Posts Tagged 'methods'

Using stable isotope analysis to determine the effects of ocean acidification and warming on trophic interactions in a maerl bed community

Ocean acidification and warming are likely to affect the structure and functioning of marine benthic communities. This study experimentally examined the effects of ocean acidification and warming on trophic interactions within a maerl bed community by using stable carbon and nitrogen isotope analysis. Two three‐month experiments were conducted in winter and summer seasons with four different combinations of pCO2 (ambient and elevated pCO2) and temperature (ambient and +3°C). Experimental assemblages were created in tanks held in the laboratory and were composed of calcareous (Lithothamnion corallioides) and fleshy algae (Rhodymenia ardissonei, Solieria chordalis, and Ulva sp.), gastropods (Gibbula magus and Jujubinus exasperatus), and sea urchins (Psammechinus miliaris). Our results showed higher seaweed availability for grazers in summer than winter. Therefore, grazers were able to adapt their diet seasonally. Increased pCO2 and temperature did not modify the trophic structure in winter, while shifts in the contribution of seaweed were found in summer. Combined acidification and warming increased the contribution of biofilm in gastropods diet in summer conditions. Psammechinus miliaris mostly consumed L. corallioides under ambient conditions, while the alga S. chordalis became the dominant food source under high pCO2 in summer. Predicted changes in pCO2 and temperature had complex effects on assemblage trophic structure. Direct effects of acidification and warming on seaweed metabolism may modify their abundance and biomass, affecting their availability for grazers. Climate change may also modify seaweeds’ nutritive value and their palatability for grazers. The grazers we investigated were able to change their diet in response to changes in algal assemblages, an advantage given that warming and acidification alter the composition of algal communities.

Continue reading ‘Using stable isotope analysis to determine the effects of ocean acidification and warming on trophic interactions in a maerl bed community’

Incorporation of minor and trace elements into cultured brachiopods: implications for proxy application with new insights from a biomineralisation model

Brachiopods present a key fossil group for Phanerozoic palaeo-environmental and palaeo-oceanographical reconstructions, owing to their good preservation and abundance in the geological record. Yet to date, hardly any geochemical proxies have been calibrated in cultured brachiopods and only little is known on the mechanisms that control the incorporation of various key elements into brachiopod calcite. To evaluate the feasibility and robustness of multiple Element/Ca ratios as proxies in brachiopods, specifically Li/Ca, B/Ca, Na/Ca, Mg/Ca, Sr/Ca, Ba/Ca, as well as Li/Mg, we cultured Magellania venosa, Terebratella dorsata and Pajaudina atlantica under controlled experimental settings over a period of more than two years with closely monitored ambient conditions, carbonate system parameters and elemental composition of the culture medium. The experimental setup comprised of two control aquariums (pH0 = 8.0 and 8.15, T = 10 °C) and treatments where pCO2 − pH (pH1 = 7.6 and pH2 = 7.35), temperature (T = 16 °C) and chemical composition of the culture medium were manipulated. Our results indicate that the incorporation of Li and Mg is strongly influenced by temperature, growth effects as well as carbonate chemistry, complicating the use of Li/Ca, Mg/Ca and Li/Mg ratios as straightforward reliable proxies. Boron partitioning varied greatly between the treatments, however without a clear link to carbonate system parameters or other environmental factors. The partitioning of both Ba and Na varied between individuals, but was not systematically affected by changes in the ambient conditions. We highlight Sr as a potential proxy for DIC, based on a positive trend between Sr partitioning and carbonate chemistry in the culture medium. To explain the observed dependency and provide a quantitative framework for exploring elemental variations, we devise the first biomineralisation model for brachiopods, which results in a close agreement between modelled and measured Sr distribution coefficients. We propose that in order to sustain shell growth under increased DIC, a decreased influx of Ca2+ to the calcifying fluid is necessary, driving the preferential substitution of Sr2+ for Ca2+ in the crystal lattice. Finally, we conducted micro-computed tomography analyses of the shells grown in the different experimental treatments. We present pore space – punctae – content quantification that indicates that shells built under increased environmental stress, and in particular elevated temperature, contain relatively more pore space than calcite, suggesting this parameter as a potential novel proxy for physiological stress and even environmental conditions.

