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  • 1
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    Cold‐water coral ecosystems under future ocean change: Live coral performance vs. framework dissolution and bioerosion (2022)
    John Wiley & Sons, Inc. | Hoboken, USA
    Details
    Publication Date: 2023-01-15
    Description: Physiological sensitivity of cold‐water corals to ocean change is far less understood than of tropical corals and very little is known about the impacts of ocean acidification and warming on degradative processes of dead coral framework. In a 13‐month laboratory experiment, we examined the interactive effects of gradually increasing temperature and pCO2 levels on survival, growth, and respiration of two prominent color morphotypes (colormorphs) of the framework‐forming cold‐water coral Lophelia pertusa, as well as bioerosion and dissolution of dead framework. Calcification rates tended to increase with warming, showing temperature optima at ~ 14°C (white colormorph) and 10–12°C (orange colormorph) and decreased with increasing pCO2. Net dissolution occurred at aragonite undersaturation (ΩAr 〈 1) at ~ 1000 μatm pCO2. Under combined warming and acidification, the negative effects of acidification on growth were initially mitigated, but at ~ 1600 μatm dissolution prevailed. Respiration rates increased with warming, more strongly in orange corals, while acidification slightly suppressed respiration. Calcification and respiration rates as well as polyp mortality were consistently higher in orange corals. Mortality increased considerably at 14–15°C in both colormorphs. Bioerosion/dissolution of dead framework was not affected by warming alone but was significantly enhanced by acidification. While live corals may cope with intermediate levels of elevated pCO2 and temperature, long‐term impacts beyond levels projected for the end of this century will likely lead to skeletal dissolution and increased mortality. Our findings further suggest that acidification causes accelerated degradation of dead framework even at aragonite saturated conditions, which will eventually compromise the structural integrity of cold‐water coral reefs.
    Description: Bundesministerium für Bildung und Forschung http://dx.doi.org/10.13039/501100002347
    Description: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Description: Marine Research in Ireland
    Description: French National Research Agency http://dx.doi.org/10.13039/501100001665
    Keywords: ddc:577.7 ; cold-water corals ; ocean change ; laboratory experiments ; framwork dissolution ; bioerosion
    Language: English
    Type: doc-type:article
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    CITATION GEO-LEO
  • 2
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    A comparison across non-model animals suggests an optimal sequencing depth for de novo transcriptome assembly (2013)
    BioMed Central
    In:  BMC Genomics, 14 (1). p. 167.
    Details
    Publication Date: 2019-01-21
    Description: Background: The lack of genomic resources can present challenges for studies of non-model organisms. Transcriptome sequencing offers an attractive method to gather information about genes and gene expression without the need for a reference genome. However, it is unclear what sequencing depth is adequate to assemble the transcriptome de novo for these purposes. Results: We assembled transcriptomes of animals from six different phyla (Annelids, Arthropods, Chordates, Cnidarians, Ctenophores, and Molluscs) at regular increments of reads using Velvet/Oases and Trinity to determine how read count affects the assembly. This included an assembly of mouse heart reads because we could compare those against the reference genome that is available. We found qualitative differences in the assemblies of whole-animals versus tissues. With increasing reads, whole-animal assemblies show rapid increase of transcripts and discovery of conserved genes, while single-tissue assemblies show a slower discovery of conserved genes though the assembled transcripts were often longer. A deeper examination of the mouse assemblies shows that with more reads, assembly errors become more frequent but such errors can be mitigated with more stringent assembly parameters. Conclusions: These assembly trends suggest that representative assemblies are generated with as few as 20 million reads for tissue samples and 30 million reads for whole-animals for RNA-level coverage. These depths provide a good balance between coverage and noise. Beyond 60 million reads, the discovery of new genes is low and sequencing errors of highly-expressed genes are likely to accumulate. Finally, siphonophores (polymorphic Cnidarians) are an exception and possibly require alternate assembly strategies.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1186/1471-2164-14-167
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 3
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    Effects of elevated seawater pCO2 on gene expression patterns in the gills of the green crab, Carcinus maenas (2011)
    BioMed Central
    In:  BMC Genomics, 12 (1). p. 488.
