Reaction- and sample-specific inhibition affect standardization of qPCR assays of soil bacterial communities

Soil Biology and Biochemistry

Volumn 59, Issue , 2013, Pages 89-97

  Hargreaves, Sarah K ^a   Roberto, Alescia A ^a   Hofmockel, Kirsten S ^a  

^a IOWA STATE UNIVERSITY   (United States)

Author keywords

Functional genes; Gene copy number; Inhibition; Methods; QPCR efficiency; QPCR sensitivity; Quantitative PCR; Soil microbial community

Indexed keywords

FUNCTIONAL GENES; GENE COPY NUMBER; METHODS; QPCR SENSITIVITY; QUANTITATIVE PCR; SOIL MICROBIAL COMMUNITY;

DNA SEQUENCES; EFFICIENCY; ENZYME INHIBITION; GENES; GENETIC ENGINEERING; LAKES; SOILS;

POLYMERASE CHAIN REACTION;

ANNEALING; BIOASSAY; DATA SET; DNA; ENZYME ACTIVITY; GENETIC ANALYSIS; MATHEMATICAL ANALYSIS; MICROBIAL ACTIVITY; POLYMERASE CHAIN REACTION; QUANTITATIVE ANALYSIS; REACTION KINETICS; SAMPLING; SOIL MICROORGANISM;

BACTERIA (MICROORGANISMS);

EID: 84873652748     PISSN: 00380717     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.soilbio.2013.01.007     Document Type: Article

References (41)

