Amphibian skin microbiomes exhibited high microeukaryote diversity
and were dominated by Proteobacteria
In this study, we examined amphibian skin microbiome structure and
diversity with respect to geography and host genetics. In analyzing both
bacterial and microeukaryote sequences, we recovered microbial
associations with geographic and host genetic factors, as well as
unexpected patterns of microbial co-occurrence across domains. The
diversity of microeukaryotes we recovered is higher than that previously
reported from other wild frogs: we recovered 845 OTUs in our study
compared with e.g. , 255 OTUs on Rana cascadae (16). In
contrast, the level of bacterial diversity we recovered is lower than
has been previously reported: in our study we recovered 303 bacterial
OTUs compared with ~600 OTUs on Rana italica in
Federici et al. 2015). However, our recovery of bacteria from 11 phyla
is within the range of taxonomic diversity previously recovered from
amphibian skin, with for example 10-18 bacterial phyla reported from
three species (55). Our analysis showed that total microeukaryotic and
bacterial diversity were positively correlated across all samples, which
is a novel finding to our knowledge. It seems unlikely that this pattern
is an artifact of sequencing: different MiSeq runs (and different
research facilities) were used to sequence microeukaryotes and bacteria.
Proteobacteria were the most dominant bacterial phylum on T.
taophora skin across all study populations, in terms of both OTUs and
reads (Fig. 3). This is similar to findings from bacterial microbiome
studies of other tropical post-metamorphic anurans (56–59). One
hypothesis for the dominance of Proteobacteria on frog skin is that many
members of the Proteobacteria produce anti-Bd metabolites
(60,61). The presence of a high number of Proteobacteria on T.
taophora skin could hypothetically contribute to the low apparent
susceptibility to Bd previously observed in this species (17). It
is important to note however that the present study is correlative;
without experimental manipulations it is difficult to pinpoint which
factors (e.g. , the physiology of the skin, mucosal biochemistry,
host-microbial evolutionary processes, or interactions with the saline
coastal environment) are responsible for the overwhelming dominance of
Proteobacteria on anuran skin.
Although bacteria were less diverse than microeukaryotes in our samples,
bacteria could nevertheless dominate the skin microbiome according to
microbial biomass, which we did not quantify in our study. Sequence
reads are sometimes used as a proxy for relative abundance, but this has
been shown to be an unreliable measure due to known sequencing biases
among microbial taxa (62). It is possible that taxa representing fewer
OTUs (i.e. , bacteria) represent a higher proportion of microbial
biomass, and this should be considered in interpretations of our
results. Future research to address the relationship between microbial
diversity and abundance could utilize high-throughput sequencing
alongside quantitative analyses, for example quantitative PCR.