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Stanislas F. Dubois – One of the best experts on this subject based on the ideXlab platform.

  • Integration of close‐range underwater photogrammetry with inspection and mesh processing software: a novel approach for quantifying ecological dynamics of temperate biogenic reefs
    Remote Sensing in Ecology and Conservation, 2020
    Co-Authors: Daniele Ventura, Stanislas F. Dubois, Andrea Bonifazi, Maria Flavia Gravina, Giovanna Jona Lasinio, Marco Seminara, Giandomenico Ardizzone
    Abstract:

    Characterizing and monitoring changes in biogenic 3-dimensional (3D) structures at multiple scales over time is challenging within the practical constraints of conventional ecological tools. Therefore, we developed a structure-from-motion (SfM)-based photogrammetry method, coupled with inspection and mesh processing software, to estimate important ecological parameters of underwater worm colonies (hummocks) constructed by the sabellariid polychaete Sabellaria Alveolata, using non-destructive, 3D modeling and mesh analysis. High resolution digital images of bioconstructions (hummocks) were taken in situ under natural conditions to generate digital 3D models over different sampling periods to analyse the morphological evolution of four targeted hummocks. 3D models were analysed in GOM Inspect software, a powerful and freely available mesh processing software to follow growth as well as morphology changes over time of each hummock. Linear regressions showed 3D models only slightly overestimated the real dimensions of the reference objects with an average error < 5% between measured and model-estimated dimensions for both length and volume. Manual inspection of models and semi-automated surface-to-surface comparison allowed the computation of important metrics linked to the ecology of temperate reefs such as volume, surface area, surface complexity/rugosity, number and size of holes and creeks and the mean density of living worms per colony. Moreover we demonstrated the reliability of 3D surface complexity estimates against two linear rugosity measures: a traditional and a virtual variant of the ‘chain-and-tape’ method. Finally, besides 3D models deviation analysis via surface comparison, a Bayesian latent variable model approach was adopted to highlight the significative effects of sea state conditions on S. Alveolata hummocks metrics. We demonstrated without damaging the benthic organisms that SfM approach allow continuous study of temperate bioconstruction leading to a fine description of short-term structural modification mediated by hydrodynamics, making this technique accessible and repeatable to many other areas of ecological research.

  • Linking multiple facets of biodiversity and ecosystem functions in a coastal reef habitat.
    Marine environmental research, 2020
    Co-Authors: Auriane G Jones, Jerome Fournier, Nicolas Desroy, Lionel Denis, Gwendoline Duong, Stanislas F. Dubois
    Abstract:

    Abstract Reef-building species play key roles in promoting local species richness and regulating ecosystem functions like biogeochemical fluxes. We evaluated the functioning of a habitat engineered by the reef-building polychaete Sabellaria Alveolata, by measuring oxygen and nutrient fluxes in the reef structures and in the soft-sediments nearby. Then, we investigated the relative importance of temperature, the engineer S. Alveolata, and different facets of macrofauna diversity (taxonomic, functional diversity and identity), on the reef biogeochemical fluxes using multiple linear regressions and effect sizes. The reef fluxes were more intense than the soft-sediment fluxes and mainly driven by the engineer biomass and abundance, stressing the importance of these biogenic structures. Higher water temperatures and an intermediate level of associated macrofauna functional dispersion weighted only by abundance (i.e. intermediate biological trait variability) maximized the reef’s global biogeochemical functioning. Ultimately, the physical degradation of the reefs could lead to lower levels of functioning.

