Integrated field, laboratory, and theoretical study of PKD spread in a Swiss prealpine river

When does a parasite become a disease? eDNA unravels complex host-pathogen dynamics across environmental stress gradients in wild salmonid populations

Infectious diseases stem from disrupted interactions among hosts, parasites, and the environment. Both abiotic and biotic factors can influence infection outcomes by shaping the abundance of a parasite's infective stages, as well as the host's ability to fight infection. However, disentangling these mechanisms within natural ecosystems remains challenging. Here, combining environmental DNA analysis and niche modelling at a regional scale, we uncovered the biotic and abiotic drivers of an infectious disease of salmonid fish, triggered by the parasite Tetracapsuloides bryosalmonae. We found that the occurrence and abundance of the parasite in the water-i.e., the propagule pressure- were mainly correlated to the abundances of its two primary hosts, the bryozoan Fredericella sultana and the fish Salmo trutta, but poorly to local abiotic environmental stressors. In contrast, the occurrence and abundance of parasites within fish hosts-i.e., proxies for disease emergence-were closely linked to environmental stressors (water temperature, agricultural activities, dams), and to a lesser extent to parasite propagule pressure. These results suggest that pathogen distribution alone cannot predict the risk of disease in wildlife, and that local anthropogenic stressors may play a pivotal role in disease emergence among wild host populations, likely by modulating the hosts' immune response. Our study sheds light on the intricate interplay between biotic and abiotic factors in shaping pathogen distribution and raises concerns about the effects of global change on pathogen emergence.

Description, life cycle, and development of the myxozoan Myxobolus rasmusseni n. sp. in fathead minnows, Pimephales promelas: A possible emerging pathogen in southern Alberta, Canada

Morphological, gene sequence, host tissue tropism, and life cycle characteristics were utilized to describe the myxozoan, Myxobolus rasmusseni n. sp. from fathead minnow, Pimephales promelas, collected from reservoirs in southern Alberta. Results from serial histological sections of whole heads showed that myxospores were contained within irregular-shaped and sized coelozoic capsules (=plasmodia). Clusters of membrane-bound, myxospore-filled plasmodia filled the head cavities of juvenile fathead minnows, leading to the development of large, white, disfiguring lesions in mid to late summer. Bilateral exopthalmia (pop-eye disease) was a common outcome of M. rasmusseni n. sp. development. BLASTn search of a 1974 bp sequence of the 18S rDNA gene isolated from myxospores indicated that M. rasmusseni n. sp. was distinct from other coelozoic and histozoic Myxobolus spp. cataloged in GenBank. 18S rDNA gene sequences from triactinomyxon spores released from the oligochaete Tubifex were 100% identical to sequences from myxospores collected from syntopic fathead minnows. Results from a longitudinal survey of the 2020 cohort of fathead minnows showed that young-of-the-year are exposed at 1-5 mo and that 60-90% of these had developed myxospore-filled lesions approximately one year later. Data regarding potential sources and timing of M. rasmusseni n. sp. emergence in fathead minnow populations are needed.

Helminth ecological requirements shape the impact of climate change on the hazard of infection

Outbreaks and spread of infectious diseases are often associated with seasonality and environmental changes, including global warming. Free-living stages of soil-transmitted helminths are highly susceptible to climatic drivers; however, how multiple climatic variables affect helminth species, and the long-term consequences of these interactions, is poorly understood. We used experiments on nine trichostrongylid species of herbivores to develop a temperature- and humidity-dependent model of infection hazard, which was then implemented at the European scale under climate change scenarios. Intestinal and stomach helminths exhibited contrasting climatic responses, with the former group strongly affected by temperature while the latter primarily impacted by humidity. Among the demographic traits, larval survival heavily modulated the infection hazard. According to the specific climatic responses of the two groups, climate change is expected to generate differences in the seasonal and spatial shifts of the infection hazard and group co-circulation. In the future, an intensification of these trends could create new opportunities for species range expansion and co-occurrence at European central-northern latitudes.

Spatial and intra-host distribution of myxozoan parasite Tetracapsuloides bryosalmonae among Baltic sea trout (Salmo trutta)

Proliferative kidney disease caused by the myxozoan parasite Tetracapsuloides bryosalmonae has been actively studied in juvenile salmonids for decades. However, very little is known about parasite prevalence and its geographical and intra-host distribution at older life stages. We screened T. bryosalmonae among adult sea trout (Salmo trutta) (n = 295) collected along the Estonian Baltic Sea coastline together with juvenile trout from 33 coastal rivers (n = 1752) to assess spatial infection patterns of the adult and juvenile fish. The parasite was detected among 38.6% of adult sea trout with the prevalence increasing from west to east, and south to north, along the coastline. A similar pattern was observed in juvenile trout. Infected sea trout were also older than uninfected fish and the parasite was detected in sea trout up to the age of 6 years. Analysis of intra-host distribution of the parasite and strontium to calcium ratios from the otoliths revealed that (re)infection through freshwater migration may occur among adult sea trout. The results of this study indicate that T. bryosalmonae can persist in a brackish water environment for several years and that returning sea trout spawners most likely contribute to the parasite life cycle by transmitting infective spores.

Using environmental DNA metabarcoding to monitor fish communities in small rivers and large brooks: Insights on the spatial scale of information

Monitoring fish communities is central to the evaluation of ecological health of rivers. Both presence/absence of fish species and their relative quantity in local fish assemblages are crucial parameters to measure. Fish communities in lotic systems are traditionally monitored via electrofishing, characterized by a known limited efficiency and high survey costs. Analysis of environmental DNA could serve as a non-destructive alternative for detection and quantification of lotic fish communities, but this approach still requires further insights in practical sampling schemes incorporating transport and dilution of the eDNA particles; optimization of predictive power and quality assurance of the molecular detection method. Via a controlled cage experiment, we aim to extend the knowledge on streamreach of eDNA in small rivers and large brooks, as laid out in the European Water Framework Directive's water typology. Using a high and low source biomass in two river transects of a species-poor river characterized by contrasting river discharge rates, we found strong and significant correlations between the eDNA relative species abundances and the relative biomass per species in the cage community. Despite a decreasing correlation over distance, the underlying community composition remained stable from 25 to 300 m, or up to 1 km downstream of the eDNA source, depending on the river discharge rate. Such decrease in similarity between relative source biomass and the corresponding eDNA-based community profile with increasing distance downstream from the source, might be attributed to variation in species-specific eDNA persistence. Our findings offer crucial insights on eDNA behaviour and characterization of riverine fish communities. We conclude that water sampled from a relatively small river offers an adequate eDNA snapshot of the total fish community in the 300-1000 m upstream transect. The potential application for other river systems is further discussed.

