Assessment of the specificity of Burkholderia and Pseudomonas qPCR assays for detection of these genera in soil using 454 pyrosequencing

FEMS Microbiology Letters

Volumn 333, Issue 1, 2012, Pages 77-84

  Bergmark, Lasse ^a   Poulsen, Pernille Hasse Busk ^a   Al Soud, Waleed Abu ^a   Norman, Anders ^a   Hansen, Lars Hestbjerg ^a   Sørensen, Søren Johannes ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

Bacterial diversity; Primer specificity; qPCR optimization

Indexed keywords

ARTICLE; BACTERIAL GROWTH; BACTERIAL STRAIN; BURKHOLDERIA; GENE SEQUENCE; GENETIC VARIABILITY; HYDROLYSIS; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PSEUDOMONAS; PYROSEQUENCING; QUANTITATIVE ANALYSIS; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SOIL ANALYSIS; TAXONOMY;

BACTERIAL LOAD; BIOTA; BURKHOLDERIA; DNA PRIMERS; DNA, BACTERIAL; GENES, BACTERIAL; GENES, RRNA; POLYMERASE CHAIN REACTION; PSEUDOMONAS; RNA, RIBOSOMAL, 16S; SENSITIVITY AND SPECIFICITY; SOIL MICROBIOLOGY;

BACTERIA (MICROORGANISMS); BURKHOLDERIA; PSEUDOMONAS;

EID: 84863836804     PISSN: 03781097     EISSN: 15746968     Source Type: Journal    
DOI: 10.1111/j.1574-6968.2012.02601.x     Document Type: Article

References (30)

