Analyses of soil fungal communities in adjacent natural forest and hoop pine plantation ecosystems of subtropical Australia using molecular approaches based on 18S rRNA genes
Open Access
- 1 June 2005
- journal article
- research article
- Published by Oxford University Press (OUP) in FEMS Microbiology Letters
- Vol. 247 (1), 91-100
- https://doi.org/10.1016/j.femsle.2005.04.033
Abstract
Soil fungal communities were studied using 18S rDNA-based molecular techniques. Soil DNA was analyzed using temperature gradient gel electrophoresis (TGGE), single-stranded conformational polymorphism (SSCP), cloning and sequencing methods, following community DNA extraction and polymerase chain reaction (PCR). The extracted community DNA was successfully amplified using the primer pair of EF4f-Fung5r which produced ca. 550 bp 18S rDNA fragments. TGGE screening of the PCR products showed some differences in band position and intensity between two soil samples in adjacent natural forest (YNF) and hoop pine plantation (YHP) ecosystems at Yarraman in subtropical Australia. TGGE and SSCP could be used for screening PCR products. However, care must be exercised when interpreting the TGGE and SSCP results with respect to microbial diversity, because one band may not necessarily represent one species. It is recommended that the PCR products should be purified before TGGE or SSCP screening. SSCP screening of the clone sequences revealed differences among the clones. Sequence and phylogenetic analyses revealed that all obtained clones were affiliated to the kingdom Fungi, including three phyla, i.e., Zygomycota, Ascomycota and Basidiomycota. Our results suggested that community DNA extraction, PCR, cloning, SSCP screening of clones, sequencing of selected clones and phylogentic analyses could be a good strategy in investigation of soil fungal community and diversity.Keywords
This publication has 27 references indexed in Scilit:
- Dynamics of Fungal Communities in Bulk and Maize Rhizosphere Soil in the TropicsApplied and Environmental Microbiology, 2003
- Soil fungal community structure in a temperate upland grassland soilFEMS Microbiology Ecology, 2003
- Oligonucleotide Fingerprinting of rRNA Genes for Analysis of Fungal Community CompositionApplied and Environmental Microbiology, 2002
- Structure and activity of the bacterial community in the rhizosphere of different plant species and the effect of arbuscular mycorrhizal colonisationFEMS Microbiology Ecology, 2002
- Extensive Fungal Diversity in Plant RootsScience, 2002
- Arbuscular mycorrhizal infection changes the bacterial 16 S rDNA community composition in the rhizosphere of maizeMycorrhiza, 2001
- Rapid PCR-based method for the direct analysis of fungal communities in complex environmental samplesSoil Biology and Biochemistry, 2001
- Soil fungi: diversity and detectionPlant and Soil, 2001
- Methods for assessing the composition and diversity of soil microbial communitiesApplied Soil Ecology, 2000
- Soil health and sustainability: managing the biotic component of soil qualityApplied Soil Ecology, 2000