Nutrients and oxygen concentrations measured in water samples from the North Atlantic during the James Cook cruise JC087 in March 2013

Analysis for micro-molar concentrations of nitrate and nitrite, nitrite, phosphate, silicate and ammonia was undertaken on a SEAL Analytical UK Ltd, AA3 segmented flow autoanalyser following methods described by Kirkwood (1996). Samples were drawn from Niskin bottles on the CTD into 15ml polycarbonate centrifuge tubes and kept refrigerated at approximately 4oC until analysis, which generally commenced within 30 minutes. Overall 23 runs with 597 samples were analysed. This is a total of 502 CTD samples, 69 underway samples and 26 from other sources. An artificial seawater matrix (ASW) of 40g/litre sodium chloride was used as the inter-sample wash and standard matrix. The nutrient free status of this solution was checked by running Ocean Scientific International (OSI) low nutrient seawater (LNS) on every run. A single set of mixed standards were made up by diluting 5mM solutions made from weighed dried salts in 1litre of ASW into plastic 250ml volumetric flasks that had been cleaned by washing in MilliQ water (MQ). Data processing was undertaken using SEAL Analytical UK Ltd proprietary software (AACE 6.07) and was performed within a few hours of the run being finished. The sample time was 60 seconds and the wash time was 30 seconds. The lines were washed daily with wash solutions specific for each chemistry, but comprised of MQ, MQ and SDS, MQ and Triton-X, or MQ and Brij-35. Three times during the cruise the phosphate and silicate channels were washed with a weak sodium hypochlorite solution.

Per-field land use and land cover data set of the Haean catchment, South Korea

Detailed data on land use and land cover constitute important information for Earth system models, environmental monitoring and ecosystem services research. Global land cover products are evolving rapidly; however, there is still a lack of information particularly for heterogeneous agricultural landscapes. We censused land use and land cover field by field in the agricultural mosaic catchment Haean in South Korea. We recorded the land cover types with additional information on agricultural practice. In this paper we introduce the data, their collection and the post-processing protocol. Furthermore, because it is important to quantitatively evaluate available land use and land cover products, we compared our data with the MODIS Land Cover Type product (MCD12Q1). During the studied period, a large portion of dry fields was converted to perennial crops. Compared to our data, the forested area was underrepresented and the agricultural area overrepresented in MCD12Q1. In addition, linear landscape elements such as waterbodies were missing in the MODIS product due to its coarse spatial resolution. The data presented here can be useful for earth science and ecosystem services research.

Carbonate chemistry, community metabolism, PAR, temperature and salinity of One Tree Island reef

There are few in situ studies showing how net community calcification (Gnet) of coral reefs is related to carbonate chemistry, and the studies to date have demonstrated different predicted rates of change. In this study, we measured net community production (Pnet), Gnet, and carbonate chemistry of a reef flat at One Tree Island, Great Barrier Reef. Diurnal pCO2 variability of 289-724 µatm was driven primarily by photosynthesis and respiration. The reef flat was found to be net autotrophic, with daily production of ? 35 mmol C/m**2/d and net calcification of ? 33 mmol C/m**2/d . Gnet was strongly related to Pnet, which drove a hysteresis pattern in the relationship between Gnet and aragonite saturation state (Omega ar). Although Pnet was the main driver of Gnet, Omega ar was still an important factor, where 95% of the variance in Gnet could be described by Pnet and Omega ar. Based on the observed in situ relationship, Gnet would be expected to reach zero when Omega ar is 2.5. It is unknown what proportion of a decline in Gnet would be through reduced calcification and what would occur through increased dissolution, but the results here support predictions that overall calcium carbonate production will decline in coral reefs as a result of ocean acidification.

Nd and Sr isotopic compositions and isotope dilution trace element concentrations from 7 sediment cores along the southeast Greenland margin

