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Auteur Lliros, M.; Gich, F.; Plasencia, A.; Auguet, J.C.; Darchambeau, F.; Casamayor, E.O.; Descy, J.P.; Borrego, C. doi  openurl
  Titre Vertical distribution of ammonia-oxidizing crenarchaeota and methanogens in the epipelagic waters of Lake Kivu (Rwanda-Democratic Republic of the Congo) Type Article scientifique
  Année 2010 Publication Revue Abrégée Appl Environ Microbiol  
  Volume 76 Numéro 20 Pages 6853-6863  
  Mots-Clés (up) 16S/genetics Sequence Analysis; Ammonia/*metabolism Animals *Biodiversity Cluster Analysis Crenarchaeota/*classification/genetics/isolation & purification/*metabolism DNA Fingerprinting DNA; Archaeal/chemistry/genetics DNA; Archaeal/genetics RNA; DNA Sequence Homology; Fluorescence Methane/*metabolism Molecular Sequence Data Nucleic Acid Denaturation Oxidation-Reduction Phylogeny Polymerase Chain Reaction RNA; Nucleic Acid *Water Microbiology; Polyacrylamide Gel Genes; Ribosomal; Ribosomal/chemistry/genetics Democratic Republic of the Congo Electrophoresis; rRNA In Situ Hybridization  
  Résumé Four stratified basins in Lake Kivu (Rwanda-Democratic Republic of the Congo) were sampled in March 2007 to investigate the abundance, distribution, and potential biogeochemical role of planktonic archaea. We used fluorescence in situ hybridization with catalyzed-reported deposition microscopic counts (CARD-FISH), denaturing gradient gel electrophoresis (DGGE) fingerprinting, and quantitative PCR (qPCR) of signature genes for ammonia-oxidizing archaea (16S rRNA for marine Crenarchaeota group 1.1a [MCG1] and ammonia monooxygenase subunit A [amoA]). Abundance of archaea ranged from 1 to 4.5% of total DAPI (4',6-diamidino-2-phenylindole) counts with maximal concentrations at the oxic-anoxic transition zone ( approximately 50-m depth). Phylogenetic analysis of the archaeal planktonic community revealed a higher level of richness of crenarchaeal 16S rRNA gene sequences (21 of the 28 operational taxonomic units [OTUs] identified [75%]) over euryarchaeotal ones (7 OTUs). Sequences affiliated with the kingdom Euryarchaeota were mainly recovered from the anoxic water compartment and mostly grouped into methanogenic lineages (Methanosarcinales and Methanocellales). In turn, crenarchaeal phylotypes were recovered throughout the sampled epipelagic waters (0- to 100-m depth), with clear phylogenetic segregation along the transition from oxic to anoxic water masses. Thus, whereas in the anoxic hypolimnion crenarchaeotal OTUs were mainly assigned to the miscellaneous crenarchaeotic group, the OTUs from the oxic-anoxic transition and above belonged to Crenarchaeota groups 1.1a and 1.1b, two lineages containing most of the ammonia-oxidizing representatives known so far. The concomitant vertical distribution of both nitrite and nitrate maxima and the copy numbers of both MCG1 16S rRNA and amoA genes suggest the potential implication of Crenarchaeota in nitrification processes occurring in the epilimnetic waters of the lake.  
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Auteur 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 (up) 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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Auteur Auguet, J.C.; Casamayor, E.O. doi  openurl
  Titre A hotspot for cold crenarchaeota in the neuston of high mountain lakes Type Article scientifique
  Année 2008 Publication Revue Abrégée Environ Microbiol  
  Volume 10 Numéro 4 Pages 1080-1086  
  Mots-Clés (up) 16S/genetics Spain *Water Microbiology; Archaeal/genetics RNA; Biodiversity Crenarchaeota/*classification/genetics/*isolation & purification Fresh Water/*microbiology In Situ Hybridization; Fluorescence Indoles Phylogeny RNA; Ribosomal  
  Résumé We have surveyed the first 1 m of 10 oligotrophic high mountain lakes in the Central Pyrenees (Spain) for both abundance and predominant phylotypes richness of the archaeaplankton assemblage, using CARD-FISH and 16S rRNA gene sequencing respectively. Archaea inhabiting the air-water surface microlayer (neuston) ranged between 3% and 37% of total 4,6-diamidino-2-phenylindole (DAPI) counts and were mainly Crenarchaeota of a new freshwater cluster distantly related to the Marine Group 1.1a. Conversely, most of the Archaea from the underlying waters (the remaining first 1 m integrated) were mainly Euryarchaeota of three distantly related branches ranging between 0.4% and 27% of total DAPI counts. Therefore, a consistent qualitative and quantitative spatial segregation was observed for the two main archaeal phyla between neuston and underlying waters at a regional scale. We also observed a consistent pattern along the lakes surveyed between lake area, lake depth and water residence time, and the archaeal enrichment in the neuston: the larger the lake the higher the proportion of archaea in the neuston as compared with abundances from the underlying waters (n = 10 lakes; R(2) > 0.80; P < 0.001, in all three cases). This is the first report identifying a widespread non-thermophilic habitat where freshwater planktonic Crenarchaeota can be found naturally enriched. High mountain lakes offer great research opportunities to explore the ecology of one of the most enigmatic and far from being understood group of prokaryotes.  
