Lilian Pukk

Migratory hosts are key vectors of long-distance parasite dispersal. In the North Atlantic, migratory connectivity of avian hosts suggests that diplostomid trematodes with broad host specificity could potentially exhibit widespread distributions. However, host migration does not necessarily result in successful parasite dispersal. We investigated the diversity and distribution of Diplostomum spp. infecting freshwater salmonids in Greenland and the Faroe Islands using a metabarcoding approach. In Greenland, infection prevalence in Arctic char and Atlantic salmon ranged from 0% to 100% across locations. Molecular analysis revealed four lineages, including the first records of Diplostomum sp. 6, 7, and 9 (Locke et al. 2010a; 2010b), and a novel lineage/species showing 92.6–94.2% sequence identity to its closest relatives. In contrast, no evidence of diplostomid infection was found in brown trout and Atlantic salmon collected from sixteen streams in the Faroe Islands. The presence of a novel, locally abundant (28.9% prevalence) parasite lineage/species in Greenland, the affinity of these parasite assemblages with those in North America, the lack of overlap with Icelandic and Norwegian communities, and the absence of diplostomids in Faroese salmonids indicate limited bird-mediated dispersal of diplostomids across the North Atlantic. We propose that a ‘short transmission window’ at high latitudes during the breeding season, combined with specific avian migration routes, may limit long-distance dispersal and promote regional isolation between Nearctic and Palearctic diplostomid communities across the North Atlantic.

Freshwater ecosystems provide critical services to human societies; however, the plant communities that sustain these ecosystems face increasing threats from human activities, highlighting the need for effective monitoring strategies. While environmental DNA (eDNA) metabarcoding has emerged as a powerful, non‐invasive tool for biodiversity monitoring, its application to plant community monitoring remains underutilized. This study evaluated the use of eDNA metabarcoding based on the orbcL2 marker to simultaneously quantify aquatic, terrestrial, and wetland plant community composition and diversity within and among 22 inland lakes in Michigan, USA. eDNA metabarcoding surveys identified 221 plant species, including 28 aquatic, 62 wetland, and 131 terrestrial species. Notably, the richness of terrestrial species exceeded those reported in previous studies, comprising 44%–81% of all taxa detected per lake, with wind‐pollinated trees constituting a substantial component of the dataset. Terrestrial species were more prevalent in lakes within landscapes characterized by greater forest cover and lower human development. Sampling timing affected species richness. Lakes sampled early in the season had greater species richness from both terrestrial and wetland communities. Wind‐pollinated species dominated early‐season detections, indicating their disproportionate influence on diversity measures. The diversity of aquatic plants showed minimal sensitivity to sampling date, and no significant seasonal variation in alpha diversity, contrasting with previous studies. However, the relatively short duration of our sampling may explain the absence of trends typically observed later in the season when plant decay increases. Beta diversity of aquatic plant communities was affected by land use, particularly agricultural activity in surrounding landscapes. Results highlight how seasonal and landscape characteristics can affect diversity estimates of freshwater plant communities, underscoring the need to account for temporal and spatial dynamics in eDNA‐based biodiversity monitoring. The study also emphasizes the limitations of relying on a single marker for accurate detection of aquatic invasive plant species.

The myxozoan endoparasite Tetracapsuloides bryosalmonae ( Tb ), the causative agent of proliferative kidney disease (PKD) in salmonids, has predominantly been reported in temperate regions of continental Europe and North America. Here, we present the first record of Tb in the Faroe Islands, extending the known northern distribution of the parasite. We sampled 161 brown trout ( Salmo trutta ) and three Atlantic salmon ( Salmo salar ) from 16 streams across the Faroes. Quantitative PCR (qPCR) analysis of kidney tissue detected Tb in 14 streams, with mean prevalence of 65.6%, reaching 100% in six streams. Parasite load, quantified as Tb 18S rRNA gene copies per qPCR reaction, ranged from 109.5 to 281,219 (mean 16,127) among infected fish. Despite high Tb prevalence and load, no clinical signs of renal hyperplasia, indicative of PKD, were observed. Sanger sequencing of the Tb 18S rRNA gene showed 99.8% to 100% identity with European isolates. These results indicate Tb is well established in Faroese freshwater and is genetically similar to European isolates. Given the known temperature dependence of PKD, climate warming is likely to increase disease risk in northern regions. Continued monitoring is essential to assess the potential long‐term ecological impacts of Tb on wild salmonid populations under changing environmental conditions.

