ORIGINAL RESEARCH article
Front. Microbiol.
Sec. Microbe and Virus Interactions with Plants
This article is part of the Research TopicPlant Microbiomes in a Changing World: Adaptation, Resilience, and ApplicationsView all 9 articles
Functional and ecological characterization of Labrys methylaminiphilus subsp. lupini subsp. nov., associated with Lupinus luteus nodules in acidic soils of southern Chile
Provisionally accepted
Grace Armijo-Godoy1*
Luis Cottet2Annally Rupayan1Makarena Carrasco1Daniela Levicoy1Haroldo Salvo-Garrido1*- 1Agriaquaculture Nutritional Genomic Center, Temuco, Chile
- 2Univeridad Mayor Temuco, Temuco, Chile
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Background: Members of the genus Labrys are widely distributed in soil and plant-associated environments, yet their ecological roles and functional contributions within plant-associated microbiomes remain poorly understood. Labrys methylaminiphilus strain La1 was isolated from nodules of Lupinus luteus growing in acidic soils of southern Chile, providing an opportunity to investigate strain-level traits relevant to plant–microbe interactions under environmental stress. Methods: Strain La1 was characterized using physiological and biochemical, chemotaxonomic, and genomic approaches, including whole-genome sequencing and comparative genomics. Functional traits related to plant interaction were assessed through in vitro assays for indole-3-acetic acid (IAA) production, antifungal activity against lupine pathogens, and in planta experiments evaluating plant growth under salinity and osmotic stress. The ecological distribution of closely related taxa was inferred from screening of publicly available environmental microbiomes using protologger pipeline. Results: Although strain La1 showed high genomic similarity to L. methylaminiphilus JLW10ᵀ, it exhibited distinct phenotypic, metabolic, and ecological features. These included tolerance to acidic and moderately saline conditions, utilization of rhizosphere-associated carbon sources, and a fatty acid profile consistent with adaptation to terrestrial environments. Genomic analyses revealed genes related to stress tolerance, exopolysaccharide biosynthesis, carbohydrate-active enzymes, siderophore production, IAA synthesis, and nonribosomal peptide synthetases. Consistent with these traits, La1 inhibited the growth of Colletotrichum lupini and Pleiochaeta setosa and significantly enhanced L. luteus biomass under osmotic and salinity stress. Metagenomic screening indicated that sequences closely related to La1 are predominantly associated with soil, rhizosphere, and plant-associated habitats. Conclusion: This study demonstrates that strain La1 represents a functionally versatile and ecologically specialized lineage within L. methylaminiphilus, contributing traits relevant to plant-associated microbiomes in acidic soils. This integrated functional and ecological evidence supports the designation of Labrys methylaminiphilus subsp. lupini subsp. nov. and highlights the relevance of strain-level analyses for understanding plant–microbe interactions.
Keywords: beneficial bacteria, Labrys methylaminiphilus subsp. Lupini, Lupinus luteus, nodules, plant-associated bacteria
Received: 03 Dec 2025; Accepted: 02 Feb 2026.
Copyright: © 2026 Armijo-Godoy, Cottet, Rupayan, Carrasco, Levicoy and Salvo-Garrido. 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:
Grace Armijo-Godoy
Haroldo Salvo-Garrido
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