Analysis of composition and abundance of viral communities associated with coral \(\textit{Acropora formosa}\)

Doan Thi Nhung; Bui Van Ngoc

doi:10.15625/2615-9023/15595

Author affiliations

Authors

Doan Thi Nhung Institute of Biotechnology
Bui Van Ngoc Institute of Biotechnology

DOI:

https://doi.org/10.15625/2615-9023/15595

Keywords:

Acropora formosa sp., DADA2, Kaiju, Krona, metagenomics, R programming language, virus, whole genome sequencing

Abstract

Coral reefs harbor the extraordinary biodiversity and not only provide livelihoods for coastal communities but also play a crucial role in economic development generally. Unfortunately, they are in decline in Vietnam and around the world because mass coral bleaching events have become more common worldwide. However, little is discovered, about viruses that infect corals and their symbionts. Herein, we present metagenomic analyses of the viral communities in coral mucus associated with healthy and bleached coral Acropora formosa which was collected at Con Dao Island, Vietnam. Interestingly, the number of viral species in bleached specimens are higher than those in healthy status. Viruses similar to those that infect humans and some marine animals also appeared in the coral viral assemblage. The results indicated that the proportion of shared viruses were quite small, and represented extremely abundance. Among the phage identified, vibriophage and cyanophage were only presented in healthy and bleached coral, respectively. Therefore, coral-associated viruses could prospectively infect all constituents of the holobiont - coral, microalgal and microbial. Thus, we expect viruses to be illustrated prominently in the preservation and breakdown of coral health.

Downloads

Download data is not yet available.

Metrics

Metrics Loading ...

References

Bak R., Joenje M. I. J., Lambrechts D., Nieuwland G., 1998. Bacterial suspension feeding by coral reef benthic organisms. Mar. Ecol. Progr. Ser., 175: 285–288.

Ben-Haim Y., Zicherman-Keren M., Rosenberg E., 2003. Temperature-regulated bleaching and lysis of the coral Pocillopora damicomis by the novel pathogen Vibrio coralliilyticus. Appl. Environ. Microbiol., 69(7): 4236–4242.

Bythella C. J., Wild C., 2011. Biology and ecology of coral mucus release. J. Exp. Mar. Biol. Ecol., 408: 88–93.

Callahan B.J., McMurdie P.J., Rosen M.J., Han A.W., Johnson A.J.A., Holmes S.P., 2016. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods., 13(7): 581–583.

Davy S. K, Burchett S. G., Dale A. L., Davies P., Davy J. E., Muncke C., Hoegh-Guldberg O., Wilson W.H., 2006. Viruses: agents of coral disease? Dis. Aquat. Organ., 69(1): 101–110.

Dana J. D., 1846–1849. Zoophytes. United States Exploring Expedition during the years 1838–1842. Lea and Blanchard, Philadelphia., 7: 1–740.

Dung L. D., 2020. The status of coral reefs in central Vietnam’s coastal water under climate change. Aquat. Ecosyst. Health. Manag., 23(3): 323–331.

Fuhrman J. A., Schwalbach M., 2003. Viral influence on aquatic bacterial communities. Biol. Bull., 204(2): 192–195.

Kim B. R., 2006. Regulation of microbial populations by coral surface mucus and mucus- associated bacteria. Mar. Ecol. Progr. Ser., 322: 929−933.

Kushmaro A., Banin E., Loya Y., Stackebrandt E., Rosenberg E., 2001. Vibrio shiloi sp. nov., the causative agent of bleaching of the coral Oculina patagonica. Int. J. Syst. Evol. Microbiol., 51(4): 1383–1388.

Kvennefors E. C. E., Sampayo E., Kerr C., Vieira G., Roff G., Barnes A. C., 2012. Regulation of bacterial communities through antimicrobial activity by the coral holobiont. Microb. Ecol., 63(3): 605–618.

Kysela D. T., Palacios C., Sogin M. L., 2005. Serial analysis of V6 ribosomal sequence tags (SARST-V6): a method for efficient, high-throughput analysis of microbial community composition. Environ. Microbiol., 7(3): 356–364.

