Consulta: subjectFacets:"Metabarcoding"
Registros recuperados: 19
Data/hora: 07/06/2024 02:58:17

Microbiota Composition and Evenness Predict Survival Rate of Oysters Confronted to Pacific Oyster Mortality Syndrome
Provedor de dados: 5
Autores: Clerissi, Camille; De Lorgeril, Julien; Petton, Bruno; Lucasson, Aude; Escoubas, Jean Michel; Gueguen, Yannick; Dégremont, Lionel; Mitta, Guillaume; Toulza, Eve.
Pacific Oyster Mortality Syndrome (POMS) affects Crassostrea gigas oysters worldwide and causes important economic losses. Disease dynamic was recently deciphered and revealed a multiple and progressive infection caused by the Ostreid herpesvirus OsHV-1 μVar, triggering an immunosuppression followed by microbiota destabilization and bacteraemia by opportunistic bacterial pathogens. However, it remains unknown if microbiota might participate to protect oysters against POMS, and if microbiota characteristics might be predictive of oyster mortalities. To tackle this issue, we transferred full-sib progenies of resistant and susceptible oyster families from hatchery to the field during a period in favor of POMS. After 5 days of transplantation, oysters from...
Tipo: Text
Palavras-chave: Holobiont; Microbiome; Metabarcoding; Fitness; Bacteria.
Ano: 2020
URL: https://archimer.ifremer.fr/doc/00621/73332/72500.pdf

Protists Within Corals: The Hidden Diversity
Provedor de dados: 5
Autores: Clerissi, Camille; Brunet, Sebastien; Vidal-dupiol, Jeremie; Adjeroud, Mehdi; Lepage, Pierre; Guillou, Laure; Escoubas, Jean Michel; Toulza, Eve.
Previous observations suggested that microbial communities contribute to coral health and the ecological resilience of coral reefs. However, most studies of coral microbiology focused on prokaryotes and the endosymbiotic algae Symbiodinium. In contrast, knowledge concerning diversity of other protists is still lacking, possibly due to methodological constraints. As most eukaryotic DNA in coral samples was derived from hosts, protist diversity was missed in metagenome analyses. To tackle this issue, we designed blocking primers for Scleractinia sequences amplified with two primer sets that targeted variable loops of the 18S rRNA gene (18SV1V2 and 18SV4). These blocking primers were used on environmental colonies of Pocillopora damicornis sensu lato from two...
Tipo: Text
Palavras-chave: Holobiont; Protists; Symbiosis; Metabarcoding; Blocking primer; Scleractinia; Pocillopora damicornis.
Ano: 2018
URL: http://archimer.ifremer.fr/doc/00457/56823/58661.pdf

Deep-Sea Nematodes of the Mozambique Channel: Evidence of Random Community Assembly Dynamics in Seep Sediments
Provedor de dados: 5
Autores: Macheriotou, Lara; Rigaux, Annelien; Olu, Karine; Zeppilli, Daniela; Derycke, Sofie; Vanreusel, Ann.
Cold seeps occur globally in areas where gases escape from the seafloor, occasionally resulting in the formation of topographic depressions (pockmarks), characterised by unique physicochemical conditions such as anoxic and sulphuric sediments. Free-living marine nematodes tend to dominate the meiofaunal component in such environments, often occurring at extremely high densities and low richness; the mechanisms defining community assembly in areas of fluid seepage, however, have received little attention. Here we focus on a low-activity pockmark at 789 m in the Mozambique Channel (MC). We assessed the diversity, co-occurrence patterns and phylogenetic community structure of nematodes at this bathyal site to that of a nearby reference area as well as abyssal...
Tipo: Text
Palavras-chave: Cold seeps; Nematoda; Metabarcoding; Community structure; Phylogenetic community structure.
Ano: 2021
URL: https://archimer.ifremer.fr/doc/00679/79080/81524.pdf

