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.