Something from (almost) nothing: The impact of multiple displacement amplification on microbial ecology

ISME Journal

Volumn 2, Issue 3, 2008, Pages 233-241

  Binga, Erik K ^a   Lasken, Roger S ^b   Neufeld, Josh D ^a  

^a UNIVERSITY OF WATERLOO   (Canada)

^b J CRAIG VENTER INSTITUTE   (United States)

Author keywords

Metagenomics; Microbial ecology; Multiple displacement amplification; phi29 DNA polymerase; Single cell microbiology; Whole genome amplification

Indexed keywords

DNA;

ARTICLE; ECOLOGY; ECOSYSTEM; GENOMICS; METHODOLOGY; MICROBIAL GENETICS; NUCLEIC ACID AMPLIFICATION;

DNA; ECOLOGY; ECOSYSTEM; GENETICS, MICROBIAL; GENOMICS; NUCLEIC ACID AMPLIFICATION TECHNIQUES;

EID: 40249095175     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2008.10     Document Type: Article

References (79)

1. Abulencia CB, Wyborski DL, Garcia JA, Podar M, Chen W, Chang SH et al. (2006). Environmental whole-genome amplification to access microbial populations in contaminated sediments. Appl Environ Microbiol 72: 3291-3301.
2. Angly FE, Felts B, Breitbart M, Salamon P, Edwards RA, Carlson C et al. (2006). The marine viromes of four oceanic regions. PLoS Biol 4: e368.
3. Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ. (2005). At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Appl Environ Microbiol 71: 7724-7736.
4. Ballantyne K, van Oorschot R, Mitchell R. (2007). Increasing amplification success of forensic DNA samples using multiple displacement amplification. Forensic Science, Medicine, and Pathology 3: 182-187.
5. Barber AL, Foran DR. (2006). The utility of whole genome amplification for typing compromised forensic samples. J Forensic Sci 51: 1344-1349.
6. Barker DL, Hansen MST, Faruqi AF, Giannola D, Irsula OR, Lasken RS et al. (2004). Two methods of wholegenome amplification enable accurate genotyping across a 2320-SNP linkage panel. Genome Res 14: 901-907.
7. Bergen AW, Qi Y, Haque KA, Welch RA, Chanock SJ. (2005). Effects of DNA mass on multiple displacement whole genome amplification and genotyping performance. BMC Biotechnol 5: 24.
8. Blanco L, Bemad A, Lazaro JM, Martin G, Garmendia C, Salas M. (1989). Highly efficient DNA synthesis by the phage Φ29 DNA polymerase. Symmetrical mode of DNA replication. J Biol Chem 264: 8935-8940.
9. Blanco L, Salas M. (1984). Characterization and purification of a phage Φ29-encoded DNA polymerase required for the initiation of replication. Proc Natl Acad Sci USA 81: 5325-5329.
10. Blanco L, Salas M. (1985). Characterization of a 3′-5′ exonuclease activity in the phage Φ29-encoded DNA polymerase. Nucl Acids Res 13: 1239.
11. Breitbart M, Rohwer F. (2005). Method for discovering novel DNA viruses in blood using viral particle selection and shotgun sequencing. Biotechniques 39: 729-736.
12. Broderick NA, Raffa KF, Goodman RM, Handelsman J. (2004). Census of the bacterial community of the gypsy moth larval midgut by using culturing and cultureindependent methods. Appl Environ Microbiol 70: 293-300.
13. Brodie EL, DeSantis TZ, Parker JPM, Zubietta IX, Piceno YM, Andersen GL. (2007). Urban aerosols harbor diverse and dynamic bacterial populations. Proc Natl Acad Sci USA 104: 299-304.
14. Cheung VG, Nelson SF. (1996). Whole genome amplification using a degenerate oligonucleotide primer allows hundreds of genotypes to be performed on less than one nanogram of genomic DNA. Proc Natl Acad Sei USA 93: 14676-14679.
15. Christner BC, Mosley-Thompson E, Thompson LG, Reeve JN. (2001). Isolation of bacteria and 16S rDNAs from Lake Vostok accretion ice. Environ Microbiol 3: 570-577.
16. Dean FB, Hosono S, Fang L, Wu X, Faruqi AF, Bray-Ward P et al. (2002). Comprehensive human genome amplification using multiple displacement amplification. Proc Natl Acad Sci USA 99: 5261-5266.
17. Dean FB, Nelson JR, Giesler TL, Lasken RS. (2001). Rapid amplification of plasmid and phage DNA using phi29 DNA polymerase and multiply-primed rolling circle amplification. Genome Res 11: 1095-1099.
