Reef Monitoring Program Research Articles

Developing a population assessment for Caribbean spiny lobster Panulirus argus in the United States Virgin Islands: lessons learned

The Caribbean spiny lobster (Panulirus argus) is one of the most important fisheries in the US Virgin Islands. Low densities and life-history characteristics of lobsters have made reliable surveys in the region notoriously difficult, contributing to sparse and inconsistent fisheries- independent datasets to inform management decisions. Many existing and historical surveys are limited in their temporal and spatial coverage. In 2019, the National Park Service initiated a long-term monitoring effort of spiny lobsters in Buck Island Reef National Monument and Salt River National Historical Park and Ecological Preserve, St. Croix, US Virgin Islands, and Virgin Islands National Park, St. John, US Virgin Islands. Initial surveys show both density (3.06–7.07 lobsters ha –1) and occupancy (0.11–0.12 sites with lobster) are low and not significantly different between the three parks. While survey efforts are currently focused on national parks, the 50 × 50 m gridded sample frame and stratification scheme are adaptable to the wider US Caribbean region, modelled after the multi-agency design to monitor reef fish with the National Coral Reef Monitoring Program. With the same survey footprint as reef fish surveys, the two methods could conceivably be co-located in the future, improving cost-efficiency and overall data quality. If expanded, this methodology could provide regional fishery managers with much needed density indices, though future surveys would benefit from a greater sample size or by supplementing with other methods that increase the number of observed lobsters to allow for robust size-frequency analyses.

Integrating the US Caribbean Reef Fish Visual Census into fishery stock assessments

The United States Caribbean Reef Fish Visual Census (RVC) is a fishery-independent survey of the coral reef fish community, comprised of hundreds of species, designed to provide quantitative information for data-poor fisheries to support regional stock assessments. The Caribbean RVC, implemented in 2014 as part of the National Coral Reef Monitoring Program (NCRMP), uses a probabilistic stratified random sampling design capitalizing on the strong mean-variance relationship of population abundance dependent on hardbottom habitats and depths. Here we highlight RVC data for queen triggerfish in Puerto Rico, where survey precision improved from CVs of 20.6% in 2014 to 12.6% in 2021, which produced accurate and cost-effective estimates of key assessment metrics like size- structured relative population abundance and biomass. We estimated a relatively stable exploited-phase average population abundance for 2014–2021 at 2.3 million queen triggerfish with a biomass of 1246 metric tons. To support stock assessments using "statistical catch at age" models, we generated a 2001–2021 time series of several population metrics by a statistical conversion of spatially-restricted, pre- NCRMP data to the RVC frame. To cross-check assessment modeling, we combined 2014–2021 RVC results with life history demographics in an alternative length-based risk analysis (LBRA) model to evaluate stock sustainability consequences using two lifetime growth scenarios. LBRA models indicated low overfishing risks. We concluded that only a few quality fishery-independent surveys are needed to obtain understanding of stock sustainability status, and that RVC not only provides reliable data for single-species stock assessments, but also for design evaluation of marine protected areas and ecosystem-based fishery management.

Expansion of an established fishery-independent survey into the US Virgin Islands' upper mesophotic zone: feasibility and management implications

A three-year pilot study, the Deep Coral Reef Monitoring Program (DCRMP), expanded the National Coral Reef Monitoring Program's (NCRMP) established fishery-independent, diver-based reef fish visual survey to upper mesophotic reefs (>30 to 50 m) in the United States Caribbean for the first time. The new DCRMP sample domain (>30 to 50 m) encompassed 2.4 times more survey area than NCRMP (0 to ≤30 m) and collected high quality data (CV <20%) on coral reef fishes [three survey years, 29 (5) species; mean (standard deviation)]. For the four representative, fishery-targeted, analysis species selected (i. e., grouper, snapper, triggerfish, and parrotfish), domain-wide density and length comparisons between surveys showed similar or statistically higher abundances and larger lengths for fishes at deeper depths (>30 to 50 m). These results highlight the importance of surveying the entire insular shelf in St. Thomas and St. John, US Virgin Islands for fisheries management applications. Furthermore, the DCRMP survey leveraged NCRMP's methods and resources resulting in a seamless extension to deeper waters. However, if these programs were fully integrated and optimized within a single survey design, approximately half the sites would be needed to achieve the same level of precision, offering substantial time and cost savings. The principles of probabilistic sampling successfully used in the present fishery-independent survey design (0 to 50 m) can be applied more broadly to develop an "ideal" large-scale, multi-gear survey from 0 to about 500 m to encompass the entire depth ranges of managed species in the US Caribbean.

