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Changes in Bacterial and Fungal Microbiomes Associated with Tomatoes of Healthy and Infected by Fusarium oxysporum f. sp. lycopersici

Microbial Ecology volume 81, pages 1004–1017 (2021)Cite this article

Abstract

Fusarium wilt of tomato caused by the pathogen Fusarium oxysporum f. sp. lycopersici (Fol) is one of the most devastating soilborne diseases of tomato. To evaluate whether microbial community composition associated with Fol-infected tomato is different from healthy tomato, we analyzed the tomato-associated microbes in both healthy and Fol-infected tomato plants at both the taxonomic and functional levels; both bacterial and fungal communities have been characterized from bulk soil, rhizosphere, rhizoplane, and endosphere of tomatoes using metabarcoding and metagenomics approaches. The microbial community (bacteria and fungi) composition of healthy tomato was significantly different from that of diseased tomato, despite similar soil physicochemical characteristics. Both fungal and bacterial diversities were significantly higher in the tomato plants that remained healthy than in those that became diseased; microbial diversities were also negatively correlated with the concentration of Fol pathogen. Network analysis revealed the microbial community of healthy tomato formed a larger and more complex network than that of diseased tomato, probably providing a more stable community beneficial to plant health. Our findings also suggested that healthy tomato contained significantly greater microbial consortia, including some well-known biocontrol agents (BCAs), and enriched more functional genes than diseased tomato. The microbial taxa enriched in healthy tomato plants are recognized as potential suppressors of Fol pathogen invasion.

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Acknowledgments

We thank Dr. Wei Liu and Dr. Shenyong Fu (Institute of Microbiology, CAS) for the greenhouse experiments and sample collections, and Dr. Junmin Liang (Institute of Microbiology, CAS) for the editorial support of the manuscript.

Funding

This study was financially supported by NSFC 31725001. X. Zhou received financial support for his studentship (QYZDB-SSW-SMC044). C.K. Tsui acknowledges CAS153211KYSB20160029 for supporting his visit to Chinese Academy of Sciences.

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Authors and Affiliations

  1. State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People’s Republic of China

    Xin Zhou, Jin-Ting Wang & Lei Cai

  2. University of Chinese Academy of Sciences, Beijing, 100101, People’s Republic of China

    Xin Zhou, Jin-Ting Wang & Lei Cai

  3. Shandong Hetianwang Biological Technology Co., Ltd, Weifang, People’s Republic of China

    Wei-Hua Wang

  4. Department of Pathology, Sidra Medicine, Doha, Qatar

    Clement KM Tsui

  5. Department of Pathology and Laboratory Medicine, Weill Cornell Medicine-Qatar, Doha, Qatar

    Clement KM Tsui

  6. Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, Canada

    Clement KM Tsui

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  1. Xin Zhou
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  3. Wei-Hua Wang
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Contributions

L. Cai planned and supervised this research; X. Zhou performed the experiments with the assistant of J.T. Wang; X. Zhou conducted the bioinformatic analyses and mainly wrote the manuscript. W.H. Wang and C. K. Tsui contributed to the data analysis and revision of the manuscript. All authors read and approved the final manuscript.

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Correspondence to Lei Cai.

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Electronic supplementary material

Fig. S1

Rarefaction curves of tomato bacterial and fungal OTUs. a) Rarefaction curves of tomato bacterial OTUs. b) Rarefaction curves of tomato fungal OTUs. (EPS 835 kb)

Fig. S2

Concentrations of Fol in healthy and diseased tomato plants. a) Comparison of relative abundance of Fol in healthy and diseased tomato groups. b) Comparison of absolute abundance of Fol in healthy and diseased tomato groups. (EPS 757 kb)

Fig. S3

Relative abundance of different bacterial and fungal taxa at the phylum level as revealed by shotgun metagenomics. (EPS 3112 kb)

Fig. S4

Relative abundance of different bacterial and fungal taxa at the genus level as revealed by shotgun metagenomics. (EPS 2394 kb)

Fig. S5

Distinct active functions identified using the LEfSe method. The functional annotations were obtained using HUMAnN2 against the KO database. LDA scores showed significant functional differences between the healthy and diseased groups. Green represents the functions enriched in healthy tomato samples, and the red represents the functions enriched in diseased tomato samples. (EPS 1953 kb)

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Zhou, X., Wang, JT., Wang, WH. et al. Changes in Bacterial and Fungal Microbiomes Associated with Tomatoes of Healthy and Infected by Fusarium oxysporum f. sp. lycopersici. Microb Ecol 81, 1004–1017 (2021). https://doi.org/10.1007/s00248-020-01535-4

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Keywords

  • Fusarium oxysporum
  • Tomato Fusarium wilt
  • Microbiome
  • Mycobiome
  • Metabarcoding
  • Shotgun metagenomics