A sequence of autonomous underwater glider deployments were used to characterize the spatial-temporal variability of the region over an eight month period from late September to May. Strongly stratified system was found in early fall with significant gradients in both temperature (T) and salinity (S), during winter T < 23°C and minimum S of 40.3 psu was observed and resulting in weakened stratification that enables deep convective mixing and upwelling of deep water by cyclonic circulations in the region leading to significant biomass increase. Throughout the entire observational period the slope of the 28 and 28.5 kg/m3 isopycnals remained sloping downward from offshore toward the coast reflected a persistent northward geostrophic flow. The depth of the 180 μmol/kg isopleth of oxygen, indicative of the top of the nutricline, paralleled the depth of the 28 kg/m3, but remained slightly deeper than the isopycnal. The deep winter mixing did not penetrate the nutricline where the mixed layer was deeper near the coast. However, because of the cyclonic signature the 28 kg/m3 rose to the surface offshore, injecting nutrients into the surface layer and promoting increased biomass in the central Red Sea. With the presence of cyclonic eddies, there was evidence of subduction associated with the cross-eddy circulation. This subducted flow was toward the coast within the domain of the glider observations. During this period, increases in the particulate backscatter were associated with increased chlorophyll indicating that the suspended particles were primarily phytoplankton particles. Within the mean northward flow there is a cross-basin flow wherein water is upwelled near the center of the Red Sea, there is a eastward component to the northward flow, and subsequent downwelling near the coasts. Within the surface flow subductive processes lead not only to a horizontal flow, but also a downward component toward the coast. Overall transport is very 3-dimensional in the northern Red Sea, such that northward transport and its associated embedded circulations are northward, while southward transport occurs on the western side of the Red Sea, in contrast to some of the descriptions of flow provided in earlier papers.

Coral reef ecosystems are in rapid decline due to global and local anthropogenic factors. Being among the most diverse ecosystems on Earth, a loss will decrease species diversity, and remove food source for people along the coast. The coral together with its symbionts (i.e. Symbiodinium, bacteria, and other microorganisms) is called the ‘coral holobiont’. The coral host offers its associated symbionts suitable habitats and nutrients, while Symbiodinium and coral-associated bacteria provide the host with photosynthates and vital nutrients. Association of corals with certain types of Symbiodinium and bacteria confer coral stress tolerance, and lack or loss of these symbionts coincides with diseased or bleached corals. However, a detailed understanding of the coral holobiont diversity and structure in regard to diseases and health states or across global scales is missing. This dissertation addressed coral-associated symbiont diversity, specifically of Symbiodinium and bacteria, in various coral species from different geographic locations and different health states. The main aims were (1) to expand the scope of existing technologies, (2) to establish a standardized framework to facilitate comparison of symbiont assemblages over coral species and sites, (3) to assess Symbiodinium diversity in the Arabian Seas, and (4) to elucidate whether coral health states have conserved bacterial footprints. In summary, a next generation sequencing pipeline for Symbiodinium diversity typing of the ITS2 marker is developed and applied to describe Symbiodinium diversity in corals around the Arabian Peninsula. The data show that corals in the Arabian Seas are dominated by a single Symbiodinium type, but harbor a rich variety of types in low abundant. Further, association with different Symbiodinium types is structured according to geographic locations. In addition, the application of 16S rRNA gene microarrays to investigate how differences in microbiome structure relate to differences in health and disease demonstrate that coral species share common microbial footprints in phenotypically similar diseases that are conserved between regional seas. Moreover, corals harbor bacteria that are species-specific and distinct from the diseased microbial footprints. The existence of conserved coral disease microbiomes allows for cataloging diseases based on bacterial assemblage over coral species boundaries and will greatly facilitate future comparative analyses.

Deep-sea corals have long been regarded as cold-water coral; however a reevaluation of their habitat limitations has been suggested after the discovery of deep-sea coral in the Red Sea where temperatures exceed 20˚C. To gain further insight into the biology of deep-sea corals at these temperatures, the work in this PhD employed a holotranscriptomic approach, looking at coral animal host and bacterial symbiont gene expression in Dendrophyllia sp., Eguchipsammia fistula, and Rhizotrochus sp. sampled from the deep Red Sea. Bacterial community composition was analyzed via amplicon-based 16S surveys and cultured bacterial strains were subjected to bioprospecting in order to gauge the pharmaceutical potential of coralassociated microbes. Coral host transcriptome data suggest that coral can employ mitochondrial hypometabolism, anaerobic glycolysis, and surface cilia to enhance mass transport rates to manage the low oxygen and highly oligotrophic Red Sea waters. In the microbial community associated with these corals, ribokinases and retron-type reverse transcriptases are abundantly expressed. In its first application to deep-sea coral associated microbial communities, 16S-based next-generation sequencing found that a single operational taxonomic unit can comprise the majority of sequence reads and that a large number of low abundance populations are present, which cannot be visualized with first generation sequencing. Bioactivity testing of selected bacterial isolates was surveyed over 100 cytological parameters with high content screening, covering several major organelles and key proteins involved in a variety of signaling cascades. Some of these cytological profiles were similar to those of several reference pharmacologically active compounds, which suggest that the bacteria isolates produce compounds with similar mechanisms of action as the reference compounds. The sum of this work offers several mechanisms by which Red Sea deep-sea corals cope with environmental conditions in which no other deep-sea corals have yet to be reported. These deep-sea coral are associated with rich microbial communities, which produce molecules that induce bioactivity. The aggregate of this work provides direction for future research of Red Sea deep-sea coral and highlights the potential pharmacological benefit of conserving these species and their unique ecosystem.

