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Appl. Environ. Microbiol. doi:10.1128/AEM.03003-06
Copyright (c) 2007, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved.

Evaluation of two library-independent microbial source tracking methods to identify sources of faecal contamination in French estuaries

EMP, Laboratoire de Microbiologie, Ifremer, 29280 Plouzané, France, LERCC, Ifremer, 29280 Plouzané, France; Laboratoire de Microbiologie de l'Environnement, USC INRA 2017, EA 956, IRBA Université de Caen 14032 Caen, France

^* To whom correspondence should be addressed. Email: Michele.Gourmelon{at}ifremer.fr.

	Abstract

In order to identify the origin of the faecal contamination observed in French estuaries, two library-independent microbial source tracking (MST) methods were selected: (i) Bacteroidales host-specific 16S rRNA gene markers and (ii) F-specific RNA bacteriophages genotyping. The specificity of the Bacteroidales markers was evaluated on human and animal (bovine, pig, sheep, bird) faeces. Two human-specific (HF183 and HF134), one ruminant-specific (CF193') and one pig-specific (PF163) markers showed a high level of specificity (> 90%). However, the data suggest that the proposed ruminant-specific CF128 marker would be better described as an animal marker, as it was observed in all bovine and sheep faeces and 96% of pig faeces. F RNA bacteriophages were detected in only 21% of individual fecal samples tested, in 60% of pig slurries but in all sewage samples. Most detected F RNA bacteriophage were from genotypes II and III in sewage samples and from genotypes I and IV in bovine, pig, and bird faeces, and from pig slurries. Both MST methods were applied to 28 water samples collected from three watersheds at different times. Classification of water samples as subject to human, animal or mixed faecal contamination was more frequent when using Bacteroidales markers (82.1% of water samples) than by bacteriophage genotyping (50%). The ability to classify a water sample increased with increasing E. coli or enterococci concentration. For the samples that could be classified by bacteriophage genotyping, 78% agreed with the classification obtained from Bacteroidales markers.

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