非培养方法和培养方法对水稻内生细菌和根结合细菌的研究
|
摘要
本文对非培养方法在水稻内生细菌和根结合细菌研究中的应用进行了探索。主要采用了构建16S rRNA基因克隆文库、DGGE两种非培养方法并结合传统的细菌分离培养方法，对水稻(Oryza sativa L.)内生细菌和根结合细菌群落多样性及群落动态变化进行了研究。
建立了直接从水稻根组织扩增内生细菌16S rDNA的方法。选择了扩增细菌16S rDNA的引物(799f-1492r)，该对引物可以通过PCR的方法直接从水稻根总DNA中扩增出内生细菌的16S rDNA片段，而不扩增水稻叶绿体DNA。水稻线粒体DNA可通过扩增产物中片段大小差异与细菌的16S rDNA分开。通过对水稻内生细菌16S rRNA基因克隆文库中阳性克隆的序列测定证实该对引物完全适用于非培养的分子生物学方法对水稻内生细菌的研究。该项研究结果尚未见报道。
对分蘖期水稻(Oryza sativa L. japonica 90-3)的内生细菌16S rRNA基因克隆文库中192个阳性克隆的16S rDNA片段进行ARDRA分型，根据ARDRA分型结果将该克隆文库分为52个OTUs；16S rDNA序列系统发育分析揭示水稻根内生细菌中包含α-、β-、γ-、δ-、ε-五个亚类的Proteobacteria，其中γ-Proteobacteria为克隆文库中最优势的细菌类群，占克隆总数的25％。除此之外水稻根内生细菌中还含有低GC的革兰氏阳性细菌及Cytophaga／Flexibacter／Bacteroides(CFB)类细菌。文库中28.64％的克隆与尚未培养的细菌具有较高的序列相似性。该文库中还有6个克隆属于古菌，这是首次通过非培养方法研究证实水稻内生菌群落中包含有古菌。这些结果均说明水稻内生菌具有丰富的种群多样性。
采用构建细菌16S rDNA克隆文库并结合分离培养方法，研究了水稻根结合细菌群落结构。ARDRA分型结果显示，克隆文库包含43个OTUs，分离培养物包含17个OTUs。两种研究方法的结果均说明γ-Proteobacteria为水稻根结合细菌群落中的优势类群。气单胞菌属为克隆文库中的最优势菌群；与16S rDNA克隆文库比较，分离培养物中的最优势菌群则为假单胞菌属。
采用PCR-DGGE技术研究了在水稻生长的不同年份及不同生长时期两个品种的水稻(Oryza sativa L. japonica 90-3，Oryza sativa L. japonica 90-12)根内生细菌和根结合细菌的群落多样性及其动态变化。DGGE图谱中主要条带的序列分析结果显示，水稻内生细菌和根结合细菌群落中均有α-、β-、γ-、δ-四个亚类的Proteobacteria及低GC的革兰氏
The rice endophytic bacteria and root-associated bacteria were explored with culture-independent approaches. The diversity and population dynamics of endophytic bacteria and root-associated bacteria of two rice cultivars (Oryza saliva L. japonica 90-3 and Oryza sativa L. japonica 90-12) grown in the same paddy field were studied by using both 16S rDNA cloning, sequencing and denaturing gradient gel electrophoresis (DGGE) as well as traditional cultivation technique.
The method of amplifying endophytic bacterial 16S rDNA from rice roots directly was established. A pair of bacterial 16S rDNA primers (799f-1492r) was selected to amplify bacterial sequences directly from rice root tissues by PCR for exclusion of chloroplast DNA. The mitochondrial sequence from rice was separated from the PCR-amplified bacterial 16S rDNA sequence by the different size of fractionations. Sequence analysis of clones in the 16S rDNA library of rice endophytic bacteria indicated that this pair of primers was available for the study of endophytic bacteria communities associated with rice plant. To our knowledge, this is the only one report of the primers used for culture-independent approaches on the analysis of endophytic bacterial communities associated with rice plants.
Among the 196 positive clones in the 16S rDNA library of endophytic bacteria, 52 OTUs were formed according to the similarity of the banding patterns obtained by amplified DNA restriction analysis (ARDRA). The sequence analysis revealed a broad phylogenetic spectrum of bacteria, including α 、 β、 γ、 δ and ε subgroup of the Proteobacteria, low G+C gram-positive bacteria, and some microbes belonging to the Cytophaga/Flexibacter/Bacteroides (CFB) phylum in the library. The most dominant group was y - Proteobacteria (25% of the total). 28.64% of the total clones showed the highest similarity to uncultured bacteria. To our knowledge, it is the first report that archaea was identified as endophytic bacteria associated with rice by the culture-independent approach. It is suggested that a abundant diversity of endophytic bacterial community occurred within rice roots.
The structure of bacterial community associated with rice roots was studied with both construction of 16S rDNA clone library and culture-dependent approache. ARDRA patterns showed 43 OTUs in the 16S rDNA clone library as well as 17 OTUs in the bacterial isolates. Y
建立了直接从水稻根组织扩增内生细菌16S rDNA的方法。选择了扩增细菌16S rDNA的引物(799f-1492r)，该对引物可以通过PCR的方法直接从水稻根总DNA中扩增出内生细菌的16S rDNA片段，而不扩增水稻叶绿体DNA。水稻线粒体DNA可通过扩增产物中片段大小差异与细菌的16S rDNA分开。通过对水稻内生细菌16S rRNA基因克隆文库中阳性克隆的序列测定证实该对引物完全适用于非培养的分子生物学方法对水稻内生细菌的研究。该项研究结果尚未见报道。
对分蘖期水稻(Oryza sativa L. japonica 90-3)的内生细菌16S rRNA基因克隆文库中192个阳性克隆的16S rDNA片段进行ARDRA分型，根据ARDRA分型结果将该克隆文库分为52个OTUs；16S rDNA序列系统发育分析揭示水稻根内生细菌中包含α-、β-、γ-、δ-、ε-五个亚类的Proteobacteria，其中γ-Proteobacteria为克隆文库中最优势的细菌类群，占克隆总数的25％。除此之外水稻根内生细菌中还含有低GC的革兰氏阳性细菌及Cytophaga／Flexibacter／Bacteroides(CFB)类细菌。文库中28.64％的克隆与尚未培养的细菌具有较高的序列相似性。该文库中还有6个克隆属于古菌，这是首次通过非培养方法研究证实水稻内生菌群落中包含有古菌。这些结果均说明水稻内生菌具有丰富的种群多样性。
采用构建细菌16S rDNA克隆文库并结合分离培养方法，研究了水稻根结合细菌群落结构。ARDRA分型结果显示，克隆文库包含43个OTUs，分离培养物包含17个OTUs。两种研究方法的结果均说明γ-Proteobacteria为水稻根结合细菌群落中的优势类群。气单胞菌属为克隆文库中的最优势菌群；与16S rDNA克隆文库比较，分离培养物中的最优势菌群则为假单胞菌属。
采用PCR-DGGE技术研究了在水稻生长的不同年份及不同生长时期两个品种的水稻(Oryza sativa L. japonica 90-3，Oryza sativa L. japonica 90-12)根内生细菌和根结合细菌的群落多样性及其动态变化。DGGE图谱中主要条带的序列分析结果显示，水稻内生细菌和根结合细菌群落中均有α-、β-、γ-、δ-四个亚类的Proteobacteria及低GC的革兰氏
The rice endophytic bacteria and root-associated bacteria were explored with culture-independent approaches. The diversity and population dynamics of endophytic bacteria and root-associated bacteria of two rice cultivars (Oryza saliva L. japonica 90-3 and Oryza sativa L. japonica 90-12) grown in the same paddy field were studied by using both 16S rDNA cloning, sequencing and denaturing gradient gel electrophoresis (DGGE) as well as traditional cultivation technique.
The method of amplifying endophytic bacterial 16S rDNA from rice roots directly was established. A pair of bacterial 16S rDNA primers (799f-1492r) was selected to amplify bacterial sequences directly from rice root tissues by PCR for exclusion of chloroplast DNA. The mitochondrial sequence from rice was separated from the PCR-amplified bacterial 16S rDNA sequence by the different size of fractionations. Sequence analysis of clones in the 16S rDNA library of rice endophytic bacteria indicated that this pair of primers was available for the study of endophytic bacteria communities associated with rice plant. To our knowledge, this is the only one report of the primers used for culture-independent approaches on the analysis of endophytic bacterial communities associated with rice plants.
Among the 196 positive clones in the 16S rDNA library of endophytic bacteria, 52 OTUs were formed according to the similarity of the banding patterns obtained by amplified DNA restriction analysis (ARDRA). The sequence analysis revealed a broad phylogenetic spectrum of bacteria, including α 、 β、 γ、 δ and ε subgroup of the Proteobacteria, low G+C gram-positive bacteria, and some microbes belonging to the Cytophaga/Flexibacter/Bacteroides (CFB) phylum in the library. The most dominant group was y - Proteobacteria (25% of the total). 28.64% of the total clones showed the highest similarity to uncultured bacteria. To our knowledge, it is the first report that archaea was identified as endophytic bacteria associated with rice by the culture-independent approach. It is suggested that a abundant diversity of endophytic bacterial community occurred within rice roots.
The structure of bacterial community associated with rice roots was studied with both construction of 16S rDNA clone library and culture-dependent approache. ARDRA patterns showed 43 OTUs in the 16S rDNA clone library as well as 17 OTUs in the bacterial isolates. Y
引文
1. Abraham W-R, Strompl C, Meyer H. et al. Phylogeny and polyphasic taxonomy of Caulobacter species. Proposal of Maricaulis gen. nov. with Maricaulis maris (Poindexter) comb. nov. as the type species, and emended description of the genera Brevundimonas and Caulobacter. Int J Syst Bacteriol, 1999, 49:1053-1073
2. Achenbach L A, Michaelidou U,Bruce R A, Fryman J, Coates j D. Dechloromonas agitata gen. nov., sp. nov. and Dechlorosoma suillum gen. nov., sp. nov., two novel environmentally dominant (per)chlorate-reducing bacteria and their phylogenetic position, Int J Syst Evol Microbiol, 2001, 51:527-33
3. Achouak W, Sutra L, Hulin T, Meyer J-M, Fromin N, Degraeve S, Christen R, Garden L. Peseudomonas brassicacearum sp. nov. and Pseudomonas thivervalensis sp. nov., two root-associated bacteria isolated from Brassica napus and Arabidopsis thaliana, Int J Syst Evol Microbiol, 2000, 50:9-18
4. Adams P D & Kloepper J W. Effect of host genotype on indigenous bacterial endophytes of cotton (Gossypium hirsutum L.). Plant and Soil 240:181-189,2002
5. Ait Barka E, Gognies S, Nowak J, Audran J-C and Beiarbi A. Inhibitory effect of endophyte bacteria on Botrytis cinerea and its influence to promote the grapevine growth. Biol. Control, 2002, 24:135-142
6. Akkermans A D L, EIsas J D V, Bruijn F J D E. Molecular Microbial Ecology Manual. Netherlands: Kluwer Academic Publishers, 1995, 2:1-8
7. Amann R I, Ludwig W, Schleifer K H. Phylogenetic identification and in situ detection of individual microbialcell without cultivation. Microbiol Rev, 1995, 59:143-169
8. Ampe F, Sirvent A, Zakhia N. Dynamics of the microbial community responsible for traditional sour cassava strch fementation studied by denaturing gradient gel electrophoresis and quantitative rRNA hybridization, Int J Food Microbiol, 2001, 65:45-54
9. Araujo W L, Macron J, Maccheroni W, et al. Diversity of endophytic bacterial populations and their interaction with Xylella fastidiosas in Citrus plants. Appl Environ Microbiol, 2002, 68:4906-4914
10. Arshad M and Ftankenberger W T. Mirobial production of plant hormones, in: The Rhizosphere and Plant Growth. 1991, pp.327-334
11. Avrahami S and Conrad R. Patterns of community change among ammonia oxidizers in meadow soils upon long-term incubation at different temperatures. Appl Environ Microbiol, 2003,69:6152-6164
12. Baere T D, Mendonca R, Claeys G. Evaluation of amplified rDNA restriction analysis (ARDRA) for the identification of cultured mycobacteria in a diagnostic laboratory. BMC Microbiology, 2002, 2(1):4-15
13. Baldani J, Caruso, Baldani V L F, Goi S R, Dbbereinner J. Recent advance in BNF with non-legume plant. Soil Biol Biochem, 1997, 29:911-922
14. Balestra G M, Misaghi I J. Increasing the efficiency of the plate counting method for estimating bacterial diversity. J Microbiol Meth, 1997, 30: 111-117
15. Bano N, Hollibaugh J T. Diversity and distribution of DNA sequencesw ith affinity to ammonia-oxidizing bacteria of the B2subdivision of the class P roteobacteria in the A rctic Ocean. Appi Environ Microbiol, 2000, 66:1960-1969
16. Barbieri P, Galli E. Effect on wheat development of inoculation with an Azospirllum brasilense mutant with altered indole-3-acetic acid production. Res Microbiol, 1993, 144:69-75
17. Bashan Y and Holguin G. Azosprillwn-plant relationships: environmental and physiological advance (1990-1996). Can J Microbiol, 1997,43:103-121
18. Bashan Y and Holguin G Proposal for the division of plant growth-promoting rhizobacteria into two classifications: biocontrol-PGPB (plant growth-promoting bacteria) and PGPB. Soil Biol Biochem, 1998. 30:1225-1228
19. Biswas J C, Ladha J K, Dazzo F B. Rhizobia inoculation improves nutrient uptake and growth of lowland rice. Soil Sci Soc Am J, 2000a, 64:1644-1650
20. Biswas J C, Ladha J K, Dazzo F B, Yanni Y G, Rolfe B G Rhizobial inoculation influences seedling vigour and yield of rice. Agron J, 2000b, 92:880-886
21. Baudoin E, Benizri E, Guckert A. Impact of growth stage on the bacterial community structure along maize roots , as determined by metabolic and genetic fingerprinting. Applied Soil Ecology, 2002, 19:135-145
22. Belimov A A, Safronova V I, Sergeveva T A, Egorova T N, Matvcveva V A, el al. Characterization of plant growth promoting rhizobacteria isolated from polluted soils and containing 1-aminocyclopropane-1-carboxylate deaminase. Can J Microbiol, 2001, 47(7):642-52.
