Since the beginning of the Industrial Revolution, carbon dioxide (CO2) has been emitted into the atmosphere at rates unprecedented to Earth’s history. Nearly 30% of the anthropogenic CO2 in the atmosphere has been absorbed in surface waters of the ocean, pushing carbonate chemistry towards increased bicarbonate ions and hydrogen protons and decreased carbonate ions. Consequently, seawater pH has decreased from pre-Industrial Revolution levels of 8.2 to current levels of 8.1, and it is expected to continue to drop to 7.8 by the year 2100 if carbon emissions continue as predicted. The combination of these effects is referred to as ocean acidification. It is at the forefront of marine research as it poses a serious threat to several marine organisms and ecosystems. Ocean acidification has the most notable direct effect on calcifying organisms with calcium carbonate skeletons and shells, because fewer carbonate ions in the water column result in reduced calcification. Coral reefs are especially vulnerable to ocean acidification since reefs are composed of complex carbonate structures. Coral reefs have a high biodiversity; thus, not only will the corals themselves be affected by ocean acidification, but so will many of the animals that dwell in them. The primary objective of this thesis was to examine the effects of ocean acidification on demersal zooplankton that reside in coral reefs. Ocean acidification research on zooplankton has primarily been single- species experiments on calcifying species or generalist copepod species. Scaling-up to experiments examining ocean acidification effects on entire zooplankton communities is logistically difficult, thus the ability to predict community changes in zooplankton due to ocean acidification has been rather limited. However, a few locations around the world have submarine volcanic CO2 seeps that can be used as natural laboratories to study ecosystem effects of ocean acidification. Two CO2 seeps located in coral reefs in Papua New Guinea were used as windows into the future to examine the effects of ocean acidification on entire zooplankton communities while they live naturally in their environment. Over three expeditions to two CO2 seeps, nocturnal plankton were sampled with horizontal net tows and emergence traps. Additional experiments were also conducted, and collectively this work is summarized in chapters 2-5 as outlined below. Chapter 2 reports on the observed changes in zooplankton abundance and community composition between control and high-CO2 sites. Consistent results between seep sites and expeditions showed that zooplankton abundances were reduced three-fold under high-CO2 conditions. The abundance loss was partially attributed to habitat change within the coral reef, from more structurally complex corals in the control sites to a replacement of massive bouldering corals in the high-CO2 sites. The loss of structural complexity in the reef meant there were fewer hiding spaces for the zooplankton to seek refuge in during the day. All zooplankton taxa were reduced under high-CO2 conditions but to varying levels, suggesting that each taxon reacts differently to ocean acidification. Since each taxonomic group within the zooplankton communities was reduced to varying levels under ocean acidification, the copepod genus with the largest reduction in abundance was investigated in more detail. Labidocera spp. are pontellid copepods that are generally considered surface-dwellers and are not known to inhabit coral reefs. Therefore, as a preface to the ocean acidification study, the new discovery of these copepods living in coral reefs is first described (Chapter 3). Not only were they found to be residential to the reef, but Labidocera spp. living at the control reefs preferred to reside in coral rubble, macroalgae, and turf algae. Labidocera spp. were one of the most sensitive copepods to high-CO2 conditions and were reduced by nearly 70% in abundance, prompting a more detailed investigation about the effect of ocean acidification on their physiology and habitat preference (Chapter 4). Physiological parameters, e.g. size, feeding, and oocyte development, were unaffected by ocean acidification. Unlike the zooplankton community as a whole, the main cause for the abundance loss of Labidocera spp. was not a shift in the habitat because their preferred substrata were of equal percent coverage across high-CO2 and control sites. Instead, Labidocera spp. were no longer associated with any substrata type. Multiple direct and indirect effects of ocean acidification will act on each zooplankton taxa separately, and their collective response will contribute to the community response. The effects of ocean acidification on zooplankton communities were then scaled up to potential impacts on entire ecosystems. Zooplankton are the primary food source for corals, fish, and other zooplanktivores. The impacts of ocean acidification on zooplankton communities will have cascade effects on the food chain via the pathway of zooplanktivorous organisms. A case study on the stony coral Galaxea fascicularis explored the effects of ocean acidification on the ability of corals, which had lived their entire lives under high-CO2 conditions, to feed on zooplankton (Chapter 5). Under anthropogenic changes, whether it is from bleaching, high turbidity, or ocean acidification, some corals rely more on heterotrophy and consume more zooplankton. Contrary to expectation, this study showed that when given equal quantities of food particles these corals consumed less zooplankton under ocean acidification. Corals rely on heterotrophy for essential nutrients, like nitrogen and phosphorus, which they cannot otherwise obtain from autotrophy and their symbiotic zooxanthellae. In conclusion, my thesis shows that not only is there fewer zooplankton available to consume, but the existing zooplankton is consumed with lower capture rates under high CO2 conditions. Coral reefs in future oceans will likely have reduced zooplankton abundances as an indirect effect of ocean acidification, partially caused by a change in habitat from branching corals to more massive bouldering corals. Zooplankton abundances were reduced yet the community composition was unaffected by ocean acidification. All zooplankton taxa were reduced yet present under high-CO2 conditions suggesting that the zooplankton are at least able to survive under ocean acidification. Fewer zooplankton will be available to zooplanktivores, but the fatty acid content and nutritional value of the zooplankton as a food source is expected to be similar to current food. Together this is expected to negatively impact the entire coral reef ecosystem, with some coral species unable to consume zooplankton at normal rates. In an ecosystem already highly vulnerable to ocean acidification, coral reefs may be even more threatened if the very basis of their food webs is reduced.

