Biology:Marine bacteriophage

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Electron micrograph of negative-stained Prochlorococcusmyoviruses

Marine viruses are small infectious agents found in the ocean that require living host machinery for replication.[1] They consist of a core of nucleic acids coated with protein, as they have the traditional virus assemblage. The dominant hosts for viruses in the ocean are marine microorganisms such as cyanobacteria.[2] Viruses that that live as obligate parasitic agents in marine bacteria are known as marine bacteriophages or marine phages.[2] The existence of viruses in the ocean was discovered through electron microscopy and epifluorescence microscopy of ecological water samples, and later through metagenomic sampling of uncultured viral samples.[2][3] Marine viruses, although microscopic and essentially unnoticed by scientists until recently, are the most abundant and diverse biological entities in the ocean. Viruses have an estimated abundance of 1030 in the ocean, or between 1 and 100,000x106 per millilitre.[1] Quantification of marine viruses was originally performed using transmission electron microscopy but has been replaced by epifluorescence or flow cytometry.[4]

Distribution

Viruses are highly host specific.[5] Studies have shown that marine viruses are more likely to infect cooccurring organisms, those that live in the same region a virus exists in.[6] Therefore, biogeography is an important factor in a virion’s ability to infect.

The knowledge of variation of viral populations across spatiotemporal and other environmental gradients is supported viral morphology, determined by transmission electron microscopy (TEM).  Non-tailed viruses appear to be dominant in multiple depths and oceanic regions, followed by the Caudovirales myoviruses, podoviruses, and siphoviruses.[7] However, viruses belonging to families Corticoviridae,[8] Inoviridae[9] and Microviridae[10] are also known to infect diverse marine bacteria. Metagenomic evidence suggests that microviruses (icosahedral ssDNA phages) are particularly prevalent in marine habitats.[10]

Metagenomic approaches to assess viral diversity are often limited by a lack of reference sequences, leaving many sequences unannotated.[11]  However, viral contigs are generated through direct sequencing of a viral fraction, typically generated after 0.02-um filtration of a marine water sample, or through bioinformatics approaches to identify viral contigs or viral genomes from a microbial metagenome.  Novel tools to identify putative viral contigs, such as VirSorter[12] and VirFinder,[13] allow for the assessment of patterns of viral abundance, host range, and functional content of marine bacteriophage.[14][15]

Virus-to-Prokaryote Ratio

The virus-to-prokaryote ratio, VPR, is often used as an indicator of the relationship between viruses and hosts. Studies have used VPR to indirectly infer virus impact on marine microbial productivity, mortality, and biogeochemical cycling.[16] However, in making these approximations, scientists assume a VPR of 10:1, the median observed VPR in the surface ocean.[16][17][7] The actual VPR varies greatly depending on location, so VPR may not be the accurate proxy for viral activity or abundance as it has been treated.[16][18]

Ecological Importance

Although marine viruses have only recently been studied extensively, they are already known to hold critical roles in many ecosystem functions and cycles. Marine bacteriophages and other viruses appear to influence biogeochemical cycles globally, provide and regulate microbial biodiversity, cycle carbon through marine food webs, and are essential in preventing bacterial population explosions.[19] Scientists are exploring the potential of marine cyanophages to be used to prevent or reverse eutrophication.

In the water column

Marine viral activity presents a potential explanation of the Paradox of the Plankton, proposed by George Evelyn Hutchinson in 1961.[20] The Paradox of the Plankton is that many plankton species have been identified in small regions in the ocean, where limited resources should create competitive exclusion, limiting the number of coexisting species.[20] Marine viruses could play a role in this effect, as viral infection increases as potential contact with hosts increases.[1] Viruses could therefore control the populations of plankton species that grow too abundant, allowing a wide diversity of species to coexist.[1]