Modelling environmental DNA transport in rivers reveals highly resolved spatio-temporal biodiversity patterns

The ever-increasing threats to riverine ecosystems call for novel approaches for highly resolved biodiversity assessments across taxonomic groups and spatio-temporal scales. Recent advances in the joint use of environmental DNA (eDNA) data and eDNA transport models in rivers (e.g., eDITH) allow uncovering the full structure of riverine biodiversity, hence elucidating ecosystem processes and supporting conservation measures. We applied eDITH to a metabarcoding dataset covering three taxonomic groups (fish, invertebrates, bacteria) and three seasons for a catchment sampled for eDNA at 73 sites. We upscaled eDNA-based biodiversity predictions to approximately 1900 reaches, and assessed α- and β-diversity patterns across seasons and taxonomic groups over the whole network. Genus richness predicted by eDITH was generally higher than values from direct eDNA analysis. Both predicted α- and β-diversity varied depending on season and taxonomic group. Predicted fish α-diversity increased downstream in all seasons, while invertebrate and bacteria α-diversity either decreased downstream or were unrelated to network position. Spatial β-diversity mostly decreased downstream, especially for bacteria. The eDITH model yielded a more refined assessment of freshwater biodiversity as compared to raw eDNA data, both in terms of spatial coverage, diversity patterns and effect of covariates, thus providing a more complete picture of freshwater biodiversity.

Environmental DNA/RNA for pathogen and parasite detection, surveillance, and ecology

Detection of pathogens, parasites, and other symbionts in environmental samples via eDNA/eRNA (collectively eNA) is an increasingly important source of information about their occurrence and activity. There is great potential for using such detections as a proxy for infection of host organisms in connected habitats, for pathogen monitoring and surveillance, and for early warning systems for disease. However, many factors require consideration, and appropriate methods developed and verified, in order that eNA detections can be reliably interpreted and adopted for surveillance and assessment of disease risk, and potentially inclusion in international standards, such as the World Organisation for Animal Health guidelines. Disease manifestation results from host-symbiont-environment interactions between hosts, demanding a multifactorial approach to interpretation of eNA signals.

Ecohydrology 2.0

This paper aims at a definition of the domain of ecohydrology, a relatively new discipline borne out of an intrusion-as advertised by this Topical Collection of the Rendiconti Lincei-of hydrology and geomorphology into ecology (or vice-versa, depending on the reader's background). The study of hydrologic controls on the biota proves, in our view, significantly broader than envisioned by its original focus that was centered on the critical zone where much of the action of soil, climate and vegetation interactions takes place. In this review of related topics and contributions, we propose a reasoned broadening of perspective, in particular by firmly centering ecohydrology on the fluvial catchment as its fundamental control volume. A substantial unity of materials and methods suggests that our advocacy may be considered legitimate.

Mitigating human impacts including climate change on proliferative kidney disease in salmonids of running waters

Over the last two decades, an increasing number of reports have identified a decline in salmonid populations, possibly linked to infection with the parasite Tetracapsuloides bryosalmonae and the corresponding disease, that is, proliferative kidney disease (PKD). The life cycle of this myxozoan parasite includes sessile bryozoan species as invertebrate host, which facilitates the distribution of the parasite in running waters. As the disease outcome is temperature dependent, the impact of the disease on salmonid populations is increasing with global warming due to climate change. The goal of this review is to provide a detailed overview of measures to mitigate the effects of PKD on salmonid populations. It first summarizes the parasite life cycle, temperature-driven disease dynamics and new immunological and molecular research into disease resistance and, based on this, discusses management possibilities. Sophisticated management actions focusing on local adaptation of salmonid populations, restoration of the riverine ecosystem and keeping water temperatures cool are necessary to reduce the negative effects of PKD. Such actions include temporary stocking with PKD-resistant salmonids, as this may assist in conserving current populations that fail to reproduce.

Method for Isolation of Myxozoan Proliferative Stages from Fish at High Yield and Purity: An Essential Prerequisite for In Vitro, In Vivo and Genomics-Based Research Developments

Myxozoans are a diverse group of microscopic cnidarian parasites and some representatives are associated with important diseases in fish, in both marine and freshwater aquaculture systems. Research on myxozoans has been largely hampered by the inability to isolate myxozoan parasites from their host tissues. In this study, we developed and optimized a method to isolate the myxozoan proliferative stages of different size and cellularity from fish blood, using DEAE-cellulose ion exchange chromatography. We optimized several parameters and obtained 99–100% parasite purity, as well as high survival and infectivity. Using polyclonal pan-carp blood cell-specific antibodies, we further developed a rapid cytometric assay for quantification of the proliferative stages, not only in highly concentrated DEAE-C isolates but also in dilute conditions in full blood. Early developmental stages of myxozoans are key to parasite proliferation, establishment, and pathology in their hosts. The isolation of these stages not only opens new possibilities for in vivo and in vitro studies, but also for obtaining purified DNA and protein extracts for downstream analyses. Hence, we provide a long-desired tool that will advance the functional research into the mechanisms of host exploitation and immune stimulation/evasion in this group, which could contribute greatly to the development of therapeutic strategies against myxozoans.

