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  • 1
    Online Resource
    Online Resource
    Viruses of a key coral symbiont exhibit temperature-driven productivity across a reefscape
    Springer Science and Business Media LLC ; 2023
    In:  ISME Communications Vol. 3, No. 1 ( 2023-04-03)
    Details
    In: ISME Communications, Springer Science and Business Media LLC, Vol. 3, No. 1 ( 2023-04-03)
    Abstract: Viruses can affect coral health by infecting their symbiotic dinoflagellate partners (Symbiodiniaceae). Yet, viral dynamics in coral colonies exposed to environmental stress have not been studied at the reef scale, particularly within individual viral lineages. We sequenced the viral major capsid protein ( mcp ) gene of positive-sense single-stranded RNA viruses known to infect symbiotic dinoflagellates (‘dinoRNAVs’) to analyze their dynamics in the reef-building coral, Porites lobata . We repeatedly sampled 54 colonies harboring Cladocopium C15 dinoflagellates, across three environmentally distinct reef zones (fringing reef, back reef, and forereef) around the island of Moorea, French Polynesia over a 3-year period and spanning a reef-wide thermal stress event. By the end of the sampling period, 28% (5/18) of corals in the fringing reef experienced partial mortality versus 78% (14/18) of corals in the forereef. Over 90% (50/54) of colonies had detectable dinoRNAV infections. Reef zone influenced the composition and richness of viral mcp amino acid types (‘aminotypes’), with the fringing reef containing the highest aminotype richness. The reef-wide thermal stress event significantly increased aminotype dispersion, and this pattern was strongest in the colonies that experienced partial mortality. These findings demonstrate that dinoRNAV infections respond to environmental fluctuations experienced in situ on reefs. Further, viral productivity will likely increase as ocean temperatures continue to rise, potentially impacting the foundational symbiosis underpinning coral reef ecosystems.
    Type of Medium: Online Resource
    ISSN: 2730-6151
    URL: Article
    DOI: 10.1038/s43705-023-00227-7
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
    detail.hit.zdb_id: 3041786-7
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  • 2
    Online Resource
    Online Resource
    Stony coral tissue loss disease induces transcriptional signatures of in situ degradation of dysfunctional Symbiodiniaceae
    Springer Science and Business Media LLC ; 2023
    In:  Nature Communications Vol. 14, No. 1 ( 2023-05-22)
    Details
    In: Nature Communications, Springer Science and Business Media LLC, Vol. 14, No. 1 ( 2023-05-22)
    Abstract: Stony coral tissue loss disease (SCTLD), one of the most pervasive and virulent coral diseases on record, affects over 22 species of reef-building coral and is decimating reefs throughout the Caribbean. To understand how different coral species and their algal symbionts (family Symbiodiniaceae) respond to this disease, we examine the gene expression profiles of colonies of five species of coral from a SCTLD transmission experiment. The included species vary in their purported susceptibilities to SCTLD, and we use this to inform gene expression analyses of both the coral animal and their Symbiodiniaceae. We identify orthologous coral genes exhibiting lineage-specific differences in expression that correlate to disease susceptibility, as well as genes that are differentially expressed in all coral species in response to SCTLD infection. We find that SCTLD infection induces increased expression of rab7 , an established marker of in situ degradation of dysfunctional Symbiodiniaceae, in all coral species accompanied by genus-level shifts in Symbiodiniaceae photosystem and metabolism gene expression. Overall, our results indicate that SCTLD infection induces symbiophagy across coral species and that the severity of disease is influenced by Symbiodiniaceae identity.
    Type of Medium: Online Resource
    ISSN: 2041-1723
    URL: Article
    DOI: 10.1038/s41467-023-38612-4
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
    detail.hit.zdb_id: 2553671-0
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  • 3
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    Online Resource
    Characterizing population structure of coral-associated fauna from mesophotic and shallow habitats in the Caribbean
    Cambridge University Press (CUP) ; 2019
    In:  Journal of the Marine Biological Association of the United Kingdom Vol. 99, No. 3 ( 2019-05), p. 619-629
    Details
    In: Journal of the Marine Biological Association of the United Kingdom, Cambridge University Press (CUP), Vol. 99, No. 3 ( 2019-05), p. 619-629
    Abstract: Symbiotic relationships are a common phenomenon among marine invertebrates, forming both obligatory and facultative dependencies with their host. Here, we investigate and compare the population structure of two crustacean species associated with both shallow and mesophotic ecosystems: an obligate symbiont barnacle (Ceratoconcha domingensis) , of the coral Agaricia lamarcki and a meiobenthic, free-living harpacticoid copepod (Laophontella armata) . Molecular analyses of the Cytochrome Oxidase Subunit I ( COI ) gene revealed no population structure between mesophotic and shallow barnacle populations within south-west Puerto Rico ( Φ ST = 0.0079, P = 0.33 ) . The absence of population structure was expected due to the pelagic naupliar larvae of the barnacles and the connectivity patterns exhibited by the coral itself within the same region. Laophontella armata exhibited significant structure based on the mitochondrial COI gene between the mesophotic reef ecosystem of El Seco, Puerto Rico and mangrove sediments of Curaçao ( Φ ST = 0.2804, P = 0.0 ) . The El Seco and Curaçao copepods shared three COI haplotypes despite the obligatory benthic development of harpacticoid copepods and the geographic distance between the two locations. Three other COI haplotypes from El Seco exhibited higher than expected ( up to 7% ) intra-species variability, potentially representing three new cryptic species of harpacticoid copepods or rare, deeply divergent lineages of L. armata . This result is evidence for the urgent need of a deeper investigation into the meiofauna diversity associated with mesophotic coral ecosystems ( MCEs ) , arguably the most diverse metazoan component of MCEs.
