Research in soil microbiology has concerned the determination of the presence of gene sequences so as to assess microbial diversity rather than the determination of gene expression. Generally these molecular techniques are based on the specific amplification of the target nucleic acid by polymerase chain reaction (PCR) with either restriction analysis or separation by denaturing or conformational properties of the resulting amplicons (Lynch et al. 2004). On the other hand microbial activities in soil have been measured by classical techniques such as those for determining soil respiration, enzyme activities, N mineralization, adenylate energy charge, leucine and thymidine incorporation, etc., with no idea of gene expression. The rhizosphere effects on microbial diversity and activity are discussed in Chap. 14 of this book.
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Keywords
- Microbial Community
- Bacterial Artificial Chromosome
- Horizontal Gene Transfer
- Rhizosphere Soil
- Pseudomonas Fluorescens
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
References
Adamczyk J, Hesselsoe M, Iversen N, Horn M, Lehner A, Nielsen PH, Scloter 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
Allaway D, Schofield NA, Leonard ME, Gilardoni L, Finan TM, Poole PS (2001) Use of differ-ential fluorescence induction and optical trapping to isolate environmentally induced genes. Environ Microbiol 3:397-406
Amin-Hanjani S, Meikle A, Glover LA, Prosser JI, Killham K (1993) Plasmid and chromosomally encoded luminescence marker systems for detection of Pseudomonas fluorescens in soil. Mol Ecol 2:47-54
Andersen JB, Heydorn A, Hentzer M, Eberl L, Geisenberger O, Christensen BB, Molin S, Givskov M (2001) gfp-Based N-acyl homoserine-lactone sensor systems for detection of bac-terial communication. Appl Environ Microbiol 67:575-585
Anukool U, Gaze WH, Wellington EMH (2004) In situ monitoring of streptothricin production by Streptomyces rochei F20 in soil and rhizosphere. Appl Environ Microbiol 70:5222-5228
Arevalo-Ferro C, Reil G, 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
Assmann EM, Ottoboni LM, Ferraz A, Rodriguez J, De Mello MP (2003) Iron-responsive genes of Phanerochaete chrysosporium isolated by differential display reverse transcription poly-merase chain reaction. Environ Microbiol 9:777-786
Avarre JC, Lajudie P, Bén G (2007) Hybridization of genomic DNA to microarrays: a challenge for the analysis of environmental samples. J Microbiol Method 69:242-248
Badalucco L, Kuikman P (2001) Mineralization and immobilization in the rhizosphere. In: Pinton R, Varanini Z, Nannipieri P (eds) The rhizosphere. Biochemistry and organic substances at the soil-plant interface. Marcel Dekker, New York, pp 159-196
Bahl MI, Hestbjerg Hansen L, Rask Licht T, Sorensen SJ (2004) In vivo detection and quantifica-tion of tetracycline by use of a whole-cell biosensor in the rat intestine. Antimicrob Agents Chemother 48:1112-1117
Bakken LR, Frostegård A (2006) Nucleic acid extraction from soil. In: Nannipieri P, Smalla K (eds) Nucleic acids and proteins in soil. Springer, Berlin Heidelberg New York, pp 49-73
Bechor O, Smulski DR, Van Dyk TK, LaRossa RA, Belkin S (2002) Recombinant microorgan-isms as environmental biosensors: pollutants detection by Escherichia coli bearing fabA:lux fusions. J Biotechnol 94:125-132
Béjà O, Suzuki MT, Koonin EV, Aravind L, Hadd A, Nguyen LP, Villacorta R, Amjadi M, Garrigues C, Jovanovich SB, Feldman RA, DeLong EF (2000) Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environ Microbiol 2:516-529
