Characterization of myxomycete communities in soil by reverse transcription polymerase chain reaction (RT-PCR)-based method

• Published in: Soil biology & biochemistry 2009-06, Vol.41 (6), p.1324-1330
• Main Authors: Kamono, Akiko, Matsumoto, Jun, Kojima, Hisaya, Fukui, Manabu
• Format: Article
• Language: English
• Subjects: Agronomy. Soil science and plant productions; Biochemistry and biology; Biological and medical sciences; Chemical, physicochemical, biochemical and biological properties; Community composition; community structure; DGGE; Didymiaceae; fruiting bodies; Fundamental and applied biological sciences. Psychology; gel electrophoresis; Myxomycetes; optimization; Physaraceae; Physics, chemistry, biochemistry and biology of agricultural and forest soils; reverse transcriptase polymerase chain reaction; RNA; RT-PCR; seasons; soil fungi; Soil science; soil-plant interactions
• ISSN: 0038-0717; 1879-3428
• DOI: 10.1016/j.soilbio.2009.04.001

Myxomycetes are amoeboid organisms, and their life cycle includes a stage in which they produce fruiting bodies. Extensive field collections of their fruiting bodies have been conducted in various terrestrial ecosystems. However, little is known about the ecology of myxomycetes in their natural habitat, especially during their trophic stages. To study the presence and distribution of myxomycetes such as those belonging to Didymiaceae and Physaraceae in soil, we used a polymerase chain reaction (PCR)-based method. First, optimization of the reverse transcription (RT)-PCR conditions was performed with the RNA extracted from soil samples. A semi-nested RT-PCR approach was used to improve the specificity of detection. We used newly and previously designed primers in the first round of amplification, which was followed by a second round with the previously described primer pair for PCR-denaturing gradient gel electrophoresis. Next, this method and nucleotide sequence analyses were applied to study several soil samples collected from five study sites. While no marked dynamic seasonal change was detected in the community composition of myxomycetes belonging to Didymiaceae and Physaraceae in the soil samples collected from the single site, their composition significantly differed between different sites. This is the first study that demonstrates the presence of myxomycetes in the soil and characterizes their community composition by RNA-based molecular analysis.