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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Marta Coll; Lynne J. Shannon; Kristin M. Kleisner; M. J. Juan-Jorda; +34 Authors

    IndiSeas (>Indicators for the Seas>) is a collaborative international working group that was established in 2005 to evaluate the status of exploited marine ecosystems using a suite of indicators in a comparative framework. An initial shortlist of seven ecological indicators was selected to quantify the effects of fishing on the broader ecosystem using several criteria (i.e., ecological meaning, sensitivity to fishing, data availability, management objectives and public awareness). The suite comprised: (i) the inverse coefficient of variation of total biomass of surveyed species, (ii) mean fish length in the surveyed community, (iii) mean maximum life span of surveyed fish species, (iv) proportion of predatory fish in the surveyed community, (v) proportion of under and moderately exploited stocks, (vi) total biomass of surveyed species, and (vii) mean trophic level of the landed catch. In line with the Nagoya Strategic Plan of the Convention on Biological Diversity (2011-2020), we extended this suite to emphasize the broader biodiversity and conservation risks in exploited marine ecosystems. We selected a subset of indicators from a list of empirically based candidate biodiversity indicators initially established based on ecological significance to complement the original IndiSeas indicators. The additional selected indicators were: (viii) mean intrinsic vulnerability index of the fish landed catch, (ix) proportion of non-declining exploited species in the surveyed community, (x) catch-based marine trophic index, and (xi) mean trophic level of the surveyed community. Despite the lack of data in some ecosystems, we also selected (xii) mean trophic level of the modelled community, and (xiii) proportion of discards in the fishery as extra indicators. These additional indicators were examined, along with the initial set of IndiSeas ecological indicators, to evaluate whether adding new biodiversity indicators provided useful additional information to refine our understanding of the status evaluation of 29 exploited marine ecosystems. We used state and trend analyses, and we performed correlation, redundancy and multivariate tests. Existing developments in ecosystem-based fisheries management have largely focused on exploited species. Our study, using mostly fisheries independent survey-based indicators, highlights that biodiversity and conservation-based indicators are complementary to ecological indicators of fishing pressure. Thus, they should be used to provide additional information to evaluate the overall impact of fishing on exploited marine ecosystems. © 2015 Elsevier Ltd. All rights reserved We thank the Euroceans IndiSeas Working Group funded by the European Network of Excellence EUR-OCEANS (FP6, Contract N° 511106), the European collaborative project MEECE – Marine Ecosystem Evolution in a Changing Environment (FP7, Contract N° 212085) and IRD (Institute of Research for Development) and IOC/UNESCO. [...] MC was partially funded by the European Commission through the Marie Curie Career Integration Grant Fellowships – PCIG10-GA-2011-303534 – to the BIOWEB project and by the Spanish National Program Ramon y Cajal. LJS was supported through the South African Research Chair Initiative, funded through the South African Department of Science and Technology (DST) and administered by the South African National Research Foundation (NRF). LJS and YS were also funded by the European collaborative project MEECE – Marine Ecosystem Evolution in a Changing Environment – (FP7, Contract N° 212085). KMK was supported by the Northeast Fisheries Science Center and the Nature Conservancy through a grant from the Gordon and Betty Moore Foundation. MJJJ was supported by an EU Marie Curie International Outgoing Fellowship – PIOF-GA-2013-628116. MFB was supported by the Portuguese Oceanic and Atmospheric Institute and the trawl survey data collected under Biological Sampling (PNAB) Program. LJG would like to thank the Joint Research Centre of the European Commission for support. HO was financed by the Estonian Ministry of Education and Research (Grant SF0180005s10). JJH was supported by the Natural Environment Research Council and Department for Environment, Food and Rural Affairs [Grant Number NE/L003279/1, Marine Ecosystems Research Programme]. GIvdM was supported by the Institute of Marine Research, Norway. KT was partially funded by the project PERSEUS (Policy-oriented marine Environmental Research in the Southern EUropean Seas; FP7 Contract N° 287600). MAT was funded by the Spanish Institute of Oceanography (IEO) through a Predoctoral FPI fellowship. KNM was supported by a National Research Council fellowship at the Northwest Fishery Science Center. YJS and MTT were partially supported by the French project EMIBIOS (FRB, Contract No. APP-SCEN-2010-II). Chatham Rise trawl survey data were provided by the Ministry for Primary Industries. CL acknowledges DEVOTES – Development of innovative tools for understanding marine biodiversity and assessing good Environmental Status – EC project (FP7 Grant Agreement 308392) Coll, Marta ... et al.-- 16 pages, 6 figures, 6 tables Peer Reviewed