Bever JD (2003) Soil community feedback and the coexistence of competitors: conceptual frame-work and empirical tests. New Phytol 157:465-473
Bhagwat AA, Keister DL (1992) Identification and cloning of Bradyrhizobium japonicum genes expressed strain selectively in soil and rhizosphere. Appl Environ Microbiol 58:1490-1495
Blum SAE, Lorenz MG, Wackernagel W (1997) Mechanisms of retarded DNA degradation and prokaryotic origin of DNases in non-sterile soil. Syst Appl Microbiol 20:513-521
Bodrossy L, Stralis-Pavese N, Konrad-Köszler M, Weilharter A, Reichenauer TG, Schöfer D, Sessitsch A (2006) mRNA-based parallel detection of active methanotroph populations by use of a diagnostic microarray. Appl Environ Microbiol 72:1672-1676
Bogan BW, Schoenike B, Lamar RT, Cullen D (1996a) Manganese peroxidase mRNA and enzyme activity levels during bioremediation of polycyclic hydrocarbon-contaminated soil with Phanerochaete chrysosporium. Appl Environ Microbiol 62:2381-2386
Bogan BW, Schoenike B, Lamar RT, Cullen D (1996b) Expression of lip genes during growth in soil and oxidation of anthracene by Phanerochaete chrysosporium. Appl Environ Microbiol 62:3697-3703
Bolanos Vasquez MC, Warner D (1997) Effects of Rhizobium tropici, R. etli, and R. leguminosa-rum bv phaseoli on nod gene-inducing flavonoids in root exudates of Phaseolus vulgaris. Mol Plant-Microbe Interact 10:339-346
Bollag J-M, Chen C-M, Sarkar JM, Loll MJ (1987) Extraction and purification of a peroxidase from soil. Soil Biol Biochem 19:61-67
Borneman J (1999) Culture-independent identification of microorganisms that respond to speci-fied stimuli. Appl Environ Microbiol 65:3398-3400
Boschker HTS, Nold SC, Wellsbury P, Bos D, de Graaf W, Pel R, Parkes RJ, Cappenberg TE (1998) Direct linking of microbial populations to specific biogeochemical cycles by 13C-labe-ling of biomarkers. Nature 392:801-805
Briones AM, Okabe S, Umemiya Y, Ramsing NB, Reichardt W, Okuyama H (2003) Ammonia-oxidising bacteria on root biofilms and their possible contribution to N use efficiency of dif-ferent rice cultivars. Plant Soil 250:335-348
Burmǿlle M, Hestbjerg Hansen L, Sǿrensen JS (2006) Reporter gene technology in soil ecol-ogy; detection of bioavailability and microbial interactions. In: Nannipieri P, Smalla K (eds) Nucleic acids and proteins in soil. Springer, Berlin Heidelberg New York, pp 397-419
Ceccherini MT, Potè J, Kay E, Tran Van V, Marèchal J, Pietramellara G, Nannipieri P, Vogel TM, Simonet P (2003) Degradation and transformability of DNA from transgenic leaves. Appl Environ Microbiol 69:673-678
Cho JC, Tiedje JM (2002) Quantitative detection of microbial genes by using DNA microrrays. Appl Environ Microbiol 68:1425-1430
Cho Y, Qiu YL, Kuhlman P, Palmer JD (1998). Explosive invasion of plant mitochondria by a group I intron. Proc Nat Acad Sci 95:14244-14249
Cocking EC (2003) Endophytic colonisation of plant roots by nitrogen-fixing bacteria. Plant Soil 252:169-175
Cowan D, Meyer Q, Stafford W, Muyanga S, Cameron R, Wittwer P (2005) Metagenomic gene discovery: past, present and future. TRENDS Biotechnol 23:321-329
Crowley D (2001) Function of siderophores in the plant rhizosphere. In: Pinton R, Varanini Z, Nannipieri P (eds) The rhizosphere. Biochemistry and organic substances at the soil-plant interface. Marcel Dekker, New York, pp 223-261
Darwent MJ, Paterson E, McDonald AJS, Tomos AD (2003) Biosensor reporting of root exuda-tion from Hordeum vulgare in relation to shoot nitrate concentration. J Exp Bot 54: 325-334
