pH Proxy Research Articles

Connexin26 mediates CO2-dependent regulation of breathing via glial cells of the medulla oblongata

Breathing is highly sensitive to the PCO2 of arterial blood. Although CO2 is detected via the proxy of pH, CO2 acting directly via Cx26 may also contribute to the regulation of breathing. Here we exploit our knowledge of the structural motif of CO2-binding to Cx26 to devise a dominant negative subunit (Cx26DN) that removes the CO2-sensitivity from endogenously expressed wild type Cx26. Expression of Cx26DN in glial cells of a circumscribed region of the mouse medulla - the caudal parapyramidal area – reduced the adaptive change in tidal volume and minute ventilation by approximately 30% at 6% inspired CO2. As central chemosensors mediate about 70% of the total response to hypercapnia, CO2-sensing via Cx26 in the caudal parapyramidal area contributed about 45% of the centrally-mediated ventilatory response to CO2. Our data unequivocally link the direct sensing of CO2 to the chemosensory control of breathing and demonstrates that CO2-binding to Cx26 is a key transduction step in this fundamental process.

Thermal flux, fugitive gas emission and geotechnical instability in a complex tailings legacy site

Several years after decommissioning, a magnesium dross and mixed waste heap at a former industrial facility is still reactive, as evidenced by the emission of heat, Volatile Organic Carbon (VOCs), acetylene (C2H2), cyanide (HCN) and ammonia (NH3) from deep, discordant, epigenetic fissures. To evaluate the longer-term stability of the waste heap material, four cores were collected to evaluate vertical variations in temperature, moisture, gas composition, geochemistry, and mineralogy. Temperature increased with depth and peaked at around 8 m, reaching in excess of 90 °C. The waste heap was a mixture of unreacted materials (mainly MgO and CaO) and a variety of hydrated secondary reaction products. Formation of the latter could account for the generation of heat and creation of the fissures via thermal and secondary mineral volumetric expansion. With a large inventory of unreacted CaO and MgO and substantial in situ water present, the waste heap will probably remain reactive in the foreseeable future. Importantly, the CaO/MgO ratio of solid materials in the waste heap provides a useful proxy for down hole temperature, pH, and fugitive gas concentrations. Fugitive gases emitted by the waste heap are related to the reaction of co-existing minerals in the heap based on an historical analysis of site waste disposal. These waste materials include calcium carbide (CaC2), magnesium nitride (Mg3N2) and calcium cyanamide (CaCN2). Capping to limit the ingress of additional meteoric water and targeted venting to facilitate cooling and the controlled release and dispersion of gases are recommended to manage the environmental risk.

TEX86 as a potential proxy of lake water pH in the Tibetan Plateau

Water pH represents one of the most important indicators of chemical and biological changes in lacustrine systems. However, although water pH is also a major influence on inland water bodies and related ecosystems, it is not well studied in the lakes of the Tibetan Plateau (TP). The applicability of diatom assemblages, an effective proxy of variations in water pH in freshwater lakes, is greatly limited in the TP because the alkaline environment in most of the lakes is unfavorable for the preservation of diatom frustules. Isoprenoid glycerol dialkyl glycerol tetraethers (iGDGTs) are a series of specific membrane lipids biosynthesized by archaea, which appear to be a promising method for reflecting lake water pH variations. In this study, we analyzed the distribution of iGDGTs in the surface sediments of 34 alpine TP lakes and combined the data with published iGDGTs results from across the TP, in order to examine the effect of various environmental factors on iGDGT cyclization. The results show that water pH appears to be the most important factor affecting the degree of cyclization of iGDGTs in high-elevation alkaline lakes. This also suggests that the novel temperature proxy, TEX86, is also a promising water pH proxy for alpine lakes in the region. Despite a moderate correlation is observed between TEX86 and water pH, caution is needed in the interpretation of the TEX86 records, since other factors, such as temperature and the dissolved oxygen level, may also have an influence. Nevertheless, TEX86 appears to be a promising indicator of water pH for the alkaline lakes of the TP, and it could be a potentially useful tool for reconstructing pH in alkaline lakes in other areas, after regional calibrations.

