Succession and phylogenetic composition of eubacterial communities in rice straw during decomposition on the surface of paddy field soil

Abstract

To estimate the bacterial communities in rice straw left on the soil surface of paddy fields, polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis was conducted. Rice straw samples were placed on the soil surface in a Japanese paddy field under drained conditions after harvest and under flooded conditions after the transplanting of rice. The residual samples on the soil surface under upland conditions were collected just before spring plowing and were replaced again on the soil surface after transplanting, under flooded conditions. The DGGE patterns of the bacterial communities in rice straw on the surface of paddy field soil were divided into three groups, namely rice straw samples before placement, under drained conditions and under flooded conditions. Sequence analysis of DGGE bands indicated that most of the bacterial members in rice straw during decomposition on the soil surface in the paddy field belonged to Gram-negative bacteria. The bands that commonly existed throughout the periods under flooded and upland conditions were closely related to α-Proteobacteria. The groups of Spirochaetes and δ-Proteobacteria were often observed during flooded periods, although the members of Bacteroidetes, α-Proteobacteria, Gemmatimonadetes and Actinobacteria were also detected under flooded conditions. In contrast, the bands characteristic to the rice straw left on the soil surface of the paddy field under drained conditions belonged to Bacteroidetes and γ-Proteobacteria. This finding clearly indicates that the bacterial communities responsible for rice straw decomposition were determined by the water regime in the paddy field, and various members of Gram-negative bacteria have contributed to the decomposition of rice straw left on the soil surface in a paddy field.

Molecular characterization of T4‐type bacteriophages in a rice field

“…The rice field was located at Anjo Research and Extension Center in Japan, and experiment set‐up has been described in detail by Asari and colleagues (2007). Briefly, during the flooding period aerobic surface soil and the sheath part of rice straw in the surface layer of the rice field were collected in triplicate.…”

Incorporation of plant residue-derived carbon into the microeukaryotic community in a rice field soil revealed by DNA stable-isotope probing

“…In our recent study, dried rice callus labelled with 13 C was used as a model of plant residue to trace the incorporation of callus‐derived carbon into bacteria in a rice field soil under drained conditions through DNA‐SIP (Lee et al ., ). Results demonstrated that the bacterial community incorporating callus carbon was more diverse than expected from the results of the previous studies on the bacterial community inhabiting plant residues (Sugano et al ., ; Asari et al ., ; Matsuyama et al ., ).…”

“…Phospholipid fatty acids (PLFAs) profiling revealed the seasonal change in the bacterial community structure and fungal biomass of rice straw in a rice field (Nakamura et al ., ). Nucleic acid‐based analysis gave detailed phylogenetic information of the microbial community inhabiting plant residues (Weber et al ., , b; Sugano et al ., , b, ; Asari et al ., ). Comparison of the results from different microbial habitats in a rice field demonstrated that the microbial community of plant residues in rice field soil is distinct from that of the bulk soil (Kimura & Asakawa, ; Asakawa & Kimura, ).…”

Bacterial diversity and bioaugmentation in floodwater of a paddy field in the presence of the herbicide molinate

“…Floodwater is a complex habitat where organic matter is produced by algae and phytoplankton, with the contribution of floating weeds, and where microorganisms promote different catabolic processes (Asari et al 2007;Kimura et al 2002;Nakayama et al 2006). When compared with other natural aquatic environments, the floodwater ecosystem is unstable, being presumably affected by an interrelated set of factors (Shibagaki-Shimizu et al 2006).…”