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 By January 2015, a total of 581 data sets (over 4 000 000 data points) from 539 papers had been archived.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

Diversity of zooplankton assemblages at Station L4, Western English Channel, measured using next generation DNA sequencing

Background: Zooplankton play an important role in our oceans, in biogeochemical cycling and providing a food source for commercially important fish larvae. However, difficulties in correctly identifying zooplankton hinder our understanding of their roles in marine ecosystem functioning, and can prevent detection of long term changes in their community structure. The advent of massively parallel Next Generation Sequencing technology allows DNA sequence data to be recovered directly from whole community samples. Here we assess the ability of such sequencing to quantify the richness and diversity of a mixed zooplankton assemblage from a productive monitoring site in the Western English Channel. Methodology/Principle Findings: Plankton WP2 replicate net hauls (200 µm) were taken at the Western Channel Observatory long-term monitoring station L4 in September 2010 and January 2011. These samples were analysed by microscopy and metagenetic analysis of the 18S nuclear small subunit ribosomal RNA gene using the 454 pyrosequencing platform. Following quality control a total of 419,042 sequences were obtained for all samples. The sequences clustered in to 205 operational taxonomic units using a 97% similarity cut-off. Allocation of taxonomy by comparison with the National Centre for Biotechnology Information database identified 138 OTUs to species level, 11 to genus level and 1 to order, <2.5% of sequences were classified as unknowns. By comparison a skilled microscopic analyst was able to routinely enumerate only 75 taxonomic groups. Conclusions: The percentage of OTUs assigned to major eukaryotic taxonomic groups broadly aligns between the metagenetic and morphological analysis and are dominated by Copepoda. However, the metagenetics reveals a previously hidden taxonomic richness, especially for Copepoda and meroplankton such as Bivalvia, Gastropoda and Polychaeta. It also reveals rare species and parasites. We conclude that Next Generation Sequencing of 18S amplicons is a powerful tool for estimating diversity and species richness of zooplankton communities.

Heavy minerals, grain size distribution, and ice-rafted debris in the Greenland Sea during 44 to 30 Ma

The widely accepted age estimate for the onset of glaciation in the Northern Hemisphere ranges between 2 and 15 million years ago (Ma). However, recent studies indicate the date for glacial onset may be significantly older. We report the presence of ice-rafted debris (IRD) in ~44 to 30 Ma sediments from the Greenland Sea, evidence for glaciation in the North Atlantic during the Middle Eocene to Early Oligocene. Detailed sedimentological evidence indicates that glaciers extended to sea level in the region, allowing icebergs to be produced. IRD may have been sourced from tidewater glaciers, small ice caps, and/or a continental ice sheet.

Seawater carbonate chemistry and dissolution rates by boring microflora during ex situ experiments with dead corals (Porites lobata), 2009

Eight-month-old blocks of the coral Porites lobata colonized by natural Hawaiian euendolithic and epilithic communities were experimentally exposed to two different aqueous pCO2 treatments, 400 ppmv and 750 ppmv, for 3 months. The chlorophyte Ostreobium quekettii dominated communities at the start and at the end of the experiment (65-90%). There were no significant differences in the relative abundance of euendolithic species, nor were there any differences in bioeroded area at the surface of blocks (27%) between pCO2 treatments. The depth of penetration of filaments of O. quekettii was, however, significantly higher under 750 ppmv (1.4 mm) than under 400 ppmv (1 mm). Consequently, rates of carbonate dissolution measured under elevated pCO2 were 48% higher than under ambient pCO2 (0.46 kg CaCO3 dissolved m2/a versus 0.31 kg /m2/a). Thus, biogenic dissolution of carbonates by euendoliths in coral reefs may be a dominant mechanism of carbonate dissolution in a more acidic ocean.