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Enabling the Development of Sustainable Aquaculture in Qatar Razan Khalifa (21043289) Uncategorised value Achieving food security is a major global challenge for the growing human population. Aquaculture offers a promising solution, and it is expanding rapidly; however, aquatic production systems are highly susceptible to a number of challenges including disease emergence. In Qatar, aquaculture is still developing and presents specific challenges given that it is set in an arid region with limited water resources and an extreme environment with high temperature and salinity. The main aims of this thesis were: (i) to establish the first histological atlas for two important teleost species for aquaculture in Qatar, the hamour (Epinephelus coioides) and the safi (Siganus canaliculatus), (ii) to investigate the presence of pathogens in wild and farmed aquatic species of relevance to Arabian Gulf aquaculture, and (iii) to document the gill bacterial communities in the wild and aquaculture setting for the hamour using a microbiome approach. For both atlases, the histological analysis was conducted for nine organs including the skin and muscle, gill, liver, intestine, male and female gonads, heart, kidney, and spleen, (excluding skin for hamour). These atlas presents, for the first time, the histological characterization of the heart, kidney and spleen in the safi, and the heart in the hamour, addressing a critical knowledge gap in the literature. The findings confirm that the histological features of organs previously studied for both species (skin and muscle, gills, liver, intestine, and gonads), are largely consistent with existing literature. All organs in both species displayed well-preserved histoarchitecture consistent with healthy teleost anatomy, with some tissue-specific characteristics likely reflecting adaptation to the high-salinity environment. The safi gills showed epithelial lifting, while the hamour kidney exhibited multi-glomerular arrangements. Pathogen screening revealed no pathogens in farmed fish; however, non-infectious lesions were observed in several individuals. These included a hepatic lesion, consistent with cholangiofibrosis observed in the liver of an individual hamour and nephrocalcinosis diagnosed in the kidneys of five safi individuals in aquaculture settings. In wild individuals, histopathological analysis identified granulomatous lesions in 26 % of the safi individuals studied and nematodes in the liver of one hamour. Microbiome analysis showed that microbial diversity (Shannon entropy) 2 was consistently higher in swab samples compared to gill tissue biopsies in both wild and aquaculture groups. Microbial richness was generally higher in wild fish compared to aquaculture, with the swab samples being more representative of the gill surface. Taxonomic analysis identified a core set of genera shared across sample types, with Vibrio present in all groups. Vibrio abundance was higher in wild samples, while Algibacter was prominent in aquaculture fish. Based on these data, it is recommended that swabs, a non-invasive technique, can be useful for routine health monitoring, early pathogen detection, and environmental microbiome assessments, however, they may underrepresent tightly associated microbes or internal microbiota. These findings are particularly relevant for aquaculture in Qatar, where baseline microbial data are limited and were incorporating microbial monitoring as part of fish health surveillance could improve early disease detection. As aquaculture continues to grow in Qatar and across the Arabian Gulf, understanding the responses of hamour and safi to captive rearing conditions is essential for promoting physiological resilience, welfare and productivity and contribute to the sustainability of food production systems.<p></p> 2025-11-17T00:00:00Z Text Thesis 10779/exe.31361797.v1 https://figshare.com/articles/thesis/Enabling_the_Development_of_Sustainable_Aquaculture_in_Qatar/31361797 All rights reserved Open Access after 2030-02-18