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Molecular tools in rhizosphere microbiology—from single-cell to whole-community analysis

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Abstract

It is the aim of this chapter to present an overview of new, molecular tools that have been developed over recent years to study individual, single cells and composite, complex communities of microorganisms in the rhizosphere. We have carefully focused on culture-independent assays and selected methodologies that have already been or will soon be applicable for rhizosphere microbiology. Emphasis is placed on rhizosphere bacteria and the review first describes a number of the new methodologies developed for detection and localization of specific bacterial populations using modern electron and fluorescence microscopy combined with specific tagging techniques. First half of the chapter further comprises a thorough treatise of the recent development of reporter gene technology, i.e. using specific reporter bacteria to detect microscale distributions of rhizosphere compounds such as nutrients, metals and organic exudates or contaminants. Second half of the chapter devoted to microbial community analysis contains a thorough treatise of nucleotide- and PCR-based technologies to study composition and diversity of indigenous bacteria in the natural rhizosphere. Also included are the most recent developments of functional gene and gene expression analyses in the rhizosphere based on specific mRNA transcript or transcriptome analysis, proteome analysis and construction of metagenomic libraries.

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References

  • Adamczyk J, Hesselsoe M, Iversen N, Horn M, Lehner A, Nielsen PH, Schloter M, Roslev P, Wagner M (2003) The isotope array, a new tool that employs substrate-mediated labeling of rRNA for determination of microbial community structure and function. Appl Environ Microbiol 69:6875–6887. doi:10.1128/AEM.69.11.6875-6887.2003

    Article  PubMed  CAS  Google Scholar 

  • Allaway D, Schofield NA, Leonard ME, Gilardoni L, Finan TM, Poole PS (2001) Use of differential fluorescence induction and optical trapping to isolate environmentally induced genes. Environ Microbiol 3:397–406. doi:10.1046/j.1462-2920.2001.00205.x

    Article  PubMed  CAS  Google Scholar 

  • Andersen JB, Sternberg C, Poulsen JK, Bjørn SP, Givskov M, Molin S (1998) New unstable variants of Green Fluorescent Protein for studies of transient gene expression in bacteria. Appl Environ Microbiol 64:2240–2246

    PubMed  CAS  Google Scholar 

  • Anguish LJ, Ghiorse WC (1997) Computer-assisted laser scanning and video microscopy for analysis of Cryptosporidium parvum oocysts in soil, sediment, and feces. Appl Environ Microbiol 63:724–733

    PubMed  CAS  Google Scholar 

  • Assmus B, Hutzler P, Kirchhof G, Amann RI, Lawrence JR, Hartmann A (1995) In situ localization of Azospirillum brasilense in the rhizosphere of wheat with fluorescently labelled, ribosomal-RNA targeted oligonucleotide probes and scanning confocal laser microscopy. Appl Environ Microbiol 61:1013–1019

    PubMed  CAS  Google Scholar 

  • Assmus B, Schloter M, Kirchhof G, Hutzler P, Hartmann A (1997) Improved in situ tracking of rhizosphere bacteria using dual staining with fluorescence-labelled antibodies and rRNA-targeted oligonucleotides. Microb Ecol 33:32–40. doi:10.1007/s002489900005

    Article  PubMed  Google Scholar 

  • Babić KH, Schauss K, Hai B, Sikora S, Redzepović S, Radl V, Schloter M (2008) Influence of different Sinorhizobium meliloti inocula on abundance of genes involved in nitrogen transformations in the rhizosphere of alfalfa (Medicago sativa L.) Environ Microbiol 10: 2922–2930

    Article  PubMed  CAS  Google Scholar 

  • Bae YS, Knudsen GR (2000) Cotransformation of Trichoderma harzianum with beta-glucuronidase and green fluorescent protein genes provides a useful tool for monitoring fungal growth and activity in natural soils. Appl Environ Microbiol 66:810–815. doi:10.1128/AEM.66.2.810-815.2000

    Article  PubMed  CAS  Google Scholar 

  • Bælum J, Nicolaisen MH, Holben WE, Strobel BW, Sørensen J, Jacobsen CS (2008) Direct analysis of tfdA gene expression by indigenous bacteria in phenoxy acid amended agricultural soil. ISME J 2:677–687. doi:10.1038/ismej.2008.21

    Article  PubMed  CAS  Google Scholar 

  • Bammler T (2005) Standardizing global gene expression analysis between laboratories and across platforms. Nat Methods 2:351–356. doi:10.1038/nmeth0605-477a

    Article  PubMed  CAS  Google Scholar 

  • Barr M, East AK, Leonard M, Mauchline TH, Poole PS (2008) In vivo expression technology (IVET) selection of genes of Rhizobium leguminosarum biovar viciae A34 expressed in the rhizosphere. FEMS Microbiol Lett 282:219–227. doi:10.1111/j.1574-6968.2008.01131.x

    Article  PubMed  CAS  Google Scholar 

  • Beja O, Suzuki MT, Koonin EV, Aravind L, Hadd A, Nguyen LP, Villacorta R, Amjadi M (2000) Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environ Microbiol 2:516–529. doi:10.1046/j.1462-2920.2000.00133.x

    Article  PubMed  CAS  Google Scholar 

  • Bernhardt J, Buttner K, Scharf C, Hecker M (1999) Dual channel imaging of two-dimensional electropherograms in Bacillus subtilis. Electrophoresis 20:2225–2240. doi:10.1002/(SICI) 1522-2683(19990801) 20:11<2225::AID-ELPS2225>3.0.CO;2-8

    Article  PubMed  CAS  Google Scholar 

  • Bodrossy L, Stralis-Pavese N, Murrell JC, Radajewski S, Weilharter A, Sessitsch A (2003) Development and validation of a diagnostic microbial microarray for methanotrophs. Environ Microbiol 5:566–582. doi:10.1046/j.1462-2920.2003.00450.x

    Article  PubMed  CAS  Google Scholar 

  • Bolanos Vasquez MC, Warner D (1997) Effects of Rhizobium tropici, R. etli, and R. leguminosarum bv phaseoli on nod gene-inducing flavonoids in root exudates of Phaseolus vulgaris. Mol Plant Microbe Interact 10:339–346. doi:10.1094/MPMI.1997.10.3.339

    Article  CAS  Google Scholar 

  • Boldt T, Sørensen J, Karlson U, Molin S, Ramos C (2004) Combined use of different Gfp reporters for monitoring single-cell activities of a genetically modified PCB degrader in the rhizosphere of alfalfa. FEMS Microbiol Ecol 48:139–148. doi:10.1016/j.femsec.2004.01.002

    Article  CAS  PubMed  Google Scholar 

  • Borneman J, Triplett EW (1997) Rapid and direct method for extraction of RNA from soil. Soil Biol Biochem 29:1621–1624. doi:10.1016/S0038-0717(97) 00084-9

    Article  CAS  Google Scholar 

  • Bottin A, Larche L, Villalba F, Gaulin E, Esquerre-Tugaye MT, Rickauer M (1999) Green fluorescent protein (GFP) as gene expression reporter and vital marker for studying development and microbe-plant interaction in the tobacco pathogen Phytophthora parasitica var. nicotianae. FEMS Microbiol Lett 176:51–56. doi:10.1111/j.1574-6968.1999.tb13641.x

    Article  PubMed  CAS  Google Scholar 

  • Brazil GM, Kenefick L, Callanan M, Haro A, De Lorenzo V, Dowling DN, O’Gara F (1995) Construction of a rhizosphere pseudomonad with potential to degrade polychlorinated biphenyls and detection of bph gene expression in the rhizosphere. Appl Environ Microbiol 61:1946–1952

    PubMed  CAS  Google Scholar 

  • Brown MM, Friez MJ, Lovell CR (2003) Expression of nifH genes by diazotrophic bacteria in the rhizosphere of short form Spartina alterniflora. FEMS Microbiol Ecol 43:411–417. doi:10.1111/j.1574-6941.2003.tb01081.x

