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  • Elsevier  (593,885)
  • Public Library of Science  (118,079)
  • 2010-2014  (711,964)
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  • 1
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    Granulites and charnockites of the Gruf Complex : evidence for Permian ultra-high temperature metamorphism in the Central Alps (2011)
    Elsevier
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    Publication Date: 2024-06-07
    Description: We present a detailed field and petrological study of charnockites and ultra-high temperature (UHT) granulites from the Gruf Complex, eastern Central Alps. Charnockites occur as up to 0.5 km wide and 8 km long, internally boudinaged, opx-bearing sheet-like bodies within the regionally dominant migmatitic biotite-orthogneisses. Granulites occur as garnet–orthopyroxene–biotite–alkali feldspar-bearing schlieren (± sapphirine, sillimanite, cordierite, corundum, spinel, plagioclase, and quartz) within charnockites and as residual enclaves both in the charnockites and the migmatitic orthogneisses. Thermobarometric calculations, P–T pseudosections and orthopyroxene Al content, show that both charnockites and granulites equilibrated at metamorphic peak conditions of T = 920–940 °C and P = 8.5–9.5 kbar. Peak assemblages were subsequently overprinted by intergrowth, symplectite and corona textures involving orthopyroxene, sapphirine, cordierite and spinel at T = 720–740 °C and P = 7–7.5 kbar. We suggest that granulites and charnockites are lower crustal relicts preserved in the migmatitic orthogneisses. Garnet diffusion modelling shows that metamorphic garnet–opx ± sapphirine ± sillimanite peak assemblages and post-peak reaction textures always involving cordierite developed during two separate metamorphic cycles. Peak assemblages reflect UHT metamorphism related to post-Varican Permian extension, but post-peak coronae and symplectites formed during the mid-Tertiary, upper amphibolite facies, Alpine regional metamorphism. Fluid-absent partial melting of pelitic and psammitic sediments during the Permian UHT event lead to the formation of charnockitic magmas and granulitic residues. Intense melt loss and thorough dehydration of the granulites (although retaining biotite) favoured the partial preservation of peak mineral assemblages during Alpine metamorphism.
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  • 2
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    Fluid geochemistry and geothermometry in the western sector of the Sabatini Volcanic District and the Tolfa Mountains (Central Italy) (2011)
    Elsevier
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    Publication Date: 2024-05-09
    Description: A geochemical survey of 197 fluid discharges (cold and thermal waters and bubbling pools) and 15 gas emissions from the western sector of the Sabatini Volcanic District and the Tolfa Mountains (Latium, Central Italy) was carried out in 2007–2008. The chemical and isotopic compositions of the fluid discharges indicate the occurrence of two main sources: 1) relatively shallow aquifers with Ca(Na,K)–HCO3 and Ca(Mg)–HCO3 compositions when trapped in volcanic and sedimentary formations, respectively; and 2) a deep reservoir, which is hosted in the Mesozoic carbonate sequence, rich in CO2 and having a Ca–SO4(HCO3) composition. Dissolution of a CO2-rich gas phase into the shallow aquifers produces high-TDS and high-pCO2 cold waters, while oxidation of deep-derived H2S to SO4 2− generates low-pH (b4) sulfate waters. The δ13C–CO2 values for gas emissions (from−2.8 to+2.7‰vs. VPDB) suggest that the origin of CO2 associated with the deep fluids ismainly related to thermo-metamorphic reactions within the carbonate reservoir, although significant mantle contribution may also occur. However, R/Ra values (0.37–0.62) indicate that He is mainly produced by a crustal source, with a minor component from a crust-contaminated mantle. On the basis of the δ13C–CH4 and δD–CH4 values (from −25.7 to −19.5‰ vs. VPDB and from −152 to −93.4‰ vs. VSMOW, respectively) CH4 production is associated with thermogenic processes, possibly related to abiogenic CO2 reduction within the carbonate reservoir. The δ34S–H2S values (from+9.3 to +10.4‰ vs. VCDT) are consistent with the hypothesis of a sedimentary source of sulfur from thermogenic reduction of Triassic sulfates. Geothermometric evaluations based on chemical equilibria CO2–CH4 and, separately, H2S suggest that the reservoir equilibriumtemperature is up to ~300 °C. The δDand δ18O data indicate thatwater recharging both the shallow and deep aquifers has a meteoric origin. Fluid geochemistry, coupled with gravimetric data and tectonic lineaments, supports the idea that significant contributions from a deep-seated geothermal brine are present in the Stigliano thermal fluid discharges. Exploration surveys investigated this area during 70's–90's for geothermal purposes. Nevertheless, presently the area is still under-exploited. The presence of thermal waters and anomalous heat flow together with the demographic growth of the last years,makes this site a suitable location for direct applications of the geothermal resource.
    Description: Published
    Description: 160-181
    Description: 2.4. TTC - Laboratori di geochimica dei fluidi
    Description: JCR Journal
    Description: reserved
    Keywords: Geochemistry Water Gas Stable isotope Geothermometry Central Italy ; 03. Hydrosphere::03.04. Chemical and biological::03.04.03. Chemistry of waters ; 03. Hydrosphere::03.04. Chemical and biological::03.04.05. Gases ; 03. Hydrosphere::03.04. Chemical and biological::03.04.06. Hydrothermal systems
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 3
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    Deciphering the pathways for the deep limb of the Meridional Overturning Circulation (2011)
    Elsevier
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    Publication Date: 2024-04-08
    Description: For the past 50 years it has been assumed that the principal pathway for the deep limb of the Atlantic Meridional Overturning Circulation (AMOC) is the Deep Western Boundary Current (DWBC). However, recent observations of Lagrangian floats have shown that the DWBC is not necessarily a unique, dominant, or continuous pathway for these deep waters. A significant portion of the deep water export from the subpolar to the subtropical gyres follows a pathway through the interior of the Newfoundland and subtropical basins, which is constrained by the western boundary and the western flank of the Mid-Atlantic Ridge. The hypothesis that deep eddy-driven recirculation gyres are a mechanism for partitioning the deep limb of the AMOC into the DWBC and this interior pathway is investigated here. Eulerian and Lagrangian analyses of the output of ocean general circulation models at eddy-resolving, eddy-permitting, and non-eddy permitting resolutions are used to test this hypothesis. Eddy-driven recirculation gyres, simulated in the eddy-resolving and eddy-permitting models and similar to recirculations inferred from hydrographic data, are shown to shape the export pathways of deep water from the subpolar to the subtropical gyres.
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  • 4
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    The Phanerozoic δ88/86Sr Record of Seawater: New Constraints on Past Changes in Oceanic Carbonate Fluxes (2014)
    Elsevier
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    Publication Date: 2024-03-23
    Description: The isotopic composition of Phanerozoic marine sediments provides important information about changes in seawater chemistry. In particular, the radiogenic strontium isotope (87Sr/86Sr) system is a powerful tool for constraining plate tectonic processes and their influence on atmospheric CO2 concentrations. However, the 87Sr/86Sr isotope ratio of seawater is not sensitive to temporal changes in the marine strontium (Sr) output flux, which is primarily controlled by the burial of calcium carbonate (CaCO3) at the ocean floor. The Sr budget of the Phanerozoic ocean, including the associated changes in the amount of CaCO3 burial, is therefore only poorly constrained. Here, we present the first stable isotope record of Sr for Phanerozoic skeletal carbonates, and by inference for Phanerozoic seawater (δ88/86Srsw), which we find to be sensitive to imbalances in the Sr input and output fluxes. This δ88/86Srsw record varies from ∼0.25‰ to ∼0.60‰ (vs. SRM987) with a mean of ∼0.37‰. The fractionation factor between modern seawater and skeletal calcite Δ88/86Srcc-sw, based on the analysis of 13 modern brachiopods (mean δ88/86Sr of 0.176±0.016‰, 2 standard deviations (s.d.)), is -0.21‰ and was found to be independent of species, water temperature, and habitat location. Overall, the Phanerozoic δ88/86Srsw record is positively correlated with the Ca isotope record (δ44/40Casw), but not with the radiogenic Sr isotope record ((87Sr/86Sr)sw). A new numerical modeling approach, which considers both δ88/86Srsw and (87Sr/86Sr)sw, yields improved estimates for Phanerozoic fluxes and concentrations for seawater Sr. The oceanic net carbonate flux of Sr (F(Sr)carb) varied between an output of -4.7x1010mol/Myr and an input of +2.3x1010mol/Myr with a mean of -1.6x1010mol/Myr. On time scales in excess of 100Myrs the F(Sr)carb is proposed to have been controlled by the relative importance of calcium carbonate precipitates during the “aragonite” and “calcite” sea episodes. On time scales less than 20Myrs the F(Sr)carb seems to be controlled by variable combinations of carbonate burial rate, shelf carbonate weathering and recrystallization, ocean acidification, and ocean anoxia. In particular, the Permian/Triassic transition is marked by a prominent positive δ88/86Srsw-peak that reflects a significantly enhanced burial flux of Sr and carbonate, likely driven by bacterial sulfate reduction (BSR) and the related alkalinity production in deeper anoxic waters. We also argue that the residence time of Sr in the Phanerozoic ocean ranged from ∼1Myrs to ∼20Myrs.
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  • 5
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    Environmental boundary conditions of cold-water coral mound growth over the last 3 Million years in the Porcupine Seabight, Northeast Atlantic (2014)
    Elsevier
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    Publication Date: 2024-03-22
    Description: IODP Expedition 307 made it for the first time possible to investigate the entire body of a cold-water coral carbonate mound. Here we provide new insights into the long-term history of Challenger Mound on the European continental margin off Ireland. This study is based on age determinations (230Th/U, 87Sr/86Sr) and geochemical signals (Mg/Li and Ba/Ca) measured in the scleractinian cold-water coral Lophelia pertusa from IODP Site 1317 in the Porcupine Seabight. The paleoceanographic reconstructions reveal that coral growth in the Porcupine Seabight was restricted to specific oceanographic conditions such as enhanced export of primary production and Bottom-Water Temperatures (BWT) between ∼8–10 °C, related to the water mass stratification of the Mediterranean Outflow Water (MOW) and Eastern North Atlantic Water (ENAW). The geochemical signals from the coral skeletons can be explained by the close interaction between cold-water coral growth, sea-surface productivity and the surrounding water masses - the boundary layer between MOW and ENAW. Enhanced sea-surface productivity and the build-up of a stable water mass stratification between ENAW and MOW caused enhanced nutrient supply at intermediate water depths and facilitated a steady mound growth between∼3.0 - 2.1 Ma. With the decrease in sea-surface productivity and related reduced export productivity the food supply was insufficient for rapid coral mound growth between∼1.7 - 1 Ma. During the late Pleistocene (over the last∼0.5 Myr) mound growth was restricted to interglacial periods. During glacials the water mass boundary between ENAW/MOW probably was below the mound summit and hence food supply was not sufficient for corals to grow.
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  • 6
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    Stable Sr-isotope, Sr/Ca, Mg/Ca, Li/Ca and Mg/Li ratios in the scleractinian cold-water coral Lophelia pertusa (2013)
    Elsevier
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    Publication Date: 2024-03-22
    Description: The aragonitic skeletons of scleractinian cold-water corals can serve as valuable archives in paleoceanographic studies. The potential of δ88/86Sr, Sr/Ca, Mg/Ca, Li/Ca and Mg/Li ratios of the cold-water coral Lophelia pertusa to record intermediate water mass properties has been investigated. Here we used samples from several locations along the European continental margin spanning a large temperature range from 6 to 14 °C. Stable strontium isotope measurements were carried out with the recently developed double spike TIMS technique and our results differ from those obtained with less precise methods. In contrast to the strong positive relationship with temperature of previous studies, our results suggest that δ88/86Sr measured in scleractinian cold-water corals is not controlled by seawater temperature, but reflects the Sr isotopic composition of seawater with an offset of Δ88/86Sr = − 0.196‰. As found in previous studies, the elemental ratios Sr/Ca, Li/Ca and Mg/Li measured in corals are significantly related to water temperature and do not correlate with salinity. Moreover, Sr/Ca ratios in L. pertusa display the expected inverse correlation with temperature. However, the variance in the Sr/Ca data severely limits the accuracy of paleotemperature estimates. The Li/Ca and Mg/Ca ratios reveal other influences besides temperature such as pH and/or growth or calcification rate. However, corresponding Mg/Li ratios in L. pertusa are more tightly related to temperature as they remove these secondary effects. In particular, the Mg/Li ratio in L. pertusa may serve as a new promising paleotemperature proxy for intermediate water masses. Our dataset represents the most extensive geochemical examination of L. pertusa to date, revealing a temperature sensitivity of 0.015 mol/mmol/°C for Mg/Li. However, using this temperature dependence and the precision of 5.3% (2SD) only temperature variations larger than ~ 1.5 °C can be resolved with 95% confidence.
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  • 7
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    Paleoenvironmental reconstruction of Challenger Mound initiation in the Porcupine Seabight, NE Atlantic (2011)
    Elsevier
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    Publication Date: 2024-03-22
    Description: The understanding of the paleoenvironment during initiation and early development of deep cold-water coral carbonate mounds in the NE Atlantic is currently a focus of international research. The Integrated Ocean Drilling Program (IODP) Expedition 307 drilled the 155 m high Challenger Mound in the Porcupine Seabight (SW off Ireland) in order to investigate for the first time sediments from the base of a giant carbonate mound. In this study we focus in high resolution on 12 m of sediments from Site 1317 encompassing the mound base. The mound initiation and start-up phase coincide with the intensification of the Northern Hemisphere Glaciation (INHG) at around 2.7 Ma. Further carbonate mound development seems to be strongly dependent on rapid changes in paleoceanographic and climatic conditions at the Pliocene–Pleistocene boundary, especially characterized and caused by the interaction of intermediate water masses, the Mediterranean Outflow Water (MOW), the Eastern North Atlantic Water (ENAW) and the influence of Southern Component Water (SCW). This study is based on well-established proxies such as δ18O and δ13C of planktonic (Globigerina bulloides) and benthic foraminifera (Fontbotia wuellerstorfi, Discanomalina coronata, Lobatula lobatula, Lobatula antarctica, and Planulina ariminensis) as well as grain size parameters to identify the paleoenvironmental and paleoecological setting favourable for the initial coral colonization on the mound. Stable oxygen and carbon isotope records of benthic foraminiferal species indicate that L. lobatula provides a reliable isotopic signature for paleoenvironmental reconstructions. In particular, δ18O values of L. lobatula indicate that initial mound growth started in a glacial mode with moderate excursions in δ18O values. Carbon isotope values of D. coronata are significantly offset compared to other epibenthic species. This offset may be related to vital effects. Bottom water temperatures, calculated using standard equations based on δ18O of foraminiferal tests, range between 7 and 11 °C, consistent with the known temperature range conducive for cold-water coral growth and development. Bottom currents transporting intermediate water masses of southern origin (Mediterranean and Bay of Biscay) enhanced at 2.6 Ma supporting first coral settlements with the INHG. The benthic δ13C and the sortable silt records indicate that the early Pleistocene hydrodynamic regime was characterized by weaker current intensities associated with vertical movements of MOW or its replacement by SCW at intermediate depth. After these sluggish phases enhanced MOW flow dominated again and led to stronger current intensities and most probably sediment erosion on Challenger Mound. Erosion in combination with early diagenetic (oxidation) processes overprinted the sediment layers as indicated by dissolved coral skeletons, the increase in Ca-content and sediment density, minimum δ13Cplanktonic values, as well as the occurrence of gypsum and pyrite, implying a careful evaluation of original and overprinted geochemical signals. We conclude that the Challenger Mound development was already influenced by short-term variability of water masses from southern origin and possible erosional events comparable to the late Pleistocene setting.
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  • 8
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    Semidiurnal tides in the Laptev Sea Shelf zone in the summer season (2014)
    Elsevier
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    Publication Date: 2024-01-01
    Description: Tidal processes play an important role in the dynamics of shelf circulation in the Laptev Sea. The Unstructured Grid Finite Volume Coastal Ocean Model (FVCOM) is used to simulate the tidal dynamics in the Lena Delta region of the Laptev Sea in ice-free barotropic case. The grid element size ranges from 400 m to 5 km. The major semidiurnal tidal waves M2M2 and S2S2 are investigated with the M2M2 being the most important in generating large sea level amplitudes and currents over shallow areas. A correction to the tidal elevation at the open boundary is proposed, which minimizes the discrepancy between the model prediction and observations. The observations include both recent mooring data and the standard set of tide gauge measurements used in previous studies. The comparison of results to known tidal solutions is carried out. The paper also discusses the residual circulation and energy fluxes and assesses the impact of additional bathymetric information. Highlights • Our simulations reproduce the semidiurnal tidal waves M2M2 and S2S2 in the Laptev Sea region. • We develop special procedure for the construction of optimal open boundary conditions for tidal elevation for M2M2 and S2S2 constituents. • The simulated tidal maps show an improved agreement with observations. • We analyze barotropic currents, residual circulation and evolution of energy fluxes in the region. • We consider the energy balance for the M2M2 and S2S2 waves and the sensitivity to the bathymetry.
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  • 9
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    Late Quaternary evolution of sediment provenances in the Central Arctic Ocean : mineral assemblage, trace element composition and Nd and Pb isotope fingerprints of detrital fraction from the Northern Mendeleev Ridge (2014)
    Elsevier
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    Publication Date: 2024-01-01
    Description: Mineral assemblage, trace element content and Nd and Pb isotope signatures were analysed on the fine fraction (〈20 μm) of sedimentary records from the Northern Mendeleev Ridge in the Central Arctic Ocean. Our aim was to identify the detrital particle provenance and to interpret the changes over the past ∼250 ka in the relative contribution of the different source-areas in relation to paleoenvironmental conditions. The clay mineral assemblage and the Nd and Pb isotope signatures depict systematic changes over the Late Quaternary. The bulk mineralogy exhibits increases in the relative contribution of carbonate minerals vs. silicates in interglacial/deglacial intervals. In glacial intervals, the mineral assemblage of the 〈20 μm fraction is characterised by an enrichment in kaolinite, counterbalanced by a decrease in illite. The Nd and Pb isotope signatures of 〈20 μm fraction are interpreted using a three end-member mixing model, involving crustal supplies from North America and Canada, from the Siberian margin and some from volcanic material. A compilation of geochemical signatures of geological terraines surrounding the Arctic Ocean allowed each end-member to be assigned a representative signature, averaging the signal of the eroded terraines. The Suspended Particulate Matter (SPM) of the MacKenzie River represents an average signature of the sedimentary supplies delivered from the North American platform and Canadian margin. The SPM of the Lena River reflects the mean sedimentary signature of the Siberian platform. The Okhotsh-Chukotka province from the Eastern border of Siberia is identified as the most probable volcanic source. Late Quaternary evolution of the estimated relative contribution of the three end-members confirms that the sediment provenances in the Central Arctic Ocean remain close to the current conditions during past interglacials/deglacials MIS1–3, MIS5/TII and MIS7/TIII. In contrast, glacial conditions (MIS4 and MIS6) record minimum supplies from the American margin, associated with increased volcanic contribution, to the Mendeleev Ridge core location suggesting a different sea-ice circulation associated with a low sea-level and reduced shelf area. Highlights • Nd and Pb isotope signatures of fine detrital sediment fraction are tracer of sources. • Glacial and interglacials are characterised by systematic changes in sediment sources. • The volcanic Okhotsh-Chukotka province has major contribution during glacials.
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  • 10
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    Bathymetric variations in vertical distribution patterns of meiofauna in the surface sediments of the deep Arctic ocean (HAUSGARTEN, Fram strait) (2014)
    Elsevier
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    Publication Date: 2024-01-01
    Description: Deep-sea benthic communities and their structural and functional characteristics are regulated by surface water processes. Our study focused on the impact of changes in water depth and food supplies on small-sized metazoan bottom-fauna (meiobenthos) along a bathymetric transect (1200–5500 m) in the western Fram Strait. The samples were collected every summer season from 2005 to 2009 within the scope of the HAUSGARTEN monitoring program. In comparison to other polar regions, the large inflow of organic matter to the sea floor translates into relatively high meiofaunal densities in this region. Densities along the bathymetric gradient range from approximately 2400 ind. 10 cm-2 at 1200 m to approximately 300 ind. 10 cm-2 at 4000 m. Differences in meiofaunal distribution among sediment layers (i.e., vertical profile) were stronger than among stations (i.e., bathymetric gradient). At all the stations meiofaunal densities and number of taxa were the highest in the surface sediment layer (0–1 cm), and these decreased with increasing sediment depth (down to 4–5 cm). However, the shape of the decreasing pattern differed significantly among stations. Meiofaunal densities and taxonomic richness decreased gradually with increasing sediment depth at the shallower stations with higher food availability. At deeper stations, where the availability of organic matter is generally lower, meiofaunal densities decreased sharply to minor proportions at sediment depths already at 2–3 cm. Nematodes were the most abundant organisms (60–98%) in all the sediment layers. The environmental factors best correlated to the vertical patterns of the meiofaunal community were sediment-bound chloroplastic pigments that indicate phytodetrital matter. Highlights • Small-scale heterogeneity is the main source of variation in meiofauna community. • Trophic conditions influence vertical patterns of meiofauna distribution. • Meiofauna abundance and biomass decrease with increasing water depth.
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  • 11
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    Appraisal of TEX86 and TEXL86 thermometries in subpolar and polar regions (2014)
    Elsevier
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    Publication Date: 2024-01-01
    Description: TEX86 (TetraEther indeX of tetraethers consisting of 86 carbon atoms) is a sea surface temperature (SST) proxy based on the distribution of archaeal isoprenoid glycerol dialkyl glycerol tetraethers (GDGTs). In this study, we appraise the applicability of TEX86 and View the MathML sourceTEX86L in subpolar and polar regions using surface sediments. We present TEX86 and View the MathML sourceTEX86L data from 160 surface sediment samples collected in the Arctic, the Southern Ocean and the North Pacific. Most of the SST estimates derived from both TEX86 and View the MathML sourceTEX86L are anomalously high in the Arctic, especially in the vicinity of Siberian river mouths and the sea ice margin, plausibly due to additional archaeal contributions linked to terrigenous input. We found unusual GDGT distributions at five sites in the North Pacific. High GDGT-0/crenarchaeol and GDGT-2/crenarchaeol ratios at these sites suggest a substantial contribution of methanogenic and/or methanotrophic archaea to the sedimentary GDGT pool here. Apart from these anomalous findings, TEX86 and View the MathML sourceTEX86L values in the surface sediments from the Southern Ocean and the North Pacific do usually vary with overlaying SSTs. In these regions, the sedimentary TEX86-SST relationship is similar to the global calibration, and the derived temperature estimates agree well with overlaying annual mean SSTs at the sites. However, there is a systematic offset between the regional View the MathML sourceTEX86L-SST relationships and the global calibration. At these sites, temperature estimates based on the global View the MathML sourceTEX86L calibration are closer to summer SSTs than annual mean SSTs. This finding suggests that in these subpolar settings a regional View the MathML sourceTEX86L calibration may be a more suitable equation for temperature reconstruction than the global calibration.
