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Impact of the chemical composition of applied organic materials on bacterial and archaeal community compositions in paddy soil


Microcosm experiments were performed to investigate the effect of organic material composition on soil bacterial and archaeal communities under paddy soil conditions. Rice straw and farmyard manure were used as the original organic materials, and three types of residues were prepared by sequential extraction from the original materials as follows: Residue 1 was obtained by lipid extraction with an ethanol–benzene mixture from the original material, Residue 2 was obtained by hot water extraction from Residue 1, and Residue 3 was obtained by hemicellulose extraction with 2% HCl from Residue 2. The organic material application did not affect soil pH and redox potential (Eh). The alpha diversities of bacterial and archaeal communities were significantly affected by the incubation period, chemical component differences, and organic material type. The relative abundance of Clostridiaceae and Bacillaceae increased in the microcosms treated with rice straw and farmyard manure, respectively, suggesting that they are important bacterial groups that may facilitate degradation of easily degradable organic fractions under waterlogged and anaerobic soil conditions. In the archaeal communities, the relative abundance of acetoclastic methanogens (Methanosarcinaceae) was increased by rice straw application. Principal coordinate analysis based on the weighted UniFrac distances showed that the application of rice straw caused greater changes in the soil bacterial and archaeal communities than farmyard manure. The bacterial and archaeal communities in the microcosms treated with organic materials differed even after lipid and water-soluble sugar extraction (Residue 1 and 2) depending on the type of the original organic materials used; however, when hemicellulose-free materials (Residue 3) were applied, the bacterial and archaeal community composition changed similarly during incubation. These results suggest that the difference in the proportions of hemicelluloses in rice straw and farmyard manure was the most significant factor in changing the bacterial and archaeal community compositions differently.

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The 16S rRNA gene amplicon sequences for this study were deposited in the DDBJ under the following accession number: DRR331204-DRR331380.


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This work was the result of using research equipment shared in the MEXT Project for promoting public utilization of advanced research infrastructure (Program for supporting introduction of the new sharing system) at Niigata University, Grant Number JPMXS0421100320.

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Correspondence to Kazuki Suzuki.

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Chowdhury, S.A., Kaneko, A., Baki, M.Z.I. et al. Impact of the chemical composition of applied organic materials on bacterial and archaeal community compositions in paddy soil. Biol Fertil Soils 58, 135–148 (2022).

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  • Organic materials
  • Sequential extraction
  • Bacterial and archaeal community
  • Paddy soil
  • Hemicellulose
  • High-throughput sequencing