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Auteur (up) Brandt, M.; Trouche, B.; Henry, N.; Liautard-Haag, C.; Maignien, L.; de Vargas, C.; Wincker, P.; Poulain, J.; Zeppilli, D.; Arnaud-Haond, S. doi  openurl
  Titre An Assessment of Environmental Metabarcoding Protocols Aiming at Favoring Contemporary Biodiversity in Inventories of Deep-Sea Communities Type Article scientifique
  Année 2020 Publication Revue Abrégée Front. Mar. Sci.  
  Volume 7 Numéro Pages 234  
  Mots-Clés benthic ecology; biomonitoring; deep-sea biodiversity; diversity; environmental metabarcoding; extracellular dna; extracellular DNA; extraction; foraminifera; impacts; method testing; preservation; RNA versus DNA; sediments; taxa  
  Résumé The abyssal seafloor covers more than 50% of planet Earth and is a large reservoir of still mostly undescribed biodiversity. It is increasingly targeted by resource-extraction industries and yet is drastically understudied. In such remote and hard-to-access ecosystems, environmental DNA (eDNA) metabarcoding is a useful and efficient tool for studying biodiversity and implementing environmental impact assessments. Yet, eDNA analysis outcomes may be biased toward describing past rather than present communities as sediments contain both contemporary and ancient DNA. Using commercially available kits, we investigated the impacts of five molecular processing methods on eDNA metabarcoding biodiversity inventories targeting prokaryotes (16S), unicellular eukaryotes (18S-V4), and metazoans (18S-V1, COI). As the size distribution of ancient DNA is skewed toward small fragments, we evaluated the effect of removing short DNA fragments via size selection and ethanol reconcentration using eDNA extracted from 10 g of sediment at five deep-sea sites. We also compare communities revealed by eDNA and environmental RNA (eRNA) co-extracted from similar to 2 g of sediment at the same sites. Results show that removing short DNA fragments does not affect alpha and beta diversity estimates in any of the biological compartments investigated. Results also confirm doubts regarding the possibility to better describe live communities using eRNA. With ribosomal loci, eRNA, while resolving similar spatial patterns than co-extracted eDNA, resulted in significantly higher richness estimates, supporting hypotheses of increased persistence of ribosomal RNA (rRNA) in the environment and unmeasured bias due to overabundance of rRNA and RNA release. With the mitochondrial locus, eRNA detected lower metazoan richness and resolved fewer spatial patterns than co-extracted eDNA, reflecting high messenger RNA lability. Results also highlight the importance of using large amounts of sediment (>= 10 g) for accurately surveying eukaryotic diversity. We conclude that eDNA should be favored over eRNA for logistically realistic, repeatable, and reliable surveys and confirm that large sediment samples (>= 10 g) deliver more complete and accurate assessments of benthic eukaryotic biodiversity and that increasing the number of biological rather than technical replicates is important to infer robust ecological patterns.  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2791  
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Auteur (up) Brosset, P.; Le Bourg, B.; Costalago, D.; Banaru, D.; Van Beveren, E.; Bourdeix, J.-H.; Fromentin, J.-M.; Menard, F.; Saraux, C. doi  openurl
  Titre Linking small pelagic dietary shifts with ecosystem changes in the Gulf of Lions Type Article scientifique
  Année 2016 Publication Revue Abrégée Mar. Ecol.-Prog. Ser.  
