Viral activities and life cycles in deep subseafloor sediments

Environmental Microbiology Reports

Volumn 7, Issue 6, 2015, Pages 868-873

  Engelhardt, Tim ^a   Orsi, William D ^b   Jørgensen, Bo Barker ^a  

^a AARHUS UNIVERSITY   (Denmark)

^b WOODS HOLE OCEANOGRAPHIC INSTITUTION   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

VIRUS DNA; VIRUS RNA;

BIODIVERSITY; CLASSIFICATION; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; GENE EXPRESSION REGULATION; GENETICS; METAGENOME; METAGENOMICS; MICROBIOLOGY; SEDIMENT; VIROLOGY; VIRUS;

BIODIVERSITY; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEATS; DNA, VIRAL; ENVIRONMENTAL MICROBIOLOGY; GENE EXPRESSION REGULATION, VIRAL; GEOLOGIC SEDIMENTS; METAGENOME; METAGENOMICS; RNA, VIRAL; VIRUSES;

EID: 84955216670     PISSN: None     EISSN: 17582229     Source Type: Journal    
DOI: 10.1111/1758-2229.12316     Document Type: Article

References (36)

1. Ackermann, H.-W., and DuBow, M.S. (1987) Viruses of prokaryotes. In General Properties of Bacteriophages, Vol. I. DuBow, M.S. (ed.). Boca Raton: CRC Press.
2. Anderson, R.E., Brazelton, W.J., and Baross, J.A. (2011) Using CRISPRs as a metagenomic tool to identify microbial hosts of a diffuse flow hydrothermal vent viral assemblage. FEMS Microbiol Ecol 77: 120-133.
3. Baltimore, D. (1971) Expression of animal virus genomes. Bacteriol Rev 35: 235-241.
4. Barrangou, R. (2013) CRISPR-Cas systems and RNA-guided interference. Wiley Interdiscip Rev RNA 4: 267-278.
5. Barrangou, R., and Marraffini, L.A. (2014) CRISPR-Cas systems: prokaryotes upgrade to adaptive immunity. Mol Cell 54: 234-244.
6. Bengtson, S., Ivarsson, M., Astolfo, A., Belivanova, V., Broman, C., Marone, F., and Stampanoni, M. (2014) Deep-biosphere consortium of fungi and prokaryotes in Eocene subseafloor basalts. Geobiology 12: 489-496.
7. Bhaya, D., Davison, M., and Barrangou, R. (2011) CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation. Annu Rev Genet 45: 273-297.
8. Bird, D.F., Juniper, S.K., Ricciardi-Rigault, M., Martineu, P., Prairie, Y.T., and Calvert, S.E. (2001) Subsurface viruses and bacteria in Holocene/Late Pleistocene sediments of Saanich Inlet, BC: ODP Holes 1033B and 1034B, Leg 169S. Mar Geol 174: 227-239.
9. Breitbart, M. (2012) Marine viruses: truth or dare. Annu Rev Mar Sci 4: 425-448.
10. Davis, B.M., Kimsey, H.H., Kane, A.V., and Waldor, M.K. (2002) A satellite phage-encoded antirepressor induces repressor aggregation and cholera toxin gene transfer. Embo J 21: 4240-4249.
11. Engelhardt, T., Sahlberg, M., Cypionka, H., and Engelen, B. (2011) Induction of prophages from deep-subseafloor bacteria. Environ Microbiol Rep 3: 459-465.
12. Engelhardt, T., Sahlberg, M., Cypionka, H., and Engelen, B. (2013) Biogeography of Rhizobium radiobacter and distribution of associated temperate phages in deep subseafloor sediments. Isme J 7: 199-209.
13. Engelhardt, T., Kallmeyer, J., Cypionka, H., and Engelen, B. (2014) High virus-to-cell ratios indicate ongoing production of viruses in deep subsurface sediments. Isme J 8: 1503-1509.
14. Fell, J.W., and Master, I.M. (1980) The association and potential role of fungi in mangrove detrital systems. Botanica Marina 23: 257-263.
15. Fell, J.W., and Newell, S.Y. (1981) Role of fungi in carbon flow and nitrogen immobilization in coastal marine plant litter systems. In The Fungal Community, its Organization and Role in the Ecosystem. Wicklow, D.T., and Carroll, G.C. (eds). NY, USA: Marcel Dekker.
16. Hoehler, T.M., and Jørgensen, B.B. (2013) Microbial life under extreme energy limitation. Nat Rev Microbiol 11: 83-94.
