Apprill Amy

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Apprill

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Amy

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0000-0002-4249-2977

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Alphaflexivirus genomes in stony coral tissue loss disease-affected, disease-exposed, and disease-unexposed coral colonies in the U.S. Virgin Islands

(American Society for Microbiology, 2022-02-17) Veglia, Alex J. ; Beavers, Kelsey ; Van Buren, Emily W. ; Meiling, Sonora S. ; Muller, Erinn ; Smith, Tyler B. ; Holstein, Daniel M. ; Apprill, Amy ; Brandt, Marilyn ; Mydlarz, Laura ; Correa, Adrienne M.S.

Stony coral tissue loss disease (SCTLD) is decimating Caribbean corals. Here, through the metatranscriptomic assembly and annotation of two alphaflexivirus-like strains, we provide genomic evidence of filamentous viruses in SCTLD-affected, -exposed, and -unexposed coral colonies. These data will assist in clarifying the roles of viruses in SCTLD.
Coordinated transformation of the gut microbiome and lipidome of bowhead whales provides novel insights into digestion

(Springer Nature, 2019-12-02) Miller, Carolyn A. ; Holm, Henry C. ; Horstmann, Lara ; George, John C. ; Fredricks, Helen F. ; Van Mooy, Benjamin A. S. ; Apprill, Amy

Whale digestion plays an integral role in many ocean ecosystems. By digesting enormous quantities of lipid-rich prey, whales support their energy intensive lifestyle, but also excrete nutrients important to ocean biogeochemical cycles. Nevertheless, whale digestion is poorly understood. Gastrointestinal microorganisms play a significant role in vertebrate digestion, but few studies have examined them in whales. To investigate digestion of lipids, and the potential contribution of microbes to lipid digestion in whales, we characterized lipid composition (lipidomes) and bacterial communities (microbiotas) in 126 digesta samples collected throughout the gastrointestinal tracts of 38 bowhead whales (Balaena mysticetus) harvested by Alaskan Eskimos. Lipidomes and microbiotas were strongly correlated throughout the gastrointestinal tract. Lipidomes and microbiotas were most variable in the small intestine and most similar in the large intestine, where microbiota richness was greatest. Our results suggest digestion of wax esters, the primary lipids in B. mysticetus prey representing more than 80% of total dietary lipids, occurred in the mid- to distal small intestine and was correlated with specific microorganisms. Because wax esters are difficult to digest by other marine vertebrates and constitute a large reservoir of carbon in the ocean, our results further elucidate the essential roles that whales and their gastrointestinal microbiotas play in the biogeochemical cycling of carbon and nutrients in high-latitude seas.
The coral ecosphere: a unique coral reef habitat that fosters coral-microbial interactions

(Wiley, 2019-05-21) Weber, Laura ; Gonzalez‐Díaz, Patricia ; Armenteros, Maickel ; Apprill, Amy

Scleractinian corals are bathed in a sea of planktonic and particle‐associated microorganisms. The metabolic products of corals influence the growth and composition of microorganisms, but interactions between corals and seawater microorganisms are underexplored. We conducted a field‐based survey to compare the biomass, diversity, composition, and functional capacity of microorganisms in small‐volume seawater samples collected adjacent to five coral species with seawater collected > 1 m away from the reef substrate on the same reefs. Seawater collected close to corals generally harbored copiotrophic‐type bacteria and its bacterial and archaeal composition was influenced by coral species as well as the local reef environment. Trends in picoplankton abundances were variable and either increased or decreased away from coral colonies based on coral species and picoplankton functional group. Genes characteristic of surface‐attached and potentially virulent microbial lifestyles were enriched in near‐coral seawater compared to reef seawater. There was a prominent association between the coral Porites astreoides and the coral symbiont Endozoicomonas, suggesting recruitment and/or shedding of these cells into the surrounding seawater. This evidence extends our understanding of potential species‐specific and reef site‐influenced microbial interactions that occur between corals and microorganisms within this near‐coral seawater environment that we propose to call the “coral ecosphere.” Microbial interactions that occur within the coral ecosphere could influence recruitment of coral‐associated microorganisms and facilitate the transfer of coral metabolites into the microbial food web, thus fostering reef biogeochemical cycling and a linkage between corals and the water column.
Discovery and quantification of anaerobic nitrogen metabolisms among oxygenated tropical Cuban stony corals

