases the total number of recorded benthic Antarctic deep-sea gastropods (below 750 m) from 115 to 177. The previously known depth ranges have been extended, often considerably, for 31 species. The collected deep-sea gastropods comprise both eurybathic shelf species (29%) and apparently true deep-sea species (58%); some of the latter may belong to a so far unknown Antarctic abyssal fauna. Geographical ranges of the collected Antarctic benthic deep-sea gastropod species appear limited

  14. Engineering concepts for the placement of wastes on the abyssal seafloor

    Valent, Philip J.; Palowitch, Andrew W.; Young, David K.

    1998-05-01

    The Naval Research Laboratory (NRL), with industry and academic participation, has completed a study of the concept of isolating industrial wastes (i.e., sewage sludge, fly ash from municipal incinerators, and dredged material) on the abyssal seafloor. This paper presents results of the technical and economic assessment of this waste management concept. The results of the environmental impacts portion of the study are presented in a companion paper. The technical assessment began with identification of 128 patents addressing waste disposal in the ocean. From these 128 patents, five methods for transporting wastes through the water column and emplacing wastes within an easily monitored area on the abyssal seafloor were synthesized for technical assessment. In one method waste is lowered to the seafloor in a bucket of 190 m 3. In a second method waste is pumped down to the seafloor in pipes, 1.37 m in diameter and 6100 m in length. In a third method waste is free-fallen from the ocean surface in 380-m 3 geosynthetic fabric containers (GFCs). In the fourth and fifth methods, waste is carried to near the seafloor in GFCs transported in (a) a 20,000 metric ton displacement (loaded), unpowered, unmanned submersible glider, or (b) a 2085 metric ton displacement (loaded) disk-shaped transporter traversing to and from the seafloor much like an untethered elevator. In the last two methods the transporter releases the GFCs to free-fall the last few hundred meters to the seafloor. Two reliability analyses, a Fault Tree Analysis (FTA), and a Failure Modes, Effects, and Criticality Analysis (FMECA), showed that the free-fall GFC method posed the least overall relative risk, provided that fabric container and transporter designs eliminate the potential for tearing of the containers on release from the surface transporter. Of the five methods, the three GFC methods were shown to offer cost-effective waste management options when compared with present-day waste management

  15. Implications of spinel compositions for the petrotectonic history of abyssal peridotite from Southwest Indian Ridge (SWIR)

    Chen, T.; Jin, Z.; Wang, Y.; Tao, C.

    2012-12-01

    Abyssal peridotites generate at mid-ocean ridges. Lherzolite and harzburgite are the main rock types of peridotites in the uppermost mantle. The lherzolite subtype, less depleted and less common in ophiolites, characterizes mantle diapirs and slow-spreading ridges. Along the Earth's mid-ocean ridges, abyssal peridotites undergo hydration reactions to become serpentinite minerals, especially in slow to ultraslow spreading mid-ocean ridges. Spinel is common in small quantities in peridotites, and its compositions have often been used as petrogenetic indicators [1]. The Southwest Indian Ridge (SWIR) is one of the two ultraslow spreading ridges in the world. The studied serpentinized peridotite sample was collected by the 21st Voyage of the Chinese oceanic research ship Dayang Yihao (aka Ocean No. 1) from a hydrothermal field (63.5°E, 28.0°S, and 3660 m deep) in SWIR. The studied spinels in serpentinized lherzolite have four zones with different compositions: relic, unaltered core is magmatic Al-spinels; micro- to nano- sized ferrichromite zoned particles; narrow and discontinuous magnetite rim; and chlorite aureoles. The values Cr# of the primary Al-spinels indicate the range of melting for abyssal peridotites from SWIR extends from ~4% to ~7% [2]. The alteration rims of ferrichromite have a chemical composition characterized by Fe enrichment and Cr# increase indicating chromite altered under greenschist-amphibolite facies. Magnetites formed in syn- and post- serpentinization. Chlorite (clinochlore) formed at the boundary and crack of spinel indicating it had undergone with low-temperature MgO- and SiO2-rich hydrothermal fluids [3]. It suggests that serpentinized lherzolite from SWIR had undergone poly-stage hydration reactions with a wide range of temperature. Acknowledgments: EMPA experiment was carried out by Xihao Zhu and Shu Zheng in The Second Institute of Oceanography and China University of Geosciences, respectively. The work was supported by NSFC

  16. Kuril-Kamchatka deep sea revisited - insights into the amphipod abyssal fauna

    Jażdżewska, Anna

    2015-01-01

    During the KuramBIO expedition to the Kuril-Kamchatka Trench and abyssal plain, benthic samples from the depths from 4987 to 5422 m were collected using a camera-epibenthic sledge. In this collection more than 1200 individuals of Amphipoda were found. They were assigned to 60 taxa (including 47 morphospecies) and 21 families. Until now 28 species being new to science have been found: six in the superfamily Eusiroidea and in the Oedicerotidae and Synopiidae families, four in the Phoxocephalidae, three in the Pardaliscidae, two in the Stenothoidae and one in the Pachynidae. The Synopiidae, Stenothoidae and Pachynidae were recorded for the first time in North-West Pacific area. The dominant and most speciose families were Oedicerotidae, Phoxocephalidae, Synopiidae, Eusiridae s.l. and Lysianassidae. The cluster analysis clearly separated the shallowest sample from the others, which were divided further into two groups. The shallowest sample was characterized by the highest number of species and number of individuals.

  17. Vesicomyinae (Bivalvia: Vesicomyidae) of the Kuril-Kamchatka Trench and adjacent abyssal regions

    Krylova, Elena M.; Kamenev, Gennady M.; Vladychenskaya, Irina P.; Petrov, Nikolai B.

    2015-01-01

    Representatives of the subfamily Vesicomyinae (Bivalvia, Vesicomyidae) are tiny deep-sea molluscs distributed worldwide and reaching huge abundances of hundreds and thousands of specimens in trawl catches. During the German-Russian deep-sea expedition KuramBio (R/V Sonne, 2012) for the first time two vesicomyin species were collected from the abyssal plain adjacent to the Kuril-Kamchatka Trench from the depths of 4861-5787 m, Vesicomya pacifica (Smith, 1885) and "Vesicomya" filatovae sp.n. Two species of vesicomyins, V. sergeeviFilatova, 1971 and V. profundiFilatova, 1971, which were previously reported from the hadal of the Kuril-Kamchatka Trench, were not collected at the abyssal depth despite of the close geographical proximity of the sampling area to their distribution ranges. Altogether nine species of vesicomyins are recorded now from the West and Indo-West Pacific; data on distribution and morpho-anatomical characters of these species are provided. Taxonomic description of V. pacifica is revised including information on its soft part anatomy, new localities and COI sequences. For the first time for a vesicomyin bivalve molecular data is given for a species with an explicit morphological description and unambiguous taxonomic affiliation. Molecular analysis of 160 published COI sequences of vesicomyids and newly obtained molecular data on V. pacifica showed that V. pacifica and two undescribed vesicomyin species forming a monophyletic clade which exhibits sister relationships with the Pliocardiinae, the group of chemosymbiotic vesicomyids. "Vesicomya" filatovae sp.n. is provisionally assigned to the genus Vesicomya (s.l.) until additional morphological and molecular data are obtained. It differs from Vesicomya s.s. by a broader hinge margin with more radiating teeth and the presence of only one pair of demibranchs.

  18. Recoding of the stop codon UGA to glycine by a BD1-5/SN-2 bacterium and niche partitioning between Alpha- and Gammaproteobacteria in a tidal sediment microbial community naturally selected in a laboratory chemostat

    Hanke, Anna [Max Planck Institute for Marine Microbiology; Hamann, Emmo [Max Planck Institute for Marine Microbiology; Sharma, Ritin [ORNL; Geelhoed, Jeanine [Max Planck Institute for Marine Microbiology; Hargesheimer, Theresa [Max Planck Institute for Marine Microbiology; Kraft, Beate [Max Planck Institute for Marine Microbiology; Meyer, Volker [Max Planck Institute for Marine Microbiology; Lenk, Sabine [Max Planck Institute for Marine Microbiology; Osmers, Harald [Max Planck Institute for Marine Microbiology; Wu, Rong [Delft University of Technology, Delft, Netherlands; Makinwa, Kofi [Delft University of Technology, Delft, Netherlands; Hettich, Robert {Bob} L [ORNL; Banfield, Jillian F. [University of California, Berkeley; Tegetmeyer, Halina [Max Planck Institute for Marine Microbiology; Strouss, Marc [University of Calgary, ALberta, Canada

    2014-01-01

    Sandy coastal sediments are global hot spots for microbial mineralization of organic matter and denitrification. These sediments are characterized by advective pore water flow, tidal cycling and an active and complex microbial community. Metagenomic sequencing of microbial communities sampled from such sediments showed that potential sulfuroxidizing Gammaproteobacteria and members of the enigmaticBD1-5/ SN-2 candidatephylumwereabundantinsitu (>10% and 2% respectively). By mimicking the dynamic oxic/anoxic environmental conditions of the sedimentin a laboratory chemostat, a simplified microbial community was selected from the more complex inoculum. Metagenomics, proteomics and fluorescenceinsituhybridization showed that this simplified community contained both a potential sulfuroxidizing Gamma proteobacteria (at 24 2% abundance) and a member of the BD1-5 / SN-2candidatephylum (at 7 6%abundance). Despite the abundant supply of organic substrates to the chemostat, proteomic analysis suggested that the selected gamma proteobacterium grew partially auto trophically and performed hydrogen/formate oxidation. The enrichment of a member of the BD1-5/SN-2candidatephylum enabled, for the first time, direct microscopic observation by fluorescent insitu hybridization and the experimental validation of the previously predicted translation of the stop codon UGA into glycine.

  19. Phylogenetic identification of marine bacteria isolated from deep-sea sediments of the eastern South Atlantic Ocean

    da Silva, Marcus Adonai Castro; Cavalett, Angélica; Spinner, Ananda; Rosa, Daniele Cristina; Jasper, Regina Beltrame; Quecine, Maria Carolina; Bonatelli, Maria Letícia; Pizzirani-Kleiner, Aline; Corção, Gertrudes; Lima, André Oliveira de Souza

    2013-01-01

    The deep-sea environments of the South Atlantic Ocean are less studied in comparison to the North Atlantic and Pacific Oceans. With the aim of identifying the deep-sea bacteria in this less known ocean, 70 strains were isolated from eight sediment samples (depth range between 1905 to 5560 m) collected in the eastern part of the South Atlantic, from the equatorial region to the Cape Abyssal Plain, using three different culture media. The strains were classified into three phylogenetic groups, ...

  20. Microbial community structure and nitrogenase gene diversity of sediment from a deep-sea hydrothermal vent field on the Southwest Indian Ridge

    WU Yuehong; CAO Yi; WANG Chunsheng; WU Min; AHARON Oren; XU Xuewei

    2014-01-01

    A sediment sample was collected from a deep-sea hydrothermal vent field located at a depth of 2 951 m on the Southwest Indian Ridge. Phylogenetic analyses were performed on the prokaryotic community using polymerase chain reaction (PCR) amplification of the 16S rRNA and nifH genes. Within the Archaea, the dominant clones were from marine benthic group E (MBGE) and marine group I (MGI) belonging to the phyla Euryarchaeota and Thaumarchaeota, respectively. More than half of the bacterial clones belonged to the Proteobacteria, and most fell within the Gammaproteobacteria. No epsilonproteobacterial sequence was observed. Additional phyla were detected including the Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Nitrospirae, Chloroflexi, Chlorobi, Chlamydiae, Verrucomicrobia, and candidate divisions OD1, OP11, WS3 and TM6, confirming their existence in hydrothermal vent environments. The detection of nifH gene suggests that biological nitrogen fixation may occur in the hydrothermal vent field of the South-west Indian Ridge. Phylogenetic analysis indicated that only Clusters I and III NifH were present. This is consistent with the phylogenetic analysis of the microbial 16S rRNA genes, indicating that Bacteria play the main role in nitrogen fixation in this hydrothermal vent environment.

  1. An End-to-End DNA Taxonomy Methodology for Benthic Biodiversity Survey in the Clarion-Clipperton Zone, Central Pacific Abyss

    Adrian G. Glover

    2015-12-01

    Full Text Available Recent years have seen increased survey and sampling expeditions to the Clarion-Clipperton Zone (CCZ, central Pacific Ocean abyss, driven by commercial interests from contractors in the potential extraction of polymetallic nodules in the region. Part of the International Seabed Authority (ISA regulatory requirements are that these contractors undertake environmental research expeditions to their CCZ exploration claims following guidelines approved by the ISA Legal and Technical Commission (ISA, 2010. Section 9 (e of these guidelines instructs contractors to “…collect data on the sea floor communities specifically relating to megafauna, macrofauna, meiofauna, microfauna, nodule fauna and demersal scavengers”. There are a number of methodological challenges to this, including the water depth (4000–5000 m, extremely warm surface waters (~28 °C compared to bottom water (~1.5 °C and great distances to ports requiring a large and long seagoing expedition with only a limited number of scientists. Both scientists and regulators have recently realized that a major gap in our knowledge of the region is the fundamental taxonomy of the animals that live there; this is essential to inform our knowledge of the biogeography, natural history and ultimately our stewardship of the region. Recognising this, the ISA is currently sponsoring a series of taxonomic workshops on the CCZ fauna and to assist in this process we present here a series of methodological pipelines for DNA taxonomy (incorporating both molecular and morphological data of the macrofauna and megafauna from the CCZ benthic habitat in the recent ABYSSLINE cruise program to the UK-1 exploration claim. A major problem on recent CCZ cruises has been the collection of high-quality samples suitable for both morphology and DNA taxonomy, coupled with a workflow that ensures these data are made available. The DNA sequencing techniques themselves are relatively standard, once good samples have been

  2. Tephra records from abyssal sediments off western Sumatra in recent 135 ka:evidence from Core IR-GC1

    QIU Zhongyan; HAN Xiqiu; JIN Xianglong; WANG Yejian; ZHU Jihao

    2014-01-01

    Three volcanic ash layers were identified in a deep-sea Core IR-GC1 from the north-eastern Indian Ocean, adjacent to western Indonesian arc. They were dominated by glass shards with minor mineral crystals, such as plagioclase, biotite, and hornblende. According to the morphology and major element compositions of the representative glass shards, combined with theδ18O-based age, it is suggested that ash Layer A is cor-related to the youngest Toba tuff (YTT), Layer B is supposed to be associated with a new eruption of Toba caldera in an age of 98 to 100 ka. Ash Layer C is different the geochemistry characteristics than those of Layer A and Layer B, suggesting that Layer C was not originated from Toba but registered another volcanic erup-tion event.

  3. Paleoceanographic interpretations of late Pleistocene to Holocene sedimentological and geochemical proxy-data from SE-Atlantic abyssal plains (Cape, Angola and Guinea Basin)

    Piller, W. E.; Müllegger, S.

    2009-04-01

    Sediments of the deep abyssal regions of the Southeast Atlantic (Cape Basin, Angola Basin and Guinea Basin) were studied to reconstruct changes in surface and deep water circulation, bioproductivity, and terrigenous sediment flux. To gain these results various sedimentological and geochemical proxies were imposed, including grain size data, foraminiferal fragmentation, carbonate and organic carbon content, as well as stable oxygen and carbon isotope contents of foraminiferal tests. Samples were gained with a multicorer device during Meteor cruise 63/2 (2005) in water depths between ~5,100 and ~5,600 m. The superficial 30 cm of sediment, sampled in 1/2, 1 and 5 cm steps, were processed for this study. The record covers parts of the Pleistocene and Holocene. Even if the sedimentation conditions seem to be similar in the deep-sea regions of the SE-Atlantic there are clear differences between the three sampled locations. This is caused by major changes in deep water corrosiveness leading to fluctuations in the sedimentation rate and carbonate preservation. Cape Basin localities show a pattern of enhanced carbonate preservation around 12 ka BP possibly indicating a delayed Last Glacial Maximum signal. This pattern, which is typical for Indo-Pacific records, clearly points to an influence of Antarctic Bottom Water (AABW) at water depths below 5000 m in the Northern Cape Basin. The non-correlation between carbonate content and grain size distribution is owing to a coccoliths' dominated carbonate production possibly caused by low nutrient availability in surface waters and the higher dissolution susceptibility of foraminiferal tests. Angola Basin samples delivered highest sand contents, a carbonate peak and low organic carbon values around 8.2 ka BP which indicate a reduced bioproduction and nutrient supply in superficial waters. A connection of the 8.2 ka cold event in the northern hemisphere and central African precipitation, equatorial East Atlantic (EEA) upwelling

  4. iodine diagenesis in pelagic deep sea sediments

    Measurements of sediment geochemistry and porewater speciation and fluxes, made using nineteen sediment cores from the Madeira, Seine, Tagus and Nares Abyssal plains and the Alboran Sea, and a benthic flux experiment in the San Clemente Basin have been used to evaluate the early diagenesis of iodine in the deep sea. The observations result from a quasi-closed cycle for I at the sediment-seawater interface involving release of I from decomposing marine organic matter, oxidation of porewater I- to molecular 2 which is rapidly removed by reactive organic matter and the build up of I/C regeneration ratios of up to 200 x 10-4. Below this surficial zone the absence of reactive organic matter allows disproportionation of I2 leading to a net interconversion of porewater I- to 103-. Iodate reduction occurs during suboxic diagenesis, after denitrification and before MnO2 reduction, consistent with the sequence of reactions predicted from the free energy yields for organic matter oxidation. There is some further I-production in the anoxic section of sediments but at much smaller rates than occur during the interfacial diagenetic cycling. (author)

  5. Uppermost Jurassic to Lower Cretaceous benthic foraminiferal biostratigraphy at ODP Site 765 on the Argo Abyssal Plain.

    Kaminski, M.A.; Gradstein, F.M.; Geroch, S.

    1992-01-01

    Benthic foraminifers were studied in 99 samples collected from the lower 200 m of Hole 765C. The studied section ranges from the Tithonian to Aptian, and benthic foraminifers can be subdivided into five assemblages on the basis of faunal diversity and stratigraphic ranges of distinctive species. Compared with deep-water assemblages from Atlantic DSDP sites and Poland, assemblages from the Argo Abyssal Plain display a higher diversity of agglutinated forms, which comprise the autochthonous ...

  6. Morphological, histochemical and immunohistochemical study of the gill epithelium in the abyssal teleost fish Coelorhynchus coelorhynchus

    Aurelio Licata; Silvestro Martella; Eugenia Rita Lauriano; Maria Pia Albanese; Concetta Calabrò

    2011-01-01

    Histochemical and immunohistochemical study was carried out on nitrinergic innervation and neuroendocrine system in the gill epithelium of the abyssal fish Coelorhynchus coelorhynchus. The results showed that nNOS-positive nerve fibers, originating from the branchial arch were present in the subepithelial tissue of branchial primary filament. nNOS-positive neuroendocrine cells were also present in the primary filaments and secondary lamellae. Numerous mucous cells in the gi...

  7. On A Simple Parameterization and Global Extrapolation of Topography-Catalyzed Diapycnal Mixing in the Abyssal Ocean

    Decloedt, T.; Luther, D. S.

    2006-12-01

    The potential role of topography-catalyzed mixing in maintaining the observed abyssal stratification is re- examined in light of the growing body of fine- and micro-structure data revealing energetic mixing near rough topography. A large collection of these fine- and micro-structure data sets from various oceanic regions are employed to develop a simple parameterization of the mean vertical structure of diapycnal mixing. The parameterization depends only on seafloor roughness and a power law function of height above bottom. Resulting global diffusivity maps show considerable spatial variability and suggest the need for more exploration of regions where non-tidal energy sources may generate near-boundary mixing. Basin-average diffusivity profiles and total dissipation rate estimates are found to be sensitive to the strength of mixing very close to the boundary (within 200 m). The contention that topography-catalyzed mixing is an important factor in maintaining the abyssal stratification is supported. Near-boundary mixing is perhaps the dominant factor below 3 km of depth, and is a significant factor at depths as shallow as one kilometer where it may provide as much as 1/3 of the bulk diffusivity required to maintain the stratification (under the assumption that diapycnal mixing is the sole mechanism for maintaining the stratification). The power required by the model to sustain this basin-average diffusivity profile in the abyssal oceans (1-4 km depth, 40 S to 48 N) is 0.41 TW to 0.89 TW (depending on the maximum near-boundary diffusivity prescribed in the power law model), in contrast to about 0.65 TW to maintain a diffusivity of 1 Stoke in the abyssal oceans.

  8. Community Structure of Denitrifiers, Bacteria, and Archaea along Redox Gradients in Pacific Northwest Marine Sediments by Terminal Restriction Fragment Length Polymorphism Analysis of Amplified Nitrite Reductase (nirS) and 16S rRNA Genes

    Braker, Gesche; Ayala-del-Río, Héctor L.; Devol, Allan H.; Fesefeldt, Andreas; Tiedje, James M.