Premières propositions pour un indice de composition du phytoplancton, basé sur les résultats des méthodes pigments et diversité génétique. Action 3 - Indice Composition - Livrable 1. Rapport final, mars 2015.
Provedor de dados: 5
Autores: Siano, Raffaele; Delmas, Daniel; Lampert, Luis.
Tipo: Text
Palavras-chave: Phytoplancton; Pigments; Indice composition; Diversité pigmentaire; Metabarcoding; Picoplancton; Mamiellophyceae; Chlb; Golfe de Gascogne; Panache de la Gironde; Phytoplankton; Pigments; Composition index; Pigment diversity; Metabarcoding; Picoplankton; Mamiellophyceae; Chlb; Gulf of Biscay; River Gironde plume.
Ano: 2015
URL: http://archimer.ifremer.fr/doc/00361/47263/47228.pdf

Définition d’un indice composition pour le phytoplancton en Manche- Atlantique, à partir des données du micro-phytoplancton du REPHY et des réseaux régionaux, et des mesures complémentaires de la flore phytoplanctonique acquises avec des techniques novatrices. Action 3 – Livrable 1. Propositions pour un indice de composition du phytoplancton, basé sur les résultats des méthodes microscopie, pigments et diversité génétique. Rapport final, février 2016
Provedor de dados: 5
Autores: Hernandez Farinas, Tania; Brun, Melanie; Siano, Raffaele; Delmas, Daniel.
This deliverable is composed of two reports which propose indice of phytoplankton composition, based respectively on the results of pigment and genetic diversity methods, and the results of microscopy method. Proposals based on the results of pigment and genetic diversity methods. The present work is a continuation of several studies carried out in the past (Siano and Delmas, 2013, 2015) on investigating an indicator of phytoplankton diversity using two methods complementary to optical microscopy: the genetic diversity analyzed with metabarcoding (exhaustive analysis of the diversity and relative abundance of OTUs, i.e. groups of sequences identified by their genetic resemblance) and the pigmentary diversity (analysis of the diversity and abundance of...
Tipo: Text
Palavras-chave: Metabarcoding; OTUs; Pigments; Picophytoplancton; Indice composition; Niche ecologique; Mamiellophyceae; Chlorophylle b; Rade de Brest; Bretagne sud; Panache de la Gironde; Denombrements du micro-phytoplancton; Abondance totale; Monotonicite; Linearite; Pressions; Facade Manche-Atlantique; Metabarcoding; OTUs; Pigments; Picophytoplankton; Composition indice; Ecological niche; Mamiellophyceae; Chlorophyll b; Brest Bay; Southern Britain; Gironde plume; Micro-phytoplankton counts; Total abundance; Monotonicity; Linearity; Pressure; Channel-Atlantic coast.
Ano: 2016
URL: http://archimer.ifremer.fr/doc/00363/47421/47426.pdf

Blind assessment of vertebrate taxonomic diversity across spatial scales by clustering environmental DNA metabarcoding sequences
Provedor de dados: 5
Autores: Marques, Virginie; Guérin, Pierre-édouard; Rocle, Mathieu; Valentini, Alice; Manel, Stéphanie; Mouillot, David; Dejean, Tony.
Human activities impact all ecosystems on Earth, which urges scientists to better understand biodiversity changes across temporal and spatial scales. Environmental DNA (eDNA) metabarcoding is a promising non‐invasive method to assess species composition in a wide range of ecosystems. Yet, this method requires the completeness of a reference database, i.e. a list of DNA sequences attached to each species of the regional pool, which is rarely met. As an alternative, molecular operational taxonomic units (MOTUs) can be extracted as clusters of sequences. However, the extent to which the diversity of MOTUs can predict the diversity of species across spatial scales is unknown. Here, we used 196 samples along the Rhone river (France) for which the reference...
Tipo: Text
Palavras-chave: 12S primer; Alpha-beta-delta-diversity; Clustering; Metabarcoding; MOTUs; Reference database.
Ano: 2020
URL: https://archimer.ifremer.fr/doc/00643/75506/76373.pdf