    Article  CAS  PubMed  Google Scholar 

  • Burgmann H, Widmer F, Sigler WV, Zeyer J (2003) mRNA extraction and reverse transcription-PCR protocol for detection of nifH gene expression by Azotobacter vinelandii in soil. Appl Environ Microbiol 69:1928–1935. doi:10.1128/AEM.69.4.1928-1935.2003

    Article  PubMed  CAS  Google Scholar 

  • Cabala J, Teper L (2007) Metalliferous constituents of rhizosphere soils contaminated by Zn-Pb mining in Southern Poland. Water Air Soil Pollut 178:351–362. doi:10.1007/s11270-006-9203-1

    Article  CAS  Google Scholar 

  • Case RJ, Boucher Y, Dahllöf I, Holmstrom C, Doolittle WF, Kjelleberg S (2007) Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies. Appl Environ Microbiol 73:278–288. doi:10.1128/AEM.01177-06

    Article  PubMed  CAS  Google Scholar 

  • Chen XP, Zhu YG, Xia Y, Shen JP, He JZ (2008) Ammonia-oxidizing archaea: important players in paddy rhizosphere soil? Environ Microbiol 10:1978–1987. doi:10.1111/j.1462-2920.2008.01613.x

    Article  PubMed  CAS  Google Scholar 

  • Clarke JD, Zhu T (2006) Microarray analysis of the transcriptome as a stepping stone towards understanding biological systems: practical considerations and perspectives. Plant J 45:630–650. doi:10.1111/j.1365-313X.2006.02668.x

    Article  PubMed  CAS  Google Scholar 

  • Coelho MRR, Da Mota FF, Carneiro NP, Marriel IE, Paiva E, Rosado AS, Seldin L (2007) Diversity of Paenibacillus spp. in the rhizosphere of four sorghum (Sorghum bicolor) cultivars sown with two contrasting levels of nitrogen fertilizer assessed by rpoB-based PCR-DGGE and sequencing analysis. J Microbiol Biotechnol 17:753–760

    PubMed  CAS  Google Scholar 

  • Costa R, Gomes NCM, Krogerrecklenfort E, Opelt K, Berg G, Smalla K (2007) Pseudomonas community structure and antagonistic potential in the rhizosphere: insights gained by combining phylogenetic and functional gene-based analyses. Environ Microbiol 9:2260–2273. doi:10.1111/j.1462-2920.2007.01340.x

    Article  PubMed  CAS  Google Scholar 

  • Courtois S, Frostegard A, Goransson P, Depret G, Jeannin P, Simonet P (2001) Quantification of bacterial subgroups in soil: comparison of DNA extracted directly from soil or from cells previously released by density gradient centrifugation. Environ Microbiol 3:431–439. doi:10.1046/j.1462-2920.2001.00208.x

    Article  PubMed  CAS  Google Scholar 

  • Courtois S, Cappellano CM, Ball M, Francou FX, Normand P, Helynck G, Martinez A, Kolvek SJ, Hopke J, Osburne MS, August PR, Nalin R, Guerineau M, Jeannin P, Simonet P, Pernodet JL (2003) Recombinant environmental libraries provide access to microbial diversity for drug discovery from natural products. Appl Environ Microbiol 69:49–55. doi:10.1128/AEM.69.1.49-55.2003

    Article  PubMed  CAS  Google Scholar 

  • Dahllöf I, Baillie H, Kjelleberg S (2000) rpoB-based microbial community analysis avoids limitations inherent in 16S rRNA gene intraspecies heterogeneity. Appl Environ Microbiol 66:3376–3380. doi:10.1128/AEM.66.8.3376-3380.2000

    Article  PubMed  Google Scholar 

  • Daime H, Lücker S, Wagner M (2006) daime, a novel image analysis program for microbial ecology and biofilm research. Environ Microbiol 8:200–213. doi:10.1111/j.1462-2920.2005.00880.x

    Article  CAS  Google Scholar 

  • Dandurand LM, Schotzko DJ, Knudsen GR (1997) Spatial patterns of rhizoplane populations of Pseudomonas fluorescens. Appl Environ Microbiol 63:3211–3217

    PubMed  CAS  Google Scholar 

  • Dazzo FB, Schmid M, Hartmann A (2007) Immunofluorescence microscopy and fluorescence in situ hybridization combined with CMEIAS and other image analysis tools for soil- and plant-associated microbial autecology. In: Hurst C et al (eds) Manual of environmental microbiology. ASM Press, Washington DC, pp 712–733

    Google Scholar 

  • De Werra P, Baehler E, Huser A, Keel C, Maurhofer M (2008) Detection of palnt-modulated alterations in antifungal gene expression in Pseudomonas fluorescens CHA0 on roots by flow cytometry. Appl Environ Microbiol 74:1339–1349. doi:10.1128/AEM.02126-07

    Article  PubMed  CAS  Google Scholar 

  • DeAngelis KM, Ji P, Firestone MK, Lindow SE (2005) Two novel bacterial biosensors for detection of nitrate availability in the rhizosphere. Appl Environ Microbiol 71:8537–8547. doi:10.1128/AEM.71.12.8537-8547.2005

    Article  PubMed  CAS  Google Scholar 

  • DeAngelis KM, Lindow SE, Firestone MK (2008) Bacterial quorum sensing and nitrogen cycling in rhizosphere soil. FEMS Microbiol Ecol 66:197–207. doi:10.1111/j.1574-6941.2008.00550.x

    Article  PubMed  CAS  Google Scholar 

  • DeLeo PC, Baveye P, Ghiorse WC (1997) Use of confocal laser scanning microscopy on soil thin-sections for improved characterization of microbial growth in unconsolidated soils and aquifer materials. J Microbiol Methods 30:193–203. doi:10.1016/S0167-7012(97) 00065-1

    Article  Google Scholar 

  • Demaneche S, David MM, Navarro E, Simonet P, Vogel TM (2009) Evaluation of functional gene enrichment in a soil metagenomic clone library. J Microbiol Methods 76:105–107. doi:10.1016/j.mimet.2008.09.009

    Article  PubMed  CAS  Google Scholar 

  • Desantis TZ, Brodie EL, Moberg JP, Zubieta IX, Piceno YM, Andersen GL (2007) High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microb Ecol 53:371–383. doi:10.1007/s00248-006-9134-9

    Article  PubMed  CAS  Google Scholar 

  • Dorn JG, Frye RJ, Maier RM (2003) Effect of temperature, pH and initial cell number on luxCDABE and nah gene expression during naphthalene and salicylate catabolism in the reporter bacterium Pseudomonas putida RB1353. Appl Environ Microbiol 69:2209–2216. doi:10.1128/AEM.69.4.2209-2216.2003

    Article  PubMed  CAS  Google Scholar 

  • Drissner D, Blum H, Tscherko D, Kandeler E (2007) Nine years of enriched CO2 changes the function and structural diversity of soil microorganisms in a grassland. Eur J Soil Sci 58:260–269. doi:10.1111/j.1365-2389.2006.00838.x

    Article  Google Scholar 

  • Eickhorst T, Tippkötter R (2008) Detection of microorganisms in undisturbed soil by combining fluorescence in situ hybridization (FISH) and micropedological methods. Soil Biol Biochem 40:1284–1293. doi:10.1016/j.soilbio.2007.06.019

    Article  CAS  Google Scholar 

  • El Zahar Haichar F, Achouak W, Christen R, Heulin T, Marol C, Marais MF, Mougel C, Ranjard L, Balesdent J, Berge O (2007) Identification of cellulolytic bacteria in soil by stable isotope probing. Environ Microbiol 9:625–634. doi:10.1111/j.1462-2920.2006.01182.x

    Article  CAS  Google Scholar 

  • Elasri M, Delorme S, Lemanceau P, Stewart G, Laue B, Glickmann E, Oger PM, Dessaux Y (2001) Acyl-homoserine lactone production is more common among plant-associated Pseudomonas spp. than among soilborne Pseudomonas spp. Appl Environ Microbiol 67:1198–1209. doi:10.1128/AEM.67.3.1198-1209.2001

    Article  PubMed  CAS  Google Scholar 

  • Espinosa-Urgel M, Ramos JL (2001) Expression of a Pseudomonas putida involved in lysine metabolism is induced in the rhizosphere. Appl Environ Microbiol 67:5219–5224. doi:10.1128/AEM.67.11.5219-5224.2001