    2001-01-01

    Steep vertical gradients of oxidants (O2 and NO3−) in Puget Sound and Washington continental margin sediments indicate that aerobic respiration and denitrification occur within the top few millimeters to centimeters. To systematically explore the underlying communities of denitrifiers, Bacteria, and Archaea along redox gradients at distant geographic locations, nitrite reductase (nirS) genes and bacterial and archaeal 16S rRNA genes (rDNAs) were PCR amplified and analyzed by terminal restrict...

  9. 14C and 210Pb in NE Atlantic sediments: evidence of biological reworking in the context of radioactive waste disposal

    Scavenging by the seabed and sediments in the deep ocean may have a significant effect on the removal of artificial radionuclides released in radioactive waste disposal operations. Biological activity in the upper layers of the sediment column will enhance the rate of removal for those particle-reactive radionuclides with a short half-life relative to the turnover time of the upper mixed layer. For longer-lived radionuclides the rate of sediment accumulation will determine the ultimate rate of removal. The rate of sediment accumulation and extent of biological mixing of a deep-sea sediment from three areas of the NE Atlantic Ocean have been investigated using 14C and 210Pb data. For 14C, box cores from the Iberia Abyssal Plain, Madeira Abyssal Plain and from the NEA low-level radioactive waste dumpsite yielded sedimentation rates in the range 0.8 to 2.2 cm ky-1 over the upper 16-25 cm. Continuous particle mixing appears to be taking place to a depth of 4 to 6 cm below the present sediment-water interface. Closely spaced vertical sampling of core 161-2 for 210Pb allowed a biodiffusion coefficient (Dsub(B)) to be calculated (4 x 10-9 cm2s-1). (author)

  10. Abyssal fauna of the UK-1 polymetallic nodule exploration claim, Clarion-Clipperton Zone, central Pacific Ocean: Echinodermata.

    Glover, Adrian G; Wiklund, Helena; Rabone, Muriel; Amon, Diva J; Smith, Craig R; O'Hara, Tim; Mah, Christopher L; Dahlgren, Thomas G

    2016-01-01

    We present data from a DNA taxonomy register of the abyssal benthic Echinodermata collected as part of the Abyssal Baseline (ABYSSLINE) environmental survey cruise 'AB01' to the UK Seabed Resources Ltd (UKSRL) polymetallic-nodule exploration claim 'UK-1' in the eastern Clarion-Clipperton Zone (CCZ), central Pacific Ocean abyssal plain. Morphological and genetic data are presented for 17 species (4 Asteroidea, 4 Crinoidea, 2 Holothuroidea and 7 Ophiuroidea) identified by a combination of morphological and genetic data. No taxa matched previously published genetic sequences, but 8 taxa could be assigned to previously-described species based on morphology, although here we have used a precautionary approach in taxon assignments to avoid over-estimating species ranges. The Clarion-Clipperton Zone is a region undergoing intense exploration for potential deep-sea mineral extraction. We present these data to facilitate future taxonomic and environmental impact study by making both data and voucher materials available through curated and accessible biological collections. PMID:26929713

  11. Morphological, histochemical and immunohistochemical study of the gill epithelium in the abyssal teleost fish Coelorhynchus coelorhynchus

    Aurelio Licata

    2011-08-01

    Full Text Available Histochemical and immunohistochemical study was carried out on nitrinergic innervation and neuroendocrine system in the gill epithelium of the abyssal fish Coelorhynchus coelorhynchus. The results showed that nNOS-positive nerve fibers, originating from the branchial arch were present in the subepithelial tissue of branchial primary filament. nNOS-positive neuroendocrine cells were also present in the primary filaments and secondary lamellae. Numerous mucous cells in the gill epithelium were AB/PAS-positive, while sialic acid was absent as confirmed by neuraminidase reaction and WGA lectin histochemistry. The mucus compounds in abyssal teleost fish are different from those found in pelagic species, being related to their living conditions. In abyssal species, greater numbers of chloride and neuroendocrine cells are involved in the movement of water and electrolytes. Neuroendocrine cells possess oxygen receptors which mediate the cardiovascular and ventilatory response to oxygen deficiency, as reported in teleost species. Besides, NO contributes through nervous stimulation to the regulation of vascular tone and blood circulation in the gill.

  12. Community structure of foraminiferal communities within temporal biozones from the western Arctic Ocean

    Hayek, Lee-Ann C.; Buzas, Martin A.; Osterman, Lisa A.

    2007-01-01

    Community structure is often an overlooked dimension of biodiversity. Knowledge of community structure, the statistical distribution of the relative species abundance vector, makes possible comparisons and contrasts across time, space, and/or environmental conditions. Our results indicate that species of Arctic foraminifera in age-correlated cores from abyssal depths are each best described by log-series distributions. Using this structural information, we were able to determine that structural stability exists for at least 50 ka. The foraminiferal communities in this study show remarkable concordance, distributional similarity and support the neutral theory of biodiversity.

  13. Diversity and distribution of Porifera in the bathyal and abyssal Weddell Sea and adjacent areas

    Janussen, Dorte; Tendal, Ole Secher

    2007-08-01

    During the ANDEEP I-III expeditions, we obtained a rich and highly diverse sponge collection from the deep Weddell Sea. All the three Poriferan classes, Calcarea, Demospongiae and Hexactinellida, were well represented. Among this material, we have identified a total of 76 species from 47 genera and 30 families. Of these, 17 species (22%) are new to science and 37 (49%) new for the Southern Ocean. Particularly remarkable is the considerable depth of the boundary between bathyal and abyssal sponge faunas. Both Demospongiae and Hexactinellida show a strong shift in their taxonomic composition from a typical shelf assemblage to a more cosmopolitan deep-sea fauna at around 2500 m. Within the Demospongiae, the families Polymastiidae and Cladorhizidae (carnivorous sponges) are particularly abundant and very diverse. The Calcarea are recorded for the first time from the Antarctic deep sea. The type of sampling gear used, especially the epibenthic sledge, was an important factor for the successful collection of deep-sea sponges during the ANDEEP campaigns.

  14. Mineralogy of the mid-ocean-ridge basalt source from neodymium isotopic composition of abyssal peridotites.

    Salters, Vincent J M; Dick, Henry J B

    2002-07-01

    Inferring the melting process at mid-ocean ridges, and the physical conditions under which melting takes place, usually relies on the assumption of compositional similarity between all mid-ocean-ridge basalt sources. Models of mantle melting therefore tend to be restricted to those that consider the presence of only one lithology in the mantle, peridotite. Evidence from xenoliths and peridotite massifs show that after peridotite, pyroxenite and eclogite are the most abundant rock types in the mantle. But at mid-ocean ridges, where most of the melting takes place, and in ophiolites, pyroxenite is rarely found. Here we present neodymium isotopic compositions of abyssal peridotites to investigate whether peridotite can indeed be the sole source for mid-ocean-ridge basalts. By comparing the isotopic compositions of basalts and peridotites at two segments of the southwest Indian ridge, we show that a component other than peridotite is required to explain the low end of the (143)Nd/(144)Nd variations of the basalts. This component is likely to have a lower melting temperature than peridotite, such as pyroxenite or eclogite, which could explain why it is not observed at mid-ocean ridges. PMID:12097907

  15. Surprises in abyssal peridotites: implications for melt migration beneath ocean ridges

    Niu, Y.

    2003-04-01

    Since Mike's two classic papers [1,2], the last 35 years have seen much progress on MORB petrogenesis because of improved experimental/theoretical approaches and because of rapid growth of geochemical database on MORB samples from the global ocean ridge system. Our current understanding of MORB genesis also owes a great deal to the studies [3-5] of abyssal peridotites - interpreted as mantle melting residues for MORB. Recent studies [6,7] have confirmed the complementary relationship between MORB and abyssal peridotites, but also revealed the hidden complexities in these peridotites such as olivine addition [6-8] and melt refertilization [7-9]. These same studies [6,7] have simultaneously excited serious debates on the petrogenesis of abyssal peridotites [10-14]. These debates are actually different views on the same observations: modes and major element compositions of residual minerals, and trace element data on residual clinopyroxene (Cpx) [3-5]. I report here whole-rock ICP-MS trace element data on abyssal peridotites including samples previously studied for Cpx trace elements [5]. Residual Cpx shows highly depleted light rare earth elements (LREEs) with flat-to-elevated middle-heavy REEs (e.g., [Ce]_N = 0.25±0.51 [mean±1σ]; [Yb]_N = 6.09±2.59; [Nd/Sm]_N = 0.29±0.14; [Nd/Dy]_N = 0.14±0.11), which is consistent with varying extents of melt depletion [5]. In contrast, whole-rock data of the same samples [15] show elevated abundances of LREEs with flat to enriched LREE patterns (e.g., [Ce]_N = 0.57±0.74; [Yb]_N, 0.72±0.41; [Nd/Sm]_N = 1.18±0.41; [Nd/Dy]_N = 0.70±0.38). If the constituent Cpx records the melting process, the whole-rock data would suggest post-melting LREE addition. The significant correlations of LREEs with high-field strength elements (HFSEs) (e.g., RCe-Zr = 0.730, RNd-Zr = 0.789, RCe-Nb = 0.836, RNd-Nb = 0.900) suggest that this LREE addition is magmatic refertilization (vs. serpentinization). The observation that this magmatic

  16. Molluscs of an intertidal soft-sediment area in China: Does overfishing explain a high density but low diversity community that benefits staging shorebirds?

    Yang, Hong-Yan; Chen, Bing; Piersma, Theunis; Zhang, Zhengwang; Ding, Changqing

    2016-03-01

    The Yellow Sea is a key staging ground for shorebirds that migrate from Australasia to the Arctic each spring. A lot of attention has been paid to the impact of habitat loss due to land reclamation on shorebird survival, but any effects of overfishing of coastal resources are unclear. In this study, the abundance of molluscs in the intertidal mudflats of northern Bohai Bay on the Chinese Yellow Sea was investigated in 2008-2014 from the perspective of their importance as food for northward migrating shorebirds, especially Red Knots Calidris canutus. Numerically contributing 96% to the numbers of 17 species found in spring 2008, the bivalve Potamocorbula laevis (the staple food of Red Knots and other shorebirds) dominated the intertidal mollusc community. In the spring of 2008-2014, the densities of P. laevis were surprisingly high, varying between 3900 and 41,000 individuals/m2 at distinctly small sizes (average shell lengths of 1.1 to 4.8 mm), and thus reaching some of the highest densities of marine bivalves recorded worldwide and providing good food for shorebirds. The distribution of P. laevis was associated with relatively soft sediments in close proximity to the recently built seawalls. A monthly sampling programme showed steep seasonal changes in abundance and size. P. laevis were nearly absent in winter, each year settling on the intertidal mudflats anew. Peak densities were reached in spring, when 0-age P. laevis were 1-3 mm long. The findings point to a highly unusual demographic structure of the species, suggesting that some interfering factors are at play. We hypothesise that the current dominance of young P. laevis in Bohai Bay reflects the combined pressures of a nearly complete active removal of adult populations from mid-summer to autumn for shrimp farming (this clearing of adults may offer space for recruitment during the next spring) and low numbers of epibenthic predators of bivalves, such as shrimps and crabs, due to persistent overfishing in

  17. Dense microbial community on a ferromanganese nodule from the ultra-oligotrophic South Pacific Gyre: Implications for biogeochemical cycles

    Shiraishi, Fumito; Mitsunobu, Satoshi; Suzuki, Katsuhiko; Hoshino, Tatsuhiko; Morono, Yuki; Inagaki, Fumio

    2016-08-01

    During Integrated Ocean Drilling Program (IODP) Expedition 329, a deep-sea ferromanganese nodule and surrounding sediment were collected from the South Pacific Gyre, the most oligotrophic oceanic environment on earth. Using a combination of cryo-sectioning and fluorescence-based cell counting techniques, we determined that the microbial cell density at the very surface of the nodule was ∼108 cells cm-3, three orders of magnitude higher than that in the surrounding sediment. Analysis of bacterial and archaeal 16S rRNA gene sequences (∼1400 bp) indicated that the taxonomic composition of the nodule-associated community differed markedly from that of the sediment-associated community. Members of Marine Group I (MGI) Thaumarchaeota are potentially crucial for sustaining the high cell density because both ammonia and Cu were available on the nodule surface, making it suitable for ammonia-oxidizing chemolithoautotrophy mediated by copper enzymes. Combined cryo-sectioning and synchrotron analysis of the nodule surface revealed both hexagonal birnessite resembling δ-MnO2 and triclinic birnessite, minerals characteristic of biogenic oxide and its secondary product, respectively. Regardless of these possible biogenic features, only one gene sequence exhibited some similarity to previously identified manganese-oxidizing bacteria. On the other hand, MGI Thaumarchaeota were assumed as potential candidate of manganese oxidizers because they have multi-copper oxidase that is utilized by most known manganese oxidizers. Therefore, this archaeal group is considered to play a significant ecological role as a primary producer in biogeochemical elemental cycles in the ultra-oligotrophic abyssal plain.

  18. Aquatic Sediments.

    Sanville, W. D.; And Others

    1978-01-01

    Presents a literature review of aquatic sediments and its effect upon water quality, covering publications of 1976-77. This review includes: (1) sediment water interchange; (2) chemical and physical characterization; and (3) heavy water in sediments. A list of 129 references is also presented. (HM)

  19. The bacterial community of coastal sediments influenced by cage culture in Xiangshan Bay, Zhejiang, China%象山港网箱养殖对近海沉积物细菌群落的影响

    裘琼芬; 张德民; 叶仙森; 郑珍珍

    2013-01-01

    Microorganisms play important roles in biogeochemical cycling such as organic matter decomposition and energy transformation. Recently, rapid development of aquaculture has caused a large influx of introduced organic matter into Xiangshan Bay, Zhejiang Province, China. At the same time, many ecological problems have developed in this coastal site. Study of the influence of aquaculture on microbial diversity in sediments is important for the structural and functional assessment of coastal ecosystems. In this paper, sediments in three sites were investigated in July 2011: a control or check site ( CK) , an intersection site 6-8 km from the aquaculture site (IS ) , and a cage culture site ( AC ). As the physicochemical background showed, total organic carbon in those three sites was different. Several physiochemical factors (T, pH, Eh and SO2-4 ) were analyzed. The temperatures of sediments in Xiangshan Bay decreased with depth, but remained between 23.0-26.5℃ in the upper 55 cm layer. The pH of sediments was slightly alkaline, but was elevated slightly in the AC site, although all of the sediments had pH values of 7.6-7.9. The effect of aquaculture on SO2-4 was not significant. However, as expected, the measurement of Eh showed sediment in the CK site had the highest oxidation-reduction potential. Following with physiochemical analysis, the structure and diversity of bacterial communities in sediments from Xiangshan Bay were analyzed by Terminal Restriction Fragment Length Polymorphism (T-RFLP) analysis and cloning/sequencing. Total nucleic acids was extracted from the sediment core, T-RFLP analysis was conducted after amplification of the bacterial 16S rRNA partial gene using a fluorescent primer pair 27-FAM/907R and digestion by Msp I (C'CGG). A bacterial 16S rRNA partial gene clone library was constructed using DNA extracted from the upper 5 cm sediment layer of the CK region, and the phylogenic relationships were analyzed using the neighbor-joining method in

  20. Moored observation of abyssal flow and temperature near a hydrothermal vent on the Southwest Indian Ridge

    Liao, Guanghong; Zhou, Beifeng; Liang, Chujin; Zhou, Huaiyang; Ding, Tao; Wang, Yuan; Dong, Changming

    2016-01-01

    Four moorings were deployed near "Dragon Flag," an active hydrothermal vent in the valley of the Southwest Indian Ridge. The goal was to examine the variability of currents and temperature, which will guide the trajectory of spreading plumes. The mean current was cross-isobath, and the circulation was characterized by a submesoscale circulation. Observed currents also showed fluctuations with periods of 1-15 days. The inferred phase speed and wavelength for the wave with a period of 4.4 day are 10.4 km d-1 and 45.8km, respectively, which are consistent with the topographic Rossby wave theory. The persistent warming tendency with corresponding variation of salinity based on background θ-S properties may be caused by background circulation and divergence of the water column. The warming or cooling episodes were most likely as signatures of isopycnal surface depression or uplifting induced by the moving of mesoscale eddies. Well-resolved rotary spectra exhibited important nonlinear interactions between inertial and semidiurnal tide in the velocity and temperature records. Amplification of near-inertial currents in the near bottom is also exposed. These discoveries provided new evidence for the nonlinear interaction and trapped near-inertial waves by the ridge, which occurred in the deep ocean of the Southern Hemisphere. Such nonlinear interaction may represent a significant energy loss pathway for the internal waves, and part of the decay of such motion would likely result in increased mixing to maintain the abyssal stratification. Enhanced near-inertial motions can play a major role for the local advection of hydrothermal plumes.

  1. Long-term nutrient addition differentially alters community composition and diversity of genes that control nitrous oxide flux from salt marsh sediments

    Kearns, Patrick J.; Angell, John H.; Feinman, Sarah G.; Bowen, Jennifer L.

    2015-03-01

    Enrichment of natural waters, soils, and sediments by inorganic nutrients, including nitrogen, is occurring at an increasing rate and has fundamentally altered global biogeochemical cycles. Salt marshes are critical for the removal of land-derived nitrogen before it enters coastal waters. This is accomplished via multiple microbially mediated pathways, including denitrification. Many of these pathways, however, are also a source of the greenhouse gas nitrous oxide (N2O). We used clone libraries and quantative PCR (qPCR) to examine the effect of fertilization on the diversity and abundance of two functional genes associated with denitrification and N2O production (norB and nosZ) in experimental plots at the Great Sippewissett Salt Marsh (Falmouth, MA, USA) that have been enriched with nutrients for over 40 years. Our data showed distinct nosZ and norB community structures at different nitrogen loads, especially at the highest level of fertilization. Furthermore, calculations of the Shannon Diversity Index and Chao1 Richness Estimator indicated that nosZ gene diversity and richness increased with increased nitrogen supply, however no such relationship existed with regard to richness and diversity of the norB gene. Results from qPCR demonstrated that nosZ gene abundance was an order of magnitude lower in the extra-highly fertilized plots compared to the other plots, but the abundance of norB was not affected by fertilization. The majority of sequences obtained from the marsh plots had no close cultured relatives and they were divergent from previously sequenced norB and nosZ fragments. Despite their divergence from any cultured representatives, most of the norB and nosZ sequences appeared to be from members of the Alpha- and Betaproteobacteria, suggesting that these classes are particularly important in salt marsh nitrogen cycling. Our results suggest that both norB and nosZ containing microbes are affected by fertilization and that the Great Sippewissett Marsh may

  2. Disposal in sea-bed geological formations. Properties of ocean sediments in relation to the disposal of radioactive waste

    Work on the permeability and consolidation characteristics of sediment cores from the north-east Atlantic has shown that each sediment type studied has a unique void ratio/permeability relationship and that the permeability decreases with effective stress more rapidly for fine than for coarser grained material. Significant over-consolidation is also present in Pacific red clays from the deep-sea drilling project. Their permeability is less for a given void ratio than that of their Atlantic counterparts. A theoretical analysis is given of the effects on permeability of deep open burrows revealed by improved core handling techniques. Mineralogy and sediment and water chemistry of six cores from the Nares Abyssal Plain have demonstrated the effects of lateral sediment redistribution and have shown only mildly reducing conditions. Pore water studies on a 4 m Kasten core from Great Meteor East show oxygen falling to zero within 30 cm of the sediment surface

  3. Great Meteor East (distal Madeira Abyssal Plain): geological studies of its suitability for disposal of heat-emitting radioactive wastes

    This report summarises geological and geophysical studies carried out by the Institute of Oceanographic Sciences up to December 1983 in an area of the Madeira Abyssal Plain in order to assess its suitability for the disposal of heat-emitting radioactive waste. The results of work carried out in the same area by the Rijks Geologische Dienst of the Netherlands are also reviewed in the report. Other oceanographic studies in the area in the fields of geochemistry, biology and oceanography are briefly touched upon. (author)

  4. Sediment Transport

    Liu, Zhou

    Flow and sediment transport are important in relation to several engineering topics, e.g. erosion around structures, backfilling of dredged channels and nearshore morphological change. The purpose of the present book is to describe both the basic hydrodynamics and the basic sediment transport...... mechanics. Chapter 1 deals with fundamentals in fluid mechanics with emphasis on bed shear stress by currents, while chapter 3 discusses wave boundary layer theory. They are both written with a view to sediment transport. Sediment transport in rivers, cross-shore and longshore are dealt with in chapters 2...

  5. Composition and distribution of bivalves of the abyssal plain adjacent to the Kuril-Kamchatka Trench (Pacific Ocean)

    Kamenev, Gennady M.