23. Bell C R, Dickie G A, Harvey W L G Chan J W Y F. Endophytic bacteria in grapevine. Can J Microbiol, 1995,41:46-53
24. Berga G, Krechel J, Ditz M. Sikora R A, Irich A, Allmann J. Endophytic and ectophytic potato-associated bacterial communities differ in structure and antagonistic function against plant pathogenic fungi. FEMS Microbiology Ecology , 2005, 51: 215-229
25. Bergsma-Vlami M, Prins M E, Staats M, Raaijmakers J M. Assessment of genotypic diversity of antibiotic-producing Pseudomonas species in the rhizosphere by denaturing gradient gel electrophoresis. Appl Environ Microbiol, 2005, 71: 993-1003
26. Bevivino A, Sarrocco S, Dalmastri C, et al. Characterization of a free-living maize-rhizosphere population of Burkholderia cepacia: effect of seed treatment on disease suppression and growth promotion of maize. FEMS Microbiology Ecology, 1998, 27:225-237
27. Bligh E G, Dyer W J. A rapid method of total lipid extraction and purification. Can J Biochem Physiol, 1959, 37: 911- 917
28. Boddey R M. Biological nitrogen fixation in sugar cane: A key to energetically viable bio-fuel production. Crit Rev Plant Sci, 1995,14:263-279
29. Boon N, Top E M, Verstraete W, Siciliano S D. Bioaugmentation as a tool to protect the structure and function of an activated-sludge microbial community against a 3-chluroaniline shock load. Appl Environ Microbiol. 2003,69:1511-1520
30. Bowman J P, McCammon S A, Gibson J A E, Robertson L, Nichols P D. Prokaryotic metabolic activity and community structure in antarctic continental shelfsediments. Appl Environ Microbiol, 2003, 69: 2448-2462
31. Bramwell P A, Barallon R A, Rogers H J, et al. Extraction and PCR amplification of DNA from the rhizoplane. In Akkermans A D L, van Elsas J D, Bruijn F J DE (Eds), Molecular Microbial Ecology Manual, Kluwer Academic Publishers, London, 1995, pp. 1.4.2.1-1.4.2.20
32. Brettar I, Christen R, Hofle M G Rheinheimera baltica gen nov., sp. nov., a blue-coloured bacterium isolated from the central Baltic Sea. Int J Syst Evol Microbiol, 2002,52: 1851-1857
33. Briones A M, Okabe S, Umemiya Y, et al. On root biofilms and their possible contribution to N use efficiency of different ammonia-oxidizaing bacteria rice cultivars. Plant and Soil, 2003, 250:335-348
34. Briones A M, Okabe S, Umemiya Y, Ramsing N-B, Reichardt W, Okuyama H. Influence of different cultivars on populations of ammonia-oxidizing bacteria in the root environment of rice. Appl Environ Microbiol, 2002,68:3067-3075
35. Brosius J, Palmer M L, Kennedy P L, Noller H F. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc Nat Acad Sci USA, 1978,75:4801-4805
36. Brown M E. Seed and root bacterization. Annual Review of Phytopathology, 1974,12: 181-197
37. Brun E, Moriaud F, Gans P, et al. Solution structure of the cellulose-binding domain of the endoglucanase Z secreted by Erwinia chrysanthemi. Biochemistry, 1997,36:16074-16086
38. Burke D J, Hamerlynck E P, Hahn D. Effect of arbuscular mycorrhizae on soil microbial populations and associated plant performance of the salt marsh grass Spartina patens. Plant and Soil, 2002, 239:141 -154
39. Cankar K, Kraigher H, Ravnikar M, Maja Rupnik M. Bacterial endophytes from seeds of Norway spruce (Picea abies L. Karst). FEMS Microbiology Letters, 2005, 244:341-345
40. Cariello N F, Skopek T R. Mutation analysis using denaturing gradient gel eletrophoresis and PCR. Mutat Res, 1993, 288:103-112
41. Chanway C P, Nelson L M. Cultivar-specific growth promotion of spring wheat by coexistent Bacillus species. Can J Microbiol, 1988, 34:925-929
42. Chelius M K, Tiplet E W. The diversity of archaea and bacteria in association with the root of Zea mays L. Microbial Ecology, 2001,41:252-263
43. Chiarini L, Bevivno A, Tabacchioni S, et al. Inoculation of Burkholderia cepac(?)a , Pseudomonas fluorescens and Enterobacter sp. on Sorghum bicolor: root colonization and plant growth promotion of dual strain inocula. Soil Biol Biochem, 1998,30:81-87
44. Chow M L, Radomski C C, McDermott J M, et al. Molecular characterization of bacterial diversity in Lodgepole pine (Pinus contorta) rhizosphere soils from British Columbia forest soil differing in disturbance and geographic source. FEMS Microbiology Ecology, 2002,42: 347-357
45. Chrnin L, Chet I. Microbial enzymes in biocontrol of plant pathogens and pest. In: enzymes in the environment: activity, ecology, and application. (eds.) R G Burns and R P Dick. Marcel dekker, New York, 2002, p. 171 -225
46. Collins M D, Lawson P A, Willems A, Cordoba J J, Fernandez- Garayzabal J, Garcia P, Cai J, Hippe H, Farrow J A E. The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. Int J Syst Bacteriol, 1994,44:812-826.
47. Compant S, Duffy B, Nowak J, Clement C, Ait Barka E. Use of plant growth-promoting bacteria for biocontrol of paint diseases: principles, mechanisms of action, and future prospects. Appl Environ Microbiol, 2005,71:4951-4959
48. Conn V M, Franco C M M. Analysis of the endophytic actinobacterial population in the roots of wheat (Triticum aestivum L.) by terminal restriction fragment length polymorphism and sequencing of 16S rRNA clones. Appl Environ Microbiol, 2004,70:1787-1794
49. Coskuner G, Curtis T P. In situ characterization of nitrifiers in an activated sludge plant: detection of Nitrobacter spp.. Journal of Applied Microbiology, 2002,93: 431- 437
50. Dahllof I, Baillie H, Kjelleberg S. rpoB-based microbial community analysis avoids limitations inherent in 16S rRNA gene intraspecies heterogeneity. Appl Environ Microbiol, 2000,66: 3376-3380
51. Daubaras D L, Danganan C E, Hubner A, Ye R W, Hendrickson W, Chakrabarty A M. Biodegradation of 2 , 4 , 5-trichlorophenoxyacetic acid by Burkholderia cepacia strain AC1100: evolutionary insight. Gene, 1996, 179:1-8
52. Davison J. Plant beneficial bacteria. Biotechnology, 1988,6:282-286
53. Di Fiore S, Del Gallo M. Endophytic bacteria their possible role in the host plant. In: Azospirillum VI and Related Microorganisms: Geneticsa, Physiology, Ecology. Fendrik et al. (eds.). Heidelberg: Springer. 1995, pp. 169-187
54. Dobereinner J, Baldani V L D, Reis V M. Endophytic occurrence of diazotrophic bacteria in tropical agriculture. Fert Res. 1995,42:339-346
55. Duffy B K, Defago G Environmental factors modulating antibiotic and siderophores biosynthesis by Pseudomonas fluorescens biocontrol strains. Appl Environ Microbiol, 1999,65:2429-2438
56. Duijff B J, Gianinazzi-Pearson V, Lemanceau P. Involvement of the outer membrane lipopolysaccharides in the endophytic colonization of tomato roots by biocontrol Pseudomonas fluorescens strain WCS417r. New Phytol, 1997, 135:325-334
57. Duineveld B M, Kowalchuk G A, Keijzer A, et al. Analysis of bacterial communities in the rhizosphere of chrysanthemum via denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA as well as DNA fragments coding for 16S rRNA. Appl Environ Microbiol, 2001, 67: 172-178
58. Duineveld B M, Rosado A S, van Eisas J D, et al. Analysis of the dynamic of bacterial community in the rhizosphere of the Chrysanthemun via denaturing gradient gel electrophoresis and substrate utilization patterns. Appl Environ Microbiol, 1998, 64: 4950-4957
59. Dunbar J, Takala S, Barns S M, et al. Levels of bacterial community diversity in four arid soils compared by cultivation and 16S rRNA gene cloning. Appl Environ Microbiol, 1999,65: 1662-1669
60. Dunne C, Crowley J J, Monne-Loccoz Y, et al. Biological controi of Pythium ultimum by Stenotrophomonas mal(?)ophilia W81 is mediated by an extracellular proteolytic activity. Microbiology, 1997, 143:3921-3931
61. Edwards U, Rogall T, Blocker H, et al. Isolation and direct complete nucleotide determination of entire genes: characterization of a gene coding for 16S ribosomal RN A. Nucleic Acids Res, 1989. 17:7843-7853
62. Elbeltagy A, Nishioka K, Sato T, et al. Endophytic colonization and in planta nitrogen fixation by a Herbaspirillum sp. isolated from wild rice species. Appl Environ Microbiol, 2001, 67:5285-5293
63. Eller G, Frenzel P. Changes in activity and community structure of methane-oxidizing bacteria over the growth period of rice. Appl Environ Microbil, 2001, 67:2395-2403
64. Ellis R J, Morgan P, Weightman A J, Fry J C. Cultivation-dependeent and independent approaches for determining bacterial diversity in heavy-metal-contaminated soil. Appl Environ Microbiol, 2003, 69:3223-3230
65. Elsas J D V, Wellington E M H, Trevors J T. Modern Soil Microbiology. New York; Marcel Dekker, Inc, 1997, pp. 353-374
66. Esahi Y. Ethylene and seed germination. In The Plant Hormone Ethylene,(eds) A K matoo and J C Suttle, CRC Press, Boca Raton, F1. 1991, pp: 133-157
67. Fang C, Radosevich M, Fuhrmann J J. Characterization of rhizosphere microbial community structure in five similar grass species using FAME and BIOLOG analyses. Soil Biology & Biochemistry, 2001, 33:679-682
68. Fang M, Kremer R J, Motavalli P P, Georgia D. Bacterial diversity in rhizosphere of nontransgenic and transgenic corn. Appl Environ Microbiol, 2005, 71: 4132-4136
69. Farrelly V, Rainey F A, Stackebrandt E. Effect of genome size and rm gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl Environ Microbiol, 1995, 61:2798-2801
70. Felske A, AkkermansA D L. Prominent occurrence of ribo somes from an uncultured bacterium of the Verrucomicrobiales cluster in grassland soils. Lett Appl Microbiol, 1998, 26: 219- 223
71. Felske A, Wolterink A, van Lis R, Akkermans A D L. Phylogeny of the main bacterial 16S rRNA sequences in Drentse A grassland soils (The Netherlands). Appl Environ Microbiol, 1998,64:871-879
72. Ferris M J , Ward D M. Seasonal distributions of dominant 16S rDNA-defined populations in a hot spring microbialmat examined by denaturing gradient gel eiectropho resis. Appl Environ Microbiol, 1997,63: 1375-1381.
73. Ferris M J, Muyzer G, Ward D M. Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabitong a hot spring microbial mat community. Appl Environ Microbiol, 1996,62:1375-1381
74. Fischer S G, Lerman S L. DNA fragments differing by single base-pair substitutions are separated in denaturing gradient gel: correspondence with melting theory. Proc Natl Acad Sci USA, 1983, 80:1579-1583
75. Foster Jamie S, Palmer Robert J J. Human oral cavity as a model for the study of genome-genome interactions. Biological Bulletin, 2003,204:200- 204
76. Frostegard A, Cour S, Ranmisse V, et al. Quantification of bias related to the extraction of DNA directly from soils. Appl Environ Microbiol. 1999, 65:5409-5420
77. Garbeva P, Overbeek L S. Vuurde J W, et al. Analysis of cndophytic bacterial communities of potato by plating and denaturing gradient gel electrophoresis of 16S rDNA based PCR fragments. Microbial Ecology, 2001. 41:369-383
78. Gaston K J. Biodiversity. A biology of numbers and difference. Oxford, UK:Blackwell Sci. 1996
79. Germida J J, Siciliano S D, de Freitas J R, Seib A M. Diversity of root-associated with field-grown canola (Brassica napus L.) and wheat (Triticum aeslivum L.). FEMS Microbiol Ecology, 1998, 26:43-50
80. Giesler L J. Yuen G Y. Evaluation of Stenotrophomonas maltophilia strain C3 for biocontrol of brown patch disease. Crop Protection, 1998. 17:509-513
81. Giovannoni S J, Britschgi T B, Moyer C L, Field K G Genetic diversity in Sargasso Sea bacterioplankton. Nature, 1990, 345:60-63
82. Glick B R, Patten C L, Holguin G,Penrose D M. Biochemical and genetic mechanisma used by plant growth-promoting bacteria. Imperial College Press, London UK, 1999
83. Glick B R,Penrose D M, Li J. A model for the lowing of plant ethylene concentrations by plant growth promoting bacteria. J Theor Biol, 1998. 190:63-68
84. Gomes N C M, Heuer H, Schonfeld J. et al. Bacterial diversity of the rhizosphere of maize (Zea mays)grown in tropical soil studied by temperature gradient ge! eicctrophoresis. Plant and soil, 2001, 232:167-180
85. Gomes N C, Fagbola O.Costa R. Rumjanek N G, Buchner A, Mendona-Hagler L, Smalla K. Dynamics of fungal communities in bulk and maize rhizosphere soil in the tropics. Appl Environ Microbiol, 2003.69:3758-3766
86. Good I L. The population frequencies of species and the estimation of population parameters. Biometrika, 1953, 40: 237-264
87. Gray E J and Smith D. Interacellular and extracellular PGPR: commonalities and distinction in the plant-bacteria signaling rocesses. Soil Biol Biocheim, 2005, 37:395-412
88. Groβkopf R, Stubner S, Liesack W. Novel euryarchaeotal lineages detected on rice roots and in the anoxic bulk soil of flooded rice microcosms. Appl Environ Microbiol, 1998,64: 4983-4989
89. Hadrys H, Balick M, Schierwater B. Application of random amplified polymorphic DNA (RAPD) in molecular ecology. Mol Ecol, 1992, 1:55-63
90. Hallmann J, Quadt-Hallmann A, Mahaffee W F, et al. Bacterial endophytes in agricultural crops. Can J Microbiol, 1997, 43:895-914
91. Hallmann J, Quadt-Hallmann A, Rodriguez-Kabana R, et al. Interactions between meloidogyne incognita and endophytic bacteria in cotton and cucumber. Soil Biol Biochem, 1998,30:92-937
92. Han J G, Sun L, Dong X Z, et al. Characterization of a novel plant growth-promoting bacteria strain Delftia tsuruhatensis HR4 both as a diazotroph and a potentiawl biocontrol agent against various plant pathogens. Syst Appl Microbiol, 2005, 28:66-76
93. Hebbar K P, Martel M H, Heulin T. Suppression of pre- and postemergence damping-off in corn by Burkholderia cepacia. Eur J Plant Pathol, 1998, 104:29-36
94. Hedges R W, Messens E. Genetic aspects of rhizosphere interactions. In: Lynch J M (ed) The Rhizosphere. John Wiley and Sons Ltd, Chichester, UK, 1990, pp 129-176
95. Hcucr H M, Baker K P, Smalla K, Wellington E M. Analysis of actinomycete communities by specific amplification of genes encoding 16S rDNA and gel-eletrophoretic separation in denaturing gradients. Appl Environ Microbiol, 1997, 63:3222-3241
96. Heuer H, Smalla K. Application of denaturing gradient gel electrophoresis and temperature gradient gel electrophoresis for studying soil microbial communities. In: van Elsas JD, Trevors JT, Wellington EMH (eds),
97. Heuer H, Smalla k. Evaluation of community-level catabolic profiling using BIOLOG GN microplates to study microbial community changes in potato phyllosphere. J Microbiol Methods, 1997, 30:49-61
98. Heyndrickx M,Vauterin L, Vandamme P, Kersters K, De Vos P. Applicability of combined amplified ribosomal DNA restriction analysis (ARDRA) patterns in bacterial phylogeny and taxonomy. J Microbiol Methods, 1996, 26:247-259
99. Hilla G T, Mitkowskia N A, Aldrich-Wolfeb L, et al. Methods for assessing the composition and diversity of soil microbial communities. Applied Soil Ecology, 2000, 15: 25- 36
100. Hinton D M, Bacon C W. Enterobacter cloacae is an endophytic symbiont of corn. Mycopathologia, 1995, 129:117-125
101. Holben W E, Feris K. P, Kettunen A, Apajaiahti H A. GC fractionation enhances microbial community diversity assessment and detection of minority populations of bacteria by denaturing gradient gel electrophoresis. Appl Environ Microbiol, 2004, 70: 2263-2270
102. Hong Y, Pasternak J J, Glick B R. Biological consequences of plasmid transformation of the plant growth-promoting rhizobacterium Pseudomonas putida GR12-2. Can J Microbiol, 1991, 37:796-799
103. Hugenholtz P, Goebet B M and Pace N R. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. Journal of bacteriology, 1998, 180:4765-4774
104. Hugenholtz P, Pace N R. Identifying microbial diversity in the natural environment: a molecular phylogenetic approach. Trend in Biotechnology, 1996, 14(6): 190-197
105. Hurek T, Reinhold-Hurek B, Van Montagu M, et al. Root colonization and systemic spreading of Azoarcus sp. Strain BH72 in grasses. J Bacteriol, 1994, 176:1913-1923
106. Ibekwe A M, Grieve C M. Change in developing plant microbial community structure as affected by contaminated water. FEMS Microbiol Ecology, 2004,48:239-248
107. Idris R, Trifonova R, Puschenreiter M, Wenzel W W, Sessitsch A. Bacterial Communities Associated with Flowering Plants of the Ni Hyperaccumulator Thlaspi goesingense. Appl Envion Microbiol, 2004, 70: 2667-2677
108. Ikenaga M, Muraoka Y, Toyota K, et al. Community structure of the microbiota associated with nodal roots of rice plants along with the growth stages: estimation by PCR-RFLP analysis. Biol Fertil Soils, 2002, 36:397-404
109. Jackson C R, Roden ￡ E. Churchill P F. Denaturing gradient gel electrophoresis can fail to separate 16S rDNA fragment with multiple base differences. Mol Biol Today, 2000,1(2): 49-51
110. Jackson M B, Pasternak J J, Glick B R. Partial purification and characterization of ACC deaminase from the plant growth-promoting rhizobacterium Pseudomonas putida GR12-2. Can J Microbiol. 1994,40:1019-1025
111. Jackson M B. Ethylene in root growth and development. In The Plant Hormone Ethylene , (eds) A K matoo and J C Suttie, CRC Press, Boca Raton, F1. 1991, pp: 159-181
112. Jacob M J, Bugbee W M, Gabrielson D A. Enumeration, location, and characterization of endophytic bacteria within sugar beet roots. Can J Bot, 1985,45:757-766
113. Jaeger C H III, Lindow S E, Miller W, Clark E, Firestone M K. Mapping of sugar and amino acid availability in soil around roots with bacterial sensors of sucrose and trytophan. Appl Environ Microbiol, 1999, 65: 2685-2690
114. Jakobi M, Winkelmann G Maltophilin: a new antifungal compound produced by Stenotrophomonas maltophilia R3089. J Antibiot, 1996,49: 1101-1104
115. Jensen M, Straus N. Effect of PCR conditions on the formation of heteroduplex and single-stranded DNA products in the amplification of bacterial ribosomal DNA spacer regions. PCR Methods Appl, 1993, 3:186-194
116. Kaiser O, Puhler A, Selbitschka W. Phylogenetic Analysis of Microbial diversity in the rhizoplane of Oilseed Rape (Brassica napus cv. Westar) employing cultivation-dependent and cultivation-independent approaches. Microbial Ecology, 2001, 42:136-149
117. Kandeler E, Marschner P. Tscherko D, et al. Microbial community composition and functional diversity in the rhizosphere of maize. Plant and soil, 2002, 238:301-312
118. Kemp P F. Aller J Y. Bacterial diversity in aquatic and other environments: what 16S rDNA libraries and tell us. FEMS Microbiology Ecology, 2004, 47:167-177
119. Keohavong P. Thilly W G. Fidelity of DNA polymerases in DNA amplification. Proc Nail Acad Sci USA, 1989, 86:9253-9257
120. Kirchhof G. Eckert B, Stoffels M. et al. Herbaspirillum frisingense sp. nov., a new nitrogen-fixing bacterial species that occurs in C4-fibre plants. Int J Syst Environ Microbiol, 2001, 51:157-168
121. Kitts C L. Terminal restriction fragment patterns: a tool for comparing microbial communities and assessing community dynamics. Curt Issues Intest Microbiol, 2001.2:17-25
122. Kloepper J W, Schroth M N. Miller T D. Effect of rhizosphere colonization by plant growth promoting rhizobacteria on potato development and yield. Phytopathology, 1980, 70:1078-1082
123. Kloepper J W, Schroth M N. Plant growth promoting rhizobacteria on radishes, in proceedings of the 4th International Cnference on Plant Pathogenic Bacteria, ed. Station de Pathologic Vegetal et phytobacteriologie, 1978, vol. 2, pp. 879-882. Angers France.
124. Klopper J W, Rodriguez-Ubna R, Zehnder G W. Murphy J F. Sikora E, Fernandez C. Plant root-bacterial interactions in biological control of soilborne disease and potential extension to systemic and foliar diseases. Austral lant Pathol, 1999, 28:21-26
125. Klopper J, Tuzum S, Kuc J. Proposed definitions related to induced disease resistance. Biocontrol Science and Technology, 1992, 2:347-349
126. Kobayashi D Y, Reedy R M, Bick JA, et al. Characterization of a chitinase gene from Stenotrophomonas maltophilia strain 34S1 and its involvement in biological control. Appl Environ Microbiol., 2002, 68:1047-1054
127. Koizumi Y, Kojima H, Fukui M. Characterization of depth-related microbial community structure in lake sediment by denaturing gradient gel electrophoresis of amplied 16S rDNA and reversely transcribed 16S rRNA fragments. FEMS Microbiol Ecology, 2003, 46:147-157
128. Kowa; chuk G A, Stephen J R, Boer W De, Prosser J I, Embley T M and Woldendorp J W. Analysis of ammonia-oxidizing bacteria of the eta subdivision of the clad Proteobacteria in coastal sand dunes by denaturing gradient gel eletrophoresis sequencing of PCR-amplified 16S ribosomal DNA fragments. Appl Environ microbilol, 1997, 63:1489-1497
129. Kozdroj J, Elsas J D. Application of polymerase chain recreation-denaturing gradient gel electrophoresis for comparison of direct and indirect extraction methods of soil DNA used for microbial community fingerprinting. Biology and Fertility of Soil, 2000, 31:372-378
130. Kuklinsky-sobral J, Araujo W L, Mendes R, et al. Isolation and characterization of endophytic bacteria from soybean (Glycine max) grown in soil treated with glyphosate herbicide. Plant and Soil, 2005, 273:91-99
131. Lagace L, Pitre M, Jacques M, Roy D. Identification of the bacterial community of Maple sap by using amplified ribosomal DNA (rDNA) restriction analysis and rDNA sequencing. Appl Environ Microbiol, 2004, 70:2052-2060
132. Lambert B, Frederik L, van Rooyen L, et al. Rhizobacteria of maize and their antifungal activities. Appl Environ Microbiol, 1987, 53:1866-1871
133. Lazarovits G, Nowak J. Rhizobacteria for improvement of plant growth and establishment. Hortscience, 1997, 32:188-192
134. Lee T J, Kawaharasaki M. Matsumura M, et al. Microbial community structures of activated sludges dominated with polyphosphate-accumulating bacteria and glycogen-accumulating bacteria. Environmental Technology, 2002,23: 747- 755
135. Leifert C, Morris C E, Waites W M. Ecology of microbial saprophytes and pathogens in tissue culture and fiels grown plant: reasons for contamination problems in vitro. Crit Rev Plant Sci, 1994, 13:139-183
136. Lerman L S, Fischer S G, Silverstein H K, Lumelsky N. Sequence-detemined DNA separations. Annu Rev Biophys Bioeng, 1984, 13:399-423
137. Liu J, Leff L G Temporal changes in the bacterioplankton of a Northeast Ohio (USA) River. Hydrobiologia, 2002, 489: 151-159
138. Liu W T, Marsh T L, Cheng H, Forney L J. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol, 1997, 63:4516-4522.
139. Lodewyck C, Vangronsveld J, Porteous F, Moore E R B, Taghavi S, Mezgeay M, van der Lelie D. Endophytic bacteria and their potential application. Crit Rev Plant Sci, 2002, 86(6):583-606
140. Loper J E, Henkels M D. Utilization of heterologous siderophores enhances level of iron available to Pseudomonas putida in the rhizosphere. Appl Environ Microbiol, 1999, 65:5357-5363
141. Lu Y, Conrad R. In situ stable isotope probing of Methanogenic archaea in the rice rhizosphere. Science, 2005, 309:1088-1090
142. Lucy M, Reed E, Glick B R. Application of free living plant growth-promoting rhizobacteria. Antonic van Leeuwenhoke, 2004,86 : 1-25
143. Lueders T, Friedrich M W. Evaluation of PCR amplification bias by terminal restriction fragment length polymorphism analysis of small-subunit rRNA and mcrA genes by using defined template mixtures of methanogenic pure cultures and soil DNA extracts. Appl Environ Microbiol, 2003, 69:320-326
144. Luo H F, Qi H Y, Zhang H X. Assessment of the bacterial diversity in fenvalerate-treated soil. World Journal of Microbiology & biotechnology, 2004, 20: 509-515
145. Lynch J M. Introduction: Some consequences of microbial rhizosphere competence for plant and soil. In: Lynch J M (ed) The Rhizosphere. John Wiley-SonsLtd , ChichesterUK, 1990, pp. 1-10
146. Maarit-Niemi R, Heiskanen L, Wallenius K, Lindstrom K. Extraction and purification of DNA in rhizosphere soil samples for PCR-DGGE analysis of bacterial consortia J Microbiol Methods, 2001,45: 155-165
147. Macrae A, Rimmer D L, O'Donnell A G Novel bacterial diversity recovered from the rhizosphere of oilseed rape (Brassica napus) determined by the analysis of 16S ribosomal DNA. Antonie van Leeuwenhoek, 2000, 78: 13-21
148. Marilley L, Aragno M. Phylogenetic diversity of bacterial communities differing in degree of p(?)oximity of Lolium perenne and Trifolium repens root. Appl Soil Ecol, 1999, 13:127-136
149. Marilley L, Vogt G, Blanc M, et al. Bacterial diversity in the bulk soil and rhizosphere fractions of Lolium perenne and Trifolium repens as revealed by PCR estriction analysis of 16S rDNA. Plant and Soil, 1998, 198:219-224
150. Marilly B L, Aragno M. Phylogenetic diversity of bacterial communities differing in degree of proximity of Lolium perernne and Trifolium repens roots. Appl Soil Ecol, 1999, 13:127-136
151. Marschner P, Baumann K. Changes in bacterial community induced by mycorrhizal colonization in split-root maize. Plant and soil, 2003,251:279-289
152. Marschner P, Neumann G, Kania A, et al. Spatial and temporal dynamics of the microbial community structure in the rhizosphere of cluster roots of white lupin (Lupin albus L.).Plant and Soil, 2002, 246:167-174
153. Marschner P, Yang C-H, Leiberei R, el al. Soil and plant specific effects on bacterial community composition in the rhizosphere. Soil Biol Biochem, 2001, 33:1437-1445
154. Martin-Laurent F, Philippot L, Hallet S, et al. DNA extraction from soil: old bias for new microbial diversity analysis method. Appl Environ Microbiol. 2001. 67: 2354-2359
155. Massol-Deya A A. Odelsonn D A, Hickey R F, Tiedje J M. Bacterial community fingerprinting of amplified 16S and 16-23S ribosomal DNA gene sequence and restriction endonuclease analysis (ARDRA), In Molecular Microbial Ecology Manual(eds) ADL Akkermans. JD van Elsas, FJ de Bruijn, 1995. pp. 2:1-8.
156. Mazzola M, Stahlman P W, Leach J E. Application method affects the distribution and efficacy of rhizobacteria suppressive of downy brome (Bromus tectorum). Soil Biol. Biochem, 1995, 27:1271-2178
157. McCaig A E, Glover L A, Prosser J I. Molecular analysis of bacterial community structure and diversity in unimproved and improved upland grass pastures. Appl Environ Microbiol, 1999, 65.1721-1730
158. McInroy J A, Kloepper J W. Survey of indigenous bacterial endophytes from cotton and sweet corn. Plant Soil, 1995, 173:337-342
159. McNamara C J, Lemke M J, Leff L G Culturable and non-culturable fractions of bacterial populations in sediments of a South Carolina stream. Hydrobiologia. 2002, 482: 151-159
160. Mchnaz S, Mirza M S, Haurat J, Bally R, et al. Isolation and 16S rRNA sequence analysis of the beneficial from the rhizosphere of rice. Can J Microbiol, 2001,47:110-117
161. Miethling R, Wieland G, Backhaus H, et al. Variation of microbial rhizosphere communities in response to crop species , soil origin, and inoculation with Sinorhizobium meliloti L33. Microbial Ecology. 2000. 41:43-56
162. Minamisawa K, Nishioka K, Miyaki T, et al. Anaerobic nitrogen-fixing consortia consisting of clostridia isolated from gramineous plants. Appl Environ Microbiol, 2004, 70:3096-3102.
