ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Plant Symbiotic Interactions
This article is part of the Research TopicEngineering Plant-Microbiomes to Improve the Health of Economic CropsView all 9 articles
Nature's Pre-Installed Helpers: Diverse Seed Endophytes Enhance Rice Nitrogen Use Efficiency
Provisionally accepted
- 1Kunming University of Science and Technology, Kunming, China
- 2Yunnan University, Kunming, China
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Nitrogen is a key limiting factor for crop growth, and improving nitrogen use efficiency (NUE) is critical for achieving high crop yields. In this study, both culture-independent and culture-dependent approaches were employed to systematically analyze the community composition and functional traits of seed endophytic bacteria in rice varieties with contrasting NUE. The results revealed diverse endophytic bacterial communities across the four rice varieties, with Shannon indices ranging from 2.95 to 3.23. However, significant compositional differences were observed among varieties. Rare taxa accounted for over 51% of operational taxonomic units (OTUs) in each variety and were the primary drivers of community diversity and differentiation. In contrast, core taxa (shared OTUs) were highly conserved across varieties, largely composed of abundant taxa (OTUs > 39%, total relative abundance > 93%), and occupied central positions in co-occurrence networks, thereby contributing to community stability. Five representative strains exhibited diverse plant growth-promoting (PGP) traits in vitro, including siderophore production, phosphate solubilization, and indole - 3 - acetic acid (IAA) synthesis. These functions were partially redundant, but individual strains exhibited distinct strengths, indicating functional complementarity. Inoculation experiments demonstrated that all strains improved rice growth, nitrogen accumulation, and NUE, with their effectiveness modulated by both strain identity and nitrogen availability. This study reveals rice seed endophytic bacteria as "natural microbial allies" that support host growth and adaptation under low-nitrogen conditions. These endophytes represent valuable microbial resources for the development of next-generation biofertilizers in sustainable agriculture.
Keywords: Rice seed endophytes, microbial communities, Rata taxa, Core taxa, PlantGrowth promotion (PGP), Nitrogen use efficiency (NUE)
Received: 20 Sep 2025; Accepted: 22 Dec 2025.
Copyright: © 2025 Lao, Fang, Fang, Zhao, Li and Li. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Tao Li
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