1887

Abstract

We have been using a mutational approach to determine how plant-beneficial bacteria such as 501R3 obtain carbon and energy for colonization of subterranean portions of cucumber and other plants. Reduced carbon detected in cucumber root exudate consisted of 73.3 % amino acids, 22.2 % organic acids and 4.4 % carbohydrate. M2, a mini-Tn Km transposon mutant of strain 501R3, was severely reduced in growth relative to strain 501R3 on the mixture of amino acids and organic acids detected in cucumber root exudate when these compounds were supplied as the sole source of carbon and energy, but was similar in growth on the mixture of carbohydrates detected in this exudate. Molecular and biochemical characterization of M2 indicated that the transposon was inserted in , which encodes a subunit of succinate dehydrogenase. A-11, a mutant of strain 501R3 with a mini-Tn Km insertion in was severely reduced in growth relative to strain 501R3 on the mixture of carbohydrates detected in cucumber root exudate, but similar in growth on the mixture of amino acids and organic acids. When strains A-11 and M2 were coapplied with strain 501R3 to cucumber seeds above carrying capacity in competitive root colonization assays, populations of strains A-11 and M2 were roughly one order of magnitude lower than those of strain 501R3 in cucumber rhizosphere, while populations of strains A-11 and M2 were similar to one other when coapplied to cucumber seeds. When strains were coapplied to cucumber seeds below carrying capacity, populations of A-11 and M2 were roughly two to three orders of magnitude lower than those of 501R3 in cucumber rhizosphere, and populations of A-11 were significantly lower than those of M2 when these two strains were coapplied to cucumber seed. The experiments reported here indicate an important role for and and the catabolism of carbohydrates, and of amino acids and organic acids, respectively, in the colonization of cucumber roots by . The results reported here also indicate that catabolism of carbohydrates by this bacterium is more important than catabolism of amino acids and organic acids at lower population densities, despite the much higher relative quantities of amino acids and organic acids detected in cucumber root exudate.

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.2006/005538-0
2007-09-01
2024-04-23
Loading full text...

Full text loading...

/deliver/fulltext/micro/153/9/3196.html?itemId=/content/journal/micro/10.1099/mic.0.2006/005538-0&mimeType=html&fmt=ahah