Kinetics of Parasite-Specific Antibody and B-Cell-Associated Gene Expression in Brown Trout, Salmo trutta during Proliferative Kidney Disease

Tetracapsuloides bryosalmonae, a myxozoan endoparasite often causes chronic infection in brown trout. Antiparasite immunity mediated by antibodies and B cells is known as an important determinant of host survival and parasite proliferation during chronic infections. Accordingly, studying their time course during proliferative kidney disease (PKD) might be helpful in improving our understanding of its chronic nature. Therefore, we conducted this study to examine parasite specific serum antibody and B-cell-mediated response in laboratory-infected brown trout at different time points. Brown trout were exposed to the spores of T. bryosalmonae, derived from infected bryozoans. Samples were collected at different time points and processed for indirect ELISA, histopathology, and qRT-PCR. T. bryosalmonae specific antibody was detected at 4 weeks post exposure (wpe) and it persisted until 17 wpe. Additionally, the expressions of C4A, CD34, CD79A, BLNK, CD74, BCL7, and CD22 were differentially regulated in the important immune organs, kidney and spleen. To our knowledge, this is the first study addressing anti-T. bryosalmonae antibody response in brown trout at different time points. The results from this study provide valuable insights into the processes leading to changes in B cell development, inflammation and antibody production during the course of PKD in brown trout.

Parasite DNA detection in water samples enhances crayfish plague monitoring in asymptomatic invasive populations

Invasive species can facilitate the spread of pathogens by first providing asymptomatic host reservoirs, and then driving disease outbreaks in native populations through pathogen spillover. An example of this are invasive crayfish species in Europe (Faxonius limosus, Pacifastacus leniusculus, Procambarus clarkii), which carry the deadly plague agent (Aphanomyces astaci). Effective disease management requires comprehensive monitoring, however, pathogen detection in carrier populations with low pathogen prevalence and intensities is challenging. We simultaneously collected and analysed crayfish tissue samples of invasive crayfish populations and water samples to compare A. astaci detection in different sample types using quantitative PCR. Combined, the two sampling methods revealed A. astaci presence with DNA concentrations above limit of detection (LOD; the lowest concentration which can be detected with reasonable certainty) in 13 of 23 invasive crayfish populations. In four additional sites, A. astaci DNA concentrations below LOD were found in water. In four populations only were A. astaci concentrations above LOD detected in both sample types and in three populations in concentrations above LOD in tissue but below LOD in water. The likely reason for these discrepancies is the low A. astaci prevalence and concentration in resistant invasive crayfish, which limit detection reliability. Consistency may be improved by timing surveys with seasonal periods of high A. astaci abundance and by increasing water sampling effort. Considering the ease of collecting eDNA samples, compared to crayfish tissue sampling, eDNA methods would facilitate frequent and comprehensive surveys. However, remaining uncertainties in eDNA-based detection reveal the relevance of combining monitoring tools to improve detection of invasive pathogens and their management.

Effect of water temperature on the morbidity of Tetracapsuloides bryosalmonae (Myxozoa) to brown trout (Salmo trutta) under laboratory conditions

Proliferative kidney disease (PKD) is a disease found in salmonid fish that is widespread in Europe and North America. The dependency of the clinical signs on the water temperature is extensively reported in rainbow trout, but detailed information on brown trout is lacking. In this study, juvenile brown trout were exposed to the spores of Tetracapsuloides bryosalmonae and then kept at different ambient water temperatures (16°C, 19°C and 22°C) for 10 weeks along with recording of morbidity throughout the experiment. At 6, 8 and 10 weeks post-exposure, fish from each temperature group were sampled and underwent pathoanatomical examination to survey disease progression. At 16°C, brown trout showed a significantly higher survival probability compared to those kept in 19°C and 22°C water. Additionally, the parasitic burden (MSQ) was higher and the clinical signs were more pronounced in the brown trout kept at 19°C and 22°C compared with the ones kept at 16°C. This study highlights the correlation of PKD outbreaks and water temperature increases related to global climate change, which will impact the future distribution of brown trout in natural waters.

It's a hard knock life for some: Heterogeneity in infection life history of salmonids influences parasite disease outcomes

Heterogeneity in immunity occurs across numerous disease systems with individuals from the same population having diverse disease outcomes. Proliferative kidney disease (PKD) caused by Tetracapsuloides bryosalmonae, is a persistent parasitic disease negatively impacting both wild and farmed salmonids. Little is known of how PKD is spread or maintained within wild susceptible populations. We investigated an aspect of fish disease that has been largely overlooked, that is, the role of the host phenotypic heterogeneity in disease outcome. We examined how host susceptibility to T. bryosalmonae infection, and the disease PKD, varied across different infection life-history stages and how it differs between naïve, re-infected and persistently infected hosts. We investigated the response to parasite exposure in host phenotypes with (a) different ages and (b) heterogeneous infection life histories. Among (a) the age phenotypes were young-of-the-year (YOY) fish and juvenile 1+ fish (fish older than one) and, for (b) juvenile 1+ infection survivors were either re-exposed or not re- exposed to the parasite and response phenotypes were assigned post-hoc dependant on infection status. In fish not re-exposed this included fish that cleared infection (CI) or had a persistent infection (PI). In fish re-exposed these included fish that were re-infected (RI), or re-exposed and uninfected (RCI). We assessed both parasite-centric (infection prevalence, parasite burden, malacospore transmission) and host-centric parameters (growth rates, disease severity, infection tolerance and the immune response). In (a), YOY fish, parasite success and disease severity were greater and differences in the immune response occurred, demonstrating an ontogenetic decline of susceptibility in older fish. In (b), in PI and RI fish, parasite success and disease severity were comparable. However, expression of several adaptive immunity markers was greater in RI fish, indicating concomitant immunity, as re-exposure did not intensify infection. We demonstrate the relevance of heterogeneity in infection life history on disease outcome and describe several distinctive features of immune ontogeny and protective immunity in this model not previously reported. The relevance of such themes on a population level requires greater research in many aquatic disease systems to generate clearer framework for understanding the spread and maintenance of aquatic pathogens.