17. Hopkins, M., Kailasan, S., Cohen, A., Roux, S., Tucker, K.P., Shevenell, A., etal. (2014) Diversity of environmental single-stranded DNA phages revealed by PCR amplification of the partial major capsid protein. Isme J 8: 2093-2103.
18. Jørgensen, B.B. (2012) Shrinking majority of the deep biosphere. Proc Natl Acad Sci USA 109: 15976-15977.
19. Kallmeyer, J., Pockalny, R., Adhikari, R.R., Smith, D.C., and D'Hondt, S. (2012) Global distribution of microbial abundance and biomass in subseafloor sediment. Proc Natl Acad Sci USA 109: 16213-16216.
20. Kim, K.H., and Bae, J.W. (2011) Amplification methods bias metagenomic libraries of uncultured single-stranded and double-stranded DNA viruses. Appl Environ Microbiol 77: 7663-7668.
21. Krupovic, M., Forterre, P., and Bamford, D.H. (2010) Comparative analysis of the mosaic genomes of tailed archaeal viruses and proviruses suggests common themes for virion architecture and assembly with tailed viruses of bacteria. J Mol Biol 397: 144-160.
22. Krupovic, M., Prangishvili, D., Hendrix, R.W., and Bamford, D.H. (2011) Genomics of bacterial and archaeal viruses: dynamics within the prokaryotic virosphere. Microbiol Mol Biol Rev 75: 610-635.
23. Langerhuus, A.T., Røy, H., Lever, M.A., Morono, Y., Inagaki, F., Jørgensen, B.B., and Lomstein, B.A. (2012) Endospore abundance and D:L-amino acid modeling of bacterial turnover in holocene marine sediment (Aarhus Bay). Geochim Cosmochim Acta 99: 87-99.
24. Lemire, S., Figueroa-Bossi, N., and Bossi, L. (2011) Bacteriophage crosstalk: coordination of prophage induction by trans-acting antirepressors. PLoS Genet 7: e1002149.
25. Lomstein, B.A., Langerhuus, A.T., D'Hondt, S., Jorgensen, B.B., and Spivack, A.J. (2012) Endospore abundance, microbial growth and necromass turnover in deep sub-seafloor sediment. Nature 484: 101-104.
26. Marvin, D.A. (1998) Filamentous phage structure, infection and assembly. Curr Opin Struct Biol 8: 150-158.
27. Middelboe, M., and Glud, R.N. (2006) Viral activity along a trophic gradient in continental margin sediments off central Chile. Mar Biol Res 2: 41-51.
28. Middelboe, M., Glud, R.N., and Finster, K. (2003) Distribution of viruses and bacteria in relation to diagenetic activity in an estuarine sediment. Limnol Oceanogr 48: 1447-1456.
29. Middelboe, M., Glud, R.N., and Filippini, M. (2011) Viral abundance and activity in the deep sub-seafloor biosphere. Aquat Microb Ecol 63: 1-8.
30. Orsi, W., Biddle, J.F., and Edgcomb, V. (2013a) Deep sequencing of subseafloor eukaryotic RRNA reveals active fungi across marine subsurface provinces. PLoS ONE 8: e56335.
31. Orsi, W.D., Edgcomb, V.P., Christman, G.D., and Biddle, J.F. (2013b) Gene expression in the deep biosphere. Nature 499: 205-211.
32. Røy, H., Kallmeyer, J., Adhikari, R.R., Pockalny, R., Jorgensen, B.B., and D'Hondt, S. (2012) Aerobic microbial respiration in 86-million-year-old deep-sea red clay. Science 336: 922-925.
33. Weinbauer, M.G., Brettar, I., and Hofle, M.G. (2003) Lysogeny and virus-induced mortality of bacterioplankton in surface, deep, and anoxic marine waters. Limnol Oceanogr 48: 1457-1465.
34. Williamson, S.J., Cary, S.C., Williamson, K.E., Helton, R.R., Bench, S.R., Winget, D., and Wommack, K.E. (2008) Lysogenic virus-host interactions predominate at deep-sea diffuse-flow hydrothermal vents. Isme J 2: 1112-1121.
35. Yanagawa, K., Morono, Y., Yoshida-Takashima, Y., Eitoku, M., Sunamura, M., Inagaki, F., etal. (2014) Variability of subseafloor viral abundance at the geographically and geologically distinct continental margins. FEMS Microbiol Ecol 88: 60-68.
36. Yoshida, M., Takaki, Y., Eitoku, M., Nunoura, T., and Takai, K. (2013) Metagenomic analysis of viral communities in (Hado)pelagic sediments. PLoS ONE 8: e57271.