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16S rDNA-Based Analysis of Dominant Bacterial Populations Associated with Early Life Stages of Coho Salmon (Oncorhynchus kisutch)

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Abstract

In this study, we used a 16S rDNA–based approach to determine bacterial populations associated with coho salmon (Oncorhynchus kisutch) in its early life stages, highlighting dominant bacteria in the gastrointestinal tract during growth in freshwater. The present article is the first molecular analysis of bacterial communities of coho salmon. Cultivability of the salmon gastrointestinal microbiota was estimated by comparison of direct microscopic counts (using acridine orange) with colony counts (in tryptone soy agar). In general, a low fraction (about 1%) of the microbiota could be recovered as cultivable bacteria. Using DNA extracted directly from individuals belonging to the same lot, bacterial communities present in eggs and gastrointestinal tract of first-feeding fries and juveniles were monitored by polymerase chain reaction–denaturing gradient gel electrophoresis (PCR–DGGE). The DGGE profiles revealed simple communities in all stages and exposed changes in bacterial community during growth. Sequencing and phylogenetic analysis of excised DGGE bands revealed the nature of the main bacteria found in each stage. In eggs, the dominant bacteria belonged to β-Proteobacteria (Janthinobacterium and Rhodoferax). During the first feeding stage, the most abundant bacteria in the gastrointestinal tract clustered with γ-Proteobacteria (Shewanella and Aeromonas). In juveniles ranging from 2 to 15 g, prevailing bacteria were Pseudomonas and Aeromonas. To determine the putative origin of dominant Pseudomonas and Aeromonas found in juvenile gastrointestinal tracts, primers for these groups were designed based on sequences retrieved from DGGE gel. Subsequently, samples of the water influent, pelletized feed, and eggs were analyzed by PCR amplification. Only those amplicons obtained from samples of eggs and the water influent presented identical sequences to the dominant bands of DGGE. Overall, our results suggest that a stable microbiota is established after the first feeding stages and its major components could be derived from water and egg epibiota.

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Acknowledgments

This project was supported by grant DID INC 03/07-2 from the University of Chile. P. Navarrete acknowledges a scholarship from the Comisión Nacional de Ciencia y Tecnología CONICYT–Chile. The authors thank Harriet V. Harrison and Dr. Mariana Cifuentes for editing and revising the English grammar, R.T. Espejo for his helpful discussions and review, and Dr. Rafael Opazo for technical assistance.

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Authors and Affiliations

  1. Laboratorio de Biotecnología, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile

    Jaime Romero & Paola Navarrete

  2. El Líbano 5524, Macul, 6903625, Santiago, Chile

    Jaime Romero

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  1. Jaime Romero
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  2. Paola Navarrete
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Correspondence to Jaime Romero.

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Romero, J., Navarrete, P. 16S rDNA-Based Analysis of Dominant Bacterial Populations Associated with Early Life Stages of Coho Salmon (Oncorhynchus kisutch). Microb Ecol 51, 422–430 (2006). https://doi.org/10.1007/s00248-006-9037-9

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  • DOI: https://doi.org/10.1007/s00248-006-9037-9

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