Biology subjects

Neely, K. L.

Publications and source records attributed to Neely, K. L..

9 recordsLinked to original sources

bioRxiv2025

Markers of resilience to stony coral tissue loss disease and probiotic potential in the microbiome of the threatened coral, Orbicella faveolata

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.

microbiology↗

bioRxiv2025

Multidisciplinary assessments of a potentially novel acute tissue loss disease on Florida Orbicella corals

Coral disease outbreaks are an increasingly common threat to reefs. While coral disease research is expanding rapidly, there are still monumental challenges in diagnosing and differentiating among the different diseases on a reef. We used a collaborative multidisciplinary approach to characterize a potentially novel disease affecting Orbicella faveolata colonies in the Florida Keys. We tagged and fate-tracked individual lesions for progression and cessation rates, reanalyzed in situ photographs of previously monitored corals to determine prevalence and seasonality, and assessed the efficacy of amoxicillin treatments. Samples collected from lesions as well as unaffected and healthy controls were used to examine microbiomes, assess nine coral pathological parameters via histology, and measure 19 symbiont-specific physiological metrics using transmission electron microscopy (TEM). Across all analyses, we concluded that the observed disease is unlikely to be SCTLD. Many, but not all, metrics had similarities to previous descriptions of white plague, and so we additionally conducted preliminary histology on presumed white plague samples of O. franksi for comparison. However, the dearth of quantifiable histology and TEM studies on white plague did not allow us to conclusively confirm or refute comparisons to white plague. Using the recommended coral disease nomenclature, we define this specific outbreak as "Orbicella acute tissue loss disease" (OATLD). We provide unprecedented, quantified descriptions across numerous metrics of both diseased and control colonies. We suggest that these data lay the groundwork for future efforts on this disease as well as a comprehensive set of parameters against which other diseases can be compared.

physiology↗

bioRxiv2025

Status of Florida's pillar coral population: in situ declines and ex situ successes

The population of the pillar coral, Dendrogyra cylindrus, in Florida was decimated from 2013-2020, primarily by the emergence of stony coral tissue loss disease (SCTLD). Monitoring of survivors from 2021 - early 2025 showed that the population underwent an additional 96% decline in live tissue, 78% loss in living colonies, and 57% loss of genotypes. SCTLD continued to be the primary cause of these losses. Though some surviving tissue isolates exhibited small amounts of growth, the population remains extremely small, with only an estimated 9.6 square meters of tissue remaining on 23 colonies (15 genotypes). Additionally, colonies are far too dispersed to successfully fertilize spawned gametes. The further declines in the population since 2020 highlight the instability of the remnant population, as well as the value of the pillar coral rescue program and ongoing propagation efforts. As of February 2025, eight different in situ and ex situ facilities were caring for rescued D. cylindrus. Experimental fragmentation at one in situ nursery identified variable, but continually increasing, growth rates across multiple fragmentation events. Sexual propagation efforts at an ex situ nursery documented 105 different rescue fragments spawning across five years. The smallest fragment was 9 x 7 x 9 cm, establishing a potential "minimum colony size" for reproductive capacity for this species. From these spawning events, 82 juveniles were being raised ex situ in early 2025. Two of these sexually propagated juveniles spawned six years after settlement, thus establishing a potential minimum age for reproduction.

ecology↗

bioRxiv2025

Survival and reinfection rates of SCTLD-affected corals treated in situ with amoxicillin