Lesser M. P., Mazel C. H., Gorbunov M. Y., Falkowski P. G., 2004. Discovery of symbiotic nitrogen-fixing cyanobacteria in corals. Science (New York, N.Y.)., 305(5686): 997–1000.

Marhaver K. L., Edwards R. A., Rohwer F., 2008. Viral communities associated with healthy and bleaching corals. Environ. Microbiol., 10(9): 2277–2286.

Menzel P., Ng K. L., Krogh A., 2016. Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nat. Commun., 7: 11257.

Nguyen-Kim H., Bettarel Y., Bouvier T., Bouvier C., Doan-Nhu H., Nguyen-Ngoc L., Nguyen-Thanh T., Tran-Quang H., Brune J., 2015. Coral mucus is a hot spot for viral infections. Appl. Environ. Microbiol., 81(17): 5773–5783.

Nguyen-Kim H., Bouvier T., Bouvier C., Bui V. N., Le-Lan H., Bettarel Y., 2015. Viral and bacterial epibionts in thermally-stressed corals. J. Mar. Sci. Eng., 3(4): 1272–1286.

Nguyen Manh Linh, Pham The Thu, Nguyen Van Quan, Pham Van Chien, Dao Huong Ly, Dinh Van Nhan, Dam Thi Len, 2019. DNA barcoding application of mitochondrial COI gene to identify some fish species of family Gobiidae in Vietnam. Vietnam Journal of Marine Science and Technology, 18(4): 443–451.

Nguyen Van Lam, Pham Quang Huy, Nguyen Quoc Dai, Hoang Minh Hien, Dang Diem Hong, Le Van Son, Chu Hoang Ha, Truong Nam Hai, Nguyen Cuong, 2015. Genome assembly and annotation of the heterotrophic microalga Schizochytrium Mangrovei PQ6 in Viet Nam. Vietnam. J. Sci. Technol., 2(6).

Ondov B., Bergman N., Phillippy A., 2011. Krona: Interactive Metagenomic Visualization. BMC. Bioinform., 12: 385.

Pham The Thu, 2014. Correlation between viruses and bacteria in coral mucus at Cat Ba and Long Chau areas, Vietnam. Academia Journal of Biology, 36(3): 301–308.

Reshef L., Koren O., Loya Y., Zilber-Rosenberg I., Rosenberg E., 2006. The coral probiotic hypothesis. Environ. Microbiol., 8(12): 2068–2073.

Rosenberg E., Kushmaro A., Kramarsky-Winter E., Banin E., Yossi L., 2009. The role of microorganisms in coral bleaching. ISME. J., 3(2): 139–146.

Sato Y., Ling E., Turaev D., Laffy P., Weynberg K., Rattei T., Willis B., Bourne D., 2017. Unraveling the microbial processes of black band disease in corals through integrated genomics. Sci. Rep., 7(1): 1–14.

Soffer N., Brandt M. E., Correa A. M. S., Smith T. B., Thurber R. V., 2014. Potential role of viruses in white plague coral disease. ISME. J., 8(2): 271–283.

Suttle C. A., 2007. Marine viruses–major players in the global ecosystem. Nat. Rev. Microbioly., 5(10): 801–812.

Tran Thi Hong, Pham Viet Cuong, Nguyen Thi Kim Cuc, 2019. Screening genes encoding protein protease inhibitor from metagenome of sponge-associated microorganisms in Quang Tri sea, Vietnam. Academia Journal of Biology, 41(2): 49–60.

Vo S. T. 2000. The corals at Con Dao Archipelago (South Vietnam): Before, during and after the bleaching event in 1998. International Coral Reef Symposium Indonesia, 9: 23–27.

Vo S. T., Phan K. H., Hua T. T., Thai M. Q., Hoang X. B., 2020. Genus-specific bleaching at Con Dao Islands, Southern Vietnam, June 2019. Galaxea, J. C. R. S., 22(1): 27–28.

Vollmer V. S., Baker C. A., Coffroth M-A., Harvell C. D., Medina M., 2013. Understanding the coral holobiont through science and scuba. Smithson. Contrib. Mar. Sci., 173–186.