Seawater carbonate chemistry and Ruditapes decussatus biological processes during experiments, 2011

We investigated the effects of ocean acidification on juvenile clams Ruditapes decussatus (average shell length 10.24 mm) in a controlled CO2 perturbation experiment. The carbonate chemistry of seawater was manipulated by diffusing pure CO2, to attain two reduced pH levels (by -0.4 and -0.7 pH units), which were compared to unmanipulated seawater. After 75 days we found no differences among pH treatments in terms of net calcification, size or weight of the clams. The naturally elevated total alkalinity of local seawater probably contributed to buffer the effects of increased pCO2 and reduced pH. Marine organisms may, therefore, show diverse responses to ocean acidification at local scales, particularly in coastal, estuarine and transitional waters, where the physical-chemical characteristics of seawater are most variable. Mortality was significantly reduced in the acidified treatments. This trend was probably related to the occurrence of spontaneous spawning events in the control and intermediate acidification treatments. Spawning, which was unexpected due to the small size of the clams, was not observed for the pH -0.7 treatment, suggesting that the increased survival under acidified conditions may have been associated with a delay in the reproductive cycle of the clams. Future research about the impacts of ocean acidification on marine biodiversity should be extended to other types of biological and ecological processes, apart from biological calcification.

Seawater carbonate chemistry and biological processes during experiments with haploid and diploid life stages of Emiliania huxleyi, Calcidiscus leptoporus and Syracosphaera pulchra

The response of Emiliania huxleyi (Lohmann), Calcidiscus leptoporus (Murray and Blackman), and Syracosphaera pulchra (Lohmann) to elevated partial pressure of carbon dioxide (pCO2) was investigated in batch cultures. For the first time, we reported on the response of the non-calcifying (haploid) life stage of these three species. Growth rate, cell size, particulate inorganic (PIC) and particulate organic carbon (POC) of both life stages were measured at two different pCO2 (400 and 760 ppm) and their organic and inorganic carbon production calculated. The two life stages within the same species generally exhibited a similar response to elevated pCO2, the response of the haploid stage being often more pronounced than that of the diploid stage. The growth rate was consistently higher at elevated pCO2 but the response of other processes varied among species. Calcification rate of C. leptoporus and of S. pulchra did not change at elevated pCO2 while it increased in E. huxleyi. Particulate organic carbon production and cell size of both life stages of S. pulchra and of the haploid stage of E. huxleyi markedly decreased at elevated pCO2. It remained unaltered in the diploid stage of E. huxleyi and C. leptoporus and increased in the haploid stage of the latter. The PIC:POC ratio increased in E. huxleyi and was constant in C. leptoporus and S. pulchra. Elevated pCO2 has a significant effect on these three coccolithophores species, the haploid stage being more sensitive. This must be taken into account when predicting the fate of coccolithophores in the future ocean.

Seawater carbonate chemistry and biological processes of Porites panamensis during experiments, 2011

Survival of coral planulae, and the successful settlement and healthy growth of primary polyps are critical for the dispersal of scleractinian corals and hence the recovery of degraded coral reefs. It is therefore important to explore how the warmer and more acidic oceanic conditions predicted for the future could affect these processes. This study used controlled culture to investigate the effects of a 1 °C increase in temperature and a 0.2-0.25 unit decrease in pH on the settlement and survival of planulae and the growth of primary polyps in the Tropical Eastern Pacific coral Porites panamensis. We found that primary polyp growth was reduced only marginally by more acidic seawater but the combined effect of high temperature and lowered pH caused a significant reduction in growth of primary polyps by almost a third. Elevated temperature was found to significantly reduce the amount of zooxanthellae in primary polyps, and when combined with lowered pH resulted in a significant reduction in biomass of primary polyps. However, survival and settlement of planula larvae were unaffected by increased temperature, lowered acidity or the combination of both. These results indicate that in future scenarios of increased temperature and oceanic acidity coral planulae will be able to disperse and settle successfully but primary polyp growth may be hampered. The recovery of reefs may therefore be impeded by global change even if local stressors are curbed and sufficient sources of planulae are available.

Benthic cover map of Heron Reef derived from a high-spatial-resolution multi-spectral satellite image using object based image analysis

Providing accurate maps of coral reefs where the spatial scale and labels of the mapped features correspond to map units appropriate for examining biological and geomorphic structures and processes is a major challenge for remote sensing. The objective of this work is to assess the accuracy and relevance of the process used to derive geomorphic zone and benthic community zone maps for three western Pacific coral reefs produced from multi-scale, object-based image analysis (OBIA) of high-spatial-resolution multi-spectral images, guided by field survey data. Three Quickbird-2 multi-spectral data sets from reefs in Australia, Palau and Fiji and georeferenced field photographs were used in a multi-scale segmentation and object-based image classification to map geomorphic zones and benthic community zones. A per-pixel approach was also tested for mapping benthic community zones. Validation of the maps and comparison to past approaches indicated the multi-scale OBIA process enabled field data, operator field experience and a conceptual hierarchical model of the coral reef environment to be linked to provide output maps at geomorphic zone and benthic community scales on coral reefs. The OBIA mapping accuracies were comparable with previously published work using other methods; however, the classes mapped were matched to a predetermined set of features on the reef.