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  • 12
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    A state-of-the-art review of techno-economic models predicting the costs of CO2 pipeline transport (2013)
    Elsevier
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    Publication Date: 2023-12-12
    Description: This study aims to provide a systematic overview and comparison of capital and O&M costs models for CO2 pipelines and booster stations currently available in literature. Our findings indicate significantly large cost ranges for the results provided by the different cost models. Two main types of capital cost models for pipeline transport were found in literature, models relating diameter to costs and models relating mass flow to costs. For the nine diameter based models examined, a capital cost range is found of, for instance, 0.8–5.5 M€2010/km for a pipeline diameter of 0.8 m and a length of 25 km. For the five mass flow based cost models evaluated in this study, a cost range is found of, for instance, 0.9–2.1 M€2010/km for a mass flow of 750 kg/s over 25 km (TRUNK-25). An important additional factor is that all capital costs models for CO2 pipeline transport, directly or indirectly, depend on the diameter. Therefore, a systematic overview is made of the various equations and parameter used to calculate the diameter. By applying these equations and parameters to a common mass flow, height difference and length result in diameters between 0.59 and 0.91 m for TRUNK-25. The main reason for this range was different assumptions about specific pressure drop and velocity. Combining the range for diameter, mass flow and diameter based cost models gives a capital and levelized cost range which varied by a factor 10 for a given mass flow and length. The levelized cost range will further increase if the discrepancy in O&M costs is added, for which estimations vary between 4.5 and 75 €/m/year for a pipeline diameter of 0.8 m. On top of this, most cost models underestimate the capital costs of CO2 pipelines. Only two cost models (namely the models who relate the costs to the weight of the pipeline) take into account the higher material requirements which are typically required for CO2 pipelines. The other sources use existing onshore natural gas pipelines as the basis for their cost estimations, and thereby underestimating the material costs for CO2 pipelines. Additionally, most cost models are based on relatively old pipelines constructed in the United States in the 1990s and early 2000s and do not consider the large increase in material prices in the last several years. Furthermore, key model characteristics are identified for a general cost comparison of CCS with other technologies and a system analysis over time. For a general cost comparison of CCS with other technologies, pipeline cost models with parameters which have physical or economic meaning are the preferred option. These are easy to interpret and can be adjusted to new conditions. A linear cost model is an example of such an model. For a system analysis over time, it is advised to adapt a pipeline cost model related to the weight of the pipeline, which is the only cost model that specifically models thickness of the pipeline and include material prices, to incorporate the effect of impurities and pipeline technology development. For modeling booster station costs, a relation between capacity and costs including some economies of scale seems to be the most appropriate. However, the cost range found in literature is very large, for instance, 3.1–3.6 M€2010 for a booster station with a capacity of 1.25 MWe. Therefore, validation of the booster station cost is required before such models are applied in further research.
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  • 13
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    Toxicity of proton–metal mixtures in the field: Linking stream macroinvertebrate species diversity to chemical speciation and bioavailability (2010)
    Elsevier
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    Publication Date: 2023-11-29
    Description: Understanding metal and proton toxicity under field conditions requires consideration of the complex nature of chemicals in mixtures. Here, we demonstrate a novel method that relates streamwater concentrations of cationic metallic species and protons to a field ecological index of biodiversity. The model WHAM-FTOX postulates that cation binding sites of aquatic macroinvertebrates can be represented by the functional groups of natural organic matter (humic acid), as described by the Windermere Humic Aqueous Model (WHAM6), and supporting field evidence is presented. We define a toxicity function (FTOX) by summing the products: (amount of invertebrate-bound cation) × (cation-specific toxicity coefficient, αi). Species richness data for Ephemeroptera, Plecoptera and Trichoptera (EPT), are then described with a lower threshold of FTOX, below which all organisms are present and toxic effects are absent, and an upper threshold above which organisms are absent. Between the thresholds the number of species declines linearly with FTOX. We parameterised the model with chemistry and EPT data for low-order streamwaters affected by acid deposition and/or abandoned mines, representing a total of 412 sites across three continents. The fitting made use of quantile regression, to take into account reduced species richness caused by (unknown) factors other than cation toxicity. Parameters were derived for the four most common or abundant cations, with values of αi following the sequence (increasing toxicity) H+ 〈 Al 〈 Zn 〈 Cu. For waters affected mainly by H+ and Al, FTOX shows a steady decline with increasing pH, crossing the lower threshold near to pH 7. Competition effects among cations mean that toxicity due to Cu and Zn is rare at lower pH values, and occurs mostly between pH 6 and 8.
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    Geochemical and physical constraints for the occurrence of living cold-water corals (2014)
    Elsevier
    Details
    Publication Date: 2023-11-08
    Description: Cold-water coral communities cover a wide range of possible habitats in terms of latitude, ocean basins, and depth, with ongoing studies continually expanding occurrences in various regions of the global ocean. A range of factors determines the formation of cold-water coral reefs, such as physical, hydrochemical, and biological (e.g. food supply) factors. Recently, more and more modeling studies have emerged using a variety of mathematical approaches have emerged including environmental niche factor analysis (ENFA) and predictive habitat suitability models. However, only few studies have attempted to characterize the underlying suite of hydro-biogeochemical and physical constraints of cold-water coral reefs and to differentiate between pristine reef growth vs. sites with reduced or no coral occurrences. This study concentrates on new data and a compilation of existing data sets on the physical and chemical properties in the NE Atlantic and the Mediterranean. It explores the influence of ambient bottom waters and its characteristics on living cold-water reefs and mounds formed by Lophelia pertusa. Several questions are addressed: (1) what are the physical and geochemical boundary conditions of living cold-water corals? (2) Do these geochemical parameters correlate with proposed physical prerequisites? (3) Is there a general difference in the signature of living and dead coral sites?
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    A Perspective on Decadal Climate Variability and Predictability (2011)
    Elsevier
    Details
    Publication Date: 2023-11-08
    Description: The global surface air temperature record of the last 150 years is characterized by a long-term warming trend, with strong multidecadal variability superimposed. Similar multidecadal variability is also seen in other (societal important) parameters such as Sahel rainfall or Atlantic hurricane activity. The existence of the multidecadal variability makes climate change detection a challenge, since Global Warming evolves on a similar timescale. The ongoing discussion about a potential anthropogenic signal in the Atlantic hurricane activity is an example. A lot of work was devoted during the last years to understand the dynamics of the multidecadal variability, and external as well as internal mechanisms were proposed. This review paper focuses on two aspects. First, it describes the mechanisms for internal variability using a stochastic framework. Specific attention is given to variability of the Atlantic Meridional Overturning Circulation (AMOC), which is likely the origin of a considerable part of decadal variability and predictability in the Atlantic Sector. Second, the paper discusses the decadal predictability and the factors limiting its realisation. These include a poor understanding of the mechanisms involved and large biases in state-of-the-art climate models. Enhanced model resolution, improved subgrid scale parameterisations, and the inclusion of additional climate subsystems, such as a resolved stratosphere, may help overcome these limitations.
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    The toxicity of ozone-produced oxidants to the Pacific White Shrimp Litopenaeus vannamei (2010)
    Elsevier
    Details
    Publication Date: 2023-11-08
    Description: In marine recirculating aquaculture systems ozone, as a strong oxidant, is often used to improve water quality by reducing the pathogen load and removing inorganic and organic wastes. However, mainly when disinfection of recirculating water is desired, high ozone dosage is required, which may lead to toxicity problems for the cultured species. Acute toxicity of ozone-produced oxidants (OPO) to juvenile Pacific white shrimp, Litopenaeus vannamei, was assessed by determining the medium lethal concentration (LC50). Shrimp were exposed to a series of OPO concentrations for 96 h. Toxicity was analysed using standard probit regression. The 24, 48, 72 and 96 h LC50 values were 0.84, 0.61, 0.54 and 0.50 mg/l chlorine equivalent, respectively. A safe level for residual oxidant concentration was calculated and further verified by chronic exposure experiments. While long-term exposure of juvenile white shrimp to an OPO concentration of 0.06 mg/l revealed no observable effect, long-term exposures to 0.10 and 0.15 mg/l induced incidence of soft shell syndrome which led to mortalities due to cannibalism. Thus, an OPO concentration of 0.06 mg/l is suggested to be the maximum safe exposure level for rearing juvenile L. vannamei. Furthermore, we proved this safe level to be sufficient to control and reduce bacterial biomass in the recirculating process water.
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    Comparative mass balance of volcanic edifices at the Southern Volcanic Zone of the Andes between 33°S and 46°S (2011)
    Elsevier
    Details
    Publication Date: 2023-11-08
    Description: Volcano edifice volume calculations are presented for 65 volcanoes of the 1400 km long Chilean Southern Volcanic Zone (SVZ) as a basic step in subduction zone mass budgets. Volume calculations are performed in a Geographical Information System that integrates Digital Elevation Models based on of Shuttle Radar Topography Mission as well as ASTER-GDEM topographic data, LANDSAT satellite images and geological maps. The method of volume calculation is straightforward for isolated, morphologically well-defined stratovolcanoes. Uncertainties increase for volcanic edifices that formed on pre-existing rugged terrain, for multi-phase eruptive centers, as well as for eroded edifices. A revised segmentation of the arc is used to describe the spatial volume distribution of extruded magma along the SVZ and to discuss controlling tectonic factors. Peak volumes between arc and back arc are offset by 400 km. The total volcanic extrusion is in the range of 10–13 km3/km/Ma. Major differences between the SVZ and the Central American subduction system are notable with regard to volcano density and maximum volumes.
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    Parameter optimization and uncertainty analysis in a model of oceanic CO2 uptake using a hybrid algorithm and algorithmic differentiation (2010)
    Elsevier
    Details
    Publication Date: 2023-11-03
    Description: Methods and results for parameter optimization and uncertainty analysis for a one-dimensional marine biogeochemical model of NPZD type are presented. The model, developed by Schartau and Oschlies, simulates the distribution of nitrogen, phytoplankton, zooplankton and detritus in a water column and is driven by ocean circulation data. Our aim is to identify parameters and fit the model output to given observational data. For this model, it has been shown that a satisfactory fit could not be obtained, and that parameters with comparable fits can vary significantly. Since these results were obtained by evolutionary algorithms (EA), we used a wider range of optimization methods: A special type of EA (called quantum-EA) with coordinate line search and a quasi-Newton SQP method, where exact gradients were generated by Automatic/Algorithmic Differentiation. Both methods are parallelized and can be viewed as instances of a hybrid, mixed evolutionary and deterministic optimization algorithm that we present in detail. This algorithm provides a flexible and robust tool for parameter identification and model validation. We show how the obtained parameters depend on data sparsity and given data error. We present an uncertainty analysis of the optimized parameters w.r.t. Gaussian perturbed data. We show that the model is well suited for parameter identification if the data are attainable. On the other hand, the result that it cannot be fitted to the real observational data without extension or modification, is confirmed. (C) 2010 Elsevier Ltd. All rights reserved.
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  • 19
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    A stable (Li, O) and radiogenic (Sr, Nd) isotope perspective on metasomatic processes in a subducting slab (2011)
    Elsevier
    Details
    Publication Date: 2023-09-26
    Description: Two distinct types of eclogites from the Raspas Complex (Ecuador), which can be distinguished based on petrography and trace element geochemistry, were analyzed for their stable (Li, O) and radiogenic (Sr, Nd) isotope signature to constrain metasomatic changes due to fluid-overprinting in metabasaltic rocks at high-pressure conditions and to identify fluid sources. MORB-type eclogites are characterized by a relative LREE depletion similar to MORB. High-pressure (HP) minerals from this type of eclogite have highly variable oxygen isotope compositions (garnet: + 4.1 to + 9.8 ‰; omphacite: + 6.1 to + 11.0 ‰; phengite: 8.7 to 10.4 ‰; amphibole: 6.2 to 10.1 ‰) and generally show equilibrium oxygen isotope fractionation. Initial 87Sr/86Sr isotope ratios are also variable (0.7037-0.7063), whereas εNd130Ma values (+ 8.3 to + 11.0) are relatively similar. Sr and O isotopic compositional differences among rocks on outcrop scale, the preservation of O isotopic compositions of low-temperature altered oceanic crust, and Sr-Nd isotopic trends typical for seafloor alteration suggest inheritance from variably altered oceanic crust. However, decreasing δ7Li values (-0.5 to -12.9 ‰) with increasing Li concentrations (11-94 ppm) indicate Li isotope fractionation by diffusion related to fluid-rock interaction. Li isotopes prove to be a very sensitive tracer of metasomatism, although the small effects on the Sr-Nd-O isotope systems suggest that the fluid-induced metasomatic event in the MORB-type eclogites was small-scale at low-water/rock ratios. This metasomatic fluid is thought to predominantly derive from in situ dehydration of MORB-type rocks. Zoisite eclogites, the second eclogite type from the Raspas Complex, are characterized by the presence of zoisite and enrichment in many incompatible trace elements compared to the MORB-type eclogites. The zoisite eclogites have a homogenous Sr-Nd isotopic signature (Initial 87Sr/86Sr = 0.7075-0.7081, εNd130Ma = -6.7 to -8.7), interpreted to reflect a metasomatic overprint. The isotopic signature can be attributed to the metasomatic formation of zoisite because associated zoisite veins are isotopically similar. Relatively homogenous O isotope values for garnet (10.9-12.3 ‰) omphacite (9.4 to 10.8 ‰), amphibole (10.0-10.1 ‰) and zoisite (10.5-11.9 ‰) and inter-mineral O isotopic disequilibria are consistent with a metasomatic overprint via open-system fluid input. Li concentrations (46-76 ppm) and δ7Li values of the zoisite eclogites overlap the range of the MORB-type eclogites. The large amount of fluid required for isotopic homogenization, combined with the results from fluid inclusion studies, suggests that deserpentinization played a major role in generating the metasomatic fluid that altered the zoisite eclogites. However, influence of a (meta)sedimentary source is required based on Sr-Nd isotope data and trace element enrichments. The significant geochemical variation in the various eclogites generated by interaction with metasomatic fluids has to be considered in attempts to constrain recycling at convergent margins.
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    Magmatic evolution of a dying spreading axis: evidence for the interaction of tectonics and mantle heterogeneity from the fossil Phoenix Ridge, Drake Passage (2011)
    Elsevier
    Details
    Publication Date: 2023-09-19
    Description: New 40Ar-39Ar ages of 5.6 to 1.3 Ma for lavas from the fossil Phoenix Ridge in the Drake Passage show that magmatism continued for at least 2 Ma after the cessation of spreading at 3.3 ± 0.2 Ma. The Phoenix Ridge lavas are incompatible element-enriched relative to average MORB and show an increasing enrichment with decreasing age, corresponding to progressively decreasing degrees of partial melting of spinel peridotite after spreading stopped. The low-degree partial melts increasingly tap a mantle source with radiogenic Sr and Pb but unradiogenic Nd isotope ratios implying an ancient enrichment. The post-spreading magmas apparently form by buoyant ascent of enriched and easily fusible portions of the upper mantle. Only segments of fossil spreading ridges underlain by such enriched and fertile mantle show post-spreading volcanism frequently forming bathymetric highs. The Phoenix Ridge lavas belong to the Pacific, rather than the Atlantic, mantle domain in regional Sr-Nd-Pb space. Our new data show that the southern Pacific Ocean mantle is heterogeneous containing significant enriched portions that are preferentially tapped at low melt fractions. Isotopic mapping reveals that Pacific-type upper mantle flows eastward through Drake Passage and surrounds the subducting Phoenix Plate beneath the Bransfield Basin.
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  • 21
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    Comparative evaluation of preprocessing freeware on chromatography/mass spectrometry data for signature discovery (2014)
    Elsevier
    Details
    Publication Date: 2023-08-15
    Description: Preprocessing software, which converts large instrumental data sets into a manageable format for data analysis, is crucial for the discovery of chemical signatures in metabolomics, chemical forensics, and other signature-focused disciplines. Here, four freely available and published preprocessing tools known as MetAlign, MZmine, SpectConnect, and XCMS were evaluated for impurity profiling using nominal mass GC/MS data and accurate mass LC/MS data. Both data sets were previously collected from the analysis of replicate samples from multiple stocks of a nerve-agent precursor and method blanks. Parameters were optimized for each of the four tools for the untargeted detection, matching, and cataloging of chromatographic peaks from impurities present in the stock samples. The peak table generated by each preprocessing tool was analyzed to determine the number of impurity components detected in all replicate samples per stock and absent in the method blanks. A cumulative set of impurity components was then generated using all available peak tables and used as a reference to calculate the percent of component detections for each tool, in which 100% indicated the detection of every known component present in a stock. For the nominal mass GC/MS data, MetAlign had the most component detections followed by MZmine, SpectConnect, and XCMS with detection percentages of 83, 60, 47, and 41%, respectively. For the accurate mass LC/MS data, the order was MetAlign, XCMS, and MZmine with detection percentages of 80, 45, and 35%, respectively. SpectConnect did not function for the accurate mass LC/MS data. Larger detection percentages were obtained by combining the top performer with at least one of the other tools such as 96% by combining MetAlign with MZmine for the GC/MS data and 93% by combining MetAlign with XCMS for the LC/MS data. In terms of quantitative performance, the reported peak intensities from each tool had averaged absolute biases (relative to peak intensities obtained using instrument software) of 41, 4.4, 1.3 and 1.3% for SpectConnect, MetAlign, XCMS, and MZmine, respectively, for the GC/MS data. For the LC/MS data, the averaged absolute biases were 22, 4.5, and 3.1% for MetAlign, MZmine, and XCMS, respectively. In summary, MetAlign performed the best in terms of the number of component detections; however, more than one preprocessing tool should be considered to avoid missing impurities or other trace components as potential chemical signatures.
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    Development and evaluation of a fluorescence microplate assay for quantification of heparins and other sulfated carbohydrates (2010)
    Elsevier
    Details
    Publication Date: 2023-07-19
    Description: Due to their complex composition, quantification of heparins is difficult. On the one hand there are many biological tests, which only indirectly detect effects of the antithrombin-binding material. On the other hand direct quantitative methods are available but they are often insensitive, challenging, time-consuming or expensive. The aim of this study was to develop a sensitive, rapid, simple as well as inexpensive direct quantification assay suitable for routine analysis. Based on Polymer-H, a novel heparin complexing, fluorescent labeled synthetic polymer (λ(ex) 320 nm, λ(em) 510 nm), a microplate assay was developed and optimized. The specificity of the assay was evaluated by structure–assay response relationships studies using structurally defined glucan sulfates, heparins, and other natural and synthetic sulfated carbohydrates. The fluorescence intensity of Polymer-H (7.5 μg/ml) showed to be concentration-dependently amplified by heparins as well as by other sulfated carbohydrates. The best sensitivity, accuracy and linearity were observed in a range from 0.63 to 5.0 μg/ml heparins. No differences in the fluorescence between various heparins were observed, so that only one calibration curve is needed. In addition, all types of carbohydrates with a degree of sulfation (DS) 〉 ∼1.2 and a Mr 〉 3000 can be quantified as well. By own calibration curves also other sulfated carbohydrates like fondaparinux or other glycosaminoglycans (DS 〉 0.4) can be determined.
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  • 23
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    Limits to adaptation to climate change: a risk approach (2013)
    Elsevier
    Details
    Publication Date: 2023-06-30
    Description: As attention to adaptation to climate change increases, there is a growing call for adaptation approaches that focus on risk management. There is also greater recognition that the rate and magnitude of climate variability and change may exceed the limits to adaptation of socio-ecological systems. We offer an actor-centered, risk-based definition for adaptation limits in social systems. Specifically, we frame adaptation limits as the point at which an actor's objectives cannot be secured from intolerable risks through adaptive actions. These limits are significant because exceeding a limit will either result in intolerable losses on the affected actor or system, or precipitate a discontinuous (or transformational) change of behavior by actors. Such discontinuities in behavior have implications for the distribution of risks, with potentially significant governance consequences. We further argue that some adaptation limits are dynamic through time. We conclude with recommendations for further research into adaptation limits and challenges to risk governance.
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    Earth and Life Processes Discovered from Subseafloor Environment - A Decade of Science Achieved by the Integrated Ocean Drilling Program (IODP) (2014)
    Elsevier
    In:  EPIC3Amsterdam, Elsevier, 804 p., ISBN: 978-0-444-62617-2
    Details
    Publication Date: 2023-06-21
    Repository Name: EPIC Alfred Wegener Institut
    Type: Book , peerRev
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    Optimization and mathematical modeling of mass transfer between Zostera marina residues and supercritical CO2 modified with ethanol (2012)
    Elsevier
    Details
    Publication Date: 2023-06-19
    Description: Supercritical CO2 extraction of phenolic compounds from Zostera marina residues was optimized by developing a mathematical model based on mass transfer balances. A linear driving force model was applied considering model parameters such as solute concentration on the surface of the solid (Cs) and in the supercritical fluid phase (Cf), film mass transfer coefficient (kf) and molecular diffusivity (DAB) and axial dispersion (Dax) coefficients. Henry's law was used to describe the equilibrium state of solid and fluid phases. The results of the proposed model were compared to that of the experimental data in terms of transport properties and extraction yield at various temperatures (303.15, 323.15, 353.15 K), pressures (15, 25, 35 MPa) and co-solvent mass ratios (0, 10, 20%). The optimum parameters were elicited as 25 MPa, 353.15 K and a co-solvent ratio of 20% yielding 77.22 μg g−1 dry feed. The model satisfactorily described the extraction yield which can be used for scale-up purposes.
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    An integrated process for conversion of Zostera marina residues to bioethanol (2012)
    Elsevier
    Details
    Publication Date: 2023-06-19
    Description: Zostera marina is an aquatic plant forming wide grasslands and considered as the lungs of the marine ecosystems. However, the residues reaching the coastlines create nuisance and high costs are required for their disposal. The objective was to investigate the potential of Z. marina residues as a source of secondary metabolites and feedstock in order to propose alternative solutions to the landfill. The supercritical CO2 extract had a total phenol value of 55.4 mg GAE/g extract and a radical scavenging capacity of 71.4%. Considering the raffinate phase, 3% higher hemicellulose content was reached after supercritical CO2 treatment. Enzymatic hydrolysis revealed 31.45% and the yield of simultaneous saccharification and fermentation was 8.72% corresponding to a productivity of 0.273 kg/(m3 h). An integrated process is proposed, where supercritical fluid extraction can act both as the main process to obtain solvent-free pharmaceutical compounds and a pretreatment method in order to loosen the lignin structure, thereby liberating some of the hemicellulose in the matrix.