Climate change-driven disease in sympatric hosts: Temporal dynamics of parasite burden and proliferative kidney disease in wild brown trout and Atlantic salmon

Global climate change is altering the abundance and spread of various parasites, which has important consequences not only for host-parasite interactions but also for the relationships between different host species. Here, we focus on the myxozoan endoparasite Tetracapsuloides bryosalmonae that causes temperature-dependent proliferative kidney disease (PKD) in salmonids. We characterized the temporal changes in the parasite load and the severity of PKD signs (renal hyperplasia, haematocrit) in two sympatric populations of wild brown trout (Salmo trutta) and Atlantic salmon (Salmo salar). We found that both the parasite load and disease signs vary considerably between individuals, species, rivers and sampling periods. We showed that Atlantic salmon was able to slow down the initial parasite proliferation rate and subsequently tolerate high parasite burden without obvious disease signs. In contrast, the initial parasite proliferation rate was much higher in brown trout, which was followed by the development of severe PKD signs. Thus, the speed of parasite proliferation, rather than the absolute number of the parasites in the host kidney, may play an important role in interspecific variation in PKD susceptibility. To conclude, this study illustrates the usefulness of temporal perspective for understanding host defence mechanisms and climate change-mediated impacts in the wild.

The role of migration barriers for dispersion of Proliferative Kidney Disease-Balance between disease emergence and habitat connectivity

Natural and uninterrupted water courses are important for biodiversity and fish population stability. Nowadays, many streams and rivers are obstructed by artificial migration barriers, often preventing the migration of fish. On the other hand, distribution of pathogens by migrating fishes is still a point of concern. Pathogen transport and transmission is a driving force in the dynamics of many infectious diseases. The aim of the study was to investigate the possible consequences of the removal of an artificial migration barrier for the upstream transport of Tetracapsuloides bryosalmonae, the causative agent of Proliferative Kidney Disease (PKD) in brown trout, by migrating fish. To test this question, a river system was selected with a migration barrier separating a PKD positive river from a PKD negative tributary. After removal of the barrier, PKD prevalence and pathology was examined during five years after elimination of the barrier. In the tributary, no PKD was recorded at any time of the survey. By means of unidirectional PIT (passive integrated transponder)-tagging, we confirmed upstream migration of adult brown trout into the tributary during the cold season, presumably for spawning. By eDNA, we confirmed presence of T. bryoalmonae and Fredericella sp., the definitive host, DNA in water from the PKD positive river stretch, but not in the PKD negative tributary. Our study illustrates the importance of the connectivity of streams for habitat maintenance. Although migration of brown trout from a PKD-positive river into a PKD-negative tributary, mainly for spawning, was confirmed, upstream spreading of PKD was not observed.

Advances and Discoveries in Myxozoan Genomics

Myxozoans are highly diverse and globally distributed cnidarian endoparasites in freshwater and marine habitats. They have adopted a heteroxenous life cycle, including invertebrate and fish hosts, and have been associated with diseases in aquaculture and wild fish stocks. Despite their importance, genomic resources of myxozoans have proven difficult to obtain due to their miniaturized and derived genome character and close associations with fish tissues. The first 'omic' datasets have now become the main resource for a better understanding of host-parasite interactions, virulence, and diversity, but also the evolutionary history of myxozoans. In this review, we discuss recent genomic advances in the field and outline outstanding questions to be answered with continuous and improved efforts of generating myxozoan genomic data.

Comparative transcriptomics and host-specific parasite gene expression profiles inform on drivers of proliferative kidney disease

The myxozoan parasite, Tetracapsuloidesbryosalmonae has a two-host life cycle alternating between freshwater bryozoans and salmonid fish. Infected fish can develop Proliferative Kidney Disease, characterised by a gross lymphoid-driven kidney pathology in wild and farmed salmonids. To facilitate an in-depth understanding of T.bryosalmonae-host interactions, we have used a two-host parasite transcriptome sequencing approach in generating two parasite transcriptome assemblies; the first derived from parasite spore sacs isolated from infected bryozoans and the second from infected fish kidney tissues. This approach was adopted to minimize host contamination in the absence of a complete T.bryosalmonae genome. Parasite contigs common to both infected hosts (the intersect transcriptome; 7362 contigs) were typically AT-rich (60–75% AT). 5432 contigs within the intersect were annotated. 1930 unannotated contigs encoded for unknown transcripts. We have focused on transcripts encoding proteins involved in; nutrient acquisition, host–parasite interactions, development, cell-to-cell communication and proteins of unknown function, establishing their potential importance in each host by RT-qPCR. Host-specific expression profiles were evident, particularly in transcripts encoding proteases and proteins involved in lipid metabolism, cell adhesion, and development. We confirm for the first time the presence of homeobox proteins and a frizzled homologue in myxozoan parasites. The novel insights into myxozoan biology that this study reveals will help to focus research in developing future disease control strategies.

Natural Feed Additives Modulate Immunity and Mitigate Infection with Sphaerospora molnari (Myxozoa:Cnidaria) in Common Carp: A Pilot Study

Myxozoans are a diverse group of cnidarian parasites, including important pathogens in different aquaculture species, without effective legalized treatments for fish destined for human consumption. We tested the effect of natural feed additives on immune parameters of common carp and in the course of a controlled laboratory infection with the myxozoan Sphaerospora molnari. Carp were fed a base diet enriched with 0.5% curcumin or 0.12% of a multi-strain yeast fraction, before intraperitoneal injection with blood stages of S. molnari. We demonstrate the impact of these treatments on respiratory burst, phagocytosis, nitric oxide production, adaptive IgM+ B cell responses, S. molnari-specific antibody titers, and on parasite numbers. Both experimental diets enriched B cell populations prior to infection and postponed initial parasite proliferation in the blood. Curcumin-fed fish showed a decrease in reactive oxygen species, nitric oxide production and B cell density at late-stage infection, likely due to its anti-inflammatory properties, favoring parasite propagation. In contrast, multi-strain yeast fraction (MsYF)-fed fish harbored the highest S. molnari-specific antibody titer, in combination with the overall lowest parasite numbers. The results demonstrate that yeast products can be highly beneficial for the outcome of myxozoan infections and could be used as effective feed additives in aquaculture.

