Biology subjects

Apprill, A.

Publications and source records attributed to Apprill, A..

8 recordsLinked to original sources

bioRxiv2026

Global diversity and distribution of coral-associated protists

Coral reefs are critical ecosystems and biodiversity hotspots that provide ecological stability and essential services to coastal communities. The coral holobiont, a complex symbiotic system composed of the coral animal and a diverse array of associated microbes, plays a central role in coral health and resilience. While Symbiodiniaceae and bacterial symbionts have been extensively studied, much less is known about the diversity and function of microbial eukaryotes such as protists and fungi. These organisms are increasingly recognized as important, yet remain vastly underexplored. Here, we present the first global survey of the coral-associated eukaryome using an anti-metazoan 18S rRNA primer set to bypass host DNA amplification. Our dataset includes corals and related anthozoans from the Caribbean Sea, the Red Sea, and several locations in the Pacific Ocean, spanning a broad taxonomic and geographic range, and includes both healthy and diseased specimens. They reveal a eukaryome that is not only more diverse than that of global coastal waters but also surpasses the diversity of the well-studied coral bacterial microbiome. We recover diverse microbial eukaryotic communities, including Symbiodiniaceae, other known symbionts, potential pathogens, and previously uncharacterized lineages. These results reveal consistent patterns across coral groups and geographic regions. This study provides the most comprehensive taxonomic overview of coral-associated microbial eukaryotes to date, offering new insights into their roles within the holobiont. Our findings highlight the ecological significance of microbial eukaryotes and underscore the importance of incorporating them into broader coral reef research and conservation strategies.

microbiology↗

bioRxiv2026

Habitat and Hydrodynamics Influence Coral Reef and Seagrass Microbial and Exometabolite Dynamics

Coral reef and seagrass ecosystems provide critical storm protection and economic revenue to tropical coastal communities. Effective monitoring and restoration strategies are essential given increasing impacts from climate change and human development. Microorganisms, and the metabolites they produce and consume, are key drivers of coastal ecosystem function. However, microbially-mediated metabolite recycling remains poorly understood, limiting its inclusion in conservation and restoration strategies. Here we examine how seawater exometabolites and microorganisms in coastal ecosystems vary in relation to habitat (seagrass or coral reef), temporal scales and hydrodynamics. We characterized benthic seawater from two St. John, U.S. Virgin Islands coral reefs (Yawzi and Tektite) and one seagrass meadow at dawn and mid-day over four consecutive days. Using quantitative metabolomics and SSU rRNA gene amplicon sequencing, we found that habitat served as the primary driver of exometabolite and microbial community composition, while daily changes and hydrodynamics strongly influenced system variability. Hydrodynamic modeling indicated offshore water intrusion at mid-day at Yawzi reef, likely driving exometabolite and microbial shifts towards oligotrophic taxa (e.g., SAR11, SAR86). In contrast, a high percentage of coastal source water in the seagrass habitat maintained stable exometabolite pools and supported diverse microbial communities. These findings demonstrate that coastal habitat and hydrodynamics strongly influence exometabolite and microbial assemblages, with lesser contributions from temporal changes. Integrating exometabolites, microorganisms, and hydrodynamics provides new insights into coastal ecosystem functioning useful for habitat monitoring and restoration strategies.

ecology↗

bioRxiv2024

Characterizing gene expression profiles of various tissue states in stony coral tissue loss disease using a feature selection algorithm