  • Connecting organic to mineral: How the physiological state of an ecosystem-engineer is linked to its habitat structure
    Ecological Indicators, 2019
    Co-Authors: Amelia Curd, Louise B. Firth, Fabrice Pernet, Flavia L. D. Nunes, Charlotte Corporeau, Lizenn Delisle, Stanislas F. Dubois
    Abstract:

    The honeycomb worm Sabellaria Alveolata is capable of building extensive bioconstructions, including what are currently considered Europe’s largest biogenic reefs. The size and volume of these bioconstructions, however, vary greatly, such that not all habitats engineered by S. Alveolata may be easily identified as reefs. Given that European environmental legislation protects marine habitats that are classified as “reefs”, it is important to identity a clear set of definition criteria. Furthermore, quantifiable and unequivocal criteria are also needed to evaluate the ecological (health) state of these reefs, in order to best monitor and protect them. Here we propose new terminology to describe the physical appearance of these bioconstructions and attempt to link these physical criteria to the physiological state of the tube-building polychaete. We tested whether a bioconstruction displaying outward signs of growth is built by “healthy” worms devoid of physiological stress by analysing three macromolecules (carbohydrates, proteins, lipids), four polar lipid fatty acids, six neutral lipid fatty acid markers and three metabolic enzymes (citrate synthase, catalase and superoxide dismutase). The worms were sampled in bioconstructions of different “Type” (veneer vs. hummock), “Phase” (progradation vs. retrogradation), and “Shore Level” (high shore vs. low shore) at Champeaux in Mont-Saint-Michel Bay, France. Our results show that worms sampled in retrograding reefs (i.e. displaying signs of erosion and colonisation by epibionts such as oysters or mussels), were less physiologically stressed than worms sampled in prograding bioconstructions, possibly due to lower intraspecific competition and hence greater food availability. We therefore suggest management measures should encompass the whole mosaic of biogenic construction Types and Phases. We propose the inclusion of the polar lipid fatty acid arachidonic acid, in combination with the activity of two metabolic enzymes, citrate synthase and superoxide dismutase, as the three key biochemical markers to consider for quantitative information on the physiological state of this particular ecosystem engineer. Our results also revealed the influence of both sex and size on fatty acid and enzyme levels, highlighting the importance of taking into account both these variables when sampling and subsequently pooling individuals by sex and size category for laboratory analyses. Once seasonal and site variation have been addressed, these biochemical indicators could be examined in parallel with S. Alveolata bioconstruction physical criteria as part of a European-wide protocol for monitoring ecological status in this potential reef habitat.

Fabrice Pernet – One of the best experts on this subject based on the ideXlab platform.

  • Connecting organic to mineral: How the physiological state of an ecosystem-engineer is linked to its habitat structure
    Ecological Indicators, 2019
    Co-Authors: Amelia Curd, Louise B. Firth, Fabrice Pernet, Flavia L. D. Nunes, Charlotte Corporeau, Lizenn Delisle, Stanislas F. Dubois
    Abstract:

    The honeycomb worm Sabellaria Alveolata is capable of building extensive bioconstructions, including what are currently considered Europe’s largest biogenic reefs. The size and volume of these bioconstructions, however, vary greatly, such that not all habitats engineered by S. Alveolata may be easily identified as reefs. Given that European environmental legislation protects marine habitats that are classified as “reefs”, it is important to identity a clear set of definition criteria. Furthermore, quantifiable and unequivocal criteria are also needed to evaluate the ecological (health) state of these reefs, in order to best monitor and protect them. Here we propose new terminology to describe the physical appearance of these bioconstructions and attempt to link these physical criteria to the physiological state of the tube-building polychaete. We tested whether a bioconstruction displaying outward signs of growth is built by “healthy” worms devoid of physiological stress by analysing three macromolecules (carbohydrates, proteins, lipids), four polar lipid fatty acids, six neutral lipid fatty acid markers and three metabolic enzymes (citrate synthase, catalase and superoxide dismutase). The worms were sampled in bioconstructions of different “Type” (veneer vs. hummock), “Phase” (progradation vs. retrogradation), and “Shore Level” (high shore vs. low shore) at Champeaux in Mont-Saint-Michel Bay, France. Our results show that worms sampled in retrograding reefs (i.e. displaying signs of erosion and colonisation by epibionts such as oysters or mussels), were less physiologically stressed than worms sampled in prograding bioconstructions, possibly due to lower intraspecific competition and hence greater food availability. We therefore suggest management measures should encompass the whole mosaic of biogenic construction Types and Phases. We propose the inclusion of the polar lipid fatty acid arachidonic acid, in combination with the activity of two metabolic enzymes, citrate synthase and superoxide dismutase, as the three key biochemical markers to consider for quantitative information on the physiological state of this particular ecosystem engineer. Our results also revealed the influence of both sex and size on fatty acid and enzyme levels, highlighting the importance of taking into account both these variables when sampling and subsequently pooling individuals by sex and size category for laboratory analyses. Once seasonal and site variation have been addressed, these biochemical indicators could be examined in parallel with S. Alveolata bioconstruction physical criteria as part of a European-wide protocol for monitoring ecological status in this potential reef habitat.

