Despite high temperature and salinity conditions that challenge reef growth in other oceans, the Red Sea maintains amongst the most biodiverse and productive coral reefs worldwide. It is therefore an important region for the exploration of coral reef functioning, and expected to contribute valuable insights towards the understanding of coral reefs in challenging environments. This dissertation assessed the baseline variability of in situ abiotic conditions (temperature, dissolved oxygen, pH, and total alkalinity, among others) in the central Red Sea and highlights these environmental regimes in a global context. Further, focus was directed on biotic factors (biofilm community dynamics, calcification and bioerosion), which underlie reef growth processes and are crucial for maintaining coral reef functioning and ecosystem services. Using full-year data from an environmental cross-shelf gradient, the dynamic interplay of abiotic and biotic factors was investigated. In situ observations demonstrate that central Red Sea coral reefs were highly variable on spatial, seasonal, and diel scales, and exhibited comparably high temperature, high salinity, and low dissolved oxygen levels, which on the one hand reflect future ocean predictions. Under these conditions epilithic bacterial and algal assemblages were mainly driven by variables (i.e., temperature, salinity, dissolved oxygen) which are predicted to change strongly in the progression of global climate change, implying an influential bottom up effect on reef-building communities. On the other hand, measured alkalinity and other carbonate chemistry value were close to the estimates of preindustrial global ocean surface water and thus in favor of reef growth processes. Despite this beneficial carbonate chemistry, calcification and carbonate budgets in the reefs were not higher than in other coral reef regions. In this regard, seasonal calcification patterns suggest that summer temperatures may be exceeding the optima of calcifiers. As a possible interpretation of the here observed environmental regimes, it can be concluded that the central Red Sea may be less sensitive to ocean acidification, but is already impacted by ocean warming. Importantly, this dissertation provides valuable present-day baseline data of the natural variability of relevant abiotic drivers together with benthic community and reef growth dynamics. These data will be important for future comparative studies and efforts to quantify the impact of future environmental change in the region.

Herbivorous coral reef fishes play an important role in helping to structure their environment directly by consuming algae and indirectly by promoting coral health and growth. These fishes are generally separated into three broad groups: browsers, grazers, and excavators/scrapers, with these groupings often thought to have a fixed general function and all fishes within a group thought to have similar ecological roles. This categorization assumes a high level of functional redundancy within herbivorous fishes. However, recent evidence questions the use of this broad classification scheme, and posits that there may actually be more resource partitioning within these functional groupings. Here, I use a compound-specific stable isotope approach (CSIA) to show there appears to be a greater diversity of functional roles than previously assumed within broad functional groups. The δ13C signatures from essential amino acids of reef end-members (coral, macroalgae, detritus, and phytoplankton) and fish muscle were analyzed to investigate differences in resource use between fishes. Most end-members displayed clear isotopic differences, and most fishes within functional groups were dissimilar in their isotopic signature, implying differences in the resources they target. No grazers closely resembled each other isotopically, implying a much lower level of functional redundancy within this group; scraping parrotfish were also distinct from excavating parrotfish and to a lesser degree distinct between scrapers. This study highlights the potential of CSIA to help distinguish fine-scale ecological differences within other groups of reef organisms as well. These results question the utility of lumping nominally herbivorous fishes into broad groups with assumed similar roles. Given the apparent functional differences between nominally herbivorous reef fishes, it is important for managers to incorporate the diversity of functional roles these fish play.

The exceptional environment of the Red Sea has lead to high rates of endemism and biodiversity. Located at the periphery of the world’s coral reefs distribution, its relatively young reefs offer an ideal opportunity to study biogeography and underlying evolutionary and ecological triggers. Here, I provide baseline information on putative seasonal recruitment patterns of reef fishes along a cross shelf gradient at an inshore, mid-shelf, and shelf-edge reef in the central Saudi Arabian Red Sea. I propose a basic comparative model to resolve biogeographic patterns in endemic and cosmopolitan reef fishes. Therefore, I chose the genetically, biologically, and ecologically similar coral-dwelling damselfishes Dascyllus aruanus and D. marginatus as a model species-group. As a first step, basic information on the distribution, population structure, and genetic diversity is evaluated within and outside the Red Sea along most of their global distribution. Second, pelagic larval durations (PLDs) within the Red Sea environmental gradient are explored. For the aforementioned, PLDs of the only other Red Sea Dascyllus, D. trimaculatus, are included for a more comprehensive comparison. Third, to further assess ongoing pathways of connectivity and geneflow related to larval behavior and dispersal in Red Sea reef fishes, the genetic composition and kinship of a single recruitment cohort of D. aruanus arriving together at one single reef is quantified using single nuclear polymorphisms (SNPs). Genetic diversity and relatedness of the recruits are compared to that of the standing population at the settlement reef, providing insight into putative dispersal strategies and behavior of coral reef fish larvae. As a fourth component to study traits shaping biogeography, the ecology and adaptive potential of the cosmopolitan D. aruanus is described by studying morphometric-geometrics of the body structure in relation to the stomach content and prey type from specimen along the cross-shelf of the central Red Sea and at a site outside the Red Sea, in Madagascar, and approach whether foraging strategies change depending on geographic location and environment, and if differences in diet are followed by phenotypic plasticity. Jointly, results suggest that biological responses and putative adaptive strategies are correlated with different biogeographic ranges and habitat preferences.