Seawater temperature and buffering capacity modulate coral calcifying pH

Scleractinian corals promote the precipitation of their carbonate skeleton by elevating the pH and dissolved inorganic carbon (DIC) concentration of their calcifying fluid above that of seawater. The fact corals actively regulate their calcifying fluid chemistry implies the potential for acclimation to ocean acidification. However, the extent to which corals can adjust their regulation mechanism in the face of decreasing ocean pH has not been rigorously tested. Here I present a numerical model simulating pH and DIC up-regulation by corals, and use it to determine the relative importance of physiological regulation versus seawater conditions in controlling coral calcifying fluid chemistry. I show that external seawater temperature and buffering capacity exert the first-order control on the extent of pH elevation in the calcifying fluid and explain most of the observed inter- and intra-species variability. Conversely, physiological regulation, represented by the interplay between enzymatic proton pumping, carbon influx and the exchange of calcifying fluid with external seawater, contributes to some variability but remain relatively constant as seawater conditions change. The model quantitatively reproduces variations of calcifying fluid pH in natural Porites colonies, and predicts an average 0.16 unit decrease in Porites calcifying fluid pH, i.e., ~43% increase in H+ concentration, by the end of this century as a combined result of projected ocean warming and acidification, highlighting the susceptibility of coral calcification to future changes in ocean conditions. In addition, my findings support the development of coral-based seawater pH proxies, but suggest the influences of physicochemical and biological factors other than seawater pH must be considered.

Evaluation of 3-hydroxy fatty acids as a pH and temperature proxy in soils from temperate and tropical altitudinal gradients

Three hydroxy (3-OH) fatty acids (FAs), containing 10 to 18 C and a hydroxyl group in third position are characteristic components of Gram-negative bacteria. These compounds were used previously to detect and quantify Gram-negative bacterial communities in various types of samples, from terrestrial, aquatic and atmospheric environments. The relative abundance of 3-OH FAs in soils was recently shown to vary with mean annual air temperature (MAAT) and pH in soils from Mt. Shennongjia (China). In the current study, the concentrations and abundances of 3-OH FAs were determined in soils from altitudinal transects under tropical and temperate climates: Mt. Rungwe (SW Tanzania) and Mt. Majella (Central Italy), respectively. The aim was to (i) examine and compare the distributions of 3-OH FAs in soils from different climatic zones and (ii) to investigate the potential of 3-OH FAs as temperature and pH proxies. When combined with previously published data, a moderate correlation (R2 0.62) between the summed iso and anteiso to the total amount of normal 3-OH FAs (RIAN index) and pH was obtained. We show that Gram-negative bacteria respond in the same way to temperature variations in soils from different latitudes, with a relative increase of the anteiso to normal 3-OH FA ratios of the C15 and C17 compounds (RAN15 and RAN17 indices, respectively) with decreasing temperature. Nevertheless, the intercepts of the relationships between RAN15 and MAAT are mountain-dependent, suggesting that regional calibrations may be required to use RAN15 as a temperature proxy. In contrast with RAN15, the statistical similarity of the local relationships between RAN17 and MAAT leads to a combined calibration (R2 0.60, residual mean error 5.1 °C) covering a wide range of temperature (ca. 0–25 °C). As 3-OH FAs seem well-preserved in sedimentary archives, this strengthens the potential of these compounds as a temperature and pH proxy for paleoreconstructions in terrestrial settings.

An integrated open-coastal biogeochemistry, ecosystem and biodiversity observatory of the eastern Mediterranean – the Cretan Sea component of the POSEIDON system

Abstract. There is a general scarcity of oceanic observations that concurrently examine air–sea interactions, coastal–open-ocean processes and physical–biogeochemical processes, in appropriate spatiotemporal scales and under continuous, long-term data acquisition schemes. In the Mediterranean Sea, the resulting knowledge gaps and observing challenges increase due to its oligotrophic character, especially in the eastern part of the basin. The oligotrophic open Cretan Sea's biogeochemistry is considered to be representative of a greater Mediterranean area up to 106 km2, and understanding its features may be useful on even larger oceanic scales, since the Mediterranean Sea has been considered a miniature model of the global ocean. The spatiotemporal coverage of biogeochemical (BGC) observations in the Cretan Sea has progressively increased over the last decades, especially since the creation of the POSEIDON observing system, which has adopted a multiplatform, multivariable approach, supporting BGC data acquisition. The current POSEIDON system's status includes open and coastal sea fixed platforms, a Ferrybox (FB) system and Bio-Argo autonomous floats that remotely deliver fluorescence as a proxy of chlorophyll-a (Chl-a), O2, pH and pCO2 data, as well as BGC-related physical variables. Since 2010, the list has been further expanded to other BGC (nutrients, vertical particulate matter fluxes), ecosystem and biodiversity (from viruses up to zooplankton) variables, thanks to the addition of sediment traps, frequent research vessel (R/V) visits for seawater–plankton sampling and an acoustic Doppler current profiler (ADCP) delivering information on macrozooplankton–micronekton vertical migration (in the epipelagic to mesopelagic layer). Gliders and drifters are the new (currently under integration to the existing system) platforms, supporting BGC monitoring. Land-based facilities, such as data centres, technical support infrastructure, calibration laboratory and mesocosms, support and give added value to the observatory. The data gathered from these platforms are used to improve the quality of the BGC-ecosystem model predictions, which have recently incorporated atmospheric nutrient deposition processes and assimilation of satellite Chl-a data. Besides addressing open scientific questions at regional and international levels, examples of which are presented, the observatory provides user-oriented services to marine policy makers and the society, and is a technological test bed for new and/or cost-efficient BGC sensor technology and marine equipment. It is part of European and international observing programs, playing a key role in regional data handling and participating in harmonization and best practices procedures. Future expansion plans consider the evolving scientific and society priorities, balanced with sustainable management.

