Comparison of environmental and culture-derived bacterial communities through 16S metabarcoding: A powerful tool to assess media selectivity and detect rare taxa
| Autor: | Odile Berge, Léa Guyon, Marie-Anne Barny, Amandine Lecomte, Jacques Pédron, Xavier Raynaud, Charlotte Chandeysson, Lydie Blottière, Emma Rochelle-Newall |
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| Přispěvatelé: | Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Pathologie Végétale (PV), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ec2co CNRS project CARTOBACTER, ANR-17-CE32-0004,SPREE,Stratégie préemptive de surveillance de l'air et de l'eau pour anticiper l'émergence de maladies des plantes liés aux changements paysagers(2017), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) |
| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
Microbiology (medical)
Pectobacterium Range (biology) river Zoology microbial ecology Microbiology Article 03 medical and health sciences Microbial ecology Abundance (ecology) Virology Pseudomonas medium selectivity lcsh:QH301-705.5 030304 developmental biology 0303 health sciences [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE] biology 030306 microbiology 16S barcoding Anthropization biology.organism_classification 16S ribosomal RNA bacterial communities 6. Clean water [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology lcsh:Biology (General) cultivation [SDE.BE]Environmental Sciences/Biodiversity and Ecology Bacteria |
| Zdroj: | Microorganisms Microorganisms, MDPI, 2020, 8 (8), ⟨10.3390/microorganisms8081129⟩ Microorganisms, 2020, 8 (8), pp.1129. ⟨10.3390/microorganisms8081129⟩ Microorganisms, Vol 8, Iss 1129, p 1129 (2020) Volume 8 Issue 8 Microorganisms, MDPI, 2020, 8 (8), pp.1129. ⟨10.3390/microorganisms8081129⟩ |
| ISSN: | 2076-2607 |
| Popis: | 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&ndash 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. |
| Databáze: | OpenAIRE |
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