Validation of an eDNA-based method for the detection of wildlife pathogens in water

Monitoring the occurrence and density of parasites and pathogens can identify high infection-risk areas and facilitates disease control and eradication measures. Environmental DNA (eDNA) techniques are increasingly used for pathogen detection due to their relative ease of application. Since many factors affect the reliability and efficacy of eDNA-based detection, rigorous validation and assessment of method limitations is a crucial first step. We evaluated an eDNA detection method using in situ filtration of large-volume water samples, developed to detect and quantify aquatic wildlife parasites by quantitative PCR (qPCR). We assessed method reliability using Batrachochytrium dendrobatidis, a pathogenic fungus of amphibians and the myxozoan Tetracapsuloides bryosalmonae, causative agent of salmonid proliferative kidney disease, in a controlled experimental setup. Different amounts of parasite spores were added to tanks containing either clean tap water or water from a semi-natural mesocosm community. Overall detection rates were higher than 80%, but detection was not consistent among replicate samples. Within-tank variation in detection emphasises the need for increased site-level replication when dealing with parasites and pathogens. Estimated parasite DNA concentrations in water samples were highly variable, and a significant increase with higher spore concentrations was observed only for B. dendrobatidis. Despite evidence for PCR inhibition in DNA extractions from mesocosm water samples, the type of water did not affect detection rates significantly. Direct spiking controls revealed that the filtration step reduced detection sensitivity. Our study identifies sensitive quantification and sufficient replication as major remaining challenges for the eDNA-based methods for detection of parasites in water.

A portrait of the immune response to proliferative kidney disease (PKD) in rainbow trout

Proliferative kidney disease (PKD), caused by the myxozoan Tetracapsuloides bryosalmonae, is one of the most serious parasitic diseases of salmonids in which outbreaks cause severe economic constraints for the aquaculture industry and declines of wild species throughout Europe and North America. Given that rainbow trout (Oncorhynchus mykiss) is one of the most widely farmed freshwater fish and an important model species for fish immunology, most of the knowledge on how the fish immune response is affected during PKD is from this organism. Once rainbow trout are infected, PKD pathogenesis results in a chronic kidney immunopathology mediated by decreasing myeloid cells and increasing lymphocytes. Transcriptional studies have revealed the regulation of essential genes related to T-helper (Th)-like functions and a dysregulated B-cell antibody type response. Recent reports have discovered unique details of teleost B-cell differentiation and functionality and characterized the differential immunoglobulin (Ig)-mediated response. These studies have solidified the rainbow trout T. bryosalmonae system as a sophisticated disease model capable of feeding key advances into mainstream immunology and have contributed essential information to design novel parasite disease prevention strategies. In our following perspective, we summarize these efforts to evaluate the immune mechanisms of rainbow trout during PKD pathogenesis.

On the potential role of Mergus merganser as transport hosts for Tetracapsuloides bryosalmonae

Transmission paths in the distribution of proliferative kidney disease (PKD) of salmonids are still largely unknown. In this study, the role of goosander (Mergus merganser) as possible transport host for Tetracapsuloides bryosalmonae through faeces was examined. Goosander fledglings were fed exclusively with diseased brown trout (Salmo trutta fario). In all trout used for feeding, intratubular sporogonic stage of the parasite was confirmed histologically. Between one to 10 hours post-feeding, the goosander faeces were sampled and tested for T. bryosalmonae DNA. In qPCR, only DNA fragments were found, and in conventional PCR, no amplification was confirmed. Therefore, we hypothesize that the role of goosander as transport hosts for T. bryosalmonae via their faeces can be neglected.

Environmental DNA allows upscaling spatial patterns of biodiversity in freshwater ecosystems

The alarming declines of freshwater biodiversity call for efficient biomonitoring at fine spatiotemporal scales, such that conservation measures be grounded upon accurate biodiversity data. Here, we show that combining environmental DNA (eDNA) extracted from stream water samples with models based on hydrological first principles allows upscaling biodiversity estimates for aquatic insects at very high spatial resolution. Our model decouples the diverse upstream contributions to the eDNA data, enabling the reconstruction of taxa distribution patterns. Across a 740-km2 basin, we obtain a space-filling biodiversity prediction at a grain size resolution of 1-km long stream sections. The model's accuracy in matching direct observations of aquatic insects' local occurrence ranges between 57-100%. Our results demonstrate how eDNA can be used for high-resolution biodiversity assessments in rivers with minimal prior knowledge of the system. Our approach allows identification of biodiversity hotspots that could be otherwise overlooked, enabling implementation of focused conservation strategies.

Transcriptome of Sphaerospora molnari (Cnidaria, Myxosporea) blood stages provides proteolytic arsenal as potential therapeutic targets against sphaerosporosis in common carp

Background

Parasites employ proteases to evade host immune systems, feed and replicate and are often the target of anti-parasite strategies to disrupt these interactions. Myxozoans are obligate cnidarian parasites, alternating between invertebrate and fish hosts. Their genes are highly divergent from other metazoans, and available genomic and transcriptomic datasets are limited. Some myxozoans are important aquaculture pathogens such as Sphaerospora molnari replicating in the blood of farmed carp before reaching the gills for sporogenesis and transmission. Proliferative stages cause a massive systemic lymphocyte response and the disruption of the gill epithelia by spore-forming stages leads to respiratory problems and mortalities. In the absence of a S. molnari genome, we utilized a de novo approach to assemble the first transcriptome of proliferative myxozoan stages to identify S. molnari proteases that are upregulated during the first stages of infection when the parasite multiplies massively, rather than in late spore-forming plasmodia. Furthermore, a subset of orthologs was used to characterize 3D structures and putative druggable targets.