Diverse and abundant coral associated microbial communities may play a key role in coral resistance to and recovery from unwavering stressors currently threatening coral reefs worldwide. The composition and structure of the coral microbiome is integral to coral health as microbes can play beneficial (e.g. nutritional or protective) or negative (e.g. pathogenic or opportunistic) roles in the coral. To review the impacts of stressors on the coral microbiome, I compiled data from 39 studies, each tracking microbial community shifts in corals experiencing stress from climate change, pollution or overfishing. Stress was associated with shifts in coral microbial communities. I found that regardless of stressor, microbial alpha diversity increased under stress, with Vibrionales, Flavobacteriales and Rhodobacterales commonly found on stressed corals, and Oceanospirillales not as abundant on stressed corals. In addition, I used 16S rRNA sequencing to evaluate how local and global stressors affect the community structure of the coral microbiome for the two coral species, Porites lobata and Montipora foliosa. I monitored tagged coral colonies at two human disturbance levels (i.e. high and low), before and during a thermal bleaching hotspot at Kiritimati, Kiribati. Human disturbance, a bleaching hotspot, and coral species were all important drivers of coral microbiome community structure. My results suggest that human disturbance increases microbial alpha and beta diversity, although results vary between coral species, with P. lobata having more of a difference between disturbance levels. Similarly, bleaching increased beta diversity at low disturbance sites. Both human disturbance and thermal stress appeared to homogenize coral microbiomes between species and thermal stress appeared to homogenize communities between disturbance levels. Thus, both human disturbance and bleaching appear to stress the coral and destabilize its microbiome. However, intense thermal stress (i.e. 12.86 DHWs) appears to have a greater influence than human disturbance, probably due to corals responding to stressful conditions in a similar manner. In conclusion, my results highlight the impact of local and global stressors on coral microbiome community structure. / Graduate / 2018-04-26 / 0359

