Rocky intertidal habitats are highly diverse coastal ecosystems that may be disproportionately affected by climate change due to their susceptibility to marine and terrestrial heat waves and sea level rise. It is important to enhance understanding of community dynamics as well as habitat preferences for canopy forming taxa in order to better inform conservation efforts in the face of climate change. This study investigates variation in community composition with a focus on the role that elevation and structural complexity measured as rugosity plays on the presence of the functionally important surfgrass, Phyllospadix at Cabrillo National Monument in San Diego, California. Three long term monitoring sites were analyzed using large area imaging and 3D models across 3 timepoints from 2019-2020. We found that community composition varied between all sites with the most abundant taxa across sites being turf algae and the functionally important surfgrass Phyllospadix. Elevation and structural complexity both proved to be significant factors in determining the presence of Phyllospadix with it generally being found between the lowest elevation measured and 0.4 m tidal heights and in areas of relatively low structural complexity. The results from the elevation analysis of Phyllospadix align with conclusions from previous studies, while there is no comparison for the results showing the dependence of Phyllospadix on structural complexity as no previous research has investigated this relationship. It is likely that habitat heterogeneity affects Phyllospadix abundance in a variety of ways but further research is needed to understand these patterns.

Coral reefs are valuable ecosystems that provide billions of dollars globally in ecological goods and services, but they are facing widespread degradation due to climate change. This dissertation provides insights into the dynamics of coral bleaching and recovery, responses of other key taxa such as algae, and broader ecological implications for coral reef communities in the context of thermal stress. Chapter 1 of the dissertation synthesizes results from past studies on coral bleaching: while bleaching severity was highly variable as expected, this was complicated by inconsistent response metrics and the fact that bleaching measurements are often taken at different timing with respect to the onset of thermal stress. By standardizing existing observations, this chapter allows for inter-study comparison of coral bleaching susceptibility by genus, morphology, and/or region. Chapter 2 uses a time series of underwater imagery taken yearly for the past decade from two habitats on Palmyra Atoll to quantify the cover of reef-building corals, crustose coralline algae, macroalgae, turf, and other invertebrates. One year after each of the thermal anomalies in 2009 and 2015, some sites experienced reductions in coral cover which were replaced by turf or crustose coralline algae. However, across the entire decade, benthic community structure changed minimally at the functional group level, with greater stability at the reef terrace as compared to the fore reef. Chapter 3 of the dissertation tracks the growth, discoloration (i.e., lack of pigmentation), partial or whole-colony mortality, survival, and/or regrowth of individual coral colonies on Palmyra. This chapter explores which species were more sensitive or tolerant than others when exposed to thermal stress, and whether a colony’s level of discoloration at the time of warming corresponds to its fate one year later. Finally, Chapter 4 evaluates the long-term effects of increased seawater temperatures on benthic algae. This chapter investigates the abundance of fleshy and calcareous algae on Palmyra’s reef habitats over time, and suggests that a major macroalgal genus, Halimeda spp., showed evidence of temperature sensitivity. Long-term monitoring data sets from Palmyra can be used to establish baseline information for the conservation and restoration of more-threatened reefs at risk of decline.

In 2015, prolonged warming caused severe bleaching across reefs in the Main Hawaiian Islands resulting in widespread coral mortality. In addition to understanding changes in coral populations, it is also important to study algal dynamics on these reefs, especially with a focus on crustose coralline algae (CCA) and turf algae. CCA can serve as indicator for coral growth and recovery, thus playing a significant role in determining the future of bleached coral reefs. Meanwhile, turf algae quickly occupies available space, competes with corals and prevents coral settlement. To assess the state of these Hawaiian reefs, a large-scale mosaic imaging technique has been in use since 2014 to document the conditions of select sites before and after the bleaching event. These 33 m2 photomosaics cover three reefs in leeward Maui across a gradient of herbivore biomass and sediment input. Analysis of the mosaics shows marked differences in turf and CCA spatial dynamics and percent cover between sites. Sites more protected from anthropogenic influences had the greatest CCA growth, while the site most impacted by local stressors lost CCA abundance and had the highest increase in turf algae. This suggests local management and stressors around a reef may affect CCA and turf growth, and therefore influence coral recovery. The large-area mosaic imaging method may serve as a useful model for analyses of reef resilience on coral reefs.

Herbivores on coral reefs are instrumental in mitigating the competitive interactions between reef-building corals and fleshy algae; however, not all herbivores provide the same ecological function. Grazers/ detritivores consume turf algae (and associated organic matter), which are the primary spatial competitors to corals in the Main Hawaiian Islands. This study highlights functional diversity among surgeonfishes through observations of foraging behavior, analysis of stomachcontents, and analysis of stable isotopic signatures of muscle tissue (δ13C and δ15N) for three common species (Acanthurus nigrofuscus, Acanthurus olivaceus, and Ctenochaetus strigosus) on the leeward side of Maui. Similar foraging behavior was observed in A. nigrofuscus and C. strigosus, with both biting primarily on turf; A. olivaceus grazed primarily sand in addition to turf. Diet composition based on stomach contents was different among species, and variation in composition was influenced by site. Measured δ15N values indicate similar trophic position in the three species; however, δ13C values varied among species at different sites, indicating consumption of different algal resources. Collectively, these data suggest that surgeonfish grazers exhibit significant within-guild functional diversity; however, the differences and degree of divergence revealed depend on the methods used.

