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Auteur (up) Restrepo-Ortiz, C.X.; Merbt, S.N.; Barrero-Canossa, J.; Fuchs, B.M.; Casamayor, E.O. doi  openurl
  Titre Development of a 16S rRNA-targeted fluorescence in situ hybridization probe for quantification of the ammonia-oxidizer Nitrosotalea devanaterra and its relatives Type Article scientifique
  Année 2018 Publication Revue Abrégée Syst. Appl. Microbiol.  
  Volume 41 Numéro 4 Pages 408-413  
  Mots-Clés Ammonia oxidizing; archaea; bacteria; card-fish; catalyzed reporter deposition; cells; crenarchaeota; environments; high-mountain lakes; identification; Nitrosotalea devanaterra; oligonucleotide probes; SAGMCG-1 Group; Soil; thaumarchaeota; Thaumarchaeota  
  Résumé The Thaumarchaeota SAGMCG-1 group and, in particular, members of the genus Nitrosotalea have high occurrence in acidic soils, the rhizosphere, groundwater and oligotrophic lakes, and play a potential role in nitrogen cycling. In this study, the specific oligonucleotide fluorescence in situ hybridization probe SAG357 was designed for this Thaumarchaeota group based on the available 16S rRNA gene sequences in databases, and included the ammonia-oxidizing species Nitrosotalea devanaterra. Cell permeabilization for catalyzed reporter deposition fluorescence in situ detection and the hybridization conditions were optimized on enrichment cultures of the target species N. devanaterra, as well as the non-target ammonia-oxidizing archaeon Nitrosopumilus maritimus. Probe specificity was improved with a competitor oligonucleotide, and fluorescence intensity and cell visualization were enhanced by the design and application of two adjacent helpers. Probe performance was tested in soil samples along a pH gradient, and counting results matched the expected in situ distributions. Probe SAG357 and the CARD-FISH protocol developed in the present study will help to improve the current understanding of the ecology and physiology of N. devanaterra and its relatives in natural environments. (C) 2018 Elsevier GmbH. All rights reserved.  
  Auteur institutionnel Thèse  
  Editeur Lieu de Publication Éditeur  
  Langue English Langue du Résumé Titre Original  
  Éditeur de collection Titre de collection Titre de collection Abrégé  
  Volume de collection Numéro de collection Edition  
  ISSN 0723-2020 ISBN Médium  
  Région Expédition Conférence  
  Notes Approuvé pas de  
  Numéro d'Appel MARBEC @ alain.herve @ collection 2393  
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