The marine biological carbon pump (BCP) leads to the transfer of carbon from the atmosphere to the ocean interior through the growth of photosynthetic plankton in the euphotic zone and subsequent sinking of particulate matter to depth. In the subarctic northeast Pacific Ocean, the BCP is limited by the availability of the micro-nutrient iron (Fe) in the offshore, high nutrient, low chlorophyll (HNLC) region and by the macronutrient nitrate in the coastal region. In the last decade, two atmospheric events led to anomalously high sea surface temperatures, or marine heatwaves, in 2014-2015 and 2019 that were related to changes in the phytoplankton community composition and the BCP. Given that the bioavailability of trace metals can control microbial community composition, and important rate processes related to the BCP, we studied the spatial and temporal variation in the distribution of dissolved trace metals manganese, iron, cobalt, nickel, copper, and cadmium and macronutrients nitrate, phosphate, and silicic acid from 5 stations along the Line P Time Series transect in the subarctic northeast Pacific Ocean from winter (February) and summer (August) 2012-2019. In 2014 the mixed layer shallowed by diminished winter storm mixing, resulted in lower trace metal and macronutrient concentrations, but sustained dissolved iron and net community production (NCP) in the offshore, while the coastal region biogeochemistry remained similar to previous years (2012-2013). In 2015, further mixed layer shallowing allowed for similarly diminished trace metal (most notably iron), macronutrient concentrations, and NCP in the offshore and coastal regions. The phytoplankton community in the offshore shifted towards a higher relative abundance of pico-nano size species in both 2014 and 2015, with biomass sustained in 2014 and reduced in 2015. During the second marine heatwave event in 2019, the offshore was subject to similar winter mixed layer shallowing, warming, and reduced macronutrient concentrations. In the summer, surface trace metal and macronutrient concentrations were greatly diminished, resulting in nitrate limitation in the offshore. As the oceans continue to warm in response to anthropogenic CO2, a likely consequence may be more frequent, and severe, marine heatwaves that can have internal and external effects on micro-macronutrient distributions, phytoplankton production, and the efficiency of the biological carbon pump. / Graduate

Hermatypic, or reef-building, corals (Order Scleractinia) are the foundation of coral reefs, providing a diversity of structurally complex habitats for the myriad species in these biologically diverse ecosystems. However, both local and global anthropogenic stressors threaten the persistence of these corals. For this thesis, thirty 16m2 permanent photoquadrats at 10 shallow forereef sites around Kiritimati (Christmas Island, Republic of Kiribati) were monitored across a four-year study encompassing the 2015-2016 El Niño derived marine heatwave, and subsequent mass coral mortality event. Sites were exposed to either low, medium, or high levels of local anthropogenic disturbance. My objective herein was to examine the effects of a mass coral mortality event on reef structural complexity, from the end of the event to three years afterwards. To do so, I digitally quantified six metrics of structural complexity for each photoquadrat sampled across three resolution scales for each of the five expeditions. Plots from 2015, 2017, and 2019 were later annotated based on the morphological structure present. I found that while significant declines in multiple of habitat metrics occurred by the end of the heatwave, no further significant declines occurred thereafter. However, this trend was lost as resolution scale increased, indicating the trends seen in the habitat metrics at 1.0 cm were likely documenting the shift from live coral towards abiotic dominated reefs. Anthropogenic disturbance compounded the El Niño’s effect, ensuring high disturbance sites had the lowest structural complexity values throughout the study. Lastly, live branching, tabulate, foliose, and submassive coral morphologies were found to be most closely associated with the different habitat complexity metrics. These results highlight the importance live coral structure has on reef structural complexity, illustrate the importance of model resolution when quantifying trends in structural complexity, pinpoint coral morphologies creating reef structural complexity, and further emphasize the need to limit the effects of local anthropogenic disturbance on coral reefs. / Graduate / 2023-04-15

