Succession and phylogenetic profile of eukaryotic communities in the composting process of rice straw estimated by PCR-DGGE analysis

Abstract

The succession and phylogenetic profile of eukaryotic communities during the composting process of rice straw (RS) were studied by applying polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis followed by sequencing of 18S rDNA. Principal component analysis and cluster analysis of the DGGE band patterns of eukaryotic communities resulted in exactly the same grouping as found with phospholipid fatty acid (PLFA) analysis (Cahyani et al. in Soil Sci Plant Nutr 48:735, 2002) and by the DGGE pattern analysis of the bacterial communities (Cahyani et al. in Soil Sci Plant Nutr 49:619, 2003) for the same samples, namely the communities characterizing the pre-composting stage (initial RS materials), and thermophilic, middle, and curing stages of the compost. Different eukaryotic members characterized the respective stages as follows: fungi (Ascomycota) for the initial RS materials, protozoans (Apicomplexa) as well as the fungi (Ascomycota) of the initial RS materials for the thermophilic stage, fungi (Ascomycota and Basidiomycota), protozoans (Opalozoa, Ciliophora and Leptomyxida), nematodes and stramenopiles for the middle stage, and fungi (Ascomycota, Zygomycota and Oomycota), algae (Haptophyceae and Chrysophyceae), and nematodes for the curing stage, respectively. Temperature, moisture content, and substrates available seemed to play a key role in determining the composition of eukaryotic members present at the respective stages of the composting process of RS.