In sediments

Marine bacteriophages play an important role in deep sea ecosystems. There are between 5x1012 and 1x1013 phages per square metre in deep sea sediments and their abundance closely correlates with the number of prokaryotes found in the sediments. They are responsible for the death of 80% of the prokaryotes found in the sediments, and almost all of these deaths are caused by cell lysis (bursting). This allows nitrogen, carbon, and phosphorus from the living cells to be converted into dissolved organic matter and detritus, contributing to the high rate of nutrient turnover in deep sea sediments. Because of the importance of deep sea sediments in biogeochemical cycles, marine bacteriophages influence the carbon, nitrogen and phosphorus cycles. More research needs to be done to more precisely elucidate these influences.[21]

Nutrient cycles

Marine viruses are thought to play an important role in nutrient cycles by increasing the efficiency of the biological pump. Viruses cause lysis of living cells, releasing compounds such as amino acids and nucleic acids, which tend to be recycled near the surface. Lysis also releases more indigestible carbon-rich material like that found in cell walls, which is likely exported to deeper waters. Thus, the material that is exported to deeper waters by the 'viral shunt' is probably more carbon rich than the material from which it was derived. This would increase the efficiency of the biological pump.[22][23]

Marine bacteriophages often contain auxiliary metabolic genes, host-derived genes thought to sustain viral replication by supplementing host metabolism during viral infection.[24]  These genes can impact multiple biogeochemical cycles, including carbon, phosphorus, sulfur, and nitrogen.[25][26][27][28]