(Springer Nature, 2020-12-20) Babbin, Andrew ; Tamasi, Tyler ; Dumit, Diana ; Weber, Laura ; Rodríguez, María Victoria Iglesias ; Schwartz, Sarah L. ; Armenteros, Maickel ; Wankel, Scott D. ; Apprill, Amy

Coral reef health depends on an intricate relationship among the coral animal, photosynthetic algae, and a complex microbial community. The holobiont can impact the nutrient balance of their hosts amid an otherwise oligotrophic environment, including by cycling physiologically important nitrogen compounds. Here we use 15N-tracer experiments to produce the first simultaneous measurements of ammonium oxidation, nitrate reduction, and nitrous oxide (N2O) production among five iconic species of reef-building corals (Acropora palmata, Diploria labyrinthiformis, Orbicella faveolata, Porites astreoides, and Porites porites) in the highly protected Jardines de la Reina reefs of Cuba. Nitrate reduction is present in most species, but ammonium oxidation is low potentially due to photoinhibition and assimilatory competition. Coral-associated rates of N2O production indicate a widespread potential for denitrification, especially among D. labyrinthiformis, at rates of ~1 nmol cm−2 d−1. In contrast, A. palmata displays minimal active nitrogen metabolism. Enhanced rates of nitrate reduction and N2O production are observed coincident with dark net respiration periods. Genomes of bacterial cultures isolated from multiple coral species confirm that microorganisms with the ability to respire nitrate anaerobically to either dinitrogen gas or ammonium exist within the holobiont. This confirmation of anaerobic nitrogen metabolisms by coral-associated microorganisms sheds new light on coral and reef productivity.
Microbial signatures of protected and impacted Northern Caribbean reefs: changes from Cuba to the Florida Keys.

(Wiley, 2019-11-19) Weber, Laura ; Gonzalez‐Díaz, Patricia ; Armenteros, Maickel ; Ferrer, Víctor M. ; Bretos, Fernando ; Bartels, Erich ; Santoro, Alyson E. ; Apprill, Amy

There are a few baseline reef‐systems available for understanding the microbiology of healthy coral reefs and their surrounding seawater. Here, we examined the seawater microbial ecology of 25 Northern Caribbean reefs varying in human impact and protection in Cuba and the Florida Keys, USA, by measuring nutrient concentrations, microbial abundances, and respiration rates as well as sequencing bacterial and archaeal amplicons and community functional genes. Overall, seawater microbial composition and biogeochemistry were influenced by reef location and hydrogeography. Seawater from the highly protected ‘crown jewel’ offshore reefs in Jardines de la Reina, Cuba had low concentrations of nutrients and organic carbon, abundant Prochlorococcus, and high microbial community alpha diversity. Seawater from the less protected system of Los Canarreos, Cuba had elevated microbial community beta‐diversity whereas waters from the most impacted nearshore reefs in the Florida Keys contained high organic carbon and nitrogen concentrations and potential microbial functions characteristic of microbialized reefs. Each reef system had distinct microbial signatures and within this context, we propose that the protection and offshore nature of Jardines de la Reina may preserve the oligotrophic paradigm and the metabolic dependence of the community on primary production by picocyanobacteria.
Ground-truthing daily and lunar patterns of coral reef fish call rates on a US Virgin Island reef

(Inter Research, 2022-07-28) Ferguson, Sophie R. ; Jensen, Frants H. ; Hyer, Matthew D. ; Noble, Allison ; Apprill, Amy ; Mooney, T. Aran