Results

An assembled and host filtered transcriptome containing 9436 proteins, mapping to 29,560 contigs was mined for protease virulence factors and revealed that cysteine proteases were most common (38%), at a higher percentage than other myxozoans or cnidarians (25–30%). Two cathepsin Ls that were found upregulated in spore-forming stages with a presenilin like aspartic protease and a dipeptidyl peptidase. We also identified downregulated proteases in the spore-forming development when compared with proliferative stages including an astacin metallopeptidase and lipases (qPCR). In total, 235 transcripts were identified as putative proteases using a MEROPS database. In silico analysis of highly transcribed cathepsins revealed potential drug targets within this data set that should be prioritised for development.

Conclusions

In silico surveys for proteins are essential in drug discovery and understanding host-parasite interactions in non-model systems. The present study of S. molnari’s protease arsenal reveals previously unknown proteases potentially used for host exploitation and immune evasion. The pioneering dataset serves as a model for myxozoan virulence research, which is of particular importance as myxozoan diseases have recently been shown to emerge and expand geographically, due to climate change.

Proliferative kidney disease in Alaskan salmonids with evidence that pathogenic myxozoans may be emerging north

Proliferative kidney disease (PKD) of salmonids, a chronic immunopathology caused by the myxozoan parasite Tetracapsuloides bryosalmonae, is exacerbated by increased water temperatures. PKD causes economic concerns to trout farmers and contributes to the decline of wild salmonid populations in North America and Europe. The parasite occurs as far north as Norway and Iceland in Europe and was confirmed from California to southern British Columbia in the American continent. In mid-September 2011 adult chum salmon (Oncorhynchus keta) were sampled from Kantishna River, a tributary to Yukon River in Alaska. Clinical PKD was diagnosed based on the macroscopic appearance of mottled kidneys that were uniformly swollen and by the detection of tumultuous histozoic extrasporogonic and coelozoic sporogonic stages of T. bryosalmonae in renal tissue by histopathology. Archived samples provided the molecular confirmation and local strain identification, representing the first confirmed case of PKD in wild adult chum salmon, also co-infected with Parvicapsula minibicornis that represents another novel myxozoan detection in Alaska. Our investigation was extended to another case from August/September 1997, with mortality following furunculosis and ectoparasite co-infections, in sockeye salmon (Oncorhynchus nerka) pre-smolts net-pen reared in English Bay Lakes, Alaska. Immunohistochemistry on archived histological preparations confirmed T. bryosalmonae sporogonic and extrasporogonic stages, indicating a severe to resolving PKD, with concomitant Chloromyxum spp. infection. Those cases provide the first documentation that this parasite is present in Alaska and causes PKD in wild and cultured salmonids in the region. The known geographic range of T. bryosalmonae can be extended to ~267 km south of the Arctic Circle, representing the northernmost detection in America. Given the vast size of Alaska and small resident population, it is likely that T. bryosalmonae remained undetected, but more recently became evident due to the clinical manifestation of PKD, possibly linked to increasing water temperatures reported at the sample locations.

Effects of parasite concentrations on infection dynamics and proliferative kidney disease pathogenesis in brown trout (Salmo trutta)

Proliferative kidney disease (PKD) is an emerging disease of salmonids, which is exacerbating with increasing water temperature. Its causative agent, the myxozoan parasite Tetracapsuloides bryosalmonae, exploits freshwater bryozoans as primary hosts and salmonids as intermediate hosts. Our experiments showed that the manipulation of exposure concentrations of infective malacospores had relatively minor impacts for the disease outcomes in the fish host. In this study, brown trout (Salmo trutta) were exposed to three different exposure concentrations of T. bryosalmonae malacospores: (a) a single low parasite concentration (LC), (b) a single high parasite concentration (HC) and (c) three times a low concentration (repeat exposure, RE). Parasite dynamics in the fish host and release of fish malacospores were quantified and fish kidney histopathology was evaluated to determine PKD pathogenesis. Infection prevalence was always lower in the LC group than in the other groups over the course of the study. While the parasite proliferation phase was slower in the LC group, the maximum parasite burden did not differ significantly amongst treatments. The onset of fish malacospore release (day 45 post-exposure), indicated by detection of T. bryosalmonae DNA in the tank water, occurred at the same time point for all groups. Reduced intensity of kidney pathological development was observed in the LC treatment indicating lower disease severity. While the LC treatment resulted in reduced outcomes across several infection parameters (infection prevalence, parasite proliferation, total fish malacospores released), the overall differences were small. The RE and HC treatment outcomes were for most parameters comparable. Our results suggest that repeated exposure, as is likely to occur in the wild during the summer months, might play a more important role in the dynamics of PKD as an emerging infectious disease than the actual concentration of spores.

The Malacosporean Myxozoan Parasite Tetracapsuloides bryosalmonae: A Threat to Wild Salmonids

Tetracapsuloides bryosalmonae is a myxozoan parasite responsible for proliferative kidney disease (PKD) in a wide range of salmonids. PKD, characterized by high mortality and morbidity, is well known for affecting aquaculture operations and wild salmonid populations across Europe and North America. The life cycle of T. bryosalmonae revolves around freshwater bryozoan and salmonid fish hosts. In recent years, T. bryosalmonae has been reported among wild salmonids from the European countries where it has not been reported previously. T. bryosalmonae is believed to be a possible reason for the diminishing wild salmonid populations in the natural water bodies of many European countries. Climate crisis driven rising water temperature can further accelerate the distribution of T. bryosalmonae. Expansion of the geographical distribution of T. bryosalmonae may further advocate the decline of wild salmonid populations, especially brown trout (Salmo trutta) in their habitats. Mathematical models are used to understand the pattern and distribution of T. bryosalmonae among the host in the natural water bodies. The present manuscript not only summarizes the incidences of T. bryosalmonae among the wild salmonid populations, but also discusses the contemporary understanding about the development of T. bryosalmonae in its hosts and the influences of various factors in the spread of the disease in the wild.

