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A community perspective on the concept of marine holobionts: state-of-the-art, challenges, and future directions ArchiMer
Dittami, Simon M; Arboleda, Enrique; Auguet, Jean-christophe; Bigalke, Arite; Briand, Enora; Cardenas, Paco; Cardini, Ulisse; Decelle, Johan; Engelen, Aschwin; Eveillard, Damien; Gachon, Claire Mm; Griffiths, Sarah; Harder, Tilmann; Kayal, Ehsan; Kazamia, Elena; Lallier, François H; Media, Monica; Marzinelli, Ezequiel M; Morganti, Teresa; Nunez Pons, Laura; Prado, Soizik; Pintado, José; Saha, Mahasweta; Selosse, Marc-andré; Skillings, Derek; Stock, Willem; Sunagawa, Shinichi; Toulza, Eve; Vorobev, Alexey; Leblanc, Catherine; Not, Fabrice.
Host-microbe interactions play crucial roles in marine ecosystems, but we still have very little understanding of the mechanisms that govern these relationships, the evolutionary processes that shape them, and their ecological consequences. The holobiont concept is a renewed paradigm in biology that can help describe and understand these complex systems. It posits that a host and its associated microbiota, living together in a long-lasting relationship, form the holobiont, and have to be studied together, as a coherent biological and functional unit, in order to understand the biology, ecology and evolution of the organisms. Here we discuss critical concepts and opportunities in marine holobiont research and identify key challenges in the field. We...
Tipo: Text
Ano: 2019 URL: https://archimer.ifremer.fr/doc/00480/59209/61904.pdf
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Chronic Polyaromatic Hydrocarbon (PAH) Contamination Is a Marginal Driver for Community Diversity and Prokaryotic Predicted Functioning in Coastal Sediments ArchiMer
Jeanbille, Mathilde; Gury, Jérôme; Duran, Robert; Tronczynski, Jacek; Ghiglione, Jean-françois; Agogué, Hélène; Saïd, Olfa Ben; Taïb, Najwa; Debroas, Didier; Garnier, Cédric; Auguet, Jean-christophe.
Benthic microorganisms are key players in the recycling of organic matter and recalcitrant compounds such as polyaromatic hydrocarbons (PAHs) in coastal sediments. Despite their ecological importance, the response of microbial communities to chronic PAH pollution, one of the major threats to coastal ecosystems, has received very little attention. In one of the largest surveys performed so far on coastal sediments, the diversity and composition of microbial communities inhabiting both chronically contaminated and non-contaminated coastal sediments were investigated using high-throughput sequencing on the 18S and 16S rRNA genes. Prokaryotic alpha-diversity showed significant association with salinity, temperature, and organic carbon content. The effect of...
Tipo: Text Palavras-chave: Microbial communities; PAH; Chronic contamination; Coastal sediment; Functional diversity.
Ano: 2016 URL: http://archimer.ifremer.fr/doc/00347/45854/45522.pdf
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Comparative analysis of the food webs of two intertidal mudflats during two seasons using inverse modelling: Aiguillon Cove and Brouage Mudflat, France ArchiMer
Degre, Delphine; Leguerrier, D; Du Chatelet, E; Rzeznik, J; Auguet, Jean-christophe; Dupuy, Christine; Marquis, E; Fichet, Denis; Struski, Caroline; Joyeux, E; Sauriau, Pierre-guy; Niquil, Nathalie.
Inverse analysis was used to model the food webs of two intertidal mudflat ecosystems: Aiguillon Cove (AC) and Brouage Mudflat (BM) (south-western Atlantic coast, France). The aim of the present study is to describe and compare the functioning of these two ecosystems. The method of inverse analysis has been adapted in order to take into account, in a single calculation, two seasons: spring/summer (mid-March to mid-October) and autumn/winter (the rest of the year). Gathering all available data on the two sites, the most important gaps in knowledge were identified with the help of sensitivity analyses: they concerned mainly the exports of material by grazing fish (such as mullet Liza ramada), resuspension of microphytobenthos, and fluxes linked to microfauna...
Tipo: Text Palavras-chave: Atlantic coast; Sensitivity analysis; Tidal flat; Inverse analysis; Steady state; Food web.
Ano: 2006 URL: http://archimer.ifremer.fr/doc/2006/publication-1863.pdf
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Genomic ecology of Marine Group II, the most common marine planktonic Archaea across the surface ocean ArchiMer
Pereira, Olivier; Hochart, Corentin; Auguet, Jean-christophe; Debroas, Didier; Galand, Pierre E..
Planktonic Archaea have been detected in all the world's oceans and are found from surface waters to the deep sea. The two most common Archaea phyla are Thaumarchaeota and Euryarchaeota. Euryarchaeota are generally more common in surface waters, but very little is known about their ecology and their potential metabolisms. In this study, we explore the genomic ecology of the Marine Group II (MGII), the main marine planktonic Euryarchaeota, and test if it is composed of different ecologically relevant units. We re‐analyzed Tara Oceans metagenomes from the photic layer and the deep ocean by annotating sequences against a custom MGII database and by mapping gene co‐occurrences. Our data provide a global view of the distribution of Euryarchaeota, and more...
Tipo: Text Palavras-chave: 16S rRNA; Euryarchaeota; Global ocean; Metagenomics; Poseidoniales; Proteorhodopsin.