Coral reefs comprise some of the most biodiverse habitats on the planet. These ecosystems face a range of stressors, making quantifying community assemblages and potential changes vital to effective management. To understand short- and long-term changes in biodiversity and detect early warning signals of decline, new methods for quantifying biodiversity at scale are necessary. Acoustic monitoring techniques have proven useful in observing species activities and biodiversity on coral reefs through aggregate approaches (i.e. energy as a proxy). However, few studies have ground-truthed these acoustic analyses with human-based observations. In this study, we sought to expand these passive acoustic methods by investigating biological sounds and fish call rates on a healthy reef, providing a unique set of human-confirmed, labeled acoustic observations. We analyzed acoustic data from Tektite Reef, St. John, US Virgin Islands, over a 2 mo period. A subset of acoustic files was manually inspected to identify recurring biotic sounds and quantify reef activity throughout the day. We found a high variety of acoustic signals in this soundscape. General patterns of call rates across time conformed to expectations, with dusk and dawn showing important and significantly elevated peaks in soniferous fish activity. The data reflected high variability in call rates across days and lunar phases. Call rates did not correspond to sound pressure levels, suggesting that certain call types may drive crepuscular trends in sound levels while lower-level critical calls, likely key for estimating biodiversity and behavior, may be missed by gross sound level analyses.
Characterizing the culturable surface microbiomes of diverse marine animals

(Oxford University Press, 2021-03-03) Keller, Abigail G. ; Apprill, Amy ; Lebaron, Philippe ; Robbins, Jooke ; Romano, Tracy ; Overton, Ellysia ; Rong, Yuying ; Yuan, Ruiyi ; Pollara, Scott B. ; Whalen, Kristen E.

Biofilm-forming bacteria have the potential to contribute to the health, physiology, behavior and ecology of the host and serve as its first line of defense against adverse conditions in the environment. While metabarcoding and metagenomic information furthers our understanding of microbiome composition, fewer studies use cultured samples to study the diverse interactions among the host and its microbiome, as cultured representatives are often lacking. This study examines the surface microbiomes cultured from three shallow-water coral species and two whale species. These unique marine animals place strong selective pressures on their microbial symbionts and contain members under similar environmental and anthropogenic stress. We developed an intense cultivation procedure, utilizing a suite of culture conditions targeting a rich assortment of biofilm-forming microorganisms. We identified 592 microbial isolates contained within 15 bacterial orders representing 50 bacterial genera, and two fungal species. Culturable bacteria from coral and whale samples paralleled taxonomic groups identified in culture-independent surveys, including 29% of all bacterial genera identified in the Megaptera novaeangliae skin microbiome through culture-independent methods. This microbial repository provides raw material and biological input for more nuanced studies which can explore how members of the microbiome both shape their micro-niche and impact host fitness.
Incubation experiments were conducted in St. John, US Virgin Islands to investigate the macronutrient drawdown response of reef seawater microbial communities to exudates released from the coral species Porites astreoides and Gorgonia ventalina.

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2022-11-10) Weber, Laura ; Apprill, Amy ; Kujawinski, Elizabeth

Incubation experiments were conducted in St. John, US Virgin Islands to investigate the composition of exudates released from different species of benthic organisms, and the response of reef seawater microbial communities to mixed exudates released from different species and to specific metabolites. Exudates were collected from the stony coral Porites astreoides, and the octocoral Gorgonia ventalina after an 8 hour incubation. Reef seawater microbial communities were incubated separately in the presence of exudates from P. astreoides and G. ventalina for 48 hours and samples were collected to monitor changes in macronutrient concentrations. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/865193
Soundscape monitoring acoustic data collected in July of 2017 during an in situ larval coral settlement experiment in St. John, US Virgin Islands

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2020-01-21) Apprill, Amy ; Mooney, T. Aran ; Lillis, Ashlee

Matlab R2016 was used to process acoustic data from raw wave audio files. Mean power spectral densities were estimated (Hamming window, non-overlapping 0.5-sec windows, frequency resolution: 1.47 Hz) within 1-minute samples across the total experiment length (62 hours). For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/742573
Isotopic analysis of ¹³C and ¹⁵N for sponges, coral, and zooxanthellae (family Symbiodiniaceae) used in a 'pulse-chase' experiment to examine the uptake of sponge-derived nutrients by the coral holobiont

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2023-02-24) Reigel, Alicia M. ; Easson, Cole G. ; Apprill, Amy ; Freeman, Christopher J. ; Bartley, Michaela M. ; Fiore, Cara L.

