메뉴 건너뛰기




Volumn 75, Issue 1, 2008, Pages 12-18

A novel method for sampling bacteria on plant root and soil surfaces at the microhabitat scale

Author keywords

Micro sampling; Microhabitat; Rhizosphere bacteria; Soil bacteria

Indexed keywords

TUNGSTEN;

EID: 48749124898     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mimet.2008.04.013     Document Type: Article
Times cited : (21)

References (40)
  • 1
    • 0029890507 scopus 로고    scopus 로고
    • In situ visualization of high genetic diversity in a natural microbial community
    • Amann R., Snaidr J., Wagner M., Ludwig W., and Schleifer K.H. In situ visualization of high genetic diversity in a natural microbial community. J. Bacteriol. 178 (1996) 3496-3500
    • (1996) J. Bacteriol. , vol.178 , pp. 3496-3500
    • Amann, R.1    Snaidr, J.2    Wagner, M.3    Ludwig, W.4    Schleifer, K.H.5
  • 2
    • 0034808993 scopus 로고    scopus 로고
    • Survival of Listeria monocytogenes attached to stainless steel surfaces in the presence or absence of Flavobacterium spp
    • Bremer P.J., Monk I., and Osborne C.M. Survival of Listeria monocytogenes attached to stainless steel surfaces in the presence or absence of Flavobacterium spp. J. Food Prot. 64 (2001) 1369-1376
    • (2001) J. Food Prot. , vol.64 , pp. 1369-1376
    • Bremer, P.J.1    Monk, I.2    Osborne, C.M.3
  • 3
    • 0032834486 scopus 로고    scopus 로고
    • Elimination of bacterial DNA from Taq DNA polymerases by restriction endonuclease digestion
    • Carroll N.M., Adamson P.O., and Khravi N. Elimination of bacterial DNA from Taq DNA polymerases by restriction endonuclease digestion. J. Clin. Microbiol. 37 (1999) 3402-3404
    • (1999) J. Clin. Microbiol. , vol.37 , pp. 3402-3404
    • Carroll, N.M.1    Adamson, P.O.2    Khravi, N.3
  • 4
    • 0031028808 scopus 로고    scopus 로고
    • Description of the colonization of a gnotobiotic tomato rhizosphere by Pseudomonas fluorescens biocontrol strain WCS365, using scanning electron microscopy
    • Chin-A-Woeng T.F.C., de Priester W., van der Bij A.J., and Lugtenberg B.J.J. Description of the colonization of a gnotobiotic tomato rhizosphere by Pseudomonas fluorescens biocontrol strain WCS365, using scanning electron microscopy. Mol. Plant-Microb. Interact. 10 (1997) 79-86
    • (1997) Mol. Plant-Microb. Interact. , vol.10 , pp. 79-86
    • Chin-A-Woeng, T.F.C.1    de Priester, W.2    van der Bij, A.J.3    Lugtenberg, B.J.J.4
  • 6
    • 7544236217 scopus 로고    scopus 로고
    • Interpolating, extrapolating, and comparing incidence-based species accumulation curves
    • Colwell R.K., Mao C.X., and Chang J. Interpolating, extrapolating, and comparing incidence-based species accumulation curves. Ecology 85 (2004) 2717-2727
    • (2004) Ecology , vol.85 , pp. 2717-2727
    • Colwell, R.K.1    Mao, C.X.2    Chang, J.3
  • 8
    • 13544277388 scopus 로고    scopus 로고
    • Effects of growth medium, inoculum size, and incubation time on culturability and isolation of soil bacteria
    • Davis K.E.R., Joseph S.J., and Janssen P.H. Effects of growth medium, inoculum size, and incubation time on culturability and isolation of soil bacteria. Appl. Environ. Microb. 71 (2005) 826-834
    • (2005) Appl. Environ. Microb. , vol.71 , pp. 826-834
    • Davis, K.E.R.1    Joseph, S.J.2    Janssen, P.H.3
  • 9
    • 0032891962 scopus 로고    scopus 로고
    • The number of bacteria in the rhizosphere during plant development: relating colony-forming units to different reference units
