Understanding how coral reefs respond to natural disturbances is fundamental to assess their resistance and resilience, particularly in a context of climate change. Therefore, and given the escalating frequency and intensity of bleaching events, it is essential to evaluate responses of communities in space and time to disentangle the mechanisms underlying ecological changes. Here, I analyzed a dataset comprising 59 reefs, resulting from 6 years (2014-2016) of a coral reef benthic monitoring program in the Saudi Arabian Red Sea. It encompasses the 2015/2016 mass bleaching event and spans three different geographic regions: north (Duba and Al Wajh), central (Jeddah and Thuwal), and south (Al Lith, Farasan Islands and Farasan Banks). The results indicate significant differences between regions and through time. Coral assemblages from the southern region were the most affected by the 2015 bleaching event, where in some reefs, hard and soft corals cover dropped to <2% in 2017. Important changes in community structure were observed through time in the three regions, with a shift to a macroalgae, turf algae and CCA dominance. Different environmental drivers (salinity, sea surface temperature, fishing index, distance to shore, and photosynthetically active radiation) were analyzed, and highlighted a regionally-based response of the communities to these potential drivers of change. Overall, the examined Red Sea benthic communities presented dynamic patterns in composition. Distance decay plots based on presence/absence showed a general increase in similarity throughout multiple spatial scales in 2019, when compared to previous years. This finding suggests a loss in biodiversity due to thermal anomalies and bleaching events, evidenced by a homogenization (i.e., increase similarity) in the composition of the benthic communities. I document here a patterns of dominance of a few benthic groups with time and a decrease in branching corals. This study provides baseline information about changes in coral reef benthic community structure and identifies environmental factors with a higher impact on a regional scale. This information can be used to guide conservation efforts in these highly biodiverse ecosystems.The resulting datasets can be valuable for anticipating responses of coral communities under future climate scenarios.

As a part of Saudi Arabia’s Vision 2030, the Al Wajh Bank will soon undergo major coastal development to be transformed into a sustainable luxury tourist destination, with goals to safeguard the marine and coastal habitats in order to achieve a net conservation benefit of 30%. To realize these objectives, it is essential to establish baseline data on the marine communities to gauge the success of conservation goals. In this study, we evaluated and compared the taxonomic and functional diversity of reef fish assemblages between two areas in the Al Wajh Bank, sites inside the lagoon and those outside of it, in order to establish differences in fish communities across environmental gradients. Conditions within the lagoon, such as temperature and salinity, have been shown to differ from most other Red Sea areas and are thought to result in unique fish assemblages. Underwater assessments of fish communities and benthic composition were conducted throughout the Al Wajh Bank during cruises in 2016 and 2017. We found that of the 168 fish species recorded, 75 species were exclusive outside the lagoon, 22 were exclusive inside the lagoon, and 71 species were shared between inside and outside. Sites within the lagoon had significantly less species richness as well as lower abundances. While taxonomic composition differed between the two areas, functionally they were very similar. Two functional metrics (functional richness and functional dispersion) indicated different levels of functional diversity, while two other metrics (functional evenness and functional specialization) showed no differences in functional diversity. The outside had five groups comprising eleven species with functional redundancy; in contrast, the inside had two species which were functionally redundant. This study was able to establish that the inside and outside habitats are different and have dissimilar species compositions, yet the functional characterization of fish assemblages in conserved. These results advocate for the use of functional diversity metrics as a way to evaluate changes to community composition, and is an initial assessment towards tracking changes in the fish communities as coastal development progresses

Microorganisms are widespread in all ecosystems and play critical roles in nature. They are major players in global biogeochemical cycles that are fundamental in nutrient cycling. Molecular ecology surveys that investigate the microbial diversity of many different environments have revealed an impressive diversity of microbes in nature and have highlighted our inability to cultivate the vast majority of them in the laboratory. The improvement of our ability to grow uncultivable microbes in laboratory conditions will help us in this challenging task. Standard cultivation methods that have helped to bring to culture many relevant microorganisms in the past century are, however, characterized by limitations which hamper the isolation of novel microbes. For this reason, alternative cultivation strategies have been developed in recent decades which have allowed to expand the collection of environmentally relevant but poorly represented microbial strains. The use of such novel approaches for investigating the microbial diversity of underexplored natural ecosystems, such as sub-tropical mangrove forests, can result in the isolation, in laboratory conditions, of bacterial strains belonging to previously undescribed taxa. Mangroves are unique environments exposed to strong selection forces with respect to other marine environments, including high temperatures, salinity and oligotrophy. I hypothesize that these unique combinations of environmental features have selected microbiomes with unique characteristics. The aim of this PhD research is to explore the bacterial diversity of the Red Sea mangrove ecosystem, by applying an alternative cultivation strategy that uses oligotrophic conditions and long incubation time. I also exploited the diffusion chamber to cultivate bacterial taxa belonging to rarely isolated or even novel genera. This approach allowed me to isolate four novel bacterial taxa. Using 16S rRNA gene sequencing, the isolated bacteria were identified as one novel species and three novel genera belonging to Alpha-proteobacteria, Bacteroidetes, and Firmicutes, respectively. These isolates were further characterized and described through genomic, phylogenetic, chemotaxonomic, and phenotypic analysis to describe their ecological significance in the ecosystem of origin (i.e., mangrove sediments). This study reveals that the extreme conditions of the Red Sea mangroves have selected a unique and yet mostly untapped culturable microbiome with great potential for environmental applications.

