Intraspecific Variation in the Skin-Associated Microbiome of a Terrestrial Salamander

Abstract

Resident microbial communities living on amphibian skin can have significant effects on host health, yet the basic ecology of the host-microbiome relationship of many amphibian taxa is poorly understood. We characterized intraspecific variation in the skin microbiome of the salamander Ensatina eschscholtzii xanthoptica, a subspecies composed of four genetically distinct populations distributed throughout the San Francisco Bay Area and the Sierra Nevada mountains in California, USA. We found that salamanders from four geographically and genetically isolated populations harbor similar skin microbial communities, which are dominated by a common core set of bacterial taxa. Additionally, within a population, the skin microbiome does not appear to differ significantly between salamanders of different ages or sexes. In all cases, the salamander skin microbiomes were significantly different from those of the surrounding terrestrial environment. These results suggest that the relationship between E. e. xanthoptica salamanders and their resident skin microbiomes is conserved, possibly indicating a stable mutualism between the host and microbiome.

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Acknowledgements

The authors would like to thank S. Ellison for his great help with lab work and troubleshooting. We would also like to thank F. Cipriano and A. Swei for advice on methodology. J. de la Torre provided valuable advice as a member of SPI’s Master’s thesis committee. SPI would also like to thank her classmates from OEB210 for valuable feedback on the manuscript. We would also like to thank four anonymous reviewers whose comments greatly improved the manuscript. The National Science Foundation provided funding through a research grant (IOS-1258133) awarded to AGZ and VTV as well as a GRFP (DGE-1144152) awarded to SPI. The National Institutes of Health also provided financial support through MBRS-RISE fellowships awarded to SPI and AKB (R25-GM059298).

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Correspondence to Sofia R. Prado-Irwin.

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Ethical Approval

All procedures performed with live animals in this study were approved by the Institutional Animal Care and Use Committee at San Francisco State University (Protocol no. A12-07). All sampling of wild salamanders was performed with approval from the California Department of Fish and Wildlife (SC-12920) and California State Parks.

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The authors declare that they have no conflict of interest.

Electronic Supplementary Material

Supplementary Table 1

Sequences of Illumina primers used for amplicon sequencing (Illumina Inc., San Diego, CA, USA). (XLSX 8 kb)

Supplementary Table 2

Complete list of core bacterial OTUs and average abundances by sample group. (*) indicates an OTU with previously-documented antifungal properties. (XLSX 18 kb)

Supplementary Table 3

List of bacterial OTUs unique to one population. All unique OTUs were present at <0.01% abundance. The East Bay population had the most unique OTUs. (XLSX 15 kb)

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Prado-Irwin, S.R., Bird, A.K., Zink, A.G. et al. Intraspecific Variation in the Skin-Associated Microbiome of a Terrestrial Salamander. Microb Ecol 74, 745–756 (2017). https://doi.org/10.1007/s00248-017-0986-y

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Keywords

  • Amphibian
  • Microbiome
  • Symbiosis
  • Ensatina eschscholtzii