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Amidst rapidly changing ocean soundscapes, research is still unraveling how marine animals use sound to communicate, detect predators, seek prey, and find suitable habitat. These vital behaviors may also be impacted by anthropogenic noise. Here, we describe a new tool, a Reef Acoustic Playback System, or RAPS, designed to be a cost-effective, extended-duration device that allows researchers to remotely and replay sound cues, manipulate soundscapes, and introduce “noise” into field-based experiments to address key questions regarding sound use or noise impacts within ocean ecology and conservation. The RAPS, outlined herein, has been deployed in the field for days to weeks, powered by renewable solar energy. The tool has been proven to be flexible in applications and robust to a range of ocean conditions. We outline the tool and describe several use cases, including use of the RAPS to replay healthy soundscapes to enhance the settlement of coral larvae, a fundamental ecological process sustaining coral reefs. Fundamentally, the RAPS is a new, potentially scalable means of supporting both healthy and imperiled reefs undergoing restoration, enhancing settlement of reef larvae, and broadening our ability to conduct a range of acoustic behavior studies. 

Acoustic enrichment can facilitate coral and fish larval settlement, offering a promising method to rebuild degraded reefs. Yet it is critical to understand sound propagation in complex shallow-water coral reefs to effectively apply this method over large restoration-scale areas. In this field-based study, we quantified propagation features of multiple sound types emitted through a custom playback system over varying coral reef habitat. Sound levels were computed at different distances from the source in both pressure and particle motion, the latter being detected by marine invertebrates. Detection distances were primarily determined by source levels, and depth-dependent transmission losses. Transmission losses and detection distances were similar for sound pressure and particle acceleration measurements. Importantly, broadband particle acceleration levels could be closely estimated at distances >10 m using a single hydrophone and a plane wave approximation. Using empirically determined coral larvae sound detection thresholds, we found that low frequency sounds (<1 kHz) such as fish calls from healthy coral reef soundscapes may be detectable by larvae hundreds of meters away. These results provide key data to help design standardized methods and protocols for scientists, managers and restoration practitioners aiming to rebuild coral reef ecosystems over reasonably large spatial scales using acoustic enrichment. 

The quantity of passive acoustic data collected in marine environments is rapidly expanding; however, the software developments required to meaningfully process large volumes of soundscape data have lagged behind. A significant bottleneck in the analysis of biological patterns in soundscape datasets is the human effort required to identify and annotate individual acoustic events, such as diverse and abundant fish sounds. This paper addresses this problem by training a YOLOv5 convolutional neural network (CNN) to automate the detection of tonal and pulsed fish calls in spectrogram data from five tropical coral reefs in the U.S. Virgin Islands, building from over 22 h of annotated data with 55 015 fish calls. The network identified fish calls with a mean average precision of up to 0.633, while processing data over 25× faster than it is recorded. We compare the CNN to human annotators on five datasets, including three used for training and two untrained reefs. CNN-detected call rates reflected baseline reef fish and coral cover observations; and both expected biological (e.g., crepuscular choruses) and novel call patterns were identified. Given the importance of reef-fish communities, their bioacoustic patterns, and the impending biodiversity crisis, these results provide a vital and scalable means to assess reef community health. 

Reef-building corals contain a complex consortium of organisms, a holobiont, which responds dynamically to disease, making pathogen identification difficult. While coral transcriptomics and microbiome communities have previously been characterized, similarities and differences in their responses to different pathogenic sources has not yet been assessed. In this study, we inoculated four genets of the Caribbean branching coral Acropora palmata with a known coral pathogen ( Serratia marcescens ) and white band disease. We then characterized the coral’s transcriptomic and prokaryotic microbiomes’ (prokaryiome) responses to the disease inoculations, as well as how these responses were affected by a short-term heat stress prior to disease inoculation. We found strong commonality in both the transcriptomic and prokaryiomes responses, regardless of disease inoculation. Differences, however, were observed between inoculated corals that either remained healthy or developed active disease signs. Transcriptomic co-expression analysis identified that corals inoculated with disease increased gene expression of immune, wound healing, and fatty acid metabolic processes. Co-abundance analysis of the prokaryiome identified sets of both healthy-and-disease-state bacteria, while co-expression analysis of the prokaryiomes’ inferred metagenomic function revealed infected corals’ prokaryiomes shifted from free-living to biofilm states, as well as increasing metabolic processes. The short-term heat stress did not increase disease susceptibility for any of the four genets with any of the disease inoculations, and there was only a weak effect captured in the coral hosts’ transcriptomic and prokaryiomes response. Genet identity, however, was a major driver of the transcriptomic variance, primarily due to differences in baseline immune gene expression. Despite genotypic differences in baseline gene expression, we have identified a common response for components of the coral holobiont to different disease inoculations. This work has identified genes and prokaryiome members that can be focused on for future coral disease work, specifically, putative disease diagnostic tools. 

Once one of the predominant reef-building corals in the region,Acropora cervicornisis now a focal species of coral restoration efforts in Florida and the western Caribbean. Scientists and restoration practitioners have been independently collecting phenotypic data on genets ofA. cervicornisgrown in restoration nurseries. While these data are important for understanding the intraspecific response to varying environmental conditions, and thus the potential genetic contribution to phenotypic variation, in isolation these observations are of limited use for large-scale, multi- institution restoration efforts that are becoming increasingly necessary. Here, we present theAcropora cervicornisData Coordination Hub, a web-accessible relational database to align disparate datasets to compare genet-specific performance. In this data descriptor, we release data for 248 genets evaluated across 38 separate traits. We present a framework to align datasets with the ultimate goal of facilitating informed, data-driven restoration throughout the Caribbean.