qPCR counts of mRNA for hepatic reference gene selection in adult female Atlantic salmon from perturbation experiments under artificial temperature conditions

The dataset contains raw data (quantification cycle) for a study which determined the most suitable hepatic reference genes for normalisation of qPCR data orginating from adult (entire reproductive season) Atlantic salmon (14 days) exposed to 14 and 22 degrees C. These results will be useful for anyone wanting to study the effects of climate change/elevated temperature on reproductive physiology of fish (and perhaphs other vertebrates). In addition, a target gene (vitellogenin) has normalised using an inappropriate and an 'ideal' reference gene to demonstrate the consequences of using an unstable reference gene for normalisation. For the adult experiment, maiden and repeat adult females were held at the Salmon Enterprises of Tasmania (SALTAS) Wayatinah Hatchery (Tasmania, Australia) at ambient temperature and photoperiod in either 200 (maidens) or 50 (repeats) m3 circular tanks at stocking densities of 12-18, and 24-36 kg m-3 for maidens and repeats, respectively, until transfered to the experimental tanks.

Temperature Dependent Effects of Elevated CO2 on Shell Composition and Mechanical Properties of Hydroides elegans: Insights from a Multiple Stressor Experiment

The majority of marine benthic invertebrates protect themselves from predators by producing calcareous tubes or shells that have remarkable mechanical strength. An elevation of CO2 or a decrease in pH in the environment can reduce intracellular pH at the site of calcification and thus interfere with animal's ability to accrete CaCO3. In nature, decreased pH in combination with stressors associated with climate change may result in the animal producing severely damaged and mechanically weak tubes. This study investigated how the interaction of environmental drivers affects production of calcareous tubes by the serpulid tubeworm, Hydroides elegans. In a factorial manipulative experiment, we analyzed the effects of pH (8.1 and 7.8), salinity (34 and 27), and temperature (23°C and 29°C) on the biomineral composition, ultrastructure and mechanical properties of the tubes. At an elevated temperature of 29°C, the tube calcite/aragonite ratio and Mg/Ca ratio were both increased, the Sr/Ca ratio was decreased, and the amorphous CaCO3 content was reduced. Notably, at elevated temperature with decreased pH and reduced salinity, the constructed tubes had a more compact ultrastructure with enhanced hardness and elasticity compared to decreased pH at ambient temperature. Thus, elevated temperature rescued the decreased pH-induced tube impairments. This indicates that tubeworms are likely to thrive in early subtropical summer climate. In the context of climate change, tubeworms could be resilient to the projected near-future decreased pH or salinity as long as surface seawater temperature rise at least by 4°C.

Seawater carbonate chemistry and physiological response of the Mediterranean crustose coralline alga Lithophyllum cabiochae to elevated pCO2 and temperature

The response of respiration, photosynthesis, and calcification to elevated pCO2 and temperature was investigated in isolation and in combination in the Mediterranean crustose coralline alga Lithophyllum cabiochae. Algae were maintained in aquaria during 1 year at near-ambient conditions of irradiance, at ambient or elevated temperature (+3 °C), and at ambient (ca. 400 µatm) or elevated pCO2 (ca. 700 µatm). Respiration, photosynthesis, and net calcification showed a strong seasonal pattern following the seasonal variations of temperature and irradiance, with higher rates in summer than in winter. Respiration was unaffected by pCO2 but showed a general trend of increase at elevated temperature at all seasons, except in summer under elevated pCO2. Conversely, photosynthesis was strongly affected by pCO2 with a decline under elevated pCO2 in summer, autumn, and winter. In particular, photosynthetic efficiency was reduced under elevated pCO2. Net calcification showed different responses depending on the season. In summer, net calcification increased with rising temperature under ambient pCO2 but decreased with rising temperature under elevated pCO2. Surprisingly, the highest rates in summer were found under elevated pCO2 and ambient temperature. In autumn, winter, and spring, net calcification exhibited a positive or no response at elevated temperature but was unaffected by pCO2. The rate of calcification of L. cabiochae was thus maintained or even enhanced under increased pCO2. However, there is likely a trade-off with other physiological processes. For example, photosynthesis declines in response to increased pCO2 under ambient irradiance. The present study reports only on the physiological response of healthy specimens to ocean warming and acidification, however, these environmental changes may affect the vulnerability of coralline algae to other stresses such as pathogens and necroses that can cause major dissolution, which would have critical consequence for the sustainability of coralligenous habitats and the budgets of carbon and calcium carbonate in coastal Mediterranean ecosystems.

