The structure and function of the global citrus rhizosphere microbiome

First author: Jin Xu; Affiliations: University of Florida (佛罗里达大学): Lake Alfred, USA

Corresponding author: Nian Wang

Citrus is a globally important, perennial fruit crop whose rhizosphere microbiome (根际微生物群) 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 (非根际土) and rhizosphere samples collected across distinct biogeographical regions from six continents. Predominant taxa include Proteobacteria (变形菌), Actinobacteria (放线菌), Acidobacteria (酸杆菌) and Bacteroidetes(拟杆菌). The core citrus rhizosphere microbiome comprises Pseudomonas (假单胞菌属), Agrobacterium (土壤杆菌属), Cupriavidus (贪铜菌属), Bradyrhizobium (慢生根瘤菌属), Rhizobium (根瘤菌属), Mesorhizobium (中生根瘤菌属), Burkholderia (伯克氏菌属), Cellvibrio (纤维弧菌属), Sphingomonas(鞘氨醇单胞菌属), Variovorax (贪噬菌属) 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.

柑橘是全球比较重要的、多年生水果作物，并且其根际微生物群对于柑橘的生长和健康方面发挥非常重要的作用。本文中，作者对柑橘的根际微生物群落进行了结构和功能的综合分析。作者通过扩增和深度鸟枪法宏基因组测序方法对从6大洲不同地理区域收集的非根际土壤和根际土壤进行了测序分析。研究发现柑橘根际优势微生物主要是变形菌、放线菌、酸杆菌和拟杆菌四大门。核心的柑橘根基微生物群落主要由假单胞菌属、土壤杆菌属、贪铜菌属、慢生根瘤菌属、根瘤菌属、中生根瘤菌属、伯克氏菌属、纤维弧菌属、鞘氨醇单胞菌属、贪噬菌属以及Paraburkholderia属所构成，其中某些微生物对于植物来说是益生菌。作者还鉴定了柑橘根际与植物-微生物和微生物-微生物互作、营养获取和植物生长促进等相关的微生物功能性状。本文的结果为微生物分离、培养以及未来利用微生物改良作物产量和生长提供了宝贵的信息。

通讯：Nian Wang (https://crec.ifas.ufl.edu/faculty/dr-nian-wang-faculty-profile-page/)

研究方向：植物-病菌互作的分子遗传与功能基因组学研究。

doi: https://doi.org/10.1038/s41467-018-07343-2

Journal: Nature Communications

Published date: 20 November, 2018