    2015-01-01

    The KuramBio German-Russian deep-sea expedition ("Sonne", 2012) revealed a rich fauna of bivalves (55 species belonging to 21 families) on the abyssal plain (4861-5787 m) adjacent to the Kuril-Kamchatka Trench. Per station species richness varied from 18 to 33 species. The richest families were Cuspidariidae (7 species), Tindariidae (6 species), Thyasiridae (6 species), and Xylophagidae (5 species). The families Nuculidae, Malletidae, Yoldiidae, Mytilidae, Protocuspidariidae, and Verticordiidae were represented by a single species. Representatives of the family Siliculidae were recorded in the northwestern Pacific for the first time. Thirteen species (23.6%) were most common in the investigated northwestern Pacific region. Nine species (16.4%) were only found at one of the stations. Eight species (14.5%) are first records for the northwestern Pacific, of which Yoldiella cf. jeffreysi (Hidalgo, 1877), Pristigloma cf. albaSanders and Allen, 1973, and Syssitomya cf. pourtalesianaOliver, 2012 were previously known only for the Atlantic Ocean. The high diversity and richness of the bivalve fauna on the abyssal plain in the Kuril-Kamchatka Trench area may be connected to the favorable feeding conditions in this, one of the most highly productive areas of the Pacific Ocean.

  6. Morphological and ontogenetic stratification of abyssal and hadal Eurythenes gryllus sensu lato (Amphipoda: Lysianassoidea) from the Peru-Chile Trench

    Eustace, Ryan M.; Ritchie, Heather; Kilgallen, Niamh M.; Piertney, Stuart B.; Jamieson, Alan J.

    2016-03-01

    The globally ubiquitous lysianassoid amphipod, Eurythenes gryllus, has been shown to consist of multiple genetically distinct cryptic taxa, with depth considered a major driver of speciation and morphological divergence. Here we examine morphological variation of E. gryllus sensu lato through a continuous depth distribution that spans from abyssal (3000-6000 m) into hadal depths (>6000 m) in the Peru-Chile Trench (SE Pacific Ocean). Three distinct morphospecies were identified: one was confirmed as being E. magellanicus (4602-5329 m) based on DNA sequence and morphological similarity. The other two morphologically distinct species were named based upon depth of occurrence; Abyssal (4602-6173 m) and Hadal (6173-8074 m). The three Eurythenes morphospecies showed vertical ontogenetic stratification across their bathymetric range, where juveniles were found shallower in their depth range and mature females deeper. Potential ecological and evolutionary drivers that explain the observed patterns of intra and inter-specific structure, such as hydrostatic pressure and topographical isolation, are discussed.

  7. Microbial community characterization and functional gene quantification in RDX-degrading microcosms derived from sediment and groundwater at two naval sites.

    Wilson, Fernanda Paes; Cupples, Alison M

    2016-08-01

    The explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) has long been recognized as a problematic environmental pollutant, and efforts to remediate contaminated soils, sediments, and groundwater have been going on for decades. In recent years, much interest has focused on using bioremediation to clean up these sites. The current study investigated the microorganisms (16S rRNA genes, Illumina) and functional genes (xenA, xenB, and xplA) linked to RDX biodegradation in microcosms composed of sediment or groundwater from two Navy sites. For this, experiments included sediment samples from three depths (5 to 30 ft) from two wells located in one Navy site. In addition, the groundwater upstream and downstream of an emulsified oil biobarrier was examined from another Navy site. Further, for the groundwater experiments, the effect of glucose addition was explored. For the sediment experiments, the most enriched phylotypes during RDX degradation varied over time, by depth and well locations. However, several trends were noted, including the enrichment of Pseudomonas, Rhodococcus, Arthrobacter, and Sporolactobacillus in the sediment microcosms. For the groundwater-based experiments, Pseudomonas, unclassified Rhodocyclaceae, Sphingomonas, and Rhodococcus were also highly abundant during RDX degradation. The abundance of both xplA and xenA significantly increased during RDX degradation compared to the control microcosms for many treatments (both groundwater and sediment microcosms). In a limited number of microcosms, the copy number of the xenB gene increased. Phylotype data were correlated with functional gene data to highlight potentially important biomarkers for RDX biodegradation at these two Navy sites. PMID:27118012

  8. Feasibility of high level radioactive waste disposal in deep sea sediments

    For the past ten years, an international program has been conducted to investigate the concept feasibility for disposing of spent nuclear fuel waste in deep ocean sediments. These studies by the Seabed Working Group were coordinated by the Nuclear Energy Agency of the Organization for Economic Cooperation and Development. Penetrators have been considered as the primary method of waste emplacement. This required emphasis on studies of the nature of the plastic sediments which would form the primary barrier to the release of radionuclides into the biosphere. Site qualification guidelines, included criteria for tectonic and sedimentary stability over periods of at least 105 years. Using these guidelines two potential areas were identified: one in the Madeira Abyssal Plain; and one in the Southern Nares Abyssal Plain, both in the North Atlantic. The sediment barrier properties are quite different in terms of dominant mineralogy (carbonates in MAP, and silicous clays in SNAP). The MAP is dominated by thick wide-spread turbidites, but SNAP is dominated by thin discontinuous turbidites

  9. The Light-Field of Microbenthic Communities - Radiance Distribution and Microscale Optics of Sandy Coastal Sediments Rid A-1977-2009

    KUHL, M.; JØRGENSEN, BB

    1994-01-01

    relative to vertically incident collimated light in rinsed quartz sand and in a coastal sandy sediment colonized by microalgae. Upwelling and downwelling components of irradiance and scalar irradiance were calculated from the radiance distributions. Calculated total scalar irradiance agreed well with the...

  10. "First" abyssal record of Stenosemus exaratus (G.O. Sars, 1878) (Mollusca, Polyplacophora) in the North-Atlantic Ocean.

    Allcock, Louise; Schwabe, Enrico

    2013-01-01

    The first proven abyssal record of Stenosemus exaratus (G.O. Sars, 1878) is presented on the basis of an ROV study in the Irish Sea. For the first time in situ images of the species and data on the environmental parameters are provided. PMID:23794838

  11. “First” abyssal record of Stenosemus exaratus (G.O. Sars, 1878) (Mollusca, Polyplacophora) in the North-Atlantic Ocean

    Allcock, Louise; Schwabe, Enrico

    2013-01-01

    Abstract The first proven abyssal record of Stenosemus exaratus (G.O. Sars, 1878) is presented on the basis of an ROV study in the Irish Sea. For the first time in situ images of the species and data on the environmental parameters are provided. PMID:23794838

  12. “First” abyssal record of Stenosemus exaratus (G.O. Sars, 1878 (Mollusca, Polyplacophora in the North-Atlantic Ocean

    Louise Allcock

    2013-04-01

    Full Text Available The first proven abyssal record of Stenosemus exaratus (G.O. Sars, 1878 is presented on the basis of an ROV study in the Irish Sea. For the first time in situ images of the species and data on the environmental parameters are provided.

  13. Population ecology and community structure of sub-tidal soft sediment dwelling macro-invertebrates of Konkan, west coast of India

    Vizakat, L.; Harkantra, S.N.; Parulekar, A.H.

    (Shannon Wiener index) varied from 0.44 to 3.58 (X = 1.94, SD = + or - 0.89). Population and community structure were more stable in premonsoon months. Carnivorous species Glycera alba modified the community structure mainly due to prey-predator...

  14. Rates of sediment reworking at the HEBBLE site based on measurements of Th-234, Cs-137 and Pb-210

    Th-234, Cs-137 and Pb-210 measurements have been made on ten cores from the HEBBLE site on the Nova Scotian continental rise. Th-234 mixing coefficients from HEBBLE sediments show substantial lateral variability with values ranging from 1 to 33 cm2 yr-1. These mixing coefficients are one to two orders of magnitude greater than values from typical continental-rise and abyssal sediments because of high densities of benthic macrofauna. Th-234 data from HEBBLE cores indicate that particles at the sediment-water interface are mixed to depths of 1-5 cm on a 100-day time scale. Cs-137 and Pb-210 data indicate that on time scales of 30-100 yrs surface sediments are reworked to depths ranging from 1 to 12 cm. Based on Th-234 profiles from two HEBBLE cores collected less than 200 m apart during consecutive years, no temporal variability in mixing rate could be resolved. (Auth.)

  15. Global sediment thickness data set updated for the Australian-Antarctic Southern Ocean

    Whittaker, Joanne M.; Goncharov, Alexey; Williams, Simon E.; Müller, R. Dietmar; Leitchenkov, German

    2013-08-01

    We present a new, 5 min sediment thickness grid for the Australian-Antarctic region (60°E-155°E, 30°S-70°S). New seismic reflection and refraction data have been used to add detail to the conjugate Australian and Antarctic margins and intervening ocean floor where regional sediment thickness patterns were poorly known previously. On the margins, sediment thickness estimates were computed from velocity-depth functions from sonobuoy/refraction velocity solutions ground-truthed against seismic reflection data. For the Southeast Indian Ridge abyssal plains, sediment thickness contours from Geli et al. (2007) were used. The new regional minimum sediment thickness grid was combined with the global National Geophysical Data Center (NGDC) sediment grid to create an updated global grid. Even using the minimum estimates, sediment accumulations on the extended Australian and Antarctic continental margins are 2 km thicker across large regions and up to 9 km thicker in the Ceduna Basin compared to the global NGDC compilation of sediment thickness data.

  16. Shift in detrital sedimentation in the eastern Bay of Bengal during the late Quaternary

    C Prakash Babu; J N Pattan; K Dutta; N Basavaiah; G V Ravi Prasad; D K Ray; P Govil

    2010-06-01

    Down-core variations of granulometric, geochemical and mineral magnetism of a 70-cm long sediment core retrieved from the eastern Bay of Bengal abyssal region were studied to understand sedimentation pattern and sediment provenance during the last ∼12 kyr BP. Based on down-core physical and elemental variations, three units were identified: unit 3 (70–43 cm) is a ∼30 cm thick clayey silt organic carbon-rich (0.5–0.92%) turbidite probably delivered by the Brahmaputra River during the late Quaternary period. Units 2 (43–24 cm) and 1 (24–0 cm) represent enhanced and reduced supply of coarse-grained detrital sediments from the Ganges River during early and late Holocene period, respectively. Increased terrigenous supply dilutes calcium carbonate (CaCO3) and biogenic elements (P, Ba and Cu) in units 3 and 2. On the contrary, a reduction in detrital input enhances CaCO3 and biogenic elements in unit 1. Lithogenic elements (Ti, Al, K and Rb) and shale-normalized REE patterns in all three units suggest terrigenous source. The shift in provenance from the Brahmaputra to the Ganges derived sediments is evident by a sharp increase in sediment grain size, increased concentration and grain size assemblages of magnetic minerals, lithogenic elements concentration and Lan/Ybn ratio. This study highlights terrigenous dilution on biogenic sedimentation in the eastern Bay of Bengal sediments.

  17. Nitrite Reductase Genes (nirK and nirS) as Functional Markers To Investigate Diversity of Denitrifying Bacteria in Pacific Northwest Marine Sediment Communities

    Braker, Gesche; Zhou, Jizhong; Wu, Liyou; Devol, Allan H.; Tiedje, James M.

    2000-01-01

    Genetic heterogeneity of denitrifying bacteria in sediment samples from Puget Sound and two sites on the Washington continental margin was studied by PCR approaches amplifying nirK and nirS genes. These structurally different but functionally equivalent single-copy genes coding for nitrite reductases, a key enzyme of the denitrification process, were used as a molecular marker for denitrifying bacteria. nirS sequences could be amplified from samples of both sampling sites, whereas nirK sequen...

  18. Quantification of Tinto River Sediment Microbial Communities: Importance of Sulfate-Reducing Bacteria and Their Role in Attenuating Acid Mine Drainage

    Sanchez-Andrea, I.; Knittel, K; Amann, R; Amils, R.; Sanz, J.L.

    2012-01-01

    Tinto River (Huelva, Spain) is a natural acidic rock drainage (ARD) environment produced by the bio-oxidation of metallic sulfides from the Iberian Pyritic Belt. This study quantified the abundance of diverse microbial populations inhabiting ARD-related sediments from two physicochemically contrasting sampling sites (SN and JL dams). Depth profiles of total cell numbers differed greatly between the two sites yet were consistent in decreasing sharply at greater depths. Although catalyzed repor...

  19. Population sizes and growth pressure responses of intestinal microfloras of deep-sea fish retrieved from the abyssal zone.

    Yano, Y; Nakayama, A; Yoshida, K

    1995-12-01

    The intestinal floras of seven deep-sea fish retrieved at depths of from 3,200 to 5,900 m were examined for population sizes and growth responses to pressure. Large populations of culturable bacteria, ranging from 1.1 x 10(sup6) to 3.6 x 10(sup8) cells per ml of contents, were detected when samples were incubated at conditions characteristic of those of the deep sea. Culturable cell counts at in situ pressures were greater than those at atmospheric pressure in all samples. Most of the strains isolated by the spread-plating method at atmospheric pressure later proved barophilic. Barophilic bacteria were the predominant inhabitants of the abyssal fish intestines. PMID:16535199

  20. Comparison of communities of both methane-producing and metabolizing archaea and bacteria in sediments between the northern South China Sea and coastal Mai Po Nature Reserve revealed by PCR amplification of mcrA and pmoA genes

    Zhichao eZhou

    2015-02-01

    Full Text Available Communities of methanogens, anaerobic methanotrophic (ANME archaea and aerobic methantrophic bacteria were compared by profiling mcrA and pmoA genes encoded by methyl-coenzyme M reductase alpha subunit and particulate methane monooxygenase alpha subunit, respectively, in sediments of northern South China Sea (nSCS and Mai Po mangrove wetland. Community structures representing by mcrA gene based on 12 clone libraries from nSCS showed separate clusters indicating niche specificity, while, Methanomicrobiales, Methanosarcinales clade 1,2 and Methanomassiliicoccus like groups of methanogens were the most abundant constitutional parts in nSCS sediment samples . Novel clusters specific to the SCS were identified and the phylogeny of mcrA gene-harboring archaea was completely updated. Mai Po mangrove wetland surface layer exhibited lower diversity than subsurface, but similar community structures were shared in both layers. Quantitative PCR was used to detect mcrA gene abundance in all samples: similar abundance of mcrA gene in the surface layers of mangrove (3.4~3.9×106 copies per gram dry weight and of intertidal mudflat (5.5~5.8×106 copies per gram dry weight was observed, but higher abundance (6.9×106 to 1.02×108 copies per gram dry weight was found in subsurface samples of both sediment types. Aerobic methanotrophic bacteria were more abundant in surface layers (6.7~11.1×105 copies per gram dry weight than the subsurface layers (1.2~5.9×105copies per gram dry weight based on pmoA gene. Mangrove surface layers harbored more abundant pmoA gene than intertidal, but fewer abundant pmoA genes in the subsurface layers. Meanwhile, it is also noted that in surface layers of all samples, more pmoA gene copies were detected than the subsurface layers. Reedbed rhizosphere exhibited the highest gene abundance of mcrA gene (8.51×108 copies per g dry weight and pmoA gene (1.56×107 copies per g dry weight.

  1. Anthropogenic metal contamination and sapropel imprints in deep Mediterranean sediments

    Research highlights: → Metal pollution was recorded in deep Mediterranean sediments. → Atmospheric imprint was characterized with radioactive and stable Pb isotopes. → 210Pb data suggests metal pollution from atmospheric deposition. → Pollutant Pb input to the western basin is 20-25% of coastal atmospheric inventories. → Trace element redistribution is associated with sapropel and turbidite events. - Abstract: Sediment cores from the deep Balearic basin and the Cretan Sea provide evidence for the accumulation of Cd, Pd and Zn in the top few centimeters of the abyssal Mediterranean sea-bottom. In both cores, 206Pb/207Pb profiles confirm this anthropogenic impact with less radiogenic imprints toward surface sediments. The similarity between excess 210Pb accumulated in the top core and the 210Pb flux suggests that top core metal inventories reasonably reflect long-term atmospheric deposition to the open Mediterranean. Pb inventory in the western core for the past 100 years represents 20-30% of sediment coastal inventories, suggesting that long-term atmospheric deposition determined from coastal areas has to be used cautiously for mass balance calculations in the open Mediterranean. In the deeper section of both cores, Al normalized trace metal profiles suggest diagenetic remobilization of Fe, Mn, Cu and, to a lesser extent, Pb that likely corresponds to sapropel event S1.

  2. Diversity, Persistence and Evolution in Marine Sediments

    Starnawski, Piotr

    2016-01-01

    . No evidence for selection of repair and recombination functions in the deeper sediment was found, and high number of motility and chemotaxis was detected through the sediment column. This work casts new light on marine sediment communities, describes their vertical structure and assembly in detail......72 % of our planet is covered by saline water, which at its bottom gradually forms a layer of deposited material. This layer of marine sediments harbors active and diverse prokaryotic communities, of which we know little more than just the phylogenetical associ- ation with their often distant...... treat the whole community as equal, not knowing who and what are the contributions of hydrolyzers, fermenters and terminal oxidizers. In order to address these unknowns I have focused my work on three main aspects of the marine sediments: (i) systematic, analytical description of the microbial...

  3. Site-specific sediment clean-up objectives developed by the sediment quality triad

    Sediment chemistry, sediment toxicity, and benthic macroinvertebrate community data were collected and evaluated in concert (1) to characterize adverse effects of hydrocarbon and metal contaminants in the sediments of a small inlet of Superior Bay, Lake Superior and a tributary creek and (2) to derive numeric objectives for the clean up of this system. Sediments from reference locations and eight study sites were analyzed for a range of contaminants, including hydrocarbons (measured both as diesel range organics (DRO) and oil and grease), lead, chromium, and ammonia. A range of sediment toxicity was observed across the eight study sites using a variety of tests and endpoints: Hyalella azteca (10 day survival and growth), Chironomus tentans (10 day survival and growth), Ceriodaphnia dubia (48 hour survival), and Daphnia magna (48 hour survival and 10 day survival and reproduction). A range of alterations of the benthic macroinvertebrate community compared with communities from reference locations were observed. Benthic community alterations were summarized quantitatively by taxa richness and Shannon-Weiner mean diversity. Lowest effect levels determined through this study included 150 microg/g dry sediment for DRO (as measured in this study) and 40 microg/g dry sediment for lead. Effects thresholds determined through this study included 1,500 microg/g dry sediment for DRO and 90 microg/g dry sediment for lead. These levels and concentrations measured in relevant reference locations are being used to define objectives for sediment clean up in the inlet and creek

  4. Meiofauna Metabolism in Suboxic Sediments: Currently Overestimated

    Braeckman, U.; Vanaverbeke, J.; Vincx, M.; van Oevelen, D.; Soetaert, K.

    2013-01-01

    Oxygen is recognized as a structuring factor of metazoan communities in marine sediments. The importance of oxygen as a controlling factor on meiofauna (32 µm-1 mm in size) respiration rates is however less clear. Typically, respiration rates are measured under oxic conditions, after which these rates are used in food web studies to quantify the role of meiofauna in sediment carbon turnover. Sediment oxygen concentration ([O2]) is generally far from saturated, implying that (1) current estima...

  5. Quantification of Tinto River sediment microbial communities: importance of sulfate-reducing bacteria and their role in attenuating acid mine drainage.

    Sánchez-Andrea, Irene; Knittel, Katrin; Amann, Rudolf; Amils, Ricardo; Sanz, José Luis

    2012-07-01

    Tinto River (Huelva, Spain) is a natural acidic rock drainage (ARD) environment produced by the bio-oxidation of metallic sulfides from the Iberian Pyritic Belt. This study quantified the abundance of diverse microbial populations inhabiting ARD-related sediments from two physicochemically contrasting sampling sites (SN and JL dams). Depth profiles of total cell numbers differed greatly between the two sites yet were consistent in decreasing sharply at greater depths. Although catalyzed reporter deposition fluorescence in situ hybridization with domain-specific probes showed that Bacteria (>98%) dominated over Archaea (water column (pH 2.5 and +400 mV), the most abundant organisms were identified as iron-reducing bacteria: Acidithiobacillus spp. and Acidiphilium spp., probably related to the higher iron solubility at low pH. At the JL dam, characterized by a banded sediment with higher pH (4.2 to 6.2), more reducing redox potential (-210 mV to 50 mV), and a lower solubility of iron, members of sulfate-reducing genera Syntrophobacter, Desulfosporosinus, and Desulfurella were dominant. The latter was quantified with a newly designed CARD-FISH probe. In layers where sulfate-reducing bacteria were abundant, pH was higher and redox potential and levels of dissolved metals and iron were lower. These results suggest that the attenuation of ARD characteristics is biologically driven by sulfate reducers and the consequent precipitation of metals and iron as sulfides. PMID:22544246

  6. Invertebrates in stormwater wet detention ponds - Sediment accumulation and bioaccumulation of heavy metals have no effect on biodiversity and community structure.

