Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction.

PubWeight™: 5.50‹?› | Rank: Top 1%

🔗 View Article (PMC 182998)

Published in Appl Environ Microbiol on September 01, 1992

Authors

C Picard1, C Ponsonnet, E Paget, X Nesme, P Simonet

Author Affiliations

1: Laboratoire d'Ecologie Microbienne du Sol, URA 1450, Centre National de la Recherche Scientifique, Villerbanne, France.

Articles citing this

Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol (1997) 17.04

Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl Environ Microbiol (1995) 11.09

Microbial biofilms: from ecology to molecular genetics. Microbiol Mol Biol Rev (2000) 9.83

Interference of humic acids and DNA extracted directly from soil in detection and transformation of recombinant DNA from bacteria and a yeast. Appl Environ Microbiol (1993) 6.24

Quantitative cell lysis of indigenous microorganisms and rapid extraction of microbial DNA from sediment. Appl Environ Microbiol (1994) 6.03

Phylogenetic analysis and in situ identification of bacteria in activated sludge. Appl Environ Microbiol (1997) 5.61

Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples. Appl Environ Microbiol (1999) 4.53

A computer analysis of primer and probe hybridization potential with bacterial small-subunit rRNA sequences. Appl Environ Microbiol (1996) 3.92

PCR amplification and direct sequencing of gyrB genes with universal primers and their application to the detection and taxonomic analysis of Pseudomonas putida strains. Appl Environ Microbiol (1995) 3.52

Biology of Frankia strains, actinomycete symbionts of actinorhizal plants. Microbiol Rev (1993) 3.15

Flow sorting of microorganisms for molecular analysis. Appl Environ Microbiol (1997) 3.13

Quantification of bias related to the extraction of DNA directly from soils. Appl Environ Microbiol (1999) 3.12

16S rRNA gene-based detection of tetrachloroethene-dechlorinating Desulfuromonas and Dehalococcoides species. Appl Environ Microbiol (2000) 2.75

Survival and activity of Pseudomonas sp. strain B13(FR1) in a marine microcosm determined by quantitative PCR and an rRNA-targeting probe and its effect on the indigenous bacterioplankton. Appl Environ Microbiol (1995) 2.74

Expression of nifH genes in natural microbial assemblages in Lake George, New York, detected by reverse transcriptase PCR. Appl Environ Microbiol (2000) 2.61

Detection of polychlorinated biphenyl degradation genes in polluted sediments by direct DNA extraction and polymerase chain reaction. Appl Environ Microbiol (1993) 2.48

Simultaneous recovery of RNA and DNA from soils and sediments. Appl Environ Microbiol (2001) 2.38

Detection of methanotrophic bacteria in environmental samples with the PCR. Appl Environ Microbiol (1995) 2.37

Small-Scale DNA Sample Preparation Method for Field PCR Detection of Microbial Cells and Spores in Soil. Appl Environ Microbiol (1998) 2.28

Direct DNA extraction for PCR-mediated assays of soil organisms. Appl Environ Microbiol (1995) 2.16

Methods for microbial DNA extraction from soil for PCR amplification. Biol Proced Online (1998) 1.95

Detection and counting of Nitrobacter populations in soil by PCR. Appl Environ Microbiol (1995) 1.87

Geographical distribution and diversity of bacteria associated with natural populations of Drosophila melanogaster. Appl Environ Microbiol (2007) 1.80

Use of 5-cyano-2,3-ditolyl tetrazolium chloride for quantifying planktonic and sessile respiring bacteria in drinking water. Appl Environ Microbiol (1993) 1.76

Quantitative community fingerprinting methods for estimating the abundance of operational taxonomic units in natural microbial communities. Appl Environ Microbiol (2009) 1.75

Development of a method for detection of enteroviruses in shellfish by PCR with poliovirus as a model. Appl Environ Microbiol (1994) 1.53

Microscale detection of specific bacterial DNA in soil with a magnetic capture-hybridization and PCR amplification assay. Appl Environ Microbiol (1995) 1.38

A pyrosequencing-based metagenomic study of methane-producing microbial community in solid-state biogas reactor. Biotechnol Biofuels (2013) 1.37

Detection of Xanthomonas campestris pv. citri by the polymerase chain reaction method. Appl Environ Microbiol (1993) 1.35

Symbiotic Role of the Viable but Nonculturable State of Vibrio fischeri in Hawaiian Coastal Seawater. Appl Environ Microbiol (1995) 1.33

