Seawater carbonate chemistry and carbon allocation, growth and morphology of the coccolithophore Emiliania huxleyi (calcifying strain CCMP 371) during experiments, 2011

Coccolithophores are unicellular phytoplankton that produce calcium carbonate coccoliths as an exoskeleton. Emiliania huxleyi, the most abundant coccolithophore in the world's ocean, plays a major role in the global carbon cycle by regulating the exchange of CO2 across the ocean-atmosphere interface through photosynthesis and calcium carbonate precipitation. As CO2 concentration is rising in the atmosphere, the ocean is acidifying and ammonium (NH4) concentration of future ocean water is expected to rise. The latter is attributed to increasing anthropogenic nitrogen (N) deposition, increasing rates of cyanobacterial N2 fixation due to warmer and more stratified oceans, and decreased rates of nitrification due to ocean acidification. Thus future global climate change will cause oceanic phytoplankton to experience changes in multiple environmental parameters including CO2, pH, temperature and nitrogen source. This study reports on the combined effect of elevated pCO2 and increased NH4 to nitrate (NO3) ratio (NH4/NO3) on E. huxleyi, maintained in continuous cultures for more than 200 generations under two pCO2 levels and two different N sources. Here we show that NH4 assimilation under N-replete conditions depresses calcification at both low and high pCO2, alters coccolith morphology, and increases primary production. We observed that N source and pCO2 synergistically drive growth rates, cell size and the ratio of inorganic to organic carbon. These responses to N source suggest that, compared to increasing CO2 alone, a greater disruption of the organic carbon pump could be expected in response to the combined effect of increased NH4/NO3 ratio and CO2 level in the future acidified ocean. Additional experiments conducted under lower nutrient conditions are needed prior to extrapolating our findings to the global oceans. Nonetheless, our results emphasize the need to assess combined effects of multiple environmental parameters on phytoplankton biology in order to develop accurate predictions of phytoplankton responses to ocean acidification.

Seawater carbonate chemistry and processes during experiments with Emiliania huxleyi (PML B93/11A)

The formation of calcareous skeletons by marine planktonic organisms and their subsequent sinking to depth generates a continuous rain of calcium carbonate to the deep ocean and underlying sediments. This is important in regulating marine carbon cycling and ocean-atmosphere CO2 exchange. The present rise in atmospheric CO2 levels causes significant changes in surface ocean pH and carbonate chemistry. Such changes have been shown to slow down calcification in corals and coralline macroalgae, but the majority of marine calcification occurs in planktonic organisms. Here we report reduced calcite production at increased CO2 concentrations in monospecific cultures of two dominant marine calcifying phytoplankton species, the coccolithophorids Emiliania huxleyi and Gephyrocapsa oceanica . This was accompanied by an increased proportion of malformed coccoliths and incomplete coccospheres. Diminished calcification led to a reduction in the ratio of calcite precipitation to organic matter production. Similar results were obtained in incubations of natural plankton assemblages from the north Pacific ocean when exposed to experimentally elevated CO2 levels. We suggest that the progressive increase in atmospheric CO2 concentrations may therefore slow down the production of calcium carbonate in the surface ocean. As the process of calcification releases CO2 to the atmosphere, the response observed here could potentially act as a negative feedback on atmospheric CO2 levels.

Seawater carbonate chemistry and processes during experiments with Emiliania huxleyi (TW1), 2003

