bascule de visibilité Search & Display Options

Tout Sélectionner    Désélectionner
 |   | 
Détails
   print
  Enregistrements Liens
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 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.  
  Adresse  
  Auteur institutionnel Thèse (up)  
  Editeur Lieu de Publication Éditeur  
  Langue Langue du Résumé Titre Original  
  Éditeur de collection Titre de collection Titre de collection Abrégé  
  Volume de collection Numéro de collection Edition  
  ISSN ISBN Médium  
  Région Expédition Conférence  
  Notes Approuvé pas de  
  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1303  
Lien permanent pour cet enregistrement
 

 
Auteur 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.  
  Adresse  
  Auteur institutionnel Thèse (up)  
  Editeur Lieu de Publication Éditeur  
  Langue Langue du Résumé Titre Original  
  Éditeur de collection Titre de collection Titre de collection Abrégé  
  Volume de collection Numéro de collection Edition  
  ISSN ISBN Médium  
  Région Expédition Conférence  
  Notes Approuvé pas de  
  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1304  
Lien permanent pour cet enregistrement
 

 
Auteur Misson, B.; Garnier, C.; Lauga, B.; Dang, D.H.; Ghiglione, J.-F.; Mullot, J.-U.; Duran, R.; Pringault, O. url  doi
openurl 
  Titre Chemical multi-contamination drives benthic prokaryotic diversity in the anthropized Toulon Bay Type Article scientifique
  Année 2016 Publication Revue Abrégée Science of The Total Environment  
  Volume 556 Numéro Pages 319-329  
  Mots-Clés Marine sediment; Microbial ecotoxicology; Multi-contamination; Prokaryotic diversity  
  Résumé Investigating the impact of human activities on marine coastal ecosystems remains difficult because of the co-occurrence of numerous natural and human-induced gradients. Our aims were (i) to evaluate the links between the chemical environment as a whole and microbial diversity in the benthic compartment, and (ii) to compare the contributions of anthropogenic and natural chemical gradients to microbial diversity shifts. We studied surface sediments from 54 sampling sites in the semi-enclosed Toulon Bay (NW Mediterranean) exposed to high anthropogenic pressure. Previously published chemical data were completed by new measurements, resulting in an in depth geochemical characterization by 29 representative environmental variables. Bacterial and archaeal diversity was assessed by terminal restriction fragment length polymorphism profiling on a selection of samples distributed along chemical gradients. Multivariate statistical analyses explained from 45% to 80% of the spatial variation in microbial diversity, considering only the chemical variables. A selection of trace metals of anthropogenic origin appeared to be strong structural factors for both bacterial and archaeal communities. Bacterial terminal restriction fragment (T-RF) richness correlated strongly with both anthropogenic and natural chemical gradients, whereas archaeal T-RF richness demonstrated fewer links with chemical variables. No significant decrease in diversity was evidenced in relation to chemical contamination, suggesting a high adaptive potential of benthic microbial communities in Toulon Bay.  
  Adresse  
  Auteur institutionnel Thèse (up)  
  Editeur Lieu de Publication Éditeur  
  Langue Langue du Résumé Titre Original  
  Éditeur de collection Titre de collection Titre de collection Abrégé  
  Volume de collection Numéro de collection Edition  
  ISSN 0048-9697 ISBN Médium  
  Région Expédition Conférence  
  Notes Approuvé pas de  
  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1560  
Lien permanent pour cet enregistrement
 

 
Auteur Alves-Júnior, F.D.A.; Silva, E.D.S.; Araújo, M.D.S.L.C.D.; Cardoso, I.; Bertrand, A.; Souza-Filho, J.F. url  doi
openurl 
  Titre Taxonomy of deep-sea shrimps of the Superfamily Oplophoroidea Dana 1852 (Decapoda: Caridea) from Southwestern Atlantic Type Article scientifique
  Année 2019 Publication Revue Abrégée Zootaxa  
  Volume 4613 Numéro 3 Pages 401-442  
  Mots-Clés Crustacea; Acanthephyridae; New Records; bathypelagic shrimps; deep waters; deep-sea biodiversity; Northeastern Brazil; Oplophoridae  
  Résumé In this paper, we provide some available information about the occurrence and some taxonomic aspects of 19 species from the Superfamily Oplophoroidea in the southwestern Atlantic (Brazilian waters), with the update to 22 species of Oplophoroidea occurring in Brazilian waters. Samples were collected during two sets of surveys. The first was performed in 2009 and 2011 in the Potiguar Basin in northeast of Brazil (03–05°S; 38–35°W; between the States of Ceará and Rio Grande do Norte) under the framework of the project “Avaliação da biota bentônica e planctônica da Bacia Potiguar e Ceará (Bpot)”, with samples collected from bottom trawls in the continental slope at depth ranging from 150–2068 m. Second, under the in the framework of the ABRACOS (Acoustic along the Brazilian coast), performed in 2015 and 2017 on seamounts and offshore areas in Northeast Brazil (Ceará Chain, Rio Grande do Norte and Rocas Atoll, Fernando de Noronha Archipelago and Pernambuco State), with samples with pelagic micronekton and mesopelagic nets, in depths ranging from 50–1260 m. We highlight the occurrence of 14 species of the family Acanthephyridae and 5 species of the family Oplophoridae, including the first occurrences of five species to Brazilian deep waters: Acanthephyra kingsleyi Spence Bate, 1888, Ephyrina ombango Crosnier & Forest, 1973, Meningodora compsa (Chace, 1940), M. longisulca Kikuchi, 1985 and Systellapsis curvispina Crosnier, 1987. These records increase the knowledge on deep-sea shrimps occurring in Southwestern Atlantic.  
  Adresse  
  Auteur institutionnel Thèse (up)  
  Editeur Lieu de Publication Éditeur  
  Langue en Langue du Résumé Titre Original  
  Éditeur de collection Titre de collection Titre de collection Abrégé  
  Volume de collection Numéro de collection Edition  
  ISSN 1175-5334 ISBN Médium  
  Région Expédition Conférence  
  Notes Approuvé pas de  
  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2584  
Lien permanent pour cet enregistrement
 

 
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 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.  
  Adresse  
  Auteur institutionnel Thèse (up)  
  Editeur Lieu de Publication Éditeur  
  Langue Langue du Résumé Titre Original  
  Éditeur de collection Titre de collection Titre de collection Abrégé  
  Volume de collection Numéro de collection Edition  
  ISSN ISBN Médium  
  Région Expédition Conférence  
  Notes Approuvé pas de  
  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1305  
Lien permanent pour cet enregistrement
Tout Sélectionner    Désélectionner
 |   | 
Détails
   print

Save Citations:
Export Records: