Terminal restriction fragment length polymorphism analysis of ribosomal RNA genes to assess changes in fungal community structure in soils
Open Access
- 1 March 2004
- journal article
- research article
- Published by Oxford University Press (OUP) in FEMS Microbiology Ecology
- Vol. 47 (3), 397-404
- https://doi.org/10.1016/s0168-6496(04)00002-9
Abstract
Monitoring the structure and dynamics of fungal communities in soils under agricultural and environmental disturbances is currently a challenge. In this study, a terminal restriction fragment length polymorphism (T-RFLP) fingerprinting method was developed for the rapid comparison of fungal community structures. The terminal restriction fragment polymorphism of different regions of the small-subunit (SSU) ribosomal RNA (rRNA) gene was simulated by sequence comparison using 10 restriction enzymes, and analyzed among three different soils using fungal-specific primers. Polymerase chain reaction amplification of the 3′ end of the SSU rRNA gene with the primer nu-SSU-0817-5′ and with the fluorescently labelled primer nu-SSU-1536-3′, and digestion of the amplicons with AluI and MboI were found to be optimal and were used in a standardized T-RFLP procedure. Both the number and the intensity of terminal restriction fragments detected by capillary gel electrophoresis were integrated in correspondence analyses. Three soils with contrasting physicochemical properties were differentiated according to the structure of their fungal communities. Assessment of the impact on the fungal community structure of the amendment of two soils with compost or manure confirmed the reproducibility and the sensitivity of the method. Shifts in the community structure were detected between non-amended and amended soil samples. In both soils, the shift differed with the organic amendment applied. In addition, the fungal community structures of the two soils were affected in a different way by the same organic amendment. The fingerprinting method provides a rapid tool to investigate the effect of various perturbations on the fungal communities in soils.Keywords
This publication has 17 references indexed in Scilit:
- Application of New Primer-Enzyme Combinations to Terminal Restriction Fragment Length Polymorphism Profiling of Bacterial Populations in Human FecesApplied and Environmental Microbiology, 2003
- Assessment of fungal diversity using terminal restriction fragment (TRF) pattern analysis: comparison of 18S and ITS ribosomal regionsFEMS Microbiology Ecology, 2002
- Vertical niche differentiation of ectomycorrhizal hyphae in soil as shown by T‐RFLP analysisNew Phytologist, 2002
- Influence of Elevated CO 2 on the Fungal Community in a Coastal Scrub Oak Forest Soil Investigated with Terminal-Restriction Fragment Length Polymorphism AnalysisApplied and Environmental Microbiology, 2002
- Extensive Fungal Diversity in Plant RootsScience, 2002
- Microbial Population Structures in Soil Particle Size Fractions of a Long-Term Fertilizer Field ExperimentApplied and Environmental Microbiology, 2001
- DNA Extraction from Soils: Old Bias for New Microbial Diversity Analysis MethodsApplied and Environmental Microbiology, 2001
- Community Structure of Denitrifiers, Bacteria , and Archaea along Redox Gradients in Pacific Northwest Marine Sediments by Terminal Restriction Fragment Length Polymorphism Analysis of Amplified Nitrite Reductase ( nirS ) and 16S rRNA GenesApplied and Environmental Microbiology, 2001
- A soil microscale study to reveal the heterogeneity of Hg(II) impact on indigenous bacteria by quantification of adapted phenotypes and analysis of community DNA fingerprintsFEMS Microbiology Ecology, 2000
- Simple and rapid method fordirect extraction of microbial DNA fromsoil for PCRSoil Biology and Biochemistry, 1998