Paddy-upland rotation makes distinct impacts on the abundance of methane-oxidizing and ammonia-oxidizing microbial communities in paddy field soil

Paddy-upland rotation systems have been used as a major land management of paddy fields in Japan. In the paddy-upland rotational fields, upland crops are cultivated under drained conditions in summer for one year to several years, followed by paddy rice cropping for one year to several years. The soil conditions are kept oxic during the upland periods in these fields. Microbial communities in paddy field soil are greatly affected by these managements. In the present study, effect of paddy-upland rotation on the abundance of methane-oxidizing bacteria (MOB) and ammonia-oxidizing bacteria (AOB) and archaea (AOA) was investigated. Soil samples were collected from the rotational plots and consecutive paddy (control) plots at the experimental fields, where paddy rice under flooded conditions was rotated with soybean under upland conditions at different rotation histories. Abundance of MOB, AOB, and AOA communities was estimated by the quantitative PCR analyses of <i>pmoA</i> and <i>amoA</i> genes for DNAs extracted from the soil samples. The gene abundance of <i>pmoA</i> of MOB was an order of magnitude greater in the consecutive paddy plots (10⁶ copies g⁻¹ dry soil) than in the rotational plots (10⁵ copies g⁻¹ dry soil). In contrast, the gene abundance of <i>amoA</i> of AOB was an order of magnitude greater in the rotational plots (10⁸ copies g⁻¹ dry soil) than in the consecutive paddy plots (10⁷ copies g⁻¹ dry soil). The gene abundance of <i>amoA</i> of AOA was on the order of 10⁹ copies g⁻¹ dry soil both in the rotational and consecutive paddy plots and showed very small differences between the plots. These results indicated that the factors affecting fluctuation in the community abundance caused by the paddy-upland rotation could be different among MOB, AOB, and AOA in the paddy field soil.