Skip to main content

Rhizosphere Colonization: Molecular Determinants from Plant-Microbe Coexistence Perspective

  • Chapter

Part of the book series: Soil Biology ((SOILBIOL,volume 15))

Inoculation of plants with beneficial microbes can be traced back for centuries. Although bacteria were not proven to exist until in 1683 von Leeuwenhoek discovered microscopic ‘animals’ under the lens of his microscope, their utilisation to stimulate plant growth in agriculture has been exploited since ancient times. Theophrastus (372-287 BC) suggested the mixing of different soils as a means of ‘remedying defects and adding heart to the soil’ (Vessey 2003). Colonisation of plant root system is the very first step in nearly all interactions between plants and soil borne microbes. The importance of this compartment for plant growth and soil microbiology had already been realised in the very pioneer times of microbiology in the late 19th century. In 1888, Hellriegel and Wilfarth proved the special case of nitrogen nutrition of legumes through their root nodule bacteria, which Beijerinck finally isolated in 1889. In 1887–1888 Hiltner was certainly fascinated by the findings of Hellriegel and Wilfarth about the special case of nitrogen nutrition in legumes. Together with Professor Nobbe, intensive studies were conducted about the nature of the symbiotic interaction of nodule bacteria and legume roots (Nobbe and Hiltner 1896). Apparently during these studies, Hiltner became aware of the importance of the ecological interactions in the root zone. Together with his teacher he developed the first inoculant based on root nodule bacteria for agricultural practice which they called ‘Nitragin’ in 1890. As agricultural practice was in close contact to the new achievements of basic sciences, the challenge quickly arose whether at all, and how, these discoveries of the — at that time — very young science ‘soil bacteriology’ could be applied in the field. Region of contact between root and soil where soil is affected by roots was designated as “rhizosphere” by Hiltner (1904).

This is a preview of subscription content, log in via an institution.

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   169.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Ahn IP, Park K, Kim CH (2002) Rhizobacteria-induced resistance perturbs viral disease progress and triggers defense-related gene expression. Mol Cell 13:302-308

    Google Scholar 

  • Akopyants NS, Fradkov A, Diatchenko L, Hill JE, Siebert PD, Lukyanov SA, Sverdlov ED, Berg DE (1998) PCR-based subtractive hybridization and differences in gene content among strains of Helicobacter pylori. Proc Natl Acad Sci USA 95:13108-13113

    PubMed  Google Scholar 

  • Alejandro P, Aloza V, Mohamed KF, Ana MB, Carol LB (2004) AlgR functions in algC expres-sion and virulence in Pseudomonas syringae pv. Syringe. Plant-Microbe Interact 150:2727-2737

    Google Scholar 

  • Andrews JH, Harris RF (2000) The ecology and biogeography of microorganisms on plant sur-faces. Annu Rev Phytopathol 38:145-180

    PubMed  Google Scholar 

  • Angela S, Hongqiao L, Helge W, Stephan A, Antje B, Katharina F, Alexander S, Matthias SU (2001) Thermoregulated expression of virulence factors in plant-associated bacteria. Arch Microbiol 176:393-399

    Google Scholar 

  • Anraku Y, Gennis R (1987) The aerobic respiratory chain of Escherichia coli. Trend Biochem Sci 12:262-266

    Google Scholar 

  • Apel K, Hirt H (2004) Reactive oxygen species: metabolism, oxidative stress, and signal transduc-tion. Ann Rev Plant Biol 55:373-399

    Google Scholar 

  • Arden A, Kelli P, Marvin W (2006) Microarray analysis of the osmotic stress response in Pseudomonas aeruginosa. J Bacteriol 188:2721-2725

    Google Scholar 

  • Arevalo-Ferro C, Reil C, Görg A, Eberl L, Riedel K (2005) Biofilm formation of Pseudomonas putida IsoF: the role of quorum sensing as assessed by proteomics. Syst Appl Microbiol 28:87-114

    PubMed  Google Scholar 

  • Aspedon A, Palmer K, Whiteley M (2006) Microarray analysis of the osmotic stress response in Pseudomonas aeruginosa. J Bacteriol 188:2721-2725

    PubMed  Google Scholar 

  • Bais HP, Tiffany LW, Laura GP, Simon G, Jorge MV (2006) The role of root exudates in rhizo-sphere interactions with plants and other organisms. Ann Rev Plant Biol 57:233-266