Biocatalysis is considered a green and environmentally friendly technology. Therefore, novel enzymes and enzymatic systems, together with cascades and protein engineering approaches, are in high demand. Here, three very different biocatalytic approaches have been studied. First, the richness of enzymes in the Red Sea brine pools has been assessed, and the discovery and characterization of a novel halophilic γ-carbonic anhydrase is described, together with the protein engineering approach, which boosted the initial catalytic activity of the γ- carbonic anhydrase. The understanding of polyextremophilicity principles from enzymes from the Red Sea brine pool, contributes to the bioengineering effort of turning mesophilic enzymes into more stable variants. Next, focus is given to the use of amine-transaminases in cascades for chiral amine synthesis. This resulted in the development of a self-sufficient sustainable cascade for chiral and non-chiral amine synthesis. This cascade was achieved by combining a lysine decarboxylase with an amine-transaminase to generate a cheap amino donor source for a more sustainable reaction economy. Finally, gas vesicle nanoparticles are functionalized by various engineering principles to create floating platforms for the immobilization of enzymes. The proof-of-concept was achieved by anchoring a phytase via anchoring peptides on the gas vesicle nanoparticles surface. These bioengineering approaches contributed to the effort of generating first principles for protein engineering.

To meet ambitious net-zero greenhouse gas emission targets by 2050, large-scale CO₂ reduction and removal are required. Nature-based solutions have been proposed as a potential aid to this process. Mangrove ecosystems, as well as their conservation and restoration, have the potential to make significant contributions in Saudi Arabia and other coastal regions. While field measurements of carbon assimilation rate and leaf area index (LAI) in mangroves provide important insights into carbon fluxes, they are time-consuming, labor-intensive, and limited when covering large areas. To address this issue, multispectral images captured by unmanned aerial vehicles (UAV) are used to generate spectral vegetation indices, which can then be used to build regression models for estimating mangrove LAI and carbon capture capabilities. The carbon assimilation rate measurements in the field for studying both diurnal and sub-seasonal fluxes revealed that Avicennia marina has a high carbon assimilation rate peak in the morning, which decreases thereafter, and a smaller peak in the afternoon. Furthermore, comparing all the studied sites, the KAM site (June) had the highest morning overall carbon assimilation rate values, ranging from 15- 20 μmol CO₂ m⁻² s⁻¹, followed by Island (October) ranging from 10- 17 μmol CO₂ m⁻² s⁻¹, and finally Rheem (February) ranging from 5- 15 μmol CO₂ m⁻² s⁻¹. Moreover, the acquired multispectral images were used to generate spectral vegetation indices, which were then used as input to build a random forest algorithm for estimating the LAI of mangroves. Following an evaluation of each mangrove site, the Rheem site dataset yielded the best Random forest algorithm (R²= 0.88 and RMSE= 0.39), so this model was used to create high resolution spatially distributed LAI-based maps for all of the mangrove sites studied. Knowing the carbon uptake per leaf area as well as the total leaf area (based on UAV-derived LAI estimates) within a mangrove site enabled us to create carbon capture maps (kg C yr⁻¹ per pixel) for all of the sites studied. To enable a more complete carbon accounting of mangrove ecosystems, future research should explore remote sensing approaches for inferring carbon assimilation in both belowground biomass and soils.

Plastic pollution has become of public concern recently and only in the last decades the need of quantifying loads of plastic in the marine environment and identifying their ultimate destination has been urged as a mean to point at where interventions should concentrate. The Arabian seas (Red Sea and Arabian Gulf) have oceanographic features that candidate them as accumulation zones for marine plastics, but, especially the Red Sea, are largely unexplored. The dissertation here presented provides significant advances in the understanding of the marine plastic distribution in the two basins. Despite the initial hypothesis, the Red Sea was found to hold a remarkably low abundance of plastic particles in its surface waters. Similarly, previous assessments have reported the same in the Arabian Gulf. In line with the global estimates, only a small portion of the plastic that is discarded yearly in the marine environment is found in its surface waters, implying the presence of removal processes. However, the unexpectedly low loads of floating plastics in the Arabian seas indicate that sinks are likely more significant here than elsewhere. In the Red Sea, an extensive survey of macroplastic stranded on shores, globally considered a major sink of marine plastic, has indicated that Avicennia marina mangrove forests, through the mesh created by their pneumatophores, contribute significantly more than unvegetated shores in retaining plastics. Loads of plastic in the Arabian Gulf mangrove stands, more impacted by coastal development than stands in the Red Sea, are even larger. The role of mangroves as significant sinks of plastics is further corroborated by the finding that the burial rates of plastic in their sediments follow an exponential increase in line with the global plastic production increase, ultimately demonstrating that plastic is likely sequestered there permanently. Mangrove forests alone are, however, not enough to justify the mismatch between plastic inputs and loads in surface waters. The experimental finding showed here that coral structures can passively trap substantial loads of microplastics and the large extension of reefs, especially in the Red Sea, suggest that reefs might constitute a missing sink of marine plastic in the basin worth exploring.