To remain or leave: Dispersal variation and its genetic consequences in benthic freshwater invertebrates

Variation in dispersal capacity may influence population genetic variation and relatedness of freshwater animals thus demonstrating how life-history traits influence patterns and processes that in turn influence biodiversity. The majority of studies have focused on the consequences of dispersal variation in taxa inhabiting riverine systems whose dendritic nature and upstream/downstream gradients facilitate characterizing populations along networks. We undertook extensive, large-scale investigations of the impacts of hydrological connectivity on population genetic variation in two freshwater bryozoan species whose dispersive propagules (statoblasts) are either attached to surfaces (Fredericella sultana) or are released as buoyant stages (Cristatella mucedo) and that live primarily in either lotic (F. sultana) or lentic environments (C. mucedo). Describing population genetic structure in multiple sites characterized by varying degrees of hydrological connectivity within each of three (or four) UK regions enabled us to test the following hypotheses: (1) genetic diversity and gene flow will be more influenced by hydrological connectivity in populations of C. mucedo (because F. sultana dispersal stages are retained); (2) populations of F. sultana will be characterized by greater genetic divergence than those of C. mucedo (reflecting their relative dispersal capacities); and (3) genetic variation will be greatest in F. sultana (reflecting a propensity for genetic divergence as a result of its low dispersal potential). We found that hydrological connectivity enhanced genetic diversity and gene flow among C. mucedo populations but not in F. sultana while higher overall measures of clonal diversity and greater genetic divergence characterized populations of F. sultana. We suggest that genetic divergence over time within F. sultana populations reflects a general constraint of releasing propagules that might eventually be swept to sea when taxa inhabit running waters. In contrast, taxa that primarily inhabit lakes and ponds may colonize across hydrologically connected regions, establishing genetically related populations. Our study contributes more nuanced views about drivers of population genetic structures in passively dispersing freshwater invertebrates as outlined by the Monopolization Hypothesis (Acta Oecologica, 23, 2002, 121) by highlighting how a range of demographic and evolutionary processes reflect life-history attributes of benthic colonial invertebrates (bryozoans) and cyclically parthenogenetic zooplankton. In addition, growing evidence that genetic divergence may commonly characterize populations of diverse groups of riverine taxa suggests that organisms inhabiting lotic systems may be particularly challenged by environmental change. Such change may predispose riverine populations to extinction as a result of genetic divergence combined with limited dispersal and gene flow.

OPEN RESEARCH BADGES

This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at https://doi.org/10.5061/dryad.1tm8705.

Keeping an Eye on Wild Brown Trout (Salmo trutta) Populations: Correlation Between Temperature, Environmental Parameters, and Proliferative Kidney Disease

Proliferative kidney disease (PKD) is an emerging disease of salmonids caused by the myxozoan parasite Tetracapsuloides bryosalmonae, which plays a major role in the decrease of wild brown trout (Salmo trutta) populations in Switzerland. Strong evidence demonstrated that water temperature modulates parasite infection. However, less knowledge exists on how seasonal water temperature fluctuations influence PKD manifestation under field conditions, how further environmental factors such as water quality may modulate the disease, and whether these factors coalesce with temperatures role possibly giving rise to cumulative effects on PKD. The aims of this study were to (1) determine the correlation between seasonal course of water temperature and PKD prevalence and intensity in wild brown trout populations, (2) assess if other factors such as water quality or ecomorphology correlate with the infection, and (3) quantitatively predict the implication of these factors on PKD prevalence with a statistical model. Young-of-the-year brown trout were sampled in 45 sites through the Canton of Vaud (Switzerland). For each site, longitudinal time series of water temperature, water quality (macroinvertebrate community index, presence of wastewater treatment plant effluent) and ecomorphological data were collected and correlated with PKD prevalence and intensity. 251 T. bryosalmonae-infected trout of 1,118 were found (overall prevalence 22.5%) at 19 of 45 study sites (42.2%). Relation between PKD infection and seasonal water temperature underlined that the mean water temperature for June and the number of days with mean temperature ≥15°C were the most significantly correlated parameters with parasite prevalence and intensity. The presence of a wastewater treatment plant effluent was significantly correlated with the prevalence and infection intensity. In contrast, macroinvertebrate diversity and river ecomorphology were shown to have little impact on disease parameters. Linear and logistic regressions highlighted quantitatively the prediction of PKD prevalence depending on environmental parameters at a given site and its possible increase due to rising temperatures. The model developed within this study could serve as a useful tool for identifying and predicting disease hot spots. These results support the importance of temperature for PKD in salmonids and provides evidence for a modulating influence of additional environmental stress factors.

Stream Transport and Retention of Environmental DNA Pulse Releases in Relation to Hydrogeomorphic Scaling Factors

The DNA of aquatic organisms can be identified in water sampled from freshwater ecosystems to detect species presence. Because these DNA-based methods (termed environmental DNA, eDNA) confirm species presence by proxy of DNA in water, the processes influencing eDNA transport and removal from water are critical to the method's efficacy and interpretation of results. Previous studies of aquatic eDNA transport and fate have employed uncontrolled field experiments, controlled studies in experimental streams, and laboratory column tests. As a step toward understanding the processes controlling eDNA transport and retention, we released and tracked experimental pulses of white sturgeon eDNA (novel to the system) in five fourth-order stream reaches with varied hydrology and geomorphology. We found strong support that stream water transient storage controls eDNA areal uptake rate (or spiraling length). We calculated the median spiraling length to be ∼260 m. Down channel slope correlated with transient storage, suggesting that this slope could be used as a proximate measure of eDNA removal into the benthic zone. Our results suggest that sampling effort should be increased in reaches with longer transient storage (or lower slopes) to compensate for the increase in eDNA retention.

