Analysis of rhizosphere fungal communities using rRNA and rDNA

TitleAnalysis of rhizosphere fungal communities using rRNA and rDNA
Publication TypeBook Chapter
Year of Publication2009
AuthorsJumpponen, A
EditorVarma, A, Kharkwal, AC
Book TitleSymbiotic Fungi, Soil Biology
Pagination29 -40
PublisherSpringer-Verlag, Berlin
Accession NumberKNZ001309

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.