163. Miyamoto T, Kawahara M, Minamisawa K. Novel Endophytic Nitrogen-Fixing Clostridia from the Grass Miscanthus sinensis as Revealed by Terminal Restriction Fragment Length Polymorphism Analysis. Appl Environ Microbiol, 2004, 70:6580-6586
164. Mocali S, Bertelli E, Cello F D, et al. Fluctuation of bacteria isolated from elm tissues during different seasons and from different plant organs. Res Microbiol, 2003,154:105-114
165. Moeseneder M, Arrieta J M, Muyzer G, Winter C, Herndl G J. Optimization of terminal-restriction fragment length polymorphism analysis for complex marine bacterioplankton communities and comparison with denaturing gradient gel clectrophoresis. Appl Environ Microbiol, 1999,65:3518-3525
166. Mueller J G, Devereux R, Santavy D L, Lantz S E, Willis S G, Pritchard P H. Phylogenetic and physiological compartment of PAH-degrading bacteria from geographically diverse soils. Antonie Leeuwenhoek, 1997, 71:329-343.
167. Mundt J O, Hinkle N F. Bacteria within ovules and seeds. Appl Environ Microbiol, 1976,32:694-698
168. Muyzer G, Smalla K. Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophorcsis (TGGE) in microbial ecology. Antonie Van Leeuwenhoke, 1998, 73:127-141
169. Muyzer G, de Waal E C, Uitterlinden AG Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol, 1993, 59: 687-694
170. Myres R M, Fischer S G, Lerman L S, Maniatis T. Nearly all single base substitutions in DNA fragments joined to a GC-clamp can be detected by denaturing gradient gel electrophoresis. Nucleic Acids Res, 1985,13: 3131-3145
171. Niemi R M, Heiskanen I, Wallenius K, et al. Extraction and purification of DNA in rhizosphere soil samples for PCR-DGGE analysis of bacterial consortia. J Microbiol Methods, 2001,45:155-165
172. Normander B, Prosser J I. Bacterial origin and community composition in the barely phytosphere as a function of habitat and presowing conditions. Appl Environ Microbiol, 2000,66:4372-4377
173. Nowak J, Shulaev V. Priming for transplant stress resistance in in vitro propagation. In Vitro cell Dev Biol-Plant, 2003, 39:107-124
174. Ongcna M, Daayf F, Jacques P, et al. Protection of cucumber against Pythium root rot by fluorescent pseudomonads: predominant role of induced resistance over siderophores and antibiosis. Plant Pathology. 1999. 48: 66-76
175. Ordentlich A, Elad Y, Chet I. The role of chitinase of Serratia marcescens in biocontrol of Sclerotium rolfsii. Phytopathology, 1988, 78:84-88
176. (?)veras L, Forney L, Daae F L, et al. Distribution of bacterioplankton in menomictic lake Saelenvannet, As determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl Environ Microbiol. 1997, 63:3367-3373
177. (?)veras L, Torsvik V. Microbial diversity and community structure in two different agriculture soil communities. Microbio Ecol, 1998,36.303-315
178. Picard C, Di Cello F, Ventura M, Fani R, Guckert A. Frequency and biodiversity of 2, 4-diacethyphoroglucinol-producing bacteria isolated from the maize rhizosphere at different stages of plant growth. Appl Environ Microbiol, 2000,66: 948-955
179. Picard C, Ponsonnet C, Pager E, Nesme X, Simonet P. Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction. Appl Environ Microbiol, 1992. 58:2712-2722
180. Piceno Y M, Lovell C R. Stability in natural bacterial communities: Ⅱ.plant resource allocation effect on rhizosphere diazotroph assemblage composition. Microbial Ecology, 2000, 39 : 41-48
181. Piceno Y M, Lovell C R. Stability in natural bacterial vommunities Ⅰ .nutrient addition effect on rhizosphere diazotroph assemblage composition. Microbial Ecology. 2000,39:32-40
182. Qiu X, Wu L, Huang H, McDonel P E, Palumbo A V, Tiedje J M, Zhou J. Evaluation of PCR-generated chimeras , mutations , and heteroduplexes with 16S rRNA gene-bsed cloning. Appl Environ Microbiol. 2001, 67:880-887
183. Ramamoorthy V, Viswanathan R, Raguchander T, Prakasam V, Smajyappan R. Induction of systemic resistance by plant growth-promoting rhizobacteria in crop plants against pest and diseases. Crop Prot, 2001, 20:1 -11
184. Rangarajan S, Saleena L M, Nair S. Diversity of Pseudomonas spp. isolated rice rhizosphere population grown along a salinity gradient. Microbial Ecology, 2002,3:280-289
185. Reinhold-Hurek B, Hurek T. Life in grasses diazotrophic endophytes, Trend Microbiol, 1998,6:139-144
186. Reiter B, Pfeifer U, Schwab H, et al. Response of endophytic bacterial communities in potato plant to infection with Erwinia carotovora subsp. Atroseptica. Appl Environ Microbiol, 2002, 68:2261-2268
187. Reiter B, Wermbter N, Gyamfi S, et al. Endophytic Pseudomonas spp. Populations of pathogen-infected potato plants analysed by 16S rDNA-and 16S rRNA-based denaturating gradient gel electrophoresis. Plant and Soil, 2003, 257:397-405
188. Reysenbach A L, Giver L J, Wickham G S, Pace N R. Differential amplification of rPNA genes by poiymerase chain reaction. Appl Environ Microbiol, 1992,58:3417-3418
189. Robleto E A, Borneman J, Triplett E W. Effect of bacterial antibiotic production on rhizosphere microbial communities from a culture-independent perspective. Appl Environ Microbiol, 1998,64:5020-5022
190. Romanenko L A, Uchino M, Falsen E, Zhukova N V, Mikhailov V V, Uchimura T. Rheinheimera pacifica ap. nov. , a novel halotolerant bacterium isolated from deep sea water of the Pacific. Int J Syst Evol Microbiol, 2003, 53:1973-1977
191. Roslev P, Iversen N, Henrik sen K. Direct fingerp rinting of metabo lically active bacteria in environmental samples by substrate specific radio labelling and lipid analysis. J Microbiol Methods, 1998, 31:99-111.
192. Ruben A, Katsuji T, Tatsuya T. Bacterial activity and community composition in stream water and biofilm from an urban river determined by fluorescent in situ hybridization and DGGE analysis. FEMS Microbiol Ecology, 2003,43: 111-119
193. Sandaa R A, Enger A, Torsvik V. A bundance and diversity of archaea in heavy metal contaminated soils. Appl Environ Microbiol. 1999. 65:3293- 3297
194. Sanguinetti C J. Nego E D. Simpson A J G Rapid silver staining and recovery of PCR products separated on polyacrylamide gels. BioTechniques, 1994, 17(5): 914-921
195. Santegoeds C M. Nolf S C. Ward D M Denaturing gradient gel eletrophoresis used to monitor the enrichment culture of aerobic chemoorganotrophic bacteria from a hot spring cyanobacterial mat. Appl Environ Microbiol, 1996, 62:3922-3928
196. Schafer H, Bernard L, Courties C, et al. Microbial dynamics in mediterranean nutrient enriched seawater mesocosms: changes in the genetic diversity of bacterial populations. FEMS Microbiol Ecology, 2001, 33 : 243- 253
197. Scheid D, Stubner S, Conrad R. Identification of rice root associated nitrate , sulfate and ferriciron reducing bacteria during root decomposition. FEMS Microbiol Ecology, 2004, 50:101-110
198. Seghers D, Wittebolle L, Top E M, et al. Impact of Agricultural practices on the Zea mays L. endophytic community. Appl Environ Microbiol, 2004. 70: 1475-1482
199. Sekiguchi H, Tomioka N, Nakahara T. Uchiyama H. A single band dose not always represent single bacterial strains in denaturing gradient gel electrophoresis analysis. Biotechnology Letters. 2001, 23:1205-1208
200. Sessitsch A, Gyamfi S. Dagmar Tscherko D, Martin H. Gerzabek M H, Kandeler E. Activity of microorganisms in the rhizosphere of herbicide treated and untreated transgenic glufosinate-tolerant and wildtype oilseed rape grown in containment. Plant and Soil, 2004, 266: 105-116
201. Sessitsch A, Reiter B, Berg G Endophytic bacterial communities of field-grown potato plants and their plant-growth-promoiing and antagonistic abilities. Can J Microbiol, 2004, 50:239-249
202. Sessitsch A, Reiter B, Pfeifer U, et al. Cultivation-independent population analysis of bacterial endophytes in three potato varieties based on eubacterial and Actinomycetes-specific PCR of 16S rDNA genes. FEMS Microbiol Ecology, 2002, 39:23-32
203. Shah S, Li J, Moffatt B A and Glick B R. Isolation and characterization of ACC deaminase genes from two different plant growth promoting rhizobacteria. Can J Microbiol, 1998,44:833-843
204. Simposn J M, McCracken V J, White B A, Gaskins H R, Mackie R I. Application of denaturant gradient gel electrophoresis for the analysis of the porcine gastrointestinal microbiota. J Microbiol Methods, 1999,36: 167-179
205. Singh P P, Shin Y C, Park C S, Chung Y R. Biological control of Fusarium wilt of cucumber by chitinolytic bcteria. Phytopathology, 1999, 89:92-99
206. Smalla K, Wachtendorf U, Liu W-T, Forney L. Analysis of BIOLOG GN substrate utilization patterns by microbial communities. Appl Environ Microbiol, 1998,64:1220-1225
207. Smalla K, Wieland G, Buchner A, et al. Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed. Appl Environ Microbiol, 2001,67:4742-4751
208. Smith K P, Handelsman J, Goodman R M. Genetic basis in plants for interactions with disease-suppressive bacteria. Proc Natl Acad Sci USA, 1999,96:4786-4790
209. Soderberg KH, Probanza A, Jumpponen A, E. Baath E. The microbial community in the rhizosphere determined by community-level physiological profiles (CLPP) and direct soil- and cfu-PLFA techniques. Applied Soil Ecology, 2004, 25: 135-145
210. Stackebrandt E, Liesack W, Geobel B M. Bacteial diversity in a soil sample from a subtropical Australian environment as determined by 16S rDNA analysis. FASEB J, 1993, 7: 232-236
211. Steer J, Harris A. Shifts in the microbial community in rhizosphere and non-rhizosphere soils during the growth of Agrostis stolonifera. Soil Biology & Biochemistry, 2000,32: 869-878
212. Stoltzfus J R, So R, Malarvithi P P, Ladha J K, de Bruijn F J. Isolation of endophytic bacteria from rice and assessment of their potential for supplying rice with biologically fixed nitrogen. Plant and Soil, 1997,194: 25-36
213. Sturz A V. The role of endophytic bacteria during seed piece decay and tomato tuberization. Plant Soil, 1995,175:257-263
214. Sturz A V, Christie B R, Matheson B G Association of bacterial endophyte populations from red clover and potato crops with potential for beneficial allelopanthy. Can J microbial, 1998, 44:162-167
215. Sturz A V, Christie B R, Matheson B G, Nowak J, et al. Biodiversity of endophytic bacteria which colonize red clover nodules , roots , stems and foliages and their influence on host growth. Biol Fertil Soil, 1997, 25:13-19
216. Sturz A V, Christie B R, Matheson B G, et al. Endophytic bacterial communities in the periderm of potato tubes and their potential to improve resistance to soil-born plant pathogens. Plant Pathol, 1999,48:360-369
217. Sturz A V, Christie B R, Nowak J. Bacterial endophytes: potential role in developing sustainable systems of crop production. Crit Rev Plant Sci, 2000, 19:1-30
218. Surettel M A, Sturz A V, Lada R R, et al. Bacterial endophytes in processing carrots (Daucus carota L. var. sativus): their localization, population density, biodiversity and their effects on plant growth. Plant and Soil, 2003, 253:381-390
219. Suzuki M T, Giovannoni S J. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol, 1996,62:625-630
220. Tabacchioni S, Bevivno A, Chiarini L, et al. Characteristics of two rhizosphere isolates of Pseudomonas cepacia and their potential plant-promoting activity. Microb Release, 1993,2:161-168
221. Tholozan J L, CAppelier J M, Tissier J P, Delattre G. Federighi M. Physiological characterization of viable-but-nonculturable Campylobacter jejuni cell. Appl.Environ Microbiol, 1999,65.1110-1116
222. Timms-Wilson T M, Kilshaw K, Bailey M J. Risk assessment for engineered bacteria used in biocontrol of fungal disease in agricultural crops. Plant and Soil, 2004,266: 57-67
223. Tran Van V, Berge O, S. Ngo Ke, Balandreau J, Heulin T. Repeated beneficial effects of rice inoculation with a strain of Burkholderia vietnamiensis on early and late yield component in low fertility sulphate acid soils of Vietnam. Plant and Soil, 2000, 218:273-284.
224. Triplerr E W. Dizaotrophic endophytes: progress and prospects for nitrogen fixation in monocots. Plant and Soil, 1996, 186:29-38
225. Tsuda K, Kosaka Y Tsuge S, et al. Evaluation of the Endophyte Enterobacter cloacae SM10 Isolated from Spinach Roots for Biological Control against Fusarium Wilt of Spinach. J Gen Plant Pathol, 2001,67:78-84
226. Ueda T, Suga Y, Yahiro N, et al. Remberkable N2-Fix bacterial diverdity detected in rice roots by molecular evolutionary analysis of nifH gene sequence. Journal of Bacteriology, 1995,177(5): 1414-1417
227. Vallaeys T, Topp E, Muyzer G, et al. Evaluation of denaturing gradient gel electrophoresis in the detection of 16S rDNA sequence variation in rhizobia and methanotrophs. FEMS Microbiol. Ecology, 1997, 24: 279- 285
228. Van Loon L C, Bakker PHAM, Pieterse C M J. Systemic resistance induced by rhizosphere bacteria. Annu Rev Phytopathol, 1998,36:453-483
229. Vaneechoutte M, Riegel P, de Briel D, Monteik H, Verschraegen G, De Rouck A, Claeys G Evaluation of the applicability of amplified rDNA-restriction anslysis (ARDRA) to identification of species of the genus Corynebacterium. Res Microbiol, 1995,146:633-641
230. Vetriani C, Jannasch H W, MacGregor B, et al. Population structure and phylo-genetic characterization of marine benthic archaea in deep-sea sediments. Appl Environ Microbiol, 1999,65:4375-4383
231. Von Bulow J F W, Dobereiner J. Potential for nitrogen-fixation in maize genotypes in Brazil. Proc. Natl. Acad. Sci. USA, 1975,72:2389-2393
232. Ward G C, Santegoeds C M, Nold S C, Ramsing N B, Ferris M J, Bateson M M. Biodiversity within hot spring microbial mat communities: molecular monitoring of enrichment cultures. Antonie Van Leeuwenhoek, 1997, 71: 143-150
233. Watanabe K, Teramoto M, Futmata H, Harayama S. Molecular detection isolation, and physiological characterization of functionally dominant phenol-degrading bacteria in activated sludge. Appl Environ Microbiol. 1998. 64:4396-4402
234. Weisskopf L, Fromin N. Tomasi N, Aragno M, Martinoia E. Secretion activity of white lupin's cluster roots influences bacterial abundance, function and community structure, Plant and Soil. 2005, 268:181-194
235. Whipps J M Microbial interaction and biocontrol in the rhizosphere. J Exp Bot, 2001,52:487-511
236. Wieland G, Neumann R, Horst Backhaus. Variation of microbial communities in soil. rhizosphere, and crop development. Appl Ehviron Microbiol, 2001.67:5849-5854
237. Wilkinson S C, Anderson J M. Spatial patterns of soil microbial communities in a Norway. Microbial Ecology, 2001, 42:248-255
238. Wilson M J, Weightman A J, Wade W G. Applications of molecular ecology in the characterization of uncultured microorganisms associated with human disease. Rev Med Microbiol, 1997, 8:91-101
239. Yang C H, Crowley D E, Borneman J, Keen N T. Microbial phylloshere populations are more comlex than previously realized. Proc Natl Acad Sci USA, 2001, 98:3889-3894
240. Yang C H, Crowley D E. Rhizosphere microbioal community structure in relation to root location and plant iron nutritional status. Appl Environ Microbiol. 2000, 66:345-351
241. Yanni YG. Rizk RY, Corich V, Squartini A, et al. Natural endophytic association between Rhizobium leguminosarum by. trifolii and rice and assessment of its potential to promote rice growth. Plant and Soil, 1997, 194:99-114
242. Zinniel D K, Pat Lambrecht P, Beth Harris N, et al. Isolation and characterization of endophytic colonizing bacteria from agronomic crops and prairie plants. Appl Environ Microbiol, 2002, 68:2198-2208
243. Zou W X, Tan R X. Biological and chemical diversity of endophytes and their potential application. In: Advances in Plant Sciences. Vol. 2, Li G S (eds). China Higher Education press, Beijing, 1999, pp. 183-190
244．东秀珠，蔡妙英等．常见细菌系统鉴定手册．北京：科学出版社，1999
245．高平平，晁群芳，张学礼，王凌华，赵立平．TGGE分析焦化废水处理系统活性污泥细菌种群动态变化及多样性．生态学报，2003，23(10)：1963-1969
246．韩继刚，宋未．植物内生细菌研究进展及其应用潜力．自然科学进展，2004，14(4)：374-379
247．韩继刚．一株新的水稻植物内生固氮细菌Delftia tsuruhatensis HR4的坚定及其生物学特性．博士学位论文，首都师范大学，2004
248．胡楷，吴庆书．单细胞生物进化研究的进步．遗传，2002．24：104-110
249．雷娟利，周艳虹，丁桔，王礼，俞景权．不同蔬菜连作对土壤细菌DNA分子水平多态性影响的研究，中国农业科学，2005，38(10)：2076-2083
250．萨姆布鲁克 J．费里奇 E F，曼尼阿蒂斯 T，分子克隆实验指南(第二版)．北京：科学出版社，1999
251．沈德龙．水稻内生成团肠杆菌的分类鉴定及其生物学特性的研究。博士学位论文，中国农科院原子能所，1999
252．宋铁英．包晓东，郑伟文，Ulla R.DGGE法监测稻田蓝细菌及硅藻的遗传多样性，厦门大学学报(自然科学版)，2002，41：670-673
253．孙晓璐．水稻根面植物促生细菌的研究，硕士学位论文，中国农业科学院原子能利用研究所，1997
254．谢中稳，葛颂，洪德元．从普通野生稻硅胶干燥的小量叶片中制备DNA用于RAPD分析和总DNA库的建立(英文)．植物学报，1999，41(8)：802-807
255．杨海莲．水稻植株内生细菌的研究．博士学位论文，中国农业科学院原子能利用研究所，1997
2. Achenbach L A, Michaelidou U,Bruce R A, Fryman J, Coates j D. Dechloromonas agitata gen. nov., sp. nov. and Dechlorosoma suillum gen. nov., sp. nov., two novel environmentally dominant (per)chlorate-reducing bacteria and their phylogenetic position, Int J Syst Evol Microbiol, 2001, 51:527-33
3. Achouak W, Sutra L, Hulin T, Meyer J-M, Fromin N, Degraeve S, Christen R, Garden L. Peseudomonas brassicacearum sp. nov. and Pseudomonas thivervalensis sp. nov., two root-associated bacteria isolated from Brassica napus and Arabidopsis thaliana, Int J Syst Evol Microbiol, 2000, 50:9-18
4. Adams P D & Kloepper J W. Effect of host genotype on indigenous bacterial endophytes of cotton (Gossypium hirsutum L.). Plant and Soil 240:181-189,2002
5. Ait Barka E, Gognies S, Nowak J, Audran J-C and Beiarbi A. Inhibitory effect of endophyte bacteria on Botrytis cinerea and its influence to promote the grapevine growth. Biol. Control, 2002, 24:135-142
6. Akkermans A D L, EIsas J D V, Bruijn F J D E. Molecular Microbial Ecology Manual. Netherlands: Kluwer Academic Publishers, 1995, 2:1-8
7. Amann R I, Ludwig W, Schleifer K H. Phylogenetic identification and in situ detection of individual microbialcell without cultivation. Microbiol Rev, 1995, 59:143-169
8. Ampe F, Sirvent A, Zakhia N. Dynamics of the microbial community responsible for traditional sour cassava strch fementation studied by denaturing gradient gel electrophoresis and quantitative rRNA hybridization, Int J Food Microbiol, 2001, 65:45-54
9. Araujo W L, Macron J, Maccheroni W, et al. Diversity of endophytic bacterial populations and their interaction with Xylella fastidiosas in Citrus plants. Appl Environ Microbiol, 2002, 68:4906-4914
10. Arshad M and Ftankenberger W T. Mirobial production of plant hormones, in: The Rhizosphere and Plant Growth. 1991, pp.327-334
11. Avrahami S and Conrad R. Patterns of community change among ammonia oxidizers in meadow soils upon long-term incubation at different temperatures. Appl Environ Microbiol, 2003,69:6152-6164
12. Baere T D, Mendonca R, Claeys G. Evaluation of amplified rDNA restriction analysis (ARDRA) for the identification of cultured mycobacteria in a diagnostic laboratory. BMC Microbiology, 2002, 2(1):4-15
13. Baldani J, Caruso, Baldani V L F, Goi S R, Dbbereinner J. Recent advance in BNF with non-legume plant. Soil Biol Biochem, 1997, 29:911-922
14. Balestra G M, Misaghi I J. Increasing the efficiency of the plate counting method for estimating bacterial diversity. J Microbiol Meth, 1997, 30: 111-117
15. Bano N, Hollibaugh J T. Diversity and distribution of DNA sequencesw ith affinity to ammonia-oxidizing bacteria of the B2subdivision of the class P roteobacteria in the A rctic Ocean. Appi Environ Microbiol, 2000, 66:1960-1969
16. Barbieri P, Galli E. Effect on wheat development of inoculation with an Azospirllum brasilense mutant with altered indole-3-acetic acid production. Res Microbiol, 1993, 144:69-75
17. Bashan Y and Holguin G. Azosprillwn-plant relationships: environmental and physiological advance (1990-1996). Can J Microbiol, 1997,43:103-121
18. Bashan Y and Holguin G Proposal for the division of plant growth-promoting rhizobacteria into two classifications: biocontrol-PGPB (plant growth-promoting bacteria) and PGPB. Soil Biol Biochem, 1998. 30:1225-1228
19. Biswas J C, Ladha J K, Dazzo F B. Rhizobia inoculation improves nutrient uptake and growth of lowland rice. Soil Sci Soc Am J, 2000a, 64:1644-1650
20. Biswas J C, Ladha J K, Dazzo F B, Yanni Y G, Rolfe B G Rhizobial inoculation influences seedling vigour and yield of rice. Agron J, 2000b, 92:880-886
21. Baudoin E, Benizri E, Guckert A. Impact of growth stage on the bacterial community structure along maize roots , as determined by metabolic and genetic fingerprinting. Applied Soil Ecology, 2002, 19:135-145
22. Belimov A A, Safronova V I, Sergeveva T A, Egorova T N, Matvcveva V A, el al. Characterization of plant growth promoting rhizobacteria isolated from polluted soils and containing 1-aminocyclopropane-1-carboxylate deaminase. Can J Microbiol, 2001, 47(7):642-52.
23. Bell C R, Dickie G A, Harvey W L G Chan J W Y F. Endophytic bacteria in grapevine. Can J Microbiol, 1995,41:46-53
24. Berga G, Krechel J, Ditz M. Sikora R A, Irich A, Allmann J. Endophytic and ectophytic potato-associated bacterial communities differ in structure and antagonistic function against plant pathogenic fungi. FEMS Microbiology Ecology , 2005, 51: 215-229
25. Bergsma-Vlami M, Prins M E, Staats M, Raaijmakers J M. Assessment of genotypic diversity of antibiotic-producing Pseudomonas species in the rhizosphere by denaturing gradient gel electrophoresis. Appl Environ Microbiol, 2005, 71: 993-1003
26. Bevivino A, Sarrocco S, Dalmastri C, et al. Characterization of a free-living maize-rhizosphere population of Burkholderia cepacia: effect of seed treatment on disease suppression and growth promotion of maize. FEMS Microbiology Ecology, 1998, 27:225-237
27. Bligh E G, Dyer W J. A rapid method of total lipid extraction and purification. Can J Biochem Physiol, 1959, 37: 911- 917
28. Boddey R M. Biological nitrogen fixation in sugar cane: A key to energetically viable bio-fuel production. Crit Rev Plant Sci, 1995,14:263-279
29. Boon N, Top E M, Verstraete W, Siciliano S D. Bioaugmentation as a tool to protect the structure and function of an activated-sludge microbial community against a 3-chluroaniline shock load. Appl Environ Microbiol. 2003,69:1511-1520
30. Bowman J P, McCammon S A, Gibson J A E, Robertson L, Nichols P D. Prokaryotic metabolic activity and community structure in antarctic continental shelfsediments. Appl Environ Microbiol, 2003, 69: 2448-2462
31. Bramwell P A, Barallon R A, Rogers H J, et al. Extraction and PCR amplification of DNA from the rhizoplane. In Akkermans A D L, van Elsas J D, Bruijn F J DE (Eds), Molecular Microbial Ecology Manual, Kluwer Academic Publishers, London, 1995, pp. 1.4.2.1-1.4.2.20
32. Brettar I, Christen R, Hofle M G Rheinheimera baltica gen nov., sp. nov., a blue-coloured bacterium isolated from the central Baltic Sea. Int J Syst Evol Microbiol, 2002,52: 1851-1857
33. Briones A M, Okabe S, Umemiya Y, et al. On root biofilms and their possible contribution to N use efficiency of different ammonia-oxidizaing bacteria rice cultivars. Plant and Soil, 2003, 250:335-348
34. Briones A M, Okabe S, Umemiya Y, Ramsing N-B, Reichardt W, Okuyama H. Influence of different cultivars on populations of ammonia-oxidizing bacteria in the root environment of rice. Appl Environ Microbiol, 2002,68:3067-3075
35. Brosius J, Palmer M L, Kennedy P L, Noller H F. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc Nat Acad Sci USA, 1978,75:4801-4805
36. Brown M E. Seed and root bacterization. Annual Review of Phytopathology, 1974,12: 181-197
37. Brun E, Moriaud F, Gans P, et al. Solution structure of the cellulose-binding domain of the endoglucanase Z secreted by Erwinia chrysanthemi. Biochemistry, 1997,36:16074-16086
38. Burke D J, Hamerlynck E P, Hahn D. Effect of arbuscular mycorrhizae on soil microbial populations and associated plant performance of the salt marsh grass Spartina patens. Plant and Soil, 2002, 239:141 -154
39. Cankar K, Kraigher H, Ravnikar M, Maja Rupnik M. Bacterial endophytes from seeds of Norway spruce (Picea abies L. Karst). FEMS Microbiology Letters, 2005, 244:341-345
40. Cariello N F, Skopek T R. Mutation analysis using denaturing gradient gel eletrophoresis and PCR. Mutat Res, 1993, 288:103-112
41. Chanway C P, Nelson L M. Cultivar-specific growth promotion of spring wheat by coexistent Bacillus species. Can J Microbiol, 1988, 34:925-929
42. Chelius M K, Tiplet E W. The diversity of archaea and bacteria in association with the root of Zea mays L. Microbial Ecology, 2001,41:252-263
43. Chiarini L, Bevivno A, Tabacchioni S, et al. Inoculation of Burkholderia cepac(?)a , Pseudomonas fluorescens and Enterobacter sp. on Sorghum bicolor: root colonization and plant growth promotion of dual strain inocula. Soil Biol Biochem, 1998,30:81-87
44. Chow M L, Radomski C C, McDermott J M, et al. Molecular characterization of bacterial diversity in Lodgepole pine (Pinus contorta) rhizosphere soils from British Columbia forest soil differing in disturbance and geographic source. FEMS Microbiology Ecology, 2002,42: 347-357
45. Chrnin L, Chet I. Microbial enzymes in biocontrol of plant pathogens and pest. In: enzymes in the environment: activity, ecology, and application. (eds.) R G Burns and R P Dick. Marcel dekker, New York, 2002, p. 171 -225
46. Collins M D, Lawson P A, Willems A, Cordoba J J, Fernandez- Garayzabal J, Garcia P, Cai J, Hippe H, Farrow J A E. The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. Int J Syst Bacteriol, 1994,44:812-826.
47. Compant S, Duffy B, Nowak J, Clement C, Ait Barka E. Use of plant growth-promoting bacteria for biocontrol of paint diseases: principles, mechanisms of action, and future prospects. Appl Environ Microbiol, 2005,71:4951-4959
48. Conn V M, Franco C M M. Analysis of the endophytic actinobacterial population in the roots of wheat (Triticum aestivum L.) by terminal restriction fragment length polymorphism and sequencing of 16S rRNA clones. Appl Environ Microbiol, 2004,70:1787-1794
49. Coskuner G, Curtis T P. In situ characterization of nitrifiers in an activated sludge plant: detection of Nitrobacter spp.. Journal of Applied Microbiology, 2002,93: 431- 437
50. Dahllof I, Baillie H, Kjelleberg S. rpoB-based microbial community analysis avoids limitations inherent in 16S rRNA gene intraspecies heterogeneity. Appl Environ Microbiol, 2000,66: 3376-3380
51. Daubaras D L, Danganan C E, Hubner A, Ye R W, Hendrickson W, Chakrabarty A M. Biodegradation of 2 , 4 , 5-trichlorophenoxyacetic acid by Burkholderia cepacia strain AC1100: evolutionary insight. Gene, 1996, 179:1-8
52. Davison J. Plant beneficial bacteria. Biotechnology, 1988,6:282-286
53. Di Fiore S, Del Gallo M. Endophytic bacteria their possible role in the host plant. In: Azospirillum VI and Related Microorganisms: Geneticsa, Physiology, Ecology. Fendrik et al. (eds.). Heidelberg: Springer. 1995, pp. 169-187
54. Dobereinner J, Baldani V L D, Reis V M. Endophytic occurrence of diazotrophic bacteria in tropical agriculture. Fert Res. 1995,42:339-346
55. Duffy B K, Defago G Environmental factors modulating antibiotic and siderophores biosynthesis by Pseudomonas fluorescens biocontrol strains. Appl Environ Microbiol, 1999,65:2429-2438
56. Duijff B J, Gianinazzi-Pearson V, Lemanceau P. Involvement of the outer membrane lipopolysaccharides in the endophytic colonization of tomato roots by biocontrol Pseudomonas fluorescens strain WCS417r. New Phytol, 1997, 135:325-334
57. Duineveld B M, Kowalchuk G A, Keijzer A, et al. Analysis of bacterial communities in the rhizosphere of chrysanthemum via denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA as well as DNA fragments coding for 16S rRNA. Appl Environ Microbiol, 2001, 67: 172-178
58. Duineveld B M, Rosado A S, van Eisas J D, et al. Analysis of the dynamic of bacterial community in the rhizosphere of the Chrysanthemun via denaturing gradient gel electrophoresis and substrate utilization patterns. Appl Environ Microbiol, 1998, 64: 4950-4957
59. Dunbar J, Takala S, Barns S M, et al. Levels of bacterial community diversity in four arid soils compared by cultivation and 16S rRNA gene cloning. Appl Environ Microbiol, 1999,65: 1662-1669
60. Dunne C, Crowley J J, Monne-Loccoz Y, et al. Biological controi of Pythium ultimum by Stenotrophomonas mal(?)ophilia W81 is mediated by an extracellular proteolytic activity. Microbiology, 1997, 143:3921-3931
61. Edwards U, Rogall T, Blocker H, et al. Isolation and direct complete nucleotide determination of entire genes: characterization of a gene coding for 16S ribosomal RN A. Nucleic Acids Res, 1989. 17:7843-7853
62. Elbeltagy A, Nishioka K, Sato T, et al. Endophytic colonization and in planta nitrogen fixation by a Herbaspirillum sp. isolated from wild rice species. Appl Environ Microbiol, 2001, 67:5285-5293
63. Eller G, Frenzel P. Changes in activity and community structure of methane-oxidizing bacteria over the growth period of rice. Appl Environ Microbil, 2001, 67:2395-2403
64. Ellis R J, Morgan P, Weightman A J, Fry J C. Cultivation-dependeent and independent approaches for determining bacterial diversity in heavy-metal-contaminated soil. Appl Environ Microbiol, 2003, 69:3223-3230
65. Elsas J D V, Wellington E M H, Trevors J T. Modern Soil Microbiology. New York; Marcel Dekker, Inc, 1997, pp. 353-374
66. Esahi Y. Ethylene and seed germination. In The Plant Hormone Ethylene,(eds) A K matoo and J C Suttle, CRC Press, Boca Raton, F1. 1991, pp: 133-157
67. Fang C, Radosevich M, Fuhrmann J J. Characterization of rhizosphere microbial community structure in five similar grass species using FAME and BIOLOG analyses. Soil Biology & Biochemistry, 2001, 33:679-682
68. Fang M, Kremer R J, Motavalli P P, Georgia D. Bacterial diversity in rhizosphere of nontransgenic and transgenic corn. Appl Environ Microbiol, 2005, 71: 4132-4136
69. Farrelly V, Rainey F A, Stackebrandt E. Effect of genome size and rm gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl Environ Microbiol, 1995, 61:2798-2801
70. Felske A, AkkermansA D L. Prominent occurrence of ribo somes from an uncultured bacterium of the Verrucomicrobiales cluster in grassland soils. Lett Appl Microbiol, 1998, 26: 219- 223
71. Felske A, Wolterink A, van Lis R, Akkermans A D L. Phylogeny of the main bacterial 16S rRNA sequences in Drentse A grassland soils (The Netherlands). Appl Environ Microbiol, 1998,64:871-879
72. Ferris M J , Ward D M. Seasonal distributions of dominant 16S rDNA-defined populations in a hot spring microbialmat examined by denaturing gradient gel eiectropho resis. Appl Environ Microbiol, 1997,63: 1375-1381.
73. Ferris M J, Muyzer G, Ward D M. Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabitong a hot spring microbial mat community. Appl Environ Microbiol, 1996,62:1375-1381
74. Fischer S G, Lerman S L. DNA fragments differing by single base-pair substitutions are separated in denaturing gradient gel: correspondence with melting theory. Proc Natl Acad Sci USA, 1983, 80:1579-1583
75. Foster Jamie S, Palmer Robert J J. Human oral cavity as a model for the study of genome-genome interactions. Biological Bulletin, 2003,204:200- 204
76. Frostegard A, Cour S, Ranmisse V, et al. Quantification of bias related to the extraction of DNA directly from soils. Appl Environ Microbiol. 1999, 65:5409-5420
77. Garbeva P, Overbeek L S. Vuurde J W, et al. Analysis of cndophytic bacterial communities of potato by plating and denaturing gradient gel electrophoresis of 16S rDNA based PCR fragments. Microbial Ecology, 2001. 41:369-383
78. Gaston K J. Biodiversity. A biology of numbers and difference. Oxford, UK:Blackwell Sci. 1996
79. Germida J J, Siciliano S D, de Freitas J R, Seib A M. Diversity of root-associated with field-grown canola (Brassica napus L.) and wheat (Triticum aeslivum L.). FEMS Microbiol Ecology, 1998, 26:43-50
80. Giesler L J. Yuen G Y. Evaluation of Stenotrophomonas maltophilia strain C3 for biocontrol of brown patch disease. Crop Protection, 1998. 17:509-513
81. Giovannoni S J, Britschgi T B, Moyer C L, Field K G Genetic diversity in Sargasso Sea bacterioplankton. Nature, 1990, 345:60-63
82. Glick B R, Patten C L, Holguin G,Penrose D M. Biochemical and genetic mechanisma used by plant growth-promoting bacteria. Imperial College Press, London UK, 1999
83. Glick B R,Penrose D M, Li J. A model for the lowing of plant ethylene concentrations by plant growth promoting bacteria. J Theor Biol, 1998. 190:63-68
84. Gomes N C M, Heuer H, Schonfeld J. et al. Bacterial diversity of the rhizosphere of maize (Zea mays)grown in tropical soil studied by temperature gradient ge! eicctrophoresis. Plant and soil, 2001, 232:167-180
85. Gomes N C, Fagbola O.Costa R. Rumjanek N G, Buchner A, Mendona-Hagler L, Smalla K. Dynamics of fungal communities in bulk and maize rhizosphere soil in the tropics. Appl Environ Microbiol, 2003.69:3758-3766
86. Good I L. The population frequencies of species and the estimation of population parameters. Biometrika, 1953, 40: 237-264
87. Gray E J and Smith D. Interacellular and extracellular PGPR: commonalities and distinction in the plant-bacteria signaling rocesses. Soil Biol Biocheim, 2005, 37:395-412
88. Groβkopf R, Stubner S, Liesack W. Novel euryarchaeotal lineages detected on rice roots and in the anoxic bulk soil of flooded rice microcosms. Appl Environ Microbiol, 1998,64: 4983-4989
89. Hadrys H, Balick M, Schierwater B. Application of random amplified polymorphic DNA (RAPD) in molecular ecology. Mol Ecol, 1992, 1:55-63
90. Hallmann J, Quadt-Hallmann A, Mahaffee W F, et al. Bacterial endophytes in agricultural crops. Can J Microbiol, 1997, 43:895-914
91. Hallmann J, Quadt-Hallmann A, Rodriguez-Kabana R, et al. Interactions between meloidogyne incognita and endophytic bacteria in cotton and cucumber. Soil Biol Biochem, 1998,30:92-937
92. Han J G, Sun L, Dong X Z, et al. Characterization of a novel plant growth-promoting bacteria strain Delftia tsuruhatensis HR4 both as a diazotroph and a potentiawl biocontrol agent against various plant pathogens. Syst Appl Microbiol, 2005, 28:66-76
93. Hebbar K P, Martel M H, Heulin T. Suppression of pre- and postemergence damping-off in corn by Burkholderia cepacia. Eur J Plant Pathol, 1998, 104:29-36
94. Hedges R W, Messens E. Genetic aspects of rhizosphere interactions. In: Lynch J M (ed) The Rhizosphere. John Wiley and Sons Ltd, Chichester, UK, 1990, pp 129-176
95. Hcucr H M, Baker K P, Smalla K, Wellington E M. Analysis of actinomycete communities by specific amplification of genes encoding 16S rDNA and gel-eletrophoretic separation in denaturing gradients. Appl Environ Microbiol, 1997, 63:3222-3241
96. Heuer H, Smalla K. Application of denaturing gradient gel electrophoresis and temperature gradient gel electrophoresis for studying soil microbial communities. In: van Elsas JD, Trevors JT, Wellington EMH (eds),
97. Heuer H, Smalla k. Evaluation of community-level catabolic profiling using BIOLOG GN microplates to study microbial community changes in potato phyllosphere. J Microbiol Methods, 1997, 30:49-61
98. Heyndrickx M,Vauterin L, Vandamme P, Kersters K, De Vos P. Applicability of combined amplified ribosomal DNA restriction analysis (ARDRA) patterns in bacterial phylogeny and taxonomy. J Microbiol Methods, 1996, 26:247-259
99. Hilla G T, Mitkowskia N A, Aldrich-Wolfeb L, et al. Methods for assessing the composition and diversity of soil microbial communities. Applied Soil Ecology, 2000, 15: 25- 36
100. Hinton D M, Bacon C W. Enterobacter cloacae is an endophytic symbiont of corn. Mycopathologia, 1995, 129:117-125
101. Holben W E, Feris K. P, Kettunen A, Apajaiahti H A. GC fractionation enhances microbial community diversity assessment and detection of minority populations of bacteria by denaturing gradient gel electrophoresis. Appl Environ Microbiol, 2004, 70: 2263-2270
102. Hong Y, Pasternak J J, Glick B R. Biological consequences of plasmid transformation of the plant growth-promoting rhizobacterium Pseudomonas putida GR12-2. Can J Microbiol, 1991, 37:796-799
103. Hugenholtz P, Goebet B M and Pace N R. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. Journal of bacteriology, 1998, 180:4765-4774
104. Hugenholtz P, Pace N R. Identifying microbial diversity in the natural environment: a molecular phylogenetic approach. Trend in Biotechnology, 1996, 14(6): 190-197
105. Hurek T, Reinhold-Hurek B, Van Montagu M, et al. Root colonization and systemic spreading of Azoarcus sp. Strain BH72 in grasses. J Bacteriol, 1994, 176:1913-1923
106. Ibekwe A M, Grieve C M. Change in developing plant microbial community structure as affected by contaminated water. FEMS Microbiol Ecology, 2004,48:239-248
107. Idris R, Trifonova R, Puschenreiter M, Wenzel W W, Sessitsch A. Bacterial Communities Associated with Flowering Plants of the Ni Hyperaccumulator Thlaspi goesingense. Appl Envion Microbiol, 2004, 70: 2667-2677
108. Ikenaga M, Muraoka Y, Toyota K, et al. Community structure of the microbiota associated with nodal roots of rice plants along with the growth stages: estimation by PCR-RFLP analysis. Biol Fertil Soils, 2002, 36:397-404
109. Jackson C R, Roden ￡ E. Churchill P F. Denaturing gradient gel electrophoresis can fail to separate 16S rDNA fragment with multiple base differences. Mol Biol Today, 2000,1(2): 49-51
110. Jackson M B, Pasternak J J, Glick B R. Partial purification and characterization of ACC deaminase from the plant growth-promoting rhizobacterium Pseudomonas putida GR12-2. Can J Microbiol. 1994,40:1019-1025
111. Jackson M B. Ethylene in root growth and development. In The Plant Hormone Ethylene , (eds) A K matoo and J C Suttie, CRC Press, Boca Raton, F1. 1991, pp: 159-181
112. Jacob M J, Bugbee W M, Gabrielson D A. Enumeration, location, and characterization of endophytic bacteria within sugar beet roots. Can J Bot, 1985,45:757-766
113. Jaeger C H III, Lindow S E, Miller W, Clark E, Firestone M K. Mapping of sugar and amino acid availability in soil around roots with bacterial sensors of sucrose and trytophan. Appl Environ Microbiol, 1999, 65: 2685-2690
114. Jakobi M, Winkelmann G Maltophilin: a new antifungal compound produced by Stenotrophomonas maltophilia R3089. J Antibiot, 1996,49: 1101-1104
115. Jensen M, Straus N. Effect of PCR conditions on the formation of heteroduplex and single-stranded DNA products in the amplification of bacterial ribosomal DNA spacer regions. PCR Methods Appl, 1993, 3:186-194
116. Kaiser O, Puhler A, Selbitschka W. Phylogenetic Analysis of Microbial diversity in the rhizoplane of Oilseed Rape (Brassica napus cv. Westar) employing cultivation-dependent and cultivation-independent approaches. Microbial Ecology, 2001, 42:136-149
117. Kandeler E, Marschner P. Tscherko D, et al. Microbial community composition and functional diversity in the rhizosphere of maize. Plant and soil, 2002, 238:301-312
118. Kemp P F. Aller J Y. Bacterial diversity in aquatic and other environments: what 16S rDNA libraries and tell us. FEMS Microbiology Ecology, 2004, 47:167-177
119. Keohavong P. Thilly W G. Fidelity of DNA polymerases in DNA amplification. Proc Nail Acad Sci USA, 1989, 86:9253-9257
120. Kirchhof G. Eckert B, Stoffels M. et al. Herbaspirillum frisingense sp. nov., a new nitrogen-fixing bacterial species that occurs in C4-fibre plants. Int J Syst Environ Microbiol, 2001, 51:157-168
121. Kitts C L. Terminal restriction fragment patterns: a tool for comparing microbial communities and assessing community dynamics. Curt Issues Intest Microbiol, 2001.2:17-25
122. Kloepper J W, Schroth M N. Miller T D. Effect of rhizosphere colonization by plant growth promoting rhizobacteria on potato development and yield. Phytopathology, 1980, 70:1078-1082
123. Kloepper J W, Schroth M N. Plant growth promoting rhizobacteria on radishes, in proceedings of the 4th International Cnference on Plant Pathogenic Bacteria, ed. Station de Pathologic Vegetal et phytobacteriologie, 1978, vol. 2, pp. 879-882. Angers France.
