Comparative transcriptomics of stickleback immune gene responses upon infection by two helminth parasites, Diplostomum pseudospathaceum and Schistocephalus solidus

Population-level immunologic variation in wild threespine stickleback (Gasterosteusaculeatus)

Wild organisms are regularly exposed to a wide range of parasites, requiring the management of an effective immune response while avoiding immunopathology. Currently, our knowledge of immunoparasitology primarily derives from controlled laboratory studies, neglecting the genetic and environmental diversity that contribute to immune phenotypes observed in wild populations. To gain insight into the immunologic variability in natural settings, we examined differences in immune gene expression of two Alaskan stickleback (Gasterosteus aculeatus) populations with varying susceptibility to infection by the cestode Schistocephalus solidus. Between these two populations, we found distinct immune gene expression patterns at the population level in response to infection with fish from the high-infection population displaying signs of parasite-driven immune manipulation. Further, we found significant differences in baseline immune gene profiles between the populations, with uninfected low-infection population fish showing signatures of inflammation compared to uninfected high-infection population fish. These results shed light on divergent responses of wild populations to the same parasite, providing valuable insights into host-parasite interactions in natural ecosystems.

Subtle transcriptomic response of Eurasian perch (Perca fluviatilis) associated with Triaenophorus nodulosus plerocercoid infection

Determining the physiological effects of parasites and characterizing genes involved in host responses to infections are essential to improving our understanding of host-parasite interactions and their ecological and evolutionary consequences. This task, however, is complicated by high diversity and complex life histories of many parasite species. The use of transcriptomics in the context of wild-caught specimens can help ameliorate this by providing both qualitative and quantitative information on gene expression patterns in response to parasites in specific host organs and tissues. Here, we evaluated the physiological impact of the widespread parasite, the pike tapeworm (Triaenophorus nodulosus), on its second intermediate host, the Eurasian perch (Perca fluviatilis). We used an RNAseq approach to analyse gene expression in the liver, the target organ of T. nodulosus plerocercoids, and spleen which is one of the main immune organs in teleost fishes. We compared perch collected from multiple lakes consisting of individuals with (n = 8) and without (n = 6) T. nodulosus plerocercoids in the liver. Results revealed a small number of differentially expressed genes (DEGs, adjusted p-value ≤0.05) in both spleen (n = 22) and liver (n = 10). DEGs in spleen consisted of mostly upregulated immune related genes (e.g., JUN, SIK1, THSB1), while those in the liver were often linked to metabolic functions (e.g., FABP1, CADM4, CDAB). However, Gene Ontology (GO) analysis showed lack of functional enrichment among DEGs. This study demonstrates that Eurasian perch displays a subtle response at a gene expression level to T. nodulosus plerocercoid infection. Given that plerocercoids are low-metabolic activity transmission stages, our results suggest that moderate T. nodulosus plerocercoid infection most likely does not provoke an extensive host immune response and have relatively low physiological costs for the host. Our findings illustrate that not all conspicuous infections have severe effects on host gene regulation.

Evolutionary gain and loss of a pathological immune response to parasitism

Parasites impose fitness costs on their hosts. Biologists often assume that natural selection favors infection-resistant hosts. Yet, when the immune response itself is costly, theory suggests that selection may sometimes favor loss of resistance, which may result in alternative stable states where some populations are resistant and others are tolerant. Intraspecific variation in immune costs is rarely surveyed in a manner that tests evolutionary patterns, and there are few examples of adaptive loss of resistance. Here, we show that when marine threespine stickleback colonized freshwater lakes, they gained resistance to the freshwater-associated cestode Schistocephalus solidus. Extensive peritoneal fibrosis and inflammation are a commonly observed phenotype that contributes to suppression of cestode growth and viability but also imposes a substantial cost on fecundity. Combining genetic mapping and population genomics, we find that opposing selection generates immune system differences between tolerant and resistant populations, consistent with divergent optimization.