Precipitation of calcium carbonate by phytoplankton in the photic oceanic layer is an important process regulating the carbon cycling and the exchange of CO2 at the ocean-atmosphere interface. Previous experiments have demonstrated that, under nutrient-sufficient conditions, doubling the partial pressure of CO2 (pCO2) in seawater-a likely scenario for the end of the century-can significantly decrease both the rate of calcification by coccolithophorids and the ratio of inorganic to organic carbon production. The present work investigates the effects of high pCO2 on calcification by the coccolithophore Emiliania huxleyi (Strain TW1) grown under nitrogen-limiting conditions, a situation that can also prevail in the ocean. Nitrogen limitation was achieved in NO3-limited continuous cultures renewed at the rate of 0.5 d-1 and exposed to a saturating light level. pCO2 was increased from 400 to 700 ppm and controlled by bubbling CO2-rich or CO2-free air into the cultures. The pCO2 shift has a rapid effect on cell physiology that occurs within 2 cell divisions subsequent to the perturbation. Net calcification rate (C) decreased by 25% and, in contrast to previous studies with N-replete cultures, gross community production (GCP) and dark community respiration (DCR) also decreased. These results suggest that increasing pCO2 has no noticeable effect on the calcification/photosynthesis ratio (C/P) when cells of E. huxleyi are NO3-limited.

Temperature, water level and bathymetry of thermokarst lakes in the continuous permafrost zone of northern Siberia - Lena River Delta, Siberia

Thermokarst lakes are typical features of the northern permafrost ecosystems, and play an important role in the thermal exchange between atmosphere and subsurface. The objective of this study is to describe the main thermal processes of the lakes and to quantify the heat exchange with the underlying sediments. The thermal regimes of five lakes located within the continuous permafrost zone of northern Siberia (Lena River Delta) were investigated using hourly water temperature and water level records covering a 3-year period (2009-2012), together with bathymetric survey data. The lakes included thermokarst lakes located on Holocene river terraces that may be connected to Lena River water during spring flooding, and a thermokarst lake located on deposits of the Pleistocene Ice Complex. Lakes were covered by ice up to 2 m thick that persisted for more than 7 months of the year, from October until about mid-June. Lake-bottom temperatures increased at the start of the ice-covered period due to upward-directed heat flux from the underlying thawed sediment. Prior to ice break-up, solar radiation effectively warmed the water beneath the ice cover and induced convective mixing. Ice break-up started at the beginning of June and lasted until the middle or end of June. Mixing occurred within the entire water column from the start of ice break-up and continued during the ice-free periods, as confirmed by the Wedderburn numbers, a quantitative measure of the balance between wind mixing and stratification that is important for describing the biogeochemical cycles of lakes. The lake thermal regime was modeled numerically using the FLake model. The model demonstrated good agreement with observations with regard to the mean lake temperature, with a good reproduction of the summer stratification during the ice-free period, but poor agreement during the ice-covered period. Modeled sensitivity to lake depth demonstrated that lakes in this climatic zone with mean depths > 5 m develop continuous stratification in summer for at least 1 month. The modeled vertical heat flux across the bottom sediment tends towards an annual mean of zero, with maximum downward fluxes of about 5 W/m**2 in summer and with heat released back into the water column at a rate of less than 1 W/m**2 during the ice-covered period. The lakes are shown to be efficient heat absorbers and effectively distribute the heat through mixing. Monthly bottom water temperatures during the ice-free period range up to 15 °C and are therefore higher than the associated monthly air or ground temperatures in the surrounding frozen permafrost landscape. The investigated lakes remain unfrozen at depth, with mean annual lake-bottom temperatures of between 2.7 and 4 °C.

Pore water geochemistry of Håkon Mosby mud volcano sediments measured at station PS74/169-1_PUC-15 (Z1-S1, new flow surface)

Pore water and turnover rates were determined for surface sediment cores obtained in 2009 and 2010. The pore water was extracted with Rhizons (Rhizon CSS: length 5 cm, pore diameter 0.15 µm; Rhizosphere Research Products, Wageningen, Netherlands) in 1 cm-resolution and immediately fixed in 5% zinc acetate (ZnAc) solution for sulfate, and sulfide analyses. The samples were diluted, filtered and the concentrations measured with non-suppressed anion exchange chromatography (Waters IC-Pak anion exchange column, waters 430 conductivity detector). The total sulfide concentrations (H2S + HS- + S**2-) were determined using the diamine complexation method (doi:10.4319/lo.1969.14.3.0454). Samples for dissolved inorganic carbon (DIC) and alkalinity measurements were preserved by adding 2 µl saturated mercury chloride (HgCl2) solution and stored headspace-free in gas-tight glass vials. DIC and alkalinity were measured using the flow injection method (detector VWR scientific model 1054) (doi:10.4319/lo.1992.37.5.1113). Dissolved sulfide was eliminated prior to the DIC measurement by adding 0.5 M molybdate solution (doi:10.4319/lo.1995.40.5.1011). Nutrient subsamples (10 - 15 ml) were stored at - 20 °C prior to concentration measurements with a Skalar Continuous-Flow Analyzer (doi:10.1002/9783527613984).