    Details
    Publication Date: 2019-09-23
    Description: Background: The green crab Carcinus maenas is known for its high acclimation potential to varying environmental abiotic conditions. A high ability for ion and acid-base regulation is mainly based on an efficient regulation apparatus located in gill epithelia. However, at present it is neither known which ion transport proteins play a key role in the acid-base compensation response nor how gill epithelia respond to elevated seawater pCO2 as predicted for the future. In order to promote our understanding of the responses of green crab acid-base regulatory epithelia to high pCO2, Baltic Sea green crabs were exposed to a pCO2 of 400 Pa. Gills were screened for differentially expressed gene transcripts using a 4,462-feature microarray and quantitative real-time PCR. Results: Crabs responded mainly through fine scale adjustment of gene expression to elevated pCO2. However, 2% of all investigated transcripts were significantly regulated 1.3 to 2.2-fold upon one-week exposure to CO2 stress. Most of the genes known to code for proteins involved in osmo- and acid-base regulation, as well as cellular stress response, were were not impacted by elevated pCO2. However, after one week of exposure, significant changes were detected in a calcium-activated chloride channel, a hyperpolarization activated nucleotide-gated potassium channel, a tetraspanin, and an integrin. Furthermore, a putative syntaxin-binding protein, a protein of the transmembrane 9 superfamily, and a Cl-/HCO3 - exchanger of the SLC 4 family were differentially regulated. These genes were also affected in a previously published hypoosmotic acclimation response study. Conclusions: The moderate, but specific response of C. maenas gill gene expression indicates that (1) seawater acidification does not act as a strong stressor on the cellular level in gill epithelia; (2) the response to hypercapnia is to some degree comparable to a hypoosmotic acclimation response; (3) the specialization of each of the posterior gill arches might go beyond what has been demonstrated up to date; and (4) a re-configuration of gill epithelia might occur in response to hypercapnia.
    Type: Article , PeerReviewed
    Format: text
    Format: text
    Format: other
    DOI: 10.1186/1471-2164-12-488
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 4
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    Simultaneous recording of filtration and respiration in marine organisms in response to short‐term environmental variability (2021)
    John Wiley & Sons, Inc. | Hoboken, USA
    Details
    Publication Date: 2021-06-16
    Description: Climate change imposes unusual long‐term trends in environmental conditions, plus some tremendous shifts in short‐term environmental variability, exerting additional stress on marine ecosystems. This paper describes an empirical method that aims to improve our understanding of the performance of benthic filter feeders experiencing changes in environmental conditions, such as temperature, on time scales of minutes to hours, especially during daily cycles or extreme events such as marine heatwaves or hypoxic upwelling. We describe the Fluorometer and Oximeter equipped Flow‐through Setup (FOFS), experimental design, and methodological protocols to evaluate the flood of data, enabling researchers to monitor important energy budget traits, including filtration and respiration of benthic filter‐feeders in response to fine‐tuned environmental variability. FOFS allows online recording of deviations in chlorophyll and dissolved oxygen concentrations induced by the study organism. Transparent data processing through Python scripts provides the possibility to adjust procedures to needs when working in different environmental contexts (e.g., temperature vs. pH, salinity, oxygen, biological cues) and with different filter‐feeding species. We successfully demonstrate the functionality of the method through recording responses of Baltic Sea blue mussels (Mytilus) during one‐day thermal cycles. This method practically provides a tool to help researchers exposing organisms to environmental variability for some weeks or months, to relate the observed long‐term performance responses to short‐term energy budget responses, and to explain their findings with the potential to generalize patterns. The method, therefore, allows a more detailed description of stress‐response relationships and the detection of species' tolerance limits.
    Description: Climate‐Biogeochemistry Interactions in the Tropical Ocean
    Description: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Description: Exzellenzcluster Ozean der Zukunft http://dx.doi.org/10.13039/501100010783
    Description: GEOMAR Helmholtz‐Zentrum für Ozeanforschung Kiel http://dx.doi.org/10.13039/501100003153
    Description: Helmholtz‐Gemeinschaft http://dx.doi.org/10.13039/501100001656
    Description: Programme d’Investissements d’Avenir
    Description: Studienstiftung des Deutschen Volkes http://dx.doi.org/10.13039/501100004350
    Keywords: 578.77 ; benthic filter-feeders ; shallow-water marine habitats ; environmental changes ; monitoring energy budget responses
    Type: article
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    CITATION GEO-LEO
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