Eye fluke effects on Danish freshwater fish: Field and experimental investigations

Eye flukes in fish are common in freshwater lakes. Fish become infected by the penetration of cercariae released from freshwater snails, and high infection pressures may be associated with mortalities in a Danish lake. Examination of two other freshwater lakes, combined with laboratory study, supported the notion. We investigated 77 freshwater fish from two lakes and the infection level suggested the occurrence of a high cercarial infection pressure in the Danish lakes. Dominant genera were Tylodelphys and Diplostomum covering a range of species identified by PCR and sequencing of the 18S (partial)-ITS1-5.8S-ITS2-28S (partial) of the rDNA. Cercariae of the prevalent species Diplostomum pseudospathaceum were used to infect zebrafish Danio rerio for the elucidation of short-term effects on the fish host. Zebrafish did not display abnormal behaviour when exposed to 200-400 cercariae, but a dosage of 600 and 1,000 cercariae/fish proved lethal. When fish were exposed to sublethal dosages, 19 out of 27 immune genes were significantly regulated and three genes encoding cytokine (IL 4/13B, IL-6 and IL-8) were upregulated at 3 hr post-infection (hpi), whereas others were downregulated especially at a later time point. We suggest that direct massive cercarial penetration of fish surfaces may be detrimental and may represent a threat to fish populations.

Between-population differences in constitutive and infection-induced gene expression in threespine stickleback

Vertebrate immunity is a complex system consisting of a mix of constitutive and inducible defences. Furthermore, host immunity is subject to selective pressure from a range of parasites and pathogens which can produce variation in these defences across populations. As populations evolve immune responses to parasites, they may adapt via a combination of (1) constitutive differences, (2) shared inducible responses, or (3) divergent inducible responses. Here, we leverage a powerful natural host‐parasite model system (Gasterosteus aculeatus and Schistochephalus solidus) to tease apart the relative contributions of these three types of adaptations to among‐population divergence in response to parasites. Gene expression analyses revealed limited evidence of significant divergence in constitutive expression of immune defence, and strong signatures of conserved inducible responses to the parasite. Furthermore, our results highlight a handful of immune‐related genes which show divergent inducible responses which may contribute disproportionately to functional differences in infection success or failure. In addition to investigating variation in evolutionary adaptation to parasite selection, we also leverage this unique data set to improve understanding of cellular mechanisms underlying a putative resistance phenotype (fibrosis). Combined, our results provide a case study in evolutionary immunology showing that a very small number of genes may contribute to genotype differences in infection response.

Characterization of viruses in a tapeworm: phylogenetic position, vertical transmission, and transmission to the parasitized host

Parasitic flatworms (Neodermata) infect all vertebrates and represent a significant health and economic burden worldwide due to the debilitating diseases they cause. This study sheds light for the first time into the virome of a tapeworm by describing six novel RNA virus candidate species associated with Schistocephalus solidus, including three negative-strand RNA viruses (order Jingchuvirales, Mononegavirales, and Bunyavirales) and three double-stranded RNA viruses. Using in vitro culture of S. solidus, controlled experimental infections and field sampling, we demonstrate that five of these viruses are vertically transmitted, and persist throughout the S. solidus complex life cycle. Moreover, we show that one of the viruses, named Schistocephalus solidus rhabdovirus (SsRV1), is excreted by the parasite and transmitted to parasitized hosts indicating that it may impact S. solidus-host interactions. In addition, SsRV1 has a basal phylogenetic position relative to vertebrate rhabdoviruses suggesting that parasitic flatworms could have contributed to virus emergence. Viruses similar to four of the S. solidus viruses identified here were found in geographically distant S. solidus populations through data mining. Further studies are necessary to determine if flatworm viruses can replicate in parasitized hosts, how they contribute to parasite infection dynamics and if these viruses could be targeted for treatment of parasitic disease.

Gene expression response to a nematode parasite in novel and native eel hosts

Invasive parasites are involved in population declines of new host species worldwide. The high susceptibilities observed in many novel hosts have been attributed to the lack of protective immunity to the parasites which native hosts acquired during their shared evolution. We experimentally infected Japanese eels (Anguilla japonica) and European eels (Anguilla anguilla) with Anguillicola crassus, a nematode parasite that is native to the Japanese eel and invasive in the European eel. We inferred gene expression changes in head kidney tissue from both species, using RNA-seq data to determine the responses at two time points during the early stages of infection (3 and 23 days postinfection). At both time points, the novel host modified the expression of a larger and functionally more diverse set of genes than the native host. Strikingly, the native host regulated immune gene expression only at the earlier time point and to a small extent while the novel host regulated these genes at both time points. A low number of differentially expressed immune genes, especially in the native host, suggest that a systemic immune response was of minor importance during the early stages of infection. Transcript abundance of genes involved in cell respiration was reduced in the novel host which may affect its ability to cope with harsh conditions and energetically demanding activities. The observed gene expression changes in response to a novel parasite that we observed in a fish follow a general pattern observed in amphibians and mammals, and suggest that the disruption of physiological processes, rather than the absence of an immediate immune response, is responsible for the higher susceptibility of the novel host.

