Coral reef environments have been degrading steadily over the last few decades. It is generally accepted now that coral reefs are one of the first marine ecosystems to show measurable perturbations driven by global warming. Some of theses perturbations are consequence of extreme stochastic disturbances like hurricanes or extreme thermal anomalies and therefore, can be easily identified using broad indicators like coral cover. These indicators are easy to measure and provide a general description of the system in question. The detection and interpretation of more subtle perturbation in coral communities is more complicated, both logistically and conceptually. However, detecting chronic perturbations at an early stage can increase significantly the success of early mitigating management strategies. This thesis focuses on the development and application of highly sensitive indicators that can detect subtle perturbations in coral communities. It also studies the ecological interpretation of mild perturbations and their effect on the future structure of coral reef environments. The mild thermal disturbance experienced by the Heron Island reef in the south of the Great Barrier Reef during the 2005-2006 summer, and an environmental gradient along the central coast of Venezuela (south Caribbean Sea), were used as models to test the sensitivity of coral reefs to mild disturbances at different organisation levels (organism, population, and community). At the organismal level my results showed that the intensity of bleaching that a colony shows during a mild thermal disturbance is affected by the morphology of the colony as well as the substrates surrounding the colony. Colonies surrounded by sand bleached more than colonies surrounded by dead coral or rubble. I propose that reef specific information on the relative cover of sand, rubble, and dead coral can improve the fine scale accuracy of bleaching predicting models. Studying the same mild thermal disturbance at Heron Island, I showed how demographic parameters of some populations are more sensitive to mild thermal disturbances than coral cover (the most widely used response variable in coral monitoring programs around the world). Furthermore, my results suggest that the response of coral populations to mild thermal disturbance is different in nature and intensity to the respond observed during extreme thermal disturbances. Some taxa like Stylophora pistillata, are highly sensitive to extreme thermal disturbances, and tend to be the first to die under these conditions. In contrast, this taxon was extremely tolerant to the mild thermal disturbance of early 2006 in comparison to other taxa identified previously as more tolerant than S. pistillata. This difference in the response of coral environments to milder more common disturbances can have great influence in the trajectory that coral reefs follow in a rapidly changing world. Finally at a community level, I demonstrated how the power to detect the effect of environmental conditions on coral environments is drastically increased when the coral host-endosymbiotic algae relationship is interpreted holistically. The percentage of the variability of the community structure that can be explained by environmental variables in the central coast of Venezuela is doubled when the unit of selection considered is the holobiont instead of the coral host or the endosymbiont independently. This approach can be crucial for the detection of subtle changes in coral communities as the frequency and intensity of disturbances increase rapidly. The increase in detection power provided by the different approaches developed in this project can both improve our understanding of the structuring role of mild disturbances in coral communities as well as help identify the effect of disturbances in an early stage before the perturbation reaches catastrophic proportions. This early identification of perturbations can be used for the development of adaptive management strategies that can increase the resistance and resilience of coral reefs in the future.

Thesis (Ph.D.) -- McMaster University, 1998. / Includes bibliographical references (p. 223-258). Also available via World Wide Web.

Thesis (M.Sc.). / Written for the Dept. of Bioresource Engineering. Title from title page of PDF (viewed 2008/05/30). Includes bibliographical references.

Thesis (Ph. D.)--University of Texas at Austin, 2008. / Vita. Includes bibliographical references.

Thesis (M.Sc.(Hons.)--Victoria University of Wellington, 2009. / Includes bibliographical references.

Thesis (M.S.)--University of North Carolina Wilmington, 2009. / Vita. Title from PDF title page (January 15, 2010) Includes bibliographical references (p. 67-70)

Thesis (M.A.)--University of Alberta, 2010. / Title from pdf file main screen (viewed July 27, 2010). "A thesis submitted to the Faculty of Graduate Studies and Research in partial fulfillment of the requirements for the degree of Master of Arts, Dept. of Anthropology". Includes bibliographical references.

Thesis (Ph.D.) - University of Queensland, 2005. / Includes bibliography.

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