Unprecedented N2O production by nitrate-ammonifying Geobacteraceae with distinctive N2O isotopocule signatures
ABSTRACT Dissimilatory nitrate reduction to ammonium (DNRA), driven by nitrate-ammonifying bacteria, is an increasingly appreciated nitrogen-cycling pathway in terrestrial ecosystems. This process reportedly generates nitrous oxide (N2O), a strong greenhouse gas with ozone-depleting effects. However...
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American Society for Microbiology
2024-12-01
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| Series: | mBio |
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| Online Access: | https://journals.asm.org/doi/10.1128/mbio.02540-24 |
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| author | Zhenxing Xu Shohei Hattori Yoko Masuda Sakae Toyoda Keisuke Koba Pei Yu Naohiro Yoshida Zong-Jun Du Keishi Senoo |
| author_facet | Zhenxing Xu Shohei Hattori Yoko Masuda Sakae Toyoda Keisuke Koba Pei Yu Naohiro Yoshida Zong-Jun Du Keishi Senoo |
| author_sort | Zhenxing Xu |
| collection | DOAJ |
| description | ABSTRACT Dissimilatory nitrate reduction to ammonium (DNRA), driven by nitrate-ammonifying bacteria, is an increasingly appreciated nitrogen-cycling pathway in terrestrial ecosystems. This process reportedly generates nitrous oxide (N2O), a strong greenhouse gas with ozone-depleting effects. However, it remains poorly understood how N2O is produced by environmental nitrate-ammonifiers and how to identify DNRA-derived N2O. In this study, we characterize two novel enzymatic pathways responsible for N2O production in Geobacteraceae strains, which are predominant nitrate-ammonifying bacteria in paddy soils. The first pathway involves a membrane-bound nitrate reductase (Nar) and a hybrid cluster protein complex (Hcp–Hcr) that catalyzes the conversion of NO2− to NO and subsequently to N2O. The second pathway is observed in Nar-deficient bacteria, where the nitrite reductase (NrfA) generates NO, which is then reduced to N2O by Hcp–Hcr. These enzyme combinations are prevalent across the domain Bacteria. Moreover, we observe distinctive isotopocule signatures of DNRA-derived N2O from other established N2O production pathways, especially through the highest 15N-site preference (SP) values (43.0‰–49.9‰) reported so far, indicating a robust means for N2O source partitioning. Our findings demonstrate two novel N2O production pathways in DNRA that can be isotopically distinguished from other pathways.IMPORTANCEStimulation of DNRA is a promising strategy to improve fertilizer efficiency and reduce N2O emission in agriculture soils. This process converts water-leachable NO3− and NO2− into soil-adsorbable NH4+, thereby alleviating nitrogen loss and N2O emission resulting from denitrification. However, several studies have noted that DNRA can also be a source of N2O, contributing to global warming. This contribution is often masked by other N2O generation processes, leading to a limited understanding of DNRA as an N2O source. Our study reveals two widespread yet overlooked N2O production pathways in Geobacteraceae, the predominant DNRA bacteria in paddy soils, along with their distinctive isotopocule signatures. These findings offer novel insights into the role of the DNRA bacteria in N2O production and underscore the significance of N2O isotopocule signatures in microbial N2O source tracking. |
| format | Article |
| id | doaj-art-cebaa0e05fd8400eb10e7041aa37f4fe |
| institution | OA Journals |
| issn | 2150-7511 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mBio |
