The structure and function of the global citrus rhizosphere microbiome

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.

between bulk soil and rhizosphere samples based on ITS2 and metagenomic data; (b) The distribution of eukaryotic microbes at phylum level for bulk soil samples based on metagenomic data; (c) The distribution of eukaryotic microbes at phylum level for rhizosphere samples based on metagenomic data. CN, China; SA, South Africa; BR, Brazil; SP, Spain; FR, French Réunion island; IT, Italy; AUS, Australia. Figure 7. The rhizosphere-enriched and rhizosphere-depleted genera using metagenomic data. (a) The relative abundance of rhizosphere-enriched genera. (b) The relative abundance of rhizosphere-depleted genera. Scale, relative abundance of genus at row normalization by removing the mean (centering) and dividing by the standard deviation (scaling). The color from blue to yellow represents a relative abundance of each taxa from low to high.
Supplementary Figure 9. The relative abundance of core and universally depleted KOs for rhizosphere microbiome involved in bacterial secretion system, including type I, II, III, IV, V, VI, Sec and Tat (a) and two component system (b). Scale, relative abundance of KO at row normalization by removing the mean (centering) and dividing by the standard deviation (scaling). The color from blue to yellow represents a relative abundance of each KO from low to high.

a b
Supplementary Figure 10. The relative abundance of core and universally depleted KOs for rhizosphere microbiome involved in biofilm formation and quorum sensing (a) and antimicrobial resistant genes (ARGs), antibiotic synthesis genes (ASGs) and CRISPR associated proteins (CAS) (b). Scale, relative abundance of KO at row normalization by removing the mean (centering) and dividing by the standard deviation (scaling). The color from blue to yellow represents a relative abundance of each KO from low to high.

a b
Supplementary Figure 11. The relative abundance of core and universally depleted KOs for rhizosphere microbiome involved in ABC transporters (a) and xenobiotics biodegradation and metabolism (b). Scale, relative abundance of KO at row normalization by removing the mean (centering) and dividing by the standard deviation (scaling). The color from blue to yellow represents a relative abundance of each KO from low to high.

a b
Supplementary Figure 12. The relative abundance of core and universally depleted KOs for rhizosphere microbiome involved in amino acid degradation (a) and biosynthesis (b), respectively. APD, arginine and proline degradation; CMD, cysteine and methionine degradation; LD, lysine degradation; PD, phenylalanine degradation; TD, tyrosine degradation. AAGM, alanine , aspartate and glutamate metabolism; AB, Arginine biosynthesis; CMB, cysteine and methionine biosynthesis; LB, lysine biosynthesis; PTTB, phenylalanine, tyrosine and tryptophan biosynthesis; PB, Proline biosynthesis; VLIB, Valine, leucine and isoleucine biosynthesis. Scale, relative abundance of KO at row normalization by removing the mean (centering) and dividing by the standard deviation (scaling). The color from blue to yellow represents a relative abundance of each KO from low to high.

a b
Supplementary Figure 13. The relative abundance of core and universally depleted KOs for rhizosphere microbiome involved in peptidases (a) and transcription factors (b). Scale, relative abundance of KO at row normalization by removing the mean (centering) and dividing by the standard deviation (scaling). The color from blue to yellow represents a relative abundance of each KO from low to high.

a b
Supplementary Figure 14. The relative abundance of core and universally depleted KOs for rhizosphere microbiome involved in plant nutrition promotion, plant hormone balance, adaptation to drought and pathogen inhibition. Scale, relative abundance of KO at row normalization by removing the mean (centering) and dividing by the standard deviation (scaling). The color from blue to yellow represents a relative abundance of each KO from low to high.

Supplementary Tables
Supplementary Table 1. Summary of the rhizosphere soil and the corresponding bulk soil samples collected from citrus groves worldwide.
Note: NA, the information was not available. *, only rhizosphere soil samples were collected. For other sites, both rhizosphere and bulk soil samples were collected. #, the trees were from seedlings, not from grafting.