Originally presented as the author's Thesis (Ph. D.--North Carolina State University, 1980). / Includes indexes. In Arabic. Includes bibliographical references (p. 315-336).

As anthropogenically-forced ocean temperatures continue to rise, the physiological response of marine macrophytes becomes exceedingly relevant. The Red Sea is a semi-isolated sea- the warmest in the world (SST up to 34°C) - already exhibiting signs of rapid warming rates exceeding those of other tropical oceans. This will have profound effects on the physiology of marine organisms, specifically marine macrophytes, which have direct influence on the dynamic carbonate system of the Red Sea. The aim of this paper is to define the physiological capability and thermal optima and limits of six ecologically important Red Sea macrophytes- ranging from seagrasses to calcifying and non-calcifying algae- and to describe the effects of increasing thermal stress on the performance and limits of each macrophyte in terms of activation energy. Of the species considered, Halophila stipulacae, Halimeda optunia, Halimeda monile and Padina pavonica thrive in thermal extremes and may be more successful in future Red Sea warming scenarios. Specifically, Halimeda opuntia increased productivity and calcification rates up to 38°C, making it the most thermally resilient macrophyte. Halophila stipulacae is the most productive seagrass, and hence has the greatest positive effect on Omega saturation state and offers chemical buffer capacity to future ocean acidification.

Prokaryotes are the main actors in biogeochemical cycles that are fundamental in global nutrient cycling. The characterization of microbial communities and isolates can enhance the comprehension of such cycles. Potentially novel biochemical processes can be discovered in particular environments with unique characteristics. The Red Sea can be considered as a unique natural laboratory due to its peculiar hydrology and physical features including temperature, salinity and water circulation. Moreover the Red Sea is subjected to hydrocarbon pollution by both anthropogenic and natural sources that select hydrocarbon degrading prokaryotes. Due to its unique features the Red Sea has the potential to host uncharacterized novel microorganisms with hydrocarbondegrading pathways. The focus of this thesis is on the characterization at the metagenomic level of the water column of the Red Sea and on the isolation and characterization of novel hydrocarbon-degrading species and genomes adapted to the unique environmental characteristics of the basin. The presence of metabolic genes responsible of both linear and aromatic hydrocarbon degradation has been evaluated from a metagenomic survey and a meta-analysis of already available datasets. In parallel, water column-based microcosms have been established with crude oil as the sole carbon source, with aim to isolate potential novel bacterial species and provide new genome-based insights on the hydrocarbon degradation potential available in the Red Sea.

The genus Albula includes marine fish species, commonly called bonefish, that occur in tropical coastal ecosystems worldwide. Their association to nearshore marine environments makes bonefish especially vulnerable to habitat loss and overharvest. Artisanal fisheries often harvest bonefish, although, in certain areas, bonefish support lucrative catch-and-release recreational fisheries. Bonefish are largely understudied compared to other economically significant fish species, and the presence of cryptic species within the Albula genus has further complicated the establishment of conservation measures. In particular, there is no detailed biological information available on bonefish from the Red Sea despite the unregulated harvest of bonefish that occurs there. To facilitate the establishment of management and contribute to the overall knowledge of Albula biology, I assessed the genetic diversity, growth, and seasonal reproduction of bonefish in Saudi Arabia. Based on samples collected from local fish markets and coastal waters, my findings provide the first genetically verified records of A. glossodonta in the Red Sea and A. oligolepis in the northwest Indian Ocean. Moreover, my results indicate a genetically distinct Red Sea population of A. glossodonta that reaches smaller sizes than documented for the species in the Pacific Ocean and exhibits distinct seasonal spawning activity over the winter months. This information enables fishery managers to make informed decisions regarding bonefish size limits and seasonal colures around peak spawning activity. My results may become increasingly relevant as the potential for lucrative recreational fisheries for Albula glossodonta will likely increase with the ambitious Red Sea tourism development plans.

The demand for novel and robust microbial biocatalysts for industrial and pharmaceutical applications continue to grow at a fast pace.This warrants a continuous need for advanced tools and technologies to exploit the vast metabolic potential of microorganisms in different environments. Unlike culture-based studies that can only reveal the metabolic potential of cultivable microorganisms, functional metagenomics charts the enzymatic potential of the entire microbial communities in a given environment. This method has substantially contributed to the effective discovery of unique microbial genes for industrial and medical applications. Functional metagenomics involves the extraction of microbial DNA directly from environmental samples,construction of an expression library containing the entire microbial genome, and screening the libraries for the presence of desired phenotypes. Therefore, development of a pipeline for analyzing and screening metagenomic libraries is essential for rapid detection of the desired features from thousands of clones of a single library. Here, we developed a pipeline for high-throughput screening of the lipolytic genes from the Red Sea.Further, a high-throughput single cell microfluidics platform combined with a laser-based fluorescent screening bioassay was deployed to discover new lipolytic genes. Our analysis led to the identification of 24 microbial genes for lipases and esterase from a metagenomic library of the Red Sea water. The results further showed that the constructed pipeline is robust in conducting functional metagenomics and for the discovery of new genes. It also implies that the Red Sea is a rich under- investigated source of natural resources of new genes and gene products.

