A doubling of stony coral cover on shallow forereefs at Carrie Bow Cay, Belize from 2014 to 2019.

To better understand the decline of one of earth's most biodiverse habitats, coral reefs, many survey programs employ regular photographs of the benthos. An emerging challenge is the time required to annotate the large volume of digital imagery generated by these surveys. Here, we leverage existing machine-learning tools (CoralNet) and develop new fit-to-purpose programs to process and score benthic photoquadrats using five years of data from the Smithsonian MarineGEO Network's biodiversity monitoring program at Carrie Bow Cay, Belize. Our analysis shows that scleractinian coral cover on forereef sites (at depths of 3-10 m) along our surveyed transects increased significantly from 6 to 13% during this period. More modest changes in macroalgae, turf algae, and sponge cover were also observed. Community-wide analysis confirmed a significant shift in benthic structure, and follow-up in situ surveys of coral demographics in 2019 revealed that the emerging coral communities are dominated by fast-recruiting and growing coral species belonging to the genera Agaricia and Porites. While the positive trajectory reported here is promising, Belizean reefs face persistent challenges related to overfishing and climate change. Open-source computational toolkits offer promise for increasing the efficiency of reef monitoring, and therefore our ability to assess the future of coral reefs in the face of rapid environmental change.

Environmental DNA survey captures patterns of fish and invertebrate diversity across a tropical seascape.

Accurate, rapid, and comprehensive biodiversity assessments are critical for investigating ecological processes and supporting conservation efforts. Environmental DNA (eDNA) surveys show promise as a way to effectively characterize fine-scale patterns of community composition. We tested whether a single PCR survey of eDNA in seawater using a broad metazoan primer could identify differences in community composition between five adjacent habitats at 19 sites across a tropical Caribbean bay in Panama. We paired this effort with visual fish surveys to compare methods for a conspicuous taxonomic group. eDNA revealed a tremendous diversity of animals (8,586 operational taxonomic units), including many small taxa that would be undetected in traditional in situ surveys. Fish comprised only 0.07% of the taxa detected by a broad COI primer, yet included 43 species not observed in the visual survey. eDNA revealed significant differences in fish and invertebrate community composition across adjacent habitats and areas of the bay driven in part by taxa known to be habitat-specialists or tolerant to wave action. Our results demonstrate the ability of broad eDNA surveys to identify biodiversity patterns in the ocean.

The importance of sponges and mangroves in supporting fish communities on degraded coral reefs in Caribbean Panama.

Fish communities associated with coral reefs worldwide are threatened by habitat degradation and overexploitation. We assessed coral reefs, mangrove fringes, and seagrass meadows on the Caribbean coast of Panama to explore the influences of their proximity to one another, habitat cover, and environmental characteristics in sustaining biomass, species richness and trophic structure of fish communities in a degraded tropical ecosystem. We found 94% of all fish across all habitat types were of small body size (≤10 cm), with communities dominated by fishes that usually live in habitats of low complexity, such as Pomacentridae (damselfishes) and Gobiidae (gobies). Total fish biomass was very low, with the trend of small fishes from low trophic levels over-represented, and top predators under-represented, relative to coral reefs elsewhere in the Caribbean. For example, herbivorous fishes comprised 27% of total fish biomass in Panama relative to 10% in the wider Caribbean, and the small parrotfish Scarus iseri comprised 72% of the parrotfish biomass. We found evidence that non-coral biogenic habitats support reef-associated fish communities. In particular, the abundance of sponges on a given reef and proximity of mangroves were found to be important positive correlates of reef fish species richness, biomass, abundance and trophic structure. Our study indicates that a diverse fish community can persist on degraded coral reefs, and that the availability and arrangement within the seascape of other habitat-forming organisms, including sponges and mangroves, is critical to the maintenance of functional processes in such ecosystems.

Tropical dead zones and mass mortalities on coral reefs.