Stony coral tissue loss disease (SCTLD) remains a substantial threat to coral reef diversity already threatened by global climate change. Restoration efforts and effective treatment of SCTLD requires an in-depth understanding of its pathogenesis in the coral holobiont as well as mechanisms of disease resistance. Here, we present a supervised machine learning framework to describe SCTLD progression in a major reef-building coral, Montastraea cavernosa, and its dominant algal endosymbiont, Cladocopium goreaui. Utilizing support vector machine recursive feature elimination (SVM-RFE) in conjunction with differential expression analysis, we identify a subset of biologically relevant genes that exhibit the highest classification performance across three types of coral tissues collected from a natural reef environment: apparently healthy tissue on an apparently healthy colony, apparently healthy tissue on a SCTLD-affected colony, and lesion tissue on a SCTLD-affected colony. By analyzing gene expression signatures associated with these tissue health states in both the coral host and its algal endosymbiont (family Symbiodiniaceae), we describe key processes involved in SCTLD resistance and disease progression within the coral holobiont. Our findings further support evidence that SCTLD causes dysbiosis between the coral host and its Symbiodinaiceae and additionally describes the metabolic and immune shifts that occur as the holobiont transitions from a healthy to a diseased state. This supervised machine learning framework offers a novel approach to accurately assess the health states of endangered coral species and brings us closer to developing effective solutions for disease monitoring and intervention. AUTHOR SUMMARYCoral reefs are under increasing threat due to climate change, with rising ocean temperatures and disease outbreaks accelerating reef degradation. Stony coral tissue loss disease (SCTLD) has been particularly destructive, leading to widespread coral mortality across Floridas Coral Reef and the wider Caribbean since its emergence in 2014. While the cause of SCTLD remains unknown, the rapid decline in coral reef health highlights the urgent need for innovative approaches to understanding threats to coral health. In this study, we applied a supervised machine learning approach, previously used in cancer research, to identify key genes associated with SCTLD progression in the coral Montastraea cavernosa and its symbiotic algae, which the coral relies on to meet its nutritional requirements. By analyzing gene expression patterns across tissues representing different health states, we find that SCTLD affects the metabolic interactions between the coral and their symbionts and causes shifts in coral immune signaling pathways, even in tissue on a SCTLD-affected colony that appears to be healthy. This study presents a novel framework for applying supervised machine learning in coral gene expression research and could lead to new methods for monitoring coral health and combatting SCTLD.

genomics↗

bioRxiv2024

Environmental and Population influences on Mummichog (Fundulus heteroclitus) Gut Microbiomes

The mummichog, Fundulus heteroclitus, an abundant estuarine fish broadly distributed along the eastern coast of North America, has repeatedly evolved tolerance to otherwise lethal levels of aromatic hydrocarbon exposure. This tolerance is linked to reduced activation of the aryl hydrocarbon receptor (AHR) signaling pathway. In other animals, the AHR has been shown to influence the gastrointestinal-associated microbial community, or gut microbiome, particularly when activated by the model toxic pollutant 3,3,4,4,5-pentachlorobiphenyl (PCB-126) and other dioxin-like compounds. In order to understand host population and PCB-126 exposure effects on mummichog gut microbiota, we sampled two populations of wild fish, one from a PCB-contaminated environment (New Bedford Harbor, MA) and the other from a non-polluted location (Scorton Creek, MA), as well as laboratory-reared F2 generation fish originating from each of these populations. We examined the bacteria and archaea associated with the gut of these fish using amplicon sequencing of small subunit ribosomal RNA genes. Fish living in the PCB-polluted site had high microbial alpha and beta diversity and an altered microbial network structure compared to fish from the non-polluted site. These differences between wild fish were not present in laboratory-reared F2 fish that originated from the same populations. Microbial compositional differences existed between the wild and lab-reared fish, with the wild fish dominated by Vibrionaceae and the lab-reared fish by Enterococceae. These results suggest that mummichog habitat and/or environmental conditions has a stronger influence on the mummichog gut microbiome compared to population or hereditary-based influences. Mummichog are important eco-evolutionary model organisms; this work reveals their importance for exploring host-environmental-microbiome dynamics.

ecology↗

bioRxiv2023

Advancing Reef Monitoring Techniques through Exometabolomics: Quantification of Labile Dissolved Organic Metabolites on Coral Reefs

Extracellular chemical cues constitute much of the language of life among marine organisms from microbes to mammals. These chemical cues shape foraging and feeding strategies, symbiotic interactions, selection of mates and habitats, and the transfer of energy and nutrients within and among ecosystems. Changes in the chemical pool flux within these ecosystems serve as invisible signals of overall ecosystem health and, conversely, disruption to this finely tuned equilibrium. In coral reef systems, the full scope and magnitude of the chemicals involved in maintaining reef equilibria are largely unknown. In particular, processes involving small, polar molecules, which form the majority components of labile dissolved organic carbon (DOC), are often poorly captured using traditional techniques and therefore remain unconstrained. In this study, we employed a recently developed chemical derivatization method and mass spectrometry-based targeted exometabolomics to capture and quantify polar dissolved phase metabolites on five coral reefs in the U.S. Virgin Islands. We detected and quantified 45 polar exometabolites, and further demonstrate their variability across the investigated geographic landscape and contextualize these findings in terms of geographic and benthic cover differences. By comparing our results to previously published coral reef exometabolomes that did not employ chemical derivatization, we show the novel quantification of 23 metabolites which were previously undetected in the coral reef exometabolome, including compounds involved in central carbon metabolism (e.g., glutamate) and novel metabolites such as homoserine betaine. We highlight the immense potential of chemical derivatization-based exometabolomics for quantifying labile chemical cues on coral reefs and measuring molecular level responses to environmental stressors. Overall, improving our understanding of the composition and dynamics of reef exometabolites is vital for effective ecosystem monitoring and management strategies. SynopsisMinimal research exists on the polar exometabolites on coral reefs, an essential component of reef health and the majority component of labile DOC. This study reports 23 newly quantified polar metabolites on coral reefs and highlights significant differences in the exometabolome composition across geographically distinct reefs and bays.

