These data are associated with a study that explores variation in microbial communities on western tiger salamander skin (Ambystoma mavortium) through space, time, and across life history stages. Lake water and lake substrate microbiome samples were collected to observe microbial taxa which were disproportionately abundant between salamander skin and the environment. Microbiome samples were collected at two lakes during the summer and fall of 2018, and sampling occurred at each lake every other week. During each sampling event, water quality data were collected at four or five locations within the lake and are associated with microbiome samples collected in the lake's respective regions. For each sample, bacterial and fungal communities were examined through metabarcoding of the 16S and ITS metabarcoding regions, respectively, using Illumina next-generation sequencing. The dataset includes negative control samples to aid in detecting contamination, and the dataset includes mock community samples to aid in validating our bioinformatics methods. Each sample received spike-ins of cross-contamination oligos and synthetic genes to observe cross-contamination during library preparation and to allow for the estimation of absolute microbial abundances, respectively. This dataset includes spatiotemporal, ontogenetic, morphometric, and water quality metadata for microbiome samples along with essential information for processing the DNA sequence data.

Microbiome samples from western tiger salamander (Ambystoma mavortium) skin, lake water, and lake substrate were collected at two Rocky Mountain lakes throughout the summer and fall of 2018. Sampling at each lake occurred every other week, and negative control wet and dry swab samples were collected after sampling each lake. Distilled water samples were taken as negative water controls. Twelve negative control extraction blanks were included. Two positive control mock community samples were used. 16S rRNA V4 and ITS1 metabarcoding for bacteria and fungi, respectively, were performed for each microbiome sample. DNA was extracted using the Qiagen DNeasy PowerSoil Pro Kit. Prior to library preparation, each sample received spike-ins of cross-contamination oligos and synthetic genes. During library preparation, samples were normalized and each received two PCR replicates with unique dual index combinations. Magnetic bead cleanups were performed following PCR. DNA sequencing was performed on both Illumina MiSeq and NextSeq. Sample metadata and essential information for processing the DNA sequence data are included in this dataset.

No specialized software is required to open the data files. All files are provided in csv format.