Environmental DNA approaches and host genomics for myxozoan parasite ecology and disease prediction
Publication Date
July 31, 2026
Creator
Melzer, Florian
Abstract
Host-parasite relations shape evolution, community biodiversity and disease dynamics. Myxozoa are a group of diverse, internal parasites belonging to phylum Cnidaria with a wide range of invertebrate and fish hosts. In riverine freshwater ecosystems the complex around the myxozoan parasite Tetracapsuloides bryosalmonae with the bryozoan Fredericella sultana as its primary host and salmonids as its intermediate host has been in focus because T. bryosalmonae can cause the high-mortality Proliferative Kidney Disease (PKD) impacting wild and farmed fish. Spatial and temporal variation in host-parasite co-occurrences influences disease dynamics but makes research through conventional methods challenging. I present here an optimised, simultaneous capture approach of both host environmental DNA (eDNA) and parasite spores from river water. Detection and quantification of host and parasite(s) through highly sensitive, species-specific qPCR and broad-range metabarcoding reveals variation across a single river catchment. I demonstrate that eDNA-based methods work at a practical scale and will be crucial in modelling host and parasite co-occurrence and prediction of seasonal population changes. Host population genetics let us trace community (structural) changes and can relate to parasitic infection susceptibility. The genomics of the host F. sultana are still largely unexplored. The mitogenome sequence, widely used in detection, quantification and population genetics for both tissue and eDNA-based studies, is unknown. We developed a direct sequencing and de-novo assembly approach for the complete mitogenome, including gene annotation and order, expression profiles and discovery of a group II intron. Knowledge of sequence, gene order and transcription profiles expands metabarcoding, direct or long-range sequencing and eRNA possibilities, and, crucially for PKD dynamics, leads to insights into population genetics of the host F. sultana. Based on the complete mitogenome we establish the mitogenomic diversity of F. sultana on a single river-basin scale to explore intra-species variability with a simple single gene marker and the more informative full mitogenome. Both approaches reveal similar population structures with distinct haplotypes spread through the river. Additionally, we designed a mitogenomic marker panel for future tissue and eDNA work. We present a case study that can be applied in other host-parasite systems to investigate population level tolerance and resistance, spatial and temporal patterns of local adaptation, and dispersal and range expansion dynamics. Besides population genetics biodiversity, ecology and environmental factors shared by hosts and parasites lead to similarities and co-occurrence patterns between communities. To understand if co-occurrence alone can be informative, we combined myxozoan parasite metabarcoding with physical site characteristics, biodiversity and ecological traits of fish and invertebrate species. While the comparisons highlighted concordant patterns of fish and invertebrate occurrence, they could not explain co-occurrence with parasites. Host presence and shared biodiversity are crucial determinants of parasite occurrence. However, the resulting theoretical ecological niche is not always realised leading to complex parasite distribution and prevalence of infections. Simultaneous eDNA detection of parasites and hosts, host mitogenome population genetics and interaction study between local ecology and parasite co-occurrence are important steps to better understand host-parasite relationships and disease dynamics. This thesis contributes to the conceptual and methodological foundation to the identification of areas and local populations that are threatened by PKD.
Item Type
ethesis
Thesis Type
PhD
Supervisors
Hartikainen, Hanna
Dugdale, Stephen
Subjects (LC)
Associated Schools / Departments
UoN Repository URI
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PhD_thesis_final_FlorianMelzer_20316105_corr_final_notrack.pdf
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8.71 MB
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Adobe PDF
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