Analysis of Rhizosphere Fungal Communities Using rRNA and rDNA
- 1.6k Downloads
Microbial communities in soil and rhizosphere are diverse. Use of sequence data derived from environmental samples has become somewhat of a standard to explore the microbial diversity and community composition in soils. While the DNA encoding the ribosomal RNA genes can be easily PCR-amplified from many environmental samples, this DNA may carry a historical fingerprint, as naked DNA or as dormant, but inactive organisms. The use of ribosomal RNA may provide a tool to focus on the active organisms. This chapter describes kit-based methods to simultaneously extract DNA and RNA from environmental samples, and outlines a protocol for reverse-transcribing ribosomal RNA for PCR amplification of the produced cDNA. The fungal communities observed via sequencing the ribosomal RNA or the ribosomal RNA encoding DNA from Andropogon gerardii rhizosphere are compared, and the results briefly discussed.
KeywordsClone Library Panicum Virgatum Fungal Community Tallgrass Prairie Andropogon Gerardii
This material is based upon work supported by the National Science Foundation under Grants 0344838 and 0516456. Stacie Kageyama assisted in sampling Andropogon gerardii roots. Konza Prairie Biological Station and its personnel maintain the research site, and are funded partly through the National Science Foundation Long Term Ecological Research program.
- Bentivenga SP, Hetrick BAD (1992) Seasonal and temperature effects on mycorrhizal activity and dependence of cool- and warm-season tallgrass prairie grases. Can J Bot 70:1596–1602Google Scholar
- Domsch KH, Gams W, Anderson T-H (1980) Compendium of soil fungi. Academic, New YorkGoogle Scholar
- Duineveld BM, Kowalchuk GA, Keijzer A, van Elsas JD, van Veen JA (2001) Analysis of bacterial communities in the rhizosphere of chrysanthemum via denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA as well as DNA fragments coding for 16S rRNA. Appl Environ Microbiol 67:172–178CrossRefPubMedGoogle Scholar
- Kowalchuk GA, Drigo B, Yergeau E, van Veen JA (2006) Assessing bacterial and fungal community structure in soil using ribosomal RNA and other structural gene markers. In: Nannipieri P, Smalla K (eds) Nucleic acids and proteins in soil, vol 7. Springer, Berlin, pp 159–188Google Scholar
- Rambelli A, Persiani AM, Maggi O, Lunghini D, Onofri S, Riess S, Dowgiallo G, Puppi G (1983) Comparative studies on microfungi in tropical ecosystems. UNESCO, RomeGoogle Scholar
- White TJ, Bruns TD, Lee SB, Taylor JW (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ (eds) PCR protocols: a guide to methods and applications. Academic, New York, pp 315–322Google Scholar