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References
Akkermanns ADL, Elsas JDV, De Bruijn FJ (eds) (1998) Molecular microbial ecology manual. Kluwer Academic Publishers, Dordrecht, The Netherlands
Amann RI, Krumholz L, Stahl DA (1990) Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J Bacteriol 172:762–770
Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143–169
Amikam D, Glaser G, Razin S (1984) Mycoplasmas (Mollicutes) have a low number of rRNA genes. J Bacteriol 158:376–378
Avaniss-Aghajani E, Jones K, Chapman D, Brunk C (1994) A molecular technique for identification of bacteria using small subunit ribosomal RNA sequences. Biotechniques 17:144–149
Avise JC (1994) Molecular markers. Natural history and evolution. Chapman and Hall, New York
Azcon-Aguilar C, Bago B (1994) Physiological characteristics of the host plant promoting an undisturbed functioning of the mycorrhizal symbiosis. In: Gianiazzi S, Schuepp H (eds) Impact of arbuscular mycorrhizas on sustainable agriculture and natural ecosystems. ALS Birkhäuser, Basel, Switzerland, pp 47–60
Azcon-Aguilar C, Barea JM (1992) Interactions between mycorrhizal fungi and other rhizosphere microorganisms. In: Allen MJ (ed) Mycorrhizal functioning: an integrative plant-fungal process. Routledge, Chapmann and Hill, New York, pp 163–198
Baker GC, Smith JJ, Cowan DA (2003) Review and re-analysis of domain specific 16S primers. J Microbiol Meth 55:541–555
Barea JM (1997) Mycorrhiza/bacteria interactions on plant growth promotion. In: Ogoshi A, Kobayashi L, Homma Y, Kodama F, Kondon N, Akino S (eds) Plant growth-promoting rhizobacteria, present status and future prospects. OECD, Paris, pp 150–158
Barea JM (2000) Rhizosphere and mycorrhiza of field crops. In: Toutant JP, Balaz E, Galante E, Lynch JM, Schepers JS, Werner D, Werry PA (eds) Biological resource management: connecting science and policy. (OECD) INRA Editions and Springer, pp 110–125
Barea JM, Azcon R, Azcon-Aguilar C (2002) Mycorrhizosphere interactions to improve plant fitness and soil quality. Antonie van Leeuwenhoek 81:343–351
Barns SM, Fundyga RE, Jeffries MW, Pace NR (1994) Remarkable archaeal diversity detected in Yellowstone National Park hot spring environment. Proc Natl Acad Sci USA 91:1609–1613
Bjourson AJ, Stone CE, Cooper JE (1992) Combined subtraction hybridization and polymerase chain reaction amplification procedure for isolation of strain-specific Rhizobium DNA sequences. Appl Environ Microbiol 58:296–301
Bohlool BB, Schmidt EL (1980) The immuno fluorescence approach in microbial ecology. Adv Microb Ecol 4:203–241
Borneman J, Hartin RJ (2000) PCR primers that amplify fungal rRNA genes from environmental samples. Appl Environ Microbiol 66:4356–4360
Bourgault AM, Lamothe F (1988) Evaluation of the KOH test and the antibiotic disk test in routine clinical anaerobic bacteriology. J Clin Microbiol 26:2144–2146
Bowen GD, Rovira AD (1999) The rhizosphere and its management to improve plant growth. Adv Agron 66:1–102
Braker G, Ayala-del-Rio HL, Devol AH, Fesefeldt A, Tiedje JM (2001) Community structure of denitrifiers, bacteria, and archaea along redox gradients in Pacific Northwest marine sediments by terminal restriction fragment length polymorphism analysis of amplified nitrite reductase (nirS) and 16S rRNA genes. Appl Environ Microbiol 19:421–430
Brunk CF, Eis N (1998) Quantitative measure of small subunit rRNA gene sequences of the Kingdom Korarchaeota. Appl Environ Microbiol 64:5064–5066
Buehaille R, Couble ML, Magloire H, Bleicher F (2000) A subtractive PCR based cDNA library from human odontoblast cells: identification of novel genes expressed in tooth forming cells. Matrix Biol 19:421–430
Buissiere J, Nardon P (1968) Micromethode d'identification des batteries. I. Iniret de la quantification des characttres biochimiques. Ann Inst Pasteur, Paris 115:218
Busse H, Denner EBM, Lubitz WJ (1996) Classification and identification of bacteria: current approaches to an old problem. Overview of methods used in bacterial systematics. J Biotechnol 47:3–38