Marine aquaculture is already vital to global food security and will continue to become more important in the coming years. Crassostrea gigas (Pacific oysters) is the primary oyster species cultivated worldwide. The FAO and IPCC predict that climate change will create uncertainty and challenges for marine aquaculture. Baynes Sound, British Columbia, is a productive region for aquaculture, producing >50% of British Columbia’s total annual bivalve production by live weight and value. Major summer mortality events have been documented in farmed Crassostrea gigas globally since the 1950’s. These events are believed to be caused by a multiplicity of factors including changes induced by anthropogenic climate change. One of the major contributors to summer mortality is the proliferation of Vibrio bacteria, specifically Vibrio aestuarianus, which has been shown to increase in abundance and virulence when seawater temperatures rise. Despite this connection and the economic importance of oyster farming in the region, little is known about the presence of V. aestuarianus in Baynes Sound. Our 17-month study sampled 7 sites in Baynes Sound on 33 occasions from May 2019 to September 2020. We found a positive correlation between seawater temperature and total Vibrio detected in water samples in Baynes Sound, an association that was stronger when the overall temperature regime was warmer. We found no significant correlation between any of the bacterial assays tested and salinity, pH, or Ωarag saturation. We also did not identify a geographic pattern to bacterial abundance or virulence amongst test C. gigas in the field. Understanding that flagellates are the predominant type of microalgae present in Baynes Sound when summer mortality events occur, in lab trials, we found that incorporating V. aestuarianus into marine aggregates with flagellate microalgae caused higher mortality than aggregates with diatoms or planktonic V. aestuarianus. These results were not statistically significant but led us to look at how exposure to husbandry stress pre and post inoculation with V. aestuarianus incorporated into marine aggregates affects mortality. We found that stress was a significant driver of mortality, particularly when administered 24h post inoculation, suggesting that farmers should avoid sorting or tumbling their oysters in the summer, and particularly immediately after a marine heatwave. Oysters lack adaptive immune systems and are grown in an open ocean environment where it is not possible to eliminate their exposure to pathogens. These factors make it impossible to use vaccines or antibacterial disinfectants to combat diseases. Therefore, breeding genetic resistance to V. aestuarianus may be the most effective way to fight summer mortality. Creating a repeatable and accurate protocol for inoculating oysters with marine bacteria is key to accurate heritability measurements and the estimation of breeding values of different families. Key factors include controlling for dose per animal, laboratory efficiency, and inoculation via a mechanism that mimics real-world infection and does not bypass the animal’s immune defenses. We designed a protocol which controls for these factors, separating each animal into individual containers and adding a controlled dose of planktonic bacteria to each. Previously used methods of injection or using an infected “donor” animal in a group tank do not control for dose or bypass parts of the oysters’ natural immune system, potentially creating inaccuracies in survival data generated with these methods. After designing this protocol, we tested 32 full-sib families and estimated the heritability of survival to V. aestuarianus on the observed and underlying liability scales to be 0.095 (SE = 0.043), and 0.15 (SE = 0.068) respectively. We also found a strong negative correlation between oyster size and survival, with a gram of additional weight creating a 73% increase in the risk of death. Fast growth and large size are two traits which have been explicitly bred into C. gigas stock. Our work suggests that breeding a slower-growing, smaller animal may reduce summer mortality. / Graduate / 2022-09-15

Global biodiversity losses are being driven by human actions, and coral reef communities are not immune. Local anthropogenic stress and global climate change are rapidly changing coral reefs, through coral bleaching and mortality. How these stressors impact the biodiversity and community structure of corals on tropical reefs will not only affect the communities of fish and invertebrates that rely on coral reefs, but they could have lasting impacts on ecosystem functioning. The record-breaking marine heatwave caused by the 2015/2016 El Niño was superimposed on a strong local human disturbance gradient on Kiritimati, Kiribati, allowing for the investigation of how these combined disturbances affect coral communities. In Chapter 2, I investigated how soft coral cover varies with these disturbances and natural environmental factors, using benthic photoquadrats collected on Kiritimati’s forereefs from 2007 to 2019. Additionally, I conducted a literature review to establish what is already known about soft coral and disturbances, to compare Kiritimati data to that found in the literature. I show that soft corals are grossly understudied, with only a fifth (19/94) of coral studies presenting any results of heat stress