Methanogenic archaeal communities in paddy field soils in north-east China as evaluated by PCR-DGGE, sequencing and real-time PCR analyses

Abstract Community structures of methanogenic archaea in north-east China (NE China) were investigated by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), sequencing and real-time PCR methods. Plow layer soil samples were collected from 15 paddy fields over a broad area in NE China during March and April 2007. The DGGE banding patterns of methanogenic archaeal 16S rRNA genes amplified with primers 1106F-GC and 1378R in NE China were distinctly different from those obtained from Anjo and Chikugo paddy fields in Japan, and were also influenced by soil types and sampling locations inNE China. Real-time PCR quantification showed that the numbers of methanogenic archaeal 16S rRNA genes and mcrA genes, encoding the methyl-coenzyme M reductase a subunit of methanogenic archaea, ranged from 4.0 × 106 to 2.7 × 108 and from 4.7 × 105 to 3.2 × 107 g−1 dry soil, respectively. In total, 53 DGGE bands were sequenced and 42 sequences with different nucleotides were detected; 85.7% of the sequences were identified as methanogenic archaea. Phylogenetic analysis of the sequenced 16S rRNA genes indicated that methanogenic archaea belonging to Methanosaetaceae, Methanocellales, Methanomicrobiales and Methanosarcinaceae dominated the paddy fields in NE China.