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oai:figshare.com:article/31341910 2026-02-18T10:47:39Z portal_1132 item_type_8 month_year_02_2026

Enabling the Development of Sustainable Aquaculture in Qatar Razan Khalifa (21043289) Aquaculture, histology atlas histopathology microbiome Qatar <p dir="ltr">Achieving food security is a major global challenge for the growing human population.</p><p dir="ltr">Aquaculture offers a promising solution, and it is expanding rapidly; however, aquatic</p><p dir="ltr">production systems are highly susceptible to a number of challenges including disease</p><p dir="ltr">emergence. In Qatar, aquaculture is still developing and presents specific challenges</p><p dir="ltr">given that it is set in an arid region with limited water resources and an extreme</p><p dir="ltr">environment with high temperature and salinity. The main aims of this thesis were: (i) to</p><p dir="ltr">establish the first histological atlas for two important teleost species for aquaculture in</p><p dir="ltr">Qatar, the hamour (<i>Epinephelus coioides</i>) and the safi (<i>Siganus canaliculatus</i>), (ii) to</p><p dir="ltr">investigate the presence of pathogens in wild and farmed aquatic species of relevance to</p><p dir="ltr">Arabian Gulf aquaculture, and (iii) to document the gill bacterial communities in the wild</p><p dir="ltr">and aquaculture setting for the hamour using a microbiome approach. For both atlases,</p><p dir="ltr">the histological analysis was conducted for nine organs including the skin and muscle,</p><p dir="ltr">gill, liver, intestine, male and female gonads, heart, kidney, and spleen, (excluding skin</p><p dir="ltr">for hamour). These atlas presents, for the first time, the histological characterization of</p><p dir="ltr">the heart, kidney and spleen in the safi, and the heart in the hamour, addressing a critical</p><p dir="ltr">knowledge gap in the literature. The findings confirm that the histological features of</p><p dir="ltr">organs previously studied for both species (skin and muscle, gills, liver, intestine, and</p><p dir="ltr">gonads), are largely consistent with existing literature. All organs in both species</p><p dir="ltr">displayed well-preserved histoarchitecture consistent with healthy teleost anatomy, with</p><p dir="ltr">some tissue-specific characteristics likely reflecting adaptation to the high-salinity</p><p dir="ltr">environment. The safi gills showed epithelial lifting, while the hamour kidney exhibited</p><p dir="ltr">multi-glomerular arrangements. Pathogen screening revealed no pathogens in farmed</p><p dir="ltr">fish; however, non-infectious lesions were observed in several individuals. These included</p><p dir="ltr">a hepatic lesion, consistent with cholangiofibrosis observed in the liver of an individual</p><p dir="ltr">hamour and nephrocalcinosis diagnosed in the kidneys of five safi individuals in</p><p dir="ltr">aquaculture settings. In wild individuals, histopathological analysis identified</p><p dir="ltr">granulomatous lesions in 26 % of the safi individuals studied and nematodes in the liver</p><p dir="ltr">of one hamour. Microbiome analysis showed that microbial diversity (Shannon entropy)</p><p dir="ltr">2was consistently higher in swab samples compared to gill tissue biopsies in both wild and</p><p dir="ltr">aquaculture groups. Microbial richness was generally higher in wild fish compared to</p><p dir="ltr">aquaculture, with the swab samples being more representative of the gill surface.</p><p dir="ltr">Taxonomic analysis identified a core set of genera shared across sample types, with</p><p dir="ltr"><i>Vibrio</i> present in all groups. <i>Vibrio</i> abundance was higher in wild samples, while</p><p dir="ltr"><i>Algibacter</i> was prominent in aquaculture fish. Based on these data, it is recommended</p><p dir="ltr">that swabs, a non-invasive technique, can be useful for routine health monitoring, early</p><p dir="ltr">pathogen detection, and environmental microbiome assessments, however, they may</p><p dir="ltr">underrepresent tightly associated microbes or internal microbiota. These findings are</p><p dir="ltr">particularly relevant for aquaculture in Qatar, where baseline microbial data are limited</p><p dir="ltr">and were incorporating microbial monitoring as part of fish health surveillance could</p><p dir="ltr">improve early disease detection. As aquaculture continues to grow in Qatar and across</p><p dir="ltr">the Arabian Gulf, understanding the responses of hamour and safi to captive rearing</p><p dir="ltr">conditions is essential for promoting physiological resilience, welfare and productivity and</p><p dir="ltr">contribute to the sustainability of food production systems.</p> 2026-02-18T10:47:39Z Text Thesis 10779/exe.31341910.v1 https://figshare.com/articles/thesis/Enabling_the_Development_of_Sustainable_Aquaculture_in_Qatar/31341910 CC BY Open Access after 2028-02-15