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Auteur (up) Thomas, F.; Dittami, S.M.; Brunet, M.; Le Duff, N.; Tanguy, G.; Leblanc, C.; Gobet, A. doi  openurl
  Titre Evaluation of a new primer combination to minimize plastid contamination in 16S rDNA metabarcoding analyses of alga-associated bacterial communities Type Article scientifique
  Année Publication Revue Abrégée Environ. Microbiol. Rep.  
  Volume Numéro Pages  
  Mots-Clés diversity; phylogenetic analysis; ribosomal-rna sequences; surfaces  
  Résumé Plant- and alga-associated bacterial communities are generally described via 16S rDNA metabarcoding using universal primers. As plastid genomes encode 16S rDNA related to cyanobacteria, these data sets frequently contain >90% plastidial sequences, and the bacterial diversity may be under-sampled. To overcome this limitation we evaluated in silico the taxonomic coverage for four primer combinations targeting the 16S rDNA V3-V4 region. They included a forward primer universal to Bacteria (S-D-Bact-0341-b-S-17) and four reverse primers designed to avoid plastid DNA amplification. The best primer combination (NOCHL) was compared to the universal primer set in the wet lab using a synthetic community and samples from three macroalgal species. The proportion of plastid sequences was reduced by 99%-100% with the NOCHL primers compared to the universal primers, irrespective of algal hosts, sample collection and extraction protocols. Additionally, the NOCHL primers yielded a higher richness while maintaining the community structure. As Planctomycetes, Verrucomicrobia and Cyanobacteria were underrepresented (70%-90%) compared to universal primers, combining the NOCHL set with taxon-specific primers may be useful for a complete description of the alga-associated bacterial diversity. The NOCHL primers represent an innovation to study algal holobionts without amplifying host plastid sequences and may further be applied to other photosynthetic hosts.  
  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 1758-2229 ISBN Médium  
  Région Expédition Conférence  
  Notes WOS:000498132200001 Approuvé pas de  
  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2661  
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