Cerny G (1976) Method for distinction of the Gram-negative from Gram-positive bacteria. Eur J Appl Microbiol 3:223–225
Cowan ST, Steel KJ (1964) Comparison of differentiating criteria for Staphylococci and Micrococci. J Bacteriol 88:804
Curtis TP, Sloan WT, Scannell JW (2002) Estimating prokaryotic diversity and its limits. Proc Natl Acad Sci USA 99:10494–10499
D'Amato RF, Bottone EJ, Amsterdam D (1991) Substrate profile systems for the identification of bacteria and yeasts by rapid and automated appoaches. In: Balows A, Hausler WJ Jr, Hermann KL, Isenberg HD Shadomy HJ (eds) Manual of clinical microbiology, 5th edn. American Society for Microbiology, Washington, DC, pp 128–136
Das Sarma S, Fleischmann EF (1995) Archea: a laboratory manual – halophiles. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, pp 269–272
DeLong EF, Wickham GS, Pace NR (1989) Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells. Science 243:1360–1363
De Ley J (1970) Reexamination of the association between melting point, buoyant density, and chemical base composition of deoxyribonucleic acid. J Bacteriol 101:738–754
De Ley J, Cattoir H, Reynaerts A (1970) The quantitative measurements of DNA hybridization from renaturation rates. Eur J Biochem 12:133–142
De Smedt J, De Ley J (1977) Intra- and intergeneric similarities of Agrobacterium ribosomal acid cistrons. Int J Syst Bacteriol 27:222–240
De Vos P, De Ley J (1983) Intra- and intergeneric similarities of Pseudomonas and Xanthomonas ribosomal ribonucleic acid cistrons. Int J Syst Bacteriol 33:487–509
Elwood HJ, Olsen GJ, Sogin ML (1985) The small subunit rRNA gene sequences from the hypotrichous ciliates Oxytricha nova and Stylonychia pustulata. Mol Biol Evol 2:399
Farelly V, Rainey FA, Stackebrandt E (1995) Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes mixture of bacterial species. Appl Environ Microbiol 61:2798–2801
Ferris MJ, Ward DM (1997) Seasonal distribution of dominant 16S rRNA-defined populations in a hot spring microbial mat examined by denaturing gradient gel electrophoresis. Appl Environ Microbiol 63:1375–1381
Gaby WL, Hadley L (1957) Practical laboratory test for the identification of Pseudomonas aeruginosa. J Bacteriol 74:356
Gagnon M, Hunting WM (1959) New method for the catalase determination. Anal Chem 31:144
Gillis PBM, De Leg J (1992) The genus Aquaspirillum. In: Balows A, Truper HG, Dworkin M, Harder W, Schleifer KH (eds.) The prokaryotes: a handbook on the biology of bacterial ecophysiology, isolation, identification, and applications. Springer, Berlin Heidelberg New York, pp 2569–2582
Giovannoni SJ, DeLong EF, Olsen GJ, Pace NR (1988) Phylogenetic group-specific oligodeoxynucleotide probes for identification of single microbial cells. J Bacteriol 170:720–726
Giovannoni SJ, Britschgi TB, Moyer CL, Field KG (1990a) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60–63
Giovannoni SJ, DeLong EF, Schmidt TM, Pace NR (1990b) Tangential flow filtration and preliminary phylogenetic analysis of marine picoplankton. Appl Environ Microbiol 56:2572–2575
Gonzalez JM, Ortiz-Martinez A, Gonzalez-delvalle MA, Laiz L, Saiz-Jimenez (2003) An efficient strategy for screening large cloned libraries of amplified 16S rDNA sequence from complex environmental communities. J Microbiol Meth 55:459–463
Gregersen T (1978) Rapid method for distinction of Gramnegative from Grampositive bacteria. Eur J Appl Microbiol Biotechnol 5:123–127
Gryndler M, Hrselova H, Striteska D (2000) Effect of soil bacteria on growth of hyphae of the arbuscular mycorrhizal (AM) fungus Glomus claroideum. Folia Microbiol 45:545–551
Halebian S, Harris B, Finegold M, Rolfe RD (1981) Rapid method that aids in distinguishing Gram-positive from Gram-negative anaerobic bacteria. J Clin Microbiol 13:444–448
Hansen MC, Tolker-Neilson T, Givskov M, Molin S (1998) Biased 16S rDNA PCR amplification caused by interference from DNA flanking template region. FEMS Microbiol Ecol 26:141–149