Changes in sea floor productivity are crucial to understanding the impact of climate change in temperate coastal ecosystems according to a new size-based model

The multifaceted effects of climate change on physical and biogeochemical processes are rapidly altering marine ecosystems but often are considered in isolation, leaving our understanding of interactions between these drivers of ecosystem change relatively poor. This is particularly true for shallow coastal ecosystems, which are fuelled by a combination of distinct pelagic and benthic energy pathways that may respond to climate change in fundamentally distinct ways. The fish production supported by these systems is likely to be impacted by climate change differently to those of offshore and shelf ecosystems, which have relatively simpler food webs and mostly lack benthic primary production sources. We developed a novel, multispecies size spectrum model for shallow coastal reefs, specifically designed to simulate potential interactive outcomes of changing benthic and pelagic energy inputs and temperatures and calculate the relative importance of these variables for the fish community. Our model, calibrated using field data from an extensive temperate reef monitoring program, predicts that changes in resource levels will have much stronger impacts on fish biomass and yields than changes driven by physiological responses to temperature. Under increased plankton abundance, species in all fish trophic groups were predicted to increase in biomass, average size, and yields. By contrast, changes in benthic resources produced variable responses across fish trophic groups. Increased benthic resources led to increasing benthivorous and piscivorous fish biomasses, yields, and mean body sizes, but biomass decreases among herbivore and planktivore species. When resource changes were combined with warming seas, physiological responses generally decreased species’ biomass and yields. Our results suggest that understanding changes in benthic production and its implications for coastal fisheries should be a priority research area. Our modified size spectrum model provides a framework for further study of benthic and pelagic energy pathways that can be easily adapted to other ecosystems.

Ecological and environmental predictors of juvenile coral density across the central and western Pacific

The persistence of Pacific coral reefs is threatened by large-scale mortality resulting from heat stress, storms, overfishing, disease, and land-based pollution. While reefs have demonstrated the ability to recover from these disturbances, recovery potential is highly variable; in part driven by the high spatial variability in the abundance of coral juveniles. However, our understanding of the patterns and predictors of juvenile coral density is hampered by the limited geographic scope of previous studies. Our objectives in this study were to: (1) explore the spatial and temporal patterns of juvenile (1- < 5cm in diameter) colony density across the U.S.-affiliated Pacific islands and atolls; and (2) identify the potential role of ecological and environmental factors which may influence coral juvenile abundance. Juvenile density was quantified as part of NOAA’s National Coral Reef Monitoring Program between 2013 and 2019 using a stratified sampling design across 1,405 forereef sites on 34 islands and atolls. Regional mean juvenile density varied from 1.4 to 10.5 colonies m-2 with the highest densities observed in the northern Mariana Islands, Northwestern Hawaiian Islands, and southern Mariana Islands. Juvenile density significantly increased between sampling periods in the Main Hawaiian Islands, Line Islands and northern Mariana Islands. Survey-weighted generalized linear modeling demonstrated that juvenile density was best predicted by the interaction between time since a heat stress event and heat stress severity, depth, site and sector-level percent coral cover, human density, percent unconsolidated substrate, macroalgal cover, herbivore biomass, and the interaction of sector coral cover area and heat stress, and the interaction of wave power (combination of wave height and period) and heat stress. With the unique scale and gradients across the U.S. Pacific, our study found that the high latitude regions have enhanced juvenile density compared to their lower latitude counterparts. Our results also suggest density is most dependent on the timing and severity of heat stress, depth, stock-recruitment with an open adult population, availability of suitable habitat at the site-scale, and the number of humans in the system.