These are raw data from isotopic analysis of ¹³C and ¹⁵N for sponges, coral, and zooxanthellae (family Symbiodiniaceae) used in a 'pulse-chase' experiment to examine the uptake of sponge-derived nutrients by the coral holobiont. Coral were collected from the Florida Keys National Marine Sanctuary and the experiments were carried out at the Climate and Acidification Ocean Simulator (CAOS) at Mote Marine Laboratory at Summerland Key, Florida, USA. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/889857
Dates and locations of hydrophone deployments at coral reefs in St. John, U.S. Virgin Islands in 2016 and 2017

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2020-12-15) Mooney, T. Aran ; Apprill, Amy ; Dinh, Jason

A passive acoustic recorder was deployed at various coral reefs in St. John, U.S. Virgin Islands between 2016-03-28 and 2017-07-11. This dataset contains deployment dates and locations. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/748536
Incubation experiments were conducted in St. John, US Virgin Islands to investigate the response of reef seawater microbial communities to the mixed exudates released from the coral species Porites astreoides and Gorgonia ventalina.

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2022-11-10) Weber, Laura ; Apprill, Amy ; Kujawinski, Elizabeth

Incubation experiments were conducted in St. John, US Virgin Islands to investigate the composition of exudates released from different species of benthic organisms, and the response of reef seawater microbial communities to mixed exudates released from different species and to specific metabolites. Exudates were collected from the stony coral Porites astreoides, and the octocoral Gorgonia ventalina after an 8 hour incubation. Reef seawater microbial communities were incubated separately in the presence of exudates from P. astreoides and G. ventalina for 48 hours and samples were collected to monitor changes in microbial abundance via flow cytometry and microbial community composition via 16S rRNA gene sequencing. Complementary Targeted and Untargeted metabolomic data from these incubation experiments is available on the MetaboLights database under accession number MTBLS2855. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/865739
Coral reef fish assemblages exhibit signs of depletion in two protected areas from the eastern of Los Canarreos archipelago (Cuba, Caribbean Sea)

(PeerJ, 2022-10-04) Navarro-Martínez, Zenaida María ; Armenteros, Maickel ; Espinosa, Leonardo ; González-Díaz, Patricia ; Apprill, Amy

Understanding the impact of marine protected areas on the distribution and composition of fishes is key to the protection and management of coral reef ecosystems, and especially for fish-based activities such as SCUBA diving and recreational fishing. The aim of this research is to compare the ichthyofauna structure in three areas in the eastern part of Los Canarreos archipelago in Cuba with different management schemes: Cayo Campos-Cayo Rosario Fauna Refuge (CCCR), Cayo Largo Ecological Reserve (CL) and non-protected area (nMPA), and considering habitat differences and depth variation. A total of 131 video transects were conducted using diver operated stereo-video (stereo-DOV) in November, 2015 in backreef and forereef along the CCCR, CL and the adjacent nMPA. We recorded 84 species and 27 functional groups suggesting high complementarity of functions. Several multispecies schools were observed along surveys, which explain the biomass peaks in some sites, mainly for Lutjanidae, Haemulidae and Carangidae. A concerning issue was the bare representation of critical functional groups and threatened species. The effect of sites nested within habitats was significant and the most important driver structuring fish assemblages, while MPA condition was not evident. Favorable habitat features (habitat heterogeneity and surrounding coastal ecosystems) are likely enhancing fish assemblages and counteracting the effects of pouching derived from insufficient management. We recommend immediate actions within a strategy of precautionary management including, but not limited to, the appointment of staff for the administration of CL, frequent monitoring and effective enforcement.
Benthic exometabolites and their ecological significance on threatened Caribbean coral reefs

(Springer, 2022-10-17) Weber, Laura ; Soule, Melissa Kido ; Longnecker, Krista ; Becker, Cynthia C. ; Huntley, Naomi ; Kujawinski, Elizabeth B. ; Apprill, Amy

