Composition and variation of the skin microbiota in sympatric species of European newts (Salamandridae)

in Amphibia-Reptilia
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The mucous skin of amphibians provides a habitat for microorganisms which may interact with their hosts and thereby affect their condition and health. Cultivation-independent analyses of the bacterial communities based on the detection of PCR-amplified bacterial 16S rRNA genes provides a direct approach to characterize their diversity. In the present pilot study we utilized this approach in combination with a high-throughput DNA sequencing technology (454 pyrosequencing), to characterize the bacterial community structure of the skin of three newt species (Lissotriton vulgaris, Ichthyosaura alpestris, Triturus cristatus), collected near Braunschweig, Germany. 16S rDNA sequences were obtained from 19 unique samples. On average, 6113 amplicon sequences were obtained per sample and these could phylogenetically be assigned to a total of 1615 different operational taxonomic units (OTUs). Altogether, most samples were rather similar in their dominant bacterial taxa. Most represented were Betaproteobacteria (46%; mostly Janthinobacterium), Gammaproteobacteria (28%; mostly Pseudomonas), Flavobacteria (phylum Bacteroidetes: 19%, mostly Flavobacterium), and Sphingobacteria (Bacteroidetes: 5%, mostly Pedobacter). We found no significant differences between the three newt species, or between hemi-nested vs. non-nested PCR, but a strong difference among sampling dates (15 and 17 April 2013) which might be explained by the ongoing transition of the newts from their terrestrial to aquatic phase which coincided with this period, or by differences between sexes as these were unevenly sampled on the two dates. 16S rRNA gene sequences retrieved in this study in several cases were identical or very similar to those previously found on the skin of North American salamanders.

Amphibia-Reptilia

Publication of the Societas Europaea Herpetologica

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Figures

  • Proportion of the five most common genera of bacteria (proportion > 3%) plus Ralstonia among 16S rRNA sequences obtained from skin swab samples of three species of newts (from 15 and 17 April 2013). Numbers with asterisk indicate those samples amplified with hemi-nested PCR. A capital F or M at the end of the name indicates samples taken from female or male newts, respectively. Note that especially in the alpine newt (I. alpestris) but also in the other species, a distinct reduction of the percentage of Janthinobacterium sequences and an augmentation of Pseudomonas is observed from 15 to 17 April 2013, concordant with increasing water temperatures in the pond. This figure is published in color in the online version.

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  • NMDS plots of samples of skin bacterial composition of three newt species, based on a weighted Unifrac distance matrix that considers phylogenetic relatedness among bacterial sequences. Only samples from 2013 included. NMDS stress: 0.117, R-squared for configuration: 0.959. As supported by ANOSIM analysis, sampling date and sex are significant predictor of the bacterial community (due to uneven sampling of sexes on the two dates) while host species and PCR method have no significant influence.

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