Predicting Coral Reef Carbonate Chemistry Through Statistical Modeling: Constraining Nearshore Residence Time Around Guam

To accurately predict the impacts of ocean acidification on shallow-water ecosystems, we must account for the biogeochemical impact of local benthic communities, as well as the connectivity between offshore and onshore water masses. Estimation of residence time can help quantify this connectivity and determine the degree to which the benthos can influence the chemistry of the overlying water column. We present estimates of nearshore residence time for Guam and utilize these estimates to model the effects of benthic ecosystem metabolism on the coral reef carbonate system. Control volume and particle tracking approaches were used to estimate nearshore residence time. These estimates were paired with observed patterns in the reef carbonate system around Guam using water samples collected by NOAA’s National Coral Reef Monitoring Program. Model performance results suggest that when considering the effects of benthic metabolism on the carbonate system, it is paramount to represent the contact time of the water volume with the benthos. Even coarse estimates of residence time significantly increase model skill. We observed the highest predictive skill in models including control volume derived estimates of residence time, but only when those estimates were included as an interaction with benthic composition. This work shows that not only is residence time critically important to better predict biogeochemical variability in coral reef environments, but that even coarse hydrodynamic models can provide useful residence time estimates at management relevant, whole-ecosystem scales.

Low net carbonate accretion characterizes Florida’s coral reef

Coral reef habitat is created when calcium carbonate production by calcifiers exceeds removal by physical and biological erosion. Carbonate budget surveys provide a means of quantifying the framework-altering actions of diverse assemblages of marine species to determine net carbonate production, a single metric that encapsulates reef habitat persistence. In this study, carbonate budgets were calculated for 723 sites across the Florida Reef Tract (FRT) using benthic cover and parrotfish demographic data from NOAA’s National Coral Reef Monitoring Program, as well as high-resolution LiDAR topobathymetry. Results highlight the erosional state of the majority of the study sites, with a trend towards more vulnerable habitat in the northern FRT, especially in the Southeast Florida region (− 0.51 kg CaCO3 m−2 year−1), which is in close proximity to urban centers. Detailed comparison of reef types reveals that mid-channel reefs in the Florida Keys have the highest net carbonate production (0.84 kg CaCO3 m−2 year−1) and indicates that these reefs may be hold-outs for reef development throughout the region. This study reports that Florida reefs, specifically their physical structure, are in a net erosional state. As these reefs lose structure, the ecosystem services they provide will be diminished, signifying the importance of increased protections and management efforts to offset these trends.

Biak and Wakatobi reefs are the two hottest hotspots of coral reef fish diversity and abundance in the Indonesian Archipelago

The Indonesian Archipelago has a very complex geological history, along with equatorial warm sea temperature, resulting in diverse types of coral reefs and high diversity of coral reef fish. Many livelihoods of the coastal community are dependent on coral reef fisheries. The present study aimed to determine which region and location in the Indonesian Archipelago has the most diverse and abundant coral reef fish. The archipelago was divided into four regions: the Indian Ocean, Sunda Shelf, Wallacea, and the Pacific Ocean. Data were obtained from a national coral reef monitoring program of the Indonesian Research Center for Oceanography (RCO)-the National Board for Research and Innovation (BRIN). The reef fish data were collected using the underwater visual census method, from 321 belt transects on 24 locations (districts) across the archipelago. The results show that coral reef fish diversity of the Pacific region was the highest across the archipelago for all three trophic levels, i.e., corallivore, herbivore, and carnivore fish. The Pacific Ocean region also had the highest fish abundance for the three trophic levels. Comparison among locations revealed that the best ten locations in reef fish diversity and abundance were Sabang, Mentawai, Makassar, Selayar, Buton, Luwuk, Ternate, Raja Ampat, Biak, and Wakatobi. Wakatobi reefs showed their supremacy in carnivore fish diversity and abundance, while Biak reefs were the best in herbivore fish. The abundance of corallivore fish was also considerably high in Sabang reefs, but it is still lower than in Raja Ampat, Biak, and Wakatobi reefs. These results provide empirical evidence that the coral reefs of Wakatobi and Biak are the hottest hotspots of coral reef fish diversity and abundance in the Indonesian Archipelago.