DeAngelis KM, Ji P, Firestone MK, Lindow SE (2005) Two novel bacterial biosensors for detec-tion of nitrate availability in the rhizosphere. Appl Environ Microbiol 71:8537-8547
Dekkers LC, Muelders IH, Phoelich CC, Chin-A-Woeng TFC, Wijfjes AH, Lugtenberg BJJ (1998a) The sss colonization gene of the tomato-Fusarium oxysporumf. Sp. Radicis-lycopersici biocontrol strain Pseudomonas fluorescen WCS365 can improve root colonization of other wild-type Pseudomonas spp bacteria. Mol Plant Microbe Interact 13:1177-1183
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
DeLong EF (2002) Microbial population genomics and ecology. Curr Opin Microbiol 5:520-524
Desbrow C, Routledge EJ, Brighty GC, Sumpter JP, Waldock M (1998) Identification of estro-genic chemicals in STW effluent. 1. Chemical fractionation and in vitro biological screening. Environ Sci Technol 34:1548-1558
Espinosa-Urgel M (2004) Plant-associated Pseudomonas populations: molecular biology, DNA dynamcs, and gene transfer. Plasmid 52:139-150
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
Falchini L, Naumova N, Kuikman PJ, Bloem J, Nannipieri P (2003) CO2 evolution and denaturing gradient gel electrophoresis profiles of bacterial communities in soil following addition of low molecular weight substrates to simulate root exudation. Soil Biol Biochem 36:775-782
Fleming JT, Sanseverino J, Sayler GS (1993) Quantitative relationship between naphthalene cata-bolic gene frequency and expression in predicting PAH degradation in soil at town gas manu-facturing sites. Environ Sci Technol 27:1068-1074
Gebhard F, Smalla K (1999). Monitoring field releases of genetically modified sugar beets for persistence of transgenic plant DNA and horizontal gene transfer. FEMS Microbiol Ecol 28:261-272
Graves PR, Haystead TAJ (2002) Molecular biologist's guide to proteomics. Microbiol Mol Biol Rev 66:39-63
Gray ND, Head IM (2001) Linking genetic identity and function in communities of uncultured bacteria. Environ Microbiol 3:481-492
Gray ND, Howarth R, Pickup RW, Gwyn Jones J, Head IM (2000) Use of combined microautora-diography and fluorescence in situ hybridization to determine carbon metabolism in mixed natural communities of uncultured bacteria from the genus Achromatium. Appl Environ Microbiol 66:4518-4522
Griffiths RI (2003) Carbon flux and soil bacteria: the correlation with diversity and perturbation. PhD Thesis, The University of Newcastle
Hall-Stoodley L, Costerton JW, Stoodley P (2004) Bacterial biofilms: from the natural environ-ment to infectious diseases. Nat Rev 2:95-108
Handelsman J, Rondon MR, Brady SP, Clady J, Goodman RM (1998) Molecular biological access to the chemistry of unknown soil microbe: a new frontier for natural products. Chem Biol 5R:245-249
Hoshino T, Furukawa K, Tsuneda S, Inamori Y (2007) RNA microarray for estimating relative abundance of 16 S rRNA in microbial communities. J Microbiol Meth 69:406-410
Jaeger CH III, Lindow SE, Miller W, Clark E, 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
Jain, R, Rivera MC, Lake JA (1999) Horizontal gene transfer among genomes: the complexity hypothesis. Proc Nat Acad Sci USA 96:3801-3806
Janse BJH, Gaskell J, Aktar M, Cullen D (1998) Expression of Phanerochaete chrysosporium genes encoding lignin peroxidase, manganese peroxidase, and glyoxal oxidase in wood. Appl Environ Microbiol 64:3536-3538
Jeon CO, Park W, Padmanabhan P, DeRito C, Snape JR, Madsen EL (2003) Discovery of a bacte-rium, with distinctive dioxygenase, that is responsible for in situ biodegradation in contami-nated sediment. Proc Natl Acad Sci USA 100:13591-13596