In agreement with global patterns of climate change and increasing temperatures in the tropical oceans, the Northern Red Sea (NRS) has been warming over the last few decades. Using 18 years of remotely-sensed chlorophyll-a data (Chl-a, an index of phytoplankton biomass), we investigate the potential impacts of climate warming on phytoplankton abundance and phenology in the Northern Red Sea by exploring the mechanistic links with the regional physical environment. The results of the analysis reveal that, in accordance with other tropical ecosystems, phytoplankton biomass in the NRS will decrease in response to warmer climate scenarios. This is attributed to lower heat fluxes (heat loss to the atmosphere) during the bloom period, and enhanced vertical stratification, which prevents vertical mixing of nutrients into the euphotic layer. In addition, we show that during warmer conditions (when heat fluxes are weakened), the winter bloom initiates significantly later (by up to 10 weeks) and its duration is considerably reduced. The biological implications of alterations to phytoplankton phenology may include increased larval mortality of pelagic species, reduced recruitment, fisheries impacts and changes to community structure.

Aquatic primary productivity mainly depends on pelagic phytoplankton. The globally abundant marine picocyanobacteria Prochlorococcus comprises a significant fraction of the photosynthetic biomass in most tropical, oligotrophic oceans. The Red Sea is an enclosed narrow body of water characterized by continuous solar irradiance, and negligible annual rainfall, in addition to elevated temperatures and salinity levels, which mimics a global warming scenario. Analysis of 16S rRNA sequences of bacterioplankton communities indicated the predominance of a high-light adapted ecotype (HL II) of Prochlorococcus at the surface of the Northern and Central Red Sea. To this end, we analyzed the distribution of Prochlorococcus at multiple depths within and below the euphotic zone in different regions of the Red Sea, using clone libraries of the 16S–23S rRNA internal transcribed spacer (ITS) region. Results indicated a high diversity of Prochlorococcus ecotypes at the 100 m depth in the water column and an unusual dominance of HL II-related sequences in deeper waters of the Red Sea. To further investigate the microdiversity of Prochlorococcus over a wider biogeographical scope, we used a 454-pyrosequencing approach to analyze rpoC1 gene pyrotags. Samples were collected from the surface of the water column to up to 500 m at 45 stations that span the Red Sea’s main basin from 4 north to south. Phylogenetic analysis of abundant rpoC1 OTUs revealed genotypes of recently discovered strains that belong to the high-light and lowlight clades. In addition, we used a rapid community-profiling tool (GraftM) and quantitatively analyzed rpoC1 gene abundance from 45 metagenomes to assess the Prochlorococcus community structure across vertical and horizontal physicochemical gradients. Results revealed the clustering of samples according to their depth and a strong influence on ecotypic distribution by temperature and oxygen levels. In efforts to better understand how the cells survive the unusual features of the Red Sea, a Prochlorococcus strain of the HL II adapted clade from the euphotic zone was cultured, enabling morphological analyses and growth rates measurements for the strain. In addition, we successfully sequenced and annotated the genome of the strain, which was then used for genomic comparison with other ecotypes. Interestingly, the set of unique genes identified in the draft genome included genes encoding proteins involved in salt tolerance mechanisms. The expression level and pattern of these genes in the Red Sea water column was explored through metatranscriptomic mapping and revealed their occurrence throughout, independent of the diel cycle. This led to the hypothesis that Prochlorococcus populations in the highly saline Red Sea are able to biosynthesize additional compatible solutes via several pathways to counterbalance the effects of salt stress. The results presented in this dissertation provide the first glimpse on how the environmental parameters of the Red Sea can affect the evolution, diversity and distribution patterns of Prochlorococcus ecotypes.