Robust Constraints on Past CO2 Climate Forcing From the Boron Isotope Proxy

AbstractThe atmospheric concentration of the greenhouse gas carbon dioxide, CO2, is intimately coupled to the carbon chemistry of seawater, such that the radiative climate forcing from CO2 can be changed by an array of physical, geochemical, and biological ocean processes. For instance, biological carbon sequestration, seawater cooling, and net CaCO3 dissolution are commonly invoked as the primary drivers of CO2 change that amplify the orbitally paced ice age cycles of the late Pleistocene. Based on first‐principle arguments with regard to ocean chemistry, we demonstrate that seawater pH change (ΔpH) is the dominant control that effectively sets CO2 radiative forcing (ΔF) on orbital timescales, as is evident from independent late Pleistocene reconstructions of pH and CO2. In short, all processes relevant for CO2on orbital timescales, including temperature change, cause pH to change to bring about fractional CO2 change so as to yield a linear relationship of ΔpH to CO2 climate forcing. Further, we show that ΔpH and CO2 climate forcing can be reconstructed using the boron isotope pH proxy more accurately than absolute pH or CO2, even if seawater boron isotope composition is poorly constrained and without information on a second carbonate system parameter. Thus, our formalism relaxes otherwise necessary assumptions to allow the accurate determination of orbital timescale CO2 radiative forcing from boron isotope pH reconstructions alone, thereby eliminating a major limitation of current methods to estimate our planet's climate sensitivity from the geologic record.

Zinc isotope fractionation during the inorganic precipitation of calcite – Towards a new pH proxy

Zinc was co-precipitated with calcite in mixed-flow reactors at 25 °C and 6.1 ≤ pH ≤ 8.5 to quantify Zn isotope fractionation between calcite and the reactive fluid. The results suggest that the difference between the isotopic composition of the solid and the fluid (Δ66Zncalcite-fluid = δ66Zncalcite − δ66Znfluid) increases by about 0.6‰ as the solution pH decreases from 8.5 to 6.1. In contrast, based on Zn aqueous speciation and the theoretical values of the reduced partition function ratios for zinc species, lnβ, the isotopic fractionation between calcite and aqueous Zn2+, Δ66Zncalcite - Zn2+, remains constant at 0.58 ± 0.05‰ over the entire pH range investigated. The constant value of Δ66Zncalcite - Zn2+ suggests that irrespective of the solution pH, the same Zn aqueous species, likely free Zn2+ ions, interacts with calcite surface sites during the growth of this mineral via ion by ion attachment. The enrichment of calcite in 66Zn is consistent with the formation of mononuclear, inner-sphere tetrahedral Zn surface complexes at the calcite surface and the increase of Zn coordination to 6 following its incorporation in the crystal lattice with no further isotopic fractionation. Overall, the results suggest that Zn isotopic composition of natural calcite has the potential to shed light on the prevailing pH at the time of calcite formation in the geological past.

Boron isotopic fractionation during adsorption by calcite – Implication for the seawater pH proxy