Coral bleaching is now the main driver of reef degradation. The common notion is that most corals bleach and suffer mortality at just 1-2°C above their mean summer maximum temperatures, but some species and genotypes resist or recover better than others. Here we conducted a series of 18-hour short-term heat stress assays side-by-side with a long-term heat stress experiment to assess the ability of both approaches to resolve putative differences in coral thermotolerance and provide a measure of in situ reef temperature thresholds. Using a suite of measures (photosynthetic performance, coral whitening, chlorophyll a, host protein, algal symbiont counts, and algal type association), we assessed bleaching sensitivity/resilience of Stylophora pistillata colonies from the exposed and protected sides of a near-shore coral reef in the central Red Sea. As suggested by the differential mortality during a previous bleaching event, coral colonies from the protected site exhibited less impacted physiological performance in comparison to their exposed site counterparts, and these differences were resolved using both experimental setups. Notably, the long-term experiment provided better resolution with regard to the different measures collected, but at the price of portability, cost, and duration of the experiment. Variability in resilience to ocean warming is critical to reef persistence, yet we lack standardized diagnostics to rapidly assess bleaching severity or resilience across different corals and locations. Using a newly developed portable experimental system termed CBASS (the Coral Bleaching Automated Stress System), we demonstrate that mobile, short-term heat stress assays can resolve fine-scale differences in coral thermotolerance across reef sites. Based on our results, photosynthetic efficiency measured by non-invasive PAM fluorometry provides a rapid and representative proxy of coral resilience. Our system holds the potential to be employed for large-scale determination of in situ bleaching temperature thresholds across reef sites and species. Such data can then be used to identify resistant genotypes (and reefs) for downstream experimental examination and to complement existing remote-sensing approaches.

Phages are the most abundant components of the marine environments and can control host abundances. The severity of viral infections may depend on whether phages are lytic, lysogenic, or chronic, which can be influenced by host activity and by environmental conditions. Lysogeny remains the least understood process. Knowledge of virioplankton dynamics and their life strategies in the Red Sea remain unexplored. In this Ph.D. research we aimed to quantify virioplankton abundance, the variability on viral and bacterial dynamics, and to investigate the occurrence of lytic and lysogenic phages in the Red Sea. Accordingly, we used the flow cytometric technique to enumerate viral and bacterial abundances in the coastal pelagic area during two years of sampling and in the coastal lagoon waters for one year, together with water column distribution in open Red Sea waters. We conducted incubations of natural microbial communities in the laboratory to induce lysogenic bacteria by using the chemical mutagenic mitomycin C. We also explored the influence of host abundance, temperature, and ultraviolet radiation on viral dynamics and lysogeny. Our results showed that abundances of virses in the Red Sea ranged from 106 to 107 virus-like particles per mL, and bacteria ranged from 104 to 105 cells per mL. We observed a large variability i the values of virus-to-bacterium ratios, and lower values of viral production to those for temperate coastal waters and relatively close to values reported in other oligotrophic areas. Although the lytic phase was prevalent, lysogeny was detected when bacterial abundances decreased. We determined inducible lysogenic bacteria from undetectable to ~56% in the coastal Red Sea, although we found a lower maximum of 29.1% at a eutrophic coastal lagoon. The decay rates of viruses were influenced by UVB exposure, suggesting their susceptibility to solar radiation. Exposure to UVB radiation-induced prophage varied between 4 and 34%. Our findings identified the significant role of viral infections in controlling bacterial abundance and the importance of both lytic and lysogenic phases in the Red Sea waters. This study contributes to the understanding of lysogeny in marine phages.