The Nd and Sr isotopic compositions of Quaternary glacial and glacimarine siliciclastic sediments deposited along the margin of southeast Greenland were determined to assess the roles of the Greenland, Iceland, and more distal ice sheets in delivering detritus to this portion of the northern North Atlantic. The isotopic compositions of detritus generated by portions of the southern Greenland Ice Sheet were defined through measurements of till and trough mouth fan sediments. Massive diamicts from the Scoresby Sund trough mouth fan show a restricted range of e-Nd (-11.8 to -16.6) and 87Sr/86Sr (0.7192-0.7246) consistent with their derivation from mixtures of sediments derived from Paleoproterozoic and/or Caledonian basement and Tertiary Greenland basalts. Further south at Kangerlussuaq, till isotopic compositions covary with the underlying basement type, with low e-Nd values in the inner fiord (-18.1) reflecting the erosion of the local Precambrian gneisses, but with higher e-Nd values (-2.3 to 2.5) found where the trough crosses East Greenland Tertiary basalts. Fine-grained (< 63 µm) sediments deposited along the southeast Greenland margin also show regular spatial isotopic variations. Ambient sediments and ice-rafted detritus in the southern Irminger Basin trend towards low e-Nd values (to ~ -28) and 87Sr/86Sr ratios (~ 0.711 to ~ 0.715) and are likely derived from proximal Archean gneisses of SE Greenland. Further north in the northern Irminger and Blosseville Basins, sediments trend toward much higher e-Nd (> -4) and low 87Sr/86Sr (< 0.709) reflecting a component derived from the local Iceland volcanic rocks and/or the East Greenland Tertiary basalts. In all three regions, the locally-derived detritus is intermixed with sediment with an intermediate e-Nd value (~ -10) and 87Sr/86Sr (~ 0.718) that was likely delivered by icebergs emanating from the Eurasian Ice Sheets and not from eastern Greenland. Deposition of glacial sediments from both proximal and distal (Eurasian) sources occurred adjacent to SE Greenland throughout the past 50 Ka, with periodic increases in IRD deposition at various times including those of Heinrich events 1, 2 and 4. These results suggest that at least the southern portions of the Greenland Ice Sheet experienced periodic instabilities during the Last Glacial period.

Shotgun proteomics reveals physiological response to ocean acidification in Crassostrea gigas

Background. Ocean acidification as a result of increased anthropogenic CO2 emissions is occurring in marine and estuarine environments worldwide. The coastal ocean experiences additional daily and seasonal fluctuations in pH that can be lower than projected end of century open ocean pH reductions. Projected and current ocean acidification have wide-ranging effects on many aquatic organisms, however the exact mechanisms of the impacts of ocean acidification on many of these animals remains to be characterized. Methods. In order to assess the impact of ocean acidification on marine invertebrates, Pacific oysters (Crassostrea gigas) were exposed to one of four different pCO2 levels for four weeks: 400 µatm (pH 8.0), 800 µatm (pH 7.7), 1000 µatm (pH 7.6), or 2800 µatm (pH 7.3). At the end of 4 weeks a variety of physiological parameters were measured to assess the impacts of ocean acidification: tissue glycogen content and fatty acid profile, shell micromechanical properties, and response to acute heat shock. To determine the effects of ocean acidification on the underlying molecular physiology of oysters and their stress response, some of the oysters from 400 µatm and 2800 µatm were exposed to an additional mechanical stress and shotgun proteomics were done on oysters from high and low pCO2 and from with and without mechanical stress. Results. At the end of the four week exposure period, oysters in all four pCO2 environments deposited new shell, but growth rate was not different among the treatments. However, micromechanical properties of the new shell were compromised by elevated pCO2. Elevated pCO2 affected neither whole body fatty acid composition, nor glycogen content, nor mortality rate associated with acute heat shock. Shotgun proteomics revealed that several physiological pathways were significantly affected by ocean acidification, including antioxidant response, carbohydrate metabolism, and transcription and translation. Additionally, the proteomic response to a second stress differed with pCO2, with numerous processes significantly affected by mechanical stimulation at high versus low pCO2 (all proteomics data are available in the ProteomeXchange under the identifier PXD000835). Discussion. Oyster physiology is significantly altered by exposure to elevated pCO2, indicating changes in energy resource use. This is especially apparent in the assessment of the effects of pCO2 on the proteomic response to a second stress. The altered stress response illustrates that ocean acidification may impact how oysters respond to other changes in their environment. These data contribute to an integrative view of the effects of ocean acidification on oysters as well as physiological trade-offs during environmental stress.

Petrology and origin of basalts at DSDP Hole 66-487

The volcanism of Central America, according to current theory (Pichler and Weyl, 1973; Stoiber and Carr, 1974; Hey, 1977), is related to the subduction of the Cocos Plate under the North American lithospheric plate and the melting of ocean crust material in the subduction zone (Green and Ringwood, 1968; Dickinson, 1970, Fitton, 1971). Since Cocos Plate subduction occurs at the rate of more than 7 cm/y. (Hey et al., 1977), basalts underlying upper Miocene sediments of the Middle America Trench outer slope, penetrated in Hole 487 (Fig. 1) during Leg 66 (Moore et al., 1979), should have formed far from their present position if current theory is accurate. Present manifestations of basaltic magmatism in adjacent areas of the Pacific derive from the axial part of the East Pacific Rise, the Galapagos spreading center, and transform fracture zones. The question arises: Are there analogs of the Middle America Trench basalts among magmatic cock associated with these modern features, or do the trench basalts have some other origin?

