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Auteur (up) Auguet, J.C.; Montanie, H.; Hartmann, H.J.; Lebaron, P.; Casamayor, E.O.; Catala, P.; Delmas, D.
Titre Potential effect of freshwater virus on the structure and activity of bacterial communities in the Marennes-Oleron Bay (France) Type Article scientifique
Année 2009 Publication Revue Abrégée Microb Ecol
Volume 57 Numéro 2 Pages 295-306
Mots-Clés 16S/genetics Seasons Seawater/microbiology/virology Viruses/*growth & development *Water Microbiology; Bacteria/genetics/*growth & development/*virology Biodiversity Colony Count; Bacterial/genetics France Fresh Water/virology Polymorphism; Microbial DNA Fingerprinting DNA; Ribosomal; Single-Stranded Conformational Population Dynamics RNA
Résumé 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 (r2=0.91, n=12, p<0.0001) to bacterial production, making this value a good predictor of active cell dynamics along the study. While confinement and temperature were the two principal experimental factors affecting bacterial community composition and dynamics, respectively, additions of freshwater viruses had significant effects on coastal bacterial communities. Thus, foreign viruses significantly reduced net bacterial population increase as compared to the enrichment treated with inactivated virus. Moreover, freshwater viruses recurrently and specifically affected bacterial community composition, as compared to addition of autochthonous viruses. In most cases, the combined treatment viruses and freshwater dissolved organic matter helped to maintain or even enhance species richness in coastal bacterial communities in agreement to the 'killing the winner' hypothesis. Thus, riverine virus input could potentially influence bacterial community composition of the coastal bay albeit with modest modification of bulk bacterial growth.
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Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1301
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Auteur (up) Auguet, J.C.; Nomokonova, N.; Camarero, L.; Casamayor, E.O.
Titre Seasonal changes of freshwater ammonia-oxidizing archaeal assemblages and nitrogen species in oligotrophic alpine lakes Type Article scientifique
Année 2011 Publication Revue Abrégée Appl Environ Microbiol
Volume 77 Numéro 6 Pages 1937-1945
Mots-Clés 16S/genetics Seasons Spain; Ammonia/*metabolism Archaea/classification/genetics/*metabolism Biodiversity Fresh Water Molecular Sequence Data Nitrogen/*metabolism Oxidoreductases/genetics Phylogeny Polymerase Chain Reaction RNA; Ribosomal
Résumé The annual changes in the composition and abundance of ammonia-oxidizing archaea (AOA) were analyzed monthly in surface waters of three high mountain lakes within the Limnological Observatory of the Pyrenees (LOOP; northeast Spain) using both 16S rRNA and functional (ammonia monooxygenase gene, amoA) gene sequencing as well as quantitative PCR amplification. The set of biological data was related to changes in nitrogen species and to other relevant environmental variables. The whole archaeal assemblage was dominated by phylotypes closely related to the crenarchaeal 1.1a group (58% +/- 18% of total 16S rRNA gene sequences), and consistent structural changes were detected during the study. Water temperature was the environmental variable that better explained spring, summer, and winter (ice-covered lakes) archaeal assemblage structure. The amoA gene was detected year round, and seasonal changes in amoA gene composition were well correlated with changes in the archaeal 16S rRNA gene pool. In addition, copy numbers of both the specific 1.1a group 16 rRNA and archaeal amoA genes were well correlated, suggesting that most freshwater 1.1a Crenarchaeota had the potential to carry out ammonia oxidation. Seasonal changes in the diversity and abundance of AOA (i.e., amoA) were better explained by temporal changes in ammonium, the substrate for nitrification, and mostly nitrite, the product of ammonia oxidation. Lacustrine amoA gene sequences grouped in coherent freshwater phylogenetic clusters, suggesting that freshwater habitats harbor typical amoA-containing ecotypes, which is different from soils and seas. We observed within the freshwater amoA gene sequence pool a high genetic divergence (translating to up to 32% amino acid divergence) between the spring and the remaining AOA assemblages. This suggests that different AOA ecotypes are adapted to different temporal ecological niches in these lakes.
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Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1304
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Auteur (up) Bachiller, E.; Albo-Puigserver, M.; Gimenez, J.; Grazia Pennino, M.; Mari-Mena, N.; Esteban, A.; Lloret-Lloret, E.; Jadaud, A.; Carro, B.; Maria Bellido, J.; Coll, M.