    Google Scholar 

  • Beerling DJ, Berner RA (2005) Feedbacks and the coevolution of plants and atmospheric CO2. Proc Natl Acad Sci USA 102:1302-1305

    PubMed  Google Scholar 

  • Benchamas S, Thomas Mark S, Katzenmeier G, Jonathan GS, Tungpradabkul S, Kunakorn M (2003) Role of the stationary growth phase sigma factor RpoS of Burkholderia pseudomallei in response to physiological stress conditions. J Bacteriol 185:7008-7014

    Google Scholar 

  • Benizri E, Nguyen C, Piutti S, Slezack-Deschaumes S, Philippot L (2007) Additions of maize root mucilage to soil changed the structure of the bacterial community. Soil Biol Biochem 39:1230-1233

    Google Scholar 

  • Blaha D, Sanguin H, Robe P, Nalin R, Bally R, Moënne-Loccoz R (2005) Physical organization of phytobeneficial genes nifH and ipdC in the plant growth-promoting rhizobacterium Azospirillum lipoferum 4VI. FEMS Microbiol Lett 244:157-163

    PubMed  Google Scholar 

  • Blomberg GV, Lugtenberg BJJ (2001) Molecular basis of plant growth promotion and biocontrol by rhizobacteria. Curr Opin Plant Biol 4:343-350

    Google Scholar 

  • Brandl MT, Lindow SE (1997) Environmental signals modulate the expression of an indole-3-acetic acid biosynthetic gene in Erwinia herbicola. Mol Plant Microb Interact 10:499-505

    Google Scholar 

  • Cardon ZG, Gage DJ (2006) Resource exchange in the rhizosphere: molecular yools and the microbial perspective. Annu Rev Ecol Evol Syst 37:459-488

    Google Scholar 

  • Castanjeda M, Sanchez J, Moreno S, Nunez C, Espi NG (2001) The global regulators GacA and GacAS form part of a cascade that controls alginate production in Azotobacter Vinelandii. J Bacteriol 183:787-793

    Google Scholar 

  • Chinnusamy V, Schumaker K, Zhu JK (2004) Molecular genetic perspectives on cross-talk and specificity in abiotic stress signaling in plants. J Exp Bot 55:225-236

    PubMed  Google Scholar 

  • Cortina C, Culiáñez-Macià FA (2005) Tomato abiotic stress enhanced tolerance by trehalose biosynthesis. Plant Sci 169:75-82

    Google Scholar 

  • Danhorn T, Fuqua C (2007) Biofilm formation by plant-associated bacteria. Ann Rev Microbiol (in press) De La Fuente L, Mavrodi DV, Landa BB, Thomashow LS, Weller DM (2006) phlD-based genetic diversity and detection of genotypes of 2,4-diacetylphloroglucinol-producing Pseudomonas fluorescens. FEMS Microbio Ecol 56:64-78

    Google Scholar 

  • Dekkers LC, Bloemendaal CP, de Weger LA, Wijffelman CA, Spaink HP, Lugtenberg BJJ (1998a) A two-component system plays an important role in the root-colonizing ability of Pseudomonas fluorescens strain WCS365. Mol Plant Microbe Interact 11:45-56

    PubMed  Google Scholar 

  • Dekkers LC, Phoelich CC, van der Fits L, Lugtenberg BJJ (1998b) A site-specific recombinase is required for competitive root colonization by Pseudomonas fluorescens WCS365. Proc Natl Acad Sci 95:7051-7056

    PubMed  Google Scholar 

  • Dekkers LC, van der Bij AJ, Mulders IHM, Phoelich CC, Wentwoord RAR, Glandorf DC, Wijffelman CA, Lugtenberg BJJ (1998c) Role of the O-antigen of lipopolysaccharide, and possible roles of growth rate and NADH: ubiquinone oxidoreductase in competitive tomato root-tip colonization by Pseudomonas fluorescens WCS365. Mol Plant Microb Interact 11:763-771

    Google Scholar 

  • Dewar K, Sabbagh L, Cardinal G, Veilleux F, Sanschagrin F, Birren B, Levesque RC (1998) Pseudomonas aeruginosa PAO1 bacterial artificial chromosomes: strategies for mapping, screening, and sequencing100 kb loci of the5.9 Mb genome. Microb Comp Genomic 2:105-117

    Google Scholar 

  • Dorman CJ (1991) DNA supercoiling and environmental regulation of gene expression in pathogenic bacteria. Infect Immun 59:745-749