18. Detter JC, Jett JM, Lucas SM, Dalin E, Arellano AR, Wang M et al. (2002). Isothermal strand-displacement amplification applications for high-throughput genomics. Genomics 80: 691-698.
19. Dickson PA, Montgomery GW, Henders A, Campbell MJ, Martin NG, RJames M. (2005). Evaluation of multiple displacement amplification in a 5 cM STR genomewide scan. Nucl Acids Res 33: e119.
20. Dunning AM, Talmud P, Humphries SE. (1988). Errors in the polymerase chain reaction. Nucleic Acids Res 18:10393.
21. Edwards RA, Rodriguez-Brito B, Wegley L, Haynes M, Breitbart M, Peterson DM et al. (2006). Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics 7: 57.
22. Esteban JA, Salas M, Blanco L. (1993). Fidelity of Φ29 DNA polymerase: comparison between proteinprimed initiation and DNA polymerization. J Biol Chem 268: 2719-2726.
23. Fernández-Ortuño D, Torés J, de Vicente A, Pérez-García A. (2007). Multiple displacement amplification, a powerful tool for molecular genetic analysis of powdery mildew fungi. Curr Genet 51: 209-219.
24. Foster SJ, Monahan BJ. (2005). Whole genome amplification from filamentous fungi using Phi29-mediated multiple displacement amplification. Fungal Genet Biol 42: 367-375.
25. Gadkar V, Rillig MC. (2005). Application of Phi29 DNA polymerase mediated whole genome amplification on single spores of arbuscular mycorrhizal (AM) fungi. FEMS Microbiol Lett 342: 65-71.
26. Gonzalez JM, Portillo MC, Saiz-Jimenez C. (2005). Multiple displacement amplification as a pre-polymerase chain reaction (pre-PCR) to process difficult to amplify samples and low copy number sequences from natural environments. Environ Microbiol 7: 1024-1028.
27. Gorrochotegui-Escalante N, Black IV WC. (2003). Amplifying whole insect genomes with multiple displacement amplification. Insect Mol Biol 12: 195-200.
28. Groathouse NA, Brown SE, Knudson DL, Brennan PJ, Slayden RA. (2006). Isothermal amplification and molecular typing of the obligate intracellular pathogen Mycobacterium leprae isolated from tissues of unknown origins. }Clin Microbiol 44: 1502-1508.
29. Holbrook JF, Stabley D, Sol-Church K. (2005). Exploring whole genome amplification as a DNA recovery tool for molecular genetic studies. J Biomol Tech 16: 125-133.
30. Hosono S, Faruqi AF, Dean FB, Du Y, Sun Z, Wu X et al. (2003). Unbiased whole-genome amplification directly from clinical samples. Genome Res 13: 954-964.
31. Huang WE, Stoecker K, Griffiths R, Newbold L, Daims H, Whiteley AS et al. (2007). Raman-FISH: combining stable-isotope Raman spectroscopy and fluorescence in situ hybridization for single cell analysis of identity and function. Environ Microbiol 9: 1878-1889.
32. Hugenholtz P, Huber T. (2003). Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases. Int J Syst Evol Microbiol 53: 289-293.
33. Hutchison III CA, Smith HO, Pfannkoch C, Venter JC. (2005). Cell-free cloning using Φ29 DNA polymerase. Proc Natl Acad Sci USA 102: 17332-17336.
34. Inoue J, Shigemori Y, Mikawa T. (2006). Improvements of rolling circle amplification (RCA) efficiency and accuracy using Thermus thermophilus SSB mutant protein. Nucleic Acids Res 34: e69.
35. Ishøy T, Kvist T, Westermann P, Ahring BK. (2006). An improved method for single cell isolation of prokaryotes from meso-, thermo-and hyperthermophilic environments using micromanipulation. Appl Microbiol Biotechnol 69: 510-514.
36. Jeyaprakash A, Hoy MA. (2004). Multiple displacement amplification in combination with high-fidelity PCR improves detection of bacteria from single females or eggs of Metaseiulus occidentalis (Nesbitt) (Acari: Phytoseiidae). 7/21 vertebr Pathol 86: 111-116.
37. Jiang Z, Zhang X, Deka R, Jin L. (2005). Genome amplification of single sperm using multiple displacement amplification. Nucleic Acids Res 33: e91.
