Dynamics of methanogenic archaeal communities based on rRNA analysis and their relation to methanogenic activity in Japanese paddy field soils

We investigated the relationships between dynamics of methanogenic archaeal communities and methanogenic activities in Japanese paddy field soils by reverse transcription-PCR-denaturing gradient gel electrophoresis (RT-PCR-DGGE) and real-time PCR targeting 16S rRNA gene (16S rDNA) and 16S rRNA. The investigated paddy fields were managed on a double-cropping system, where rice was cultivated under flooded conditions in summer and wheat was cropped after drainage in winter under drained conditions. Methanogenic archaeal 16S rRNAs were retrieved from all collected soil samples even under drained conditions by RT-PCR. DGGE band patterns from methanogenic archaeal 16S rRNAs were stable throughout the year and were similar to the patterns from their 16S rDNAs. Sequences of main DGGE bands were closely related to Methanomicrobiales, Methanosarcinales and Rice cluster I, indicating those methanogenic archaea predominantly maintained basal metabolism in the paddy fields. Numbers of methanogenic archaeal 16S rDNAs and 16S rRNAs ranged from 5.9×107 to 1.3×109 and from 5.3×109 to 2.9×1011 g−1 dry soil, respectively. The ratio of 16S rRNAs per one 16S rDNA fragment fluctuated between 9.4 and 1.2×103 and increased during rice cultivations although contrary results were also obtained in some investigated plots. Methanogenic activities under flooded conditions were higher than those under drained conditions. These results suggested that activities of methanogenic archaeal communities fluctuated in a year depending on soil conditions. Surprisingly, 6.7×107 g−1 dry soil of methanogenic archaeal 16S rDNAs and certain number of their 16S rRNAs were detected even in a long-term air-dried paddy soil (15 years). When the air-dried soil was incubated under anoxic flooded condition, methane was vigorously produced after 6 days and the number of methanogenic archaeal 16S rRNA gradually increased during the incubation. These results indicated that methanogenic archaea were dormant or starved, but survived in oxic paddy soils, and their activity increased under the conditions suitable for growth.