Abstract
Purpose
Plant residues are one of the main sources of soil organic matter in paddy fields, and elucidation of the bacterial communities decomposing plant residues was important to understand their function and roles, as the microbial decomposition of plant residues is linked to soil fertility. We conducted a DNA stable isotope probing (SIP) experiment to elucidate the bacterial community assimilating 13-carbon (13C) derived from plant residue under an anoxic soil condition. In addition, we compared the bacterial community with that under the oxic soil condition, which was elucidated in our previous study (Lee et al. in Soil Biol Biochem 43:814–822, 2011).
Materials and methods
We used the 13C-labeled dried rice callus cells as a model of rice plant residue. A paddy field soil was incubated with unlabeled and 13C-labeled callus cells. DNA extracted from the soils was subjected to buoyant density gradient centrifugation to fractionate 13C-enriched DNA. Then, polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE) analysis of bacterial 16S rDNA band patterns and band sequencing method were used to evaluate bacterial community.
Results and discussion
DGGE analysis showed that the band patterns in the 13C-enriched fractions were distinctly changed over time, while the changes in the community structure before fractionation were minor. Sequencing of the 13C-labeled DGGE bands revealed that Clostridia were a major group in the bacterial communities incorporating the callus-derived carbon although Gram-negative bacteria, and Actinobacteria also participated in the carbon flow from the callus under the anoxic condition. The proportion of Gram-negative bacteria and Actinobacteria increased on 14 days after the onset of incubation, suggesting that the callus was decomposed by diverse bacterial members on this phase. When the bacterial groups incorporating the 13C were compared between under anoxic and oxic soil conditions, the composition was largely different under the two opposite conditions. However, some members of Gram-negative bacteria were commonly found under the anoxic and oxic soil conditions.
Conclusions
The majority of bacterial members assimilating the callus carbon was Clostridia in the soil under anoxic conditions. However, several Gram-negative bacterial members, such as Acidobacteria, Bacteroidetes, and Proteobacteria, also participated in the decomposition of callus under anoxic soil conditions. Our study showed that carbon flow into the diverse bacterial members during the callus decomposition and the distinctiveness of the bacterial communities was formed under the anoxic and oxic soil conditions.
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Acknowledgements
We thank Professors Makoto Kimura and Akira Watanabe and Associate Professor Jun Murase, Graduate School of Bioagricultural Sciences, Nagoya University, for their valuable criticisms, comments, and suggestions. We also thank Dr. Yutaka Sato, Graduate School of Bioagricultural Sciences, Nagoya University, for preparing callus cells. We wish to thank the members of Aichi-ken Anjo Research and Extension Center for allowing us to use the soil samples.
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Lee, C.G., Watanabe, T. & Asakawa, S. Bacterial community incorporating carbon derived from plant residue in an anoxic non-rhizosphere soil estimated by DNA-SIP analysis. J Soils Sediments 17, 1084–1091 (2017). https://doi.org/10.1007/s11368-016-1621-0
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DOI: https://doi.org/10.1007/s11368-016-1621-0