Metadata und statistic analysis of archael and bacterial sequences originating from sediments of the Håkon Mosby mud volcano (Z1-Z3, all habitats)

DNA extraction was carried out as described on the MICROBIS project pages (http://icomm.mbl.edu/microbis ) using a commercially available extraction kit. We amplified the hypervariable regions V4-V6 of archaeal and bacterial 16S rRNA genes using PCR and several sets of forward and reverse primers (http://vamps.mbl.edu/resources/primers.php). Massively parallel tag sequencing of the PCR products was carried out on a 454 Life Sciences GS FLX sequencer at Marine Biological Laboratory, Woods Hole, MA, following the same experimental conditions for all samples. Sequence reads were submitted to a rigorous quality control procedure based on mothur v30 (doi:10.1128/AEM.01541-09) including denoising of the flow grams using an algorithm based on PyroNoise (doi:10.1038/nmeth.1361), removal of PCR errors and a chimera check using uchime (doi:10.1093/bioinformatics/btr381). The reads were taxonomically assigned according to the SILVA taxonomy (SSURef v119, 07-2014; doi:10.1093/nar/gks1219) implemented in mothur and clustered at 98% ribosomal RNA gene V4-V6 sequence identity. V4-V6 amplicon sequence abundance tables were standardized to account for unequal sampling effort using 1000 (Archaea) and 2300 (Bacteria) randomly chosen sequences without replacement using mothur and then used to calculate inverse Simpson diversity indices and Chao1 richness (doi:10.2307/4615964). Bray-Curtis dissimilarities (doi:10.2307/1942268) between all samples were calculated and used for 2-dimensional non metric multidimensional scaling (NMDS) ordinations with 20 random starts (doi:10.1007/BF02289694). Stress values below 0.2 indicated that the multidimensional dataset was well represented by the 2D ordination. NMDS ordinations were compared and tested using Procrustes correlation analysis (doi:10.1007/BF02291478). All analyses were carried out with the R statistical environment and the packages vegan (available at: http://cran.r-project.org/package=vegan), labdsv (available at: http://cran.r-project.org/package=labdsv), as well as with custom R scripts. Operational taxonomic units at 98% sequence identity (OTU0.03) that occurred only once in the whole dataset were termed absolute single sequence OTUs (SSOabs; doi:10.1038/ismej.2011.132). OTU0.03 sequences that occurred only once in at least one sample, but may occur more often in other samples were termed relative single sequence OTUs (SSOrel). SSOrel are particularly interesting for community ecology, since they comprise rare organisms that might become abundant when conditions change.16S rRNA amplicons and metagenomic reads have been stored in the sequence read archive under SRA project accession number SRP042162.

Seawater carbonate chemistry, fertilization rate and biological processes of sea urchin Paracentrotus lividus during experiments, 2011

The effect of pH ranging from 8.0 to 6.8 (total scale - pHT) on fertilization, cleavage and larval development until pluteus stage was assessed in an intertidal temperate sea urchin. Gametes were obtained from adults collected in two contrasting tide pools, one showing a significant nocturnal pH decrease (lowest pHT = 7.4) and another where pH was more stable (lowest pHT = 7.8). The highest pHT at which significant effects on fertilization and cleavage were recorded was 7.6. On the contrary, larval development was only affected below pHT 7.4, a value equal or lower than that reported for several subtidal species. This suggests that sea urchins inhabiting stressful intertidal environments produce offspring that may better resist future ocean acidification. Moreover, at pHT 7.4, the fertilization rate of gametes whose progenitors came from the tide pool with higher pH decrease was significantly higher, indicating a possible acclimatization or adaptation of gametes to pH stress.

Seawater carbonate chemistry and biological processes during experiments with Limacina helicina, 2009

Thecosome pteropods (pelagic mollusks) can play a key role in the food web of various marine ecosystems. They are a food source for zooplankton or higher predators such as fishes, whales and birds that is particularly important in high latitude areas. Since they harbor a highly soluble aragonitic shell, they could be very sensitive to ocean acidification driven by the increase of anthropogenic CO2 emissions. The effect of changes in the seawater chemistry was investigated on Limacina helicina, a key species of Arctic pelagic ecosystems. Individuals were kept in the laboratory under controlled pCO2 levels of 280, 380, 550, 760 and 1020 µatm and at control (0°C) and elevated (4°C) temperatures. The respiration rate was unaffected by pCO2 at control temperature, but significantly increased as a function of the pCO2 level at elevated temperature. pCO2 had no effect on the gut clearance rate at either temperature. Precipitation of CaCO3, measured as the incorporation of 45Ca, significantly declined as a function of pCO2 at both temperatures. The decrease in calcium carbonate precipitation was highly correlated to the aragonite saturation state. Even though this study demonstrates that pteropods are able to precipitate calcium carbonate at low aragonite saturation state, the results support the current concern for the future of Arctic pteropods, as the production of their shell appears to be very sensitive to decreased pH. A decline of pteropod populations would likely cause dramatic changes to various pelagic ecosystems.

Stable isotope analysis on sediment core RC11-86

Oxygen isotope measurements have been made in foraminifera from over 60 deep-sea sediment cores. Taken together with the oxygen isotope measurements published by Emiliani from Caribbean and Equatorial Atlantic cores, this comprises a unique body of stratigraphic data covering most of the important areas of calcareous sediment over the whole world ocean. The oxygen isotopic composition of foraminifera from cores of Late Pleistocene sediment varies in a similar manner in nearly all areas; the variations reflect changes in the oxygen isotopic composition of the ocean. The oceans are mixed in about 1 ka so that ocean isotopic changes, resulting from fluctuations in the quantity of ice stored on the continents, must have occurred almost synchronously in all regions. Thus the oxygen isotope record provides an excellent means of stratigraphic correlation. Cores accumulated at rates of over about 5 cm/ka provide records of oxygen isotopic composition change that are almost unaffected by post-depositional mixing of the sediment. Thus they preserve a detailed record of the advance and retreat of the ice masses in the northern hemisphere, and provide a unique source of information for the study of ice-sheet dynamics.