The red alga, Asparagopsis taxiformis, has recently been recognized for its unique ability to drastically reduce methane emissions from livestock. The main obstacle in using this seaweed is the complete lack of commercially available A. taxiformis. Little is known about how to develop large-scale cultivation systems for this red alga and the factors that influence its performance. This study examined the effect of the key factors including temperature and CO2 concentration, on the growth, photophysiology and the concentration of bromoform, the secondary metabolite responsible for methane reduction in A. taxiformis. A series of single and multifactor closed culture experiments, conducted on A. taxiformis collected, isolated, and cultured in southern California, identified the temperature and CO2 concentration required to optimize growing conditions. The findings indicate that through environmental control and addressing limiting factors, significant increases in biomass production can be achieved, making A. taxiformis a viable species for large-scale cultivation.

Understanding how relatively healthy coral communities respond to disturbance provides an important baseline to which the response and recovery of more degraded ecosystems can be compared. Here, Palmyra Atoll was used as a case study to examine the response of an intact coral reef community to biotic and abiotic stressors in the form of a species invasion and bleaching event. Techniques from the fields of spatial, chemical, and microbial ecology were used to investigate the response of benthic communities to these disturbances. A decade-long, spatially robust dataset found contrasting patterns in the invasion of a corallimorph, Rhodactis howesii, around the atoll. Decreasing cover of R. howesii was observed at the epicenter of the invasion, but contrasted sharply with increased spread and cover of the corallimorph at additional sites. Sites with high coral cover and low levels of disturbance experienced lower levels of invasion, while sites with high wave energy and lower coral cover experienced increased corallimorph growth. Competitive mechanisms of the corallimorph were examined using an assay that found evidence of bioactive chemical compounds present in R. howesii tissue that caused coral mortality. To further investigate the impact of invasion on coral health, 16S rRNA amplicon sequencing of coral-corallimorph interaction zones showed shifts in coral-associated microbial communities with increasing proximity to R. howesii. Overgrown coral tissue was dominated by bacterial families strongly associated with stress and disease, suggesting that the corallimorph can directly impact coral colonies through microbial community alteration. Evidence of acclimatization was found by studying the response and recovery of coral-associated bacterial communities to the global stressor of the 2015-16 bleaching event. Although microbial community composition shifted as a result of bleaching, healthy symbionts were maintained in coral tissue and pathogenic bacterial invasion was not observed. These data, in combination with the low mortality at Palmyra, support the hypothesis that natural temperature variability may lead to a more resilient community in the face of thermal stress. Collectively, the results of my dissertation provide valuable insight into the response of coral communities to invasion and their ability to adapt to increasing thermal stress events over time. This dissertation also highlights the importance of long-term and spatially robust data sets that allow for accurate quantification of reef trajectories in response to disturbance events.

Understanding the natural processes that drive resource distribution and the associated response of organisms is a principal goal in ecology. Mixotrophic organisms are particularly interesting in this regard because their fitness is linked to the resources essential for both primary producers (e.g., light and nutrients) and consumers (e.g., food). Reef-building corals are among the most widely distributed mixotrophs and form the foundation of one of the most productive and diverse marine ecosystems, coral reefs. To date, a disproportionate amount of research has focused on the role of endosymbiotic microalgae in defining coral nutrition and we have a limited understanding of how corals respond to variation in food availability through time and space. This dissertation examines how mixotrophic corals can modify their nutritional modes in accordance with resource availability at multiple spatial scales. The Southern Line Islands of Kiribati in the central Pacific Ocean span a known upwelling gradient and have distinct differences in nearshore primary production. Combining remotely sensed estimates of surface chl-a as a proxy for food availability and stable isotope analysis of a common coral species, I found that corals are more heterotrophic at more productive islands. I then extended this relationship globally by synthesizing published isotopic data on corals and found that large-scale patterns of chl-a can predict how heterotrophic corals are likely to be. I then developed a more precise method to studying coral trophic ecology at finer spatial scales. Using δ13C analysis of amino acids, I found extreme trophic plasticity (0-100% contribution of heterotrophic nutrition) among conspecific corals at the scale of meters to kilometers around Palmyra Atoll. Finally, I conducted a nutrient enrichment experiment to examine the physiological responses of corals to changes in autotrophic nutrition in the absence of heterotrophic nutrition. I found that elevated nutrient concentrations have species-specific effects on coral calcification likely due to modifications in resource sharing between corals and their endosymbionts. Collectively, the results of my dissertation address a critical knowledge gap in coral biology and provide a framework to resolve the importance of heterotrophic nutrition in the persistence of coral reef ecosystems in an era of global change.