Kowalchuk GA, Drigo B, Yergeau E, Van Veen JA (2006) Assessing bacterial and fungal commu-nity structure in soil using ribosomal RNA and other structural gene markers. In: Nannipieri P, Smalla K (eds) Nucleic acids and proteins in soil. Springer, Berlin Heidelberg New York, pp 159-188
Kragelund L, Christofersen B, Nybroe O, de Bruijn FJ (1995) Isolation of lux reporter gene fusions in Pseudomonas fluorescens DF57 inducible by nitrogen or phosphorus starvation. FEMS Microbiol Ecol 17:95-106
Kragelund L, Hosbond C, Nybroe O (1997) Distribution of metabolic activity and phosphate star-vation response of lux-tagged Pseudomonas fluorescens reporter bacteria in the barley rhizo-sphere. Appl Environ Microbiol 63:4920-4928
Krsek M, Gaze WH, Morris NZ, Wellington EMH (2006) Gene detection, expression and related enzyme activity in soil. In: Nannipieri P, Smalla K (eds) Nucleic acids and proetins in soil. Springer, Berlin Heidelberg New York, pp 217-255
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 fluo-rescens strain WCS365. Mol Plant Microbe Interact 14:1096-1104
Lambert B, Leyns F, Van Rooyen L, Gosele F, Papon Y, Swings J (1987) Rhizobacteria of maize and their antifungal activities. Appl Environ Microbiol 53 1866-1871
Lambert B, Meire P, Joos H, Lens P, Swings J (1990) Fast-growing, aerobic, heterotrophic bacteria from the rhizosphere of young sugar beet plants Appl Environ Microbiol 56:3375-3381
Lee N, Nielsen PH, Andreasen KH, Juretschko S, Nielsen JL, Schleifer KH, Wagner M (1999) Combination of fluorescent in situ hybridization and microautoradiography - a new tool for structure-function analyses in microbial ecology. Appl Environ Microbiol 65:1289-1297
Lee SW, Cooksey DA (2000) Genes expressed in Pseudomonas putida during colonization of a plant-pathogenic fungus. Appl Environ Microbiol 66:2764-2772
Liley AK, Bailey MJ (1997) Impact of pQBR103 acquisition and carriage on the phytosphere fit-ness of Pseudomonas fluorescens SBW25: burden and benefit. Appl Environ Microbiol 63:1584-1587
Loper JE, Henkels MD (1997) Availability of iron to Pseudomonas fluorescens in rhizosphere and bulk soil evaluated with an ice nucleation reporter gene. Appl Environ Microbiol 63:99-105
Loy A, Kusel K, Lehner A, Drake HL, Wgner M (2004) Microrray and functional gene analysis of sulfate reducing prokaryote in low sulfate acidic fens reveal coocurrence of recognizedgeneral and novel linages. Appl Environ Microbiol 70:6998-7009
Lueders T, Wagner B, Claus P, Friedrich MW (2004a) Stable isotope probing of rRNA and DNA reveals a dynamic methylotroph community and trophic interactions with fungi and protozoa in oxic rice field soil. Environ Microbiol 6:60-72
Lueders T, Pommerenke B, Friedrich MW (2004b) Stable isotope probing of microorganisms thriving at thermodynamic limits: syntrophic propionate oxidation in flooded soil. Appl Environ Microbiol 70:5778-5786
Lynch JM, Benedetti A, Insam H, Nuti PM, Smalla K, Torsvik V, Nannipieri P (2004) Microbial diversity in soil: ecological theories, the contribution of molecular techniques and the impact of transgenic plants and transgenic microorganisms. Biol Fertil Soils 40:363-385
Manefield M, Whiteley AS, Ostle N, Ineson P, Bailey MJ (2002a) Technical considerations for RNA-based stable isotope probing: an approach to associating microbial diversity with micro-bial community function. Rapid Commun Mass Spectrom 16:2179-2183
Manefield M, Whiteley AS, Griffiths RJ, Bailey MJ (2002b) RNA stable isotope probing, a novel means of linking microbial community function to phylogeny. Appl Environ Microbiol 68:5367-5373