Although adsorption at the solid surface is the first step controlling boron incorporation in the crystal lattice during the standard growth mechanism of calcite and aragonite, little is known about the identity, structure and isotopic composition of the boron complexes formed at the CaCO3-solution interface. To generate this important information, we investigated experimentally the boron chemical and isotopic fractionation during adsorption at the calcite-water interface as a function of pH (6.5–11.7) at 4 and 20 °C in 0.01 and 0.1 M NaCl aqueous solutions. The surface complexation modeling of B adsorption and isotopic composition data showed that boron is sorbed at the calcite surface as a tetrahedral complex (>CaB(OH)40) formed by reaction of borate ions with Ca-protonated surface sites (log Kint0 = 1.54 ± 0.37 at 20 °C) and excluded the formation of trigonal B surface complexes (>CaB(OH)3+). The B isotopic composition of >CaB(OH)40 is ∼5‰ and 2‰ heavier than that of aqueous B(OH)4− in 0.01 and 0.1 M NaCl solution, respectively. Consistently, these values suggest that adsorbed borate ions have isotopic compositions intermediate between those of aqueous borate and structural tetrahedral species in calcite, which have been recently predicted to be ∼12‰ heavier than aqueous borate using quantum mechanical calculations (Balan et al., 2018). The good agreement between the isotopic composition of adsorbed boron measured in this study and boron experimentally co-precipitated with calcite in the 8–9 pH range at close to equilibrium conditions (i.e. via ion-by-ion attachment at advancing steps) (Noireaux et al., 2015) indicate that the isotopic composition of structural boron can be inherited from the boron surface complexes formed at the calcite/water interface. The results of this study contradict the assumption of no isotopic fractionation between tetrahedral boron in calcite and the borate ion that sustains the boron paleo-pH proxy, but confirm that trigonal B cannot be directly incorporated in the crystal structure during near equilibrium growth of calcite.

A simple role of coral-algal symbiosis in coral calcification based on multiple geochemical tracers

Light-enhanced calcification of reef-building corals, which eventually create vast coral reefs, is well known and based on coral-algal symbiosis. Several controversial hypotheses have been proposed as possible mechanisms for connecting symbiont photosynthesis and coral calcification, including pH rise in the internal pool, role of organic matrix secretion, and enzyme activities. Here, based on the skeletal chemical and isotopic compositions of symbiotic and asymbiotic primary polyps of Acropora digitifera corals, we show a simple pH increase in the calcification medium as the predominant contribution of symbionts to calcification of host corals. We used the symbiotic and asymbiotic primary polyps reared for 10 days at four temperatures (27, 29, 31, and 33 °C), five salinities (34, 32, 30, 28, and 26), and four pCO2 levels (<300, 400, 800, and 1000 µatm). As a result of analyzing multiple geochemical tracers (U/Ca, Mg/Ca, Sr/Ca, δ18O, δ13C, and δ44Ca), a clear and systematic decrease in skeletal U/Ca ratio (used as a proxy for calcification fluid pH) was observed, indicating a higher pH of the fluid in symbiotic compared to asymbiotic polyps. In contrast, Mg/Ca ratios (used as a tentative proxy for organic matrix secretion) and δ44Ca (used as an indicator of Ca2+ pathway to the fluid) did not differ between symbiotic and asymbiotic polyps. This suggests that organic matrix secretion related to coral calcification is controlled mainly by the coral host itself, and a transmembrane transport of Ca2+ does not vary according to symbiosis relationship. Skeletal δ18O values of both symbiotic and asymbiotic polyps showed offsets between them with identical temperature dependence. Based on a newly proposed model, behavior of δ18O in the present study seems to reflect the rate of CO2 hydration in the calcifying fluid. Since CO2 hydration is promoted by enzyme carbonic anhydrase, the offset of δ18O values between symbiotic and asymbiotic polyps is attributed to the differences of enzyme activity, although the enzyme is functional even in the asymbiotic polyp. Symbiotic δ13C values in the temperature and salinity experiments were higher compared to those in the asymbiotic polyps due to photosynthesis, although photosynthetic δ13C signals in the pCO2 experiment were masked by the dominant δ13C gradient in dissolved inorganic carbon in seawater caused by 13C-depletd CO2 gas addition in the higher pCO2 treatments. Sr/Ca ratios showed a negligible relationship according to variation of temperature, salinity, and pCO2, although it might be attributed to relatively large deviations of replicates of Sr/Ca ratios in the present study. Overall, only the U/Ca ratio showed a significant difference between symbiotic and asymbiotic polyps throughout all experiments, indicating that the critical effect on coral calcification caused by symbiotic algae is the increase of pH of the calcifying fluid by photosynthesis.

