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Potassium phosphite enhanced the suppressive capacity of the soil microbiome against the tomato pathogen Ralstonia solanacearum

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Abstract

High-throughput sequencing, culture-dependent workflows, and microbiome transfer experiments reveal whether potassium phosphite (KP), an environmentally acceptable agricultural chemical, could specifically enrich the antagonistic bacterial community that inhibited the growth of the pathogen Ralstonia solanacearum. The application of KP enriched the potential antagonistic bacteria Paenibacillus and Streptomyces in soil, but depleted most dominant genera belonging to gram negative bacteria, such as Pseudomonas, Massilia, and Flavobacterium on day 7. Moreover, the KP-modulated soil microbiome suppressed R. solanacearum growth in soil. The predicted functions related to the synthesis of antagonistic substances, such as streptomycin, and the predicted functions related to tellurite resistance and nickel transport system were significantly enriched, but the synthesis of lipopolysaccharide (distinct component lipopolysaccharide in gram negative bacteria) were significantly depleted in the KP-treated soils. In addition, the copy numbers of specific sequences for Streptomyces coelicoflavus and Paenibacillus favisporus were significantly increased in the soil amended with KP, inhibited the growth of R. solanacearum, and had a higher tolerance of KP than R. solanacearum. Our study linked the application of fertilizers to the enrichment of antagonistic bacteria, which could support future work that aims to precisely regulate the soil microbiome to protect the host from infection by soil-borne pathogens.

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Availability of data and material

The raw sequences were submitted to the NCBI Sequence Read Archive (SRA) under BioProject accession PRJNA577427. The whole-genome shotgun project has been deposited in GenBank under the accession numbers PRJNA579492 (strain Y7) and PRJNA577208 (strain F13).

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Acknowledgements

The authors thank Ms. Chao Zhou and Ms. Zhenghua Wu for technical assistance. Publication number 7417 of the Netherlands Institute of Ecology (NIOO-KNAW).

Funding

This work was supported by the Chinese Natural Science Fund Program (41571242).

Author information

Author notes

  1. The authors Lv Su and Haichao Feng contributed equally to this paper.

Authors and Affiliations

  1. Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People’s Republic of China

    Lv Su, Haichao Feng, Xingxia Mo, Juan Sun, Pengfei Qiu, Ruifu Zhang, Biao Shen & Qirong Shen

  2. Key Laboratory of Agricultural Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People’s Republic of China

    Lv Su, Yunpeng Liu & Ruifu Zhang

  3. Microbial Ecology Department, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands

    Eiko E. Kuramae

  4. Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands

    Eiko E. Kuramae

Authors
  1. Lv Su
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  9. Biao Shen
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Contributions

Lv Su composed the main text, conceived the project, and performed almost all experiments except for the following. Haichao Feng analyzed the data of high throughput sequencing and provided suggestions of ecology concepts. Xingxia Mo and Juan Sun isolated strains from soils. Pengfei Qiu extracted soil DNA. Yunpeng Liu, Eiko E. Kuramae, and Ruifu Zhang provided suggestions for the manuscript. Biao Shen and Qirong Shen organized and supervised the project, respectively.

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Correspondence to Biao Shen.

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Su, L., Feng, H., Mo, X. et al. Potassium phosphite enhanced the suppressive capacity of the soil microbiome against the tomato pathogen Ralstonia solanacearum. Biol Fertil Soils 58, 553–563 (2022). https://doi.org/10.1007/s00374-022-01634-z

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