Continue reading ‘Incorporation of minor and trace elements into cultured brachiopods: implications for proxy application with new insights from a biomineralisation model’

Controls on the spatio-temporal distribution of microbialite crusts on the Great Barrier Reef over the past 30,000 years


  • Comprehensive dataset of reefal microbial crusts over the past 30,000 years.
  • Modern 3D analysis to assess heterogeneity of microbialites in reef frameworks.
  • Radiocarbon ages show microbialite development coeval with and postdating framework.
  • Microbialite thickness correlates with changes in carbonate saturation level and pH.


Calcification of microbial mats adds significant amounts of calcium carbonate to primary coral reef structures that stabilizes and binds reef frameworks. Previous studies have shown that the distribution and thicknesses of late Quaternary microbial crusts have responded to changes in environmental parameters such as seawater pH, carbonate saturation state, and sediment and nutrient fluxes. However, these studies are few and limited in their spatio-temporal coverage. In this study, we used 3D and 2D examination techniques to investigate the spatio-temporal distribution of microbial crusts and their responses to environmental changes in Integrated Ocean Drilling Program (IODP) Expedition 325 (Great Barrier Reef Environmental Changes) fossil reef cores that span 30 to 10 ka at two locations on the GBR reef margin. Our GBR microbialite record was then combined with a meta-analysis of 17 other reef records to assess global scale changes in microbialite development (i.e., presence/absence, thickness) over the same period. The 3D results were compared with 2D surface area measurements to assess the accuracy of 2D methodology. The 2D technique represents an efficient and accurate proxy for the 3D volume of reef framework components within the bounds of uncertainty (average: 9.45 ± 4.5%). We found that deep water reef frameworks were most suitable for abundant microbial crust development. Consistent with a previous Exp. 325 study (Braga et al., 2019), we also found that crust ages were broadly coeval with coralgal communities in both shallow water and fore-reef settings. However, in some shallow water settings they also occur as the last reef framework binding stage, hundreds of years after the demise of coralgal communities. Lastly, comparisons of crust thickness with changes in environmental conditions between 30 and 10 ka, show a temporal correlation with variations in partial pressure of CO2 (pCO2), calcite saturation state (Ωcalcite), and pH of seawater, particularly during the past ~15 kyr, indicating that these environmental factors likely played a major role in microbialite crust development in the GBR. This supports the view that microbialite crust development can be used as an indicator of ocean acidification.

Continue reading ‘Controls on the spatio-temporal distribution of microbialite crusts on the Great Barrier Reef over the past 30,000 years’

Preparation of 2‐amino‐2‐hydroxymethyl‐1,3‐propanediol (TRIS) pHT buffers in synthetic seawater

Buffers of known quality for the calibration of seawater pHT measurements are not widely or commercially available. Although there exist published compositions for the 0.04 mol kg‐H2O−1 equimolar buffer 2‐amino‐2‐hydroxymethyl‐1,3‐propanediol (TRIS)‐TRIS · H+ in synthetic seawater, there are no explicit procedures that describe preparing this buffer to achieve a particular pHT with a known uncertainty. Such a procedure is described here which makes use of easily acquired laboratory equipment and techniques to produce a buffer with a pHT within 0.006 of the published pHT value originally assigned by DelValls and Dickson (1998), 8.094 at 25°C. Such a buffer will be suitable for the calibration of pH measurements expected to fulfil the “weather” uncertainty goal of the Global Ocean Acidification Observation Network of 0.02 in pHT, an uncertainty goal appropriate to “identify relative spatial patterns and short‐term variation.”

Continue reading ‘Preparation of 2‐amino‐2‐hydroxymethyl‐1,3‐propanediol (TRIS) pHT buffers in synthetic seawater’

Interpreting measurements of total alkalinity in marine and estuarine waters in the presence of proton-binding organic matter


• Model simulates alkalinity differences arising from different titration methodologies.

