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 By January 2015, a total of 581 data sets (over 4 000 000 data points) from 539 papers had been archived.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.

Seawater carbonate chemistry and calcification during experiments with corals, 2003

Biogenic calcification is influenced by the concentration of available carbonate ions. The recent confirmation of this for hermatypic corals has raised concern over the future of coral reefs because [CO3] is a decreasing function of increasing pCO2 in the atmosphere. As one of the overriding features of coral reefs is their diversity, understanding the degree of variability between species in their ability to cope with a change in [CO3] is a priority. We cultured four phylogenetically and physiologically different species of hermatypic coral (Acropora verweyi, Galaxea fascicularis, Pavona cactus and Turbinaria reniformis) under 'normal' (280 µmol/kg) and 'low' (140 µmol/kg) carbonate-ion concentrations. The effect on skeletogenesis was investigated quantitatively (by calcification rate) and qualitatively (by microstructural appearance of growing crystalline fibres using scanning electron microscopy (SEM)). The 'low carbonate' treatment resulted in a significant suppression of calcification rate and a tendency for weaker crystallization at the distal tips of fibres. However, while the calcification rate was affected uniformly across species (13-18% reduction), the magnitude of the microstructural response was highly species specific: crystallization was most markedly affected in A. verweyi and least in T. reniformis. These results are discussed in relation to past records and future predictions of carbonate variability in the oceans.

(Table 1) Position and astronomical ages of sedimentary cycles in the eastern Mediterranean Sea

An astronomically calibrated timescale has recently been established [Hilgen, 1991, doi:10.1016/0012-821X(91)90082-S; doi:10.1016/0012-821X(91)90206-W] for the Pliocene and earliest Pleistocene based on the correlation of dominantly precession controlled sedimentary cycles (sapropels and carbonate cycles) in Mediterranean marine sequences to the precession time series of the astronomical solution of Berger and Loutre [1991, doi:10.1016/0277-3791(91)90033-Q ] (hereinafter referred to as Ber90). Here we evaluate the accuracy of this timescale by (1) comparing the sedimentary cycle patterns with 65°N summer insolation time series of different astronomical solutions and (2) a cross-spectral comparison between the obliquity-related components in the 65°N summer insolation curves and high-resolution paleoclimatic records derived from the same sections used to construct the timescale. Our results show that the carbonate cycles older than 3.5 m.y. should be calibrated to one precession cycle older than previously proposed. Application of the astronomical solution of Laskar [1990, doi:10.1016/0019-1035(90)90084-M], (hereinafter referred to as La90) with present-day values for the dynamical ellipticity of the Earth and tidal dissipation by the Sun and Moon results in the best fit with the geological record, indicating that this solution is the most accurate from a geological point of view. Application of Ber90, or La90 solutions with dynamical ellipticity values smaller or larger than the present-day value, results in a less obvious fit with the geological record. This implies that the change in the planetary shape of the Earth associated with ice loading and unloading near the poles during the last 5.3 million years was too small to drive the precession into resonance with the perturbation term, s6-g6+g5, of Jupiter and Saturn. Our new timescale results in a slight but significant modification of all ages of the sedimentary cycles, bioevents, reversal boundaries, chronostratigraphic boundaries, and glacial cycles. Moreover, a comparison of this timescale with the astronomical timescales of ODP site 846 [Shackleton et al., 1995, doi:10.2973/odp.proc.sr.138.106.1995; doi:10.2973/odp.proc.sr.138.117.1995] and ODP site 659 [Tiedemann et al., 1994, doi:10.1029/94PA00208] indicates that all obliquity-related glacial cycles prior to ~4.7 Ma in ODP sites 659 and 846 should be correlated with one obliquity cycle older than previously proposed.

PumaPlex 1.0: Data generated during the development of the SNP markers and SNP genotypes of pumas

Pumas are one of the most studied terrestrial mammals because of their widespread distribution, substantial ecological impacts, and conflicts with humans. Extensive efforts, often employing genetic methods, are undertaken to manage this species. However, the comparison of population genetic data is difficult because few of the microsatellite loci chosen are shared across research programs. Here, we describe the development of PumaPlex, a high-throughput assay to genotype 25 single nucleotide polymorphisms in pumas. We validated PumaPlex in more than 700 North American pumas (Puma concolor couguar), and demonstrated its ability to generate reproducible genotypes and accurately identify individuals. Furthermore, we compared PumaPlex with traditional genotyping of 12 microsatellite loci in fecal DNA samples and found that PumaPlex produced significantly more genotypes with fewer false alleles. PumaPlex promotes the cross-laboratory comparison of genotypes, is easily expandable in the future, and is a valuable tool for the genetic monitoring and management of North American puma populations.

(Table 1) Stable oxygen and carbon isotopic ratios of tree rings, and tree ring width of white spruce (Picea glauca), Ennadai Lake

Stable isotope ratios from tree rings and peatland mosses have become important proxies of past climate variations. We here compare recent stable carbon and oxygen isotope ratios in cellulose of tree rings from white spruce (Picea glauca), growing near the arctic tree line; and cellulose of Sphagnum fuscum stems, growing in a hummock of a subarctic peatland, in west-central Canada. Results show that carbon isotopes in S. fuscum correlate significantly with July temperatures over the past ~20 yr. The oxygen isotopes correlate with both summer temperature and precipitation. Analyses of the tree-ring isotopes revealed summer temperatures to be the main controlling factor for carbon isotope variations, whereas tree-ring oxygen isotope ratios are controlled by a combination of spring temperatures and precipitation totals. We also explore the potential of combining high-frequency (annual) climate signals derived from long tree-ring series with low-frequency (decadal to centennial) climate signals derived from the moss remains in peat deposits. This cross-archive comparison revealed no association between the oxygen isotopes, which likely results from the varying sensitivity of the archives to different seasons. For the carbon isotopes, common variance could be achieved through adjustments of the Sphagnum age model within dating error.