Biology and Fertility of Soils

, Volume 52, Issue 7, pp 997–1005 | Cite as

Pathogen invasion indirectly changes the composition of soil microbiome via shifts in root exudation profile

  • Yian Gu
  • Zhong Wei
  • Xueqi Wang
  • Ville-Petri Friman
  • Jianfeng Huang
  • Xiaofang Wang
  • Xinlan Mei
  • Yangchun Xu
  • Qirong Shen
  • Alexandre Jousset
Original Paper


Plant-derived root exudates modulate plant-microbe interactions and may play an important role in pathogen suppression. Root exudates may, for instance, directly inhibit pathogens or alter microbiome composition. Here, we tested if plants modulate their root exudation in the presence of a pathogen and if these shifts alter the rhizosphere microbiome composition. We added exudates from healthy and Ralstonia solanacearum-infected tomato plants to an unplanted soil and followed changes in bacterial community composition. The presence of pathogen changed the exudation of phenolic compounds and increased the release of caffeic acid. The amendment of soils with exudates from the infected plants led to a development of distinct and less diverse soil microbiome communities. Crucially, we could reproduce similar shift in microbiome composition by adding pure caffeic acid into the soil. Caffeic acid further suppressed R. solanacearum growth in vitro. We conclude that pathogen-induced changes in root exudation profile may serve to control pathogen both by direct inhibition and by indirectly shifting the composition of rhizosphere microbiome.


Amplicon sequencing Phenolics Ralstonia solanacearum Root exudation Root-pathogen interaction Soil microbiome 



We thank Wu Xiong from Nanjing Agricultural University for help with bioinformatic analysis. Joana Falcao Salles from University of Groningen is acknowledged for providing helpful advices. This research was financially supported by the National Key Basic Research Program of China (2015CB150503), the National Natural Science Foundation of China (31501837, 41301262, 41471213), the Natural Science Foundation of Jiangsu Province (BK20130677), the 111 project (B12009), the Priority Academic Program Development (PAPD) of Jiangsu Higher Education Institutions (Qirong Shen), the China Post-doctoral Science Foundation (2013M541687) and the Qing Lan Project (Yangchun Xu and Zhong Wei).

Supplementary material

374_2016_1136_Fig5_ESM.gif (32 kb)
Fig. S1

High-performance liquid chromatography (HPLC) profile of exudates originating from pathogen-only (RS; blue line), plant-only (Tomato; red line) and plant-and-pathogen together (Tomato + RS; green line) treatments. (GIF 31 kb)

374_2016_1136_MOESM1_ESM.tif (481 kb)
High Resolution Image (TIF 480 kb)
374_2016_1136_Fig6_ESM.gif (59 kb)
Fig. S2

The relative abundance of the major bacterial phyla in the control, caffeic acid, plant-only (Tomato) and plant-and-pathogen (Tomato + RS) treatments. (GIF 58 kb)

374_2016_1136_MOESM2_ESM.tif (374 kb)
High Resolution Image (TIF 374 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  • Yian Gu
    • 1
  • Zhong Wei
    • 1
  • Xueqi Wang
    • 1
  • Ville-Petri Friman
    • 2
  • Jianfeng Huang
    • 3
  • Xiaofang Wang
    • 1
  • Xinlan Mei
    • 1
  • Yangchun Xu
    • 1
  • Qirong Shen
    • 1
  • Alexandre Jousset
    • 1
    • 4
  1. 1.Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based FertilizersNanjing Agricultural UniversityNanjingPeople’s Republic of China
  2. 2.Department of BiologyUniversity of YorkYorkUK
  3. 3.Institute of Agricultural Resources and EnvironmentGuangdong Key Laboratory of Nutrient Cycling and Farmland Conservation, Guangdong Academy of Agricultural SciencesGuangzhouPeople’s Republic of China
  4. 4.Institute for Environmental Biology, Ecology & BiodiversityUtrecht UniversityUtrechtThe Netherlands

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