Cultivated single-stranded DNA phages that infect marine bacteroidetes prove difficult to detect with DNA-binding stains

Applied and Environmental Microbiology

Volumn 78, Issue 3, 2012, Pages 892-894

  Holmfeldt, Karin ^a,b   Odić, Duško ^a   Sullivan, Matthew B ^b   Middelboe, Mathias ^c   Riemann, Lasse ^a,c  

^a LINNAEUS UNIVERSITY   (Sweden)

^b UNIVERSITY OF ARIZONA   (United States)

^c UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

CONVENTIONAL METHODS; DNA-BINDING; IN-SITU; MARINE BACTERIOPLANKTON; SINGLE-STRANDED DNA; SINGLE-STRANDED DNA (SS-DNA);

BACTERIOPHAGES;

DNA;

SEA WATER; SINGLE STRANDED DNA;

BACTERIOPHAGE; BACTERIOPLANKTON; BACTERIUM; HETEROTROPHY; INFECTIVITY; MARINE ECOSYSTEM;

ARTICLE; BACTERIOPHAGE; BACTEROIDETES; ELECTRON MICROSCOPY; GENETICS; ISOLATION AND PURIFICATION; METHODOLOGY; STAINING; ULTRASTRUCTURE; VIRION; VIROLOGY; VIRUS LOAD;

BACTERIOPHAGES; BACTEROIDETES; DNA, SINGLE-STRANDED; MICROSCOPY, ELECTRON; SEAWATER; STAINING AND LABELING; VIRAL LOAD; VIRION; VIROLOGY;

BACTEROIDETES;

EID: 84856148335     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.06580-11     Document Type: Article

References (24)

1. Angly FE, et al. 2006. The marine viromes of four oceanic regions. PLoS Biol. 4:e368.
2. Ausubel FM, et al. 1995. Short protocols in molecular biology, 3rd ed. John Wiley & Sons, Inc, Hoboken, NJ.
3. Brussaard CP. 2004. Optimization of procedures for counting viruses by flow cytometry. Appl. Environ. Microbiol. 70:1506-1513.
4. Casas V, Rohwer F. 2007. Phage metagenomics. Methods Enzymol. 421:259-268.
5. Chen F, Lu JR, Binder BJ, Liu YC, Hodson RE. 2001. Application of digital image analysis and flow cytometry to enumerate marine viruses stained with SYBR gold. Appl. Environ. Microbiol. 67:539-545.
6. Desnues C, et al. 2008. Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature 452:340-343.
7. Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA. 2005. Virus taxonomy: eighth report of the international committee on taxonomy of viruses. Elsevier Inc., London, United Kingdom.
8. Hennes KP, Suttle CA. 1995. Direct counts of viruses in natural waters and laboratory cultures by epifluorescence microscopy. Limnol. Oceanogr. 40:1050-1055.
9. Holmfeldt K, Middelboe M, Nybroe O, Riemann L. 2007. Large variabilities in host strain susceptibility and phage host range govern interactions between lytic marine phages and their Flavobacterium hosts. Appl. Environ. Microbiol. 73:6730-6739.
10. Krupovic M, Forterre P. 2011. Microviridae goes temperate: microvirusrelated proviruses reside in the genomes of bacteroidetes. PLoS One 6:e19893.
11. Martin WJ. 1996. Genetic instability and fragmentation of a stealth viral genome. Pathobiology 64:9-17.
12. McDaniel LD, delaRosa M, Paul JH. 2006. Temperate and lytic cyanophages from the Gulf of Mexico. J. Mar. Biol. Assoc. U.K. 86:517-527.
13. Nagasaki K, et al. 2005. Previously unknown virus infects marine diatom. Appl. Environ. Microbiol. 71:3528-3535.
14. Noble RT, Fuhrman JA. 1998. Use of SYBR green I for rapid epifluorescence counts of marine viruses and bacteria. Aquat. Microb. Ecol. 14:113-118.
15. Sambrook J, Fritsch EF, Maniatis T. 1989. Molecular cloning: a laboratory manual, 2nd ed, vol 1. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
16. Steward GF. 2001. Fingerprinting viral assemblages by pulsed field gel electrophoresis (PFGE), p 85-104. In Paul JH (ed), Methods in microbiology. Academic Press, New York, NY.
17. Suttle CA, Fuhrman JA. 2010. Enumeration of virus particles in aquatic or sediment samples by epifluorescence microscopy, p 145-153. In Wilhelm SW, Weinbauer MG, Suttle CA(ed), Manual of aquatic viral ecology. ASLO, Waco, TX.
18. Thurber RV, Haynes M, Breitbart M, Wegley L, Rohwer F. 2009. Laboratory procedures to generate viral metagenomes. Nat. Protoc. 4:470-483.
19. Tomaru Y, Nagasaki K. 2007. Flow cytometric detection and enumeration of DNA and RNA viruses infecting marine eucaryotic microalgae. J. Oceanogr. 63:215-221.
20. Tomaru Y, Shirai Y, Suzuki H, Nagumo T, Nagasaki K. 2008. Isolation and characterization of a new single-stranded DNA virus infecting the cosmopolitan marine diatom Chaetoceros debilis. Aquat. Microb. Ecol. 50:103-112.
21. Tomaru Y, et al. 2011. Isolation and characterization of a singlestranded DNA virus infecting Chaetoceros lorenzianus Grunow. Appl. Environ. Microbiol. 77:5285-5293.
22. Tucker KP, Parsons R, Symonds EM, Breitbart M. 2011. Diversity and distribution of single-stranded DNA phages in the North Atlantic Ocean. ISME J. 5:822-830.
23. Wegley L, Edwards R, Rodriguez-Brito B, Liu H, Rohwer F. 2007. Metagenomic analysis of the microbial community associated with the coral Porites astreoides. Environ. Microbiol. 9:2707-2719.
24. Wilhelm SW, Brigden SM, Suttle CA. 2002. A dilution technique for the direct measurement of viral production: a comparison in stratified and tidally mixed coastal waters. Microb. Ecol. 43:168-173.