RNA-Seq analysis of the guppy immune response against Gyrodactylus bullatarudis infection

Sex-dependent effects of infection on guppy reproductive fitness and offspring parasite resistance

Infection imposes energetic costs on hosts. Hosts typically respond by shifting resources, potentially affecting the quantity and quality of offspring they produce. As the sexes differ in their optimal reproductive strategies, the infection of mothers versus fathers may affect offspring quantity and quality in different ways. Here, we test how experimental infection of guppies Poecilia reticulata with the ectoparasite Gyrodactylus turnbulli affects parental reproductive fitness and offspring parasite resistance. We compared breeding pairs in which one or neither parent had previously been infected. In terms of reproductive fitness, pairs in which fathers had been infected produced more offspring than those in which mothers had been infected. Additionally, fathers who experienced the heaviest infections produced offspring ~55 days sooner than average. This result may represent terminal investment by males, especially those most affected by infection, or that males invest in reproduction at the expense of parasite defence. We found that offspring age, parental infection experience, and parental infection severity together strongly predicted offspring parasite resistance. Only among pairs in which one parent had been infected did older offspring, which were those born soonest after the parent's infection, tend to experience heavier infections. This result may reflect temporary infection-induced reductions in parental investment in offspring quality. Beyond this effect of offspring age, offspring of infected mothers experienced 105 fewer worm days than those of infected fathers: fathers, but not mothers, who experienced heavy infections themselves produced offspring that also experienced heavy infections. The parent-offspring regression for infected fathers is consistent with previous evidence that parasite resistance is heritable in this system and yields a narrow sense heritability estimate of 0.62 ± 0.12. By contrast, the mother-offspring regression (slope: -0.12 ± 0.14) provides novel insight that mothers may engage in transgenerational immune priming. Our results suggest that the sexes strike a different balance between offspring quantity and quality when faced with infection, with potentially broad implications for disease and host-parasite co-evolutionary dynamics in nature.

Transcriptomic analysis of immune-related genes in Pacific white snook (Centropomus viridis) gills infected with the monogenean parasite Rhabdosynochus viridisi

The parasite Rhabdosynochus viridisi (Platyhelminthes: Monogenea) infects the Pacific white snook Centropomus viridis gills and can cause adverse effects in the aquaculture industry. The immune responses of Pacific white snook to monogenean infections are poorly understood. Thus, this study aimed to identify differentially expressed genes (DEGs) in the gills of Pacific white snook juveniles experimentally infected with R. viridisi, emphasizing immune-related genes and pathways activated or suppressed during the infection. RNA sequencing was performed on the gills of uninfected (control) and infected fish. The algorithm Seq2Fun was selected without a reference transcriptome to map the reads to transcripts of fishes available from a database for gene orthologs (EcoOmics) and obtain the counting table. The ExpressAnalyst software was used for differential expression and functional analyses. A total of 20,106 transcripts were found, and 1430 (7 %) were differentially expressed genes (DEGs) between infected and control groups. We identified 860 (60 %) downregulated and 570 (40 %) upregulated genes. Thirteen canonical pathways after the Kyoto Encyclopedia of Genes and Genomes (KEGG) database were overrepresented, and most of the DEGs were downregulated, suggesting the inactivation of these pathways. The functions of most of the DEGs with higher fold change found in this study are poorly understood in fish. Even though the well-known pro-inflammatory cytokines remained unchanged in infected gills of C. viridis, and transforming growth factor β (tgfβ) was downregulated, interleukin-17 ligands il17d and il17a/f1, as well as C-X-C motif chemokine receptor 2 (cxcr2) genes were upregulated, indicating that the infection with R. viridisi promotes Th17-like immunity. Overexpression of plasma B cell activity markers such as immunoglobulin light chain-like genes and the v-set pre-B cell surrogate light chain 3 (vpreb3) was also detected in this study. The possible implications of DEGs related to calcium imbalance, hypoxia adaptation, hemostasis, and immunity are discussed. These results will support future studies to improve the prevention and treatment of monogenean infections in finfish aquaculture.

