Functional and ecological characterization of Labrys methylaminiphilus subsp. lupini subsp. nov., associated with Lupinus luteus nodules in acidic soils of southern Chile

Abstract

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 JLW10 T , 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 non-ribosomal 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.