A robust PCR primer design platform applied to the detection of Acidobacteria group 1 in soil

Nucleic Acids Research

Volumn 40, Issue 12, 2012, Pages

  Gans, Jason D ^a   Dunbar, John ^a   Eichorst, Stephanie A ^a,b   Gallegos Graves, La Verne ^a   Wolinsky, Murray ^a   Kuske, Cheryl R ^a  

^a LOS ALAMOS NATIONAL LABORATORY   (United States)

^b UNIVERSITY OF VIENNA   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

CARBON DIOXIDE; RNA 16S;

ACIDOBACTERIA; ARTICLE; ATMOSPHERE; BACTERIUM DETECTION; CLASSIFICATION ALGORITHM; COMPUTER PROGRAM; CONTROLLED STUDY; DNA SEQUENCE; GENE CLUSTER; GENE SEQUENCE; MAXIMUM LIKELIHOOD METHOD; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; QUANTITATIVE ASSAY; SEQUENCE ANALYSIS; SOIL MICROFLORA; VALIDATION PROCESS;

ACIDOBACTERIA; ALGORITHMS; DNA PRIMERS; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SOFTWARE; SOIL MICROBIOLOGY;

ACIDOBACTERIA; BACTERIA (MICROORGANISMS); GROUP 1 SPECIES;

EID: 84863219983     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks238     Document Type: Article

References (62)