This work is aimed at investigating diurnal cycle variability of the planetary boundary layer characteristics over the Arabian Peninsula and the Red Sea region. To fulfill this goal the downscaling simulations are performed using Weather Research and Forecasting (WRF) model. We analyze planetary boundary layer height, latent and sensible heat fluxes, and surface air temperature. The model results are compared with observations in different areas, for different seasons, and for different model resolutions. The model results are analyzed in order to better quantify the diurnal cycle variability over the Arabian Peninsula and the Red Sea. The specific features of this region are investigated and discussed.

Reef-building corals are cornerstones of life in the oceans. Understanding their interactions with microorganisms and their surrounding physicochemical conditions is important to comprehend reef functioning and ultimately protect coral reef ecosystems. Corals associate with a complex and specific array of microorganisms that supposedly affect their physiology and therefore can significantly determine the condition of a coral ecosystem. As environmental conditions may shape bacterial diversity and ecology in the coral symbiosis, ecosystem changes might have unfavorable consequences for the holobiont, to date poorly understood. Here, we were studying microbial community changes in A. hemprichii as a consequence of simulated eutrophication and overfishing over a period of 16 weeks by using in situ caging and slow release fertilizer treatments in an undisturbed Red Sea reef (22.18ºN, 38.57ºW). We used 16S rDNA amplicon sequencing to evaluate the individual and combined effects of overnutrification and fishing pressure, two of the most common local threats to coral reefs. With our data we hope to better understand bacterial population dynamics under anthropogenic influences and its role in coral resilience. Projecting further, this data will be useful to better predict the consequences of human activity on reef ecosystems.

It has been estimated that coral reefs shelter 830 000 species. Well-studied biodiversity patterns provide tools for better representation of species in marine protected areas. A cross-shelf gradient in biodiversity exists for fishes, corals, and macroalgae. Here, an inshore to offshore gradient in biodiversity on the Saudi Arabian coast of the Red Sea was sampled using Autonomous Reef Monitoring Structures (ARMS) with barcoding and metabarcoding techniques. It was hypothesized that differences in community structure would be driven by an increase in habitat area. The difference was attributed to the greater accumulation of sediments close to shore that increases the area habitable for sediment dwelling organisms and favors macroalgal cover. Macroalgae are inhabited by a greater number of species than live coral. Only 10% of the sequences of the barcoded fraction and <1% of the metabarcoded fraction had a BLAST hit on the NCBI database with a previously identified species sequence. In addition, the rarefaction curves for all fractions did not plateau. The ARMS community composition changed from inshore to offshore and was significantly correlated with the percentage of algal and bryozoan plate cover. The differences in community composition were related to changes in habitat but not to sediments retrieved from the ARMS.

In a recent global study of whale shark population genetics, aggregations were found to belong to either the Indo-Pacific or Atlantic population. This overview included an aggregation found within the Red Sea near Al Lith, Saudi Arabia, however the Mafia Island, Tanzania, aggregation was not part of the study. Both aggregations have unique aspects with the Saudi Arabian individuals showing sexual parity with no segregation, while recent acoustic results have revealed cryptic residency at Mafia Island. Genetic analysis using 11 microsatellite markers was performed on whale sharks from both locations. A combination of primers sourced from previous studies and newly designed primers were used to compare both aggregations and the individuals within. Samples were collected in the Red Sea for 5 seasons spanning 6 years, and for 2 seasons in Tanzania. Analysis with STRUCTURE showed a lack of significant genetic differences between the two aggregations, confirming that whale sharks in Tanzania are part of the Indo-Pacific population. Kinship analysis using COLONY found two potential pairs of full siblings in Tanzania. One pair had a high probability (.993) of being a full sibling dyad while the other had a lower probability (.357). There were no sibling pairs identified from the Red Sea aggregation. Genetic diversity was investigated using allelic richness over the 6 seasons at Al Lith, with values showing no significant change. This is in contrast to results that showed a decline in genetic diversity at Western Australia’s Ningaloo reef. These differences, however, only highlight the need for genetic diversity studies over longer time periods and at other aggregations within the Indo-Pacific.