A National Status Report on United States Coral Reefs Based on 2012–2018 Data From National Oceanic and Atmospheric Administration’s National Coral Reef Monitoring Program

National Oceanic and Atmospheric Administration’s Coral Reef Conservation Program supports the National Coral Reef Monitoring Program (NCRMP) in the United States Pacific, Atlantic, Caribbean, and Gulf of Mexico. NCRMP conducts standardized observations of biological, climatic, and socioeconomic indicators across American Samoa, Guam, the Main Hawaiian Islands, the Northwestern Hawaiian Islands, the Northern Mariana Islands, the Pacific Remote Islands, Florida, the Flower Garden Banks, Puerto Rico, and the United States Virgin Islands. NCRMP provides periodic, national-level assessments of the status of United States coral reef ecosystems and communities connected to them. In 2014, NCRMP partnered with the University of Maryland Center for Environmental Science on an unprecedented collaboration between federal and jurisdictional/state agencies, academia, and non-governmental organizations to synthesize NCRMP data into a reporting format designed to be accessible and relevant to the public and policy makers. The process involved multi-year data analyses of key benthic, fish, and climate indicators. In populated jurisdictions, socioeconomic data were integrated to assess public support for management actions, participation in pro-environmental behaviors, and awareness of threats to coral reefs. Jurisdictions were scored using a report-card scale (0–100%) by establishing references for each indicator using best-available historical data or expert opinion where historical data did not exist or were not statistically comparable. Despite overall ecosystem scores of Fair for all combined Atlantic (70%) and Pacific (74%) jurisdictions, the current trend is downward with a majority of United States coral reefs declining and vulnerable to further degradation. Remote, uninhabited reefs had an advantage with respect to reef fish population scores, i.e., Flower Garden Banks (85%) and Pacific Remote Islands (93%), when compared to populated location scores, i.e., Puerto Rico (63%) and Main Hawaiian Islands (66%). All coral reefs are highly impacted by climate change, and climate impacts were more pronounced than expected on remote reefs, i.e., the Northwestern Hawaiian Islands (58%). Presenting results in a report-card style facilitates communication to the public and policy makers, and provides a useful mechanism to garner support for management actions such as expanding protected areas; enforcing existing regulations; increasing climate change education; reducing land-based sources of pollution; and other actions to improve the trajectory of coral reef ecosystem conditions.

Dynamics of large benthic foraminiferal assemblages: A tool to foreshadow reef degradation?

Ecological regime shifts in the marine realm have been recorded from a variety of systems and locations around the world. Coral reefs have been especially affected, with their benthic habitat changing from a dominance of stony corals to a dominance of other organisms such as fleshy algae. To detect changes in the benthic habitat of coral reefs, simple tools applicable on a global scale are necessary for future monitoring programs. Hence, the aim of this research is to explore the hypothesis that shifts in assemblages of large benthic foraminifera (LBF) can detect early signs of degradation in the reef benthic habitat. To do so, data on living assemblages of LBF collected between 1997 and 2018 at 12 islands in the Spermonde Archipelago (South Sulawesi, Indonesia) were analyzed. Foraminiferal specimens were morphologically identified to the species level and statistical analyses performed to assess changes in their assemblage composition. A clear temporal shift was observed. Typical foraminiferal assemblages in a coral-dominated (e.g., Amphistegina lobifera, Calcarina spengleri, Heterostegina depressa) and fleshy algae-dominated (e.g., Neorotalia gaimardi, C. mayori) reef habitats were identified and significantly linked to the substrate type. Other species (e.g., Elphidium spp., Peneroplis planatus and Sphaerogypsina globulus) seem to reflect a spatial and temporal gradient of anthropogenic pollution from local inhabited islands and ongoing urban development on the mainland. Hence communities of LBF consistently follow gradual shifts in environmental conditions. Additionally to foraminiferal assemblages being an indicator for actual reef condition, closely monitoring LBF may provide early information on reef degradation, in time to take action against identified stressors (e.g., eutrophication or intensive fishing) at local and regional scales. The circumtropical distribution of LBF is such that they can be included worldwide in reef monitoring programs, conditional to calibration to the regional species pool.

