Seawater carbonate chemistry and benthic marine community during experiments, 2011

Ocean acidification is predicted to impact all areas of the oceans and affect a diversity of marine organisms. However, the diversity of responses among species prevents clear predictions about the impact of acidification at the ecosystem level. Here, we used shallow water CO2 vents in the Mediterranean Sea as a model system to examine emergent ecosystem responses to ocean acidification in rocky reef communities. We assessed in situ benthic invertebrate communities in three distinct pH zones (ambient, low, and extreme low), which differed in both the mean and variability of seawater pH along a continuous gradient. We found fewer taxa, reduced taxonomic evenness, and lower biomass in the extreme low pH zones. However, the number of individuals did not differ among pH zones, suggesting that there is density compensation through population blooms of small acidification-tolerant taxa. Furthermore, the trophic structure of the invertebrate community shifted to fewer trophic groups and dominance by generalists in extreme low pH, suggesting that there may be a simplification of food webs with ocean acidification. Despite high variation in individual species' responses, our findings indicate that ocean acidification decreases the diversity, biomass, and trophic complexity of benthic marine communities. These results suggest that a loss of biodiversity and ecosystem function is expected under extreme acidification scenarios.

Alkenone accumulation and SST reconstruction for the Benguela upwelling zone

A feature of Pliocene climate is the occurrence of "permanent El Niño-like" or "El Padre" conditions in the Pacific Ocean. From the analysis of sediment cores in the modern northern Benguela upwelling, we show that the mean oceanographic state off Southwest Africa during the warm Pliocene epoch was also analogous to that of a persistent Benguela "El Niño". At present these events occur when massive southward flows of warm and nutrient-poor waters extend along the coasts of Angola and Namibia, with dramatic effects on regional marine ecosystems and rainfall. We propose that the persistent warmth across the Pliocene in the Benguela upwelling ended synchronously with the narrowing of the Indonesian seaway, and the early intensification of the Northern Hemisphere Glaciations around 3.0-3.5 Ma. The emergence of obliquity-related cycles in the Benguela sea surface temperatures (SST) after 3 Ma highlights the development of strengthened links to high latitude orbital forcing. The subsequent evolution of the Benguela upwelling system was characterized by the progressive intensification of the meridional SST gradients, and the emergence of the 100 ky cycle, until the modern mean conditions were set at the end of the Mid Pleistocene transition, around 0.6 Ma. These findings support the notion that the interplay of changes in the depth of the global thermocline, atmospheric circulation and tectonics preconditioned the climate system for the end of the warm Pliocene epoch and the subsequent intensification of the ice ages.

Table 6 Generalised properties of Utsira caprocks, based on analysis of cuttings (page 79)

Executive Summary: Carbon dioxide capture and storage (CCS) is one option for mitigating atmospheric emissions of carbon dioxide and thereby contributes in actions for stabilization of atmospheric greenhouse gas concentrations. The Bellona Foundation is striving to achieve wide implementation of carbon dioxide (CO2) capture and storage both in Norway and internationally. Bellona considers CCS as the only viable large scale option to close the gap between energy production and demand in an environmentally sound way, thereby ensuring that climate changes and acidification of the oceans due to increased CO2 concentrations in the atmosphere will be stabilised. ff

N2 fixation in marine heterotrophic bacteria: dynamics of environmental and molecular regulation.

Molecular and immunological techniques were used to examine N2 fixation in a ubiquitous heterotrophic marine bacterium, the facultative anaerobic Vibrio natriegens. When batch cultures were shifted from aerobic N-replete to anaerobic N-deplete conditions, transcriptional and post-translational regulation of N2 fixation was observed. Levels of nifHDK mRNA encoding the nitrogenase enzyme were highest at 140 min postshift and undetectable between 6 and 9 h later. Immunologically determined levels of nitrogenase enzyme (Fe protein) were highest between 6 and 15 h postshift, and nitrogenase activity peaked between 6 and 9 h postshift, declining by a factor of 2 after 12-15 h. Unlike their regulation in cyanobacteria, Fe protein and nitrogenase activity were present when nifHDK mRNA was absent in V. natriegens, indicating that nitrogenase is stored and stable under anaerobic conditions. Both nifHDK mRNA and Fe protein disappeared within 40 min after cultures were shifted from N2-fixing conditions (anaerobic, N-deplete) to non- N2-fixing conditions (aerobic, N-enriched) but reappeared when shifted to conditions favoring N2 fixation. Thus, unlike other N2-fixing heterotrophic bacteria, nitrogenase must be resynthesized after aerobic exposure in V. natriegens. Immunological detection based on immunoblot (Western) analysis and immunogold labeling correlated positively with nitrogenase activity; no localization of nitrogenase was observed. Because V. natriegens continues to fix N2 for many hours after anaerobic induction, this species may play an important role in providing "new" nitrogen in marine ecosystems.

