title: The amphibian skin-associated microbiome across species, space and life history stages.
abstract: Skin-associated bacteria of amphibians are increasingly recognized for their role in defence against pathogens, yet we have little understanding of their basic ecology. Here, we use high-throughput 16S rRNA gene sequencing to examine the host and environmental influences on the skin microbiota of the cohabiting amphibian species Anaxyrus boreas, Pseudacris regilla, Taricha torosa and Lithobates catesbeianus from the Central Valley in California. We also studied populations of Rana cascadae over a large geographic range in the Klamath Mountain range of Northern California, and across developmental stages within a single site. Dominant bacterial phylotypes on amphibian skin included taxa from Bacteroidetes, Gammaproteobacteria, Alphaproteobacteria, Firmicutes, Sphingobacteria and Actinobacteria. Amphibian species identity was the strongest predictor of microbial community composition. Secondarily, within a given amphibian species, wetland site explained significant variation. Amphibian-associated microbiota differed systematically from microbial assemblages in their environments. Rana cascadae tadpoles have skin bacterial communities distinct from postmetamorphic conspecifics, indicating a strong developmental shift in the skin microbes following metamorphosis. Establishing patterns observed in the skin microbiota of wild amphibians and environmental factors that underlie them is necessary to understand skin symbiont community assembly, and ultimately, the role skin microbiota play in the extended host phenotype including disease resistance.
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Colorado, Ramaley N-122, UCB 334, Boulder, CO, 80309, USA.
authors.forename: Jordan G
authors.initials: JG
authors.lastname: Kueneman
authors.affiliation: Biofrontiers Institute, University of Colorado, Boulder, CO, 80309, USA.
authors.forename: Laura Wegener
authors.initials: LW
authors.lastname: Parfrey
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Colorado, Ramaley N-122, UCB 334, Boulder, CO, 80309, USA.
authors.forename: Douglas C
authors.initials: DC
authors.lastname: Woodhams
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Colorado, Ramaley N-122, UCB 334, Boulder, CO, 80309, USA.
authors.forename: Holly M
authors.initials: HM
authors.lastname: Archer
authors.affiliation: Biofrontiers Institute, University of Colorado, Boulder, CO, 80309, USA.|Howard Hughes Medical Institute, University of Colorado, Boulder, CO, USA.
authors.forename: Rob
authors.initials: R
authors.lastname: Knight
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Colorado, Ramaley N-122, UCB 334, Boulder, CO, 80309, USA.
authors.forename: Valerie J
authors.initials: VJ
authors.lastname: McKenzie
mesh_terms: D000663:Amphibians / Q000382:microbiology*; D000818:Animals; D001419:Bacteria / Q000145:classification* / Q000235:genetics; D044822:Biodiversity; D002140:California; D004269:DNA, Bacterial / Q000235:genetics; D060106:Lakes; D007814:Larva / Q000382:microbiology; D064307:Microbiota; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D011898:Ranidae / Q000382:microbiology*; D017422:Sequence Analysis, DNA; D012867:Skin / Q000382:microbiology*; D012988:Soil Microbiology; D013045:Species Specificity; D014871:Water Microbiology
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S
keywords: California; amphibians; bacteria; metamorphosis; microbiome; skin