    Type of Medium: Online Resource
    ISSN: 0025-3154 , 1469-7769
    URL: Article
    DOI: 10.1017/S0025315418000413
    RVK:
    WA 15000
    Language: English
    Publisher: Cambridge University Press (CUP)
    Publication Date: 2019
    detail.hit.zdb_id: 1491269-7
    detail.hit.zdb_id: 281325-7
    SSG: 12
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  • 4
    Online Resource
    Online Resource
    DataSheet_7.docx
    Frontiers Media SA ; 2023
    In:  Frontiers in Marine Science Vol. 10 ( 2023-4-13)
    Details
    In: Frontiers in Marine Science, Frontiers Media SA, Vol. 10 ( 2023-4-13)
    Abstract: Animal waste products are an important component of nutrient cycles and result in the trophic transmission of diverse microorganisms. There is growing recognition that the feces of consumers, such as predators, may impact resource species, their prey, via physical effects and/or microbial activity. We tested the effect of feces from distinct fish trophic groups on coral health and used heat-killed fecal controls to tease apart physical versus microbial effects of contact with fecal material. Fresh grazer/detritivore fish feces caused lesions more frequently on corals, and lesions were 4.2-fold larger than those from sterilized grazer/detritivore feces; in contrast, fresh corallivore feces did not cause more frequent or larger lesions than sterilized corallivore feces. Thus, microbial activity in grazer/detritivore feces, but not corallivore feces, was harmful to corals. Characterization of bacterial diversity in feces of 10 reef fish species, ranging from obligate corallivores to grazer/detritivores, indicated that our experimental findings may be broadly generalizable to consumer guild, since feces of some obligate corallivores contained ~2-fold higher relative abundances of coral mutualist bacteria ( e.g., Endozoicomonadaceae), and lower abundances of the coral pathogen, Vibrio coralliilyticus , than feces of some grazer/detritivores. These findings recontextualize the ecological roles of consumers on coral reefs: although grazer/detritivores support coral reef health in various ways ( e.g. , promoting coral settlement and herbivory through the removal of detritus and sediments from the algal matrix), they also disperse coral pathogens. Corallivore predation can wound corals, yet their feces contain potentially beneficial coral-associated bacteria, supporting the hypothesized role of consumers, and corallivores in particular, in coral symbiont dispersal. Such consumer-mediated microbial dispersal as demonstrated here has broad implications for environmental management.
