Between 33 and 91 percent of marine species are currently undescribed, with the majority occurring in tropical and offshore environments. Sponges act as important microhabitats and promote biodiversity by harboring a wide variety of macrofauna and microbiota, but little is known about the relationships between the sponges and their symbionts. This study uses DNA barcoding to examine the macrofaunal communities associated with sponges of the central Saudi Arabian Red Sea, a drastically understudied ecosystem with high biodiversity and endemism. In total, 185 epifaunal and infaunal operational taxonomic units (OTUs) were distinguished from the 1399 successfully-sequenced macrofauna individuals from 129 sponges representing seven sponge species, one of which (Stylissa carteri) was intensively studied. A significant difference was found in the macrofaunal community composition of Stylissa carteri along a cross-shelf gradient using relative OTU abundance (Bray-Curtis diversity index). The abundance of S. carteri also follows a cross-shelf gradient, increasing with proximity to shore. The difference in macrofaunal communities of several species of sponges at one location was found to be significant as well, using OTU presence (binary Jaccard diversity index). Four of the seven sponge species collected were dominated by a single annelid OTU, each unique to one sponge species. A fifth was dominated by four arthropod OTUs, all species-specific as well. Region-based diversity differences may be attributed to environmental factors such as reef morphology, water flow, and sedimentation, whereas species-based differences may be caused by sponge morphology, microbial abundances, and chemical defenses. As climate change and ocean acidification continue to modify coral reef ecosystems, understanding the ecology of sponges and their role as microhabitats may become more important. This thesis also includes a supplemental document in the form of a spreadsheet showing the number of macrofauna individuals of each OTU found within each sponge sample.

Wind and waves play a major role in important ocean dynamical processes, such as the exchange of heat, momentum and gases between atmosphere and ocean, that greatly contributes to the earth climate and marine lives. Knowledge on wind and wave weather and climate is crucial for a wide range of applications, including oceanographic studies, maritime activities and ocean engineering. Despite being one of the important world shipping routes, the wind-wave characteristics in the Red Sea are yet to be fully explored. Because of the scarcity of waves data in the Red Sea, numerical models become crucial and provide very powerful tools to extrapolate wind and wave data in space, and backward and forward in time. Unlike open oceans, enclosed basins wave have different characteristics, mainly because of their local generation processes. The complex orography on both sides of the Red Sea makes the local wind, and consequently wave, modeling very challenging. This thesis considers the modeling of wind-wave characteristics in the Red Sea, including their climate variability and trends using state-of-the-art numerical models and all available observations. Different approaches are investigated to model and understand the general and unusual wind and wave conditions in the basin using standard global meteorological products and customised regional wind and wave models. After studying and identifying the main characteristics of the wind-wave variability in the Red Sea, we demonstrate the importance of generating accurate atmospheric forcing through data assimilation for reliable wave simulations. In particular, we show that the state-of-the-art physical formulation of wave models is not suitable to model the unique situation of the two opposing wind-waves systems in the Red Sea Convergence Zone, and propose and successfully test a modification to the input and white-capping source functions to address this problem. We further investigate the climate variability and trends of wind and waves in the Red Sea using high-resolution wind and wave reanalyses that have been generated as part of this thesis. An innovative spectral partition technique is first applied to distinguish the dominant wave systems. Our analysis demonstrates that winds, and consequently waves, exhibit a decreasing trend in the Red Sea. This is mainly attributed to a remarkable weakening of the winds protruding from the Mediterranean Sea. We also use these highresolution reanalyses to assess the potential for harvesting wind and wave energy from the Red Sea.