Genetic diversity and expression of the [NiFe] hydrogenase large-subunit gene of Desulfovibrio spp. in environmental samples. Appl Environ Microbiol (1997) 1.31

Identification of a novel group of bacteria in sludge from a deteriorated biological phosphorus removal reactor. Appl Environ Microbiol (1999) 1.30

Amplification of the amoA gene from diverse species of ammonium-oxidizing bacteria and from an indigenous bacterial population from seawater. Appl Environ Microbiol (1995) 1.22

Genetic diversity among Frankia strains nodulating members of the family Casuarinaceae in Australia revealed by PCR and restriction fragment length polymorphism analysis with crushed root nodules. Appl Environ Microbiol (1996) 1.21

Detection of Phanerochaete chrysosporium in soil by PCR and restriction enzyme analysis. Appl Environ Microbiol (1994) 1.10

Kinetics of the persistence of chromosomal DNA from genetically engineered Escherichia coli introduced into soil. Appl Environ Microbiol (1993) 1.06

Molecular detection of streptomycin-producing streptomycetes in Brazilian soils. Appl Environ Microbiol (1997) 1.03

Detection of Tn5-like sequences in kanamycin-resistant stream bacteria and environmental DNA. Appl Environ Microbiol (1993) 1.01

Engineering root exudation of Lotus toward the production of two novel carbon compounds leads to the selection of distinct microbial populations in the rhizosphere. Microb Ecol (2004) 1.00

Rapid quantitative detection of Vibrio parahaemolyticus in seafood by MPN-PCR. Curr Microbiol (2008) 0.97

Diversity of Geobacteraceae species inhabiting metal-polluted freshwater lake sediments ascertained by 16S rDNA analyses. Microb Ecol (2003) 0.97

Rapid and sensitive method for the detection of Mycobacterium chlorophenolicum PCP-1 in soil based on 16S rRNA gene-targeted PCR. Appl Environ Microbiol (1996) 0.96

Development and application of a most-probable-number-pcr assay to quantify flagellate populations in soil samples. Appl Environ Microbiol (2001) 0.95

A real-time PCR method for quantifying viable ascaris eggs using the first internally transcribed spacer region of ribosomal DNA. Appl Environ Microbiol (2006) 0.89

Impacts of inter- and intralaboratory variations on the reproducibility of microbial community analyses. Appl Environ Microbiol (2010) 0.89

pH gradient-induced heterogeneity of Fe(III)-reducing microorganisms in coal mining-associated lake sediments. Appl Environ Microbiol (2007) 0.88

Affinity purification of DNA and RNA from environmental samples with peptide nucleic acid clamps. Appl Environ Microbiol (2000) 0.88

Universal PCR primers for detection of phytopathogenic Agrobacterium strains. Appl Environ Microbiol (1995) 0.87

Protein extraction and fingerprinting optimization of bacterial communities in natural environment. Microb Ecol (2006) 0.87

Molecular characterization of Frankia microsymbionts from spore-positive and spore-negative nodules in a natural alder stand. Appl Environ Microbiol (1994) 0.85

Seasonal fluctuations and long-term persistence of pathogenic populations of Agrobacterium spp. in soils. Appl Environ Microbiol (2002) 0.84

Spatial distribution of bacterial communities and phenanthrene degradation in the rhizosphere of Lolium perenne L. Appl Environ Microbiol (2004) 0.84

PCR-restriction fragment length polymorphism identification and host range of single-spore isolates of the flexible Frankia sp. strain UFI 132715. Appl Environ Microbiol (1996) 0.83

Estimating biodegradative gene numbers at a JP-5 contaminated site using PCR. Appl Biochem Biotechnol (1996) 0.83

Habitable worlds with no signs of life. Philos Trans A Math Phys Eng Sci (2014) 0.82

Strategy for extracting DNA from clay soil and detecting a specific target sequence via selective enrichment and real-time (quantitative) PCR amplification. Appl Environ Microbiol (2009) 0.80

Abundance and Relative Distribution of Frankia Host Infection Groups Under Actinorhizal Alnus glutinosa and Non-actinorhizal Betula nigra Trees. Microb Ecol (2015) 0.79

Methods for detection of Anticarsia gemmatalis nucleopolyhedrovirus DNA in soil. Appl Environ Microbiol (1999) 0.79

Direct Detection of Cylindrocarpon destructans, Root Rot Pathogen of Ginseng by Nested PCR from Soil Samples. Mycobiology (2010) 0.79

An efficient and cost-effective method for DNA extraction from athalassohaline soil using a newly formulated cell extraction buffer. 3 Biotech (2016) 0.78

