Characterization of duckweed-associated bacteria from the Wolffia globosa microbiome: Strain-level effects on host growth and key determinants.

Abstract

Wolffia, a rootless duckweed in the family Lemnaceae, is increasingly recognized as a sustainable bioresource for food, animal feed, bioenergy, and biomaterials. Its productivity depends strongly on the associated microbiome, yet the functional roles of individual duckweed-associated bacteria (DAB) remain poorly understood. In this study, we evaluated the effects of DAB isolated from Wolffia globosa microbiomes on host plant growth and characterized their physiological traits. A total of 98 DAB strains were isolated from seven W. globosa microbiomes and individually co-cultivated with W. globosa, exhibiting diverse effects on host growth ranging from promotion to inhibition, with -14.6 to +12.9% of final effects on plant growth. Ten strains consistently promoted host growth and nine strains inhibited growth, which were identified as plant growth-promoting and growth-inhibiting bacteria, respectively. Of these, seven and four strains were identified within the core taxa of W. globosa microbiomes. At the community level, growth-promoting strains tended to be enriched in the growth-promoting microbiomes, whereas neutral or negative strains appeared to be enriched in the growth-inhibiting microbiomes. Taxonomic evaluation demonstrated that prominent promotive and inhibitory phenotypes occurred across six and five genera, respectively, with strain-level characteristics likely determining plant growth effects. Indole-related compound production by DAB emerged as a key physiological determinant associated with Wolffia growth. These findings provide a traceable strain set to advance our understanding of Wolffia-microbiome interactions and offer practical clues on microbiome engineering strategies to enhance Wolffia biomass productivity.