Microbial genomic database of the Yangtze River, the third-longest river on Earth
Abstract Microbes play an important role in mediating the nutrient cycling in the river ecosystem as a hotspot for biogeochemical processes. Due to scattered sampling efforts, however, there is a lack of a systematic study of the diversity of prokaryotic genomes in the Yangtze River, the third longe...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-07-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-025-05548-x |
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| author | Minglei Ren Bensheng You Xue Gong Peixuan Zhang Jianjun Wang |
| author_facet | Minglei Ren Bensheng You Xue Gong Peixuan Zhang Jianjun Wang |
| author_sort | Minglei Ren |
| collection | DOAJ |
| description | Abstract Microbes play an important role in mediating the nutrient cycling in the river ecosystem as a hotspot for biogeochemical processes. Due to scattered sampling efforts, however, there is a lack of a systematic study of the diversity of prokaryotic genomes in the Yangtze River, the third longest river on Earth. Here, we collected 602 metagenomic datasets of water, sediment and riparian soil samples spanning the Upper, Middle, and Lower basins of the Yangtze River over a 6,300 km continuum. We reconstructed 8,110 qualified genomes represented by 927 species-level genomes at the 95% ANI threshold, spanning 31 bacterial and five archaeal phyla. We further showed that more than half of these species (61.3% ~ 82.4%) were novel according to the genomic comparison against the curated databases, greatly expanding the known diversity of river prokaryotes. This dataset depicts an overview of microbial genomic diversity in the Yangtze River and provides a resource for in-depth investigation of metabolic potential, ecology, and evolution of riverine microbiomes. |
| format | Article |
| id | doaj-art-c1efc870d40c45e9894f0ea62d87209d |
| institution | Kabale University |
| issn | 2052-4463 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Data |
| spelling | doaj-art-c1efc870d40c45e9894f0ea62d87209d2025-08-20T03:45:45ZengNature PortfolioScientific Data2052-44632025-07-011211610.1038/s41597-025-05548-xMicrobial genomic database of the Yangtze River, the third-longest river on EarthMinglei Ren0Bensheng You1Xue Gong2Peixuan Zhang3Jianjun Wang4State Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and Limnology, Chinese Academy of SciencesState Environmental Protection Key Laboratory of Aquatic Ecosystem Health in the Middle and Lower Reaches of Yangtze RiverState Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and Limnology, Chinese Academy of SciencesState Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and Limnology, Chinese Academy of SciencesState Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and Limnology, Chinese Academy of SciencesAbstract Microbes play an important role in mediating the nutrient cycling in the river ecosystem as a hotspot for biogeochemical processes. Due to scattered sampling efforts, however, there is a lack of a systematic study of the diversity of prokaryotic genomes in the Yangtze River, the third longest river on Earth. Here, we collected 602 metagenomic datasets of water, sediment and riparian soil samples spanning the Upper, Middle, and Lower basins of the Yangtze River over a 6,300 km continuum. We reconstructed 8,110 qualified genomes represented by 927 species-level genomes at the 95% ANI threshold, spanning 31 bacterial and five archaeal phyla. We further showed that more than half of these species (61.3% ~ 82.4%) were novel according to the genomic comparison against the curated databases, greatly expanding the known diversity of river prokaryotes. This dataset depicts an overview of microbial genomic diversity in the Yangtze River and provides a resource for in-depth investigation of metabolic potential, ecology, and evolution of riverine microbiomes.https://doi.org/10.1038/s41597-025-05548-x |
| spellingShingle | Minglei Ren Bensheng You Xue Gong Peixuan Zhang Jianjun Wang Microbial genomic database of the Yangtze River, the third-longest river on Earth Scientific Data |
| title | Microbial genomic database of the Yangtze River, the third-longest river on Earth |
| title_full | Microbial genomic database of the Yangtze River, the third-longest river on Earth |
| title_fullStr | Microbial genomic database of the Yangtze River, the third-longest river on Earth |
| title_full_unstemmed | Microbial genomic database of the Yangtze River, the third-longest river on Earth |
| title_short | Microbial genomic database of the Yangtze River, the third-longest river on Earth |
| title_sort | microbial genomic database of the yangtze river the third longest river on earth |
| url | https://doi.org/10.1038/s41597-025-05548-x |
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