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    Ecological Indicators
    Article . 2016 . Peer-reviewed
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    Hal-Diderot
    Article . 2016
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      Other literature type . 2016
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      Other literature type . 2016
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      Ecological Indicators
      Article . 2016 . Peer-reviewed
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      Hal-Diderot
      Article . 2016
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    Authors: Ana, Popovic; Tran, Hai; Anatoly, Tchigvintsev; Mahbod, Hajighasemi; +17 Authors

    AbstractMetagenomics has made accessible an enormous reserve of global biochemical diversity. To tap into this vast resource of novel enzymes, we have screened over one million clones from metagenome DNA libraries derived from sixteen different environments for carboxylesterase activity and identified 714 positive hits. We have validated the esterase activity of 80 selected genes, which belong to 17 different protein families including unknown and cyclase-like proteins. Three metagenomic enzymes exhibited lipase activity, and seven proteins showed polyester depolymerization activity against polylactic acid and polycaprolactone. Detailed biochemical characterization of four new enzymes revealed their substrate preference, whereas their catalytic residues were identified using site-directed mutagenesis. The crystal structure of the metal-ion dependent esterase MGS0169 from the amidohydrolase superfamily revealed a novel active site with a bound unknown ligand. Thus, activity-centered metagenomics has revealed diverse enzymes and novel families of microbial carboxylesterases, whose activity could not have been predicted using bioinformatics tools.

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    Scientific Reports
    Other literature type . Article . 2017 . Peer-reviewed
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    Europe PubMed Central
    Article . 2017
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    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    CNR ExploRA
    Article . 2017
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      Other literature type . Article . 2017 . Peer-reviewed
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      Europe PubMed Central
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      CNR ExploRA
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    Authors: Diego Robledo; Juan A. Rubiolo; Santiago Cabaleiro; Paulino Martínez; +1 Authors

    Growth is among the most important traits for animal breeding. Understanding the mechanisms underlying growth differences between individuals can contribute to improving growth rates through more efficient breeding schemes. Here, we report a transcriptomic study in muscle and brain of fast- and slow-growing turbot (Scophthalmus maximus), a relevant flatfish in European and Asian aquaculture. Gene expression and allelic association between the two groups were explored. Up-regulation of the anaerobic glycolytic pathway in the muscle of fast-growing fish was observed, indicating a higher metabolic rate of white muscle. Brain expression differences were smaller and not associated with major growth-related genes, but with regulation of feeding-related sensory pathways. Further, SNP variants showing frequency differences between fast- and slow-growing fish pointed to genomic regions likely involved in growth regulation, and three of them were individually validated through SNP typing. Although different mechanisms appear to explain growth differences among families, general mechanisms seem also to be involved, and thus, results provide a set of useful candidate genes and markers to be evaluated for more efficient growth breeding programs and to perform comparative genomic studies of growth in fish and vertebrates This work was funded by Spanish Ministry of Economy and Competitiveness and European Regional Development Funds (AGL2012-35904), Ministry of Science and Innovation (Consolider Ingenio, Aquagenomics, CSD2007-00002), and Local Government. Xunta de Galicia (GRC2014/010). DR was supported by a FPU fellowship funded by Spanish Ministry of Education, Culture and Sport (AP2012-0254) and a postdoctoral contract funded by the Biotechnology and Biological Science Research Council (BBSRC) grant BB/N024044/1 SI

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    Europe PubMed Central
    Article . 2017
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    Scientific Reports
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    Scientific Reports
    Article . 2017 . Peer-reviewed
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      Scientific Reports
      Article . 2017 . Peer-reviewed
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    Authors: Alan Baudron; Paul G. Fernandes;

    Outputs from simulations done with the ecosystem model Ecopath with Ecosim. Data contain future estimates of catch and biomass calculated for a given climate scenario (i.e. IPCC projection), for each species included in the model.