Pore water geochemistry of Håkon Mosby mud volcano sediments measured at station MSM16/2_847-1 (Z2-S2, aged flow surface)

Pore water and turnover rates were determined for surface sediment cores obtained in 2009 and 2010. The pore water was extracted with Rhizons (Rhizon CSS: length 5 cm, pore diameter 0.15 µm; Rhizosphere Research Products, Wageningen, Netherlands) in 1 cm-resolution and immediately fixed in 5% zinc acetate (ZnAc) solution for sulfate, and sulfide analyses. The samples were diluted, filtered and the concentrations measured with non-suppressed anion exchange chromatography (Waters IC-Pak anion exchange column, waters 430 conductivity detector). The total sulfide concentrations (H2S + HS- + S**2-) were determined using the diamine complexation method (doi:10.4319/lo.1969.14.3.0454). Samples for dissolved inorganic carbon (DIC) and alkalinity measurements were preserved by adding 2 µl saturated mercury chloride (HgCl2) solution and stored headspace-free in gas-tight glass vials. DIC and alkalinity were measured using the flow injection method (detector VWR scientific model 1054) (doi:10.4319/lo.1992.37.5.1113). Dissolved sulfide was eliminated prior to the DIC measurement by adding 0.5 M molybdate solution (doi:10.4319/lo.1995.40.5.1011). Nutrient subsamples (10 - 15 ml) were stored at - 20 °C prior to concentration measurements with a Skalar Continuous-Flow Analyzer (doi:10.1002/9783527613984).

Pore water geochemistry of arctic deep sea sediments measured at station MSM16/2_809-1 (REF, Reference)

Pore water and turnover rates were determined for surface sediment cores obtained in 2009 and 2010. The pore water was extracted with Rhizons (Rhizon CSS: length 5 cm, pore diameter 0.15 µm; Rhizosphere Research Products, Wageningen, Netherlands) in 1 cm-resolution and immediately fixed in 5% zinc acetate (ZnAc) solution for sulfate, and sulfide analyses. The samples were diluted, filtered and the concentrations measured with non-suppressed anion exchange chromatography (Waters IC-Pak anion exchange column, waters 430 conductivity detector). The total sulfide concentrations (H2S + HS- + S**2-) were determined using the diamine complexation method (doi:10.4319/lo.1969.14.3.0454). Samples for dissolved inorganic carbon (DIC) and alkalinity measurements were preserved by adding 2 µl saturated mercury chloride (HgCl2) solution and stored headspace-free in gas-tight glass vials. DIC and alkalinity were measured using the flow injection method (detector VWR scientific model 1054) (doi:10.4319/lo.1992.37.5.1113). Dissolved sulfide was eliminated prior to the DIC measurement by adding 0.5 M molybdate solution (doi:10.4319/lo.1995.40.5.1011). Nutrient subsamples (10 - 15 ml) were stored at - 20 °C prior to concentration measurements with a Skalar Continuous-Flow Analyzer (doi:10.1002/9783527613984).