    • Duineveld B.M., and van Veen J.A. The number of bacteria in the rhizosphere during plant development: relating colony-forming units to different reference units. Biol. Fertil. Soils 28 (1999) 285-291
    • (1999) Biol. Fertil. Soils , vol.28 , pp. 285-291
    • Duineveld, B.M.1    van Veen, J.A.2
  • 10
    • 1642328667 scopus 로고    scopus 로고
    • Colonization pattern of primary tomato roots by Pseudomonas fluorescens A6ri characterized by dilution plating, flow cytometry, fluorescence, confocal and scanning electron microscopy
    • Gamalero E., Lingua G., Giusy Capri F., Fusconi A., Berta G., and Lemanceau P. Colonization pattern of primary tomato roots by Pseudomonas fluorescens A6ri characterized by dilution plating, flow cytometry, fluorescence, confocal and scanning electron microscopy. FEMS Microbiol. Ecol. 48 (2004) 79-87
    • (2004) FEMS Microbiol. Ecol. , vol.48 , pp. 79-87
    • Gamalero, E.1    Lingua, G.2    Giusy Capri, F.3    Fusconi, A.4    Berta, G.5    Lemanceau, P.6
  • 11
    • 0030745504 scopus 로고    scopus 로고
    • Repetitive element PCR fingerprinting (rep-PCR) using enterobacterial repetitive intergenic consensus (ERIC) primers is not necessarily directed at ERIC elements
    • Gillings M., and Holley M. Repetitive element PCR fingerprinting (rep-PCR) using enterobacterial repetitive intergenic consensus (ERIC) primers is not necessarily directed at ERIC elements. Lett. Appl. Microbiol. 25 (1997) 17-21
    • (1997) Lett. Appl. Microbiol. , vol.25 , pp. 17-21
    • Gillings, M.1    Holley, M.2
  • 12
    • 0033780249 scopus 로고    scopus 로고
    • -oxidizing bacteria and serotypes at the millimeter scale along a soil transect
    • -oxidizing bacteria and serotypes at the millimeter scale along a soil transect. FEMS Microbiol. Ecol. 34 (2000) 57-62
    • (2000) FEMS Microbiol. Ecol. , vol.34 , pp. 57-62
    • Grundmann, G.L.1    Debouzie, D.2
  • 13
    • 0033779659 scopus 로고    scopus 로고
    • Microscale diversity of the genus nitrobacter in soil on the basis of analysis of genes encoding rRNA
    • Grundmann G.L., and Normand P. Microscale diversity of the genus nitrobacter in soil on the basis of analysis of genes encoding rRNA. Appl. Environ. Microb. 66 (2000) 4543-4546
    • (2000) Appl. Environ. Microb. , vol.66 , pp. 4543-4546
    • Grundmann, G.L.1    Normand, P.2
  • 14
    • 33646575278 scopus 로고    scopus 로고
    • Quantitative microbial risk assessment models for consumption of raw vegetables irrigated with reclaimed water
    • Hamilton A.J., Stagnitti F., Premier R., Boland A.M., and Hale G. Quantitative microbial risk assessment models for consumption of raw vegetables irrigated with reclaimed water. Appl. Environ. Microb. 72 (2006) 3284-3290
    • (2006) Appl. Environ. Microb. , vol.72 , pp. 3284-3290
    • Hamilton, A.J.1    Stagnitti, F.2    Premier, R.3    Boland, A.M.4    Hale, G.5
  • 15
    • 0025761156 scopus 로고
    • ERIC sequences - a novel family of repetitive elements in the genomes of Escherichia coli, Salmonella typhimurium and other enterobacteria
    • Hulton C.S.J., Higgins C.F., and Sharp P.M. ERIC sequences - a novel family of repetitive elements in the genomes of Escherichia coli, Salmonella typhimurium and other enterobacteria. Mol. Microbiol. 5 (1991) 825-834
    • (1991) Mol. Microbiol. , vol.5 , pp. 825-834
    • Hulton, C.S.J.1    Higgins, C.F.2    Sharp, P.M.3
  • 16
    • 0027570115 scopus 로고
    • Alkali treatment for rapid preparation of plant-material for reliable PCR analysis
    • Klimyuk V.I., Carroll B.J., Thomas C.M., and Jones J.D.G. Alkali treatment for rapid preparation of plant-material for reliable PCR analysis. Plant J. 3 (1993) 493-494
