A global soil plasmidome resource unveils functional and ecological roles of plasmids in soil microbiomes

Mateus B. Fiamenghi (), Antonio Pedro Camargo, Natalia N. Ivanova, Emily B. Graham, Ruonan Wu, Kirsten S. Hofmockel and Nikos C. Kyrpides ()
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Mateus B. Fiamenghi: Lawrence Berkeley National Laboratory
Antonio Pedro Camargo: Lawrence Berkeley National Laboratory
Natalia N. Ivanova: Lawrence Berkeley National Laboratory
Emily B. Graham: Pacific Northwest National Laboratory
Ruonan Wu: Pacific Northwest National Laboratory
Kirsten S. Hofmockel: Pacific Northwest National Laboratory
Nikos C. Kyrpides: Lawrence Berkeley National Laboratory

Nature Communications, 2025, vol. 16, issue 1, 1-16

Abstract: Abstract Plasmids play significant roles in microbial adaptation to ecosystems, yet their dynamics remain poorly understood due to identification challenges. We present the Global Soil Plasmidome Resource (GSPR), a comprehensive dataset of 98,728 plasmid sequences amassed from 6860 terrestrial microbial communities and isolates. We explore this resource through various computational approaches, including phylogenetic diversity analysis, host prediction, and extensive functional annotation, to understand the contribution of plasmids to the genetic and functional diversity in soil, correlating these findings with sample type, as well as the soil habitat they were retrieved from. Our analysis reveals insights into plasmid-encoded functions such as effector modules, quorum sensing, and stress resistance, which may contribute to their persistence and microbial adaptation in soil. Furthermore, CRISPR analysis suggests a prevalent role of these elements related to intra-plasmid competition. By contrasting plasmids from cultivated and uncultivated organisms, we identify important functions that expand existing knowledge of plasmid roles in these habitats. This study represents a notable step forward in elucidating plasmid diversity and function within soil microbiomes and establishes a foundational framework for exploring their roles in natural environments.

Date: 2025
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DOI: 10.1038/s41467-025-65102-6

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