http://hdl.handle.net/1893/13 Electronic theses of Aquaculture Students. Wed, 30 Sep 2026 10:34:11 GMT 2026-09-30T10:34:11Z http://hdl.handle.net/1893/38224 Title: Host immunology and pathogen-bacteriophage interactions in Black Soldier Fly Larvae (BSFL; Hermetia illucens) Author(s): McDonald, Emma Abstract: The Black Soldier Fly (Hermetia illucens) has emerged as a sustainable bioconversion species with considerable potential for a circular economy. While extensively studied for waste management and protein production, its innate immune system remains comparatively underexplored. This thesis aims to establish and optimise experimental and molecular approaches to investigate host immune responses and bacteriophage-pathogen interactions in H. illucens, providing new insight into its immunological potential and implications for sustainable disease control. Methodological optimisation included refining larval rearing conditions, bioactive administration, and RNA extraction techniques tailored to the physiological characteristics of H. illucens. Using pathogen-associated molecular patterns (PAMPS), lipopolysaccharide (LPS) and polyinosinic:polycytidylic [Poly (I:C)], the dose-dependent induction of pattern-recognition receptors and antimicrobial peptide genes was quantified through qPCR analysis. Responses showed thresholds and paralogue-specific expression profiles, indicating scalable innate activation. A directional poly (A) RNA-seq transcriptome was generated from pooled whole-body larvae and subjected to genome-guided, orthology-informed annotation to produce a curated immune gene database. Canonical innate immune pathways, including Toll, IMD, JAK/STAT and JNK signalling, were characterised through Gene Ontology, KEGG, Reactome, and STRING protein-protein interaction analyses, providing a comprehensive molecular framework for future functional and comparative studies. Finally, prophylactic administration of bacteriophage SPFM14 significantly reduced Salmonella enterica serovar Typhimurium (SL1344) colonisation in H. illucens, supporting the potential of phage-based biocontrol as an alternative to antibiotics in insect production systems. Time-course experiments further demonstrated rapid phage shedding from the larval gut, providing important context for interpreting in vivo phage persistence and bacteriophage-mediated bacterial control. Mon, 27 Jul 2026 00:00:00 GMT http://hdl.handle.net/1893/38224 2026-07-27T00:00:00Z http://hdl.handle.net/1893/37928 Title: The effects and genetic diversity of salmon gill poxvirus in freshwater Atlantic salmon in Scotland Author(s): Allshire, Rosa Abstract: Salmon gill poxvirus (SGPV) is an emerging pathogen causing significant losses in the Scottish Atlantic salmon farming industry. Clinical presentation varies widely, from sub-clinical infection to severe clinical signs and gill pathology. Understanding the causes for this variation in clinical presentation and mortality is key to mitigating the significant economic losses caused by this virus. To date, little research has been done in Scotland on the effects of SGPV infection, and why disease presentation is so unpredictable. In this thesis, a natural outbreak of SGPV disease in an enclosed freshwater system was studied. A range of SGPV positive samples from geographically distinct detections were sequenced to explore the genetic diversity of SGPV in Scotland. During the naturally-occurring outbreak, histological findings showed the gills to be the primary target organ, with severe pathology correlating with high viral loads. Common pathologies associated with SGPV disease (SGPVD) were found in the gills, including severe hyperplasia, hypertrophy and widespread inflammation. However, epithelial apoptosis, described in many published studies as the pathognomonic clinical sign of SGPV infection, was only found in low levels during this study. Downregulation of anti-viral immune markers MDA-5 and Mx was observed in clinically diseased fish, when compared with sub-clinically infected fish, which suggests that the host antiviral immune response is being differentially modulated. Samples positive for SGPV were collected from outbreaks and incidental detections across six geographically distinct sites in Scotland and used for whole-genome sequencing and phylogenetic analysis. Genetic diversity was found to be limited between these cases, with sequence similarity of >85% in near-complete genomes. Some areas of nucleotide variation were also identified, possibly representing targets for phylogenetic studies. This work provides an insight into the pathogenesis of a natural outbreak that will aid the control and monitoring of SGPVD on freshwater Atlantic salmon farms. Mon, 01 Jul 2024 00:00:00 GMT http://hdl.handle.net/1893/37928 2024-07-01T00:00:00Z http://hdl.handle.net/1893/37927 