Over the last four decades, coral reefs have suffered a ~50% decline of across the tropics. Consequently, most research efforts have focused on the impacts of anthropogenic pressures on corals, including ocean warming, ocean acidification, and overfishing. However, recent discoveries indicate that coral reefs are becoming increasingly vulnerable to acute deoxygenation events, which can drive severe and widespread coral bleaching, and in some cases, mortality of corals and other reef organisms. On unimpacted coral reefs, dissolved oxygen (DO) availability can vary between 50% and 200% air saturation, depending on the location, proximity to the open-ocean, and time of the day. During the daytime, Symbiodiniaceae spp. produce more O$_2$ than the coral host can consume, releasing excess O$_2$ to the surrounding tissues. However, at nighttime Symbiodiniaceae spp. cease O$_2$ production. Hence, corals may suffer to O$_2$ deprivation at nighttime when the photosynthesis ceases, and holobiont respiration consumes oxygen. To assess the O$_2$ thresholds and aftereffects of two Red Sea coral species: ${{P. lobata}}$ and ${{G. fascicularis}}$ corals were exposed to reduced DO concentrations. Coral fragments from both species were exposed to one control treatment (6.8 mg O$_2$ l$^{−1}$) and three reduced DO concentrations treatments (5.25 mg O$_2$ l$^{−1}$, 3.5 mg O$_2$ l$^{−1}$, and 1.25 mg O$_2$ l$^{−1}$). Experiments were held at a stable temperature (32°C ± 0.25) and stable pH levels (pH 8.2 ± 0.08). Corals in these experiments displayed different thresholds to low O$_2$ concentrations. ${{P. lobata}}$ coral fragments didn’t exhibit any bleaching symptoms throughout complete experiment. However, ${{G. fascicularis}}$ fragments showed signs of bleaching after the third night of exposure to the low O$_2$ treatment (1.25 mg O$_2$ l$^{−1}$). Physiological variables such as maximum and effective photochemical efficiency, Chl ${{a}}$, cell density, and dark respiration experienced the lowest values under the low O$_2$ treatment for both species. These results highlight the need for further experimental assessments of deoxygenation thresholds for corals across the globe. These assessments are of great importance to create better conservation strategies for the preservation of coral reefs.

Given the high salinity, prevailing annual high temperatures, and ultra-oligotrophic conditions in the Red Sea isolation and characterization of important microbial groups thriving in this environment is important in understanding the ecological significance and metabolic capabilities of these communities. By using a high-­throughput cultivation technique in natural seawater amended with minute amounts of nutrients, members of the rare biosphere (PS1), methylotrophic Betaproteobacteria (OM43), and the ubiquitous and abundant SAR11 group (Pelagibacterales), were isolated in pure culture. Phylogenetic analyses of Red Sea isolates along with comparative genomics with close representatives from disparate provinces revealed ecotypes and genomic differentiation among the groups. Firstly, the PS1 alphaproteobacterial clade was found to be present in very low abundance in several metagenomic datasets form divergent environments. While strain RS24 (Red Sea) harbored genomic islands involved in polymer degradation, IMCC14465 (East (Japan) Sea) contained unique genes for degradation of aromatic compounds. Secondly, methylotrophic OM43 bacteria from the Red Sea (F5, G12 and H7) showed higher similarities with KB13 isolate from Hawaii, forming a ‘H-­RS’ (Hawaii-­Red Sea) cluster separate from HTCC2181 (Oregon isolate). HTCC2181 members were shown to prevail in cold, productive coastal environments and had an nqrA-­F system for energy generation by sodium motive force. On the contrary, H-­RS cluster members may be better adapted to warm and oligotrophic environments, and seem to generate energy by using a proton-­translocating NADH:Quinone oxidoreductase (complex I; nuoA-­N subunits). Moreover, F5, G12, and H7 had unique proteins related to resistance to UV, temperature and salinity, in addition to a heavy metal ‘resistance island’ as adaptive traits to cope with the environmental conditions in the Red Sea. Finally, description of the Red Sea Pelagibacterales isolates from the Ia (RS39) and Ib (RS40) subgroups, principally revealed unique putative systems for iron uptake and myo-inositol utilization in RS39, and a potential phosphonates biosynthetic pathway present in RS40. The findings presented here reflect how environments influence the genomic repertoire of microbial communities and shows novel metabolisms and putative pathways as unique adaptive qualities in diverse microbes encompassing from rare to predominant bacterioplankton groups from the Red Sea.

