Microbial potential to mitigate neurotoxic methylmercury accumulation in farmlands and rice
Abstract Toxic methylmercury (CH3Hg+) is produced by microbial conversion of inorganic mercury in hypoxic environments such as rice paddy soils, and can accumulate in rice grains. Although microbial demethylation has been recognized as a crucial pathway for CH3Hg+ degradation, the identities of micr...
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Nature Portfolio
2025-06-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-60458-1 |
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| author | Xin-Quan Zhou Kang-Hua Chen Ri-Qing Yu Man Yang Qin Liu Yun-Yun Hao Jibing Li Hui-Wen Liu Jiao Feng Wenfeng Tan Qiaoyun Huang Baohua Gu Yu-Rong Liu |
| author_facet | Xin-Quan Zhou Kang-Hua Chen Ri-Qing Yu Man Yang Qin Liu Yun-Yun Hao Jibing Li Hui-Wen Liu Jiao Feng Wenfeng Tan Qiaoyun Huang Baohua Gu Yu-Rong Liu |
| author_sort | Xin-Quan Zhou |
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| description | Abstract Toxic methylmercury (CH3Hg+) is produced by microbial conversion of inorganic mercury in hypoxic environments such as rice paddy soils, and can accumulate in rice grains. Although microbial demethylation has been recognized as a crucial pathway for CH3Hg+ degradation, the identities of microbes and pathways accountable for CH3Hg+ degradation in soil remain elusive. Here, we combine 13CH3Hg+-DNA stable-isotope probing experiments with shotgun metagenomics to explore microbial taxa and associated biochemical processes involved in CH3Hg+ degradation in paddy and upland soils. We identify Pseudarthrobacter, Methylophilaceae (MM2), and Dechloromonas as the most significant taxa potentially engaged in the degradation of 13CH3Hg+ in paddy soil with high mercury contamination. We confirm that strains affiliated with two of those taxa (species Dechloromonas denitrificans and Methylovorus menthalis) can degrade CH3Hg+ in pure culture assays. Metagenomic analysis further reveals that most of these candidate 13CH3Hg+ degraders carry genes associated with the Wood-Ljungdahl pathway, dicarboxylate-hydroxybutyrate cycle, methanogenesis, and denitrification, but apparently lack the merB and merA genes involved in CH3Hg+ reductive demethylation. Finally, we estimate that microbial degradation of soil CH3Hg+ contributes to 0.08–0.64 fold decreases in CH3Hg+ accumulation in rice grains across China (hazard quotient (HQ) decrements of 0.62–13.75%). Thus, our results provide insights into microorganisms and pathways responsible for CH3Hg+ degradation in soil, with potential implications for development of bioremediation strategies. |
| format | Article |
| id | doaj-art-82eb84e889404b9095dd52fea6177cca |
| institution | OA Journals |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | Nature Portfolio |
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| series | Nature Communications |
| spelling | doaj-art-82eb84e889404b9095dd52fea6177cca2025-08-20T02:30:42ZengNature PortfolioNature Communications2041-17232025-06-0116111310.1038/s41467-025-60458-1Microbial potential to mitigate neurotoxic methylmercury accumulation in farmlands and riceXin-Quan Zhou0Kang-Hua Chen1Ri-Qing Yu2Man Yang3Qin Liu4Yun-Yun Hao5Jibing Li6Hui-Wen Liu7Jiao Feng8Wenfeng Tan9Qiaoyun Huang10Baohua Gu11Yu-Rong Liu12National Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural UniversityNational Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural UniversityDepartment of Biology, Center for Environment, Biodiversity and Conservation, The University of Texas at TylerNational Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural UniversityNational Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural UniversityNational Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural UniversityState Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of SciencesNational Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural UniversityNational Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural UniversityNational Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural UniversityNational Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural UniversityEnvironmental Sciences Division, Oak Ridge National LaboratoryNational Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural UniversityAbstract Toxic methylmercury (CH3Hg+) is produced by microbial conversion of inorganic mercury in hypoxic environments such as rice paddy soils, and can accumulate in rice grains. Although microbial demethylation has been recognized as a crucial pathway for CH3Hg+ degradation, the identities of microbes and pathways accountable for CH3Hg+ degradation in soil remain elusive. Here, we combine 13CH3Hg+-DNA stable-isotope probing experiments with shotgun metagenomics to explore microbial taxa and associated biochemical processes involved in CH3Hg+ degradation in paddy and upland soils. We identify Pseudarthrobacter, Methylophilaceae (MM2), and Dechloromonas as the most significant taxa potentially engaged in the degradation of 13CH3Hg+ in paddy soil with high mercury contamination. We confirm that strains affiliated with two of those taxa (species Dechloromonas denitrificans and Methylovorus menthalis) can degrade CH3Hg+ in pure culture assays. Metagenomic analysis further reveals that most of these candidate 13CH3Hg+ degraders carry genes associated with the Wood-Ljungdahl pathway, dicarboxylate-hydroxybutyrate cycle, methanogenesis, and denitrification, but apparently lack the merB and merA genes involved in CH3Hg+ reductive demethylation. Finally, we estimate that microbial degradation of soil CH3Hg+ contributes to 0.08–0.64 fold decreases in CH3Hg+ accumulation in rice grains across China (hazard quotient (HQ) decrements of 0.62–13.75%). Thus, our results provide insights into microorganisms and pathways responsible for CH3Hg+ degradation in soil, with potential implications for development of bioremediation strategies.https://doi.org/10.1038/s41467-025-60458-1 |
| spellingShingle | Xin-Quan Zhou Kang-Hua Chen Ri-Qing Yu Man Yang Qin Liu Yun-Yun Hao Jibing Li Hui-Wen Liu Jiao Feng Wenfeng Tan Qiaoyun Huang Baohua Gu Yu-Rong Liu Microbial potential to mitigate neurotoxic methylmercury accumulation in farmlands and rice Nature Communications |
| title | Microbial potential to mitigate neurotoxic methylmercury accumulation in farmlands and rice |
| title_full | Microbial potential to mitigate neurotoxic methylmercury accumulation in farmlands and rice |
| title_fullStr | Microbial potential to mitigate neurotoxic methylmercury accumulation in farmlands and rice |
| title_full_unstemmed | Microbial potential to mitigate neurotoxic methylmercury accumulation in farmlands and rice |
| title_short | Microbial potential to mitigate neurotoxic methylmercury accumulation in farmlands and rice |
| title_sort | microbial potential to mitigate neurotoxic methylmercury accumulation in farmlands and rice |
| url | https://doi.org/10.1038/s41467-025-60458-1 |
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