Habitat Map for Lizard Island reef, Australia derived from a photo-transect survey field data collected in December 2011 and September/October 2012

An object based image analysis approach (OBIA) was used to create a habitat map of the Lizard Reef. Briefly, georeferenced dive and snorkel photo-transect surveys were conducted at different locations surrounding Lizard Island, Australia. For the surveys, a snorkeler or diver swam over the bottom at a depth of 1-2m in the lagoon, One Tree Beach and Research Station areas, and 7m depth in Watson's Bay, while taking photos of the benthos at a set height using a standard digital camera and towing a surface float GPS which was logging its track every five seconds. The camera lens provided a 1.0 m x 1.0 m footprint, at 0.5 m height above the benthos. Horizontal distance between photos was estimated by fin kicks, and corresponded to a surface distance of approximately 2.0 - 4.0 m. Approximation of coordinates of each benthic photo was done based on the photo timestamp and GPS coordinate time stamp, using GPS Photo Link Software (www.geospatialexperts.com). Coordinates of each photo were interpolated by finding the gps coordinates that were logged at a set time before and after the photo was captured. Dominant benthic or substrate cover type was assigned to each photo by placing 24 points random over each image using the Coral Point Count excel program (Kohler and Gill, 2006). Each point was then assigned a dominant cover type using a benthic cover type classification scheme containing nine first-level categories - seagrass high (>=70%), seagrass moderate (40-70%), seagrass low (<= 30%), coral, reef matrix, algae, rubble, rock and sand. Benthic cover composition summaries of each photo were generated automatically in CPCe. The resulting benthic cover data for each photo was linked to GPS coordinates, saved as an ArcMap point shapefile, and projected to Universal Transverse Mercator WGS84 Zone 56 South. The OBIA class assignment followed a hierarchical assignment based on membership rules with levels for "reef", "geomorphic zone" and "benthic community" (above).

Seawater carbonate chemistry and biological processes during experiments with four species of marine diatoms

The effect of pCO2 on carbon acquisition and intracellular assimilation was investigated in the three bloom-forming diatom species, Eucampia zodiacus (Ehrenberg), Skeletonema costatum (Greville) Cleve, Thalassionema nitzschioides (Grunow) Mereschkowsky and the non-bloom-forming Thalassiosira pseudonana (Hust.) Hasle and Heimdal. In vivo activities of carbonic anhydrase (CA), photosynthetic O2 evolution, CO2 and HCO3? uptake rates were measured by membrane-inlet mass spectrometry (MIMS) in cells acclimated to pCO2 levels of 370 and 800 ?atm. To investigate whether the cells operate a C4-like pathway, activities of ribulose-1,5-bisphosphate carboxylase (RubisCO) and phosphoenolpyruvate carboxylase (PEPC) were measured at the mentioned pCO2 levels and a lower pCO2 level of 50 ?atm. In the bloom-forming species, extracellular CA activities strongly increased with decreasing CO2 supply while constantly low activities were obtained for T. pseudonana. Half-saturation concentrations (K1/2) for photosynthetic O2 evolution decreased with decreasing CO2 supply in the two bloom-forming species S. costatum and T. nitzschioides, but not in T. pseudonana and E. zodiacus. With the exception of S. costatum, maximum rates (Vmax) of photosynthesis remained constant in all investigated diatom species. Independent of the pCO2 level, PEPC activities were significantly lower than those for RubisCO, averaging generally less than 3%. All examined diatom species operate highly efficient CCMs under ambient and high pCO2, but differ strongly in the degree of regulation of individual components of the CCM such as Ci uptake kinetics and extracellular CA activities. The present data do not suggest C4 metabolism in the investigated species.