In order to properly assess human impacts and appropriate restoration goals, baselines of pristine conditions on coral reefs are required. In Saudi Arabian waters of the central Red Sea, widespread and heavy fishing pressure has been ongoing for decades. To evaluate this influence, we surveyed the assemblage of offshore reef fishes in both this region as well as those of remote and largely unfished southern Sudan. At comparable latitudes, of similar oceanographic influence, and hosting the same array of species, the offshore reefs of southern Sudan provided an ideal location for comparison. We found that top predators (jacks, large snappers, groupers, and others) dominated the reef fish community biomass in Sudan’s deep south region, resulting in an inverted (top-heavy) biomass pyramid. In contrast, the Red Sea reefs of central Saudi Arabia exhibited the typical bottom-heavy pyramid and show evidence for trophic cascades in the form of mesopredator release. Biomass values from Sudan’s deep south are quite similar to those previously reported in the remote and uninhabited Northwest Hawaiian Islands, northern Line Islands, Pitcairn Islands, and other remote Pacific islands and atolls. The findings of this study suggest that heavy fishing pressure has significantly altered the fish community structure of Saudi Arabian Red Sea reefs. The results point towards the urgent need for enhanced regulation and enforcement of fishing practices in Saudi Arabia while simultaneously making a strong case for protection in the form of marine protected areas in the southern Sudanese Red Sea.

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.

Coral reef ecosystems are under increasing threat from ocean warming and deoxygenation. Mass coral bleaching events in recent years have been linked to marine heatwaves but reporting of hypoxia-induced bleaching has also been increasing. Oxygen availability in coral reefs is driven by community metabolism and they experience a dynamic range of oxygen concentrations throughout diel cycles, hyperoxia during the day and hypoxia during the night. It has been suggested that the highest oxygen concentrations coincide with the hottest part of the day and this may protect marine taxa from high temperatures. We evaluated experimentally whether excess oxygen availability would increase the thermal threshold of the branching coral Stylophora pistillata, from the Southern Red Sea. We did this by exposing coral fragments of this species to varying dissolved oxygen concentrations (hypoxia, normoxia and hyperoxia) and a short-term temperature ramping regime (1˚C h-1). Hyperoxia did extend the thermal tolerance of S. pistillata fragments, with an LT50 of 39.1˚C as opposed to 39.0˚C for the normoxic treatment and 38.7˚C for the hypoxic treatment. Hyperoxia also increased respiration and gross photosynthesis and had a negative effect on photochemical efficiency at high temperatures. Net photosynthesis, P:R ratio and symbiont density were not significantly affected by oxygen concentration. Corals in this experiment displayed exceedingly high thermal thresholds, which were at least 2˚C higher than previously reported for the same species in the Central Red Sea. The corals used in the experiment had previously survived mass bleaching events in 2015 and hence we may have selected for individuals adapted to thermal stress. This is the first study to investigate the role of oxygen in the thermal tolerance of hermatypic corals and the first assessment of thermal thresholds from corals in the Southern Red Sea, where previously thermal thresholds have been based on a 1-2˚C increase in maximum mean monthly temperatures and visual bleaching observations. This highlights the need for increased experimental assessments of thermal thresholds in the Southern regions of the Red Sea and the important role of oxygen in moderating thermal stress.

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.

No description available.