Pore water geochemistry of Håkon Mosby mud volcano sediments measured at station MSM16/2_838-1 (Z1-S3, new flow surface)

Pore water and turnover rates were determined for surface sediment cores obtained in 2009 and 2010. The pore water was extracted with Rhizons (Rhizon CSS: length 5 cm, pore diameter 0.15 µm; Rhizosphere Research Products, Wageningen, Netherlands) in 1 cm-resolution and immediately fixed in 5% zinc acetate (ZnAc) solution for sulfate, and sulfide analyses. The samples were diluted, filtered and the concentrations measured with non-suppressed anion exchange chromatography (Waters IC-Pak anion exchange column, waters 430 conductivity detector). The total sulfide concentrations (H2S + HS- + S**2-) were determined using the diamine complexation method (doi:10.4319/lo.1969.14.3.0454). Samples for dissolved inorganic carbon (DIC) and alkalinity measurements were preserved by adding 2 µl saturated mercury chloride (HgCl2) solution and stored headspace-free in gas-tight glass vials. DIC and alkalinity were measured using the flow injection method (detector VWR scientific model 1054) (doi:10.4319/lo.1992.37.5.1113). Dissolved sulfide was eliminated prior to the DIC measurement by adding 0.5 M molybdate solution (doi:10.4319/lo.1995.40.5.1011). Nutrient subsamples (10 - 15 ml) were stored at - 20 °C prior to concentration measurements with a Skalar Continuous-Flow Analyzer (doi:10.1002/9783527613984).

Pore water geochemistry of Håkon Mosby mud volcano sediments measured at station MSM16/2_855-1 (Z2-S3, aged flow surface)

Pore water and turnover rates were determined for surface sediment cores obtained in 2009 and 2010. The pore water was extracted with Rhizons (Rhizon CSS: length 5 cm, pore diameter 0.15 µm; Rhizosphere Research Products, Wageningen, Netherlands) in 1 cm-resolution and immediately fixed in 5% zinc acetate (ZnAc) solution for sulfate, and sulfide analyses. The samples were diluted, filtered and the concentrations measured with non-suppressed anion exchange chromatography (Waters IC-Pak anion exchange column, waters 430 conductivity detector). The total sulfide concentrations (H2S + HS- + S**2-) were determined using the diamine complexation method (doi:10.4319/lo.1969.14.3.0454). Samples for dissolved inorganic carbon (DIC) and alkalinity measurements were preserved by adding 2 µl saturated mercury chloride (HgCl2) solution and stored headspace-free in gas-tight glass vials. DIC and alkalinity were measured using the flow injection method (detector VWR scientific model 1054) (doi:10.4319/lo.1992.37.5.1113). Dissolved sulfide was eliminated prior to the DIC measurement by adding 0.5 M molybdate solution (doi:10.4319/lo.1995.40.5.1011). Nutrient subsamples (10 - 15 ml) were stored at - 20 °C prior to concentration measurements with a Skalar Continuous-Flow Analyzer (doi:10.1002/9783527613984).

Pore water geochemistry of Håkon Mosby mud volcano sediments measured at station PS74/168-1 (Z1-S2, new flow surface)

Pore water and turnover rates were determined for surface sediment cores obtained in 2009 and 2010. The pore water was extracted with Rhizons (Rhizon CSS: length 5 cm, pore diameter 0.15 µm; Rhizosphere Research Products, Wageningen, Netherlands) in 1 cm-resolution and immediately fixed in 5% zinc acetate (ZnAc) solution for sulfate, and sulfide analyses. The samples were diluted, filtered and the concentrations measured with non-suppressed anion exchange chromatography (Waters IC-Pak anion exchange column, waters 430 conductivity detector). The total sulfide concentrations (H2S + HS- + S**2-) were determined using the diamine complexation method (doi:10.4319/lo.1969.14.3.0454). Samples for dissolved inorganic carbon (DIC) and alkalinity measurements were preserved by adding 2 µl saturated mercury chloride (HgCl2) solution and stored headspace-free in gas-tight glass vials. DIC and alkalinity were measured using the flow injection method (detector VWR scientific model 1054) (doi:10.4319/lo.1992.37.5.1113). Dissolved sulfide was eliminated prior to the DIC measurement by adding 0.5 M molybdate solution (doi:10.4319/lo.1995.40.5.1011). Nutrient subsamples (10 - 15 ml) were stored at - 20 °C prior to concentration measurements with a Skalar Continuous-Flow Analyzer (doi:10.1002/9783527613984).