Lithium isotopic composition of benthic foraminifera: A new proxy for paleo-pH reconstruction

The lithium isotopic composition of foraminifera is an established tracer of long-term changes in the global silicate weathering cycle, following the assumption that foraminifera faithfully record the lithium isotopic composition (δ7Li) of seawater. In this study, we demonstrate by utilising benthic foraminifera (Amphistegina lessonii) that were cultured under decoupled pH-[CO32–] conditions, that foraminifera δ7Li is strongly dependent on pH. This is reinforced with δ7Li data from globally distributed core-top samples of Cibicidoides mundulus and Cibicidoides wuellerstorfi, which show the same negative correlation with pH. The dependency of δ7Li on pH is perhaps a surprising result given that lithium speciation in seawater is independent of both pH and carbonate ion speciation. The dependence of lithium incorporation on growth rate was assessed by measuring the calcium isotopic composition; no growth rate dependent incorporation was observed. Instead, we propose that the strength of the 6Li and 7Li hydration spheres (and hence their respective desolvation energy) is pH-dependent, resulting in a significant isotopic fractionation during the incorporation of lithium into foraminifer calcite. The core-top derived δ7Li-pH calibration is used to demonstrate the applicability of this δ11B-independent pH proxy in reconstructing deglacial variations in pH in the South Pacific. The use of foraminifera δ7Li to compliment δ11B-based pH reconstructions has the potential to provide insight into time-dependent variations in porewater/seawater δ11B, temperature and salinity, which were previously unresolvable.

Theoretical isotopic fractionation between structural boron in carbonates and aqueous boric acid and borate ion

The 11B/10B ratio in calcite and aragonite is an important proxy of oceanic water pH. However, the physico-chemical mechanisms underpinning this approach are still poorly known. In the present study, we theoretically determine the equilibrium isotopic fractionation properties of structural boron species in calcium carbonates, BO33−, BO2(OH)2− and B(OH)4− anions substituted for carbonate groups, as well as those of B(OH)4− and B(OH)3 species in vacuum. Significant variability of equilibrium isotopic fractionation properties is observed among these structural species which is related to their contrasted coordination state, BO bond lengths and atomic-scale environment. The isotopic composition of structural boron does not only depend on its coordination number but also on its medium range environment, i.e. farther than its first coordination shell. The isotopic fractionation between aqueous species and their counterparts in vacuum are assessed using previous investigations based on similar quantum-mechanical modeling approaches. At 300 K, the equilibrium isotope composition of structural trigonal species is 7–15‰ lighter than that of aqueous boric acid molecules, whereas substituted tetrahedral borate ions are heavier than their aqueous counterparts by 10–13‰. Although significant uncertainties are known to affect the theoretical prediction of fractionation factors between solids and solutions, the usually assumed lack of isotopic fractionation during borate incorporation in carbonates is challenged by these theoretical results. The present theoretical equilibrium fractionation factors between structural boron and aqueous species differ from those inferred from experiments which may indicate that isotopic equilibrium, unlike chemical equilibrium, was not reached in most experiments. Further research into the isotopic fractionation processes at the interface between calcium carbonates and aqueous solution as well as long duration experiments aimed at investigating the kinetics of equilibration of boron environment and isotopic composition are therefore required to refine our understanding of boron coprecipitation in carbonates and thus the theory behind the use of boron isotopes as an ocean pH proxy.

Kinetic stable Cr isotopic fractionation between aqueous Cr(III)-Cl-H2O complexes at 25 °C: Implications for Cr(III) mobility and isotopic variations in modern and ancient natural systems

