A novel approach to wildlife transcriptomics provides evidence of disease‐mediated differential expression and changes to the microbiome of amphibian populations

Abstract

Ranaviruses are responsible for a lethal, emerging infectious disease in amphibians and threaten their populations throughout the world. Despite this, little is known about how amphibian populations respond to ranaviral infection. In the United Kingdom, ranaviruses impact the common frog (Rana temporaria). Extensive public engagement in the study of ranaviruses in the UK has led to the formation of a unique system of field sites containing frog populations of known ranaviral disease history. Within this unique natural field system, we used RNA sequencing (RNA-Seq) to compare the gene expression profiles of R. temporaria populations with a history of ranaviral disease and those without. We have applied a RNA read-filtering protocol that incorporates Bloom filters, previously used in clinical settings, to limit the potential for contamination that comes with the use of RNA-Seq in nonlaboratory systems. We have identified a suite of 407 transcripts that are differentially expressed between populations of different ranaviral disease history. This suite contains genes with functions related to immunity, development, protein transport and olfactory reception among others. A large proportion of potential noncoding RNA transcripts present in our differentially expressed set provide first evidence of a possible role for long noncoding RNA (lncRNA) in amphibian response to viruses. Our read-filtering approach also removed significantly more bacterial reads from libraries generated from positive disease history populations. Subsequent analysis revealed these bacterial read sets to represent distinct communities of bacterial species, which is suggestive of an interaction between ranavirus and the host microbiome in the wild.

Diversity-Stability Dynamics of the Amphibian Skin Microbiome and Susceptibility to a Lethal Viral Pathogen

“…Results from our experimental work here are well supported by counterpart investigations into the structure of the microbiota of wild common frogs. These studies have illustrated distinct differences in bacterial community structure at sites suffering mass mortality events due to ranavirus compared to sites where no such outbreaks have been detected (Campbell et al, 2018b(Campbell et al, , 2019, even after accounting for differences among populations (Campbell et al, 2019). These correlative data from wild frogs could represent bacterial communities in some populations associated with protection of the host from viral infection, or marked shifts in microbiome structure in populations suffering ranaviral infection.…”

An emerging viral pathogen truncates population age structure in a European amphibian and may reduce population viability

“…Evidence from the same populations studied herein suggests that ranaviruses may be more ubiquitous within amphibian populations in the UK than previously thought, being detectable even in populations with no history of ranavirosis ( Campbell et al, 2018 ). We therefore used a history of ranavirosis related mortality (or lack of), rather than detectable ranavirus burden, to differentiate between populations that are impacted by ranaviruses and those which are not.…”

“…Second, mortality due to ranavirosis is annually recurrent ( Daszak et al, 1999 ; Teacher, Cunningham & Garner, 2010 ), and unlike all other host-ranavirus systems, infection in the UK primarily affects adult life stages of R. temporaria ( Cunningham et al, 1996 ; Duffus, Nichols & Garner, 2013 ). Third, adaptive immune response to ranaviruses are apparently limited in R. temporaria ( Price et al, 2015 ; Campbell et al, 2018 ). Consequently, it is possible that adult mortality within populations with a history of ranavirosis is maintained in such a way that an individual is more likely to become infected and succumb to ranavirosis the more often it returns to spawn.…”

“…Though population recovery has been observed in some instances, often population size remains supressed, and some populations decline to local extinction ( Teacher, Cunningham & Garner, 2010 ). Campbell et al (2018) demonstrated that ranaviruses are potentially more widespread than previously thought, and present within the environment even when resident frog populations show no overt signs of disease. These findings suggests that whether or not an outbreak of ranavirosis occurs may depend on currently unknown biotic or abiotic factors of an environment, although there is evidence for a role of the cutaneous or environmental microbiome ( Campbell et al, 2018 ), secondary host species, and chemical usage ( North et al, 2015 ).…”

“… Campbell et al (2018) demonstrated that ranaviruses are potentially more widespread than previously thought, and present within the environment even when resident frog populations show no overt signs of disease. These findings suggests that whether or not an outbreak of ranavirosis occurs may depend on currently unknown biotic or abiotic factors of an environment, although there is evidence for a role of the cutaneous or environmental microbiome ( Campbell et al, 2018 ), secondary host species, and chemical usage ( North et al, 2015 ). Susceptibility to ranavirosis outbreaks varies among species, but a number of ecological risk factors, including life history strategy (the species specific cycle of growth, maturation, reproduction and death), have been identified ( Hoverman et al, 2011 ).…”