A Level III fugacity-type model was applied to southern Belize (Stann Creek and Toledo Districts) to predict which of the pesticides most heavily used in banana and citrus farms are most likely to end up in streams and coastal waters via surface runoff. Concentrations of all target pesticides in coastal waters of southern Belize were then measured during two sampling campaigns (dry season and rainy season) in 2008. Several pesticides were measured in significant levels, including some as far out as waters overlying coral reefs. The presence of these pesticides in the coastal waters indicates that agricultural activities in southern Belize may have a potential impact on coral reefs offshore. Results of the predictive model were compared with the empirical data to determine how well the model works in a tropical region such as southern Belize. Overall, there is considerable agreement between the two, indicating that the model employed herein can be applied to other tropical areas. Concentrations of mercury and lead were also measured in the same study area. Mercury levels were uniform and low, suggesting natural sources. Lead levels varied and are most likely explained by the presence of unregulated and illegal waste dumps near streams in the region. An analysis was carried out to examine government policy on pesticide use. Findings indicate a lack of a coherent governmental policy on the sale and use of pesticides, most likely because of too many agencies/ministries being involved and the lack of national standards for these pesticides in the environment.

Many organisms form mutually beneficial, symbiotic partnerships with other organisms. Corals and sea anemones undergo mutualistic symbioses with photosynthetic algae of the family Symbiodiniaceae, and these partnerships are key for the viability of coral reef ecosystems. Cnidarian-Symbiodiniaceae symbioses are sensitive to climate change-induced ocean warming, which causes the disruption of symbiosis, commonly referred to as bleaching, and can lead to coral mortality. Cellular and molecular aspects of how this symbiosis is established and disrupted by heat stress are not well understood. The research presented herein characterizes immunity transcription factor NF-kappaB in the cnidarian model organism Exaiptasia pallida (Aiptasia). It is shown that the DNA-binding site specificity of Aiptasia NF-kappaB is similar to mammalian NF-kappaB subunit p50 and that this binding specificity is conserved across a broad expanse of metazoans. Moreover, Aiptasia and human IkappaB kinases can phosphorylate serine residues in the C-terminus of NF-kappaB, signaling the protein for proteasomal processing to allow for nuclear localization, DNA binding, and transactivation. In Aiptasia, NF-kappaB expression is downregulated by symbiosis onset in larvae, and NF-kappaB total expression, DNA-binding activity, and tissue-specific expression are increased following laboratory-induced loss of symbiosis in adult Aiptasia. NF-kappaB downregulation during the onset of symbiosis occurs only with the compatible symbiont Breviolum minutum and data suggest that host TGFbeta plays a role in NF-kappaB downregulation. Results demonstrate that aposymbiotic Aiptasia (with high NF-kappaB levels) have increased survival following bacterial infection as compared to symbiotic anemones. A bioinformatic analysis shows that potential NF-kappaB binding sites are enriched in promoter regions of immune-related genes that are upregulated in aposymbiotic Aiptasia. Increased levels of NF-kappaB are also found in a genet of the coral Pocillopora damicornis that exhibits resilience to heat-induced bleaching. Overall, the results in this thesis suggest a role for NF-kappaB-directed immunity in symbiosis onset, bleaching, and resistance to biological stressors in cnidarians. It is proposed that NF-kappaB downregulation in Aiptasia is a mechanism to lower host immunity and promote the establishment of symbiosis, but that this process compromises host immunity to pathogen infection. Nevertheless, constitutively high basal levels of NF-kappaB may be protective against bleaching in cnidarians.

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.