    Article  PubMed  CAS  Google Scholar 

  • Faegri A, Torsvik VL, Goksoyr J (1977) Bacterial and fungal activities in soil: Separation of bacteria and fungi by a rapid fractionated centrifugation technique. Soil Biol Biochem 9:105–112. doi:10.1016/0038-0717(77) 90045-1

    Article  Google Scholar 

  • Fakhouri W, Kang Z, Buchenauer H (2001) Ultrastructural studies on the mode of action of fluorescent pseudomonads alone and in combination with acibenzolar-S-methyl effective against Fusarium oxysporum f. sp lycopersici in tomato plants. Z Pflanzenk 108:513–529

    CAS  Google Scholar 

  • Fieseler L, Horn M, Wagner M, Hentschel U (2004) Discovery of the novel candidate phylum “Poribacteria” in marine sponges. Appl Environ Microbiol 70:3724–3732. doi:10.1128/AEM.70.6.3724-3732.2004

    Article  PubMed  CAS  Google Scholar 

  • Füchslin HP, Rüegg I, van der Meer JR, Egli T (2003) Effect of integration of a GFP reporter gene on fitness of Ralstonia eutropha during growth with 2, 4-dichlorophenoxyacetic acid. Environ Microbiol 5:878–887. doi:10.1046/j.1462-2920.2003.00479.x

    Article  PubMed  CAS  Google Scholar 

  • Fukui R, Poinar EI, Bauer PH, Schroth MN, Hendson M, Wang XL, Hancock JG (1994) Spatial colonization patterns and interaction of bacteria on inoculated sugar-beet seed. Phytopathol 84:1338–1345. doi:10.1094/Phyto-84-1338

    Article  Google Scholar 

  • Gage DJ, Bobo T, Long SR (1996) Use of green fluorescent protein to visualize the early events of symbiosis between Rhizobium meliloti and alfalfa (Medicago sativa). J Bacteriol 178:7159–7166

    PubMed  CAS  Google Scholar 

  • Ghiglione JL, Gourbiere F, Potier P, Phillippot L, Lensi R (2000) Role of respiratory nitrate reductase in ability of Pseudomonas fluorescens YT101 to colonize the rhizosphere of maize. Appl Environ Microbiol 66:4012–4016. doi:10.1128/AEM.66.9.4012-4016.2000

    Article  PubMed  CAS  Google Scholar 

  • Ginolhac A, Jarrin C, Gillet B, Robe P, Pujic P, Tuphile K, Bertrand H, Vogel TM, Perriere G, Simonet P, Nalin R (2004) Phylogenetic analysis of polyketide synthase I domains from soil metagenomic libraries allows selection of promising clones. Appl Environ Microbiol 70:5522–5527. doi:10.1128/AEM.70.9.5522-5527.2004

    Article  PubMed  CAS  Google Scholar 

  • Gorg A, Postel W, Domscheit A, Gunther S (1988) Two-dimensional electrophoresis with immobilized pH gradients of leaf proteins from barley (Hordeum vulgare): method, reproducibility and genetic aspects. Electrophoresis 9:681–692. doi:10.1002/elps.1150091103

    Article  PubMed  CAS  Google Scholar 

  • Gottesman S, McCullen CA, Guillier M, Vanderpool CK, Majdalani N, Benhammou J, Thompson KM, FitzGerald PC, Sowa NA, FitzGerald DJ (2006) Small RNA regulators and the bacterial response to stress. Cold Spring Harb Symp Quant Biol 71:1–11. doi:10.1101/sqb.2006.71.016

    Article  PubMed  CAS  Google Scholar 

  • Götz M, Gomes NCM, Dratwinski A, Costa R, Berg G, Peixoto R, Mendonca-Hagler L, Smalla K (2006) Survival of gfp-tagged antagonistic bacteria in the rhizosphere of tomato plants and their effects on the indigenous bacterial community. FEMS Microbiol Ecol 56:207–218. doi:10.1111/j.1574-6941.2006.00093.x

    Article  PubMed  CAS  Google Scholar 

  • Griffiths RI, Whiteley AS, O'Donnell A, Bailey MJ (2000) Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition. Appl Environ Microbiol 66:5488–5491. doi:10.1128/AEM.66.12.5488-5491.2000

    Article  PubMed  CAS  Google Scholar 

  • Han JI, Semrau JD (2004) Quantification of gene expression in methanotrophs by competitive reverse transcription-polymerase chain reaction. Environ Microbiol 6:388–399. doi:10.1111/j.1462-2920.2004.00572.x

    Article  PubMed  CAS  Google Scholar 

  • Hansen M, Kragelund L, Nybroe O, Sørensen J (1997) Early colonization of barley roots by Pseudomonas fluorescens studied by immunofluorescence technique and confocal laser scanning microscopy. FEMS Microbiol Ecol 23:353–360. doi:10.1111/j.1574-6941.1997.tb00416.x

    Article  CAS  Google Scholar 

  • Harris K, Crabb D, Young IM, Weaver H, Gilligan CA, Otten W, Ritz K (2002) In situ visualisation of fungi in soil thin sections: problems with crystallisation of the fluorochrome FB28 (Calcofluor M2R) and improved staining by SCRI Renaissance 2200. Mycol Res 106:293–297. doi:10.1017/S0953756202005749

    Article  CAS  Google Scholar 

  • Hay AG, Rice JF, Applegate BM, Bright NG, Sayler GS (2000) A bioluminescent whole-cell reporter for detection of 2, 4-dichloroophenoxyacetic acid and 2, 4-dichlorophenol in soil. Appl Environ Microbiol 66:4589–4594. doi:10.1128/AEM.66.10.4589-4594.2000

    Article  PubMed  CAS  Google Scholar 

  • He Z, Gentry TJ, Schadt CW, Wu L, Liebich J, Chong SC, Huang Z, Wu W, Gu B, Jardine P, Criddle C, Zhou J (2007) GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes. ISME J 1:67–77. doi:10.1038/ismej.2007.2

    Article  PubMed  CAS  Google Scholar 

  • Heid CA, Stevens J, Livak KJ, Williams PM (1996) Real time quantitative PCR. Genome Res 6:986–994. doi:10.1101/gr.6.10.986

    Article  PubMed  CAS  Google Scholar 

  • Heitzer A, Malachowsky K, Thonnard JE, Bienkowski PR, White D, Sayler GS (1994) Optical biosensor for environmental on-line monitoring of naphthalene and salicylate bioavailability with an immobilized bioluminescent catabolic reporter bacterium. Appl Environ Microbiol 60:1487–1494

    PubMed  CAS  Google Scholar 

  • Hoheisel JD (2006) Microarray technology: beyond transcript profiling and genotype analysis. Nat Rev Genet 7:200–210. doi:10.1038/nrg1809

    Article  PubMed  CAS  Google Scholar 

  • Højberg O, Schnider U, Winteler HV, Sørensen J, Haas D (1999) Oxygen-sensing reporter strain of Pseudomonas fluorescens for monitoring the distribution of low-oxygen habitats in soil. Appl Environ Microbiol 65:4085–4093

    PubMed  Google Scholar 

  • Holben WE, Jansson JK, Chelm BK, Tiedje JM (1988) DNA probe method for the detection of specific microorganisms in the soil bacterial community. Appl Environ Microbiol 54:703–711

    PubMed  CAS  Google Scholar 

  • Hugenholtz P 2002 Exploring prokaryotic diversity in the genomic era. Genome Biol. 3:reviews0003.1-reviews0003.8.