Mangrove plants are a productive ecosystem that provide several benefits for marine organisms and industry. They are considered to be a food source and habitat for many organisms. However, mangrove growth is limited by nutrient availability. According to some recent studies, the dwarfism of the mangrove plants is due to the limitation of nitrogen in the environment. Biological nitrogen fixation is the process by which atmospheric nitrogen is fixed into ammonium. Then, this fixed nitrogen can be uptaken by plants. Hence, biological nitrogen fixation increases the input of nitrogen in the mangrove ecosystem. In this project, we focus on measuring the rates of nitrogen fixation on Red Sea mangrove (Avicennia marina) located at Thuwal, Saudi Arabia. The nitrogen fixation rates are calculated by the acetylene reduction assay. The experimental setup will allow us to analyze the effect of crab bioturbation on nitrogen fixing rates. This study will help to better understand the nitrogen dynamics in mangrove ecosystems in Saudi Arabia. Furthermore, this study points out the importance of the sediment microbial community in mangrove trees development. Finally, the role of nitrogen fixing bacteria should be taken in account for future restoration activities.

Seagrass ecosystems are intense carbon sinks, but they can also emit greenhouse gases (GHG), such as carbon dioxide (CO2) and methane (CH4), to the atmosphere. Yet, GHG emissions by seagrasses are not considered when estimating global CH4 production rates by natural sources, although these estimations will help predict future scenarios and potential changes in CH4 emissions. In addition, the effect of warming on GHG emissions by seagrasses has not yet been reported. The present study aims to assess the CO2 and CH4 production rates by vegetated and adjacent bare sediment of a monospecific seagrass meadow (Halophila stipulacea) located in the central Red Sea. We measured CH4 and CO2 fluxes and their isotopic signatures by cavity ringdown spectroscopy on chambers containing vegetated and bare sediment. The fluxes were measured at temperatures from 25 °C (winter seawater temperature) to 37 °C to cover the natural thermal range and future seawater temperatures in the Red Sea. Additional parameters analyzed included changes in the sediment microbial community composition, sediment organic matter, organic carbon, nitrogen, and phosphorus concentration. We detected up to 100-fold higher CH4 (up tp 571.65 µmol CH4 m−2 d−1) and up to six-fold higher CO2 (up to 13,930.18 µmol CO2 m−2 d−1) fluxes in vegetated sediment compared to bare sediment, and an increase in CH4 and CO2 production with increasing temperature. In contrast, CH4 and CO2 production rates decreased in communities that were maintained at 25 °C, while communities that were exposed to prolonged darkness showed a decrease in CH4 and an increase in CO2 production rates. However, only minor changes were seen in the microbial community composition with increasing temperatures. These results show that GHG emissions by seagrasses might be affected by natural temperature extremes and warming due to climate change in the Red Sea. The findings will have critical implications for the estimation of natural GHG sources, especially when predicting future changes in the global CH4 budget.

Saudi Arabia is highly accessible to marine water, receives year-round availability of sunlight and generates a high annual carbon dioxide emission, all of which are justifications that merits the deployment of cyanobacterial cell factories. However, industrial cyanobacterial strains capable of thriving in conditions of the Arabian Peninsula are currently lacking. Given the fact that native cyanobacteria from the Red Sea are adapted to the local conditions, they are therefore good cell factory candidates where their inherent attributes can be harnessed. In this dissertation, an isolation and screening pipeline was developed to specifically identify physiologically robust cyanobacterial strains from the central Red Sea. Seventeen unicellular cyanobacterial strains were extensively cataloged through a series of physiological characterization and their evolutionary relationships were ascertained through phylogenetic analyses. Arising from this survey work, a high light, thermo- and halo-tolerant Synechococcus sp. RSCCF101 was selected for metabolic analysis under various growth conditions to assess its suitability as a platform for cell factory development. Significant metabolic changes were observed in cells subjected to different light regimes. High phycocyanin and chlorophyll a content were obtained under the low-light growth (50 μmol photons.m-2.s-1) while high biomass was accumulated, along with an increase external nitrate demand, under the high light growth (200 μmol photons.m-2.s-1). A genomic and transcriptomic approach was undertaken to elucidate the molecular signatures of Synechococcus sp. RSCCF101. Synechococcus sp. RSCCF101 contains a small genome (3 Mbp) that is rich in guanine cytosine content (68%) and harbors genes that encode for compatible solutes biosynthetic pathway and phycobilisome subunits which may account for its halo-tolerant and phycocyanin rich phenotype. Upon high-light treatment, the light harvesting machineries of Synechococcus sp. RSCCF101 was downregulated while the photosystem protection and carbon fixation capacity were upregulated. Taken together, the findings of this research will facilitate in the development of a new model system for industrial applications in high-light, high temperature and high salinity environments in general and Saudi Arabia in particular.

