ORIGINAL RESEARCH article
Front. Microbiol.
Sec. Terrestrial Microbiology
Volume 16 - 2025 | doi: 10.3389/fmicb.2025.1595810
This article is part of the Research TopicBiogeochemical Processes of Nutrients: Impacts of Global Changes and Human Activities on Microbial Communities in Terrestrial EcosystemsView all 5 articles
Structure and function of the topsoil microbiome in Chinese terrestrial ecosystems
Provisionally accepted
Yuqiang Li1
Yulong Duan1*
Junbiao Zhang2
Evangelos Petropoulos3
Jianhua Zhao2
Fasi Wu4
Lilong Wang1
Yun Chen1
Xuyang Wang1- 1Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou, China
- 2Shanghai Majorbio Bio-Pharm Technology Co. Ltd, Shanghai, China
- 3Stantec, Ltd., Newcastle, United Kingdom
- 4National Engineering Technology Research Center for the Protection of Ancient Murals and Earthen Sites, Dunhuang Research Academy, Lanzhou, Gansu Province, China
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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, geographydriven clustering patterns, strongly correlated with eight environmental drivers (Latitude, NDVI, pH, EC, SOC, TN, C: N ratio, 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.
Keywords: terrestrial ecosystem, Metagenomics, functional genes, SOC decomposition and biosynthesis, N cycle, S cycle
Received: 18 Mar 2025; Accepted: 31 Jul 2025.
Copyright: © 2025 Li, Duan, Zhang, Petropoulos, Zhao, Wu, Wang, Chen and Wang. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Yulong Duan, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou, China
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