References

  1. Altschul S. F., Madden T. L., Schaffer A. A., Zhang J., Miller W., Lipman D. J. 1997; Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402
    [Google Scholar]
  2. Andrews J. H. 1992; Biological control in the phyllosphere. Annu Rev Phytopathol 30:603–635
    [Google Scholar]
  3. Bennet R. A., Lynch J. M. 1981; Colonization potential of bacteria in the rhizosphere. Curr Microbiol 6:137–138
    [Google Scholar]
  4. Botsford J. L., Harman J. G. 1992; Cyclic AMP in prokaryotes. Microbiol Rev 56:100–122
    [Google Scholar]
  5. Bradford M. M. 1976; A rapid and sensitive method for the quantitation of milligram quantities of protein utilizing the principle of protein–dye binding. Anal Biochem 72:248–254
    [Google Scholar]
  6. Bringhurst R. M., Cardon Z. G., Gage D. J. 2001; Galactosides in the rhizosphere: utilization by Sinorhizobium meliloti and development of a biosensor. Proc Natl Acad Sci U S A 98:4540–4545
    [Google Scholar]
  7. Bull C. T., Weller D. M., Thomashow L. S. 1991; Relationship between root colonization and suppression of Gaeumannomyces graminis var. tritici by Pseudomonas fluorescens 2–79. Phytopathology 81:954–959
    [Google Scholar]
  8. Canonaco F., Hess T. A., Heri S., Wang T., Szyperski T., Sauer U. 2001; Metabolic flux response to phosphoglucose isomerase knock-out in Escherichia coli and impact of overexpression of the soluble transhydrogenase UdhA. FEMS Microbiol Lett 204:247–252
    [Google Scholar]
  9. Carlton B. C., Brown B. J. 1981; Gene Mutation. In Manual of Methods for General Bacteriology, pp. 222–242 Edited by Gerhardt P., Murray R. G. E., Costilow R. N., Nester E. W., Wood W. A., Krieg N. R., Phillips G. B. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  10. Cecchini G., Schroeder I., Gunsalus R. P., Macklashina E. 2002; Succinate dehydrogenase and fumarate reductase from Escherichia coli. Biochim Biophys Acta 1553140–157
    [Google Scholar]
  11. Chang K. J., Roberts J. K. M. 1989; Observation of cytoplasmic and vacuolar malate in maize root tips by 13C-NMR spectroscopy. Plant Physiol 89:197–203
    [Google Scholar]
  12. Chin-A-Woeng T. F. C., Bloemberg G. V., Mulders I. H. M., Dekkers L. C., Lugtenberg B. J. J. 2000; Root colonization by phenazine-1-carboxamide-producing bacterium Pseudomonas chlororaphis PCL1391 is essential for biocontrol of tomato foot and root rot. Mol Plant Microbe Interact 13:1340–1345
    [Google Scholar]
  13. Collier D. N., Hagar P. W., Phibbs P. V. Jr 1996; Catabolite repression control in the pseudomonads. Res Microbiol 147:551–561
    [Google Scholar]
  14. Crozat Y., Cleyet-Marel J. C., Giraud J. J., Obaton M. 1982; Survival rates of Rhizobium japonicum populations introduced into different soils. Soil Biol Biochem 14:401–405
    [Google Scholar]
  15. Cunningham L., Guest J. R. 1998; Transcription and transcript processing in the sdhCDAB- sucABCD operon of Escherichia coli. Microbiology 144:2113–2123
    [Google Scholar]
  16. Curl E. A., Truelove B. 1986 The Rhizosphere New York: Springer-Verlag;
  17. De Leij F. A. A. M., Thomas C. E., Bailey M. J., Whipps J. M., Lynch J. M. 1998; Effect of insertion site and metabolic load on the environmental fitness of a genetically modified Pseudomonas fluorescens isolate. Appl Environ Microbiol 64:2634–2638
    [Google Scholar]
  18. de Weert S., Vermeiren H., Mulders I. H. M., Kuiper I., Hendrickx N., Bloemberg G. V., Vanderleyden J., De Mot R., Lugtenberg B. J. J. 2002; Flagella-driven chemotaxis towards exudate components is an important trait for tomato root colonization by Pseudomonas fluorescens. Mol Plant Microbe Interact 15:1173–1180
    [Google Scholar]
  19. Egli T., Zinn M. 2003; The concept of multiple-nutrient-limited growth of microorganisms and its application in biotechnological processes. Biotechnol Adv 22:35–43
    [Google Scholar]
  20. Emmerling M., Dauner M., Ponti A., Fiaux J., Hochuli M., Szyperski T., Wüthrich K., Bailey J. E., Sauer U. 2002; Metabolic flux responses to pyruvate kinase knockout in Escherichia coli. J Bacteriol 184:152–164
    [Google Scholar]
  21. Farrar J., Hawes M., Jones D., Lindow S. 2003; How roots control the flux of carbon to the rhizosphere. Ecology 84:827–837
    [Google Scholar]