From Vineyard Soil to Wine Fermentation: Microbiome Approximations to Explain the "terroir" Concept. Front Microbiol (2017) 0.76

Identification of Rhizobium spp. in peat-based inoculants by DNA hybridization and PCR and its application in inoculant quality control. Appl Environ Microbiol (1995) 0.75

SPION-mediated soil DNA extraction and comparative analysis with conventional and commercial kit-based protocol. 3 Biotech (2014) 0.75

PCR-Based detection of the causal agent of watermark disease in willows (Salix spp.) Appl Environ Microbiol (1998) 0.75

Soil pretreatment and fast cell lysis for direct polymerase chain reaction from forest soils for terminal restriction fragment length polymorphism analysis of fungal communities. Braz J Microbiol (2016) 0.75

Comparative assessment of methods for metagenomic DNA isolation from soils of different crop growing fields. 3 Biotech (2016) 0.75

Optimization of high-yielding protocol for DNA extraction from the forest rhizosphere microbes. 3 Biotech (2017) 0.75

Articles cited by this

Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science (1988) 220.77

Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods Enzymol (1987) 58.68

16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature (1990) 26.48

Methods of multilocus enzyme electrophoresis for bacterial population genetics and systematics. Appl Environ Microbiol (1986) 24.31

High diversity in DNA of soil bacteria. Appl Environ Microbiol (1990) 19.16

Rapid method for direct extraction of DNA from soil and sediments. Appl Environ Microbiol (1991) 10.11

Recovery of DNA from soils and sediments. Appl Environ Microbiol (1988) 8.02

DNA amplification to enhance detection of genetically engineered bacteria in environmental samples. Appl Environ Microbiol (1988) 7.65

Plasmids, recombination and chromosome mapping in Streptomyces lividans 66. J Gen Microbiol (1983) 5.06

Detection of coliform bacteria in water by polymerase chain reaction and gene probes. Appl Environ Microbiol (1990) 4.89

Polymerase chain reaction for the detection of Mycobacterium leprae. J Gen Microbiol (1989) 4.82

Protection of sediment-adsorbed transforming DNA against enzymatic inactivation. Appl Environ Microbiol (1983) 3.71

Formamide can dramatically improve the specificity of PCR. Nucleic Acids Res (1990) 3.38

Adsorption of DNA to sand and variable degradation rates of adsorbed DNA. Appl Environ Microbiol (1987) 3.17

A simple method for the isolation of chromosomal DNA from gram positive or acid-fast bacteria. Nucleic Acids Res (1991) 2.82

Biphasic amplification of very dilute DNA samples via 'booster' PCR. Nucleic Acids Res (1989) 2.74

Sensitive and specific detection of Listeria monocytogenes in milk and ground beef with the polymerase chain reaction. Appl Environ Microbiol (1991) 2.25

Frankia genus-specific characterization by polymerase chain reaction. Appl Environ Microbiol (1991) 2.20

DNA recovery and direct detection of Tn5 sequences from soil. Lett Appl Microbiol (1991) 2.18

Isolation of different agrobacterium biovars from a natural oak savanna and tallgrass prairie. Appl Environ Microbiol (1987) 2.09

Short PCR product yields improved by lower denaturation temperatures. Nucleic Acids Res (1991) 1.58

Effect of ionic and nonionic detergents on the Taq polymerase. Biotechniques (1990) 1.45

Fractionation and Estimation of Particle-Attached and Unattached Bradyrhizobium japonicum Strains in Soils. Appl Environ Microbiol (1986) 1.04

French Mathematicians Push the Panic Button: A lack of university teaching posts is fueling a new brain drain to the United States which, some claim, threatens to erode one of the country's most prized intellectual achievements. Science (1988) 0.95

Articles by these authors

Drug-resistance genotyping in HIV-1 therapy: the VIRADAPT randomised controlled trial. Lancet (1999) 4.68

Quantification of bias related to the extraction of DNA directly from soils. Appl Environ Microbiol (1999) 3.12

Characterization of natural populations of Nitrobacter spp. using PCR/RFLP analysis of the ribosomal intergenic spacer. Arch Microbiol (1992) 2.34

Quantification of bacterial subgroups in soil: comparison of DNA extracted directly from soil or from cells previously released by density gradient centrifugation. Environ Microbiol (2001) 1.54

Analysis of a ribosomal RNA operon in the actinomycete Frankia. Gene (1992) 1.54

Phylogenetic relationships among Frankia genomic species determined by use of amplified 16S rDNA sequences. J Bacteriol (1991) 1.49