Resident Perceptions of Ecosystem Services Provided by U.S. Coral Reefs: Highlights from the First Cycle of the National Coral Reef Monitoring Program’s Socioeconomic Survey

Despite being among the most valuable ecosystems on Earth, coral reefs face ongoing threats that could negatively impact the human populations who depend on them. The National Coral Reef Monitoring Program (NCRMP) collects and monitors data on various aspects of U.S. coral reefs to provide a holistic understanding of the status of the reefs and adjacent human communities. This paper explores results from the NCRMP’s first socioeconomic monitoring cycle using an ecosystem services framework and examines how these results can be used to improve coral reef management in the following U.S. coral reef jurisdictions: American Samoa, the Commonwealth of the Northern Mariana Islands, Florida, Guam, Hawai’i, Puerto Rico, and the U.S. Virgin Islands. Results suggest that residents in the U.S. Pacific coral reef basin may hold stronger cultural and provisioning values, whereas residents in the U.S. Atlantic coral reef basin may hold stronger regulating values. These findings suggest that outreach efforts have been successful in communicating benefits provided by coral reef ecosystems to the public. They also provide insight into which ecosystem services are valued in each jurisdiction, allowing resource managers to make science-based decisions about how to communicate conservation and management initiatives.

Diversity and Disease: The Effects of Coral Diversity on Prevalence and Impacts of Stony Coral Tissue Loss Disease in Saint Thomas, U.S. Virgin Islands

Stony coral tissue loss disease (SCTLD) was first observed in St. Thomas, U.S. Virgin Islands (USVI) in January 2019. This disease affects at least 20 scleractinian coral species; however, it is not well understood how reef diversity affects its spread or its impacts on reef ecosystems. With a large number of susceptible species, SCTLD may not follow the diversity-disease hypothesis, which proposes that high species diversity is negatively correlated with disease prevalence. Instead, SCTLD may have a higher prevalence and a greater impact on reefs with higher coral diversity. To test this, in 2020 we resampled 54 sites around St. Thomas previously surveyed in 2017 or 2019 by the National Oceanic and Atmospheric Administration National Coral Reef Monitoring Program. These sites represented a variety of species diversity values [categorized into poor (<12 spp. rich.) and rich (≥12 spp. rich.)] in multiple disease zones (Endemic: disease present ≥ 9 months; Epidemic: disease present 2–6 months; Control and Emergent: disease present no disease/<2 months). We hypothesized that, contrary to the diversity-disease hypothesis, sites with high species diversity (as measured by species richness or Simpson’s index) would have higher disease prevalence within the epidemic zone, and that high species diversity sites would have a greater impact from disease within the endemic zone. Results indicated a significant positive relationship between disease prevalence and diversity in the epidemic zone, and a similar trend in the endemic zones. Additionally, a negative relationship was seen between pre-outbreak diversity and loss of diversity and coral cover within the endemic zone. This supports the hypothesis that higher diversity predicts greater disease impact and suggests that SCTLD does not follow the diversity-disease hypothesis. Within the epidemic zone, the species with the highest SCTLD prevalence were Dendrogyra cylindrus, Colpophyllia natans, and Meandrina meandrites, while in the endemic zone, Diploria labyrinthiformis, Pseudodiploria strigosa, Montastraea cavernosa, and Siderastrea siderea had the highest SCTLD prevalence. Understanding the relationship between species diversity and SCTLD will help managers predict the most vulnerable reefs, which should be prioritized within the USVI and greater Caribbean region.

