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Abstract Stony coral tissue loss disease (SCTLD) has been causing significant whole colony mortality on reefs in Florida and the Caribbean. The cause of SCTLD remains unknown, with the limited concurrence of SCTLD-associated bacteria among studies. We conducted a meta-analysis of 16S ribosomal RNA gene datasets generated by 16 field and laboratory SCTLD studies to find consistent bacteria associated with SCTLD across disease zones (vulnerable, endemic, and epidemic), coral species, coral compartments (mucus, tissue, and skeleton), and colony health states (apparently healthy colony tissue (AH), and unaffected (DU) and lesion (DL) tissue from diseased colonies). We also evaluated bacteria in seawater and sediment, which may be sources of SCTLD transmission. Although AH colonies in endemic and epidemic zones harbor bacteria associated with SCTLD lesions, and aquaria and field samples had distinct microbial compositions, there were still clear differences in the microbial composition among AH, DU, and DL in the combined dataset. Alpha-diversity between AH and DL was not different; however, DU showed increased alpha-diversity compared to AH, indicating that, prior to lesion formation, corals may undergo a disturbance to the microbiome. This disturbance may be driven by Flavobacteriales, which were especially enriched in DU. In DL, Rhodobacterales and Peptostreptococcales–Tissierellales were prominent in structuring microbial interactions. We also predict an enrichment of an alpha-toxin in DL samples which is typically found in Clostridia. We provide a consensus of SCTLD-associated bacteria prior to and during lesion formation and identify how these taxa vary across studies, coral species, coral compartments, seawater, and sediment.

IntroductionThough bacterial pathogens and parasites can compromise coral health, coral microbiome research increasingly suggests a beneficial role for bacterial species living in coral tissue and mucus. Recent studies suggest the application of targeted antibiotic treatments, while inhibiting the growth of harmful bacteria, may have unintended and persistent impacts on coral health. Land-based coral nurseries use antiseptic treatments such as Lugol’s solution and KoralMD™ dip to reduce infectious agents as part of restoration best practices. These antiseptic treatments often halt tissue loss, but the short- or long-term effects of these treatments on the coral microbiome is unknown.MethodsWe conducted a controlled tank experiment to assess the effects of these broad-spectrum treatments on coral growth rates and microbial communities when used as a prophylactic measure on healthy corals. Sixty individuals from each of two genotypes of the coral species Acropora palmata and Orbicella faveolata were treated with either Lugol’s solution or KoralMD™. Coral tissue, mucus, and skeleton were sampled pre-treatment, during treatment, and 1 and 2 months after treatment to assess microbiome shifts and recovery. The impact of the two treatments on coral growth was assessed using surface area measurements from 3D imagery.ResultsAlthough we found that A. palmata treated with Lugol’s solution had significantly reduced growth rates compared with untreated controls, impacts of antiseptic treatment were otherwise limited and microbiomes were not significantly different by treatment either immediately after application or 2 months thereafter. DiscussionStudy of the effects of these widely-used interventions may have significant repercussions on management and propagation strategies for corals reared in land-based nurseries. Furthermore, our findings indicate that antiseptic treatments can be applied to mitigate coral health issues without long-term harmful effects or significant microbiome shifts.

Effective coral restoration must include comprehensive investigations of the targeted coral community that consider all aspects of the coral holobiont—the coral host, symbiotic algae, and microbiome. For example, the richness and composition of microorganisms associated with corals may be indicative of the corals’ health status and thus help guide restoration activities. Potential differences in microbiomes of restoration corals due to differences in host genetics, environmental condition, or geographic location, may then influence outplant success. The objective of the present study was to characterize and compare the microbiomes of apparently healthy Acropora cervicornis genotypes that were originally collected from environmentally distinct regions of Florida’s Coral Reef and sampled after residing within Mote Marine Laboratory’s in situ nursery near Looe Key, FL (USA) for multiple years. By using 16S rRNA high-throughput sequencing, we described the microbial communities of 74 A. cervicornis genotypes originating from the Lower Florida Keys (n = 40 genotypes), the Middle Florida Keys (n = 15 genotypes), and the Upper Florida Keys (n = 19 genotypes). Our findings demonstrated that the bacterial communities of A. cervicornis originating from the Lower Keys were significantly different from the bacterial communities of those originating from the Upper and Middle Keys even after these corals were held within the same common garden nursery for an average of 3.4 years. However, the bacterial communities of corals originating in the Upper Keys were not significantly different from those in the Middle Keys. The majority of the genotypes, regardless of collection region, were dominated by Alphaproteobacteria, namely an obligate intracellular parasite of the genus Ca. Aquarickettsia. Genotypes from the Upper and Middle Keys also had high relative abundances of Spirochaeta bacteria. Several genotypes originating from both the Lower and Upper Keys had lower abundances of Aquarickettsia, resulting in significantly higher species richness and diversity. Low abundance of Aquarickettsia has been previously identified as a signature of disease resistance. While the low-Aquarickettsia corals from both the Upper and Lower Keys had high abundances of an unclassified Proteobacteria, the genotypes in the Upper Keys were also dominated by Spirochaeta. The results of this study suggest that the abundance of Aquarickettsia and Spirochaeta may play an important role in distinguishing bacterial communities among A. cervicornis populations and compositional differences of these bacterial communities may be driven by regional processes that are influenced by both the environmental history and genetic relatedness of the host. Additionally, the high microbial diversity of low-Aquarickettsia genotypes may provide resilience to their hosts, and these genotypes may be a potential resource for restoration practices and management.