  22. Fraenkel D. G. 1996; Glycolysis. In Escherichia coli and Salmonella Cellular and Molecular Biology pp 189–198 Edited by Neidhardt F. C., Curtis R. III, Ingraham J. L., Lin E. C. C., Low K. B., Magasanik B., Reznikoff W. S., Riley M., Schaechter M., Umbarger H. E. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  23. Gottschal J. C. 1993; Growth kinetics and competition – some contemporary comments. Antonie van Leeuwenhoek 63:299–313
    [Google Scholar]
  24. Grayston S. J., Vaughan D., Jones D. 1997; Rhizosphere carbon flow in trees, in comparison with annual plants: the importance of root exudation and its impact on microbial activity and nutrient availability. Appl Soil Ecol 5:29–56
    [Google Scholar]
  25. Guest J. R., Russell G. C. 1992; Complexes and complexities of the citric acid cycle in Escherichia coli. Curr Top Cell Regul 33:231–247
    [Google Scholar]
  26. Hadar Y., Harman G. E., Taylor A. G., Horton J. M. 1983; Effects of pregermination of pea and cucumber seeds and of seed treatment with Enterobacter cloacae on rots caused by Pythium spp. Phytopathology 73:1322–1325
    [Google Scholar]
  27. Hall T. A. 1999; BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98
    [Google Scholar]
  28. Harder W., Dijkhuizen L. 1983; Physiological responses to nutrient limitation. Annu Rev Microbiol 37:1–23
    [Google Scholar]
  29. Helal H. M., Sauerbeck D. 1986; Effect of plant roots on carbon metabolism of soil microbial biomass. Z Pflanzenernaehr Bodenkd 149:181–188
    [Google Scholar]
  30. Herbert A. A., Guest J. R. 1971; Two mutations affecting utilization of C4-dicarboxylic acids by Escherichia coli. J Gen Microbiol 63:151–162
    [Google Scholar]
  31. Hirsch C. A., Rasminsky M., Davis B. D., Lin E. C. C. 1963; A fumarate reductase in Escherichia coli distinct from succinate dehydrogenase. J Biol Chem 238:3770–3774
    [Google Scholar]
  32. Hoagland D. R., Arnon D. I. 1950; The Water-Culture Method for Growing Plants without Soil. Circular no: 347 Berkeley, CA: University of California Agricultural Experiment Station;
    [Google Scholar]
  33. Hua Q., Yang C., Oshima T., Mori H., Shimizu K. 2004; Analysis of gene expression in Escherichia coli in response to changes of growth-limiting nutrient in chemostat cultures. Appl Environ Microbiol 70:2354–2366
    [Google Scholar]
  34. Jaeger C. H. III, Lindow S. E., Miller W., Clark E., Firestone M. K. 1999; Mapping of sugar and amino acid availability in soil around roots with bacterial sensors of sucrose and tryptophan. Appl Environ Microbiol 65:2685–2690
    [Google Scholar]
  35. Jones D. L. 1998; Organic acids in the rhizosphere – a critical review. Plant Soil 205:25–44
    [Google Scholar]
  36. Jones D. L., Darrah P. R. 1993; Re-sorption of organic compounds by roots of Zea mays L. and its consequences in the rhizosphere. II. Experimental and model evidence for simultaneous exudation and re-sorption of soluble C compounds. Plant Soil 153:47–57
    [Google Scholar]
  37. Jones D. L., Darrah P. R. 1994a; Amino-acid influx at the soil–root interface of Zea mays L. and its implications in the rhizosphere. Plant Soil 163:1–12
    [Google Scholar]
  38. Jones D. L., Darrah P. R. 1994b; Role of root derived organic-acids in the mobilization of nutrients from the rhizosphere. Plant Soil 166:247–257
    [Google Scholar]
  39. Jones D. L., Darrah P. R. 1995; Influx and efflux of organic-acids across the soil–root interface of Zea mays L. and its implications in the rhizosphere C flow. Plant Soil 173:103–109
    [Google Scholar]
  40. Jones H. M., Gunsalus R. P. 1985; Transcription of Escherichia coli fumarate reductase genes ( frdABCD) and their coordinate regulation by oxygen, nitrate, and fumarate. J Bacteriol 164:1100–1109
    [Google Scholar]
  41. Keseler I. M., Collado-Vides J., Gama-Castro S., Ingraham J., Paley S., Paulsen I. T., Peralta-Gil M., Karp P. D. 2005; EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Res 33:D334–D337
    [Google Scholar]
  42. Koch A. L. 2001; Oligotrophs versus copiotrophs. Bioessays 23:657–661
    [Google Scholar]
  43. Kovarova-Kovar K., Egli T. 1998; Growth kinetics of suspended microbial cells: from single-substrate-controlled growth to mixed-substrate kinetics. Microbiol Mol Biol Rev 62:646–666
    [Google Scholar]
  44. Kraffczyk I., Trolldeiner G., Beringer H. 1984; Soluble root exudates of maize: influence of potassium supply and rhizosphere microorganisms. Soil Biol Biochem 16:315–322
    [Google Scholar]
