Brian Keith Walker

Spatially-integrated marine benthic data provide the foundation for effective spatial decision-support tools that address critical issues in marine and coastal systems. However, the diversity of benthic data types and forms often presents challenges for proper data integration. Without common standards, these data cannot be easily integrated and reused. Here, we proposed standards for data collection, processing, archiving, and publication, as well as metadata standards, for various types of commonly integrated marine data (i.e., bathymetric, backscatter, biological, chemical, geological, and physical oceanographic data). The standards are aimed at Florida data producers and users and, as a result, leverage existing state, regional, and national infrastructure. The standards recommendations were shared with the Florida-based stakeholder community to quantify the overall level of agreement, the likelihood of their widespread adoption, and the types of tools needed to increase that likelihood. Overall, the Florida community reported varying but positive agreement with the recommended standards and expressed willingness to adopt them, on the condition that easy-to-use tools and comprehensive documentation are provided to facilitate the implementation. We also found that while relatively few individuals or organizations establish standards themselves, most researchers and users are willing to adopt recommended practices when they are easy and efficient to implement. In an era where scientific data are digitally processed and archived, scientists must foster a culture that consistently shares data, workflows, and use cases. However, this requires tools and accessible resources to facilitate the broader adoption of standards within the scientific community.

Stony coral tissue loss disease (SCTLD) is widespread within the Caribbean and affects at least 22 species of reef-building coral. Bacteria have been implicated in the etiology of SCTLD, but the community of bacteria and archaea may also contribute to SCTLD resistance. To identify potential mechanisms through which microbes contribute to SCTLD resistance, we sequenced metagenomes from 41 colonies of the threatened coral, Orbicella faveolata, in the lower Florida Keys. All colonies were fate-tracked for 4 to 5 years, treated with amoxicillin if needed to prevent SCTLD-related mortality, and categorized into 4 health status categories following the monitoring period: never diseased (20%), diseased before sampling but recovered (10%), apparently healthy during sampling but eventually diseased (22%), and diseased (49%). Within the coral microbiome, diseased and yet-to-be diseased colonies exhibited higher variability in functional genes. In contrast, corals that remained unaffected or recovered had less variable microbiomes with greater abundances of vitamin and antibiotic biosynthesis, secretion system, and quorum-sensing genes that may support host health and resilience to pathogens. Despite repeated antibiotic treatments on some colonies, there was no effect on the diversity of beta-lactamases, antibiotic resistance genes that may confer amoxicillin resistance. Additional potentially probiotic gene clusters for the production of antimicrobial and bioactive compounds were present in many colonies regardless of fate. Taken together, we find significant putative probiotic functions in the coral microbiome to armor host O. faveolata corals against SCTLD infection, which may underpin intraspecific variation in stony coral tissue loss disease resilience and susceptibility.

Stony coral tissue loss disease (SCTLD) is widespread within the Caribbean and affects at least 22 species of reef-building coral. Bacteria have been implicated in the etiology of SCTLD, but the community of bacteria and archaea may also contribute to SCTLD resistance. To identify potential mechanisms through which microbes contribute to SCTLD resistance, we sequenced metagenomes from 41 colonies of the threatened coral, Orbicella faveolata, in the lower Florida Keys. All colonies were fate-tracked for three to five years and disease lesions were treated with amoxicillin. By 2024, 20% were never diseased, 10% had lesions before sampling but recovered, 22% were apparently healthy but were eventually susceptible to infection, and 49% had regular repeated infections. Within the coral microbiome, diseased and yet-to-be diseased colonies exhibited higher variability in functional genes. In contrast, corals that remained unaffected or recovered had less variable microbiomes with greater abundances of vitamin and antibiotic biosynthesis, secretion system, and quorum sensing genes that may support host health and resilience to pathogens. Though on some colonies antibiotic treatments were applied repeatedly, there was no effect on the diversity of beta-lactamases, antibiotic resistance genes that may confer amoxicillin resistance. Additional potentially probiotic gene clusters for the production of antimicrobial and bioactive compounds were present in many colonies regardless of fate. Taken together, we find significant probiotic potential in the coral microbiome to armor host O. faveolata corals against SCTLD infection, which may underpin intraspecific variation in stony coral tissue loss disease resilience and susceptibility.