Comparing Coral Colony Surveys From In-Water Observations and Structure-From-Motion Imagery Shows Low Methodological Bias

As the threats to coral reefs mount, scientists and managers are looking for innovative ways to increase the scope, scale, and efficiency of coral reef monitoring. Monitoring changes in coral communities and demographic features provides key information about ecosystem function and resilience of reefs. While most monitoring programs continue to rely on in-water visual survey methods, scientists are exploring 3D imaging technologies such as photogrammetry, also known as Structure-from-Motion (SfM), to enhance precision of monitoring, increase logistical efficiency in the field, and generate a permanent record of the reef. Here, we quantitatively compare data generated from in-water surveys to SfM-derived metrics for assessing coral demography, bleaching, and diversity in the main Hawaiian Islands as part of NOAA’s National Coral Reef Monitoring Program. Our objectives were to compare between-method error to within-method error, test for bias between methods, and identify strengths and weaknesses of both methods. Colony density, average colony diameter, average partial mortality, prevalence of bleaching, species richness, and species diversity were recorded using both methods within the same survey areas. For all metrics, the magnitude of between-method error was comparable to the within-method error for the in-water method and between method error was significantly higher than within-method error for SfM for one of the seven metrics. Our results also reveal that a majority of the metrics do not vary significantly between methods, nor did we observe a significant interaction between method and habitat type or method and depth. Exceptions include estimates of partial mortality, bleaching prevalence, and Porites juvenile density–though differences between methods are generally small. Our study also highlights that SfM offers a unique opportunity to more rigorously quantify and mitigate inter-observer error by providing observers unlimited “bottom time” and the opportunity to work together to resolve difficult annotations. However, the necessary investment in equipment and expertise does present substantial up-front costs, and the time associated with curating imagery, photogrammetric modeling, and manual image annotation can reduce the timeliness of data reporting. SfM provides a powerful tool to reimagine how we study and manage coral reefs, and this study provides the first quantified methodological comparison to validate the transition from standard in-water methods to SfM survey methods for estimates of coral colony-level surveys.

Coral monitoring in northwest Australia with environmental DNA metabarcoding using a curated reference database for optimized detection

AbstractThe need for efficient and more accurate ways of monitoring threatened ecosystems is becoming increasingly urgent as climate change intensifies. Coral reefs are an example of an ecosystem in crisis, with widespread declines in coral cover and diversity documented over recent decades. Novel molecular approaches such as biomonitoring using environmental DNA (eDNA) from seawater samples show great potential to complement future coral reef monitoring programs, especially when used in combination with conventional methods. However, eDNA metabarcoding studies often rely on public databases (e.g., GenBank) for assigning taxonomy, which generally limits the number of sequences that can be taxonomically identified. The extent to which building reference tissue sequences improves taxonomic resolution has yet to be fully examined. Here, we combined traditional coral reef monitoring data with eDNA assessments derived from seawater collected at the highly diverse Rowley Shoals in Western Australia. Using two ITS2 assays developed to target basal metazoan DNA and a reference database spiked with 70 local coral specimens, we identified 37 genera and 40 species from 56 1 L seawater samples. We identified considerable overlap of taxa with visual survey data and showed that assignment of amplicon sequence variants was significantly improved when “spiking” the taxonomic classifier with curated sequences of locally collected species. Our findings showcase the potential of eDNA metabarcoding for monitoring the biodiversity of reef corals and highlight the importance of custom reference sequence databases for improving taxonomic resolution in metabarcoding studies.

