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Auteur Thomas, F.; Dittami, S.M.; Brunet, M.; Le Duff, N.; Tanguy, G.; Leblanc, C.; Gobet, A.
Titre Evaluation of a new primer combination to minimize plastid contamination in 16S rDNA metabarcoding analyses of alga-associated bacterial communities Type Article scientifique
Année (down) 2020 Publication Revue Abrégée Environ. Microbiol. Rep.
Volume 12 Numéro 1 Pages 30-37
Mots-Clés diversity; phylogenetic analysis; ribosomal-rna sequences; surfaces
Résumé Plant- and alga-associated bacterial communities are generally described via 16S rDNA metabarcoding using universal primers. As plastid genomes encode 16S rDNA related to cyanobacteria, these data sets frequently contain >90% plastidial sequences, and the bacterial diversity may be under-sampled. To overcome this limitation we evaluated in silico the taxonomic coverage for four primer combinations targeting the 16S rDNA V3-V4 region. They included a forward primer universal to Bacteria (S-D-Bact-0341-b-S-17) and four reverse primers designed to avoid plastid DNA amplification. The best primer combination (NOCHL) was compared to the universal primer set in the wet lab using a synthetic community and samples from three macroalgal species. The proportion of plastid sequences was reduced by 99%-100% with the NOCHL primers compared to the universal primers, irrespective of algal hosts, sample collection and extraction protocols. Additionally, the NOCHL primers yielded a higher richness while maintaining the community structure. As Planctomycetes, Verrucomicrobia and Cyanobacteria were underrepresented (70%-90%) compared to universal primers, combining the NOCHL set with taxon-specific primers may be useful for a complete description of the alga-associated bacterial diversity. The NOCHL primers represent an innovation to study algal holobionts without amplifying host plastid sequences and may further be applied to other photosynthetic hosts.
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Volume de collection Numéro de collection Edition
ISSN 1758-2229 ISBN Médium
Région Expédition Conférence
Notes WOS:000498132200001 Approuvé pas de
Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2759
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Auteur Ramirez-Romero, E.; Molinero, J.C.; Sommer, U.; Salhi, N.; Yahia, O.K.-D.; Yahia, M.N.D.
Titre Phytoplankton size changes and diversity loss in the southwestern Mediterranean Sea in relation to long-term hydrographic variability Type Article scientifique
Année (down) 2020 Publication Revue Abrégée Estuar. Coast. Shelf Sci.
Volume 235 Numéro Pages 106574
Mots-Clés bay; climate-change; Diversity loss; dynamics; evolution; jellyfish; marine; Nanophytoplankton; Ocean warming; patterns; Phytoplankton diversity; plankton communities; Size structural changes; Southwestern mediterranean; temperature; time-series
Résumé Structural changes in plankton primary producers have large implications for food web dynamics, energy fluxes and the vertical export of biogenic particulate carbon. Here we examine phytoplankton data spanning the period 1993-2008 from the Bay of Tunis, southwestern Mediterranean Sea, in relation to long term hydroclimate variability. We show a conspicuous shift in the structure of the phytoplankton community characterized by an increase of small-sized species and diversity loss, revealing a dominance of smaller blooming diatoms and cyanobacteria. Such changes were concurrent with marked modifications in hydroclimatic patterns experienced in the Bay of Tunis consisting of a shift towards enhanced winter precipitation together with rising temperatures. This novel study shows an overall rise in the proportion of small phytoplankton cells and a decreasing trend in phytoplankton diversity in the southern Mediterranean area. These findings warn of a potential decline of trophic efficiency and lesser food web stability resulting from mean size reduction and the diversity loss.
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Volume de collection Numéro de collection Edition
ISSN 0272-7714 ISBN Médium
Région Expédition Conférence
Notes WOS:000527915700034 Approuvé pas de
Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2766
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Auteur Puerta, P.; Johnson, C.; Carreiro-Silva, M.; Henry, L.-A.; Kenchington, E.; Morato, T.; Kazanidis, G.; Luis Rueda, J.; Urra, J.; Ross, S.; Wei, C.-L.; Manuel Gonzalez-Irusta, J.; Arnaud-Haond, S.; Orejas, C.
Titre Influence of Water Masses on the Biodiversity and Biogeography of Deep-Sea Benthic Ecosystems in the North Atlantic Type Article scientifique
Année (down) 2020 Publication Revue Abrégée Front. Mar. Sci.