Age and chemical composition of apatites from five DSDP and ODP Sites in the Pacific, Atlantic and Indian Oceans

Since studies on deep-sea cores were carried out in the early 1990s it has been known that ambient temperature may have a marked affect on apatite fission track annealing. Due to sluggish annealing kinetics, this effect cannot be quantified by laboratory annealing experiments. The unknown amount of low-temperature annealing remains one of the main uncertainties for extracting thermal histories from fission track data, particularly for samples which experienced slow cooling in shallow crustal levels. To further elucidate these uncertainties, we studied volcanogenic sediments from five deep-sea drill cores, that were exposed to maximum temperatures between ~10° and 70°C over geological time scales of ~15-120 Ma. Mean track lengths (MTL) and etch pit diameters (Dpar) of all samples were measured, and the chemical composition of each grain analyzed for age and track length measurements was determined by electron microprobe analysis. Thermal histories of the sampled sites were independently reconstructed, based on vitrinite reflectance measurements and/or 1D numerical modelling. These reconstructions were used to test the most widely used annealing models for their ability to predict low-temperature annealing. Our results show that long-term exposure to temperatures below the temperature range of the nominal apatite fission track partial annealing zone results in track shortening ranging between 4 and 11%. Both chlorine content and Dpar values explain the downhole annealing patterns equally well. Low chlorine apatite from one drill core revealed a systematic relation between Si-content and Dpar value. The question whether Si-substitution in apatite has direct and systematic effects on annealing properties however, cannot be addressed by our data. For samples, which remained at temperatures <30°C, and which are low in chlorine, the Laslett et al. [Laslett G., Green P., Duddy I. and Gleadow A. (1987) Thermal annealing of fission tracks in apatite. Chem. Geol. 65, 1-13] annealing model predicts MTL up to 0.6 µm longer than those actually measured, whereas for apatites with intermediate to high chlorine content, which experienced temperatures >30°C, the predictions of the Laslett et al. (1987) model agree with the measured MTL data within error levels. With few exceptions, predictions by the Ketcham et al. [Ketcham R., Donelick R. and Carlson W. (1999) Variability of apatite fission-track annealing kinetics. III: Extrapolation to geological time scales. Am. Mineral. 84/9, 1235-1255] annealing model are consistent with the measured data for samples which remained at temperatures below ~30°C. For samples which experienced maximum temperatures between ~30 and 70°C, and which are rich in chlorine, the Ketcham et al. (1999) model overestimates track annealing.

Interstitial water chemistry at DSDP Leg 57 Holes

Analyses of water samples taken by means of an in-hole sampler generally show good agreement with analyses of samples collected by routine shipboard squeezing techniques. At Sites 438 and 439, a decrease in salinity with depth is related to former freshwater flow from an aquifer that crops out at an anticline on a deep sea terrace between Japan and the top of the trench slope of the Japan Trench. This former subaerial recharge suggests significant late Cenozoic subsidence of the terrace, because it now lies at a water depth of 1500 meters. Samples from the trench slope at Site 440 have extremely high values of alkalinity and ammonia, presumably because of a favorable combination of high sedimentation rate and organic carbon content. Diagenetic conditions on the trench slope favor formation of the Fe-Mg carbonate mineral, ankerite; at Site 440 it first occurs at a depth below the sea floor of only 29 meters in late Pleistocene strata. Undissolved diatoms persist to relatively great depth at the sites of Leg 57 because of a low geothermal gradient caused by subduction. Secondary silica lepispheres first appear at 851 meters at the most landward and warmest site, Site 438, in strata 16 million years old with an ambient temperature of 31 °C.