Identification of Agrobacterium strains by PCR-RFLP analysis of pTi and chromosomal regions. Arch Microbiol (1994) 1.46

Plasmids in Frankia sp. J Bacteriol (1983) 1.45

Novel Ti plasmids in Agrobacterium strains isolated from fig tree and chrysanthemum tumors and their opinelike molecules. Mol Plant Microbe Interact (1995) 1.44

Resistance of plastic ophthalmic lenses: the effect of base curve on different materials during static load testing. Optom Vis Sci (2001) 1.38

Conservation of nif sequences in Frankia. Mol Gen Genet (1988) 1.38

Evidence that some Frankia sp. strains are able to cross boundaries between Alnus and Elaeagnus host specificity groups. Appl Environ Microbiol (1992) 1.26

Genetic diversity among Frankia strains nodulating members of the family Casuarinaceae in Australia revealed by PCR and restriction fragment length polymorphism analysis with crushed root nodules. Appl Environ Microbiol (1996) 1.21

Comparison of Randomly Amplified Polymorphic DNA with Amplified Fragment Length Polymorphism To Assess Genetic Diversity and Genetic Relatedness within Genospecies III of Pseudomonas syringae. Appl Environ Microbiol (1998) 1.17

Conditions for natural transformation of Ralstonia solanacearum. Appl Environ Microbiol (1997) 1.12

Rhodanobacter lindaniclasticus gen. nov., sp. nov., a lindane-degrading bacterium. Int J Syst Bacteriol (1999) 1.11

Nucleotide sequence of nifD from Frankia alni strain ArI3: phylogenetic inferences. Mol Biol Evol (1992) 1.09

The nodular endophytes of Coriaria spp. form a distinct lineage within the genus Frankia. Mol Ecol (1992) 1.08

Horizontal gene transfers in the environment: natural transformation as a putative process for gene transfers between transgenic plants and microorganisms. Res Microbiol (1999) 1.07

Kinetics of the persistence of chromosomal DNA from genetically engineered Escherichia coli introduced into soil. Appl Environ Microbiol (1993) 1.06

Novel tellurite-amended media and specific chromosomal and Ti plasmid probes for direct analysis of soil populations of Agrobacterium biovars 1 and 2. Appl Environ Microbiol (2001) 1.03

Isolation and characterization of a novel gamma-hexachlorocyclohexane-degrading bacterium. J Bacteriol (1996) 1.03

The Julius F. Neumueller Award in Optics, 1989: change of pupil centration with change of illumination and pupil size. Optom Vis Sci (1992) 1.01

[Recommendations for the care of the patient with chronic obstructive pulmonary disease]. Arch Bronconeumol (2001) 1.01

Engineering root exudation of Lotus toward the production of two novel carbon compounds leads to the selection of distinct microbial populations in the rhizosphere. Microb Ecol (2004) 1.00

A new Agrobacterium strain isolated from aerial tumors on Ficus benjamina L. Appl Environ Microbiol (1995) 1.00

Natural transformation of Pseudomonas fluorescens and Agrobacterium tumefaciens in soil. Appl Environ Microbiol (2001) 1.00

Evaluation of biological and physical protection against nuclease degradation of clay-bound plasmid DNA. Appl Environ Microbiol (2001) 0.99

Inter-laboratory evaluation of the ISO standard 11063 "Soil quality - Method to directly extract DNA from soil samples". J Microbiol Methods (2011) 0.98

Relationship between spatial and genetic distance in Agrobacterium spp. in 1 cubic centimeter of soil. Appl Environ Microbiol (2003) 0.97

Opportunistic colonization of Ralstonia solanacearum-infected plants by Acinetobacter sp. and its natural competence development. Microb Ecol (2002) 0.96

Polyphasic characterization of xanthomonads pathogenic to members of the Anacardiaceae and their relatedness to species of Xanthomonas. Int J Syst Evol Microbiol (2009) 0.91

Molecular tools for the characterisation of antibiotic-resistant bacteria. Vet Res (2001) 0.91

Laboratory-scale evidence for lightning-mediated gene transfer in soil. Appl Environ Microbiol (2001) 0.86

Plant genome complexity may be a factor limiting in situ the transfer of transgenic plant genes to the phytopathogen Ralstonia solanacearum. Appl Environ Microbiol (2000) 0.86