1. Braker G., Conrad R. Diversity, structure, and size of n(2)o-producing microbial communities in soils-what matters for their functioning?. Advances in Applied Microbiology 2011, 75:33-70.
2. Braker G., Tiedje J.M. Nitric oxide reductase (norB) genes from pure cultures and environmental samples. Applied and Environmental Microbiology 2003, 69:3476-3483.
3. Bustin S.A., Benes V., Garson J.A., Hellemans J., Huggett J., Kubista M., Mueller R., Nolan T., Pfaffl M.W., Shipley G.L., Vandesompele J., Wittwer C.T. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clinical Chemistry 2009, 55:611-622.
4. Bustin S.A. A-Z of Quantitative PCR 2004, International University Line, California. first ed.
5. Crawley M.J. The R Book 2007, Wiley, England. first ed.
6. Dandie C.E., Miller M.N., Burton D.L., Zebarth B.J., Trevors J.T., Goyer C. Nitric oxide reductase-targeted real-time PCR quantification of denitrifier populations in soil. Applied and Environmental Microbiology 2007, 73:4250-4258.
7. Fierer N., Jackson J., Vilgalys R., Jackson R.B. Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays. Applied and Environmental Microbiology 2005, 71:4117.
8. Frostegård A., Courtois S., Ramisse V., Clerc S., Bernillon D., Le Gall F., Jeannin P., Nesme X., Simonet P. Quantification of bias related to the extraction of DNA directly from soils. Applied and Environmental Microbiology 1999, 65:5409-5420.
9. Gallup J.M., Ackermann M.R. Addressing fluorogenic real-time qpcr inhibition using the novel custom excel file system 'FocusField2-6GallupqPCRSet-upTool-001' to attain consistently high fidelity qPCR reactions. Biological Procedures Online 2006, 8:87-153.
10. Gallup J.M., Ackermann M.R. The 'PREXCEL-Q Method' for qPCR. International Journal of Biomedical Science 2008, 4:273-293.
11. Gallup J.M., Sow F.B., Van Geelen A., Ackermann M.R. SPUD qPCR assay confirms PREXCEL-Q softwares ability to avoid qPCR inhibition. Current Issues in Molecular Biology 2010, 12:129-134.
12. Grayston S.J., Griffith G.S., Mawdsley J.L., Campbell C.D., Bardgett R.D. Accounting for variability in soil microbial communities of temperate upland grassland ecosystems. Soil Biology and Biochemistry 2001, 33:533-551.
13. Hallin S., Jones C.M., Schloter M., Philippot L. Relationship between N-cycling communities and ecosystem functioning in a 50-year-old fertilization experiment. The ISME Journal 2009, 3:597-605.
14. Henry S., Bru D., Stres B., Hallet S., Philippot L. Quantitative detection of the nosZ gene, encoding nitrous oxide reductase, and comparison of the abundances of 16S rRNA, narG, nirK, and nosZ genes in soils. Applied and Environmental Microbiology 2006, 72:5181-5189.
15. 3 deposition alter the abundance and activity of ligninolytic fungi in forest soils?. Ecosystems 2007, 10:1278-1286.
16. Huggett J.F., Novak T., Garson J.A., Green C., Morris-Jones S.D., Miller R.F., Zumla A. Differential susceptibility of PCR reactions to inhibitors: an important and unrecognised phenomenon. BMC Research Notes 2008, 1:70.
17. Jones C.M., Stres B., Rosenquist M., Hallin S. Phylogenetic analysis of nitrite, nitric oxide, and nitrous oxide respiratory enzymes reveal a complex evolutionary history for denitrification. Molecular Biology and Evolution 2008, 25:1955-1966.
18. Krsek M., Wellington E.M. Comparison of different methods for the isolation and purification of total community DNA from soil. Journal of Microbiological Methods 1999, 39:1-16.
19. Lauber C.L., Strickland M.S., Bradford M.A., Fierer N. The influence of soil properties on the structure of bacterial and fungal communities across land-use types. Soil Biology and Biochemistry 2008, 40:2407-2415.
20. Lloyd-Jones G., Hunter D. Comparison of rapid DNA extraction methods applied to contrasting New Zealand soils. Soil Biology and Biochemistry 2001, 33:2053-2059.
21. Martin-Laurent F., Philippot L., Hallet S., Chaussod R., Germon J.C., Soulas G., Catroux G. DNA extraction from soils: old bias for new microbial diversity analysis methods. Applied and Environmental Microbiology 2001, 67:2354-2359.
22. Miller D.N., Bryant J.E., Madsen E.L., Ghiorse W.C. Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples. Applied and Environmental Microbiology 1999, 65:4715-4724.
23. 2O emissions and denitrifier community abundance in soil. Soil Biology and Biochemistry 2008, 40:2553-2562.
24. Nicol G.W., Leininger S., Schleper C., Prosser J.I. The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria. Environmental Microbiology 2008, 10:2966-2978.
25. Philippot L., Hallin S. Finding the missing link between diversity and activity using denitrifying bacteria as a model functional community. Current Opinion in Microbiology 2005, 8:234-239.
26. Philippot L., čuhel J., Saby N.P.A., Chèneby D., Chroňáková A., Bru D., Arrouays D., Martin-Laurent F., Šimek M. Mapping field-scale spatial patterns of size and activity of the denitrifier community. Environmental Microbiology 2009, 11:1518-1526.
27. Ramakers C., Ruijter J.M., Deprez R.H.L., Moorman A.F.M. Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data. Neuroscience Letters 2003, 339:62-66.
28. Rasche F., Knapp D., Kaiser C., Koranda M., Kitzler B., Zechmeister-Boltenstern S., Richter A., Sessitsch A. Seasonality and resource availability control bacterial and archaeal communities in soils of a temperate beech forest. The ISME Journal 2011, 5:389-402.
29. Robe P., Nalin R., Capellano C., Vogel T.M., Simonet P. Extraction of DNA from soil. European Journal of Soil Biology 2003, 39:183-190.
30. Roh C., Villatte F., Kim B.G., Schmid R.D. Comparative study of methods for extraction and purification of environmental DNA from soil and sludge samples. Applied Biochemistry and Biotechnology 2006, 134:97-112.
31. Ruijter J.M., Ramakers C., Hoogaars W.M.H., Karlen Y., Bakker O., Van Den Hoff M.J.B., Moorman A.F.M. Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data. Nucleic Acids Research 2009, 37:e45.
32. Sagova-Mareckova M., Cermak L., Novotna J., Plhackova K., Forstova J., Kopecky J. Innovative methods for soil DNA purification tested in soils with widely differing characteristics. Applied and Environmental Microbiology 2008, 74:2902-2907.
33. Schmidt S.K., Costello E.K., Nemergut D.R., Cleveland C.C., Reed S.C., Weintraub M.N., Meyer A.F., Martin A.M. Biogeochemical consequences of rapid microbial turnover and seasonal succession in soil. Ecology 2007, 88:1379-1385.
34. Siciliano S.D., Ma W.K., Ferguson S., Farrell R.E. Nitrifier dominance of Arctic soil nitrous oxide emissions arises due to fungal competition with denitrifiers for nitrate. Soil Biology and Biochemistry 2009, 41:1104-1110.
35. Sieber M.W., Recknagel P., Glaser F., Witte O.W., Bauer M., Claus R.A., Frahm C. Substantial performance discrepancies among commercially available kits for reverse transcription quantitative polymerase chain reaction: a systematic comparative investigator-driven approach. Analytical Biochemistry 2010, 401:1-9.
36. Smith C.J., Osborn A.M. Advantages and limitations of quantitative PCR (Q-PCR)-based approaches in microbial ecology. FEMS Microbiology Ecology 2009, 67:6-20.
37. Smith C.J., Nedwell D.B., Dong L.F., Osborn A.M. Evaluation of quantitative polymerase chain reaction-based approaches for determining gene copy and gene transcript numbers in environmental samples. Environmental Microbiology 2006, 8:804-815.
38. Throbäck I.N., Enwall K., Jarvis A., Hallin S. Reassessing PCR primers targeting nirS, nirK and nosZ genes for community surveys of denitrifying bacteria with DGGE. FEMS Microbiology Ecology 2004, 49:401-417.
39. Töwe S., Kleineidam K., Schloter M. Differences in amplification efficiency of standard curves in quantitative real-time PCR assays and consequences for gene quantification in environmental samples. Journal of Microbiological Methods 2010, 82:338-341.
40. Whitehouse C.A., Hottel H.E. Comparison of five commercial DNA extraction kits for the recovery of Francisella tularensis DNA from spiked soil samples. Molecular and Cellular Probes 2007, 21:92-96.
41. Wilson I. Inhibition and facilitation of nucleic acid amplification. Applied and Environmental Microbiology 1997, 63:3741.