This dissertation characterizes the genetic diversity and thermal tolerance of the coral holobiont Stylophora pistillata and Pocillopora verrucosa (family Pocilloporidae) across the Saudi Arabian Red Sea coast (~1500 km). The population genetic structure and holobiont diversity was assessed using genome-wide single nucleotide polymorphisms (SNPs) identified with reference genome-based RAD-Seq, while the associated microbial communities of the algal symbiont (Symbiodiniaceae) and bacteria were inferred from metabarcoding analyses of the ITS2 and 16S rRNA gene. Thermal tolerance of Stylophora pistillata colonies was assessed using standardized short-term heat stress assays on the novel Coral Bleaching Automated Stress System (CBASS). Chapter 1 details the assembly and annotation of the P. verrucosa genome (~380 Mbp; 27,439 gene models), which was highly complete and compared well to the already available S. pistillata genome. Chapter 2 presents population genetic analyses of both coral species, which revealed pronounced differences in their population genetic structure. While P. verrucosa seemed to be highly connected across the Red Sea basin with the exception of the far south, S. pistillata depicted a complex population genetic structure. Microbial communities of Symbiodiniaceae and bacteria were overall less diverse in P. verrucosa than in S. pistillata, and followed an association pattern that was partly determined by the environment and partly by host genotype. Chapter 3 identifies thermally tolerant S. pistillata genotypes by comparing the heat stress response of colonies collected at two sites within the same reef. Ex-situ heat-stress assays confirmed that colonies from the more temperature stable site (fore reef) were less thermally tolerant than their conspecifics from the back reef, where the diel temperature is more variable. This chapter also highlights the utility of acute heat-stress assays as a tool to identify thermotolerant colonies. Taken together, the work of this dissertation provides a foundation for coral conservation in the Red Sea. It highlights that the genetic structure differs between coral species, suggesting that effective conservation through marine protected areas need to incorporate data from multiple species. Coral population genetic data should further be complemented by thermal tolerance assays across the Red Sea to associate genetic diversity with patterns of heat stress tolerance.

Parasitism is a common phenomenon in nature, where one species benefits at the expense of another. In marine environments, fungal parasites are known to infect phytoplankton, causing disease and death, and contributing to the loss of phytoplankton populations. The impact of fungal parasites on phytoplankton communities can be significant, as selective parasitism on one species of phytoplankton can encourage the development of other species and may be one of the factors influencing communities' seasonal succession. Fungi parasites play a crucial role in sinking by inducing cell death and promoting cell aggregation, which can lead to the export of phytoplankton to the deep sea. Although fungal parasites are well studied in freshwater phytoplankton, there is still little information on marine phytoplankton parasites. Recent studies have shown that large diatoms are the preferred hosts for fungal parasites in cold waters, while the infection of dinoflagellates is reported in the oligotrophic Mediterranean Sea. However, the occurrence and impact of fungal parasites on phytoplankton communities in the Red Sea remain largely unknown. Therefore, the proposed project aims to investigate the occurrence of fungal parasites that infect phytoplankton and analyze their role in the export of phytoplankton to the deep sea in the Red Sea. By understanding the ecological impacts, life cycle, host range, and infection strategies of fungal parasites on populations of Red Sea phytoplankton, this study can provide critical information on the dynamics of marine ecosystems and carbon cycling.

