Academic Journal
Specific detection and quantification of the marine flavobacterial genus Zobellia on macroalgae using novel qPCR and CARD-FISH assays
| Title: | Specific detection and quantification of the marine flavobacterial genus Zobellia on macroalgae using novel qPCR and CARD-FISH assays |
|---|---|
| Authors: | Brunet, Maéva, Le Duff, Nolwen, Fuchs, Bernhard, M, Amann, Rudolf, Barbeyron, Tristan, Thomas, François |
| Contributors: | Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff = Roscoff Marine Station (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Max Planck Institute for Marine Microbiology, Max-Planck-Gesellschaft, ANR-18-CE02-0001,ALGAVOR,Stratégies écologiques et métaboliques de bactéries spécialistes de la dégradation des macroalgues(2018) |
| Superior Title: | ISSN: 0723-2020 ; Systematic and Applied Microbiology ; https://hal.sorbonne-universite.fr/hal-03417302 ; Systematic and Applied Microbiology, 2021, 44 (6), pp.126269. ⟨10.1016/j.syapm.2021.126269⟩. |
| Publisher Information: | HAL CCSD Elsevier |
| Publication Year: | 2021 |
| Subject Terms: | Zobellia, qPCR, CARD-FISH, macroalgae, marine flavobacteria, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology |
| Description: | International audience ; The flavobacterial genus Zobellia is considered as a model to study macroalgal polysaccharide degradation. The lack of data regarding its prevalence and abundance in coastal habitats constitutes a bottleneck to assess its ecological strategies. To overcome this issue, real-time quantitative PCR (qPCR) and fluorescence in situ hybridization (FISH) methods targeting the 16S rRNA gene were optimized to specifically detect and quantify Zobellia on the surface of diverse macroalgae. The newly designed qPCR primers and FISH probes targeted 98 and 100% of the Zobellia strains in silico and their specificity was confirmed using pure bacterial cultures. The dynamic range of the qPCR assay spanned 8 orders of magnitude from 10 to 10 8 16S rRNA gene copies and the detection limit was 0.01% relative abundance of Zobellia in environmental samples. Zobellia-16S rRNA gene copies were detected on all surveyed brown, green and red macroalgae, in proportion varying between 0.1 and 0.9% of the total bacterial copies. The absolute and relative abundance of Zobellia varied with tissue aging on the kelp Laminaria digitata. Zobellia cells were successfully visualized in Ulva lactuca and stranded Palmaria palmata surface biofilm using CARD-FISH, representing in the latter 10 5 Zobellia cells.cm-2 and 0.43% of total bacterial cells. Overall, qPCR and CARD-FISH assays enabled robust detection, quantification and localization of Zobellia representatives in complex samples, underlining their ecological relevance as primary biomass degraders potentially cross-feeding other microorganisms. |
| Document Type: | article in journal/newspaper |
| Language: | English |
| Relation: | hal-03417302; https://hal.sorbonne-universite.fr/hal-03417302; https://hal.sorbonne-universite.fr/hal-03417302/document; https://hal.sorbonne-universite.fr/hal-03417302/file/qPCR-FISH_SAM_revised.pdf |
| DOI: | 10.1016/j.syapm.2021.126269 |
| Availability: | https://doi.org/10.1016/j.syapm.2021.126269 https://hal.sorbonne-universite.fr/hal-03417302 https://hal.sorbonne-universite.fr/hal-03417302/document https://hal.sorbonne-universite.fr/hal-03417302/file/qPCR-FISH_SAM_revised.pdf |
| Rights: | info:eu-repo/semantics/OpenAccess |
| Accession Number: | edsbas.F102F122 |
| Database: | BASE |
| Description not available. |