PMID- 34673434
OWN - NLM
STAT- MEDLINE
DCOM- 20211125
LR  - 20211125
IS  - 1618-0984 (Electronic)
IS  - 0723-2020 (Linking)
VI  - 44
IP  - 6
DP  - 2021 Nov
TI  - Specific detection and quantification of the marine flavobacterial genus Zobellia 
      on macroalgae using novel qPCR and CARD-FISH assays.
PG  - 126269
LID - S0723-2020(21)00092-8 [pii]
LID - 10.1016/j.syapm.2021.126269 [doi]
AB  - 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.
CI  - Copyright (c) 2021 Elsevier GmbH. All rights reserved.
FAU - Brunet, Maeva
AU  - Brunet M
AD  - Sorbonne Universite, CNRS, Integrative Biology of Marine Models (LBI2M), Station 
      Biologique de Roscoff (SBR), 29680 Roscoff, France.
FAU - Le Duff, Nolwen
AU  - Le Duff N
AD  - Sorbonne Universite, CNRS, Integrative Biology of Marine Models (LBI2M), Station 
      Biologique de Roscoff (SBR), 29680 Roscoff, France.
FAU - Fuchs, Bernhard M
AU  - Fuchs BM
AD  - Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 
      Bremen, Germany.
FAU - Amann, Rudolf
AU  - Amann R
AD  - Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 
      Bremen, Germany.
FAU - Barbeyron, Tristan
AU  - Barbeyron T
AD  - Sorbonne Universite, CNRS, Integrative Biology of Marine Models (LBI2M), Station 
      Biologique de Roscoff (SBR), 29680 Roscoff, France.
FAU - Thomas, Francois
AU  - Thomas F
AD  - Sorbonne Universite, CNRS, Integrative Biology of Marine Models (LBI2M), Station 
      Biologique de Roscoff (SBR), 29680 Roscoff, France. Electronic address: 
      francois.thomas@sb-roscoff.fr.
LA  - eng
PT  - Journal Article
DEP - 20211004
PL  - Germany
TA  - Syst Appl Microbiol
JT  - Systematic and applied microbiology
JID - 8306133
RN  - 0 (RNA, Ribosomal, 16S)
SB  - IM
MH  - *Flavobacteriaceae/genetics
MH  - In Situ Hybridization, Fluorescence
MH  - RNA, Ribosomal, 16S/genetics
MH  - Seawater
MH  - *Seaweed
OTO - NOTNLM
OT  - CARD-FISH
OT  - Macroalgae
OT  - Marine flavobacteria
OT  - Zobellia
OT  - qPCR
EDAT- 2021/10/22 06:00
MHDA- 2021/11/26 06:00
CRDT- 2021/10/21 21:01
PHST- 2021/06/08 00:00 [received]
PHST- 2021/09/16 00:00 [revised]
PHST- 2021/09/25 00:00 [accepted]
PHST- 2021/10/22 06:00 [pubmed]
PHST- 2021/11/26 06:00 [medline]
PHST- 2021/10/21 21:01 [entrez]
AID - S0723-2020(21)00092-8 [pii]
AID - 10.1016/j.syapm.2021.126269 [doi]
PST - ppublish
SO  - Syst Appl Microbiol. 2021 Nov;44(6):126269. doi: 10.1016/j.syapm.2021.126269. 
      Epub 2021 Oct 4.