Degradation of coastal water quality in the form of low dissolved oxygen levels (hypoxia) can harm biodiversity, ecosystem function, and human wellbeing. Extreme hypoxic conditions along the coast, leading to what are often referred to as "dead zones," are known primarily from temperate regions. However, little is known about the potential threat of hypoxia in the tropics, even though the known risk factors, including eutrophication and elevated temperatures, are common. Here we document an unprecedented hypoxic event on the Caribbean coast of Panama and assess the risk of dead zones to coral reefs worldwide. The event caused coral bleaching and massive mortality of corals and other reef-associated organisms, but observed shifts in community structure combined with laboratory experiments revealed that not all coral species are equally sensitive to hypoxia. Analyses of global databases showed that coral reefs are associated with more than half of the known tropical dead zones worldwide, with >10% of all coral reefs at elevated risk for hypoxia based on local and global risk factors. Hypoxic events in the tropics and associated mortality events have likely been underreported, perhaps by an order of magnitude, because of the lack of local scientific capacity for their detection. Monitoring and management plans for coral reef resilience should incorporate the growing threat of coastal hypoxia and include support for increased detection and research capacity.

Assessing the ecological effects of human impacts on coral reefs in Bocas del Toro, Panama.

Environmental and biological reef monitoring was conducted in Almirante Bay (Bahía Almirante) in Bocas del Toro, Panama, to assess impacts from anthropogenic developments. An integrated monitoring investigated how seasonal temperature stress, turbidity, eutrophication and physical impacts threatened reef health and biodiversity throughout the region. Environmental parameters such as total suspended solids [TSS], carbon isotopes (δ(13)C), C/N ratios, chlorophyll a, irradiance, secchi depth, size fractions of the sediments and isotope composition of dissolved inorganic carbon [DIC] of the water were measured throughout the years 2010 and 2011 and were analysed in order to identify different impact sources. Compared to data from Collin et al. (Smithsonian Contributions to the Marine Sciences 38:324-334, 2009) chlorophyll a has doubled at sites close to the city and the port Almirante (from 0.46-0.49 to 0.78-0.97 µg l(-1)) and suspension load increased, visible by a decrease in secchi depth values. Visibility decreased from 9-13 m down to 4 m at the bay inlet Boca del Drago, which is strongly exposed to river run off and dredging for the shipping traffic. Eutrophication and turbidity levels seemed to be the determining factor for the loss of hard coral diversity, most significant at chlorophyll a levels higher than 0.5 µg l(-1) and TSS levels higher than 4.7 mg l(-1). Hard coral cover within the bay has also declined, at some sites down to <10 % with extremely low diversities (7 hard coral species). The hard coral species Porites furcata dominated the reefs in highly impacted areas and showed a strong recovery after bleaching and a higher tolerance to turbidity and eutrophication compared to other hard coral species in the bay. Serious overfishing was detected in the region by a lack of adult and carnivorous fish species, such as grunts, snappers and groupers. Study sites less impacted by anthropogenic activities and/or those with local protection showed a higher hard coral cover and fish abundance; however, an overall loss of hard coral diversity was observed.

Sources and spatial distribution of heavy metals in scleractinian coral tissues and sediments from the Bocas del Toro Archipelago, Panama.

Marine ecosystems worldwide are threatened by aquatic pollution; however, there is a paucity in data from the Caribbean region. As such, five heavy metals (arsenic, cadmium, copper, zinc, mercury) were measured in tissues of the scleractinian corals Porites furcata and Agaricia tenuifolia and in adjacent sediments in the Bocas del Toro Archipelago, Panama. Samples were collected from five reef sites along a gradient of distance from an international shipping port and were analysed using inductively coupled plasma optical emission spectrometry and atomic absorption spectrophotometry for mercury. Copper and zinc were the most abundant metals and ranged from 11 to 63 mg kg(-1) and from 31 to 185 mg kg(-1) in coral tissues, respectively. The highest concentration of each metal was measured in P. furcata tissues, with copper and mercury concentrations significantly higher in P. furcata than in A. tenuifolia at every site. These results suggest that P. furcata has a higher affinity for metal accumulation and storage than A. tenuifolia. With the exception of cadmium, metal concentrations in coral tissues were generally elevated at coral reefs in closer proximity to the port; however, this pattern was not observed in sediments. Hard coral cover was lowest at reefs in closest proximity to the port, suggesting that metal pollution from port-related activities is influencing hard coral abundance at nearby coral reefs.