The stable Cr isotope fractionation preserved in natural substances has been attributed predominantly to Cr(III)-Cr(VI) redox transformations. However, non-redox reaction pathways (e.g., ligand-promoted dissolution, ligand exchange, adsorption of Cr(III)) are liable to contribute to isotopic fractionation in natural systems given that soluble Cr(III)-ligands have been directly documented or modeled in several marine, continental, and hydrothermal environments.This study isolates the stable Cr isotope fractionation accompanying Cl-H2O ligand exchange during the transformation of three aqueous species in the Cr(III)-Cl-H2O system, [CrCl2(H2O)4]+aq (abr. CrCl2+ or S1), [CrCl(H2O)5]2+aq (abr. CrCl2+ or S2), and [Cr(H2O)6]3+aq (abr. Cr3+ or S3), at low pH (≤2). In dilute HCl (0.01 to 1 M), Cr3+ is the kinetically favoured species and transformation of CrCl2+ to CrCl2+ to Cr3+ via 2 steps of dechlorination/hydrolyzation begins immediately upon dissolution of a Cr(III)-Cl solid. Individual species are separated with cation exchange chromatography at different stages of transformation and inter- and intra-species (across an elution peak of one species) isotopic fractionation of up to 1 and 2‰ (δ53/52Cr), respectively, is documented. Comparison of peak elution characteristics with Cr-Cl-H-O isotopologue mass abundances suggests mass-dependent sorting of isotopologues alone cannot explain intra-species fractionation, supporting a previously published proposal that preferential adsorption of light Cr isotopes on the resin is driven by vibrational energy effects. The transformation of CrCl2+ to CrCl2+ is faster than CrCl2+ to Cr3+ and the rates of both transformations increase with solution pH. Preferential reaction of light Cr(III) isotopes into product species occurs during each transformation, consistent with closed-system, kinetic fractionation during Cl-H2O ligand exchange. Inter-species fractionation is assessed using time-series experiments beginning from the dissolution of two Cr(III)-Cl solids (dried NIST SRM979 standard and commercial CrCl3·6H2O salt) in 0.01 M HCl (pH ≈ 2). The ε53/52Cr(CrCl2+/CrCl2+) for the CrCl2+ to CrCl2+ reaction is −0.19‰ (SRM979) and −0.38‰ (salt) and the ε53/52Cr(Cr3+/CrCl2+) for the CrCl2+ to Cr3+ reaction is consistent for both experiments at −0.49‰ (SRM979) and −0.51‰ (salt). Experiments where SRM979 is dissolved in 0.1 and 1 M HCl for a longer aging period provide preliminary evidence that the Cr3+/CrCl2+ Cr(III) isotopic fractionation scales with HCl concentration (transformation rate). Chromium(III) dissolved in 6 M HCl and aged 5 months still yields an inter-species Cr isotope distribution that is apparently inherited from kinetic effects (light Cr isotopes in Cr3+), attesting to the slow development of inter-species isotopic equilibrium, which instead predicts progressively heavier Cr isotopes from CrCl2+ to CrCl2+ to Cr3+.The kinetic Cr(III) isotopic fractionation documented herein is proposed to be relevant to understanding systems where aqueous Cr(III)-Cl species may be temporarily stable (e.g., metamorphic and hydrothermal systems or lateritic weathering). Further, the complexation of Cr(III) with other ligands (e.g., CO32−, organics), combined with additional kinetic effects of Cr(III) potentially occurring in soils or sediment, must be explored prior to establishing the significance of empirical stable Cr isotope signatures in marine and continental environments. Further understanding of non-redox effects may lead to stable Cr isotopes developing as a proxy for system pH or ligand chemistry.

An improved boron isotope pH proxy calibration for the deep-sea coral Desmophyllum dianthus through sub-sampling of fibrous aragonite

The isotopic composition of boron (δ11B) in marine carbonates is well established as a proxy for past ocean pH, however, its robust application to palaeo-environments relies on the generation of species-specific calibrations. Existing calibrations utilising the deep-sea coral (DSC) Desmophyllum dianthus highlight the potential application of this pervasive species to pH reconstructions of intermediate depth waters. Nevertheless, considerable uncertainty remains regarding the estimation of seawater pH from these bulk skeletal δ11B measurements, likely resulting from microstructural heterogeneities in δ11B of D. dianthus. To circumvent this problem, thus improving the reliability of the D. dianthus δ11B-pH calibration, we present a new δ11B calibration of micro-sampled fibrous aragonite from this species.Modern coral specimens recovered from the Atlantic, Pacific, and Southern Oceans, micro-sampled using microdrilling, micromilling, and laser cutting extraction, were analysed for trace element (B/Ca, Mg/Ca, Sr/Ca, and U/Ca) and boron isotopic composition. We find the best calibration against the δ11B of borate in local ambient seawater (a function of pH and taken from hydrographic data sets; pH range 7.57 to 8.05) utilises δ11B measurements of fibres with likely slow growth rates and minimal contamination from adjacent microstructures (identified by low Mg/Ca) for each coral specimen. This new calibration exhibits a stronger, and better-defined dependence on ambient seawater pH compared to bulk coral δ11B; δ11Bfibre=(0.93±0.17)×δ11Bborate+(12.02±2.63). We suggest that the majority of the variability in measured δ11B between replicate bands of fibrous aragonite from a D. dianthus specimen can be explained by small incorporation of non-fibrous aragonite and surface impurities during microsampling and growth rate effects. This study confirms the utility of D. dianthus as an archive of precise palaeo-pH (±0.07pH units), provided that suitable sampling strategies are applied.

