Abstract
The phyllosphere represents the largest surface area of any terrestrial habitat and is colonized by a diverse and specialized community of microorganisms which include epiphytes, saprophytes and phytopathogens (Andrews and Hirano 1991). This specialization has been reflected in studies which distinguish leaf isolates from soil or rhizosphere bacteria of the same genus (Thompson et al. 1993a). The phyllosphere is highly variable both within and between plant species where the diversity of microflora can be enhanced by non-resident colonisers dispersed by wind and rain and via animal faeces. To survive this harsh environment, leaf colonisers have to respond rapidly to extremes of temperature, humidity, ultraviolet irradiation and nutrient concentrations which fluctuate over short periods of time (O’Brian and Lindow 1988). The ability of bacteria to exhibit a broad range of phenotypes (phenotypic plasticity) by the habitat dependent expression of a subset of genes has been proposed as an important survival mechanism for bacteria in highly variable environments such as the leaf (Lindow 1993). Despite studies which describe microbial diversity and population succession in maturing plants, the microbiology of the leaf remains poorly understood. Of the common residents, pseudomonads have been best studied. Detailed investigations by extraction and plate count enumeration demonstrate that pseudomonads and other epiphytes exhibit diurnal fluctuations in population densities and a log-normal distribution in this habitat (Hirano and Upper 1989).
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References
Amann RI, Zarda B, Stahl DA and Schleifer H-H (1992) Identification of individual prokaryotie cells by using enzyme labelled, rRNA targeted oligonucleotide probes. Appl Environ Microbiol 58: 3007–3011
Andrews JH, Hirano SS (1991) Microbial ecology of leaves. Springer, Berlin, Heidelberg, New York
Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K (1989) Current protocols in molecular biology. Wiley, New York
Bailey MJ, Thompson IP (1992) Detection systems for phylloplane pseudomonads. In: Wellington EM, van Elsas JD (eds) Genetic interactions between microorganisms in the natural environment. Pergamon, Oxford, pp 126–141
Barry GF (1988) A broad host range shuttle system for gene insertion into the chromosome of gram negative bacteria. Gene 71: 75–84
Bender CL, Cooksey DA (1986) Indigenous plasmids in Pseudomonas syringae pv. tomato: conjugative transfer and role in copper resistance. JBacteriol 165: 534–541
Brayton PR, Colwell RR (1987) Fluorescent antibody staining method for the enumeration of viable environmental Vibrio cholerae 01. J Microbiol Methods 6: 309–314
Carlton BC, Gawron-Burke C, Johnson TB (1990) Exploiting the genetic diversity of Bacillus thuringiensis for the creation of new biocides. In: Proceedings of the fifth International colloquium on invertebrate pathology and microbial control. Society for Invertebrate Pathology, Adelaide, pp 18–22
Coplin DL, Frederick RD, McCammon SL (1985) Characterization of a conjugative plasmid from Erwinia stewartii. J Gen Microbiol 131: 2985–2991
De Bruijn FJ (1992) Use of repetitive (repetitive extragenic palindromic and enterobacterial repetitive intergeneric consensus) sequences and the polymerase chain reaction to fingerprint the genomes of Rhizobium meliloti isolates and other soil bacteria. Appl Environ Microbiol 58: 2180–2187
de Leij FAAM, Bailey MJ, Whipps JM, Lynch JM (1993) A simple most probable number technique for the sensitive recovery of a genetically modified Pseudomonas aureofaciens from soil. Lett Appl Microbiol 16: 307–310
deLong EG, Wickham GS, Pace NR (1989) Phylogenese stains: ribosomal RNA based probes for the identification of single cells. Science 243: 1260–1263
Donegan K. Matyac C, Seidler R, Porteous A (1991) Evaluation of methods for sampling, recovery and enumeration of bacteria applied to the phylloplane. Appl Environ Microbiol 57: 51–56
Drahos DL (1992) Methods for detection, identification and enumeration of microbes. In: Andrews JH, Hirano SS, (eds) Microbial ecology of leaves. Springer, Berlin, Heidelberg, New York pp 135–157
