Heterotrophic bacterioplankton dynamics have seldom been assessed in the Red Sea, an exceptionally warm oligotrophic basin, which could be used as a model for the future ocean. To understand the function of heterotrophic bacteria in biogeochemical cycles and the flows of matter and energy to higher trophic levels, it is peremptory to understand how bacterial growth is controlled. Bottom-up (resources availability), top-down (mortality by predators and viruses) and temperature are the main hypotheses of control of bacterial activity and stocks. This dissertation aims to assess the spatial-temporal variability of heterotrophic bacteria and their interactions with diverse sources of dissolved organic matter (DOM) through the observed effects on bacterial growth rates and productivity in coastal environments of the central Red Sea. To that end we conducted a total of 66 shortterm incubations (4-6 days) concurrently with the whole microbial community and predator-free (by filtration) in various shallow ecosystems characterized by different dominant sources of DOM. Frequent sampling combined flow cytometry and biogeochemical analysis allowed us to measure bacterial standing stocks, including the carrying capacity (maximum abundances), growth rates, characterize DOM concentrations and lability, assess bacterial DOM consumption rates and biomass production and ultimately quantify bacterial growth efficiencies. Our findings suggest that although bacteria seemed to thrive in nutrient-sufficient waters, the central coastal Red Sea is characterized by unusually low bacterial standing stocks (4.05 ± 0.31 x105 cells ml-1), probably controlled by protistan grazing. At the same time, bacterioplankton showed high potential to grow (0.35-1.75 d-1, reaching 4.16 d-1 when dilution and pre-filtration were performed). Even though the highest specific growth rates were observed during the warmer periods, we did not find any consistent relationship with temperature. While temperature seemed not to constrain bacterial specific growth rates, we observed a tight link between bacterial growth and resource availability in terms of both quantity and quality. Overall, by surveying one of the warmest marine regions on Earth, this dissertation provides detailed insights into heterotrophic bacterioplankton dynamics and how bottomup, top-down and temperature regulate them in tropical waters, a vast geographical extension of the world oceans that had remained strongly undersampled to date.

Polyaromatic hydrocarbons (PAHs) are oil derived toxic and persistent pollutants prevalent across the oceans from pelagic waters to coral reefs. The Great Barrier Reef (GBR) in Australia and the Red Sea are important oligotrophic marine ecosystems susceptible to oil contamination. This Ph.D. dissertation aims to advance our understanding on PAH tolerance, accumulation dynamics and trophic transfer in oligotrophic ecosystems where those aspects remain poorly explored. In this dissertation, a new, highly-sensitive method combining stable carbon isotope labelling and cavity ring-down spectroscopy (CRDS) was developed to quantify PAH accumulation and applied in a series of ex situ food chain experiments with two representative PAHs, 13C-phenanthrene and 13C-pyrene. The experiments conducted with Acropora millepora – a common reef-building coral in the GBR, showed faster accumulation of both PAHs by dissolved uptake, although dietary exposure caused more consistent accumulation. Phenanthrene was not toxic to the coral photosystem II in either exposure mode but biomagnification increased with increasing food-chain complexity. In contrary, pyrene led to loss of symbionts accompanied by reduction in photosynthetic efficiency and coral bleaching, especially via dietary uptake. Also, microbial communities and food webs are relevant components of oligotrophic waters. We identified contrasting sensitivities among key autotrophic and heterotrophic microbial populations in the chronically oil exposed Red Sea to a mixture of 16 PAHs recognized as priority pollutants. The differential tolerance pointed towards localized selection for resistant strains in some populations. Some PAH toxicity thresholds approached ambient PAHs concentrations suggesting that any increase in pollution loads will hold consequences for these important microbial groups and their ecological functions.