Acquisition de données complémentaires aux dénombrements, avec les techniques d’analyses pigmentaires et de diversité génétique. Etat d’avancement et premiers résultats. Action Indice Composition. Livrable n° AIV. Rapport final, 16 juillet 2014.
Provedor de dados: 5
Autores: Delmas, Daniel; Siano, Raffaele.
Studies on phytoplankton community diversity cannot be limited microphytoplankton (cells&gt;20 ìm), it is indeed necessary to take into account also the nano (3-20ìm) picophytoplankton (&lt;3 ìm) components. In the frame of this work aimed at studying temporal phytoplankton community diversity two complementary methodologies of phytoplankton sample analysis, pigment and genetic (metarbarcoding) diversity, have been used as alternative to routine morphological analysis carried out at light microscopy. The REPHY station (047-P-016 Concarneau Large) off-shore the Concarneau Bay has been sampled during the annual highest phytoplankton production (March-July 2012) with a frequent sample interval strategy (twice per week). Results obtained by both pigment and...
Tipo: Text
Palavras-chave: Phytoplancton; Structure de taille; Picophytoplancton; Nanophytoplancton; Microphytoplancton; Diversité génétique; Metabarcoding; Taxonomie pigmentaire; Façade atlantique; Baie de Concarneau; Phytoplankton; Size classes; Picophytoplankton; Nanophytoplankton; Microphytoplankton; Genetic diversity; Metabarcoding; Pigment taxonomy; Atlantic coasts; Concarneau Bay.
Ano: 2014
URL: http://archimer.ifremer.fr/doc/00361/47260/47225.pdf

A test of community assembly rules using foliar endophytes from a tropical forest canopy
Provedor de dados: 5
Autores: Donald, Julian; Roy, Mélanie; Suescun, Uxue; Iribar, Amaia; Manzi, Sophie; Péllissier, Léonie; Gaucher, Philippe; Chave, Jérôme.
1.Community assembly theory assumes that ecological communities are spatially delimited into patches. Within these patches, coexistence results from environmental filtering, competition, and immigration. Truly delineated communities exist in laboratory studies of microbial cultures in Petri dishes, yet empirical tests conducted in continuous environments often use patches defined by convention as opposed to realised boundaries. 2.Here we perform a test of ecological community assembly rules using foliar endophyte communities from a tropical rainforest, where leaves are considered as patches for both fungal and bacterial communities. We determined the diversity of fungal and bacterial endophytes using environmental DNA sequencing of 365 top‐canopy leaves,...
Tipo: Text
Palavras-chave: Bacteria; Distribution; French Guiana; Fungi; Metabarcoding; Plant–pathogen interactions; Rainforest.
Ano: 2020
URL: https://archimer.ifremer.fr/doc/00606/71808/70296.pdf

Malacological survey in a bottle of water: A comparative study between manual sampling and environmental DNA metabarcoding approaches
Provedor de dados: 5
Autores: Mulero, Stephen; Toulza, Eve; Loisier, Anaïs; Zimmerman, Meryl; Allienne, Jean-françois; Foata, Joséphine; Quilichini, Yann; Pointier, Jean-pierre; Rey, Olivier; Boissier, Jérôme.
To assess the effect of anthropogenic activities on ecosystems, it is of prime importance to develop new tools enabling a rapid characterization of ecological communities. Freshwater ecosystems are particularly impacted and threatened by human activities and need thorough attention to preserve their biodiversity and the ecological services they provide. Studying such ecosystems is generally difficult because the associated organisms are hard to sample and to monitor. We present a ready-to-use environmental metabarcoding protocol to characterize and monitor the freshwater gastropods communities from water samples. The efficiency of this new tool was compared to a classical malacological survey at 19 sampled sites from 10 distinct rivers distributed over...
Tipo: Text
Palavras-chave: Biomonitoring; Corsica; Environmental DNA; Malacology; Metabarcoding; Snail communities.
Ano: 2021
URL: https://archimer.ifremer.fr/doc/00666/77777/79917.docx