    Stephansen, Diana Agnete; Nielsen, Asbjørn Haaning; Hvitved-Jacobsen, Thorkild; Pedersen, Morten Lauge; Vollertsen, Jes

    2016-10-01

    The invertebrate diversity in nine stormwater wet detention ponds (SWDP) was compared with the diversity in eleven small shallow lakes in the western part of Denmark. The SWDPs and lakes were chosen to reflect as large a gradient of pollutant loads and urbanization as possible. The invertebrates as well as the bottom sediments of the ponds and shallow lakes were analyzed for copper, iron, zinc, cadmium, chromium, lead, aluminum, nickel, arsenic and the potentially limiting nutrient, phosphorus. The Principal Component Analysis showed that invertebrates in SWDPs and lakes differed with respect to bioaccumulation of these elements, as did the sediments, albeit to a lesser degree. However, the Detrended Correspondence Analysis and the TWINSPAN showed that the invertebrate populations of the ponds and lakes could not be distinguished, with the possible exception of highway ponds presenting a distinct sub-group of wet detention ponds. The SWDPs and shallow lakes studied seemed to constitute aquatic ecosystems of similar taxon richness and composition as did the 11 small and shallow lakes. This indicates that SWDPs, originally constructed for treatment and flood protection purposes, become aquatic environments which play a local role for biodiversity similar to that of natural small and shallow lakes. PMID:27302374

  7. Community structure and diversity of scavenging amphipods from bathyal to hadal depths in three South Pacific Trenches

    Lacey, Nichola C.; Rowden, Ashley A.; Clark, Malcolm R.; Kilgallen, Niamh M.; Linley, Thomas; Mayor, Dan J.; Jamieson, Alan J.

    2016-05-01

    There are few biological datasets that span large bathymetric ranges with sufficient resolution to identify trends across the abyssal and hadal transition zone, particularly over multiple trenches. Here, scavenging Amphipoda were collected from three trenches in the South Pacific Ocean at bathyal to hadal depths. Diversity and community structure were examined from stations within the Kermadec Trench (1490-9908 m) and New Hebrides Trench (2000-6948 m) and additional data were included from the South Fiji Basin (4000 m) and Peru-Chile Trench (4602-8074 m). The hadal community structure of the Kermadec and New Hebrides trenches were distinct from the surrounding abyssal and bathyal depths and correlated to hydrostatic pressure and POC flux. Low POC flux in the New Hebrides Trench and South Fiji Basin best explained the dissimilarity in abyssal community structure from those of the disparate Kermadec and Peru-Chile trenches. POC flux also best explained patterns in hadal community structure with the Kermadec and New Hebrides Trench communities showing greater similarity to each other than to the eutrophic Peru-Chile Trench. Hydrostatic pressure was the strongest driver of intra-trench assemblage composition in all trench environments. A unimodal pattern of species diversity, peaking between 4000 and 5000 m, was best explained by hydrostatic pressure and temperature.

  8. METAGENOMICS OF TONGUE RIVER SEDIMENTS: WORKING WITH TRIBAL STUDENTS TO ASSESS THE IMPACTS OF CLIMATE, SEASON AND RESOURCE EXTRACTION ON FRESHWATER MICROBIAL COMMUNITY STRUCTURE AND GENE CONTENT

    It is expected to find a strong relationship between season and microbial community structure. Also, it is expected to find an increased prevalence of genes associated with hydrocarbon metabolism and osmotic stress near the Decker Coal Mine and around coal-bed methane extra...

  9. Tectonic and Sedimentation Interactions in the East Caribbean Subduction Zone: AN Overview from the Orinoco Delta to the Barbados Accretionary Prism

    Deville, E.

    2011-12-01

    Recent marine geophysical acquisitions and piston-coring allow to better understand the close interactions between the sand-rich Orinoco turbidite system and the compressional structures of the Barbados prism. Because of the morphologic and tectonic control in the east-Caribbean active margin, the Orinoco turbiditic pattern system does not exhibit a classic fan geometry. The sea-floor geometry between the slope of the front of the Barbados prism and the slope of the South-American margin induces the convergence of the turbidite channels toward the abyssal plain, at the front of the accretionary prism. Also, whereas in most passive margins the turbidite systems are organized upstream to downstream as canyon, then channel-levee, then lobes, here, due to the tectonic control, the sedimentary system is organized as channel-levee, then canyons, then channelized lobes. At the edge of the Orinoco platform, the system has multiple sources with several distributaries and downward the channel courses are complex with frequent convergences or divergences that are emphasized by the effects of the undulating seafloor tectonic morphologies associated with active thrust tectonics and mud volcanism. On top of the accretionary prism, turbidite sediments are filling transported piggy-back basins whose timing of sedimentation vs. deformation is complex. Erosion processes are almost absent on the highly subsiding Orinoco platform and in the upper part of the turbidite system. Erosion processes develop mostly between 2000 and 4000 m of water depth, above the compressional structures of the Barbados prism (canyons up to 3 km wide and 300 m deep). In the abyssal plain, turbiditic channels develop on very long distance (> 1000 km) joining the mid-Atlantic channel (sourced mostly by the Amazon), filling several elongated basins corresponding to transform faults (notably the Barracuda Basin), and finally sourcing the Puerto-Rico trench, the deepest morphologic depression of this region

  10. Desmosomatidae (Isopoda: Asellota) from the abyssal plain to the east of the Kuril-Kamchatka Trench: New data on diversity with the description of two new species

    Golovan, Olga A.

    2015-01-01

    In the material from the KuramBio expedition (Kuril-Kamchatka Biodiversity Study) Desmosomatidae constituted 20% of all isopod specimens (Crustacea: Malacostraca). 29 species in 10 genera (Desmosoma, Chelator, Eugerda, Eugerdella, Mirabilicoxa, Momedossa, Parvochelus, Prochelator, Pseudomesus and Torwolia) were found in the Pacific Ocean to the east of the Kuril-Kamchatka Trench at depth of 4830-5780 m. From these taxa five genera are reported for the first time in the Northwest Pacific, 26 species (90%) are new to science. Two species, Chelator michaeli sp.nov. and Prochelator keenani sp.nov. are described. Both described species appear to be very close to the two species previously known from the abyssal of the North Atlantic. Keys to the species of ChelatorHessler, 1970a and ProchelatorHessler, 1970a and the discussion of the genera are provided. The discussion of the Northwest Pacific desmosomatid fauna is presented. The diversity and the generic composition of the Desmosomatidae in the open abyssal of the Northwest Pacific are comparable with those known in other non-isolated deep-sea regions. On the contrary, the generic composition of Desmosomatidae in the adjacent semi-isolated Sea of Japan is impoverished versus the open Pacific abyssal.

  11. Sediment transport and fan deposition in the Gulf of Alaska: Effects of transform motion on deep sea sedimentation

    Stevenson, A.J.; Bruns, T.R.; Carlson, P.R. (Geological Survey, Palo Alto, CA (USA)); Dobson, M.R. (Univ. of College of Wales, Aberystwyth (Wales))

    1990-06-01

    GLORIA side-scan sonar images and two channel seismic profiles recently collected in the Gulf of Alaska reveal a major site of late Miocene to Recent terrigenous sediment accumulation on the oceanic plate adjacent to the Fairweather-Queen Charlotte transform and the Yakutat Terrane. Sediment moving across this margin has formed several large channel dominated fan systems that blanket the entire gulf and spill westward onto the Tufts Abyssal Plain. The Surveyor Fan, fed by the glaciers of the Yakutat Terrane and insulated from transform sediment source offset by the Terrane, has maintained a single channel course over the entire life of the fan. The Chirikov and Baranof fans receive their sediment supply from glaciofluvial point sources along the SE Alaska margin, separated from the fans by an active transform. The fans show a southward younging of channel ages consistent with the sense of plate motion. Early (late Miocene) deposition within the gulf was limited to the structural basin between the continental margin and the Kodiak-Bowie seamount chain. The geometry of these early depositional systems is poorly known, but available data suggest their channels were oriented NW-SE. Subsequent establishment of a depositional slope between the margin and the seamount chain, coupled with the filling of the basin, led to a reorganization into SW-NE channel systems. The fan bodies of the Gulf of Alaska are members of a distinct class of fans that are characterized by long distributary channels which persist to near the fan limits. This type of fan morphology is most often attributed to a predominantly fine-grained sediment supply. This is difficult to reconcile with the obvious proximal glacial source for much of the sediment supplied to these fans.

  12. Fatty acid compositions and trophic relationships of shelled molluscs from the Kuril-Kamchatka Trench and the adjacent abyssal plain

    Kharlamenko, Vladimir I.; Würzberg, Laura; Peters, Janna; Borisovets, Evgeny E.

    2015-01-01

    Fatty acid (FA) compositions of 12 species of shelled molluscs (gastropods, bivalves, and scaphopods) from the Kuril-Kamchatka Trench and the adjacent abyssal plain were studied. According to the results of multivariate statistical analysis, molluscs were divided into three groups. Group I consisted of three scaphopod species, the bivalve Nucula profundorum and the gastropod Solariella delicata. FA compositions of this group were characterized by high levels of 20:4(n-6). We suggest that the FA pattern found in scaphopods with high values of 20:4(n-6) is most likely typical for that of benthic organisms feeding preferentially on foraminiferans. Group II included the bivalves Neilonella politissima, Bentharca asperula, and Rhinoclama filatovae. Bivalves from the second group had elevated concentrations of 22:6(n-3), and the ratio of 20:4(n-6) to 20:5(n-3) was lower than 1. Bivalves from the second group had elevated concentrations of 22:6(n-3). We propose that high concentrations of this FA can be used as a specific marker for a carnivorous feeding mode of deep-sea benthic invertebrates. The bivalve Bathyspinula calcarella as well as the scaphopod Polyschides sakuraii could not unambiguously be assigned to one group. Within the similarity analysis they rather clustered together with the foraminiferans feeders (group I), but forming an own subgroup. In the PCA on the other hand, P. sakuraii showed a position close to the other bivalves, while B. calcarella had an intermediate position between all three groups. Group III consisted of the gastropods Tacita holoserica and Paracteocina sp., which contained high concentrations of 20:5(n-3) and 22:5(n-3). Both are known to exhibit a carnivorous/scavenging feeding strategy. The very low content of DHA in both species is on first sight not consistent with the suggested carnivorous feeding behavior. A characteristic feature of Paracteocina sp. and T. holoserica was a high level of 22:5(n-3), and HUFA ratios indicate that DHA

  13. Simple models for disequilibrium fractional melting and batch melting with application to REE fractionation in abyssal peridotites

    Liang, Yan; Liu, Boda

    2016-01-01

    Disequilibrium melting arises when the kinetics of chemical exchange between a residual mineral and partial melt is sluggish compare to the rate of melting. To better understand the role of a finite crystal-melt exchange rate on trace element fractionation during mantle melting, we have developed a disequilibrium melting model for partial melting in an upwelling steady-state column. We use linear kinetics to approximate crystal-melt mass exchange rate and obtain simple analytical solutions for cases of perfect fractional melting and batch melting. A key parameter determining the extent of chemical disequilibrium during partial melting is an element specific dimensionless ratio (ε) defined as the melting rate relative to the solid-melt chemical exchange rate for the trace element of interest. In the case of diffusion in mineral limited chemical exchange, ε is inversely proportional to diffusivity of the element of interest. Disequilibrium melting is important for the trace element when ε is comparable to or greater than the bulk solid-melt partition coefficient for the trace element (k). The disequilibrium fractional melting model is reduced to the equilibrium perfect fractional melting model when ε is much smaller than k. Hence highly incompatible trace elements with smaller mobilities in minerals are more susceptible to disequilibrium melting than moderately incompatible and compatible trace elements. Effect of chemical disequilibrium is to hinder the extent of fractionation between residual solid and partial melt, making the residual solid less depleted and the accumulated melt more depleted in incompatible trace element abundances relative the case of equilibrium melting. Application of the disequilibrium fractional melting model to REE and Y abundances in clinopyroxene in abyssal peridotites from the Central Indian Ridge and the Vema Lithospheric Section, Mid-Atlantic Ridge revealed a positive correlation between the disequilibrium parameter ε and the

  14. Relationship between polymetallic nodule genesis and sediment distribution in the KODOS (Korea Deep Ocean Study) Area, Northeastern Pacific

    Kim, Jonguk; Hyeong, Kiseong; Lee, Hyun-Bok; Ko, Young-Tak

    2012-09-01

    Polymetallic nodule and sediment characteristics were investigated for two blocks (KR2 and KR5) in the Korea Deep Ocean Study (KODOS) area in order to better understand nodule distribution and the potential effects of sediments on nodule genesis. The northern block (KR2) is dominated by hydrogenetic nodules, whereas the southern block (KR5) is dominated by diagenetic nodules. Sediments in the study area are assigned to three major lithologic units which are distinctive in color and texture. The northern block is characterized by a thick, metalpoor Unit 1 sediment, which is thin in the southern block, where metal-rich Units 2b and 3 occur close to the surface. The distribution of different nodule genetic types in the northern and southern blocks can be attributed to topographic variations (topographic high near seamounts in KR2 and abyssal plain in KR5) and different sedimentation rates (0.1 and 0.32 mm/kyr in blocks KR2 and KR5, respectively). The southern block has a geologic setting more conducive to diagenetic nodule formation, such as flat topography and sediment composition. Nodule distribution in the studied blocks might also be explained by the distribution of the sediment units of different metal contents. The northern block, in which Unit 1 is thicker, has more abundant hydrogenetic nodules, possibly because Unit 1 prevents metals that are remobilized from the underlying sediments from reaching the seabed where the nodules are forming.

  15. Interactions between pesticides and microorganisms in freshwater sediments

    Widenfalk, Anneli

    2005-01-01

    In aquatic ecosystems sediment microbial communities provide many important functions, such as organic matter decomposition and by constituting a major food source for organisms at higher trophic levels. Sediments are also sites were pesti-cides have been frequently detected. In this thesis, laboratory microcosm experi-ments on the interactions between pesticides and microorganisms in fresh-water sediments were performed. Natural microbial communities were exposed to both environmentally rele...

  16. Microbial interactions with naturally occurring hydrophobic sediments: Influence on sediment and associated contaminant mobility.

    Droppo, I G; Krishnappan, B G; Lawrence, J R

    2016-04-01

    The erosion, transport and fate of sediments and associated contaminants are known to be influenced by both particle characteristics and the flow dynamics imparted onto the sediment. The influential role of bitumen containing hydrophobic sediments and the microbial community on sediment dynamics are however less understood. This study links an experimental evaluation of sediment erosion with measured sediment-associated contaminant concentrations and microbial community analysis to provide an estimate of the potential for sediment to control the erosion, transport and fate of contaminants. Specifically the paper addresses the unique behaviour of hydrophobic sediments and the role that the microbial community associated with hydrophobic sediment may play in the transport of contaminated sediment. Results demonstrate that the hydrophobic cohesive sediment demonstrates unique transport and particle characteristics (poor settling and small floc size). Biofilms were observed to increase with consolidation/biostabilization times and generated a unique microbial consortium relative to the eroded flocs. Natural oil associated with the flocs appeared to be preferentially associated with microbial derived extracellular polymeric substances. While PAHs and naphthenic acid increased with increasing shear (indicative of increasing loads), they tended to decrease with consolidation/biostabilization (CB) time at similar shears suggesting a chemical and/or biological degradation. PAH and napthenic acid degrading microbes decreased with time as well, which may suggest that there was a reduced pool of PAHs and naphthenic acids available resulting in their die off. This study emphasizes the importance that any management strategies and operational assessments for the protection of human and aquatic health incorporate the sediment (suspended and bed sediment) and biological (biofilm) compartments and the energy dynamics within the system in order to better predict contaminant

  17. Par Pond Fish, Water, and Sediment Chemistry

    The objectives of this report are to describe the Par Pond fish community and the impact of the drawdown and refill on the community, describe contaminant levels in Par Pond fish, sediments, and water and indicate how contaminant concentrations and distributions were affected by the drawdown and refill, and predict possible effects of future water level fluctuations in Par Pond

  18. 枸杞岛海藻场沉积物细菌群落组成的初步研究%A preliminary study on the composition of bacterial community in the seaweed bed sediment of Gouqi Island

    尹冰玉; 章守宇

    2011-01-01

    提取枸杞岛海藻场沉积物样品总DNA,以细菌16S rDNA通用引物进行PCR扩增,经分子克隆、测序与序列分析,构建了沉积物细菌16S rDNA文库和系统发育树,进行沉积物中细菌多样性及系统发育分析.结果表明,沉积物中细菌分属5个类群,分别为变形细菌门(Proteobacteria,48.2%)、厚壁菌门(Firmicutes,22.2%)、放线菌门(Actinobacteria,14.8%)、绿屈挠菌门(Chlorofiexi,3.7%)和酸杆菌门(Acidobacteria,3.7%),还有一些尚未确定其分类(7.4%).在枸杞岛海藻场沉积物变形细菌门类群中,γ-变形菌占主导地位,约为46.1%,其次为α-变形菌(23.1%)、β-变形菌(15.4%)、ε-变形菌(7.7%)和δ-变形菌(7.7%).作为海洋沉积物中的优势菌群,不同生态系统中变形细菌门类群的组成略有不同,功能类群的组成与生态系统机制密切相关.厚壁菌门和放线菌门作为革兰氏阳性菌的两个分支,在枸杞岛海藻场中主要参与分解碎屑及异养营养素的循环过程.%The clone library of 16S rDNA and the phylogenetic tree were constructed with extraction of bacterial DNA from seaweed bed sediment sample of Gouqi Island , PCR amplification of bacterial 16S rDNA by universal primers, molecular clone, sequencing of 16S rDNA fragments and sequence analysis.The biodiversity of bacteria and phylogenetic analysis showed that the bacterial community fell into five main lineages: Proteobacteria (48.2%), Firmicutes (22.2%), Actinobacteria ( 14.8% ), Chloroflexi (3.7%),Acidobacteria (3.7%), In addition, a part of unidentified bacteria (7.4%) was detected.Gammaproteobacteria played the dominant role in the Proteobacteria community of the seaweed bed sediment,it was about 46.1%, followed by the Alphaproteobacteria (23.1% ), Betaproteobacteria ( 15.4% ),Epsilonproteobacteria ( 7.7% ), Deltaproteobacteria ( 7.7% ).As the preponderant bacteria of marine sediment, the composition of Proteobacteria community was different in

  19. Triticella minini - a new ctenostome bryozoan from the abyssal plain adjacent to the Kuril-Kamchatka Trench

    Grischenko, Andrei V.; Chernyshev, Alexei V.

    2015-01-01

    A new species of ctenostome bryozoan, Triticella minini sp. nov., is described from the abyssal plain adjacent to the Kuril-Kamchatka Trench, based on material collected by the Russian-German deep-sea expedition KuramBio 2012. Colonies of T. minini sp. nov. were found attached to the oral spines of irregular sea urchin Echinosigra (Echinogutta) amphoraMironov, 1974 by means of rhizoid fibers that penetrated the substratum through circular borings. The specimens were examined by light microscopy, scanning electron microscopy, and confocal laser scanning microscopy with phalloidin and nuclear labeling. The description of T. minini sp. nov. combines a general taxonomic description with a description of the anatomy of the muscular system. The new species differs from congeners in lacking a stolon. It has an intertentacular organ. T. minini sp. nov. is the eleventh species described in the genus TriticellaDalyell, 1848, and the first record for this genus from the northwestern Pacific. The new species is the fifth ctenostome bryozoan known to occur in 5001-5500 m depth interval worldwide, and the deepest record reported for Triticella.

  20. Three new species and one new genus of abyssal Cumacea (Crustacea, Malacostraca, Peracarida) from the Kuril-Kamchatka Trench area

    Lavrenteva, Anna V.; Mühlenhardt-Siegel, Ute

    2015-01-01

    Only two species of crustacean Cumacea have been reported in publications for the Kuril-Kamchatka Trench area after nine expeditions on board of the RV "Vityaz". During the KuramBio expedition 2012 to the Kuril-Kamchatka Trench and the adjacent abyssal plain at depths 4830-5780 m no less than 72 species of cumaceans from 23 genera and 6 families were sampled. Five genera were recorded for the first time in the studied region: the genera Pseudoleptostyloides and Platycuma were detected for the first time for the Pacific Ocean; Cyclaspoides, Bathylamprops and Styloptocuma were firstly sampled in North Pacific. About 90% of the sampled species appear to be new to science. Three new deep-sea cumacean species and one new genus from the Kurile Kamchatka area are described in the present paper: Abyssoleucon tzarevae gen. n., sp. n. belonging to the family Leuconidae, Cyclaspoides borisovetsi sp. n. and Bathycuma sonne sp. n. of the family Bodotriidae. A distribution map for the species of the genus Cyclaspoides is provided.

  1. Hyalinecia (sic) Edwardsi Roule, 1898-the enigmatic ghost from abyssal depths-redescribed as Nothria edwardsi (Annelida: Onuphidae).