1. Gervais,A.L., Marques,M. and Gaudreau,L. (2010) PCRTiler: automated design of tiled and specific PCR primer pairs. Nucleic Acids Res., 38, W308-W312.
2. Kaderali,L. and Schliep,A. (2002) Selecting signature oligonucleotides to identify organisms using DNA arrays. Bioinformatics, 18, 1340-1349. (Pubitemid 35244191)
3. Li,K., Brownley,A., Stockwell,T.B., Beeson,K., McIntosh,T.C., Busam,D., Ferriera,S., Murphy,S. and Levy,S. (2008) Novel computational methods for increasing PCR primer design effectiveness in directed sequencing. BMC Bioinformatics, 9, 191.
4. Rozen,S. and Skaletsky,H. (2000) Primer3 on the WWW for General Users and for Biologist Programmers. Humana Press, Totowa, NJ.
5. Balla,S. and Rajasekaran,S. (2007) An efficient algorithm for minimum degeneracy primer selection. IEEE Trans. Nanobiosci., 6, 12-17. (Pubitemid 46397104)
6. Boyce,R., Chilana,P. and Rose,T.M. (2009) iCODEHOP: a new interactive program for designing COnsensus-DEgenerate Hybrid Oligonucleotide Primers from multiply aligned protein sequences. Nucleic Acids Res., 37, W222-W228.
7. Contreras-Moreira,B., Sachman-Ruiz,B., Figueroa-Palacios,I. and Vinuesa,P. (2009) primers4clades: a web server that uses phylogenetic trees to design lineage-specific PCR primers for metagenomic and diversity studies. Nucleic Acids Res., 37, W95-W100.
8. Gadberry,M.D., Malcomber,S.T., Doust,A.N. and Kellogg,E.A. (2005) Primaclade-a flexible tool to find conserved PCR primers across multiple species. Bioinformatics, 21, 1263-1264. (Pubitemid 40467953)
9. Giegerich,R., Meyer,F. and Schleiermacher,C. (1996) Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology, Vol. 4. AAAI Press, St. Louis, MI, pp. 68-77.
10. Graham,K.J. and Holland,M. (2005) PrimerSelect: a transcriptome-wide oligonucleotide primer pair design program for kinetic RT-PCR-based transcript profiling. Methods Enzymol., 395, 544-553. (Pubitemid 40754385)
11. Jabado,O.J., Palacios,G., Kapoor,V., Hui,J., Renwick,N., Zhai,J., Briese,T. and Lipkin,W.I. (2006) Greene SCPrimer: a rapid comprehensive tool for designing degenerate primers from multiple sequence alignments. Nucleic Acids Res., 34, 6605-6611. (Pubitemid 46017954)
12. Linhart,C. and Shamir,R. (2002) The degenerate primer design problem. Bioinformatics, 18, S172-S181.
13. Najafabadi,H.S., Torabi,N. and Chamankhah,M. (2008) Designing multiple degenerate primers via consecutive pairwise alignments. BMC Bioinformatics, 9, 55.
14. Souvenir,R., Buhler,J., Stromo,G. and Zhang,W. (2003) String Algorithms. In: Benson,G. and Page,R. (eds), Workshop on Algorithms in Bioinformatics. Springer, Budapest, Hungary, pp. 512-526.
15. Wei,X., Kuhn,D. and Narasimhan,G. (2003) IEEE Computer Society Bioinformatics Conference. Stanford, CA, pp. 75-83.
16. Frech,C., Breuer,K., Ronacher,B., Kern,T., Sohn,C. and Gebauer,G. (2009) hybseek: pathogen primer design tool for diagnostic multi-analyte assays. Comput. Methods Programs Biomed., 94, 152-160.
17. Nordberg,E.K. (2005) YODA: selecting signature oligonucleotides. Bioinformatics, 21, 1365-1370.
18. Tembe,W., Zavaljevski,N., Bode,E., Chase,C., Geyer,J., Wasieloski,L., Benson,G. and Reifman,J. (2007) Oligonucleotide fingerprint identification for microarray-based pathogen diagnostic assays. Bioinformatics, 23, 5-13. (Pubitemid 46017849)
19. Ashelford,K., Weightman,A. and Fry,J. (2002) PRIMROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNA oligonuleotide probes and primers in conjunction with the RDP-II database. Nucleic Acids Res., 30, 3481-3489. (Pubitemid 34845945)
20. Bader,K., Grothoff,C. and Meier,H. (2011) Comprehensive and relaxed search for oligonucleotide signatures in hierarchically clustered sequence datasets. Bioinformatics, 27, 1546-1554.
21. Fitch,J., Gardner,S., Kuczmarski,T., Kurtz,S., Myers,R., Ott,L., Slezak,T., Vitalis,E., Zelma,A. and McCready,P. (2002) Rapid development of nucleic acid diagnostics. Proc IEEE, 90, 1708-1720.
22. Fu,Q., Ruegger,P., Bent,E., Chrobak,M. and Borneman,J. (2008) PRISE (PRImer SElector): software for designing sequence-selective PCR primers. J. Microbiol. Methods, 72, 263-267.
