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Microbiota Diversity Within and Between the Tissues of Two Wild Interbreeding Species

  • Host Microbe Interactions
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Abstract

Understanding the role of microbiota as reproductive barriers or sources of adaptive novelty in the fundamental biological phenomenon of speciation is an exciting new challenge necessitating exploration of microbiota variation in wild interbreeding species. We focused on two interbreeding cyprinid species, Chondrostoma nasus and Parachondrostoma toxostoma, which have geographic distributions characterized by a mosaic of hybrid zones. We described microbiota diversity and composition in the three main teleost mucosal tissues, the skin, gills and gut, in the parental parapatric populations. We found that tissue type was the principal determinant of bacterial community composition. In particular, there was strong microbiota differentiation between external and internal tissues, with secondary discrimination between the two species. These findings suggest that specific environmental and genetic filters associated with each species have shaped the bacterial communities, potentially reflecting deterministic assemblages of bacteria. We defined the core microbiota common to both Chondrostoma species for each tissue, highlighting the occurrence of microbe-host genome interactions at this critical level for studies of the functional consequences of hybridization. Further investigations will explore to what extend these specific tissue-associated microbiota signatures could be profoundly altered in hybrids, with functional consequences for post-mating reproductive isolation in relation to environmental constraints.

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Acknowledgements

We are grateful to Maxime Galan (UMR CBGP, Montferrier-sur-lez) for technical advices. We thank the plateform Genotypage—Séquençage (Université Montpellier, IRD, CNRS, EPHE), and particularly Frédérique Cerqueira for her technical help. We are also grateful to Benjamin Hérodet (Fédération de l’Ain pour la pêche et la protection des milieux aquatiques) for help in the carrying out of the field sampling.

Funding

The study has been funded by Electricité de France within the project FACIES developing scientific advances in favor of Aquatic System Biodiversity.

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Authors and Affiliations

  1. IMBE, Aix Marseille Université, CNRS, IRD, Avignon Université, Centre Saint-Charles, 3 place Victor Hugo, 13331, Marseille Cedex 3, France

    Emmanuel Guivier, Nicolas Pech, Arnaud Ungaro, Rémi Chappaz & André Gilles

  2. Montpellier SupAgro, UMR CBGP, F-34988, Montferrier-sur-Lez, France

    Jean-François Martin

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  1. Emmanuel Guivier
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  2. Jean-François Martin
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Correspondence to Emmanuel Guivier.

Electronic Supplementary Material

ESM 1

Supplementary Fig. S1. Alpha diversity rarefactions curves. Procedure of rarefactions from 10 to 100,000 sequences with 20 steps and 100 iterations for A) Shannon and B) Phylogenetic Diversity indices. (PDF 135 kb)

ESM 2

Supplementary Fig. S2. Principal Coordinates Analysis exploring the effect tissues and species on the dissimilarities of microbiota compositions. For the A) Bray-Curtis, B) Jaccard and C) weighted Unifrac distance matrices we present the two first axes of independent PCoA analyses performed. Each point corresponds to one microbiota sample colored following 1) the 4 mucosal tissues: caudal fin (blue triangle), gills (orange circle), midgut (green triangle) and hindgut (purple triangle); 2) the two species: C. nasus (orange triangle) and P. toxostoma (green square). (PDF 159 kb)

ESM 3

Supplementary Fig. S3. Common and specific OTUs of P. toxostoma and C. nasus in the different mucosal tissues. Venn diagram showed numbers and percentages of OTUs specific to P. toxostoma, C. nasus and shared by the two species in caudal fin, gills, midgut and hindgut. (PDF 194 kb)

ESM 4

Supplementary Fig. S4. Cumulative bar charts of main bacterial phyla present in mucosal tissues of C. nasus and P. toxostoma. Percentages show the mean relative abundance of each phylum for each sample from the 1000 rarefied OTU tables by A) caudal fin, B) gills, C) midgut and D) hindgut (PDF 258 kb)

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Guivier, E., Martin, JF., Pech, N. et al. Microbiota Diversity Within and Between the Tissues of Two Wild Interbreeding Species. Microb Ecol 75, 799–810 (2018). https://doi.org/10.1007/s00248-017-1077-9

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