Geochemistry of Miocene "blue tuff" samples

Distinctive, massive to stratified, pale blue volcaniclastics, initially referred to as the "blue tuff," were encountered at all four sites drilled during ODP Leg 127 in the Japan Sea. Detailed vertical sequence analysis, plagioclase chemistry, plagioclase 87Sr/86Sr isotopic composition, and 40Ar/39Ar age dating indicate that thick sequences of the blue tuff are not genetically related. Blue tuffs at Hole 794B were apparently deposited by density flows at ambient temperature. Deposition was penecontemporaneous with a large submarine phreatomagmatic eruption at 14.9 Ma in bathyal or deeper water depths. The blue tuffs at this location comprise mostly reworked hydroclastic glass shards and lesser amounts of plagioclase crystals. Pyrogenic plagioclase has an average An mole% of 18±3. Comparison of blue tuff plagioclase compositions with the composition of plagioclase from acoustic basement at Site 794 suggests that these rocks are not genetically related. As such, the extrapolation of sediment accumulation rate data in conjunction with this more precise age for the blue tuff corroborates previous minimum age estimates of 16.2 Ma for acoustic basement at Site 794. Blue tuffs at Hole 796B were probably deposited at ambient temperatures by downslope slumping and density flow of reworked pyrogenic debris. This debris includes abundant bubble wall glass shards and plagioclase crystals, with variable admixture of volcanic lithic and intrabasinal fragments. Pyrogenic fragments were produced by subaerial or shallow submarine, magmatic eruptions dated at 7.6 Ma. Blue tuffs contain a heterogeneous mixture of unrelated fragments including a mixed population of plagioclase crystals. The average An mole% of the predominant, probable comagmatic, plagioclase population is 30±4. The two sequences of blue tuff studied are distinct in age, mineral composition, and the eruptive origin of pyroclastic fragments. Preliminary 87Sr/86Sr isotopic compositions of plagioclase, however, indicates that blue tuffs at both locations are the product of typical, subduction-related island arc magmatism. Based on the results of this study, there is no justification for stratigraphic correlation of widespread, Miocene, blue to blue-gray bentonitic tuff and tuffaceous sandstones nor the interpretation that these strata are indicative of regional, explosive submarine volcanism genetically related to rifting and formation of the Japan Sea. Rather, these reworked pyroclastic strata of intermediate composition were deposited over a protracted 6-8 m.y. period in association with widespread, subduction-related submarine to subaerial volcanism in the Japan Sea backarc basin.

Impacts of passive warming chambers on soil parameters in Antarctica

Passive chambers are used to examine the impacts of summer warming in Antarctica but, so far, impacts occurring outside the growing season, or related to extreme temperatures, have not been reported, despite their potentially large biological significance. In this review, we synthesise and discuss the microclimate impacts of passive warming chambers (closed, ventilated and Open Top Chamber-OTC) commonly used in Antarctic terrestrial habitats, paying special attention to seasonal warming, during the growing season and outside, extreme temperatures and freeze-thaw events. Both temperature increases and decreases were recorded throughout the year. Closed chambers caused earlier spring soil thaw (8-28 days) while OTCs delayed soil thaw (3-13 days). Smaller closed chamber types recorded the largest temperature extremes (up to 20°C higher than ambient) and longest periods (up to 11 h) of above ambient extreme temperatures, and even OTCs had above ambient temperature extremes over up to 5 consecutive hours. The frequency of freeze-thaw events was reduced by ~25%. All chamber types experienced extreme temperature ranges that could negatively affect biological responses, while warming during winter could result in depletion of limited metabolic resources. The effects outside the growing season could be as important in driving biological responses as the mean summer warming. We make suggestions for improving season-specific warming simulations and propose that seasonal and changed temperature patterns achieved under climate manipulations should be recognised explicitly in descriptions of treatment effects.

FISH analysis of biofilm samples from five CANON reactors in Beijing

Completely autotrophic nitrogen removal over nitrite (CANON) has been regarded as an efficient and economical process for nitrogen removal from wastewater. The distribution and genetic diversity of the functional microorganisms in five lab-scale CANON reactors have been investigated by using some molecular biology methods. Nitrosomonas-like aerobic ammonium oxidizing bacteria (AerAOB) and Candidatus Brocadia-related anaerobic ammonium oxidizing bacteria (AnAOB) were detected as predominant functional microbes in the five reactors while Nitrobacter-like nitrite oxidizing bacteria (NOB) existed only in the systems operated at ambient temperature. Communities of AerAOB and AnAOB were almost similar among the five reactors while the distribution of the functional microbes was either scattered or densely packed. Meanwhile, this study has demonstrated the feasibility of starting up CANON by inoculating conventional activated sludge in low ammonium content at ambient temperature.