23. Jarman,S.N. (2004) Amplicon: software for designing PCR primers on aligned DNA sequences. Bioinformatics, 20, 1644-1645.
24. Phillippy,A.M., Ayanbule,K., Edwards,N.J. and Salzberg,S.L. (2009) Insignia: a DNA signature search web server for diagnostic assay development. Nucleic Acids Res., 37, W229-W234.
25. Drosten,C., Gottig,S., Schilling,S., Asper,M., Panning,M., Schmitz,H. and Gunther,S. (2002) Rapid detection and quantification of RNA of Ebola and Marburg Viruses, Lassa Virus, Crimean-Congo Hemorrhagic Fever Virus, Rift Valley Fever Virus, Dengue Virus, and Yellow Fever Virus by real-time reverse transcription-PCR. J. Clin. Microbiol., 40, 2323-2330. (Pubitemid 34747327)
26. Radnedge,L., Agron,P.G., Hill,K.K., Jackson,P.J., Ticknor,L.O., Keim,P. and Andersen,G.L. (2003) Genome differences that distinguish Bacillus anthracis from Bacillus cereus and Bacillus thuringiensis. Appl. Environ. Microbiol., 69, 2755-2764. (Pubitemid 36560354)
27. Barns,S.M., Grow,C.C., Okinaka,R.T., Keim,P. and Kuske,C.R. (2005) Detection of diverse new Francisella-like bacteria in environmental samples. Appl. Environ. Microbiol., 71, 5494-5500. (Pubitemid 41338285)
28. Larkin,M.J., Osborn,A.M. and Fairley,D. (2005) A molecular toolbox for bacterial ecologists: PCR primers for functional gene analysis. In: Osborn,A.M. and Smith,C.J. (eds), Molecular Microbial Ecology. Taylor and Francis, NY, New York, pp. 249-270.
29. Pereyra,L.P., Hiibel,S.R., Riquelme,M.V., Reardon,K.F. and Pruden,A. (2010) Detection and quantification of functional genes of cellulose- degrading, fermentative, and sulfate-reducing bacteria and methanogenic archaea. Appl. Environ. Microbiol., 76, 2192-2202.
30. Smith,C.J. and Osborn,A.M. (2008) Advantages and limitations of quantitative PCR (Q-PCR)-based approaches in microbial ecology. FEMS Microbiol. Ecol., 67, 6-20.
31. Fierer,N., Bradford,M.A. and Jackson,R.B. (2007) Toward an ecological classification of soil bacteria. Ecology, 88, 1354-1364. (Pubitemid 351345211)
32. Lim,J., Shin,S.G., Lee,S. and Hwang,S. (2011) Design and use of group-specific primers and probes for real-time quantitative PCR. Front. Environ. Sci. Eng. China, 5, 28-39.
33. Cole,J.R., Wang,Q., Cardenas,E., Fish,J., Chai,B., Farris,R.J., Kulam-Syed-Mohideen,A.S., McGarrell,D.M., Marsh,T., Garrity,G.M. et al. (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res., 37, D141-D145.
34. Probert,W.S., Schrader,K.N., Khuong,N.Y., Bystrom,S.L. and Graves,M.H. (2004) Real-time multiplex PCR assay for detection of Brucella spp., B. abortus, and B. melitensis. J. Clin. Microbiol., 42, 1290-1293. (Pubitemid 38332870)
35. Janssen,P.H. (2006) Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl. Environ. Microbiol., 72, 1719-1728.
36. Eichorst,S.A., Breznak,J.A. and Schmidt,T.M. (2007) Isolation and characterization of soil bacteria that define Terriglobus gen. nov., in the phylum. Acidobacteria Appl. Environ. Microbiol. gen. nov., 73, 2708-2717.
37. Jones,R.T., Robeson,M.S., Lauber,C.L., Hamady,M., Knight,R. and Fierer,N. (2009) A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. ISME J., 3, 442-453.
38. Sait,M., Davis,K.E. and Janssen,P.H. (2006) Effect of pH on isolation and distribution of members of subdivision 1 of the phylum Acidobacteria occurring in soil. Appl. Environ. Microbiol., 72, 1852-1857.
39. Eichorst,S.A., Kuske,C.R. and Schmidt,T.M. (2011) Influence of plant polymers on the distribution and cultivation of bacteria in the phylum Acidobacteria. Appl. Environ. Microbiol., 77, 586-596.
40. Thomson,B.C., Ostle,N., McNamara,N., Bailey,M.J., Whiteley,A.S. and Griffiths,R.I. (2010) Vegetation affects the relative abundances of dominant soil bacterial taxa and soil respiration Rates in an upland grassland soil. Microb. Ecol., 59, 335-343.
41. Yin,C., Jones,K.L., Peterson,D.E., Garrett,K.A., Hulbert,S.H. and Paulitz,T.C. (2010) Members of soil bacterial communities sensitive to tillage and crop rotation. Soil Biol. Biochem., 42, 2111-2118.