Assessing the chemical interactions and biological effects of a petrochemical and bio-based plastic with a common plastic flame retardant and solvent

Microplastic pollution remains a persistent environmental challenge for aquatic environments. Yet, health impact assessments of microplastics focus largely on the polymers themselves. It is important to understand the chemical behaviour and biological effects of both plastics and chemicals associated with their production, such as additives and solvents. Here, the individual and interactive chemical behaviour and biological impacts of two microplastics and two associated chemicals are assessed: polyvinyl chloride (PVC), a traditional petroleum-based plastic; polyhydroxyalkanoate (PHA) a novel bio-based plastic; triphenyl phosphate (TPhP), a common plastic flame retardant; and a widely use solvent dimethyl sulfoxide (DMSO). Thermogravimetric analysis and Nuclear Magnetic Resonance revealed no significant polymer chemical adsorption and desorption of TPhP or DMSO nor any evidence of reaction products between TPhP and DMSO. Biological assays on a freshwater fish host-parasite system, assessed fish growth, feeding, disease resistance and parasite survival. Both microplastics, the TPhP and solvent DMSO individually and interactively had no significant impact on fish growth. However, PVC alone and PHA + TPhP + DMSO significantly inhibited feeding behaviour of fish and increased mortality. Fish exposed to the solvent DMSO alone experienced the highest disease burdens. Interestingly, off-host survival of parasitic worms exposed to DMSO or TPhP + DMSO was higher than unexposed control worms. This study highlights the complex effects of microplastics and plastic associated chemicals on biological systems, and that novel bio-based plastics are not necessarily 'better' especially when associated with the same chemicals. Industry must be required to declare which chemicals are used in the manufacture of plastic products.

Role of the Pseudomonas plecoglossicida fliL gene in immune response of infected hybrid groupers (Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂)

Pseudomonas plecoglossicida, a gram-negative bacterium, is the main pathogen of visceral white-point disease in marine fish, responsible for substantial economic losses in the aquaculture industry. The FliL protein, involved in torque production of the bacterial flagella motor, is essential for the pathogenicity of a variety of bacteria. In the current study, the fliL gene deletion strain (ΔfliL), fliL gene complement strain (C-ΔfliL), and wild-type strain (NZBD9) were compared to explore the influence of the fliL gene on P. plecoglossicida pathogenicity and its role in host immune response. Results showed that fliL gene deletion increased the survival rate (50%) and reduced white spot disease progression in the hybrid groupers. Moreover, compared to the NZBD9 strain, the ΔfliL strain was consistently associated with lower bacterial loads in the grouper spleen, head kidney, liver, and intestine, coupled with reduced tissue damage. Transcriptomic analysis identified 2 238 differentially expressed genes (DEGs) in the spleens of fish infected with the ΔfliL strain compared to the NZBD9 strain. Based on Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, the DEGs were significantly enriched in seven immune system-associated pathways and three signaling molecule and interaction pathways. Upon infection with the ΔfliL strain, the toll-like receptor (TLR) signaling pathway was activated in the hybrid groupers, leading to the activation of transcription factors (NF-κB and AP1) and cytokines. The expression levels of proinflammatory cytokine-related genes IL-1β, IL-12B, and IL-6 and chemokine-related genes CXCL9, CXCL10, and CCL4 were significantly up-regulated. In conclusion, the fliL gene markedly influenced the pathogenicity of P. plecoglossicida infection in the hybrid groupers. Notably, deletion of fliL gene in P. plecoglossicida induced a robust immune response in the groupers, promoting defense against and elimination of pathogens via an inflammatory response involving multiple cytokines.

Restless nights when sick: ectoparasite infections alter rest-activity cycles of diurnal fish hosts

Circadian rhythms are timekeeping mechanisms responsible for an array of biological processes. Disruption of such cycles can detrimentally affect animal health. Circadian rhythms are critical in the co-evolution of host–parasite systems, as synchronization of parasite rhythms to the host can influence infection dynamics and transmission potential. This study examines the circadian rhythms in behaviour and activity of a model fish species (Poecilia reticulata) in isolation and in shoals, both when uninfected and infected with an ectoparasite (Gyrodactylus turnbulli). Additionally, the rhythmical variance of parasite activity under different light conditions as well as rhythmical variance in parasite transmissibility was explored. Overall, infection alters the circadian rhythm of fish, causing nocturnal restlessness. Increased activity of gyrodactylids on the host's skin at night could potentially contribute to this elevated host activity. Whilst migration of gyrodactylids across the host's skin may have caused irritation to the host resulting in nocturnal restlessness, the disruption in guppy activity rhythm caused by the expression of host innate immunity cannot be excluded. We discuss the wider repercussions such behavioural responses to infection have for host health, the implications for animal behaviour studies of diurnal species as well as the application of chronotherapeutic approaches to aquaculture.