Application of remotely sensed sea surface temperature for assessment of recurrent coral bleaching (2014–2019) impact on a marginal coral ecosystem

The 2014–2016 El Niño Southern Oscillation (ENSO) caused a prolonged marine heatwave that led to widespread coral bleaching and mortality across the Indo-pacific coral reefs. Prediction of coral bleaching and assessment of bleaching impact on corals is vital for reef ecosystem functioning, services and management. Wherein, advanced satellite remote sensing approach to determine and quantify the thermal stress on corals can assist as an alternative and convenient tool for reef monitoring programs. The present study examines the impact of consecutive coral bleaching episodes on shallow-water marginalized patch reef ecosystems on the Eastern Arabian Sea. Advanced Very High-Resolution Radiometer (AVHRR) satellite data from the NOAA Coral Reef Watch’s (NOAA-CRW) platform, known as CoralTemp, were used to analyze the thermal stress on the coral reefs. Coral bleaching indices like Bleaching Threshold (BT), Positive Anomaly (PA), and Degree Heating Weeks (DHW) were calculated. Ground-truthing revealed that detected thermal stress from satellite-derived Sea Surface Temperature (SST) data over this region well corroborate with the mass coral bleaching events, and found reliable for detecting coral bleaching episodes in the marginalized turbid coral habitats. This study signifies the potential benefit of incorporating remote sensed SST data in coral bleaching monitoring program, which may guide to undertake targeted coral surveys and aid in decision-making and conservation of the vulnerable coral reef ecosystems.

The use of pseudo-multivariate standard error to improve the sampling design of coral monitoring programs.

The characteristics of coral reef sampling and monitoring are highly variable, with numbers of units and sampling effort varying from one study to another. Numerous works have been carried out to determine an appropriate effect size through statistical power; however, these were always from a univariate perspective. In this work, we used the pseudo multivariate dissimilarity-based standard error (MultSE) approach to assess the precision of sampling scleractinian coral assemblages in reefs of Venezuela between 2017 and 2018 when using different combinations of number of transects, quadrats and points. For this, the MultSE of 36 sites previously sampled was estimated, using four 30m-transects with 15 photo-quadrats each and 25 random points per quadrat. We obtained that the MultSE was highly variable between sites and is not correlated with the univariate standard error nor with the richness of species. Then, a subset of sites was re-annotated using 100 uniformly distributed points, which allowed the simulation of different numbers of transects per site, quadrats per transect and points per quadrat using resampling techniques. The magnitude of the MultSE stabilized by adding more transects, however, adding more quadrats or points does not improve the estimate. For this case study, the error was reduced by half when using 10 transects, 10 quadrats per transect and 25 points per quadrat. We recommend the use of MultSE in reef monitoring programs, in particular when conducting pilot surveys to optimize the estimation of the community structure.

Representation and complementarity of the long-term coral monitoring on the Great Barrier Reef.

Effective environmental management hinges on efficient and targeted monitoring, which in turn should adapt to increasing disturbance regimes that now characterize most ecosystems. Habitats and biodiversity of Australia's Great Barrier Reef (GBR), the world's largest coral reef ecosystem, are in declining condition, prompting a review of the effectiveness of existing coral monitoring programs. Applying a regional model of coral cover (i.e., the most widely used proxy for coral reef condition globally) within major benthic communities, we assess the representation and complementarity of existing long-term coral reef monitoring programs on the GBR. We show that existing monitoring has captured up to 45% of the environmental diversity on the GBR, while some geographic areas (including major hotspots of cyclone activity over the last 30yr) have remained unmonitored. Further, we identified complementary groups of reefs characterized by similar benthic community composition and similar coral cover trajectories since 1996. The mosaic of their distribution across the GBR reflects spatial variation in the cumulative impact of multiple acute disturbances, as well as spatial gradients in coral recovery potential. Representation and complementarity, in combination with other performance assessment criteria, can inform the cost-effective design and stratification of future surveys. Based on these results, we formulate recommendations to assist with the design of future long-term coral reef monitoring programs.

Shifts in coralline algae, macroalgae, and coral juveniles in the Great Barrier Reef associated with present-day ocean acidification.

