Novel primers and PCR protocols for the specific detection and quantification of Sphingobium suberifaciens in situ

Molecular and Cellular Probes

Volumn 28, Issue 5-6, 2014, Pages 211-217

  Bull, Carolee T ^a   Goldman, Polly H ^a   Martin, Kendall J ^b  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

^b WILLIAM PATERSON UNIVERSITY   (United States)

Author keywords

Quantitative PCR; Real time PCR; Rhizomonas; Rhizorhapis; Sphingomonas

Indexed keywords

BACTERIAL DNA; DNA 16S; PRIMER DNA; RNA 16S;

ARTICLE; BACTERIAL GENETICS; BACTERIAL STRAIN; BACTERIUM DETECTION; BACTERIUM ISOLATION; COMPUTER MODEL; CORRELATION ANALYSIS; DISEASE COURSE; DISEASE SEVERITY; LETTUCE; LIMIT OF DETECTION; NATURAL POPULATION; NONHUMAN; POLYMERASE CHAIN REACTION; PRACTICE GUIDELINE; PRIORITY JOURNAL; QUANTITATIVE POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; SOIL; SOIL INOCULATION; SPHINGOBIUM SUBERIFACIENS; SPHINGOMONADACEAE; BACTERIUM IDENTIFICATION; CHEMISTRY; CLASSIFICATION; DNA SEQUENCE; GENETIC VARIABILITY; GENETICS; MICROBIOLOGY; MOLECULAR GENETICS; PLANT ROOT; PROCEDURES; REPRODUCIBILITY; SPECIES DIFFERENCE;

LACTUCA; SPHINGOBIUM; SPHINGOMONADACEAE; SPHINGOMONAS;

BACTERIAL TYPING TECHNIQUES; DNA PRIMERS; DNA, BACTERIAL; GENETIC VARIATION; LETTUCE; MOLECULAR SEQUENCE DATA; PLANT ROOTS; POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY; SPECIES SPECIFICITY; SPHINGOMONADACEAE;

EID: 84922064551     PISSN: 08908508     EISSN: 10961194     Source Type: Journal    
DOI: 10.1016/j.mcp.2014.03.001     Document Type: Article

References (32)

