Cargando…

Comparison of Environmental and Culture-Derived Bacterial Communities through 16S Metabarcoding: A Powerful Tool to Assess Media Selectivity and Detect Rare Taxa

To compare environmental and culture-derived microbial communities, we performed 16S metabarcoding of uncultured samples and their culture-derived bacterial lawns. Microbial communities were obtained from freshwater river samples representative of an anthropization gradient along a river stream. The...

Descripción completa

Detalles Bibliográficos
Autores principales: Pédron, Jacques, Guyon, Léa, Lecomte, Amandine, Blottière, Lydie, Chandeysson, Charlotte, Rochelle-Newall, Emma, Raynaud, Xavier, Berge, Odile, Barny, Marie-Anne
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7464939/
https://www.ncbi.nlm.nih.gov/pubmed/32727027
http://dx.doi.org/10.3390/microorganisms8081129
_version_ 1783577477377949696
author Pédron, Jacques
Guyon, Léa
Lecomte, Amandine
Blottière, Lydie
Chandeysson, Charlotte
Rochelle-Newall, Emma
Raynaud, Xavier
Berge, Odile
Barny, Marie-Anne
author_facet Pédron, Jacques
Guyon, Léa
Lecomte, Amandine
Blottière, Lydie
Chandeysson, Charlotte
Rochelle-Newall, Emma
Raynaud, Xavier
Berge, Odile
Barny, Marie-Anne
author_sort Pédron, Jacques
collection PubMed
description To compare environmental and culture-derived microbial communities, we performed 16S metabarcoding of uncultured samples and their culture-derived bacterial lawns. Microbial communities were obtained from freshwater river samples representative of an anthropization gradient along a river stream. Their culture-derived bacterial lawns were obtained by growing aliquots of the samples on a broad range medium and on two different semi-selective media. The V3–V4 16S rRNA region was amplified and sequenced. The bacterial diversity of water samples decreased from the upper to lower stream sampling sites and, as expected, these differences were mostly suppressed by the culture step. Overall, the diversity of cultured-derived bacterial communities reflected selectivity of each tested medium. Comparison of treatments indicated that the culture selected both detected and rare undetected environmental species. Accurate detection of rare environmental bacteria of the Pectobacterium genus by 16S metabarcoding of the culture lawn was demonstrated. Interestingly, for abundant taxa, such as those of the Pseudomonas genus, the culture/environment ratio varied between sampled sites, indicating the difficulty of comparing cultured-derived taxa abundance between environmental sites. Finally, our study also highlighted media specificity and complementarity: bacterial communities grown on the two selective media, while selecting a small set of specific species, were mostly a subset of the bacterial community observed on the broad range medium.
format Online
Article
Text
id pubmed-7464939
institution National Center for Biotechnology Information
language English
publishDate 2020
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-74649392020-09-04 Comparison of Environmental and Culture-Derived Bacterial Communities through 16S Metabarcoding: A Powerful Tool to Assess Media Selectivity and Detect Rare Taxa Pédron, Jacques Guyon, Léa Lecomte, Amandine Blottière, Lydie Chandeysson, Charlotte Rochelle-Newall, Emma Raynaud, Xavier Berge, Odile Barny, Marie-Anne Microorganisms Article To compare environmental and culture-derived microbial communities, we performed 16S metabarcoding of uncultured samples and their culture-derived bacterial lawns. Microbial communities were obtained from freshwater river samples representative of an anthropization gradient along a river stream. Their culture-derived bacterial lawns were obtained by growing aliquots of the samples on a broad range medium and on two different semi-selective media. The V3–V4 16S rRNA region was amplified and sequenced. The bacterial diversity of water samples decreased from the upper to lower stream sampling sites and, as expected, these differences were