    • (1993) Plant J. , vol.3 , pp. 493-494
    • Klimyuk, V.I.1    Carroll, B.J.2    Thomas, C.M.3    Jones, J.D.G.4
  • 17
    • 33947371287 scopus 로고    scopus 로고
    • Improved fluorescent in situ hybridization method for detection of bacteria from activated sludge and river water by using DNA molecular beacons and flow cytometry
    • Lenaerts J., Lappin-Scott H.M., and Porter J. Improved fluorescent in situ hybridization method for detection of bacteria from activated sludge and river water by using DNA molecular beacons and flow cytometry. Appl. Environ. Microb. 73 (2007) 2020-2023
    • (2007) Appl. Environ. Microb. , vol.73 , pp. 2020-2023
    • Lenaerts, J.1    Lappin-Scott, H.M.2    Porter, J.3
  • 18
    • 0026287027 scopus 로고
    • Changes in bacterial populations along roots of wheat (Triticum aestivum L) seedlings
    • Liljeroth E., Burgers S., and van Veen J.A. Changes in bacterial populations along roots of wheat (Triticum aestivum L) seedlings. Biol. Fertil. Soils 10 (1991) 276-280
    • (1991) Biol. Fertil. Soils , vol.10 , pp. 276-280
    • Liljeroth, E.1    Burgers, S.2    van Veen, J.A.3
  • 19
    • 0028355774 scopus 로고
    • Characterization of contaminating DNA in Taq polymerase which occurs during amplification with a primer set for legionella 5S ribosomal-RNA
    • Maiwald M., Ditton H.J., Sonntag H.G., and Vonknebeldoeberitz M. Characterization of contaminating DNA in Taq polymerase which occurs during amplification with a primer set for legionella 5S ribosomal-RNA. Mol. Cell. Probes 8 (1994) 11-14
    • (1994) Mol. Cell. Probes , vol.8 , pp. 11-14
    • Maiwald, M.1    Ditton, H.J.2    Sonntag, H.G.3    Vonknebeldoeberitz, M.4
  • 20
    • 0032835208 scopus 로고    scopus 로고
    • Phylogenetic diversity of bacterial communities differing in degree of proximity of Lolium perenne and Trifolium repens roots
    • Marilley L., and Aragno M. Phylogenetic diversity of bacterial communities differing in degree of proximity of Lolium perenne and Trifolium repens roots. Appl. Soil Ecol. 13 (1999) 127-136
    • (1999) Appl. Soil Ecol. , vol.13 , pp. 127-136
    • Marilley, L.1    Aragno, M.2
  • 21
    • 0031956351 scopus 로고    scopus 로고
    • Bacterial diversity in the bulk soil and rhizosphere fractions of Lolium perenne and Trifolium repens as revealed by PCR restriction analysis of 16S rDNA
    • Marilley L., Vogt G., Blanc M., and Aragno M. Bacterial diversity in the bulk soil and rhizosphere fractions of Lolium perenne and Trifolium repens as revealed by PCR restriction analysis of 16S rDNA. Plant Soil 198 (1998) 219-224
    • (1998) Plant Soil , vol.198 , pp. 219-224
    • Marilley, L.1    Vogt, G.2    Blanc, M.3    Aragno, M.4
  • 22
    • 0030186138 scopus 로고    scopus 로고
    • Physiological activity of a bioluminescent Pseudomonas fluorescens (strain 2-79) in the rhizosphere of mycorrhizal and non-mycorrhizal pepper (Capsicum annuum L)
    • Marschner P., and Crowley D.E. Physiological activity of a bioluminescent Pseudomonas fluorescens (strain 2-79) in the rhizosphere of mycorrhizal and non-mycorrhizal pepper (Capsicum annuum L). Soil Biol. Biochem. 28 (1996) 869-876
    • (1996) Soil Biol. Biochem. , vol.28 , pp. 869-876
    • Marschner, P.1    Crowley, D.E.2
  • 23
    • 0036146824 scopus 로고    scopus 로고
    • Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set
    • Nadkarni M.A., Martin F.E., Jacques N.A., and Hunter N. Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set. Microbiology-SGM 148 (2002) 257-266
    • (2002) Microbiology-SGM , vol.148 , pp. 257-266