Knowledge about cetaceans in the Red Sea is limited with only a handful of sporadic or spatially-limited studies carried out to date. Funded by the Italian Cooperation through a Debt-for-Nature Swap programme and carried out in collaboration with the Egyptian NGO HEPCA, this thesis presents the results from the first ever systematic vessel-based surveys conducted in the southern Egyptian Red Sea from 2010 to 2013 using linetransect methodology. The main aims of the thesis were (a) to estimate cetacean abundance, (b) to determine distribution patterns and habitat use of the cetacean species, (c) to investigate movement patterns for species for which individual recognition techniques were suitable and (d) to identify areas of conservation concern for cetaceans with a particular focus on existing protected areas. Eight species were identified, of which five were commonly encountered (Stenella longirostris, S. attenuata, Tursiops truncatus, T. aduncus, and Grampus griseus) and three were rare (Pseudorca crassidens, Sousa plumbea, Balaenoptera edeni). Estimates of abundance using design-based line transect sampling techniques were obtained for five species: S. attenuata 10,268 (CV=0.26); S. longirostris 6,961 (CV=0.26); T. aduncus 659 (CV=0.69); T. truncatus 509 (CV=0.33), and G. griseus 367 (CV=0.37). Habitat modelling revealed that the two Stenella species were widely distributed across the study area. In contrast, T. truncatus was concentrated in waters around Ras Banas peninsula (in particular Satayah offshore reef), and T. aduncus was mainly found along the coast with possibly separate sub-populations in the northern and southern study area. G. griseus was only encountered in the southern part. The information provided in this study will allow the development of a conservation strategy for the protected areas and will serve as baseline information to carry out future survey work in the Red Sea.

Marine ecosystems can be exposed to natural and anthropogenic disturbances that can lead to ecological failures. Marine reserves have been lately suggested to protect marine populations and communities that have been affected by habitat destruction and harvest. This research evaluates the potential role of two marine reserves established in Oregon in 1967 (Whale Cove) and 1993 (Gregory Point). The red sea urchin (Strongylocentrotus franciscanus) was selected as indicator of population recovery since it is the only species that is commercially harvested. Changes in density, biomass, average size, size structure, growth and mortality rates were evaluated through time to assess population recovery. These parameters were also compared between reserves and adjacent exploited areas to evaluate the effect of exploitation. Results from Whale Cove (old reserve) indicate that the population in this area is fully recovered. On the contrary, the population in Gregory Point (new reserve) showed signs of recovery after six years of being protected. The importance of red urchins as source populations to provide larvae to adjacent areas was explored by the analysis of drifter's trajectories. Both reserves might be connected in a network where larvae produced in Whale Cove will provide recruits to Gregory Point and adjacent exploited areas, as well as populations in northern California. Gregory Point releases larvae that become recruits for Whale Cove only when spawning takes place in winter, otherwise larvae travel to central California. No clear trends were found in growth and mortality rates between reserves and non-reserves; differences were more related with food availability, competitors, and age specific mortality. We applied qualitative simulations to characterize and differentiate the community network inside reserves and exploited areas. Results suggest that communities from a particular site can be represented by a set of alternative models with consistent species interactions. Differences in predator-prey interactions as well as non-predatory relationships (interference competition, mutualism, amensalism) were found among sites. Each set of models represents a hypothesis of community organization that agreed with natural history information. Alternative models suggest that kelp forest communities are dynamic and can shift from one network configuration to another providing a buffer against a variable environment. / Graduation date: 2002

Nowadays, the market environment is getting more radical and dynamic, such condition boosts up intensive competition make numerous organization toward red sea. Under such circumstance, however, the most important thing is not only to get survive but having additional earnings to sustain business. Thus lots organizations struggle to do renewal in strategizing, planning in order to differentiate themselves to outperform in their industry. Based on practical experience and integrate theoretical finds, the framework in analyzing how organization crafts sustainable capacity form coopetition(Äv¦X) is explored. Real practical case is illustrated in this study try to explain how L Company is integrated under a serious competitive condition and outperform then it shapes synergy from merging six parallel businesses into one big company. Through such merging story, finds are emerged as followings: 1. Small business can compete with big company by cooperation with others. 2. Relationship is critical element to integrate forces and accumulate common sense from business partners. 3. In integration, how effective result will come out through intensive compromising and negotiating among business partners. Keywords: Coopetition strategy, Red sea, Blue sea strategy, Zero-sum, Win-win.