    Type of Medium: Online Resource
    ISSN: 2296-7745
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    DOI: 10.3389/fmars.2023.1110346
    DOI: 10.3389/fmars.2023.1110346.s001
    DOI: 10.3389/fmars.2023.1110346.s002
    DOI: 10.3389/fmars.2023.1110346.s003
    DOI: 10.3389/fmars.2023.1110346.s004
    DOI: 10.3389/fmars.2023.1110346.s005
    DOI: 10.3389/fmars.2023.1110346.s006
    DOI: 10.3389/fmars.2023.1110346.s007
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2023
    detail.hit.zdb_id: 2757748-X
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  • 5
    Online Resource
    Online Resource
    Isolation and genotyping of novel T4 cyanophages associated with diverse coral reef invertebrates
    Springer Science and Business Media LLC ; 2021
    In:  Coral Reefs Vol. 40, No. 2 ( 2021-04), p. 485-504
    Details
    In: Coral Reefs, Springer Science and Business Media LLC, Vol. 40, No. 2 ( 2021-04), p. 485-504
    Type of Medium: Online Resource
    ISSN: 0722-4028 , 1432-0975
    URL: Article
    DOI: 10.1007/s00338-021-02056-3
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 9047-5
    detail.hit.zdb_id: 1472576-9
    SSG: 12
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  • 6
    Online Resource
    Online Resource
    Thermal stress triggers productive viral infection of a key coral reef symbiont
    Oxford University Press (OUP) ; 2022
    In:  The ISME Journal Vol. 16, No. 5 ( 2022-05-01), p. 1430-1441
    Details
    In: The ISME Journal, Oxford University Press (OUP), Vol. 16, No. 5 ( 2022-05-01), p. 1430-1441
    Abstract: Climate change-driven ocean warming is increasing the frequency and severity of bleaching events, in which corals appear whitened after losing their dinoflagellate endosymbionts (family Symbiodiniaceae). Viral infections of Symbiodiniaceae may contribute to some bleaching signs, but little empirical evidence exists to support this hypothesis. We present the first temporal analysis of a lineage of Symbiodiniaceae-infecting positive-sense single-stranded RNA viruses (“dinoRNAVs”) in coral colonies, which were exposed to a 5-day heat treatment (+2.1 °C). A total of 124 dinoRNAV major capsid protein gene “aminotypes” (unique amino acid sequences) were detected from five colonies of two closely related Pocillopora-Cladocopium (coral-symbiont) combinations in the experiment; most dinoRNAV aminotypes were shared between the two coral-symbiont combinations (64%) and among multiple colonies (82%). Throughout the experiment, seventeen dinoRNAV aminotypes were found only in heat-treated fragments, and 22 aminotypes were detected at higher relative abundances in heat-treated fragments. DinoRNAVs in fragments of some colonies exhibited higher alpha diversity and dispersion under heat stress. Together, these findings provide the first empirical evidence that exposure to high temperatures triggers some dinoRNAVs to switch from a persistent to a productive infection mode within heat-stressed corals. Over extended time frames, we hypothesize that cumulative dinoRNAV production in the Pocillopora-Cladocopium system could affect colony symbiotic status, for example, by decreasing Symbiodiniaceae densities within corals. This study sets the stage for reef-scale investigations of dinoRNAV dynamics during bleaching events.
    Type of Medium: Online Resource
    ISSN: 1751-7362 , 1751-7370
    URL: Article
    DOI: 10.1038/s41396-022-01194-y
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2299378-2
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  • 7
    Online Resource
    Online Resource
    Variable Species Responses to Experimental Stony Coral Tissue Loss Disease (SCTLD) Exposure
    Frontiers Media SA ; 2021
    In:  Frontiers in Marine Science Vol. 8 ( 2021-4-30)
    Details
    In: Frontiers in Marine Science, Frontiers Media SA, Vol. 8 ( 2021-4-30)
    Abstract: Stony coral tissue loss disease (SCTLD) was initially documented in Florida in 2014 and outbreaks with similar characteristics have since appeared in disparate areas throughout the northern Caribbean, causing significant declines in coral communities. SCTLD is characterized by focal or multifocal lesions of denuded skeleton caused by rapid tissue loss and affects at least 22 reef-building species of Caribbean corals. A tissue-loss disease consistent with the case definition of SCTLD was first observed in the U.S. Virgin Islands (USVI) in January of 2019 off the south shore of St. Thomas at Flat Cay. The objective of the present study was to characterize species susceptibility to the disease present in St. Thomas in a controlled laboratory transmission experiment. Fragments of six species of corals ( Colpophyllia natans , Montastraea cavernosa , Orbicella annularis , Porites astreoides , Pseudodiploria strigosa , and Siderastrea siderea ) were simultaneously incubated with (but did not physically contact) SCTLD-affected colonies of Diploria labyrinthiformis and monitored for lesion appearance over an 8 day experimental period. Paired fragments from each corresponding coral genotype were equivalently exposed to apparently healthy colonies of D. labyrinthiformis to serve as controls; none of these fragments developed lesions throughout the experiment. When tissue-loss lesions appeared and progressed in a disease treatment, the affected coral fragment, and its corresponding control genet, were removed and preserved for future analysis. Based on measures including disease prevalence and incidence, relative risk of lesion development, and lesion progression rates, O. annularis, C. natans , and S. siderea showed the greatest susceptibility to SCTLD in the USVI. These species exhibited earlier average development of lesions, higher relative risk of lesion development, greater lesion prevalence, and faster lesion progression rates compared with the other species, some of which are considered to be more susceptible based on field observations (e.g., P. strigosa ). The average transmission rate in the present study was comparable to tank studies in Florida, even though disease donor species differed. Our findings suggest that the tissue loss disease affecting reefs of the USVI has a similar epizootiology to that observed in other regions, particularly Florida.
