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Phylogenetic diversity and functional characterization of the Manila clam microbiota: a culture-based approach

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Abstract

According to the hologenome theory, the microbiota contributes to the fitness of the holobiont having an important role in its adaptation, survival, development, health, and evolution. Environmental stress also affects the microbiota and its capability to assist the holobiont in coping with stress factors. Here, we analyzed the diversity of cultivable bacteria associated with Manila clam tissues (mantle, gills, hemolymph) in two non-contaminated sites (Portugal and France) and one metal-contaminated site (Portugal). A total of 240 isolates were obtained. Representative isolates (n = 198) of the overall diversity were identified by 16S rDNA sequencing and subjected to functional characterization. Isolates affiliated with Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. Proteobacteria (mostly Pseudoalteromonadaceae and Vibrionaceae) were dominant in non-contaminated sites while Actinobacteria (mostly Microbacteriaceae) dominated in the metal-contaminated site. The main factor affecting the microbiota composition was contamination. No significant differences were observed between clam tissues and geographic regions. Several isolates tested positive for antibacterial activity, biofilm formation, protease, and siderophore production. The results show that the Manila clam harbors a diverse microbiota that may contribute to clam protection and overall fitness, as well as to its adaptation to stressful environments. In addition, the Manila clam microbiota is revealed as a promising source of novel probiotics with potential application in aquaculture.

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Acknowledgments

This work was supported by European Funds (FEDER) through COMPETE and by National Funds through the Portuguese Foundation for Science and Technology (FCT) to CESAM (UID/AMB/50017/2013-POCI-01-0145-FEDER-007638), Artur Alves (FCT Investigator Programme-IF/00835/2013), Isabel Henriques (FCT Investigator Programme-IF/00492/2013), and Laura Leite (PhD grant SFRH/BD/86879/2012). The authors acknowledge financing from the Programa de Ações Universitárias Integradas Luso-Francesas (PAUILF-ref.: TC-08_12).

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  1. Departamento de Biologia, CESAM, Campus de Santiago, Universidade de Aveiro, 3810-193, Aveiro, Portugal

    Laura Leite, Isabel Henriques & Artur Alves

  2. Université de Bordeaux, UMR 5805 EPOC, 33120, Arcachon, France

    Laura Leite, Florence Jude-Lemeilleur, Natalie Raymond & Frédéric Garabetian

  3. CNRS, UMR 5805 EPOC, 33120, Arcachon, France

    Laura Leite, Florence Jude-Lemeilleur, Natalie Raymond & Frédéric Garabetian

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  1. Laura Leite
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Leite, L., Jude-Lemeilleur, F., Raymond, N. et al. Phylogenetic diversity and functional characterization of the Manila clam microbiota: a culture-based approach. Environ Sci Pollut Res 24, 21721–21732 (2017). https://doi.org/10.1007/s11356-017-9838-z

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