Data compilation on the biological response to ocean acidification: environmental and experimental context of data sets and related literature

The exponential growth of studies on the biological response to ocean acidification over the last few decades has generated a large amount of data. To facilitate data comparison, a data compilation hosted at the data publisher PANGAEA was initiated in 2008 and is updated on a regular basis (doi:10.1594/PANGAEA.149999). By January 2015, a total of 581 data sets (over 4 000 000 data points) from 539 papers had been archived. Here we present the developments of this data compilation five years since its first description by Nisumaa et al. (2010). Most of study sites from which data archived are still in the Northern Hemisphere and the number of archived data from studies from the Southern Hemisphere and polar oceans are still relatively low. Data from 60 studies that investigated the response of a mix of organisms or natural communities were all added after 2010, indicating a welcomed shift from the study of individual organisms to communities and ecosystems. The initial imbalance of considerably more data archived on calcification and primary production than on other processes has improved. There is also a clear tendency towards more data archived from multifactorial studies after 2010. For easier and more effective access to ocean acidification data, the ocean acidification community is strongly encouraged to contribute to the data archiving effort, and help develop standard vocabularies describing the variables and define best practices for archiving ocean acidification data.

Organic geochemistry of deep sea sediments from the Nankai Trough and the Southwest Japan forearc region

Earth's largest reactive carbon pool, marine sedimentary organic matter, becomes increasingly recalcitrant during burial, making it almost inaccessible as a substrate for microorganisms, and thereby limiting metabolic activity in the deep biosphere. Because elevated temperature acting over geological time leads to the massive thermal breakdown of the organic matter into volatiles, including petroleum, the question arises whether microorganisms can directly utilize these maturation products as a substrate. While migrated thermogenic fluids are known to sustain microbial consortia in shallow sediments, an in situ coupling of abiotic generation and microbial utilization has not been demonstrated. Here we show, using a combination of basin modelling, kinetic modelling, geomicrobiology and biogeochemistry, that microorganisms inhabit the active generation zone in the Nankai Trough, offshore Japan. Three sites from ODP Leg 190 have been evaluated, namely 1173, 1174 and 1177, drilled in nearly undeformed Quaternary and Tertiary sedimentary sequences seaward of the Nankai Trough itself. Paleotemperatures were reconstructed based on subsidence profiles, compaction modelling, present-day heat flow, downhole temperature measurements and organic maturity parameters. Today's heat flow distribution can be considered mainly conductive, and is extremely high in places, reaching 180 mW/m**2. The kinetic parameters describing total hydrocarbon generation, determined by laboratory pyrolysis experiments, were utilized by the model in order to predict the timing of generation in time and space. The model predicts that the onset of present day generation lies between 300 and 500 m below sea floor (5100-5300 m below mean sea level), depending on well location. In the case of Site 1174, 5-10% conversion has taken place by a present day temperature of ca. 85 °C. Predictions were largely validated by on-site hydrocarbon gas measurements. Viable organisms in the same depth range have been proven using 14C-radiolabelled substrates for methanogenesis, bacterial cell counts and intact phospholipids. Altogether, these results point to an overlap of abiotic thermal degradation reactions going on in the same part of the sedimentary column as where a deep biosphere exists. The organic matter preserved in Nankai Trough sediments is of the type that generates putative feedstocks for microbial activity, namely oxygenated compounds and hydrocarbons. Furthermore, the rates of thermal degradation calculated from the kinetic model closely resemble rates of respiration and electron donor consumption independently measured in other deep biosphere environments. We deduce that abiotically driven degradation reactions have provided substrates for microbial activity in deep sediments at this convergent continental margin.

Pore water (SO4, CH4, alkalinity, HS-, Ca, Sr, Mg, Ba) and solid phase (Ca, Sr, Mg, Ba) data measured in pockmark sediments of the Northern Congo Fan