    • Nadkarni, M.A.1    Martin, F.E.2    Jacques, N.A.3    Hunter, N.4
  • 24
    • 0001352419 scopus 로고
    • Patterns of distribution of bacteria on root surfaces
    • Newman E.I., and Bowen H.J. Patterns of distribution of bacteria on root surfaces. Soil Biol. Biochem. 6 (1974) 205-209
    • (1974) Soil Biol. Biochem. , vol.6 , pp. 205-209
    • Newman, E.I.1    Bowen, H.J.2
  • 25
    • 0034869048 scopus 로고    scopus 로고
    • Quantification of the in situ distribution of soil bacteria by large-scale imaging of thin sections of undisturbed soil
    • Nunan N., Ritz K., Crabb D., Harris K., Wu K.J., Crawford J.W., et al. Quantification of the in situ distribution of soil bacteria by large-scale imaging of thin sections of undisturbed soil. FEMS Microbiol. Ecol. 37 (2001) 67-77
    • (2001) FEMS Microbiol. Ecol. , vol.37 , pp. 67-77
    • Nunan, N.1    Ritz, K.2    Crabb, D.3    Harris, K.4    Wu, K.J.5    Crawford, J.W.6
  • 26
    • 0037447853 scopus 로고    scopus 로고
    • Spatial distribution of bacterial communities and their relationships with the micro-architecture of soil
    • Nunan N., Wu K.J., Young I.M., Crawford J.W., and Ritz K. Spatial distribution of bacterial communities and their relationships with the micro-architecture of soil. FEMS Microbiol. Ecol. 44 (2003) 203-215
    • (2003) FEMS Microbiol. Ecol. , vol.44 , pp. 203-215
    • Nunan, N.1    Wu, K.J.2    Young, I.M.3    Crawford, J.W.4    Ritz, K.5
  • 27
    • 6544262110 scopus 로고
    • Growth of Verticillium dahliae Kleb. hyphae and of bacteria along the roots of rape (Brassica napus L) seedlings
    • Olsson S., Baath E., and Soderstrom B. Growth of Verticillium dahliae Kleb. hyphae and of bacteria along the roots of rape (Brassica napus L) seedlings. Can. J. Microbiol. 33 (1987) 916-919
    • (1987) Can. J. Microbiol. , vol.33 , pp. 916-919
    • Olsson, S.1    Baath, E.2    Soderstrom, B.3
  • 28
    • 0022823630 scopus 로고
    • Soil water flow affects the rhizosphere distribution of a seed borne biological control agent, Pseudomonas fluorescens
    • Parke J.L., Moen R., Rovira A.D., and Bowen G.D. Soil water flow affects the rhizosphere distribution of a seed borne biological control agent, Pseudomonas fluorescens. Soil Biol. Biochem. 18 (1986) 583-588
    • (1986) Soil Biol. Biochem. , vol.18 , pp. 583-588
    • Parke, J.L.1    Moen, R.2    Rovira, A.D.3    Bowen, G.D.4
  • 29
    • 77956889208 scopus 로고
    • Recovery of inter-block information when block sizes are unequal
    • Patterson H.D., and Thompson R. Recovery of inter-block information when block sizes are unequal. Biometrika 58 (1971) 545-554
    • (1971) Biometrika , vol.58 , pp. 545-554
    • Patterson, H.D.1    Thompson, R.2
  • 30
    • 0036159413 scopus 로고    scopus 로고
    • Local measurements of nitrate and potassium fluxes along roots of maritime pine. Effects of ectomycorrhizal symbiosis
    • Plassard C., Guerin-Laguette A., Very A.A., Casarin V., and Thibaud J.B. Local measurements of nitrate and potassium fluxes along roots of maritime pine. Effects of ectomycorrhizal symbiosis. Plant Cell Environ. 25 (2002) 75-84
    • (2002) Plant Cell Environ. , vol.25 , pp. 75-84
    • Plassard, C.1    Guerin-Laguette, A.2    Very, A.A.3    Casarin, V.4    Thibaud, J.B.5
  • 31
    • 0026768316 scopus 로고
    • DNAse-I treatment of Taq DNA-polymerase for complete PCR decontamination
    • Rochelle P.A., Weightman A.J., and Fry J.C. DNAse-I treatment of Taq DNA-polymerase for complete PCR decontamination. Biotechniques 13 (1992) 520