The epizootic disease outbreak known as stony coral tissue loss disease (SCTLD) is arguably the most devastating coral disease in recorded history. SCTLD emerged off the coast of South Florida in 2014 and has since moved into the Caribbean, resulting in coral mortality rates that have changed reef structure and function. Currently, the cause of SCTLD is unknown, but there is evidence from 16S rRNA gene sequencing and bacterial culture studies that the microbial community plays a role in the progression of SCTLD lesions. In this study, we applied shotgun metagenomics to characterize the potential function of bacteria, as well as the composition of the micro-eukaryotic community, associated with SCTLD lesions. We re-examined samples that were previously analyzed using 16S rRNA gene high-throughput sequencing from four coral species: Stephanocoenia intersepta, Diploria labyrinthiformis, Dichocoenia stokesii, and Meandrina meandrites. For each species, tissue from apparently healthy (AH) corals, and unaffected tissue (DU) and lesion tissue (DL) on diseased corals, were collected from sites within the epidemic zone of SCTLD in the Florida Keys. Within the micro-eukaryotic community, the taxa most prominently enriched in DL compared to AH and DU tissue were members of Ciliophora. We also found that DL samples were relatively more abundant in less energy-efficient pathways like the pentose phosphate pathways. While less energy-efficient processes were identified, there were also relatively higher abundances of nucleotide biosynthesis and peptidoglycan maturation pathways in diseased corals compared to AH, which suggests there was more bacteria growth in diseased colonies. In addition, we generated 16 metagenome-assembled genomes (MAGs) belonging to the orders Pseudomonadales, Beggiatoales, Rhodobacterales, Rhizobiales, Rs-D84, Flavobacteriales, and Campylobacterales, and all MAGs were enriched in DL samples compared to AH samples. Across all MAGs there were antibiotic resistance genes that may have implications for the treatment of SCTLD with antibiotics. We also identified genes and pathways linked to virulence, such as nucleotide biosynthesis, succinate dehydrogenase, ureases, nickel/iron transporters, Type-1 secretion system, and metalloproteases. Some of these enzymes/pathways have been previously targeted in the treatment of other bacterial diseases and they may be of interest to mitigate SCTLD lesion progression.

Infectious disease outbreaks are a primary contributor to coral reef decline worldwide. A particularly lethal disease, black band disease (BBD), was one of the first coral diseases reported and has since been documented on reefs worldwide. BBD is described as a microbial consortium of photosynthetic cyanobacteria, sulfate-reducing and sulfide-oxidizing bacteria, and heterotrophic bacteria and archaea. The disease is visually identified by a characteristic dark band that moves across apparently healthy coral tissue leaving behind bare skeleton. Despite its virulence, attempts to effectively treat corals with BBD in the field have been limited. Here, we developed and tested several different therapeutic agents on Pseudodiploria spp. corals with signs of active BBD at Buck Island Reef National Monument in St. Croix, USVI. A variety of therapies were tested, including hydrogen peroxide-based treatments, ointment containing antibiotics, and antiviral/antimicrobial-based ointments (referred to as CoralCure). The CoralCure ointments, created by Ocean Alchemists LLC, focused on the dosing regimen and delivery mechanisms of the different active ingredients. Active ingredients included carbamide peroxide, Lugol's iodine solution, along with several proprietary essential oil and natural product blends. Additionally, the active ingredients had different release times based on treatment: CoralCure A-C had a release time of 24 hours, CoralCure D-F had a release time of 72 hours. The ointments were applied directly to the BBD lesion. Also, jute rope was saturated with a subset of these CoralCure ointment formulations to assist with adhesion. These ropes were then applied to the leading edge of the BBD lesion for one week to ensure sufficient exposure. Corals were revisited approximately three to five months after treatment application to assess disease progression rates and the presence/absence of lesions-the metrics used to quantify the efficacy of each treatment. Although most of the treatments were unsuccessful, two CoralCure rope formulations-CoralCure D rope and CoralCure E rope, eliminated the appearance of BBD in 100% of the corals treated. As such, these treatments significantly reduced the likelihood of BBD occurrence compared to the untreated controls. Additionally, lesions treated with these formulations lost significantly less tissue compared with controls. These results provide the mechanisms for an easily employable method to effectively treat a worldwide coral disease.