124. Klopper J W, Rodriguez-Ubna R, Zehnder G W. Murphy J F. Sikora E, Fernandez C. Plant root-bacterial interactions in biological control of soilborne disease and potential extension to systemic and foliar diseases. Austral lant Pathol, 1999, 28:21-26
125. Klopper J, Tuzum S, Kuc J. Proposed definitions related to induced disease resistance. Biocontrol Science and Technology, 1992, 2:347-349
126. Kobayashi D Y, Reedy R M, Bick JA, et al. Characterization of a chitinase gene from Stenotrophomonas maltophilia strain 34S1 and its involvement in biological control. Appl Environ Microbiol., 2002, 68:1047-1054
127. Koizumi Y, Kojima H, Fukui M. Characterization of depth-related microbial community structure in lake sediment by denaturing gradient gel electrophoresis of amplied 16S rDNA and reversely transcribed 16S rRNA fragments. FEMS Microbiol Ecology, 2003, 46:147-157
128. Kowa; chuk G A, Stephen J R, Boer W De, Prosser J I, Embley T M and Woldendorp J W. Analysis of ammonia-oxidizing bacteria of the eta subdivision of the clad Proteobacteria in coastal sand dunes by denaturing gradient gel eletrophoresis sequencing of PCR-amplified 16S ribosomal DNA fragments. Appl Environ microbilol, 1997, 63:1489-1497
129. Kozdroj J, Elsas J D. Application of polymerase chain recreation-denaturing gradient gel electrophoresis for comparison of direct and indirect extraction methods of soil DNA used for microbial community fingerprinting. Biology and Fertility of Soil, 2000, 31:372-378
130. Kuklinsky-sobral J, Araujo W L, Mendes R, et al. Isolation and characterization of endophytic bacteria from soybean (Glycine max) grown in soil treated with glyphosate herbicide. Plant and Soil, 2005, 273:91-99
131. Lagace L, Pitre M, Jacques M, Roy D. Identification of the bacterial community of Maple sap by using amplified ribosomal DNA (rDNA) restriction analysis and rDNA sequencing. Appl Environ Microbiol, 2004, 70:2052-2060
132. Lambert B, Frederik L, van Rooyen L, et al. Rhizobacteria of maize and their antifungal activities. Appl Environ Microbiol, 1987, 53:1866-1871
133. Lazarovits G, Nowak J. Rhizobacteria for improvement of plant growth and establishment. Hortscience, 1997, 32:188-192
134. Lee T J, Kawaharasaki M. Matsumura M, et al. Microbial community structures of activated sludges dominated with polyphosphate-accumulating bacteria and glycogen-accumulating bacteria. Environmental Technology, 2002,23: 747- 755
135. Leifert C, Morris C E, Waites W M. Ecology of microbial saprophytes and pathogens in tissue culture and fiels grown plant: reasons for contamination problems in vitro. Crit Rev Plant Sci, 1994, 13:139-183
136. Lerman L S, Fischer S G, Silverstein H K, Lumelsky N. Sequence-detemined DNA separations. Annu Rev Biophys Bioeng, 1984, 13:399-423
137. Liu J, Leff L G Temporal changes in the bacterioplankton of a Northeast Ohio (USA) River. Hydrobiologia, 2002, 489: 151-159
138. Liu W T, Marsh T L, Cheng H, Forney L J. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol, 1997, 63:4516-4522.
139. Lodewyck C, Vangronsveld J, Porteous F, Moore E R B, Taghavi S, Mezgeay M, van der Lelie D. Endophytic bacteria and their potential application. Crit Rev Plant Sci, 2002, 86(6):583-606
140. Loper J E, Henkels M D. Utilization of heterologous siderophores enhances level of iron available to Pseudomonas putida in the rhizosphere. Appl Environ Microbiol, 1999, 65:5357-5363
141. Lu Y, Conrad R. In situ stable isotope probing of Methanogenic archaea in the rice rhizosphere. Science, 2005, 309:1088-1090
142. Lucy M, Reed E, Glick B R. Application of free living plant growth-promoting rhizobacteria. Antonic van Leeuwenhoke, 2004,86 : 1-25
143. Lueders T, Friedrich M W. Evaluation of PCR amplification bias by terminal restriction fragment length polymorphism analysis of small-subunit rRNA and mcrA genes by using defined template mixtures of methanogenic pure cultures and soil DNA extracts. Appl Environ Microbiol, 2003, 69:320-326
144. Luo H F, Qi H Y, Zhang H X. Assessment of the bacterial diversity in fenvalerate-treated soil. World Journal of Microbiology & biotechnology, 2004, 20: 509-515
145. Lynch J M. Introduction: Some consequences of microbial rhizosphere competence for plant and soil. In: Lynch J M (ed) The Rhizosphere. John Wiley-SonsLtd , ChichesterUK, 1990, pp. 1-10
146. Maarit-Niemi R, Heiskanen L, Wallenius K, Lindstrom K. Extraction and purification of DNA in rhizosphere soil samples for PCR-DGGE analysis of bacterial consortia J Microbiol Methods, 2001,45: 155-165
147. Macrae A, Rimmer D L, O'Donnell A G Novel bacterial diversity recovered from the rhizosphere of oilseed rape (Brassica napus) determined by the analysis of 16S ribosomal DNA. Antonie van Leeuwenhoek, 2000, 78: 13-21
148. Marilley L, Aragno M. Phylogenetic diversity of bacterial communities differing in degree of p(?)oximity of Lolium perenne and Trifolium repens root. Appl Soil Ecol, 1999, 13:127-136
149. Marilley L, Vogt G, Blanc M, et al. Bacterial diversity in the bulk soil and rhizosphere fractions of Lolium perenne and Trifolium repens as revealed by PCR estriction analysis of 16S rDNA. Plant and Soil, 1998, 198:219-224
150. Marilly B L, Aragno M. Phylogenetic diversity of bacterial communities differing in degree of proximity of Lolium perernne and Trifolium repens roots. Appl Soil Ecol, 1999, 13:127-136
151. Marschner P, Baumann K. Changes in bacterial community induced by mycorrhizal colonization in split-root maize. Plant and soil, 2003,251:279-289
152. Marschner P, Neumann G, Kania A, et al. Spatial and temporal dynamics of the microbial community structure in the rhizosphere of cluster roots of white lupin (Lupin albus L.).Plant and Soil, 2002, 246:167-174
153. Marschner P, Yang C-H, Leiberei R, el al. Soil and plant specific effects on bacterial community composition in the rhizosphere. Soil Biol Biochem, 2001, 33:1437-1445
154. Martin-Laurent F, Philippot L, Hallet S, et al. DNA extraction from soil: old bias for new microbial diversity analysis method. Appl Environ Microbiol. 2001. 67: 2354-2359
155. Massol-Deya A A. Odelsonn D A, Hickey R F, Tiedje J M. Bacterial community fingerprinting of amplified 16S and 16-23S ribosomal DNA gene sequence and restriction endonuclease analysis (ARDRA), In Molecular Microbial Ecology Manual(eds) ADL Akkermans. JD van Elsas, FJ de Bruijn, 1995. pp. 2:1-8.
156. Mazzola M, Stahlman P W, Leach J E. Application method affects the distribution and efficacy of rhizobacteria suppressive of downy brome (Bromus tectorum). Soil Biol. Biochem, 1995, 27:1271-2178
157. McCaig A E, Glover L A, Prosser J I. Molecular analysis of bacterial community structure and diversity in unimproved and improved upland grass pastures. Appl Environ Microbiol, 1999, 65.1721-1730
158. McInroy J A, Kloepper J W. Survey of indigenous bacterial endophytes from cotton and sweet corn. Plant Soil, 1995, 173:337-342
159. McNamara C J, Lemke M J, Leff L G Culturable and non-culturable fractions of bacterial populations in sediments of a South Carolina stream. Hydrobiologia. 2002, 482: 151-159
160. Mchnaz S, Mirza M S, Haurat J, Bally R, et al. Isolation and 16S rRNA sequence analysis of the beneficial from the rhizosphere of rice. Can J Microbiol, 2001,47:110-117
161. Miethling R, Wieland G, Backhaus H, et al. Variation of microbial rhizosphere communities in response to crop species , soil origin, and inoculation with Sinorhizobium meliloti L33. Microbial Ecology. 2000. 41:43-56
162. Minamisawa K, Nishioka K, Miyaki T, et al. Anaerobic nitrogen-fixing consortia consisting of clostridia isolated from gramineous plants. Appl Environ Microbiol, 2004, 70:3096-3102.
163. Miyamoto T, Kawahara M, Minamisawa K. Novel Endophytic Nitrogen-Fixing Clostridia from the Grass Miscanthus sinensis as Revealed by Terminal Restriction Fragment Length Polymorphism Analysis. Appl Environ Microbiol, 2004, 70:6580-6586
164. Mocali S, Bertelli E, Cello F D, et al. Fluctuation of bacteria isolated from elm tissues during different seasons and from different plant organs. Res Microbiol, 2003,154:105-114
165. Moeseneder M, Arrieta J M, Muyzer G, Winter C, Herndl G J. Optimization of terminal-restriction fragment length polymorphism analysis for complex marine bacterioplankton communities and comparison with denaturing gradient gel clectrophoresis. Appl Environ Microbiol, 1999,65:3518-3525
166. Mueller J G, Devereux R, Santavy D L, Lantz S E, Willis S G, Pritchard P H. Phylogenetic and physiological compartment of PAH-degrading bacteria from geographically diverse soils. Antonie Leeuwenhoek, 1997, 71:329-343.
167. Mundt J O, Hinkle N F. Bacteria within ovules and seeds. Appl Environ Microbiol, 1976,32:694-698
168. Muyzer G, Smalla K. Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophorcsis (TGGE) in microbial ecology. Antonie Van Leeuwenhoke, 1998, 73:127-141
169. Muyzer G, de Waal E C, Uitterlinden AG Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol, 1993, 59: 687-694
170. Myres R M, Fischer S G, Lerman L S, Maniatis T. Nearly all single base substitutions in DNA fragments joined to a GC-clamp can be detected by denaturing gradient gel electrophoresis. Nucleic Acids Res, 1985,13: 3131-3145
171. Niemi R M, Heiskanen I, Wallenius K, et al. Extraction and purification of DNA in rhizosphere soil samples for PCR-DGGE analysis of bacterial consortia. J Microbiol Methods, 2001,45:155-165
172. Normander B, Prosser J I. Bacterial origin and community composition in the barely phytosphere as a function of habitat and presowing conditions. Appl Environ Microbiol, 2000,66:4372-4377
173. Nowak J, Shulaev V. Priming for transplant stress resistance in in vitro propagation. In Vitro cell Dev Biol-Plant, 2003, 39:107-124
174. Ongcna M, Daayf F, Jacques P, et al. Protection of cucumber against Pythium root rot by fluorescent pseudomonads: predominant role of induced resistance over siderophores and antibiosis. Plant Pathology. 1999. 48: 66-76
175. Ordentlich A, Elad Y, Chet I. The role of chitinase of Serratia marcescens in biocontrol of Sclerotium rolfsii. Phytopathology, 1988, 78:84-88
176. (?)veras L, Forney L, Daae F L, et al. Distribution of bacterioplankton in menomictic lake Saelenvannet, As determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl Environ Microbiol. 1997, 63:3367-3373
177. (?)veras L, Torsvik V. Microbial diversity and community structure in two different agriculture soil communities. Microbio Ecol, 1998,36.303-315
178. Picard C, Di Cello F, Ventura M, Fani R, Guckert A. Frequency and biodiversity of 2, 4-diacethyphoroglucinol-producing bacteria isolated from the maize rhizosphere at different stages of plant growth. Appl Environ Microbiol, 2000,66: 948-955
179. Picard C, Ponsonnet C, Pager E, Nesme X, Simonet P. Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction. Appl Environ Microbiol, 1992. 58:2712-2722
180. Piceno Y M, Lovell C R. Stability in natural bacterial communities: Ⅱ.plant resource allocation effect on rhizosphere diazotroph assemblage composition. Microbial Ecology, 2000, 39 : 41-48
181. Piceno Y M, Lovell C R. Stability in natural bacterial vommunities Ⅰ .nutrient addition effect on rhizosphere diazotroph assemblage composition. Microbial Ecology. 2000,39:32-40
182. Qiu X, Wu L, Huang H, McDonel P E, Palumbo A V, Tiedje J M, Zhou J. Evaluation of PCR-generated chimeras , mutations , and heteroduplexes with 16S rRNA gene-bsed cloning. Appl Environ Microbiol. 2001, 67:880-887
183. Ramamoorthy V, Viswanathan R, Raguchander T, Prakasam V, Smajyappan R. Induction of systemic resistance by plant growth-promoting rhizobacteria in crop plants against pest and diseases. Crop Prot, 2001, 20:1 -11
184. Rangarajan S, Saleena L M, Nair S. Diversity of Pseudomonas spp. isolated rice rhizosphere population grown along a salinity gradient. Microbial Ecology, 2002,3:280-289
185. Reinhold-Hurek B, Hurek T. Life in grasses diazotrophic endophytes, Trend Microbiol, 1998,6:139-144
186. Reiter B, Pfeifer U, Schwab H, et al. Response of endophytic bacterial communities in potato plant to infection with Erwinia carotovora subsp. Atroseptica. Appl Environ Microbiol, 2002, 68:2261-2268
187. Reiter B, Wermbter N, Gyamfi S, et al. Endophytic Pseudomonas spp. Populations of pathogen-infected potato plants analysed by 16S rDNA-and 16S rRNA-based denaturating gradient gel electrophoresis. Plant and Soil, 2003, 257:397-405
188. Reysenbach A L, Giver L J, Wickham G S, Pace N R. Differential amplification of rPNA genes by poiymerase chain reaction. Appl Environ Microbiol, 1992,58:3417-3418
189. Robleto E A, Borneman J, Triplett E W. Effect of bacterial antibiotic production on rhizosphere microbial communities from a culture-independent perspective. Appl Environ Microbiol, 1998,64:5020-5022
190. Romanenko L A, Uchino M, Falsen E, Zhukova N V, Mikhailov V V, Uchimura T. Rheinheimera pacifica ap. nov. , a novel halotolerant bacterium isolated from deep sea water of the Pacific. Int J Syst Evol Microbiol, 2003, 53:1973-1977
191. Roslev P, Iversen N, Henrik sen K. Direct fingerp rinting of metabo lically active bacteria in environmental samples by substrate specific radio labelling and lipid analysis. J Microbiol Methods, 1998, 31:99-111.