Drahos DJ, Hemming BC, McPherson S (1986) Tracking recombinant organisms in the environment: ß-galactosidase as a selectable, non-antibiotic marker for fluorescent pseudomonads. Bio/Technology 4: 439–443
Drahos DL, Barry GF, Hemming BC, Brandt EJ, Kline EL, Skipper HD, Kluepfel DA, Gooden DT, Hughes TA (1992) Spread and survival of genetically marked bacteria in soil. In: Fry JC, Day MJ (eds) Release of genetically engineered and other micro-organisms. Cambridge University Press, Cambridge pp 147–159
Entwistle PF, Coiy JS, Bailey MJ, Higgs S (eds) (1993) Bacillus thuringiensis, an environmental biopesticide: theory and practice, Wiley, Chichester
Fry JC (1990) Direct methods for biomass estimation. Methods Microbiol 22: 41–86
Fry JC, Day MJ (1990) Plasmid transfer in the epilithon. In: Fry JC, Day MJ (eds) Bacterial genetics in natural environments. Chapman and Hall, London pp 55–80
Grothues D, Tümmler B (1991) New approaches in genome analysis by pulsed-field gel electrophoresis: application to the analysis of Pseudomonas species. Mol Microbiol 5: 502–539
Hahn D, Amann RI, Ludwig W, Akkermans ADL, Schleifer K-H (1992) Detection of microorganisms in soil after in situ hybridisation with rRNA targeted, fluorescently labelled oligonucleotides. J Gen Microbiol 138: 879–887
Herrero M, de Lorenzo V, Timmis K (1990) Transposon vectors contaning non-antibiotic resistance selection markers for cloning and stable chromosomal insertion of foreign genes in gram-negative bacteria. J Bacterol 172: 6557–6567
Hirano SS, Upper CD, (1989) Diel variation in population size and ice nucleation activity of Pseudomonas syringae on snap bean leaves. Appl Environ Microbiol 55: 623–630
Holben WE, Tiedje JM (1988) Applications of nucleic acid hybridisation in microbial ecology. Ecology 69: 561–568
Jackman SC, Lee H, Trevors, JT (1992) Survival, detection and containment of bacteria. Microb Rel 1: 125–154
Kado CI, Liu S-T (1981) Rapid procedure for detection and isolation of large and small plasmids. J Bacteriol 145: 1365–1373
Knight IT, Holben WE, Tiedje, JM, Colwell RR (1992) Nucleic acid hybridisation techniques for the detection, identification and enumeration of microorganisms in the environment. In: Levin MA, Seidler RJ, Rogul M (eds) Microbial ecology. McGraw Hill, New York, pp 65–91
Knudsen GR (1991) Models for the survival of bacteria applied to the foliage of crop plants. In: Hurst CJ (ed) Modelling the environmental fate of microorganisms. American Society for Microbiology, Washington, pp 191–216
Knudsen GR, Spurr HW (1987) Field persistence and efficacy of five bacterial preparations for control of peanut leaf spot. Plant Dis 71: 442–445
Leach JE, Rhoads ML, Vera Cruz CM, White FF, Mew, TW, Leung H (1992) Assessment of genetic diversity and population structure of Xanthomonas oryzae pv. oryzae with a repetitive DNA element. Appl Environ Microbiol 58: 2188–2195
Levin MA, Strauss H (eds) (1991) Risk assessment in genetic engineering. McGraw Hill, New York
Lilley AK,Fry JC, Day MJ, Bailey MJ (1994) In situ transfer of an exogenously isolated plasmid between Pseudomonas spp. in sugar beet rhizosphere. Microbiology 140:27–33
Lindow SE (1986) Strategies and practice of biological control of ice nucleation active bacteria on plants. In:Fokkema NJ, van den Heuvel J (eds) Microbiology of the phyllosphere, Cambridge University Press, Cambridge, pp. 293–311
Lindow SE (1993) Novel method for identifying bacterial mutants with reduced epiphytic fitness. Appl Environ Microbiol 59: 1586–1592
Maniatis T, Fritsch EF, Sambrook J (1982) Molecular cloning a laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor
Nakai C, Kagamiyama H, Nozaki M, Nakazawa T Inouye S, Ebika Y, Nakazawa A (1983) Complete nucleotide sequence of the metapyrocatechase gene on the TOL plasmid of Pseudomonasputida mt-2. J Biol Chem 258: 2923–2928
O’Brian RD, Lindow SE (1988) Effect of plant species and environmental conditions on epiphytic population sizes of Pseudomonas syringae and other bacteria. Phytopathol 79: 619–627