| spelling | doaj-art-cebaa0e05fd8400eb10e7041aa37f4fe2025-08-20T02:33:47ZengAmerican Society for MicrobiologymBio2150-75112024-12-01151210.1128/mbio.02540-24Unprecedented N2O production by nitrate-ammonifying Geobacteraceae with distinctive N2O isotopocule signaturesZhenxing Xu0Shohei Hattori1Yoko Masuda2Sakae Toyoda3Keisuke Koba4Pei Yu5Naohiro Yoshida6Zong-Jun Du7Keishi Senoo8Marine College, Shandong University, Weihai, ChinaInternational Center for Isotope Effects Research (ICIER), Nanjing University, Nanjing, ChinaDepartment of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, JapanSchool of Materials and Chemical Technology, Institute of Science Tokyo, Yokohama, JapanCenter for Ecological Research, Kyoto University, Shiga, JapanSDU-ANU Joint Science College, Shandong University, Weihai, ChinaEarth-Life Science Institute, Institute of Science Tokyo, Tokyo, JapanMarine College, Shandong University, Weihai, ChinaDepartment of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, JapanABSTRACT Dissimilatory nitrate reduction to ammonium (DNRA), driven by nitrate-ammonifying bacteria, is an increasingly appreciated nitrogen-cycling pathway in terrestrial ecosystems. This process reportedly generates nitrous oxide (N2O), a strong greenhouse gas with ozone-depleting effects. However, it remains poorly understood how N2O is produced by environmental nitrate-ammonifiers and how to identify DNRA-derived N2O. In this study, we characterize two novel enzymatic pathways responsible for N2O production in Geobacteraceae strains, which are predominant nitrate-ammonifying bacteria in paddy soils. The first pathway involves a membrane-bound nitrate reductase (Nar) and a hybrid cluster protein complex (Hcp–Hcr) that catalyzes the conversion of NO2− to NO and subsequently to N2O. The second pathway is observed in Nar-deficient bacteria, where the nitrite reductase (NrfA) generates NO, which is then reduced to N2O by Hcp–Hcr. These enzyme combinations are prevalent across the domain Bacteria. Moreover, we observe distinctive isotopocule signatures of DNRA-derived N2O from other established N2O production pathways, especially through the highest 15N-site preference (SP) values (43.0‰–49.9‰) reported so far, indicating a robust means for N2O source partitioning. Our findings demonstrate two novel N2O production pathways in DNRA that can be isotopically distinguished from other pathways.IMPORTANCEStimulation of DNRA is a promising strategy to improve fertilizer efficiency and reduce N2O emission in agriculture soils. This process converts water-leachable NO3− and NO2− into soil-adsorbable NH4+, thereby alleviating nitrogen loss and N2O emission resulting from denitrification. However, several studies have noted that DNRA can also be a source of N2O, contributing to global warming. This contribution is often masked by other N2O generation processes, leading to a limited understanding of DNRA as an N2O source. Our study reveals two widespread yet overlooked N2O production pathways in Geobacteraceae, the predominant DNRA bacteria in paddy soils, along with their distinctive isotopocule signatures. These findings offer novel insights into the role of the DNRA bacteria in N2O production and underscore the significance of N2O isotopocule signatures in microbial N2O source tracking.https://journals.asm.org/doi/10.1128/mbio.02540-24nitrate-ammonifying bacteriaDNRAGeobacteraceaeN2O productionN2O isotopocule signaturespaddy soils |
| spellingShingle | Zhenxing Xu Shohei Hattori Yoko Masuda Sakae Toyoda Keisuke Koba Pei Yu Naohiro Yoshida Zong-Jun Du Keishi Senoo Unprecedented N2O production by nitrate-ammonifying Geobacteraceae with distinctive N2O isotopocule signatures mBio nitrate-ammonifying bacteria DNRA Geobacteraceae N2O production N2O isotopocule signatures paddy soils |
| title | Unprecedented N2O production by nitrate-ammonifying Geobacteraceae with distinctive N2O isotopocule signatures |
| title_full | Unprecedented N2O production by nitrate-ammonifying Geobacteraceae with distinctive N2O isotopocule signatures |
| title_fullStr | Unprecedented N2O production by nitrate-ammonifying Geobacteraceae with distinctive N2O isotopocule signatures |
| title_full_unstemmed | Unprecedented N2O production by nitrate-ammonifying Geobacteraceae with distinctive N2O isotopocule signatures |
| title_short | Unprecedented N2O production by nitrate-ammonifying Geobacteraceae with distinctive N2O isotopocule signatures |
| title_sort | unprecedented n2o production by nitrate ammonifying geobacteraceae with distinctive n2o isotopocule signatures |
| topic | nitrate-ammonifying bacteria DNRA Geobacteraceae N2O production N2O isotopocule signatures paddy soils |
| url | https://journals.asm.org/doi/10.1128/mbio.02540-24 |
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