effects on soft corals, and even fewer (5%) presenting taxonomic-specific results. On Kiritimati, prior to the 2015/2016 El Niño, soft corals were more common at sheltered sites with lower net primary productivity, but no effect of local disturbance was found. Soft corals were, however, highly vulnerable to heat stress, with a documented complete loss after the heatwave. I also show that soft coral skeletons persisted for years after the heatwave and provided substrate for hard coral recruitment. In Chapter 3, I examined how local and global stressors affected coral diversity, using community composition photoquadrat data collected from 2013 to 2017, and developed a conceptual framework for understanding effects of multiple stressors, when there are both discrete and continuous stressors. Coral alpha diversity (assessed as Hill diversity) exhibited a non-linear relationship with local anthropogenic stress, peaking at intermediate levels, and was negatively impacted by the marine heatwave, such that sites tended to decrease in both coral richness and evenness. Coral beta diversity (assessed as community composition turnover) was significantly impacted by both stressors, but sites exposed to higher levels of anthropogenic stress tended to experience less turnover during the heatwave. Explicitly considering the relationships between the two stressors, I found that it varied depending on the intensity of anthropogenic stress and the diversity metric (i.e., richness vs. composition) examined. For Hill-Richness, I found a tipping point at moderate levels of local anthropogenic stress, below which there was an additive response and above which the response tended towards synergy. In contrast, for Hill-Shannon and Hill-Simpson the responses were additive and there was an antagonistic effect between stressors for community composition. By using the frameworks outlined in this thesis for reporting changes to soft coral due to disturbances, and examining relationships between discrete and continuous stressors, we may better predict how reefs will look in the future and what actions will conserve and assist in the recovery of coral reef ecosystems. / Graduate / 2022-08-10

Coral reefs around the world are threatened by a variety of sources, from localized impacts, including overfishing and coastal development, to global temperature increases and ocean acidification. Conserving these marine biodiversity havens requires both global and local action informed by scientific research. In this thesis, I use data collected from the coral reefs around Kiritimati atoll (Republic of Kiribati) in the central equatorial Pacific, first to assess the applicability of two common metrics used in passive underwater acoustic research, and second to examine the effects of a marine heatwave and local human disturbance on an assemblage of corallivorous fish. Using acoustic data recorded in 2017 and 2018 on reefs around Kiritimati, I assess how sound pressure level (SPL) and the acoustic complexity index (ACI) respond to changes in fish sounds in a low frequency band (160 Hz – 1 kHz) and snapping shrimp snaps in a high frequency band (1 kHz – 22 kHz). I found that while SPL was positively correlated with increases in fish sounds and snap density, changes in ACI were dependent upon the settings chosen for its calculation, with the density of snaps negatively correlated with ACI across all settings. These findings provide evidence that despite its quick and prolific adoption, acoustic metrics like ACI should be thoroughly field-tested and standardized before they are applied to new ecosystems like coral reefs. Next, using underwater visual censuses (UVCs) of reef fish assemblages, I quantified how two functional groups of corallivores, obligate and facultative, responded to a mass coral mortality event created by the 2015-2016 El Niño. Declines in abundance of both groups were largely driven by the response of coral-associated damselfishes, Plectroglyphidodon johnstonianus in the obligate group and Plectroglyphidodon dickii in the facultative group, to heat stress and subsequent coral mortality. I also observed a significant decline in the species richness of obligate corallivores, and a continued decline in the abundance of obligate corallivores three years after the mass coral mortality event. Additionally, facultative corallivore abundance increased with disturbance, although the effect was modulated by year, likely due to their more adaptable diets. Corallivore assemblage structure was also influenced by the heat stress event, recovery, and local human disturbance. These results detail how an entire corallivorous assemblage is impacted by a coral mortality event and incidentally provide a timeline for corallivore decline. Together, these results provide information about new ways of monitoring coral reefs, and the ways in which two components of the reef fish community, obligate and facultative corallivores, respond to a mass coral mortality event. / Graduate / 2022-01-15