    PubMed  Google Scholar 

  • Dubern JF, Lugtenberg BJJ, Bloemberg GV (2006) The ppuI-rsaL-ppuR quorum-sensing system regulates biofilm formation of Pseudomonas putida PCL1445 by controlling biosynthesis of the cyclic lipopeptides putisolvins I and II. J Bacteriol 188:2898-2906

    PubMed  Google Scholar 

  • Duijff BJ, Gianinazzi-Pearson V, Lemanceau P (1997) Involvement of the outer membrane lipopolysaccharides in the endophytic colonisation of tomato roots by biocontrol Pseudomonas fluorescens strain WCS417r. New Phytol 135:325-334

    Google Scholar 

  • Dybvig K (1993) DNA rearrangements and phenotypic switching in prokaryotes. Mol Microbiol 10:465-471

    PubMed  Google Scholar 

  • Edwards KJ, Saunders NA (2001) Real-time PCR used to measure stress-induced changes in the expression of the genes of the alginate pathway of Pseudomonas aeruginosa. J Appl Microbiol 91:29-37

    PubMed  Google Scholar 

  • Franklin MJ, Ohman DE (2002) Mutant analysis and cellular localization of the AlgI, AlgJ, and AlgF Proteins required for O acetylation of alginate in Pseudomonas aeruginosa. J Bacteriol 184:3000-3007

    PubMed  Google Scholar 

  • Gal M, Preston GM, Massey RC, Spiers AJ, Rainey PB (2003) Genes encoding a cellulosic polymer contribute toward the ecological success of Pseudomonas fluorescens SBW25 on plant surfaces. Mol Ecol 12:3109-3121

    PubMed  Google Scholar 

  • Glick BR, Penrose DM, Jiping LA (1998) Model for the lowering of plant ethylene concentrations by plant growth promoting bacteria. J Theor Biol 190:63-68

    PubMed  Google Scholar 

  • Gray KM (1997) Intercellular communication and group behavior in bacteria. Trends Microbiol 5:184-188

    PubMed  Google Scholar 

  • Hamon MA, Stanley NR, Britton RA, Grossman AD, Lazazzera BA (2004) Identification of AbrB-regulated genes involved in biofilm formation by Bacillus subtilis. Mol Microbiol 52 (3):847-860

    PubMed  Google Scholar 

  • Hassan NE, Vereecke D, Goethals K, Jaziri M, Baucher M (2003) Screening for differential gene expression in Atropa belladonna leafy gall induced following Rhodococcus fascians Infection. Euro J Plant Pathol 109:327-330

    Google Scholar 

  • Henge-Aronis R (1996) Regulation of gene expression during entry into stationary phase. In: Neidhardt FC, Curtiss R III, Ingraham JL, Lin ECC, Low KB, Magasanik B, Reznikoff WS, Riley M, Schaechter M, Umbarger HE (eds) Escherichia coli and Salmonella: cellular and molecular biology, 2nd edn, vol 1. ASM Press, Washington, pp 1497-1512

    Google Scholar 

  • Hiltner L (1904) Uber neuere Erfahrungen und Probleme auf dem Gebiete der Bodenbakteriologie unter bessonderer Ber&$$$;¨ ucksichtigung der Gr&$$$;¨ undung und Brache. Arb Dtsch Landwirtsch Ges Berl 98:59-78

    Google Scholar 

  • Howie WJ, Cook RJ, Weller DM (1987) Effects of soil matrix potential and cell motility on wheat root colonization by fluorescent pseudomonads suppressive to takeall. Phytopathol 77:286-292

    Google Scholar 

  • Huang B, Liu JY (2006) Cloning and functional analysis of the novel gene GhDBP3 encoding a DRE-binding transcription factor from Gossypium hirsutum. Biochim Biophys Acta 1759:263-269

    PubMed  Google Scholar 

  • Huang TP, Eileen BS, Wong ACL (2006) Differential biofilm formation and motility associated with lipopolysaccharide/exopolysaccharide-coupled biosynthetic genes in Stenotrophomonas maltophilia. J Bacteriol 188:3116-3120

    PubMed  Google Scholar 

  • Hulsmann A, Rosche TM, Kong IS, Hassan HM, Beam DM, Oliver JD (2003) RpoS-dependent stress response and exoenzyme production in Vibrio vulnificus. Appl Environ Microbiol 69:6114-6120