Nearshore declines in water quality are potentially exacerbating the negative impacts of climate change-induced ocean warming on many coastal coral reefs. While the relationship between...

The Anthropocene rise in global temperatures is facilitating the expansion of tropical species into historically non-native subtropical locales, including coral reef fish. This redistribution of species, known as tropicalization, has serious consequences for economic development, livelihoods, food security, human health, and culture. Measuring the tropicalization of subtropical reef fish assemblages is difficult due to expansive species ranges, temporal distribution shifts with the movement of isotherms, and many dynamic density-dependent factors affecting occurrence and density. Therefore, in locales where tropical and subtropical species co-occur, detecting tropicalization changes relies on regional analyses of the relative densities and occurrence of species. This study provides a baseline for monitoring reef fish tropicalization by utilizing extensive monitoring data from a pivotal location in southeast Florida along a known transition between tropical and subtropical ecotones to define regional reef fish assemblages and use benthic habitat maps to spatially represent their zoogeography. Assemblages varied significantly by ecoregion, habitat depth, habitat type, and topographic relief. Generally, the southern assemblages had higher occurrences and densities of tropical species, whereas the northern assemblages had a higher occurrence and density of subtropical species. A total of 108 species were exclusive to regions south of the Bahamas Fracture Zone (BFZ) (South Palm Beach, Deerfield, Broward-Miami) and 35 were exclusive to the north (North Palm Beach, Martin), supporting the BFZ as a pivotal location that affects the coastal biogeographic extent of tropical marine species in eastern North America. Future tropicalization of reef fish assemblages are expected to be evident in temporal deviance of percent occurrence and/or relative species densities between baseline assemblages, where the poleward expansion of tropical species is expected to show the homogenization of assemblage regions as adjacent regions become more similar or the regional boundaries expand poleward. Ecoregions, habitat depth, habitat type, and relief should be incorporated into the stratification and analyses of reef fish surveys to statistically determine assemblage differences across the seascape, including those from tropicalization.

Climate change, overfishing, and pollution have driven changes in the composition of many extant reef fish assemblages. As global temperatures rise, historically temperate locales are becoming inhabited by vagrant tropical species as their ranges expand poleward in a process known as tropicalization. Severe reef fish biomass declines are predicted by 2100 under high ocean warming scenarios. This redistribution of species has serious consequences for economic development, livelihoods, food security, human health and culture. Determining the tropicalization of Western Atlantic reef fish is challenging because ranges are expansive, their distributions temporally shift with the movement of isotherms, and many dynamic density-dependent factors affect occurrence and density. Since fish assemblages are known to vary with depth, habitat type, topography, and regionality and local benthic habitat map classifications include these descriptors in their scheme, we used benthic habitat maps to spatially represent the zoogeography of regional reef fish assemblages. The outcomes illustrate that the southeast Florida coast is a pivotal location in the transition between tropical and temperate marine fauna for North America driven by geology and Florida Current upwelling dynamics. The southern assemblages had a higher occurrence and density of tropical species, whereas the northern assemblages had a higher occurrence and density of temperate species. Delineating the spatial distribution of reef fish assemblages facilitates monitoring and detection of future poleward tropicalization, as will be evident in temporal changes in percent occurrence, assemblage relative abundance, and the homogenization of assemblage regions. These delineations contextualize restoration expectations and success by providing a spatial reference to focus conservation actions based on expectations from natural environmental variability, especially in transitional areas between ecoregions.