Pore water geochemistry of Håkon Mosby mud volcano sediments measured at station PS74/172-1_PUC-136 (Z3-S2, old flow surface)

Pore water and turnover rates were determined for surface sediment cores obtained in 2009 and 2010. The pore water was extracted with Rhizons (Rhizon CSS: length 5 cm, pore diameter 0.15 µm; Rhizosphere Research Products, Wageningen, Netherlands) in 1 cm-resolution and immediately fixed in 5% zinc acetate (ZnAc) solution for sulfate, and sulfide analyses. The samples were diluted, filtered and the concentrations measured with non-suppressed anion exchange chromatography (Waters IC-Pak anion exchange column, waters 430 conductivity detector). The total sulfide concentrations (H2S + HS- + S**2-) were determined using the diamine complexation method (doi:10.4319/lo.1969.14.3.0454). Samples for dissolved inorganic carbon (DIC) and alkalinity measurements were preserved by adding 2 µl saturated mercury chloride (HgCl2) solution and stored headspace-free in gas-tight glass vials. DIC and alkalinity were measured using the flow injection method (detector VWR scientific model 1054) (doi:10.4319/lo.1992.37.5.1113). Dissolved sulfide was eliminated prior to the DIC measurement by adding 0.5 M molybdate solution (doi:10.4319/lo.1995.40.5.1011). Nutrient subsamples (10 - 15 ml) were stored at - 20 °C prior to concentration measurements with a Skalar Continuous-Flow Analyzer (doi:10.1002/9783527613984).

Properties of seawater (pH total scale) from a Satlantic SeaFET instrument mounted on the continuous surface water sampling system during the Tara Oceans expedition 2009-2013

The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data set provides continuous pH measurements made during 2013 expedition with a Satlantic SeaFET instrument that was connected to the flowthrough system. Data calibration was performed according to Bresnahan et al. (2014) (using spectrophotometric pH measurements on discrete samples (Clayton and Byrne 1993). pH_internal values were taken to calibrate the data (rather than pH_external) because of the better calibration coefficient (there was no trend associated with it). The equations of Clayton and Byrne (1993) was used to compute pH from the measured absorbance values at the temperature of measurement. The data was converted to in situ temperature using the "CO2-sys" program which can be downloaded from http://cdiac.ornl.gov/ftp/co2sys/.

Bicarbonate uptake via an anion exchange protein is the main mechanism of inorganic carbon acquisition by the giant kelp Macrocystis pyrifera (Laminariales, Phaeophyceae) under variable pH

Macrocystis pyrifera is a widely distributed, highly productive, seaweed. It is known to use bicarbonate (HCO3-) from seawater in photosynthesis and the main mechanism of utilization is attributed to the external catalyzed dehydration of HCO3- by the surface-bound enzyme carbonic anhydrase (CAext). Here, we examined other putative HCO3- uptake mechanisms in M. pyrifera under pHT 9.00 (HCO3-: CO2 = 940:1) and pHT 7.65 (HCO3-: CO2 = 51:1). Rates of photosynthesis, and internal CA (CAint) and CAext activity were measured following the application of AZ which inhibits CAext, and DIDS which inhibits a different HCO3- uptake system, via an anion exchange (AE) protein. We found that the main mechanism of HCO3- uptake by M. pyrifera is via an AE protein, regardless of the HCO3-: CO2 ratio, with CAext making little contribution. Inhibiting the AE protein led to a 55%-65% decrease in photosynthetic rates. Inhibiting both the AE protein and CAext at pHT 9.00 led to 80%-100% inhibition of photosynthesis, whereas at pHT 7.65, passive CO2 diffusion supported 33% of photosynthesis. CAint was active at pHT 7.65 and 9.00, and activity was always higher than CAext, because of its role in dehydrating HCO3- to supply CO2 to RuBisCO. Interestingly, the main mechanism of HCO3- uptake in M. pyrifera was different than that in other Laminariales studied (CAext-catalyzed reaction) and we suggest that species-specific knowledge of carbon uptake mechanisms is required in order to elucidate how seaweeds might respond to future changes in HCO3-:CO2 due to ocean acidification.

