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Volume 14
Issue 21
10.3390/plants14213325
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This is an early access version, the complete PDF, HTML, and XML versions will be available soon.
Article

Amplicon Sequencing Reveals Rhizosphere Fungal Dysbiosis Facilitates Goji Berry Root Rot Onset

by
Tianyu Wang
1,†,
Yao Chen
1,†,
Meng Yan
1,
Haonan Wang
1,
Kai Guo
1,
Xudong Zhou
1,
Hexing Qi
2 and
Lifeng Zhou
1,*
1
State Key Laboratory for Development and Utilization of Forest Food Resources, Zhejiang A&F University, Hangzhou 311300, China
2
College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Plants 2025, 14(21), 3325; https://doi.org/10.3390/plants14213325 (registering DOI)
Submission received: 24 September 2025 / Revised: 19 October 2025 / Accepted: 28 October 2025 / Published: 30 October 2025
(This article belongs to the Special Issue Nutrient Management on Soil Microbiome Dynamics and Plant Health)
Versions Notes

Abstract

Root rot in Lycium barbarum, an economically vital crop, is a critical barrier to its sustainable development in China. To elucidate the underlying micro-ecological mechanisms, this study aimed to characterize and compare the rhizosphere microbial communities of healthy and diseased plants from the Qaidam Basin. We employed PacBio full-length amplicon sequencing to analyze bacterial and fungal populations, complemented by network analysis and in vitro antagonistic assays. The results indicated that while microbial species richness was similar, the community structures of healthy and diseased soils were fundamentally different, suggesting that the disease is primarily driven by microbial dysbiosis rather than species loss. Healthy soil was enriched with beneficial Trichoderma, whereas diseased soil was dominated by the pathogen Fusarium, with an abundance 6.7 times higher than that in healthy soil. Network analysis revealed the healthy fungal community was significantly more stable (modularity index: 0.818) than the diseased network (0.4131), where Fusarium occupied a core hub position. Crucially, Trichoderma strains isolated from healthy soil exhibited strong antagonistic activity against Fusarium, with an average inhibition rate exceeding 75%. This study identifies Fusarium as the key pathogen of Goji root rot and native Trichoderma as a potent biocontrol agent, providing a scientific basis for a sustainable, micro-ecological control strategy.
Keywords: microflora; species abundance; ecological diversity; arid climate microflora; species abundance; ecological diversity; arid climate

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MDPI and ACS Style

Wang, T.; Chen, Y.; Yan, M.; Wang, H.; Guo, K.; Zhou, X.; Qi, H.; Zhou, L. Amplicon Sequencing Reveals Rhizosphere Fungal Dysbiosis Facilitates Goji Berry Root Rot Onset. Plants 2025, 14, 3325. https://doi.org/10.3390/plants14213325

AMA Style

Wang T, Chen Y, Yan M, Wang H, Guo K, Zhou X, Qi H, Zhou L. Amplicon Sequencing Reveals Rhizosphere Fungal Dysbiosis Facilitates Goji Berry Root Rot Onset. Plants. 2025; 14(21):3325. https://doi.org/10.3390/plants14213325

Chicago/Turabian Style

Wang, Tianyu, Yao Chen, Meng Yan, Haonan Wang, Kai Guo, Xudong Zhou, Hexing Qi, and Lifeng Zhou. 2025. "Amplicon Sequencing Reveals Rhizosphere Fungal Dysbiosis Facilitates Goji Berry Root Rot Onset" Plants 14, no. 21: 3325. https://doi.org/10.3390/plants14213325

APA Style

Wang, T., Chen, Y., Yan, M., Wang, H., Guo, K., Zhou, X., Qi, H., & Zhou, L. (2025). Amplicon Sequencing Reveals Rhizosphere Fungal Dysbiosis Facilitates Goji Berry Root Rot Onset. Plants, 14(21), 3325. https://doi.org/10.3390/plants14213325

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