Heuer H, Krsek M, Baker P, Smalla K, Wellington EMH (1997) Analysis of actinmycetes communities by specific amplification of genes encoding 16S rDNA and gel electrophoretic separation in denaturing gradients. Appl Environ Microbiol 63:3233–3241
Heuer H, Hartung K, Wieland G, Kramer I, Smalla K (1999) Polynucleotide probes that target a hypervariable region of 16S rRNA genes to identify bacterial isolates corresponding to bands of community fingerprints. Appl Environ Microbiol 65:1045–1049
Hugenholtz P, Pitulle C, Hershberger KL, Pace NR (1998) Novel division level bacterial diversity in a Yellowstone hot spring. J Bacteriol 180:366–376
Hugh R, Leifson E (1953) The taxonomic significance of fermentative versus oxidative metabolism of carbohydrates by various Gram negative bacteria. J Bacteriol 66:24–26
Hughes JB, Hellmann JJ, Ricketts TH, Bohannan BJM (2001) Counting the uncountable: statistical approaches to estimating microbial diversity. Appl Environ Microbiol 67:4399–4406
Innis MA, Gelfand DH, Sninsky JJ, White TJ (1990) PCR protocols: a guide to methods and applications. Academic Press, New York
Jarvis ED, Widom RL, LaFauci G, Setoguchi Y, Richter IR, Rudner R (1988) Chromosomal organization of rRNA operons in Bacillus subtilis. Genetics 120:625–635
Kaneko T, Katoh K, Fujimoto M, Kumagai M, Tamaoka J, Kataydma-Fujimura Y (1986) Determnation of the nucleotide composition of a deoxyribonucleic acid by high-performance liquid chromatography of its enzymatic hydrolysate: a review. J Microbiol Meth 4:229–240
Karp A, Seberg O, Buiatti M (1996) Molecular techniques in the assessment of botanical diversity. Ann Bot 78:143–149
Katayama-Fujimura Y, Tsuzaki N, Kuraishi H (1982) Ubiquinone, fatty acid and DNA base composition determination as a guide to the taxonomy of the genus Thiobucillus. J Gen Microbiol 128:1599–1611
Kirschner P, Bottger EC (1992) Microheterogenisity within rRNA of Mycobacterium gordonae. J Clin Microbiol 30:1049
Kloepper JW (1994) Plant growth promoting rhizobacteria (other systems) In: Okon Y (ed) Azospirillum/plant associations. CRC Press, Boca Raton, pp 111–118
Kolganova TV, Kuznetsov BB, Tourova TP (2002) Designing and testing oligonucleotide primers for amplification and sequencing of Archael 16S rRNA genes. Mikrobiologiya 71:283–286
Kovacs N (1928) Eine vereinfachte Methode zum Nachweis der Indolbildung durch Bakterien. Z Immunitaetsforsch Exp Ther 55:311–315
Kovacs N (1956) Identification of Pseudomonas pyocyanae by the oxidase reaction. Nature 178:703
Krieg NR, Holt JG (1984) Bergey's manual of systematic bacteriology, vol. I. Williams and Wilkins, Baltimore
Larsen N, Olsen GJ, Maidak BL, McCaughey MJ, Overbeek R, Macke TJ, Marsh TL, Woese CR (1993) The ribosomal database project. Nucleic Acids Res 21:3021–3023
Lee N, Neilsen PH, Andreasen KH, Juretschko S, Schleifer JL, Wagner M (1999) Combination of fluorescent in situ hybridization and microautoradiography – a new tool for structure-function analysis in microbial ecology. Appl Environ Microbiol 65:1289–1297
Liesack W, Weyland H, Stackebrandt E (1991) Potential risks of gene amplification by PCR as determined by 16S rDNA analysis of a mixed culture of strict barophilic bacteria. Microbial Ecol 21:191–198
Linderman RG (1992) Vescicular-arbuscular mycorrhizae and soil microbial interactions. In: Bethlenfalvay GJ, Linderman RG (eds) Mycorrhizae in sustainable agriculture. ASA Spec Publ, Madison, Wisconsin, pp 45–70
Linderman RG (2000) Effects of mycorrhizas on plant tolerance to diseases. In: Kapulnick Y, Douds DD (eds) Arbuscular mycorrhizas: physiology and function. Kluwer Academic Press, pp 345–366
Liu W, Marsh TL, Cheng H, Fomey LJ (1997) Charecterization of microbial diversity by determining terminal restriction length polymorphism of genes encoding 16S rDNA. Appl Environ Microbiol 63:4516–4522
Lynch JM (1990) The rhizosphere. John Wiley, New York
