Formel Nathan

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Formel
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Nathan
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  • Article
    Coral persistence despite marginal conditions in the Port of Miami
    (Nature Research, 2023-04-25) Enochs, Ian C. ; Studivan, Michael S. ; Kolodziej, Graham ; Foord, Colin ; Basden, Isabelle ; Boyd, Albert ; Formel, Nathan ; Kirkland, Amanda ; Rubin, Ewelina ; Jankulak, Mike ; Smith, Ian ; Kelble, Christopher R. ; Manzello, Derek P.
    Coral cover has declined worldwide due to anthropogenic stressors that manifest on both global and local scales. Coral communities that exist in extreme conditions can provide information on how these stressors influence ecosystem structure, with implications for their persistence under future conditions. The Port of Miami is located within an urbanized environment, with active coastal development, as well as commercial shipping and recreational boating activity. Monitoring of sites throughout the Port since 2018 has revealed periodic extremes in temperature, seawater pH, and salinity, far in excess of what have been measured in most coral reef environments. Despite conditions that would kill many reef species, we have documented diverse coral communities growing on artificial substrates at these sites-reflecting remarkable tolerance to environmental stressors. Furthermore, many of the more prevalent species within these communities are now conspicuously absent or in low abundance on nearby reefs, owing to their susceptibility and exposure to stony coral tissue loss disease. Natural reef frameworks, however, are largely absent at the urban sites and while diverse fish communities are documented, it is unlikely that these communities provide the same goods and services as natural reef habitats. Regardless, the existence of these communities indicates unlikely persistence and highlights the potential for coexistence of threatened species in anthropogenic environments, provided that suitable stewardship strategies are in place.
  • Article
    Different disease inoculations cause common responses of the host immune system and prokaryotic component of the microbiome in Acropora palmata.
    (Public Library of Science, 2023-05-25) Young, Benjamin D. ; Rosales, Stephanie M. ; Enochs, Ian C. ; Kolodziej, Graham ; Formel, Nathan ; Moura, Amelia ; DAlonso, Gabrielle L. ; Traylor-Knowles, Nikki
    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.
  • Article
    Acropora cervicornis Data Coordination Hub, an open access database for evaluating genet performance
    (Rosenstiel School of Marine and Atmospheric Science, 2023-03-24) Kiel, Patrick M. ; Formel, Nathan ; Jankulak, Mike ; Baker, Andrew C. ; Cunning, Ross ; Gilliam, David S. ; Kenkel, Carly ; Langdon, Chris ; Lirman, Diego ; Lustic, Caitlin ; Maxwell, Kerry ; Moulding, Alison L. ; Moura, Amelia ; Muller, Erinn M. ; Schopmeyer, Stephanie ; Winters, R. Scott ; Enochs, Ian C.
    Once one of the predominant reef-building corals in the region, Acropora cervicornis is 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 of A. cervicornis grown 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 the Acropora cervicornis Data 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.
  • Article
    Unidentified fish sounds as indicators of coral reef health and comparison to other acoustic methods
    (Frontiers Media, 2024-02-29) Jarriel, Sierra D. ; Formel, Nathan ; Ferguson, Sophie R. ; Jensen, Frants H. ; Apprill, Amy ; Mooney, T. Aran
    The global decline of coral reefs is a major contributor to the global biodiversity crisis and requires improved monitoring at these critically important habitats. Non-invasive passive acoustic assessments may address this need, leveraging the rich variety and spatiotemporal variability of biological sounds present in coral reef environments and offering near-continuous temporal coverage. Despite this, acoustic metrics that reliably represent coral reef health are still debated, and ground-truthing of methods is limited. Here we investigated how the prevalence of low frequency biotic sounds (without species information) relates to coral reef health, providing a foundation from which one can compare assessment methods. We first quantified call rates of these low frequency sounds for three reefs exhibiting different community assemblages around St. John, U.S. Virgin Islands, by manually annotating presumed fish noises for 1 min every 30 min across 8 days for each site. Annotated days were selected at key points across lunar cycles. These call rates were then compared with traditional visual surveys, and several acoustic methods and indices commonly used in underwater soundscape research. We found that, overall, manually detected fish call rates successfully differentiated between the three reefs, capturing variation in crepuscular activity levels–a pattern consistent with previous work that highlights the importance of diel choruses. Moreover, fish vocal rates were predictors of hard coral cover, fish abundance, and fish species richness, while most acoustic indices failed to parse out fine distinctions among the three sites. Some, such as the Acoustic Complexity Index, failed to reveal any expected differences between sites or times of day, while the Bioacoustic Index could only identify the most acoustically active reef, otherwise having weak correlations to visual metrics. Of the indices tested, root-mean-squared sound pressure level and Acoustic Entropy, both calculated in the low frequency fish band (50–1,200 Hz), showed the strongest association with visual health measures. These findings present an important step toward using soundscape cues for reef health assessments. The limited generalizability of acoustic indices across different locations emphasizes the need for caution in their application. Therefore, it is crucial to improve methods utilizing fish sounds, such as automatic fish call detectors that are able to generalize well to new soundscapes.