In recent years, European countries have intensified efforts to control or limit the spread of invasive freshwater crayfish and the crayfish plague pathogen Aphanomyces astaci , while working to conserve native species such as the noble crayfish ( Astacus astacus ). Although crayfish shed relatively low amounts of DNA into their environment, environmental DNA (eDNA) approaches have proven effective for detecting their presence. A range of protocols and equipment is currently used in eDNA‐based monitoring of freshwater crayfish. To evaluate how methodological variation influences detection accuracy, we conducted the first European interlaboratory ring test using eDNA to detect A. astacus , the invasive signal crayfish Pacifastacus leniusculus , a chronic carrier of A. astaci , and the pathogen itself. The aim is to harmonize monitoring methods for crayfish and disease surveillance across laboratories. Eleven teams from thirteen European countries participated, each using its own equipment and protocols to collect and filter water from indoor tanks and outdoor ponds where the presence of A. astacus and P. leniusculus had been experimentally manipulated, as well as from a natural lake containing a P. leniusculus population. The resulting samples were analyzed in each team's laboratory. Despite methodological differences, all teams successfully detected DNA from both crayfish species in indoor tanks (3–10 crayfish/m ³ ). However, detection accuracy declined in outdoor ponds where crayfish density was an order of magnitude lower (0.32 crayfish/m ³ ). Detection was most variable for A. astaci , likely due to its very low prevalence in the host stock. Our study demonstrates the challenges of achieving consistent eDNA results across laboratories and highlights the importance of interlaboratory comparisons. It also underscores the need to identify sources of variability and error, an essential step toward developing robust and standardized protocols. This multinational intercalibration and exchange of knowledge improved methodology and enhanced reliability in crayfish detection.

Dams provide different services for human society, but they also significantly disrupt ecosystems by altering natural flow and temperature regimes. Here, we describe a novel, unappreciated threat posed by reservoirs to one of the world’s most popular game fish, brown trout ( Salmo trutta ). We show that small river impoundments elevate downstream water temperature during summer, which increases the prevalence and abundance of Tetracapsuloides bryosalmonae parasite triggering proliferative kidney disease (PKD), an emerging disorder in salmonids across North America and Europe. Our study highlights the role of reservoirs in creating parasite and disease hotspots, while providing limited evidence that dams act as barriers to parasite spread. This makes downstream areas from reservoirs valuable sentinel sites for monitoring climate impacts on riverine ecosystems. Ultimately, the assessment of dams requires a more holistic approach, where the disease risks are included in the decision-making process balancing human needs with the health of aquatic ecosystems.

Host–parasite interactions are influenced by both abiotic and biotic factors. While abiotic drivers, particularly temperature, have received considerable attention in recent years due to global climate change, the role of biotic factors remains comparatively underexplored. The malacosporean parasite Tetracapsuloides bryosalmonae ( Tb ), which causes proliferative kidney disease in salmonids, is a well‐documented example, where elevated temperature and eutrophication have been shown to intensify disease prevalence and severity. In this study, we investigated whether freshwater sponges, known for their particle‐filtering capabilities, can graze on malacosporean spores in the aquatic environment, potentially acting as biotic filters that may influence parasite transmission dynamics. Using an experimental setup, we employed environmental DNA sampling to (1) characterise the short‐term release of Tb spores from infected 1+ brown trout ( Salmo trutta ) and (2) assess the ability of freshwater sponge ( Ephydatia muelleri ) to remove Tb spores from water and function as a bio‐sampler. Our results show that sponges significantly reduced Tb DNA concentrations in water. However, their effectiveness as bio‐samplers and concentrators of Tb was limited, likely due to the rapid degradation of ingested Tb DNA. These results suggest that freshwater sponges may function as natural biological controllers of Tb by filter feeding on its infectious planktonic stages in natural environments.