U-series ages from calcitic cold-water corals from the Amundsen Sea

Radiocarbon and uranium-thorium dating results are presented from a genus of calcitic Antarctic cold-water octocorals (family Coralliidae), which were collected from the Marie Byrd Seamounts in the Amundsen Sea (Pacific sector of the Southern Ocean) and which to date have not been investigated geochemically. The geochronological results are set in context with solution and laser ablation-based element/Ca ratios (Li, B, Mg, Mn, Sr, Ba, U, Th). Octocoral radiocarbon ages on living corals are in excellent agreement with modern ambient deep-water D14C, while multiple samples of individual fossil coral specimens yielded reproducible radiocarbon ages. Provided that local radiocarbon reservoir ages can be derived for a given time, fossil Amundsen Sea octocorals should be reliably dateable by means of radiocarbon. In contrast to the encouraging radiocarbon findings, the uranium-series data are more difficult to interpret. The uranium concentration of these calcitic octocorals is an order of magnitude lower than in the aragonitic hexacorals that are conventionally used for geochronological investigations. While modern and Late Holocene octocorals yield initial d234U in good agreement with modern seawater, our results reveal preferential inward diffusion of dissolved alpha-recoiled 234U and its impact on fossil coral d234U. Besides alpha-recoil related 234U diffusion, high-resolution sampling of two fossil octocorals further demonstrates that diagenetic uranium mobility has offset apparent coral U-series ages. Combined with the preferential alpha-recoil 234U diffusion, this process has prevented fossil octocorals from preserving a closed system U-series calendar age for longer than a few thousand years. Moreover, several corals investigated contain significant initial thorium, which cannot be adequately corrected for because of an apparently variable initial 232Th/230Th. Our results demonstrate that calcitic cold-water corals are unsuitable for reliable U-series dating. Mg/Ca ratios within single octocoral specimens are internally strikingly homogeneous, and appear promising in terms of their response to ambient temperature. Magnesium/lithium ratios are significantly higher than usually observed in other deep marine calcifiers and for many of our studied corals are remarkably close to seawater compositions. Although this family of octocorals is unsuitable for glacial deep-water D14C reconstructions, our findings highlight some important differences between hexacoral (aragonitic) and octocoral (calcitic) biomineralisation. Calcitic octocorals could still be useful for trace element and some isotopic studies, such as reconstruction of ambient deep water neodymium isotope composition or pH, via boron isotopic measurements.

Respiration and ingestion rates of calanoid copepod in the northern Benguela Current System measured ex situ during the RSS Discovery D356 cruise in 2010

Respiration rates of 16 calanoid copepod species from the northern Benguela upwelling system were measured on board RRS Discovery in September/October 2010 to determine their energy requirements and assess their significance in the carbon cycle. Copepod species were sampled by different net types. Immediately after the hauls, samples were sorted to species and stages (16 species; females, males and C5 copepodids) according to Bradford-Grieve et al. (1999). Specimens were kept in temperature-controlled refrigerators for at least 12 h before they were used in experiments. Respiration rates of different copepod species were measured onboard by optode respirometry (for details see Köster et al., 2008) with a 10-channel optode respirometer (PreSens Precision Sensing Oxy-10 Mini, Regensburg, Germany) under simulated in situ conditions in temperature-controlled refrigerators. Experiments were run in gas-tight glass bottles (12-13 ml). For each set of experiments, two controls without animals were measured under exactly the same conditions to compensate for potential bias. The number of animals per bottle depended on the copepods size, stage and metabolic activity. Animals were not fed during the experiments but they showed natural species-specific movements. Immediately after the experiments, all specimens were deep-frozen at - 80 °C for later dry mass determination (after lyophilisation for 48 h) in the home lab. The carbon content (% of dry mass) of each species was measured by mass-spectrometry in association with stable isotope analysis and body dry mass was converted to units of carbon. For species without available carbon data, the mean value of all copepod species (44% dry mass) was applied. For the estimation of carbon requirements of copepod species, individual oxygen consumption rates were converted to carbon units, assuming that the expiration of 1 ml oxygen mobilises 0.44 mg of organic carbon by using a respiratory quotient (RQ) of 0.82 for a mixed diet consisting of proteins (RQ = 0.8-1.0), lipids (RQ = 0.7) and carbohydrates (RQ = 1.0) (Auel and Werner, 2003). The carbon ingestion rates were calculated using the energy budget and the potential maximum ingestion rate approach. To allow for physiological comparisons of respiration rates of deep- and shallow-living copepod species without the effects of ambient temperature and different individual body mass, individual respiration rates were temperature- (15°C, Q10=2) and size-adjusted. The scaling coefficient of 0.76 (R2=0.556) is used for the standardisation of body dry mass to 0.3 mg (mean dry mass of all analysed copepods), applying the allometric equation R= (R15°C/M0.76)×0.30.76, where R is respiration and M is individual dry mass in mg.