Seawater acidification from increasing CO2 is often enhanced in coastal waters due to elevated nutrients and sedimentation. Our understanding of the effects of ocean and coastal acidification on present-day ecosystems is limited. Here we use data from three independent large-scale reef monitoring programs to assess coral reef responses associated with changes in mean aragonite saturation state (Ωar ) in the Great Barrier Reef World Heritage Area (GBR). Spatial declines in mean Ωar are associated with monotonic declines in crustose coralline algae (up to 3.1-fold) and coral juvenile densities (1.3-fold), while non-calcifying macroalgae greatly increase (up to 3.2-fold), additionally to their natural changes across and along the GBR. These three key groups of organisms are important proxies for coral reef health. Our data suggest a tipping point at Ωar 3.5-3.6 for these coral reef health indicators. Suspended sediments acted as an additive stressor. The latter suggests that effective water quality management to reduce suspended sediments might locally and temporarily reduce the pressure from ocean acidification on these organisms.

Switching between standard coral reef benthic monitoring protocols is complicated: proof of concept.

Monitoring the state of coral reefs is necessary to identify drivers of change and assess effectiveness of management actions. There are several widely-used survey methods, each of which is likely to exhibit different biases that should be quantified if the purpose is to combine datasets obtained via different survey methods. The latter is a particularly important consideration when switching methodologies in long-term monitoring programs and is highly relevant to the Caribbean today. This is because of the continuing need for regionally comparable coral reef monitoring datasets and the fact that the Global Coral Reef Monitoring Network (GCRMN)-Caribbean node is now recommending a photoquadrat (PQ) method over the chain intercept transect method widely adopted by the members of the first truly regional monitoring network, Caribbean Coastal Marine Productivity Program (CARICOMP), in the early-1990s. Barbados, a member of the CARICOMP network, has been using a variation of the chain intercept method in its long-term coral reef monitoring program for more than two decades. Now a member of GCRMN-Caribbean, Barbados is considering switching to the PQ method in conformity with other regional members. Since we expect differences between methods, this study seeks to quantify the nature of those differences to inform Barbados and others considering switching methods. In 2017, both methods were concurrently implemented at 21 permanent monitoring plots across three major reef types in Barbados. Differences in % cover estimates for the six major benthic components, that is, hard corals, sponges, gorgonians, macroalgae, turf algae and crustose coralline algae, were examined within and among reef types. Overall, we found a complex pattern of differences between methods that depended on the benthic component, its relative abundance, and the reef type. We conclude that most benthic components would require a different conversion procedure depending on the reef type, and we provide an example of these procedures for Barbados. The factors that likely contribute to the complex pattern of between-method differences are discussed. Overall, our findings highlight that switching methods will be complicated, but not impossible. Finally, our study fills an important gap by underscoring a promising analytical framework to guide the comparison of ecological survey methods on coral reefs.

Oxidative stress biomarkers as potential tools in reef degradation monitoring: A study case in a South Atlantic reef under influence of the 2015–2016 El Niño/Southern Oscillation (ENSO)

Abstract The third global-scale coral bleaching event, triggered by the 2015–2016 El Nino, presented unprecedented levels of thermal stress and bleaching occurrence. Identification of potential cellular biomarkers in key reef species can greatly improve coral reef resource manager’s ability to make ecological forecasts and develop efficient mitigation strategies. In this context, the present study evaluated ecologically relevant biochemical parameters involved in thermal-stress response in two important reef building species of southwestern Atlantic Reefs – the scleractinian coral Mussismilia harttii and the hydrocoral Millepora alcicornis – aiming to assess their potential to forecast bleaching occurrence in corals/hydrocorals. Bleaching frequency, lipid peroxidation (LPO) and total antioxidant capacity (TAC), as well as thermal stress parameters (Degree Heating Weeks, DHW), were monitored during a six-month period in a reef area under influence of the 2015–2016 El Nino event. LPO is suggested as an informative, cost-effective and logical complement to reef monitoring programs; and TAC basal level as a potential measurement for predicting corals/hydrocorals susceptibility to bleaching. Further, results indicate M. alcicornis as a promising bioindicator in South Atlantic reefs. Findings presented here are expected to improve South Atlantic coral reef monitoring programs, as well as to contribute with potential biomarker-monitoring techniques to be used as additional tools in traditional reef monitoring programs worldwide. Further, observations on oxidative stress responses of a hydrocoral undergoing thermal stress conditions in the field are reported here for the first time.