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A ciliate belonging to theDiadema antillarumscuticociliatosis (DaSc)-associatedPhilasterclade (DaScPc) caused catastrophic long-spined urchin mass mortality in spring and summer of 2022. The ciliate can be grown in culture in both the presence and absence ofD. antillarumtissues, suggesting that it may persist outside its host by consuming microorganisms or dissolved organic nutrients. We hypothesized that DaScPc was present outside its host during and after mass mortality and absent prior to 2022. We examined DaScPc in DNA extracted from 500 swabs of sympatric metazoa and abiotic surfaces, and plankton samples, collected at 35 sites in the Caribbean in 2022 and 2023. DaScPc was detected on corals, turf algae, and a sponge, predominantly at sites with active or prior DaSc. We examined whether it was present prior to 2022 by surveying extracted DNA from Caribbean corals and water collected near corals by PCR and by mining publicly available transcriptomes and metagenomes for DaScPc rRNAs. These efforts yielded no DaScPc genes. We further hypothesized that DaScPc may recruit to the specific corals detected in field surveys, and that these may then infect naïve hosts. A mesocosm experiment to test DaScPc recruitment suggested that, while it recruited to corals, it did so inconsistently between coral species. Incubation of corals that recruited DaScPc with naïve urchins yielded inconclusive results since urchins died without characteristic DaSc signs. Overall, our results suggest that DaScPc may occur outside its urchin host, and that it may have been absent in the region prior to 2022. 

Coral reefs comprise some of the most biodiverse habitats on the planet. These ecosystems face a range of stressors, making quantifying community assemblages and potential changes vital to effective management. To understand short- and long-term changes in biodiversity and detect early warning signals of decline, new methods for quantifying biodiversity at scale are necessary. Acoustic monitoring techniques have proven useful in observing species activities and biodiversity on coral reefs through aggregate approaches (i.e. energy as a proxy). However, few studies have ground-truthed these acoustic analyses with human-based observations. In this study, we sought to expand these passive acoustic methods by investigating biological sounds and fish call rates on a healthy reef, providing a unique set of human-confirmed, labeled acoustic observations. We analyzed acoustic data from Tektite Reef, St. John, US Virgin Islands, over a 2 mo period. A subset of acoustic files was manually inspected to identify recurring biotic sounds and quantify reef activity throughout the day. We found a high variety of acoustic signals in this soundscape. General patterns of call rates across time conformed to expectations, with dusk and dawn showing important and significantly elevated peaks in soniferous fish activity. The data reflected high variability in call rates across days and lunar phases. Call rates did not correspond to sound pressure levels, suggesting that certain call types may drive crepuscular trends in sound levels while lower-level critical calls, likely key for estimating biodiversity and behavior, may be missed by gross sound level analyses. 

Seawater microorganisms play an important role in coral reef ecosystem functioning and can be influenced by biological, chemical, and physical features of reefs. As coral reefs continue to respond to environmental changes, the reef seawater microbiome has been proposed as a conservation tool for monitoring perturbations. However, the spatial variability of reef seawater microbial communities is not well studied, limiting our ability to make generalizable inferences across reefs. In order to better understand how microorganisms are distributed at multiple spatial scales, we examined seawater microbial communities in Florida Reef Tract and US Virgin Islands reef systems using a nested sampling design. On 3 reefs per reef system, we sampled seawater at regular spatial intervals close to the benthos. We assessed the microbial community composition of these waters using ribosomal RNA gene amplicon sequencing. Our analysis revealed that reef water microbial communities varied as a function of reef system and individual reefs, but communities did not differ within reefs and were not significantly influenced by benthic composition. For the reef system and inter-reef differences, abundant microbial taxa were found to be potentially useful indicators of environmental difference due to their high prevalence and variance. We further examined reef water microbial biogeography on a global scale using a secondary analysis of 5 studies, which revealed that microbial communities were more distinct with increasing geographic distance. These results suggest that biogeography is a distinguishing feature for reef water microbiomes, and that development of monitoring criteria may necessitate regionally specific sampling and analyses. 