mostly suppressed by the culture step. Overall, the diversity of cultured-derived bacterial communities reflected selectivity of each tested medium. Comparison of treatments indicated that the culture selected both detected and rare undetected environmental species. Accurate detection of rare environmental bacteria of the Pectobacterium genus by 16S metabarcoding of the culture lawn was demonstrated. Interestingly, for abundant taxa, such as those of the Pseudomonas genus, the culture/environment ratio varied between sampled sites, indicating the difficulty of comparing cultured-derived taxa abundance between environmental sites. Finally, our study also highlighted media specificity and complementarity: bacterial communities grown on the two selective media, while selecting a small set of specific species, were mostly a subset of the bacterial community observed on the broad range medium. MDPI 2020-07-27 /pmc/articles/PMC7464939/ /pubmed/32727027 http://dx.doi.org/10.3390/microorganisms8081129 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Pédron, Jacques
Guyon, Léa
Lecomte, Amandine
Blottière, Lydie
Chandeysson, Charlotte
Rochelle-Newall, Emma
Raynaud, Xavier
Berge, Odile
Barny, Marie-Anne
Comparison of Environmental and Culture-Derived Bacterial Communities through 16S Metabarcoding: A Powerful Tool to Assess Media Selectivity and Detect Rare Taxa
title Comparison of Environmental and Culture-Derived Bacterial Communities through 16S Metabarcoding: A Powerful Tool to Assess Media Selectivity and Detect Rare Taxa
title_full Comparison of Environmental and Culture-Derived Bacterial Communities through 16S Metabarcoding: A Powerful Tool to Assess Media Selectivity and Detect Rare Taxa
title_fullStr Comparison of Environmental and Culture-Derived Bacterial Communities through 16S Metabarcoding: A Powerful Tool to Assess Media Selectivity and Detect Rare Taxa
title_full_unstemmed Comparison of Environmental and Culture-Derived Bacterial Communities through 16S Metabarcoding: A Powerful Tool to Assess Media Selectivity and Detect Rare Taxa
title_short Comparison of Environmental and Culture-Derived Bacterial Communities through 16S Metabarcoding: A Powerful Tool to Assess Media Selectivity and Detect Rare Taxa
title_sort comparison of environmental and culture-derived bacterial communities through 16s metabarcoding: a powerful tool to assess media selectivity and detect rare taxa
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7464939/
https://www.ncbi.nlm.nih.gov/pubmed/32727027
http://dx.doi.org/10.3390/microorganisms8081129
work_keys_str_mv AT pedronjacques comparisonofenvironmentalandculturederivedbacterialcommunitiesthrough16smetabarcodingapowerfultooltoassessmediaselectivityanddetectraretaxa
AT guyonlea comparisonofenvironmentalandculturederivedbacterialcommunitiesthrough16smetabarcodingapowerfultooltoassessmediaselectivityanddetectraretaxa
AT lecomteamandine comparisonofenvironmentalandculturederivedbacterialcommunitiesthrough16smetabarcodingapowerfultooltoassessmediaselectivityanddetectraretaxa
AT blottierelydie comparisonofenvironmentalandculturederivedbacterialcommunitiesthrough16smetabarcodingapowerfultooltoassessmediaselectivityanddetectraretaxa
AT chandeyssoncharlotte comparisonofenvironmentalandculturederivedbacterialcommunitiesthrough16smetabarcodingapowerfultooltoassessmediaselectivityanddetectraretaxa
AT rochellenewallemma comparisonofenvironmentalandculturederivedbacterialcommunitiesthrough16smetabarcodingapowerfultooltoassessmediaselectivityanddetectraretaxa
AT raynaudxavier comparisonofenvironmentalandculturederivedbacterialcommunitiesthrough16smetabarcodingapowerfultooltoassessmediaselectivityanddetectraretaxa
AT bergeodile comparisonofenvironmentalandculturederivedbacterialcommunitiesthrough16smetabarcodingapowerfultooltoassessmediaselectivityanddetectraretaxa
AT barnymarieanne comparisonofenvironmentalandculturederivedbacterialcommunitiesthrough16smetabarcodingapowerfultooltoassessmediaselectivityanddetectraretaxa