  45. Larkin R. P., Roberts D. P., Gracia-Garza J. A. 1998; Biological control of fungal diseases. In Fungicidal Activity. Chemical and Biological Approaches to Plant Protection pp 149–191 Edited by Hutson D., Miyamoto J. New York: Wiley;
    [Google Scholar]
  46. Lendenmann U., Snozzi M., Egli T. 1996; Kinetics of the simultaneous utilization of sugar mixtures by Escherichia coli in continuous culture. Appl Environ Microbiol 62:1493–1499
    [Google Scholar]
  47. Lohrke S. M., Dery P. D., Li W., Reedy R., Kobayashi D. Y., Roberts D. P. 2002; Mutation in rpiA in Enterobacter cloacae decreases seed and root colonization and biocontrol of damping-off caused by Pythium ultimum on cucumber. Mol Plant Microbe Interact 15:817–825
    [Google Scholar]
  48. Lugtenberg B. J. J., Kravchenko L. V., Simons M. 1999; Tomato seed and root exudate sugars: composition, utilization by Pseudomonas biocontrol strains and role in rhizosphere colonization. Environ Microbiol 1:439–446
    [Google Scholar]
  49. Lugtenberg B. J. J., Dekkers L., Bloemberg G. V. 2001; Molecular determinants of rhizosphere colonization by Pseudomonas. Annu Rev Plant Phytopathol 39:461–490
    [Google Scholar]
  50. Lynch A. S., Lin E. C. 1996; Transcriptional control mediated by the ArcA two-component response regulator protein of Escherichia coli: characterization of DNA binding at target promoters. J Bacteriol 178:6238–6249
    [Google Scholar]
  51. Lynch J. M., Whipps J. M. 1990; Substrate flow in the rhizosphere. Plant Soil 129:1–10
    [Google Scholar]
  52. MacKenzie S. L. 1987; Gas chromatographic analysis of amino acids as the N-heptafluorobutyryl isobutyl esters. J Assoc Off Anal Chem 70:151–160
    [Google Scholar]
  53. Martínez-Granero F., Capdevila S., Sánchez-Contreras M., Martín M., Rivilla R. 2005; Two site-specific recombinases are implicated in phenotypic variation and competitive rhizosphere colonization in Pseudomonas fluorescens. Microbiology 151:975–983
    [Google Scholar]
  54. Mazzola M., Cook R. J., Thomashow L. S., Weller D. M., Pierson L. S. III 1992; Contribution of phenazine antibiotic biosynthesis to the ecological competence of fluorescent pseudomonads in soil habitats. Appl Environ Microbiol 58:2616–2624
    [Google Scholar]
  55. McDougall B. M., Rovira A. D. 1970; Sites of exudation of 14C-labeled compounds from wheat roots. New Phytol 69:999–1003
    [Google Scholar]
  56. Meharg A. A. 1994; A critical review of labeling techniques used to quantify rhizosphere carbon flow. Plant Soil 166:55–62
    [Google Scholar]
  57. Melal H. M., Sauerbeck E. R. 1983; Method to study turnover processes in soil layers of different proximity to roots. Soil Biol Biochem 15:223–225
    [Google Scholar]
  58. Meyer S. L. F., Roberts D. P. 2002; Combinations of biocontrol agents for management of plant-parasitic nematodes and soilborne plant-pathogenic fungi. J Nematol 34:1–8
    [Google Scholar]
  59. Miller J. H. 1972 Experiments in Molecular Genetics Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
  60. Nelson E. B. 1988; Biological control of Pythium seed rot and preemergence damping-off of cotton with Enterobacter cloacae and Erwinia herbicola applied as seed treatments. Plant Dis 72:140–142
    [Google Scholar]
  61. Owen A. G., Jones D. L. 2001; Competition for amino acids between wheat roots and rhizosphere microorganisms and the role of amino acids in plant N acquisition. Soil Biol Biochem 33:651–657
    [Google Scholar]
  62. Park S.-J., Chao G., Gunsalus R. P. 1997; Aerobic regulation of the sucABCD genes of Escherichia coli, which encode α-ketoglutarate dehydrogenase and succinyl coenzyme A synthetase: roles of ArcA, Fnr, and the upstream sdhCDAB promoter. J Bacteriol 179:4138–4142
    [Google Scholar]
  63. Paulitz T. C. 1990; Biochemical and ecological aspects of competition in biological control. . In Alternatives for Suppressing Agricultural Pests and Diseases pp 713–724 Edited by Baker R. R., Dunn P. E. New York: Alan R. Liss;
    [Google Scholar]
  64. Peekhaus N., Conway T. 1998; What's for Dinner?: Entner-Doudoroff metabolism in Escherichia coli. J Bacteriol 180:3495–3502
    [Google Scholar]
  65. Postma J., Hok-A-Hin C. H., Oude Voshaar J. H. 1990; Influence of the inoculum density on the growth and survival of Rhizobium leguminosarum biovar trifolii introduced into sterile and non-sterile loamy sand and silt loam. FEMS Microbiol Ecol 73:49–58