Seawater carbonate chemistry and processes during experiments with marine mussel, Mytilus galloprovincialis, 2005

In the context of future scenarios of progressive accumulation of anthropogenic CO2 in marine surface waters, the present study addresses the effects of long-term hypercapnia on a Mediterranean bivalve, Mytilus galloprovincialis. Sea-water pH was lowered to a value of 7.3 by equilibration with elevated CO2 levels. This is close to the maximum pH drop expected in marine surface waters during atmosextracellular pHric CO2 accumulation. Intra- and extracellular acid-base parameters as well as changes in metabolic rate and growth were studied under both normocapnia and hypercapnia. Long-term hypercapnia caused a permanent reduction in haemolymph pH. To limit the degree of acidosis, mussels increased haemolymph bicarbonate levels, which are derived mainly from the dissolution of shell CaCO3. Intracellular pH in various tissues was at least partly compensated; no deviation from control values occurred during long-term measurements in whole soft-body tissues. The rate of oxygen consumption fell significantly, indicating a lower metabolic rate. In line with previous reports, a close correlation became evident between the reduction in extracellular pH and the reduction in metabolic rate of mussels during hypercapnia. Analysis of frequency histograms of growth rate revealed that hypercapnia caused a slowing of growth, possibly related to the reduction in metabolic rate and the dissolution of shell CaCO3 as a result of extracellular acidosis. In addition, increased nitrogen excretion by hypercapnic mussels indicates the net degradation of protein, thereby contributing to growth reduction. The results obtained in the present study strongly indicate that a reduction in sea-water pH to 7.3 may be fatal for the mussels. They also confirm previous observations that a reduction in sea-water pH below 7.5 is harmful for shelled molluscs.

Purine catabolic pathway revealed by transcriptomics in the model marine bacteriumRuegeria pomeroyiDSS-3

Purines are nitrogen-rich compounds that are widely distributed in the marine environment and are an important component of the dissolved organic nitrogen (DON) pool. Even though purines have been shown to be degraded by bacterioplankton, the identities of marine bacteria capable of purine degradation and their underlying catabolic mechanisms are currently unknown. This study shows that Ruegeria pomeroyi, a model marine bacterium and Marine Roseobacter Clade (MRC) representative, utilizes xanthine as a source of carbon and nitrogen. The R. pomeroyi genome contains putative genes that encode xanthine dehydrogenase (XDH), which is expressed during growth with xanthine. RNAseq-based analysis of the R. pomeroyi transcriptome revealed that the transcription of an XDH-initiated catabolic pathway is up-regulated during growth with xanthine, with transcription greatest when xanthine was the only available carbon source. The RNAseq-deduced pathway indicates that glyoxylate and ammonia are the key intermediates from xanthine degradation. Utilising a laboratory model, this study has identified the potential genes and catabolic pathway active during xanthine degradation. The ability of R. pomeroyi to utilize xanthine provides novel insights into the capabilities of the MRC that may contribute to their success in marine ecosystems and the potential biogeochemical importance of the group in processing DON.

Purine catabolic pathway revealed by transcriptomics in the model marine bacteriumRuegeria pomeroyiDSS-3

Purines are nitrogen-rich compounds that are widely distributed in the marine environment and are an important component of the dissolved organic nitrogen (DON) pool. Even though purines have been shown to be degraded by bacterioplankton, the identities of marine bacteria capable of purine degradation and their underlying catabolic mechanisms are currently unknown. This study shows that Ruegeria pomeroyi, a model marine bacterium and Marine Roseobacter Clade (MRC) representative, utilizes xanthine as a source of carbon and nitrogen. The R. pomeroyi genome contains putative genes that encode xanthine dehydrogenase (XDH), which is expressed during growth with xanthine. RNAseq-based analysis of the R. pomeroyi transcriptome revealed that the transcription of an XDH-initiated catabolic pathway is up-regulated during growth with xanthine, with transcription greatest when xanthine was the only available carbon source. The RNAseq-deduced pathway indicates that glyoxylate and ammonia are the key intermediates from xanthine degradation. Utilising a laboratory model, this study has identified the potential genes and catabolic pathway active during xanthine degradation. The ability of R. pomeroyi to utilize xanthine provides novel insights into the capabilities of the MRC that may contribute to their success in marine ecosystems and the potential biogeochemical importance of the group in processing DON.