Rapid responses of pristine marine planktonic communities in experimental approach to diuron and naphthalene (Juan de Nova Island, Western Indian Ocean)
Provedor de dados: 5
Autores: Bouvy, Marc; Dupuy, Christine; Got, Patrice; Domaizon, Isabelle; Carré, Claire; Pagano, Marc; Debroas, Didier; Roques, Cécile; Leboulanger, Christophe.
Planktonic communities from Juan de Nova lagoon were submitted to a single exposure of diuron or naphthalene in triplicate outdoor 40-L mesocosms for 5 days. The study followed the temporal changes of the assemblages by determining abundances and taxonomic level of microbial (heterotrophic prokaryotes, picocyanobacteria, heterotrophic protists and phytoplankton) and metazooplankton communities. Exposure to both contaminants did not result in significant changes in phytoplankton abundances. Microscopic identification demonstrated the dominance of Bacillariophyta (mostly Chaetoceros tenuissimus) accounting for more than 95% of the microalgae detected in all mesocosms. Using 18S rRNA metabarcoding, temporal changes in the proportion of eukaryotic operational...
Tipo: Text
Palavras-chave: Contaminant; Taxonomy; Metabarcoding; Plankton; Experiments; Lagoon.
Ano: 2021
URL: https://archimer.ifremer.fr/doc/00681/79348/81853.pdf

Novel Widespread Marine Oomycetes Parasitising Diatoms, Including the Toxic Genus Pseudo-nitzschia: Genetic, Morphological, and Ecological Characterisation
Provedor de dados: 5
Autores: Garvette, Andrea; Nezan, Elisabeth; Badis, Yacine; Bilien, Gwenael; Arce, Paola; Bresnan, Eileen; Gachon, Claire M. M.; Siano, Raffaele.
Parasites are key drivers of phytoplankton bloom dynamics and related aquatic ecosystem processes. Yet, the dearth of morphological and molecular information hinders the assessment of their diversity and ecological role. Using single-cell techniques, we characterise morphologically and molecularly, intracellular parasitoids infecting four potentially toxin-producing Pseudo-nitzschia and one Melosira species on the North Atlantic coast. These sequences define two, morphologically indistinguishable clades within the phylum Oomycota, related to the genera of algal parasites Anisolpidium and Olpidiopsis and the diatom parasitoid species Miracula helgolandica. Our morphological data are insufficient to attribute either clade to the still unsequenced genus...
Tipo: Text
Palavras-chave: Pseudo-nitzschia; Diatoms; Marine oomycetes; Plankton parasites; Single-cell analysis; Metabarcoding.
Ano: 2018
URL: https://archimer.ifremer.fr/doc/00470/58135/60593.pdf

Schistosomiasis Vector Snails and Their Microbiota Display a Phylosymbiosis Pattern
Provedor de dados: 5
Autores: Huot, Camille; Clerissi, Camille; Gourbal, Benjamin; Galinier, Richard; Duval, David; Toulza, Eve.
Planorbidae snails are the intermediate host for the trematode parasite of the Schistosoma genus, which is responsible for schistosomiasis, a disease that affects both humans and cattle. The microbiota for Schistosoma has already been described as having an effect on host/parasite interactions, specifically through immunological interactions. Here, we sought to characterize the microbiota composition of seven Planorbidae species and strains. Individual snail microbiota was determined using 16S ribosomal DNA amplicon sequencing. The bacterial composition was highly specific to the host strain with limited interindividual variation. In addition, it displayed complete congruence with host phylogeny, revealing a phylosymbiosis pattern. These results were...
Tipo: Text
Palavras-chave: Microbiota; Phylosymbiosis; Metabarcoding; Planorbid snails; Tripartite interactions; Schistosomiasis.
Ano: 2020
URL: https://archimer.ifremer.fr/doc/00606/71807/70295.pdf

The marine intertidal zone shapes oyster and clam digestive bacterial microbiota
Provedor de dados: 5
Autores: Offret, Clement; Paulino, Sauvann; Gauthier, Olivier; Château, Kevin; Bidault, Adeline; Corporeau, Charlotte; Miner, Philippe; Petton, Bruno; Pernet, Fabrice; Fabioux, Caroline; Paillard, Christine; Blay, Gwenaelle Le.
Digestive microbiota provides a wide range of beneficial effects on host physiology and are therefore likely to play a key role in marine intertidal bivalve ability to acclimatize to the intertidal zone. This study investigated the effect of intertidal levels on the digestive bacterial microbiota of oysters Crassostrea gigas and clams Ruditapes philippinarum, two bivalves with different ecological niches. Based on the 16S rRNA region sequencing, digestive glands, seawater and sediments harbored specific bacterial communities, dominated by OTUs assigned to the Mycoplasmatales, Desulfobacterales and Rhodobacterales orders, respectively. Field implantation modified digestive bacterial microbiota of both bivalve species according to their intertidal position....
Tipo: Text
Palavras-chave: Microbiota; Oysters; Clams; Intertidal zone; Digestive gland; Metabarcoding.
Ano: 2020
URL: https://archimer.ifremer.fr/doc/00628/73961/73320.pdf