This thesis presents our efforts to build an operational ensemble forecasting system for the Red Sea, based on the Data Research Testbed (DART) package for ensemble data assimilation and the Massachusetts Institute of Technology general circulation ocean model (MITgcm) for forecasting. The Red Sea DART-MITgcm system efficiently integrates all the ensemble members in parallel, while accommodating different ensemble assimilation schemes. The promising ensemble adjustment Kalman filter (EAKF), designed to avoid manipulating the gigantic covariance matrices involved in the ensemble assimilation process, possesses relevant features required for an operational setting. The need for more efficient filtering schemes to implement a high resolution assimilation system for the Red Sea and to handle large ensembles for proper description of the assimilation statistics prompted the design and implementation of new filtering approaches. Making the most of our world-class supercomputer, Shaheen, we first pushed the system limits by designing a fault-tolerant scheduler extension that allowed us to test for the first time a fully realistic and high resolution 1000 ensemble members ocean ensemble assimilation system. In an operational setting, however, timely forecasts are of essence, and running large ensembles, albeit preferable and desirable, is not sustainable. New schemes aiming at lowering the computational burden while preserving reliable assimilation results, were developed. The ensemble Optimal Interpolation (EnOI) algorithm requires only a single model integration in the forecast step, using a static ensemble of preselected members for assimilation, and is therefore computationally significantly cheaper than the EAKF. To account for the strong seasonal variability of the Red Sea circulation, an EnOI with seasonally-varying ensembles (SEnOI) was first implemented. To better handle intra-seasonal variabilities and enhance the developed seasonal EnOI system, an automatic procedure to adaptively select the ensemble members through the assimilation cycles was then introduced. Finally, an efficient Hybrid scheme combining the dynamical flow-dependent covariance of the EAKF and a static covariance of the EnOI was proposed and successfully tested in the Red Sea. The developed Hybrid ensemble data assimilation system will form the basis of the first operational Red Sea forecasting system that is currently being implemented to support Saudi Aramco operations in this basin.

Coral reefs are under considerable decline. The framework builders in coral reefs are scleractinian corals, which comprise so-called holobionts, consisting of cnidarian host, algal symbionts (genus Symbiodinium), and other associated microbes. Corals are commonly considered stenohaline osmoconformers, possessing limited capability to adjust to salinity changes. However, corals differ in their ability to cope with different salinities. The underlying mechanisms have not yet been addressed. To further understand putative mechanisms involved, I examined coral holobiont osmoregulation conducting a range of experiments on the coral Fungia granulosa. In my research F. granulosa from the Red Sea exhibited pronounced physiological reactions (decreased photosynthesis, cessation of calcification) upon short-term incubations (4 h) to high salinity (55). However, during a 29-day in situ salinity transect experiment, coral holobiont photosynthesis was unimpaired under high salinity (49) indicating acclimatization. F. granulosa microbiome changes after the 29-day high salinity exposure aligned with a bacterial community restructuring that putatively supports the coral salinity acclimatization (osmolyte synthesis, nutrient fixation/cycling). Long-term incubations (7 d) of cultured Symbiodinium exhibited cell growth even at ‘extreme’ salinity levels of 25 and 55. Metabolic profiles of four Symbiodinium strains exposed to increased (55) and decreased (25) salinities for 4 h indicated distinct carbohydrates and amino acids to be putatively involved in the osmoadjustment. Importantly, under high salinity the osmolyte floridoside was consistently increased. This could be corroborated in the coral model Aiptasia and in corals from the Persian/Arabian Gulf, where floridoside was also markedly increased upon short- (15 h) and long-term (>24 months) exposure to high salinity, confirming an important role of floridoside in the osmoadjustment of cnidarian holobionts. This thesis demonstrates osmoacclimatization of F. granulosa and osmoadjustment of cultured Symbiodinium. All three main compartments (i.e. coral host, Symbiodinium, bacteria) seem to contribute to the coral holobionts salinity adjustment. However, the exact mechanisms of coral host and bacteria contribution remain to be determined. Floridoside likely constitutes a conserved osmolyte increasing the salinity resilience of Symbiodinium and also of the cnidarian/coral holobiont. Floridoside further possess’ antioxidative properties, possibly providing a protection from reactive oxygen species formation as a result of salinity stress or/and other environmental stressors.