The unprecedented mortality to Caribbean corals caused by stony coral tissue loss disease (SCTLD) led to the use of an in-water medicine applied directly to disease lesions. This topical amoxicillin paste is highly effective in halting lesions and has been used on tens of thousands of wild corals since 2019, but long-term survival rates of treated corals as well as the frequency of potential reinfections remained speculative. We fate-tracked thousands of corals treated for SCTLD in the Florida Keys across numerous species and two habitats (inshore patch reefs and offshore spur and groove) every two months, assessing health condition and providing additional treatments if necessary. After three years, 84% of corals remained alive. Inshore corals had higher survival rates than offshore corals, and there were species-specific differences in survival, with the boulder corals Montastraea cavernosa and Orbicella faveolata having higher survivorship than brain coral species. Across all treated corals, 36% remained disease-free for at least one year after the initial treatment, and an additional 18% remained disease-free if any new lesions were treated within three months after the initial treatment. Reinfection rates were influenced by both habitat and species, with inshore corals more likely to remain disease-free than offshore corals. Among the species assessed, Montastraea cavernosa was the most likely to remain disease free, while the brain corals Diploria labyrinthiformis and Colpophyllia natans were the most prone to reinfection. These measurements can help guide expectations for disease intervention projects, including survival estimates if corals are regularly visited, as well as predictions of survivorship if diseased corals are visited only once or twice.

ecology↗

bioRxiv2024

Two methodologies and timescales show no promotion of antibiotic resistance from in-water coral disease treatments

The decimation of reefs caused by stony coral tissue loss disease prompted the use of a topical amoxicillin treatment to prevent coral mortality. Application of this treatment led to concerns about unintentional impacts such as potential alteration of the coral microbiome and possible spread of antibiotic resistance. We used two different methodologies - microbial RNA sequencing and microbial qPCR array - to assess these concerns and to establish a baseline of antimicrobial resistance genes in coral microbes. RNA sequencing was conducted on coral mucus samples collected before and 24 hours after amoxicillin application on wild Montastraea cavernosa. While diverse antibiotic resistance genes (ARGs) were expressed, no differences were detected in ARG expression after amoxicillin treatment. Additionally, there were no notable changes in the microbial communities between the before and after samples. Microbial qPCR array was used to assess differences in ARGs over longer timescales in wild Colpophyllia natans, comparing never-treated corals with ones treated a single time seven months prior and with those treated multiple times seven months and more prior. No clinically relevant ARGs represented in the arrays were detected across any samples. A small number of above-detection reads (4 in the never-treated corals, 2 in the once-treated corals, and 0 in the multi-treated corals) may indicate weak amplification of similar environmental (non-anthropogenic) ARGs in the corals. Results indicate that the localized topical application of amoxicillin to prevent mortality of SCTLD-affected corals is neither immediately disrupting the microbiome of treated corals at the colony level nor driving the development of ARGs over immediate or longer-term time scales.

microbiology↗

bioRxiv2024

Too hot to handle? The impact of the 2023 marine heatwave on Florida Keys coral

The marine heatwave in the summer of 2023 was the most severe on record for Floridas Coral Reef, with unprecedented water temperatures and cumulative thermal stress precipitating near 100% coral bleaching levels. An existing SCTLD coral fate-tracking program assessed over 4200 coral colonies across five offshore and four inshore reef sites approximately every two months, allowing for analyses of bleaching-related mortality and diseases during and after the marine heatwave. Across the vast majority of assessed corals, including multiple sites and species, there was no partial or full mortality as a result of the 2023 bleaching event. The two sites that did experience substantial bleaching-related mortality were those experiencing the highest levels of cumulative thermal stress. However, the substantial acute mortality at one of them occurred at relatively low levels of cumulative stress, suggesting death was the result of exceeding thermal maxima. At the two sites with notable mortality, 43% and 24% of all monitored corals died, but mortality varied among species. Brain corals fared worse than boulder corals, with Pseudodiploria strigosa the most heavily impacted species. The health status of corals before the bleaching event had little impact on whether they experienced disease or bleaching-related mortality during the event. At three sites, we observed unusual lesions on Orbicella faveolata colonies shortly after color returned to the corals; the lesions were only observed for a few months but on some colonies led to substantial tissue loss. Though not part of the coral monitoring program, we also observed substantial losses and local extinctions of Acroporid corals at most sites, as well as probable local extinctions of octocorals at three of the four inshore reefs. Though most reef-building corals came through the 2023 event with no mortality, continually rising temperatures are likely to make these temperature regimes more common and widespread. We encourage future research on what the unusual O. faveolata lesions are, and why the brain and boulder corals fared differently at highly-impacted sites. Our results also provide perspective on how restoration strategies, particularly those focused on species likely to die under current and future climate regimes, should consider shifting focus to species likely to survive. Finally, these results highlight the importance of this type of monitoring, with a focus on fate-tracking individuals through disturbance events, including a large number of individuals of multiple species across a geographic range and multiple habitats.