Unveiling protist diversity associated with the Pacific oyster Crassostrea gigas using blocking and excluding primers
Provedor de dados: 5
Autores: Clerissi, Camille; Guillou, Laure; Escoubas, Jean Michel; Toulza, Eve.
Background Microbiome of macroorganisms might directly or indirectly influence host development and homeostasis. Many studies focused on the diversity and distribution of prokaryotes within these assemblages, but the eukaryotic microbial compartment remains underexplored so far. Results To tackle this issue, we compared blocking and excluding primers to analyze microeukaryotic communities associated with Crassostrea gigas oysters. High-throughput sequencing of 18S rRNA genes variable loops revealed that excluding primers performed better by not amplifying oyster DNA, whereas the blocking primer did not totally prevent host contaminations. However, blocking and excluding primers showed similar pattern of alpha and beta diversities when protist communities...
Tipo: Text
Palavras-chave: Holobiont; Metabarcoding; Microbiome; Ostreoida; Crassostrea.
Ano: 2020
URL: https://archimer.ifremer.fr/doc/00636/74799/75165.pdf

Microplastic bacterial communities in the Bay of Brest: Influence of polymer type and size
Provedor de dados: 5
Autores: Frere, Laura; Maignien, Lois; Chalopin, Morgane; Huvet, Arnaud; Rinnert, Emmanuel; Morrison, Hilary; Kerninon, Sandrine; Cassone, Anne-laure; Lambert, Christophe; Reveillaud, Julie; Paul-pont, Ika.
Microplastics (&lt;5 mm) exhibit intrinsic features such as density, hydrophobic surface, or high surface/volume ratio, that are known to promote microbial colonization and biofilm formation in marine ecosystems. Yet, a relatively low number of studies have investigated the nature of microplastic associated bacterial communities in coastal ecosystems and the potential factors influencing their composition and structure. Here, we characterized microplastics collected in the Bay of Brest by manual sorting followed by Raman spectroscopy and studied their associated bacterial assemblages using 16S amplicon high-throughput sequencing. Our methodology allowed discriminating polymer type (polyethylene, polypropylene and polystyrene) within small size ranges...
Tipo: Text
Palavras-chave: Bacteria; Microplastics; Coastal ecosystem; Metabarcoding; Vibrios.
Ano: 2018
URL: https://archimer.ifremer.fr/doc/00449/56082/57614.pdf

Molecular mechanisms of acclimation to long‐term elevated temperature exposure in marine symbioses
Provedor de dados: 5
Autores: Alves Monteiro, H.j.; Brahmi, C.; Mayfield, A.b.; Vidal‐dupiol, J.; Lapeyre, B.; Le Luyer, Jeremy.
Seawater temperature rise in French Polynesia has repeatedly resulted in the bleaching of corals and giant clams. Because giant clams possess distinctive ectosymbiotic features, they represent a unique and powerful model for comparing molecular pathways involved in 1) maintenance of symbiosis and 2) acquisition of thermo‐tolerance among coral reef organisms. Herein, we explored the physiological and transcriptomic responses of the clam hosts and their photosynthetically active symbionts over a 65‐day experiment in which clams were exposed to either normal or environmentally relevant elevated seawater temperatures. Additionally, we used metabarcoding data coupled with in situ sampling/survey data to explore the relative importance of holobiont adaptation...
Tipo: Text
Palavras-chave: Co-expression network analysis; Giant clams; Metabarcoding; RNA-Seq; Symbiodiniaceae; Thermo-acclimation.
Ano: 2020
URL: https://archimer.ifremer.fr/doc/00591/70271/68331.pdf

