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Auteur (up) Auguet, J.C.; Montanie, H.; Hartmann, H.J.; Lebaron, P.; Casamayor, E.O.; Catala, P.; Delmas, D. doi  openurl
  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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Auteur (up) Auguet, J.C.; Nomokonova, N.; Camarero, L.; Casamayor, E.O. doi  openurl
  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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Auteur (up) Bailleul, D.; Stoeckel, S.; Arnaud-Haond, S. doi  openurl
  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. doi  openurl
  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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  ISSN 2045-2322 ISBN Médium  
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  Numéro d'Appel MARBEC @ alain.herve @ collection 2244  
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Auteur (up) Barberan, A.; Fernandez-Guerra, A.; Auguet, J.C.; Galand, P.E.; Casamayor, E.O. doi  openurl
  Titre Phylogenetic ecology of widespread uncultured clades of the Kingdom Euryarchaeota Type Article scientifique
  Année 2011 Publication Revue Abrégée Mol Ecol  
  Volume 20 Numéro 9 Pages 1988-1996  
  Mots-Clés 16S/genetics Sequence Analysis; Biodiversity Databases; dna; Genetic *Ecosystem Environment Euryarchaeota/*classification/*genetics Genes; Ribosomal; rRNA/*genetics Phylogeny RNA  
  Résumé Despite its widespread distribution and high levels of phylogenetic diversity, microbes are poorly understood creatures. We applied a phylogenetic ecology approach in the Kingdom Euryarchaeota (Archaea) to gain insight into the environmental distribution and evolutionary history of one of the most ubiquitous and largely unknown microbial groups. We compiled 16S rRNA gene sequences from our own sequence libraries and public genetic databases for two of the most widespread mesophilic Euryarchaeota clades, Lake Dagow Sediment (LDS) and Rice Cluster-V (RC-V). The inferred population history indicated that both groups have undergone specific nonrandom evolution within environments, with several noteworthy habitat transition events. Remarkably, the LDS and RC-V groups had enormous levels of genetic diversity when compared with other microbial groups, and proliferation of sequences within each single clade was accompanied by significant ecological differentiation. Additionally, the freshwater Euryarchaeota counterparts unexpectedly showed high phylogenetic diversity, possibly promoted by their environmental adaptability and the heterogeneous nature of freshwater ecosystems. The temporal phylogenetic diversification pattern of these freshwater Euryarchaeota was concentrated both in early times and recently, similarly to other much less diverse but deeply sampled archaeal groups, further stressing that their genetic diversity is a function of environment plasticity. For the vast majority of living beings on Earth (i.e. the uncultured microorganisms), how they differ in the genetic or physiological traits used to exploit the environmental resources is largely unknown. Inferring population history from 16S rRNA gene-based molecular phylogenies under an ecological perspective may shed light on the intriguing relationships between lineage, environment, evolution and diversity in the microbial world.  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1305  
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