• Differences between measured and calculated alkalinity caused by organics are computed.

• Alkalinity differences vary with titration method and organic proton-binding affinity.

• Organics create errors in carbonate system calculations and interpretations.

• Marine alkalinity assessments should account for the ubiquitous presence of organics


Total alkalinity (AT) is one of four measurable cornerstone parameters for characterizing the marine carbonate system, yet its measurement by standard titration methods is subject to systematic misinterpretations in the presence of uncharacterized dissolved organic molecules in ocean and estuarine waters. A consequence of these misinterpretations may be the lack of thermodynamic consistency that is routinely observed among measured and calculated parameters of the carbonate system. In this work, a numerical model is used to illustrate (a) how proton-binding dissolved organic molecules influence the reported results of total alkalinity titrations in marine and estuarine settings and (b) how errors in interpretations of reported AT values can then propagate through carbonate system calculations, thus distorting biogeochemical interpretations of calculated parameters. We examine five distinct approaches for alkalinity measurement by titration. Ideally, the difference between the measured (reported) AT and the conventional (thermodynamic) definition of inorganic alkalinity (Ainorg) would be zero. However, in the presence of titratable organic matter, our model results show consistent non-zero differences that vary with the chemical properties of the organic matter. For all five titration approaches, the differences between reported AT and Ainorg are greatest when the negative logarithm of the organic acid dissociation constant (pKorg) is between approximately 5 and 7. The differences between reported AT and Ainorg also display previously undescribed variation among measurement approaches, most significantly when pKorg is between approximately 3 and 6 (typical of carboxylic acid groups). The measurement approaches that are most effective at limiting the unfavorable influence of these relatively low-pK organic acids on AT are closed-cell titrations and single-step titrations that are terminated at a relatively high pH. For calculated carbonate system parameters relevant to in situ conditions (e.g., pH, pCO2, calcium carbonate mineral saturation states), errors resulting from the presence of proton-binding organics are largest when calculations are based on the input pair of directly measured dissolved inorganic carbon (CT) and directly measured AT, and can vary in magnitude depending on the titration approach that is used to obtain AT. The modeling results presented in this work emphasize the importance of (a) determining AT in a manner that accounts for the ubiquity of organic alkalinity in marine and estuarine waters and (b) working toward a clearer understanding of the phenomena underlying the routine lack of internal consistency between measured versus calculated carbonate system parameters. Total alkalinity measurements should begin to incorporate either implicit or explicit evaluations of the titration characteristics of the natural organic carbon present in each sample. To that end, we recommend use of secondary titrations to directly measure organic alkalinity (sample-by-sample), characterization of relationships between total dissolved organic carbon concentrations and organic alkalinity (on local to regional scales), and/or exploration of novel curve-fitting procedures to infer the behavior of organic functional groups from titration data.

Continue reading ‘Interpreting measurements of total alkalinity in marine and estuarine waters in the presence of proton-binding organic matter’

Purified meta-cresol purple dye perturbation: how it influences spectrophotometric pH measurements


• The addition of an indicator dye perturbs the sample original pH and limits the spectrophotometric pH measurement accuracy.

• Dye perturbation on the sample pH varies depending on the sample properties and the indicator dye properties.

• To experimentally correct dye perturbation, sample properties like total alkalinity and salinity should be taken into consideration.

• A MATLAB function is proposed to calculate theoretical dye perturbation.