Ano: 2019 URL: https://archimer.ifremer.fr/doc/00505/61676/65607.pdf
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Les virus de l'estuaire de la Charente el du bassin de Marennes-Oleron. Dynamiques spatio-temporelles et interactions avec les communautés bactériennes ArchiMer
Auguet, Jean-christophe.
This study is divided in two parts; one aim is to evaluate the in situ spalio-temporal dynamics of viral communities in the Charante estuary in order to define the appropriate seasons to conduct in vitro viral enrichment experiments. These experiments, that constitute the second part of this study, were performed to assess the impact of freshwater viruses carried by the Charante River on the dynamics and composition of coastal bacterial communities. With abundance ranging from 1.4 x 107 to 208 x I07 VLPml-1. viruses are the most abundant component among plankton microorganisms in surface waters of the Charente estuary. Thre temporal dynamics of this component reflects the indirect influence of temperature through the control of bacterial abundance,...
Tipo: Text Palavras-chave: Richesse spécifique; Composition clonale; Enrichissement vital; Infection lyrique; Structure des communautés; MET; PPGE; Dynamique temporelle; Gradient de salinité; Estuaire; Bactérioplancton; Virioplancton; Species richness; Clonal composition; Viral enrichment; Lytic infection; Community structure; Diversity; TEM; PEGE; Temporal dynamic; Gradient; Salinity; Estuary; Bacterioplankton; Virioplankton.
Ano: 2005 URL: http://archimer.ifremer.fr/doc/2005/these-3071.pdf
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Oyster hemolymph is a complex and dynamic ecosystem hosting bacteria, protists and viruses ArchiMer
Dupont, Samuel; Lokmer, A.; Corre, E.; Auguet, Jean-christophe; Petton, Bruno; Toulza, E.; Montagnani, Caroline; Tanguy, G.; Pecqueur, D.; Salmeron, C.; Guillou, L.; Desnues, C.; La Scola, B.; Bou Khalil, J.; De Lorgeril, Julien; Mitta, Guillaume; Gueguen, Yannick; Escoubas, Jean Michel.
Background The impact of the microbiota on host fitness has so far mainly been demonstrated for the bacterial microbiome. We know much less about host-associated protist and viral communities, largely due to technical issues. However, all microorganisms within a microbiome potentially interact with each other as well as with the host and the environment, therefore likely affecting the host health. Results We set out to explore how environmental and host factors shape the composition and diversity of bacterial, protist and viral microbial communities in the Pacific oyster hemolymph, both in health and disease. To do so, five oyster families differing in susceptibility to the Pacific oyster mortality syndrome were reared in hatchery and transplanted into a...
Tipo: Text Palavras-chave: Oyster genetic background; Hemolymph microbiota dynamics; Early-life microbiota; Trans-kingdom interactions; Crassostrea gigas; Within-host ecosystem.
Ano: 2020 URL: https://archimer.ifremer.fr/doc/00627/73916/73254.pdf
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Potential Effect of Freshwater Virus on the Structure and Activity of Bacterial Communities in the Marennes-Oléron Bay (France) ArchiMer
Auguet, Jean-christophe; Montanie, Helene; Hartmann, Hans; Lebaron, P.; Casamayor, E. O.; Catala, P.; Delmas, Daniel.
Batch culture experiments using viral enrichment were conducted to test the response of a coastal bacterial community to autochthonous (i.e., co-existing) or allochthonous riverine viruses. The effects of viral infections on bacterial dynamics and activity were assessed by epifluorescence microscopy and thymidine incorporation, respectively, whereas the effect of viral infection on bacterial community composition was examined by polymerase chain reaction-single strand conformation polymorphism 16S ribosomal RNA fingerprinting. The percentages of high nucleic acid-containing cells, evaluated by flow cytometry, were significantly correlated (r (2) = 0.91, n = 12, p < 0.0001) to bacterial production, making this value a good predictor of active cell...
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Ano: 2009 URL: http://archimer.ifremer.fr/doc/2009/publication-6636.pdf
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Response of Core Microbial Consortia to Chronic Hydrocarbon Contaminations in Coastal Sediment Habitats ArchiMer
Jeanbille, Mathilde; Gury, Jerome; Duran, Robert; Tronczynski, Jacek; Agogue, Helene; Ben Said, Olfa; Ghiglione, Jean-francois; Auguet, Jean-christophe.
Traditionally, microbial surveys investigating the effect of chronic anthropogenic pressure such as polyaromatic hydrocarbons (PAHs) contaminations consider just the alpha and beta diversity and ignore the interactions among the different taxa forming the microbial community. Here, we investigated the ecological relationships between the three domains of life (i.e., Bacteria, Archaea, and Eukarya) using 454 pyrosequencing on the 16S rRNA and 18S rRNA genes from chronically impacted and pristine sediments, along the coasts of the Mediterranean Sea (Gulf of Lion, Vermillion coast, Corsica, Bizerte lagoon and Lebanon) and the French Atlantic Ocean (Bay of Biscay and English Channel). Our approach provided a robust ecological framework for the partition of the...
Tipo: Text Palavras-chave: Co-occurrence network; Core community; Microbial consortia; PAH; Chronic contamination; Coastal sediment.
Ano: 2016 URL: https://archimer.ifremer.fr/doc/00355/46586/46394.pdf
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