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ORIGINAL RESEARCH article

Front. Microbiol.

Sec. Terrestrial Microbiology

Volume 16 - 2025 | doi: 10.3389/fmicb.2025.1670956

This article is part of the Research TopicMicrobial Community Dynamics in Agroecosystems: From Disease Suppression to Soil HealthView all 6 articles

Wilt disease reshapes rhizosphere microbiota in small yellow ginger soils

Provisionally accepted
Qing  SunQing Sun1,2Sitian  FeiSitian Fei1Sihao  HuangSihao Huang2Runtao  TanRuntao Tan2Haibo  ChenHaibo Chen3*Songquan  SongSongquan Song1Bin  WangBin Wang1
  • 1Nanling Research Institute for Modern Seed Industry, Xiangnan University, Chenzhou, China
  • 2School of Chemistry and Environmental Science, Xiangnan University, Chenzhou, China
  • 3School of Basic Medical Sciences, Xiangnan University, Chenzhou, China

The final, formatted version of the article will be published soon.

Introduction: Continuous cropping obstacles, particularly the prevalent ginger wilt disease (bacterial wilt), severely constrain the sustainable development of the small yellow ginger (Zingiber officinale Roscoe) industry in Rucheng County, China. However, the primary pathogen responsible for this disease in the local cultivar and the associated microbiome shifts within the rhizosphere remain unidentified. This study aimed to elucidate the distinctive rhizosphere microbial community changes induced by ginger wilt disease, identify the potential key pathogen responsible for this disease in Rucheng, and provide a scientific basis for overcoming continuous cropping obstacles in small yellow ginger cultivation. Methods: Soil samples were collected from an uncultivated plot, and from the rhizosphere of healthy and wilted small yellow ginger plants. Microbial community structure and composition were analyzed using 16S rRNA gene high-throughput sequencing. Linear Discriminant Analysis (LDA) effect size (LEfSe) was employed to identify differential biomarkers, and functional prediction was performed using BugBase. Results: Ginger wilt disease significantly altered the rhizosphere soil bacterial community structure and composition: the relative abundance of Proteobacteria increased significantly, primarily due to the enrichment of the genus Ralstonia; conversely, the relative abundance of Acidobacteriota, Firmicutes, and Chloroflexi significantly decreased. Ginger wilt disease also significantly reduced the diversity of the rhizosphere soil bacterial community. LEfSe further confirmed Ralstonia as a diagnostic biomarker for ginger wilt disease. BugBase phenotypic prediction indicated that the microbiota enriched in the diseased ginger rhizosphere exhibited higher capabilities for oxidative stress resistance, pathogenic potential, and mobile element content, attributed to a functional consortium of multiple genera, including Ralstonia as the dominant contributor alongside major contributors such as Rhodanobacter and Dokdonella. Discussion: Our findings highlight that the enrichment of Ralstonia is strongly associated with ginger wilt in Rucheng County and concomitant with profound changes in the rhizospheric microbiota of wilted ginger, involving alterations in both community structure and functional potential.

Keywords: Ginger, wilt disease, Ralstonia, Soil microbiota, Microbial Diversity

Received: 22 Jul 2025; Accepted: 29 Sep 2025.

Copyright: © 2025 Sun, Fei, Huang, Tan, Chen, Song and Wang. 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: Haibo Chen, chenhaibo526@hotmail.com

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