Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, 33885, FL, USA.
Citrus Research and Education Center, Department of Plant Pathology, IFAS, University of Florida, Lake Alfred, 33885, FL, USA.
Nat Commun. 2018 Nov 20;9(1):4894. doi: 10.1038/s41467-018-07343-2.
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.
柑橘是一种具有全球重要意义的多年生水果作物，其根际微生物组被认为在促进柑橘生长和健康方面发挥着重要作用。在这里，我们报告了对柑橘根际微生物组的结构和功能组成的全面分析。我们使用扩增子和深度 shotgun 宏基因组测序技术，对来自六大洲不同生物地理区域的大量土壤和根际样本进行了测序。主要类群包括变形菌门、放线菌门、酸杆菌门和拟杆菌门。核心柑橘根际微生物组包括假单胞菌、根瘤菌、土壤杆菌、考克氏菌、布克氏菌、中慢生根瘤菌、慢生根瘤菌、伯克氏菌、纤维弧菌、鞘氨醇单胞菌、交替单胞菌和副伯克氏菌，其中一些是潜在的有益植物微生物。我们还鉴定了在柑橘根际中过度表达的微生物功能特征，这些特征介导了植物-微生物和微生物-微生物之间的相互作用、营养获取和植物生长促进。研究结果为指导微生物的分离和培养提供了有价值的信息，并可能利用微生物组的力量来提高植物的产量和健康。