References

  1. ↑ 1.0 1.1 1.2 1.3 Brussaard, Corina P.D.; Baudoux, Anne-Claire; Rodríguez-Valera, Francisco (2016). Stal, Lucas J.; Cretoiu, Mariana Silvia. eds (in en). Marine Viruses. Springer International Publishing. pp. 155–183. doi:10.1007/978-3-319-33000-6_5. ISBN 9783319329987. 
  2. ↑ 2.0 2.1 2.2 "The third age of phage". PLoS Biology 3 (5): e182. May 2005. doi:10.1371/journal.pbio.0030182. PMID 15884981. 
  3. ↑ "Effects of sunlight on bacteriophage viability and structure". Applied and Environmental Microbiology 62 (4): 1336–41. April 1996. PMID 8919794. 
  4. ↑ "Enumeration of marine viruses in culture and natural samples by flow cytometry". Applied and Environmental Microbiology 65 (1): 45–52. January 1999. PMID 9872758. 
  5. ↑ "Generalism and the evolution of parasite virulence" (in English). Trends in Ecology & Evolution 28 (10): 592–6. October 2013. doi:10.1016/j.tree.2013.07.002. PMID 23968968. 
  6. ↑ "Multi-scale structure and geographic drivers of cross-infection within marine bacteria and phages". The ISME Journal 7 (3): 520–32. March 2013. doi:10.1038/ismej.2012.135. PMID 23178671. 
  7. ↑ 7.0 7.1 "Global morphological analysis of marine viruses shows minimal regional variation and dominance of non-tailed viruses". The ISME Journal 7 (9): 1738–51. September 2013. doi:10.1038/ismej.2013.67. PMID 23635867. 
  8. ↑ "Putative prophages related to lytic tailless marine dsDNA phage PM2 are widespread in the genomes of aquatic bacteria". BMC Genomics 8: 236. July 2007. doi:10.1186/1471-2164-8-236. PMID 17634101. 
  9. ↑ "High frequency of a novel filamentous phage, VCY φ, within an environmental Vibrio cholerae population". Applied and Environmental Microbiology 78 (1): 28–33. January 2012. doi:10.1128/AEM.06297-11. PMID 22020507. 
  10. ↑ 10.0 10.1 "Evolution and diversity of the Microviridae viral family through a collection of 81 new complete genomes assembled from virome reads". PLOS ONE 7 (7): e40418. 2012. doi:10.1371/journal.pone.0040418. PMID 22808158. Bibcode: 2012PLoSO...740418R. 
  11. ↑ "The Pacific Ocean virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology". PLOS ONE 8 (2): e57355. 2013. doi:10.1371/journal.pone.0057355. PMID 23468974. Bibcode: 2013PLoSO...857355H. 
  12. ↑ "VirSorter: mining viral signal from microbial genomic data". PeerJ 3: e985. 2015-05-28. doi:10.7717/peerj.985. PMID 26038737. 
  13. ↑ "VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data". Microbiome 5 (1): 69. July 2017. doi:10.1186/s40168-017-0283-5. PMID 28683828. 
  14. ↑ "Uncovering Earth's virome". Nature 536 (7617): 425–30. August 2016. doi:10.1038/nature19094. PMID 27533034. Bibcode: 2016Natur.536..425P. http://www.escholarship.org/uc/item/4zh090xt. 
  15. ↑ "Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans". Nature Communications 8: 15955. July 2017. doi:10.1038/ncomms15955. PMID 28677677. Bibcode: 2017NatCo...815955C. 
  16. ↑ 16.0 16.1 16.2 "Re-examining the relationship between virus and microbial cell abundances in the global oceans". bioRxiv: 025544. 2015-08-26. doi:10.1101/025544. 
  17. ↑ "Virioplankton: viruses in aquatic ecosystems". Microbiology and Molecular Biology Reviews 64 (1): 69–114. March 2000. doi:10.1128/mmbr.64.1.69-114.2000. PMID 10704475. 
  18. ↑ "Deciphering the virus-to-prokaryote ratio (VPR): insights into virus-host relationships in a variety of ecosystems". Biological Reviews of the Cambridge Philosophical Society 92 (2): 1081–1100. May 2017. doi:10.1111/brv.12271. PMID 27113012. 
  19. ↑ Phages: their role in bacterial pathogenesis and biotechnology. Washington DC: ASM Press. 2005. pp. 450. ISBN 978-1-55581-307-9. 
  20. ↑ 20.0 20.1 "The Paradox of the Plankton". The American Naturalist 95 (882): 137–145. 1961. doi:10.1086/282171. 
  21. ↑ "Major viral impact on the functioning of benthic deep-sea ecosystems". Nature 454 (7208): 1084–7. August 2008. doi:10.1038/nature07268. PMID 18756250. Bibcode: 2008Natur.454.1084D. 
  22. ↑ Suttle CA. Marine viruses—major players in the global ecosystem. Nature Reviews Microbiology. October 2007;5(10):801–12. doi:10.1038/nrmicro1750. PMID 17853907.
  23. ↑ "Viruses in the sea". Nature 437 (7057): 356–61. September 2005. doi:10.1038/nature04160. PMID 16163346. Bibcode: 2005Natur.437..356S. 
  24. ↑ Breitbart, Mya; Thompson, Luke; Suttle, Curtis; Sullivan, Matthew (2007-06-01). "Exploring the Vast Diversity of Marine Viruses". Oceanography 20 (2): 135–139. doi:10.5670/oceanog.2007.58. https://tos.org/oceanography/assets/docs/20-2_breitbart.pdf. 
  25. ↑ "Viral metabolic reprogramming in marine ecosystems". Current Opinion in Microbiology 31: 161–168. June 2016. doi:10.1016/j.mib.2016.04.002. PMID 27088500. 
  26. ↑ "Metabolic reprogramming by viruses in the sunlit and dark ocean". Genome Biology 14 (11): R123. November 2013. doi:10.1186/gb-2013-14-11-r123. PMID 24200126. 
  27. ↑ "Sulfur oxidation genes in diverse deep-sea viruses". Science 344 (6185): 757–60. May 2014. doi:10.1126/science.1252229. PMID 24789974. Bibcode: 2014Sci...344..757A. 
  28. ↑ "Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics". eLife 3: e03125. August 2014. doi:10.7554/elife.03125. PMID 25171894. 




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