First-principles study of boron speciation in calcite and aragonite

Despite the importance of boron as a proxy of past ocean pH, the crystal-chemical factors controlling its incorporation in the structure of calcium carbonates are still poorly understood. This is partly linked to an imperfect knowledge of the coordination, protonation state and local environment of boron species in these minerals. In the present study, we use first-principles quantum mechanical tools to model selected trigonal and tetragonal boron species in calcite and aragonite. The stable geometry of the models is obtained from standard energy minimization schemes or using a more advanced metadynamics exploration of their configurational space. The computation of 11B NMR chemical shifts and quadrupolar coupling parameters enables a straightforward comparison of the models to existing experimental NMR data. The results show that B in calcium carbonates does occur as structural species substituted for CO32− anions. The B speciation depends on the polymorph considered. In calcite, structural boron is present as partially deprotonated trigonal BO2(OH)2− species coexisting with a fraction of substituted B(OH)4− groups. In aragonite, the B(OH)4− substitution for CO32− anions is dominant. Different species, including entrapped B(OH)3 molecules and substituted BO33− groups also occur in biogenic samples. The diversity of B speciation reflects a diversity of B incorporation mechanisms and sheds light on previous studies confronting B isotopic composition determination with NMR observations. The mechanisms of boron incorporation in calcium carbonates are probably more complex than usually assumed in the literature using boron isotopes as a proxy of paleo-atmospheric CO2 reconstructions. Although not invalidating the empirical paleo-pH proxy, these results call for a better understanding of the fundamental mechanisms of boron incorporation in carbonates.

Coral Sr‐U thermometry

AbstractCoral skeletons archive past climate variability with unrivaled temporal resolution. However, extraction of accurate temperature information from coral skeletons has been limited by “vital effects,” which confound, and sometimes override, the temperature dependence of geochemical proxies. We present a new approach to coral paleothermometry based on results of abiogenic precipitation experiments interpreted within a framework provided by a quantitative model of the coral biomineralization process. DeCarlo et al. (2015a) investigated temperature and carbonate chemistry controls on abiogenic partitioning of Sr/Ca and U/Ca between aragonite and seawater and modeled the sensitivity of skeletal composition to processes occurring at the site of calcification. The model predicts that temperature can be accurately reconstructed from coral skeleton by combining Sr/Ca and U/Ca ratios into a new proxy, which we refer to hereafter as the Sr‐U thermometer. Here we test the model predictions with measured Sr/Ca and U/Ca ratios of 14 Porites sp. corals collected from the tropical Pacific Ocean and the Red Sea, with a subset also analyzed using the boron isotope (δ11B) pH proxy. Observed relationships among Sr/Ca, U/Ca, and δ11B agree with model predictions, indicating that the model accounts for the key features of the coral biomineralization process. By calibrating to instrumental temperature records, we show that Sr‐U captures 93% of mean annual temperature variability (26–30°C) and has a standard deviation of prediction of 0.5°C, compared to 1°C using Sr/Ca alone. The Sr‐U thermometer may offer significantly improved reliability for reconstructing past ocean temperatures from coral skeletons.

Factors affecting B/Ca ratios in synthetic aragonite

Measurements of B/Ca ratios in marine carbonates have been suggested to record seawater carbonate chemistry, however experimental calibration of such proxies based on inorganic partitioning remains limited. Here we conducted a series of synthetic aragonite precipitation experiments to evaluate the factors influencing the partitioning of B/Ca between aragonite and seawater. Our results indicate that the B/Ca ratio of synthetic aragonites depends primarily on the relative concentrations of borate and carbonate ions in the solution from which the aragonite precipitates; not on bicarbonate concentration as has been previously suggested. The influence of temperature was not significant over the range investigated (20–40°C), however, partitioning may be influenced by saturation state (and/or growth rate). Based on our experimental results, we suggest that aragonite B/Ca ratios can be utilized as a proxy of [CO32–]. Boron isotopic composition (δ11B) is an established pH proxy, thus B/Ca and δ11B together allow the full carbonate chemistry of the solution from which the aragonite precipitated to be calculated. To the extent that aragonite precipitation by marine organisms is affected by seawater chemistry, B/Ca may also prove useful in reconstructing seawater chemistry. A simplified boron purification protocol based on amberlite resin and the organic buffer TRIS is also described.

Carbon isotope fractionation in phytoplankton as a potential proxy for pH rather than for [CO2(aq)]: Observations from a carbonate lake

AbstractThe method of reconstructing paleoatmospheric CO2 levels using carbon isotope signatures of organic matter buried in sediments has been questioned due to the dubious foundation that carbon isotope fractionation during phytoplankton photosynthesis (εp) is controlled primarily by aquatic CO2 concentration ([CO2(aq)]). Consequently, what carbon isotope data from bulk sedimentary organic matter reflects is a puzzle. In this study, we determined the carbon isotope compositions of dissolved inorganic carbon and particulate organic carbon in a lake located in a carbonate area. Partial correlation analysis was employed to distinguish between direct and indirect factors in controlling εp. The results show that εp is more closely, and more steadily related with pH than with [CO2(aq)], which is in accordance with recent advances in our understanding of the physiology of carbon utilization by phytoplankton for CO2 and . Therefore, we propose that carbon isotope fractionation in phytoplankton is more suitable as a proxy of pH than of [CO2(aq)]. One advantage of this amendment is that information on , the main species of carbon uptake by phytoplankton, is likewise included. In the future, culture experiments aiming at revealing the relationship between pH and cellular carbon isotope signatures is necessary to construct a new isotope fractionation formula to couple the different effects of CO2 and , which is of critical importance to improve the understanding of carbon isotope fractionation, and to more precisely model pH and CO2.