    • (1992) Biotechniques , vol.13 , pp. 520
    • Rochelle, P.A.1    Weightman, A.J.2    Fry, J.C.3
  • 32
    • 0002288590 scopus 로고
    • Quantitative assessment of the rhizoplane microflora by direct microscopy
    • Rovira A.D., Newman E.I., Bowen H.J., and Campbell R. Quantitative assessment of the rhizoplane microflora by direct microscopy. Soil Biol. Biochem. 6 (1974) 211-216
    • (1974) Soil Biol. Biochem. , vol.6 , pp. 211-216
    • Rovira, A.D.1    Newman, E.I.2    Bowen, H.J.3    Campbell, R.4
  • 33
    • 33646271604 scopus 로고    scopus 로고
    • Sensitive, real-time PCR detects low-levels of contamination by Legionella pneumophila in commercial reagents
    • Shen H., Rogej S., and Kieft T.L. Sensitive, real-time PCR detects low-levels of contamination by Legionella pneumophila in commercial reagents. Mol. Cell. Probes 20 (2006) 147-153
    • (2006) Mol. Cell. Probes , vol.20 , pp. 147-153
    • Shen, H.1    Rogej, S.2    Kieft, T.L.3
  • 34
    • 0034884297 scopus 로고    scopus 로고
    • Detection of bacteraemia in critically ill patients using 16S rDNA polymerase chain reaction and DNA sequencing
    • Sleigh J., Cursons R., and La Pine M. Detection of bacteraemia in critically ill patients using 16S rDNA polymerase chain reaction and DNA sequencing. Intensive Care Med. 27 (2001) 1269-1273
    • (2001) Intensive Care Med. , vol.27 , pp. 1269-1273
    • Sleigh, J.1    Cursons, R.2    La Pine, M.3
  • 35
    • 0031568295 scopus 로고    scopus 로고
    • Domain-directed polymerase chain reaction capable of distinguishing bacterial from host DNA at the single-cell level: characterization of a systematic method to investigate putative bacterial infection in idiopathic disease
    • Steinman C.R., Muralidhar B., Nuovo G.J., Rumore P.M., Yu D., and Mukai M. Domain-directed polymerase chain reaction capable of distinguishing bacterial from host DNA at the single-cell level: characterization of a systematic method to investigate putative bacterial infection in idiopathic disease. Anal. Biochem. 244 (1997) 328-339
    • (1997) Anal. Biochem. , vol.244 , pp. 328-339
    • Steinman, C.R.1    Muralidhar, B.2    Nuovo, G.J.3    Rumore, P.M.4    Yu, D.5    Mukai, M.6
  • 37
    • 0026323259 scopus 로고
    • Distribution of repetitive DNA-sequences in Eubacteria and application to fingerprinting of bacterial genomes
    • Versalovic J., Koeuth T., and Lupski J.R. Distribution of repetitive DNA-sequences in Eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res. 19 (1991) 6823-6831
    • (1991) Nucleic Acids Res. , vol.19 , pp. 6823-6831
    • Versalovic, J.1    Koeuth, T.2    Lupski, J.R.3
  • 38
    • 33645457143 scopus 로고    scopus 로고
    • Numbers and locations of native bacteria on field-grown wheat roots quantified by fluorescence in situ hybridization (FISH)
    • Watt M., Hugenholtz P., White R., and Vinall K. Numbers and locations of native bacteria on field-grown wheat roots quantified by fluorescence in situ hybridization (FISH). Environ. Microbiol. 8 (2006) 871-884
    • (2006) Environ. Microbiol. , vol.8 , pp. 871-884
    • Watt, M.1    Hugenholtz, P.2    White, R.3    Vinall, K.4
  • 40
    • 0001309175 scopus 로고    scopus 로고
    • Likelihood ratio tests for fixed model terms using residual maximum likelihood
    • Welham S.J., and Thompson R. Likelihood ratio tests for fixed model terms using residual maximum likelihood. J. R. Stat. Soc., B Meth. 59 (1997) 701-714
    • (1997) J. R. Stat. Soc., B Meth. , vol.59 , pp. 701-714
    • Welham, S.J.1    Thompson, R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.