    Arias, Andrés; Paxton, Hannelore

    2016-01-01

    The deep sea is one of the largest ecosystems on earth, extending from 200 m, where sunlight becomes inadequate for photosynthesis, to the deepest trenches. However, it is still one of the least explored. Polychaetes are among the dominant groups in these environments worldwide and play a critical role in the deep sea food chain. Within polychaetes, the onuphids are one the best represented families from 2000 m deep to the hadal zone, with 46 recorded species (Paterson et al. 2009). Hyalinoecia edwardsi Roule, 1898 is one of the early described abyssal onuphids. The species was described from the Talisman station 136, located between the Azores archipelago and the Iberian Peninsula (referred as "l'Espagne") at 4255 m depth (Roule 1898). The original description is rather brief without illustrations and the species was characterised as follows: thick antennae, lateral ones reaching chaetiger 3; first chaetiger twice as long as second one; parapodia of first chaetiger with thick falcate hooks; parapodia of second chaetiger with bidentate hooks; parapodia of third chaetiger with limbate chaetae; following chaetigers with limbate, pectinate chaetae and subacicular hooks; oval tube looking flattened and covered by small particles, mainly quartzites of different colours (Roule 1898). PMID:27515609

  2. APPLICATION OF SEDIMENT QUALITY GUIDELINES IN THE ASSESSMENT OF MANGROVE SURFACE SEDIMENT IN MENGKABONG LAGOON, SABAH, MALAYSIA

    S. M. Praveena, M. Radojevic, M. H. Abdullah, A. Z. Aris

    2008-01-01

    Full Text Available There have been numerous sediment quality guidelines developed to monitor the sediments. Sediment quality guidelines are very useful to screen sediment contamination by comparing sediment contaminant concentration with the corresponding quality guideline, provide useful tools for screening sediment chemical data to identify pollutants of concern and prioritise problem sites and relatively good predictors of contaminations. However, these guidelines are chemical specific and do not include biological parameters. Aquatic ecosystems, including sediments, must be assessed in multiple components (biological data, toxicity, physicochemistry by using intregrated approaches in order to establish a complete and comprehensive set of sediment quality guidelines. Numerous sediment quality guidelines Washington Department of Ecology Sediment Quality Guideline, Australian and New Zealand Environment and Conservation Council, Swedish Environmental Sediment Quality, Screening Quick Reference Table, Portuguese Legislation on the Classification of Dredged Materials in Coastal Zones and Interim Sediment Quality Guideline for Hong Kong have been applied to the Mengkabong lagoon mangrove sediment and discussed. The most appropriate guideline that meets the prioritization criteria consistent with international initiatives and regulations is interim sediment quality values for Hong Kong. The guideline verifies that all the metals are below the Interim Sediment Quality Value-low. However, site-specific, biological testing and ecological analysis of exisiting benthics community structure related to sediment contamination are needed for final decision making in the case of Mengkabong lagoon.

  3. A new Capitella polychaete worm (Annelida: Capitellidae) living inside whale bones in the abyssal South Atlantic

    Silva, Camila F.; Shimabukuro, Maurício; Alfaro-Lucas, Joan M.; Fujiwara, Yoshihiro; Sumida, Paulo Y. G.; Amaral, Antonia C. Z.

    2016-02-01

    A new species of the genus Capitella, Capitella iatapiuna sp. nov., has been found in deep sea whale-fall samples, São Paulo Ridge-Southwest Atlantic. The new species is mainly characterized by a bluntly rounded prostomium and a very distinct peristomium forming a complete ring. Ribosomal 16S sequences were obtained and used for inter-specific comparisons. This species is herein described and compared to others species of the genus. Its ecological role in the whale-fall community is also discussed.

  4. Links between deep-sea respiration and community dynamics.

    Ruhl, Henry A; Bett, Brian J; Hughes, Sarah J M; Alt, Claudia H S; Ross, Elizabeth J; Lampitt, Richard S; Pebody, Corinne A; Smith, Kenneth L; Billett, David S M

    2014-06-01

    It has been challenging to establish the mechanisms that link ecosystem functioning to environmental and resource variation, as well as community structure, composition, and compensatory dynamics. A compelling hypothesis of compensatory dynamics, known as "zero-sum" dynamics, is framed in terms of energy resource and demand units, where there is an inverse link between the number of individuals in a community and the mean individual metabolic rate. However, body size energy distributions that are nonuniform suggest a niche advantage at a particular size class, which suggests a limit to which metabolism can explain community structuring. Since 1989, the composition and structure of abyssal seafloor communities in the northeast Pacific and northeast Atlantic have varied interannually with links to climate and resource variation. Here, for the first time, class and mass-specific individual respiration rates were examined along with resource supply and time series of density and biomass data of the dominant abyssal megafauna, echinoderms. Both sites had inverse relationships between density and mean individual metabolic rate. We found fourfold variation in echinoderm respiration over interannual timescales at both sites, which were linked to shifts in species composition and structure. In the northeastern Pacific, the respiration of mobile surface deposit feeding echinoderms was positively linked to climate-driven particulate organic carbon fluxes with a temporal lag of about one year, respiring - 1-6% of the annual particulate organic carbon flux. PMID:25039229

  5. The community structure and abundance of microcystin-producing cyanobacteria in surface sediment of Lake Taihu in winter%冬季太湖表层底泥产毒蓝藻群落结构和种群丰度

    李大命; 孔繁翔; 于洋; 阳振; 史小丽

    2011-01-01

    targeting toxin-producing genes. The microcystin gene cluster which contains 10 genes, namely from nicyA to mcyJ has been widely used to reveal microcystin-producing species in genera Anabaena, Microcystis and Planktothrix. Detection of cyanobacteria and their toxin-producing ability using molecular methods has been successfully applied to a diverse range of water and sediment environments. In this study, we use quantitative real time PCR to quantify the abundance of microcystin-producing cyanobacteria and Microcystis, and PCR-denaturing gradient gel electrophoresis technique to investigate the community structure of microcystin-producing cyanobacteria in surface sediment of Lake Taihu in winter. qPCR data showed that Microcystis and microcystin-producing cyanobacteria were present in all of sediment samples and their abundance varied significantly in different lake areas, ranging from 1. 23×104copies/g dry weight to 3.75×l06copies/g dry weight and from 2. 56×104 to 1. 07×10 copies/g dry weight, respectively. The proportion of microcystin-producing cyanobacteria to Microcystis ranged from 4. 8% to 35. 2%. DGGE patterns indicated that the composition of microcystin-producing cyanobacteria were very similar in surface sediments collected from different lake areas, and the similarity values were between 70. 2% and 96. 0% . Although the composition of genotypes of microcystin-producing cyanobacteria slightly varied among samples, the dominant band is same. The number of dominant band was negatively correlated with Shannon index. Taking into consideration of qPCR analysis and the concentration of Chlorophyll-a and Phycocyanin, we concluded that in the winter of 2010 cyanobacteria of Lake Taihu mainly overwinter in four lake areas, Mei Hang bay, Zhu shan bay,Gong hu bay and center part of Lake Taihu. Our results showed that quantitative real time PCR is a feasible method to investigate the dynamics of toxic cyanobacteria in lake sediment.

  6. How Specific Microbial Communities Benefit the Oil Industry: Dynamics of Alcanivorax spp. in Oil-Contaminated Intertidal Beach Sediments Undergoing Bioremediation

    Singh, Arvind K.; Sherry, Angela; Gray, Neil D.; Jones, Martin D.; Röling, Wilfred F. M.; Head, Ian M.

    The industrial revolution has led to significant increases in the consumption of petroleum hydrocarbons. Concomitant with this increase, hydrocarbon pollution has become a global problem resulting from emissions related to operational use, releases during production, pipeline failures and tanker spills. Importantly, in addition to these anthropogenic sources of hydrocarbon pollution, natural seeps alone account for about 50% of total petroleum hydrocarbon releases in the aquatic environment (National Research Council, 2003). The annual input from natural seeps would form a layer of hydrocarbons 20 molecules thick on the sea surface globally if it remained un-degraded (Prince, 2005). By contrast with natural seeps, many oil spills, e.g. Sea Empress (Milford Haven, UK), Prestige (Galicia, Spain), EXXON Valdez (Prince William Sound, Alaska, USA), released huge amounts of oil (thousands to hundreds of thousand tonnes; Table 24.1) in a locally confined area over a short period of time with a huge acute impact on the marine environment. These incidents have attracted the attention of both the general public and the scientific community due to their great impact on coastal ecosystems. Although many petroleum hydrocarbons are toxic, they are degraded by microbial consortia naturally present in marine ecosystems.

  7. What is the pollution status of North Sea sediments?

    A March 1990 international sea-going workshop in Bremerhaven, Germany provided the opportunity to conduct detailed sediment toxicity testing in concert with studies of fish histopathology, bioaccumulation, benthic community structure, and sediment chemical contamination in the North Sea. Two gradients of sediment chemical contamination were tested, one from an abandoned oil platform and the other from the mouth of the Elbe River northward to the Dogger Bank. Using a preponderance of evidence approach, it was determined that sediments nearest the Elbe are moderately polluted (pollution is defined as contamination, toxicity, and community alteration) and that sediments offshore and at the Dogger Bank are unpolluted. Sediments nearest the oil platform showed evidence for a low level of pollution, but there was no evidence of pollution 125 m from the platform. The results suggest the testable hypothesis that North Sea sediments away from point sources of pollution such as coastal areas and drilling platforms are presently not polluted. 46 refs., 2 figs., 6 tabs

  8. Nature, source and composition of volcanic ash in sediments from a fracture zone trace of Rodriguez Triple Junction in the Central Indian Basin

    Mascarenhas-Pereira, M.B.L.; Nath, B.N.; Borole, D.V.; Gupta, S.M.

    and Petrology 75, 153-184. Gupta, S.M., 1987. Paleogene ichthyoliths from the substrates of ferromanganese encrustations and nuclei of manganese nodules from the Central Indian Basin. J. Palaeontol. Soc. India. 32, 85-91. Gupta, S.M., 1988. Radiolarian... tephrochronology. J Volcanol Geotherm Res. 34, 153-172. Pattan, J.N., Shane, P., Banakar, V.K., 1999. New occurrence of youngest Toba Tuff in abyssal sediments of the Central Indian Basin. Mar. Geol. 155, 243-248. Price, R.C., Kennedy, A.K., Riggs-Sneeringer, M...

  9. Activity and growth of microbial populations in pressurized deep-sea sediment and animal gut samples.

    Tabor, P S; Deming, J W; Ohwada, K; Colwell, R R

    1982-08-01

    Benthic animals and sediment samples were collected at deep-sea stations in the northwest (3,600-m depth) and southeast (4,300- and 5200-m depths) Atlantic Ocean. Utilization rates of [14C]glutamate (0.67 to 0.74 nmol) in sediment suspensions incubated at in situ temperatures and pressures (3 to 5 degrees C and 360, 430, or 520 atmospheres) were relatively slow, ranging from 0.09 to 0.39 nmol g-1 day-1, whereas rates for pressurized samples of gut suspensions varied widely, ranging from no detectable activity to a rapid rate of 986 nmol g-1 day-1. Gut flora from a holothurian specimen and a fish demonstrated rapid, barophilic substrate utilization, based on relative rates calculated for pressurized samples and samples held at 1 atm (101.325 kPa). Substrate utilization by microbial populations in several sediment samples was not inhibited by in situ pressure. Deep-sea pressures did not restrict growth, measured as doubling time, of culturable bacteria present in a northwest Atlantic sediment sample and in a gut suspension prepared from an abyssal scavenging amphipod. From the results of this study, it was concluded that microbial populations in benthic environments can demonstrate significant metabolic activity under deep-ocean conditions of temperature and pressure. Furthermore, rates of microbial activity in the guts of benthic macrofauna are potentially more rapid than in surrounding deep-sea sediments. PMID:6127054

  10. Ecological effects of contaminated sediments following a decade of no industrial effluents emissions: the Sediment Quality Triad approach.

    Lopes, Marta Lobão; Rodrigues, Ana Maria; Quintino, Victor

    2014-10-15

    Sediments contaminated by industrial effluents a decade after the emissions were stopped were statistically compared to sediments from reference channels, using the Sediment Quality Triad approach. The metals and metalloid concentrations, mainly Hg and As, increased towards the upper part of a contaminated channel, where the industrial discharge was located. A bioaccumulation assay with Scrobicularia plana showed the highest bioaccumulation and mortality in the most contaminated sediments and bioaccumulation strongly correlated with the sediments metals and metalloid concentrations. The resident macroinvertebrate community also showed significant differences between the contaminated and reference channels, in the upper areas, where the community was most affected. All three elements of the quality triad rejected the null hypothesis and indicated that despite the emissions ceasing in 2004, sediments remain contaminated by high levels of metals and metalloid, leading to bioaccumulation and with severe community level consequences. PMID:25152187

  11. Water in orthopyroxene from abyssal spinel peridotites of the East Pacific Rise (ODP Leg 147: Hess Deep)

    Hesse, Kirsten T.; Gose, Jürgen; Stalder, Roland; Schmädicke, Esther

    2015-09-01

    Abyssal spinel peridotites from Hess Deep, East Pacific Rise (ODP Leg 147) were investigated concerning their major, minor, and trace element mineral chemistry and the incorporation of structural water in orthopyroxene. The rocks are partially serpentinized harzburgites containing primary minerals of olivine, orthopyroxene, clinopyroxene, and spinel. Orthopyroxene is enstatitic with Mg# (Mg/(Mg + Fe)) between 0.90 and 0.92 and Al2O3 from 0.5 to 2.9 wt.%. The residual harzburgite experienced high degrees of melt removal in the spinel peridotite stability field. The average degree of partial melting was calculated to be 17.5% (range: 16.4-17.8%). Trace element data of ortho- and clinopyroxenes reflect this strong depletion, characteristic for the restitic nature of abyssal peridotites. Mantle re-equilibration temperatures around 1000 °C indicate that, after melt extraction and before exhumation to the ocean floor, the rocks experienced significant cooling in the spinel peridotite facies. Water contents of orthopyroxene range from 86 to 233 wt. ppm H2O with an average concentration of 142 wt. ppm H2O. These results represent the first data on water contents in the sub-pacific mantle obtained by direct measurements of sub-oceanic peridotite. The water contents are not related to mineral chemistry, stratigraphy, melting degree, mantle equilibrium conditions or oxidation state. Calculated post-melt peridotite water contents vary between 40 and 100 wt. ppm H2O. Compared to Mid-Atlantic Ridge peridotites, the East Pacific Rise samples of Leg 147 contain somewhat lower water concentrations than samples from Leg 153 and considerably higher contents than those of Leg 209 (Gose et al., 2009; Schmädicke et al., 2011). In Leg 147, the strongest OH absorbtion band occurs at 3420 cm- 1, wheras orthopyroxene from MAR peridotite (Legs 153 and 209) has its strongest absorbtion band at 3566 and 3522 cm- 1. The mantle equilibrium temperature of Leg 147 peridotites is lower than that

  12. Application of Markov Chain Monte Carlo Method to Mantle Melting: An Example from REE Abundances in Abyssal Peridotites

    LIU, B.; Liang, Y.

    2015-12-01

    Markov chain Monte Carlo (MCMC) simulation is a powerful statistical method in solving inverse problems that arise from a wide range of applications, such as nuclear physics, computational biology, financial engineering, among others. In Earth sciences applications of MCMC are primarily in the field of geophysics [1]. The purpose of this study is to introduce MCMC to geochemical inverse problems related to trace element fractionation during concurrent melting, melt transport and melt-rock reaction in the mantle. MCMC method has several advantages over linearized least squares methods in inverting trace element patterns in basalts and mantle rocks. First, MCMC can handle equations that have no explicit analytical solutions which are required by linearized least squares methods for gradient calculation. Second, MCMC converges to global minimum while linearized least squares methods may be stuck at a local minimum or converge slowly due to nonlinearity. Furthermore, MCMC can provide insight into uncertainties of model parameters with non-normal trade-off. We use MCMC to invert for extent of melting, amount of trapped melt, and extent of chemical disequilibrium between the melt and residual solid from REE data in abyssal peridotites from Central Indian Ridge and Mid-Atlantic Ridge. In the first step, we conduct forward calculation of REE evolution with melting models in a reasonable model space. We then build up a chain of melting models according to Metropolis-Hastings algorithm to represent the probability of specific model. We show that chemical disequilibrium is likely to play an important role in fractionating LREE in residual peridotites. In the future, MCMC will be applied to more realistic but also more complicated melting models in which partition coefficients, diffusion coefficients, as well as melting and melt suction rates vary as functions of temperature, pressure and mineral compositions. [1]. Sambridge & Mosegarrd [2002] Rev. Geophys.

  13. The Late Pliocene Eltanin Impact: Documentation From Sediment Core Analyses

    Gersonde, R.; Kyte, F.; Flores, J. A.; Becquey, S.

    2002-01-01

    The expeditions ANT-XII/4 (1995) and ANT-XVIII/5a (2001) of the RV POLARSTERN collected extensive bathymetric and seismic data sets as well as sediment cores from an area in the Bellingshausen Sea (eastern Pacific Southern Ocean) that allow the first comprehensive geoscientific documentation of an asteroid impact into a deep ocean (approx. 5 km) basin, named the Eltanin impact. Impact deposits have now been recovered from a total of more than 20 sediment cores collected in an area covering about 80,000 km2. Combined biomagnetostratigraphic dating places the impact event into the earliest Matuyama Chron, a period of enhanced climate variability. Sediment texture analyses and studies of sediment composition including grain size and microfossil distribution reveal the pattern of impact- related sediment disturbance and the sedimentary processes immediately following the impact event. The pattern is complicated by the San Martin Seamounts (approx. 57.5 S, 91 W), a large topographic elevation that rises up to 3000 m above the surrounding abyssal plain in the area affected by the Eltanin impact. The impact ripped up sediments as old as Eocene and probably Paleocene that have been redeposited in a chaotic assemblage. This is followed by a sequence sedimented from a turbulent flow at the sea floor, overprinted by fall-out of airborne meteoritic ejecta that settled trough the water column. Grain size distribution reveals the timing and interaction of the different sedimentary processes. The gathered estimate of ejecta mass deposited over the studied area, composed of shock-melted asteroidal material and unmelted meteorites including fragments up to 2.5 cm in diameter, point to an Eltanin asteroid larger than the 1 km in diameter size originally suggested as a minimum based on the ANT-XII/4 results. This places the energy released by the impact at the threshold of those considered to cause environmental disturbance at a global scale and it makes the impact a likely transport

  14. The Late Pliocene Eltanin Impact - Documentation From Sediment Core Analyses

    Gersonde, R.; Kuhn, G.; Kyte, F. T.; Flores, J.; Becquey, S.

    2002-12-01

    The expeditions ANT-XII/4 (1995) and ANT-XVIII/5a (2001) of the RV POLARSTERN collected extensive bathymetric and seismic data sets as well as sediment cores from an area in the Bellingshausen Sea (eastern Pacific Southern Ocean) that allow the first comprehensive geoscientific documentation of an asteroid impact into a deep ocean (~ 5 km) basin, named the Eltanin impact. Impact deposits have now been recovered from a total of more than 20 sediment cores collected in an area covering about 80,000 km2. Combined biomagnetostratigraphic dating places the impact event into the earliest Matuyama Chron, a period of enhanced climate variability. Sediment texture analyses and studies of sediment composition including grain size and microfossil distribution reveal the pattern of impact-related sediment disturbance and the sedimentary processes immediately following the impact event. The pattern is complicated by the San Martin Seamounts (~57.5 S, 91 W), a large topographic elevation that rises up to 3000 m above the surrounding abyssal plain in the area affected by the Eltanin impact. The impact ripped up sediments as old as Eocene and probably Paleocene that have been redeposited in a chaotic assemblage. This is followed by a sequence sedimented from a turbulent flow at the sea floor, overprinted by fall-out of airborne meteoritic ejecta that settled trough the water column. Grain size distribution reveals the timing and interaction of the different sedimentary processes. The gathered estimate of ejecta mass deposited over the studied area, composed of shock-melted asteroidal matrial and unmelted meteorites including fragments up to 2.5 cm in diameter, point to an Eltanin asteroid larger than the 1 km in diameter size originally suggested as a minimum based on the ANT-XII/4 results. This places the energy released by the impact at the threshold of those considered to cause environmental disturbance at a global scale and it makes the impact a likely transport mechanism

  15. Description and phylogenetic position of the first abyssal solitary kamptozoan species from the Kuril-Kamchatka Trench area: Loxosomella profundorum sp. nov. (Kamptozoa: Loxosomatidae)

    Borisanova, Anastasia O.; Chernyshev, Alexei V.; Neretina, Tatyana V.; Stupnikova, Alexandra N.

    2015-01-01

    One of two orders of a small phylum Kamptozoa, Solitaria, consisting of one family Loxosomatidae of about 140 species, has never been recorded deeper than 700 m. All known for the north-western Pacific loxosomatids (about 17 species) occur in shallow waters. The first abyssal solitary kamptozoan, Loxosomella profundorum sp. nov. is described herein. It was collected during the German-Russian deep-sea expedition KuramBio aboard RV Sonne in the summer of 2012 in the abyssal plain adjacent to the Kuril-Kamchatka Trench. It is the deepest finding of Kamptozoa to date. The new species was found living on the anthozoan polyp Corallimorpharia. L. profundorum sp. nov. is a largest solitary kamptozoan species, up to 4 mm in length, with a stalk of up to 3.5 mm, with 10-12 tentacles, with two conspicuous lateral papillae, and a row of glandular cells in its stalk. A preliminary molecular phylogenetic analysis based on partial 18S rDNA indicated that L. profundorum sp. nov. is a sister clade to the clade, which includes other Loxosomella and two species of Loxomitra.