Fish-associated microorganisms are known to be affected by the environment and other external factors, such as microbial transfer between interacting partners. One of the most iconic mutualistic interactions on coral reefs is the cleaning interactions between cleaner fishes and their clients, during which direct physical contact occurs. Here, we characterized the skin bacteria of the Caribbean cleaner sharknose goby, Elacatinus evelynae, in four coral reefs of the US Virgin Islands using sequencing of the V4 region of the 16S rRNA gene. We specifically tested the relationship between gobies’ level of interaction with clients and skin microbiota diversity and composition. Our results showed differences in microbial alpha- and beta-diversity in the skin of gobies from different reef habitats and high inter-individual variation in microbiota diversity and structure. Overall, the results showed that fish-to-fish direct contact and specifically, access to a diverse clientele, influences the bacterial diversity and structure of cleaner gobies’ skin. Because of their frequent contact with clients, and therefore, high potential for microbial exchange, cleaner fish may serve as models in future studies aiming to understand the role of social microbial transfer in reef fish communities. 

ABSTRACT Stony coral tissue loss disease (SCTLD) is decimating Caribbean corals. Here, through the metatranscriptomic assembly and annotation of two alphaflexivirus-like strains, we provide genomic evidence of filamentous viruses in SCTLD-affected, -exposed, and -unexposed coral colonies. These data will assist in clarifying the roles of viruses in SCTLD. 

In coral reefs and adjacent seagrass meadow and mangrove environments, short temporal scales (i.e. tidal, diurnal) may have important influences on ecosystem processes and community structure, but these scales are rarely investigated. This study examines how tidal and diurnal forcings influence pelagic microorganisms and nutrient dynamics in 3 important and adjacent coastal biomes: mangroves, coral reefs, and seagrass meadows. We sampled for microbial ( Bacteria and Archaea ) community composition, cell abundances and environmental parameters at 9 coastal sites on St. John, US Virgin Islands that spanned 4 km in distance (4 coral reefs, 2 seagrass meadows and 3 mangrove locations within 2 larger bays). Eight samplings occurred over a 48 h period, capturing day and night microbial dynamics over 2 tidal cycles. The seagrass and reef biomes exhibited relatively consistent environmental conditions and microbial community structure but were dominated by shifts in picocyanobacterial abundances that were most likely attributed to diel dynamics. In contrast, mangrove ecosystems exhibited substantial daily shifts in environmental parameters, heterotrophic cell abundances and microbial community structure that were consistent with the tidal cycle. Differential abundance analysis of mangrove-associated microorganisms revealed enrichment of pelagic oligotrophic taxa during high tide and enrichment of putative sediment-associated microbes during low tide. Our study underpins the importance of tidal and diurnal time scales in structuring coastal microbial and nutrient dynamics, with diel and tidal cycles contributing to a highly dynamic microbial environment in mangroves, and time of day likely contributing to microbial dynamics in seagrass and reef biomes. 

Microorganisms are central to the functioning of coral reef ecosystems, but their dynamics are unstudied on most reefs. We examined the microbial ecology of shallow reefs within the Federated States of Micronesia. We surveyed 20 reefs surrounding 7 islands and atolls (Yap, Woleai, Olimarao, Kosrae, Kapingamarangi, Nukuoro, and Pohnpei), spanning 875053 km 2 . On the reefs, we found consistently higher coral coverage (mean ± SD = 36.9 ± 22.2%; max 77%) compared to macroalgae coverage (15.2 ± 15.5%; max 58%), and low abundances of fish. Reef waters had low inorganic nutrient concentrations and were dominated by Synechococcus, Prochlorococcus, and SAR11 bacteria. The richness of bacterial and archaeal communities was significantly related to interactions between island/atoll and depth. High coral coverage on reefs was linked to higher relative abundances of Flavobacteriaceae, Leisingera, Owenweeksia, Vibrio, and the OM27 clade, as well as other heterotrophic bacterial groups, consistent with communities residing in waters near corals and within coral mucus. Microbial community structure at reef depth was significantly correlated with geographic distance, suggesting that island biogeography influences reef microbial communities. Reefs at Kosrae Island, which hosted the highest coral abundance and diversity, were unique compared to other locations; seawater from Kosrae reefs had the lowest organic carbon (59.8-67.9 µM), highest organic nitrogen (4.5-5.3 µM), and harbored consistent microbial communities (>85% similar), which were dominated by heterotrophic cells. This study suggests that the reef-water microbial ecology on Micronesian reefs is influenced by the density and diversity of corals as well as other biogeographical features.