Integrated shotgun metagenomic and culture-based characterization of plant growth-promoting rhizobacteria associated with Sangyod Rice

IF 6.7 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Current Research in Biotechnology Pub Date : 2026-01-01 Epub Date: 2026-10-09 DOI:10.1016/j.crbiot.2026.100427

Jannisuta Rangchai, Natthasap Moolika, Khunanon Chanasongkhram, Ponsit Sathapondecha, Jutarut Iewkittayakorn, Unitsa Sangket

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引用次数: 0

Abstract

Sangyod rice (Oryza sativa L. var. indica) is a high-value traditional rice variety in southern Thailand. Organic farming practices may enhance rhizosphere microbial diversity and promote beneficial plant growth-promoting rhizobacteria (PGPR), but the microbial composition and functional potential of the Sangyod rice rhizosphere remain poorly understood. Long-read shotgun metagenomic sequencing (Oxford Nanopore) was used to characterize rhizosphere bacterial communities in organic and chemical cultivation systems. Six samples, comprising three samples the chemical cultivation system (C2, C3, and C4) and three from the organic cultivation system (O2, O3, and O4), were sequenced and analyzed individually. Culturable rhizobacteria were isolated and screened for plant growth-promoting traits, including potential nitrogen-fixing ability, phosphate-solubilizing potential and IAA-producing potential. Selected isolates were identified by 16S rRNA gene sequencing and evaluated for antagonistic interactions using a reciprocal agar disc diffusion assay. Shotgun metagenomic analysis identified Pseudomonadota and Actinomycetota as the predominant phyla, with Streptomyces as the most abundant genus across all samples. Alpha-diversity indices did not differ significantly between the cultivation systems. Isolate SSY16, closely related to Streptomyces sp., showed the highest phosphate-solubilizing index (PSI = 1.799 ± 0.088), while SSN34, closely related to Bacillus sp., showed IAA-producing potential (estimated IAA concentration: 38.96 μg mL⁻¹) and no detectable antagonism with SSY16 under the tested agar conditions. The integration of shotgun metagenomic analysis and culture-based screening enabled the characterization of the rhizosphere bacterial community and the identification of cultivable rhizobacteria with plant growth-promoting traits. SSY16 and SSN34 represent a preliminary candidate consortium requiring further validation in pot experiments.

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桑稻促生根瘤菌的综合元基因组和培养鉴定

Sangyod水稻（Oryza sativa L. var. indica）是泰国南部一个高价值的传统水稻品种。有机耕作可以提高根际微生物多样性，促进有益植物生长的根际细菌（PGPR）的产生，但对桑古稻根际微生物组成和功能潜力的了解尚不充分。采用长读散弹枪宏基因组测序（Oxford Nanopore）对有机和化学栽培系统的根际细菌群落进行了表征。对化学栽培体系（C2、C3、C4） 3个样品和有机栽培体系（O2、O3、O4） 3个样品分别进行测序和分析。对可培养的根细菌进行了分离和筛选，并对其促进植物生长的特性进行了研究，包括潜在的固氮能力、溶解磷酸盐的潜力和产生iaa的潜力。选定的分离株通过16S rRNA基因测序鉴定，并使用互惠琼脂盘扩散试验评估其拮抗相互作用。散弹枪宏基因组分析发现假单胞菌门和放线菌门是优势门，链霉菌属是所有样本中数量最多的属。不同栽培体系间α多样性指数差异不显著。与Streptomyces sp.亲缘关系密切的分离物SSY16表现出最高的磷酸盐溶解指数（PSI = 1.799 ± 0.088），而与芽孢杆菌sp.亲缘关系密切的分离物SSN34表现出产生IAA的潜力（估计IAA浓度为38.96 μg mL−1），在所测试的agar条件下未检测到与SSY16的拮抗作用。将散弹枪宏基因组分析与基于培养的筛选相结合，实现了根际细菌群落的鉴定和具有植物生长促进性状的可培养根际细菌的鉴定。SSY16和SSN34是初步候选组合，需要在盆栽试验中进一步验证。

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来源期刊

Current Research in Biotechnology Biochemistry, Genetics and Molecular Biology-Biotechnology

CiteScore

6.70

自引率

3.60%

发文量

审稿时长

38 days

期刊介绍： Current Research in Biotechnology (CRBIOT) is a new primary research, gold open access journal from Elsevier. CRBIOT publishes original papers, reviews, and short communications (including viewpoints and perspectives) resulting from research in biotechnology and biotech-associated disciplines. Current Research in Biotechnology is a peer-reviewed gold open access (OA) journal and upon acceptance all articles are permanently and freely available. It is a companion to the highly regarded review journal Current Opinion in Biotechnology (2018 CiteScore 8.450) and is part of the Current Opinion and Research (CO+RE) suite of journals. All CO+RE journals leverage the Current Opinion legacy-of editorial excellence, high-impact, and global reach-to ensure they are a widely read resource that is integral to scientists' workflow.