Archaeal community structures in rice soils from different geographical regions before and after initiation of methane production

Abstract

The methane production potential of rice soils, which are situated in different geographical regions, shows inherent variations and is catalyzed by archaeal methanogens. We therefore investigated the archaeal community structure in 11 rice field soils which represent a range of climatic conditions (temperate to subtropical zones) and soil properties. Retrieval of environmental partial SSU rDNA sequences from the rice soils of Shenyang (China) and Gapan (The Philippines) showed that the communities were different from each other. However, despite the differences in soil properties and geographical region the sequences clustered in similar phylogenetic groups to those obtained earlier from rice fields of Vercelli (Italy). The archaeal community structure in the other rice field soils was compared using terminal restriction fragment length polymorphism (T-RFLP) analysis targeting the SSU rRNA gene and the methyl-coenzyme M reductase α-subunit gene (mcrA). The relative abundance of each terminal restriction fragment (T-RF) was determined by fluorescence peak area integration. The 182-bp SSU rDNA T-RF (representing members of Methanosarcinaceae and rice cluster (RC) VI) was dominant (40–80% contribution) in Chinese soils (Zhenjiang, Changchun, Jurong, Beiyuan, Shenyang) and the Philippine soil of Gapan. The other Philippine soils (Luisiana, Guangzhou, Pila) and the Italian soils (Vercelli, Pavia) showed a dominant 389-bp T-RF (35–40% contribution), representing mainly the novel methanogenic RC-I. All the other T-RF (80, 88, 280, 375 and >800 bp) contributed <20%. Prolonged anoxic incubation (30–200 days) of the air-dried soils resulted in the production of CH4, which was in some soils preceded by a characteristic halt phase. T-RFLP analysis revealed that the soils with a methanogenic halt phase also showed dramatic archaeal population dynamics which were related to the length of the halt phase. Our results show that the archaeal communities in rice field soils of different geographical origin are highly related, but nevertheless exhibit individual patterns and dynamics, thus providing evidence for the active participation of the community members in energy and carbon flow.