The recovery of 12,789 genomes revealed the diversity, function, and microbial interactions of the geothermal spring microbiome

Li, Y.-x.; Rao, Y.-z.; Li, Z.-w.; Li, S.-p.; Qu, Y.-n.; Kuang, J.-l.; Chen, Y.-j.; Qi, Y.-l.; Xie, Q.-j.; Jiao, J.-y.; Shu, W.-s.; Li, W.-J.; Hua, Z.-S.

doi:10.64898/2026.03.10.710734

bioRxiv · 10.64898/2026.03.10.710734

The recovery of 12,789 genomes revealed the diversity, function, and microbial interactions of the geothermal spring microbiome

Li, Y.-x.·Rao, Y.-z.·Li, Z.-w.·Li, S.-p.·Qu, Y.-n.·Kuang, J.-l.·Chen, Y.-j.·Qi, Y.-l.·Xie, Q.-j.·Jiao, J.-y.·Shu, W.-s.·Li, W.-J.·Hua, Z.-S.

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Abstract

Geothermal springs, characterized by extreme physicochemical conditions, represent ecologically and evolutionarily significant habitats that foster unique microbial communities and drive adaptive evolutionary processes. Despite their importance, the complex microbial interactions and underlying mechanisms governing community assembly in these environments remain poorly understood. In this study, we conducted systematic sampling across 49 geothermal springs in Tengchong, Yunnan, over a six-year period (2016-2021), and performed metagenomic sequencing on 152 samples. We successfully reconstructed 12,789 non-redundant microbial genomes, revealing an exceptionally high level of phylogenetic and functional diversity within the spring microbiomes. Our analyses demonstrate that pH and temperature are the primary deterministic drivers shaping both microbial species composition and functional potential, thereby segregating the communities into three distinct groups: acidic, hyperthermal, and thermal. Furthermore, ecological network analysis revealed that extreme environmental conditions significantly alter network topology, resulting in less complex but more efficient microbial interaction networks. Collectively, this study provides a comprehensive resource and mechanistic insights into the microbial diversity, community structure, and species interactions in geothermal spring ecosystems.

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Li, Y.-x., Rao, Y.-z., Li, Z.-w., Li, S.-p., Qu, Y.-n., Kuang, J.-l., Chen, Y.-j., Qi, Y.-l., Xie, Q.-j., Jiao, J.-y., Shu, W.-s., Li, W.-J., Hua, Z.-S.. 2026-03-10. The recovery of 12,789 genomes revealed the diversity, function, and microbial interactions of the geothermal spring microbiome. https://doi.org/10.64898/2026.03.10.710734

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