Abstract
The succession and phylogenetic profiles of methanogenic archaeal communities associated with rice straw decomposition in rice-field soil were studied by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis followed by 16S rDNA sequencing. Nylon bags containing either leaf sheaths or blades were buried in the plowed layer of a Japanese rice field under drained conditions during the off-crop season and under flooded conditions after transplanting. In addition, rice straw samples that had been buried in the rice field under drained conditions during the off-crop season were temporarily removed during spring plowing and then re-buried in the same rice field under flooded conditions at transplanting. Populations of methanogenic archaea were examined by amplification of the 16S rRNA genes in the DNA extracted from the rice straw samples. No PCR product was produced for samples of leaf sheath or blade prior to burial or after burial under drained conditions, indicating that the methanogen population was very small during decomposition of rice straw under oxic conditions. Many common bands were observed in rice straw samples of leaf sheath and blade during decomposition of rice straw under flooded conditions. Cluster analysis based on DGGE patterns divided methanogenic archaeal communities into two groups before and after the mid-season drainage. Sequence analysis of DGGE bands that were commonly present were closely related to Methanomicrobiales and Rice cluster I. Methanomicrobiales, Rice cluster I and Methanosarcinales were major members before the mid-season drainage, whereas the DGGE bands that characterized methanogenic archaeal communities after the mid-season drainage were closely related to Methanomicrobiales. These results indicate that mid-season drainage affected the methanogenic archaeal communities irrespective of their location on rice straw (sheath and blade) and the previous history of decomposition during the off-crop season.
Highlights
Rice fields are usually flooded during most of the cultivation period
Methanogenic archaeal communities involved in the decomposition of rice straw in anoxic rice soil microcosms have been determined by sequencing rRNA gene libraries, terminal restriction fragment length polymorphisms (T-RFLP) and slot blot hybridizations to include Methanobacterium, Methanosarcina and Rice cluster I (Weber et al 2001)
Methanogenic archaeal 16S rRNA genes were successfully amplified by PCR from rice straw samples under flooded conditions in both Experiments 1 and 2
Summary
Rice fields are usually flooded during most of the cultivation period. Anaerobic decomposition of organic matter in flooded rice fields produces methane, making the fields a major source of atmospheric methane. Acetate and syntrophically degraded propionate are the main precursors of methane during decomposition of rice straw in anoxic rice-field soils (Glissmann and Conrad 2000). The dynamics of methanogenic populations and their activities in rice fields amended with rice straw have been investigated (Adachi et al 1996, Joulian et al 1996, Asakawa et al 1998, Kaku et al 2000). Methanogenic archaeal communities involved in the decomposition of rice straw in anoxic rice soil microcosms have been determined by sequencing rRNA gene libraries, terminal restriction fragment length polymorphisms (T-RFLP) and slot blot hybridizations to include Methanobacterium, Methanosarcina and Rice cluster I (Weber et al 2001). The methanogenic archaeal communities responsible for decomposition of rice straw in fields have not yet been investigated using molecular biological methods
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