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Environmental Virology

blue sky and white clouds over the ocean
blue sky and white clouds over the ocean
yellow fish over corals
yellow fish over corals
body of water between grasses
body of water between grasses
green trees on forest during daytime
green trees on forest during daytime
Environmental Virology studies viruses in natural environments, focusing on their roles in ecosystems, including oceans, soils, and the atmosphere. It is crucial for understanding viral impacts on microbial communities, nutrient cycles, and global ecological processes. Current knowledge gaps include the diversity of environmental viruses and their specific functions, highlighting the need for further research to uncover the full extent of viral influence on ecological and evolutionary dynamics.
Take a moment to review the above photos showcasing these incredibly biodiverse ecosystems. Beyond the visible diversity, there is a remarkable amount of unseen biodiversity, particularly among the inhabiting viruses. Viruses are among the most abundant entities on Earth, with concentrations reaching approximately 10 million per milliliter of ocean water and up to a billion per gram of soil. This unseen viral diversity plays a crucial role in regulating ecological processes and maintaining the balance within these ecosystems!

Overarching ViDaB Lab Research Directions

  1. Investigate the diversity and ecology of viruses in plant and animal tissues, focusing on their role in health and disease.

  2. Explore virus-host and virus-virus interactions across various environmental contexts to understand their ecological and evolutionary impacts.

  3. Develop and refine bioinformatics tools to analyze virus sequencing data, enhancing our ability to detect and interpret patterns in viral communities across different ecosystems.

  4. Apply insights from these studies to inform ecosystem conservation and management practices, aiming to protect biodiversity and ecosystem health through targeted interventions.
Our Publications
Ongoing ViDaB Lab Projects

The Puerto Rico Coral Reef Virus Project investigates the diversity and ecological roles of viruses within marine invertebrate holobionts, such as corals and sponges. The project employs traditional microbiological and virological techniques to isolate and culture virus-host pairs from these holobionts for laboratory experimentation. Additionally, we utilize long-term monitoring and high-throughput sequencing techniques to explore virus diversity and population dynamics across time and space on the reef, providing a comprehensive look into viral influences on marine ecosystems.

Questions addressed:

Q1. How does virome composition vary spatially across different reef locations and temporally across sampling years?
Q2. To what extent does seasonal variability in environmental conditions (e.g., temperature, rainfall) affect the virome composition of marine invertebrates?
Q3. Which symbiotic viruses and their cellular hosts can be isolated from marine invertebrate holobionts?
Q4. To what extent do environmental factors influence holobiont-associated virus-host and virus-virus interactions?
Puerto Rico Cyanophage Project

The Puerto Rico Cyanophage Project investigates the diversity and dynamics of cyanophages across different aquatic environments, including coastal waters, wetlands, and lakes. We conduct monthly sampling at coastal sites in Mayagüez Bay and La Parguera Natural Reserve, using most-probable-number assays to measure cyanophage abundance and isolating viruses to assess diversity. Additionally, we perform extinction dilution assays across various water bodies to isolate cyanophages infecting different cyanobacteria strains. We sequence these isolates to analyze single genes or entire genomes, comparing our findings—abundance, genetic diversity, and ecological diversity—with global cyanophage populations to understand broader ecological patterns.

Questions addressed:

Q1. What is the diversity of cyanophages across different aquatic systems in Puerto Rico?

Q2. How do cyanophage abundance and diversity fluctuate over time in Puerto Rico's coastal marine environments, and how do these patterns compare to those observed in more temperate regions like Rhode Island?

Q3. How do Puerto Rican cyanophages compare to those from other regions in terms of genome content and host range?

Extremophillic Virus Project

The Extremophilic Virus Project explores the diversity of viruses associated with extreme environments around Puerto Rico, employing isolation, culturing, and high-throughput sequencing techniques. Currently, we are focusing on isolating archaea-infecting viruses and cyanophages from Las Salinas in Cabo Rojo. Additionally, we are mining publicly available metagenomes to investigate virus-mediated host persistence in extreme environments. This involves identifying metabolically important genes within virus genomes and prophage elements that may aid cellular hosts in surviving extreme habitats.

Questions addressed:

Q1. What is the diversity of viruses inhabiting Las Salinas, Cabo Rojo hypersaline lagoons?

Q2. How do viruses contribute to host persistance in extreme environments?

Puerto Rico Coral Reef Virus Project

Publications

(ViDaB Lab Member; *Indicates undergraduate student; #Indicates equal authorship)
[16.] Vega Thurber, R. L., Silva, D., Speare, L., Croquer, A., Veglia, A. J., Alvarez-Filip, L., Zaneveld, J. R., Muller, E. M., & Correa, A. M. S. (2024). Coral disease: Direct and indirect agents, mechanisms of disease, and innovations for increasing resistance and resilience. Annual Review of Marine Science, 17, 20.1–20.29. https://doi.org/10.1146/annurev-marine-011123-102337
[15.] ^Toledo-Rodriguez, D. A., Veglia, A.J., Marrero, N. M. J., Gomez-Samot, J. M., McFadden, C. S., Weil, E., & Schizas, N. V. (2024). Shadows over Caribbean reefs: Identification of a new invasive soft coral species, Xenia umbellata, in southwest Puerto Rico. bioRxiv. DOI: 10.1101/2024.05.07.592775
[14.] Veglia, A.J., Rivera-Vicéns, R.E., Grupstra, C.G.B., Howe-Kerr, L.I., Correa, A.M.S. (2024) vAMPirus: A versatile amplicon processing and analysis program for studying viruses. Molecular Ecology Resources. https://doi.org/10.1111/1755-0998.13978