Ocean acidification, a phenomenon of seawater pH decreasing due to increasing atmospheric CO2, has a global effect on seawater chemistry, marine biology, and ecosystems. Ocean acidification is a gradual and global long-term process, the study of which demands high-quality pH data. The spectrophotometric technique is capable of generating accurate and precise pH measurements but requires adding an indicator dye that perturbs the sample original pH. While the perturbation is modest in well-buffered seawater, applications of the method in environments with lower buffer capacity such as riverine, estuarine, sea-ice meltwater and lacustrine environments are increasingly common, and uncertainties related to larger potential dye perturbations need further evaluation. In this paper, we assess the effect of purified meta-Cresol Purple (mCP) dye addition on the sample pH and how to correct for this dye perturbation. We conducted numerical simulations by incorporating mCP speciation into the MATLAB CO2SYS program to examine the changes in water sample pH caused by the dye addition and to reveal the dye perturbation mechanisms. Then, laboratory experiments were carried out to verify the simulation results. The simulations suggest that the dye perturbation on sample pH is a result of total alkalinity (TA) contributions from the indicator dye and chemical equilibrium shifts that are related to both the water sample properties (pH, TA, and salinity) and the indicator dye solution properties (pH and solvent matrix). The laboratory experiments supported the simulation results; the same dye solution can lead to different dye perturbations in water samples with different pH, TA, and salinity values. The modeled adjustments agreed well with the empirically determined adjustments for salinities >5, but it showed greater errors for lower salinities with disagreements as large as 0.005 pH units. Adjustments are minimized when the pH and salinity of the dye are matched to the sample. When the dye is used over a wide range of salinity, we suggest that it should be prepared in deionized water to minimize the dye perturbation effect on pH in the fresher sample waters with less well-constrained perturbation adjustments. We also suggest that the dye perturbation correction should be based on double dye addition experiments performed over a wide range of pH, TA, and salinity. Otherwise, multiple volume dye addition experiments are recommended for each sample to determine the dye perturbation adjustment. We further create a MATLAB function dyeperturbation.m that calculates the expected dye perturbation. This function can be used to validate empirically-derived adjustments or in lieu of empirical adjustments if dye addition experiments are unfeasible (e.g., for historical data). This study of dye perturbation evaluation and correction will improve the accuracy of the pH data, necessary for monitoring the long-term anthropogenic-driven changes in the seawater carbonate system.

Continue reading ‘Purified meta-cresol purple dye perturbation: how it influences spectrophotometric pH measurements’

Evaluation of a new carbon dioxide system for autonomous surface vehicles

Current carbon measurement strategies leave spatiotemporal gaps that hinder the scientific understanding of the oceanic carbon biogeochemical cycle. Data products and models are subject to bias because they rely on data that inadequately capture mesoscale spatiotemporal (kilometers and days to weeks) changes. High-resolution measurement strategies need to be implemented to adequately evaluate the global ocean carbon cycle. To augment the spatial and temporal coverage of ocean-atmosphere carbon measurements, an Autonomous Surface Vehicle CO2 (⁠⁠) system was developed. From 2011 to 2018, ASVCO2 systems were deployed on seven Wave Glider and Saildrone missions along the U.S. Pacific and Australia’s Tasmanian coastlines and in the tropical Pacific to evaluate the viability of the sensors and their applicability to carbon cycle research. Here we illustrate that the ASVCO2 systems are capable of long-term oceanic deployment and robust collection of air and seawater pCO2 within ± 2 µatm based on comparisons with established ship-board underway systems, with previously described MAPCO2 systems, and with companion ASVCO2 systems deployed side-by-side.

Continue reading ‘Evaluation of a new carbon dioxide system for autonomous surface vehicles’

Reversible and high accuracy pH colorimetric sensor array based on a single acid-base indicator working in a wide pH interval


• Reversible pH CSA working within 7 pH units by using only one pH indicator.

• Use of a suitable surfactant to vary the pKa of the indicator over 7 pH units.

• Error minimization (0.01 pH units) with a model computing the optimal spots number.

• A pH CSA with analytical performance comparable to the glass electrode.