ecology↗

bioRxiv2020

Rapid Population Decline of the Pillar Coral Dendrogyra cylindrus Along the Florida Reef Tract

Coral reefs worldwide are in a state of decline, but the status of populations and stressors for rare species are generally not well documented using broad-scale monitoring protocol. We fate-tracked all known colonies of the pillar coral Dendrogyra cylindrus on the Florida Reef Tract from 2013 - 2020 to assess the population and document the impacts of chronic and acute stressors. Large average colony size, an absence of juveniles, and large geographic distances between genotypes suggest that the Florida D. cylindrus population has been reproductively extinct for decades. During the study period, low-intensity chronic stressors were balanced by regrowth, while back-to-back years of coral bleaching and thermally-exacerbated disease led to declines that the subsequent years of recovery suggest would take 11 uninterrupted years to overcome. The most recent stressor on Floridas D. cylindrus population is "stony coral tissue loss disease." Following the appearance of the disease in Florida in 2015, it resulted in unrecoverable losses to the D. cylindrus population as tissue, colonies, and whole genotypes were driven to extinction. Losses of 91% of coral tissue, 88% of colonies, and 73% of genotypes between 2014 and early 2020 have led to functional extinction of D. cylindrus on the Florida Reef Tract.

ecology↗

bioRxiv2019

Effectiveness of topical antibiotics in treating corals affected by Stony Coral Tissue Loss Disease

Since 2014, Stony Coral Tissue Loss Disease (SCTLD) has led to mass mortality of the majority of hard coral species on the Florida Reef Tract. Following the successful treatment of SCTLD lesions on corals in closed aquaria using water dosed with antibiotics, two pastes were developed as vehicles for direct antibiotic treatments on wild corals. These pastes were tested as placebos and with additions of amoxicillin via topical applications over active SCTLD margins on multiple coral species. The effectiveness of the pastes without antibiotics (placebo treatments) was less than 10%. Adding amoxicillin to both pastes increased effectiveness. For one of the two pastes, which was silicone based with a time-release mechanism for the antibiotics, effectiveness in halting disease lesions reached 86% when amoxicillin was added. Topical antibiotic application is a viable tool for the preservation of priority corals affected by SCTLD.

ecology↗

bioRxiv2018

Fallen Pillars: The Past, Present, and Future Population Dynamics of a Rare, Specialist Coral-Algal Symbiosis

Rare and ecologically specialized species are at greater risk of extinction. Rarity in terms of low genotypic diversity may be obscured in sessile foundation species that can reproduce asexually. Asexual propagules are often only distinguishable from sexual recruits through molecular tools. Thus, molecular markers are necessary to assess genotypic variation and population structure in clonal organisms such as corals. The global decline of corals has necessitated marker development for improved conservation of rare coral species. We infer past demographic changes, describe modern population structure, and quantify asexual reproduction of the uncommon Caribbean pillar coral, Dendrogyra cylindrus and its endosymbiotic dinoflagellate, Symbiodinium dendrogyrum using de novo microsatellite markers. Results show that D. cylindrus comprises three distinct populations in the Caribbean whereas the symbiont was differentiated into four populations. Thus, barriers to gene flow differ between host and symbiont. In Florida, host and symbiont reproduced mainly asexually, yielding lower genotypic diversity than predicted from census size. Models of past demographic events revealed no evidence of historical changes in population size, consistent with the geological record of D. cylindrus indicating it has been rare for hundreds of thousands of years. The most recent global thermal stress event triggered a severe disease outbreak among D. cylindrus in Florida, resulting in a precipitous population decline. Projections indicate a high likelihood that this species may become locally extinct within the coming decades. The ecosystem consequences of losing rare coral species and their symbionts with increasingly frequent extreme warming events are not known but require urgent study.

genetics↗