Structure and function of the topsoil microbiome in Chinese terrestrial ecosystems
While soil microorganisms underpin terrestrial ecosystem functioning, how their functional potential adapts across environmental gradients remains poorly understood, particularly for ubiquitous taxa. Employing a comprehensive metagenomic approach across China’s six major terrestrial ecosystems (41 t...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2025-08-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2025.1595810/full |
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| author | Yuqiang Li Yuqiang Li Yuqiang Li Yulong Duan Yulong Duan Yulong Duan Junbiao Zhang Evangelos Petropoulos Jianhua Zhao Fasi Wu Lilong Wang Lilong Wang Yun Chen Yun Chen Xuyang Wang Xuyang Wang Xuyang Wang |
| author_facet | Yuqiang Li Yuqiang Li Yuqiang Li Yulong Duan Yulong Duan Yulong Duan Junbiao Zhang Evangelos Petropoulos Jianhua Zhao Fasi Wu Lilong Wang Lilong Wang Yun Chen Yun Chen Xuyang Wang Xuyang Wang Xuyang Wang |
| author_sort | Yuqiang Li |
| collection | DOAJ |
| description | While soil microorganisms underpin terrestrial ecosystem functioning, how their functional potential adapts across environmental gradients remains poorly understood, particularly for ubiquitous taxa. Employing a comprehensive metagenomic approach across China’s six major terrestrial ecosystems (41 topsoil samples, 0–20 cm depth), we reveal a counterintuitive pattern: oligotrophic environments (deserts, karst) harbor microbiomes with significantly greater metabolic pathway diversity (KEGG) compared to resource-rich ecosystems. We provide a systematic catalog of key functional genes governing biogeochemical cycles in these soils, identifying: 6 core CAZyme genes essential for soil organic carbon (SOC) decomposition and biosynthesis; 62 nitrogen (N)-cycling genes (KOs) across seven critical enzymatic clusters; 15 sulfur (S)-cycling genes (KOs) within three key enzymatic clusters. These functional gene abundances exhibit distinct, geography-driven clustering patterns, strongly correlated with eight environmental drivers (latitude, NDVI, pH, EC, SOC, TN, C:N ratio, and MAP). This work provides a predictive framework and actionable genetic targets (e.g., specific CAZyme, N/S cycling genes) for potentially manipulating soil microbiomes to enhance ecosystem resilience and biogeochemical functions under stress. |
| format | Article |
| id | doaj-art-abb0bebc591943dbbd2e04ff181a36bb |
| institution | Kabale University |
| issn | 1664-302X |
| language | English |
| publishDate | 2025-08-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj-art-abb0bebc591943dbbd2e04ff181a36bb2025-08-25T05:25:17ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2025-08-011610.3389/fmicb.2025.15958101595810Structure and function of the topsoil microbiome in Chinese terrestrial ecosystemsYuqiang Li0Yuqiang Li1Yuqiang Li2Yulong Duan3Yulong Duan4Yulong Duan5Junbiao Zhang6Evangelos Petropoulos7Jianhua Zhao8Fasi Wu9Lilong Wang10Lilong Wang11Yun Chen12Yun Chen13Xuyang Wang14Xuyang Wang15Xuyang Wang16State Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, ChinaNaiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Tongliao, ChinaUniversity of Chinese Academy of Sciences, Beijing, ChinaState Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, ChinaNaiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Tongliao, ChinaUniversity of Chinese Academy of Sciences, Beijing, ChinaShanghai Majorbio Bio-Pharm Technology Co., Ltd., Shanghai, ChinaStantec, Ltd., Newcastle upon Tyne, United KingdomShanghai Majorbio Bio-Pharm Technology Co., Ltd., Shanghai, ChinaNational Research Center for Conservation of Ancient Wall Paintings and Earthen Sites, Dunhuang Academy, Dunhuang, ChinaState Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, ChinaNaiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Tongliao, ChinaState Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, ChinaNaiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Tongliao, ChinaState Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, ChinaNaiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Tongliao, ChinaUniversity of Chinese Academy of Sciences, Beijing, ChinaWhile soil microorganisms underpin terrestrial ecosystem functioning, how their functional potential adapts across environmental gradients remains poorly understood, particularly for ubiquitous taxa. Employing a comprehensive metagenomic approach across China’s six major terrestrial ecosystems (41 topsoil samples, 0–20 cm depth), we reveal a counterintuitive pattern: oligotrophic environments (deserts, karst) harbor microbiomes with significantly greater metabolic pathway diversity (KEGG) compared to resource-rich ecosystems. We provide a systematic catalog of key functional genes governing biogeochemical cycles in these soils, identifying: 6 core CAZyme genes essential for soil organic carbon (SOC) decomposition and biosynthesis; 62 nitrogen (N)-cycling genes (KOs) across seven critical enzymatic clusters; 15 sulfur (S)-cycling genes (KOs) within three key enzymatic clusters. These functional gene abundances exhibit distinct, geography-driven clustering patterns, strongly correlated with eight environmental drivers (latitude, NDVI, pH, EC, SOC, TN, C:N ratio, and MAP). This work provides a predictive framework and actionable genetic targets (e.g., specific CAZyme, N/S cycling genes) for potentially manipulating soil microbiomes to enhance ecosystem resilience and biogeochemical functions under stress.https://www.frontiersin.org/articles/10.3389/fmicb.2025.1595810/fullterrestrial ecosystemmetagenomicsfunctional genesSOC decomposition and biosynthesisN cycleS cycle |
| spellingShingle | Yuqiang Li Yuqiang Li Yuqiang Li Yulong Duan Yulong Duan Yulong Duan Junbiao Zhang Evangelos Petropoulos Jianhua Zhao Fasi Wu Lilong Wang Lilong Wang Yun Chen Yun Chen Xuyang Wang Xuyang Wang Xuyang Wang Structure and function of the topsoil microbiome in Chinese terrestrial ecosystems Frontiers in Microbiology terrestrial ecosystem metagenomics functional genes SOC decomposition and biosynthesis N cycle S cycle |
| title | Structure and function of the topsoil microbiome in Chinese terrestrial ecosystems |
| title_full | Structure and function of the topsoil microbiome in Chinese terrestrial ecosystems |
| title_fullStr | Structure and function of the topsoil microbiome in Chinese terrestrial ecosystems |
| title_full_unstemmed | Structure and function of the topsoil microbiome in Chinese terrestrial ecosystems |
| title_short | Structure and function of the topsoil microbiome in Chinese terrestrial ecosystems |
| title_sort | structure and function of the topsoil microbiome in chinese terrestrial ecosystems |
| topic | terrestrial ecosystem metagenomics functional genes SOC decomposition and biosynthesis N cycle S cycle |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2025.1595810/full |
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