The amphibian microbiome exhibits poor resilience following pathogen-induced disturbance

Abstract

Infectious pathogens can disrupt the microbiome in addition to directly affecting the host. Impacts of disease may be dependent on the ability of the microbiome to recover from such disturbance, yet remarkably little is known about microbiome recovery after disease, particularly in nonhuman animals. We assessed the resilience of the amphibian skin microbial community after disturbance by the pathogen, Batrachochytrium dendrobatidis (Bd). Skin microbial communities of laboratory-reared mountain yellow-legged frogs were tracked through three experimental phases: prior to Bd infection, after Bd infection (disturbance), and after clearing Bd infection (recovery period). Bd infection disturbed microbiome composition and altered the relative abundances of several dominant bacterial taxa. After Bd infection, frogs were treated with an antifungal drug that cleared Bd infection, but this did not lead to recovery of microbiome composition (measured as Unifrac distance) or relative abundances of dominant bacterial groups. These results indicate that Bd infection can lead to an alternate stable state in the microbiome of sensitive amphibians, or that microbiome recovery is extremely slow—in either case resilience is low. Furthermore, antifungal treatment and clearance of Bd infection had the additional effect of reducing microbial community variability, which we hypothesize results from similarity across frogs in the taxa that colonize community vacancies resulting from the removal of Bd. Our results indicate that the skin microbiota of mountain yellow-legged frogs has low resilience following Bd-induced disturbance and is further altered by the process of clearing Bd infection, which may have implications for the conservation of this endangered amphibian.

Fine scale transitions of the microbiota and metabolome along the gastrointestinal tract of herbivorous fishes

“…Raw paired fastq reads were processed to generate amplicon sequence variants (ASVs) [ 53 , 54 ]. In brief, raw sequences were filtered, trimmed, and merged using the dada2 R package, triplicate technical replicates were merged bioinformatically after confirmation of replicability, and OTUs were defined as unique “amplicon sequence variants” by dada2 [ 55 ].…”

Predicting fungal infection rate and severity with skin‐associated microbial communities on amphibians

“…Therefore, there was limited opportunity for introduction of new microbes to each individual amphibians' skin. This may have reduced detectable effects on the skin microbiota after exposure to Bd, especially compared to what has been observed in previous work in non-sterile environments (Jani et al, 2021) because there was no reservoir of microbes from which new members could be recruited.…”

“…Previous studies report that skin‐associated microbial communities change after Bd infection (Jani & Briggs, 2014, 2018; Jani et al, 2017, 2021). While we did not observe shifts in any community traits (Figure 4), our PERMANOVA analysis revealed that Bd infection was associated with a significant difference in community composition between infected and noninfected individuals (Figure ).…”

Body condition, skin bacterial communities and disease status: insights from the first release trial of the limosa harlequin frog,Atelopus limosus

“…Adaptive management frameworks for amphibians that are threatened by Bd include interventions to prevent further extinctions [17,18]. For instance, efforts have focused on reducing Bd in the environment [19] and infections on the amphibian hosts [20,21], while also improving the capacity of populations to persist despite increased disease-related mortality [18]. In areas where Bd is enzootic, additional pressures, such as climate change and habitat degradation, can compromise already struggling populations [17].…”