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    ZENODO
    Dataset . 2019
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    Data sources: ZENODO; Sygma
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      ZENODO
      Dataset . 2019
      License: CC BY
      Data sources: ZENODO; Sygma
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    Authors: Fernandez, Carolina; Mascolo, Dario; Monaghan, Sean J.; Baily, Johanna L.; +5 Authors

    AbstractTwo aqueous fixation methods (modified Davidson's solution and modified Davidson's solution with 2% (w/v) Alcian blue) were compared against two non‐aqueous fixation methods (methacarn solution and methacarn solution with 2% (w/v) Alcian blue) along with the standard buffered formalin fixation method to (a) improve preservation of the mucous coat on Atlantic salmon, Salmo salar L., gills and (b) to examine the interaction between the amoebae and mucus on the gill during an infection with amoebic gill disease. Aqueous fixatives demonstrated excellent cytological preservation but failed to deliver the preservation of the mucus when compared to the non‐aqueous‐based fixatives; qualitative and semi‐quantitative analysis revealed a greater preservation of the gill mucus using the non‐aqueous methacarn solution. A combination of this fixation method and an Alcian blue/Periodic acid–Schiff staining was tested in gills of Atlantic salmon infected with amoebic gill disease; lectin labelling was also used to confirm the mucus preservation in the methacarn‐fixed tissue. Amoebae were observed closely associated with the mucus demonstrating that the techniques employed for preservation of the mucous coat can indeed avoid the loss of potential mucus‐embedded parasites, thus providing a better understanding of the relationship between the mucus and parasite.

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    Journal of Fish Diseases
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    Journal of Fish Diseases
    Other literature type . Article . 2019 . Peer-reviewed
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      Journal of Fish Diseases
      Other literature type . Article . 2019 . Peer-reviewed
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    Authors: Stahl; H.; Warnken; K.W.; +8 Authors

    A new sandwich sensor, consisting of an O2 planar optode overlain by a thin (90 µm) DGT layer is presented. This sensor can simultaneously resolve 2‐D O2 dynamics and trace metal fluxes in benthic substrates at a high spatial resolution. The DGT layer accumulates metals on a small particle size (0.2 µm) chelating resin and records the locally induced trace metal flux during the deployment, whereas the planar optode resolves the O2 dynamic in near real time at the same location in the sediment. Despite its ultrathin composition, the DGT layer has high carrying capacity for trace metals with no saturation problems during application to typical coastal‐ or contaminated sediments. Combined with laser ablation, accumulated metal fluxes could be resolved at a resolution of ~200 µm, whereas the O2 images had a resolution of ~100 µm. A 2‐D diffusion‐reaction model showed that the enhanced smearing and reduced response time of the O2 signal associated with the additional DGT layer were marginal. To test sensor performance at realistic conditions, it was applied to an artificial burrow system consisting of permeable dialysis tubing flushed with oxygenated seawater. The measurements demonstrated localized mobilization of Ni, Cu, and Pb close to the burrow wall, where O2 was elevated. The latter was also confirmed for Cu and Pb in natural sediments irrigated by the polychaete Hediste diversicolor. The sandwich sensor has great potential for investigating interrelations between O2 dynamics and metal mobilization in complex benthic systems such as burrows, rhizospheres, permeable sands, and microbial mats.