systems biology↗

bioRxiv2022

A meta-analysis of the stony coral tissue loss disease microbiome finds key bacteria in lesions and unaffected tissue of diseased colonies

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 limited concurrence of SCTLD-associated bacteria among studies. We conducted a meta-analysis of SSU 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 disease 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. While Rhodobacterales and Peptostreptococcales-Tissierellales were prominent in structuring microbial interactions in DL. Peptostreptococcales-Tissierellales specifically may contribute to lesion progression through an alpha-toxin. We provide a consensus of SCTLD-associated bacteria both prior to and during lesion progression and identify how these taxa vary across studies, coral species, coral compartments, seawater, and sediment.

microbiology↗

bioRxiv2022

Reshuffling of the coral microbiome during dormancy

Quiescence, or dormancy, is a response to stressful conditions in which an organism slows or halts physiological functioning. Although most species that undergo dormancy maintain complex microbiomes, there is little known about how dormancy influences and is influenced by the hosts microbiome, including in the temperate coral, Astrangia poculata. Northern populations of A. poculata undergo winter quiescence. Here, we characterized wild A. poculata microbiomes in a high-resolution sampling time series before, during, and after quiescence using 16S ribosomal RNA gene sequencing on active (RNA) and present (DNA) microbiomes. We observed a restructuring of the coral microbiome during quiescence that persisted after re-emergence. Upon entering quiescence, corals shed copiotrophic microbes, including putative pathogens, suggesting removal of these taxa as corals cease normal functioning. During and after quiescence, bacteria and archaea associated with nitrification were enriched, suggesting the quiescent microbiome may replace essential functions through supplying nitrate to corals and/or microbes. Overall, this study demonstrates that key microbial groups related to quiescence in A. poculata may play a role in the onset or emergence from dormancy, and long-term regulation of the microbiome composition. The predictability of dormancy in A. poculata provides an ideal natural manipulation system to further identify factors that regulate host-microbial associations. ImportanceUsing a high-resolution sampling time series, we are the first to demonstrate a persistent microbial community shift with quiescence (dormancy) in a marine organism, the temperate coral, Astrangia poculata. Furthermore, during this period of community turnover, there is a shedding of putative pathogens and copiotrophs and an enhancement of the ammonia-oxidizing bacteria (Nitrosococcales) and archaea (Ca. Nitrosopumilus). Our results suggest that quiescence represents an important period during which the coral microbiome can "reset," shedding opportunistic microbes and enriching for the re-establishment of beneficial associates, including those that may contribute nitrate while the coral animal is not actively feeding. We suggest this work provides foundational understanding of the interplay of microbes and the hosts dormancy response in marine organisms.

microbiology↗

bioRxiv2021

Stony Coral Tissue Loss Disease biomarker bacteria identified in corals and overlying waters using a rapid field-based sequencing approach

Stony Coral Tissue Loss Disease (SCTLD) is a devastating disease. Since 2014, it has spread along the entire Florida Reef Tract, presumably via a water-borne vector, and into the greater Caribbean. It was first detected in the United States Virgin Islands (USVI) in January 2019. To more quickly identify disease biomarker microbes, we developed a rapid pipeline for microbiome sequencing. Over a span of 10 days we collected, processed, and sequenced coral tissue and near-coral seawater microbiomes from diseased and apparently healthy Colpophyllia natans, Montastraea cavernosa, Meandrina meandrites and Orbicella franksi. Analysis of the resulting bacterial and archaeal 16S ribosomal RNA sequences revealed 25 biomarker amplicon sequence variants (ASVs) enriched in diseased tissue. These biomarker ASVs were additionally recovered in near-coral seawater (within 5 cm of coral surface), a potential recruitment zone for pathogens. Phylogenetic analysis of the biomarker ASVs belonging to Vibrio, Arcobacter, Rhizobiaceae, and Rhodobacteraceae revealed relatedness to other coral disease-associated bacteria and lineages novel to corals. Additionally, four ASVs (Algicola, Cohaesibacter, Thalassobius and Vibrio) were exact sequence matches to microbes previously associated with SCTLD. This work represents the first rapid coral disease sequencing effort and identifies biomarkers of SCTLD that could be targets for future SCTLD research.

microbiology↗