Cellulase-producing microorganisms are considered as a key player in various environments to degrade the plant biomass and were isolated from various environment like soils, mangroves and oceans. The Red Sea has a unique environment in terms of high seawater temperature, high salinity and low nutrients. This study aims of examining if the Red Sea is a potential resource for cellulase-producing microorganisms and cellulase genes. First, I investigated types of microbial cellulase genes in the Red Sea based on public metagenomic datasets. The analysis revealed 3,383 microbial cellulase were more abundant in shallow depth than in deep seawater, and were classified into 16 sub-GH orthologous groups. These results suggest that the Red Sea environment is potentially an excellent gene resource of microbial cellulases due to its high diversity. Next, cellulase-producing microorganisms were isolated and screened from the Red Sea. Three bacterial and one fungal strain were successfully obtained. The MLTS analysis showed that the three bacterial strains belong to Bacillus paralichiniformis. The 18S rRNA of fungal strain showed 99% similarity to Aspergillus ustus and the enzymatic assay of the four strains showed high cellulase activity. These results suggest that these four isolates secreted active cellulases. Next, I tried to identify cellulase genes actually working during their cellulolysis by conducting comparative transcriptome analysis of the candidate genes and identified cellulase genes that are highly expressed during cellulolysis. To my knowledge, it is the first attempt to find out cellulase genes functioning during their cellulolysis among distinct cellulases on genomes of microorganisms. The results showed that although all the candidate genes were upregulated in general, a limited number of cellulase genes were highly expressed, which are highly expected to have a crucial role in cellulolysis. I also identified operon structures composed of genes including cellulases. This will provide us with the information to elucidate the cellular mechanisms occurring along with the cellulolysis in bacterial strains. We can expect that the Red Sea is a potential resource for new cellulase genes applicable for the industry. These information can be significantly useful for the bio-prospecting research of microbial cellulases in the Red Sea.

The global aquaculture industry is expanding to support increased demand in global markets and supplement traditional fisheries. The rapid increase of aquaculture production relies on introducing and using species outside their native range, posing significant regional environmental and socio-economic risks. Non-native species are selected based on transferable large-scale production protocols, fast growth, and existing market demand. Aquaculture is an important sector within Saudi Arabia’s Vision 2030 (anticipated >400% production increase by 2030). Barramundi (Lates calcarifer) was introduced into the Red Sea for open sea-cage farming in 2008, with large-scale production beginning in 2014. Regionally, there are numerous anecdotal reports of escape events of this species, including an incident in 2015 involving the release of ~300,000 fish. Since then, local fishers have caught up to 15 wild individuals per month in Al Lith, central Saudi Arabia. This study presents the first biological information on L. calcarifer aquaculture escapees in the Saudi Arabian Red Sea. Wild-caught L. calcarifer (n=5) were collected from a local fish landing and measured up to 10 kg, eight years of age, were sexually mature, and consumed benthic and coral reef fishes. In contrast, individuals in aquaculture facilities are harvested at < 1 kg and < 400 mm. In their native range, L. calcarifer can reach up to 200 cm and 60 kg. To assist in detecting and monitoring escapees within the Red Sea, I designed and validated a species-specific SYBR-based environmental DNA quantitative PCR assay targeting a 16S mitochondrial region of L. calcarifer rRNA (Barramundi_16S assay). Preliminary results, using DNA metabarcoding and environmental (seawater) samples, detected L. calcarifer near active/historical aquaculture farms and north/south of areas where this species has not been reported previously in the Red Sea (10–250 km from aquaculture facilities). In the future, the Barramundi_16S assay can screen additional eDNA samples (n=250) collected for this study to delineate the geographic range of barramundi in the Red Sea. Cumulatively, this study highlights the need to consider the ecological impacts of aquaculture escapees and provides managers and industry with valuable information and a novel molecular monitoring tool for detecting aquaculture escapees.

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第21827号 / 農博第2340号 / 新制||農||1067(附属図書館) / 学位論文||H31||N5199(農学部図書室) / 京都大学大学院農学研究科応用生物科学専攻 / (主査)教授 佐藤 健司, 准教授 豊原 治彦, 准教授 田川 正朋 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

