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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 Partitioning of Thaumarchaeota populations along environmental gradients in high mountain lakes Type Article scientifique
Année 2013 Publication Revue Abrégée FEMS Microbiology Ecology
Volume 84 Numéro 1 Pages 154-164
Mots-Clés amoA gene Euryarchaeota Freshwater Nitrogen Plankton SAGMGC
Résumé We investigated the spatial distribution and diversity of ammonia-oxidizing Archaea (AOA) across gradients of pH, trophic status and altitude in a set of high mountain lakes (Limnological Observatory of the Pyrenees, north-east Spain). Both phylogeny- and taxonomy-based approaches revealed well-defined AOA community patterns with pH as the main potential driving environmental factor. The I.1a and SAGMGC-1 Thaumarchaeota clusters, and their potentially associated amoA gene variants (clusters Fresh 5 and Soil/Fresh 1, respectively) showed highest relative abundances in the most oligotrophic lakes. Euryarchaeota (i.e. HV-Fresh cluster, Methanomicrobiales and Thermoplasmatales) dominated in lakes with higher trophic status. Phylogenetic diversity (PD) in Pyrenean lakes was 1.5- to 2.3-fold higher than the PD from an equivalent number of globally distributed marine and soil sites. We observed segregated distributions for SAGMGC-1, preferentially distributed in the lakes with the lowest pH (< 5) and the highest nitrite concentration (> 0.12 μm), and I.1a in lakes with lower nitrite and dissolved organic carbon concentrations below 0.5 mg L-1. Overall, these results showed strong selection by local environmental conditions, unveiled new ecological niches for freshwater SAGMGC-1 in low pH oligotrophic lakes, and suggested specific and successful adaptations of planktonic archaea to the high mountain lakes landscape. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.
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Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1309
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Auteur (up) Auguet, J.C.; Montanie, H.; Delmas, D.; Hartmann, H.J.; Huet, V.
Titre Dynamic of virioplankton abundance and its environmental control in the Charente estuary (France) Type Article scientifique
Année 2005 Publication Revue Abrégée Microb Ecol
Volume 50 Numéro 3 Pages 337-349
Mots-Clés Bacteria/isolation & purification Ecosystem *Environment; Controlled France Plankton/*isolation & purification Rivers/chemistry/*microbiology Seasons Viruses/*isolation & purification Water Microbiology
Résumé The Charente River provides nutrient- and virus-rich freshwater input to the Marennes Oleron Basin, the largest oyster-producing region in Europe. To evaluate virioplankton distribution in the Charente Estuary and identify which environmental variables control dynamic of virioplankton abundance, five stations defined by a salinity gradient (0-0.5, 0.6-5, 13-17, 20-24, and higher than 30 PSU) were surveyed over a year. Viral abundance was related to bacterioplankton abundance and activities, photosynthetic pigments, nutrient concentration, and physical parameters (temperature and salinity). On a spatial scale, virus displayed a decreasing pattern seaward with abundance ranging over the sampling period from 1.4x10(7) to 20.8x10(7) viruses mL-1 making virioplankton the most abundant component of planktonic microorganisms in the Charente Estuary. A good correlation was found between viral and bacterial abundance (rs=0.85). Furthermore, bacterial abundance was the most important predictor of viral abundance explaining alone between 66% (winter) and 76% (summer) of viral variability. However, no relation existed between viral abundance and chlorophyll a. Temporal variations in viral distributions were mainly controlled by temperature through the control of bacterial dynamics. Spatial variations of viral abundance were influenced by hydrodynamic conditions especially during the winter season where virioplankton distribution was entirely driven by mixing processes.
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Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1296
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Auteur (up) Auguet, J.C.; Montanie, H.; Lebaron, P.
Titre Structure of virioplankton in the Charente Estuary (France): transmission electron microscopy versus pulsed field gel electrophoresis Type Article scientifique
Année 2006 Publication Revue Abrégée Microb Ecol
Volume 51 Numéro 2 Pages 197-208
Mots-Clés Capsid/chemistry *Electrophoresis; Electron Plankton Rivers/*virology Seasons Seawater/*microbiology/*virology Viruses/genetics/*isolation & purification/ultrastructure *Water Microbiology; Gel; Pulsed-Field Environmental Monitoring/methods France Genome; Viral/genetics *Microscopy
Résumé Changes in the composition of viral communities were investigated along a salinity gradient and at different times by means of transmission electron microscopy (TEM) and pulsed field gel electrophoresis (PFGE). Samples were collected in fresh (Charente River), estuarine (Charente Estuary), and coastal (Pertuis d'Antioche, French Atlantic coast) waters. Both methods revealed similar patterns in viral community structure with a dominance of small viral particles (capsid and genome size). Viruses with a head size below 65 nm made up 71 +/- 5% of total virus-like particles, and virus-like genomes (VLG) below 100 kb accounted for 89 +/- 9% of total VLG. Despite this apparent stability of virioplankton composition over spatial scale (salinity gradient), the occurrence of large viruses (capsid and genome size) in estuarine and seawater samples indicated the presence of viral populations specific to a geographical location. Temporal changes in the structure (capsid and genome size) of viral communities were more pronounced than those reported at the spatial scale. From January to May 2003, seasonal changes in viral abundance and bacterial production occurred concomitantly with an increase in viral genomic diversity (richness), suggesting that virioplankton composition was strongly linked to changes in microbial activity and/or in the structure of the host communities. Although PFGE and TEM yielded complementary results in the description of virioplankton structures, it seems that the use of PFGE alone should be enough for the monitoring of community changes.
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Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1297
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Auteur (up) Ayon, P.; Swartzman, G.; Espinoza, P.; Bertrand, A.
Titre Long-term changes in zooplankton size distribution in the Peruvian Humboldt Current System : conditions favouring sardine or anchovy Type Article scientifique
Année 2011 Publication Revue Abrégée Marine Ecology. Progress Series
Volume 422 Numéro Pages 211-222
Mots-Clés abundance; anchovy; Current; dominance; energetics; Euphausiids; Feeding; Humboldt; Sardine; size; System; Zooplankton
Résumé Changes in the size distribution of zooplankton in the Humboldt Current System have been hypothesized to underlie observed changes in sardine and anchovy populations, the dominant pelagic fish species. To examine this hypothesis, the size distribution of over 15 000 zooplankton data samples collected since the 1960s was qualitatively determined. Dominance of each size group of zooplankton (small, medium and large) and of euphausiids was modelled using generalized additive models as a function of year, latitude, time of day, distance from the 200 m isobath (a surrogate for on-shelf versus off-shelf), sea surface temperature and salinity. The temporal (yr) pattern for euphausiid dominance was highly cross-correlated (i.e. was in phase) with the time series for estimated biomass of anchovy, and small zooplankton dominance with that for estimated sardine biomass. This supports the focal hypothesis based on feeding-energetic experiments, which showed energetic advantages to sardine filter feeding on smaller zooplankton and to anchovy bite feeding on larger copepods and euphausiids. Although euphausiids predominate offshore from the shelf break, anchovy biomass is generally highest on the shelf, suggesting a possible mismatch between anchovy feeding and euphausiid dominance. However, evidence concerning the offshore expansion of the anchovy range in cooler conditions, where both anchovy and euphausiids predominate, somewhat alleviates this apparent contradiction. A strong diel component to euphausiids and large zooplankton indicated diel migration for these zooplankton groups. That anchovy will preferentially eat euphausiids when they are more available (i.e. during the night and offshore) is supported by anchovy diet data.
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Numéro d'Appel LL @ pixluser @ collection 117
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