  • Lipid remodelling in the reef-building honeycomb worm, Sabellaria Alveolata, reflects acclimation and local adaptation to temperature
    Scientific Reports, 2016
    Co-Authors: Anna P. Muir, Stanislas F. Dubois, Flavia L. D. Nunes, Fabrice Pernet
    Abstract:

    Acclimation and adaptation, which are key to species survival in a changing climate, can be observed in terms of membrane lipilipid composition. Remodelling membrane lipids, via homeoviscous adaptation (HVA), counteracts membrane dysfunction due to temperature in poikilotherms. In order to assess the potential for acclimation and adaptation in the honeycomb worm, Sabellaria Alveolata, a reef-building polychaete that supports high biodiversity, we carried out common-garden experiments using individuals from along its latitudinal range. Individuals were exposed to a stepwise temperature increase from 15 degrees C to 25 degrees C and membrane lipilipid composition assessed. Our results suggest that S. Alveolata was able to acclimate to higher temperatures, as observed by a decrease in unsaturation index and 20:5n-3. However, over the long-term at 25 degrees C, lipid composition patterns are not consistent with HVA expectations and suggest a stress response. Furthermore, unsaturation index of individuals from the two coldest sites were higher than those from the two warmest sites, with individuals from the thermally intermediate site being in-between, likely reflecting local adaptation to temperature. Therefore, lipid remodelling appears limited at the highest temperatures in S. Alveolata, suggesting that individuals inhabiting warm environments may be close to their upper thermal tolerance limits and at risk in a changing climate.

  • Lipid remodelling in the reef-building honeycomb worm, Sabellaria Alveolata, reflects acclimation and local adaptation to temperature
    Scientific reports, 2016
    Co-Authors: Anna P. Muir, Stanislas F. Dubois, Flavia L. D. Nunes, Fabrice Pernet
    Abstract:

    Acclimation and adaptation, which are key to species survival in a changing climate, can be observed in terms of membrane lipilipid composition. Remodelling membrane lipids, via homeoviscous adaptation (HVA), counteracts membrane dysfunction due to temperature in poikilotherms. In order to assess the potential for acclimation and adaptation in the honeycomb worm, Sabellaria Alveolata, a reef-building polychaete that supports high biodiversity, we carried out common-garden experiments using individuals from along its latitudinal range. Individuals were exposed to a stepwise temperature increase from 15 °C to 25 °C and membrane lipilipid composition assessed. Our results suggest that S. Alveolata was able to acclimate to higher temperatures, as observed by a decrease in unsaturation index and 20:5n-3. However, over the long-term at 25 °C, lipid composition patterns are not consistent with HVA expectations and suggest a stress response. Furthermore, unsaturation index of individuals from the two coldest sites were higher than those from the two warmest sites, with individuals from the thermally intermediate site being in-between, likely reflecting local adaptation to temperature. Therefore, lipid remodelling appears limited at the highest temperatures in S. Alveolata, suggesting that individuals inhabiting warm environments may be close to their upper thermal tolerance limits and at risk in a changing climate.

Sarah J. White – One of the best experts on this subject based on the ideXlab platform.

