Captivity and Infection by the Fungal Pathogen Batrachochytrium salamandrivorans Perturb the Amphibian Skin Microbiome

Abstract

The emerging fungal pathogen, Batrachochytrium salamandrivorans ( Bsal ) is responsible for the catastrophic decline of European salamanders and poses a threat to amphibians globally. The amphibian skin microbiome can influence disease outcome for several host-pathogen systems, yet little is known of its role in Bsal infection. In addition, many experimental in-vivo amphibian disease studies to date have relied on specimens that have been kept in captivity for long periods without considering the influence of environment on the microbiome and how this may impact the host response to pathogen exposure. We characterized the impact of captivity and exposure to Bsal on the skin bacterial and fungal communities of two co-occurring European newt species, the smooth newt, Lissotriton vulgaris and the great-crested newt, Triturus cristatus . We show that captivity led to significant losses in bacterial and fungal diversity of amphibian skin, which may be indicative of a decline in microbe-mediated protection. We further demonstrate that in both L. vulgaris and T. cristatus, Bsal infection was associated with changes in the composition of skin bacterial communities with possible negative consequences to host health. Our findings advance current understanding of the role of host-associated microbiota in Bsal infection and highlight important considerations for ex-situ amphibian conservation programmes.

Skin microbiome correlates with bioclimate and Batrachochytrium dendrobatidis infection intensity in Brazil’s Atlantic Forest treefrogs

“…GLMMs using the glmer () function 96 in the lme4 package ( https://cran.r-project.org/package=lme4 ) in R, with Poisson (for Bd infection intensity, Supplementary table S20 ) and binominal (for Bd infection status; Table 2 ) distribution were used to test the effect of the five selected bioclimatic variables from Response Screening in separated models. As further fixed factors we added elevation, latitude, and #OTUs independently from Response Screening results, due to their a priori assumed biological significance.…”

“…To select best-fit models, we added to Models 1-4 the non-bioclimatic, non-categorical predictors: 'elevation' , 'latitude' , and 'Bd infection intensity' as fixed factors, and added as nested random factor the categorical predictors 'location, sampling date, and host species' . We performed Generalized Linear Mixed Models (GLMM) using the glmer() function 96 in the lme4 package (https ://cran.r-proje ct.org/packa ge=lme4) in R, with Poisson distribution to test whether selected bioclimatic variables from Model 1-4, elevation, latitude, and Bd infection intensity are associated with richness and abundance of skin bacterial communities in treefrogs (i.e. observed #OTUs and Simpson's evenness; Supplementary Table 9 and 10).…”

Post‐epizootic microbiome associations across communities of neotropical amphibians

“…Samples with a band had sufficient genetic material to undergo ITS ‐ 2 amplification and were selected for metagenomic library preparation. ITS ‐ 2 library preparation was performed using dual‐indexed ITS‐3F and ITS‐4R primers (Kozich et al, 2013) and PCR protocols (Bates et al, 2019). Samples were run in duplicate, amplicons were visualized on a 1.5% agarose gel and samples that produced a band were pooled to yield a final per‐sample volume of 50 µl.…”

Amphibian ranaviruses in Europe: important directions for future research

“…There is substantial and growing evidence that the amphibian skin microbiome is vital to the ability of amphibians to resist or tolerate infection by pathogens (Harris et al 2006(Harris et al , 2009Becker et al 2015). Although this evidence is primarily drawn from studies concerning amphibians infected with the chytrid fungi, including Batrachochytrium dendrobatidis (Bd) (Kueneman et al 2016; and B. salamandrivorans (Bates et al 2019), recent research suggests that host-associated microbial communities in amphibians also represent a key component of their immune defense against ranaviruses. For example, skin microbiome structure has been found to correlate with population disease-status in the wild (Campbell et al 2018b(Campbell et al , 2019 and survival of acute ranaviral infection under laboratory conditions (Harrison et al 2019).…”