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)
2was 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.
","abstract_html":"<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>","abstract_has_math":false,"creators":["Razan Khalifa (21043289)"],"institution":null,"degree_name":null,"degree_level":null,"degree_discipline":null,"degree_department":null,"school":null,"contributors":[],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2026,"date_issued":"2026-02-18T10:47:39Z","date_published":"2026-02-18T10:47:39Z","updated_at":"2026-07-27T19:34:24Z","subjects":["Aquaculture,","histology atlas","histopathology","microbiome","Qatar"],"languages":[],"rights":["CC BY","Open Access after 2028-02-15"],"rights_urls":[],"identifier_entries":[{"key":"dc:identifier","label":"Identifier","values":["10779/exe.31341910.v1"],"render_values":[{"text":"10779/exe.31341910.v1","href":null,"code":true}]}]},"links":{"outbound_url":null,"outbound_label":null,"outbound_source":null},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:creator","label":"Author","values":["Razan Khalifa (21043289)"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2026-02-18T10:47:39Z"]},{"key":"dc:relation","label":"Dc Relation","values":["https://figshare.com/articles/thesis/Enabling_the_Development_of_Sustainable_Aquaculture_in_Qatar/31341910"]},{"key":"dc:type","label":"Dc Type","values":["Text","Thesis"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Aquaculture,","histology atlas","histopathology","microbiome","Qatar"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:rights","label":"Dc Rights","values":["CC BY","Open Access after 2028-02-15"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["10779/exe.31341910.v1"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["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)
2was 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.
"]},{"key":"dc:title","label":"Title","values":["Enabling the Development of Sustainable Aquaculture in Qatar"]}]}],"canonical_facts":{"dc:creator":["Razan Khalifa (21043289)"],"dc:date":["2026-02-18T10:47:39Z"],"dc:description":["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)
2was 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.
"],"dc:identifier":["10779/exe.31341910.v1"],"dc:relation":["https://figshare.com/articles/thesis/Enabling_the_Development_of_Sustainable_Aquaculture_in_Qatar/31341910"],"dc:rights":["CC BY","Open Access after 2028-02-15"],"dc:subject":["Aquaculture,","histology atlas","histopathology","microbiome","Qatar"],"dc:title":["Enabling the Development of Sustainable Aquaculture in Qatar"],"dc:type":["Text","Thesis"]},"updated_at":"2026-07-27T19:34:24Z"}