The structure and function of the global citrus rhizosphere microbiome

Jin Xu, Yunzeng Zhang, Pengfan Zhang, Pankaj Trivedi, Nadia Riera, Yayu Wang, Xin Liu, Guangyi Fan, Jiliang Tang, Helvécio D. Coletta-Filho, Jaime Cubero, Xiaoling Deng, Veronica Ancona, Zhanjun Lu, Balian Zhong, M. Caroline Roper, Nieves Capote, Vittoria Catara, Gerhard Pietersen, Christian VernièreAbdullah M. Al-Sadi, Lei Li, Fan Yang, Xun Xu, Jian Wang, Huanming Yang, Tao Jin, Nian Wang*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

279 Citations (Scopus)


Citrus is a globally important, perennial fruit crop whose rhizosphere microbiome is thought to play an important role in promoting citrus growth and health. Here, we report a comprehensive analysis of the structural and functional composition of the citrus rhizosphere microbiome. We use both amplicon and deep shotgun metagenomic sequencing of bulk soil and rhizosphere samples collected across distinct biogeographical regions from six continents. Predominant taxa include Proteobacteria, Actinobacteria, Acidobacteria and Bacteroidetes. The core citrus rhizosphere microbiome comprises Pseudomonas, Agrobacterium, Cupriavidus, Bradyrhizobium, Rhizobium, Mesorhizobium, Burkholderia, Cellvibrio, Sphingomonas, Variovorax and Paraburkholderia, some of which are potential plant beneficial microbes. We also identify over-represented microbial functional traits mediating plant-microbe and microbe-microbe interactions, nutrition acquisition and plant growth promotion in citrus rhizosphere. The results provide valuable information to guide microbial isolation and culturing and, potentially, to harness the power of the microbiome to improve plant production and health.

Original languageEnglish
Article number4894
JournalNature Communications
Issue number1
Publication statusPublished - Dec 1 2018
Externally publishedYes

ASJC Scopus subject areas

  • General Chemistry
  • General Biochemistry,Genetics and Molecular Biology
  • General Physics and Astronomy


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