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  • 27
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    Diel Vertical Migration Behaviour of the Northern Krill (Meganyctiphanes norvegica Sars) (2010)
    Elsevier
    Details
    Publication Date: 2023-06-06
    Description: The prototype of Meganyctiphanes norvegica diel vertical migration (DVM) behaviour comprises ascent around dusk, feeding near the surface at night, and descent at dawn, explained as a trade-off between feeding and predator avoidance in an environment where both food and risk of predation is highest near surface. Light is the proximate cue, and daytime distribution is deeper in clear waters and sunny weather and nocturnal distributions deeper in moonlight. However, both internal state and external factors further affect and modify the diel migration pattern. While Meganyctiphanes migrates in synchrony to the surface at sunset, part of the population may descend soon after the ascent with individuals re-entering upper layers throughout the night. This has been explained with hungry individuals being prone to take larger risks and hence stay shallower, while satiated individuals seek shelter at depth. Females migrate closer to the surface than males of equivalent size, possibly due to their greater demand for energy to fuel egg production. Freshly moulted M. norvegica remain at depth throughout the diel cycle. This has been related to the fact that that krill do not feed during moulting, to reduced swimming capacity, and as a mechanism to avoid cannibalism whilst in a vulnerable condition. In some locations large parts of the population remain at depth at night. Such behaviour may incur access to demersal food sources, provide avoidance of predators, or can be a means to avoid horizontal transport to adjacent, unfavourable areas. Environmental gradients can arrest migrations of M. norvegica, yet the effect of physics is not always distinguished from associated biological properties, like subsurface maxima of phytoplankton located at pycnocline boundaries. Deeper nocturnal distribution when predators were abundant has been reported, and krill may adjust their distribution upwards when exposed to deep-living predators. Instantaneous escape to approaching predators is a common component of the anti-predator repertoire of Meganyctiphanes. Occasionally reported schooling behaviour that overrides normal DVM behaviour may serve anti-predation purposes, as well as being related to reproduction. M. norvegica can remain within confined areas, often defined by the bottom topography, even when exposed to strong currents. Behaviourally mediated retention may be accomplished by vertical migration in depth-stratified flows, but evidence for active use of DVM for the purpose of retention is so far circumstantial among M. norvegica. In several instances, large aggregations of krill that repeatedly occur in the same location appear to be accidental consequences of krill vertical migration behaviour interacting with the mean circulation and bottom topography, rather than representing active retention behaviour.
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    Structural characterization of novel extracellular liamocins (mannitol oils) produced by Aureobasidium pullulans strain NRRL 50380 (2013)
    Elsevier
    Details
    Publication Date: 2023-05-17
    Description: Aureobasidium pullulans is a common, ubiquitous fungus, which is used industrially to produce the polysaccharide pullulan. We have previously shown that A. pullulans produces various heavier-than-water oils, first named here as liamocins, that accumulate in fermentations. Here we report the structural characterization of four liamocins, A1, A2, B1, and B2, produced by A. pullulans strain NRRL 50380 using a combination of MALDI-TOF/MS, quadrupole-TOF/MS, isotopic labeling, NMR, GC/MS, and classical carbohydrate analysis. The data showed that the liamocins are composed of a single mannitol headgroup partially O-acylated with three (for liamocin A1 and A2) or four (for liamocin B1 and B2) 3,5-dihydroxydecanoic ester groups. Liamocins A1 and B1 are non-acetylated, whereas A2 and B2 each contain a single 3′-O-acetyl group. Each of these compounds is characterized by pseudomolecular [M+Na]+ ions in the MALDI-TOF/MS spectra at m/z 763.22, 949.35, 805.22, and 991.37, respectively. The 186 Da mass difference between A-type and B-type liamocins corresponds to one O-linked 3,5-dihydroxydecanoate group. HMBC NMR showed that one 3,5-dihydroxydecanoate carbonyl group is ester linked to a primary hydroxyl on the mannitol. Other long range 13C–1H couplings across 1,5-ester bridges showed that the 3,5-dihydroxydecanoate groups form 1–5-linked polyester chains, similar in structure to the antibiotic substance exophilin A. Moreover, the MS analysis identified several non-conjugated poly-3,5-dihydroxydecanoate esters as minor components that are tentatively assigned as exophilins A1, A2, B1, and B2. The liamocins, and three of the exophilins, are new, previously unreported structures.
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  • 29
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    Parameterising meso-scale eddy momentum fluxes based on potential vorticity mixing and a gauge term (2010)
    Elsevier
    Details
    Publication Date: 2023-03-09
    Description: Meso-scale fluctuations are known to drive large-scale zonal flows in the ocean, a mechanism which is currently missing in non-eddy-resolving ocean models. A closure for meso-scale eddy momentum fluxes is evaluated in a suite of idealised eddying channel models, featuring eddy-driven zonal jets. It is shown how the appearance of zonal jets, which act as mixing barriers for turbulent exchange, and reduced lateral diffusivities are linked in a natural way by implementing mixing of potential vorticity and using a gauge term to insure that no spurious forces are introduced. It appears, therefore, possible to parameterise the appearance of zonal jets and its effect on the ventilation of interior ocean basins in non-eddy-resolving, realistic ocean models.
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    The hafnium and neodymium isotope composition of seawater in the Atlantic sector of the Southern Ocean (2012)
    Elsevier
    Details
    Publication Date: 2023-03-09
    Description: We present the first combined dissolved hafnium (Hf) and neodymium (Nd) concentrations and isotope compositions of deep water masses from the Atlantic sector of the Southern Ocean. Eight full depth profiles were analyzed for Hf and twelve for Nd. Hafnium concentrations are generally depleted in the upper few hundred meters ranging between 0.2 pmol/kg and 0.4 pmol/kg and increase to relatively constant values of around 0.6 pmol/kg in the deeper water column. At the stations north of the Polar Front (PF), Nd concentrations increase linearly from about 10 pmol/kg at depths of ~ 200 m to up to 31 pmol/kg close to the bottom indicating particle scavenging and release. Within the Weddell Gyre (WG), however, Nd concentrations are essentially constant at 25 pmol/kg at depths greater than ~ 1000 m. The distributions of both elements show a positive correlation with dissolved silicon implying a close linkage to diatom biogeochemistry. Hafnium essentially shows invariant isotope compositions with values averaging at εHf = + 4.6, whereas Nd isotopes mark distinct differences between water masses, such as modified North Atlantic Deep Water (NADW, εNd = − 11 to − 10) and Antarctic Bottom Water (AABW, εNd = − 8.6 to − 9.6), but also waters locally advected via the Agulhas Current can be identified by their unradiogenic Nd isotope compositions. Mixing calculations suggest that a small fraction of Nd is removed by particle scavenging during mixing of water masses north of the PF. Nevertheless, the Nd isotope composition has apparently not been significantly affected by uptake and release of Nd from particles, as indicated by mixing calculations. A mixing envelope of an approximated North Pacific and a North Atlantic end-member shows that Nd isotope and concentration patterns in the Lower Circumpolar Deep Water (LCDW) can be fully explained by ~ 30:70 percentage contributions of these respective end-members.
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    A review of wastewater handling in the Arctic with special reference to pharmaceuticals and personal care products (PPCPs) and microbial pollution (2013)
    Elsevier
    Details
    Publication Date: 2023-02-21
    Description: Treatment of wastewater is often inadequate or completely lacking in Arctic regions. Wastewater contains different kinds of substances that can be harmful for the environment and human health, including residues of pharmaceuticals and personal care products. Bioaccumulation and biomagnifications of chemicals in the food web are of concern. This can affect fishery that is a significant industry in many Arctic coastal regions. Wastewater from human settlements may also contain antibiotic resistant bacteria and pathogens that can cause negative impacts on human health and the environment. In the Arctic, especially, the direct release of untreated sewage may have severe consequences for the receiving environment due to low biological diversity, low ambient temperatures and consequently high vulnerability of the Arctic ecosystem to environmental contaminants. Bucket toilets are common in remote settlements but are also used in towns. In settlements having inadequate sanitary facilities the risk of contracting diseases, such as hepatitis A, is unacceptably high. Conventional centralized wastewater collection systems and treatment plants are a challenge to build in the Arctic and expensive to operate. Thus alternative methods are needed. Possible solutions are improved dry or low flush toilets with collection of toilet waste at the household level and subsequent centralized treatment by dry composting or anaerobic digestion. Both treatment methods facilitate co-treatment of wastewater along with other organic waste fractions and provide a by-product that is environmentally safe and easy to handle. Combining the above with decentralized greywater treatment will reduce the costs for expensive infrastructure.
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    Shotgun proteomic analysis of the unicellular alga Ostreococcus tauri (2011)
    Elsevier
    Details
    Publication Date: 2023-02-21
    Description: Ostreococcus tauri is a unicellular green alga and amongst the smallest and simplest free-living eukaryotes. The O. tauri genome sequence was determined in 2006. Molecular, physiological and taxonomic data that has been generated since then highlight its potential as a simple model species for algae and plants. However, its proteome remains largely unexplored. This paper describes the global proteomic study of O. tauri, using mass spectrometry-based approaches: phosphopeptide enrichment, cellular fractionation, label-free quantification and 15N metabolic labeling. The O. tauri proteome was analyzed under the following conditions: sampling at different times during the circadian cycle, after 24 h of illumination, after 24 h of darkness and under various nitrogen source supply levels. Cell cycle related proteins such as dynamin and kinesin were significantly up-regulated during the daylight-to-darkness transition. This is reflected by their higher intensity at ZT13 and this transition phase coincides with the end of mitosis. Proteins involved in several metabolic mechanisms were found to be up-regulated under low nitrogen conditions, including carbon storage pathways, glycolysis, phosphate transport, and the synthesis of inorganic polyphosphates. Ostreococcus tauri responds to low nitrogen conditions by reducing its nitrogen assimilation machinery which suggests an atypical adaptation mechanism for coping with a nutrient-limited environment.
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    Growth- and nutrient-dependent gene expression in the toxigenic marine dinoflagellate Alexandrium minutum (2011)
    Elsevier
    Details
    Publication Date: 2023-02-16
    Description: The toxigenic marine dinoflagellate Alexandrium minutum forms toxic blooms causing paralytic shellfish poisoning (PSP), primarily in coastal waters, throughout the world. We examined effects on physiology and gene expression patterns associated with growth and nutrient starvation in a toxic strain of A. minutum. Bloom-relevant factors, including growth rate, intracellular toxin content, allelochemical activity and nutrient status were investigated in A. minutum cultures grown under different environmental regimes. Allelochemical activity of A. minutum cultures, quantified with a cryptomonad Rhodomonas bioassay, increased with age but was independent of nutrient status. The phenotypic data were integrated and compared with gene expression in cell samples taken at selected points along the growth curve. We observed 489 genes consistently differentially expressed between exponentially growing and growth-limited cultures. The expression pattern of stationary-phase cultures was characterized by conspicuous down-regulation of translation-associated genes, up-regulation of sequences involved in intracellular signalling and some indications of increased activity of selfish genetic elements such as transposons. Treatment-specific patterns included five genes regulated in parallel in all nutrient-limited cultures. The conspicuous decrease in photosynthetic performance identified in N-starved cultures was paralleled by down-regulation of chloroplast-associated genes. The particular gene expression patterns we identified as specifically linked with exponential growth, cessation of growth or nutrient limitation may be suitable biomarkers for indicating the beginning of growth limitation in field- or mesocosm studies.
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    The ecophysiology and bloom dynamics of Prymnesium spp. (2012)
    Elsevier
    Details
    Publication Date: 2023-02-15
    Description: Members of Prymnesium belong to the division Haptophyta, class Prymnesiophyceae, order Prymnesiales and family Prymnesiaceae. As most haptophytes, members of the genus Prymnesium are unicellular and planktonic. The most known of these species is the ichthyotoxic P. parvum, which may form nearly monospecific dense blooms in coastal and inland waters. This species possesses extraordinary plasticity concerning life survival strategies, and is specifically addressed in this review. Toxins produced by P. parvum have hemolytic properties, that not only kill fish but also co-existing plankton. These substances are allelopathic (when other algae are killed) and grazer deterrent (when grazers are killed). Allelopathy enables P. parvum to utilize inorganic nutrients present in the surrounding water without competition from other algal species; and by eliminating its grazers P. parvum reduces cell losses. The paralized microalgae and/or zooplankton, are therefter ingested by the P. parvum cells, a process called phagotrophy. P. parvum is also able of osmotrophy, i.e. utilization of dissolved organic matter. In this review, the cellular characteristics, life cycles, bloom formation, and factors affecting toxicity, allelopathy, phagotrophy, and osmotrophy of P. parvum are discussed.
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    Transcriptomic response of the toxic prymnesiophyte Prymnesium parvum (N. Carter) to phosphorus and nitrogen starvation (2012)
    Elsevier
    Details
    Publication Date: 2023-02-15
    Description: The ichthyotoxic and mixotrophic prymnesiophyte Prymnesium parvum is known to produce dense virtually monospecific blooms in marine coastal, brackish, and inshore waters. Fish-killing Pyrmnesium blooms are often associated with macronutrient imbalanced conditions based upon shifts in ambient nitrogen (N):phosphorus (P) ratios. We therefore investigated nutrient-dependent cellular acclimation mechanisms of this microalga based upon construction of a normalized expressed sequence tag (EST) library. We then profiled the transcriptome of P. parvum under nutrient-replete conditions as well as under nitrogen (N) and phosphorus (P) limitation via microarray analyses. Twenty-three genes putatively involved in acclimation to low nutrient levels were identified, among them three phosphate transporters, which were highly upregulated under P-starvation. In contrast, the expression of genes involved in transport and acquisition of ammonium or nitrate/nitrite was unaltered in N-starved cells. We propose that genes upregulated under P- or N-starvation lend themselves as potential tools to monitor nutrient limitation effects at the cellular level and indirectly the potential for initiation and maintenance of toxic blooms of P. parvum.
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    Nitrogen uptake kinetics of Prymnesium parvum (Haptophyte) (2011)
    Elsevier
    Details
    Publication Date: 2023-02-15
    Description: The uptake rates of different nitrogen (N) forms (NO3−, urea, and the amino acids glycine and glutamic acid) by N-deficient, laboratory-grown cells of the mixotrophic haptophyte, Prymnesium parvum, were measured and the preference by the cells for the different forms determined. Cellular N uptake rates (ρcell, fmol N cell−1 h−1) were measured using 15N-labeled N substrates. P. parvum showed high preference for the tested amino acids, in particular glutamic acid, over urea and NO3− under the culture nutrient conditions. However, extrapolating these rates to Baltic Seawater summer conditions, P. parvum would be expected to show higher uptake rates of NO3− and the amino acids relative to urea because of the difference in average concentrations of these substrates. A high uptake rate of glutamic acid at low substrate concentrations suggests that this substrate is likely used through extracellular enzymes. Nitrate, urea and glycine, on the other hand, showed a non-saturating uptake over the tested substrate concentration (1–40 μM-N for NO3− and urea, 0.5–10 μM-N for glycine), indicating slower membrane-transport rates for these substrates.
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    Effects of nitrogen supply and its composition on the growth of Prorocentrum donghaiense (2012)
    Elsevier
    Details
    Publication Date: 2023-02-15
    Description: In order to better understand the complex nitrogen (N) dynamics contributing to blooms of the harmful alga, Prorocentrum donghaiense, in eutrophic environments, we compared the growth of this organism on various forms of dissolved inorganic (nitrate and ammonium) and organic N (urea, glutamic acid, peptides and cyanate) compounds both individually and in combination. Growth rates of P. donghaiense were comparable in cultures grown with ammonium, nitrate, urea, glutamic acid, or the dipeptide phenylalanine-alanine as the sole source of N. P. donghaiense could also grow with cyanate or dialanine as sole sources of N, but at lower rates. Different DONurea, glutamic acid or diala:DINnitrate or ammonium ratios and nitrate:ammonium ratios also affected the growth of P. donghaiense. Growth rates of cultures acclimated on media with combinations of nitrate or ammonium and DON (urea, glutamic acid or alanine-alanine), grew faster than those growing on DON alone. The ratio of nitrate:ammonium in the growth media had little effect on the growth of P. donghaiense. Our uptake experiments exhibited complicated interactions among different nutrients. Nitrate uptake was inhibited by ammonium, glutamic acid and urea. In contrast, ammonium uptake was stimulated by urea and glutamic acid. Further research is needed to understand how the complex mixture of N compounds found in natural systems contributes to the growth and proliferation of P. donghaiense in the environment as this has implications for nutrient management. Because nitrate concentrations are elevated in areas prone to P. donghaiense blooms, nutrient reductions have targeted nitrate. The results presented here suggest that total N loads must be reduced to prevent blooms of this organism in coastal waters.
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    Contribution of phagotrophy versus autotrophy to Prymnesium parvum growth under nitrogen and phosphorus sufficiency and deficiency (2010)
    Elsevier
    Details
    Publication Date: 2023-02-15
    Description: Laboratory experiments were conducted to test the effects of nitrogen (N) and phosphorus (P) sufficiency and deficiency on mixotrophy in Prymnesium parvum (Haptophyta). P. parvum was grown with and without algal prey (Rhodomonas salina) and observed for 120 h. Detection and enumeration of cells containing food vacuoles with prey (i.e. phagotrophy) was based on flow cytometric detection of fluorescence of an acidotropic probe. Overall, the presence of R. salina increased phagotrophy in P. parvum suggesting that, at least in this strain of P. parvum, the presence of suitable prey can stimulate phagotrophic behavior in P. parvum. Feeding frequency (the percentage of P. parvum cells containing food vacuoles in a given time) was significantly higher under N and P deficiency than in the nutrient-sufficient treatments. A nutrient budget constructed from the data indicated that ingestion of organic matter (OM) supplied with 78 ± 7% of the N (3.9 ± 0.3 μM) incorporated by P. parvum in the N-deficient treatment, and 45 ± 9% of the P (0.3 ± 0 μM) acquired in the P-deficient cultures. Even under nutrient sufficiency, ingestion of OM was estimated to have supplied 43 ± 16% of the N and 48 ± 16% of the P incorporated into P. parvum cells. Phagotrophy was observed even in the NP-sufficient cultures (non-axenic mixed and monocultures), although P. parvum cells did not lose their photosynthetic capability, suggesting that phagotrophy is probably a permanent nutritional adaptation to this species. The ingestion of organic nutrients played an important role in P. parvum growth, being a reliable source of nutrition for P. parvum inorganic nutrient limitation, and could explain its capabilities to form persistent blooms.
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    Combining various strategies to increase the coverage of the plant cell wall glycoproteome (2011)
    Elsevier
    Details
    Publication Date: 2023-02-09
    Description: Glycoproteomics recently became a very active field, mostly in mammals. The first part of this paper consists of a mini-review on the strategies used in glycoproteomics, namely methods for enrichment in glycoproteins and mass spectrometry (MS) techniques currently used. In a second part, these strategies are applied to the cell wall glycoproteome of etiolated hypocotyls of Arabidopsis thaliana, showing their complementarity. Several sub-glycoproteomes were obtained by: (i) affinity chromatography on concanavaline A (ConA) and analysis of glycoproteins by MALDI-TOF MS; (ii) multidimensional lectin chromatography (using AIL, PNA, ConA and WGA lectins) and subsequent identification of glycoproteins by MALDI-TOF MS and LC–MS/MS; (iii) boronic acid chromatography followed by identification of glycoproteins by MALDI-TOF MS. Altogether, 127 glycoproteins were identified. Most glycoproteins were found to be putative N-glycoproteins and N-glycopeptides were predicted from MS data using the ProTerNyc bioinformatics software.
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    Uptake of alkaline earth metals in Alcyonarian spicules (Octocorallia) (2012)
    Elsevier
    Details
    Publication Date: 2023-01-31
    Description: Alcyonarian corals (Octocorallia) living in shallow tropical seas produce spicules of high-Mg calcite with ∼13 mol% MgCO3. We cultured the tropical alcyonarian coral Rhythisma fulvum in experiments varying temperature (19–32 °C) and pH (8.15–8.44). Alkalinity depletion caused by spicule formation systematically varied in the temperature experiments increasing from 19 to 29 °C. Spicules were investigated for their elemental ratios (Mg/Ca, Sr/Ca) using ICP-OES, δ44/40Ca using TIMS, as well as δ18O and δ13C by IRMS. Mg/Ca increased with temperature from 146 to 164 mmol/mol, in good agreement with the range observed for marine inorganic calcite. Mg/Ca increased by 1.0 ± 0.4 mmol/mol/°C, similar to the sensitivity of Miliolid foraminifera. The pH experiments revealed a linear relationship between Mg/Ca and carbonate ion concentration of +0.03 ± 0.02 mmol/mol/μMol. Sr/Ca ranges from 2.5 to 2.9 mmol/mol being in good agreement with other high-Mg calcites. Temperature and pH experiments showed linear dependencies of Sr/Ca matching inorganic calcite trends and pointing to a decoupling of crystal precipitation rate and calcification rate. Ca isotopes range between 0.7‰ and 0.9‰ in good agreement with aragonitic scleractinian corals and calcitic coccoliths. Presumably Ca isotopes are fractionated by a biological mechanism that may be independent of the skeletal mineralogy. We observe no temperature trend, but a significant decrease of δ44/40Ca with increasing pH. This inverse correlation may characterise biologically controlled intracellular calcification. Oxygen isotope ratios are higher than expected for isotopic equilibrium with a temperature sensitivity of −0.15 ± 0.03‰/°C. Carbon isotope ratios are significantly lower than expected for equilibrium and positively correlated with temperature with a slope of 0.20 ± 0.04‰/°C. Many of our observations on trace element incorporation in R. fulvum may be explained by inorganic processes during crystal formation, which do not comply with the intracellular mode of calcification in Alcyonarian corals. The observed elemental and isotopic compositions, however, could be explained if the partitioning caused by biological mechanisms mimics the effects of inorganic processes.