Dieta do ouriço-branco, Tripneustes ventricosus (Lamarck, 1816), no Arquipélago de Fernando de Noronha, PE

Sea urchins are benthic macroinvertebrates that inhabit shallow coastal waters in tropical and temperate zones. Urchins are usually classified as generalists or omnivores as they can adjust their diet according to the food resources available in the environment. Due to the strong grazing pressure they may exert, urchins have an important role in marine ecosystems, occupying different trophic levels and stimulating the intensification of the dynamics of communities where they occur. In 2004, a monitoring program focused on the population dynamics of the white sea urchin, Tripneustes ventricosus, has been initiated in the Fernando de Noronha Archipelago. At the same time, a surprisingly lack of information on the species biology has been noted, despite their wide geographical distribution and economic importance in many parts of its range. Hence, this work was developed to provide information on the feeding habits of T. ventricosus in the archipelago. Ten specimens were collected between December 2006 and July 2007 at two sites of the archipelago, Air France and Sueste Bay for biometrics and analysis of gut contents. Test diameters ranged from 9.19 cm (± 1.1) to 10.08 cm (± 0.58). Calculated stomach repletion index (IRE) was higher (p <0.05) in the Air France site and also during January and July. The IRE was not correlated to the gonad index. Fifteen different species of algae were detected in a total of 120 stomachs examined: 4 Chlorophytas, 4 Phaeophytas and 6 Rhodophytas. Food diversity (p <0.05) was higher in December 2006 and January 2007. Although several items had a high frequency of occurrence, they were low represented in terms of weight, and consequently, had a low level of relative importance. The brown algae Dictyopteris spp and Dictyota spp, followed by the green algae Caulerpa verticillata accounted for the greatest importance in T. ventricosus diet, comprising about 90% of the consumed items

Dieta do ouriço-branco, Tripneustes ventricosus (Lamarck, 1816), no Arquipélago de Fernando de Noronha, PE

Sea urchins are benthic macroinvertebrates that inhabit shallow coastal waters in tropical and temperate zones. Urchins are usually classified as generalists or omnivores as they can adjust their diet according to the food resources available in the environment. Due to the strong grazing pressure they may exert, urchins have an important role in marine ecosystems, occupying different trophic levels and stimulating the intensification of the dynamics of communities where they occur. In 2004, a monitoring program focused on the population dynamics of the white sea urchin, Tripneustes ventricosus, has been initiated in the Fernando de Noronha Archipelago. At the same time, a surprisingly lack of information on the species biology has been noted, despite their wide geographical distribution and economic importance in many parts of its range. Hence, this work was developed to provide information on the feeding habits of T. ventricosus in the archipelago. Ten specimens were collected between December 2006 and July 2007 at two sites of the archipelago, Air France and Sueste Bay for biometrics and analysis of gut contents. Test diameters ranged from 9.19 cm (± 1.1) to 10.08 cm (± 0.58). Calculated stomach repletion index (IRE) was higher (p <0.05) in the Air France site and also during January and July. The IRE was not correlated to the gonad index. Fifteen different species of algae were detected in a total of 120 stomachs examined: 4 Chlorophytas, 4 Phaeophytas and 6 Rhodophytas. Food diversity (p <0.05) was higher in December 2006 and January 2007. Although several items had a high frequency of occurrence, they were low represented in terms of weight, and consequently, had a low level of relative importance. The brown algae Dictyopteris spp and Dictyota spp, followed by the green algae Caulerpa verticillata accounted for the greatest importance in T. ventricosus diet, comprising about 90% of the consumed items

Impact of anthropogenic stressors on the microbial communities in marine holobionts and ecosystems