Manefield M, Griffiths RI, Whiteley A, Bailey M (2006) Stable isotope probing: a critique of its role in linking phylogeny and function. In: Nannipieri P, Smalla K (eds) Nucleic acids and proteins in soil. Springer, Berlin Heidelberg New York, pp 205-255
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
Maron PA, Ranjard L, Mougel C, Lemanceau P (2007) Metaproteomics: a new approach for stud-ying functional microbial ecology. Microb Ecol 53:486-493
Marschner P, Crowley DE (1996) Physiological activity of a bioluminescent Pseudomonas fluo-rescens (strain 2-79) in the rhizosphere of mycorrhizal and non-mycorrhizal pepper (Capsicum annuum L.). Soil Biol Biochem 28:869-876
Marschner P, Crowley DE (1997) Iron stress and pyoverdin production by a fluorescent pseu-domonad in the rhizosphere of white lupine (Lupinus albus L.) and barley (Hordeum vulgare L. Appl Environ Microbiol 63:277
Marschner P, Crowley DE (1998) Phytosiderophores decrease iron stress and pyoverdine produc-tion of Pseudomonas fluorescens PF-5 (PVD-INAZ), Soil Biol Biochem 30:1275-1280
Mercier A, Kay E, Simonet P (2006) Horizontal gene transfer by natural transformation in soil environment. In: Nannipieri P, Smalla K (eds) Nucleic acids and proteins in soil. Springer, Berlin Heidelberg New York, pp 355-373
Metcalfe AC, Krsek M, Gooday GW, Prosser JI, Wellington EM (2002) Molecular analysis of a bacterial chitinolytic community in an upland pasture. Appl Environ Microbiol 68:5042-5050
Nannipieri P (2006) Role of stabilised enzymes in microbial ecology and enzyme extraction from soil with potential applications in soil proteomics. In: Nannipieri P, Smalla K (eds) Nucleic acids and proteins in soil. Springer, Berlin Heidelberg New York, pp 75-94
Nannipieri P, Ascher J, Ceccherini MT, Landi L, Pietramellara G, Renella G (2003) Microbial diversity and soil functions. Eur J Soil Sci 54:655-670
Nielsen KM, Bones AM, Smalla K, van Elsas JD (1998) Horizontal gene transfer from transgenic plants to terrestrial bacteria - a rare event? FEMS Microbiol Rev 22:79-103
Nielsen KM, Smalla K, van Elsas JD (2000) Natural transformation of Acinetobacter sp. Strain BD413 with cell lysates of Acinetobacter sp., Pseudomonas fluorescens, and Burkholderia cepacia in soil microcosms. Appl Environ Microbiol 66:206-212
Nielsen KM, van Weerelt DM, Berg TN, Bones AM, Hageler AN, van Elsas JD (1997) Natural transformation and availability of transforming chromosomal DNA to Acinetobacter calcoace-ticus in soil microcosms. Appl Environ Microbiol 63:1945-1952
Nierlich DP, Murakawa GJ (1996) The decay of bacterial messanger RNA. Prog Nucl Acids Res Mol Biol 52:153-216
O'Toole GA, Kaplan HB, Kolter R (2000) Biofilm formation as microbial development. Ann Rev Microbiol 54:49-79
Ogunseitan OA (2006) Soil proteomics: extraction and analysis of proteins from soil. In: Nannipieri P, Smalla K (eds) Nucleic acids and proteins in soil. Springer, Berlin Heidelberg New York, pp 95-115
Ostle N, Whiteley AS, Bailey MJ, Sleep D, Ineson P, Manefield M (2003) Active microbial RNA turnover in a grassland soil estimated using a 13CO2 spike. Soil Biol Biochem 35:877-885
Padmanabhan P, Padmanabhan S, DeRito C, Gray A, Gannon D, Snape JR, Tsai CS, Park W, Jeon C, Madsen EL (2003) Respiration of 13C-labeled substrates added to soil in the field and subsequent 16 S rRNA gene analysis of 13C-labeled soil DNA. Appl Environ Microbiol 69:1614-1622
Paget E, Jocteur-Monrozier L, Simonet P (1992) Adsorption of DNA on clay minerals: protection against DNase I and influence on gene transfer. FEMS Microbiol Lett 97:31-40