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    Composition and timing of carbonate vein precipitation within the igneous basement of the Early Cretaceous Shatsky Rise, NW Pacific (2014)
    Elsevier
    Details
    Publication Date: 2023-01-31
    Description: Numerous calcium carbonate veins were recovered from the igneous basement of the Early Cretaceous Shatsky Rise during Integrated Ocean Drilling Program (IODP) Expedition 324. The chemical (Sr/Ca, Mg/Ca) and isotopic (87Sr/86Sr, 143Nd/144Nd, !18O, !13C) compositions of these veins were determined to constrain the timing of vein formation. A dominant control by seawater chemistry on calcite composition is evident for most vein samples with variable contributions fromthe basaltic basement. Slightly elevated precipitation temperatures (as inferred from oxygen isotope ratios), indicative of hydrothermal vein formation, are only observed at Site U1350 in the central part of Shatsky Rise. The highest 87Sr/86Sr ratios (least basement influence) of vein samples at each drill site range from 0.70726 to 0.70755 and are believed to reflect the contemporaneous seawater composition during the time of calcite precipitation. In principle, age information can be deduced by correlating these ratios with the global seawater Sr isotope evolution. Since the Sr isotopic composition of seawater has fluctuated three times between the early and mid Cretaceous, no unambiguous precipitation ages can be constrained by this method and vein precipitation could have occurred at any time between ~80 and 140 Ma. However, based on combined chemical and isotopic data and correlations of vein compositionwith formation depth and inferred temperature, we argue for a rather early precipitation of the veins shortly after basement formation at each respective drill site.
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    Simulating the biogeochemical effects of volcanic CO2 degassing on the oxygen-state of the deep ocean during the Cenomanian/Turonian Anoxic Event (OAE2) (2011)
    Elsevier
    Details
    Publication Date: 2023-01-31
    Description: Cretaceous anoxic events may have been triggered by massive volcanic CO2 degassing as large igneous provinces (LIPs) were emplaced on the seafloor. Here, we present a comprehensive modeling study to decipher the marine biogeochemical consequences of enhanced volcanic CO2 emissions. A biogeochemical box model has been developed for transient model runs with time-dependent volcanic CO2 forcing. The box model considers continental weathering processes, marine export production, degradation processes in the water column, the rain of particles to the seafloor, benthic fluxes of dissolved species across the seabed, and burial of particulates in marine sediments. The ocean is represented by twenty-seven boxes. To estimate horizontal and vertical fluxes between boxes, a coupled ocean–atmosphere general circulation model (AOGCM) is run to derive the circulation patterns of the global ocean under Late Cretaceous boundary conditions. The AOGCM modeling predicts a strong thermohaline circulation and intense ventilation in the Late Cretaceous oceans under high pCO2 values. With an appropriate choice of parameter values such as the continental input of phosphorus, the model produces ocean anoxia at low to mid latitudes and changes in marine δ13C that are consistent with geological data such as the well established δ13C curve. The spread of anoxia is supported by an increase in riverine phosphorus fluxes under high pCO2 and a decrease in phosphorus burial efficiency in marine sediments under low oxygen conditions in ambient bottom waters. Here, we suggest that an additional mechanism might contribute to anoxia, an increase in the C:P ratio of marine plankton which is induced by high pCO2 values. According to our AOGCM model results, an intensively ventilated Cretaceous ocean turns anoxic only if the C:P ratio of marine organic particles exported into the deep ocean is allowed to increase under high pCO2 conditions. Being aware of the uncertainties such as diagenesis, this modeling study implies that potential changes in Redfield ratios might be a strong feedback mechanism to attain ocean anoxia via enhanced CO2 emissions. The formation of C-enriched marine organic matter may also explain the frequent occurrence of global anoxia during other geological periods characterized by high pCO2 values.
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    Uncertainty in climate change projections (2011)
    Elsevier
    Details
    Publication Date: 2023-01-31
    Description: Twentieth century climate exhibits a strong warming trend. There is a broad scientific consensus that the warming contains a significant contribution from enhanced atmospheric greenhouse gas (GHG) concentrations due to anthropogenic emissions. The climate will continue to warm during the 21st century due to the large inertia of the Earth System and in response to additional GHG emissions, but by how much remains highly uncertain. This is mainly due to three factors: natural variability, model uncertainty, and GHG emission scenario uncertainty. Uncertainty due to natural variability dominates at short time scales of a few years up to a few decades, while at the longer centennial time scales scenario uncertainty provides the largest contribution to the total uncertainty. Model uncertainty is important at all lead times. Furthermore, our understanding of the Earth System dynamics is incomplete. Potentially important feedbacks such as the carbon cycle feedback are not well understood and not even taken into account in many model projections. Yet the scientific evidence is overwhelming that global mean surface temperature will exceed a level toward the end of the 21st century that will be unprecedented during the history of mankind, even if strong measures are taken to reduce global GHG emissions. It is this long-term perspective that demands immediate political action.
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    Carbohydrates analysis in herbal glycomics (2013)
    Elsevier
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    Publication Date: 2023-01-27
    Description: Herbs serve primary healthcare needs and some herbs are widely used as functional foods. Analysis of carbohydrates is essential to understand their structure–function relationships in food science and herbal medicine. However, accurately defining chemical structures of glycans is a challenge due to their chemical heterogeneity and diversity. We review and discuss carbohydrates as new functional ingredients in herbs and functional foods, and their analysis, a novel aspect in quality control and herbal glycomics.
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    Dynamic plumbing system beneath volcanoes revealed by kinetic modeling, and the connection to monitoring data: An example from Mt. Etna (2012)
    Elsevier
    Details
    Publication Date: 2023-01-27
    Description: Our ability to monitor volcanoes (using seismic signals, ground deformation, gas fluxes, or other ground and satellite based observations) as well as our understanding of melt reservoirs that feed eruptions have evolved tremendously in recent years. The complex plumbing systems that are thought to feed eruptions are, however, difficult to relate to the monitoring signals. Here we show that the record preserved in compositional zoning of erupted minerals may be used to reconstruct sections of the plumbing system. Kinetic modeling of such zoning can yield information on the residence time of magma in different segments of the plumbing systems. This allows a more nuanced evaluation of the link between observed monitoring signals or eruption styles and the magmatic processes and movement of batches of melts at depth. The approach is illustrated through a study of the compositional zoning recorded in olivine crystals from the 1991–1993 SE-flank eruption products of Mt. Etna (Sicily). The zoning patterns in crystals reveal that the plumbing system of the volcano consisted of at least three different magmatic environments between which magma was transported and mixed in the year or two preceding the start of eruption. Quantification of this history indicates that two main pathways of melt migration and three timescales dominated the dynamics of the system. Combination of this information with the timing of observation of various monitoring signals allows a reconstruction of the dynamic evolution of this section of the plumbing system during the early stages of the 1991–1993 eruption. It is seen, for example, how the migration of melt through the same sections of the plumbing system can cause pre-eruptive triggering, enhance Strombolian activity, and through the ensuing eruption cleanse and flush the plumbing system. Different kinds of mixing occur simultaneously at different sections of the plumbing system on different timescales (a few days up to two years).
    Description: Published
    Description: 11-22
    Description: 1.5. TTC - Sorveglianza dell'attività eruttiva dei vulcani
    Description: 2.3. TTC - Laboratori di chimica e fisica delle rocce
    Description: 3.5. Geologia e storia dei vulcani ed evoluzione dei magmi
    Description: JCR Journal
    Description: reserved
    Keywords: Etna ; plumbing system ; olivine ; zoning ; timescales ; monitoring ; 04. Solid Earth::04.04. Geology::04.04.05. Mineralogy and petrology ; 04. Solid Earth::04.08. Volcanology::04.08.03. Magmas ; 04. Solid Earth::04.08. Volcanology::04.08.05. Volcanic rocks
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    South Pacific dissolved Nd isotope compositions and rare earth element distributions: Water mass mixing versus biogeochemical cycling (2014)
    Elsevier
    Details
    Publication Date: 2023-01-23
    Description: Despite its enormous extent and importance for global climate, the South Pacific has been poorly investigated in comparison to other regions with respect to chemical oceanography. Here we present the first detailed analysis of dissolved radiogenic Nd isotopes (εNd) and rare earth elements (REEs) in intermediate and deep waters of the mid-latitude (∼40°S) South Pacific along a meridional transect between South America and New Zealand. The goal of our study is to gain better insight into the distribution and mixing of water masses in the South Pacific and to evaluate the validity of Nd isotopes as a water mass tracer in this remote region of the ocean. The results demonstrate that biogeochemical cycling (scavenging processes in the Eastern Equatorial Pacific) and release of LREEs from the sediment clearly influence the distribution of the dissolved REE concentrations at certain locations. Nevertheless, the Nd isotope signatures clearly trace water masses including AAIW (Antarctic Intermediate Water) (average εNd = −8.2 ± 0.3), LCDW (Lower Circumpolar Deep Water) (average εNd = −8.3 ± 0.3), NPDW (North Pacific Deep Water) (average εNd = −5.9 ± 0.3), and the remnants of NADW (North Atlantic Deep Water) (average εNd = −9.7 ± 0.3). Filtered water samples taken from the sediment–water interface under the deep western boundary current off New Zealand suggest that boundary exchange processes are limited at this location and highlight the spatial and temporal variability of this process. These data will serve as a basis for the paleoceanographic application of Nd isotopes in the South Pacific.
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    Isolation and identification of chitin in three-dimensional skeleton of Aplysina fistularis marine sponge (2013)
    Elsevier
    Details
    Publication Date: 2022-12-14
    Description: The recent discovery of chitin within skeletons of numerous marine and freshwater sponges (Porifera) stimulates further experiments to identify this structural aminopolysaccharide in new species of these aquatical animals. Aplysina fistularis (Verongida: Demospongiae: Porifera) is well known to produce biologically active bromotyrosines. Here, we present a detailed study of the structural and physico-chemical properties of the three-dimensional skeletal scaffolds of this sponge. Calcofluor white staining, Raman and IR spectroscopy, ESI-MS as well as chitinase digestion test were applied in order to unequivocally prove the first discovery of α-chitin in skeleton of A. fistularis.
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    Diversity, ecological role and potential biotechnological applications of marine fungi associated to the seagrass Posidonia oceanica (2013)
    Elsevier
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    Publication Date: 2022-08-30
    Description: The marine environment is characterized by high salinity and exerts a strong selective pressure on the biota, favouring the development of halo-tolerant microorganisms. Part of this microbial diversity is made up of fungi, important organisms from ecological and biotechnological points of view. In this study, for the first time, the qualitative and quantitative composition of the mycoflora associated to leaves, rhizomes, roots and matte of the seagrass Posidonia oceanica was estimated. A total of 88 fungal taxa, mainly belonging to Ascomycota, were identified by morphological and molecular methods. The most represented genera were Penicillium, Cladosporium and Acremonium. Most of the species (70) were selectively associated with one district; only two species (Penicillium chrysogenum var. chrysogenum and P. janczewskii) were isolated from all the districts. Moreover the capability to produce laccases, peroxidases and tannases by 107 fungal isolated by the different districts of P. oceanica was carried out. These results show that the mycoflora associated to P. oceanica is very rich and characterized by fungi able to produce ligninolytic enzymes and tannases useful to degrade and detoxify lignocellulose residues in presence of high salt concentrations. These fungi, hence, may play important ecological roles in marine environments but can also be very useful in different biotechnological areas.
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    Stratigraphic evidence for a “pluvial phase” between ca 8200–7100 ka from Renella cave (Central Italy) (2012)
    Elsevier
    Details
    Publication Date: 2022-08-25
    Description: A stratigraphic and chronological study of the upper level of Renella Cave (Apuan Alps, Central Italy) reveals that two episodes of flowstone accumulation bracket a thick clastic layer deposited between ca 8.2 and 7.1 ka. This layer, which represents a period of enhanced cave flooding, is substantially in phase with an interval of depleted oxygen isotope values previously recorded in a stalagmite from nearby Corchia Cave, interpreted to have resulted from an increase in local precipitation. These data confirm that during this period of time the region experienced relatively wetter conditions, including an increase in high-magnitude events capable of invading the higher passages of Renella Cave. The timing of the clastic phase occurred when the Eastern Mediterranean experienced deposition of sapropel layer S1, which is thought to reflect the stagnation of sea water produced largely by enhanced flood activity along the Nile in response to increased monsoon intensity in northern equatorial Africa. Recent estimates suggest that S1 may have lasted from ca 10.8 to ca 6.1 ka cal BP. Combined evidence from Renella and Corchia Cave indicates that the period corresponding to the wettest phase in the Apuan Alps was much shorter than this, and suggests that there is no straightforward connection between increased advection of water vapour from the Atlantic between 8.2 and 7.1 ka, as recorded in the Corchia and Renella records, and monsoon-driven enhancement of Nile discharge and S1 deposition in the eastern Mediterranean.
    Description: Published
    Description: 409-417
    Description: 3.7. Dinamica del clima e dell'oceano
    Description: JCR Journal
    Description: reserved
    Keywords: Speleothems ; Floods ; Paleoclimate ; Holocene ; Renella cave ; Italy ; 03. Hydrosphere::03.01. General::03.01.06. Paleoceanography and paleoclimatology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    Environmental variability in northeastern Siberia during the last ~13,300 yr inferred from lake diatoms and sediment-geochemical parameters (2012)
    Elsevier
    In:  EPIC3Palaeogeography, Palaeoclimatology, Palaeoecology, Elsevier, 329-33, pp. 22-36
    Details
    Publication Date: 2022-08-12
    Repository Name: EPIC Alfred Wegener Institut
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    Phytophthora gemini sp. nov., a new species isolated from the halophilic plant Zostera marina in the Netherlands (2011)
    Elsevier
    Details
    Publication Date: 2022-06-21
    Description: Eight strains belonging to the Oomycete genus Phytophthora were isolated from Zostera marina (seagrass) in The Netherlands over the past 25 y. Based on morphology, isozymes, temperature–growth relationships and ITS sequences, these strains were found to belong to two different Phytophthora species. Five strains, four of them isolated from rotting seeds and one isolated from decaying plants, could not be assigned to a known species and hence belong to a new species for which we propose the name Phytophthora gemini sp. nov. Three strains were isolated from decaying plants and were identified as Phytophthora inundata, thereby expanding the known habitat range of this species from fresh to brackish-saline areas. The possible role of both Phytophthora species in the decline of Z. marina in The Netherlands and the evolutionary significance of the presence of Phytophthora species in marine environments are discussed.
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  • 52
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    Adventive hydrothermal circulation on Stromboli volcano (Aeolian Islands, Italy) revealed by geophysical and geochemical approaches: Implications for general fluid flow models on volcanoes (2011)
    Elsevier
    Details
    Publication Date: 2022-06-13
    Description: On March 15th 2007 a paroxysmal explosion occurred at the Stromboli volcano. This event generated a large amount of products,mostly lithic blocks, someofwhich impacted the ground as far as down to 200 m a.s.l., about 1.5 kmfaraway fromthe active vents. Two days after the explosion, a newvapouremissionwas discovered on the north-eastern flank of the volcanic edifice, at 560 m a.s.l., just above the area called “Nel Cannestrà”. This new vapour emission was due to a block impact. In order to investigate the block impact area to understand the appearance of the vapour emission, we conducted on May 2008 a multidisciplinary study involving Electrical Resistivity Tomography (ERT), Ground Penetrating Radar (GPR), Self-Potential (SP), CO2 soil diffuse degassing and soil temperature surveys. This complementary data set revealed the presence of an anomalous conductive body, probably related to a shallow hydrothermal level, at about 10–15 m depth, more or less parallel to the topography. It is the first time that such a hydrothermal fluid flow,with a temperature close to thewater boiling point (76 °C) has been evidenced at Stromboli at this low elevation on the flank of the edifice. The ERT results suggest a possible link between (1) the main central hydrothermal system of Stromboli, located just above the plumbing system feeding the active vents, with a maximum of subsurface soil temperature close to 90 °C and limited by the NeoStromboli summit crater boundary and (2) the investigated area of Nel Cannestrà, at ~500 m a.s.l., a buried eruptive fissure active 9 ka ago. In parallel, SP and CO2 soil diffuse degassingmeasurements suggest in this sector at slightly lower elevation fromthe block impact crater a magmatic and hydrothermal fluid rising system along the N41° regional fault. A complementary ERT profile, on May 2009, carried out from the NeoStromboli crater boundary downto the block impact crater displayed a flank fluid flowapparently connected to a deeper system. The concept of shallow hydrothermal level have been compared to similar ERT results recently obtained onMount Etna and La Fossa cone of Vulcano. This information needs to be taken into account in general fluid flow models on volcanoes. In particular, peripheral thermal waters (as those bordering the northeastern coast of Stromboli) could be contaminated by hydrothermal and magmatic fluids coming from regional faults but also from the summit.
    Description: Published
    Description: 111-119
    Description: 1.2. TTC - Sorveglianza geochimica delle aree vulcaniche attive
    Description: 1.5. TTC - Sorveglianza dell'attività eruttiva dei vulcani
    Description: JCR Journal
    Description: reserved
    Keywords: Stromboli ; hydrothermal system ; adventive hydrothermal flow ; electrical resistivity tomography ; self-potential ; soil diffuse degassing ; temperature ; 2007 Stromboli eruptive crisis ; 04. Solid Earth::04.08. Volcanology::04.08.04. Thermodynamics ; 04. Solid Earth::04.08. Volcanology::04.08.07. Instruments and techniques
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 53
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    Human peopling of Italian intramontane basins: The early Middle Pleistocene site of Pagliare di Sassa (L’Aquila, central Italy) (2010)
    Elsevier
    Details
    Publication Date: 2022-06-09
    Description: Multidisciplinary investigations at Pagliare di Sassa (L’Aquila, central Italy) suggest that the local succession accumulated from the late Early to the early Middle Pleistocene in a lacustrine environment. In the upper part, clastic sediments are part of an alluvial fan prograding into the lake, grading to a braided fluvial system. The pollen record confirms that a significant glacial phase occurred just before the onset of the Jaramillo inversion. These data, coupled with evidence from the nearby but earlier Madonna della Strada sequence, allow reconstruction of part of the environmental evolution of L’Aquila basin before the Jaramillo Subchron. The mammal species of Pagliare di Sassa include Stephanorhinus hundsheimensis, mostly of open environments, already present at Madonna della Strada. The faunal turnover characterizing the Early to Middle Pleistocene transition is indicated by the appearances of taxa typical of the Italian early to middle Galerian faunas, such as Praemegaceros verticornis, together with Megaloceros savini. The occurrence of Mimomys savini together with Microtus ex gr. Microtus hintonigregaloides suggests that this assemblage is earlier than the Isernia La Pineta fauna. A flint implement and a fragmentary herbivore femur with impact scars probably linked to human activity give evidence of the human peopling of intramontane basins of the Apennine chain since the early Middle Pleistocene.
    Description: Published
    Description: 170-178
    Description: 2.2. Laboratorio di paleomagnetismo
    Description: JCR Journal
    Description: restricted
    Keywords: Paleomagnetism ; Pleistocene ; L'Aquila Plain ; 04. Solid Earth::04.05. Geomagnetism::04.05.05. Main geomagnetic field
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 54
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    Cold-water coral distributions in the Drake Passage area from towed camera observations – initial interpretations (2011)
    Public Library of Science
    Details
    Publication Date: 2022-05-26
    Description: This article is distributed under the terms of the Creative Commons Public Domain. The definitive version was published in PLoS One 6 (2011): e16153, doi:10.1371/journal.pone.0016153.
    Description: Seamounts are unique deep-sea features that create habitats thought to have high levels of endemic fauna, productive fisheries and benthic communities vulnerable to anthropogenic impacts. Many seamounts are isolated features, occurring in the high seas, where access is limited and thus biological data scarce. There are numerous seamounts within the Drake Passage (Southern Ocean), yet high winds, frequent storms and strong currents make seafloor sampling particularly difficult. As a result, few attempts to collect biological data have been made, leading to a paucity of information on benthic habitats or fauna in this area, particularly those on primarily hard-bottom seamounts and ridges. During a research cruise in 2008 six locations were examined (two on the Antarctic margin, one on the Shackleton Fracture Zone, and three on seamounts within the Drake Passage), using a towed camera with onboard instruments to measure conductivity, temperature, depth and turbidity. Dominant fauna and bottom type were categorized from 200 randomized photos from each location. Cold-water corals were present in high numbers in habitats both on the Antarctic margin and on the current swept seamounts of the Drake Passage, though the diversity of orders varied. Though the Scleractinia (hard corals) were abundant on the sedimented margin, they were poorly represented in the primarily hard-bottom areas of the central Drake Passage. The two seamount sites and the Shackleton Fracture Zone showed high numbers of stylasterid (lace) and alcyonacean (soft) corals, as well as large numbers of sponges. Though data are preliminary, the geological and environmental variability (particularly in temperature) between sample sites may be influencing cold-water coral biogeography in this region. Each area observed also showed little similarity in faunal diversity with other sites examined for this study within all phyla counted. This manuscript highlights how little is understood of these isolated features, particularly in Polar regions.
    Description: This work was funded by the National Science Foundation’s Antarctic Earth Sciences Program (ANT0636787 awarded to LFR and RGW) and a CenSeam minigrant (awarded to RGW), and RGW is supported by a SOEST Young Investigator Fellowship from the University of Hawaii at Manoa.
    Repository Name: Woods Hole Open Access Server
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    Beaked whales respond to simulated and actual navy sonar (2011)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: This article is distributed under the terms of the Creative Commons Public Domain declaration. The definitive version was published in PLoS One 6 (2011): e17009, doi:10.1371/journal.pone.0017009.
    Description: Beaked whales have mass stranded during some naval sonar exercises, but the cause is unknown. They are difficult to sight but can reliably be detected by listening for echolocation clicks produced during deep foraging dives. Listening for these clicks, we documented Blainville's beaked whales, Mesoplodon densirostris, in a naval underwater range where sonars are in regular use near Andros Island, Bahamas. An array of bottom-mounted hydrophones can detect beaked whales when they click anywhere within the range. We used two complementary methods to investigate behavioral responses of beaked whales to sonar: an opportunistic approach that monitored whale responses to multi-day naval exercises involving tactical mid-frequency sonars, and an experimental approach using playbacks of simulated sonar and control sounds to whales tagged with a device that records sound, movement, and orientation. Here we show that in both exposure conditions beaked whales stopped echolocating during deep foraging dives and moved away. During actual sonar exercises, beaked whales were primarily detected near the periphery of the range, on average 16 km away from the sonar transmissions. Once the exercise stopped, beaked whales gradually filled in the center of the range over 2–3 days. A satellite tagged whale moved outside the range during an exercise, returning over 2–3 days post-exercise. The experimental approach used tags to measure acoustic exposure and behavioral reactions of beaked whales to one controlled exposure each of simulated military sonar, killer whale calls, and band-limited noise. The beaked whales reacted to these three sound playbacks at sound pressure levels below 142 dB re 1 µPa by stopping echolocation followed by unusually long and slow ascents from their foraging dives. The combined results indicate similar disruption of foraging behavior and avoidance by beaked whales in the two different contexts, at exposures well below those used by regulators to define disturbance.