Bacterial abundance in the eastern Mediteranean Sea in August and September 2008 during SES_GR2

The SES_GR2_MICROBIAL PARAMETERS dataset is based on samples collected in the framework of the project SESAME, in the Ionian, Libyan and Aegean Sea during August-September 2008. The objectives were to measure the standing stocks and calculate the production of the microbial compartment of the food web, describe the vertical distribution pattern and characterize its structure and function through the water column. Subsamples for virus, heterotrophic bacteria and cyanobacteria (Synechococcus spp. and Prochlorococcus spp.) counting were analyzed using a FACSCalibur (Becton Dickinson) flow cytometer equipped with a standard laser (488 nm) and filter set and using deionized water as sheath fluid. Fluorescent beads with a diameter of 0.97 ?m (Polysciences) were added to each sample as an internal standard, and all parameters were normalized to the beads and expressed as relative units. SYBRGreen I stain (Molecular Probe) was used to stain viral and heterotrophic bacterial DNA. Viruses were counted according to (Brussaard 1984). In order to avoid bulk consentrations of viruses samples we dilluted to Tris-EDTA (pH=8,0) buffer to a final sollution of 1/5 to 1/100. Total abundance and nucleid content classes were calculated using the Paint-A-Gate software (Becton Dickinson).

(Table 2) Composition of the deapest pore fluids from ODP Holes 168-1030B and 168-1031A

On the eastern flank of the Juan de Fuca Ridge, reaction between upwelling basement fluid and sediment alters hydrothermal fluxes of Ca, SiO2(aq), SO4, PO4, NH4, and alkalinity. We used the Global Implicit Multicomponent Reactive Transport (GIMRT) code to model the processes occurring in the sediment column (diagenesis, sediment burial, fluid advection, and multicomponent diffusion) and to estimate net seafloor fluxes of solutes. Within the sediment section, the reactions controlling the concentrations of the solutes listed above are organic matter degradation via SO4 reduction, dissolution of amorphous silica, reductive dissolution of amorphous Fe(III)-(hydr)oxide, and precipitation of calcite, carbonate fluorapatite, and amorphous Fe(II)-sulfide. Rates of specific discharge estimated from pore-water Mg profiles are 2 to 3 mm/yr. At this site the basement hydrothermal system is a source of NH4, SiO2(aq), and Ca, and a sink of SO4, PO4, and alkalinity. Reaction within the sediment column increases the hydrothermal sources of NH4 and SiO2(aq), increases the hydrothermal sinks of SO4 and PO4, and decreases the hydrothermal source of Ca. Reaction within the sediment column has a spatially variable effect on the hydrothermal flux of alkalinity. Because the model we used was capable of simulating the observed pore-water chemistry by using mechanistic descriptions of the biogeochemical processes occurring in the sediment column, it could be used to examine the physical controls on hydrothermal fluxes of solutes in this setting. Two series of simulations in which we varied fluid flow rate (1 to 100 mm/yr) and sediment thickness (10 to 100 m) predict that given the reactions modeled in this study, the sediment section will contribute most significantly to fluxes of SO4 and NH4 at slow flow rates and intermediate sediment thickness and to fluxes of SiO2(aq) at slow flow rates and large sediment thickness. Reaction within the sediment section could approximately double the hydrothermal sink of PO4 over a range of flow rates and sediment thickness, and could slightly decrease (by

Abundance and Biomass from heterotrophic bacteria, Synechococcus, Prochlorococcus and Virus in the eastern Mediteranean Sea in October 2008 during SES_GR2