Stony coral tissue loss disease (SCTLD) has persisted since 2014 in the Southeast Florida Coral Reef Ecosystem Conservation Area (Coral ECA) where it was first discovered. Most of the highly susceptible corals have perished, leaving Montastraea cavernosa as the most abundant reef-building species with high SCTLD prevalence. Disease interventions (DI) have been conducted throughout Florida’s Coral Reef to save the remaining corals and reduce the disease prevalence with varying degrees of success. The two main treatments were chlorinated (Chl) epoxy and an antibiotic paste. The antibiotic paste was highly effective in the Florida Keys, but its effectiveness in the Coral ECA was questionable. Therefore, we compared the effectiveness of the antibiotic paste and Chl epoxy treatments on M. cavernosa to optimize DI efforts on this species in the Coral ECA. Significant differences were found between the treatment materials and applications related to the proportion of quiesced lesions and corals where antibiotic paste (91.2% success) outperformed Chl epoxy (20% success). By day 351, 50.6% of the antibiotic paste disease-break tissue was fully healed compared to 2.2% of the total Chl epoxy-filled disease-break area. During the study, new lesions occurred on previously treated colonies, as well as colonies not previously treated and new lesion rates varied through time, indicating revisitation is necessary to eliminate disease. Most margin treatments failed within the first 9 days, however, most disease-breaks failed before 44 days. Considering the high treatment success of the antibiotic paste and the conditional variation of new lesion rates, about 1 month is a good practical re-visitation time for retreating failures and any new lesions. DI using antibiotic paste is currently the most effective way to intervene the SCTLD epidemic, but this is only effective as a stopgap measure while the larger causative agents are identified and remediated. Conducting DI at a reef-scape scale is time consuming and requires extensive person-power and resources, making it very expensive. But this expense pales in comparison to the current cost to restore the diversity and live tissue saved with DI. This method also comes with the risk of introducing antibiotics into coral reef environments, which may have unintended outcomes.

Florida’s west coast is a 170,000 km² bedrock shelf (west Florida shelf, WFS) comprised of north-south discontinuous carbonate outcroppings extending more than 200 km from the intertidal zone to a depth of 200 m. These outcrops support diverse benthic communities, which contribute to a multi-billion dollar recreational and commercial fishing industry, yet only about 5% of their extent has been studied in detail. Benthic communities shift over a 6.5° geographic range, but the locations of these shifts are not well-defined. Previous studies have suggested a break in biogeographic regions at Tampa Bay, south at Cape Romano, and north at Cedar Key. The goal of this study was to map and investigate the shallow WFS marine hardbottom north and south of Tampa Bay, FL to identify differences in benthic communities and identify ecoregion boundaries. Habitat mapping yielded 295.89 km² of hardbottom which differed in extent between Sarasota and Pasco counties. Benthic surveys tabulated 4,079 stony coral colonies of nine species and 1,918 soft corals. Stony corals were dominated by Siderastrea radians, Oculina robusta, Solenastrea hyades, and Cladocora arbuscula less than 10 cm in diameter. Distinct differences in these communities were evident from south to north. The main community shift indicated an ecoregion boundary at, or very near, the mouth of Tampa Bay. Another shift associated with the Bahamas Fracture Zone (BFZ) occurred at the Pinellas and Pasco County border. The outputs of this work provide the first detailed benthic habitat map of the area, a detailed survey of the composition of hardbottom benthic communities in the region, identify Tampa Bay as a coastal benthic biogeographic transition, and illustrate the influence of the BFZ on coastal communities. These findings illustrate a need for additional WFS benthic research and mapping to give a more comprehensive understanding of coral community biogeography in the context of future warming conditions and the potential tropicalization. Unifying seafloor mapping data, mapping new areas with high probability of hardbottom resources, and collecting benthic community data over broader scales will refine community biogeographic zonation. This is a necessary precursor to any long-term community monitoring to detect spatial shifts in communities and population modeling.