Peplies J, Glöckner FO, Amann R (2003) Optimization strategies for DNA microarray based detection of bacteria with 16 S rRNA-targeting oligonucleotide probes. Appl Environ Microbiol 69:1397-1407
Pietramellara G, Dal Canto L, Vettori C, Gallori E, Nannipieri P (1997) Effects of air-drying and wetting cycles on the transforming ability of DNA bound on clay minerals. Soil Biol Biochem 29:55-61
Ptitsyn LR, Horneck G, Komova O, Kozubek S, Krasavin EA, Bonev M, Rettberg P (1997) A biosensor for environmental genotoxin screening based on an SOS lux assay in recombinnt Escherichia coli cells. Appl Environ Microbiol 63:4377-4384
Radajewski S, Ineson P, Parekh NR, Murrell JC (2000) Stable-isotope probing as a tool in micro-bial ecology. Nature 403:646-649
Radajewski S, Webster G, Reay DS, Morris SA, Ineson P, Nedwell DB, Prosser JI, Murrell JC (2002) Identification of active methylotroph populations in an acidic forest soil by stable-isotope probing. Microbiology 148:2331-2342
Radajewski S, McDonald IR, Murrell JC (2003) Stable-isotope probing of nucleic acids: a win-dow to the function of uncultured microorganisms. Curr Opin Biotechnol 14:296-302
Rainey PB (1999) Adaptation of Pseudomonas fluorescens to the plant rhizosphere. Environ Microbiol 1:243-257
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
Rhee S-K, Liu X, Wu L, Song CC, Wan X, Zhou J (2004) Detection of genes involved in biodeg-radation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays. Appl Environ Microbiol 70:4303-4317
Roca C, Olson L (2001) Dynamic responses of Pseudomonas fluorescens DF57 to nitrogen or carbon source addition. J Biotechnol 86:39-50
Rondon MR, August PR, Bettermann AD, Brady SF, Grossman TH, Liles MR, Loiacono KA, Lynch BA, Mac Neil IA, Minor C, Tiong CI, 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
Saleh-Lakha S, Miller M, Campbell RG, Schneider K, Elahimanesh P, Hart MM, Trevors JT (2005) Microbial gene expression in soil: methods, applications and challenges. J Microbiol Methods 63:1-9
Sanseverino J, Werner C, Fleming J, Applegate B, King JM, Sayler GS (1993-1994) Molecular diagnostics of polycyclic aromatic hydrocarbons biodegradation in manufactured gas plant soils. Biodegradation 4:303-321
Sarkar N (1997) Polyadenylation of mRNA in prokaryotes. Annu Rev Biochem 66:173-197
Schadt CW, Zhou J (2006) Advances in microarray-based technologies for soil microbial commu-nity analyses. In: Nannipieri P, Smalla K (eds) Nucleic acids and proteins in soil. Springer, Berlin Heidelberg New York, pp 189-203
Schloss D, Handelsman J (2003) Biotechnological prospects from metagenomics. Curr Opin Biotechnol 14:303-310
Schulze WX, Gleixner G, Kaiser K, Guggenberger G, Mann M, Schulze E-D (2005) A proteomic fingerprinting of dissolved organic carbon and of soil particles. Oecologia 142:335-343
Schwaner NE, Kroer N (2001) Effect of plant species in the kinetics of conjugal transfer in the rhizosphere and relation to bacterial metabolic activity. Microb Ecol 42:458-465
Smith LM, Tola E, deBoer 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
Sǿrensen S, Nybroe O (2006) 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, Berlin Heidelberg New York, pp 375-395
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
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-medi-ated cell-cell communication between bacteria colonizing the tomato rhizosphere, Appl Environ Microbiol 67:5761-5770