    Type of Medium: Online Resource
    ISSN: 2296-7745
    URL: Article
    DOI: 10.3389/fmars.2021.670829
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2021
    detail.hit.zdb_id: 2757748-X
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  • 8
    Online Resource
    Online Resource
    Correction to: Isolation and genotyping of novel T4 cyanophages associated with diverse coral reef invertebrates
    Springer Science and Business Media LLC ; 2021
    In:  Coral Reefs Vol. 40, No. 2 ( 2021-04), p. 683-683
    Details
    In: Coral Reefs, Springer Science and Business Media LLC, Vol. 40, No. 2 ( 2021-04), p. 683-683
    Type of Medium: Online Resource
    ISSN: 0722-4028 , 1432-0975
    URL: Article
    DOI: 10.1007/s00338-021-02070-5
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 9047-5
    detail.hit.zdb_id: 1472576-9
    SSG: 12
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  • 9
    Online Resource
    Online Resource
    vAMPirus : A versatile amplicon processing and analysis program for studying viruses
    Wiley ; 2024
    In:  Molecular Ecology Resources
    Details
    In: Molecular Ecology Resources, Wiley
    Abstract: Amplicon sequencing is an effective and increasingly applied method for studying viral communities in the environment. Here, we present vAMPirus, a user‐friendly, comprehensive, and versatile DNA and RNA virus amplicon sequence analysis program, designed to support investigators in exploring virus amplicon sequencing data and running informed, reproducible analyses. vAMPirus intakes raw virus amplicon libraries and, by default, performs nucleotide‐ and amino acid‐based analyses to produce results such as sequence abundance information, taxonomic classifications, phylogenies and community diversity metrics. The vAMPirus analytical framework leverages 16 different opensource tools and provides optional approaches that can increase the ratio of biological signal‐to‐noise and thereby reveal patterns that would have otherwise been masked. Here, we validate the vAMPirus analytical framework and illustrate its implementation as a general virus amplicon sequencing workflow by recapitulating findings from two previously published double‐stranded DNA virus datasets. As a case study, we also apply the program to explore the diversity and distribution of a coral reef‐associated RNA virus. vAMPirus is streamlined within Nextflow, offering straightforward scalability, standardization and communication of virus lineage‐specific analyses. The vAMPirus framework is designed to be adaptable; community‐driven analytical standards will continue to be incorporated as the field advances. vAMPirus supports researchers in revealing patterns of virus diversity and population dynamics in nature, while promoting study reproducibility and comparability.
    Type of Medium: Online Resource
    ISSN: 1755-098X , 1755-0998
    URL: Article
    DOI: 10.1111/1755-0998.13978
    Language: English
    Publisher: Wiley
    Publication Date: 2024
    detail.hit.zdb_id: 2406833-0
    SSG: 12
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  • 10
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    Online Resource
    Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes
    Springer Science and Business Media LLC ; 2023
    In:  Communications Biology Vol. 6, No. 1 ( 2023-06-01)
    Details
    In: Communications Biology, Springer Science and Business Media LLC, Vol. 6, No. 1 ( 2023-06-01)
    Abstract: Endogenous viral elements (EVEs) offer insight into the evolutionary histories and hosts of contemporary viruses. This study leveraged DNA metagenomics and genomics to detect and infer the host of a non-retroviral dinoflagellate-infecting +ssRNA virus (dinoRNAV) common in coral reefs. As part of the Tara Pacific Expedition, this study surveyed 269 newly sequenced cnidarians and their resident symbiotic dinoflagellates (Symbiodiniaceae), associated metabarcodes, and publicly available metagenomes, revealing 178 dinoRNAV EVEs, predominantly among hydrocoral-dinoflagellate metagenomes. Putative associations between Symbiodiniaceae and dinoRNAV EVEs were corroborated by the characterization of dinoRNAV-like sequences in 17 of 18 scaffold-scale and one chromosome-scale dinoflagellate genome assembly, flanked by characteristically cellular sequences and in proximity to retroelements, suggesting potential mechanisms of integration. EVEs were not detected in dinoflagellate-free (aposymbiotic) cnidarian genome assemblies, including stony corals, hydrocorals, jellyfish, or seawater. The pervasive nature of dinoRNAV EVEs within dinoflagellate genomes (especially Symbiodinium ), as well as their inconsistent within-genome distribution and fragmented nature, suggest ancestral or recurrent integration of this virus with variable conservation. Broadly, these findings illustrate how +ssRNA viruses may obscure their genomes as members of nested symbioses, with implications for host evolution, exaptation, and immunity in the context of reef health and disease.
    Type of Medium: Online Resource
    ISSN: 2399-3642
    URL: Article
    DOI: 10.1038/s42003-023-04917-9
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
    detail.hit.zdb_id: 2919698-X
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