38. Kalyuzhnaya MG, Zabinsky R, Bowerman S, Baker DR, Lidstrom ME, Chistoserdova L. (2006). Fluorescence 221 situ hybridization-flow cytometry-cell sorting-based method for separation and enrichment of type I and type II methanotroph populations. Appl Environ Microbiol 72: 4293-4301.
39. Kvist T, Ahring BK, Lasken RS, Westermann P. (2007). Specific single-cell isolation and genomic amplification of uncultured microorganisms. Appl Environ Microbiol 74: 926-935.
40. Lage JM, Leamon JH, Pejovic T, Hamann S, Lacey M, Dillon D et al. (2003). Whole genome analysis of genetic alterations in small DNA samples using hyperbranched strand displacement amplification and array-CGH. Genome Res 13: 294-307.
41. Lasken RS. (2007). Single-cell genomic sequencing using Multiple Displacement Amplification. Curr Opin Microbiol 10: 1-7.
42. Lasken RS, Egholm M. (2003). Whole genome amplification: abundant supplies of DNA from precious samples or clinical specimens. Trends Biotechnol 21: 531-535.
43. Lasken RS, Raghunathan A, Kvist T, Ishøy T, Westermann P, Ahring BK et al. (2005). Multiple displacement amplification of genomic DNA. In: Hughes S, Lasken RS (eds). Whole Genome Amplification: Methods Express. Scion Publishing Ltd: UK. pp 119-147.
44. Lasken RS, Stockwell TB. (2007). Mechanism of chimera formation during the Multiple Displacement Amplification reaction. BMC Biotechnol 7: 19.
45. Leigh MB, Pellizari VH, Uhlik O, Sutka R, Rodrigues J, Ostrom NE et al. (2007). Biphenyl-utilizing bacteria and their functional genes in a pine root zone contaminated with polychlorinated biphenyls (PCBs). ISME J 1: 134-148.
46. Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW et al. (2006). Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442: 806-809.
47. Lovmar L, Fredriksson M, Liljedahl U, Sigurdsson S, Syvanen AC. (2003). Quantitative evaluation by minisequencing and microarrays reveals accurate multiplexed SNP genotyping of whole genome amplified DNA. Nucleic Acids Res 31: e129.
48. Lu Y, Gioia-Patricola L, Gomez JV, Plummer M, Franceschi S, Kato I et al. (2005). Use of whole genome amplification to rescue DNA from plasma samples. Biotechniques 39: 511-515.
49. Marcy Y, Ishøy T, Lasken RS, Stockwell TB, Walenz BP, Halpern AL et al. (2007a). Nanoliter reactors improve multiple displacement amplification of genomes from single cells. PLoS Genet 3: e155.
50. Marcy Y, Ouverney C, Bik EM, Lösekann T, Ivanova N, Martin HG et al. (2007b). Dissecting biological 'dark matter' with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc Natl Acad Sci USA 104: 11889-11894.
51. Mavingui P, Tran Van V, Labeyrie E, Ranees E, Vavre F, Simonet P. (2005). Efficient procedure for purification of obligate intracellular Wolbachia pipientis and representative amplification of its genome by multiple-displacement amplification. Appl Environ Microbiol 71: 6910-6917.
52. Mußmann M, Hu FZ, Richter M, de Beer D, Preisler A, Jørgensen BB et al. (2007). Insights into the genome of large sulfur bacteria revealed by analysis of single filaments. PLoS Biol 5: e230.
53. Nelson JR, Cai YC, Giesler TL, Farchaus JW, Sundaram ST, Ortiz-Rivera M et al. (2002). TempliPhi, phi29 DNA polymerase based rolling circle amplification of templates for DNA sequencing. Biotechniques 32: 44-47.
54. Neufeld JD, Chen Y, Dumont MG, Murrell JC. (2008). Marine methylotrophs revealed by stable-isotope probing, multiple displacement amplification and metagenomics. Environ Microbiol (doi:10.1111/j. 1462-2920.2008.01568.X).
55. Neufeld JD, Wagner M, Murrell JC. (2007). Who eats what, where and when? Isotope-labelling experiments are coming of age. ISME J 1: 103-110.
56. Ochsenreiter T, Selezi D, Quaiser A, Bonch-Osmolovskaya L, Schleper C. (2003). Diversity and abundance of Crenarchaeota in terrestrial habitats studied by 16S RNA surveys and real time PCR. Environ Microbiol 5: 787-797.
57. Paez JG, Lin M, Beroukhim R, Lee JC, Zhao X, Richter DJ et al. (2004). Genome coverage and sequence fidelity of 29 polymerase-based multiple strand displacement whole genome amplification. Nucl Acids Res 32: e71.