Stevenson FJ (1986) Cycles of soil. Carbon, nitrogen, phosphorus, sulfur and micronutrients. Wiley, New York
Stewart GF, Bettany D, Bees J, Ward B, Zehr JP (2004) Development and testing of a DNA micro-array to assess nitrogenase (nifH) gene diversity. Appl Environ Microbiol 70:455-465
Stewart P, Cullen D (1999) Organization and differential regulation of a cluster of lignin peroxi-dase genes of Phanerochaete chrysosporium. J Bacteriol 181:3427-3432
Stralis-Pavese N, Sessitsch A, Weilharter A, Reichenauer T, Riesing J, Csontos J, Murrell JC, Bodrossy L (2004) Optimisation of diagnostic microarray for application in analysing landfill methanotroph communities under different plant covers. Environ Microbiol 6:347-363
Taroncher-Oldenburg G, Griner EM, Francis CA, Ward BB (2003) Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment. Appl Environ Microbiol 69:1159-1171
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
Treonis AM, Ostle NJ, Stott AW, Primrose R, Grayston SJ, Ineson P (2004) Identification of groups of metabolically-active rhizosphere microorganisms by stable isotope probing of PLFAs. Soil Biol Biochem 36:533-537
Utt EA, Brousal JP, Kikut-Oshima LC, Quinn FD (1995) The identification of bacterial gene expres-sion differences using mRNA-based subtractive hybridisation. Can J Microbiol 41:152-156
van Dyk TK, Smulski DR, Reed TR, Belkin S, Vollmer AC, LaRossa R (1995) Responses to toxi-cants of an Escherichia coli strain carrying a uspA:lux genetic fusion and an E. coli strain car-rying a grpE:lux fusion are similar. Appl Environ Microbiol 61:4124-4127
Van Elsas JD, Turner S, Bailey MJ (2003) Horizontal gene transfer in the phytosphere. New Phytol 157:525-537
Veal DA, Stokes HW, Daggard G (1992) Genetic exchange in natural microbial communities. Adv Microbiol Ecol 12:383-430
Vollmer AC, Belkin S, Smulski DR, Van Dyk TK, LaRossa RA (1997) Detection of DNA damage by use of Escherichia coli carrying recA:lux, uvrA:lux, or alkA:lux reporter plasmids. Appl Environ Microbiol 63:2566-2571
Wagner M (2004) Deciphering functions of uncultured microorganisms. ASM News 70:63-70
Wellington EMH, Berry A, Krsek M (2003) Resolving functional diversity in relation to microbial community structure in soil: exploiting genomics and stable isotope probing. Curr Opin Microbiol 6:295-301
Wilmes P, Bond PL (2006) Metaproteomics: studying functional gene expression in microbial ecosystems. Trends Microbiol 14:92-97
Wren BW (2000) Microbial genome analysis: insights into virulence, host adaptation and evolu-tion. Nat Genet 1:30-39
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
Yin B, Crowley D, Sparovek G, De Melo WJ, Borneman J (2000) Bacterial functional redundancy along a soil reclamation gradient. Appl Environ Microbiol 66:4361-4365
Zhang ZG, Pierson LS (2001) A second quorum sensing system regulates cell surface properties but not phenazine antibiotic production in Pseudomonas aureofaciens. Appl Environ Microbiol 67:4305-4315
Zhou J (2003) Microarrays for bacterial detection and microbial community analysis. Curr Opin Microbiol 6:1-7
Zhou J-Z, Thompson D (2002) Microarrays: applications in environmental microbiology. In: Bitton G (ed) Encyclopedia of environmental microbiology, vol 4. Wiley, New York, pp 1968-1979
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Nannipieri, P., Ascher, J., Ceccherini, M.T., Guerri, G., Renella, G., Pietramellara, G. (2008). Recent Advances in Functional Genomics and Proteomics of Plant Associated Microbes. 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_9
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