Microbial networks within and among domains
Separate networks were constructed for bacteria and microeukaryotes based on tests of co-occurrence between OTUs within and among taxonomic groups within Domains (Fig. S1). Network connections indicate that taxa co-occur more frequently than expected by random chance. A dominant bacterial network assembled that consisted of Firmicutes and Bacteroidetes at the center with connections to Fusobacteria, Spirochaetes, Verrucomicrobia, Deferribacteres, and unidentified bacteria (Fig. S2). A second group was composed of Gemmatimonadetes and Cyanobacteria. Actinobacteria and Proteobacteria did not form network connections with any other groups, although strong connections formed among OTUs within the Proteobacteria. Within the microeukaryotes, only one small network formed that consisted of five taxonomic groups: Non-apicomplexan Alveolates were at the center of the network and formed connections with Apicomplexans, Rhizaria, and unidentified microeukaryotes, which in turn connected with Nucleariids (Fig. S3). The remaining 16 microeukaryote taxa remained unconnected to the network, though there were strong connections among OTUs within the Algae.
The construction of a cross-Domain network revealed a greater number of connections among groups than either the bacterial or microeukaryotic network (Fig. 5). A majority of taxa (12/18) that had formed no connections in the bacteria-only and microeukaryote-only networks formed connections with other taxa in the overall microbial network. Specifically, these newly connected taxa included the two previously unconnected bacterial groups, Actinobacteria and Proteobacteria, and 10/16 previously unconnected microeukaryote groups.
Associations between microbiome eukaryotes and bacteria reported to inhibit, enhance, or have no effect on Bd growth
When T. taophora skin bacterial OTU representative sequences were compared against a published FASTA of bacterial OTUs that were previously isolated from a diversity of live amphibians and tested against Bd in co-culture inhibition experiments (Woodhams et al., 2015) nearly half (45%) of bacterial OTUs matched OTUs in the database (Fig. S4). Tests of co-occurrence between eukaryote groups and these matched bacterial OTUs revealed that enhancing, inhibitory, and no effect do not generally reflect the associations of these bacteria with microeukaryotes generally or fungi specifically (Fig. 6). Bdenhancing bacteria were negatively associated with the Ascomycota and Basidiomycota fungi, and also showed strong but marginally non-significant positive associations with the Chytridiomycota and Choanoflagellates. Bd inhibitory bacteria showed significant positive associations with the Cryptomycota fungi and Choanoflagellates, and significant negative associations with the Basidiomycota fungi and other unidentified fungi. Finally, bacteria that were previously found to have no effect on Bd were positively associated with the Ascomycota, Choanoflagellates, and Rhizaria, and showed strongly but marginally non-significant positive associations with Algae, Amoebae, Ciliates, and Ichthyosporeans.