Antigen Presentation and Autophagy in Teleost Adaptive Immunity

Infectious diseases are a burden for aquaculture. Antigen processing and presentation (APP) to the immune effector cells that fight pathogens is key in the adaptive immune response. At the core of the adaptive immunity that appeared in lower vertebrates during evolution are the variable genes encoding the major histocompatibility complex (MHC). MHC class I molecules mainly present peptides processed in the cytosol by the proteasome and transported to the cell surface of all cells through secretory compartments. Professional antigen-presenting cells (pAPC) also express MHC class II molecules, which normally present peptides processed from exogenous antigens through lysosomal pathways. Autophagy is an intracellular self-degradation process that is conserved in all eukaryotes and is induced by starvation to contribute to cellular homeostasis. Self-digestion during autophagy mainly occurs by the fusion of autophagosomes, which engulf portions of cytosol and fuse with lysosomes (macroautophagy) or assisted by chaperones (chaperone-mediated autophagy, CMA) that deliver proteins to lysosomes. Thus, during self-degradation, antigens can be processed to be presented by the MHC to immune effector cells, thus, linking autophagy to APP. This review is focused on the essential components of the APP that are conserved in teleost fish and the increasing evidence related to the modulation of APP and autophagy during pathogen infection.

Transmission dynamics of ectoparasitic gyrodactylids (Platyhelminthes, Monogenea): An integrative review

Parasite transmission is the ability of pathogens to move between hosts. As a key component of the interaction between hosts and parasites, it has crucial implications for the fitness of both. Here, we review the transmission dynamics of Gyrodactylus species, which are monogenean ectoparasites of teleost fishes and a prominent model for studies of parasite transmission. Particularly, we focus on the most studied host–parasite system within this genus: guppies, Poecilia reticulata, and G. turnbulli/G. bullatarudis. Through an integrative literature examination, we identify the main variables affecting Gyrodactylus spread between hosts, and the potential factors that enhance their transmission. Previous research indicates that Gyrodactylids spread when their current conditions are unsuitable. Transmission depends on abiotic factors like temperature, and biotic variables such as gyrodactylid biology, host heterogeneity, and their interaction. Variation in the degree of social contact between hosts and sexes might also result in distinct dynamics. Our review highlights a lack of mathematical models that could help predict the dynamics of gyrodactylids, and there is also a bias to study only a few species. Future research may usefully focus on how gyrodactylid reproductive traits and host heterogeneity promote transmission and should incorporate the feedbacks between host behaviour and parasite transmission.

Assembly-free rapid differential gene expression analysis in non-model organisms using DNA-protein alignment

BACKGROUND

RNA-seq is being increasingly adopted for gene expression studies in a panoply of non-model organisms, with applications spanning the fields of agriculture, aquaculture, ecology, and environment. For organisms that lack a well-annotated reference genome or transcriptome, a conventional RNA-seq data analysis workflow requires constructing a de-novo transcriptome assembly and annotating it against a high-confidence protein database. The assembly serves as a reference for read mapping, and the annotation is necessary for functional analysis of genes found to be differentially expressed. However, assembly is computationally expensive. It is also prone to errors that impact expression analysis, especially since sequencing depth is typically much lower for expression studies than for transcript discovery.

RESULTS

We propose a shortcut, in which we obtain counts for differential expression analysis by directly aligning RNA-seq reads to the high-confidence proteome that would have been otherwise used for annotation. By avoiding assembly, we drastically cut down computational costs - the running time on a typical dataset improves from the order of tens of hours to under half an hour, and the memory requirement is reduced from the order of tens of Gbytes to tens of Mbytes. We show through experiments on simulated and real data that our pipeline not only reduces computational costs, but has higher sensitivity and precision than a typical assembly-based pipeline. A Snakemake implementation of our workflow is available at: https://bitbucket.org/project_samar/samar .

