Application of T-RFLP analysis to the study of bacterial community structure in the rhizosphere

Sakai, Masao; Matsunaga, Norihisa; Matsuka, Akira; Kanazawa, Susumu

doi:10.1080/00380768.2001.10408442

Cited by 5 publications

(3 citation statements)

References 11 publications

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“…An increasing number of studies make use of PCR‐based methods like denaturing gradient gel electrophoresis (DGGE) [79] or terminal‐restriction fragment length polymorphism (T‐RFLP) [80] for characterising complex soil bacterial communities. The advantage of DGGE is that it recognises very small differences in the nucleotide sequence, allowing a description of the community structure expressed as band patterns on a gel.…”

Section: Discussionmentioning

confidence: 99%

“…The analysis of rRNA genes has lately become an important tool for studying the diversity of soil bacterial [79,80] and mycorrhizal [13] communities in different ecosystems. The use of fatty acid patterns of phospholipids and lipopolysaccharides (reviewed by Zelles [81]) and the utility of ergosterols as bioindicators of fungi in soil [82] have also been useful tools in the characterisation of microbial communities.…”

Section: Discussionmentioning

confidence: 99%

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Microbial interactions in the mycorrhizosphere and their significance for sustainable agriculture

Johansson

Paul

Finlay

2004

FEMS Microbiology Ecology

595

312

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In sustainable, low-input cropping systems the natural roles of microorganisms in maintaining soil fertility and biocontrol of plant pathogens may be more important than in conventional agriculture where their significance has been marginalised by high inputs of agrochemicals. Better understanding of the interactions between arbuscular mycorrhizal fungi and other microorganisms is necessary for the development of sustainable management of soil fertility and crop production. Many studies of the influence of mycorrhizal colonisation on associated bacterial communities have been conducted, however, the mechanisms of interaction are still poorly understood. Novel approaches including PCR-based methods, stable isotope profiling, and molecular markers have begun to shed light on the activity, identity and spatiotemporal location of bacteria in the mycorrhizosphere. This paper reviews current knowledge concerning the interactions between arbuscular mycorrhizal fungi and other microorganisms, particularly bacteria, and discusses the implications these interactions may have in sustainable agriculture.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Microbial interactions in the mycorrhizosphere and their significance for sustainable agriculture

Johansson

Paul

Finlay

2004

FEMS Microbiology Ecology

595

312

View full text Add to dashboard Cite

show abstract

“…T-RFLP profiling has been used to examine the total bacterial community in ecosystems as diverse as sludge, sand, termite guts (24), soil (13), a phenol bioreactor (17), the rhizosphere (35), and feces (21). Although T-RFLP profiling has been used in many different contexts, as far as we are aware the present study is the first application of this technique to a clinically important scenario.…”

Section: Discussionmentioning

confidence: 99%

Bacterial Diversity in Cases of Lung Infection in Cystic Fibrosis Patients: 16S Ribosomal DNA (rDNA) Length Heterogeneity PCR and 16S rDNA Terminal Restriction Fragment Length Polymorphism Profiling

et al. 2003

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The leading cause of morbidity and mortality in cystic fibrosis (CF) patients stems from repeated bacterial respiratory infections. Many bacterial species have been cultured from CF specimens and so are associated with lung disease. Despite this, much remains to be determined. In the present study, we characterized without prior cultivation the total bacterial community present in specimens taken from adult CF patients, extracting DNA directly from 14 bronchoscopy or sputum samples. Bacterial 16S ribosomal DNA (rRNA) gene PCR products were amplified from extracted nucleic acids, with analyses by terminal restriction fragment length polymorphism (T-RFLP), length heterogeneity PCR (LH-PCR), and sequencing of individual cloned PCR products to characterize these communities. Using the same loading of PCR products, 12 distinct T-RFLP profiles were identified that had between 3 and 32 T-RFLP bands. Nine distinct LH-PCR profiles were identified containing between one and four bands. T-RFLP bands were detected in certain samples at positions that corresponded to pathogens cultured from CF samples, e.g., Burkholderia cepacia and Haemophilus influenzae. In every sample studied, one T-RFLP band was identified that corresponded to that produced by Pseudomonas aeruginosa. A total of 103 16S rRNA gene clones were examined from five patients. P. aeruginosa was the most commonly identified species (59% of clones). Stenotrophomonas species were also common, with eight other (typically anaerobic) bacterial species identified within the remaining 17 clones. In conclusion, T-RFLP analysis coupled with 16S rRNA gene sequencing is a powerful means of analyzing the composition and diversity of the bacterial community in specimens sampled from CF patients.

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A simplified procedure for terminal restriction fragment length polymorphism analysis of the soil bacterial community to study the effects of pesticides on the soil microflora using 4,6-dinitroorthocresol as a test case

et al. 2003

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Application of T-RFLP analysis to the study of bacterial community structure in the rhizosphere

Cited by 5 publications

References 11 publications

Microbial interactions in the mycorrhizosphere and their significance for sustainable agriculture

Microbial interactions in the mycorrhizosphere and their significance for sustainable agriculture

Bacterial Diversity in Cases of Lung Infection in Cystic Fibrosis Patients: 16S Ribosomal DNA (rDNA) Length Heterogeneity PCR and 16S rDNA Terminal Restriction Fragment Length Polymorphism Profiling

A simplified procedure for terminal restriction fragment length polymorphism analysis of the soil bacterial community to study the effects of pesticides on the soil microflora using 4,6-dinitroorthocresol as a test case

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