Satellite sea surface height (SSH) data over 1992-2012 are analyzed to study the spatial and temporal variability of sea level in the Red Sea. Empirical orthogonal functions (EOF) analysis suggests the remarkable seasonality of SSH in the Red Sea, and a significant correlation is found between SSH variation and seasonal wind cycle. A winding-angle based eddy identification algorithm is employed to derive the mesoscale eddy information from SSH data. Totally more than 5500 eddies are detected, belonging to 2583 eddy tracks. Statistics suggest that eddies generate over the entire Red Sea, with two regions in the central basin of high eddy frequency. 76% of the detected eddies have a radius ranging from 40km to 100km, of which both intensity and absolute vorticity decrease with eddy radius. The average eddy lifespan is about 5 weeks, and eddies with longer lifespan tend to have larger radius but less intensity. Different deformation rate exists between anticyclonic eddies (AEs) and cyclonic eddies (CEs), those eddies with higher intensity appear to be less deformed and more circular. Inspection of the 84 long-lived eddies suggests the AEs tend to move a little more northward than CEs. AE generation during summer is obviously lower than that during other seasons, while CE generation is higher during spring and summer. Other features of AEs and CEs are similar with both vorticity and intensity reaching the summer peaks in August and winter peaks in January. Inter-annual variability reveals that the eddies in the Red Sea are isolated from the global event. The eddy property tendencies are different from the south and north basin, both of which exhibit a two-year cycle. Showing a correlation coefficient of -0.91, Brunt–Väisälä frequency is negatively correlated with eddy kinetic energy (EKE), which results from AE activities in the high eddy frequency region. Climatological vertical velocity shear variation is identical with EKE except in the autumn, suggesting the vertical shear could convert the energy from baroclinic instability into eddy activity. Finally, numerical simulation results from the MIT general circulation model (MITgcm) are validated with previous studies and observations. The vertical structure of the simulated flux through Bab el Mandeb is successfully reproduced. Further validation with the 2010 cruise suggests that the thermocline occurs at ~200m, but the model vertical salinity gradient is lower than the observations. The model surface eddy variability is also examined, suggesting good agreement with satellite observations.

Eukaryotic microalgae from the Red Sea were isolated, characterized and identified with the purpose of building a culture collection that will serve future research activities in the area of industrial microbiology. Seven sampling locations were surveyed using an in-house designed isolation protocol. Microalgae enrichment was carried out in vitro using the streak plate method and fluorescence activated cell sorting approaches. Colonial and cellular microscopy, growth media preference assays, as well as temperature, pH and salinity tolerance tests were carried out to describe the isolates. DNA extraction, PCR amplification, template sequencing and in silico analyses were carried out to identify the isolates and arrange them in a proper phylogenetic description. In total, 129 isolates were obtained. From these, only 39 were selected for characterization given their increased ability of accumulating large amounts of biomass in solid and liquid media in relatively short periods of time. All of these have a green color, are unicellular, non-motile, photosynthetic organisms and have a cell size ranging from 5 to 8 µm. More than half of them showed growth preference in Walne media, followed by F/2, MN and BG-11 SW. Maximum temperature tolerance of all organisms was around 38 ºC, while optimum growth was observed close to 25 ºC. pH preference was diverse and three groups were identified: acidic (6), intermediate (8 - 9) and alkaline (> 10) growing isolates. Salinity tests showed an overall growth preference at 25 PSU, approximately 10 units lower than that found at the sampling stations. Most isolates showed diminished growth at high salinity and high pH, except for OS3S1b which grew well in both cases, and could be an interesting strain to study further. Twenty four isolates were related to Ulvophyceae sp. MBIC10591 by BLAST approaches with a maximum identity of 96 - 97%. A maximum likelihood phylogenetic tree was created for these isolates, relative to the BLAST hits and to some model eukaryotic microalgae for positioning reference. It was shown that the 24 OS isolates are related to each other with a confidence value of 84%. Differential responses of all high biomass producing isolates towards abiotic stresses might suggest that each represents a distinct, novel, unclassified marine organism.

The overall goal of this study was to elucidate the relationship between coral nutrition and the observed prey preferences exhibited by corallivorous butterflyfishes. Fifteen species of coral (thirteen hard, two soft) and stomach/hindgut contents from six species of butterflyfish were analyzed in this study, all collected from the central Saudi Arabian Red Sea. All samples were analyzed for lipid, total-nitrogen (proxy for protein), and ash (proxy for minerals and when combined with lipid data, allows for calculation of carbohydrate). Unfortunately, substantial errors were encountered in the experimental lipid data, precluding the use of this data set. Using the value of (protein/ash) as a proxy for potential nutritional quality, it was determined that Pocillopora cf. verrucosa and P. damicornis have the highest nutritional quality, while Acropora hyacinthus and Stylophora pistillata have intermediate nutritional quality, and all remaining 11 species have low nutritional quality. This suggests that the high nutritional quality of Pocillopora damicornis and Acropora hyacinthus may be the cause of the well documented predator preferences for these two species. Fish gut content samples were, on average, twice as rich in protein and half as rich in minerals as the coral tissue samples, suggesting either selective consumption of especially rich parts of the coral colony, or consumption of other food sources (facultative corallivores). In all six butterflyfish species, stomach content samples were consistently richer in protein and poorer in mineral content than the hindgut content samples; this suggests significant and measureable uptake of protein in the butterflyfish digestion process.