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Auteur (up) Auguet, J.C.; Barberan, A.; Casamayor, E.O.
Titre Global ecological patterns in uncultured Archaea Type Article scientifique
Année 2010 Publication Revue Abrégée Isme J
Volume 4 Numéro 2 Pages 182-190
Mots-Clés 16S/genetics; Archaea/classification/genetics/*physiology DNA; Ribosomal; Ribosomal/genetics *Ecosystem Multivariate Analysis Phylogeny Plankton/classification/genetics RNA; Ribosomal/genetics RNA
Résumé We have applied a global analytical approach to uncultured Archaea that for the first time reveals well-defined community patterns along broad environmental gradients and habitat types. Phylogenetic patterns and the environmental factors governing the creation and maintenance of these patterns were analyzed for c. 2000 archaeal 16S rRNA gene sequences from 67 globally distributed studies. The sequences were dereplicated at 97% identity, grouped into seven habitat types, and analyzed with both Unifrac (to explore shared phylogenetic history) and multivariate regression tree (that considers the relative abundance of the lineages or taxa) approaches. Both phylogenetic and taxon-based approaches showed salinity and not temperature as one of the principal driving forces at the global scale. Hydrothermal vents and planktonic freshwater habitats emerged as the largest reservoirs of archaeal diversity and consequently are promising environments for the discovery of new archaeal lineages. Conversely, soils were more phylogenetically clustered and archaeal diversity was the result of a high number of closely related phylotypes rather than different lineages. Applying the ecological concept of 'indicator species', we detected up to 13 indicator archaeal lineages for the seven habitats prospected. Some of these lineages (that is, hypersaline MSBL1, marine sediment FCG1 and freshwater plSA1), for which ecological importance has remained unseen to date, deserve further attention as they represent potential key archaeal groups in terms of distribution and ecological processes. Hydrothermal vents held the highest number of indicator lineages, suggesting it would be the earliest habitat colonized by Archaea. Overall, our approach provided ecological support for the often arbitrary nomenclature within uncultured Archaea, as well as phylogeographical clues on key ecological and evolutionary aspects of archaeal biology.
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Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1302
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Auteur (up) Auguet, J.C.; Casamayor, E.O.
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 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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Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1300
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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) Aumont, O.; Maury, O.; Lefort, S.; Bopp, L.
Titre Evaluating the Potential Impacts of the Diurnal Vertical Migration by Marine Organisms on Marine Biogeochemistry Type Article scientifique
Année 2018 Publication Revue Abrégée Global Biogeochemical Cycles
Volume 32 Numéro 11 Pages 1622-1643
Mots-Clés ecosystem; ocean; biogeochemistry; export; carbon cycle; diurnal vertical migration
Résumé Diurnal vertical migration (DVM) of marine organisms is an ubiquitous phenomenon in the ocean that generates an active vertical transport of organic matter. However, the magnitude and consequences of this flux are largely unknown and are currently overlooked in ocean biogeochemical models. Here we present a global model of pelagic ecosystems based on the ocean biogeochemical model NEMO-PISCES that is fully coupled to the upper trophic levels model Apex Predators ECOSystem Model, which includes an explicit description of migrating organisms. Evaluation of the model behavior proved to be challenging due to the scarcity of suitable observations. Nevertheless, the model appears to be able to simulate approximately both the migration depth and the relative biomass of migrating organisms. About one third of the epipelagic biomass is predicted to perform DVM. The flux of carbon driven by DVM is estimated to be 1.05 ± 0.15 PgC/year, about 18% of the passive flux of carbon due to sinking particles at 150 m. Comparison with local studies suggests that the model captures the correct magnitude of this flux. Oxygen is decreased in the mesopelagic domain by about 5 mmol?m?3 relative to simulations of an ocean without DVM. Our study concludes that DVM drives a significant and very efficient flux of carbon to the mesopelagic domain, similar in magnitude to the transport of DOC. Relative to a model run without DVM, the consequences of this flux seem to be quite modest on oxygen, due to compensating effects between DVM and passive fluxes.
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Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2458
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