Humic-acid-driven escape from eye parasites revealed by RNA-seq and target-specific metabarcoding

Abstract

Background Next generation sequencing (NGS) technologies are extensively used to dissect the molecular mechanisms of host-parasite interactions in human pathogens. However, ecological studies have yet to fully exploit the power of NGS as a rich source for formulating and testing new hypotheses. Methods We studied Eurasian perch (Perca fluviatilis) and its eye parasite (Trematoda, Diplostomidae) communities in fourteen lakes that differed in humic content in order to explore host-parasite-environment interactions. We hypothesised that high humic content along with low pH would decrease the abundance of the intermediate hosts (gastropods), thus limiting the occurrence of diplostomid parasites in humic lakes. This hypothesis was initially invoked by whole eye RNA-seq data analysis and subsequently tested using PCR-based detection and a novel targeted metabarcoding approach.Results Whole eye transcriptome results revealed over expression of immune-related genes and the presence of eye parasite sequences in RNA-seq data obtained from perch living in clear-water lakes. Both PCR-based and targeted-metabarcoding approach showed that perch from humic lakes were completely free from diplostomid parasites, while the prevalence of eye flukes in clear-water lakes that contain low amounts of humic substances was close to 100%, with the majority of NGS reads assigned to Tylodelphys clavata. Conclusions High intraspecific diversity of T. clavata indicates that massively parallel sequencing of naturally pooled samples represents an efficient and powerful strategy for shedding light on cryptic diversity of eye parasites. Our results demonstrate that perch populations in clear-water lakes experience contrasting eye parasite pressure compared to those from humic lakes, which is reflected by prevalent differences in the expression of immune-related genes in the eye. This study highlights the utility of NGS to discover novel host-parasite-environment interactions and provide unprecedented power to characterize the molecular diversity of cryptic parasites.

Whole‐genome sequencing illuminates multifaceted targets of selection to humic substances in Eurasian perch

“…As such, these findings contrast recent reports in three‐spine stickleback (Marques et al, 2017) and Baltic herring (Hill et al, 2019), where a single amino acid change was shown to have a major effect on ecological adaptation. Nevertheless, recent work based on RNA‐sequencing analysis of the whole eye in Eurasian perch has shown differential expression of visual red‐, green‐ and short‐wavelength‐sensitive opsins ( OPN1LW / opn1lw1 , OPN1MW / opn1mw1 and OPN1SW / opn1sw2 , respectively) between humic and clear‐water environments (Noreikiene et al, 2020), indicating that regulation of visual opsin expression still occurs in humic lakes and may represent an important mechanism of adaptation.…”

“…Hence, increased DOC can also limit whole‐lake primary production and underwater higher vegetation, supporting the microbial loop and influencing resource availability and quality for consumers (Ask et al, 2009; Cole, 2009; Karlsson et al, 2009). Thus, DOC influences whole lake food‐webs from primary producers to top predators and parasites (Grether et al, 2001; Tobler & Path, 2011; Kaeuffer et al, 2012; Noreikiene et al, 2020).…”