Picard C, Ponsonnet C, Paget E, Nesmes X, Simonet, P (1992) Detection of bacteria in soil by direct DNA extraction and PCR. Appl Environ Microbiol 58: 2717–2722
Pickup RW (1991). Development of molecular methods for the detection of specific bacteria in the environment. J Gen Microbiol 137: 1009–1019
Powell BJ, Purdy KJ, Thompson IP, Bailey MJ (1993) Demonstration of tra+ plasmid activity in bacteria indigenous to the phyllosphere of sugar beet; gene transfer to a recombinant pseudomonad. FEMS Microbiol Ecol 12: 195–206
Rainey PB, Thompson IP, Palleroni, N (1994) Genome and fatty acid analysis of Pseudomonas stutzeri. Int J System Bact 62: 93–101
Romling V, Tümmler B (1991) The impact of two dimensional pulse field electrophioresis techniques for the consistent and complete mapping of bacterial genomes: refined physical map of Pseudomonas aeruginosa PAO. Nucleic Acids Res 19: 3199–3206
Roszak DB, Colwell RR (1987) Survival strategies of bacteria in the natural environment. Microbiol Rev 51: 365–379
Scanferlato VS, Orvos DR, Lacy GH, Cairns J (1990) Enumerating low densities of genetically engineered Erwinia carotovora in soil. Lett Appl Microbiol 10: 55–59
Schleifer KH, Amann R, Ludwig W, Rothemund R, Springer N, Dorn S (1992) Nucleic acid probes for the identification and in situ detection of Pseudomonads. In: Galli E, Silver S, Witholt B (eds) Pseudomonas molecular biology and biochemistry. American Society for Microbiology, Washington, pp 127–134
Selenska S, Klingmuller W (1992) Direct recovery and molecular analysis of DNA and RNA from soil. Microb Rel 1: 41–46
Shaw J J, Kado CI (1986) Development of a Vibrio bioluminescence gene-set to monitor phytopathogenic bacteria during the ongoing disease process in a non- disruptive manner. Bio/Technology 4: 560–564
Shaw JJ, Dane F, Geiger D, Kloepper JW (1992) Use of bioluminescence for detection of genetically engineered micro-organism released into the environment. Appl Environ Microbiol 58: 267–273
Thompson IP, Bailey MJ, Ellis RJ, Purdy KJ (1993a) Subgrouping bacterial populations by cellular fatty acid composition. FEMS Microbiol Ecol 102: 75–84
Thompson IP, Bailey MJ, Fenlon JS, Fermor TR? Lilley AK, Lynch JM, McCormack PJ, McQuilken M, Purdy KJ, Rainey PB, Whipps JM (1993b) Quantitative and qualitative seasonal changes in the microbial community from the phyllosphere of sugar beet (Beta vulgaris). Plant and Soil, 150: 177–191
Trevors JT (1992) DNA extraction from soil. Microb Rel 1: 3–9
Tsai Y, Park MJ, Olson BH (1991) Rapid method for direct extraction of mRNA from seeded soils Appl Environ Microbiol 57: 765–768
Versalovic J, Koeuth T, Lupski RI (1991) Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res 19: 6823–6831
Vieira J, Messing J (1982) The pUC plasmids, a M13mp7 derived system for insertion mutagenesis and sequencing with synthetic universal primers, Gene 19: 259–268
Waalwijk C, Dullemans A, Maat C (1991) Construction of a bioinsecticidal rhizosphere isolate of Pseudomonas fluorescens. FEMS Microbiol Lett 77: 257–264
Ward DB, Weller R, Bateson MM (1990) 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345: 63–65
Waterhouse RN, Glover LA (1993) Identification of procaryotic repetitive DNA suitable for use as fingerprinting probes. Appl Environ Microbiol 59: 1391–1397
Welsh J, McClelland M (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res 18: 7213–7218
Wheateroft R, Williams PA (1981) Rapid methods for the study of both stable and unstable plasmids in Pseudomonas. J Gen Microbiol 124: 433–437
Winstanley C, Morgan, JAW, Pickup RW, Saunders JR (1991) Use of a xylE marker gene to monitor survival of recombinant Pseudomonas putida populations in lake water by culture on nonselective media. Appl Environ Microbiol 57: 1905–1913
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Bailey, M.J. (1995). Extraction of DNA from the Phyllosphere. In: Trevors, J.T., van Elsas, J.D. (eds) Nucleic Acids in the Environment. Springer Lab Manuals. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-79050-8_6
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DOI: https://doi.org/10.1007/978-3-642-79050-8_6
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