  16. Geochemistry of abyssal peridotites from the super slow-spreading Southwest Indian Ridge near 65°E: Implications for magma source and seawater alteration

    Zhigang Zeng; Qiaoyun Wang; Xiaomei Wang; Shuai Chen; Xuebo Yin; Zhaoxue Li

    2012-10-01

    The geochemical characteristics of abyssal peridotite samples from one dredge station (27° 49.74′S, 65° 02.14′E, water depth 4473 m) on the super slow-spreading Southwest Indian Ridge (SWIR) near 65°E were investigated. Abyssal peridotites recovered from this site were comprised mainly of lizardite, chlorite, carbonate and magnetite with minor amounts of talc, pyroxene phenocrysts and sparse olivines. Serpentinites exhibit talc veins and major serpentine derived from serpentinization with relict olivine granuloblasts. Olivine grains in serpentinites display exsolution lamellae, indicating the occurrence of talc reduction or decompression during seawater–rock interaction. Pyroxene shows clear cleavage in two directions, with clinopyroxene or orthopyroxene exsolution lamellae. By contrast, bulk rock trace element patterns of serpentinites reveal depletion in most incompatible elements, similarly to the depleted midocean ridge basalt mantle composition, indicating that the SWIR peridotites originated from a depleted mantle source magma and have experienced partial melting. Meanwhile, Rb, Ba, U, Pb, Sr, Li anomalies and the Ce/Pb ratio suggest that these serpentinites have been strongly altered by seawater.

  17. Characteristics of nitrogen forms in the surface sediments of southwestern Nansha Trough, South China Sea

    2008-01-01

    The area of the southwestern Nansha Trough is one of the most productive areas of the southern South China Sea. It is a typical semi-deep sea area of transition from shoal to abyssal zone. To understand distributions and roles of nitrogen forms involved in biogeochemical cycling in this area, contents of nitrogen in four extractable forms: nitrogen in ion exchangeable form (IEF-N), nitrogen in weak acid extractable form (WAEF-N), nitrogen in strong alkali extractable form (SAEF-N) and nitrogen in strong oxidation extractable form (SOEF-N), as well as in total nitrogen content (TN) in surface sediments were determined from samples collected from the cruise in April - May 1999. The study area was divided into three regions (A, B and C) in terms of clay sediment (60%, respectively. Generally, region C was the richest in the nitrogen of all forms and region A the poorest, indicating that the finer the grain size is, the richer the contents of various nitrogen are. The burial efficiency of total nitrogen in surface sediments was 28.79%, indicating that more than 70% of nitrogen had been released and participated in biogeochemical recycling through sediment-water interface.

  18. Extent and toxicity of contaminated marine sediments in Southeastern Florida

    Cantillo, A. Y.; Lauenstein, G. G.

    2004-01-01

    Thirty sites were sampled in southern Biscayne Bay and Manatee Bay in December 1999 to determine the extent of toxicity in sediments. Analyses and assays included: pesticides and phenols in seawater; chemical contaminants in sediment; amphipod mortality, HRGS P450, sea urchin sperm fertilization and embryology, MicrotoxTM, MutatoxTM, grass shrimp AChE and juvenile clam mortality assays; sea urchin sperm, amphipod and oyster DNA damage; and benthic community assessment. Sediment sites near the...

  19. Sediment Interfaces: Ecotones on a Microbial Scale

    Borchers, M. R.; Colwell, F. S.; D'Angelo, G.; Thurber, A. R.; Graw, M. F.

    2015-12-01

    Ecotones - transitions between different biomes - often support greater faunal diversity than the adjacent ecological systems. For subseafloor microorganisms, defined geological and chemical gradients have been shown to affect population sizes and community structure, but the role that sediment interfaces play is still unclear. Here, we test the hypothesis that zones of transition between two distinct sediment types increase microbial diversity and change community composition. Concurrently, we explore those factors that drive deep-subsurface microbial community structure (e.g., depth, interstitial water chemistry, methane concentrations, clay content). Samples from IODP Expedition 349 - South China Sea Tectonics - had interfaces of either ash/clay or turbidite/clay boundaries sampled , DNA extracted, and the 16S rRNA gene analyzed on an Illumina MiSeq platform. Initial analyses reveal that microbial communities in sediment samples are distinct from communities in drilling fluid, indicating that contamination is unlikely. In four of the eight complete interfaces currently analyzed we found an increase in diversity (based on the chao1 index), in certain cases doubling the diversity of the adjacent rock types. The pattern was not uniform across all interfaces. While some posit that ecotones provide a mixing of the two adjacent communities, we were surprised to find an abundance (mean = 392 OTUs) of unique microbial taxa within the ecotone itself when compared to adjacent sediment (mean=282 unique OTUs). Thus while diversity was not uniformly increased in ecotones, the interface led to divergent microbial communities that were not simply mixtures of those adjacent. We will discuss the ability of abiotic factors in explaining the among ecotone variance that we observed. Our investigation helps to characterize the factors that drive microbial community structure of the subseafloor while highlighting the need to focus on habitat heterogeneity at a scale pertinent to

  20. OU3 sediment dating and sedimentation rates

    Environmental Technologies at Rocky Flats Environmental Technology Site (RFS) investigated the sediment history of Standley Lake, Great Western Reservoir, and Mower Reservoir using 137Cs and 239,240Pu global fall-out as dating indicators. These Colorado Front Range reservoirs have been the subject of study by various city, state and national agencies due to suspected Department of Energy Rocky Flats Plant impacts. We performed sediment dating as part of the RCRA Facility Investigation/Remedial Investigation Report for Operable Unit 3. A sediment chronology profile assists scientist in determining the year of sedimentation for a particular peak concentration of contaminants. Radioisotope sediment dating for the three reservoirs indicated sedimentation rates of 0.7 to 0.8 in./yr. for Standley Lake (SL), 0.9 in./yr. for Great Western Reservoir (GWR), and 0.3 in./yr. in Mower Reservoir (MR). RFS sediment dating for Operable Unit 3 compared favorably with the Hardy, Livingston, Burke, and Volchok Standley Lake study. This report describes the cesium/plutonium sediment dating method, estimates sedimentation rates for Operable Unit 3 reservoirs, and compares these results to previous investigations

  1. Messages from the Abyss

    2003-10-01

    VLT Observes Infrared Flares from Black Hole at Galactic Centre [1] Summary An international team of astronomers led by researchers at the Max-Planck Institute for Extraterrestrial Physics (MPE) in Garching (Germany) [2] has discovered powerful infrared flares from the supermassive black hole at the heart of the Milky Way . The signals, rapidly flickering on a scale of minutes, must come from hot gas falling into the black hole, just before it disappears below the "event horizon" of the monster. The new observations strongly suggest that the Galactic Centre black hole rotates rapidly . Never before have scientists been able to study phenomena in the immediate neighbourhood of a black hole in such a detail. The new result is based on observations obtained with the NACO Adaptive Optics instrument on the 8.2-m VLT YEPUN telescope and is published in this week's edition of the research journal Nature. PR Photo 29a/03 : A powerful flare from the black hole at the galactic centre. PR Photo 29b/03 : Light curve of the flare . PR Video 01/03 : A powerful flare from the black hole at the galactic centre . Flashes of light from disappearing matter ESO PR Photo 29a/03 ESO PR Photo 29a/03 [Preview - JPEG: 650 x 400 pix - 118k [Normal - JPEG: 1300 x 800 pix - 370k] ESO PR Video Clip 01/03 [MPEG] ESO PR Video Clip 01/03 [MPEG Video; 29X k] Captions : PR Photo 29a/03 and PR Video Clip 01/03 show the detection of a powerful flare from the centre of the Milky Way galaxy. These and other adaptive optics (AO) images (with resolution 0.040 arcsec in the near-infrared H-band at wavelength 1.65 µm) of the central region of the Milky Way were obtained with the NACO imager on the 8.2-m VLT YEPUN telescope at the ESO Paranal Observatory on May 9, 2003. The image covers a sky area of about 1 x 1 arcsec, corresponding to about 45 light-days at the distance of the Galactic Centre. The time (in minutes from the beginning of the data set at 6h59m24s (UT) on May 9, 2003) is shown at the upper right of each image. North is up and East to the left. The position of the 15-year orbiting star S2 (cf. ESO Press Release 17/02 ) is marked by a cross and the astrometric location of the black hole is indicated by a circle. The scene was the usual one in the VLT Control Room at the Paranal Observatory in the early morning of May 9, 2003. Groups of astronomers from different nations were sitting in front of the computer screens, pointing the four giant telescopes in different directions and recording the sparse photons from the remotest corners of the Universe. There were the usual brief exchanges of information, numbers, wavelengths, strange acronyms, but then suddenly something happened at the YEPUN desk.... " What is that star doing there? " exclaimed Rainer Schödel , one of the MPE scientists in the team working with the NACO Adaptive Optics instrument [3] that delivers razor-sharp images. He and Reinhard Genzel, leader of the team and MPE Director, were observing the Milky Way Centre, when they saw the "new" object on the screen in front of them. The astronomers were puzzled and then became excited - something unusual must be going on, there at the centre of our galaxy! And then, a few minutes later, the "star" disappeared from view. Now the scientists had little doubt - they had just witnessed, for the first time, a powerful near-infrared flare from exactly the direction of the supermassive black hole at the heart of the Milky Way , cf. PR Photo 29a/03 and PR Video Clip 01/03 . " We had been looking for infrared emission from that black hole for more than a decade " recalls another team member, Andreas Eckart of the Cologne University. " We were certain that the black hole must be accreting matter from time to time. As this matter falls towards the surface of the black hole, it gets hotter and hotter and starts emitting infrared radiation ". But no such infrared radiation had been seen until that night at the VLT. This was the wonderful moment of breakthrough. Never before had anybody witnessed the last "scream" from matter in the deadly grip of a black hole, about to pass the point of no return towards an unknown fate. At the border ESO PR Photo 29b/03 ESO PR Photo 29b/03 [Preview - JPEG: 400 x 516 pix - 87k [Normal - JPEG: 800 x 1032 pix - 219k] Captions : PR Photo 29b/03 displays the "light curve" of a light flare from the galactic centre, as observed in the K-band (wavelength 2.2 µm) on June 16, 2003. This and a second flare discovered about 24 hours earlier show variability on a time scale of a few minutes and appear to show larger variations (arrows) with a 17-minute periodicity. The rapid variability implies that the infrared emission comes from just outside (the event horizon of) the black hole. If the periodicity is a fundamental property of the motion of gas orbiting the black hole, the Galactic Centre black hole must rotate with about half the maximum spin rate allowed by General Relativity. The present observations thus probe the space-time structure in the immediate vicinity of that event horizon. A careful analysis of the new observational data, reported in this week's issue of the Nature magazine, has revealed that the infrared emission originates from within a few thousandths of an arcsecond [4] from the position of the black hole (corresponding to a distance of a few light-hours) and that it varies on time scales of minutes ( PR Photo 29b/03 ). This proves that the infrared signals must come from just outside the so-called "event horizon" of the black hole, that is the "surface of no return" from which even light cannot escape. The rapid variability seen in all data obtained by the VLT clearly indicates that the region around this horizon must have chaotic properties - very much like those seen in thunderstorms or solar flares [5]. " Our data give us unprecedented information about what happens just outside the event horizon and let us test the predictions of General Relativity " explains Daniel Rouan , a team member from Paris-Meudon Observatory. " The most striking result is an apparent 17-minute periodicity in the light curves of two of the detected flares. If this periodicity is caused by the motion of gas orbiting the black hole, the inevitable conclusion is that the black hole must be rotating rapidly ". Reinhard Genzel is very pleased: " This is a major breakthrough. We know from theory that a black hole can only have mass, spin and electrical charge. Last year we were able to unambiguously prove the existence and determine the mass of the Galactic Centre black hole ( ESO Press Release 17/02 ). If our assumption is correct that the periodicity is the fundamental orbital time of the accreting gas, we now have also measured its spin for the first time . And that turns out to be about half of the maximum spin that General Relativity allows ". He adds: " Now the era of observational black hole physics has truly begun !" More information The results described in this ESO press release are presented in a report published today in the research journal "Nature" ("Near-IR Flares from Accreting Gas around the Supermassive Black Hole in the Galactic Centre", by Reinhard Genzel and co-authors).

  2. ABYSSES OF FIRE

    Rafael Santana

    2015-11-01

    Full Text Available The aim of this paper is to think the genesis of the poetry in the artistic universe of Mário de Sá-Carneiro, a poet who undertakes literary criticism from within his own writings while reckoning with the specificities of art. Following the path of some of the iconic figures of modern times, such as Baudelaire, Rimbaud and Mallarmé, Sá-Carneiro inscribes his poetry in a tradition of a whole lineage of poets for whom writing is above all a hand-to-hand with language.

  3. Peering into the abyss

    The multi-continent detections of the neutrinos from the core of SN 1987A open a new chapter in high energy astrophysics. For the first time, we have penetrated the supernova ejecta and glimpsed at the violent convulsions that attend stellar collapse and the birth of a neutron star. The neutrino emissions are the only good diagnostic of implosion physics, and the new data allow to test supernova theories in a unique way. The author compares the theory developed over the last 20 years with these observations to extract what information there is in these epochal detections

  4. Meiofauna metabolism in suboxic sediments: currently overestimated

    Braeckman, U.; Vanaverbeke, J.; Vincx, M.; van Oevelen, D.; Soetaert, K.

    2013-01-01

    Oxygen is recognized as a structuring factor of metazoan communities in marine sediments. The importance of oxygen as a controlling factor on meiofauna (32 µm-1 mm in size) respiration rates is however less clear. Typically, respiration rates are measured under oxic conditions, after which these rat

  5. Spatial and seasonal variation in microbial diversity in marine subtidal sediments in relation to sediment geochemistry and heavy metal pollution

    Pede, A.; Gillan, D.; Gao, Y.; Billon, G.; Lesven, L.; Leermakers, M; Baeyens, W.; Vyverman, W.; Sabbe, K

    2009-01-01

    Very little information is available on the diversity and structure of microbial communities in marine subtidal sediments, especially for micro-eukaryotes. In the framework of the Belgian MICROMET project, we investigated spatial and seasonal (February vs July) variation patterns in the molecular diversity of archaeal, bacterial and eukaryotic communities in 9 subtidal stations in the Belgian Continental Plate (BCP) in relation to sediment granulometry, geochemistry and metal contamination. M...

  6. SEAGRASS RHIZOSPHERE MICROBIAL COMMUNITIES

    Devereux, Richard. 2005. Seagrass Rhizosphere Microbial Communities. In: Interactions Between Macro- and Microorganisms in Marine Sediments. E. Kristense, J.E. Kostka and R.H. Haese, Editors. American Geophysical Union, Washington, DC. p199-216. (ERL,GB 1213). Seagrasses ...

  7. Center for Contaminated Sediments

    Federal Laboratory Consortium — The U.S. Army Corps of Engineers Center for Contaminated Sediments serves as a clearinghouse for technology and expertise concerned with contaminated sediments. The...

  8. Electrodialytic remediation of sediments

    Jensen, Pernille Erland

    Sediments of harbors and freshwaters are regularly dredged for various reasons: maintenance of navigational depths, recovery of recreational locations, and even environmental recovery. In the past, sediments dredged from harbors have been dumped at sea, however, environmental regulations now, in ...

  9. Ocean Sediment Thickness Contours

    National Oceanic and Atmospheric Administration, Department of Commerce — Ocean sediment thickness contours in 200 meter intervals for water depths ranging from 0 - 18,000 meters. These contours were derived from a global sediment...

  10. National Geochemical Database: Sediment

    U.S. Geological Survey, Department of the Interior — Geochemical analysis of sediment samples from the National Geochemical Database. Primarily inorganic elemental concentrations, most samples are of stream sediment...

  11. Polychaete composition from the abyssal plain adjacent to the Kuril-Kamchatka Trench with the description of a new species of Sphaerephesia (Polychaeta: Sphaerodoridae)

    Alalykina, Inna L.

    2015-01-01

    During the KuramBio expedition, the abyssal plain adjacent to the Kuril-Kamchatka Trench was sampled in July-August 2012. More than 5200 individuals of Polychaeta belonging to 38 families, 108 genera and about 144 species were found. Six genera have been reported for the Northwest Pacific for the first time. About 50% of the collected polychaete species are considered as new to science. One of these, Sphaerephesia lesliae sp. n., is described herein. The detailed description of the new species is presented and its differences from similar species are shown. This eighth species of the genus is characterized by the presence of macrotubercles with two paired terminal papillae. The genus Sphaerephesia Fauchald, 1972 is newly recorded in the Northwest Pacific. An updated key to the species of the genus Sphaerephesia is provided.

  12. A new species of Comephoronema (Nematoda: Cystidicolidae) from the stomach of the abyssal halosaur Halosauropsis macrochir (Teleostei) from the Mid-Atlantic Ridge.

    Moravec, Frantisek; Klimpel, Sven

    2007-08-01

    A new species of parasitic nematode Comephoronema macrochiri n. sp. (Cystidicolidae), is described from the stomach of the marine deep-sea fish Halosauropsis macrochir (abyssal halosaur) from the Mid-Atlantic Ridge (MAR). The new species, studied with both light and scanning electron microscopy, is characterized mainly by 6 pairs of preanal papillae, by which it principally differs from members of Ascarophis; the spicules are 297-375 microm and 99-120 microm long and fully developed eggs possess 2 long filaments on 1 pole. Rhabdochona beatriceinsleyae is transferred to Comephoronema as C. beatriceinsleyae (Holloway and Klewer, 1969) n. comb. Comephoronema macrochiri differs from all other congeners mainly in having eggs with filaments on 1 pole only, and from individual species by some additional features such as the number of preanal papillae, the shape of pseudolabial projections, and the body and organ measurements. PMID:17918373

  13. 10Be variation in surficial sediments of the Central Indian Basin

    Distribution of 10Be in systematically collected (degree x degree interval at 10 to 16 deg. S; 73.5 to 76.5 deg. E) surficial siliceous ooze, siliceous clay and pelagic clay sediments (top 2 cm) from the abyssal Central Indian Basin and the Andaman Sea is used to evaluate sources and to decipher the transport pathways of sediment particles, demarcate sediment depocenters and erosional areas. While 10Be concentrations display a wide variation (0.12-5.56 x 109 atoms g-1) with an average of 3.58 x 109 atoms g-1 in the Central Indian Basin, the values in the Andaman Sea are uniform with an average of 1.49 x 109 atoms g-1. The 10Be/9Be values in the Central Indian Basin sediments range between 0.06 and 2.99 x 10-8 atoms atoms-1 and average to ∼1.56 x 10-8 atoms atoms-1. Correlation of 10Be data with some selected major (Al, Mn, Ti) and trace (Rb and Ba) elements suggest that large part of the isotope has been supplied through direct atmospheric fallout from the water column and minor part from lithogenic detrital flux. Significantly lower 10Be accumulation rates in the Central Indian Basin and an order of magnitude higher in the Andaman Sea sediments compared to the estimated global average production rates indicate removal of the isotopes at the continental margins. Bottom topography seems to exert control on local 10Be variation, where sediments deposited in valleys or topographic depressions contain higher 10Be concentrations in contrast to the probably erosion-dominated areas at the slopes and troughs

  14. Cross-basin heterogeneity in lanternfish (family Myctophidae) assemblages and isotopic niches (δ13C and δ15N) in the southern Tasman Sea abyssal basin

    Flynn, A. J.; Kloser, R. J.

    2012-11-01

    A cross-basin (longitudinal) study of lanternfishes in the southern Tasman Sea abyssal basin during the austral winter of 2008 and 2009 found that mean biomass in the Western sector was higher than that in the Eastern sector, corresponding with cross-basin patterns in oceanographic heterogeneity and productivity. Dominant species over the abyssal basin differed from those previously recorded over the neighbouring continental slope. Vertical biomass profiles indicated diffuse night-time distributions in the Central sector and extensive diel vertical migrations in the Eastern sector. In the Western sector, macrocrustacean δ13C values were significantly higher, and δ15N significantly lower, than those in the Eastern sector. The results indicate a cross-basin difference in the primary productivity environment and 15N enrichment at the base of the foodweb. The cross-basin pattern in lanternfish δ15N values mirrored that for macrocrustaceans and was not correlated with standard length. Lanternfish δ13C values did not differ between sectors, but there were depth-wise differences, with values in the shallowest stratum (0-200 m) significantly higher than those in the deepest stratum (800-1000 m). Calculated trophic levels (TLs) of lanternfishes spanned the third trophic level and marked niche segregation was evident in the Eastern (mean TL 3.0-3.9) and Central (mean TL 2.5-3.6) sectors. Together, the results suggest that the Eastern and Western sectors are distinct sub-basin scale pelagic habitats, with implications for ecosystem modelling and future monitoring.