Title: Characterisation of ggcP, a Putative Virulence Protein of Vibrio anguillarum Author(s): Coskun, Batuhan Abstract: Vibrio anguillarum causes significant economic losses in aquaculture, and although vaccines are available for some species, their protection can vary. A deeper understanding of V. anguillarum virulence may inform more effective mitigation measures, but the full range of mechanisms employed by this pathogen remains unclear. A previous transposon mutagenesis study discovered a gene that, when disrupted, reduced virulence in an insect (greater wax moth, Galleria mellonella) infection model. This gene, termed here ggcP, encodes a protein with a GlyGly CTERM sorting motif, which is characteristic of some membrane-localised extracellular proteases in Vibrio species. This present study aimed to further characterise GgcP protein through a holistic approach, by combining in-silico bioinformatic analyses, phenotypic comparison of transposon mutant and parent strains, and by expressing the protein in recombinant E. coli. Homology-based searches indicated that GgcP contains a signal peptide and a Domain of Unknown Function (DUF) 3466, with high prevalence across Vibrio species and a presence in all publicly available V. anguillarum genomes with high conservation. Predictive analysis suggested GgcP is either outer membrane-associated or secreted, with mass spectrometry confirming its presence in both whole-cell and extracellular fractions. Disruption of ggcP in the transposon mutant led to the downregulation of a major outer membrane protein (OmpU), suggesting that GgcP may contribute to membrane integrity and stress response, and the mutant displayed growth defects and increased sensitivity to membrane-active compounds. Successful recombinant expression of GgcP was achieved, and its antigenicity was confirmed with rabbit anti-V. anguillarum polyclonal antibodies, suggesting GgcP is an immunogenic protein and may be a candidate for a subunit vaccine. The work presented in this thesis enhances our understanding of GgcP, although the exact role of this protein in membrane regulation remains to be determined, the new knowledge accumulated in this study may aid the development of strategies to mitigate the impact of V. anguillarum in aquaculture. Mon, 30 Jun 2025 00:00:00 GMT http://hdl.handle.net/1893/37927 2025-06-30T00:00:00Z http://hdl.handle.net/1893/37882 Title: Decision Support Approaches to Advance the Understanding and Management of European Polyculture Aquaculture Author(s): Krupandan, Amalia Grace Abstract: Aquaculture in Europe is expected to grow while policy requires lower ecological impacts. Polyculture is promoted for efficient resource use, yet farm-scale ecological functioning and management effects remain uncertain and context-dependent. The thesis investigates two contrasting European polyculture systems and how management choices alter their performance. Nutrient connectivity of a coastal salmon-kelp IMTA was tested over two production years (one kelp-only, one kelp-salmon) using stable isotope analysis. The isotopic signal of salmon feed was apparent in farmed kelp during the kelp-salmon year and dissipated as salmon harvesting began. Bayesian mixing modelling identified fish feed as the dominant nitrogen source of farmed kelp in the IMTA. An integrated IMTA model was used to couple salmon metabolism, hydrodynamics, and kelp growth. Production scenarios were applied to assess bioremediation potential. Extending the kelp production cycle increased modelled kelp nitrogen assimilation to 3.07% of salmon metabolic nitrogen. Achieving 10% removal of salmon wastes required 36 kelp lines in the most favourable scenario, which remained within the licensed area. Several diversely managed earthen carp ponds were represented with mass-balanced Ecopath models to quantify differences in trophic structure and flows. Ponds varied in trophic structure according to management type. Several polyculture scenarios were applied to each pond management type and Ecological Network Analysis derived system-level ecological indicators. Out of 11 indicators, 5 were selected as most relevant to pond management. Low-level polyculture with herbivorous carp gave little benefit where macrophytes were scarce. Under a “maximum” polyculture scenario, mass balance remained feasible only by diverting grass carp consumption to detritus and feed; plankton resources capped silver carp; indicators showed ecosystem fragility under extreme herbivory. Across both systems, models serve as tools for decision-support to help understand system functioning. This enables the mapping of feasible operating space, quantifying trade-offs and focusing effort on achievable change. Sat, 01 Nov 2025 00:00:00 GMT http://hdl.handle.net/1893/37882 2025-11-01T00:00:00Z