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

Yuparat Saimee; Ryusuke Okada; Daisuke Inoue; Michihiko Ike; Yuparat Saimee; Ryusuke Okada; Daisuke Inoue; Michihiko Ike

doi:10.3934/microbiol.2026022

AIMS Microbiology

2026, Volume 12, Issue 3: 508-525. doi: 10.3934/microbiol.2026022

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Research article

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

Division of Sustainable Energy and Environmental Engineering, The University of Osaka, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan

Received: 08 May 2026 Revised: 06 July 2026 Accepted: 17 July 2026 Published: 30 July 2026

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.
- Wolffia growth,
- duckweed-associated bacteria,
- plant growth-promoting bacteria,
- plant growth-inhibiting bacteria,
- plant growth-promoting traits
Citation: Yuparat Saimee, Ryusuke Okada, Daisuke Inoue, Michihiko Ike. Characterization of duckweed-associated bacteria from the Wolffia globosa microbiome: Strain-level effects on host growth and key determinants[J]. AIMS Microbiology, 2026, 12(3): 508-525. doi: 10.3934/microbiol.2026022

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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.

Acknowledgments

Yuparat Saimee gratefully acknowledges financial support from the Japan International Cooperation Agency (JICA) during this doctoral study. We thank Editage (www.editage.com) for the English language editing.

Conflict of interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Author contributions

Yuparat Saimee: Conceptualization, Methodology, Validation, Formal analysis, Investigation, Data Curation, Writing—Original Draft, Visualization. Ryosuke Okada: Investigation. Daisuke Inoue: Conceptualization, Validation, Resources, Data Curation, Writing—Review & Editing, Supervision, Project administration, Funding acquisition. Michihiko Ike: Resources, Writing—Review & Editing, Supervision, Project administration, Funding acquisition.

Funding

The present study was supported by the Science and Technology Research Partnership for Sustainable Development (SATREPS) in collaboration with the Japan International Cooperation Agency (JICA) and the Japan Science and Technology Agency (JST) (JPMJSA2004), and by the Japan Society for the Promotion of Science (JSPS) KAKENHI JP24K21902.

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