CONCLUSIONS

The flip side of RNA-seq becoming accessible to even modestly resourced labs has been that the time, labor, and infrastructure cost of bioinformatics analysis has become a bottleneck. Assembly is one such resource-hungry process, and we show here that it can be avoided for quick and easy, yet more sensitive and precise, differential gene expression analysis in non-model organisms.

Recurrent expansions of B30.2-associated immune receptor families in fish

B30.2 domains, also known as PRY/SPRY, are key components of specific subsets of two large families of proteins involved in innate immunity: the tripartite motif proteins (TRIMs) and the Nod-like receptors (NLRs). TRIM proteins are important, often inducible factors of antiviral innate immunity, targeting multiple steps of viral cycles through a variety of mechanisms. NLRs prime and regulate systemic innate defenses, especially against bacteria, and control inflammation. Large TRIM and NLR subsets characterized by the presence of a B30.2 domain have been reported from a few fish species including zebrafish and seem to be strongly prone to gene duplication/expansion. Here, we performed a large-scale survey of these receptors across about 150 fish genomes, focusing on ray-finned fishes. We assessed the number and genomic distribution of domains and domain combinations associated with TRIMs, NLRs, and other genes containing B30.2 domains and looked for gene expansion patterns across fish groups. We then used a model to test the impact of taxonomy, genome size, and environmental variables on the copy numbers of these genes. Our findings reveal novel domain structures, clade-specific gains and losses. They also assist with the timing of the gene expansions, reveal patterns associated with the MHC, and lay the groundwork for further studies delving deeper into the forces that drive the copy number variation of immune genes on a species level.

To React or Not to React: The Dilemma of Fish Immune Systems Facing Myxozoan Infections

Myxozoans are microscopic, metazoan, obligate parasites, belonging to the phylum Cnidaria. In contrast to the free-living lifestyle of most members of this taxon, myxozoans have complex life cycles alternating between vertebrate and invertebrate hosts. Vertebrate hosts are primarily fish, although they are also reported from amphibians, reptiles, trematodes, mollusks, birds and mammals. Invertebrate hosts include annelids and bryozoans. Most myxozoans are not overtly pathogenic to fish hosts, but some are responsible for severe economic losses in fisheries and aquaculture. In both scenarios, the interaction between the parasite and the host immune system is key to explain such different outcomes of this relationship. Innate immune responses contribute to the resistance of certain fish strains and species, and the absence or low levels of some innate and regulatory factors explain the high pathogenicity of some infections. In many cases, immune evasion explains the absence of a host response and allows the parasite to proliferate covertly during the first stages of the infection. In some infections, the lack of an appropriate regulatory response results in an excessive inflammatory response, causing immunopathological consequences that are worse than inflicted by the parasite itself. This review will update the available information about the immune responses against Myxozoa, with special focus on T and B lymphocyte and immunoglobulin responses, how these immune effectors are modulated by different biotic and abiotic factors, and on the mechanisms of immune evasion targeting specific immune effectors. The current and future design of control strategies for myxozoan diseases is based on understanding this myxozoan-fish interaction, and immune-based strategies such as improvement of innate and specific factors through diets and additives, host genetic selection, passive immunization and vaccination, are starting to be considered.

Functional immunogenetic variation, rather than local adaptation, predicts ectoparasite infection intensity in a model fish species

Natural host populations differ in their susceptibility to infection by parasites, and these intrapopulation differences are still an incompletely understood component of host‐parasite dynamics. In this study, we used controlled infection experiments with wild‐caught guppies (Poecilia reticulata) and their ectoparasite Gyrodactylus turnbulli to investigate the roles of local adaptation and host genetic composition (immunogenetic and neutral) in explaining differences in susceptibility to infection. We found differences between our four study host populations that were consistent between two parasite source populations, with no indication of local adaptation by either host or parasite at two tested spatial scales. Greater values of host population genetic variability metrics broadly aligned with lower population mean infection intensity, with the best alignments associated with major histocompatibility complex (MHC) “supertypes”. Controlling for intrapopulation differences and potential inbreeding variance, we found a significant negative relationship between individual‐level functional MHC variability and infection: fish carrying more MHC supertypes experienced infections of lower severity, with limited evidence for supertype‐specific effects. We conclude that population‐level differences in host infection susceptibility probably reflect variation in parasite selective pressure and/or host evolutionary potential, underpinned by functional immunogenetic variation.