  • Hurt RA, Qiu XY, Wu LY, Roh Y, Palumbo AV, Tiedje JM, Zhou JH (2001) Simultaneous recovery of RNA and DNA from soils and sediments. Appl Environ Microbiol 67:4495–4503. doi:10.1128/AEM.67.10.4495-4503.2001

    Article  PubMed  CAS  Google Scholar 

  • Huyghe A, Francois P, Charbonnier Y, Tangomo-Bento M, Bonetti EJ, Paster BJ, Bolivar I, Baratti-Mayer D, Pittet D, Schrenzel J (2008) Novel microarray design strategy to study complex bacterial communities. Appl Environ Microbiol 74:1876–1885. doi:10.1128/AEM.01722-07

    Article  PubMed  CAS  Google Scholar 

  • Jacobsen CS, Holben WE (2007) Quantification of mRNA in Salmonella sp. seeded soil and chicken manure using magnetic capture hybridization RT-PCR. J Microbiol Methods 69:315–321. doi:10.1016/j.mimet.2007.02.001

    Article  PubMed  CAS  Google Scholar 

  • Jaeger CH, Lindow SE, Miller W, Clark W, Firestone MK (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

    PubMed  CAS  Google Scholar 

  • Janssen PH, Yates PS, Grinton BE, Taylor PM, Sait M (2002) Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia. Appl Environ Microbiol 68:2391–2396. doi:10.1128/AEM.68.5.2391-2396.2002

    Article  PubMed  CAS  Google Scholar 

  • Jarrin C (2005) Approches metagenomiques pour l’analyse des diversites genetiques et chimiques de metabolites secondaires, etude des PKS de type I d’origine bacterienne. Thesis, University Claude Bernard, Lyon 1, France.

  • Jenkins BD, Steward GF, Short SM, Ward BB, Zehr JP (2004) Fingerprinting diazotroph communities in the Chesapeake Bay by using a DNA macroarray. Appl Environ Microbiol 70:1767–1776. doi:10.1128/AEM.70.3.1767-1776.2004

    Article  PubMed  CAS  Google Scholar 

  • Jensen LE, Nybroe O (1999) Nitrogen availability to Pseudomonas fluorescens DF57 is limited during decomposition of barley straw in bulk soil and in the barley rhizosphere. Appl Environ Microbiol 65:4320–4328

    PubMed  CAS  Google Scholar 

  • Kirchhof G, Schloter M, Assmus B, Hartmann A (1997) Molecular microbial ecology approaches applied to diazotrophs associated with non-legumes. Soil Biol Biochem 29:853–862. doi:10.1016/S0038-0717(96) 00233-7

    Article  CAS  Google Scholar 

  • Knauth S, Hurek T, Brar D, Reinhold-Hurek B (2005) Influence of different Oryza cultivars on expression of nifH gene pools in roots of rice. Environ Microbiol 7:1725–1733. doi:10.1111/j.1462-2920.2005.00841.x

    Article  PubMed  CAS  Google Scholar 

  • Koch B, Worm J, Jensen LE, Højberg O, Nybroe O (2001) Carbon limitation induces σS-dependent gene expression in Pseudomonas fluorescens in soil. Appl Environ Microbiol 67:3363–3370. doi:10.1128/AEM.67.8.3363-3370.2001

    Article  PubMed  CAS  Google Scholar 

  • Kragelund L, Hosbond C, Nybroe O (1997) Distribution of metabolic activity and phosphate starvation response of lux-tagged Pseudomonas fluorescens reporter bacteria in the barley rhizosphere. Appl Environ Microbiol 63:4920–4928

    PubMed  CAS  Google Scholar 

  • Kreuzer K, Adamczyk J, Iijima M, Wagner M, Scheu S, Bonkowski M (2006) grazing of a common species of soil protozoa (Acanthamoeba castellani) affects bacterial community composition and root architecture of rice (Oryza sativa L.). Soil Biol Biochem 38:1665-1672. doi:10.1016/j.soilbio.2005.11.027

    Google Scholar 

  • Krsek M, Wellington EM (1999) Comparison of different methods for the isolation and purification of total community DNA from soil. J Microbiol Methods 39:1–16. doi:10.1016/S0167-7012(99) 00093-7

    Article  PubMed  CAS  Google Scholar 

  • Kuiper I, Bloemberg GV, Noreen S, Thomas-Oates JE, Lugtenberg BJJ (2001) Increased uptake of putrescine in the rhizosphere inhibits competitive root colonization by Pseudomonas fluorescens strain WCS365. Mol Plant Microbe Interact 14:1096–1104. doi:10.1094/MPMI.2001.14.9.1096

    Article  PubMed  CAS  Google Scholar 

  • Kutter S, Hartmann A, Schmid M (2005) Colonization of barley (Hordeum vulgare) with Salmonella enterica and Listeria spp. FEMS Microbiol Ecol 56:262–271. doi:10.1111/j.1574-6941.2005.00053.x

    Google Scholar 

  • Lagopodi AL, Ram AFJ, Lamers GEM, Punt PJ, Van den Hondel CAMJ, Lugtenberg BJJ, Bloemberg GV (2002) Novel aspects of tomato root colonization and infection by Fusarium oxysporum f. sp radicis-lycopersici revealed by confocal laser scanning microscopic analysis using the green fluorescent protein as a marker. Mol Plant Microbe Interact 15:172–179. doi:10.1094/MPMI.2002.15.2.172

    Article  PubMed  CAS  Google Scholar 

  • Lamprecht MR, Sabatini DM, Carpenter AE (2007) CellProfiler: free, versatile software for automated biological image analysis. Biotechniques 42:71–75. doi:10.2144/000112257

    Article  PubMed  CAS  Google Scholar 

  • Layton AC, Muccini M, Ghosh MM, Sayler GS (1998) Construction of a bioluminescent reporter strain to detect polychlorinated biphenyls. Appl Environ Microbiol 64:5023–5026

    PubMed  CAS  Google Scholar 

  • Lee SW, Cooksey DA (2000) Genes expressed in Pseudomonas putida during colonization of a plant-pathogenic fungus. Appl Environ Microbiol 66:2764–2772. doi:10.1128/AEM.66.7.2764-2772.2000

    Article  PubMed  CAS  Google Scholar 

  • Leveau JHJ, Lindow SE (2002) Bioreporters in microbial ecology. Curr Opin Microbiol 5:259–265. doi:10.1016/S1369-5274(02) 00321-1

    Article  PubMed  Google Scholar 

  • Liu WT, Marsh TL, Cheng H, Forney LJ (1997) Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol 63:4516–4522

    PubMed  CAS  Google Scholar 

  • Liu XM, Germaine KJ, Ryan D, Dowling DN (2007) Development of a Gfp-based biosensor for detecting the bioavailability and biodegradation of polychlorinated biphenyls (PCBs). J. Environ. Eng. Landsc Manage 15:261–268

    Google Scholar 

  • Loy A, Bodrossy L (2006) Highly parallel microbial diagnostics using oligonucleotide microarrays. Clin Chim Acta 363:106–119. doi:10.1016/j.cccn.2005.05.041

    Article  PubMed  CAS  Google Scholar 

  • Loy A, Kusel K, Lehner A, Drake HL, Wagner M (2004) Microarray and functional gene analyses of sulfate-reducing prokaryotes in low-sulfate, acidic fens reveal cooccurrence of recognized genera and novel lineages. Appl Environ Microbiol 70:6998–7009. doi:10.1128/AEM.70.12.6998-7009.2004

    Article  PubMed  CAS  Google Scholar 

  • Lüeders T, Manefield M, Friedrich MW (2004) Enhanced sensitivity of DNA- and rRNA-based stable isotope probing by fractionation and quantitative analysis of isopycnic centrifugation gradients. Environ Microbiol 6:73–78. doi:10.1046/j.1462-2920.2003.00536.x

    Article  PubMed  CAS  Google Scholar 

  • Mahmood S, Paton GI, Prosser JI (2005) Cultivation-independent in situ molecular analysis of bacteria involved in degradation of pentachlorophenol in soil. Environ Microbiol 7:1349–1360. doi:10.1111/j.1462-2920.2005.00822.x

    Article  PubMed  CAS  Google Scholar 

  • Manefield M, Whiteley AS, Griffiths RI, Bailey MJ (2002) RNA stable isotope probing, a novel means of linking microbial community function to phylogeny. Appl Environ Microbiol 68:5367–5373

    Article  PubMed  CAS  Google Scholar 

  • Marco ML, Legac J, Lindow SE (2003) Conditional survival as a selection strategy to identify plant-inducible genes of Pseudomonas syringae. Appl Environ Microbiol 69:5793–5801. doi:10.1128/AEM.69.10.5793-5801.2003