A molecular dynamics study of swift heavy ion irradiation of amorphous silica: the role of thermal effects

Irradiation with swift heavy ions (SHI), roughly defined as those having atomic masses larger than 15 and energies exceeding 1 MeV/amu, may lead to significant modification of the irradiated material in a nanometric region around the (straight) ion trajectory (latent tracks). In the case of amorphous silica, SHI irradiation originates nano-tracks of higher density than the virgin material (densification). As a result, the refractive index is increased with respect to that of the surroundings. Moreover, track overlapping leads to continuous amorphous layers that present a significant contrast with respect to the pristine substrate. We have recently demonstrated that SHI irradiation produces a large number of point defects, easily detectable by a number of experimental techniques (work presented in the parallel conference ICDIM). The mechanisms of energy transfer from SHI to the target material have their origin in the high electronic excitation induced in the solid. A number of phenomenological approaches have been employed to describe these mechanisms: coulomb explosion, thermal spike, non-radiative exciton decay, bond weakening. However, a detailed microscopic description is missing due to the difficulty of modeling the time evolution of the electronic excitation. In this work we have employed molecular dynamics (MD) calculations to determine whether the irradiation effects are related to the thermal phenomena described by MD (in the ps domain) or to electronic phenomena (sub-ps domain), e.g., exciton localization. We have carried out simulations of up to 100 ps with large boxes (30x30x8 nm3) using a home-modified version of MDCASK that allows us to define a central hot cylinder (ion track) from which heat flows to the surrounding cold bath (unirradiated sample). We observed that once the cylinder has cooled down, the Si and O coordination numbers are 4 and 2, respectively, as in virgin silica. On the other hand, the density of the (cold) cylinder increases with respect to that of silica and, furthermore, the silica network ring size decreases. Both effects are in agreement with the observed densification. In conclusion, purely thermal effects do not explain the generation of point defects upon irradiation, but they do account for the silica densification.

Development and implementation of a virtual laboratory for training process improvement in the mechanics of continuous media

The project arises from the need to develop improved teaching methodologies in field of the mechanics of continuous media. The objective is to offer the student a learning process to acquire the necessary theoretical knowledge, cognitive skills and the responsibility and autonomy to professional development in this area. Traditionally the teaching of the concepts of these subjects was performed through lectures and laboratory practice. During these lessons the students attitude was usually passive, and therefore their effectiveness was poor. The proposed methodology has already been successfully employed in universities like University Bochum, Germany, University the South Australia and aims to improve the effectiveness of knowledge acquisition through use by the student of a virtual laboratory. This laboratory allows to adapt the curricula and learning techniques to the European Higher Education and improve current learning processes in the University School of Public Works Engineers -EUITOP- of the Technical University of Madrid -UPM-, due there are not laboratories in this specialization. The virtual space is created using a software platform built on OpenSim, manages 3D virtual worlds, and, language LSL -Linden Scripting Language-, which imprints specific powers to objects. The student or user can access this virtual world through their avatar -your character in the virtual world- and can perform practices within the space created for the purpose, at any time, just with computer with internet access and viewfinder. The virtual laboratory has three partitions. The virtual meeting rooms, where the avatar can interact with peers, solve problems and exchange existing documentation in the virtual library. The interactive game room, where the avatar is has to resolve a number of issues in time. And the video room where students can watch instructional videos and receive group lessons. Each audiovisual interactive element is accompanied by explanations framing it within the area of knowledge and enables students to begin to acquire a vocabulary and practice of the profession for which they are being formed. Plane elasticity concepts are introduced from the tension and compression testing of test pieces of steel and concrete. The behavior of reticulated and articulated structures is reinforced by some interactive games and concepts of tension, compression, local and global buckling will by tests to break articulated structures. Pure bending concepts, simple and composite torsion will be studied by observing a flexible specimen. Earthquake resistant design of buildings will be checked by a laboratory test video.