  • Regular ArticleBenthic macrofauna and sediments in the Severn Estuary
    Biological Journal of the Linnean Society, 1994
    Co-Authors: Chris Mettam, Maura E. Conneely, Sarah J. White
    Abstract:

    In the Severn Estuary and Bristol Channel, a multivariate analysis indicated eight groupings of macrobenthic fauna, each associated with a different physical habitat. Samples were faunistically impoverished, especially in sublittoral areas, but greater species richness was associated with reefs of Sabellaria Alveolata, which extended well into the estuary.

  • Benthic macrofauna and sediments in the Severn Estuary
    Biological Journal of the Linnean Society, 1994
    Co-Authors: Chris Mettam, Maura E. Conneely, Sarah J. White
    Abstract:

    In the Severn Estuary and Bristol Channel, a multivariate analysis indicated eight groupings of macrobenthic fauna, each associated with a different physical habitat. Samples were faunistically impoverished, especially in sublittoral areas, but greater species richness was associated with reefs of Sabellaria Alveolata, which extended well into the estuary.

Thomas Weide – One of the best experts on this subject based on the ideXlab platform.

  • The bifunctional dihydrofolate reductase thymidylate synthase of Tetrahymena thermophila provides a tool for molecular and biotechnology applications
    BMC Biotechnology, 2006
    Co-Authors: Lutz Herrmann, Ulrike Bockau, Arno Tiedtke, Marcus Ww Hartmann, Thomas Weide
    Abstract:

    Background Dihydrofolate reductase (DHFR) and thymidylate synthase (TS) are crucial enzymes in DNA synthesis. In Alveolata both enzymes are expressed as one bifunctional enzyme. Results Loss of this essential enzyme activities after successful allelic assortment of knock out alleles yields an auxotrophic marker in ciliates. Here the cloning, characterisation and functional analysis of Tetrahymena thermophila‘s DHFR-TS is presented. A first aspect of the presented work relates to destruction of DHFR-TS enzyme function in an alveolate thereby causing an auxotrophy for thymidine. A second aspect is to knock in an expression cassette encoding for a foreign gene with subsequent expression of the target protein. Conclusion This system avoids the use of antibiotics or other drugs and therefore is of high interest for biotechnological applications.

  • The bifunctional dihydrofolate reductase thymidylate synthase of Tetrahymena thermophila provides a tool for molecular and biotechnology applications.
    BMC biotechnology, 2006
    Co-Authors: Lutz Herrmann, Ulrike Bockau, Arno Tiedtke, Marcus Hartmann, Thomas Weide
    Abstract:

    Background Dihydrofolate reductase (DHFR) and thymidylate synthase (TS) are crucial enzymes in DNA synthesis. In Alveolata both enzymes are expressed as one bifunctional enzyme.

Chris Mettam – One of the best experts on this subject based on the ideXlab platform.

  • Regular ArticleBenthic macrofauna and sediments in the Severn Estuary
    Biological Journal of the Linnean Society, 1994
    Co-Authors: Chris Mettam, Maura E. Conneely, Sarah J. White
    Abstract:

    In the Severn Estuary and Bristol Channel, a multivariate analysis indicated eight groupings of macrobenthic fauna, each associated with a different physical habitat. Samples were faunistically impoverished, especially in sublittoral areas, but greater species richness was associated with reefs of Sabellaria Alveolata, which extended well into the estuary.

  • Benthic macrofauna and sediments in the Severn Estuary
    Biological Journal of the Linnean Society, 1994
    Co-Authors: Chris Mettam, Maura E. Conneely, Sarah J. White
    Abstract:

    In the Severn Estuary and Bristol Channel, a multivariate analysis indicated eight groupings of macrobenthic fauna, each associated with a different physical habitat. Samples were faunistically impoverished, especially in sublittoral areas, but greater species richness was associated with reefs of Sabellaria Alveolata, which extended well into the estuary.