    Description: The research reported here was financially supported by the United States (U.S.) Office of Naval Research (www.onr.navy.mil) Grants N00014-07-10988, N00014-07-11023, N00014-08-10990; the U.S. Strategic Environmental Research and Development Program (www.serdp.org) Grant SI-1539, the Environmental Readiness Division of the U.S. Navy (http://www.navy.mil/local/n45/), the U.S. Chief of Naval Operations Submarine Warfare Division (Undersea Surveillance), the U.S. National Oceanic and Atmospheric Administration (National Marine Fisheries Service, Office of Science and Technology) (http://www.st.nmfs.noaa.gov/), U.S. National Oceanic and Atmospheric Administration Ocean Acoustics Program (http://www.nmfs.noaa.gov/pr/acoustics/), and the Joint Industry Program on Sound and Marine Life of the International Association of Oil and Gas Producers (www.soundandmarinelife.org).
    Repository Name: Woods Hole Open Access Server
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    Avian cholera, a threat to the viability of an Arctic seabird colony? (2012)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 7 (2012): e29659, doi:10.1371/journal.pone.0029659.
    Description: Evidence that infectious diseases cause wildlife population extirpation or extinction remains anecdotal and it is unclear whether the impacts of a pathogen at the individual level can scale up to population level so drastically. Here, we quantify the response of a Common eider colony to emerging epidemics of avian cholera, one of the most important infectious diseases affecting wild waterfowl. We show that avian cholera has the potential to drive colony extinction, even over a very short period. Extinction depends on disease severity (the impact of the disease on adult female survival) and disease frequency (the number of annual epidemics per decade). In case of epidemics of high severity (i.e., causing 〉30% mortality of breeding females), more than one outbreak per decade will be unsustainable for the colony and will likely lead to extinction within the next century; more than four outbreaks per decade will drive extinction to within 20 years. Such severity and frequency of avian cholera are already observed, and avian cholera might thus represent a significant threat to viability of breeding populations. However, this will depend on the mechanisms underlying avian cholera transmission, maintenance, and spread, which are currently only poorly known.
    Description: The study was supported by the Canadian Wildlife Service-Environment Canada (http://www.ec.gc.ca/), Nunavut Wildlife Management Board (http:// www.nwmb.com/), Greenland Institute of Natural Resources (http://www.natur.gl/), Polar Continental Shelf Project (http://polar.nrcan.gc.ca/), Fonds Que´be´cois de la Recherche sur la Nature et les Technologies (http://www.fqrnt.gouv.qc.ca/), Canadian Network of Centres of Excellence ArcticNet (http://www.arcticnet.ulaval. ca/), Natural Sciences and Engineering Research Council of Canada (http://www.nserc-crsng.gc.ca/), and the Department of Indian Affairs and Northern Canada (http://www.ainc-inac.gc.ca/).
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    Evolution of a major drug metabolizing enzyme defect in the domestic cat and other felidae : phylogenetic timing and the role of hypercarnivory (2011)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: This is an open-access article, free of all copyright. The definitive version was published in PLoS One 6(2011): e18046, doi:10.1371/journal.pone.0018046.
    Description: The domestic cat (Felis catus) shows remarkable sensitivity to the adverse effects of phenolic drugs, including acetaminophen and aspirin, as well as structurally-related toxicants found in the diet and environment. This idiosyncrasy results from pseudogenization of the gene encoding UDP-glucuronosyltransferase (UGT) 1A6, the major species-conserved phenol detoxification enzyme. Here, we established the phylogenetic timing of disruptive UGT1A6 mutations and explored the hypothesis that gene inactivation in cats was enabled by minimal exposure to plant-derived toxicants. Fixation of the UGT1A6 pseudogene was estimated to have occurred between 35 and 11 million years ago with all extant Felidae having dysfunctional UGT1A6. Out of 22 additional taxa sampled, representative of most Carnivora families, only brown hyena (Parahyaena brunnea) and northern elephant seal (Mirounga angustirostris) showed inactivating UGT1A6 mutations. A comprehensive literature review of the natural diet of the sampled taxa indicated that all species with defective UGT1A6 were hypercarnivores (〉70% dietary animal matter). Furthermore those species with UGT1A6 defects showed evidence for reduced amino acid constraint (increased dN/dS ratios approaching the neutral selection value of 1.0) as compared with species with intact UGT1A6. In contrast, there was no evidence for reduced amino acid constraint for these same species within UGT1A1, the gene encoding the enzyme responsible for detoxification of endogenously generated bilirubin. Our results provide the first evidence suggesting that diet may have played a permissive role in the devolution of a mammalian drug metabolizing enzyme. Further work is needed to establish whether these preliminary findings can be generalized to all Carnivora.
    Description: Binu Shrestha was supported by a Fulbright scholarship from the United States Department of State. This project was funded by grant R01GM061834 from the National Institute of General Medical Sciences, contract N01-CO-12400 from the National Cancer Institute (NCI), and by the Intramural Research Program, NCI Center for Cancer Research, National Institutes of Health (NIH).
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    Gene expression profile of peripheral blood lymphocytes from renal cell carcinoma patients treated with IL-2, Interferon-α and dendritic cell vaccine (2013)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 7 (2012): e50221, doi:10.1371/journal.pone.0050221.
    Description: Lymphocytes are a key component of the immune system and their differentiation and function are directly influenced by cancer. We examined peripheral blood lymphocyte (PBL) gene expression as a biomarker of illness and treatment effect using the Affymetrix Human Gene ST1 platform in patients with metastatic renal cell carcinoma (mRCC) who received combined treatment with IL-2, interferon-?-2a and dendritic cell vaccine. We examined gene expression, cytokine levels in patient serum and lymphocyte subsets as determined by flow cytometry (FCM). Pre-treatment PBLs from patients with mRCC exhibit a gene expression profile and serum cytokine profile consistent with inflammation and proliferation not found in healthy donors (HD). PBL gene expression from patients with mRCC showed increased mRNA of genes involved with T-cell and TREG-cell activation pathways, which was also reflected in lymphocyte subset distribution. Overall, PBL gene expression post-treatment (POST) was not significantly different than pre-treatment (PRE). Nevertheless, treatment related changes in gene expression (post-treatment minus pre-treatment) revealed an increased expression of T-cell and B-cell receptor signaling pathways in responding (R) patients compared to non-responding (NR) patients. In addition, we observed down-regulation of TREG-cell pathways post-treatment in R vs. NR patients. While exploratory in nature, this study supports the hypothesis that enhanced inflammatory cytotoxic pathways coupled with blunting of the regulatory pathways is necessary for effective anti-cancer activity associated with immune therapy. This type of analysis can potentially identify additional immune therapeutic targets in patients with mRCC.
    Description: This work was supported by grants from the National Institutes of Health (RO1 CA5648, R21CA112761, P20RR016437, and P30CA023108).
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    Diversity and dynamics of a widespread bloom of the toxic dinoflagellate Alexandrium fundyense (2011)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 6 (2011): e22965, doi:10.1371/journal.pone.0022965.
    Description: Historically, cosmopolitan phytoplankton species were presumed to represent largely unstructured populations. However, the recent development of molecular tools to examine genetic diversity have revealed differences in phytoplankton taxa across geographic scales and provided insight into the physiology and ecology of blooms. Here we describe the genetic analysis of an extensive bloom of the toxic dinoflagellate Alexandrium fundyense that occurred in the Gulf of Maine in 2005. This bloom was notable for its intensity and duration, covering hundreds of kilometers and persisting for almost two months. Genotypic analyses based on microsatellite marker data indicate that the open waters of the northeastern U.S. harbor a single regional population of A. fundyense comprising two genetically distinct sub-populations. These subpopulations were characteristic of early- and late-bloom samples and were derived from the northern and southern areas of the bloom, respectively. The temporal changes observed during this study provide clear evidence of succession during a continuous bloom and show that selection can act on the timescale of weeks to significantly alter the representation of genotypes within a population. The effects of selection on population composition and turnover would be magnified if sexual reproduction were likewise influenced by environmental conditions. We hypothesize that the combined effects of differential growth and reproduction rates serves to reduce gene flow between the sub-populations, reinforcing population structure while maintaining the diversity of the overall regional population.
    Description: This work was supported by the National Institute of Environmental Health Sciences (1-P50-ES012742 to DMA and DLE), by the National Science Foundation through the Woods Hole Center for Oceans and Human Health (OCE-0430724), and by the ECOHAB program (NOAA Grant NA06NOS4780245).
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    Comparison of bacterial communities in sands and water at beaches with bacterial water quality violations (2014)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e90815, doi:10.1371/journal.pone.0090815.
    Description: Recreational water quality, as measured by culturable fecal indicator bacteria (FIB), may be influenced by persistent populations of these bacteria in local sands or wrack, in addition to varied fecal inputs from human and/or animal sources. In this study, pyrosequencing was used to generate short sequence tags of the 16S hypervariable region ribosomal DNA from shallow water samples and from sand samples collected at the high tide line and at the intertidal water line at sites with and without FIB exceedance events. These data were used to examine the sand and water bacterial communities to assess the similarity between samples, and to determine the impact of water quality exceedance events on the community composition. Sequences belonging to a group of bacteria previously identified as alternative fecal indicators were also analyzed in relationship to water quality violation events. We found that sand and water samples hosted distinctly different overall bacterial communities, and there was greater similarity in the community composition between coastal water samples from two distant sites. The dissimilarity between high tide and intertidal sand bacterial communities, although more similar to each other than to water, corresponded to greater tidal range between the samples. Within the group of alternative fecal indicators greater similarity was observed within sand and water from the same site, likely reflecting the anthropogenic contribution at each beach. This study supports the growing evidence that community-based molecular tools can be leveraged to identify the sources and potential impact of fecal pollution in the environment, and furthermore suggests that a more diverse bacterial community in beach sand and water may reflect a less contaminated site and better water quality.
    Description: This work was supported by the National Science Foundation grant OCE-0430724, and the National Institute of Environmental Health Sciences grant P0ES012742 to the Woods Hole Center for Ocean and Human Health. E. Halliday was partially supported by WHOI Academic Programs and grants from the WHOI Ocean Ventures Fund and the WHOI Coastal Ocean Institute.
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    Distinguishing seawater from geologic brine in saline coastal groundwater using radium-226; an example from the Sabkha of the UAE (2014)
    Elsevier
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    Publication Date: 2022-05-26
    Description: This paper is not subject to U.S. copyright. The definitive version was published in Chemical Geology 371 (2014): 1-8, doi:10.1016/j.chemgeo.2014.01.018.
    Description: Sabkhat (Salt flats) are common geographic features of low-lying marine coastal areas that develop under hyper-arid climatic conditions. They are characterized by the presence of highly concentrated saline solutions and evaporitic minerals, and have been cited in the geologic literature as present-day representations of hyper-arid regional paleohydrogeology, paleoclimatology, coastal processes, and sedimentation in the geologic record. It is therefore important that a correct understanding of the origin and development of these features be achieved. Knowledge of the source of solutes is an important first step in understanding these features. Historically, two theories have been advanced as to the main source of solutes in sabkha brines: an early concept entailing seawater as the obvious source, and a more recent and dynamic theory involving ascending geologic brine forced upward into the base of the sabkha by a regional hydraulic gradient in the underlying formations. Ra-226 could uniquely distinguish between these sources under certain circumstances, as it is typically present at elevated activity of hundreds to thousands of Bq/m3 (Becquerels per cubic meter) in subsurface formation brines; at exceedingly low activities in open ocean and coastal water; and not significantly supplied to water from recently formed marine sedimentary framework material. The coastal marine sabkha of the Emirate of Abu Dhabi was used to test this hypothesis. The distribution of Ra-226 in 70 samples of sabkha brine (mean: 700 Bq/m3), 7 samples of underlying deeper formation brine (mean: 3416 Bq/m3), the estimated value of seawater (〈 16 Bq/m3) and an estimate of supply from sabkha sedimentary framework grains (〈~6 Bq/m3) provide the first direct evidence that ascending geologic brine contributes significantly to the solutes of this sabkha system.
    Keywords: Sabkhat ; Radium-226 ; Geologic brine ; Seawater
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    Multiple sulfur isotope constraints on the modern sulfur cycle (2014)
    Elsevier
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Earth and Planetary Science Letters 396 (2014): 14-21, doi:10.1016/j.epsl.2014.03.057.
    Description: We present 28 multiple sulfur isotope measurements of seawater sulfate (δ34SSO4δ34SSO4 and Δ33SSO4Δ33SSO4) from the modern ocean over a range of water depths and sites along the eastern margin of the Pacific Ocean. The average measured δ34SSO4δ34SSO4 is 21.24‰ (±0.88‰,2σ±0.88‰,2σ) with a calculated Δ33SSO4Δ33SSO4 of +0.050‰+0.050‰ (±0.014‰,2σ±0.014‰,2σ). With these values, we use a box-model to place constraints on the gross fraction of pyrite burial in modern sediments. This model presents an improvement on previous estimates of the global pyrite burial flux because it does not rely on the assumed value of δ34Spyriteδ34Spyrite, which is poorly constrained, but instead uses new information about the relationship between δ34Sδ34S and δ33Sδ33S in global marine sulfate. Our calculations indicate that the pyrite burial flux from the modern ocean is between 10% and 45% of the total sulfur lost from the oceans, with a more probable range between 20% and 35%.
    Description: RT acknowledges financial support from NERC Grant NE/I00596X/1. Support was provided through NERC grant NE/H011595/1 to AVT. AVT acknowledges financial support from the ERC Starting Investigator Grant 307582. JF acknowledges support from the NASA Astrobiology Institute.
    Keywords: Sulfur isotopes ; Multiple sulfur isotopes ; Pyrite flux ; Sulfur cycle ; Sulfate reduction ; Biogeochemical cycles
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    Assessment of tsunami hazard to the U.S. Atlantic margin (2014)
    Elsevier
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    Publication Date: 2022-05-26
    Description: This paper is not subject to U.S. copyright. The definitive version was published in Marine Geology 353 (2014): 31-54, doi:10.1016/j.margeo.2014.02.011.
    Description: Tsunami hazard is a very low-probability, but potentially high-risk natural hazard, posing unique challenges to scientists and policy makers trying to mitigate its impacts. These challenges are illustrated in this assessment of tsunami hazard to the U.S. Atlantic margin. Seismic activity along the U.S. Atlantic margin in general is low, and confirmed paleo-tsunami deposits have not yet been found, suggesting a very low rate of hazard. However, the devastating 1929 Grand Banks tsunami along the Atlantic margin of Canada shows that these events continue to occur. Densely populated areas, extensive industrial and port facilities, and the presence of ten nuclear power plants along the coast, make this region highly vulnerable to flooding by tsunamis and therefore even low-probability events need to be evaluated. We can presently draw several tentative conclusions regarding tsunami hazard to the U.S. Atlantic coast. Landslide tsunamis likely constitute the biggest tsunami hazard to the coast. Only a small number of landslides have so far been dated and they are generally older than 10,000 years. The geographical distribution of landslides along the margin is expected to be uneven and to depend on the distribution of seismic activity along the margin and on the geographical distribution of Pleistocene sediment. We do not see evidence that gas hydrate dissociation contributes to the generation of landslides along the U.S. Atlantic margin. Analysis of landslide statistics along the fluvial and glacial portions of the margin indicate that most of the landslides are translational, were probably initiated by seismic acceleration, and failed as aggregate slope failures. How tsunamis are generated from aggregate landslides remains however, unclear. Estimates of the recurrence interval of earthquakes along the continental slope may provide maximum estimates for the recurrence interval of landslide along the margin. Tsunamis caused by atmospheric disturbances and by coastal earthquakes may be more frequent than those generated by landslides, but their amplitudes are probably smaller. Among the possible far-field earthquake sources, only earthquakes located within the Gulf of Cadiz or west of the Tore-Madeira Rise are likely to affect the U.S. coast. It is questionable whether earthquakes on the Puerto Rico Trench are capable of producing a large enough tsunami that will affect the U.S. Atlantic coast. More information is needed to evaluate the seismic potential of the northern Cuba fold-and-thrust belt. The hazard from a volcano flank collapse in the Canary Islands is likely smaller than originally stated, and there is not enough information to evaluate the magnitude and frequency of flank collapse from the Azores Islands. Both deterministic and probabilistic methods to evaluate the tsunami hazard from the margin are available for application to the Atlantic margin, but their implementation requires more information than is currently available.
    Description: The work was funded by the U.S.-NRC Job Code V6166: Tsunami Landslide Source Probability and Potential Impact on New and Existing Power Plants.
    Keywords: Submarine landslides ; Meteo-tsunami ; Earthquakes and landslides ; Probabilistic hazard assessment
    Repository Name: Woods Hole Open Access Server
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    Composition of hydrothermal fluids and mineralogy of associated chimney material on the East Scotia Ridge back-arc spreading centre (2014)
    Elsevier
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Geochimica et Cosmochimica Acta 139 (2014): 47-71, doi:10.1016/j.gca.2014.04.024.
    Description: The East Scotia Ridge is an active back-arc spreading centre located to the west of the South Sandwich island arc in the Southern Ocean. Initial exploration of the ridge by deep-tow surveys provided the first evidence for hydrothermal activity in a back-arc setting outside of the western Pacific, and we returned in 2010 with a remotely operated vehicle to precisely locate and sample hydrothermal sites along ridge segments E2 and E9. Here we report the chemical and isotopic composition of high- and low-temperature vent fluids, and the mineralogy of associated high-temperature chimney material, for two sites at E2 (Dog’s Head and Sepia), and four sites at E9 (Black & White, Ivory Tower, Pagoda and Launch Pad). The chemistry of the fluids is highly variable between the ridge segments. Fluid temperatures were ∼350 °C at all vent sites except Black & White, which was significantly hotter (383 °C). End-member chloride concentrations in E2 fluids (532–536 mM) were close to background seawater (540 mM), whereas Cl in E9 fluids was much lower (98–220 mM) indicating that these fluids are affected by phase separation. Concentrations of the alkali elements (Na, Li, K and Cs) and the alkaline earth elements (Ca, Sr and Ba) co-vary with Cl, due to charge balance constraints. Similarly, concentrations of Mn and Zn are highest in the high Cl fluids but, by contrast, Fe/Cl ratios are higher in E9 fluids (3.8–8.1 × 10−3) than they are in E2 fluids (1.5–2.4 × 10−3) and fluids with lowest Cl have highest Cu. Although both ridge segments are magmatically inflated, there is no compelling evidence for input of magmatic gases to the vent fluids. Fluid δD values range from 0.2‰ to 1.5‰, pH values (3.02–3.42) are not especially low, and F concentrations (34.6–54.4 μM) are lower than bottom seawater (62.8 μM). The uppermost sections of conjugate chimney material from E2, and from Ivory Tower and Pagoda at E9, typically exhibit inner zones of massive chalcopyrite enclosed within an outer zone of disseminated sulphide, principally sphalerite and pyrite, in an anhydrite matrix. By contrast, the innermost part of the chimneys that currently vent fluids with lowest Cl (Black & White and Launch Pad), is dominated by anhydrite. By defining and assessing the controls on the chemical composition of these vent fluids, and associated mineralisation, this study provides new information for evaluating the significance of hydrothermal processes at back-arc basins for ocean chemistry and the formation of seafloor mineral deposits.
    Description: This work was funded by the Natural Environment Research Council consortium grant NE/D01249X/1. C.R.G. acknowledges further support from the National Science Foundation’s Office of Polar Programs grant ANT-0739675. N.R.B. acknowledges funding from the National Sciences and Engineering Research Council of Canada, Ontario Ministry of Research and Innovation, and the Academic Development Fund at Western University.
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    A fossil winonaite-like meteorite in Ordovician limestone : a piece of the impactor that broke up the L-chondrite parent body? (2014)
    Elsevier
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Earth and Planetary Science Letters 400 (2014): 145-152, doi:10.1016/j.epsl.2014.05.034.
    Description: About a quarter of all meteorites falling on Earth today originate from the breakup of the L-chondrite parent body ∼470 Ma∼470 Ma ago, the largest documented breakup in the asteroid belt in the past ∼3 Ga∼3 Ga. A window into the flux of meteorites to Earth shortly after this event comes from the recovery of about 100 fossil L chondrites (1–21 cm in diameter) in a quarry of mid-Ordovician limestone in southern Sweden. Here we report on the first non-L-chondritic meteorite from the quarry, an 8 cm large winonaite-related meteorite of a type not known among present-day meteorite falls and finds. The noble gas data for relict spinels recovered from the meteorite show that it may be a remnant of the body that hit and broke up the L-chondrite parent body, creating one of the major asteroid families in the asteroid belt. After two decades of systematic recovery of fossil meteorites and relict extraterrestrial spinel grains from marine limestone, it appears that the meteorite flux to Earth in the mid-Ordovician was very different from that of today.
    Description: This study was supported by an European Research Council Advanced Grant to B.S., in part by NASA grant NNX08AE08G to K.K., and a grant to M.M. from the Swiss National Science Foundation.
    Keywords: Fossil meteorite ; Asteroid breakup ; Winonaite ; Ordinary chondrite ; Asteroid family ; Meteorite flux
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    Movement patterns of juvenile whale sharks tagged at an aggregation site in the Red Sea (2014)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e103536, doi:10.1371/journal.pone.0103536.
    Description: Conservation efforts aimed at the whale shark, Rhincodon typus, remain limited by a lack of basic information on most aspects of its ecology, including global population structure, population sizes and movement patterns. Here we report on the movements of 47 Red Sea whale sharks fitted with three types of satellite transmitting tags from 2009–2011. Most of these sharks were tagged at a single aggregation site near Al-Lith, on the central coast of the Saudi Arabian Red Sea. Individuals encountered at this site were all juveniles based on size estimates ranging from 2.5–7 m total length with a sex ratio of approximately 1:1. All other known aggregation sites for juvenile whale sharks are dominated by males. Results from tagging efforts showed that most individuals remained in the southern Red Sea and that some sharks returned to the same location in subsequent years. Diving data were recorded by 37 tags, revealing frequent deep dives to at least 500 m and as deep as 1360 m. The unique temperature-depth profiles of the Red Sea confirmed that several whale sharks moved out of the Red Sea while tagged. The wide-ranging horizontal movements of these individuals highlight the need for multinational, cooperative efforts to conserve R. typus populations in the Red Sea and Indian Ocean.
