First in Vivo Batrachochytrium dendrobatidis Transcriptomes Reveal Mechanisms of Host Exploitation, Host-Specific Gene Expression, and Expressed Genotype Shifts

Abstract

For generalist pathogens, host species represent distinct selective environments, providing unique challenges for resource acquisition and defense from host immunity, potentially resulting in host-dependent differences in pathogen fitness. Gene expression modulation should be advantageous, responding optimally to a given host and mitigating the costs of generalism. Batrachochytrium dendrobatidis (Bd), a fungal pathogen of amphibians, shows variability in pathogenicity among isolates, and within-strain virulence changes rapidly during serial passages through artificial culture. For the first time, we characterize the transcriptomic profile of Bd in vivo, using laser-capture microdissection. Comparison of Bd transcriptomes (strain JEL423) in culture and in two hosts (Atelopus zeteki and Hylomantis lemur), reveals >2000 differentially expressed genes that likely include key Bd defense and host exploitation mechanisms. Variation in Bd transcriptomes from different amphibian hosts demonstrates shifts in pathogen resource allocation. Furthermore, expressed genotype variant frequencies of Bd populations differ between culture and amphibian skin, and among host species, revealing potential mechanisms underlying rapid changes in virulence and the possibility that amphibian community composition shapes Bd evolutionary trajectories. Our results provide new insights into how changes in gene expression and infecting population genotypes can be key to the success of a generalist fungal pathogen.

Experimental methodologies can affect pathogenicity of Batrachochytrium salamandrivorans infections

“…Newts exposed to the P20 isolate had greater odds of dying from Bsal chytridiomycosis compared to the P200 isolate, indicating differences in pathogenicity caused by passage history. Several studies on the genetically similar Bd chytrid fungus have reported loss of pathogen virulence associated with greater number of passages in culture [16,17,27]. Increased passage number can reduce zoospore production rate and total number of zoospores produced by zoosporangia [27].…”

“…Reduced selection (i.e., attenuation) or differential expression of virulence genes in culture could have influenced pathogenicity [17], as suggested by studies comparing Bd that was recently isolated from wild hosts to Bd in cell culture. For example, Ellison et al [16]found that Bd transcriptomes isolated from two infected amphibian hosts exhibited higher expression of genes associated with increased virulence when compared to a Bd culture grown in the lab. Rosenblum et al [28] also reported that Bd cultured on frog skin displayed a greater number of genes coding for proteases that affect pathogenicity when compared to Bd cultured using tryptone media [29].…”

“…Martel et al [9] used liquid culture as the inoculum, exposed eastern newts to Bsal by pipetting it directly on the dorsum, and housed individuals terrestrially; whereas, Longo et al [14] used agar plates for culturing Bsal, exposed individuals to zoospores in a water bath, and newts could select between aquatic and terrestrial conditions [9,14]. The number of cell culture passages also differed between studies, which could affect Bsal pathogenicity due to genome attenuation or differential gene expression [16,17]. To detect infection, both studies swabbed individuals; however, Martel et al [9] swabbed once per week and Longo et al [14] swabbed once every two weeks.…”

Challenges and solutions for analysing dual RNA‐seq data for non‐model host–pathogen systems

“…The analysis of datasets with higher percentages of pathogen reads was conducted to show when and how patterns changed across the range of the percentages of pathogen reads. Some systems investigate simultaneous gene expression of host and pathogens by mechanically separating cells of each species prior to sequencing (Ellison, DiRenzo, McDonald, Lips, & Zamudio, ). Datasets with higher percentages of pathogen reads that still include host reads could represent sequencing from RNA extracted after imperfect cell sorting.…”

A review of the role of parasites in the ecology of reptiles and amphibians

“…For example, when grown in vivo in a susceptible species versus in culture, the fungus ( B. dendrobatidis) simultaneously increased expression of transcripts involved in proteolysis, transmembrane transport and cilium morphogenesis, and exhibited a shift in expressed genotype frequencies (Ellison et al . ). Disentangling the extent to which host genomic and transcriptomic variation may influence rapid evolution in parasite populations holds great promise for refining our understanding of disease dynamics.…”