Predicting rhizosphere-competence-related catabolic gene clusters in plant-associated bacteria with rhizoSMASH

Yuze Li, Mingxue Sun, Jos M. Raaijmakers, Liesje Mommer, Fusuo Zhang, Chunxu Song () and Marnix H. Medema ()
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Yuze Li: China Agricultural University
Mingxue Sun: China Agricultural University
Jos M. Raaijmakers: NIOO-KNAW
Liesje Mommer: Wageningen University
Fusuo Zhang: China Agricultural University
Chunxu Song: China Agricultural University
Marnix H. Medema: Wageningen University

Nature Communications, 2025, vol. 16, issue 1, 1-11

Abstract: Abstract Plants release a substantial fraction of their photosynthesized carbon into the rhizosphere as root exudates that drive microbiome assembly. Deciphering how plants modulate the composition and activities of rhizosphere microbiota through root exudates is challenging, as no dedicated computational methods exist to systematically identify microbial root exudate catabolic pathways. Here, we integrate published information on catabolic genes in bacteria that contribute to their rhizosphere competence and develop the rhizoSMASH algorithm for genome-synteny-based annotation of rhizosphere-competence-related catabolic gene clusters (rCGCs) in bacteria with 58 curated detection rules. Our analysis reveals heterogeneity in rCGC prevalence both across and within plant-associated bacterial taxa, indicating extensive niche specialization. Furthermore, we demonstrate the predictive value of the presence or absence of rCGCs for rhizosphere competence in machine learning with two case studies. rhizoSMASH provides an extensible framework for studying rhizosphere bacterial catabolism, facilitating microbiome-assisted breeding approaches for sustainable agriculture.

Date: 2025
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DOI: 10.1038/s41467-025-63526-8

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