Ammonium-Generating Microbial Consortia in Paddy Soil Revealed by DNA-Stable Isotope Probing and Metatranscriptomics
Rice paddy fields are sustainable agricultural systems as soil microorganisms help maintain nitrogen fertility through generating ammonium. In these soils, dissimilatory nitrate reduction to ammonium (DNRA), nitrogen fixation, and denitrification are closely linked. DNRA and denitrification share th...
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2025-06-01
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| author | Chao-Nan Wang Yoko Masuda Keishi Senoo |
| author_facet | Chao-Nan Wang Yoko Masuda Keishi Senoo |
| author_sort | Chao-Nan Wang |
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| description | Rice paddy fields are sustainable agricultural systems as soil microorganisms help maintain nitrogen fertility through generating ammonium. In these soils, dissimilatory nitrate reduction to ammonium (DNRA), nitrogen fixation, and denitrification are closely linked. DNRA and denitrification share the same initial steps and nitrogen gas, the end product of denitrification, can serve as a substrate for nitrogen fixation. However, the microorganisms responsible for these three reductive nitrogen transformations, particularly those focused on ammonium generation, have not been comprehensively characterized. In this study, we used stable isotope probing with <sup>15</sup>NO<sub>3</sub><sup>−</sup>, <sup>15</sup>N<sub>2</sub>O, and <sup>15</sup>N<sub>2</sub>, combined with 16S rRNA high-throughput sequencing and metatranscriptomics, to identify ammonium-generating microbial consortia in paddy soils. Our results revealed that several bacterial families actively contribute to ammonium generation under different nitrogen substrate conditions. Specifically, <i>Geobacteraceae</i> (N<sub>2</sub>O and +N<sub>2</sub>), <i>Bacillaceae</i> (+NO<sub>3</sub><sup>−</sup> and +N<sub>2</sub>), <i>Rhodocyclaceae</i> (+N<sub>2</sub>O and +N<sub>2</sub>), <i>Anaeromyxobacteraceae</i> (+NO<sub>3</sub><sup>−</sup> and +N<sub>2</sub>O), and <i>Clostridiaceae</i> (+NO<sub>3</sub><sup>−</sup> and +N<sub>2</sub>) were involved. Many of these bacteria participate in key ecological processes typical of paddy environments, including iron or sulfate reduction and rice straw decomposition. This study revealed the ammonium-generating microbial consortia in paddy soil that contain several key bacterial drivers of multiple reductive nitrogen transformations and suggested their diverse functions in paddy soil metabolism. |
| format | Article |
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| institution | DOAJ |
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| language | English |
| publishDate | 2025-06-01 |
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| series | Microorganisms |
| spelling | doaj-art-3e04afff50a844de97e578ed90d2a95f2025-08-20T03:08:02ZengMDPI AGMicroorganisms2076-26072025-06-01137144810.3390/microorganisms13071448Ammonium-Generating Microbial Consortia in Paddy Soil Revealed by DNA-Stable Isotope Probing and MetatranscriptomicsChao-Nan Wang0Yoko Masuda1Keishi Senoo2Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, JapanDepartment of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, JapanDepartment of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, JapanRice paddy fields are sustainable agricultural systems as soil microorganisms help maintain nitrogen fertility through generating ammonium. In these soils, dissimilatory nitrate reduction to ammonium (DNRA), nitrogen fixation, and denitrification are closely linked. DNRA and denitrification share the same initial steps and nitrogen gas, the end product of denitrification, can serve as a substrate for nitrogen fixation. However, the microorganisms responsible for these three reductive nitrogen transformations, particularly those focused on ammonium generation, have not been comprehensively characterized. In this study, we used stable isotope probing with <sup>15</sup>NO<sub>3</sub><sup>−</sup>, <sup>15</sup>N<sub>2</sub>O, and <sup>15</sup>N<sub>2</sub>, combined with 16S rRNA high-throughput sequencing and metatranscriptomics, to identify ammonium-generating microbial consortia in paddy soils. Our results revealed that several bacterial families actively contribute to ammonium generation under different nitrogen substrate conditions. Specifically, <i>Geobacteraceae</i> (N<sub>2</sub>O and +N<sub>2</sub>), <i>Bacillaceae</i> (+NO<sub>3</sub><sup>−</sup> and +N<sub>2</sub>), <i>Rhodocyclaceae</i> (+N<sub>2</sub>O and +N<sub>2</sub>), <i>Anaeromyxobacteraceae</i> (+NO<sub>3</sub><sup>−</sup> and +N<sub>2</sub>O), and <i>Clostridiaceae</i> (+NO<sub>3</sub><sup>−</sup> and +N<sub>2</sub>) were involved. Many of these bacteria participate in key ecological processes typical of paddy environments, including iron or sulfate reduction and rice straw decomposition. This study revealed the ammonium-generating microbial consortia in paddy soil that contain several key bacterial drivers of multiple reductive nitrogen transformations and suggested their diverse functions in paddy soil metabolism.https://www.mdpi.com/2076-2607/13/7/1448<sup>15</sup>N stable isotope probingmetatranscriptomicsnitrogen-fixing bacteriaammonium generationdissimilatory nitrate reduction to ammoniumdenitrification |
| spellingShingle | Chao-Nan Wang Yoko Masuda Keishi Senoo Ammonium-Generating Microbial Consortia in Paddy Soil Revealed by DNA-Stable Isotope Probing and Metatranscriptomics Microorganisms <sup>15</sup>N stable isotope probing metatranscriptomics nitrogen-fixing bacteria ammonium generation dissimilatory nitrate reduction to ammonium denitrification |
| title | Ammonium-Generating Microbial Consortia in Paddy Soil Revealed by DNA-Stable Isotope Probing and Metatranscriptomics |
| title_full | Ammonium-Generating Microbial Consortia in Paddy Soil Revealed by DNA-Stable Isotope Probing and Metatranscriptomics |
| title_fullStr | Ammonium-Generating Microbial Consortia in Paddy Soil Revealed by DNA-Stable Isotope Probing and Metatranscriptomics |
| title_full_unstemmed | Ammonium-Generating Microbial Consortia in Paddy Soil Revealed by DNA-Stable Isotope Probing and Metatranscriptomics |
| title_short | Ammonium-Generating Microbial Consortia in Paddy Soil Revealed by DNA-Stable Isotope Probing and Metatranscriptomics |
| title_sort | ammonium generating microbial consortia in paddy soil revealed by dna stable isotope probing and metatranscriptomics |
| topic | <sup>15</sup>N stable isotope probing metatranscriptomics nitrogen-fixing bacteria ammonium generation dissimilatory nitrate reduction to ammonium denitrification |
| url | https://www.mdpi.com/2076-2607/13/7/1448 |
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