    Article  PubMed  CAS  Google Scholar 

  • Marschner P, Crowley DE (1996) Physiological activity of a bioluminescent Pseudomonas fluorescens (strain 2-79) in the rhizosphere of mycorrhizal and non-mycorrhizal pepper (Capsicum annuum L.). Soil Biol Biochem 28:869–876. doi:10.1016/0038-0717(96)00072-7

    Article  CAS  Google Scholar 

  • Mauchline TH, Kerry BR, Hirsch PR (2002) Quantification in soil and the rhizosphere of the nematophagous fungus Verticillium chlamydospotium by competitive PCR and comparison with selective plating. Appl Environ Microbiol 68:1846–1853. doi:10.1128/AEM.68.4.1846-1853.2002

    Article  PubMed  CAS  Google Scholar 

  • Mavrodi OV, Mavrodi DV, Thomashow LS, Weller DM (2007) Quantification of 2, 4-diacetylphloroglucinol-producing Pseudomonas fluorescens strains in the plant rhizosphere by real-time PCR. Appl Environ Microbiol 73:5531–5538. doi:10.1128/AEM.00925-07

    Article  PubMed  CAS  Google Scholar 

  • Meckenstock R, Steinle P, van der Meer JR, Snozzi M (1998) Quantification of bacterial mRNA involved in degradation of 1,2,4-trichlorobenzene by Pseudomonas sp. strain P51 from liquid culture and from river sediment by reverse transcriptase PCR (RT/PCR). FEMS Microbiol Lett 167:123–129. doi:10.1111/j.1574-6968.1998.tb13217.x

    Article  PubMed  CAS  Google Scholar 

  • Meikle A, Amin-Hanjani S, Glover LA, Killham K, Prosser JI (1995) Matric potential and the survival and activity of a Pseudomonas fluorescens inoculum in soil. Soil Biol Biochem 27:881–892. doi:10.1016/0038-0717(95) 00020-F

    Article  CAS  Google Scholar 

  • Miethling R, Ahrends K, Tebbe CC (2003) Structural differences in the rhizosphere communities of legumes are not equally reflected in community-level physiological profiles. Soil Biol Biochem 35:1405–1410. doi:10.1016/S0038-0717(03) 00221-9

    Article  CAS  Google Scholar 

  • Militon C, Rimour S, Missaoui M, Biderre C, Barra V, Hill D, Mone A, Gagne G, Meier H, Peyretaillade E, Peyret P (2007) PhylArray: phylogenetic probe design algorithm for microarray. Bioinformatics 23:2550–2557. doi:10.1093/bioinformatics/btm392

    Article  PubMed  CAS  Google Scholar 

  • Mirete S, de Figueras CG, Gonzalez-Pastor JE (2007) Novel nickel resistance genes from the rhizosphere metagenome of plants adapted to acid mine drainage. Appl Environ Microbiol 73:6001–6011. doi:10.1128/AEM.00048-07

    Article  PubMed  CAS  Google Scholar 

  • Mollet C, Drancourt M, Raoult D (1997) rpoB sequence analysis as a novel basis for bacterial identification. Mol Microbiol 26:1005–1011. doi:10.1046/j.1365-2958.1997.6382009.x

    Article  PubMed  CAS  Google Scholar 

  • Muyzer G, De Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electroforesis analysis of polymerase chain reaction-amplified genes Coding for 16S rRNA. Appl Environ Microbiol 59:695–700

    PubMed  CAS  Google Scholar 

  • Narasimhan K, Basheer C, Bajic VB, Swarup S (2003) Enhancement of plant-microbe interactions using a rhizosphere metabolomics-driven approach and its application in the removal of polychlorinated biphenyls. Plant Physiol 132:146–153. doi:10.1104/pp. 102.016295

    Article  PubMed  CAS  Google Scholar 

  • Neidhardt FC, van Bogelen RA (2000) Proteomic analysis of bacterial stress responses. In: Storz G, Hennecke H (eds) bacterial stress responses. ASM Press, Washington DC, pp 445–452

    Google Scholar 

  • Neidhardt FC, van Bogelen RA, Lau ET (1983) Molecular cloning and expression of a gene that controls the high-temperature regulon of Escherichia coli. J Bacteriol 153:597–603

    PubMed  CAS  Google Scholar 

  • Neilson JW, Pierce SA, Maier RM (1999) Factors influencing expression of luxCDABE and nah genes in Pseudomonas putida RB1353 (NAH7, pUTK9) in dynamic systems. Appl Environ Microbiol 65:3473–3482

    PubMed  CAS  Google Scholar 

  • Nicolaisen MH, Bælum J, Jacobsen CS, Sørensen J (2008) Transcription dynamics of the functional tfdA gene during MCPA herbicide degradation by Cupriavidus necator AEO106 (pRO101) in agricultural soil. Environ Microbiol 10:571–579. doi:10.1111/j.1462-2920.2007.01476.x

    Article  PubMed  CAS  Google Scholar 

  • Nocker A, Burr M, Camper AK (2007) Genotypic microbial community profiling: A critical technical review. Microb Ecol 54:276–289. doi:10.1007/s00248-006-9199-5

    Article  PubMed  CAS  Google Scholar 

  • Normander B, Hendriksen NB, Nybroe O (1999) Green fluorescent protein-marked Pseudomonas fluorescens: Localization, viability, and activity in the natural barley rhizosphere. Appl Environ Microbiol 65:4646–4651

    PubMed  CAS  Google Scholar 

  • O'Farrell PH (1975) High resolution two-dimensional electrophoresis of proteins. J Biol Chem 250:4007–4021

    PubMed  Google Scholar 

  • Ogram A, Sayler GS, Barkay T (1987) The extraction and purification of microbial DNA from sediments. J Microbiol Methods 7:57–66. doi:10.1016/0167-7012(87) 90025-X

    Article  CAS  Google Scholar 

  • Ohlmeier S, Scharf C, Hecker M (2000) Alkaline proteins of Bacillus subtilis: first steps towards a two-dimensional alkaline master gel. Electrophoresis 21:3701–3709. doi:10.1002/1522-2683(200011) 21:17<3701::AID-ELPS3701>3.0.CO;2-5

    Article  PubMed  CAS  Google Scholar 

  • Ostle N, Whiteley AS, Bailey MJ, Sleep D, Ineson P, Manefield M (2003) Active microbial RNA turnover in a grassland soil estimated using a (CO2)-C-13 spike. Soil Biol Biochem 35:877–885. doi:10.1016/S0038-0717(03) 00117-2

    Article  CAS  Google Scholar 

  • Park SH, Lee DH, Oh KH, Lee K, Kim CK (2002) Detection of aromatic pollutants by bacterial biosensors bearing gene fusions constructed with the dnaK promoter of Pseudomonas sp DJ-12. J Microbiol Biotechnol 12:417–422

    CAS  Google Scholar 

  • Paterson E, Sim A, Standing D, Dorward M, McDonald AJS (2006) Root exudation from Hordeum vulgare in response to localized nitrate supply. J Exp Bot 57:2413–2420. doi:10.1093/jxb/erj214

    Article  PubMed  CAS  Google Scholar 

  • Pliego C, de Weert S, Lamers G, de Vicente A, Bloemberg G, Cazoria FM, Ramos C (2008) Two similar enhanced root-colonizing Pseudomonas strains fifer largely in the colonization strategies of avocado roots and Roselinia necatrix hyphae. Environ Microbiol 10:3295–3304. doi:10.1111/j.1462-2920.2008.01721.x

    Article  PubMed  Google Scholar 

  • Poonguzhali S, Madhaiyan M, Yim W-J, Kim K-A, Sa T-M (2008) Colonization pattern of plant root surfaces visualized by use of green-fluorescent-marked strain of Methylobacterium suomiense and its persistence in rhizosphere. Appl Microbiol Biotechnol 78:1033–1043. doi:10.1007/s00253-008-1398-1

    Article  PubMed  CAS  Google Scholar 

  • Porteous F, Killham K, Meharg A (2000) Use of a lux-marked rhizobacterium as a biosensor to assess changes in rhizosphere C flow due to pollutant stress. Chemosphere 41:1549–1554. doi:10.1016/S0045-6535(00) 00072-2

