Adaptive microbiota in scale-eating pupfish
Fish scales are composed of a deep layer that is mostly collagen type I (Harikrishna et al. 2017); therefore, we predicted that any adaptive microbes within the scale-eater gut would have collagen degrading properties. This includes Bacillus , Clostridium , andVibrio taxa, which are well-known for microbial collagenase enzymes (Duarte et al. 2016). We found a significant reduction ofVibrio taxa within the scale-eater gut from both lake populations (Figs. 3-4). Although it is not clear why there are fewer taxa, the significant shift in a major collagenase-producing group suggests the potential for an adaptive scale-eater microbiome, even in the absence of dietary scales (except perhaps incidental aggression and ingestion of scales among tankmates). We also found significant enrichment of the family Burkholderiaceae in both scale-eater populations (Figs. 3-4). Burkholderiaceae is a family of proteobacteria which contains many human and animal pathogens (diCenzo et al. 2019), plant and insect symbionts (Gyaneshwar et al. 2011; Takeshita and Kikuchi 2017), and can be found in soil, water, and polluted environments (Coenye and Vandamme 2003; Estrada-de los Santos et al. 2016). They also include some collagenase-producing bacteria, such as Burkholderia pseudomallei (UniProtKB - A3P3M6; Rainbow et al. 2004), which is the causative agent of melioidosis in humans (Holden et al. 2004).
In contrast to a microbiome study of the adaptive radiation of Tanganyikan cichlids (Baldo et al. 2015), we found no evidence ofClostridia enrichment in scale-eaters nor a reduction of microbial diversity in this carnivorous species. This may be due to the very young 10 kya age of the scale-eating pupfish relative to the comparatively ancient 12 Mya Tanganyikan radiation and Perissodus scale-eating clade (Koblmueller et al. 2007; Martin and Wainwright 2013).