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Coral reefs are among the most biodiverse ecosystems on the planet. Almost a third of tropical reefs lie in the Coral Triangle (CT), the epicenter of marine biodiversity, and are substantially threatened by human activity. Timor-Leste became independent in 2002 and is the newest of six nations in the CT, which include Indonesia, Malaysia, the Philippines, Papua New Guinea, and the Solomon Islands. It is important to establish a baseline for the current composition and state of coral reefs. For this thesis, the following specific objectives related to the coral reefs along the north coast of Timor-Leste were addressed: (1) assess coral reef variability based on kilometer-scale phototransects and explore environmental drivers of differences; (2) explore how the variation in the diversity of marine cryptic invertebrates varies at local scales over the same regions; and (3) quantify the condition of corals (coral health) using coral disease surveys alongside and measurements of water quality and temperature in the capital area of Dili, taken before and after the global bleaching event in 2016. The benthic structure of outer reef slope communities along the north coast was analyzed using kilometer-scale phototransects (each 1.5-2 km) collected from the 2014 XL Catlin Seaview Survey. Chapter 2 analyzed over 20,000 benthic photos using machine learning techniques, which revealed significant coral cover in Timor-Leste ranging from 5.4 to 33.0%, comparable to coral cover in other regions of the Indo-Pacific and CT. Wave exposure, distance to nearest river, and human population density were explored as potential drivers of benthic composition. A linear mixed-effects model tested the same covariates plus the ratio of branching to massive corals (i.e., structural complexity) on total coral cover. All parameters significantly explained benthic composition while there was a significant positive effect from wave exposure on coral cover that interacted with structural complexity where the effect was greatest on more complex reefs. This was due to the low incidence of storms and the comparatively protected north coast.Marine cryptic invertebrate biodiversity was explored in Chapter 3 using Autonomous Reef Monitoring Structures (ARMS) and genetic DNA barcoding of brachyuran crabs for outer reef slope sites in Timor-Leste. This was accomplished in collaboration with the US National Oceanic and Atmospheric Administration and the Smithsonian Institution National Museum of Natural History. Three size fractions (i.e., two meiofaunal and one sessile) from the ARMS were DNA metabarcoded. The results indicated several interesting trends that corroborate the biogeographic pattern of maximal diversity in the CT. For example, rarefaction curves of crabs and metabarcodes did not reach asymptotes meaning greater sampling would likely uncover more species. There was a high degree of unique operational taxonomic units (37% for brachyuran crabs) and diversity was greater than other Indo-Pacific sites as expected. The metabarcoding resulted in 19% unclassified operational taxonomic units, indicating the cryptic biodiversity of reefs is under-sampled with biodiversity being much more than previously quantified. The relationship between cryptofaunal diversity and coral cover was inconclusive. However, there was further evidence that rubble habitats promote the greatest diversity of coral reef cryptofauna.Reef condition in Timor-Leste was the focus of Chapter 4. The condition of four reefs was surveyed in November 2015 and July 2017. Temperature and nutrient data were also collected in 2015. Both surveys revealed disease prevalence was low, but had higher levels of compromised health (e.g., algal overgrowth). Interestingly, the isotope signature of nitrogen along the north coast did not match that expected for coastal pollution (8-30‰) but did match that expected from oceanic sources (2-6‰). Heat stress during the 2016-2017 global bleaching event was also quantified in Timor-Leste. Surveys before and after the event did not indicate high bleaching mortality as predicted by the Coral Reef Watch Timor-Leste (CRWTL) satellite sea surface temperature. CRWTL was significantly higher (> 1˚C) than in situ temperature during the austral summer. Both the temperature and nutrient data indicate seasonal oceanographic processes such as upwelling influence shallow reefs along the north coast.As local and global conditions change along the coastline of developing nations such as Timor-Leste, understanding the condition of reefs becomes critical. This thesis undertook the largest survey of coral reefs in the history of Timor-Leste. This study revealed rich coral reefs relatively high in biodiversity that are comparatively protected from climate change-induced ocean warming. The findings emphasize Timor-Leste’s significance as one of 50 coral reef world regions that are relatively less vulnerable to recent climate change impacts from a systematic global analysis. As such, immediate conservation priorities for Timor-Leste should focus on addressing localized anthropogenic pressures including sedimentation and overfishing. The balance between communities, ecosystems, and sustainable economies, must be further investigated using the wealth of Traditional Knowledge such as tara bandu customary law to build strong and resilient socio-ecological systems. All of this must be seen in the context of strong, intergovernmental action that is needed to address global climate change.