Herbivorous fishes include a diverse assemblage of species that target primarily benthic autotrophs. This is perhaps one of the most well-studied groups of coral reef fishes, often reputed to be key components of coral reef communities, contributing to coral reef health in numerous ways. Through their feeding ecology and benthic interactions, they help mediate algae-coral interactions which can allow for improved coral survival and health. Despite the wealth of literature documenting the prominent roles of these fishes in coral reef ecosystems, studies from the Red Sea are surprisingly lacking. The Red Sea is a marginal reef environment, with a host of unique environmental and biological characteristics making it a unique environment where dynamics of herbivory may differ. This dissertation aims to fill key gaps in our knowledge of herbivorous fishes through the study of their distribution and trophic ecology. Herein, I describe habitat-specific partitioning of Red Sea herbivorous fish assemblages, discovering higher diversity and abundance found in reefs closer to shower, dissimilar to findings from other regions. Cross-shelf variation in assemblage structure seems to be quite robust through time, indicating short-term stability in herbivore assemblages. Through the use of stomach contents and stable isotope analyses, I then investigate the trophic ecology of browsing herbivores across the same shelf-gradient. I found higher trophic redundancy on nearshore reefs through time, with increased variation in diet and high levels of complementarity on offshore reefs where macroalgae are scarce. Stable isotope analyses of both liver and muscle revealed the stability of this resource partitioning through time, demonstrating for the first-time temporal stability of resource partitioning within this group. This dissertation broadens our knowledge of herbivorous fishes, filling important gaps. It offers new insight into the role of habitat in structuring trophic ecology and how flexible the diets of browsing species can be. Together, this information creates a foundation where improved knowledge of herbivorous fish ecology could be incorporated into future management plans of ongoing giga projects within the Kingdom. Incorporating herbivores into these plans could allow for increased resiliency for Red Sea coral reefs in the face of future development and shifting climatology.

Remote sensing studies based on satellite and aerial imagery have improved our understanding of the morphology and distribution of several shallow reefs along the Red Sea Arabian coast and of the benthic assemblages associated to them (Bruckner et al., 2011; Bruckner et al., 2012; Rowlands et al., 2016). However, data concerning the deeper benthic assemblages' composition and spatial distribution in the central Red Sea are still missing. Using high-resolution acoustic technology and an underwater remotely operated vehicle (ROV), we aim to map, describe, and classify the reefs found in Thuwal's coastal area, filling the information gap by producing the first benthic habitat map of this area and making progress towards the evaluation of shallow and upper mesophotic benthic resources in the Saudi Arabian Red Sea. High-resolution acoustic data was collected using a multibeam echosounder system, which generated a bathymetric model. Based on this, the seafloor features were classified into 12 morphotypes following a visual assessment. Based on the morphotypes classification, 28 sites were visually selected for ground-truthing data acquisition and characterization of the substrate and benthic assemblages using a remotely operated vehicle equipped with an ultra-short baseline (USBL) positioning system. With the information obtained from the bathymetry data and the ROV video transects, a Top-Down approach in which we analyzed, categorized, and classified the data was used to create Thuwal's reefs benthic habitat map in which 23 different benthic habitat types were identified. This research uncovered previously poorly studied reef morphologies in the Red Sea and their associated benthic assemblages. Moreover, this work will help improve the understanding of the spatial distribution of benthic communities located on Thuwal's reefs, giving a baseline with the potential to provide fundamental information that can be used for mapping, management, conservation, and future research at other Red Sea reef sites in Saudi Arabia.

Since the Hamas attack, 7 of October 2023, instability in the Red Sea region has occurred. Due to this, the United States, along with other western countries has made a military intervention to targets in Yemen. But the question remains, how has it been possible for the US to carry out a military attack? This paper is aiming to study how the US has made this intervention possible by analyzing the securitization of the threat image from the Red Sea region. The study is going to analyze the ATA (Annual threat Assessment) material from the years 2006-2024, the report shows next year's US threat image. By the Securitization Theory the study is aiming to see how the threat image has been securitized. Combined with a discourse analysis as a method the study will investigate how the Red Sea region is expressed in the reports. This material, theory and method have not been studied before and therefore filled a gap in the previous research field.  The purpose is to contribute to a wider picture of the Securitization theory in the international arena. The analysis shows that ATA reports contain clear signs of securitization. The results show that the reports contained loaded words, an authority that was targeting an audience and macro securitization had occurred by mentioning the conflict in the Red Sea region as a proxy war. Due to these results one could draw the conclusion that Securitization had occurred in the report and therefore made possible for the military invasion.