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Auteur (up) Auguet, J.C.; Borrego, C.M.; Baneras, L.; Casamayor, E.O. doi  openurl
  Titre Fingerprinting the genetic diversity of the biotin carboxylase gene (accC) in aquatic ecosystems as a potential marker for studies of carbon dioxide assimilation in the dark Type Article scientifique
  Année 2008 Publication Revue Abrégée Environ Microbiol  
  Volume 10 Numéro 10 Pages 2527-2536  
  Mots-Clés Amino Acid Sequence Archaeal Proteins/genetics Bacterial Proteins/genetics Carbon Dioxide/*metabolism Carbon-Nitrogen Ligases/*genetics Cluster Analysis DNA Fingerprinting/*methods DNA Primers/genetics DNA; Archaeal/genetics DNA; Bacterial/genetics *Ecosystem Electrophoresis; DNA *Water Microbiology; Genetic Sequence Alignment Sequence Analysis; Polyacrylamide Gel Molecular Sequence Data Nucleic Acid Denaturation Phylogeny Polymerase Chain Reaction/methods *Polymorphism  
  Résumé We designed and tested a set of specific primers for specific PCR amplification of the biotin carboxylase subunit gene (accC) of the Acetyl CoA carboxylase (ACCase) enzyme. The primer set yielded a PCR product of c. 460 bp that was suitable for denaturing gradient gel electrophoresis (DGGE) fingerprinting followed by direct sequencing of excised DGGE bands and sequence analysis. Optimization of PCR conditions for selective amplification was carried out with pure cultures of different bacteria and archaea, and laboratory enrichments. Next, fingerprinting comparisons were done in several aerobic and anaerobic freshwater planktonic samples. The DGGE fingerprints showed between 2 and 19 bands in the different samples, and the primer set provided specific amplification in both pure cultures and natural samples. Most of the samples had sequences grouped with bacterial accC, hypothetically related to the anaplerotic fixation of inorganic carbon. Some other samples, however, yielded accC gene sequences that clustered with Crenarchaeota and were related to the 3-hydroxypropionate/4-hydroxybutyrate cycle of autotrophic crenarchaeota. Such samples came from oligotrophic high mountain lakes and the hypolimnia of a sulfide-rich lake, where crenarchaeotal populations had been previously reported by 16S rRNA surveys. This study provided a fast tool to look for presence of accC genes in natural environments as potential marker for studies of carbon dioxide assimilation in the dark. After further refinement for better specificity against archaea, the new and novel primers could be very helpful to establish a target for crenarchaeota with implications for our understanding of archaeal carbon biogeochemistry.  
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Auteur (up) Auguet, J.C.; Casamayor, E.O. doi  openurl
  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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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) Brauer, V.S.; Stomp, M.; Bouvier, T.; Fouilland, E.; Leboulanger, C.; Confurius-Guns, V.; Weissing, F.J.; Stal, L.J.; Huisman, J. url  doi
openurl 
  Titre Competition and facilitation between the marine nitrogen-fixing cyanobacteriunn Cyanothece and its associated bacterial community Type Article scientifique
  Année 2015 Publication Frontiers in Microbiology Revue Abrégée  
  Volume 5 Numéro Pages  
  Mots-Clés aerobic anoxygenic phototrophs; cyanobacteria; heterotrophic bacteria; microbiota; nitrogen fixation; Phytoplankton; resource competition; species interactions  
  Résumé N-2-fixing cyanobacteria represent a major source of new nitrogen and carbon for marine microbial communities, but little is known about their ecological interactions with associated microbiota. In this study we investigated the interactions between the unicellular N-2-fixing cyanobacterium Cyanothece sp. Miami BG043511 and its associated free-living chemotrophic bacteria at different concentrations of nitrate and dissolved organic carbon and different temperatures. High temperature strongly stimulated the growth of Cyanothece, but had less effect on the growth and community composition of the chemotrophic bacteria. Conversely, nitrate and carbon addition did not significantly increase the abundance of Cyanothece, but strongly affected the abundance and species composition of the associated chemotrophic bacteria. In nitrate-free medium the associated bacterial community was co-dominated by the putative diazotroph Mesorhizobium and the putative aerobic anoxygenic phototroph Erythrobacter and after addition of organic carbon also by the Flavobacterium Muricauda. Addition of nitrate shifted the composition toward co-dominance by Erythrobacter and the Gammaproteobacterium Marinobacter. Our results indicate that Cyanothece modified the species composition of its associated bacteria through a combination of competition and facilitation. Furthermore, within the bacterial community, niche differentiation appeared to play an important role, contributing to the coexistence of a variety of different functional groups. An important implication of these findings is that changes in nitrogen and carbon availability due to, e.g., eutrophication and climate change are likely to have a major impact on the species composition of the bacterial community associated with N-2-fixing cyanobacteria.  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1101  
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Auteur (up) Brauer, V.S.; Stomp, M.; Rosso, C.; van Beusekom, S.A.M.; Emmerich, B.; Stal, L.J.; Huisman, J. url  doi
openurl 
  Titre Low temperature delays timing and enhances the cost of nitrogen fixation in the unicellular cyanobacterium Cyanothece Type Article scientifique
  Année 2013 Publication Revue Abrégée The ISME journal  
  Volume 7 Numéro 11 Pages 2105-2115  
  Mots-Clés climate change; day-night cycle; nitrogen fixation; nitrogenase; respiration; unicellular cyanobacteria  
  Résumé Marine nitrogen-fixing cyanobacteria are largely confined to the tropical and subtropical ocean. It has been argued that their global biogeographical distribution reflects the physiologically feasible temperature range at which they can perform nitrogen fixation. In this study we refine this line of argumentation for the globally important group of unicellular diazotrophic cyanobacteria, and pose the following two hypotheses: (i) nitrogen fixation is limited by nitrogenase activity at low temperature and by oxygen diffusion at high temperature, which is manifested by a shift from strong to weak temperature dependence of nitrogenase activity, and (ii) high respiration rates are required to maintain very low levels of oxygen for nitrogenase, which results in enhanced respiratory cost per molecule of fixed nitrogen at low temperature. We tested these hypotheses in laboratory experiments with the unicellular cyanobacterium Cyanothece sp. BG043511. In line with the first hypothesis, the specific growth rate increased strongly with temperature from 18 to 30 degrees C, but leveled off at higher temperature under nitrogen-fixing conditions. As predicted by the second hypothesis, the respiratory cost of nitrogen fixation and also the cellular C:N ratio rose sharply at temperatures below 21 degrees C. In addition, we found that low temperature caused a strong delay in the onset of the nocturnal nitrogenase activity, which shortened the remaining nighttime available for nitrogen fixation. Together, these results point at a lower temperature limit for unicellular nitrogen-fixing cyanobacteria, which offers an explanation for their (sub)tropical distribution and suggests expansion of their biogeographical range by global warming.  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 696  
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