Free-living or host-associated marine microbiomes play a determinant role in supporting the functioning and biodiversity of marine ecosystems, providing essential ecological services, and promoting the health of the entire biosphere. Currently, the fast and restless increase of World’s human population strongly impacts life on Earth in the forms of ocean pollution, coastal zone destruction, overexploitation of marine resources, and climate change. Thanks to their phylogenetic, metabolic, and functional diversity, marine microbiomes represent the Earth’s biggest reservoir of solutions against the major threats that are now impacting marine ecosystems, possibly providing valuable insights for biotechnological applications to preserve the health of the ocean ecosystems. Microbial-based mitigation strategies heavily rely on the available knowledge on the specific role and composition of holobionts associated microbial communities, thus highlighting the importance of pioneer studies on microbial-mediated adaptive mechanisms in the marine habitats. In this context, we propose different models representing ecologically important, widely distributed, and habitat-forming organisms, to further investigate the ability of marine holobionts to dynamically adapt to natural environmental variations, as well as to anthropogenic stress factors. In this PhD thesis, we were able to supply the characterization of the microbial community associated with the model anthozoan cnidaria Corynactis viridis throughout a seasonal gradient, to provide critical insights into microbiome-host interactions in a biomonitoring perspective. We also dissected in details the microbial-derived mitigation strategies implemented by the benthonic anthozoan Anemonia viridis and the gastropod Patella caerulea as models of adaptation to anthropogenic stressors, in the context of bioremediation of human-impacted habitats and for the monitoring and preservation of coastal marine ecosystems, respectively. Finally, we provided a functional model of adaptation to future ocean acidification conditions by characterizing the microbial community associated with the temperate coral Balanophyllia europaea naturally living at low pH conditions, to implement microbial based actions to mitigate climate change.

Marine bioprospecting - Trawling for treasure and pleasure

This Microreview seeks to highlight the molecular diversity present in marine organisms, and illustrate by example some of the challenges encountered in exploring this resource. Marine natural products exhibit an impressive array of structural motifs, many of which are derived from biosynthetic pathways that are uniquely marine, Most importantly some marine metabolites possess noteworthy biological activities, activities that have potential application outside marine ecosystems, such as antibiotics, antiparasitics, anticancer agents etc... The isolation, spectroscopic characterisation and assignment of stereostructures to these unusual metabolites is both challenging and rewarding. Examples featured in this Microreview follow a common theme in that they are all recent accounts of the isolation of natural products from Australian marine sponges, carried out in the laboratories of the author. In addition to presenting brief comments on specific structure elucidation strategies, an effort is made to emphasize techniques for solving stereochemical issues, as well as to speculate on the biosynthetic origins of some of these exotic marine natural products.

Analysis of enamel microbiopsies in shed primary teeth by Scanning Electron Microscopy (SEM) and Polarizing Microscopy (PM)

The aims of this study were 1) to verify how close to the theoretically presumed areas are the areas of enamel microbiopsies carried out in vivo or in exfoliated teeth; 2) to test whether the etching solution penetrates beyond the tape borders: 3) to test whether the etching solution demineralizes the enamel in depth. 24 shed upper primary central incisors were randomly divided into two groups: the Rehydrated Teeth Group and the Dry Teeth Group. An enamel microbiopsy was performed, and the enamel microbiopsies were then analyzed by Scanning Electron Microscopy (SEMI) and Polarizing Microscopy (PM). Quantitative birefringence measurements were performed. The ""true"" etched area was determined by measuring the etched enamel using the NIH Image analysis program. Enamel birefringence was compared using the paired t test. There was a statistically significant difference when the etched areas in the Rehydrated teeth were compared with those of the Dry teeth (p = 0.04). The etched areas varied from -11.6% to 73.5% of the presumed area in the Rehydrated teeth, and from 6.6% to 61.3% in the Dry teeth. The mean percentage of variation in each group could be used as a correction factor for the etched area. Analysis of PM pictures shows no evidence of in-depth enamel demineralization by the etching solution. No statistically significant differences in enamel birefringence were observed between values underneath and outside the microbiopsy area in the same tooth, showing that no mineral loss occurred below the enamel superficial layer. Our data showed no evidence of in-depth enamel demineralization by the etching solution used in the enamel microbiopsy proposed for primary enamel. This study also showed a variation in the measured diameter of the enamel microbiopsy in nineteen teeth out of twenty four, indicating that in most cases the etching solution penetrated beyond the tape borders. (C) 2009 Elsevier B.V. All rights reserved.