    Article  PubMed  CAS  Google Scholar 

  • Postma J, Altemüller HJ (1990) Bacteria in thin soil sections stained with the fluorescent brightener Calcofluor White M2R. Soil Biol Biochem 22:89–96. doi:10.1016/0038-0717(90) 90065-8

    Article  CAS  Google Scholar 

  • Pratscher J, Stichternot C, Fichtl K, Schleifer K-H, Braker G (2009) Application of recognition of individual genes-fluorescence in situ hybridization (RING-FISH) to detect nitrite reductase genes (nirK) of denitrifiers in pure cultures and environmental samples. Appl Environ Microbiol 75:802–810. doi:10.1128/AEM.01992-08

    Article  PubMed  CAS  Google Scholar 

  • Prieto P, Mercado-Blanco J (2008) Endophytic colonization of olive roots by the biocontrol strain Pseudomonas fluorescens PICF7. FEMS Microbiol Ecol 64:297–306. doi:10.1111/j.1574-6941.2008.00450.x

    Article  PubMed  CAS  Google Scholar 

  • Puglisi E, Fragoulis G, Del Re AAM, Spaccini R, Piccolo A, Gigliotti G, Said-Pullicino D, Trevisan M (2008) Carbon deposition in soil rhizosphere following amendments with compost and its soluble fractions, as evaluated by combined soil-plant rhizobox and reporter gene systems. Chemosphere 73:1292–1299. doi:10.1016/j.chemosphere.2008.07.008

    Article  PubMed  CAS  Google Scholar 

  • Radajewski S, Ineson P, Parekh NR, Murrell JC (2000) Stable-isotope probing as a tool in microbial ecology. Nature 403:646–649. doi:10.1038/35001054

    Article  PubMed  CAS  Google Scholar 

  • Rainey PB (1999) Adaptation of Pseudomonas fluorescens to the plant rhizosphere. Environ Microbiol 1:243–257. doi:10.1046/j.1462-2920.1999.00040.x

    Article  PubMed  CAS  Google Scholar 

  • Ramos C, Mølbak L, Molin S (2000) Bacterial activity in the rhizosphere analysed at the single-cell level by monitoring ribosome contents and synthesis rates. Appl Environ Microbiol 66:801–809. doi:10.1128/AEM.66.2.801-809.2000

    Article  PubMed  CAS  Google Scholar 

  • Robe P, Nalin R, Capellano C, Vogel TA, Simonet P (2003) Extraction of DNA from soil. Eur J Soil Biol 39:183–190. doi:10.1016/S1164-5563(03) 00033-5

    Article  CAS  Google Scholar 

  • Rondon MR, August PR, Bettermann AD, Brady SF, Grossman TH, Liles MR, Loiacono KA, Lynch BA, MacNeil IA, Minor C, Tiong CL, Gilman M, Osburne MS, Clardy J, Handelsman J, Goodman RM (2000) Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol 66:2541–2547. doi:10.1128/AEM.66.6.2541-2547.2000

    Article  PubMed  CAS  Google Scholar 

  • Rosado AS, Seldin L, Wolters AC, van Elsas JD (1996) Quantitative 16S rDNA-targeted polymerase chain reaction and oligonucleotide hybridization for the detection of Paenibacillus azotofixans in soil and the wheat rhizosphere. FEMS Microbiol Ecol 19:153–164. doi:10.1111/j.1574-6941.1996.tb00208.x

    Article  CAS  Google Scholar 

  • Rosen R, Ron EZ (2002) Proteome analysis in the study of the bacterial heat-shock response. Mass Spectrom Rev 21:244–265. doi:10.1002/mas.10031

    Article  PubMed  CAS  Google Scholar 

  • Rosen R, Buttner K, Becher D, Nakahigashi K, Yura T, Hecker M, Ron EZ (2002) Heat shock proteome of Agrobacterium tumefaciens: evidence for new control systems. J Bacteriol 184:1772–1778. doi:10.1128/JB.184.6.1772-1778.2002

    Article  PubMed  CAS  Google Scholar 

  • Rosen R, Matthysse AG, Becher D, Biran D, Yura T, Hecker M, Ron EZ (2003) Proteome analysis of plant-induced proteins of Agrobacterium tumefaciens. FEMS Microbiol Ecol 44:355–360. doi:10.1016/S0168-6496(03) 00077-1

    Article  CAS  PubMed  Google Scholar 

  • Rosen R, Sacher A, Shechter N, Becher D, Buttner K, Biran D, Hecker M, Ron EZ (2004) Two-dimensional reference map of Agrobacterium tumefaciens proteins. Proteomics 4:1061–1073. doi:10.1002/pmic.200300640

    Article  PubMed  CAS  Google Scholar 

  • Rovira AD (1956) A study on the developemnt of the root surface microflora during the initial stages of plant growth. J Appl Microbiol 19:72–79. doi:10.1111/j.1365-2672.1956.tb00048.x

    Article  Google Scholar 

  • Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S, Wu D, Eisen JA, Hoffman JM, Remington K, Beeson K, Tran B, Smith H, Baden-Tillson H, Stewart C, Thorpe J, Freeman J, Andrews-Pfannkoch C, Venter JE, Li K, Kravitz S, Heidelberg JF, Utterback T, Rogers YH, Falcon LI, Souza V, Bonilla-Rosso G, Eguiarte LE, Karl DM, Sathyendranath S, Platt T, Bermingham E, Gallardo V, Tamayo-Castillo G, Ferrari MR, Strausberg RL, Nealson K, Friedman R, Frazier M, Venter JC (2007) The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific. PLoS Biol 5:398–431. doi:10.1371/journal.pbio.0050077

    Article  CAS  Google Scholar 

  • Sanguin H, Remenant B, Dechesne A, Thioulouse J, Vogel TM, Nesme X, Moenne-Loccoz Y, Grundmann GL (2006) Potential of a 16S rRNA-based taxonomic microarray for analyzing the rhizosphere effects of maize on Agrobacterium spp. and bacterial communities. Appl Environ Microbiol 72:4302–4312. doi:10.1128/AEM.02686-05

    Article  PubMed  CAS  Google Scholar 

  • Sanguin H, Kroneisen L, Gazengel K, Kyselkova M, Remenant B, Prigent-Combaret C, Grundmann GL, Sarniguet A, Moenne-Loccoz Y (2008) Development of a 16S rRNA microarray approach for the monitoring of rhizosphere Pseudomonas populations associated with the decline of take-all disease of wheat. Soil Biol Biochem 40:1028–1039. doi:10.1016/j.soilbio.2007.11.023

    Article  CAS  Google Scholar 

  • Santaella C, Schue M, Berge O, Heulin T, Achouak W (2008) The exopolyscaccharide of Rhizobium sp. YAS34 is not necessary for biofilm formation on Arabidopsis thaliana and Brassica napus roots but contributes to root colonization. Environ Microbiol 10:2150–2163. doi:10.1111/j.1462-2920.2008.01650.x

    Article  PubMed  CAS  Google Scholar 

  • Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467–470. doi:10.1126/science.270.5235.467

    Article  PubMed  CAS  Google Scholar 

  • Schloter M, Borlinghaus R, Bode W, Hartmann A (1993) Direct identification and localization of Azospirillum in the rhizosphere of wheat using fluorescence-labelled monoclonal antibodies and confocal laser scanning microscopy. J Microscopy-Oxford 171:173–177

    Google Scholar 

  • Schwartz E (2007) Characterization of growing microorganisms in soil by stable isotope probing with H 182 O. Appl Environ Microbiol 73:2541–2546. doi:10.1128/AEM.02021-06

    Article  PubMed  CAS  Google Scholar 

  • Schwieger F, Tebbe CC (1998) A new approach to utilize PCR-single-strand-conformation polymorphism for 16s rRNA gene-based microbial community analysis. Appl Environ Microbiol 64:4870–4876

    PubMed  CAS  Google Scholar 

  • Shalon D (1998) Gene expression micro-arrays: a new tool for genomic research. Pathol Biol 46:107–109