    [Google Scholar]
  66. Rainey P. B. 1999; Adaptation of Pseudomonas fluorescens to the plant rhizosphere. Environ Microbiol 1:243–257
    [Google Scholar]
  67. Roberts D. P., Sheets C. J., Hartung J. S. 1992; Evidence for proliferation of Enterobacter cloacae on carbohydrates in cucumber and pea spermosphere. Can J Microbiol 38:1128–1134
    [Google Scholar]
  68. Roberts D. P., Marty A. M., Dery P. D., Yucel I., Hartung J. S. 1996; Amino acids as reduced carbon sources for Enterobacter cloacae during colonization of the spermospheres of crop plants. Soil Biol Biochem 28:1015–1020
    [Google Scholar]
  69. Roberts D. P., Dery P. D., Hebbar K. P., Mao W., Lumsden R. D. 1997a; Biological control of damping-off of cucumber caused by Pythium ultimum with a root-colonization-deficient strain of Escherichia coli. J Phytopathol 145:383–388
    [Google Scholar]
  70. Roberts D. P., Dery P. D., Yucel I., Buyer J., Holtman M. A., Kobayashi D. Y. 1997b; Genetic analysis of the seed colonization mutant Enterobacter cloacae A-11. In Plant Growth-Promoting Rhizobacteria. Present Status and Future Prospects. Proceedings of the Fourth International Workshop on Plant Growth-Promoting Rhizobacteria, Japan-OECD Joint Workshop October 5–10 1997 pp 330–332 Edited by Ogashi A., Kobayashi K., Homma Y., Kodama F., Kondo N., Akino S. Sapporo, Japan: Nakanishi Printing;
    [Google Scholar]
  71. Roberts D. P., Dery P. D., Yucel I., Buyer J. S., Holtman M. A., Kobayashi D. Y. 1999; Role of pfkA and general carbohydrate catabolism in seed colonization by Enterobacter cloacae. Appl Environ Microbiol 65:2513–2519
    [Google Scholar]
  72. Roberts D. P., Dery P. D., Yucel I., Buyer J. S. 2000; Importance of pfkA for rapid growth of Enterobacter cloacae during colonization of crop seeds. Appl Environ Microbiol 66:87–91
    [Google Scholar]
  73. Roehl R. A., Vinopal R. T. 1976; Lack of glucose phosphotransferase function in phosphofructokinase mutants of Escherichia coli. J Bacteriol 126:852–860
    [Google Scholar]
  74. Sambrook J., Russell D. W. 2001 Molecular Cloning. A Laboratory Manual Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
  75. Shen J., Gunsalus R. P. 1997; Role of multiple ArcA recognition sites in anaerobic regulation of succinate dehydrogenase ( sdhCDAB) gene expression in Escherichia coli. Mol Microbiol 26:223–236
    [Google Scholar]
  76. Sørensen J., Jensen L. E., Nybroe O. 2001; Soil and rhizosphere as habitats for Pseudomonas inoculants: new knowledge on distribution, activity and physiological state derived from micro-scale and single-cell studies. Plant Soil 232:97–108
    [Google Scholar]
  77. Sullivan J. E., Schewe L. R. 1977; Preparation and gas chromatography of highly volatile trifluoroacetylated carbohydrates using N-methyl bis[trifluoroacetamide]. J Chromatog Sci 15:196–197
    [Google Scholar]
  78. Toal M. E., Yoemans C., Killham K., Meharg A. A. 2000; A review of rhizosphere carbon flow modeling. Plant Soil 222:263–281
    [Google Scholar]
  79. Veeger C., DerVartanian D. V., Zeylemaker W. P. 1969; Succinate dehydrogenase [EC 1 . 3 . 99 . 1 succinate: (acceptor) oxidoreductase]. Methods Enzymol 13:81–90
    [Google Scholar]
  80. Weller D. M. 1988; Biological control of soilborne plant pathogens in the rhizosphere with bacteria. Annu Rev Phytopathol 26:379–407
    [Google Scholar]
  81. Whipps J. M. 1990; Carbon economy. In The Rhizosphere pp 59–98 Edited by Lynch J. M. New York: Wiley Interscience;
    [Google Scholar]
  82. Wilson M., Lindow S. E. 1994; Inoculum density-dependent mortality and colonization of the phyllosphere by Pseudomonas syringae. Appl Environ Microbiol 60:2232–2237
    [Google Scholar]
  83. Wood D., Darlision M. G., Wilde R. J., Guest J. R. 1984; Nucleotide sequence encoding the flavoprotein and hydrophobic subunits of the succinate dehydrogenase of Escherichia coli. Biochem J 222:519–534
    [Google Scholar]
  84. Zhang Z., Gosset G., Barabote R., Gonzalez C. S., Cuevas W. A., Saier M. H. 2005; Functional interactions between the carbon and iron utilization regulators, Crp and Fur, in Escherichia coli. J Bacteriol 187:980–990
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.2006/005538-0
Loading
/content/journal/micro/10.1099/mic.0.2006/005538-0
Loading

Data & Media loading...

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error