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 K-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 s 800 bp) contributed 6 20%. Prolonged anoxic incubation (30^200 days) of the air-dried soils resulted in the production of CH 4 , 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. ß

Identification of iron-reducing microorganisms in anoxic rice paddy soil by 13C-acetate probing

“…Most likely, the 188 bp T-RF corresponds to Methanosarcina spp. and the 286 bp T-RF to Methanosaeta spp., as was earlier shown (Lueders and Friedrich, 2000;Ramakrishnan et al, 2001;Weber et al, 2001;Chin et al, 2004).…”

Community structure of bacteria and fungi responsible for rice straw decomposition in a paddy field estimated by PCR-RFLP analysis

“…GroSkopf et al 1998;Hengstmann et al 1999) were applied to the studies of the microbial communities in anoxic rice paddy soil. The polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method that analyzes 16S rDNA (for bacteria) and 18S rDNA (for fungi) to reveal the community structure of microbiota became popular in the last decade (Weisburg et al 1991: Amann et al 1995Fantroussi et al 1999;Montano et al 2000;Yang and Crowley 2000;Wang et al 2001) and the terminal restriction fragment length polymorphism (T-RFLP) method that can provide information not only about the diversity (species richness) of an ecosystem but also about the relative abundance of different terminal restriction fragments (species evenness) has been widely applied to rice field soil and rice roots for methanogens and methanotrophs (Chin et al I 999a, b;Fey and Conrad 2000;Lueders and Friedlich 2000: Derakshani et al 2001: Horz et al 2001Ramakrishnan et al 2001).…”

Effects of Dense Planting with Less Basal N Fertilization on Rice Yield, N Use Efficiency and Greenhouse Gas Emissions

“…As planting density increased with reduced basal N application; dense planting could enhance plant N uptake , which may cause the increase of N shortage of Methanotrophs, how planting density impact CH4 oxidation might represent an area for future research. The response of microbial processes of CH4 emission in the rice soils and rice plant growth to N application was interacted by crop management and climate conditions (Ramakrishnan et al, 2001;Zou et al, 2005;Xie et al, 2010). This study covered three major Chinese rice cropping areas with different climate features, soil properties, rice varieties and previous crop managements.…”