Manafi M, Kneifel W (1990) Rapid methods for differentiating Gram-positive from Gram-negative aerobic and facultative anaerobic bacteria. J Appl Bacteriol 69:822–827
Mandel M, Schildkraut CL, Marmur J (1968) Use of CsCl density gradient analysis for determining the guanine plus cytosine content of DNA. Meth Enzymol 12:184–195
Margulis L, Schwartz KV (1998) Five kingdoms: an illustrated guide to the phyla of life on earth. Freeman, New York
Marmur J, Doty P (1962) Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J Mol Biol 5:109–118
Marsh TL (1999) Terminal restriction fragment length polymorphism (T-RFLP): an emerging method for characterizing diversity among homologous populations of amplified products. Curr Opin Neurobiol 2:323–327
Martinez-Murcia AJ, Acinas SG, Rodriguez-Valera F (1995) Evalution of prokaryotic diversity by restrictase digestion of 16S rDNA directly amplified from hypersaline environments. FEMS Microbiol Ecol 17:247–256
McPherson MJ, Hames BD, Taylor GR (1995) PCR II. Oxford University Press, Oxford, UK
McPherson PQ, Taylor GR (1992) PCR. A practical approach. The practical approach series. IRL Press at Oxford University Press, Oxford, UK
Mesbah M, Premachandran U, Whitman WB (1989) Precise measurement of the G + C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39:159–167
Mitchell JI, Roberts PJ, Moss ST (1995) Sequence or structure? A short review on the applications of nucleic acid sequence information to fungal taxonomy. Mycologist 9:67–75
Muyzer G (1999) Genetic fingerprinting of microbial communities-present status and future perspectives. In: Microbial biosystems: new frontiers. Proceedings of the 8th International Symposium on Microbial Ecology, Halifax, Canada
Muyzer G, Smalla K (1998) Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie van Leeuwenhoek 73:127–141
Muyzer G, De Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes encoding for 16 s rRNA. Appl Environ Microbiol 59:695–700
Muyzer G, Teske A, Wirsen CO, Jannasch HW (1995) Phylogenetic relationship of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresois of 16S rDNA fragment. Arch Microbiol 164:165–172
Nielsen AT, Liu WT, Filipe C, Grady L, Molin S, Stahl DA (1999) Identification of a novel group of bacteria in a sludge from a deteriorated biological phosphorus removal reactor. Appl Environ Microbiol 65:1251–1258
Ninet B, Monod M, Emler S, Pawlowski J, Metral C, Rohner P, Auckenthaler R, Hirschel B (1996) Two different 16S rRNA genes in a Mycobacteria strain. J Clin Microbiol 34:2531–2536
Nubel U, Garcia-Pichel F, Muyzer G (1997) PCR primers to amplify 16S rRNA genes from cyanobacteria. Appl Environ Microbiol 63:3327–3332
Olsen GJ, Lane DJ, Giovannoni SJ, Pace NR, Stahl DA (1986) Microbial ecology and evolution: a ribosomal RNA approach. Ann Rev Microbiol 40:337–365
Ouverney CC, Fuhrman JA (1999) Combined microautoradiography-16S rRNA probe technique for determination of radioisotope uptake by specific microbial cell types in situ. Appl Environ Microbiol 65:1746–1752
Pandey AK, Reddy MS, Suryanarayan TS (2003) ITS-RFLP and ITS sequence analysis of a foliar endophytic Phyllosticta from different tropical trees. Mycol Res 107:439–444
Prosser JI (2002) Molecular and functional diversity in soil microorganisms. Plant Soil 244:9–17
Reysenbach AL, Pace NR (1995) In: Robb FT, Place AR (eds) Archea a laboratory manual thermophiles. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp 101–107
Rodriguez-Valera F (2002) Approaches to prokaryotic biodiversity: a population genetics perspective. Environ Microbiol 4:628–633
Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
Schildkraut CL, Marmur J, Doty P (1962) Determination of the base composition of deoxyribonucleic acid from its buoyant density in CsCl. J Mol Biol 4:430–443
Singla S, Reddy MS, Marmeisse R, Gay G (2004) Genetic variability and taxonomic position of ectomycorrhizal fungus Pisolithus from India. Microbiol Res 159:203–210