Seawater carbonate chemistry and protein content, respiration, symbiodinium densities, survivorship of Pocillopora damicornis larvae in a laboratory experiment

Efforts to evaluate the response of coral larvae to global climate change (GCC) and ocean acidification (OA) typically employ short experiments of fixed length, yet it is unknown how the response is affected by exposure duration. In this study, we exposed larvae from the brooding coral Pocillopora damicornis to contrasts of temperature (24.00 °C [ambient] versus 30.49 °C) and pCO2 (49.4 Pa versus 86.2 Pa) for varying periods (1-5 days) to test the hypothesis that exposure duration had no effect on larval response as assessed by protein content, respiration, Symbiodinium density, and survivorship; exposure times were ecologically relevant compared to representative pelagic larval durations (PLD) for corals. Larvae differed among days for all response variables, and the effects of the treatment were relatively consistent regardless of exposure duration for three of the four response variables. Protein content and Symbiodinium density were unaffected by temperature and pCO2, but respiration increased with temperature (but not pCO2) with the effect intensifying as incubations lengthened. Survival, however, differed significantly among treatments at the end of the study, and by the 5th day, 78% of the larvae were alive and swimming under ambient temperature and ambient pCO2, but only 55-59% were alive in the other treatments. These results demonstrate that the physiological effects of temperature and pCO2 on coral larvae can reliably be detected within days, but effects on survival require > or = 5 days to detect. The detection of time-dependent effects on larval survivorship suggests that the influence of GCC and OA will be stronger for corals having long PLDs.

Seawater carbonate chemistry, calcification, primary production and respiration of a temperate rhodolith Lithothamnion corallioides in a laboratory experiment

Coralline algae are considered among the most sensitive species to near future ocean acidification. We tested the effects of elevated pCO2 on the metabolism of the free-living coralline alga Lithothamnion corallioides ("maerl") and the interactions with changes in temperature. Specimens were collected in North Brittany (France) and grown for 3 months at pCO2 of 380 (ambient pCO2), 550, 750, and 1000 µatm (elevated pCO2) and at successive temperatures of 10°C (ambient temperature in winter), 16°C (ambient temperature in summer), and 19°C (ambient temperature in summer +3°C). At each temperature, gross primary production, respiration (oxygen flux), and calcification (alkalinity flux) rates were assessed in the light and dark. Pigments were determined by HPLC. Chl a, carotene, and zeaxanthin were the three major pigments found in L. corallioides thalli. Elevated pCO2 did not affect pigment content while temperature slightly decreased zeaxanthin and carotene content at 10°C. Gross production was not affected by temperature but was significantly affected by pCO2 with an increase between 380 and 550 µatm. Light, dark, and diel (24 h) calcification rates strongly decreased with increasing pCO2 regardless of the temperature. Although elevated pCO2 only slightly affected gross production in L. corallioides, diel net calcification was reduced by up to 80% under the 1,000 µatm treatment. Our findings suggested that near future levels of CO2 will have profound consequences for carbon and carbonate budgets in rhodolith beds and for the sustainability of these habitats.

