DNA stable-isotope probing (DNA-SIP)

Journal of Visualized Experiments

Volumn , Issue 42, 2010, Pages

  Dunford, Eric A ^a   Neufeld, Josh D ^a  

^a UNIVERSITY OF WATERLOO   (Canada)

Author keywords

16S rRNA gene community analysis; Cultivation independent; DNA stable isotope probing; Enrichment; Issue 42; Metagenomics; Microbial ecology; Microbiology; Substrates

Indexed keywords

EID: 80055105058     PISSN: 1940087X     EISSN: None     Source Type: Journal    
DOI: 10.3791/2027     Document Type: Article

References (19)

1. Neufeld, J. D. et al. DNA stable-isotope probing. Nat. Protocols 2, 860-866 (2007).
2. Neufeld, J. D., Boden, R., Moussard, H., Schäfer, H. & Murrell, J. C. Substrate-specific clades of active marine methylotrophs associated with a phytoplankton bloom in a temperate coastal environment. Appl. Environ. Microbiol. 74, 7321-7328 (2009).
3. Nercessian, O., Noyes, E., Kalyuzhnaya, M. G., Lidstrom, M. E. & Chistoserdova, L. Bacterial populations active in metabolism of C1 compounds in the sediment of Lake Washington, a freshwater lake. Appl. Environ. Microbiol. 71, 6885-6899 (2005).
4. Padmanabhan, P. et al. Respiration of 13C-labelled substrates added to soil in the field and subsequent 16S rRNA gene analysis of 13C-labelled soil DNA. Appl. Environ. Microbiol. 69, 1614-1622 (2003).
5. Bernard, L. et al. Dynamics and identification of soil microbial populations actively assimilating carbon from 13C-labelled wheat residue as estimated by DNA-and RNA-SIP techniques. Environ. Microbiol. 9, 752-764 (2007).
6. el Zahar Haichar, F. et al. Identification of cellulolytic bacteria in soil by stable isotope probing. Environ. Microbiol. 9, 625-634 (2007).
7. Addison, S., McDonald, I. & Lloyd-Jones, G. Stable isotope probing: Technical considerations when resolving 15N-labelled RNA in gradients. J. Microbiol. Meth. 80, 70-75 (2009).
8. Buckley, D. H., Huangyutitham, V., Hsu, S.-F. & Nelson, T. A. Stable isotope probing with 15N achieved by disentangling the effects of genome G + C content and isotope enrichment on DNA density. Appl. Environ. Microbiol. 73, 3189-3195 (2007).
9. Schwartz, E. Characterization of growing microorganisms in soil by stable isotope probing with H218O. Appl. Environ. Microbiol. 73, 2541-2546 (2007).
10. Neufeld, J. D., Dumont, M. G., Vohra, J. & Murrell, J. C. Methodological considerations for the use of stable isotope probing in microbial ecology. Microb. Ecol. 53, 435-442 (2007).
11. Martineau, C., Whyte, L. & Greer, C. Development of a SYBR safe technique for the sensitive detection of DNA in cesium chloride density gradients for stable isotope probing assays. J. Microbiol. Meth. 73, 199-202 (2008).
12. Bartram, A. K., Poon, C. & Neufeld, J. D. Nucleic acid contamination of glycogen used in nucleic acid precipitation and assessment of linear polyacrylamide as an alternative co-precipitant. Biotechniques 47, 1019-1022 (2009).
13. Chen, Y. et al. Revealing the uncultivated majority: combining DNA stable-isotope probing, multiple displacement amplification and metagenomic analyses of uncultivated Methylocystis in acidic peatlands. Environ. Microbiol. 10, 2609-2622 (2008).
14. Neufeld, J. D., Chen, Y., Dumont, M. G. & Murrell, J. C. Marine methylotrophs revealed by stable-isotope probing, multiple displacement amplification and metagenomics. Environ. Microbiol. 10, 1526-1535 (2008).
15. Kalyuzhnaya, M. et al. High-resolution metagenomics targets specific functional types in complex microbial communities. Nat. Biotechnol. 26, 1029-1034 (2008).
16. Binga, E. K., Lasken, R. S. & Neufeld, J. D. Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology. ISME J. 2, 233-241 (2008).
17. Green, S. J., Leigh, M. B. & Neufeld, J. D. in Microbiology of Hydrocarbon and Lipid Microbiology (ed K. N. Timmis) 4137-4158 (Springer-Verlag Berlin Heidelberg, 2010).
18. Neufeld, J. D., Wagner, M. & Murrell, J. C. Who eats what, where and when? Isotope-labelling experiments are coming of age. ISME J. 1, 103-110 (2007).
19. Gallagher, E., McGuinness, L., Phelps, C., Young, L. Y. & Kerkhof, L. J. 13C-carrier DNA shortens the incubation time needed to detect benzoate-utilizing denitrifying bacteria by stable-isotope probing. Appl. Environ. Microbiol. 71, 5192-5196 (2005).