A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources
Abstract Soil harbors a vast expanse of unidentified microbes, termed as microbial dark matter, presenting an untapped reservoir of microbial biodiversity and genetic resources, but has yet to be fully explored. In this study, we conduct a large-scale excavation of soil microbial dark matter by reco...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2023-11-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-023-43000-z |
| _version_ | 1797397882134855680 |
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| author | Bin Ma Caiyu Lu Yiling Wang Jingwen Yu Kankan Zhao Ran Xue Hao Ren Xiaofei Lv Ronghui Pan Jiabao Zhang Yongguan Zhu Jianming Xu |
| author_facet | Bin Ma Caiyu Lu Yiling Wang Jingwen Yu Kankan Zhao Ran Xue Hao Ren Xiaofei Lv Ronghui Pan Jiabao Zhang Yongguan Zhu Jianming Xu |
| author_sort | Bin Ma |
| collection | DOAJ |
| description | Abstract Soil harbors a vast expanse of unidentified microbes, termed as microbial dark matter, presenting an untapped reservoir of microbial biodiversity and genetic resources, but has yet to be fully explored. In this study, we conduct a large-scale excavation of soil microbial dark matter by reconstructing 40,039 metagenome-assembled genome bins (the SMAG catalogue) from 3304 soil metagenomes. We identify 16,530 of 21,077 species-level genome bins (SGBs) as unknown SGBs (uSGBs), which expand archaeal and bacterial diversity across the tree of life. We also illustrate the pivotal role of uSGBs in augmenting soil microbiome’s functional landscape and intra-species genome diversity, providing large proportions of the 43,169 biosynthetic gene clusters and 8545 CRISPR-Cas genes. Additionally, we determine that uSGBs contributed 84.6% of previously unexplored viral-host associations from the SMAG catalogue. The SMAG catalogue provides an useful genomic resource for further studies investigating soil microbial biodiversity and genetic resources. |
| first_indexed | 2024-03-09T01:16:38Z |
| format | Article |
| id | doaj.art-7cabc861d8b14dfc895935210b10216d |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-03-09T01:16:38Z |
| publishDate | 2023-11-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-7cabc861d8b14dfc895935210b10216d2023-12-10T12:25:07ZengNature PortfolioNature Communications2041-17232023-11-0114111410.1038/s41467-023-43000-zA genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resourcesBin Ma0Caiyu Lu1Yiling Wang2Jingwen Yu3Kankan Zhao4Ran Xue5Hao Ren6Xiaofei Lv7Ronghui Pan8Jiabao Zhang9Yongguan Zhu10Jianming Xu11Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang UniversityInstitute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang UniversityInstitute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang UniversityZJU-Hangzhou Global Scientific and Technological Innovation CenterInstitute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang UniversityZJU-Hangzhou Global Scientific and Technological Innovation CenterZJU-Hangzhou Global Scientific and Technological Innovation CenterDepartment of Environmental Engineering, China Jiliang UniversityZJU-Hangzhou Global Scientific and Technological Innovation CenterState Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of SciencesResearch Center for Eco-environmental Sciences, Chinese Academy of SciencesInstitute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang UniversityAbstract Soil harbors a vast expanse of unidentified microbes, termed as microbial dark matter, presenting an untapped reservoir of microbial biodiversity and genetic resources, but has yet to be fully explored. In this study, we conduct a large-scale excavation of soil microbial dark matter by reconstructing 40,039 metagenome-assembled genome bins (the SMAG catalogue) from 3304 soil metagenomes. We identify 16,530 of 21,077 species-level genome bins (SGBs) as unknown SGBs (uSGBs), which expand archaeal and bacterial diversity across the tree of life. We also illustrate the pivotal role of uSGBs in augmenting soil microbiome’s functional landscape and intra-species genome diversity, providing large proportions of the 43,169 biosynthetic gene clusters and 8545 CRISPR-Cas genes. Additionally, we determine that uSGBs contributed 84.6% of previously unexplored viral-host associations from the SMAG catalogue. The SMAG catalogue provides an useful genomic resource for further studies investigating soil microbial biodiversity and genetic resources.https://doi.org/10.1038/s41467-023-43000-z |
| spellingShingle | Bin Ma Caiyu Lu Yiling Wang Jingwen Yu Kankan Zhao Ran Xue Hao Ren Xiaofei Lv Ronghui Pan Jiabao Zhang Yongguan Zhu Jianming Xu A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources Nature Communications |
| title | A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources |
| title_full | A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources |
| title_fullStr | A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources |
| title_full_unstemmed | A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources |
| title_short | A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources |
| title_sort | genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources |
| url | https://doi.org/10.1038/s41467-023-43000-z |
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