This study focuses on the vertical distribution of authigenic carbonates (aragonite and high Mg-calcite) in the form of finely disseminated precipitates as well as massive carbonate concretions present in and above gas hydrate bearing sediments of the Northern Congo Fan. Analyses of Ca, Mg, Sr and Ba in pore water, bulk sediments and authigenic carbonates were carried out on gravity cores taken from three pockmark structures (Hydrate Hole, Black Hole and Worm Hole). In addition, a background core was retrieved from an area not influenced by fluid seepage. Pore water Sr/Ca and Mg/Ca ratios are used to reveal the current depths of carbonate formation as well as the mineralogy of the authigenic precipitates. The Sr/Ca and Mg/Ca ratios of bulk sediments and massive carbonate concretions were applied to infer the presence and depth distribution of authigenic aragonite and high Mg-calcite, based on the approach presented by Bayon et al. [Bayon et al. (2007). Sr/Ca and Mg/Ca ratios in Niger Delta sediments: Implications for authigenic carbonate genesis in cold seep environments. Marine Geology 241(1-4), 93-109, doi:10.1016/j.margeo.2007.03.007]. We show that the approach developed by Bayon et al. (2007) for sediments of cold seeps of the Niger Delta is also suitable to identify the mineralogy of authigenic carbonates in pockmark sediments of the Congo Deep-Sea Fan. We expand this approach by combining interstitial with solid phase Sr/Ca and Mg/Ca ratios, which demonstrate that high Mg-calcite is the predominant authigenic carbonate that currently forms at the sulfate/methane reaction zone (SMRZ). This is the first study which investigates both solid phase and pore water signatures typical for either aragonite or high Mg-calcite precipitation for the same sediment cores and thus is able to identify active and fossil carbonate precipitation events. At all investigated pockmark sites fossil horizons of the SMRZ were deduced from high Mg-calcite located above and below the current depths of the SMRZ. Additionally, aragonite enrichments typical for high seepage rates were detected close to the sediment surface at these sites. However, active precipitation of aragonite as indicated by pore water characteristics only occurs at the Black Hole site. Dissolved and solid phase Ba concentrations were used to estimate the time the SMRZ was fixed at the current depths of the diagenetic barite fronts. The combined pore water and solid phase elemental ratios (Mg/Ca, Sr/Ca) and Ba concentrations allow the reconstruction of past changes in methane seepage at the investigated pockmark sites. At the Hydrate Hole and Worm Hole sites the time of high methane seepage was estimated to have ceased at least 600 yr BP. In contrast, a more recent change from a high flux to a more dormant stage must have occurred at the Black Hole site as evidenced by active aragonite precipitation at the sediment surface and a lack of diagenetic Ba enrichments.

Seawater carbonate chemistry and early development of the sea urchin Lytechinus variegatus in a laboratory experiment using artificial seawater

Land-based aquaculture facilities often utilize additional bicarbonate sources such as commercial sea salts that are designed to boost alkalinity in order to buffer seawater against reductions in pH. Despite these preventative measures, many facilities are likely to face occasional reductions in pH and corresponding reductions in carbonate saturation states due to the accumulation of metabolic waste products. We investigated the impact of reduced carbonate saturation states (Omega Ca, Omega Ar) on embryonic developmental rates, larval developmental rates, and echinoplutei skeletal morphometrics in the common edible sea urchin Lytechinus variegatus under high alkalinity conditions. Commercial artificial seawater was bubbled with a mixture of air and CO2 gas to reduce the carbonate saturation state. Rates of embryonic and larval development were significantly delayed in both the low and extreme low carbonate saturation state groups relative to the control at a given time. Although symmetry of overall skeletal body lengths was not affected, allometric relationships were significantly different between treatment groups. Larvae reared under ambient conditions had significantly greater postoral arm and overall body lengths relative to body lengths than larvae grown under extreme low carbonate saturation state conditions, indicating that extreme changes in the carbonate system affected not only developmental rates but also larval skeletal shape. Reduced rates of embryonic development and delayed and altered larval skeletal growth are likely to negatively impact larval culturing of L. variegatus in land-based, intensive culture situations where calcite and aragonite saturation states are lowered by the accumulation of metabolic waste products.

Grazing under experimental hypercapnia and elevated temperature does not affect the radula of a chiton (Mollusca, Polyplacophora, Lepidopleurida)

Chitons (class Polyplacophora) are benthic grazing molluscs with an eight-part aragonitic shell armature. The radula, a serial tooth ribbon that extends internally more than half the length of the body, is mineralised on the active feeding teeth with iron magnetite apparently as an adaptation to constant grazing on rocky substrates. As the anterior feeding teeth are eroded they are shed and replaced with a new row. The efficient mineralisation and function of the radula could hypothetically be affected by changing oceans in two ways: changes in seawater chemistry (pH and pCO2) may impact the biomineralisation pathway, potentially leading to a weaker or altered density of the feeding teeth; rising temperatures could increase activity levels in these ectothermic animals, and higher feeding rates could increase wear on the feeding teeth beyond the animals' ability to synthesise, mineralise, and replace radular rows. We therefore examined the effects of pH and temperature on growth and integrity in the radula of the chiton Leptochiton asellus. Our experiment implemented three temperature (10, 15, 20 °C) and two pCO2 treatments (400 µatm, pH 8.0; 2000 µatm, pH 7.5) for six treatment groups. Animals (n = 50) were acclimated to the treatment conditions for a period of 4 weeks. This is sufficient time for growth of ca. 7-9 new tooth rows or 20% turnover of the mineralised portion. There was no significant difference in the number of new (non-mineralised) teeth or total tooth row count in any treatment. Examination of the radulae via SEM revealed no differences in microwear or breakage on the feeding cusps correlating to treatment groups. The shell valves also showed no signs of dissolution. As a lineage, chitons have survived repeated shifts in Earth's climate through geological time, and at least their radulae may be robust to future perturbations.