Salmon Gravlax Biopreservation With Lactic Acid Bacteria: A Polyphasic Approach to Assessing the Impact on Organoleptic Properties, Microbial Ecosystem and Volatilome Composition
Provedor de dados: 5
Autores: Wiernasz, Norman; Leroi, Francoise; Chevalier, Frederique; Cornet, Josiane; Cardinal, Mireille; Rohloff, Jens; Passerini, Delphine; Skırnisdóttir, Sigurlaug; Pilet, Marie-france.
Seafood and fishery products are very perishable commodities with short shelf-lives owing to rapid deterioration of their organoleptic and microbiological quality. Microbial growth and activity are responsible for up to 25% of food losses in the fishery industry. In this context and to meet consumer demand for minimally processed food, developing mild preservation technologies such as biopreservation represents a major challenge. In this work, we studied the use of six lactic acid bacteria (LAB), previously selected for their properties as bioprotective agents, for salmon dill gravlax biopreservation. Naturally contaminated salmon dill gravlax slices, with a commercial shelf-life of 21 days, were purchased from a French industrial company and inoculated by...
Tipo: Text
Palavras-chave: Metabarcoding; 16S rRNA gene; Seafood; Antilisterial activity; Volatile organic compounds; Sensory analyses.
Ano: 2020
URL: https://archimer.ifremer.fr/doc/00605/71716/70174.pdf

Première évaluation de la diversité des communautés microbiennes planctoniques au cours d'épisodes de mortalité des moules bleues en France : utilisation de l'approche de métabarcoding pour l'analyse de l'ADN environnemental
Provedor de dados: 5
Autores: Pepin, Jean-francois; Bouget, Jean-francois; Chabirand, Jean-michel; Chasselin, Leo; Costes, Louis; Grizon, James; Lejolivet, Aurore; Le Noc, Sandrine; Palvadeau, Hubert; Schmitt, Anne; Seugnet, Jean-luc; Soletchnik, Patrick; Travers, Marie-agnes; Tourbiez, Delphine; Guesdon, Stephane.
Since 2014 in France, in Charente maritime and Vendée, farmed and stocks of blue mussels experienced strong mortality events. In this context, the « MORBLEU » research project (DPMA-Ifremer agreement) was initiated to explore potentially aggravating factors, associated or correlated with mortality of mussels. Here, the work is to study biotic factors in mussels environment, looking for describe diversity and evolution of microbial communities (water column) before, during and after mortality events using NGS technology (metabarcoding) for environmental DNA analysis. We present, sampling strategy used from 2015 to 2018, Material &amp; Methods and some preliminary results.  
Tipo: Text
Palavras-chave: MORBLEU; Moules; Mortalité; ADN environnemental; EDNA; Metabarcoding; Communautés microbiennes.
Ano: 2019
URL: https://archimer.ifremer.fr/doc/00505/61664/65579.pdf

Spatiotemporal variations in microbial diversity across the three domains of life in a tropical thalassohaline lake (Dziani Dzaha, Mayotte Island)
Provedor de dados: 5
Autores: Hugoni, Mylene; Escalas, Arthur; Bernard, Cecile; Nicolas, Sebastien; Jezequel, Didier; Vazzoler, Fanny; Sarazin, Gerard; Leboulanger, Christophe; Bouvy, Marc; Got, Patrice; Ader, Magali; Troussellier, Marc; Agogue, Helene.
Thalassohaline ecosystems are hypersaline environments originating from seawater in which sodium chloride is the most abundant salt and the pH is alkaline. Studies focusing on microbial diversity in thalassohaline lakes are still scarce compared with those on athalassohaline lakes such as soda lakes that have no marine origin. In this work, we investigated multiple facets of bacterial, archaeal and eukaryotic diversity in the thalassohaline Lake Dziani Dzaha using a metabarcoding approach. We showed that bacterial and archaeal diversity were mainly affected by contrasting physicochemical conditions retrieved at different depths. While photosynthetic microorganisms were dominant in surface layers, chemotrophic phyla (Firmicutes or Bacteroidetes) and...
Tipo: Text
Palavras-chave: Archaea; Bacteria; Eukaryotes; Extreme environment; Metabarcoding; Thalassohaline lake.
Ano: 2018
URL: https://archimer.ifremer.fr/doc/00464/57564/59738.pdf