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    Limnology and Oceanography Methods
    Article . 2012 . Peer-reviewed
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      Limnology and Oceanography Methods
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    Authors: Anaid Rosas-Navarro; Gerald Langer; Patrizia Ziveri;

    Unidad de excelencia María de Maeztu MdM-2015-0552 The global warming debate has sparked an unprecedented interest in temperature effects on coccolithophores. The calcification response to temperature changes reported in the literature, however, is ambiguous. The two main sources of this ambiguity are putatively differences in experimental setup and strain specificity. In this study we therefore compare three strains isolated in the North Pacific under identical experimental conditions. Three strains of Emiliania huxleyi type A were grown under non-limiting nutrient and light conditions, at 10, 15, 20 and 25°C. All three strains displayed similar growth rate versus temperature relationships, with an optimum at 20-25°C. Elemental production (particulate inorganic carbon (PIC), particulate organic carbon (POC), total particulate nitrogen (TPN)), coccolith mass, coccolith size, and width of the tube element cycle were positively correlated with temperature over the sub-optimum to optimum temperature range. The correlation between PIC production and coccolith mass/size supports the notion that coccolith mass can be used as a proxy for PIC production in sediment samples. Increasing PIC production was significantly positively correlated with the percentage of incomplete coccoliths in one strain only. Generally, coccoliths were heavier when PIC production was higher. This shows that incompleteness of coccoliths is not due to time shortage at high PIC production. Sub-optimal growth temperatures lead to an increase in the percentage of malformed coccoliths in a strain-specific fashion. Since in total only six strains have been tested thus far, it is presently difficult to say whether sub-optimal temperature is an important factor causing malformations in the field. The most important parameter in biogeochemical terms, the PIC : POC ratio, shows a minimum at optimum growth temperature in all investigated strains. This clarifies the ambiguous picture featuring in the literature, i.e. discrepancies between PIC: POC-temperature relationships reported in different studies using different strains and different experimental setups. In summary, global warming might cause a decline in coccolithophore's PIC contribution to the rain ratio, as well as improved fitness in some genotypes due to fewer coccolith malformations.

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    Biogeosciences
    Article . 2016
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      Biogeosciences
      Article . 2016
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    Authors: De Ferrari, Luna; Mitchell, John BO;

    Background: In this work we predict enzyme function at the level of chemical mechanism, providing a finer granularity of annotation than traditional Enzyme Commission (EC) classes. Hence we can predict not only whether a putative enzyme in a newly sequenced organism has the potential to perform a certain reaction, but how the reaction is performed, using which cofactors and with susceptibility to which drugs or inhibitors, details with important consequences for drug and enzyme design. Work that predicts enzyme catalytic activity based on 3D protein structure features limits the prediction of mechanism to proteins already having either a solved structure or a close relative suitable for homology modelling. Results: In this study, we evaluate whether sequence identity, InterPro or Catalytic Site Atlas sequence signatures provide enough information for bulk prediction of enzyme mechanism. By splitting MACiE (Mechanism, Annotation and Classification in Enzymes database) mechanism labels to a finer granularity, which includes the role of the protein chain in the overall enzyme complex, the method can predict at 96% accuracy (and 96% micro-averaged precision, 99.9% macro-averaged recall) the MACiE mechanism definitions of 248 proteins available in the MACiE, EzCatDb (Database of Enzyme Catalytic Mechanisms) and SFLD (Structure Function Linkage Database) databases using an off-theshelf K-Nearest Neighbours multi-label algorithm. Conclusion: We find that InterPro signatures are critical for accurate prediction of enzyme mechanism. We also find that incorporating Catalytic Site Atlas attributes does not seem to provide additional accuracy. The software code (ml2db), data and results are available online at http://sourceforge.net/projects/ml2db/ and as supplementary files. Publisher PDF Peer reviewed

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    Europe PubMed Central
    Article . 2014
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    St Andrews Research Repository
    Article . 2014 . Peer-reviewed
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    BMC Bioinformatics
    Article . 2014 . Peer-reviewed
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    Authors: William Ross Hunter; Alan J. Jamieson; Veerle A.I. Huvenne; Ursula Witte;