    Description: Financial support was provided in part by KAUST baseline research funds (to MLB), KAUST award nos. USA00002 and KSA 00011 (to SRT), and the United States National Science Foundation (OCE 0825148 to SRT and GBS).
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    Anthropogenic nutrients and harmful algae in coastal waters (2014)
    Elsevier
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Journal of Environmental Management 146 (2014): 206-216, doi:10.1016/j.jenvman.2014.07.002.
    Description: Harmful algal blooms (HABs) are thought to be increasing in coastal waters worldwide. Anthropogenic nutrient enrichment has been proposed as a principal causative factor of this increase through elevated inorganic and/or organic nutrient concentrations and modified nutrient ratios. We assess: 1) the level of understanding of the link between the amount, form and ratio of anthropogenic nutrients and HABs; 2) the evidence for a link between anthropogenically generated HABs and negative impacts on human health; and 3) the economic implications of anthropogenic nutrient/HAB interactions. We demonstrate that an anthropogenic nutrient-HAB link is far from universal, and where it has been demonstrated, it is most frequently associated with high biomass rather than low biomass (biotoxin producing) HABs. While organic nutrients have been shown to support the growth of a range of HAB species, insufficient evidence exists to clearly establish if these nutrients specifically promote the growth of harmful species in preference to benign ones, or if/how they influence toxicity of harmful species. We conclude that the role of anthropogenic nutrients in promoting HABs is site-specific, with hydrodynamic processes often determining whether blooms occur. We also find a lack of evidence of widespread significant adverse health impacts from anthropogenic nutrient-generated HABs, although this may be partly due to a lack of human/animal health and HAB monitoring. Detailed economic evaluation and cost/benefit analysis of the impact of anthropogenically generated HABs, or nutrient reduction schemes to alleviate them, is also frequently lacking.
    Description: The work described here is based in part on a project ‘Harmful Algae, Nuisance Blooms and Anthropogenic Nutrient Enrichment’ funded by the UK Department for Environment, Food and Rural Affairs (contract ME2208). In addition KD was supported by the FP7 project Asimuth and funding from the NERC Shelf Seas Biogeochemistry and PURE Associates programmes. PJH was supported by University Grants Council of Hong Kong AoE project (AoE/P-04/0401). PH and LEF were funded by the US National Science Foundation (NSF) Award 1009106; LEF was funded in part by the European Regional Development Fund and European Social Fund (University of Exeter, Truro, Cornwall, UK). GM was supported by a NERC PhD studentship.
    Keywords: Harmful algal blooms ; HABs ; Anthropogenic nutrients ; Human health ; Economic impact
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    Aggregation and Sedimentation of Thalassiosira weissflogii (diatom) in a Warmer and More Acidified Future Ocean (2014)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e112379, doi:10.1575/1912/6845.
    Description: Increasing Transparent Exopolymer Particle (TEP) formation during diatom blooms as a result of elevated temperature and pCO2 have been suggested to result in enhanced aggregation and carbon flux, therewith potentially increasing the sequestration of carbon by the ocean. We present experimental results on TEP and aggregate formation by Thalassiosira weissflogii (diatom) in the presence or absence of bacteria under two temperature and three pCO2 scenarios. During the aggregation phase of the experiment TEP formation was elevated at the higher temperature (20°C vs. 15°C), as predicted. However, in contrast to expectations based on the established relationship between TEP and aggregation, aggregation rates and sinking velocity of aggregates were depressed in warmer treatments, especially under ocean acidification conditions. If our experimental findings can be extrapolated to natural conditions, they would imply a reduction in carbon flux and potentially reduced carbon sequestration after diatom blooms in the future ocean.
    Description: This work was supported by National Science Foundation grants OCE-0926711 & OCE-1041038 to UP and Helmholtz Graduate School for Polar and Marine Research and Jacobs University Bremen to SS.
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    A novel lineage of proteobacteria involved in formation of marine Fe-oxidizing microbial mat communities (2011)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Authors, 2007. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 2 (2007): e667, doi:10.1371/journal.pone.0000667.
    Description: For decades it has been recognized that neutrophilic Fe-oxidizing bacteria (FeOB) are associated with hydrothermal venting of Fe(II)-rich fluids associated with seamounts in the world's oceans. The evidence was based almost entirely on the mineralogical remains of the microbes, which themselves had neither been brought into culture or been assigned to a specific phylogenetic clade. We have used both cultivation and cultivation-independent techniques to study Fe-rich microbial mats associated with hydrothermal venting at Loihi Seamount, a submarine volcano. Using gradient enrichment techniques, two iron-oxidizing bacteria, strains PV-1 and JV-1, were isolated. Chemolithotrophic growth was observed under microaerobic conditions; Fe(II) and Fe0 were the only energy sources that supported growth. Both strains produced filamentous stalk-like structures composed of multiple nanometer sized fibrils of Fe-oxyhydroxide. These were consistent with mineralogical structures found in the iron mats. Phylogenetic analysis of the small subunit (SSU) rRNA gene demonstrated that strains PV-1 and JV-1 were identical and formed a monophyletic group deeply rooted within the Proteobacteria. The most similar sequence (85.3% similarity) from a cultivated isolate came from Methylophaga marina. Phylogenetic analysis of the RecA and GyrB protein sequences confirmed that these strains are distantly related to other members of the Proteobacteria. A cultivation-independent analysis of the SSU rRNA gene by terminal-restriction fragment (T-RF) profiling showed that this phylotype was most common in a variety of microbial mats collected at different times and locations at Loihi. On the basis of phylogenetic and physiological data, it is proposed that isolate PV-1T ( = 1ATCC BAA-1019: JCM 14766) represents the type strain of a novel species in a new genus, Mariprofundus ferrooxydans gen. nov., sp. nov. Furthermore, the strain is the first cultured representative of a new candidatus class of the Proteobacteria that is widely distributed in deep-sea environments, Candidatus ζ (zeta)-Proteobacteria cl. nov.
    Description: Funding was provided to DE and CLM by the National Science Foundation (0348330) and to DE through the NASA Astobiology Institute.
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    Superfast vocal muscles control song production in songbirds (2011)
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    Publication Date: 2022-05-26
    Description: © The Authors, 2008. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 3 (2008): e2581, doi:10.1371/journal.pone.0002581.
    Description: Birdsong is a widely used model for vocal learning and human speech, which exhibits high temporal and acoustic diversity. Rapid acoustic modulations are thought to arise from the vocal organ, the syrinx, by passive interactions between the two independent sound generators or intrinsic nonlinear dynamics of sound generating structures. Additionally, direct neuromuscular control could produce such rapid and precisely timed acoustic features if syringeal muscles exhibit rare superfast muscle contractile kinetics. However, no direct evidence exists that avian vocal muscles can produce modulations at such high rates. Here, we show that 1) syringeal muscles are active in phase with sound modulations during song over 200 Hz, 2) direct stimulation of the muscles in situ produces sound modulations at the frequency observed during singing, and that 3) syringeal muscles produce mechanical work at the required frequencies and up to 250 Hz in vitro. The twitch kinematics of these so-called superfast muscles are the fastest measured in any vertebrate muscle. Superfast vocal muscles enable birds to directly control the generation of many observed rapid acoustic changes and to actuate the millisecond precision of neural activity into precise temporal vocal control. Furthermore, birds now join the list of vertebrate classes in which superfast muscle kinetics evolved independently for acoustic communication.
    Description: This study was funded by NIH DC04390 and DC06876 to FG, and NIH AR38404-20 and NIH AR46125 to LCR. The work was also supported by a grant from the Pennsylvania Department of Health to LCR.
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    Analysis of expressed sequence tags of the cyclically parthenogenetic rotifer Brachionus plicatilis (2011)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Authors, 2007. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 2 (2007): e671, doi:10.1371/journal.pone.0000671.
    Description: Rotifers are among the most common non-arthropod animals and are the most experimentally tractable members of the basal assemblage of metazoan phyla known as Gnathifera. The monogonont rotifer Brachionus plicatilis is a developing model system for ecotoxicology, aquatic ecology, cryptic speciation, and the evolution of sex, and is an important food source for finfish aquaculture. However, basic knowledge of the genome and transcriptome of any rotifer species has been lacking. We generated and partially sequenced a cDNA library from B. plicatilis and constructed a database of over 2300 expressed sequence tags corresponding to more than 450 transcripts. About 20% of the transcripts had no significant similarity to database sequences by BLAST; most of these contained open reading frames of significant length but few had recognized Pfam motifs. Sixteen transcripts accounted for 25% of the ESTs; four of these had no significant similarity to BLAST or Pfam databases. Putative up- and downstream untranslated regions are relatively short and AT rich. In contrast to bdelloid rotifers, there was no evidence of a conserved trans-spliced leader sequence among the transcripts and most genes were single-copy. Despite the small size of this EST project it revealed several important features of the rotifer transcriptome and of individual monogonont genes. Because there is little genomic data for Gnathifera, the transcripts we found with no known function may represent genes that are species-, class-, phylum- or even superphylum-specific; the fact that some are among the most highly expressed indicates their importance. The absence of trans-spliced leader exons in this monogonont species contrasts with their abundance in bdelloid rotifers and indicates that the presence of this phenomenon can vary at the subphylum level. Our EST database provides a relatively large quantity of transcript-level data for B. plicatilis, and more generally of rotifers and other gnathiferan phyla, and can be browsed and searched at gmod.mbl.edu.
    Description: This research was supported by the Nagasaki Prefecture Collaboration of Regional Entities for the Advancement of Technological Excellence, Japan Science and Technology Agency to KS, YT, YS and AH, and US NSF grants EF-0412674 and MCB-0544199 to DMW.
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    Microbial diversity and potential pathogens in onamental fish aquarium water (2012)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 7 (2012): e39971, doi:10.1371/journal.pone.0039971.
    Description: Ornamental fishes are among the most popular and fastest growing categories of pets in the United States (U.S.). The global scope and scale of the ornamental fish trade and growing popularity of pet fish in the U.S. are strong indicators of the myriad economic and social benefits the pet industry provides. Relatively little is known about the microbial communities associated with these ornamental fishes or the aquarium water in which they are transported and housed. Using conventional molecular approaches and next generation high-throughput amplicon sequencing of 16S ribosomal RNA gene hypervariable regions, we characterized the bacterial community of aquarium water containing common goldfish (Carassius auratus) and Chinese algae eaters (Gyrinocheilus aymonieri) purchased from seven pet/aquarium shops in Rhode Island and identified the presence of potential pathogens. Our survey identified a total of 30 phyla, the most common being Proteobacteria (52%), Bacteroidetes (18%) and Planctomycetes (6%), with the top four phyla representing 〉80% of all sequences. Sequences from our water samples were most closely related to eleven bacterial species that have the potential to cause disease in fishes, humans and other species: Coxiella burnetii, Flavobacterium columnare, Legionella birminghamensis, L. pneumophila, Vibrio cholerae, V. mimicus. V. vulnificus, Aeromonas schubertii, A. veronii, A. hydrophila and Plesiomonas shigelloides. Our results, combined with evidence from the literature, suggest aquarium tank water harboring ornamental fish are an understudied source for novel microbial communities and pathogens that pose potential risks to the pet industry, fishes in trade, humans and other species.
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    Clicking in shallow rivers : short-range echolocation of Irrawaddy and Ganges River dolphins in a shallow, acoustically complex habitat (2013)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 8 (2013): e59284, doi:10.1371/journal.pone.0059284.
    Description: Toothed whales (Cetacea, odontoceti) use biosonar to navigate their environment and to find and catch prey. All studied toothed whale species have evolved highly directional, high-amplitude ultrasonic clicks suited for long-range echolocation of prey in open water. Little is known about the biosonar signals of toothed whale species inhabiting freshwater habitats such as endangered river dolphins. To address the evolutionary pressures shaping the echolocation signal parameters of non-marine toothed whales, we investigated the biosonar source parameters of Ganges river dolphins (Platanista gangetica gangetica) and Irrawaddy dolphins (Orcaella brevirostris) within the river systems of the Sundarban mangrove forest. Both Ganges and Irrawaddy dolphins produced echolocation clicks with a high repetition rate and low source level compared to marine species. Irrawaddy dolphins, inhabiting coastal and riverine habitats, produced a mean source level of 195 dB (max 203 dB) re 1 µPapp whereas Ganges river dolphins, living exclusively upriver, produced a mean source level of 184 dB (max 191) re 1 µPapp. These source levels are 1–2 orders of magnitude lower than those of similar sized marine delphinids and may reflect an adaptation to a shallow, acoustically complex freshwater habitat with high reverberation and acoustic clutter. The centroid frequency of Ganges river dolphin clicks are an octave lower than predicted from scaling, but with an estimated beamwidth comparable to that of porpoises. The unique bony maxillary crests found in the Platanista forehead may help achieve a higher directionality than expected using clicks nearly an octave lower than similar sized odontocetes.
    Description: This study was made possible through the logistical and field support of the Bangladesh Cetacean Diversity Project of the Wildlife Conservation Society, and funded by frame grants from the Danish Natural Science Foundation to PTM. FHJ was supported by the PhD School of Aquatic Sciences, Denmark, and is currently funded by a postdoctoral fellowship from the Danish Council for Independent Research | Natural Sciences. VMJ was supported by a fellowship of the Wissenschaftskolleg Berlin. PTM was supported by frame grants from the Danish Natural Science Foundation.
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    Assessing performance of Bayesian state-space models fit to Argos satellite telemetry locations processed with Kalman filtering (2014)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e92277, doi:10.1371/journal.pone.0092277.
    Description: Argos recently implemented a new algorithm to calculate locations of satellite-tracked animals that uses a Kalman filter (KF). The KF algorithm is reported to increase the number and accuracy of estimated positions over the traditional Least Squares (LS) algorithm, with potential advantages to the application of state-space methods to model animal movement data. We tested the performance of two Bayesian state-space models (SSMs) fitted to satellite tracking data processed with KF algorithm. Tracks from 7 harbour seals (Phoca vitulina) tagged with ARGOS satellite transmitters equipped with Fastloc GPS loggers were used to calculate the error of locations estimated from SSMs fitted to KF and LS data, by comparing those to “true” GPS locations. Data on 6 fin whales (Balaenoptera physalus) were used to investigate consistency in movement parameters, location and behavioural states estimated by switching state-space models (SSSM) fitted to data derived from KF and LS methods. The model fit to KF locations improved the accuracy of seal trips by 27% over the LS model. 82% of locations predicted from the KF model and 73% of locations from the LS model were 〈5 km from the corresponding interpolated GPS position. Uncertainty in KF model estimates (5.6±5.6 km) was nearly half that of LS estimates (11.6±8.4 km). Accuracy of KF and LS modelled locations was sensitive to precision but not to observation frequency or temporal resolution of raw Argos data. On average, 88% of whale locations estimated by KF models fell within the 95% probability ellipse of paired locations from LS models. Precision of KF locations for whales was generally higher. Whales’ behavioural mode inferred by KF models matched the classification from LS models in 94% of the cases. State-space models fit to KF data can improve spatial accuracy of location estimates over LS models and produce equally reliable behavioural estimates.
    Description: This research was primarily funded by Fundação para a Ciência e a Tecnologia (FCT), Fundo Regional da Ciência, Tecnologia (FRCT), through research projects TRACE-PTDC/MAR/74071/2006 and MAPCET-M2.1.2/F/012/2011 [FEDER], the Competitiveness Factors Operational (COMPETE), QREN European Social Fund, and Proconvergencia Açores/EU Program]. We acknowledge funds provided by FCT to LARSyS Associated Laboratory and IMAR-University of the Azores/the Thematic Area D & E of the Strategic Project PEst-OE/EEI/LA0009/2011–1012 and 2013–2014 (OE & Compete) and by the FRCT - Government of the Azores pluriannual funding. MAS was supported by an FCT postdoctoral grant (SFRH/BPD/29841/2006) and is currently supported by POPH, QREN European Social Fund and the Portuguese Ministry for Science and Education through an FCT Investigator grant. RP was supported by an FCT doctoral grant (SFRH/BD/41192/2007) and by the research grant from the Azores Regional Fund for Science and Technology (M3.1.5/F/115/2012). IJ was supported by the Natural Sciences and Engineering Research Council (NSERC) and the Canada Foundation for Innovation (CFI) through their support of the Ocean Tracking Network. DJFR is funded by the United Kingdom Department of Energy and Climate Change as part of their Offshore Energy Strategic Environmental Assessment program. DT is funded by Natural Environment Research Council and Marine Scotland.
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    Analysis, optimization and verification of Illumina-generated 16S rRNA gene amplicon surveys (2014)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e94249, doi:10.1371/journal.pone.0094249.
    Description: The exploration of microbial communities by sequencing 16S rRNA genes has expanded with low-cost, high-throughput sequencing instruments. Illumina-based 16S rRNA gene sequencing has recently gained popularity over 454 pyrosequencing due to its lower costs, higher accuracy and greater throughput. Although recent reports suggest that Illumina and 454 pyrosequencing provide similar beta diversity measures, it remains to be demonstrated that pre-existing 454 pyrosequencing workflows can transfer directly from 454 to Illumina MiSeq sequencing by simply changing the sequencing adapters of the primers. In this study, we modified 454 pyrosequencing primers targeting the V4-V5 hyper-variable regions of the 16S rRNA gene to be compatible with Illumina sequencers. Microbial communities from cows, humans, leeches, mice, sewage, and termites and a mock community were analyzed by 454 and MiSeq sequencing of the V4-V5 region and MiSeq sequencing of the V4 region. Our analysis revealed that reference-based OTU clustering alone introduced biases compared to de novo clustering, preventing certain taxa from being observed in some samples. Based on this we devised and recommend an analysis pipeline that includes read merging, contaminant filtering, and reference-based clustering followed by de novo OTU clustering, which produces diversity measures consistent with de novo OTU clustering analysis. Low levels of dataset contamination with Illumina sequencing were discovered that could affect analyses that require highly sensitive approaches. While moving to Illumina-based sequencing platforms promises to provide deeper insights into the breadth and function of microbial diversity, our results show that care must be taken to ensure that sequencing and processing artifacts do not obscure true microbial diversity.
    Description: This work was partially funded by an Emerging Frontiers in Research and Innovation – Multicellular and Inter-kingdom Signaling (EFRI-MIKS) grant awarded by the US National Science Foundation to Joerg Graf and NIH RO1 GM095390 to JG and HGM.
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    First autonomous bio-optical profiling float in the Gulf of Mexico reveals dynamic biogeochemistry in deep waters (2014)
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    Publication Date: 2022-05-26
    Description: This is an open-access article, free of all copyright. The definitive version was published in PLoS One 9 (2014): e101658, doi:10.1371/journal.pone.0101658.
    Description: Profiling floats equipped with bio-optical sensors well complement ship-based and satellite ocean color measurements by providing highly-resolved time-series data on the vertical structure of biogeochemical processes in oceanic waters. This is the first study to employ an autonomous profiling (APEX) float in the Gulf of Mexico for measuring spatiotemporal variability in bio-optics and hydrography. During the 17-month deployment (July 2011 to December 2012), the float mission collected profiles of temperature, salinity, chlorophyll fluorescence, particulate backscattering (bbp), and colored dissolved organic matter (CDOM) fluorescence from the ocean surface to a depth of 1,500 m. Biogeochemical variability was characterized by distinct depth trends and local “hot spots”, including impacts from mesoscale processes associated with each of the water masses sampled, from ambient deep waters over the Florida Plain, into the Loop Current, up the Florida Canyon, and eventually into the Florida Straits. A deep chlorophyll maximum (DCM) occurred between 30 and 120 m, with the DCM depth significantly related to the unique density layer ρ = 1023.6 (R2 = 0.62). Particulate backscattering, bbp, demonstrated multiple peaks throughout the water column, including from phytoplankton, deep scattering layers, and resuspension. The bio-optical relationship developed between bbp and chlorophyll (R2 = 0.49) was compared to a global relationship and could significantly improve regional ocean-color algorithms. Photooxidation and autochthonous production contributed to CDOM distributions in the upper water column, whereas in deep water, CDOM behaved as a semi-conservative tracer of water masses, demonstrating a tight relationship with density (R2 = 0.87). In the wake of the Deepwater Horizon oil spill, this research lends support to the use of autonomous drifting profilers as a powerful tool for consideration in the design of an expanded and integrated observing network for the Gulf of Mexico.
    Description: This project was funded by Bureau of Ocean Energy Management (BOEM) Contract M10PC00112 to Leidos, Inc. with subcontract to ASB (www.boem.gov).
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    PSP toxin levels and plankton community composition and abundance in size-fractionated vertical profiles during spring/summer blooms of the toxic dinoflagellate Alexandrium fundyense in the Gulf of Maine and on Georges Bank, 2007, 2008, and 2010 : 1. Toxin levels (2014)
    Elsevier
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    Publication Date: 2022-05-26
    Description: This paper is not subject to U.S. copyright. The definitive version was published in Deep Sea Research Part II: Topical Studies in Oceanography 103 (2014): 329–349, doi:10.1016/j.dsr2.2013.04.013.
    Description: As part of the NOAA ECOHAB funded Gulf of Maine Toxicity (GOMTOX)1 project, we determined Alexandrium fundyense abundance, paralytic shellfish poisoning (PSP) toxin composition, and concentration in quantitatively-sampled size-fractionated (20–64, 64–100, 100–200, 200–500, and 〉500 μm) particulate water samples, and the community composition of potential grazers of A. fundyense in these size fractions, at multiple depths (typically 1, 10, 20 m, and near-bottom) during 10 large-scale sampling cruises during the A. fundyense bloom season (May–August) in the coastal Gulf of Maine and on Georges Bank in 2007, 2008, and 2010. Our findings were as follows: (1) when all sampling stations and all depths were summed by year, the majority (94%±4%) of total PSP toxicity was contained in the 20–64 μm size fraction; (2) when further analyzed by depth, the 20–64 μm size fraction was the primary source of toxin for 97% of the stations and depths samples over three years; (3) overall PSP toxin profiles were fairly consistent during the three seasons of sampling with gonyautoxins (1, 2, 3, and 4) dominating (90.7%±5.5%), followed by the carbamate toxins saxitoxin (STX) and neosaxitoxin (NEO) (7.7%±4.5%), followed by n-sulfocarbamoyl toxins (C1 and 2, GTX5) (1.3%±0.6%), followed by all decarbamoyl toxins (dcSTX, dcNEO, dcGTX2&3) (〈1%), although differences were noted between PSP toxin compositions for nearshore coastal Gulf of Maine sampling stations compared to offshore Georges Bank sampling stations for 2 out of 3 years; (4) surface cell counts of A. fundyense were a fairly reliable predictor of the presence of toxins throughout the water column; and (5) nearshore surface cell counts of A. fundyense in the coastal Gulf of Maine were not a reliable predictor of A. fundyense populations offshore on Georges Bank for 2 out of the 3 years sampled.