    PubMed  Google Scholar 

  • Isabel MRG, Campos MJ, Ramos JL (2005) Analysis of Pseudomonas putida KT2440 gene expression in the maize rhizosphere: in vitro expression technology capture and identification of root-activated promoters. J Bacteriol 187:4033-4041

    Google Scholar 

  • Isabelle V, Stephen PD, Rachael ES, Miguel C, Isabelle V, Stephen L, Lazdunski A, Williams P, Filloux A (2004) Biofilm formation in Pseudomonas aeruginosa: fimbrial cup gene clusters are controlled by the transcriptional regulator MvaT. J Bacteriol 186:2880-2890

    Google Scholar 

  • Jorgensen F, Bally M, Chapon HV, Michel G, Lazdunski A, Williams P, Stewart GS (1999) RpoS-dependent stress tolerance in Pseudomonas aeruginosa. Microbiol 145:835-844 Kaiser D, Losick R (1993) How and why bacteria talk to each other. Cell 73:873-885

    Google Scholar 

  • Karen MLK, Verhagen BWM, Keurentjes Joost JB, Johan AVP, Martijn R, Loon LCV, Pieterse CMJ (2005) Colonization of the Arabidopsis rhizosphere by fluorescent Pseudomonas spp. activates a root-specific, ethylene-responsive PR-5 gene in the vascular bundle. Plant Mol Biol 57:731-748

    Google Scholar 

  • Kazmierczak MJ, Wiedmann M, Kathryn JB (2005) Alternative sigma factors and their roles in bacterial virulence. Microbiol Mol Biol Rev 69:527-543

    PubMed  Google Scholar 

  • Keel US, Lezbolle KB, Behler E, Haas D, Keel C (2001) The sigma factor AlgU(AlgT) controls exopolysaccharide production and tolerance towards dessication and osmotic stress in the biocontrol agent P. flourescens CHAO. Appl Environ Microbiol 67:5683-5693

    PubMed  Google Scholar 

  • Kiely PD, Haynes JM, Higgins CH, Franks A, Mark GL, Morrissey JP, O’Gara F (2006) Exploiting new systems-based strategies to elucidate plant-bacterial interactions in the rhizo-sphere. Microb Ecol 51:257-266

    PubMed  Google Scholar 

  • Kim U, Birren B, Slepak T, Mancino V, Boysen C, Kang H, Simon M, Shizuya H (1996). Construction and characterization of a human bacterial artificial chromosome library. Genomic 34:213-218

    Google Scholar 

  • Kitagawa M, Chieko W, Yoshioka S, Takashi Y (1991) Expression of ClpB, an analog of the ATP-dependent protease regulatory subunit in Escherichia coli is controlled by a heat shock sigma factor. J Bacteriol 173:4247-4253

    PubMed  Google Scholar 

  • Kjelleberg S, Molin S (2002) Is there a role for quorum sensing signals in bacterial biofilm? Curr Opin Microbiol 5:254-258

    PubMed  Google Scholar 

  • Knoester M, Pieterse CM, Bol JF, Van Loon LC (1999) Systemic resistance in Arabidopsis induced by rhizobacteria requires ethylene-dependent signaling at the site of application. Mol Plant Microbe Interact 12:720-727

    PubMed  Google Scholar 

  • Kulkarni S, Nautiyal CS (1999) Effects of salt and pH stress on temperature tolerant Rhizobium sp. NBRI330 nodulating Prosopis juliflora. Curr Microbiol 40:221-226

    Google Scholar 

  • Kwak KJ, Kim JY, Kim YO, Kang H (2007) Characterization of transgenic Arabidopsis plants overexpressing high mobility group B proteins under high salinity, drought or cold stress. Plant Cell Physiol 48:221-231

    PubMed  Google Scholar 

  • Lan R, Reeves PR (2000) Intraspecies variation in bacterial genomes: the need for a species genome concept. Trends Microbiol 8:396-401

    PubMed  Google Scholar 

  • Landa BB, Mavrodi OV, Raaijmakers JM, McSpadden Gardener BB, Thomashow LS, Weller DM (2002) Differential ability of genotypes of 2,4-diacetylphloroglucinol-producing Pseudomonas fluorescens strains to colonize the roots of pea plants. Appl Environ Microbiol 68:3226-3237