58. Paunio T, Reima I, Syvanen AC. (1996). Preimplantation diagnosis by whole-genome amplification, PCR amplification, and solid-phase minisequencing of blastomere DNA. Clin Chem 42: 1382-1390.
59. Podar M, Abulencia CB, Walcher M, Hutchison D, Zengler K, Garcia JA et al. (2007). Targeted access to the genomes of low-abundance organisms in complex microbial communities. Appl Environ Microbiol 73: 3205-3214.
60. Quaiser A, Ochsenreiter T, Klenk HP, Kletzin A, Treusch AH, Meurer G et al. (2002). First insight into the genome of an uncultivated crenarchaeote from soil. Environ Microbiol 4: 603-611.
61. Raghunathan A, Ferguson HR, Bornarth CJ, Song W, Driscoll M, Lasken RS. (2004). Genomic DNA amplification from a single bacterium. Appl Environ Microbiol 71: 3342-3347.
62. Rönn AC, Andrés O, Bruford M, Crouau-Roy B, Doxiadis G, Domingo-Roura X et al. (2006). Multiple displacement amplification for generating an unlimited source of DNA for genotyping in nonhuman primate species. Int J Primatol 27: 1145-1169.
63. Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S et al. (2007). The Sorcerer II global ocean sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol 5: e77.
64. Saiki RK, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R, Horn GT et al. (1988). Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239: 487-491.
65. Simon HM, Jahn CE, Bergerud LT, Sliwinski MK, Weimer PJ, Willis DK et al. (2005). Cultivation of mesophilic soil crenarchaeotes in enrichment cultures from plant roots. Appl Environ Microbiol 71: 4751-4760.
66. Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, Neal PR et al. (2006). Microbial diversity in the deep sea and the underexplored 'rare biosphere'. Proc Natl Acad Sci USA 103: 12115-12120.
67. Spits C, Le Caignec C, De Rycke M, Van Haute L, Van Steirteghem A, Liebaers I et al. (2006). Optimization and evaluation of single-cell whole-genome multiple displacement amplification. Hum Mutat 27: 496-503.
68. Stepanauskas R, Sieracki ME. (2007). Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time. Proc Nat Acad Sci USA 104: 9052-9057.
69. Steven B, Léveillé R, Pollard WH, Whyte LG. (2006). Microbial ecology and biodiversity in permafrost. Extremophiles 10: 259-267.
70. Telenius H, Carter NP, Bebb CE, Nordenskjold M, Ponder BA, Tunnacliffe A. (1992). Degenerate oligonucleotide-primed PCR: general amplification of target DNA by a single degenerate primer. Genomics 13: 718-725.
71. Teske AP. (2005). The deep subsurface biosphere is alive and well. Trends Microbiol 13: 402-404.
72. Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW et al (2005). Comparative metagenomics of microbial communities. Science 308: 554-557.
73. Vora GJ, Meador CE, Stenger DA, Andreadis JD. (2004). Nucleic acid amplification strategies for DNA microarray-based pathogen detection. Appl Environ Microbiol 70: 3047-3054.
74. Watabe K, Leusch MS, Ito J. (1984). A 3′-5′ exonuclease activity is associated with phage Φ29 DNA polymerase. Biochem Biophys Res Commun 123: 1019-1026.
75. 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.
76. Wu L, Liu X, Schadt CW, Zhou J. (2006). Microarray-based analysis of subnanogram quantities of microbial community DNAs by using whole-community genome amplification. Appl Environ Microbiol 72: 4931-4941.
77. Yokouchi H, Fukuoka Y, Mukoyama D, Calugay R, Takeyama H, Matsunaga T. (2006). Whole-metagenome amplification of a microbial community associated with scleractinian coral by multiple displacement amplification using Φ29 polymerase. Environ Microbiol 8: 1155-1163.
78. Zhang K, Martiny AC, Reppas NB, Barry KW, Malek J, Chisholm SW et al. (2006). Sequencing genomes from single cells by polymerase cloning. Nat Biotechnol 24: 680-686.
79. Zhang L, Cui X, Schmitt K, Hubert R, Navidi W, Arnheim N. (1992). Whole genome amplification from a single cell: implications for genetic analysis. Proc Natl Acad Sci USA 89: 5847-5851.