    The Whittard Canyon is a branching submarine canyon on the Celtic continental margin, which may act as a conduit for sediment and organic matter (OM) transport from the European continental slope to the abyssal sea floor. In situ stable-isotope labelling experiments were conducted in the eastern and western branches of the Whittard Canyon, testing short-term (3–7 days) responses of sediment communities to deposition of nitrogen-rich marine (<i>Thalassiosira weissflogii</i>) and nitrogen-poor terrigenous (<i>Triticum aestivum</i>) phytodetritus. <sup>13</sup>C and <sup>15</sup>N labels were traced into faunal biomass and bulk sediments, and the <sup>13</sup>C label traced into bacterial polar lipid fatty acids (PLFAs). Isotopic labels penetrated to 5 cm sediment depth, with no differences between stations or experimental treatments (substrate or time). Macrofaunal assemblage structure differed between the eastern and western canyon branches. Following deposition of marine phytodetritus, no changes in macrofaunal feeding activity were observed between the eastern and western branches, with little change between 3 and 7 days. Macrofaunal C and N uptake was substantially lower following deposition of terrigenous phytodetritus with feeding activity governed by a strong N demand. Bacterial C uptake was greatest in the western branch of the Whittard Canyon, but feeding activity decreased between 3 and 7 days. Bacterial processing of marine and terrigenous OM were similar to the macrofauna in surficial (0–1 cm) sediments. However, in deeper sediments bacteria utilised greater proportions of terrigenous OM. Bacterial biomass decreased following phytodetritus deposition and was negatively correlated to macrofaunal feeding activity. Consequently, this study suggests that macrofaunal–bacterial interactions influence benthic C cycling in the Whittard Canyon, resulting in differential fates for marine and terrigenous OM.

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    Biogeosciences
    Article . 2013
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    Biogeosciences (BG)
    Other literature type . 2018
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      Biogeosciences
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      Biogeosciences
      Article . 2013
      Data sources: DOAJ-Articles
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      Biogeosciences (BG)
      Other literature type . 2018
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    Authors: Hofstede, Coen Matthijs; Beyer, Sebastian; Corr, Hugh F J; Eisen, Olaf; +7 Authors

    Support Force Glacier (SFG) is a large ice stream feeding into the Filchner Ice Shelf. The active seismic survey is recorded at the sheet-shelf transition of SFG. We map the bed while grounded, the ocean cavity around a surface channel at the ice shelf and its counterpart at the base, the basal channel, and the seabed. The survey consists of 5 seismic reflection profiles, 2 along-flow profiles and 3 across-flow profiles. The 2.42GB seismic data were recorded with a 300 m long streamer consisting of 96 30Hz p-wave sensors. The sample rate is 0.5 ms, record length 3000 ms. The data is single fold, shot spacing is 150 m: line name: profile TC paper: direction: #shots: - 20170501 profile I along-flow 291 shots - 20170502 profile III across-flow 28 shots - 20170503 profile II along-flow 71 shots - 20170504 profile IV across-flow 40 shots - 20170506 profile V across-flow 50 shots Presented are for each line (20170501 used as example): - The raw shots: 20170501_RAW_SHOTS_EDITS_GEOM.segy - The Kirchhoff migrated and depth converted profiles: 20170501stat_TXmig_Zconv.segy - The shot x,y,z coordinates in longitude, latitude and surface height in meters above sea level (z, WGS84 ellipsoid): 20170501_GPS.txt

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    PANGAEA
    Dataset . 2021
    Data sources: B2FIND
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      PANGAEA
      Dataset . 2021
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    Authors: Marta Coll; Lynne J. Shannon; Kristin M. Kleisner; M. J. Juan-Jorda; +34 Authors