  15. Reservoir Sedimentation and Upstream Sediment Sources: Perspectives and Future Research Needs on Streambank and Gully Erosion

    Fox, G. A.; Sheshukov, A.; Cruse, R.; Kolar, R. L.; Guertault, L.; Gesch, K. R.; Dutnell, R. C.

    2016-05-01

    The future reliance on water supply and flood control reservoirs across the globe will continue to expand, especially under a variable climate. As the inventory of new potential dam sites is shrinking, construction of additional reservoirs is less likely compared to simultaneous flow and sediment management in existing reservoirs. One aspect of this sediment management is related to the control of upstream sediment sources. However, key research questions remain regarding upstream sediment loading rates. Highlighted in this article are research needs relative to measuring and predicting sediment transport rates and loading due to streambank and gully erosion within a watershed. For example, additional instream sediment transport and reservoir sedimentation rate measurements are needed across a range of watershed conditions, reservoir sizes, and geographical locations. More research is needed to understand the intricate linkage between upland practices and instream response. A need still exists to clarify the benefit of restoration or stabilization of a small reach within a channel system or maturing gully on total watershed sediment load. We need to better understand the intricate interactions between hydrological and erosion processes to improve prediction, location, and timing of streambank erosion and failure and gully formation. Also, improved process-based measurement and prediction techniques are needed that balance data requirements regarding cohesive soil erodibility and stability as compared to simpler topographic indices for gullies or stream classification systems. Such techniques will allow the research community to address the benefit of various conservation and/or stabilization practices at targeted locations within watersheds.

  16. Small ecosystem engineers as important regulators of lake's sediment respiration.

    Baranov, Victor; Lewandowski, Joerg; Krause, Stefan; Romeijn, Paul

    2016-04-01

    Although shallow lakes are covering only about 1.5% of the land surface of the Earth, they are responsible for sequestration of carbon amounts similar or even larger than those sequestered in all marine sediments. One of the most important drivers of the carbon sequestration in lakes is sediment respiration. Especially in shallow lakes, bioturbation, i.e. the biogenic reworking of the sediment matrix and the transport of fluids within the sediment, severely impacts on sediment respiration. Widespread freshwater bioturbators such as chironomid larvae (Diptera, Chironomidae) are building tubes in the sediment and actively pump water through their burrows (ventilation). In the present work we study how different organism densities and temperatures (5-30°C) impact on respiration rates. In a microcosm experiment the bioreactive resazurin/resorufin smart tracer system was applied for quantifying the impacts of different densities of Chironomidae (Diptera) larvae (0, 1000, 2000 larvae/m2) on sediment respiration. Tracer transformation rates (and sediment respiration) were correlated with larval densities with highest transformation rates occurring in microcosms with highest larval densities. Respiration differences between defaunated sediment and sediment with 1000 and 2000 larvae per m2 was insignificant at 5 °C, and was progressively increasing with rising temperatures. At 30 °C respiration rates of sediment with 2000 larvae per m2 was 4.8 times higher than those of defaunated sediment. We interpret this as an effect of temperature on larval metabolic and locomotory activity. Furthermore, bacterial communities are benefiting from the combination of the high water temperatures and bioirrigation as bacterial community are able to maintain high metabolic rates due to oxygen supplied by bioirrigation. In the context of global climate change that means that chironomid ecosystem engineering activity will have a profound and increasing impact on lake sediment respiration

  17. Chemical composition of sediments from White Sea, Russian Arctic

    Gamza, Olga; Shevchenko, Vladimir; Novigatsky, Aleksandr

    2010-05-01

    The White Sea, the only Russian inland sea, is located on the north of outlying districts of the European part of Russia, belongs to Arctic Ocean. Area of water of sea occupies about 90 tousend square kilometers. The sea can be divided into some general parts: neck, funnel, basin and 4 Bays: Dvina Bay, Kandalaksha Bay, Mezen Bay and Onega Bay. The purpose of this work was geochemical mapping of the surface sediments of this area. The main tasks were: compilation data base of element composition of the surface sediments, geochemical mapping of each element, research of the anormal concentration of elements on the surface. To detect the content of chemical elements several methods were used: atomic absorption spectrometry (P.P. Shirshov Institute of Oceanology); neutron activation analysis (Vernadsky Institute of Geochemistry and Analytical Chemistry), total and organic carbon analysis, photometric method to detection Si, Al, P (P.P. Shirshov Institute of Oceanology). Bulk composition is one of the fundamental characteristics of sediments and bottom deposites of modern basins. Coarse-grained sediments with portion of pelitic component 80%). Character of elements distribution correlates with facial distribution of sediments from White Sea. According to litologic description, bottom surface of Dvina Bay is practically everywhere covered by layer of fine-grained sand. In the border area between Dvina Bay and White Sea basin on terraced subwater slope aleurite politic silts are abundant. They tend to exhange down the slope to clay silts. In Onega Bay fractions of non-deposition are observed. They are characterized by wide spread of thin blanket poorgraded sediments, which are likely to be relic. Relief of Kandalakscha Bay bottom is presented as alternation of abyssal fosses (near 300 m) with silles and elevations (depressions and in central part of the sea, which is quite wide from both places of original sedimentation and run off sources [2]. Thus, the interrelation

  18. Effects of sedimentation on macroalgae : Species-specific responses are related to reproductive traits

    Eriksson, Klemens; Johansson, Gustav

    2005-01-01

    Although increases in sedimentation have been proposed to interfere with benthic communities in many coastal areas worldwide, few experimental studies have investigated the effect of sedimentation on community composition and assessed species-specific responses. In a field experiment on a rocky shor

  19. Sediment supply to beaches

    Aagaard, Troels

    2014-01-01

    Many beaches have been built by an onshore supply of sand from the shoreface, and future long-term coastal evolution critically depends on cross-shore sediment exchange between the upper and the lower shorefaces. Even so, cross-shore sediment supply remains poorly known in quantitative terms and...... this reduces confidence in predictions of long-term shoreline change. In this paper, field measurements of suspended sediment load and cross-shore transport on the lower shoreface are used to derive a model for sediment supply from the lower to the upper shoreface at large spatial and temporal scales....... Data collection took place at five different field sites that exhibit a wide range of wave conditions and sediment characteristics. Data analysis shows that both suspended sediment load and cross-shore sediment transport scale with the grain-related mobility number which ranged up to ψ ≈ 1000 in the...

  20. Integrated approach to the toxicity evaluation of Irish marine sediments: exotoxicological assessment

    Macken, Ailbhe

    2007-01-01

    The quality of sediment in any aquatic ecosystem is vital to the health of that system. Sediments have been recognised as a major repository for persistent toxic substances. If sediments become sufficiently polluted they can lead to the disruption of surrounding natural biological communities. Therefore the monitoring of sediment quality is essential for successful ecosystem functioning in the marine environment. The aim of the present study was to employ an integrated approach of the toxicit...

  1. The Impact of Sediment Characteristics on PCB-dechlorinating Cultures: Implications for Bioaugmentation

    Yan, Tao; Timothy M. LaPara; Novak, Paige J.

    2006-01-01

    PCB-dechlorinating cultures with complimentary activities, previously derived from estuarine Baltimore Harbor (B), marine Palos Verdes (P) and riverine Hudson River (H) sediments, were mixed and then inoculated into sterile sediments from the same sources. In the treatments containing sterile B sediment, the different inocula had limited impact on the bacterial community development and on dechlorination patterns, all of which were similar. In treatments containing sterile P or H sediment, ho...

  2. Assessing sediment contamination using six toxicity assays

    Allen G. BURTON Jr.

    2001-08-01

    Full Text Available An evaluation of sediment toxicity at Lake Orta, Italy was conducted to compare a toxicity test battery of 6 assays and to evaluate the extent of sediment contamination at various sediment depths. Lake Orta received excessive loadings of copper and ammonia during the 1900’s until a large remediation effort was conducted in 1989-90 using lime addition. Since that time, the lake has shown signs of a steady recovery of biological communities. The study results showed acute toxicity still exists in sediments at a depth of 5 cm and greater. Assays that detected the highest levels of toxicity were two whole sediment exposures (7 d using Hyalella azteca and Ceriodaphnia dubia. The MicrotoxR assay using pore water was the third most sensitive assay. The Thamnotox, Rototox, Microtox solid phase, and Seed Germination-Root Elongation (pore and solid phase assays showed occasional to no toxicity. Based on similarity of responses and assay sensitivity, the two most useful assays were the C. dubia (or H. azteca and Microtox pore water. These assays were effective at describing sediment toxicity in a weight-of-evidence approach.

  3. Unique 16S rRNA sequences of Eurythenes gryllus (Crustacea: Amphipoda: Lysianassidae) from the Gulf of Mexico abyssal plain Secuencias únicas 16SrRNA de Eurythenes gryllus (Crustacea: Amphipoda: Lysianassidae) de la planicie abisal del Golfo de México

    Elva Escobar-Briones; Eduardo Nájera-Hillman; Fernando Álvarez

    2010-01-01

    Amphipods of the species Eurythenes gryllus were collected at 2 locations on the abyssal plain (~3 400 m) of the Gulf of Mexico in order to test whether or not these scavenger amphipods are isolated in this peripheral sea or show connectivity by their predominant swimming behavior, moving horizontally along the abyssal water masses in the region. Partial sequences of the mitochondrial 16S rRNA gene from 2 individuals of E. gryllus were determined and showed small differences when compared to ...

  4. Geochemical and micropaleontological character of Deep-Sea sediments from the Northwestern Pacific near the Kuril-Kamchatka Trench

    Sattarova, Valentina V.; Artemova, Antonina V.

    2015-01-01

    Sediments from the abyssal plain adjacent to the Kuril-Kamchatka Trench were collected during the German-Russian cruise for the Kuril Kamchatka Biodiversity Study, and the chemical composition, quantitative content, and species composition of collected diatoms were studied. The collected sediments are silt and clayey silt, the SiO2 am and Corg contents range 7.58-19.38% and 0.44-1.55%, respectively. The enrichment of silts by amorphous silica indicates the presence of a significant number of organisms (predominantly diatoms) with an opal skeleton. High Corg content in sediments reflects biological productivity, which is controlled by factors such as water circulation and the distribution of nutrients. Interrelation trends among chemical constituents is investigated via multi-component statistics. Diatom assemblages reflect present-day water masses characterized by high nutrient content, surface water circulation, and sedimentation conditions for different parts of the study area. Analysis of this new data also highlights changes in the response of diatom flora due to abiotic factors.

  5. The kinetics of denitrification in permeable sediments

    Evrard, Victor; Glud, Ronnie N.; Cook, Perran L. M.

    2013-04-01

    Permeable sediments comprise the majority of shelf sediments, yet the rates of denitrification remain highly uncertain in these environments. Computational models are increasingly being used to understand the dynamics of denitrification in permeable sediments, which are complex environments to study experimentally. The realistic implementation of such models requires reliable experimentally derived data on the kinetics of denitrification. Here we undertook measurements of denitrification kinetics as a function of nitrate concentration and in the presence and absence of oxygen, in carefully controlled flow through reactor experiments on sediments taken from six shallow coastal sites in Port Phillip Bay, Victoria, Australia. The results showed that denitrification commenced rapidly (within 30 min) after the onset of anoxia and the kinetics could be well described by Michaelis-Menten kinetics with half saturation constants (apparent Km) ranging between 1.5 and 19.8 μM, and maximum denitrification rate (Vmax) were in the range of 0.9-7.5 nmol mL-1 h-1. The production of N2 through anaerobic ammonium oxidation (anammox) was generally found to be less than 10% that of denitrification. Vmax were in the same range as previously reported in cohesive sediments despite organic carbon contents one order of magnitude lower for the sediments studied here. The ratio of sediment O2 consumption to Vmax was in the range of 0.02-0.09, and was on average much lower than the theoretical ratio of 0.8. The most likely explanation for this is that the microbial community is not able to instantaneously shift or optimally use a particular electron acceptor in the highly dynamic redox environment experienced in permeable sediments. Consistent with this explanation, subsequent longer-term experiments over 5 days showed that denitrification rates increased by a factor of 10 within 3 days of the permanent onset of anoxia. In contrast to previous studies, we did not observe any significant

  6. Do abyssal scavengers use phytodetritus as a food resource? Video and biochemical evidence from the Atlantic and Mediterranean

    Jeffreys, R.M.; Lavaleye, M.S.S.; Bergman, M.J.N.; Duineveld, G.C.A.; Witbaard, R.

    2011-01-01

    Deep-sea benthic communities derive their energetic requirements from overlying surface water production, which is deposited at the seafloor as phytodetritus. Benthic invertebrates are the primary consumers of this food source, with deep-sea fish at the top of the trophic hierarchy. Recently, we dem

  7. The Communities of Ammonia-oxidizing Organisms in Pearl River Estuary Sediments%珠江口海岸带沉积物氨氧化细菌和古菌组成及定量研究

    陈金全; 郑燕平; 姜丽晶; 王风平

    2012-01-01

    [Objective] This study aimed to investigate the abundance and composition of ammonia-oxidizing organism in Pearl River Estuary sediment. [ Method] Based on amoA genes, we detected the abundance and composition of ammonia-oxidizing organism in Pearl River Estuary sediment by using quantitative real-time polymerase chain reaction (Q-PCR) , cloning and sequencing approaches. [ Result] The results of Q-PCR presented that ammonia-oxidizing archaea were more abundant than ammonia-oxidizing bacteria in the top of sediment cores, with AOA to AOB ratios 8.96 (site Q5) and 3. 69 (site Q7). It suggested that ammonia-oxidizing archaea maybe play more important roles than ammonia-oxidizing bacteria in the process of ammonia oxidation in the Pearl River Estuary sediment. In the top sediment layer of Q7, bacterial amoA-like gene sequences were dominated by Nitrosomonas-like sequence types, which could be classified into five groups (clusters A, B, C, D, and E). Interestingly, archeal amoA-like gene was successfully amplified while bacterial amoA-like gene failed to be detected. These archeal amoA-like genes fell into two groups "water column/sediment" cluster and "soil/sediment" cluster. Most of the sequences (93. 3% ) in the bottom sediment layer of Q7 fell into " soil/sediment" cluster. [ Conclusion] This study helps to realize the cycle of nitrogen in Pearl River Estuary region, and thus to provide theoretical support fur the treatment of nitrogen eutrophication.%[目的]对珠江口海岸带沉积物中的氨氧化细菌和古菌的组成进行分析,并进行定量研究.[方法]用构建克隆文库和Q - PCR定量的方法对珠江口沉积物中氨氧化细菌和古菌amoA基因的含量和多样性特征进行研究.[结果]在2个沉积物表层,氨氧化古菌的含量是细菌的9和22倍,揭示氨氧化古菌在珠江口的氨氧化过程中起主导作用;系统发育分析表明大多数古菌和细菌的amoA基因序列与不可培养的源于河口区和污染

  8. Communities and Quantitative Analysis of Ammonia-oxidizing Organisms in Pearl River Estuary Sediments%珠江口海岸带沉积物氨氧化细菌和古菌组成及定量研究

    陈金全; 郑燕平; 姜丽晶; 王风平

    2012-01-01

    [Objective] This study aimed to investigate the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea in Pearl River Estuary sediment.[Method] Firstly,the amoA gene library was constructed;then based on that,the content and diversity of amoA genes of ammonia-oxidizing bacteria and ammonia-oxidizing archaea in Pearl River Estuary sediment were detected by using quantitative real-time polymerase chain reaction(Q-PCR).[Result] The results of Q-PCR presented that ammonia-oxidizing archaea(AOA) were more abundant than ammonia-oxidizing bacteria(AOB) in the top of sediment cores,with ratios of AOA to AOB of 22 and 9 at the two sites.It suggested that ammonia-oxidizing archaea may play more important roles than ammonia-oxidizing bacteria in the process of ammonia oxidation in the Pearl River Estuary sediment.The phylogenetic tree based on amoA gene sequences revealed that the amoA sequences of both AOA and AOB shared high similarity with the clones from uncultured environment.In the top sediment layer at site Q7,AOB amoA-like gene sequences were dominated by Nitrosomonas-like sequence types,which could be classified into five groups(clusters A,B,C,D and E).Cluster A accounted for 72.1% of the library.In the top sediment layer,the AOA amoA gene fell into two groups "water column/sediment" cluster(52.2%) and "soil/sediment" cluster(47.8%).But in the bottom sediment layer of Q7,most of the AOA amoA sequences(93.3%) fell into "soil/sediment" cluster,and a little part(6.7%) fell into the "water/sediment" cluster.In addition,the total amount of amoA genes in the bottom sediment was higher than that in top sediment.[Conclusion] This study helps to realize the cycle of nitrogen in Pearl River Estuary Region,and thus to provide theoretical support for the treatment of nitrogen eutrophication.%[目的]对珠江口海岸带沉积物中的氨氧化细菌和古菌的组成进行分析,并进行定量研究。[方法]用构建克隆文库和Q-PCR定量

  9. Creation Of Constructed Tidal Flats Using Ocean Dredged Sediment

    Park, S.; Yi, B.; Lee, I.; Sung, K.

    2007-12-01

    The enforcement of London dumping convention (1972) and protocols (1996) which are comprehensive assessment system for ocean dumping wastes needs environmentally sound treatment and/or reuse of dredged sediment. Creation of constructed tidal flats using dredged sediments could be one of the useful alternatives among other dredged sediment treatments. In this study, the pilot-scale constructed tidal flats with 4 different mixing ratio of ocean dredged sediment were constructed in Nakdong river estuary, Korea. The reed was transplanted from the adjacent reed community after construction, and then the survival and growth rate of the planted reed was measured. Also the changes of Chemical Oxygen Demand (COD), Ignition loss (IL), and the heterotrophic microbial numbers were monitored. The survival rate of the planted reed decreased as the mixing ratio of dredged sediment increased. The survival rate of reed in the constructed tidal flat with 100% dredged sediment was 54% while that in the tidal flat with 0% dredged sediment (original soil of Nakdong river estuary) was 90%. There was little difference of length and diameter of the reed shoot among the 4 different constructed tidal flats. 30% of COD and 9% of IL in the tidal flat with 100% dredged sediment decreased after 202 day, however, the consistent tendency in the change of COD and IL in the other tidal flats was not found possibly due to the open system. It was suggested that the construction of tidal flats using ocean dredged sediment can be possible considering the growth rate of transplanted reeds and the contaminated ocean dredged sediment might be biologically remediated considering the results of decrease of organic matter and increased heterotrophic microbial number in the tidal flat with 100% dredged sediment. However, the continuous monitoring on the vegetation and various environmental factors in the constructed tidal flats should be necessary to evaluate the success of creation of constructed flats using

  10. Beyond the bed: Effects of metal contamination on recruitment to bedded sediments and overlying substrata

    Metal-contaminated sediments pose a recognised threat to sediment-dwelling fauna. Re-mobilisation of contaminated sediments however, may impact more broadly on benthic ecosystems, including on diverse assemblages living on hard substrata patches immediately above sediments. We used manipulative field experiments to simultaneously test for the effects of metal contamination on recruitment to marine sediments and overlying hard substrata. Recruitment to sediments was strongly and negatively affected by metal contamination. However, while assemblage-level effects on hard-substratum fauna and flora were observed, most functional groups were unaffected or slightly enhanced by exposure to contaminated sediments. Diversity of hard-substratum fauna was also enhanced by metal contamination at one site. Metal-contaminated sediments appear to pose less of a hazard to hard-substratum than sediment-dwelling assemblages, perhaps due to a lower direct contaminant exposure or to indirect effects mediated by contaminant impacts on sediment fauna. Our results indicate that current sediment quality guidelines are protective of hard-substrata organisms. - Highlights: ► Potential for contaminated sediments to exert impacts beyond the sediment communities. ► We examine effects on recruitment to sediments and overlying hard substrata simultaneously. ► Metal-contaminated sediments had a strong negative impact on sediment fauna. ► Metal-contaminated sediments pose less of a hazard to hard-substratum fauna. ► Sediment quality guidelines are likely protective of hard-substrata organisms. - Under natural disturbance regimes, metal-contaminated sediments pose less of a direct risk to hard-substratum fauna than to sediment-dwelling fauna and SQG appear appropriate.

  11. Do abyssal scavengers use phytodetritus as a food resource? Video and biochemical evidence from the Atlantic and Mediterranean

    Jeffreys, R.M.; Lavaleye, M.S.S.; Bergman, M.J.N.; Duineveld, G. C. A.; Witbaard, R.

    2011-01-01

    Deep-sea benthic communities derive their energetic requirements from overlying surface water production, which is deposited at the seafloor as phytodetritus. Benthic invertebrates are the primary consumers of this food source, with deep-sea fish at the top of the trophic hierarchy. Recently, we demonstrated with the use of baited cameras that macrourid fish rapidly respond to and feed vigorously on large plant food falls mimicked by spinach (Jeffreys et al., 2010). Since higher plant remains...