The HCMR_SES_LAGRANGIAN_GR2_ MICROBIAL PARAMETERS dataset is based on samples collected in the framework of the project SESAME, in the North Aegean Sea during October 2008. The objectives were to measure the standing stocks and calculate the production of the microbial compartment of the food web, describe the vertical distribution pattern and characterize its structure and function through the water column as influenced by the BSW. Heterotrophic bacteria, Synechococcus, Prochlorococcus and Virus abundance: Subsamples for virus, heterotrophic bacteria and cyanobacteria (Synechococcus spp. and Prochlorococcus spp.) counting were analyzed using a FACSCalibur (Becton Dickinson) flow cytometer equipped with a standard laser (488 nm) and filter set and using deionized water as sheath fluid. Fluorescent beads with a diameter of 0.97 µm (Polysciences) were added to each sample as an internal standard, and all parameters were normalized to the beads and expressed as relative units. SYBRGreen I stain (Molecular Probe) was used to stain viral and heterotrophic bacterial DNA. Viruses were counted according to (Brussaard 1984). In order to avoid bulk consentrations of viruses samples we dilluted to Tris-EDTA (pH=8,0) buffer to a final sollution of 1/5 to 1/100. Total abundance and nucleid content classes were calculated using the Paint-A-Gate software (Becton Dickinson). Heterotrophic Nanoflagellate abundance: Subsamples (30-150 ml) were concentrated on 25mm black polycarbonate filters of porosity 0.6?m and stained with DAPI for 10 min (Porter and Feig 1980). Under epifluorescence microscopy heterotrophic nanoflagellates (HNAN) were distinguished using UV and blue excitation and enumerated. Nanoflagellates were classified in size categories and the biovolume was calculated. Ciliate abundance: For ciliate identification and enumeration, 100-3000 ml samples were left for 24h-4d for sedimentation and then observed under an inverted microscope. Ciliates were counted, distinguished into size-classes and major taxonomic groups and identified down to genus or species level where possible (Pitta et al. 2005). Heterotrophic bacteria, Synechococcus, Prochlorococcus bacteria: Subsamples for virus, heterotrophic bacteria and cyanobacteria (Synechococcus spp. and Prochlorococcus spp.) counting were analyzed using a FACSCalibur (Becton Dickinson) flow cytometer equipped with a standard laser (488 nm) and filter set and using deionized water as sheath fluid. Fluorescent beads with a diameter of 0.97 µm (Polysciences) were added to each sample as an internal standard, and all parameters were normalized to the beads and expressed as relative units. SYBRGreen I stain (Molecular Probe) was used to stain viral and heterotrophic bacterial DNA. Viruses were counted according to (Brussaard 1984). In order to avoid bulk consentrations of viruses samples we dilluted to Tris-EDTA (pH=8,0) buffer to a final sollution of 1/5 to 1/100. Total abundance and nucleid content classes were calculated using the Paint-A-Gate software (Becton Dickinson). Abundance data were converted into C biomass using 250 fgC cell-1 (Kana & Glibert 1987) for Synechococcus, 50 fgC cell-1 (Campbell et al. 1994) for Prochlorococcus and 20fgC cell-1 (Lee & Fuhrman 1987) for heterotrophic bacteria. Heterotrophic Nanoflagellate biomass: Subsamples (30-150 ml) were concentrated on 25mm black polycarbonate filters of porosity 0.6µm and stained with DAPI for 10 min (Porter and Feig 1980). Under epifluorescence microscopy heterotrophic nanoflagellates (HNAN) were distinguished using UV and blue excitation and enumerated. Nanoflagellates were classified in size categories and the biovolume was calculated. Abundance data were converted into C biomass using 183 fgC µm**3 (Caron et al. 1995). Ciliate biomass: For ciliate identification and enumeration, 100-3000 ml samples were left for 24h-4d for sedimentation and then observed under an inverted microscope. Ciliates were counted, distinguished into size-classes and major taxonomic groups and identified down to genus or species level where possible (Pitta et al. 2005). Ciliate cell sizes were measured and converted into cell volumes using appropriate geometric formulae using image analysis. For biomass estimation, the conversion factor 190 fgC µm**3 was used (Putt and Stoecker 1989).

DNA alignment and Bayesian trees of partial sequences of COI, COIII and the haemocyanin functional unit f-g of 28 octopod species

Background: Octopods have successfully colonised the world's oceans from the tropics to the poles. Yet, successful persistence in these habitats has required adaptations of their advanced physiological apparatus to compensate impaired oxygen supply. Their oxygen transporter haemocyanin plays a major role in cold tolerance and accordingly has undergone functional modifications to sustain oxygen release at sub-zero temperatures. However, it remains unknown how molecular properties evolved to explain the observed functional adaptations. We thus aimed to assess whether natural selection affected molecular and structural properties of haemocyanin that explains temperature adaptation in octopods. Results: Analysis of 239 partial sequences of the haemocyanin functional units (FU) f and g of 28 octopod species of polar, temperate, subtropical and tropical origin revealed natural selection was acting primarily on charge properties of surface residues. Polar octopods contained haemocyanins with higher net surface charge due to decreased glutamic acid content and higher numbers of basic amino acids. Within the analysed partial sequences, positive selection was present at site 2545, positioned between the active copper binding centre and the FU g surface. At this site, methionine was the dominant amino acid in polar octopods and leucine was dominant in tropical octopods. Sites directly involved in oxygen binding or quaternary interactions were highly conserved within the analysed sequence. Conclusions: This study has provided the first insight into molecular and structural mechanisms that have enabled octopods to sustain oxygen supply from polar to tropical conditions. Our findings imply modulation of oxygen binding via charge-charge interaction at the protein surface, which stabilize quaternary interactions among functional units to reduce detrimental effects of high pH on venous oxygen release. Of the observed partial haemocyanin sequence, residue 2545 formed a close link between the FU g surface and the active centre, suggesting a role as allosteric binding site. The prevalence of methionine at this site in polar octopods, implies regulation of oxygen affinity via increased sensitivity to allosteric metal binding. High sequence conservation of sites directly involved in oxygen binding indicates that functional modifications of octopod haemocyanin rather occur via more subtle mechanisms, as observed in this study.