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Biofilm Formation by Rice Rhizosphere Nitrogen-Fixing Microorganisms and Its Effect on Rice Growth Promotion
Supercomputing Center, Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, 370, Jeonju-si 54874, Jeollabuk-do, Republic of Korea
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Biology 2025, 14(9), 1249; https://doi.org/10.3390/biology14091249
Submission received: 5 June 2025
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Revised: 1 September 2025
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Accepted: 8 September 2025
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Published: 11 September 2025
Simple Summary
Improving nitrogen use efficiency (NUE) in rice cultivation is crucial for sustainable agriculture and for reducing environmental pollution caused by excessive fertilizer use. In this study, we found that certain beneficial microorganisms living in the rice rhizosphere can form strong biofilms when exposed to specific natural compounds—particularly cardamomin, a flavonoid found in various plants. Among the tested strains, Azoarcus indigens KACC 11682 exhibited the highest biofilm-forming ability and significantly promoted rice growth, increasing biomass by approximately 128%. Through the screening of 1597 natural compounds, 68 were identified as strong inducers of biofilm formation. These findings suggest that enhancing the symbiosis between rice and nitrogen-fixing microbes using targeted compounds can reduce the need for synthetic fertilizers and support more eco-friendly rice farming.
Abstract
Excessive nitrogen fertilizer use contributes to environmental pollution and undermines agricultural sustainability. Enhancing symbiotic interactions between rice and nitrogen-fixing microorganisms offers a promising strategy to potentially improve nitrogen use efficiency (NUE). This study investigates the role of rice root exudates in promoting biofilm formation by nitrogen-fixing microbes to enhance nitrogen fixation. Nine nitrogen-fixing microbial strains were evaluated for biofilm formation in response to flavone and apigenin treatments, with Gluconacetobacter diazotrophicus KACC 12358 serving as the reference strain. The most responsive strain was selected, and a library of 1597 natural compounds was screened to identify those that promote biofilm formation in both the selected and reference strains. A. indigens KACC 11682 exhibited the highest biofilm-forming capacity, with apigenin treatment showing an OD595 value approximately 1.4 times higher than the DMSO control. Screening identified 68 compounds that enhanced biofilm formation by more than 500% compared to the control. Among them, eight compounds induced strong biofilm formation (O.D. > 2.0) in A. indigens. Cardamomin, a chalconoid flavonoid, emerged as one of the most effective compounds, showing a 245% increase in biofilm formation. Growth promotion assays showed that A. indigens increased rice fresh weight by approximately 128% compared to untreated controls. This study demonstrates the potential of rice root exudate-derived compounds to promote beneficial symbiosis with nitrogen-fixing microbes. These findings offer a novel approach that may contribute to enhancing rice NUE. Future research will focus on evaluating the long-term effects of these compounds and microorganisms, assessing their applicability in real agricultural settings, and conducting further validation across various rice cultivars.
