ITS of amphibian: skin
For microbiome library preparation, we extracted DNA from the swabs or soil with the PowerSoil DNA Isolation kit (MO BIO Laboratories, Carlsbad, CA, USA) with minor modifications for samples with low DNA concentration: 1) after the addition of solution C1, we incubated samples at 60C for 10 min; and 2) we allowed solution S6 to sit on the filter for five minutes before the final elution. We PCR-amplified bacterial DNA for the V3-V4 region of the 16S rRNA gene using primers 515F and 806R and fungal DNA for the nuclear ribosomal internal transcribed spacer (ITS2) with the primers ITS9F and ITS4R. PCRs were performed in triplicate in 25 l reactions containing 2x KAPPA HiFi HotStart Ready Mix (Kapa Biosystems KK2602), 0.2 M of each primer, 0.5 g/l BSA (NEB B9000S), 5% DMSO (ACS grade) and 1 l of genomic DNA. For bacteria, thermocycling conditions consisted of an initial denaturation at 95 C for 3 min and 34 cycles of 98 C for 20 s, 61 C for 45 s, 72 C for 1 min and a final elongation at 72 C for 5 min. For fungi, thermocycling conditions consisted of an initial denaturation at 95 C for 2 min and 35 cycles of 95 C for 30 s, 60 C for 45 s, 72 C for 2 min and a final elongation at 72 C for 5 min. Each pair of primers included a barcode of six nucleotides at the 5' end of both oligos. We prepared amplicon libraries following the protocol of Vo & Jedlicka 2014. Libraries generated from salamander skin swabs were sequenced at San Francisco State University (16S) or the Vincent J. Coates Sequencing Facility, UC Berkeley (ITS2). The bacterial libraries from the soil samples were prepared and sequenced at Argonne National Laboratory (16S); all the libraries were sequenced with an Illumina MiSeq sequencer v3