Whole transcriptome analysis of the Atlantic cod vaccine response reveals subtle changes in adaptive immunity

Atlantic cod has lost the Major Histocompatibility complex class II pathway - central to pathogen presentation, humoral response and immunity. Here, we investigate the immunological response of Atlantic cod subsequent to dip vaccination with Vibrioanguillarum bacterin using transcriptome sequencing. The experiment was conducted on siblings from an Atlantic cod family found to be highly susceptible towards vibriosis where vaccination has demonstrated improved pathogen resistance. Gene expression analyses at 2, 4, 21 and 42 days post vaccination revealed GO-term enrichment for muscle, neuron and metabolism-related pathways. In-depth characterization of immune-related GO terms demonstrated down-regulation of MHCI antigen presentation, C-type lectin receptor signaling and granulocyte activation over time. Phagocytosis, interferon-gamma signaling and negative regulation of innate immunity were increasingly up-regulated over time. Individual differentially expressed immune genes implies weak initiation of acute phase proteins with little or no inflammation. Furthermore, gene expression indicates presence of T-cells, NK-like cells, B-cells and monocytes/macrophages. Three MHCI transcripts were up-regulated with B2M and SEC61. Overall, we find no clear immune-related transcriptomic response which could be attributed to Atlantic cod's alternative immune system. However, we cannot rule out that this response is related to vaccination protocol/sampling strategy. Earlier functional studies demonstrate significant memory in Atlantic cod post dip vaccination and combined with our results indicate the presence of other adaptive immunity mechanisms. In particular, we suggest that further investigations should look into CD8+ memory T-cells, γδ T-cells, T-cell independent memory or memory induced through NK-like/other lymphoid cells locally in the mucosal lining for this particular vaccination strategy.

The right response at the right time: Exploring helminth immune modulation in sticklebacks by experimental coinfection

Parasites are one of the strongest selective agents in nature. They select for hosts that evolve counter‐adaptive strategies to cope with infection. Helminth parasites are special because they can modulate their hosts’ immune responses. This phenomenon is important in epidemiological contexts, where coinfections may be affected. How different types of hosts and helminths interact with each other is insufficiently investigated. We used the three‐spined stickleback (Gasterosteus aculeatus) – Schistocephalus solidus model to study mechanisms and temporal components of helminth immune modulation. Sticklebacks from two contrasting populations with either high resistance (HR) or low resistance (LR) against S. solidus, were individually exposed to S. solidus strains with characteristically high growth (HG) or low growth (LG) in G. aculeatus. We determined the susceptibility to another parasite, the eye fluke Diplostomum pseudospathaceum, and the expression of 23 key immune genes at three time points after S. solidus infection. D. pseudospathaceum infection rates and the gene expression responses depended on host and S. solidus type and changed over time. Whereas the effect of S. solidus type was not significant after three weeks, T regulatory responses and complement components were upregulated at later time points if hosts were infected with HG S. solidus. HR hosts showed a well orchestrated immune response, which was absent in LR hosts. Our results emphasize the role of regulatory T cells and the timing of specific immune responses during helminth infections. This study elucidates the importance to consider different coevolutionary trajectories and ecologies when studying host‐parasite interactions.

Omics and cytokine discovery in fish: Presenting the Yellowtail kingfish (Seriola lalandi) as a case study

A continued programme of research is essential to overcome production bottlenecks in any aquacultured fish species. Since the introduction of genetic and molecular techniques, the quality of immune research undertaken in fish has greatly improved. Thousands of species specific cytokine genes have been discovered, which can be used to conduct more sensitive studies to understand how fish physiology is affected by aquaculture environments or disease. Newly available transcriptomic technologies, make it increasingly easier to study the immunogenetics of farmed species for which little data exists. This paper reviews how the application of transcriptomic procedures such as RNA Sequencing (RNA-Seq) can advance fish research. As a case study, we present some preliminary findings using RNA-Seq to identify cytokine related genes in Seriola lalandi. These will allow in-depth investigations to understand the immune responses of these fish in response to environmental change or disease and help in the development of therapeutic approaches.