Volume 7 Numéro Pages 239
Mots-Clés antarctic intermediate water; biodiversity; biogeography; climate-change impacts; coral lophelia-pertusa; deep-sea; food-supply mechanisms; global habitat suitability; meridional overturning circulation; ne atlantic; North Atlantic; ocean acidification; porcupine seabight; rockall trough margin; vulnerable marine ecosystems; water masses
Résumé Circulation patterns in the North Atlantic Ocean have changed and re-organized multiple times over millions of years, influencing the biodiversity, distribution, and connectivity patterns of deep-sea species and ecosystems. In this study, we review the effects of the water mass properties (temperature, salinity, food supply, carbonate chemistry, and oxygen) on deep-sea benthic megafauna (from species to community level) and discussed in future scenarios of climate change. We focus on the key oceanic controls on deep-sea megafauna biodiversity and biogeography patterns. We place particular attention on cold-water corals and sponges, as these are ecosystem-engineering organisms that constitute vulnerable marine ecosystems (VME) with high associated biodiversity. Besides documenting the current state of the knowledge on this topic, a future scenario for water mass properties in the deep North Atlantic basin was predicted. The pace and severity of climate change in the deep-sea will vary across regions. However, predicted water mass properties showed that all regions in the North Atlantic will be exposed to multiple stressors by 2100, experiencing at least one critical change in water temperature (+2 degrees C), organic carbon fluxes (reduced up to 50%), ocean acidification (pH reduced up to 0.3), aragonite saturation horizon (shoaling above 1000 m) and/or reduction in dissolved oxygen (> 5%). The northernmost regions of the North Atlantic will suffer the greatest impacts. Warmer and more acidic oceans will drastically reduce the suitable habitat for ecosystem-engineers, with severe consequences such as declines in population densities, even compromising their long-term survival, loss of biodiversity and reduced biogeographic distribution that might compromise connectivity at large scales. These effects can be aggravated by reductions in carbon fluxes, particularly in areas where food availability is already limited. Declines in benthic biomass and biodiversity will diminish ecosystem services such as habitat provision, nutrient cycling, etc. This study shows that the deep-sea VME affected by contemporary anthropogenic impacts and with the ongoing climate change impacts are unlikely to withstand additional pressures from more intrusive human activities. This study serves also as a warning to protect these ecosystems through regulations and by tempering the ongoing socio-political drivers for increasing exploitation of marine resources.
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ISSN ISBN Médium
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Notes WOS:000526864100001 Approuvé pas de
Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2767
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Auteur de Melo, C.C.; Cavalcanti Soares, A.P.; Pelage, L.; Eduardo, L.N.; Fredou, T.; Lira, A.S.; Ferreira, B.P.; Bertrand, A.; Lucena-Fredou, F.
Titre Haemulidae distribution patterns along the Northeastern Brazilian continental shelf and size at first maturity of the most abundant species Type Article scientifique
Année (down) 2020 Publication Revue Abrégée Reg. Stud. Mar. Sci.
Volume 35 Numéro Pages 101226
Mots-Clés archipelago; ceara state; coral-reef fish; diversity; grunts haemulidae; habitat; maturation; pernambuco; plumieri teleostei haemulidae; seagrass
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Langue English Langue du Résumé Titre Original
Éditeur de collection Titre de collection Titre de collection Abrégé
Volume de collection Numéro de collection Edition
ISSN 2352-4855 ISBN Médium
Région Expédition Conférence
Notes WOS:000525758600056 Approuvé pas de
Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2769
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Auteur Brandt, M.; Trouche, B.; Henry, N.; Liautard-Haag, C.; Maignien, L.; de Vargas, C.; Wincker, P.; Poulain, J.; Zeppilli, D.; Arnaud-Haond, S.
Titre An Assessment of Environmental Metabarcoding Protocols Aiming at Favoring Contemporary Biodiversity in Inventories of Deep-Sea Communities Type Article scientifique
Année (down) 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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Auteur institutionnel Thèse
Editeur Lieu de Publication Éditeur
Langue English Langue du Résumé Titre Original
Éditeur de collection Titre de collection Titre de collection Abrégé
Volume de collection Numéro de collection Edition
ISSN ISBN Médium
Région Expédition Conférence
Notes WOS:000531310000001 Approuvé pas de
Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2791
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