Seawater carbonate chemistry and calcification of the crustose coralline alga Hydrolithon onkodes in a laboratory experiment

Anthropogenic CO2 emissions have exacerbated two environmental stressors, global climate warming and ocean acidification (OA), that have serious implications for marine ecosystems. Coral reefs are vulnerable to climate change yet few studies have explored the potential for interactive effects of warming temperature and OA on an important coral reef calcifier, crustose coralline algae (CCA). Coralline algae serve many important ecosystem functions on coral reefs and are one of the most sensitive organisms to ocean acidification. We investigated the effects of elevated pCO2 and temperature on calcification of Hydrolithon onkodes, an important species of reef-building coralline algae, and the subsequent effects on susceptibility to grazing by sea urchins. H. onkodes was exposed to a fully factorial combination of pCO2 (420, 530, 830 µatm) and temperature (26, 29 °C) treatments, and calcification was measured by the change in buoyant weight after 21 days of treatment exposure. Temperature and pCO2 had a significant interactive effect on net calcification of H. onkodes that was driven by the increased calcification response to moderately elevated pCO2. We demonstrate that the CCA calcification response was variable and non-linear, and that there was a trend for highest calcification at ambient temperature. H. onkodes then was exposed to grazing by the sea urchin Echinothrix diadema, and grazing was quantified by the change in CCA buoyant weight from grazing trials. E. diadema removed 60% more CaCO3 from H. onkodes grown at high temperature and high pCO2 than at ambient temperature and low pCO2. The increased susceptibility to grazing in the high pCO2 treatment is among the first evidence indicating the potential for cascading effects of OA and temperature on coral reef organisms and their ecological interactions.

Respiration rate of Themisto libellula determined experimentally

Daily ingestion rates of the pelagic hyperiid amphipod Themisto libellula were studied in the marginal ice zone of the Arctic Fram Strait by feeding experiments, respiration measurements and an allometric approach based on body mass. Amphipods were collected by stratified multiple opening/closing net hauls and Rectangular Midwater Trawl (RMT 8) in August 2000 during the expedition ARK XVI/2 of R/V "Polarstern". T. libellula occurred with abundances of 0.043 and 0.015 ind/m**3 in the upper 30 m of the water column at two RMT 8 stations. Based on respiration data, the daily ingestion necessary to cover metabolic energy demands measured 1.9±0.6% of body carbon per day. Actual prey consumption during feeding experiments with Calanus copepodids as prey was very similar and accounted for 1.9±1.5%/day, indicating that feeding on Calanus can meet the energy demands of T. libellula. In general, experimental results were slightly lower than the maximum potential ingestion (2%/day for an individual of median body dry mass of 32 mg) estimated by an allometric equation based on body mass, but feeding experiments showed a strong variability. Reduced metabolism and low ingestion rates of T. libellula are consistent with low ambient temperature, large body size, slow growth and long life span of this polar species. The effect of the active pelagic life style of T. libellula on metabolism and ingestion rate is discussed in comparison to the sympagic (i.e. ice-associated) amphipod Gammarus wilkitzkii of similar body size living in the same environment. In relation to the mesozooplankton biomass in the investigation area, the predation impact by T. libellula was low. However, high-Arctic conditions also limit the secondary production of principal prey species, such as Calanus glacialis and Calanus hyperboreus, so that even low predation rates may affect the growth of prey populations.

Sponge bioerosion accelerated by ocean acidification across species and latitudes?

In many marine biogeographic realms, bioeroding sponges dominate the internal bioerosion of calcareous substrates such as mollusc beds and coral reef framework. They biochemically dissolve part of the carbonate and liberate so-called sponge chips, a process that is expected to be facilitated and accelerated in a more acidic environment inherent to the present global change. The bioerosion capacity of the demosponge Cliona celata Grant, 1826 in subfossil oyster shells was assessed via alkalinity anomaly technique based on 4 days of experimental exposure to three different levels of carbon dioxide partial pressure (pCO2) at ambient temperature in the cold-temperate waters of Helgoland Island, North Sea. The rate of chemical bioerosion at present-day pCO2 was quantified with 0.08-0.1 kg/m**2/year. Chemical bioerosion was positively correlated with increasing pCO2, with rates more than doubling at carbon dioxide levels predicted for the end of the twenty-first century, clearly confirming that C. celata bioerosion can be expected to be enhanced with progressing ocean acidification (OA). Together with previously published experimental evidence, the present results suggest that OA accelerates sponge bioerosion (1) across latitudes and biogeographic areas, (2) independent of sponge growth form, and (3) for species with or without photosymbionts alike. A general increase in sponge bioerosion with advancing OA can be expected to have a significant impact on global carbonate (re)cycling and may result in widespread negative effects, e.g. on the stability of wild and farmed shellfish populations, as well as calcareous framework builders in tropical and cold-water coral reef ecosystems.