Phenotypic Biodiversity and Niche-Associated Functional Traits in Lactiplantibacillus plantarum

Lactiplantibacillus plantarum is a highly versatile lactic acid bacterium, widely distributed across diverse ecological niches. Although often described as a nomadic species, increasing evidence suggests that strains from different habitats may retain niche-associated functional traits. This study investigated the phenotypic biodiversity of forty L. plantarum strains isolated from four ecologically distinct environments: wine, honeybee gut, trout intestine, and pre-weaning infant feces. Growth performance at different temperatures and on various carbon sources, acidification capacity, and β-glucosidase activity were evaluated and integrated using multivariate statistical analyses. Significant differences in β-glucosidase activity were observed among ecological groups (Kruskal–Wallis, p = 0.001), with wine-associated strains exhibiting the highest enzymatic activities and trout-derived isolates the lowest. Growth and acidification traits showed more limited variation among habitats, indicating that these physiological characteristics are largely conserved within the species. Heatmap visualization, principal component analysis (PCA), and hierarchical clustering revealed substantial phenotypic heterogeneity among strains. PCA indicated that growth performance and acidification traits contributed primarily to the first principal component, whereas β-glucosidase activity and differential fructose utilization were major contributors to the second component. Permutational multivariate analysis of variance (PERMANOVA) confirmed a significant effect of ecological origin on the overall phenotypic structure (p = 0.006), although habitat explained only 15.3% of the total variance (R2 = 0.153). Overall, the results show that ecological origin contributes to the phenotypic diversification of L. plantarum populations while preserving the extensive functional versatility characteristic of this species. β-Glucosidase activity emerged as the most discriminating phenotypic trait among ecological groups and represented the principal niche-associated functional signature identified in this study.