Changes in community structure of methanogenic archaea brought about by water-saving practice in paddy field soil

Abstract

Changes in the community structure of methanogenic archaea in a paddy field soil brought about by an alternate wetting and drying (AWD) water-saving practice were shown by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and quantitative PCR analyses targeting archaeal 16S rRNA gene and methanogenic archaeal mcrA gene. Soil samples were collected four times from the field plots under the treatments of continuous flooding (CF) and AWD water-saving, where irrigation was conducted when soil water potential at 15 cm depth decreased to −20 kPa. The community analysis was performed over three rice cultivation periods in the wet season in 2008 (2008WS) and the dry and wet seasons in 2009 (2009DS and 2009WS, respectively). PCR-DGGE analysis showed that the archaeal 16S rRNA genes differed depending on water management. During the three rice cultivation periods, the community of the CF plots gradually changed with time, while the community of the AWD plots possessed a relatively large variation. Principal component analysis and sequencing analysis of selected 16S rRNA genes indicated that members of Methanosarcinales dominated in the CF plots while members of Methanocellales and uncultured group of “Thaumarchaeota” characterized the AWD plots. Numbers of archaeal 16S rRNA and methanogenic archaeal mcrA genes were significantly different between the CF and AWD plots in 2008WS, but not in 2009DS and 2009WS. Thus, the AWD water-saving practice did not reduce populations of the methanogenic archaea but moderately influenced the community structure in the paddy field soil.