The LD50 test. Acta Pharmacol Toxicol (Copenh) (1983) 0.85

Optimization and biochemical characterization of a bacteriocin from a newly isolated Bacillus subtilis strain 14B for biocontrol of Agrobacterium spp. strains. Lett Appl Microbiol (2009) 0.84

Seasonal fluctuations and long-term persistence of pathogenic populations of Agrobacterium spp. in soils. Appl Environ Microbiol (2002) 0.84

Psychophysical measurement of the blur on the retina due to optical aberrations of the eye. Vision Res (1990) 0.82

Ti plasmids from Agrobacterium characterize rootstock clones that initiated a spread of crown gall disease in Mediterranean countries. Appl Environ Microbiol (1999) 0.82

Recombinant plasmid mobilization between E. coli strains in seven sterile microcosms. Can J Microbiol (1997) 0.81

Direct conjugal transfers of Ti plasmid to soil microflora. Mol Ecol (1999) 0.81

[Polylactic acid injections (Newfill) in the treatment of facial lipodystrophy in HIV-positive patients]. Ann Dermatol Venereol (2006) 0.79

A highly selectable and highly transferable Ti plasmid to study conjugal host range and Ti plasmid dissemination in complex ecosystems. Microb Ecol (2004) 0.78

A review of available systems to investigate transfer of DNA to indigenous soil bacteria. Antonie Van Leeuwenhoek (1998) 0.77

IS292: a novel insertion element from Agrobacterium. Microbiology (1995) 0.77

Rapid and accurate species and genomic species identification and exhaustive population diversity assessment of Agrobacterium spp. using recA-based PCR. Syst Appl Microbiol (2013) 0.76

Progressive addition lens channel dimension as a function of addition power. Ophthalmic Physiol Opt (1992) 0.75

Discrepancy in the evaluation of visual impairment of elderly low-vision patients by general eye care practitioners and by low-vision practitioners. Optom Vis Sci (1993) 0.75

Precision and reliability study of a modified keratometric technique for measuring the radius of curvature of soft contact lenses. Ophthalmic Physiol Opt (1994) 0.75

Combination of a side shield with an ocular moisture chamber. Am J Optom Physiol Opt (1984) 0.75

Spectral transmittance of UV-absorbing soft and rigid gas permeable contact lenses. Optom Vis Sci (1995) 0.75

Variable virological outcomes according to the center providing antiretroviral therapy within the PharmAdapt clinical trial. HIV Clin Trials (2003) 0.75

Optical performance of aspheric concave ophthalmic lenses: the effect of vertex distance. Optom Vis Sci (1997) 0.75

Development and applications of a DNA labeling method with magnetic nanoparticles to study the role of horizontal gene transfer events between bacteria in soil pollutant bioremediation processes. Environ Sci Pollut Res Int (2015) 0.75

Clinical measurement of depth perception by means of motion parallax: a case report. Optom Vis Sci (1992) 0.75

Peripheral power variations in progressive addition lenses. Am J Optom Physiol Opt (1986) 0.75

Video monitoring of the principal ray of a Maxwellian view for the measurement of optical aberrations, the Stiles-Crawford effect, retinal resolution, and for investigating color vision. Appl Opt (1990) 0.75

Comparison between electrochemical and optoelectrochemical impedance measurements for detection of DNA hybridization. Appl Biochem Biotechnol (2001) 0.75

Potential dissemination of antibiotic resistance genes from transgenic plants to microorganisms. Infect Control Hosp Epidemiol (2000) 0.75

Yves Le Grand and the assessment of retinal acuity using interference fringes. Ophthalmic Physiol Opt (1997) 0.75

To use or not to use the refractive correction along with hand-held magnifiers. Optom Vis Sci (1992) 0.75

Effects of induced transverse chromatic aberration from an afocal prismatic lens on spatio-temporal sensitivity. Ophthalmic Physiol Opt (1999) 0.75

Genomospecies identification and phylogenomic relevance of AFLP analysis of isolated and non-isolated strains of Frankia spp. Syst Appl Microbiol (2011) 0.75

Transverse chromatic aberration and colour-defined motion. Ophthalmic Physiol Opt (2000) 0.75

[Power in the periphery of several aspheric eyeglasses for aphakic patients]. J Fr Ophtalmol (1984) 0.75

A scanning focimeter to measure peripheral lens powers. Ophthalmic Physiol Opt (1983) 0.75

[Measuring the level of tonic accomodation as a function of wavelength]. J Fr Ophtalmol (1995) 0.75

Theoretical computation of the refractive index in an ophthalmic lens. Am J Optom Physiol Opt (1987) 0.75