42. Dunbar,J., Eichorst,S.A., Gallegos-Graves,L.V., Silva,S., Xie,G., Hengartner,N., Evans,R.D., Hungate,B.A., Jackson,R.B., Megonigal,J.P. et al. (2012) Common bacterial repsonses in six ecosystems exposed to 10 years of elevated atmospheric carbon dioxide. Environ. Microbiol., 14, 1145-1158.
43. 2 affects soil microbial diversity associated with trembling aspen. Environ. Microbiol., 10, 926-941.
44. Barns,S.M., Cain,E.C., Sommerville,L. and Kuske,C.R. (2007) Acidobacteria phylum sequences in uranium-contaminated subsurface sediments greatly expand the known diversity within the phylum. Appl. Environ. Microbiol., 73, 3113-3116. (Pubitemid 46718601)
45. Pankratov,T.A., Ivanova,A.O., Dedysh,S.N. and Liesack,W. (2011) Bacterial populations and environmental factors controlling cellulose degradation in an acidic Sphagnum peat. Environ. Microbiol., 13, 1800-1814.
46. Ward,N.L., Challacombe,J.F., Janssen,P.H., Henrissat,B., Coutinho,P.M., Wu,M., Xie,G., Haft,D.H., Sait,M., Badger,J. et al. (2009) Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils. Appl. Environ. Microbiol., 75, 2046-2056.
47. Kishimoto,N., Kosako,Y. and Tano,T. (1991) Acidobacterium capsulatum gen. nov., sp. nov., an acidophilic chemoorganotrophic bacterium belonging to the phylum Acidobacteria. Curr. Microbiol., 317, 138-142.
48. Koch,I.H., Gich,F., Dunfield,P.F. and Overmann,J. (2008) Edaphobacter modestus gen. nov., sp. nov., and Edaphobacter aggregans sp. nov., acidobacteria isolated from alpine and forest soils. Int. J. Syst. Evol. Microbiol., 58, 1114-1122.
49. Männistö,M.K., Rawat,S., Starovoytov,V. and Häggblom,M.M. (2011) Terriglobus saanensis sp. nov., an acidobacterium isolated from tundra soil. Int. J. Syst. Evol. Microbiol., 61, 1823-1828.
50. Pankratov,T.A. and Dedysh,S.N. (2010) Granulicella paludicola gen. nov., sp. nov., Granulicella pectinivorans sp. nov., Granulicella aggregans sp. nov. and Granulicella rosea sp. nov., acidophilic, polymer-degrading acidobacteria from Sphagnum peat bogs. Int. J. Syst. Evol. Microbiol., 60, 2951-2959.
51. Pankratov,T.A., Kirsanova,L.A., Kaparullina,E.N., Kevbrin,V.V. and Dedysh,S.N. (2011) Telmatobacter bradus gen. nov., sp. nov., a cellulolytic facultative anaerobe from subdivision 1 of the Acidobacteria, and emended description of Acidobacterium capsulatum Kishimoto et al. 1991. Int. J. Syst. Evol. Microbiol., 62, 430-437.
52. Durbin,R., Eddy,S., Krogh,A. and Mitchison,G. (1998) Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, Cambridge, UK.
53. Alpern,B., Carter,L. and Gatlin,K. (1995) ACM/IEEE Conference on Supercomputing. ACM (Association for Computing Machinery), NY, New York.
54. SantaLucia,J. Jr and Hicks,D. (2004) The thermodynamics of DNA structural motifs. Annu. Rev. Biophys. Biomol. Struct., 33, 415-440.
55. Gans,J.D. and Wolinsky,M. (2008) Improved assay-dependent searching of nucleic acid sequence databases. Nucleic Acids Res., 36, e74.
56. Karlin,S. and Mrazek,J. (1997) Compositional differences within and between eukaryotic genomes. Proc. Natl Acad. Sci. USA, 94, 10227-10232. (Pubitemid 27407023)
57. Gardner,S.N., Kuczmarski,T.A., Vitalis,E.A. and Slezak,T.R. (2003) Limitations of TaqMan PCR for detecting divergent viral pathogens illustrated by hepatitis A, B, C, and E viruses and human immunodeficiency virus. J. Clin. Microbiol., 41, 2417-2427. (Pubitemid 36712445)
58. Pruesse,E., Quast,C., Knittel,K., Fuchs,B., Ludwig,W., Peplies,J. and Glockner,F. (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res., 35, 7188-7196.
59. Ludwig,W., Strunk,O., Westram,R., Richter,L., Meier,H., Yadhukumar., Buchner,A., Lai,T., Steppi,S., Jobb,G. et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Res., 32, 1363-1371. (Pubitemid 38854737)
60. Wang,Q., Garrity,G.M., Tiedje,J.M. and Cole,J.R. (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol., 73, 5261-5267. (Pubitemid 47326658)
61. Gans,J., Wolinsky,M. and Dunbar,J. (2005) Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science, 309, 1387.
62. Gans,J., Wolinsky,M. and Dunbar,J. (2006) Response to comment by Bunge et al. on 'Computational improvements reveal great bacterial diversity and high metal toxicity in soil'. Science, 313, 917.