    PubMed  Google Scholar 

  • Landa BB, Mavrodi DM, Thomashow LS, Weller DM (2003) Interactions between strains of 2,4-diacetylphloroglucinol-producing Pseudomonas fluorescens in the rhizosphere of wheat. Phytopathology 93:982-994

    PubMed  Google Scholar 

  • Laville J, Voisard C, Keel C, Maurhofer M, Défago G, Haas D (1992) Global control in Pseudomonas fluorescens mediating antibiotic synthesis and suppression of black root rot of tobacco. Proc Natl Acad Sci USA 189:1562-1566

    Google Scholar 

  • Lee JH, Lee KH, Gyeom KC, Young LS, Joong KG, Young HP, Oh CS (2005) Appl Microbiol Biotechnol 68:213-219

    PubMed  Google Scholar 

  • Lizewski SE, Jill RS, Debra WJ, Anders F, Alexander JC, Michael JS (2004) Identification of AlgR-regulated genes in Pseudomonas aeruginosa by use of microarray analysis. J Bacteriol 186:5672-5684

    PubMed  Google Scholar 

  • Lugtenberg BJJ, Dekkers L, Bloemberg GV (2001) Molecular determinants of rhizosphere colonization by Pseudomonas. Ann Rev Phytopathol 39:461-490

    Google Scholar 

  • Margarita M, Carvajal C, André C, Wijfjes HM, Mulders IHM, Lugtenberg BJJ, Bloemberg GV (2002) Characterization of NADH dehydrogenases of Pseudomonas fluorescens WCS365 and their role in competitive root colonization. Mol Plant Microbiol Inter 15:662-671

    Google Scholar 

  • Martínez-Granero F, Rivilla R, Martín M (2006) Rhizosphere selection of highly motile pheno-typic variants of Pseudomonas fluorescens with enhanced competitive colonization ability. Appl Environ Microbiol 72:3429-3434

    PubMed  Google Scholar 

  • Mathee K, Craig MJ, Ohman DE (1997) Posttranslational control of the algT (algU)-encoded s22 for expression of the alginate regulon in Pseudomonas aeruginosa and localization of its antagonist proteins MucA and MucB (AlgN). J Bacteriol 179:3711-3720

    PubMed  Google Scholar 

  • Mavrodi DV, Mavrodi OV, McSpadden-Gardener BB, Landa BB, Weller DM, Thomashow LS (2002) Identification of differences in genome content among phlD-positive Pseudomonas fluorescens strains by using PCR-based subtractive hybridization. Appl Envir Microbiol 68:5170-5176

    Google Scholar 

  • Mavrodi OV, Mavrodi DV, Park AA, Weller DM, Thomashow LS (2006a) The role of dsbA in colonization of the wheat rhizosphere by Pseudomonas fluorescens Q8r1-96 Microbiology 152:863-872

    Google Scholar 

  • Mavrodi OV, Mavrodi DV, Weller DM, Thomashow LS (2006b) Role of ptsP, orfT, and sss recombinase genes in root colonization by Pseudomonas fluorescens Q8r1-96. Appl Environ Microbiol 72:7111-7122

    PubMed  Google Scholar 

  • Mazzola M, Cook RJ, Thomashow LS, Weller DM, Pierson LS (1992) Contribution of phenazine antibiotic biosynthesis to the ecological competence of fluorescent pseudomonads in soil habi-tats. Appl Environ Microbiol 58:2616-2624

    PubMed  Google Scholar 

  • Miller LD, Yost CK, Hynes MF, Alexandre G (2007) The major chemotaxis gene cluster of Rhizobium leguminosarum bv. viciae is essential for competitive nodulation. Mol Microbiol 63:348-362

    PubMed  Google Scholar 

  • Moens S, Vanderleyden J (1996) Functions of bacterial flagella. Crit Rev Microbiol 22:67-100

    PubMed  Google Scholar 

  • Mohr CD, Leveau JHJ, Krieg DP, Hibler NS, Deretic V (1992) AlgR-binding sites within the algD promoter make up a set of inverted repeats separated by a large intervening segment of DNA. J Bacteriol 174:6624-6633

    PubMed  Google Scholar 

  • Nautiyal CS (2006) Biological control of plant diseases by natural and genetically engineered fluorescent Pseudomonas spp. In: Ray RC, Owen PW (eds) Microbial biotechnology in horti-culture. Science Publishers, Enfield (NH) USA, pp 125-162

    Google Scholar 

  • Nautiyal CS, Mehta S, Singh HB (2006a) Biological control and plant growth-promoting Bacillus strains from milk. J Microbiol Biotechnol 16:184-192