The kinetics of cellular and humoral immune responses of common carp to presporogonic development of the myxozoan Sphaerospora molnari

BACKGROUND

Sphaerospora molnari is a myxozoan parasite causing skin and gill sphaerosporosis in common carp (Cyprinus carpio) in central Europe. For most myxozoans, little is known about the early development and the expansion of the infection in the fish host, prior to spore formation. A major reason for this lack of information is the absence of laboratory model organisms, whose life-cycle stages are available throughout the year.

RESULTS

We have established a laboratory infection model for early proliferative stages of myxozoans, based on separation and intraperitoneal injection of motile and dividing S. molnari stages isolated from the blood of carp. In the present study we characterize the kinetics of the presporogonic development of S. molnari, while analyzing cellular host responses, cytokine and systemic immunoglobulin expression, over a 63-day period. Our study shows activation of innate immune responses followed by B cell-mediated immune responses. We observed rapid parasite efflux from the peritoneal cavity (< 40 hours), an initial covert infection period with a moderate proinflammatory response for about 1-2 weeks, followed by a period of parasite multiplication in the blood which peaked at 28 days post-infection (dpi) and was associated with a massive lymphocyte response. Our data further revealed a switch to a massive anti-inflammatory response (up to 1456-fold expression of il-10), a strong increase in the expression of IgM transcripts and increased number of IgM+ B lymphocytes, which produce specific antibodies for the elimination of most of the parasites from the fish at 35 dpi. However, despite the presence of these antibodies, S. molnari invades the liver 42 dpi, where an increase in parasite cell number and indistinguishable outer cell membranes are indicative of effective exploitation and disguise mechanisms. From 49 dpi onwards, the acute infection changes to a chronic one, with low parasite numbers remaining in the fish.

CONCLUSIONS

To our knowledge, this is the first time myxozoan early development and immune modulation mechanisms have been analyzed along with innate and adaptive immune responses of its fish host, in a controlled laboratory system. Our study adds important information on host-parasite interaction and co-evolutionary adaptation of early metazoans (Cnidaria) with basic vertebrate (fish) immune systems and the evolution of host adaptation and parasite immune evasion strategies.

eDNA as a tool for identifying freshwater species in sustainable forestry: A critical review and potential future applications

Environmental DNA (eDNA) is an emerging biological monitoring tool that can aid in assessing the effects of forestry and forest manufacturing activities on biota. Monitoring taxa across broad spatial and temporal scales is necessary to ensure forest management and forest manufacturing activities meet their environmental goals of maintaining biodiversity. Our objectives are to describe potential applications of eDNA across the wood products supply chain extending from regenerating forests, harvesting, and wood transport, to manufacturing facilities, and to review the current state of the science in this context. To meet our second objective, we summarize the taxa examined with targeted (PCR, qPCR or ddPCR) or metagenomic eDNA methods (eDNA metabarcoding), evaluate how estimated species richness compares between traditional field sampling and eDNA metabarcoding approaches, and compare the geographical representation of prior eDNA studies in freshwater ecosystems to global wood baskets. Potential applications of eDNA include evaluating the effects of forestry and forest manufacturing activities on aquatic biota, delineating fish-bearing versus non fish-bearing reaches, evaluating effectiveness of constructed road crossings for freshwater organism passage, and determining the presence of at-risk species. Studies using targeted eDNA approaches focused on fish, amphibians, and invertebrates, while metagenomic studies focused on fish, invertebrates, and microorganisms. Rare, threatened, or endangered species received the least attention in targeted eDNA research, but are arguably of greatest interest to sustainable forestry and forest manufacturing that seek to preserve freshwater biodiversity. Ultimately, using eDNA methods will enable forestry and forest manufacturing managers to have data-driven prioritization for conservation actions for all freshwater species.

Estimating species distribution and abundance in river networks using environmental DNA

All organisms leave traces of DNA in their environment. This environmental DNA (eDNA) is often used to track occurrence patterns of target species. Applications are especially promising in rivers, where eDNA can integrate information about populations upstream. The dispersion of eDNA in rivers is modulated by complex processes of transport and decay through the dendritic river network, and we currently lack a method to extract quantitative information about the location and density of populations contributing to the eDNA signal. Here, we present a general framework to reconstruct the upstream distribution and abundance of a target species across a river network, based on observed eDNA concentrations and hydro-geomorphological features of the network. The model captures well the catchment-wide spatial biomass distribution of two target species: a sessile invertebrate (the bryozoan Fredericella sultana) and its parasite (the myxozoan Tetracapsuloides bryosalmonae). Our method is designed to easily integrate general biological and hydrological data and to enable spatially explicit estimates of the distribution of sessile and mobile species in fluvial ecosystems based on eDNA sampling.

Distribution and prevalence of T. bryosalmonae in Austria: A first survey of trout from rivers with a shrinking population

The first evidence of proliferative kidney disease (PKD) in an Austrian river (the River Kamp) was documented in 2016, and no information on the PKD infection status of trout in other rivers was available. Since then, brown trout (Salmo trutta fario) and rainbow trout (Oncorhynchus mykiss) have been collected from rivers in Upper and Lower Austria for different diagnostic purposes. In this study, we summarize the recent findings of a first survey concerning the distribution of Tetracapsuloides bryosalmonae, the causative agent of proliferative kidney disease (PKD), from these samples. Between September 2015 and October 2017, a total of 280 brown trout and 39 rainbow trout were collected from 21 rivers in the provinces of Upper and Lower Austria. T. bryosalmonae was detected by PCR of kidney tissue in 17 of 21 sampled rivers and in 138 of 280 brown trout as well as in 11 of 39 rainbow trout. Pathological signs of PKD (e.g., hypertrophy of the kidney) were observed in 33 analysed brown trout and six rainbow trout samples. No correlations between fish infected by T. bryosalmonae and the parameters size and age class, condition factor, geological origin of the streams and distribution within the river course were found, while positively tested fish are significantly increased at sampling sites exceeding water temperatures of 15°C for median periods of 115 days. The prevalence within the affected streams or stream sections is highly variable, and in single rivers, infection rates of up to 90% are confirmed.