1. Patterson C.L., Grogan R.G., Campbell R.N. Economically important diseases of lettuce. Plant Dis 1986, 70:982-987.
2. van Bruggen A.H.C., Jochimsen K.N. First report of Rhizomonas sp. causing corky root of lettuce in Europe. Neth J Plant Pathol 1992, 98:45-56.
3. van Bruggen A.H.C., Jochimsen K.N. First report of Rhizomonas suberifaciens causing corky root of lettuce in Australia. Australas Plant Pathol 1993, 22:22-27.
4. van Bruggen A.H.C., Brown P.R., Jochimsen K.N. Corky root of lettuce caused by strains of a gram-negative bacterium from muck soils of Florida, New York, and Wisconsin. Appl Environ Microbiol 1989, 55:2635-2640.
5. van Bruggen A.H.C., Rubatzky V.E. Use of transplants instead of direct seeding to reduce corky root severity and losses due to corky root in iceberg lettuce. Plant Dis 1992, 76:703-708.
6. van Bruggen A.H.C. Corky root. Compendium of lettuce diseases 1997, 28-29. APS Press, St. Paul, MN. R.M. Davis, K.V. Subbarao, R.N. Raid, E.A. Kurtz (Eds.).
7. Alvarez J., Datnoff L.E., Nagata S.T. Crop rotation minimizes losses from corky root in Florida lettuce. HortScience 1992, 27:66-68.
8. Subbarao K.V., Hubbard J.C., Schulbach K.F. Comparison of lettuce diseases and yield under subsurface drip and furrow irrigation. Phytopathology 1997, 87:877-883.
9. van Bruggen A.H.C., Brown P.R. Distinction between infectious and noninfectious corky root of lettuce in relation to nitrogen fertilizer. JAm Soc Hortic Sci 1990, 115:762-770.
10. van Bruggen A.H.C., Brown P.R., Shennan C., Greathead A.S. The effect of cover crops and fertilization with ammonium nitrate on corky root of lettuce. Plant Dis 1990, 74:584-589.
11. Brown P.R., Michelmore R.W. The genetics of corky root resistance in lettuce. Phytopathology 1988, 78:1145-1150.
12. Mou B., Bull C.T. Screening lettuce germplasm for new sources of resistance to corky root. JAm Soc Hortic Sci 2004, 129:712-716.
13. Vera Cruz C.M., Bai J., Oña I., Leung H., Nelson R.J., Mew T.-W., et al. Predicting durability of a disease resistance gene based on an assessment of the fitness loss and epidemiological consequences of avirulence gene mutation. Proc Natl Acad Sci U S A 2000, 97:13501-13505.
14. Coons G.H. Diseases of field and vegetable crops in the U. S. for 1921. Plant Dis Rep Sup 1922, 22:409.
15. Hoff J.K., Newhall A.G. Corky root rot of iceberg lettuce on the mucklands of New York. Plant Dis Rep 1960, 44:333-339.
16. MacNeill B.H. Abotrytis root rot condition in lettuce. Plant Dis Rep 1953, 37:618-619.
17. Mix A.J. Aphanomyces root rot of lettuce, pepper and eggplant seedlings in Northern New Jersey. Plant Dis Rep 1945, 29:649-650.
18. Van Bruggen A.H.C., Grogan R.G., Bogdanoff G.P., Waters G.M. Corky root of lettuce in California is caused by a gram-negative bacterium. Phytopathology 1988, 78:581-584.
19. Yabuuchi E., Kosako Y., Naka T., Suzuki S., Yano I. Proposal of Sphingomonas suberifaciens (van Bruggen, Jochimsen and Brown 1990) comb. nov., Sphingomonas natatoria (Sly 1985) comb. nov., Sphingomonas ursincola (Yurkov etal. 1997) comb. nov., and emendation of the genus Sphingomonas. Microbiol Immunol 1999, 1999(43):339-349.
20. Chen H., Jogler M., Rohde M., Klenk H.-P., Busse H.-J., Tindall B.J., et al. Sphingobium limneticum sp. nov. and Sphingobium boeckii sp. nov., two freshwater planktonic members of the family Sphingomonadacae, and reclassification of Sphingomonas suberifaciens as Sphingobium suberifaciens comb. nov. Int J Syst Evol Microbiol 2013, 63:735-743.
21. van Bruggen A.H.C., Jochimsen K.N., Brown P.R. Rhizomonas suberifaciens gen. nov., sp. nov., the causal agent of corky root of lettuce. Int J Syst Bacteriol 1990, 40:175-188.
22. van Bruggen A.H.C., Jochimsen K.N., Steinberger E.M., Segers P., Gillis M. Classification of Rhizomonas suberifaciens, an unnamed Rhizomonas species, and Sphingomonas spp. in rRNA superfamily IV. Int J Syst Bacteriol 1993, 43:1-7.
23. Francis I.M., Jochimsen K.N., De Vos P., van Bruggen A.H.C. Reclassification of rhizosphere bacteria including strains causing corky root of lettuce as Rhzorhapis suberifaciens gen. nov., Spingobium mellinum sp. nov., Sphingobium xanthum sp. nov., and Rhizorhabdus argentea gen. nov., sp. nov. Int J Syst Evol Microbiol 2014, 10.1099/ijs.0.058909-0.
24. O'Brien R.D., van Bruggen A.H.C. Populations of Rhizomonas suberifaciens on roots of host and nonhost plants. Phytopathology 1991, 81:1034-1038.
25. Martin K.J., Bull C.T. Novel primers for detection and quantification of Myxococcus species in situ. Mol Ecol 2006, 10.1111/j.1471-8286.2006.01339.x.
26. Reasoner D.J., Geldreich E.E. Anew medium for the enumeration and subculture of bacteria from potable water. Appl Environ Microbiol 1985, 49:1-7.
27. Van Bruggen A.H.C., Grogan R.G., Bogdanoff C.P., Waters C.M. Corky root of lettuce in California caused by a gram-negative bacterium. Phytopathology 1988, 78:1139-1145.
28. Lane D.J. 16S/23S rRNA sequencing. Nucleic acid techniques in bacterial systematics 1991, 115-175. John Wiley and Sons, New York. E. Stackebrandt, M. Goodfellow (Eds.).
29. Weisburg W.G., Barns S.M., Pelletier D.A., Lane D.J. 16S ribosomal DNA amplification for phylogenetic study. JBacteriol 1991, 173:697-703.
30. van Bruggen A.H.C., Jochimsen K.N., Benedict A.A., Pollard L.W. Monoclonal antibodies for the detection of Rhizomonas suberifaciens, causal agent of corky root of lettuce, with enzyme immunoassays. Food Agr Immunol 1992, 4:27-40.
31. Kim H., Nishiyama M., Kunito T., Senoo K., Kawahara K., Murakami K., et al. High population of Sphingomonas species on plant surface. JAppl Microbiol 1998, 85:731-736.
32. Leys M.E.J., Rygaert A., Bastiaens L., Verstraete W., Top E.M. Occurrence and phylogenetic diversity of Sphingomonas strains in soils contaminated with polycyclic aromatic hydrocarbons. Appl Environ Microbiol 2004, 70:1944-1955.