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Hybridisation of picoeukaryotes by eubacterial probes is widespread in the marine environment

Hybridisation of picoeukaryotes by eubacterial probes is widespread in the marine environment
Hybridisation of picoeukaryotes by eubacterial probes is widespread in the marine environment
Most general and group-specific eubacterial probes hybridised picoeukaryotes in coastal waters (Brittany, France) and cultures of the dominant picoeukaryotes from this environment (Micromonas pusilla and Pelagomonas calceolata). This is either because they matched the 16S rRNA from organelles or because of the presence of symbiotic or antagonist intracellular bacteria. The general eubacterial probe (EUB338) hybridised 84% of the picoeukaryotes, while the group-specific probes hybridised 3, 16, 10 and 34% of the picoeukaryotes for cyanobacteria (CYA664), alphaproteobacteria (ALF968), gamma-proteobacteria (GAM42a) and Cytophaga-Flavo-Bacteria (CF319), respectively. The results show that the hybridisation of eukaryote 16S rRNA by prokaryote probes can lead to significant errors in prokaryote counts, in particular for less well-represented groups such as cyanobacteria, with errors of 17% in the studied sample. In addition, we revealed for the first time at this scale that up to 44% of the picoeukaryotes contained intracellular prokaryotes. This finding might have serious implications for understanding the functioning of the microbial loop. Finally, because SSU rRNA databases have significantly been extended in recent years, we showed that the probe PLA886, which targets Planctomycete 16S rRNA, labelled 87% of the picoeukaryotes by hybridising their 18S rRNA. Consequently, the design of this probe should be refined for future studies, and the presence of similar changes in probe specificity should be checked regularly when using hybridisation-based techniques.
Picoeukaryotes, bacteria, hybridisation, diversity, symbiont
0948-3055
293-297
Biegala, I.C.
088b2e90-d6ec-4c36-8199-8c916d860175
Cuttle, M.
f978bb12-c450-4d58-b333-ad0a4dbb1cd3
Mary, I.
759ba210-d47f-4199-b0cf-27e585371ca9
Zubkov, M.
b1dfb3a0-bcff-430c-9031-358a22b50743
Biegala, I.C.
088b2e90-d6ec-4c36-8199-8c916d860175
Cuttle, M.
f978bb12-c450-4d58-b333-ad0a4dbb1cd3
Mary, I.
759ba210-d47f-4199-b0cf-27e585371ca9
Zubkov, M.
b1dfb3a0-bcff-430c-9031-358a22b50743

Biegala, I.C., Cuttle, M., Mary, I. and Zubkov, M. (2005) Hybridisation of picoeukaryotes by eubacterial probes is widespread in the marine environment. Aquatic Microbial Ecology, 41 (3), 293-297.

Record type: Article

Abstract

Most general and group-specific eubacterial probes hybridised picoeukaryotes in coastal waters (Brittany, France) and cultures of the dominant picoeukaryotes from this environment (Micromonas pusilla and Pelagomonas calceolata). This is either because they matched the 16S rRNA from organelles or because of the presence of symbiotic or antagonist intracellular bacteria. The general eubacterial probe (EUB338) hybridised 84% of the picoeukaryotes, while the group-specific probes hybridised 3, 16, 10 and 34% of the picoeukaryotes for cyanobacteria (CYA664), alphaproteobacteria (ALF968), gamma-proteobacteria (GAM42a) and Cytophaga-Flavo-Bacteria (CF319), respectively. The results show that the hybridisation of eukaryote 16S rRNA by prokaryote probes can lead to significant errors in prokaryote counts, in particular for less well-represented groups such as cyanobacteria, with errors of 17% in the studied sample. In addition, we revealed for the first time at this scale that up to 44% of the picoeukaryotes contained intracellular prokaryotes. This finding might have serious implications for understanding the functioning of the microbial loop. Finally, because SSU rRNA databases have significantly been extended in recent years, we showed that the probe PLA886, which targets Planctomycete 16S rRNA, labelled 87% of the picoeukaryotes by hybridising their 18S rRNA. Consequently, the design of this probe should be refined for future studies, and the presence of similar changes in probe specificity should be checked regularly when using hybridisation-based techniques.

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More information

Published date: 2005
Keywords: Picoeukaryotes, bacteria, hybridisation, diversity, symbiont

Identifiers

Local EPrints ID: 19349
URI: https://eprints.soton.ac.uk/id/eprint/19349
ISSN: 0948-3055
PURE UUID: 2dc15be2-1b0e-4db7-9cfe-0efa8202a0d5

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Date deposited: 09 Feb 2006
Last modified: 17 Jul 2017 16:31

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Contributors

Author: I.C. Biegala
Author: M. Cuttle
Author: I. Mary
Author: M. Zubkov

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