    Description: Vangie Shue was supported through the FDA and also through the Thomas Jefferson High School for Science and Technology Mentorship Program. Research support was provided by National Oceanic and Atmospheric Administration Grant NA06NOS4780245 for the Gulf of Maine Toxicity (GOMTOX) program. BAK, DJM, and DMA were partially supported by the Woods Hole Center for Oceans and Human Health through National Science Foundation Grants OCE-0430724 and OCE-0911031 and National Institute of Environmental Health Sciences Grant 1P50-ES01274201.
    Keywords: Harmful algal bloom ; PSP toxins ; Alexandrium sp. ; Vectorial intoxication ; Gulf of Maine ; Georges Bank
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    Near-bottom circulation and dispersion of sediment containing Alexandrium fundyense cysts in the Gulf of Maine during 2010–2011 (2014)
    Elsevier
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Deep Sea Research Part II: Topical Studies in Oceanography 103 (2014): 96–111, doi:10.1016/j.dsr2.2013.11.003.
    Description: The life cycle of Alexandrium fundyense in the Gulf of Maine includes a dormant cyst stage that spends the winter predominantly in the bottom sediment. Wave-current bottom stress caused by storms and tides induces resuspension of cyst-containing sediment during winter and spring. Resuspended sediment could be transported by water flow to different locations in the Gulf and the redistribution of sediment containing A. fundyense cysts could alter the spatial and temporal manifestation of its spring bloom. The present study evaluates model near-bottom flow during storms, when sediment resuspension and redistribution are most likely to occur, between October and May when A. fundyense cells are predominantly in cyst form. Simulated water column sediment (mud) concentrations from representative locations of the Gulf are used to initialize particle tracking simulations for the period October 2010–May 2011. Particles are tracked in full three-dimensional model solutions including a sinking velocity characteristic of cyst and aggregated mud settling (0.1 mm s−1). Although most of the material was redeposited near the source areas, small percentages of total resuspended sediment from some locations in the western (~4%) and eastern (2%) Maine shelf and the Bay of Fundy (1%) traveled distances longer than 100 km before resettling. The redistribution changed seasonally and was sensitive to the prescribed sinking rate. Estimates of the amount of cysts redistributed with the sediment were small compared to the inventory of cysts in the upper few centimeters of sediment but could potentially have more relevance immediately after deposition.
    Description: Research support to all authors, except DJM and VAS, was provided by U.S. Geological Survey. DJM gratefully acknowledges financial support of the National Oceanic and Atmospheric Administration (Grant NA06NOS4780245 for the Gulf of Maine Toxicity (GOMTOX) program) and the Woods Hole Center for Oceans and Human Health through National Science Foundation Grant OCE-1314642 and National Institute of Environmental Health Sciences Grant 1P01ES021923-01. VAS was supported by the North East Consortium Grant NA05NMF4721057.
    Keywords: Sediment connectivity ; Near-bottom circulation ; Harmful Algal Bloom cysts ; Gulf of Maine ; Alexandrium fundyense ; Particle tracking
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    Transcriptome profiling of a toxic dinoflagellate reveals a gene-rich protist and a potential impact on gene expression due to bacterial presence (2010)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Authors, 2010. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 5 (2010): e9688, doi:10.1371/journal.pone.0009688.
    Description: Dinoflagellates are unicellular, often photosynthetic protists that play a major role in the dynamics of the Earth's oceans and climate. Sequencing of dinoflagellate nuclear DNA is thwarted by their massive genome sizes that are often several times that in humans. However, modern transcriptomic methods offer promising approaches to tackle this challenging system. Here, we used massively parallel signature sequencing (MPSS) to understand global transcriptional regulation patterns in Alexandrium tamarense cultures that were grown under four different conditions. We generated more than 40,000 unique short expression signatures gathered from the four conditions. Of these, about 11,000 signatures did not display detectable differential expression patterns. At a p-value 〈 1E-10, 1,124 signatures were differentially expressed in the three treatments, xenic, nitrogen-limited, and phosphorus-limited, compared to the nutrient-replete control, with the presence of bacteria explaining the largest set of these differentially expressed signatures. Among microbial eukaryotes, dinoflagellates contain the largest number of genes in their nuclear genomes. These genes occur in complex families, many of which have evolved via recent gene duplication events. Our expression data suggest that about 73% of the Alexandrium transcriptome shows no significant change in gene expression under the experimental conditions used here and may comprise a “core” component for this species. We report a fundamental shift in expression patterns in response to the presence of bacteria, highlighting the impact of biotic interaction on gene expression in dinoflagellates.
    Description: This work was primarily funded by a collaborative grant from the National Institutes of Health (R01 ES 013679-01A2) awarded to DB, DMA, and M. Bento Soares. Funding support for DMA and DLE was also provided from the Woods Hole Center for Oceans and Human Health from the NSF/NIEHS Centers for Oceans and Human Health program, NIEHS (P50 ES 012742) and (NSF OCE-043072). Additional support came from the National Science Foundation (EF-0732440) in a grant awarded to F. Gerald Plumley, DB, JDH, and DMA. AM was supported by an Institutional NRSA (T 32 GM98629).
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    Climate change, precipitation and impacts on an estuarine refuge from disease (2011)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 6 (2011): e18849, doi:10.1371/journal.pone.0018849.
    Description: Oysters play important roles in estuarine ecosystems but have suffered recently due to overfishing, pollution, and habitat loss. A tradeoff between growth rate and disease prevalence as a function of salinity makes the estuarine salinity transition of special concern for oyster survival and restoration. Estuarine salinity varies with discharge, so increases or decreases in precipitation with climate change may shift regions of low salinity and disease refuge away from optimal oyster bottom habitat, negatively impacting reproduction and survival. Temperature is an additional factor for oyster survival, and recent temperature increases have increased vulnerability to disease in higher salinity regions. We examined growth, reproduction, and survival of oysters in the New York Harbor-Hudson River region, focusing on a low-salinity refuge in the estuary. Observations were during two years when rainfall was above average and comparable to projected future increases in precipitation in the region and a past period of about 15 years with high precipitation. We found a clear tradeoff between oyster growth and vulnerability to disease. Oysters survived well when exposed to intermediate salinities during two summers (2008, 2010) with moderate discharge conditions. However, increased precipitation and discharge in 2009 reduced salinities in the region with suitable benthic habitat, greatly increasing oyster mortality. To evaluate the estuarine conditions over longer periods, we applied a numerical model of the Hudson to simulate salinities over the past century. Model results suggest that much of the region with suitable benthic habitat that historically had been a low salinity refuge region may be vulnerable to higher mortality under projected increases in precipitation and discharge. Predicted increases in precipitation in the northeastern United States due to climate change may lower salinities past important thresholds for oyster survival in estuarine regions with appropriate substrate, potentially disrupting metapopulation dynamics and impeding oyster restoration efforts, especially in the Hudson estuary where a large basin constitutes an excellent refuge from disease.
    Description: Funding was provided by the Hudson River Foundation, grant number 00607A, and the New York State Department of Environmental Conservation (MOU 2008).
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    Deep sequencing of subseafloor eukaryotic rRNA reveals active fungi across marine subsurface provinces (2013)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 8 (2013): e56335, doi:10.1371/journal.pone.0056335.
    Description: The deep marine subsurface is a vast habitat for microbial life where cells may live on geologic timescales. Because DNA in sediments may be preserved on long timescales, ribosomal RNA (rRNA) is suggested to be a proxy for the active fraction of a microbial community in the subsurface. During an investigation of eukaryotic 18S rRNA by amplicon pyrosequencing, unique profiles of Fungi were found across a range of marine subsurface provinces including ridge flanks, continental margins, and abyssal plains. Subseafloor fungal populations exhibit statistically significant correlations with total organic carbon (TOC), nitrate, sulfide, and dissolved inorganic carbon (DIC). These correlations are supported by terminal restriction length polymorphism (TRFLP) analyses of fungal rRNA. Geochemical correlations with fungal pyrosequencing and TRFLP data from this geographically broad sample set suggests environmental selection of active Fungi in the marine subsurface. Within the same dataset, ancient rRNA signatures were recovered from plants and diatoms in marine sediments ranging from 0.03 to 2.7 million years old, suggesting that rRNA from some eukaryotic taxa may be much more stable than previously considered in the marine subsurface.
    Description: This work was performed with funding from the Center for Dark Energy Biosphere Investigations (C-DEBI) to William Orsi (OCE-0939564) and The Ocean Life Institute (WHOI) to Virginia Edgcomb (OLI-27071359).
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    Swimming speed of larval snail does not correlate with size and ciliary beat frequency (2014)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 8 (2013): e82764, doi:10.1371/journal.pone.0082764.
    Description: Many marine invertebrates have planktonic larvae with cilia used for both propulsion and capturing of food particles. Hence, changes in ciliary activity have implications for larval nutrition and ability to navigate the water column, which in turn affect survival and dispersal. Using high-speed high-resolution microvideography, we examined the relationship between swimming speed, velar arrangements, and ciliary beat frequency of freely swimming veliger larvae of the gastropod Crepidula fornicata over the course of larval development. Average swimming speed was greatest 6 days post hatching, suggesting a reduction in swimming speed towards settlement. At a given age, veliger larvae have highly variable speeds (0.8–4 body lengths s−1) that are independent of shell size. Contrary to the hypothesis that an increase in ciliary beat frequency increases work done, and therefore speed, there was no significant correlation between swimming speed and ciliary beat frequency. Instead, there are significant correlations between swimming speed and visible area of the velar lobe, and distance between centroids of velum and larval shell. These observations suggest an alternative hypothesis that, instead of modifying ciliary beat frequency, larval C. fornicata modify swimming through adjustment of velum extension or orientation. The ability to adjust velum position could influence particle capture efficiency and fluid disturbance and help promote survival in the plankton.
    Description: K.Y.K. Chan was supported by the Postdoctoral Scholar 1 Program at the Woods Hole Oceanographic Institution (WHOI), with funding provided by the Coastal Ocean Institute, the Croucher Foundation, and the Royal Swedish Academy of Sciences. H. Jiang was supported by National Science Foundation grant NSF OCE-1129496 and an award from WHOI's Ocean Life Institute, and D.K. Padilla was supported by NSF IOS-0920032.
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    Indirect human impacts reverse centuries of carbon sequestration and salt marsh accretion (2014)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e93296, doi:10.1371/journal.pone.0093296.
    Description: Direct and indirect human impacts on coastal ecosystems have increased over the last several centuries, leading to unprecedented degradation of coastal habitats and loss of ecological services. Here we document a two-century temporal disparity between salt marsh accretion and subsequent loss to indirect human impacts. Field surveys, manipulative experiments and GIS analyses reveal that crab burrowing weakens the marsh peat base and facilitates further burrowing, leading to bank calving, disruption of marsh accretion, and a loss of over two centuries of sequestered carbon from the marsh edge in only three decades. Analogous temporal disparities exist in other systems and are a largely unrecognized obstacle in attaining sustainable ecosystem services in an increasingly human impacted world. In light of the growing threat of indirect impacts worldwide and despite uncertainties in the fate of lost carbon, we suggest that estimates of carbon emissions based only on direct human impacts may significantly underestimate total anthropogenic carbon emissions.
    Description: This research was made possible by a grant from the National Science Foundation Biological Oceanography Program and the Brown University Undergraduate Teaching and Research Award Program.
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    Humpback whale populations share a core skin bacterial community : towards a health index for marine mammals? (2014)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e90785, doi:10.1371/journal.pone.0090785.
    Description: Microbes are now well regarded for their important role in mammalian health. The microbiology of skin – a unique interface between the host and environment - is a major research focus in human health and skin disorders, but is less explored in other mammals. Here, we report on a cross-population study of the skin-associated bacterial community of humpback whales (Megaptera novaeangliae), and examine the potential for a core bacterial community and its variability with host (endogenous) or geographic/environmental (exogenous) specific factors. Skin biopsies or freshly sloughed skin from 56 individuals were sampled from populations in the North Atlantic, North Pacific and South Pacific oceans and bacteria were characterized using 454 pyrosequencing of SSU rRNA genes. Phylogenetic and statistical analyses revealed the ubiquity and abundance of bacteria belonging to the Flavobacteria genus Tenacibaculum and the Gammaproteobacteria genus Psychrobacter across the whale populations. Scanning electron microscopy of skin indicated that microbial cells colonize the skin surface. Despite the ubiquity of Tenacibaculum and Psychrobater spp., the relative composition of the skin-bacterial community differed significantly by geographic area as well as metabolic state of the animals (feeding versus starving during migration and breeding), suggesting that both exogenous and endogenous factors may play a role in influencing the skin-bacteria. Further, characteristics of the skin bacterial community from these free-swimming individuals were assembled and compared to two entangled and three dead individuals, revealing a decrease in the central or core bacterial community members (Tenacibaculum and Psychrobater spp.), as well as the emergence of potential pathogens in the latter cases. This is the first discovery of a cross-population, shared skin bacterial community. This research suggests that the skin bacteria may be connected to humpback health and immunity and could possibly serve as a useful index for health and skin disorder monitoring of threatened and endangered marine mammals.
    Description: A.A. was funded by a WHOI Ocean Life Institute post-doctoral scholar award, and this research was supported by a grant to A.A. and T.J.M. from Woods Hole Oceanographic Institution's (WHOI) Marine Mammal Center.
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    Genomic and metabolic diversity of Marine Group I Thaumarchaeota in the mesopelagic of two subtropical gyres (2014)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: The work is made available under the Creative Commons CC0 public domain dedication. The definitive version was published in PLoS One 9 (2014): e95380, doi:10.1371/journal.pone.0095380.
    Description: Marine Group I (MGI) Thaumarchaeota are one of the most abundant and cosmopolitan chemoautotrophs within the global dark ocean. To date, no representatives of this archaeal group retrieved from the dark ocean have been successfully cultured. We used single cell genomics to investigate the genomic and metabolic diversity of thaumarchaea within the mesopelagic of the subtropical North Pacific and South Atlantic Ocean. Phylogenetic and metagenomic recruitment analysis revealed that MGI single amplified genomes (SAGs) are genetically and biogeographically distinct from existing thaumarchaea cultures obtained from surface waters. Confirming prior studies, we found genes encoding proteins for aerobic ammonia oxidation and the hydrolysis of urea, which may be used for energy production, as well as genes involved in 3-hydroxypropionate/4-hydroxybutyrate and oxidative tricarboxylic acid pathways. A large proportion of protein sequences identified in MGI SAGs were absent in the marine cultures Cenarchaeum symbiosum and Nitrosopumilus maritimus, thus expanding the predicted protein space for this archaeal group. Identifiable genes located on genomic islands with low metagenome recruitment capacity were enriched in cellular defense functions, likely in response to viral infections or grazing. We show that MGI Thaumarchaeota in the dark ocean may have more flexibility in potential energy sources and adaptations to biotic interactions than the existing, surface-ocean cultures.
    Description: This work was supported by NSF grants EF-826924 (R.S.), OCE-821374 (R.S.) and OCE-1232982 (R.S. and B.K.S.); the DOE JGI 2010 Microbes Program grant CSP77 (R.S. and M.E.S.); National Institutes of Health grant 1UH2DK083993 (H.G.M.). Work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. The contributions of S.K. were funded under Agreement No. HSHQDC-07-C-00020 awarded by the Department of Homeland Security (DHS) for the management and operation of the National Biodefense Analysis and Countermeasures Center (NBACC), a Federally Funded Research and Development Center.
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    Investigating the importance of sediment resuspension in Alexandrium fundyense cyst population dynamics in the Gulf of Maine (2014)
    Elsevier
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Deep Sea Research Part II: Topical Studies in Oceanography 103 (2014): 79–95, doi:10.1016/j.dsr2.2013.10.011.
    Description: Cysts of Alexandrium fundyense, a dinoflagellate that causes toxic algal blooms in the Gulf of Maine, spend the winter as dormant cells in the upper layer of bottom sediment or the bottom nepheloid layer and germinate in spring to initiate new blooms. Erosion measurements were made on sediment cores collected at seven stations in the Gulf of Maine in the autumn of 2011 to explore if resuspension (by waves and currents) could change the distribution of over-wintering cysts from patterns observed in the previous autumn; or if resuspension could contribute cysts to the water column during spring when cysts are viable. The mass of sediment eroded from the core surface at 0.4 Pa ranged from 0.05 kg m−2 near Grand Manan Island, to 0.35 kg m−2 in northern Wilkinson Basin. The depth of sediment eroded ranged from about 0.05 mm at a station with sandy sediment at 70 m water depth on the western Maine shelf, to about 1.2 mm in clayey–silt sediment at 250 m water depth in northern Wilkinson Basin. The sediment erodibility measurements were used in a sediment-transport model forced with modeled waves and currents for the period October 1, 2010 to May 31, 2011 to predict resuspension and bed erosion. The simulated spatial distribution and variation of bottom shear stress was controlled by the strength of the semi-diurnal tidal currents, which decrease from east to west along the Maine coast, and oscillatory wave-induced currents, which are strongest in shallow water. Simulations showed occasional sediment resuspension along the central and western Maine coast associated with storms, steady resuspension on the eastern Maine shelf and in the Bay of Fundy associated with tidal currents, no resuspension in northern Wilkinson Basin, and very small resuspension in western Jordan Basin. The sediment response in the model depended primarily on the profile of sediment erodibility, strength and time history of bottom stress, consolidation time scale, and the current in the water column. Based on analysis of wave data from offshore buoys from 1996 to 2012, the number of wave events inducing a bottom shear stress large enough to resuspend sediment at 80 m ranged from 0 to 2 in spring (April and May) and 0 to 10 in winter (October through March). Wave-induced resuspension is unlikely in water greater than about 100 m deep. The observations and model results suggest that a millimeter or so of sediment and associated cysts may be mobilized in both winter and spring, and that the frequency of resuspension will vary interannually. Depending on cyst concentration in the sediment and the vertical distribution in the water column, these events could result in a concentration in the water column of at least 104 cysts m−3. In some years, resuspension events could episodically introduce cysts into the water column in spring, where germination is likely to be facilitated at the time of bloom formation. An assessment of the quantitative effects of cyst resuspension on bloom dynamics in any particular year requires more detailed investigation.
    Description: Research support to Donald M. Anderson and Bruce A. Keafer provided through the Woods Hole Center for Oceans and Human Health; National Science Foundation Grants OCE-0430724 and OCE-0911031; and National Institute of Environmental Health Sciences Grant 1-P50-ES012742-01; the ECOHAB Grant program through NOAA Grants NA06NOS4780245 and A09NOS4780193; the MERHAB Grant program through NOAA Grant NA11NOS4780025; and the PCMHAB Grant program through NOAA Grant NA11NOS4780023. Research support to all other authors was provided by U.S. Geological Survey.
    Keywords: Sediment transport ; Bottom stress ; Sediment resuspension ; Harmful algal blooms ; Gulf of Maine ; Alexandrium fundyense ; HAB
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    A method for studying protistan diversity using massively parallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA genes (2010)
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    Publication Date: 2022-05-26
    Description: © 2009 The Authors. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 4 (2009): e6372, doi:10.1371/journal.pone.0006372.
    Description: Massively parallel pyrosequencing of amplicons from the V6 hypervariable regions of small-subunit (SSU) ribosomal RNA (rRNA) genes is commonly used to assess diversity and richness in bacterial and archaeal populations. Recent advances in pyrosequencing technology provide read lengths of up to 240 nucleotides. Amplicon pyrosequencing can now be applied to longer variable regions of the SSU rRNA gene including the V9 region in eukaryotes. We present a protocol for the amplicon pyrosequencing of V9 regions for eukaryotic environmental samples for biodiversity inventories and species richness estimation. The International Census of Marine Microbes (ICoMM) and the Microbial Inventory Research Across Diverse Aquatic Long Term Ecological Research Sites (MIRADA-LTERs) projects are already employing this protocol for tag sequencing of eukaryotic samples in a wide diversity of both marine and freshwater environments. Massively parallel pyrosequencing of eukaryotic V9 hypervariable regions of SSU rRNA genes provides a means of estimating species richness from deeply-sampled populations and for discovering novel species from the environment.
    Description: This work was supported by grants from the W.M. Keck Foundation and the Woods Hole Center for Oceans and Human Health from the National Institutes of Health and National Science Foundation (NIH/NIEHS 1 P50 ES012742-01 and NSF/OCE 0430724-J) (LAZ and SH).
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    The taxonomic and functional diversity of microbes at a temperate coastal site : a ‘multi-omic’ study of seasonal and diel temporal variation (2011)
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    Publication Date: 2022-05-26
    Description: © The Authors, 2010. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 5 (2010): e15545, doi:10.1371/journal.pone.0015545.
    Description: How microbial communities change over time in response to the environment is poorly understood. Previously a six-year time series of 16S rRNA V6 data from the Western English Channel demonstrated robust seasonal structure within the bacterial community, with diversity negatively correlated with day-length. Here we determine whether metagenomes and metatranscriptomes follow similar patterns. We generated 16S rRNA datasets, metagenomes (1.2 GB) and metatranscriptomes (157 MB) for eight additional time points sampled in 2008, representing three seasons (Winter, Spring, Summer) and including day and night samples. This is the first microbial ‘multi-omic’ study to combine 16S rRNA amplicon sequencing with metagenomic and metatranscriptomic profiling. Five main conclusions can be drawn from analysis of these data: 1) Archaea follow the same seasonal patterns as Bacteria, but show lower relative diversity; 2) Higher 16S rRNA diversity also reflects a higher diversity of transcripts; 3) Diversity is highest in winter and at night; 4) Community-level changes in 16S-based diversity and metagenomic profiles are better explained by seasonal patterns (with samples closest in time being most similar), while metatranscriptomic profiles are better explained by diel patterns and shifts in particular categories (i.e., functional groups) of genes; 5) Changes in key genes occur among seasons and between day and night (i.e., photosynthesis); but these samples contain large numbers of orphan genes without known homologues and it is these unknown gene sets that appear to contribute most towards defining the differences observed between times. Despite the huge diversity of these microbial communities, there are clear signs of predictable patterns and detectable stability over time. Renewed and intensified efforts are required to reveal fundamental deterministic patterns in the most complex microbial communities. Further, the presence of a substantial proportion of orphan sequences underscores the need to determine the gene products of sequences with currently unknown function.
    Description: Funding for this work was provided by a Natural Environmental Research Council (www.nerc.ac.uk) grant, NE/F00138X/1.
