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Aquatic Microbial Ecology

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AME 41:293-297 (2005)  -  doi:10.3354/ame041293

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

Isabelle C. Biegala1, *, Matthew Cuttle2, Isabelle Mary3, Mike Zubkov3

1Institut de Recherche pour le Développement, UR167 CYROCO, Centre d’Océanologie de Marseille, rue de la Batterie des Lions, 13007 Marseille, France
2Neurosciences Research Group, School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK
3National Oceanography Centre, Southampton, George Deacon Department, European Way, Southampton SO14 3ZH, UK

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), alpha-proteobacteria (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.

KEY WORDS: Picoeukaryotes · Bacteria · Hybridisation · Diversity · Symbiont

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