El Niño Southern Oscillation global coral bleaching events are increasing in frequency; however, the severity of bleaching is not geographically uniform. There were two major objectives of the present project: 1) assess the state of reefs and coral health at several sites and 2) explore water quality and climate change impacts on Timorese reefs. The impacts of climate change (principally by following coral mortality) were surveyed on coral reefs before and after the 2016–2017 underwater heatwave, using temperature loggers deployed between surveys which were compared to Coral Reef Watch (CRW) experimental virtual station sea surface temperature (SST). CRW is an important and widely used tool; however, we found the SST was significantly warmer (> 1°C) than in situ temperature during the austral summer accruing 5.79 degree heating weeks. In situ temperature showed no accumulation. Change in coral cover between surveys was attributed to reef heterogeneity. There were significant differences in coral cover, coral diversity, and nutrient concentrations between site and depth and a low prevalence of disease recorded in both years. The comparison of temperature and SST indicate that bleaching stress in Timor-Leste is potentially mitigated by seasonal and oceanographic dynamics. This is corroborated by Timor-Leste’s location within the Indonesian ThroughFlow. Timor-Leste is a climate refugium and the immediate conservation work lies in the management of localized anthropogenic impacts on coral reefs such as sedimentation and fishing.

Addressing the global decline of coral reefs requires effective actions from managers, policymakers and society as a whole. Coral reef scientists are therefore challenged with the task of providing prompt and relevant inputs for science-based decision-making. Here, we provide a baseline dataset, covering 1300 km of tropical coral reef habitats globally, and comprised of over one million geo-referenced, high-resolution photo-quadrats analysed using artificial intelligence to automatically estimate the proportional cover of benthic components. The dataset contains information on five major reef regions, and spans 2012–2018, including surveys before and after the 2016 global bleaching event. The taxonomic resolution attained by image analysis, as well as the spatially explicit nature of the images, allow for multi-scale spatial analyses, temporal assessments (decline and recovery), and serve for supporting image recognition developments. This standardised dataset across broad geographies offers a significant contribution towards a sound baseline for advancing our understanding of coral reef ecology and thereby taking collective and informed actions to mitigate catastrophic losses in coral reefs worldwide., Measurement(s) ecosystem • coral reef • composition Technology Type(s) automated image annotation • machine learning Factor Type(s) year of data collection • geographic location Sample Characteristic - Organism Anthozoa • Algae • Porifera Sample Characteristic - Environment marine coral reef biome • marine coral reef fore reef Sample Characteristic - Location Atlantic Ocean • Eastern Australia • Indian Ocean • Southeast Asia • Pacific Ocean • Great Barrier Reef Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.13007516

Coral reefs are highly vulnerable habitats, threatened by climate change and local anthropogenic impacts. Management is imperative, and spatial prioritisation apportions the area of interest to inform investments of scarce conservation resources. Spatially delineated planning units used to make management decisions are typically large enough to contain significant natural variabilities, but the ecological significance of such variance is seldom considered in planning decisions. On coral reefs, the patchiness of habitat quality within planning units matters both ecologically and functionally. Here, we show that considering within-planning unit variance in spatial prioritisation influences the location and design of reserve networks. Studying Timor-Leste, we statistically model the average and variance in coral cover. We compare conservation priority areas for scenarios informed by coral cover and variance to a baseline scenario with the spatial prioritisation software Marxan. To further explain these differences, and to show the value of including coral variance as a metric in spatial prioritisation, we created a reserve quality score. We show that the similarity between reserve networks was only 57% for protection, and 44% for restoration objectives. For both objectives, the inclusion of cover variance improves the conservation benefit of management. This project has shown a novel way to target areas for restoration. These results demonstrate that not only is mean coral cover (and, by extension, reef condition) a key criterion in selecting marine conservation actions, but its variance must be considered in spatial conservation prioritisation to improve both the efficiency and benefit of management actions within marine reserve networks.

Karimunjawa National Park is one of Indonesia&rsquo, s oldest established marine parks. Coral reefs across the park are being impacted by fishing, tourism and declining water quality (local stressors), as well as climate change (global pressures). In this study, we apply a multivariate statistical model to detailed benthic ecological datasets collected across Karimunjawa&rsquo, s coral reefs, to explore drivers of community change at the park level. Eighteen sites were surveyed in 2014 and 2018, before and after the 2016 global mass coral bleaching event. Analyses revealed that average coral cover declined slightly from 29.2 &plusmn, 0.12% (Standard Deviation, SD) to 26.3 &plusmn, 0.10% SD, with bleaching driving declines in most corals. Management zone was unrelated to coral decline, but shifts from massive morphologies toward more complex foliose and branching corals were apparent across all zones, reflecting a park-wide reduction in damaging fishing practises. A doubling of sponges and associated declines in massive corals could not be related to bleaching, suggesting another driver, likely declining water quality associated with tourism and mariculture. Further investigation of this potentially emerging threat is needed. Monitoring and management of water quality across Karimunjawa may be critical to improving resilience of reef communities to future coral bleaching.