Parrotfishes (Scarinae) are dominant Caribbean herbivores that play an important role in reducing coral-algae competition by grazing algae; yet some species are also occasional coral predators (corallivores) and thereby can have direct negative impacts on coral growth and survivorship. There is concern that parrotfish corallivory may contribute to substantial long-term declines in targeted coral species, particularly in areas with a high biomass of parrotfishes and low cover of corals. However, the capacity of target coral species to heal from parrotfish predation and the ecological drivers of corallivory are poorly understood. In Chapter 1, we examined the patterns of coral healing from parrotfish predation scars on Orbicella annularis – an ecologically important framework building coral that is one of the most intensely grazed Caribbean coral species and an endangered species. While some researchers have suggested that parrotfishes may have significant long-term impacts on heavily targeted species such as O. annularis, the patterns of coral recovery from parrotfish predation scars remain poorly understood. To address this knowledge gap, we tracked the fate of parrotfish bite scars on O. annularis colonies across two Caribbean islands for up to two months. We evaluated differences in coral healing between islands in response to a number of variables including the initial scar surface area, scar abundance per coral colony, colony surface area, and water depth. We used these data to develop a predictive model of O. annularis tissue loss from recent parrotfish bite scars. We then applied this model to surveys of the distribution of bite scars at a point in time to estimate long-term tissue loss of O. annularis colonies from a standing stock of bite scars. Our findings suggest that the initial scar surface area is one of the most important predictors of coral tissue loss. The data also indicate that there are thresholds in patterns of coral tissue regeneration: we observed that small scars (≤1.25 cm2) often fully heal, while larger scars (≥8.2 cm2) had minimal tissue regeneration. The vast majority of observed scars (~87%) were 1.25 cm2 or less and our model predicted that O. annularis colonies would regenerate nearly all the corresponding scar area. In contrast, while scars greater than or equal to than 8.2 cm2 were infrequent (~6% of all observed scars), our model predicted that these larger scars would account for over 96% of the total tissue loss for grazed colonies. Overall, our results suggest that the immediate negative impacts of parrotfish predation on coral tissue loss appear to be driven primarily by a few exceptionally large bite scars. While further work is needed to understand the long-term impacts of corallivory and quantify the net impacts of parrotfish herbivory and corallivory on Caribbean coral reefs, this study is an important step in addressing factors that impact the recovery of a heavily targeted and ecologically important Caribbean coral from parrotfish predation. In Chapter 2, we examined the ecological drivers of corallivory across all coral taxa and across three regions of the Greater Caribbean – the Florida Keys, St. Croix, and Bonaire. To do so, we observed how parrotfish grazing intensity varied using both size and abundance-based metrics across multiple spatial scales. At the reef community and regional scale, we found no effect of the biomass of corallivorous parrotfishes or the percent cover of target coral species on the intensity of parrotfish corallivory. However, at the scale of individual coral colonies, we found that coral taxa and colony size were important predictors of corallivory intensity, and that predation intensity increased as colony size increased. Our findings suggest that previous assertions that conservation of corallivorous parrotfishes may have net negative impacts on coral communities, particularly as live coral cover declines, are not supported at the reef-scale. Instead, our research suggests that colony-level traits such as coral taxa and colony size may be stronger drivers of predation intensity. Additionally, our research suggests that parrotfishes do not heavily graze upon the majority of coral species, but have a higher level of grazing intensity on three taxa, Orbicella annularis, Porites astreoides and other Porites spp. across multiple regions of the Caribbean. Therefore, the direct consequences of parrotfish corallivory for coral tissue loss are likely low for the majority of coral species, but further research is needed to better understand the ultimate causes of selective predation and the long-term consequences of corallivory for heavily targeted coral taxa.

Yes / Coral reefs are important ecosystems that not only provide shelter and breeding ground for many marine species, but can also control of carbon dioxide level in ocean and act as coastal protection mechanism. Reduction of coral reefs at Singapore coastal waters (SCW) region remains as an important study to identify the environmental impact from its busy industrial activities especially at the surrounding of Jurong Island in the south. This kind of study at SCW was often being related to issues such as turbidity, sedimentation, pollutant transport (from industry activities) effects in literatures, but seldom investigated from the thermal change aspect. In this paper, a computational model was constructed using the Delft3D hydrodynamic module to produce wave simulations on sea regions surrounding Singapore Island. The complicated semi-diurnal and diurnal tidal wave events experienced by SCW were simulated for 2 weeks duration and compared to the Admiralty measured data. To simulate the thermal mapping at the south Singapore coastal waters (SSCW) region, we first adapted a conversion of industrial to thermal discharge; then from the discharge affected area a thermal map was further computed to compare with the measured coral map. The outcomes show that the proposed novel thermal modelling approach has quite precisely simulated the coral map at SSCW, with the condition that the near-field thermal sources are considered (with the coverage area in the limit of 20 km × 20 km). / The author also acknowledges the support of Nazarbayev University’s (Kazakhstan) research seed grant no. KF-12/6 for purchasing and providing the Delft3D software used in this study (which the author is the principal investigator of the grant)