Environmental impacts on the distribution of microbial tetraether lipids in Chinese lakes with contrasting pH: Implications for lacustrine paleoenvironmental reconstructions

Glycerol dialkyl glycerol tetraethers (GDGTs) in lake sediments are useful biomarkers for the continental paleoclimatic reconstruction. However, the environmental controls on the distribution of these compounds, in particular the 6-methyl isomers of bacterial branched GDGTs (bGDGTs), in the lakes with contrasting pH, are still unknown, hindering their application for paleo-reconstructions. Here, we investigated the environmental impacts on the distribution of GDGTs in 17 alkaline lakes and 1 acid lake in China. It was found that the dissolved oxygen content in water column may have an impact on the distribution of archaeal isoprenoid GDGTs (iGDGTs) by causing the change in archaeal communities. The ratio of GDGT-0/crenarchaeol increases with decreasing oxygen content, indicating that the relative abundance of anaerobic methanogenic archaea or Miscellaneous Crenarchaeotic Group (MCG) vs. aerobic Thaumarchaeota is controlled by the oxygen content dissolved in water of these lakes. Thaumarchaeota are likely to contribute only a small proportion of iGDGTs in the relatively oxygen-depleted lakes, and thus TEX86 is not suitable for the reconstruction of the surface temperature of these lakes. The abundance ratio of iGDGTs to bGDGTs (R i/b ) appears to show no relationship with water pH in all the lakes, but exhibits a significant positive correlation with the water depth of the acid Lake Qinghai in Tengchong. As expected, the methylation degree of bGDGTs (MBT′) was found to correlate with both mean annual air temperature (MAT) and water pH, and the cyclization degree of bGDGTs (CBT) correlates only with water pH in these lakes. However, the MBT′5ME, an index to measure the methylation degree of 5-methyl bGDGTs, exhibits no relationship with MAT, whereas MBT′6ME, the methylation degree of 6-methyl bGDGTs, was found to correlate significantly with MAT. This is opposite to the situation observed in the global soils, pointing to a different adaptation of bGDGT-producing bacteria to environmental variables or different microbial sources of bGDGTs in these lakes. The relative abundance of 6- vs. 5-methyl bGDGTs is controlled by pH in these lakes, similar to that observed in worldwide soils. Hence, the isomer ratio (IR) of 6-methyl bGDGTs or CBT′ can be used as a proxy for water pH, although they might be influenced by other environmental factors including temperature in the lakes with a narrow range of pH.

Global calibration of a novel, branched GDGT-based soil pH proxy

Recently, 6-methyl branched glycerol dialkyl glycerol tetraethers (brGDGTs) were separated from 5-methyl brGDGTs, which are used in brGDGT-based proxies. Here we analyzed brGDGTs in 27 soil samples along the 400mm isoline of mean annual precipitation in China by using tandem 2D liquid chromatography. The fractional abundance of 6-methyl brGDGTs showed a positive correlation with soil pH, while that of 5-methyl brGDGTs decreased with increasing soil pH. The abundance ratio of 6-/5-methyl brGDGTs, namely the isomerization of branched tetraethers (IBT), was calculated. The correlation of IBT with pH (pH=6.33−1.28×IBT; R2 0.89; root mean squared error, RMSE, 0.24) was much stronger than that of the traditionally used cyclization index of branched tetraethers (CBT) with pH (R2 0.52; RMSE 0.49) and comparable with that of CBT′ with pH (R2 0.88; RMSE 0.25). Compiling all available data from 319 soil samples resulted in a global calibration: pH=6.53−1.55×IBT (R2 0.72; RMSE 0.65), which has a better correlation than the CBT5ME-pH proxy (R2 0.63; RMSE 0.78), but a weaker correlation than the CBT′-pH proxy (R2 0.85; RMSE 0.52). Our result suggests that the IBT is a promising indicator for soil pH, particularly in cases when some compounds in the CBT′ index cannot be determined.