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Auteur Carteron, A.; Jeanmougin, M.; Leprieur, F.; Spatharis, S. url  doi
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  Titre Assessing the efficiency of clustering algorithms and goodness-of-fit measures using phytoplankton field data Type Article scientifique
  Année 2012 Publication Revue Abrégée Ecol. Inform.  
  Volume 9 Numéro Pages 64-68  
  Mots-Clés (up) 2-norm; Beta diversity; Cophenetic correlation coefficient; Dendrogram; Upgma; Ward's algorithm; beta-diversity; blooms; classification; communities; cophenetic correlation; environment; forest; functional diversity; som  
  Résumé Investigation of patterns in beta diversity has received increased attention over the last years particularly in light of new ecological theories such as the metapopulation paradigm and metacommunity theory. Traditionally, beta diversity patterns can be described by cluster analysis (i.e. dendrograms) that enables the classification of samples. Clustering algorithms define the structure of dendrograms, consequently assessing their performance is crucial. A common, although not always appropriate approach for assessing algorithm suitability is the cophenetic correlation coefficient c. Alternatively the 2-norm has been recently proposed as an increasingly informative method for evaluating the distortion engendered by clustering algorithms. In the present work, the 2-norm is applied for the first time on field data and is compared with the cophenetic correlation coefficient using a set of 105 pairwise combinations of 7 clustering methods (e.g. UPGMA) and 15 (dis)similarity/distance indices (e.g. Jaccard index). In contrast to the 2-norm, cophenetic correlation coefficient does not provide a clear indication on the efficiency of the clustering algorithms for all combinations. The two approaches were not always in agreement in the choice of the most faithful algorithm. Additionally, the 2-norm revealed that UPGMA is the most efficient clustering algorithm and Ward's the least. The present results suggest that goodness-of-fit measures such as the 2-norm should be applied prior to clustering analyses for reliable beta diversity measures. (C) 2012 Elsevier B.V. All rights reserved.  
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Auteur Cocquempot, L.; Delacourt, C.; Paillet, J.; Riou, P.; Aucan, J.; Castelle, B.; Charria, G.; Claudet, J.; Conan, P.; Coppola, L.; Hocdé, R.; Planes, S.; Raimbault, P.; Savoye, N.; Testut, L.; Vuillemin, R. doi  openurl
  Titre Coastal Ocean and Nearshore Observation: A French Case Study Type Article scientifique
  Année 2019 Publication Revue Abrégée Front. Mar. Sci.  
  Volume 6 Numéro Pages Unsp-324  
  Mots-Clés (up) 2013/2014 winter; atlantic coast; coastal ocean; coastline; diversity; ecosystem; increases; interdisciplinary; national structuration; nutrient ratios; observation infrastructure; phytoplankton community; temperature; variability; wave activity  
  Résumé To understand and predict the physical, chemical, and biological processes at play in coastal and nearshore marine areas requires an integrated, interdisciplinary approach. The case study of the French structuration of coastal ocean and nearshore observing systems provides an original overview on a federative research infrastructure named ILICO. It is a notable example of national structuration and pan-institution efforts to investigate the forefront of knowledge on the processes at work within the critical coastal zone. ILICO comprises, in a pluridisciplinary approach, eight distributed network-systems of observation and data analysis that are accredited and financially supported by French research institutions and the French Ministry for Higher Education, Research, and Innovation. ILICO observation points are implemented along metropolitan and overseas French coasts, where coastline dynamics, sea level evolution, physical and biogeochemical water properties, coastal water dynamics, phytoplankton composition, and health of coral reefs are monitored in order to address a wide range of scientific questions. To give an overview of the diversity and potential of the observations carried out, this paper offers a detailed presentation of three constituting networks: Service Observation en Milieu LITtoral (SOMLIT), with homogeneous sampling strategies, DYNALIT, with heterogeneous sampling strategies adapted to different environments, and Mediterranean Ocean Observing System for the Environment (MOOSE), an integrated, pluri-disciplinary coasta/offshore regional observatory in the north-western Mediterranean Sea. ILICO was conceived using a European framework. It addresses the great challenges of the next decade in terms of sustainability, cost-efficiency, interoperability, and innovation. This paper emphasizes the added-value of federating these systems, and highlights some recommendations for the future.  
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