Coral reefs hold immense ecologic, economic, and social value, yet these important ecosystems face an existential threat from global climate change. Coral reef conservation is thus an urgent international priority, yet it can be challenging to design and implement effective conservation measures due to the innate complexity of coral reef ecosystems. Coral reef “resilience” is shaped by numerous environmental, biotic, and anthropogenic processes that operate across a range of scales. A particular conservation strategy might be appropriate for one set of conditions but fail to adequately protect reef health in another. Robust coral reef monitoring data can help natural resource managers identify the key processes impacting a given reef and design appropriate management interventions. We demonstrate how new conservation technology, specifically large-area imagery (LAI), can enhance our ability to study ecosystem processes across multiple scales in space and time, identify drivers of ecosystem condition, and inform site-specific decision making. Here, we use Hawaiian coral reefs as a case study to investigate multiple reef processes using multi-scale LAI data, specifically 1) habitat structural complexity, 2) benthic community succession, and 3) coral bleaching, growth, and survivorship in response to thermal stress. We apply these findings to quantify “resilience” (specifically patterns of resistance and recovery) at multiple scales for forereefs in leeward Maui. We use this multi-scale data to critically evaluate the predictive accuracy of coral reef resilience assessments, a popular conservation triage and marine spatial planning tool. In doing so, we demonstrate the potential of LAI to inform conservation decision making, and we recommend steps that can be taken to make this conservation technology more accessible to practitioners.

El Niño conditions are known to alter ocean circulation patterns causing a reduction in upwelling events that leads to warmer water with reduced concentrations of inorganic nutrients in coastal waters. The 2015/16 El Niño event resulted in significant losses of the habitat forming giant kelp, Macrocystis pyrifera, with concurrent increases in the non-native, invasive brown alga Sargassum horneri across San Diego, CA. M. pyrifera is known to be highly sensitive to both temperature and nutrient availability, however much less is known about the response of S. horneri to these conditions. The goals of this study were to investigate if and how El Niño-like conditions may have facilitated the invasion of S. horneri in southern CA using both laboratory and field-based approaches. In laboratory experiments, S. horneri maintained positive growth in conditions well exceeding M. pyrifera’s thermal tolerance limits. Temperature was the main driver of growth rates for S. horneri juveniles, but nitrate concentration affected other measurements of algal physiological performance, such as photosynthetic efficiency/maximum quantum yield and pigment concentration. Further, in the field, S. horneri displayed strong seasonality, but with contrasting timing to native M. pyrifera suggesting that the phenology of these two species may be offset. Given the rise in sea surface temperatures and predicted increases in the frequency and intensity of El Niño and marine heat waves, these findings suggest there is increased risk of further invasion by the non-native S. horneri within southern California’s iconic giant kelp forests, but more research is needed to evaluate future trends.

Coral reefs are one of the most diverse and productive ecosystems on the planet. Globally, corals are declining and algae are increasing due to anthropogenic activities. While most research and conservation efforts focus on the proliferation of macroalgae, in fact most algae on coral reefs are turf algae: heterogeneous assemblages of many species of small algae. These ubiquitous and abundant algal “shag carpets” are typically overlooked or studied as a homogenous functional group. I examine characteristics that make turf algae functionally unique from other types of algae, focusing on their ecological importance as food for reef organisms, major sources of productivity, and competitors with reef-building corals. Further, I argue that turfs will become more abundant in the future because they respond positively to the many anthropogenic threats facing coral reefs, including overfishing, pollution, acidification and warming. First, I explore the spatial patterns in turf assemblages, showing that, although turfs appear visually homogenous to the naked eye, they are highly variable at the centimeter scale. This descriptive work provides a foundation for testing ecological processes that may be causing those small-scale patterns. Second, I use turf algae as a tool to demonstrate that the relative influences of top-down and bottom-up processes are context-dependent. I measured the greatest response to grazer exclusion where background herbivory was lowest, suggesting a positive feedback between the loss of herbivory and loss of resilience. Further, in contrast to high profile findings in other ecosystems, my data revealed that nutrient enrichment increased, and consumers reduced, turf diversity. Finally, I expand the traditional perspective of coral reef herbivores to include small infaunal invertebrates living in turf algae. By partitioning herbivory among fish and small invertebrates, I provide some of the first evidence that infaunal invertebrates significantly impact turf algae, but their role depends on either competition with or predation by fish. Overall, my dissertation provides a new perspective on turf algae and opportunities to test classic ecological concepts. Additionally, a better understanding of the ecology of turf algae has urgent conservation applications, including insight into how reefs of the future will function and how to best protect them.