Succession and phylogenetic profile of methanogenic archaeal communities during the composting process of rice straw estimated by PCR-DGGE analysis

Abstract

The succession and phylogenetic profile of methanogenic archaeal communities for rice straw (RS) in the composting process were studied by polymerase-chain reaction (PCR)denaturing gradient gel electrophoresis (DGGE) analysis followed by sequencing. Three groups of DGGE bands of methanogenic archaeal communities appeared successively in the present composting process. The first group of DGGE bands characterized the communities that were probably associated with soil contamination and survived during the early stage of composting. The second and the third groups of DGGE bands characterized the communities that proliferated and played a role in the anaerobic decomposition of RS during the middle and curing stages. Methanogenic archaeal communities were detected at every stage of rice straw composting except for one sampling time on day 14 at the end of the thermophilic stage. Among the 12 sequenced DGGE bands, 7 bands corresponded to Methanomicrobiales, 4 bands to novel uncultured euryarchaeota belonging to “Rice Cluster I,” and one band to Methanosarcinales. Two DGGE bands which appeared from day 28 of the second temperature peak (48°C) to the end of composting corresponded to the thermophilic strain of Methanoculleus thermophilus CR-1. Six bands corresponded to the methanogens that originated from paddy field soils, which indicated that methanogens in RS compost were derived mainly from rice fields.