A pH colorimetric sensor array (CSA) with fast response time (<1 min) using only one acid-base indicator, Bromothymol Blue (BB), was prepared and characterized by modulating the amount, C, of the surfactant Hexadecyltrimethylammonium p-toluenesulfonate between 0 and 0.3725 gCTApTs/gprecursor with a constant amount of the OrMoSil precursors. The effect of the C increase is a continuous acidic shift of the calibration position, i.e. a huge variation of the pKa value of BB in the pH range 5.80-13.50. The precision error decreased with increasing C from 0.096 pH units (lower C values) to 0.023 pH units (larger C values). This result led to the development of a model to determine the number of spots with suitable C values required for having a similar value of precision in the entire working interval of the CSA. By selecting only 4 spots the precision error is < 0.100 pH units in the pH range 5.80–13.50. With 256 spots (diameter of each spot ≈ 3 mm), the model predicted an error almost constant (≈0.010) in the entire pH range.

Continue reading ‘Reversible and high accuracy pH colorimetric sensor array based on a single acid-base indicator working in a wide pH interval’

Calcification of planktonic foraminifer Pulleniatina obliquiloculata controlled by seawater temperature rather than ocean acidification


• A method is provided to correct the dissolution effect on foraminiferal SNW

• Core-top ISNWP. obli is positively correlated with calcification temperature

• ISNWP. obli linked to seawater temperature, but not atmospheric pCO2, since 250 ka

• Temperature is the dominant factor controlling P. obliquiloculata calcification


Planktonic foraminifera represent a major component of global marine carbonate production, and understanding environmental influences on their calcification is critical to predicting marine carbon cycle responses to modern climate change. The present study investigated the effects of different environmental influences on calcification of the planktonic foraminifer Pulleniatina obliquiloculata. By correcting the dissolution effect on the size-normalized weight (SNW) of P. obliquiloculata from deep-sea sediments, we provide a means of estimating initial size-normalized weight (ISNW) from which to assess secular changes in the degree of calcification of P. obliquiloculata. Core-top ISNW in P. obliquiloculata from the global tropical oceans is significantly positively correlated with calcification temperature, suggesting that temperature is the dominant control on calcification. Using Neogloboquadrina dutertrei SNW as an independent deep-water Δ[CO32−] proxy, we present an ISNW record for P. obliquiloculata from the western tropical Pacific since 250 ka. The response of ISNW to past seawater temperature variations further confirms the dominant influence of temperature on P. obliquiloculata calcification. A potential increase in calcification as a result of ocean warming may have reduced oceanic uptake of CO2 from the atmosphere and increased atmospheric pCO2, generating a positive feedback for global warming.

Continue reading ‘Calcification of planktonic foraminifer Pulleniatina obliquiloculata controlled by seawater temperature rather than ocean acidification’

Global ocean spectrophotometric pH assessment: consistent inconsistencies

Ocean Acidification (OA)—or the decrease in seawater pH resulting from ocean uptake of CO2 released by human activities—stresses ocean ecosystems and is recognized as a Climate and Sustainable Development Goal Indicator that needs to be evaluated and monitored. Monitoring OA related pH changes requires a high level of precision and accuracy. The two most common ways to quantify seawater pH are to measure it spectrophotometrically or to calculate it from Total Alkalinity (TA) and Dissolved Inorganic Carbon (DIC). However, despite decades of research, small but important inconsistencies remain between measured and calculated pH. To date, this issue has been circumvented by examining changes only in consistently-measured properties. Currently, the oceanographic community is defining new observational strategies for OA and other key aspects of the ocean carbon cycle based on novel sensors and technologies, that rely on validation against data records and/or synthesis products. Comparison of measured spectrophotometric pH to calculated pH from TA and DIC measured during the 2000s and 2010s eras, reveals that: 1) there is an evolution towards a better agreement between measured and calculated pH over time from 0.02 pH units in the 2000s to 0.01 pH units in the 2010s at pH>7.6; 2) a disagreement greater than 0.01 pH units persists in waters with pH<7.6, and 3) inconsistencies likely stem from variations in the spectrophotometric pH standard operating procedure (SOP). A reassessment of pH measurement and calculation SOPs and metrology is urgently needed.

Continue reading ‘Global ocean spectrophotometric pH assessment: consistent inconsistencies’

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Ocean acidification in the IPCC AR5 WG II

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