Hook, Line and Infection: A Guide to Culturing Parasites, Establishing Infections and Assessing Immune Responses in the Three-Spined Stickleback

The three-spined stickleback (Gasterosteus aculeatus) is a model organism with an extremely well-characterized ecology, evolutionary history, behavioural repertoire and parasitology that is coupled with published genomic data. These small temperate zone fish therefore provide an ideal experimental system to study common diseases of coldwater fish, including those of aquacultural importance. However, detailed information on the culture of stickleback parasites, the establishment and maintenance of infections and the quantification of host responses is scattered between primary and grey literature resources, some of which is not readily accessible. Our aim is to lay out a framework of techniques based on our experience to inform new and established laboratories about culture techniques and recent advances in the field. Here, essential knowledge on the biology, capture and laboratory maintenance of sticklebacks, and their commonly studied parasites is drawn together, highlighting recent advances in our understanding of the associated immune responses. In compiling this guide on the maintenance of sticklebacks and a range of common, taxonomically diverse parasites in the laboratory, we aim to engage a broader interdisciplinary community to consider this highly tractable model when addressing pressing questions in evolution, infection and aquaculture.

Life History, Systematics and Evolution of the Diplostomoidea Poirier, 1886: Progress, Promises and Challenges Emerging From Molecular Studies

Members of the Diplostomoidea mature in amniotes and employ vertebrates, annelids and molluscs as second intermediate hosts. Diplostomoid life cycles generally follow a three-host pattern typical of digeneans, but novelties have arisen in some species, including obligate four-host life cycles, vertical transmission, and intracellular parasitism. In this review, we summarize the basic biology of diplostomoids with reference to molecular studies, and present challenges, gaps and areas where molecular data could address long-standing questions. Our analysis of published studies revealed that most molecular surveys find more diplostomoid species than expected, but this tendency is influenced by how much effort goes into examining specimens morphologically and the number of sequenced worms. To date, molecular work has concentrated disproportionately on intraspecific or species-level diversity of larval stages in the Diplostomidae in temperate northern regions. Although the higher taxonomy of the superfamily is recognized to be in need of revision, little molecular work has been conducted at this level. Our phylogenetic analysis indicates several families and subfamilies require reconsideration, and that larval morphotypes are more reflective of evolutionary relationships than definitive hosts. The host associations of adult diplostomoids result from host-switching processes, whereas molecular surveys indicate that larval diplostomoid metacercariae have narrow ranges of second intermediate hosts, consistent with coevolution. Molecular data are often used to link diplostomoid developmental stages, and we provide data from adult Neodiplostomum and Mesoophorodiplostomum that correct earlier misidentifications of their larval stages and propose alternatives to collecting definitive hosts.

Can environmental change affect host/parasite-mediated speciation?

Parasitism can be a driver of species divergence and thereby significantly alter species formation processes. While we still need to better understand how parasite-mediated speciation functions, it is even less clear how this process is affected by environmental change. Both rapid and gradual changes of the environment can modify host immune responses, parasite virulence and the specificity of their interactions. They will thereby change host-parasite evolutionary trajectories and the potential for speciation in both hosts and parasites. Here, we summarise mechanisms of host-parasite interactions affecting speciation and subsequently consider their susceptibility to environmental changes. We mainly focus on the effects of temperature change and nutrient input to ecosystems as they are major environmental stressors. There is evidence for both disruptive and accelerating effects of those pressures on speciation that seem to be context-dependent. A prerequisite for parasite-driven host speciation is that parasites significantly alter the host's Darwinian fitness. This can rapidly lead to divergent selection and genetic adaptation; however, it is likely preceded by more short-term plastic and transgenerational effects. Here, we also consider how these first responses and their susceptibility to environmental changes could lead to alterations of the species formation process and may provide alternative pathways to speciation.