    PubMed  CAS  Google Scholar 

  • Sharma S, Aneja MK, Mayer J, Munch JC, Schloter M (2005) Diversity of transcripts of nitrite reductase genes (nirK and nirS) in rhizospheres of grain legumes. Appl Environ Microbiol 71:2001–2007. doi:10.1128/AEM.71.4.2001-2007.2005

    Article  PubMed  CAS  Google Scholar 

  • Singleton DR, Hunt M, Powell SN, Frontera-Suau R, Aitken MD (2007) Stable-isotope probing with multiple growth substrates to determine substrate specificity of uncultivated bacteria. J Microbiol Methods 69:180–187. doi:10.1016/j.mimet.2006.12.019

    Article  PubMed  CAS  Google Scholar 

  • Sliwinski MK, Goodman RM (2004) Comparison of crenarchaeal consortia inhabiting the rhizosphere of diverse terrestrial plants with those in bulk soil in native environments. Appl Environ Microbiol 70:1821–1826. doi:10.1128/AEM.70.3.1821-1826.2004

    Article  PubMed  CAS  Google Scholar 

  • Smalla K, Oros-Sichler M, Milling A, Heuer H, Baumgarte S, Becker R, Neuber G, Kropf S, Ulrich A, Tebbe CC (2007) Bacterial diversity of soils assessed by DGGE, T-RFLP and SSCP fingerprints of PCR-amplified 16S rRNA gene fragments: Do the different methods provide similar results? J Microbiol Methods 69:470–479. doi:10.1016/j.mimet.2007.02.014

    Article  PubMed  CAS  Google Scholar 

  • Smith LM, Tola E, de Boer P, O’Gara F (1999) Signalling by the fungus Pythium ultimum represses expression of two ribosomal RNA operons with key roles in the rhizosphere ecology of Pseudomonas fluorescens F113. Environ Microbiol 1:495–502. doi:10.1046/j.1462-2920.1999.00067.x

    Article  PubMed  CAS  Google Scholar 

  • Sørensen J (1997) The rhizosphere as a habitat for soil microorganisms. In: van Elsas JD, Trevors JT, Wellington EMH (eds) Modern Soil Microbiology. Marcel Dekker Inc., New York, pp 21–45

    Google Scholar 

  • Sørensen J, Nybroe O (2007) Reporter genes in bacterial inoculants can monitor life conditions and functions in soil. In: Nannipieri P, Smalla K (eds) Nucleic Acids and Proteins in Soil. Springer Verlag, Berlin Heidelberg, pp 375–395

    Google Scholar 

  • Sørensen J, Sessitsch A (2007) Plant-associated bacteria—Lifestyles and molecular interactions. In: van Elsas JD, Jansson JK, Trevors JT (eds) Modern Soil Microbiology. CRC Press, Boca Raton London New York, pp 211–236

    Google Scholar 

  • Sørensen J, Jensen LE, 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. doi:10.1023/A:1010338103982

    Article  Google Scholar 

  • Standing D, Meharg AA, Killham K (2003) A tripartite microbial reporter gene system for real-time assays of soil nutrient status. FEMS Microbiol Lett 220:35–39. doi:10.1016/S0378-1097(03) 00057-0

    Article  PubMed  CAS  Google Scholar 

  • Steidle A, Sigl K, Schuhegger R, Ihring A, Schmid M, Gantner S, Stoffels M, Riedel K, Givskov M, Hartmann A, Langebartels C, Eberl L (2001) Visualization of N-acylhomoserine lactone-mediated cell-cell communication between bacteria colonizing the tomato rhizosphere. Appl Environ Microbiol 67:5761–5770. doi:10.1128/AEM.67.12.5761-5770.2001

    Article  PubMed  CAS  Google Scholar 

  • Stralis-Pavese N, Sessitsch A, Weilharter A, Reichenauer T, Riesing J, Csontos J, Murrell JC, Bodrossy L (2004) Optimization of diagnostic microarray for application in analysing landfill methanotroph communities under different plant covers. Environ Microbiol 6:347–363. doi:10.1111/j.1462-2920.2004.00582.x

    Article  PubMed  CAS  Google Scholar 

  • Tam LT, Antelmann H, Eymann C, Albrecht D, Bernhardt J, Hecker M (2006) Proteome signatures for stress and starvation in Bacillus subtilis as revealed by a 2-D gel image color coding approach. Proteomics 6:4565–4585

    Article  CAS  Google Scholar 

  • Tang T, François N, Glatigny A, Agier N, Mucchielli MH, Aggerbeck L, Delacroix H (2007) Expression ratio evaluation in two-colour microarray experiments is significantly improved by correcting image misalignment. Bioinformatics 23:2686–2691. doi:10.1093/bioinformatics/btm399

    Article  PubMed  CAS  Google Scholar 

  • Thrane C, Olsson S, Nielsen TH, Sørensen J (1999) Vital fluorescent stains for detection of stress in Pythium ultimum and Rhizoctonia solani challenged with viscosinamide from Pseudomonas fluorescens DR54. FEMS Microbiol Ecol 30:11–23. doi:10.1111/j.1574-6941.1999.tb00631.x

    Article  CAS  Google Scholar 

  • Thrane C, Nielsen TH, Nielsen MN, Sørensen J, Olsson S (2000) Viscosinamide-producing Pseudomonas fluorescens DR54 exerts a biocontrol effect on Pythium ultimum in sugar beet rhizosphere. FEMS Microbiol Ecol 33:139–146. doi:10.1111/j.1574-6941.2000.tb00736.x

    Article  PubMed  CAS  Google Scholar 

  • Timms-Wilson TM, Ellis RJ, Bailey MJ (2000) Immuno-capture differential display method (IDDM) for the detection of environmentally induced promoters in rhizobacteria. J Microbiol Methods 41:77–84. doi:10.1016/S0167-7012(00) 00139-1

    Article  PubMed  CAS  Google Scholar 

  • Timmusk S, Grantcharov N, Wagner EGH (2005) Paenibacillus polymyxa invades plant roots and forms biofilms. Appl Environ Microbiol 71:7292–7300. doi:10.1128/AEM.71.11.7292-7300.2005

    Article  PubMed  CAS  Google Scholar 

  • Tiquia SM, Wu L, Chong SC, Passovets S, Xu D, Xu Y, Zhou J (2004) Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples. Biotechniques 36:664–675

    PubMed  CAS  Google Scholar 

  • Tombolini R, van der Gaag DJ, Gerhardson B, Jansson JK (1999) Colonization pattern of the biocontrol strain Pseudomonas chlororaphis MA 342 on barley seeds visualized by using green fluorescent protein. Appl Environ Microbiol 65:3674–3680

    PubMed  CAS  Google Scholar 

  • Torsvik VL, Goksoyr J (1978) Determination of bacterial DNA in soil. Soil Biol Biochem 10:7–12. doi:10.1016/0038-0717(78) 90003-2

    Article  Google Scholar 

  • Torsvik V, Goksøyr J, Daae FL (1990) High Diversity in DNA of soil bacteria. Appl Environ Microbiol 56:782–787

    PubMed  CAS  Google Scholar 

  • Ulrich A, Becker R (2006) Soil parent material is a key determinant of the bacterial community structure in arable soils. FEMS Microbiol Ecol 56:430–443. doi:10.1111/j.1574-6941.2006.00085.x

    Article  PubMed  CAS  Google Scholar 

  • Unge A, Tombolini R, Mølbak L, Jansson JK (1999) Simultaneous monitoring of cell number and metabolic activity of specific bacterial populations with a dual gfp-luxAB marker system. Appl Environ Microbiol 65:813–821

    PubMed  CAS  Google Scholar 

  • van Dyk TK, Smulski DR, Reed TR, Belkin S, Vollmer AC, LaRossa R (1995) Responses to toxicants of an Escherichia coli strain carrying a uspA´:lux genetic fusion and an E. coli strain carrying a grpE´:lux fusion are similar. Appl Environ Microbiol 61:4124–4127

