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Auteur (up) Amossé, J.; Bettarel, Y.; Bouvier, C.; Bouvier, T.; Tran Duc, T.; Doan Thu, T.; Jouquet, P.
Titre The flows of nitrogen, bacteria and viruses from the soil to water compartments are influenced by earthworm activity and organic fertilization (compost vs. vermicompost) Type Article scientifique
Année 2013 Publication Revue Abrégée Soil Biology & Biochemistry
Volume 66 Numéro Pages 197-203
Mots-Clés Bacterial and viral abundance; Bacterial diversity; Compost; Dichogaster bolaui; Earthworms; Leaching; Organic fertilization; Vermicompost
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ISSN 0038-0717 ISBN Médium
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Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 892
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Auteur (up) Aubé, J.; Senin, P.; Pringault, O.; Bonin, P.; Deflandre, B.; Bouchez, O.; Bru, N.; Biritxinaga-Etchart, E.; Klopp, C.; Guyoneaud, R.; Goñi-Urriza, M.
Titre The impact of long-term hydrocarbon exposure on the structure, activity, and biogeochemical functioning of microbial mats Type Article scientifique
Année 2016 Publication Revue Abrégée Marine Pollution Bulletin
Volume 111 Numéro 1 Pages 115-125
Mots-Clés Biogeochemical functioning; diversity; Hydrocarbonoclastic bacteria; Microbial mats
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ISSN 0025-326x ISBN Médium
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Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2155
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Auteur (up) Auguet, J.C.; Borrego, C.M.; Baneras, L.; Casamayor, E.O.
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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Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1299
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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.; 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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