    IndiSeas (>Indicators for the Seas>) is a collaborative international working group that was established in 2005 to evaluate the status of exploited marine ecosystems using a suite of indicators in a comparative framework. An initial shortlist of seven ecological indicators was selected to quantify the effects of fishing on the broader ecosystem using several criteria (i.e., ecological meaning, sensitivity to fishing, data availability, management objectives and public awareness). The suite comprised: (i) the inverse coefficient of variation of total biomass of surveyed species, (ii) mean fish length in the surveyed community, (iii) mean maximum life span of surveyed fish species, (iv) proportion of predatory fish in the surveyed community, (v) proportion of under and moderately exploited stocks, (vi) total biomass of surveyed species, and (vii) mean trophic level of the landed catch. In line with the Nagoya Strategic Plan of the Convention on Biological Diversity (2011-2020), we extended this suite to emphasize the broader biodiversity and conservation risks in exploited marine ecosystems. We selected a subset of indicators from a list of empirically based candidate biodiversity indicators initially established based on ecological significance to complement the original IndiSeas indicators. The additional selected indicators were: (viii) mean intrinsic vulnerability index of the fish landed catch, (ix) proportion of non-declining exploited species in the surveyed community, (x) catch-based marine trophic index, and (xi) mean trophic level of the surveyed community. Despite the lack of data in some ecosystems, we also selected (xii) mean trophic level of the modelled community, and (xiii) proportion of discards in the fishery as extra indicators. These additional indicators were examined, along with the initial set of IndiSeas ecological indicators, to evaluate whether adding new biodiversity indicators provided useful additional information to refine our understanding of the status evaluation of 29 exploited marine ecosystems. We used state and trend analyses, and we performed correlation, redundancy and multivariate tests. Existing developments in ecosystem-based fisheries management have largely focused on exploited species. Our study, using mostly fisheries independent survey-based indicators, highlights that biodiversity and conservation-based indicators are complementary to ecological indicators of fishing pressure. Thus, they should be used to provide additional information to evaluate the overall impact of fishing on exploited marine ecosystems. © 2015 Elsevier Ltd. All rights reserved We thank the Euroceans IndiSeas Working Group funded by the European Network of Excellence EUR-OCEANS (FP6, Contract N° 511106), the European collaborative project MEECE – Marine Ecosystem Evolution in a Changing Environment (FP7, Contract N° 212085) and IRD (Institute of Research for Development) and IOC/UNESCO. [...] MC was partially funded by the European Commission through the Marie Curie Career Integration Grant Fellowships – PCIG10-GA-2011-303534 – to the BIOWEB project and by the Spanish National Program Ramon y Cajal. LJS was supported through the South African Research Chair Initiative, funded through the South African Department of Science and Technology (DST) and administered by the South African National Research Foundation (NRF). LJS and YS were also funded by the European collaborative project MEECE – Marine Ecosystem Evolution in a Changing Environment – (FP7, Contract N° 212085). KMK was supported by the Northeast Fisheries Science Center and the Nature Conservancy through a grant from the Gordon and Betty Moore Foundation. MJJJ was supported by an EU Marie Curie International Outgoing Fellowship – PIOF-GA-2013-628116. MFB was supported by the Portuguese Oceanic and Atmospheric Institute and the trawl survey data collected under Biological Sampling (PNAB) Program. LJG would like to thank the Joint Research Centre of the European Commission for support. HO was financed by the Estonian Ministry of Education and Research (Grant SF0180005s10). JJH was supported by the Natural Environment Research Council and Department for Environment, Food and Rural Affairs [Grant Number NE/L003279/1, Marine Ecosystems Research Programme]. GIvdM was supported by the Institute of Marine Research, Norway. KT was partially funded by the project PERSEUS (Policy-oriented marine Environmental Research in the Southern EUropean Seas; FP7 Contract N° 287600). MAT was funded by the Spanish Institute of Oceanography (IEO) through a Predoctoral FPI fellowship. KNM was supported by a National Research Council fellowship at the Northwest Fishery Science Center. YJS and MTT were partially supported by the French project EMIBIOS (FRB, Contract No. APP-SCEN-2010-II). Chatham Rise trawl survey data were provided by the Ministry for Primary Industries. CL acknowledges DEVOTES – Development of innovative tools for understanding marine biodiversity and assessing good Environmental Status – EC project (FP7 Grant Agreement 308392) Coll, Marta ... et al.-- 16 pages, 6 figures, 6 tables Peer Reviewed

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    Horizon / Pleins textes
    Other literature type . 2016
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    Other literature type . 2016
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    Ecological Indicators
    Article . 2016 . Peer-reviewed
    License: Elsevier TDM
    Data sources: Crossref
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    Hal-Diderot
    Article . 2016
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      Horizon / Pleins textes
      Other literature type . 2016
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      Other literature type . 2016
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      Ecological Indicators
      Article . 2016 . Peer-reviewed
      License: Elsevier TDM
      Data sources: Crossref
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      Hal-Diderot
      Article . 2016
      Data sources: Hal-Diderot
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