Archival samples provide a unique source of DNA, offering the potential to extend the temporal scale of genetic studies by decades to centuries. Fish hard structures, such as otoliths and scales, serve as records for fish collected during fisheries monitoring across a large spatiotemporal scale. Operculum bones are a type of fish hard structure that, although less commonly collected, have been utilized in genetic studies. However, the usefulness of archived operculum bones to provide high quality whole genome sequence information has not been thoroughly evaluated. Here, we applied a commercially available extraction protocol, with minor adjustments, to isolate genomic DNA from operculum bones of Eurasian perch collected up to 47 years ago, followed by standard short-read whole genome sequencing. By comparing the metrics of DNA and whole genome sequencing data of bones with contemporary muscle samples, we demonstrate that the application of a simple extraction protocol on boiled archival fish operculum bones yields high quality genomic information that is comparable to fresh tissue, highlighting the role of archival operculum bones as an overlooked repository of valuable genomic information.

Invasive non-indigenous crayfish species (NICS) are a major threat to the existence of native crayfish populations in European freshwater ecosystems. The discovery of signal crayfish Pacifastacus leniusculus, marbled crayfish Procambarus virginalis, and spiny-cheek crayfish Faxonius limosus in Estonia has increased the risk of extinction of Estonia’s only native crayfish species, the noble crayfish Astacus astacus. The aim of this study was to give an overview of the status, distribution, and impacts of P. leniusculus, F. limosus, and Procambarus virginalis on A. astacus populations and assess the effect of trapping on NICS abundance. Annual monitoring of crayfish has been carried out since 2008 as part of A. astacus conservation and the NICS eradication plan. In this study, we present data from nine sampling locations monitored from 2010 to 2022. The spread of NICS continues to increase beyond their distribution areas, and in two sampling locations P. leniusculus and A. astacus live in sympatry. Our results suggest that trapping has a limited effect on population abundance, as NICS have already caused the extinction of two A. astacus populations. However, intensive trapping should continue simultaneously with sensitive molecular techniques to monitor the spread of NICS.

The Eurasian perch (Perca fluviatilis) is the most common fish of the Percidae family and is widely distributed across Eurasia. Perch is a popular target for professional and recreational fisheries, and a promising freshwater aquaculture species in Europe. However, despite its high ecological, economical and societal importance, the available genomic resources for P. fluviatilis are rather limited. In this work, we report de novo assembly and annotation of the whole genome sequence of perch. The linked-read based technology with 10X Genomics Chromium chemistry and Supernova assembler produced a draft perch genome ∼1.0 Gbp assembly (scaffold N₅₀ = 6.3 Mb; the longest individual scaffold of 29.3 Mb; BUSCO completeness of 88.0%), which included 281.6 Mb of putative repeated sequences. The perch genome assembly presented here, generated from small amount of starting material (0.75 ng) and a single linked-read library, is highly continuous and considerably more complete than the currently available draft of P. fluviatilis genome. A total of 23,397 protein-coding genes were predicted, 23,171 (99%) of which were annotated functionally from either sequence homology or protein signature searches. Linked-read technology enables fast, accurate and cost-effective de novo assembly of large non-model eukaryote genomes. The highly continuous assembly of the Eurasian perch genome presented in this study will be an invaluable resource for a range of genetic, ecological, physiological, ecotoxicological, functional and comparative genomic studies in perch and other fish species of the Percidae family.