Whole transcriptome analysis of the coral Acropora millepora reveals complex responses to CO2-driven acidification during the initiation of calcification

The impact of ocean acidification (OA) on coral calcification, a subject of intense current interest, is poorly understood in part because of the presence of symbionts in adult corals. Early life history stages of Acropora spp. provide an opportunity to study the effects of elevated CO(2) on coral calcification without the complication of symbiont metabolism. Therefore, we used the Illumina RNAseq approach to study the effects of acute exposure to elevated CO(2) on gene expression in primary polyps of Acropora millepora, using as reference a novel comprehensive transcriptome assembly developed for this study. Gene ontology analysis of this whole transcriptome data set indicated that CO(2) -driven acidification strongly suppressed metabolism but enhanced extracellular organic matrix synthesis, whereas targeted analyses revealed complex effects on genes implicated in calcification. Unexpectedly, expression of most ion transport proteins was unaffected, while many membrane-associated or secreted carbonic anhydrases were expressed at lower levels. The most dramatic effect of CO(2) -driven acidification, however, was on genes encoding candidate and known components of the skeletal organic matrix that controls CaCO(3) deposition. The skeletal organic matrix effects included elevated expression of adult-type galaxins and some secreted acidic proteins, but down-regulation of other galaxins, secreted acidic proteins, SCRiPs and other coral-specific genes, suggesting specialized roles for the members of these protein families and complex impacts of OA on mineral deposition. This study is the first exhaustive exploration of the transcriptomic response of a scleractinian coral to acidification and provides an unbiased perspective on its effects during the early stages of calcification.

Nitrogen cycling driven by organic matter export in the South Pacific oxygen minimum zone

Oxygen minimum zones are expanding globally, and at present account for around 20-40% of oceanic nitrogen loss. Heterotrophic denitrification and anammox-anaerobic ammonium oxidation with nitrite-are responsible for most nitrogen loss in these low-oxygen waters. Anammox is particularly significant in the eastern tropical South Pacific, one of the largest oxygen minimum zones globally. However, the factors that regulate anammox-driven nitrogen loss have remained unclear. Here, we present a comprehensive nitrogen budget for the eastern tropical South Pacific oxygen minimum zone, using measurements of nutrient concentrations, experimentally determined rates of nitrogen transformation and a numerical model of export production. Anammox was the dominant mode of nitrogen loss at the time of sampling. Rates of anammox, and related nitrogen transformations, were greatest in the productive shelf waters, and tailed off with distance from the coast. Within the shelf region, anammox activity peaked in both upper and bottom waters. Overall, rates of nitrogen transformation, including anammox, were strongly correlated with the export of organic matter. We suggest that the sinking of organic matter, and thus the release of ammonium into the water column, together with benthic ammonium release, fuel nitrogen loss from oxygen minimum zones.

Sedimentological, geochemical, micropaleontological and rock magnetic proxies of sediment core GeoB6211-2

Surface currents and sediment distribution of the SE South American upper continental margin are under influence of the South American Monsoon System (SAMS) and the Southern Westerly Wind Belt (SWWB). Both climatic systems determine the meridional position of the Subtropical Shelf Front (STSF) and probably also of the Brazil-Malvinas Confluence (BMC). We reconstruct the changing impact of the SAMS and the SWWB on sediment composition at the upper Rio Grande Cone off southern Brazil during the last 14 cal kyr combining sedimentological, geochemical, micropaleontological and rock magnetic proxies of marine sediment core GeoB 6211-2. Sharp reciprocal changes in ferri- and paramagnetic mineral content and prominent grain-size shifts give strong clues to systematic source changes and transport modes of these mostly terrigenous sediments. Our interpretations support the assumption that the SAMS over SE South America was weaker than today during most of the Late Glacial and entire Early Holocene, while the SWWB was contracted to more southern latitudes, resembling modern austral summer-like conditions. In consequence, the STSF and the BMC were driven to more southern positions than today's, favoring the deposition of Fe-rich but weakly magnetic La Plata River silts at the Rio Grande Cone. During the Mid Holocene, the northern boundary of the SWWB migrated northward, while the STSF reached its northernmost position of the last 14 cal kyr and the BMC most likely arrived at its modern position. This shift enabled the transport of Antarctic diatoms and more strongly magnetic Argentinean shelf sands to the Rio Grande Cone, while sediment contributions from the La Plata River became less important. During the Late Holocene, the modern El Niño Southern Oscillation set in and the SAMS and the austral tradewinds intensified, causing a southward shift of the STSF to its modern position. This reinforced a significant deposition of La Plata River silts at the Rio Grande Cone. These higher magnetic silts with intermediate Fe contents mirror the modern more humid terrestrial climatic conditions over SE South America.