Titre A trophic latitudinal gradient revealed in anchovy and sardine from the Western Mediterranean Sea using a multi-proxy approach Type Article scientifique
Année 2020 Publication Revue Abrégée Sci Rep
Volume 10 Numéro 1 Pages 17598
Mots-Clés body condition; daily ration; diel feeding intensity; diversity; ecology; engraulis-encrasicolus l.; food-web; niche overlap; pilchardus; small pelagic fish
Résumé This work combines state-of-the-art methods (DNA metabarcoding) with classic approaches (visual stomach content characterization and stable isotope analyses of nitrogen (delta N-15) and carbon (delta C-13)) to investigate the trophic ecology of anchovy (Engraulis encrasicolus) and sardine (Sardina pilchardus) at high taxonomic and spatial resolution in the Western Mediterranean Sea. Gut contents observed are in accordance with the dietary plasticity generally described for anchovy and sardine, suggesting a diet related to the opportunistic ingestion of available prey in a certain area and/or time. Genetic tools also showed modest inter-specific differences regarding ingested species. However, inter-specific and intra-specific differences in ingested prey frequencies and prey biomass reflected a latitudinal signal that could indicate a more effective predation on large prey like krill by anchovy versus sardine, as well as a generalized higher large prey ingestion by both species southwards. In fact, both species presented lower delta N-15 in the northernmost area. This latitudinal gradient indicates changes in the trophic ecology of anchovy and sardine that coincide with previously described better biological conditions for fish in the southern part of the study area as well as higher landings of both species in recent years.
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ISSN 2045-2322 ISBN Médium
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Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2921
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Auteur (up) Bailleul, D.; Stoeckel, S.; Arnaud-Haond, S.
Titre RClone: a package to identify MultiLocus Clonal Lineages and handle clonal data sets in r Type Article scientifique
Année 2016 Publication Revue Abrégée Methods Ecol. Evol.
Volume 7 Numéro 8 Pages 966-970
Mots-Clés clonal diversity; clonality; clonal population; diversity; genotype; markers; multilocus genotypes; multilocus lineages; organisms; population-genetics; program; software; spatial autocorrelation
Résumé Partially, clonal species are common in the Tree of Life. And yet, population genetic models still mostly focus on the extremes: strictly sexual versus purely asexual reproduction. Here, we present an R package built upon genclone software including new functions and several improvements. The RClone package includes functions to handle clonal data sets, allowing (i) checking for data set reliability to discriminate multilocus genotypes (MLGs), (ii) ascertainment of MLG and semi-automatic determination of clonal lineages (MLL), (iii) genotypic richness and evenness indices calculation based on MLGs or MLLs and (iv) describing several spatial components of clonality. RClone allows the one-shot analysis of multipopulation data sets without size limitation, suitable for data sets now increasingly produced through next-generation sequencing. A major improvement compared to existing software is the ability to determine the threshold to cluster similar MLGs into MLLs, based on implemented simulations of sexual events. Several functions allow data importation, conversion and exportation with adegenet, Genetix or Arlequin. RClone is provided with two vignettes to handle analysis on one (RClonequickmanual) or several populations (RCloneqmsevpops).
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ISSN 2041-210x ISBN Médium
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Numéro d'Appel MARBEC @ alain.herve @ collection 1637
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Auteur (up) Bakker, J.; Wangensteen, O.S.; Chapman, D.D.; Boussarie, G.; Buddo, D.; Guttridge, T.L.; Hertler, H.; Mouillot, D.; Vigliola, L.; Mariani, S.
Titre Environmental DNA reveals tropical shark diversity in contrasting levels of anthropogenic impact Type Article scientifique
Année 2017 Publication Revue Abrégée Sci Rep
Volume 7 Numéro Pages 16886
Mots-Clés management; ecosystem; conservation; fish communities; rays; populations; collapse; aquatic biodiversity; coral-reef fisheries; wilderness
Résumé Sharks are charismatic predators that play a key role in most marine food webs. Their demonstrated vulnerability to exploitation has recently turned them into flagship species in ocean conservation. Yet, the assessment and monitoring of the distribution and abundance of such mobile species in marine environments remain challenging, often invasive and resource-intensive. Here we pilot a novel, rapid and non-invasive environmental DNA (eDNA) metabarcoding approach specifically targeted to infer shark presence, diversity and eDNA read abundance in tropical habitats. We identified at least 21 shark species, from both Caribbean and Pacific Coral Sea water samples, whose geographical patterns of diversity and read abundance coincide with geographical differences in levels of anthropogenic pressure and conservation effort. We demonstrate that eDNA metabarcoding can be effectively employed to study shark diversity. Further developments in this field have the potential to drastically enhance our ability to assess and monitor elusive oceanic predators, and lead to improved conservation strategies.
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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 2045-2322 ISBN Médium
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Numéro d'Appel MARBEC @ alain.herve @ collection 2244
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