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    The relationship among oceanography, prey fields, and beaked whale foraging habitat in the Tongue of the Ocean (2011)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: This article is distributed under the terms of the Creative Commons CC0 public domain dedication. The definitive version was published in PLoS One 6 (2011): e19269, doi:10.1371/journal.pone.0019269.
    Description: Beaked whales, specifically Blainville's (Mesoplodon densirostris) and Cuvier's (Ziphius cavirostris), are known to feed in the Tongue of the Ocean, Bahamas. These whales can be reliably detected and often localized within the Atlantic Undersea Test and Evaluation Center (AUTEC) acoustic sensor system. The AUTEC range is a regularly spaced bottom mounted hydrophone array covering 〉350 nm2 providing a valuable network to record anthropogenic noise and marine mammal vocalizations. Assessments of the potential risks of noise exposure to beaked whales have historically occurred in the absence of information about the physical and biological environments in which these animals are distributed. In the fall of 2008, we used a downward looking 38 kHz SIMRAD EK60 echosounder to measure prey scattering layers concurrent with fine scale turbulence measurements from an autonomous turbulence profiler. Using an 8 km, 4-leaf clover sampling pattern, we completed a total of 7.5 repeat surveys with concurrently measured physical and biological oceanographic parameters, so as to examine the spatiotemporal scales and relationships among turbulence levels, biological scattering layers, and beaked whale foraging activity. We found a strong correlation among increased prey density and ocean vertical structure relative to increased click densities. Understanding the habitats of these whales and their utilization patterns will improve future models of beaked whale habitat as well as allowing more comprehensive assessments of exposure risk to anthropogenic sound.
    Description: The data collection and analysis was funded by the Office of Naval Research as N00014-08-1-1162.
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    Detecting the influence of initial pioneers on succession at deep-sea vents (2013)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 7 (2012): e50015, doi:10.1371/journal.pone.0050015.
    Description: Deep-sea hydrothermal vents are subject to major disturbances that alter the physical and chemical environment and eradicate the resident faunal communities. Vent fields are isolated by uninhabitable deep seafloor, so recolonization via dispersal of planktonic larvae is critical for persistence of populations. We monitored colonization near 9°50′N on the East Pacific Rise following a catastrophic eruption in order to address questions of the relative contributions of pioneer colonists and environmental change to variation in species composition, and the role of pioneers at the disturbed site in altering community structure elsewhere in the region. Pioneer colonists included two gastropod species: Ctenopelta porifera, which was new to the vent field, and Lepetodrilus tevnianus, which had been rare before the eruption but persisted in high abundance afterward, delaying and possibly out-competing the ubiquitous pre-eruption congener L. elevatus. A decrease in abundance of C. porifera over time, and the arrival of later species, corresponded to a decrease in vent fluid flow and in the sulfide to temperature ratio. For some species these successional changes were likely due to habitat requirements, but other species persisted (L. tevnianus) or arrived (L. elevatus) in patterns unrelated to their habitat preferences. After two years, disturbed communities had started to resemble pre-eruption ones, but were lower in diversity. When compared to a prior (1991) eruption, the succession of foundation species (tubeworms and mussels) appeared to be delayed, even though habitat chemistry became similar to the pre-eruption state more quickly. Surprisingly, a nearby community that had not been disturbed by the eruption was invaded by the pioneers, possibly after they became established in the disturbed vents. These results indicate that the post-eruption arrival of species from remote locales had a strong and persistent effect on communities at both disturbed and undisturbed vents.
    Description: The authors received funding from National Science Foundation grant OCE-0424953, WHOI Deep Ocean Exploration Institute, WHOI Summer Student Fellow program, Woods Hole Partnership in Education Program, IFREMER and CNRS, Fondation TOTAL Chair Extreme Marine Environment, Biodiversity and Global change.
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    The Genomic Standards Consortium (2011)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS Biology 9 (2011): e1001088, doi:10.1371/journal.pbio.1001088.
    Description: A vast and rich body of information has grown up as a result of the world's enthusiasm for 'omics technologies. Finding ways to describe and make available this information that maximise its usefulness has become a major effort across the 'omics world. At the heart of this effort is the Genomic Standards Consortium (GSC), an open-membership organization that drives community-based standardization activities, Here we provide a short history of the GSC, provide an overview of its range of current activities, and make a call for the scientific community to join forces to improve the quality and quantity of contextual information about our public collections of genomes, metagenomes, and marker gene sequences.
    Description: NERC International Opportunities Fund Award NE/3521773/1 and NE/E007325/1 (http://www.nerc. ac.uk/funding/) and National Science Foundation grant RCN4GSC, DBI-0840989 (http://www.nsf.gov/funding/).
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    Exploring the diversity of Gardnerella vaginalis in the genitourinary tract microbiota of monogamous couples through subtle nucleotide variation (2011)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 6 (2011): e26732, doi:10.1371/journal.pone.0026732.
    Description: Bacterial vaginosis (BV) is an enigmatic disease of unknown origin that affects a large percentage of women. The vaginal microbiota of women with BV is associated with serious sequelae, including abnormal pregnancies. The etiology of BV is not fully understood, however, it has been suggested that it is transmissible, and that G. vaginalis may be an etiological agent. Studies using enzymatic assays to define G. vaginalis biotypes, as well as more recent genomic comparisons of G. vaginalis isolates from symptomatic and asymptomatic women, suggest that particular G. vaginalis strains may play a key role in the pathogenesis of BV. To explore G. vaginalis diversity, distribution and sexual transmission, we developed a Shannon entropy-based method to analyze low-level sequence variation in 65,710 G. vaginalis 16S rRNA gene segments that were PCR-amplified from vaginal samples of 53 monogamous women and from urethral and penile skin samples of their male partners. We observed a high degree of low-level diversity among G. vaginalis sequences with a total of 46 unique sequence variants (oligotypes), and also found strong correlations of these oligotypes between sexual partners. Even though Gram stain-defined normal and some Gram stain-defined intermediate oligotype profiles clustered together in UniFrac analysis, no single G. vaginalis oligotype was found to be specific to BV or normal vaginal samples. This study describes a novel method for investigating G. vaginalis diversity at a low level of taxonomic discrimination. The findings support cultivation-based studies that indicate sexual partners harbor the same strains of G. vaginalis. This study also highlights the fact that a few, reproducible nucleotide variations within the 16S rRNA gene can reveal clinical or epidemiological associations that would be missed by genus-level or species-level categorization of 16S rRNA data.
    Description: This work is supported by funding from the Research Institute for Children in New Orleans and NIH grant 5RO1AI79071-2.
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    The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) : illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing (2014)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS Biology 12 (2014): e1001889, doi:10.1371/journal.pbio.1001889.
    Description: Microbial ecology is plagued by problems of an abstract nature. Cell sizes are so small and population sizes so large that both are virtually incomprehensible. Niches are so far from our everyday experience as to make their very definition elusive. Organisms that may be abundant and critical to our survival are little understood, seldom described and/or cultured, and sometimes yet to be even seen. One way to confront these problems is to use data of an even more abstract nature: molecular sequence data. Massive environmental nucleic acid sequencing, such as metagenomics or metatranscriptomics, promises functional analysis of microbial communities as a whole, without prior knowledge of which organisms are in the environment or exactly how they are interacting. But sequence-based ecological studies nearly always use a comparative approach, and that requires relevant reference sequences, which are an extremely limited resource when it comes to microbial eukaryotes. In practice, this means sequence databases need to be populated with enormous quantities of data for which we have some certainties about the source. Most important is the taxonomic identity of the organism from which a sequence is derived and as much functional identification of the encoded proteins as possible. In an ideal world, such information would be available as a large set of complete, well-curated, and annotated genomes for all the major organisms from the environment in question. Reality substantially diverges from this ideal, but at least for bacterial molecular ecology, there is a database consisting of thousands of complete genomes from a wide range of taxa, supplemented by a phylogeny-driven approach to diversifying genomics. For eukaryotes, the number of available genomes is far, far fewer, and we have relied much more heavily on random growth of sequence databases, raising the question as to whether this is fit for purpose.
    Description: This project was funded by the Gordon and Betty Moore Foundation (GBMF; Grants GBMF2637 and GBMF3111) to the National Center for Genome Resources (NCGR) and the National Center for Marine Algae and Microbiota (NCMA).
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    Assessing the health of the U.S. west coast with a regional-scale application of the Ocean Health Index (2014)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: This is an open-access article, free of all copyright. The definitive version was published in PLoS One 9 (2014): e98995, doi:10.1371/journal.pone.0098995.
    Description: Management of marine ecosystems increasingly demands comprehensive and quantitative assessments of ocean health, but lacks a tool to do so. We applied the recently developed Ocean Health Index to assess ocean health in the relatively data-rich US west coast region. The overall region scored 71 out of 100, with sub-regions scoring from 65 (Washington) to 74 (Oregon). Highest scoring goals included tourism and recreation (99) and clean waters (87), while the lowest scoring goals were sense of place (48) and artisanal fishing opportunities (57). Surprisingly, even in this well-studied area data limitations precluded robust assessments of past trends in overall ocean health. Nonetheless, retrospective calculation of current status showed that many goals have declined, by up to 20%. In contrast, near-term future scores were on average 6% greater than current status across all goals and sub-regions. Application of hypothetical but realistic management scenarios illustrate how the Index can be used to predict and understand the tradeoffs among goals and consequences for overall ocean health. We illustrate and discuss how this index can be used to vet underlying assumptions and decisions with local stakeholders and decision-makers so that scores reflect regional knowledge, priorities and values. We also highlight the importance of ongoing and future monitoring that will provide robust data relevant to ocean health assessment.
    Description: Beau and Heather Wrigley generously provided the founding grant. Additional financial and in-kind support was provided by the Pacific Life Foundation, Thomas W. Haas Fund of the New Hampshire Charitable Foundation, the Oak Foundation, Akiko Shiraki Dynner Fund for Ocean Exploration and Conservation, Darden Restaurants Inc. Foundation, Conservation International, New England Aquarium, National Geographic, and the University of California Santa Barbara's National Center for Ecological Analysis and Synthesis, which supported the Ecosystem Health Working Group as part of the Science of Ecosystem-Based Management project funded by the David and Lucile Packard Foundation. Individual authors also acknowledge support from the U.S. National Science Foundation.
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    Modification of the Quaternary stratigraphic framework of the inner-continental shelf by Holocene marine transgression : an example offshore of Fire Island, New York (2014)
    Elsevier
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    Publication Date: 2022-05-26
    Description: This paper is not subject to U.S. copyright. The definitive version was published in Marine Geology 355 (2014): 346–360, doi:10.1016/j.margeo.2014.06.011.
    Description: The inner-continental shelf off Fire Island, New York was mapped in 2011 using interferometric sonar and high-resolution chirp seismic-reflection systems. The area mapped is approximately 50 km long by 8 km wide, extending from Moriches Inlet to Fire Island Inlet in water depths ranging from 8 to 32 m. The morphology of this inner-continental shelf region and modern sediment distribution patterns are determined by erosion of Pleistocene glaciofluvial sediments during the ongoing Holocene marine transgression; much of the shelf is thus an actively forming ravinement surface. Remnants of a Pleistocene outwash lobe define a submerged headland offshore of central Fire Island. East of the submerged headland, relatively older Pleistocene outwash is exposed over much of the inner-continental shelf and covered by asymmetric, sorted bedforms interpreted to indicate erosion and westward transport of reworked sediment. Erosion of the eastern flank of the submerged Pleistocene headland over the last ~ 8000 years yielded an abundance of modern sand that was transported westward and reworked into a field of shoreface-attached ridges offshore of western Fire Island. West of the submerged headland, erosion of Pleistocene outwash continues in troughs between the sand ridges, resulting in modification of the lower shoreface. Comparison of the modern sand ridge morphology with the morphology of the underlying ravinement surface suggests that the sand ridges have moved a minimum of ~ 1000 m westward since formation. Comparison of modern sediment thickness mapped in 1996–1997 and 2011 allows speculation that the nearshore/shoreface sedimentary deposit has gained sediment at the expense of deflation of the sand ridges.
    Description: This research was funded by the U.S. Geological Survey, Coastal and Marine Geology Program.
    Keywords: Seafloor mapping ; Inner-continental shelf ; Shoreface ; Sand ridges ; Sorted bedforms ; Sediment transport ; Ravinement surface ; Quaternary stratigraphy
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    Evolutionary strategies of viruses, bacteria and archaea in hydrothermal vent ecosystems revealed through metagenomics (2014)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e109696, doi:10.1371/journal.pone.0109696.
    Description: The deep-sea hydrothermal vent habitat hosts a diverse community of archaea and bacteria that withstand extreme fluctuations in environmental conditions. Abundant viruses in these systems, a high proportion of which are lysogenic, must also withstand these environmental extremes. Here, we explore the evolutionary strategies of both microorganisms and viruses in hydrothermal systems through comparative analysis of a cellular and viral metagenome, collected by size fractionation of high temperature fluids from a diffuse flow hydrothermal vent. We detected a high enrichment of mobile elements and proviruses in the cellular fraction relative to microorganisms in other environments. We observed a relatively high abundance of genes related to energy metabolism as well as cofactors and vitamins in the viral fraction compared to the cellular fraction, which suggest encoding of auxiliary metabolic genes on viral genomes. Moreover, the observation of stronger purifying selection in the viral versus cellular gene pool suggests viral strategies that promote prolonged host integration. Our results demonstrate that there is great potential for hydrothermal vent viruses to integrate into hosts, facilitate horizontal gene transfer, and express or transfer genes that manipulate the hosts’ functional capabilities.
    Description: Funding for sequencing of the viral metagenome was provided by the Gordon and Betty Moore Foundation. All other funding was provided by a NASA Astrobiology Institute grant through Cooperative Agreement NNA04CC09A to the Geophysical Laboratory at the Carnegie Institution for Science. R.A. was funded by a NSF Graduate Research Fellowship through NSF grant number DGE-0718124, an NSF IGERT grant to the University of Washington Astrobiology Program, and the ARCS Foundation.
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    The transcriptional response to oxidative stress during vertebrate development : effects of tert-butylhydroquinone and 2,3,7,8-tetrachlorodibenzo-p-dioxin (2014)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e113158, doi:10.1371/journal.pone.0113158.
    Description: Oxidative stress is an important mechanism of chemical toxicity, contributing to teratogenesis and to cardiovascular and neurodegenerative diseases. Developing animals may be especially sensitive to chemicals causing oxidative stress. The developmental expression and inducibility of anti-oxidant defenses through activation of NF-E2-related factor 2 (NRF2) affect susceptibility to oxidants, but the embryonic response to oxidants is not well understood. To assess the response to chemically mediated oxidative stress and how it may vary during development, zebrafish embryos, eleutheroembryos, or larvae at 1, 2, 3, 4, 5, and 6 days post fertilization (dpf) were exposed to DMSO (0.1%), tert-butylhydroquinone (tBHQ; 10 µM) or 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD; 2 nM) for 6 hr. Transcript abundance was assessed by real-time qRT-PCR and microarray. qRT-PCR showed strong (4- to 5-fold) induction of gstp1 by tBHQ as early as 1 dpf. tBHQ also induced gclc (2 dpf), but not sod1, nqo1, or cyp1a. TCDD induced cyp1a but none of the other genes. Microarray analysis showed that 1477 probes were significantly different among the DMSO-, tBHQ-, and TCDD-treated eleutheroembryos at 4 dpf. There was substantial overlap between genes induced in developing zebrafish and a set of marker genes induced by oxidative stress in mammals. Genes induced by tBHQ in 4-dpf zebrafish included those involved in glutathione synthesis and utilization, signal transduction, and DNA damage/stress response. The strong induction of hsp70 determined by microarray was confirmed by qRT-PCR and by use of transgenic zebrafish expressing enhanced green fluorescent protein (EGFP) under control of the hsp70 promoter. Genes strongly down-regulated by tBHQ included mitfa, providing a molecular explanation for the loss of pigmentation in tBHQ-exposed embryos. These data show that zebrafish embryos are responsive to oxidative stress as early as 1 dpf, that responsiveness varies with development in a gene-specific manner, and that the oxidative stress response is substantially conserved in vertebrate animals.
    Description: This research was supported in part by National Institutes of Health grants R01ES016366 (MEH), R01ES006272 (MEH), R01ES015912 (JJS), and F32ES017585 (ART-L), the Andrew W. Mellon Foundation Endowed Fund for Innovative Research, a WHOI (Woods Hole Oceanographic Institution) Postdoctoral Scholar award, and the Walter A. and Hope Noyes Smith endowed chair (MEH). AGM and MJC were supported in part by the Marine Biological Laboratory's Program in Global Infectious Disease, funded by the Ellison Medical Foundation.
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    Bisphenol A in oocytes leads to growth suppression and altered stress performance in juvenile rainbow trout (2010)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: © The Authors, 2010. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 5 (2010): e10741, doi:10.1371/journal.pone.0010741.
    Description: Bisphenol A (BPA), used in the manufacture of plastics, is ubiquitously distributed in the aquatic environment. However, the effect of maternal transfer of these xenobiotics on embryonic development and growth is poorly understood in fish. We tested the hypothesis that BPA in eggs, mimicking maternal transfer, impact development, growth and stress performance in juveniles of rainbow trout (Oncorhynchus mykiss). Trout oocytes were exposed to 0, 30 and 100 µg.mL−1 BPA for 3 h in ovarian fluid, followed by fertilization. The embryos were maintained in clean water and sampled temporally over 156-days post-fertilization (dpf), and juveniles were sampled at 400-dpf. The egg BPA levels declined steadily after exposure and were undetectable after 21- dpf. Oocyte exposure to BPA led to a delay in hatching and yolk absorption and a consistently lower body mass over 152-dpf. The growth impairment, especially in the high BPA group, correlated with higher growth hormone (GH) content and lower GH receptors gene expression. Also, mRNA abundances of insulin-like growth factors (IGF-1 and IGF-2) and their receptors were suppressed in the BPA treated groups. The juvenile fish grown from the BPA-enriched eggs had lower body mass and showed perturbations in plasma cortisol and glucose response to an acute stressor. BPA accumulation in eggs, prior to fertilization, leads to hatching delays, growth suppression and altered stress response in juvenile trout. The somatotropic axis appears to be a key target for BPA impact during early embryogenesis, leading to long term growth and stress performance defects in fish.
    Description: This work was supported by funds from the Natural Science and Engineering Research Council (NSERC) of Canada Discovery grant and the Ontario Ministry of Agriculture and Food.
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    Deep-water chemosynthetic ecosystem research during the Census of Marine Life decade and beyond : a proposed deep-ocean road map (2011)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 6 (2011): e23259, doi:10.1371/journal.pone.0023259.
    Description: The ChEss project of the Census of Marine Life (2002–2010) helped foster internationally-coordinated studies worldwide focusing on exploration for, and characterization of new deep-sea chemosynthetic ecosystem sites. This work has advanced our understanding of the nature and factors controlling the biogeography and biodiversity of these ecosystems in four geographic locations: the Atlantic Equatorial Belt (AEB), the New Zealand region, the Arctic and Antarctic and the SE Pacific off Chile. In the AEB, major discoveries include hydrothermal seeps on the Costa Rica margin, deepest vents found on the Mid-Cayman Rise and the hottest vents found on the Southern Mid-Atlantic Ridge. It was also shown that the major fracture zones on the MAR do not create barriers for the dispersal but may act as trans-Atlantic conduits for larvae. In New Zealand, investigations of a newly found large cold-seep area suggest that this region may be a new biogeographic province. In the Arctic, the newly discovered sites on the Mohns Ridge (71°N) showed extensive mats of sulfur-oxidisng bacteria, but only one gastropod potentially bears chemosynthetic symbionts, while cold seeps on the Haakon Mossby Mud Volcano (72°N) are dominated by siboglinid worms. In the Antarctic region, the first hydrothermal vents south of the Polar Front were located and biological results indicate that they may represent a new biogeographic province. The recent exploration of the South Pacific region has provided evidence for a sediment hosted hydrothermal source near a methane-rich cold-seep area. Based on our 8 years of investigations of deep-water chemosynthetic ecosystems worldwide, we suggest highest priorities for future research: (i) continued exploration of the deep-ocean ridge-crest; (ii) increased focus on anthropogenic impacts; (iii) concerted effort to coordinate a major investigation of the deep South Pacific Ocean – the largest contiguous habitat for life within Earth's biosphere, but also the world's least investigated deep-ocean basin.
    Description: Alfred P. Sloan Foundation for the ChEss-Census of Marine Life programme (2002–2010) and the SYNDEEP synthesis project (2009–2010) (www.coml.org). Fondation Total for the ChEss synthesis phase and SYNDEEP synthesis project (2007–2010) (http://fondation.total.com/). Petersen Fellowship in IFM-GEOMAR to CRG.
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    Toward an understanding of the molecular mechanisms of barnacle larval settlement : a comparative transcriptomic approach (2011)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 6 (2011): e22913, doi:10.1371/journal.pone.0022913.
    Description: The barnacle Balanus amphitrite is a globally distributed biofouler and a model species in intertidal ecology and larval settlement studies. However, a lack of genomic information has hindered the comprehensive elucidation of the molecular mechanisms coordinating its larval settlement. The pyrosequencing-based transcriptomic approach is thought to be useful to identify key molecular changes during larval settlement. Using 454 pyrosequencing, we collected totally 630,845 reads including 215,308 from the larval stages and 415,537 from the adults; 23,451 contigs were generated while 77,785 remained as singletons. We annotated 31,720 of the 92,322 predicted open reading frames, which matched hits in the NCBI NR database, and identified 7,954 putative genes that were differentially expressed between the larval and adult stages. Of these, several genes were further characterized with quantitative real-time PCR and in situ hybridization, revealing some key findings: 1) vitellogenin was uniquely expressed in late nauplius stage, suggesting it may be an energy source for the subsequent non-feeding cyprid stage; 2) the locations of mannose receptors suggested they may be involved in the sensory system of cyprids; 3) 20 kDa-cement protein homologues were expressed in the cyprid cement gland and probably function during attachment; and 4) receptor tyrosine kinases were expressed higher in cyprid stage and may be involved in signal perception during larval settlement. Our results provide not only the basis of several new hypotheses about gene functions during larval settlement, but also the availability of this large transcriptome dataset in B. amphitrite for further exploration of larval settlement and developmental pathways in this important marine species.
    Description: This work was supported by grants (N-HKUST602/09 and AoE/P-04/04-II) from the Research Grants Council of the Hong Kong Special Administrative Region and an award (SA-C0040/UK-C0016) made by KAUST to P-Y Qian.
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