Deep-sea anoxic brine pools are one of the most extreme ecosystems on Earth, which are characterized by drastic changes in salinity, temperature, and oxygen concentration. The interface between the brine and overlaying seawater represents a boundary of oxic-anoxic layer and a steep gradient of redox potential that would initiate favorable conditions for divergent metabolic activities, mainly methanogenesis and sulfate reduction. This study aimed to investigate the diversity of Bacteria, particularly sulfate-reducing communities, and their ecological roles in the interfaces of five geochemically distinct brine pools in the Red Sea. Performing a comprehensive study would enable us to understand the significant role of the microbial groups in local geochemical cycles. Therefore, we combined culture-dependent approach and molecular methods, such as 454 pyrosequencing of 16S rRNA gene, phylogenetic analysis of functional marker gene encoding for the alpha subunits of dissimilatory sulfite reductase (dsrA), and single-cell genomic analysis to address these issues. Community analysis based on 16S rRNA gene sequences demonstrated high bacterial diversity and domination of Bacteria over Archaea in most locations. In the hot and multilayered Atlantis II Deep, the bacterial communities were stratified and hardly overlapped. Meanwhile in the colder brine pools, sulfatereducing Deltaproteobacteria were the most prominent bacterial groups inhabiting the interfaces. Corresponding to the bacterial community profile, the analysis of dsrA gene sequences revealed collectively high diversity of sulfate-reducing communities. Desulfatiglans-like dsrA was the prevalent group and conserved across the Red Sea brine pools. In addition to the molecular studies, more than thirty bacterial strains were successfully isolated and remarkably were found to be cytotoxic against the cancer cell lines. However, none of them were sulfate reducers. Thus, a single-cell genomic analysis was used to study the metabolism of uncultured phyla without having them in culture. We analysed ten single-cell amplified genomes (SAGs) of the uncultivated euryarchaeal Marine Benthic Group E (MBGE), which contain a key enzyme for sulfate reduction. The results showed the possibility of MBGE to grow autotrophically only with carbon dioxide and hydrogen. In the absence of adenosine 5’-phosphosulfate reductase, we hypothesized that MBGE perform sulfite reduction rather than sulfate reduction to conserve energy.

Natural products offer many possibilities for the treatment of disease. More than 70% of the Earth’s surface is ocean, and recent exploration and access has allowed for new additions to this catalog of natural treasures. The Central Red Sea off the coast of Saudi Arabia serves as a newly accessible location, which provides the opportunity to bioprospect marine sponges with the purpose of identifying novel antiviral scaffolds. Antivirals are underrepresented in present day clinical trials, as well as in the academic screens of marine natural product libraries. Here a high-throughput pipeline was initiated by prefacing the antiviral screen with an Image-based High-Content Screening (HCS) technique in order to identify candidates with antiviral potential. Prospective candidates were tested in a biochemical or cell-based assay for the ability to inhibit the NS3 protease of the West Nile Virus (WNV NS protease) as well as replication and reverse transcription of the Human Immunodeficiency Virus 1 (HIV-1). The analytical chemistry techniques of High-Performance Liquid Chromatograpy (HPLC), Liquid Chromatography-Mass Spectrometry (LC-MS), and Nuclear Magnetic Resonance (NMR) where used in order to identify the compounds responsible for the characteristic antiviral activity of the selected sponge fractions. We have identified a 3-alkyl pyridinium from Amphimedon chloros as the causative agent of the observed WNV NS3 protease inhibition in vitro. Additionally, we identified debromohymenialdisine, hymenialdisine, and oroidin from Stylissa carteri as prospective scaffolds capable of HIV-1 inhibition.

Motivation behind the spring whale shark (Rhincodon typus) aggregation in Al-Lith, on the Saudi Arabian coast of the South Central Red Sea, is uncertain. A plausible hypothesis is that whale sharks gather to feed on high prey density, leading to questions about the cause of the prey density. A bottom-up process fueled by nutrient input or accumulation from physical advection could create a peak in prey biomass. Wastewater discharged from an aquaculture facility could affect productivity or provide a chemosensory cue for whale sharks. Yet, basic physico-biological oceanography of this region is unresolved. Monthly profiles, long-term moorings, and spatial surveys were used to describe the temporal variability of potential prey biomass and water masses in this region for the first time. Plankton abundance of individuals larger than ~0.7 cm did not peak during whale shark season. Rather, a decrease coinciding the trailing end of whale shark detections was observed. Sites 180 m apart had differences in acoustic backscatter, suggesting small-scale biomass patchiness, supporting the small-scale variability in whale shark habitat selectivity. Red Sea Deep Water, a nutrient-rich water mass formed in the northern Red Sea, appeared in July at the same time the Tokar wind jet from the Sudanese mountain gap is the highest. Gulf of Aden Water, a nutrient-rich water mass from the Indian Ocean, arrived as episodes from May to September, contrary to previous expectations that the water arrives continuously. It is unlikely that these natural nutrient sources are directly responsible for the high prey density attracting the whale sharks. The aquaculture plume, observed at the aggregation site, had a distinct seasonality from the ambient waters. The plume’s highest salinity (>48) approached the extreme limits of coral tolerances. Nutrient concentrations (nitrate, nitrite, phosphate, silica), suspended particulate matter, phytoplankton biomass, bacteria and cyanobacteria cell counts, total nitrogen, and relative abundance of genera associated with opportunistic pathogenic species (e.g., Arcobacter) were significantly higher in the plume. This study was the first to estimate the nutrient flux and spatial variability of the aquaculture plume.