Benthic organisms are the architectural framework supporting coral reef ecosystems, but their community composition has recently shifted on many reefs. Little is known about the metabolites released from these benthic organisms and how compositional shifts may influence other reef life, including prolific microorganisms. To investigate the metabolite composition of benthic exudates and their ecological significance for reef microbial communities, we harvested exudates from six species of Caribbean benthic organisms including stony corals, octocorals, and an invasive encrusting alga, and subjected these exudates to untargeted and targeted metabolomics approaches using liquid chromatography-mass spectrometry. Incubations with reef seawater microorganisms were conducted to monitor changes in microbial abundances and community composition using 16 S rRNA gene sequencing in relation to exudate source and three specific metabolites. Exudates were enriched in amino acids, nucleosides, vitamins, and indole-based metabolites, showing that benthic organisms contribute labile organic matter to reefs. Furthermore, exudate compositions were species-specific, and riboflavin and pantothenic acid emerged as significant coral-produced metabolites, while caffeine emerged as a significant invasive algal-produced metabolite. Microbial abundances and individual microbial taxa responded differently to exudates from stony corals and octocorals, demonstrating that exudate mixtures released from different coral species select for specific bacteria. In contrast, microbial communities did not respond to individual additions of riboflavin, pantothenic acid, or caffeine. This work indicates that recent shifts in benthic organisms alter exudate composition and likely impact microbial communities on coral reefs.
Incubation experiments were conducted in St. John, US Virgin Islands to investigate the response of reef seawater microbial communities to the specific metabolites riboflavin, pantothenic acid, and caffeine.

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2022-11-10) Weber, Laura ; Apprill, Amy ; Kujawinski, Elizabeth

Pre-filtered reef seawater microbial communities collected from Lameshur Bay, U.S. Virgin Islands were incubated separately in the presence of the individual metabolites riboflavin, pantothenic acid, and caffeine for 24 hours and samples were collected to monitor changes in microbial community composition using 16S rRNA gene sequencing and microbial abundances using flow cytometry. Targeted metabolomic data from these incubations is available on the MetaboLights database under accession number MTBLS3286. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/865159
Porites astreoides coral settlement counts collected in July of 2017 from an in situ larval coral settlement experiment in St. John, US Virgin Islands

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2020-01-03) Apprill, Amy ; Mooney, T. Aran ; Lillis, Ashlee

Brooding coral Porites astreoides colonies were collected on St. John, U.S. Virgin Islands on June 22nd, 2017 and used in an in-situ larval coral settlement experiment. Settlement counts were taken on June 28th, 2017. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/742565
Diel, daily, and spatial variation of coral reef seawater microbial communities from US Virgin Islands, 2017

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2019-08-19) Apprill, Amy

Bacterial and archaeal diversity and composition, microbial cell abundances, inorganic nutrient concentrations, and physicochemical conditions were determined and measured in coral reef seawater over a three-day, diel time series on one reef in St. John, U.S. Virgin Islands. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/775229
Bacterioplankton data from coral and coral mucus aquaria experiments conducted at Bermuda Institute of Ocean Sciences in 2013

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2019-06-05) Apprill, Amy

Bacterioplankton data from coral and coral mucus aquaria experiments conducted at Bermuda Institute of Ocean Sciences in 2013 For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/652849
Ecological results of SCTLD multi-species transmission experiment at the University of the Virgin Islands Center for Marine and Environmental Studies

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2022-07-20) Brandt, Marilyn ; Correa, Adrienne M.S. ; Meiling, Sonora ; Veglia, Alex J. ; Lasseigne, Danielle ; MacKnight, Nicholas ; Dimos, Bradford ; Huntley, Naomi ; Muller, Erinn ; Mydlarz, Laura ; Apprill, Amy ; Smith, Tyler ; Holstein, Daniel

This dataset represents the ecological results of a stony coral tissue loss disease (SCTLD) multi-species transmission experiment. Eight colonies of six species of corals (Colpophyllia natans, Montastraea cavernosa, Orbicella annularis, Porites astreoides, Pseudodiploria strigosa, and Siderastrea siderea) were split in half and one half of these fragments were simultaneously exposed toSCTLD-affected colonies of Diploria labyrinthiformis and the other half were exposed to healthy colonies of D. labyrinthiformis. All corals were monitored for lesion appearance over an eight day experimental period. No lesions were recorded on healthy-exposed corals. Numbers of fragments showing lesion appearance, time to lesion appearance, and expansion rates of lesions for SCTLD-exposed corals are reported here. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/875156
16S V4 rRNA gene tag sequences from reef seawater samples collected in the Florida Keys and the U.S. Virgin Islands in 2019-2020

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2021-08-24) Apprill, Amy ; Ma, Lei

This dataset describes 16S V4 rRNA gene tag sequences from reef seawater. Samples were collected from three reefs in U.S. Virgin Islands and three reefs in Florida Reef tract. Sequence data can be found in the NCBI SRA database under the bioproject PRJNA733652. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/858459

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