    PubMed  Google Scholar 

  • van Overbeek LS, van Elsas JA, van Veen JD (1997) Pseudomonas fluorescens Tn5-B20 mutant RA92 responds to carbon limitation in soil. FEMS Microbiol Ecol 24:57–71. doi:10.1016/S0168-6496(97) 00045-7

    Article  Google Scholar 

  • van West P, Reid B, Campbell TA, Sandrock RW, Fry WE, Kamoun S, Gow NAR (1999) Green fluorescent protein (GFP) as a reporter gene for the plant pathogenic oomycete Phytophthora palmivora. FEMS Microbiol Lett 178:71–80. doi:10.1016/S0378-1097(99) 00320-1

    Article  PubMed  Google Scholar 

  • Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO (2004) Environmental Genome Shotgun Sequencing of the Sargasso Sea. Science 304:66–74. doi:10.1126/science.1093857

    Article  PubMed  Google Scholar 

  • Voget S, Leggewie C, Uesbeck A, Raasch C, Jaeger KE, Streit WR (2003) Prospecting for novel biocatalysts in a soil metagenome. Appl Environ Microbiol 69:6235–6242. doi:10.1128/AEM.69.10.6235-6242.2003

    Article  PubMed  CAS  Google Scholar 

  • Volker U, Hecker M (2005) From genomics via proteomics to cellular physiology of the Gram-positive model organism Bacillus subtilis. Cell Microbiol 7:1077–1085. doi:10.1111/j.1462-5822.2005.00555.x

    Article  PubMed  CAS  Google Scholar 

  • von der Weid I, Artursson V, Seldin L, Jansson J (2005) Antifungal and root colonization patterns of GFP-tagged Paenibacillus brasiliensis PB177. World J Microbiol Biotechnol 12:1591–1597. doi:10.1007/s11274-005-8123-3

    Article  Google Scholar 

  • Wagner M, Horn M, Daims H (2003) Fluorescence in situ hybridisation for the identification and characterisation of prokaryotes. Curr Opin Microbiol 6:302–309. doi:10.1016/S1369-5274(03) 00054-7

    Article  PubMed  CAS  Google Scholar 

  • Wagner M, Smidt H, Loy A, Zhou J (2007) Unravelling microbial communities with DNA-microarrays: challenges and future directions. Microb Ecol 53:498–506. doi:10.1007/s00248-006-9197-7

    Article  PubMed  CAS  Google Scholar 

  • Ward BB, Eveillard D, Kirshtein JD, Nelson JD, Voytek MA, Jackson GA (2007) Ammonia-oxidizing bacterial community composition in estuarine and oceanic environments assessed using a functional gene microarray. Environ Microbiol 9:2522–2538. doi:10.1111/j.1462-2920.2007.01371.x

    Article  PubMed  CAS  Google Scholar 

  • Watanabe T, Kimura M, Asakawa S (2007) Dynamics of methanogenic archaeal communities based on rRNA analysis and their relation to methanogenic activity in Japanese paddy field soils. Soil Biol Biochem 39:2877–2887. doi:10.1016/j.soilbio.2007.05.030

    Article  CAS  Google Scholar 

  • Watt M, Hugenholtz P, White R, Vinall K (2006) Numbers and locations of native bacteria on field-grown wheat roots quantified by fluorescence in situ hybridization (FISH). Environ Microbiol 8:871–884. doi:10.1111/j.1462-2920.2005.00973.x

    Article  PubMed  Google Scholar 

  • Weinbauer MG, Beckmann C, Höfle MG (1998) Utility of green fluorescent nucleic acid dyes and aluminum oxide membrane filters for rapid epifluorescence enumeration of soil and sediment bacteria. Appl Environ Microbiol 64:5000–5003

    PubMed  CAS  Google Scholar 

  • Wilhelm J, Pingoud A (2003) Real-time polymerase chain reaction. ChemBioChem 4:1120–1128. doi:10.1002/cbic.200300662

    Article  PubMed  CAS  Google Scholar 

  • Wilmes P, Andersson AF, Lefsrud MG, Wexler M, Shah M, Zhang B, Hettich RL, Bond PL, VerBerkmoes NC, Banfield JF (2008a) Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal. ISME J 2:853–864. doi:10.1038/ismej.2008.38

    Article  PubMed  CAS  Google Scholar 

  • Wilmes P, Remis JP, Hwang M, Auer M, Thelen MP, Banfield JF (2008b) Natural acidophilic biofilm communities reflect distinct organismal and functional organization. ISME J (in press).

  • Wintzingerode F, Gobel UB, Stackebrandt E (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21:213–229. doi:10.1111/j.1574-6976.1997.tb00351.x

    Article  Google Scholar 

  • Woese CR, Kandler O, Wheelis ML (1990) Towards a natural system of organisms—Proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 87:4576–4579. doi:10.1073/pnas.87.12.4576

    Article  PubMed  CAS  Google Scholar 

  • Wolff S, Antelmann H, Albrecht D, Becher D, Bernhardt J, Bron S, Buttner K, van Dijl JM, Eymann C, Otto A, le Tam T, Hecker M (2007) Towards the entire proteome of the model bacterium Bacillus subtilis by gel-based and gel-free approaches. J. Chromatogr. B 849:129–140

    Article  CAS  Google Scholar 

  • Wu CH, Hwang Y-C, Lee W, Mulchandani TK, Yates MV, Chen W (2008a) Detection of recombinant Pseudomonas putida in the wheat rhizosphere by fluorescence in situ hybridization targeting mRNA and rRNA. Appl Microbiol Biotechnol 79:511–518. doi:10.1007/s00253-008-1438-x

    Article  CAS  Google Scholar 

  • Wu L, Kellogg L, Devol AH, Tiedje JM, Zhou J (2008b) Microarray-based characterization of microbial community functional structure and heterogeneity in marine sediments from the Gulf of Mexico. Appl Environ Microbiol 74:4516–4529. doi:10.1128/AEM.02751-07

    Article  CAS  Google Scholar 

  • Yeomans C, Porteous F, Paterson E, Meharg AA, Killham K (1999) Assessment of lux-marked Pseudomonas fluorescens for reporting on organic carbon compounds. FEMS Microbiol Lett 176:79–83. doi:10.1111/j.1574-6968.1999.tb13645.x

    Article  CAS  Google Scholar 

  • Yolcubal I, Piatt JJ, Pierce SA, Brusseau ML, Maier RM (2000) Fiber optic detection of in situ lux reporter gene activity in porous media: system design and performance. Anal Chim Acta 422:121–130. doi:10.1016/S0003-2670(00) 01072-2

    Article  CAS  Google Scholar 

  • Zhou T, Paulitz TC (1993) In-Vitro and In-Vivo effects of Pseudomonas spp. on Pythium-Aphanidermatum—Zoospore behavior in exudates and on the rhizoplane of bacteria-treated cucumber roots. Phytopathol 83:872–876. doi:10.1094/Phyto-83-872

    Article  Google Scholar 

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Acknowledgement

Figures 1 and 2 and certain text fractions related to the specific treatise of reporter bacteria in this review were adopted from Sørensen and Nybroe (2007) with permission from the publisher (Springer Verlag, Berlin Heidelberg). This work was supported in part by the Center for Environmental and Agricultural Microbiology (CREAM) granted to Jan Sørensen.

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Authors and Affiliations

  1. Section of Genetics and Microbiology, Department of Agriculture and Ecology, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark

    Jan Sørensen & Mette Haubjerg Nicolaisen

  2. Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, 69978, Israel

    Eliora Ron

  3. Environmental Microbial Genomics Group, Microsystems and Microbiology, Laboratoire Ampère, UMR CNRS 5005, Ecole Centrale de Lyon, 36 avenue Guy de Collongue, 69134, Ecully cedex, France

    Pascal Simonet

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  1. Jan Sørensen
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  2. Mette Haubjerg Nicolaisen
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  3. Eliora Ron
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Correspondence to Jan Sørensen.

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Responsible editor: Yves Dessaux.

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Sørensen, J., Haubjerg Nicolaisen, M., Ron, E. et al. Molecular tools in rhizosphere microbiology—from single-cell to whole-community analysis. Plant Soil 321, 483–512 (2009). https://doi.org/10.1007/s11104-009-9946-8

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