Smit E, Leeflang P, Glandorf B, van Elsas JD, Wernars K (1999) Analysis of fungal diversity in the wheat rhizosphere by sequencing of cloned PCR-amplified genes encoding 18S rRNA and temperature gradient gel electrophoresis. Appl Environ Microbiol 65:2614–2621
Smith DE, Read DJ (1997) Mycorrhizal symbiosis. Academic Press, London
Sneath PHA, Sokal RR (1973) Numerical taxonomy: the principles and practice of numerical classification. W.H. Freeman, San Francisco
Stackebrandt E, Goebel BM (1994) Taxonomic note: a place for DNA-DNA reassociation and 16 s rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846–849
Stager CE, Davis JR (1992) Automated systems for identification of microorganisms. Clin Microbiol Rev 5:302–307
Staley JT, Konopka A (1985) Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Ann Rev Microbiol 39:321–346
Sturz AV, Nowak J (2000) Endophytic communities of rhizobacteria and the strategies required to create yield enhancing associations with crops. Appl Soil Ecol 15:183–190
Tamaoka J, Komagata K (1984) Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 25:125–128
Toal ME, Yeomans C, Killham K, Meharg AA (2000) A review of rhizosphere carbon flow modelling. Plant Soil 222:263–281
Torsvik V, Ovreas L (2002) Microbial diversity and function in soil: from genes to ecosystems. Curr Opin Microbiol 5:240–245
Torsvik V, Sorheim R, Gokoyr J (1996) Total bacterial diversity in soil and sediment communities – a review. J Ind Microbiol 17:170–178
Torsvik V, Ovreas L, Thingstad TF (2002) Prokaryotic diversity – magnitude, dynamics, and controlling factors. Science 296:1064–1066
Vainio EJ, Hantula J (2000) Direct analysis of wood-inhabiting fungi using denaturing gradient gel electrophoresis of amplified ribosomal DNA. Mycol Res 104:927–936
Vallaeys T, Topp E, Muyzer G, Macheret V, Laguerre G, Rigaud A, Soulas G (1997) Evaluation of denaturing gradient gel electrophotresis in the detection of 16S rRNA sequence variation in rhizobia and methanotrophs. FEMS Microbiol Ecol 24:279–285
Vandamme P, Pot B, Gillis M, De Vos P, Kersters K, Swings J (1996) Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60:407–438
Viaud M, Pasquier A, Brygoo Y (2000) Diversity of soil fungi studied by PCR-RFLP of ITS. Mycol Res 104:1027–1032
Wallner G, Amann R, Beisker W (1993) Optimizing fluorescent in situ hybridization of suspended cells with rRNA-targeted oligonucleotide probes for the flow cytometric identification of microorganisms. Cytometry 14:136–143
Watanabe K, Kodama Y, Harayama S (2001) Design and evaluation of PCR primers to amplify 16S rDNA fragments used for community fingerprinting. J Microbiol Methods 44:253–262
Wayne LG, Brenner DJ, Cowell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Tripper HG (1987) Report of the ad hoc Committee on Reconciliation of Approaches to Bacterial Systematics. Int J Syst Bacteriol 37:463–464
White TJ, Bruns TD, Lee S, Taylor J (1990) Analysis of phylogenetic relationships by amplification and direct sequencing of ribosomal RNA genes. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ (eds) PCR protocols: a guide to methods and applications. Academy Press, New York, pp 315–322
Willems A, Gillis M, De Ley J (1991) Transfer of Rhodocyclus gelatinosus to Rubriviwu gen. nav., comb. nov., and phylogenetic relationships with Leptothrix, Sphaerotilus natans. Pseudomonas saccharophila, and Alcaligenes latus. Int J Syst Bacteriol 41:65–73
Woese CR, Kandler O, Wheelis ML (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucaryota. Proc Nat Acad Sci USA 87:4576–4579
Zuckerkandl E, Pauling L (1965) Molecules as documents of evolutionary history. J Theor Biol 8:357–366
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Krishna, P., Reddy, M.S., Satyanarayana, T. (2006). Molecular Techniques for Understanding the Microbial Community Structure in Mycorrhizosphere. In: Mukerji, K.G., Manoharachary, C., Singh, J. (eds) Microbial Activity in the Rhizoshere. Soil Biology, vol 7. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-29420-1_10
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