Seagrasses are ecosystem engineers of essential marine habitat. Their populations are rapidly declining worldwide. One potential cause of seagrass population declines is wasting disease, which is caused by opportunistic pathogens in the genus Labyrinthula. While infection with these pathogens is common in seagrasses, theory suggests that disease only occurs when environmental stressors cause immunosuppression of the host. Recent evidence suggests that host factors may also contribute to disease caused by opportunistic pathogens. In order to quantify patterns of disease, identify risk factors, and investigate responses to infection, we surveyed shoot density, shoot length, epiphyte load, production of plant defenses (phenols), and wasting disease prevalence in eelgrass Zostera marina across 11 sites in the central Salish Sea (Washington state, USA), a region where both wasting disease and eelgrass declines have been documented. Wasting disease was diagnosed by the presence of necrotic lesions, and Labyrinthula cells were identified with histology. Disease prevalence among sites varied from 6 to 79%. The probability of a shoot being diseased was higher in longer shoots, in patches of higher shoot density, and in shoots with higher levels of biofouling from epiphytes. Phenolic concentration was higher in diseased leaves. We hypothesize that this results from the induction of phenols during infection. Additional research is needed to evaluate whether phenols are an adaptive defense against Labyrinthula infection. The high site-level variation in disease prevalence emphasizes the potential for wasting disease to be causing some of the observed decline in eelgrass beds.

Opportunistic marine pathogens, like opportunistic terrestrial pathogens, are ubiquitous in the environment (waters, sediments, and organisms) and only cause disease in immune-compromised or stressed hosts. In this review, we discuss four host-pathogen interactions within the marine environment that are typically considered opportunistic: sea fan coral-fungus, eelgrass-Labyrinthula zosterae, sea fan-Labyrinthulomycetes, and hard clam-Quahog Parasite Unknown with particular focus on disease ecology, parasite pathology, host response, and known associated environmental conditions. Disease is a natural part of all ecosystems; however, in some cases, a shift in the balance between the host, pathogen, and the environment may lead to epizootics in natural or cultured populations. In marine systems, host-microbe interactions are less understood than their terrestrial counterparts. The biological and physical changes to the world's oceans, coupled with other anthropogenic influences, will likely lead to more opportunistic diseases in the marine environment.

Sewage pollution threatens the health of coastal populations and ecosystems, including coral reefs. We investigated spatial patterns of sewage pollution in Puako, Hawaii using enterococci concentrations and δ(15)N Ulva fasciata macroalgal bioassays to assess relationships with the coral disease Porites lobata growth anomalies (PGAs). PGA severity and enterococci concentrations were high, spatially variable, and positively related. Bioassay algal δ(15)N showed low sewage pollution at the reef edge while high values of resident algae indicated sewage pollution nearshore. Neither δ(15)N metric predicted PGA measures, though bioassay δ(15)N was negatively related to coral cover. Furthermore, PGA prevalence was much higher than previously recorded in Hawaii and the greater Indo-Pacific, highlighting Puako as an area of concern. Although further work is needed to resolve the relationship between sewage pollution and coral cover and disease, these results implicate sewage pollution as a contributor to diminished reef health.

Many marine pathogens are opportunists, present in the environment, but causing disease only under certain conditions such as immunosuppression due to environmental stress or host factors such as age. In the temperate eelgrass Zostera marina, the opportunistic labyrinthu- lomycete pathogen Labyrinthula zosterae is present in many populations and occasionally causes severe epidemics of wasting disease; however, risk factors associated with these epidemics are unknown. We conducted both field surveys and experimental manipulations to examine the effect of leaf age (inferred from leaf size) on wasting disease prevalence and severity in Z. marina across sites in the San Juan Archipelago, Washington, USA. We confirmed that lesions observed in the field were caused by active Labyrinthula infections both by identifying the etiologic agent through histology and by performing inoculations with cultures of Labyrinthula spp. isolated from observed lesions. We found that disease prevalence increased at shallower depths and with greater leaf size at all sites, and this effect was more pronounced at declining sites. Experimental inoculations with 2 strains of L. zosterae confirmed an increased susceptibility of older leaves to infection. Overall, this pattern suggests that mature beds and shallow beds of eelgrass may be especially susceptible to outbreaks of wasting disease. The study highlights the importance of considering host and environmental factors when evaluating risk of disease from opportunistic pathogens.