1. Baker GC, Smith JJ & Cowan DA (2003) Review and re-analysis of domain-specific 16S primers. J Microbiol Methods 55: 541-555.
2. Bustin SA, Benes V, Garson JA et al. (2009) The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem 55: 611-622.
3. Cole JR, Wang Q, Cardenas E et al. (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37: D141-D145.
4. Editorial (2011) Microbiology by numbers. Nat Rev Microbiol 9: 628.
5. Fierer N, Jackson JA, Vilgalys R & Jackson RB (2005) Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays. Appl Environ Microbiol 71: 4117-4120.
6. Gans J, Wolinsky M & Dunbar J (2005) Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309: 1387-1390.
7. Huson DH & Bryant D (2006) Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23: 254-267.
8. Johnsen K, Enger O, Jacobsen CS, Thirup L & Torsvik V (1999) Quantitative selective PCR of 16S ribosomal DNA correlates well with selective agar plating in describing population dynamics of indigenous Pseudomonas spp. in soil hot spots. Appl Environ Microbiol 65: 1786-1788.
9. Khan IU & Yadav JS (2004) Real-time PCR assays for genus-specific detection and quantification of culturable and non-culturable mycobacteria and pseudomonads in metalworking fluids. Mol Cell Probes 18: 67-73.
10. LiPuma JJ, Dulaney BJ, McMenamin JD, Whitby PW, Stull TL, Coenye T & Vandamme P (1999) Development of rRNA-based PCR assays for identification of Burkholderia cepacia complex isolates recovered from cystic fibrosis patients. J Clin Microbiol 37: 3167-3170.
11. Lloyd-Jones G, Laurie AD & Tizzard AC (2005) Quantification of the Pseudomonas population in New Zealand soils by fluorogenic PCR assay and culturing techniques. J Microbiol Methods 60: 217-224.
12. Magid J, Luxhøj J, Jensen LS, Møller J & Bruun S (2006) Establishment of a long-term field trial with urban fertilizers - is recycling of nutrients from urban areas to peri-urban organic farms feasible? Long Term Field Experiments in Organic Farming (Raupp J, Pekrun C, Oltmanns M & Köpke U, eds), pp. 59. ISOFAR Scientific Series. No 1.
13. Moore RBE, Mau M, Arnscheidt B, Hutson RA, Collins MD & Timmis KN (1996) The determinationand comparison of the 16S rRNA gene sequences of species of the genus Pseudomonas (sensu stricto) and estimation of the natural intrageneric relationships. Syst Appl Microbiol 19: 478-492.
14. Morales SE & Holben WE (2009) Empirical testing of 16S rRNA gene PCR primer pairs reveals variance in target specificity and efficacy not suggested by in silico analysis. Appl Environ Microbiol 75: 2677-2683.
15. Palleroni NJ (2005) Genus I. Pseudomonas. Bergey's Manual of Systematic Bacteriology. Part B: The Proteobacteria (Brenner DJ, Krieg NR & Staley JT, Eds), pp. 323-379. Springer, New York.
16. Pallud C, Viallard V, Balandreau J, Normand P & Grundmann G (2001) Combined use of a specific probe and PCAT medium to study Burkholderia in soil. J Microbiol Methods 47: 25-34.
17. Park JW & Crowley DE (2005) Normalization of soil DNA extraction for accurate quantification real-time PCR and of target genes by DGGE. Biotechniques 38: 579-586.
18. Peix A, Ramirez-Bahena MH & Velazquez E (2009) Historical evolution and current status of the taxonomy of genus Pseudomonas. Infect Genet Evol 9: 1132-1147.
19. Poulsen PHB, Al-Soud WA, Bergmark L, Magid J, Hansen LH & Sørensen SJ (2012) Effects of fertilization with urban and agricultural organic wastes in a field trial-Prokaryotic diversity investigated by pyrosequencing. Soil Biol Biochem.
20. Poulsen PHB, Magid J, Luxhøi J & de Neergaard A (2012) Effects of fertilization with contemporary urban and agricultural organic wastes in a field trial I. Waste imprint on soil quality. Soil Biol Biochem.
21. Saleh-Lakha S, Miller M, Campbell RG, Schneider K, Elahimanesh P, Hart MM & Trevors JT (2005) Microbial gene expression in soil: methods, applications and challenges. J Microbiol Methods 63: 1-19.
22. Salles JF, De Souza FA & van Elsas JD (2002) Molecular method to assess the diversity of Burkholderia species in environmental samples. Appl Environ Microbiol 68: 1595-1603.
23. Sharma S, Radl V, Hai B, Kloos K, Fuka MM, Engel M, Schauss K & Schloter M (2007) Quantification of functional genes from procaryotes in soil by PCR. J Microbiol Methods 68: 445-452.
24. Singh BK, Campbell CD, Sorenson SJ & Zhou J (2009) Soil genomics. Nat Rev Microbiol 7: 756; author reply 756-757.
25. Torsvik V, Goksoyr J & Daae FL (1990) High diversity in DNA of soil bacteria. Appl Environ Microbiol 56: 782-787.
26. van der Heijden MG, Bardgett RD & van Straalen NM (2008) The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecol Lett 11: 296-310.
27. Vogel TM, Simonet P, Jansson JK, Hirsch PR, Tiedje JM, van Elsas JD, Bailey MJ, Nalin R & Philippot L (2009) TerraGenome: a consortium for the sequencing of a soil metagenome. Nat Rev Microbiol 7: 252.
28. Widmer F, Seidler RJ, Gillevet PM, Watrud LS & Di Giovanni GD (1998) A highly selective PCR protocol for detecting 16S rRNA genes of the genus Pseudomonas (sensu stricto) in environmental samples. Appl Environ Microbiol 64: 2545-2553.
29. Yu Y, Lee C, Kim J & Hwang S (2005) Group-specific primer and probe sets to detect methanogenic communities using quantitative real-time polymerase chain reaction. Biotechnol Bioeng 89: 670-679.
30. Zhang T & Fang HHP (2006) Applications of real-time polymerase chain reaction for quantification of microorganisms in environmental samples. Appl Microbiol Biotechnol 70: 281-289.