Long-term coral reef monitoring programs have been established and used efficiently in many parts of the world to assess the state of coral reefs under increasing anthropogenic pressures and natural disturbances, as well as to evaluate the efficiency of established marine protected areas (MPAs) or other conservation strategies. Over the past decade, Red Sea coral reefs have experienced two major bleaching events in 2010 and five years later, in 2015/2016, with severe coral loss along the central and southern Saudi Arabian coast. With this study we present the first characterization of fish community changes through time in the Red Sea. Fish abundance data from twenty-three reefs from two different regions in Saudi Arabia, central (Thuwal) and south-central (Al Lith), surveyed between 2008 and 2019 were examined. A significant decline of hard coral was observed on nearshore reefs in both regions following two bleaching events. The results revealed a persistent cross-shelf partitioning of fish communities before and following a substantial drop in coral cover. Offshore reef fish communities appeared to be more stable and homogeneous through time, whereas nearshore reef fish communities had less similar composition throughout the study period. Species-specific analyses revealed the decline in the abundance of several obligatory corallivorous species, a contrasting response from most herbivore fish species that generally experienced an increase in their abundance since 2008. These findings indicate that the bleaching events from this period had less effect on communities as a whole, but instead cause changes in abundance in several key species, mostly affected by coral loss and subsequent algal increase. While a well-structured and standardized long-term monitoring system is yet to be established for Saudi Arabian coral reefs, our findings provide a sound baseline of fish assemblages over the last decade. These findings are critical for future studies as well as effective conservation strategies in the face of ongoing coastal developments, overfishing and climate change.

Acoustic telemetry is an important tool for studying the movement patterns, behaviour, and site fidelity of marine organisms; however, its application is challenged in coral reef environments where complex topography and intense environmental noise interferes with acoustic signals, and there has been less study. Therefore, it is particularly critical in coral reef telemetry studies to first conduct a long-term range test, a tool that provides informa- tion on the variability and periodicity of the transmitter detection range and the detection probability. A one-month range test of a coded telemetric system was conducted prior to a large-scale tagging project investigating the movement of approximately 400 fishes from 30 species on offshore coral reefs in the central Red Sea. During this range test we determined the effect of the following factors on transmitter detection efficiency: distance from receiver, time of day, depth, wind, current, moon-phase and temperature. The experiment showed that biological noise is likely to be responsible for a diel pattern of -on average- twice as many detections during the day as during the night. Biological noise appears to be the most important noise source in coral reefs overwhelming the effect of wind-driven noise, which is important in other studies. Detection probability is also heavily influenced by the location of the acoustic sensor within the reef structure. Understanding the effect of environmental factors on transmitter detection probability allowed us to design a more effective receiver array for the large-scale tagging study.

Animal and plant genomes produce numerous small RNAs (smRNAs) that regulate gene expression post-transcriptionally affecting metabolism, development, and epigenetic inheritance. In order to characterize the repertoire of endogenous microRNAs and potential gene targets, we conducted smRNA and mRNA expression profiling over nine experimental treatments of cultures from the dinoflagellate Symbiodinium sp. A1, a photosynthetic symbiont of scleractinian corals. We identified a total of 75 novel smRNAs in Symbiodinum sp. A1 that share stringent key features with functional microRNAs from other model organisms. A subset of 38 smRNAs was predicted independently over all nine treatments and their putative gene targets were identified. We found 3,187 animal-like target sites in the 3’UTRs of 12,858 mRNAs and 53 plantlike target sites in 51,917 genes. Furthermore, we identified the core RNAi protein machinery in Symbiodinium. Integration of smRNA and mRNA expression profiling identified a variety of processes that could be under microRNA control, e.g. regulation of translation, DNA modification, and chromatin silencing. Given that Symbiodinium seems to have a paucity of transcription factors and differentially expressed genes, identification and characterization of its smRNA repertoire establishes the possibility of a range of gene regulatory mechanisms in dinoflagellates acting post-transcriptionally.

Early work on the reproductive seasonality of corals in the Red Sea suggested that corals exhibit temporal reproductive isolation, unlike on the Great Barrier Reef where many species spawn in synchrony. More recent work has however shown high synchrony in the maturity of gametes in Acropora species, suggesting multi-specific spawning is likely to occur in the Red Sea. In this thesis I investigate the patterns of coral reproduction in the central Red Sea. The spawning season in the central Red Sea lasts four months, from April to July and spawning occurs on nights around the full moon. During this period Acropora species show a peak of spawning in April, with some species spawning again in May. The level of synchrony, quantified with a spawning synchrony index, is comparable to other locations where multi-specific spawning has been reported. Observations over two consecutive years show that the synchrony of spawning was lower in spring 2012 than in spring 2011, and thus that spawning patterns are variable from one year to the other. Coral settlement patterns on artificial substrata confirmed a main spawning season in the spring but also supported reproductive data suggesting that some Porites spawn in October-November. Settlement was studied over 2.5 years on a reef, which had suffered recently from high mortality after a local bleaching event. Settlement appeared low but post-bleaching studies from other locations indicated similar abundances and showed that recruits generally did not increase until 5 years after the bleaching event. Abundance of juvenile corals however started to increase significantly three years after the bleaching. Successful recruitment, although low suggests that the coral assemblage on the affected reef will most likely recover as long as it is not affected by another disturbance.