192. Ruben A, Katsuji T, Tatsuya T. Bacterial activity and community composition in stream water and biofilm from an urban river determined by fluorescent in situ hybridization and DGGE analysis. FEMS Microbiol Ecology, 2003,43: 111-119
193. Sandaa R A, Enger A, Torsvik V. A bundance and diversity of archaea in heavy metal contaminated soils. Appl Environ Microbiol. 1999. 65:3293- 3297
194. Sanguinetti C J. Nego E D. Simpson A J G Rapid silver staining and recovery of PCR products separated on polyacrylamide gels. BioTechniques, 1994, 17(5): 914-921
195. Santegoeds C M. Nolf S C. Ward D M Denaturing gradient gel eletrophoresis used to monitor the enrichment culture of aerobic chemoorganotrophic bacteria from a hot spring cyanobacterial mat. Appl Environ Microbiol, 1996, 62:3922-3928
196. Schafer H, Bernard L, Courties C, et al. Microbial dynamics in mediterranean nutrient enriched seawater mesocosms: changes in the genetic diversity of bacterial populations. FEMS Microbiol Ecology, 2001, 33 : 243- 253
197. Scheid D, Stubner S, Conrad R. Identification of rice root associated nitrate , sulfate and ferriciron reducing bacteria during root decomposition. FEMS Microbiol Ecology, 2004, 50:101-110
198. Seghers D, Wittebolle L, Top E M, et al. Impact of Agricultural practices on the Zea mays L. endophytic community. Appl Environ Microbiol, 2004. 70: 1475-1482
199. Sekiguchi H, Tomioka N, Nakahara T. Uchiyama H. A single band dose not always represent single bacterial strains in denaturing gradient gel electrophoresis analysis. Biotechnology Letters. 2001, 23:1205-1208
200. Sessitsch A, Gyamfi S. Dagmar Tscherko D, Martin H. Gerzabek M H, Kandeler E. Activity of microorganisms in the rhizosphere of herbicide treated and untreated transgenic glufosinate-tolerant and wildtype oilseed rape grown in containment. Plant and Soil, 2004, 266: 105-116
201. Sessitsch A, Reiter B, Berg G Endophytic bacterial communities of field-grown potato plants and their plant-growth-promoiing and antagonistic abilities. Can J Microbiol, 2004, 50:239-249
202. Sessitsch A, Reiter B, Pfeifer U, et al. Cultivation-independent population analysis of bacterial endophytes in three potato varieties based on eubacterial and Actinomycetes-specific PCR of 16S rDNA genes. FEMS Microbiol Ecology, 2002, 39:23-32
203. Shah S, Li J, Moffatt B A and Glick B R. Isolation and characterization of ACC deaminase genes from two different plant growth promoting rhizobacteria. Can J Microbiol, 1998,44:833-843
204. Simposn J M, McCracken V J, White B A, Gaskins H R, Mackie R I. Application of denaturant gradient gel electrophoresis for the analysis of the porcine gastrointestinal microbiota. J Microbiol Methods, 1999,36: 167-179
205. Singh P P, Shin Y C, Park C S, Chung Y R. Biological control of Fusarium wilt of cucumber by chitinolytic bcteria. Phytopathology, 1999, 89:92-99
206. Smalla K, Wachtendorf U, Liu W-T, Forney L. Analysis of BIOLOG GN substrate utilization patterns by microbial communities. Appl Environ Microbiol, 1998,64:1220-1225
207. Smalla K, Wieland G, Buchner A, et al. Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed. Appl Environ Microbiol, 2001,67:4742-4751
208. Smith K P, Handelsman J, Goodman R M. Genetic basis in plants for interactions with disease-suppressive bacteria. Proc Natl Acad Sci USA, 1999,96:4786-4790
209. Soderberg KH, Probanza A, Jumpponen A, E. Baath E. The microbial community in the rhizosphere determined by community-level physiological profiles (CLPP) and direct soil- and cfu-PLFA techniques. Applied Soil Ecology, 2004, 25: 135-145
210. Stackebrandt E, Liesack W, Geobel B M. Bacteial diversity in a soil sample from a subtropical Australian environment as determined by 16S rDNA analysis. FASEB J, 1993, 7: 232-236
211. Steer J, Harris A. Shifts in the microbial community in rhizosphere and non-rhizosphere soils during the growth of Agrostis stolonifera. Soil Biology & Biochemistry, 2000,32: 869-878
212. Stoltzfus J R, So R, Malarvithi P P, Ladha J K, de Bruijn F J. Isolation of endophytic bacteria from rice and assessment of their potential for supplying rice with biologically fixed nitrogen. Plant and Soil, 1997,194: 25-36
213. Sturz A V. The role of endophytic bacteria during seed piece decay and tomato tuberization. Plant Soil, 1995,175:257-263
214. Sturz A V, Christie B R, Matheson B G Association of bacterial endophyte populations from red clover and potato crops with potential for beneficial allelopanthy. Can J microbial, 1998, 44:162-167
215. Sturz A V, Christie B R, Matheson B G, Nowak J, et al. Biodiversity of endophytic bacteria which colonize red clover nodules , roots , stems and foliages and their influence on host growth. Biol Fertil Soil, 1997, 25:13-19
216. Sturz A V, Christie B R, Matheson B G, et al. Endophytic bacterial communities in the periderm of potato tubes and their potential to improve resistance to soil-born plant pathogens. Plant Pathol, 1999,48:360-369
217. Sturz A V, Christie B R, Nowak J. Bacterial endophytes: potential role in developing sustainable systems of crop production. Crit Rev Plant Sci, 2000, 19:1-30
218. Surettel M A, Sturz A V, Lada R R, et al. Bacterial endophytes in processing carrots (Daucus carota L. var. sativus): their localization, population density, biodiversity and their effects on plant growth. Plant and Soil, 2003, 253:381-390
219. Suzuki M T, Giovannoni S J. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol, 1996,62:625-630
220. Tabacchioni S, Bevivno A, Chiarini L, et al. Characteristics of two rhizosphere isolates of Pseudomonas cepacia and their potential plant-promoting activity. Microb Release, 1993,2:161-168
221. Tholozan J L, CAppelier J M, Tissier J P, Delattre G. Federighi M. Physiological characterization of viable-but-nonculturable Campylobacter jejuni cell. Appl.Environ Microbiol, 1999,65.1110-1116
222. Timms-Wilson T M, Kilshaw K, Bailey M J. Risk assessment for engineered bacteria used in biocontrol of fungal disease in agricultural crops. Plant and Soil, 2004,266: 57-67
223. Tran Van V, Berge O, S. Ngo Ke, Balandreau J, Heulin T. Repeated beneficial effects of rice inoculation with a strain of Burkholderia vietnamiensis on early and late yield component in low fertility sulphate acid soils of Vietnam. Plant and Soil, 2000, 218:273-284.
224. Triplerr E W. Dizaotrophic endophytes: progress and prospects for nitrogen fixation in monocots. Plant and Soil, 1996, 186:29-38
225. Tsuda K, Kosaka Y Tsuge S, et al. Evaluation of the Endophyte Enterobacter cloacae SM10 Isolated from Spinach Roots for Biological Control against Fusarium Wilt of Spinach. J Gen Plant Pathol, 2001,67:78-84
226. Ueda T, Suga Y, Yahiro N, et al. Remberkable N2-Fix bacterial diverdity detected in rice roots by molecular evolutionary analysis of nifH gene sequence. Journal of Bacteriology, 1995,177(5): 1414-1417
227. Vallaeys T, Topp E, Muyzer G, et al. Evaluation of denaturing gradient gel electrophoresis in the detection of 16S rDNA sequence variation in rhizobia and methanotrophs. FEMS Microbiol. Ecology, 1997, 24: 279- 285
228. Van Loon L C, Bakker PHAM, Pieterse C M J. Systemic resistance induced by rhizosphere bacteria. Annu Rev Phytopathol, 1998,36:453-483
229. Vaneechoutte M, Riegel P, de Briel D, Monteik H, Verschraegen G, De Rouck A, Claeys G Evaluation of the applicability of amplified rDNA-restriction anslysis (ARDRA) to identification of species of the genus Corynebacterium. Res Microbiol, 1995,146:633-641
230. Vetriani C, Jannasch H W, MacGregor B, et al. Population structure and phylo-genetic characterization of marine benthic archaea in deep-sea sediments. Appl Environ Microbiol, 1999,65:4375-4383
231. Von Bulow J F W, Dobereiner J. Potential for nitrogen-fixation in maize genotypes in Brazil. Proc. Natl. Acad. Sci. USA, 1975,72:2389-2393
232. Ward G C, Santegoeds C M, Nold S C, Ramsing N B, Ferris M J, Bateson M M. Biodiversity within hot spring microbial mat communities: molecular monitoring of enrichment cultures. Antonie Van Leeuwenhoek, 1997, 71: 143-150
233. Watanabe K, Teramoto M, Futmata H, Harayama S. Molecular detection isolation, and physiological characterization of functionally dominant phenol-degrading bacteria in activated sludge. Appl Environ Microbiol. 1998. 64:4396-4402
234. Weisskopf L, Fromin N. Tomasi N, Aragno M, Martinoia E. Secretion activity of white lupin's cluster roots influences bacterial abundance, function and community structure, Plant and Soil. 2005, 268:181-194
235. Whipps J M Microbial interaction and biocontrol in the rhizosphere. J Exp Bot, 2001,52:487-511
236. Wieland G, Neumann R, Horst Backhaus. Variation of microbial communities in soil. rhizosphere, and crop development. Appl Ehviron Microbiol, 2001.67:5849-5854
237. Wilkinson S C, Anderson J M. Spatial patterns of soil microbial communities in a Norway. Microbial Ecology, 2001, 42:248-255
238. Wilson M J, Weightman A J, Wade W G. Applications of molecular ecology in the characterization of uncultured microorganisms associated with human disease. Rev Med Microbiol, 1997, 8:91-101
239. Yang C H, Crowley D E, Borneman J, Keen N T. Microbial phylloshere populations are more comlex than previously realized. Proc Natl Acad Sci USA, 2001, 98:3889-3894
240. Yang C H, Crowley D E. Rhizosphere microbioal community structure in relation to root location and plant iron nutritional status. Appl Environ Microbiol. 2000, 66:345-351
241. Yanni YG. Rizk RY, Corich V, Squartini A, et al. Natural endophytic association between Rhizobium leguminosarum by. trifolii and rice and assessment of its potential to promote rice growth. Plant and Soil, 1997, 194:99-114
242. Zinniel D K, Pat Lambrecht P, Beth Harris N, et al. Isolation and characterization of endophytic colonizing bacteria from agronomic crops and prairie plants. Appl Environ Microbiol, 2002, 68:2198-2208
243. Zou W X, Tan R X. Biological and chemical diversity of endophytes and their potential application. In: Advances in Plant Sciences. Vol. 2, Li G S (eds). China Higher Education press, Beijing, 1999, pp. 183-190
244．东秀珠，蔡妙英等．常见细菌系统鉴定手册．北京：科学出版社，1999
245．高平平，晁群芳，张学礼，王凌华，赵立平．TGGE分析焦化废水处理系统活性污泥细菌种群动态变化及多样性．生态学报，2003，23(10)：1963-1969
246．韩继刚，宋未．植物内生细菌研究进展及其应用潜力．自然科学进展，2004，14(4)：374-379
247．韩继刚．一株新的水稻植物内生固氮细菌Delftia tsuruhatensis HR4的坚定及其生物学特性．博士学位论文，首都师范大学，2004
248．胡楷，吴庆书．单细胞生物进化研究的进步．遗传，2002．24：104-110
249．雷娟利，周艳虹，丁桔，王礼，俞景权．不同蔬菜连作对土壤细菌DNA分子水平多态性影响的研究，中国农业科学，2005，38(10)：2076-2083
250．萨姆布鲁克 J．费里奇 E F，曼尼阿蒂斯 T，分子克隆实验指南(第二版)．北京：科学出版社，1999
251．沈德龙．水稻内生成团肠杆菌的分类鉴定及其生物学特性的研究。博士学位论文，中国农科院原子能所，1999
252．宋铁英．包晓东，郑伟文，Ulla R.DGGE法监测稻田蓝细菌及硅藻的遗传多样性，厦门大学学报(自然科学版)，2002，41：670-673
253．孙晓璐．水稻根面植物促生细菌的研究，硕士学位论文，中国农业科学院原子能利用研究所，1997
254．谢中稳，葛颂，洪德元．从普通野生稻硅胶干燥的小量叶片中制备DNA用于RAPD分析和总DNA库的建立(英文)．植物学报，1999，41(8)：802-807
255．杨海莲．水稻植株内生细菌的研究．博士学位论文，中国农业科学院原子能利用研究所，1997