  Volume 554 Numéro Pages 157-171  
  Mots-Clés anchovy; anchovy engraulis-encrasicolus; climate; Dietary overlap; fish; food-web; NW Mediterranean; nw mediterranean sea; plankton; regime shifts; Sardine; size-fractionated zooplankton; southern benguela; Sprat; stable-isotope ratios; Trophic ecology  
  Résumé Since 2008, a severe decrease in size and body condition together with a demographic truncation has been observed in the sardine (secondarily in anchovy) population of the Gulf of Lions (NW Mediterranean Sea). In parallel, sprat biomass, which was negligible before, has increased tenfold. All of these changes have strongly affected the regional fisheries. Using trophic and isotopic data from contrasting periods of low versus high growth and condition, we investigated potential changes in diet and interspecific feeding interactions through time. Evidence of resource partitioning was found between sprat and both anchovy and sardine in 2004 and 2005. Since 2010, the isotopic niches of the 3 species have tended to overlap, suggesting higher risk of competition for food resources. Moreover, the wider trophic niche of sprat indicates higher variability in individual diets. Anchovy and sardine diet varied through time, with a high proportion of large copepods or cladocerans in periods of high growth and condition (1994 and 2007, respectively) versus a dominance of small copepods in the present (2011-2012). Furthermore, an important reduction in prey diversity was also identified in the diet of both anchovy and sardine during the most recent period. Our results support the hypothesis that changes in small pelagic fish growth, size and body condition and ultimately biomass could be due to bottom-up control characterized by changes in food availability and increasing potential trophic competition.  
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  ISSN 0171-8630 ISBN Médium  
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  Numéro d'Appel MARBEC @ alain.herve @ collection 1642  
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Auteur (up) Chevrinais, M.; Jacquet, C.; Cloutier, R. doi  openurl
  Titre Early establishment of vertebrate trophic interactions: Food web structure in Middle to Late Devonian fish assemblages with exceptional fossilization Type Article scientifique
  Année 2017 Publication Revue Abrégée Bull. Geosci.  
  Volume 92 Numéro 4 Pages 491-510  
  Mots-Clés north-america; bottom-up; body-size; predator; top-down; bottom-up control; coordinated stasis; Devonian; digestive contents; ecomorphology; escuminac formation; foraging ecology; fossil fish; fossil record; pahteoecology; prey size relationships; top-down control  
  Résumé In past and present ecosystems, trophic interactions determine material and energy transfers among species, regulating population dynamics and community stability. Food web studies in past ecosystems are helpful to assess the persistence of ecosystem structure throughout geological times and to explore the existence of general principles of food web assembly. We determined and compared the trophic structure of two Devonian fish assemblages [(1) the Escuminac assemblage (ca. 380 Ma), Miguasha, eastern Canada and (2) the Lode assemblage (ca. 390 Ma), Straupe, Latvia] with a closer look at the Escuminac assemblage. Both localities are representative of Middle to Late Devonian aquatic vertebrate assemblages in terms of taxonomic richness (ca. 20 species), phylogenetic diversity (all major groups of lower vertebrates) and palaeoenvironment (palaeoestuaries). Fossil food web structures were assessed using different kinds of direct (i.e. digestive contents and bite marks in fossils) and indirect (e.g. ecomoiphological measurements, stratigraphic species co-occurrences) indicators. First, the relationships between predator and prey body size established for the Escuminac fishes are comparable to those of recent aquatic ecosystems, highlighting a consistency of aquatic food web structure across geological time. Second, non-metric dimensional scaling on ecomorphological variables and cluster analysis showed a common pattern of functional groups for both fish assemblages; top predators, predators, primary and secondary consumers were identified. We conclude that Devonian communities were organized in multiple trophic levels and that size-based feeding interactions were established early in vertebrate history.  
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  ISSN 1214-1119 ISBN Médium  
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  Numéro d'Appel MARBEC @ alain.herve @ collection 2251  
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Auteur (up) Chouvelon, T.; Brach-Papa, C.; Auger, D.; Bodin, N.; Bruzac, S.; Crochet, S.; Degroote, M.; Hollanda, S.J.; Hubert, C.; Knoery, J.; Munschy, C.; Puech, A.; Rozuel, E.; Thomas, B.; West, W.; Bourjea, J.; Nikolic, N. doi  openurl
  Titre Chemical contaminants (trace metals, persistent organic pollutants) in albacore tuna from western Indian and south-eastern Atlantic Oceans: Trophic influence and potential as tracers of populations Type Article scientifique
  Année 2017 Publication Revue Abrégée Sci. Total Environ.  