  12. Feasibility of disposal of high-level radioactive wastes into the seabed: Review of laboratory investigations of radionuclide migration through deep-sea sediments

    Brush, L.H.

    1988-08-01

    The Sediment Barrier Task Group (SBTG) coordinated laboratory studies of radionuclide migration through deep-sea sediments by investigators in six countries over a period of 12 years. The objectives of these studies were to evaluate the barrier properties of a variety of deep- sea sediments from study locations characterized by the Site Assessment Task Group (SATG), and to obtain site-specific data for use by the Radiological Assessment Task Group (RATG) in models of radionuclide transport through the sediments at the Great Meteor East (GME) and Southern Nares Abyssal Plain (SNAP) study locations in the North Atlantic Ocean. This volume presents a review of these laboratory investigations and the results obtained from them. Although the SBTG also participated in numerous geochemical investigations at the study locations characterized by the SATG, these field studies are not discussed here. For the convenience of the reader, however, this volume contains a brief description of the sediments from GME and SNAP, and the Mid-Plate Mid-Gyre I (MPG I) study location in the North Pacific Ocean. 130 refs., 48 figs., 11 tabs.

  13. Dynamics of Cohesive Sediments

    Johansen, Claus

    The present thesis considers the transport processes of cohesive sediments. The cohesive sediment used in the laboratory experiments was kaolinite, a clay mineral, in order to be able to reproduce the individual experiments. In the first part of the thesis, the theoretical considerations regarding...

  14. Recovery of DNA from soils and sediments.

    Steffan, R J; Goksøyr, J; Bej, A K; Atlas, R. M.

    1988-01-01

    Experiments were performed to evaluate the effectiveness of two different methodological approaches for recovering DNA from soil and sediment bacterial communities: cell extraction followed by lysis and DNA recovery (cell extraction method) versus direct cell lysis and alkaline extraction to recover DNA (direct lysis method). Efficiency of DNA recovery by each method was determined by spectrophotometric absorbance and using a tritiated thymidine tracer. With both procedures, the use of polyvi...

  15. Isolating the impact of sediment toxicity in urban streams

    Marshall, Stephen, E-mail: s.marshall@zoology.unimelb.edu.a [Centre for Environmental Stress and Adaptation Research (CESAR), The University of Melbourne, Bio21 Institute, 30 Flemington Road, Parkville, VIC 3010 (Australia); Pettigrove, Vincent [Melbourne Water Research and Technology, Melbourne Water Corporation, PO Box 4342, VIC 3000 (Australia); Carew, Melissa; Hoffmann, Ary [Centre for Environmental Stress and Adaptation Research (CESAR), The University of Melbourne, Bio21 Institute, 30 Flemington Road, Parkville, VIC 3010 (Australia)

    2010-05-15

    Several factors can contribute to the ecological degradation of stream catchments following urbanization, but it is often difficult to separate their relative importance. We isolated the impact of polluted sediment on the condition of an urban stream in Melbourne, Australia, using two complementary approaches. Using a rapid bioassessment approach, indices of stream condition were calculated based on macroinvertebrate field surveys. Urban stream reaches supported impoverished macroinvertebrate communities, and contained potentially toxic concentrations of heavy metals and hydrocarbons. Using a field microcosm approach, a bioassay was carried out to assess sediment pollution effects on native macroinvertebrates. Sediment from urban sites substantially altered the microcosm macroinvertebrate community, most likely due to elevated heavy metal and hydrocarbon concentrations. Macroinvertebrate surveys combined with a bioassay approach based on field microcosms can help isolate the effect of stream pollutants in degraded ecosystems. - Field microcosms isolate the ecological impact of polluted sediment in an urban stream.

  16. Isolating the impact of sediment toxicity in urban streams

    Several factors can contribute to the ecological degradation of stream catchments following urbanization, but it is often difficult to separate their relative importance. We isolated the impact of polluted sediment on the condition of an urban stream in Melbourne, Australia, using two complementary approaches. Using a rapid bioassessment approach, indices of stream condition were calculated based on macroinvertebrate field surveys. Urban stream reaches supported impoverished macroinvertebrate communities, and contained potentially toxic concentrations of heavy metals and hydrocarbons. Using a field microcosm approach, a bioassay was carried out to assess sediment pollution effects on native macroinvertebrates. Sediment from urban sites substantially altered the microcosm macroinvertebrate community, most likely due to elevated heavy metal and hydrocarbon concentrations. Macroinvertebrate surveys combined with a bioassay approach based on field microcosms can help isolate the effect of stream pollutants in degraded ecosystems. - Field microcosms isolate the ecological impact of polluted sediment in an urban stream.

  17. EFFECTS OF HEAVY METALS IN SEDIMENTS OF THE MACROINVERTEBRATE COMMUNITY IN THE SHORT CREEK/EMPIRE LAKE AQUATIC SYSTEM, CHEROKEE COUNTY, KANSAS: A RECOMMENDATION FOR SITE-SPECIFIC CRITERIA.

    The study uses statistical analysis techniques to determine the effects of four heavy metals (cadmium, lead, manganese, and zinc) on the macroinvertebrate community using the data collected in the fall 1987.

  18. The effects of jellyfish (Rhopilema esculentum Kishinouye) farming on the sediment nutrients and macrobenthic community%海蜇养殖对池塘底泥营养盐和大型底栖动物群落结构的影响

    冯建祥; 董双林; 高勤峰; 孙侦龙; 王芳; 张凯

    2011-01-01

    To study the effects of jellyfish (Rhopilema esculentum Kishinouye) fanning activities on the sediment nutrients and the structure of macrobenthic community, an experimental station within the farming pond and a reference station adjacent to the farming zone were set in JingHai Bay mariculture zone and samples were collected from both stations between May 2009 and September 2009 to compare the spatio-temporal changes in the biotic and abiotic conditions due to jellyfish farming. NH4-N, NO3-N, Chla, TOM, TOC of sediment and sedimentation rate (SR) were analyzed. The macrobenthos (>0.5mm) presented in the sediment were sampled, identified and enumerated. During the three sampling months,significant differences of sediment nutrients except TOC at experimental station and of NH4-N, NO3-N and Chla at reference station were observed. In July 2009, when the jellyfish were extensively cultured, the sediment NH4-N, NO3-N and SR levels at experimental station were significantly higher than those at reference station, while Chla, TOM and TOC levels were significantly lower than those at reference station. In the other two sampling months, no significant differences of sediment nutrients except Chla in September were observed. As for the structure of the benthic communities, 15 kinds of dominant species were collected in all. Nine kinds of the dominant species were polychaete, two kinds were crustacean and four kinds were mollusc. All the collected macrobenthic invertebrates were common species in intertidal zone in North China. In May 2009, Musculus senhousia Benson accounted for 91.53% and 89.25% at experimental station and reference station respectively. The proportion of polychaete among the macrobenthos at experimental station rised in July and September 2009 due to the farming activity of jellyfish. Shannon-Wiener's diversity index (H') and Pielou's evenness index (J) increased significantly with the cultivation of jellyfish at experimental station in July 2009 and

  19. Shifting Sediment Sources in the Quaternary Nile

    Woodward, Jamie; Macklin, Mark; Fielding, Laura; Millar, Ian; Williams, Martin

    2016-04-01

    Invited Paper The Nile basin contains the longest river channel system in the world and drains about one tenth of the African continent. A dominant characteristic of the modern Nile is the marked spatial and temporal variability in the flux of water and sediment. Because the major headwater basins of the Nile are linked to key elements of the global climate system, the sedimentary records in the basin have attracted good deal of attention from the Quaternary palaeoclimate and palaeohydrology communities. Various approaches (from heavy minerals to strontium isotopes) have been employed to examine present and past patterns of sediment yield in the basin. A good deal of work has been carried out on the long sediment records in the delta and offshore which provide high resolution archives of hydrological changes in the upstream basin as well fluctuations in the input of dust from the desert. The sediment load of the modern desert Nile (downstream of Khartoum) is dominated by sediment inputs from the Blue Nile (61 +/- 5%) and Atbara (35 +/- 4%), whilst the White Nile contribution is meagre (3 +/- 2%) (Padoan et al. 2011). Recent work has shown that these values were very different during humid phases of the Quaternary when stronger Northern Hemisphere summer insolation produced wetter conditions across North Africa. In the early Holocene, for example, the Nile floodplain in Northern Sudan shows a tributary wadi input of 40-50%. This paper will review three decades of work on the sediment delivery dynamics of the Quaternary Nile and explore their palaeoclimatic implications. Padoan, M., Garzanti, E., Harlavan, Y., Villa, I.M. (2011) Tracing Nile sediment sources by Sr and Nd isotope signatures (Uganda, Ethiopia, Sudan). Geochim. Cosmochim. Acta 75 (12), 3627-3644.

  20. An account of the Ischnomesidae (Peracarida, Isopoda) from the Kuril-Kamchatka Trench and abyssal plain (Northwest Pacific) with the description of two new species

    Brandt, Angelika; Kristin Stüven, Jana; Caurant, Cyril; Oskar Elsner, Nikolaus

    2015-01-01

    During the German-Russian expedition KuramBio (Kuril-Kamchatka Biodiversity Studies) from board of the RV Sonne to the Kuril-Kamchatka Trench and adjacent abyssal plain, benthic samples were taken by means of a camera-epibenthic sledge. Amongst one of the most diverse macrobenthic taxa, the Isopoda (Crustacea, Malacostraca), Ischnomesidae were the fifth most abundant isopod family in the Kuril-Kamchatka area and were sampled with 24 species from 5 genera in 21 hauls at 12 stations. Fortimesus occurs most frequently in the samples (36% of all Ischnomesidae sampled), followed by Stylomesus (26%), Heteromesus (23%), Ischnomesus (10%) and Gracilimesus (4%). Number of ischnomesid individuals is highest at station 10-12 with 35 specimens, followed by station 12-4 (30 ind.), station 6-12 (29 ind.), station 9-9 (28), and station 1-11 (24). At station 4-3 only 1 specimen was found. A key to all genera of Ischnomesidae is provided. Two new species from two genera: StylomesusWolff, 1956 and FortimesusKavanagh and Wilson, 2007 are described from the KuramBio material. Stylomesus malyutinae sp. nov. is distinguished by the smooth body surface, the shape of pleotelson and the length of uropods from other species of the genus from the Northwest Pacific Ocean. Fortimesus trispiculum sp. nov. is characterised by anterolateral projections of pereonites 1-3 which are forming an angle of about 45° with the longitudinal body axis decreasing in length from anterior to posterior.

  1. Morphology and Late Quaternary sedimentation in the Gulf of Oman Basin

    Uchupi, Elazar; Swift, S. A.; Ross, D. A.

    The morphology of the Gulf of Oman Basin, a 3,400 m deep oceanic basin between Oman and southern Pakistan and southern Iran, ranges from a convergent margin (Makran margin) along the north side, a passive type (Oman margin) along the south side, translation types along the basin's west (Zendan Fault-Oman Line) and east (Murray Ridge) sides and a narrow continental rise and a wide abyssal plain in the centre of the basin. Sediment input into the basin during the Late Quaternary has been mainly from the north as a result of the uplift of the Coast Makran Mountains in the Late Miocene-Pliocene. Today most of this detritrus is deposited on the shelf and upper continental slope and perched basins behind the fold/fault ridges on the lower slope. The presence of fans and channels on the continental rise on the north side of the basin indicate, however, that continental derived debris was, and possibly is, being transported to the deep-sea by turbidity currents via gaps in the ridges on the lower slope. In addition to land derived terrigenous sediments, the basin deposits also contain biogenic (organic matter and calcium carbonate), eolian detritus and hydrates and authigenic carbonates from the tectonic dewatering of the Makran accretionary wedge. The eolian sediment is carried into the Gulf of Oman Basin from Arabia and the Mesopotamia Valley by the northwesterly Shamal winds. This type of detritus was particularly abundant during the glacial arid periods 21,000-20,000 and 11,000 (Younger Dryas) years ago when exposure of the Persian (Arabian) Gulf increased the area of dust entrainment and shifted the position of the source of the eolian sediments closer to the basin.

  2. Thermoluminescence dating of sediments

    Thermoluminescence (TL) dating of sediments is based on the observation that exposure of quartz and feldspar to sunlight rapidly reduces the TL level to a small residual value. Therefore, sediments transported by air or water will usually be deposited with a very small TL level. When the sediment has been covered as a result of subsequent sedimentation, the TL level again increases with time as a result of exposure of the minerals to the natural background radiation. The TL level is thus a measure of the accumulated radiation dose (the palaeodose), and the time elapsed since sedimentation is given by the ratio of the palaeodose to the annual dose. Techniques for determining the palaeodose are described including the regeneration, additive dose and R-GAMMA methods. Insufficient bleaching during transport, instability of the latent TL signal and non-linear dose response for older samples pose particular problems which are discussed. In several respects, TL dating of sediments is still at the experimental stage, but the method has a great potential for dating sediments within the last 500,000 years, a period for which there are few other absolute dating methods. (author)

  3. Archaea in Arctic Thermokarst Lake Sediments

    Matheus Carnevali, P. B.; Rohrssen, M.; Dodsworth, J. A.; Kuhn, E.; Williams, M.; Adams, H. E.; Berisford, D. F.; Hand, K. P.; Priscu, J. C.; Walter Anthony, K.; Love, G. D.; Hedlund, B. P.; Murray, A. E.

    2011-12-01

    Thermokarst lakes in the Northern Slope of Alaska are known to emit ebullient methane (CH4), some of which is of biogenic origin. Thawing of permafrost in the margins and bottom of these lakes, as a result of climate change, releases sources of carbon that could be used by methanogenic Archaea. However, the composition of Archaea inhabiting these lakes is not known. We have chosen a subset of Thermokarst lakes near Barrow Alaska to determine if there are methanogenic and methane oxidizing Archaea in these lake sediments. To describe the diversity of the archaeal community in the sediments we profiled the variable 3 (v3) region of the 16S rRNA gene of Archaea. The v3 profiles indicated surprisingly high levels of diversity, with 20 to 36 bands in the 10 sample horizons over the upper 100 cm of sediments surveyed in four lakes, at two times of the year. One of v3 rRNA gene bands was common to all lakes, and most phylotypes were grouped by depth (1-40 cm or 41-105 cm) within a lake. Likewise, cluster analysis indicated partitioning of archaeal communities between lakes. To specifically detect methanogens and anaerobic methanotrophs (ANME) in the sediments, DNA was surveyed by PCR to detect the methyl coenzyme M reductase (mcrA) gene, which is specific to the pathways of methanogenesis and anaerobic methane oxidation (AMO). An array of methanogen enrichment cultures was also set up. The expected 464-491 bp amplification product predicted for the mcrA gene was detected in all sediment samples. Assays of enrichment cultures incubated at 2 and 10 °C with substrates used in the main pathways for methanogenesis have produced positive growth and CH4 production results. Most cultures produced CH4 from carbon dioxide (CO2) reduction with hydrogen (H2), although methanol and acetate were also utilized as methanogenic substrates by a few cultures. From the experiments conducted to date we conclude that there is a great diversity of Archaea inhabiting these Thermokarst lakes

  4. Tracking the spatiotemporal variations of statistically independent components involving enrichment of rare-earth elements in deep-sea sediments.

    Yasukawa, Kazutaka; Nakamura, Kentaro; Fujinaga, Koichiro; Iwamori, Hikaru; Kato, Yasuhiro

    2016-01-01

    Deep-sea sediments have attracted much attention as a promising resource for rare-earth elements and yttrium (REY). In this study, we show statistically independent components characterising REY-enrichment in the abyssal ocean that are decoded by Independent Component Analysis of a multi-elemental dataset of 3,968 bulk sediment samples from 101 sites in the Pacific and Indian oceans. This study for the first time reconstructs the spatiotemporal variations of the geochemical signatures, including hydrothermal, hydrogenous, and biogenic calcium phosphate components that were closely involved in the formation of REY-rich mud over the past 65 million years. An underlying key factor of significant REY-enrichment is a sufficiently low sedimentation rate that enables the mud to accumulate REY from seawater. In the early Cenozoic, a remarkably small supply of aeolian dust, compared with any other time and region, facilitated the deposition of very high-grade REY-rich mud in the South Pacific. This indicates an important link between the genesis of the seafloor mineral resources and Earth's dynamic phenomena such as climate change and plate tectonics. PMID:27444949

  5. Ecological differentiation in planktonic and sediment-associated chemotrophic microbial populations in Yellowstone hot springs.

    Colman, Daniel R; Feyhl-Buska, Jayme; Robinson, Kirtland J; Fecteau, Kristopher M; Xu, Huifang; Shock, Everett L; Boyd, Eric S

    2016-09-01

    Chemosynthetic sediment and planktonic community composition and sizes, aqueous geochemistry and sediment mineralogy were determined in 15 non-photosynthetic hot springs in Yellowstone National Park (YNP). These data were used to evaluate the hypothesis that differences in the availability of dissolved or mineral substrates in the bulk fluids or sediments within springs coincides with ecologically differentiated microbial communities and their populations. Planktonic and sediment-associated communities exhibited differing ecological characteristics including community sizes, evenness and richness. pH and temperature influenced microbial community composition among springs, but within-spring partitioning of taxa into sediment or planktonic communities was widespread, statistically supported (P < 0.05) and could be best explained by the inferred metabolic strategies of the partitioned taxa. Microaerophilic genera of the Aquificales predominated in many of the planktonic communities. In contrast, taxa capable of mineral-based metabolism such as S(o) oxidation/reduction or Fe-oxide reduction predominated in sediment communities. These results indicate that ecological differentiation within thermal spring habitats is common across a range of spring geochemistry and is influenced by the availability of dissolved nutrients and minerals that can be used in metabolism. PMID:27306555

  6. Enhancing the biodegradation of oil in sandy sediments with choline: A naturally methylated nitrogen compound

    We investigated how additions of choline, a naturally occurring methylated nitrogen-containing compound, accelerated hydrocarbon degradation in sandy sediments contaminated with moderately weathered crude oil (4000 mg kg−1 sediment). Addition of lauroylcholine chloride (LCC) and tricholine citrate (TCC) to oil contaminated sediments resulted in 1.6 times higher hydrocarbon degradation rates compared to treatments without added choline derivatives. However, the degradation rate constant for the oil contaminated sediments amended with LCC was similar to that in contaminated sediments amended with inorganic nitrogen, phosphorus, and glucose. Additions of LLC and TCC to sediments containing extensively weathered oil also resulted in enhanced mineralization rates. Cultivation-free 16S rRNA analysis revealed the presence of an extant microbial community with clones closely related to known hydrocarbon degraders from the Gammaproteobacteria, Alphaproteobacteria, and Firmicutes phyla. The results demonstrate that the addition of minimal amounts of organic compounds to oil contaminated sediments enhances the degradation of hydrocarbons. -- Highlights: •Aerobic degradation of weathered crude oil in sandy sediments was determined. •The effect of input of choline on degradation rates was determined. •16S rRNA clone library analyses were used to examine the microbial phylogeny. •The bacterial community was consisted of clones related to hydrocarbon degraders. •Hydrocarbon degradation in sandy sediments was accelerated by addition of choline. -- Choline, a naturally occurring methylated nitrogen-containing compound, accelerated hydrocarbon degradation in sandy sediments by an extant microbial community

  7. Habitat heterogeneity reflected in mesophotic reef sediments

    Weinstein, D. K.; Klaus, J. S.; Smith, T. B.

    2015-11-01

    Modern reef sediments reflect the physical and chemical characteristics of the environment as well as the local reef fauna. Analysis of sedimentary reef facies can thus provide a powerful tool in interpreting ancient reef deposits. However, few studies have attempted to differentiate sedimentary facies in mesophotic coral ecosystems, low light habitats defined as residing 30-150 m below sea level. The low-angle shelf mesophotic coral ecosystem south of the northern U.S. Virgin Islands (USVI) consists of reefs with different structural characteristics ideal for studying the relationship between habitat variability and sedimentary facies. Textural, compositional, and geochemical analyses of surface sediments were used to identify mesophotic reef subfacies associated with distinct benthic communities and structural habitats. Sediment grain composition and bulk geochemistry were found to broadly record the distribution and abundance of coral and macroalgae communities, foundational mesophotic reef benthic organisms. Overall, sediment composition was found to be a good indicator of specific reef environments in low-angle mesophotic reef habitats. Sedimentological analyses indicate that hydrodynamic forces do not transport a significant amount of allochthonous sediment or potentially harmful terrigenous material to USVI mesophotic reefs. Episodic, maximum current velocities prevented deposition of most silt-size grains and smaller, but biological processes were found to have a greater influence on subfacies partitioning than hydrodynamic processes. Results provide a new analog for studies of ancient mesophotic coral ecosystem geological history and document the relationship between mesophotic reef subfacies, structural complexity, and habitat heterogeneity. They also demonstrate how mesophotic reefs along the same shelf system do not always share similar sedimentary characteristics and thus record a diverse set of ecological and environmental conditions.