    Google Scholar 

  • Nautiyal CS, Mehta S, Singh HB, Pushpangadan P (2006b) Synergistic bioinoculant composition comprising bacterial strains of accession nos. NRRL B-30486, NRRL B-30487 and NRRL B-30488 and method of producing said composition thereof. US Patent 7097830

    Google Scholar 

  • Nelson KE, Weinel C, Paulsen IT, Dodson RJ, Hilbert H, Martins VA dos Santos, Fouts DE, Gill SR, Pop M, Holmes M, Brinkac L, Beanan M, DeBoy RT, Daugherty S, Kolonay J, Madupu R, Nelson W, White O, Peterson J, Khouri H, Hance I, Chris Lee P, Holtzapple E, Scanlan D, Tran K, Moazzez A, Utterback T, Rizzo M, Lee K, Kosack D, Moestl D, Wedler H, Lauber J, Stjepandic D, Hoheisel J, Straetz M, Heim S, Kiewitz C, Eisen JA, Timmis KN, Dusterhoft A, Tummler B, Fraser CM (2002) Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environ Microbiol 4:799-808

    PubMed  Google Scholar 

  • Nishimura M, Nakamura S, Hayashi N, Asakawa S, Shimizu N, Kaku H, Hasebe A, Kawasaki S (1998) Construction of a BAC library of the rice blast fungus Magnaporthe grisea and finding specific genome regions in which its transposons tend to cluster. Biosci Biotechnol Biochem 62:1515-1521

    PubMed  Google Scholar 

  • Nobbe F, Hiltner L (1896) Inoculation of the soil for cultivating leguminous plants. US Patent 570 813

    Google Scholar 

  • O’Toole GA, Kolter R (1998) Flagellar and twitching motility are necessary for Pseudomonas aeruginosa biofilm development. Mol Microbiol 30:295-304

    PubMed  Google Scholar 

  • Penrose DM, Glick BR (2003) Methods for isolating and characterizing ACC deaminase-containing plant growth-promoting rhizobacteria. Physiol Plantar 118:10-15

    Google Scholar 

  • Pham TH, Web JS, Rehm BHA (2004) The role of polyhydroxyalkanoate biosynthesis Pseudomonas aeruginosa in rhamnolipid and alginate production as well as stress tolerance and biofilm formation. Microbiology 150:3405-3413

    PubMed  Google Scholar 

  • Raaijmakers JM, Weller DM (2001) Exploiting genotypic diversity of 2,4-diacetylphloroglucinol-producing Pseudomonas spp.: characterization of superior root-colonizing P. fluorescens strain Q8r1-96. Appl Environ Microbiol 67:2545-2554

    PubMed  Google Scholar 

  • Raaijmakers JM, Bonsall RF, Weller DM (1999) Effect of population density of Pseudomonas fluorescens on production of 2,4-diacetylphloroglucinol in the rhizosphere of wheat. Phytopathology 89:470-475

    PubMed  Google Scholar 

  • Rainey PB, Preston GM (2000) In vivo expression technology strategies: valuable tools for biotechnology. Curr Opin Biotechnol 11:440-444

    PubMed  Google Scholar 

  • Rathinasabapathi B (2000) Metabolic engineering for stress tolerance: installing osmoprotectant synthesis pathways. Ann Bot 86:709-716

    Google Scholar 

  • Reva ON, Weine C, Weine M, Bohm K, Stjepandic D, Hoheisel JD, Tummler B (2006) Functional genomics of stress response in P. putida KT2440. J Bacteriol 188:4079-4092

    PubMed  Google Scholar 

  • Roberson EB, Firestone MK (1992) Relationship between desiccation and exopolysaccharide production in a soil Pseudomonas sp. Appl Environ Microbiol 1284-1291

    Google Scholar 

  • Roberts DP, McKenna LF, Lohrke SM, Rehner S, de Souza JT (2007) Pyruvate dehydrogenase activity is important for colonization of seeds and roots by Enterobacter cloacae. Soil Biol Biochem 39:2150-2159

    Google Scholar 

  • Rodriguez NDN, Dardanelli MS, Ruíz-Saínz JE (2007). Attachment of bacteria to the roots of higher plants. FEMS Microbiol Lett 1-10

