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Microorganisms
Volume 13
Issue 8
10.3390/microorganisms13081909
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This is an early access version, the complete PDF, HTML, and XML versions will be available soon.
Article

The Role of Coffee Microbiomes in Pathogen Resistance Across Varieties and Ecological Niches

by
Yihong Wu
1,2,†,
Xiu Zhao
1,2,†,
Zuquan Wang
1,2,
Xuejun Li
1,2,
Xuesong Zhang
1,2,
Chun Xie
1,2,
Huabo Du
1,2,
Kuaile Jiang
1,2,
Peng Qu
1,2,* and
Chuanli Zhang
1,2,*
1
College of Tropical Crops, Yunnan Agricultural University, Pu’er 665001, China
2
Yunnan Provincal Key Laboratory of Coffee, Pu’er 665001, China
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Microorganisms 2025, 13(8), 1909; https://doi.org/10.3390/microorganisms13081909
Submission received: 1 July 2025 / Revised: 2 August 2025 / Accepted: 13 August 2025 / Published: 15 August 2025
(This article belongs to the Section Plant Microbe Interactions)
Versions Notes

Abstract

The plant microbiome plays a role in pathogen defense, but its role in different resistant varieties and ecological niches remains unclear. This study used 16S rRNA and ITS sequencing to investigate microbial communities and interactions in disease-resistant (PT) and susceptible (Bourbon) coffee varieties of five ecological niches: leaves, fruits, roots, rhizosphere soil, and non-rhizosphere soil. We found that the microbial communities differed significantly between the two varieties. The resistant variety was enriched in beneficial bacteria from the Actinobacteriota phylum and a stable, modular microbial network dominated by saprotrophic fungi. In contrast, the susceptible variety had a higher abundance of opportunistic pathogens and stress-indicator fungi, including Neurospora spp., which were more prominent in the rhizosphere and non-rhizosphere soils. These networks were fragile and dominated by pathotrophic fungi, reflecting ecological imbalance. Our findings show that plant disease resistance is influenced not only by host genetics but also by co-evolutionary interactions with the microbiome. These insights provide a foundation for developing targeted biocontrol strategies to manage plant-associated microbial communities.
Keywords: coffee plant microbiome; rust-resistant coffee varieties; ecological niche specialization; co-occurrence network analysis; microbial community structure coffee plant microbiome; rust-resistant coffee varieties; ecological niche specialization; co-occurrence network analysis; microbial community structure

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MDPI and ACS Style

Wu, Y.; Zhao, X.; Wang, Z.; Li, X.; Zhang, X.; Xie, C.; Du, H.; Jiang, K.; Qu, P.; Zhang, C. The Role of Coffee Microbiomes in Pathogen Resistance Across Varieties and Ecological Niches. Microorganisms 2025, 13, 1909. https://doi.org/10.3390/microorganisms13081909

AMA Style

Wu Y, Zhao X, Wang Z, Li X, Zhang X, Xie C, Du H, Jiang K, Qu P, Zhang C. The Role of Coffee Microbiomes in Pathogen Resistance Across Varieties and Ecological Niches. Microorganisms. 2025; 13(8):1909. https://doi.org/10.3390/microorganisms13081909

Chicago/Turabian Style

Wu, Yihong, Xiu Zhao, Zuquan Wang, Xuejun Li, Xuesong Zhang, Chun Xie, Huabo Du, Kuaile Jiang, Peng Qu, and Chuanli Zhang. 2025. "The Role of Coffee Microbiomes in Pathogen Resistance Across Varieties and Ecological Niches" Microorganisms 13, no. 8: 1909. https://doi.org/10.3390/microorganisms13081909

APA Style

Wu, Y., Zhao, X., Wang, Z., Li, X., Zhang, X., Xie, C., Du, H., Jiang, K., Qu, P., & Zhang, C. (2025). The Role of Coffee Microbiomes in Pathogen Resistance Across Varieties and Ecological Niches. Microorganisms, 13(8), 1909. https://doi.org/10.3390/microorganisms13081909

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