[13.] Howe-Kerr, L. I., Knochel, A. M., Meyer, M. D., Sims, J. A., Karrick, C. E., Grupstra, C. G. B., Veglia, A.J., Thurber, A. R., Vega Thurber, R. L., & Correa, A. M. S. (2023). Filamentous virus-like particles are present in coral dinoflagellates across genera and ocean basins. The ISME Journal, 1-14. https://doi.org/10.1038/s41396-023-01353-9
[12.] Veglia, A.J.#, Bistolas, K.#, The Tara Pacific Consortium, Correa, A.M.S., Vega Thurber, R. L. (2023). Endogenous viral elements reveal ancient associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes. Communications Biology. DOI: doi.org/10.1038/s42003-023-04917-9
[11.] Beavers, K., Van Buren, E., Rossin, A., Emery, M., Veglia, A.J., Karrick, C., MacKnight, N., Dimos, B., Meiling, S., Smith T., Apprill, A., Muller, E., Holstein, D., Correa, A., Brandt, M., Mydlarz, L. (2023). Stony Coral Tissue Loss Disease Induces Transcriptional Signatures of in situ Degradation of Dysfunctional Symbiodiniaceae. Nature Communications. DOI: 10.1038/s41467-023-38612-4
[10.] Howe-Kerr, L.I., Grupstra, C.G.B., Rabbitt, K., Conetta, D., Coy, S.R., Klinges, J.G., Maher, R.L., McConnell, K.M., Meiling, S.S., Messyasz, A., Schmeltzer, E.R., Seabrook, S., Sims, J., Veglia, A.J., Thurber, A.R., Vega Thurber, R.L., Correa, A.M.S. (2023). Viruses of a key coral symbiont exhibit temperature-driven productivity across a reefscape. ISME Communications. DOI: 10.1038/s43705-023-00227-7
[9.] Grupstra, C.G.B., Howe-Kerr, L.I., van der Meulen, J.A., Veglia, A.J., Coy, S.R., Correa, A.M.S. (2023). Consumer feces impacts coral health in guild-specific ways. Frontiers in Marine Science. DOI: 10.3389/fmars.2023.1110346

[8.] Veglia, A.J., Beavers, K., Van Buren, E. W., Meiling, S. S., Muller, E. M., Smith, T. B., ... & Correa, A. M. S. (2022). Alphaflexivirus genomes in stony coral tissue loss disease-affected, disease-exposed, and disease-unexposed coral colonies in the US Virgin Islands. Microbiology Resource Announcements, 11(2), e01199-21.
[7.] Grupstra, C.G.B., Howe-Kerr, L.I.#, Veglia, A.J.#, Bryant, R., Coy, S.R., Blackwelder, P.L., Correa, A.M.S. (2022). Increased water temperatures drive rapid changes to dinorna-like virus consortia in the stony coral Pocillopora verrucosa. The ISME Journal. 16 (5), 1430-1441.

[6.] Meiling, S. S., Muller, E. M., Lasseigne, D., Rossin, A., Veglia, A.J., MacKnight, N., … & Brandt, M. E. (2021). Variable species responses to experimental stony coral tissue loss disease (SCTLD) exposure. Frontiers in Marine Science. 8, 464.
[5.] Veglia, A.J., Milford, C.R., Schizas, N.V. (2021). Isolation and genotyping of novel T4 cyanophages associated with diverse coral reef invertebrates. Coral Reefs. 40(2), 485-504.

[4.] Hammerman, N.M., Williams, S., Veglia, A.J., García-Hernández, J.E., Lang, J.E., and Schizas, N.V. (2020). A new record of a cup coral (Cladopsammia manuelensis) in Hispaniola and Puerto Rico. Cahiers de Biologie Marine. 62, 1-10.

[3.] Rivera-García, L., Rivera-Vicéns, R., Veglia, A.J., and Schizas, N.V. (2019). De novo transcriptome assembly of the soft octocoral Briareum asbestinum (digitate morphology) from southwest continental shelf of Puerto Rico. Marine Genomics. doi: 10.1016/j.margen.2019.04.001

[2.] Veglia, A.J., Hammerman, N.M., Rivera-Vicéns, R.E., and Schizas, N.V. (2018). De novo transcriptome assembly of the coral Agaricia lamarcki (Lamarck’s sheet coral) from mesophotic depths in southwest Puerto Rico. Marine Genomics. 41:6-11. doi: 10.1016/j.margen.2018.08.003
[1.] Veglia, A.J., Hammerman, N.M., Rivera Rosaly, C.R., Lucas, M., Galindo Estronza, A., Corgosinho, P.H., and Schizas, N.V. (2018). Characterizing population structure of coral- associated fauna from mesophotic and shallow habitats in the Caribbean. Journal of the Marine Biological Association of the United Kingdom. 1-11. doi: doi.org/10.1017/S0025315418000413
2024
2023
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2021
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2019
In Review
[] Toledo-Rodriguez, D. A., Veglia, A.J., Marrero, N. M. J., Gomez-Samot, J. M., McFadden, C. S., Weil, E., & Schizas, N. V. (In Review). Shadows over Caribbean reefs: Identification of a new invasive soft coral species, Xenia umbellata, in southwest Puerto Rico. Coral Reefs.
[] García-Hernández, J. E., Veglia, A.J., Alfaro, M., & Schizas, N. V. (In Review). Ents of coral reefs: The giant barrel sponge Xestospongia muta functioning as OA2SIS (Oscillators, Attractors, and Amplifiers of Symbiotic Interactions between Species) for biodiversity. Marine Biodiversity.
2018