    Google Scholar 

  • Ryu CM, Chia-Hui Hu CH, Locy RD, Kloepper JW (2005) Study of mechanisms for plant growth promotion elicited by rhizobacteria in Arabidopsis thaliana. Plant Soil 268:285-292

    Google Scholar 

  • Sakuma Y, Maruyama K, Qin F, Osakabe Y, Shinozaki K, Yamaguchi-Shinozaki K (2006) Dual function of an Arabidopsis transcription factor DREB2A in water-stress-responsive and heat-stress-responsive gene expression. Proc Natl Acad Sci USA 103:18822-18827

    PubMed  Google Scholar 

  • Salmond GPC, Bycroft BW, Stewart GSAB, Williams P (1995) The bacterial ‘enigma’: cracking the code of cell-cell communication. Mol Microbiol 16:615-624

    PubMed  Google Scholar 

  • Sauer K, Camper AK (2001) Characterization of phenotypic changes in Pseudomonas putida in response to surfaceassociated growth. J Bacteriol 183:6579-6589

    PubMed  Google Scholar 

  • Scher FM, Kloepper JW, Singleton C, Zaleski I, Laliberte M (1988) Colonization of soybean roots by Pseudomonas and Serratia species: relationship to bacterial motility, chemotaxis and generation time. Phytopathology 78:1055-1059

    Google Scholar 

  • Schmidt KD, Schmidt-Rose T, Romling U, Tummler B (1998) Differential genome analysis of bacteria by genomic subtractive hybridization and pulsed field gel electrophoresis. Electrophoresis 19:509-514

    PubMed  Google Scholar 

  • Schnider U, Keel C, Blumer C, Troxler J, Defago G, Haas D (1995) Amplification of the house-keeping sigma factor in Pseudomonas fluorescens CHA0 enhances antibiotic production and improves biocontrol abilities. J Bacteriol 177:5387-5392

    PubMed  Google Scholar 

  • Shizuya H, Birren B, Kim U, Mancino V, Slepak T, Tachiiri Y, Simon M (1992) Cloning and stable maintenance of 300-kilobase-pair fragment of human DNA in Escherichia coli using an F-factor-based vector. Proc Natl Acad Sci USA 89:8794-8797

    PubMed  Google Scholar 

  • Sledjeski DD, Whitman C, Zhang A (2001) Hfq is necessary for regulation by the untranslated RNA DsrA. J Bacteriol 183:1997-2005

    PubMed  Google Scholar 

  • Sreenivasulu NA, Sopory SK, Kavi Kishor PB (2007) Deciphering the regulatory mechanisms of abiotic stress tolerance in plants by genomic approaches. Gene 388:1-13

    PubMed  Google Scholar 

  • Straus D, Ausubel FM (1990) Genomic subtraction for cloning DNA corresponding to deletion mutations. Proc Natl Acad Sci USA 87:1889-1893

    PubMed  Google Scholar 

  • Swift S, Throup JP, Williams P, Salmond GP, Stewart GS (1996) Quorum sensing: a population-density component in the determination of bacterial phenotype. Trends Biochem Sci 21:214-219

    PubMed  Google Scholar 

  • Thomashow LS, Weller DM (1996) Current concepts in the use of introduced bacteria for biological disease control: mechanisms and antifungal metabolites. In: Stacey G, Keen NT (eds) Plant microbe interactions. Chapman & Hall, New York, NY, vol 1, pp 187-236

    Google Scholar 

  • Timmusk S, Wagner EGH (1999) The plant growth promoting Rhizobacterium Pennibacillus polymyxa induces changes in Arabidopsis thaliana gene expression: a possible connection between biotic and abiotic stress responses. Mol Plant Microbe Interact 12:951-959

    PubMed  Google Scholar 

  • Timmusk S, van West P, Gow NAR, Wagner EGH (2003) Antagonistic effects of Paenibacillus polymyxa towards the oomycete plant pathogens Phytophthora palmivora and Pythium apha-nidermatum. In: Mechanism of action of the plant growth promoting bacterium Paenibacillus polymyxa. Uppsala University, Uppsala, Sweden, pp 1-28

    Google Scholar 

  • Timmusk S, Grantcharova N, Gerhart E, Wagner H (2005) Paenibacillus polymyxa Invades plant roots and forms biofilms. Appl Environ Microbiol 71:7292-7300