  Volume 596 Numéro Pages 481-495  
  Mots-Clés Bioaccumulation; biscay northeast atlantic; enhanced bioaccumulation; feeding ecology; Inorganic elements; Intrinsic markers; marine food webs; mercury concentrations; merluccius-merluccius; Organic contaminants; organochlorine compounds; polychlorinated-biphenyls; stable-isotope analysis; Stable isotopes; thunnus-alalunga; Top predator  
  Résumé Albacore tuna (Thunnus alalunga) is a highly commercial fish species harvested in the world's Oceans. Identifying the potential links between populations is one of the key tools that can improve the current management across fisheries areas. In addition to characterising populations' contamination state, chemical compounds can help refine foraging areas, individual flows and populations' structure, especially when combined with other intrinsic biogeochemical (trophic) markers such as carbon and nitrogen stable isotopes. This study investigated the bioaccumulation of seven selected trace metals – chromium, nickel, copper (Cu), zinc (Zn), cadmium (Cd), mercury (Hg) and lead – in the muscle of 443 albacore tunas, collected over two seasons and/or years in the western Indian Ocean (WIO: Reunion Island and Seychelles) and in the south-eastern Atlantic Ocean (SEAO: South Africa). The main factor that explained metal concentration variability was the geographic origin of fish, rather than the size and the sex of individuals, or the season/year of sampling. The elements Cu, Zn, Cd and Hg indicated a segregation of the geographic groups most clearly. For similar sized-individuals, tunas from SEAO had significantly higher concentrations in Cu, Zn and Cd, but lower Hg concentrations than those from WIO. Information inferred from the analysis of trophic markers (delta C-13, delta N-15) and selected persistent organic pollutants, as well as information on stomach contents, corroborated the geographical differences obtained by trace metals. It also highlighted the influence of trophic ecology on metal bioaccumulation. Finally, this study evidenced the potential of metals and chemical contaminants in general as tracers, by segregating groups of individuals using different food webs or habitats, to better understand spatial connectivity at the population scale. Limited flows of individuals between the SEAO and the WIO are suggested. Albacore as predatory fish also provided some information on environmental and food web chemical contamination in the different study areas. (C) 2017 Elsevier B.V. All rights reserved.  
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  ISSN 0048-9697 ISBN Médium  
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  Numéro d'Appel MARBEC @ alain.herve @ collection 2139  
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Auteur (up) Christensen, V.; Coll, M.; Steenbeek, J.; Buszowski, J.; Chagaris, D.; Walters, C.J. url  doi
openurl 
  Titre Representing Variable Habitat Quality in a Spatial Food Web Model Type Article scientifique
  Année 2014 Publication Revue Abrégée Ecosystems  
  Volume 17 Numéro 8 Pages 1397-1412  
  Mots-Clés Ecology; Ecopath; ecospace; Environmental Management; food web model; foraging capacity model; Geoecology/Natural Processes; habitat modeling; Hydrology/Water Resources; Plant Sciences; sampling; simulation model; species distribution model; Zoology  
  Résumé Why are marine species where they are? The scientific community is faced with an urgent need to understand aquatic ecosystem dynamics in the context of global change. This requires development of scientific tools with the capability to predict how biodiversity, natural resources, and ecosystem services will change in response to stressors such as climate change and further expansion of fishing. Species distribution models and ecosystem models are two methodologies that are being developed to further this understanding. To date, these methodologies offer limited capabilities to work jointly to produce integrated assessments that take both food web dynamics and spatial-temporal environmental variability into account. We here present a new habitat capacity model as an implementation of the spatial-temporal model Ecospace of the Ecopath with Ecosim approach. The new model offers the ability to drive foraging capacity of species from the cumulative impacts of multiple physical, oceanographic, and environmental factors such as depth, bottom type, temperature, salinity, oxygen concentrations, and so on. We use a simulation modeling procedure to evaluate sampling characteristics of the new habitat capacity model. This development bridges the gap between envelope environmental models and classic ecosystem food web models, progressing toward the ability to predict changes in marine ecosystems under scenarios of global change and explicitly taking food web direct and indirect interactions into account.  
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  ISSN 1432-9840, 1435-0629 ISBN Médium  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1196  
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