10Be/9Be-based chronostratigraphy of ODP Hole 181-1121B from the Southwest Pacific Ocean

A 10Be/9Be-based chronostratigraphy has been determined for ODP 181, Site 1121 sediment core, recovered from the foot of the Campbell Plateau, Southwest Pacific Ocean. This core was drilled through the Campbell 'skin drift' in ca. 4500 m water depth on the mid-western margin of the extensive Campbell Nodule Field, beneath the flow of the major cold-water Deep Western Boundary Current (DWBC). In the absence of detailed biostratigraphy, beryllium isotopes have provided essential time information to allow palaeo-environmental interpretation to be undertaken on the upper 7 m of the core. Measured 10Be/9Be ratios of sediment, and of ferromanganese nodules entrapped in the sediment, decrease systematically with depth in the core, in accordance with radioactive decay. However, the 10Be/9Be data diverge from ca. 3 m below the seafloor (mbsf) to the top of the core, giving rise to several possible geochronological models. The preferred model assumes that the measured 10Be/9Be ratios of the nodule rims reflect initial 10Be/9Be ratios equivalent to contemporary seawater, and that these can be used to derive the true age of the sediment where the nodules occur. The nodule rim ages can be then used to interpret the sediment 10Be/9Be data, which indicate an overall age to ca. 7 mbsf of ca. 17.5 Ma. The derived chronology is consistent with diatom biostratigraphy, which indicates an age of 2.2-3.6 Ma at 1 mbsf. Calculated sedimentation rates range from 8 to 95 cm m.y.**-1, with an overall rate to 7 mbsf of ca. 39 cm m.y.**-1. The lowest rates generally coincide with the occurrence of entrapped nodules, and reflect periods of increased bottom current flow causing net sediment loss. Growth rates of individual nodules decrease towards the top of the sediment core, similar to the observed decrease in growth rate from core to rim of seafloor nodules from the Campbell Nodule Field. This may be related to an overall increase in the vigour of the DWBC from ca. 10 Ma to the present.

Annotated record of the detailed examination of Mn deposits from the QUEBRADA (1969) and SIQUEIROS (1974) expeditions around the East Pacific Rise

Basalt samples obtained from the Siqueiros transform fault/fracture zone and the adjacent East Pacific Rise are mostly very fresh oceanic tholeiite and fractionated oceanic tholeiite with Fe+3/ Fe+2 ? 0.25; however, alkali basalts occur in the area as well. The rocks of the tholeiitic suite are ol + pl phyric and ol + pl + cpx phyric basalts, while the alkali basalts are ol and ol + pl phyric. Microprobe analyses of the tholeiitic suite phenocrysts indicate that they are Fo68-Fo86, An58-An75, and augite (Ca34Mg50Fe16). The range of olivine and plagioclase compositions represents the chemical variation of the phenocryst compositions with fractionation. The phenocyrsts in the alkali basalts are Fo81 and An69. The suite of tholeiites comprises a fractionation series characterized by relative enrichment of Fe, Ti, Mn, V, Na, K, and P and depletion of Ca, Al, Mg, Ni, and Cr. The fractionated tholeiites occur on the median ridge (which is a sliver of normal oceanic crust) of the double Siqueiros transform fault, on the western Siqueiros fracture zone, and on the adjoining East Pacific Rise, while the two transform fault troughs contain mostly unfractionated or only slightly fractionated tholeiite. We suggest that the fractionated tholeiites are produced by fractional crystallization of more 'primitive' tholeiitic liquid in a crustal magma chamber below the crest of the East Pacific Rise. This magma chamber may be disrupted by the transform fault troughs, thus explaining the paucity of fractionated tholeiites in the troughs. The alkali basalts are found only on the flanks of a topographic high near the intersection of the northern transform trough with the East Pacific Rise.

Sr/Ca and Cd/Ca ratios of benthic foraminifera in surface deep-sea sediments

Measurements of Sr/Ca of benthic foraminifera show a linear decrease with water depth which is superimposed upon significant variability identified by analyses of individual foraminifera. New data for Cd/Ca support previous work in defining a contrast between waters shallower and deeper than ~2500 m. Measured element partition coefficients in foraminiferal calcium carbonate relative to sea water (D) have been described by means of a one-box model in which elements are extracted by Rayleigh distillation from a biomineralization reservoir that serves for calcification with a constant fractionation factor (alpha), such that D = (1 - f**alpha)/(l - f), where f is the proportion of Ca remaining after precipitation. A modification to the model recognises differences in element speciation. The model is consistent with differences between D[Sr], D[Ba], and D[Cd] in benthic but not planktonic foraminifera. Depth variations in D for Sr and Ba are consistent with the model, as are differences in depth variation of D[Cd] in calcitic and aragonitic benthic foraminifera. The shallower depth variations may reflect increasing calcification rates with increasing water depth to an optimum of about 2500 m. Observations of unusually lower DCd for some deep waters, not accompanied by similar [Sr], or D[Ba] may be because of dissolution or a calcification response to a lower carbonate saturation state.