    PubMed  Google Scholar 

  • Tosa Y, Mayama S, Nakayashiki H, Ohara Y, Wang Yan Qing (2005) Microarray analysis of the gene expression profile induced by the endophytic plant growth-promoting rhizobacteria, Pseudomonas fluorescens FPT9601-T5 in Arabidopsis. Mol Plant Microb Interact 18:385-396

    Google Scholar 

  • Urgel ME, Salido A, Ramos JL (2000) Genetic analysis of functions involved in adhesion of Pseudomonas putida to seeds. J Bacteriol 182:2363-2369

    Google Scholar 

  • Valverde A, Yaacov O, Burdman S (2006) How rhizobacteria promote plant growth: direct impact on plant development. FEMS Microbiol 265:186-194

    Google Scholar 

  • Vashisht AA, Tuteja N (2006) Stress responsive DEAD-box helicases: a new pathway to engineer plant stress tolerance. J Photochem Photobiol 84:150-160

    Google Scholar 

  • Vessey JK (2003) Plant growth promoting rhizobacteria as biofertilizers. Plant Soil 255:571-586

    Google Scholar 

  • Vinocur B, Altman A (2005) Recent advances in engineering plant tolerance to abiotic stress: achievements and limitations. Curr Opin Biotechnol 16:123-132

    PubMed  Google Scholar 

  • Weber H, Polen T, Heuveling J, Wendisch VF, Hengge R (2005) Genome-wide analysis of the general stress response network in Escherichia coli: &sgr;S-dependent genes, promoters, and sigma factor selectivity. J Bacteriol 187:1591-1603

    PubMed  Google Scholar 

  • Weger de LA, van der Vlugt CIM, Wijfjes AHM, Bakker PAHM, Schippers B, Lugtenberg BJJ (1987) Flagella of a plant growth stimulating Pseudomonas fluorescens strain are required for colonization of potato roots. J Bacteriol 169:2769-2773

    PubMed  Google Scholar 

  • Weller DM, Landa BB, Mavrodi OV, Schroeder KL, De La Fuente L, Bankhead LB, Allende MS, Bonsall RRF, Mavrodi DV, Thomashow LS (2007) Role of 2,4-diacetylphloroglucinol- producing fluorescent Pseudomonas spp. in the defense of plant roots. Plant Biol 9:4-20

    PubMed  Google Scholar 

  • Westbrock-Wadman S, Sherman DR, Hickey MJ, Coulter SN, Zhu YQ, Warrener P, Nguyen LY, Shawar RM, Folger KR, Stover CK (1999) Characterization of a Pseudomonas aeruginosa efflux pump contributing to aminoglycoside impermeability. Antimicrob Agents Chemother 43:2975-2983

    PubMed  Google Scholar 

  • Whitchurch CB, Nielsen TT, Ragas PC, Mattick JS (2002a) Extracellular DNA required for bacte-rial biofilm formation. Science 295:1487

    PubMed  Google Scholar 

  • Whitchurch CB, Erova TE, Emery JA, Sargent JL, Harris JM, Semmler ABT, Young MD, Mattick JS, Wozniak DJ (2002b) Phosphorylation of the Pseudomonas aeruginosa response regulator AlgR is essential for type IV fimbria-mediated twitching motility. J Bacteriol 184:4544-4554

    PubMed  Google Scholar 

  • Woo SS, Jiang J, Gill B, Paterson AH, Wing RA (1994) Construction and characterization of a bacterial artificial chromosome library of Sorghum bicolor. Nucleic Acids Res 22:4922-4931

    PubMed  Google Scholar 

  • Xie H, Pasternak JJ, Glick BR (1996) Isolation and characterization of mutants of the plant growth-promoting rhizobacterium Pseudomonas putida GR12-2 that overproduce indoleacetic acid. Curr Microbiol 32:67-71

    Google Scholar 

  • Zuo KJ, Qin J, Zhao JY, Ling H, Zhang LD, Cao YF, Tang KS (2007) Over-expression GbERF2 transcription factor in tobacco enhances brown spots disease resistance by activating expres-sion of downstream genes. Gene 391:80-90

    PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Chandra Shekhar Nautiyal .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2008 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Nautiyal, C.S., Srivastava, S., Chauhan, P.S. (2008). Rhizosphere Colonization: Molecular Determinants from Plant-Microbe Coexistence Perspective. In: Nautiyal, C.S., Dion, P. (eds) Molecular Mechanisms of Plant and Microbe Coexistence. Soil Biology, vol 15. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-75575-3_4

Download citation

Publish with us

Policies and ethics