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.

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Main Authors: Xu, Jin, Zhang, Yunzeng, Zhang, Pengfan, Trivedi, Pankaj, Riera, Nadia, Wang, Yayu, Liu, Xin, Fan, Guangyi, Tang, Jiliang, Coletta-Filho, Helvécio D, Cubero, Jaime, Deng, Xiaoling, Ancona, Veronica, Lu, Zhanjun, Zhong, Balian, Roper, Caroline, Capote, Nieves, Catara, Vittoria, Pietersen, Gerhard, Vernière, Christian, Al-Sadi, Abdullah M., Li, Lei, Yang, Fan, Xu, Xun, Wang, Jian, Yang, Huanming, Jin, Tao, Wang, Nian
Format: article biblioteca
Language:eng
Subjects:F61 - Physiologie végétale - Nutrition, F62 - Physiologie végétale - Croissance et développement, Citrus, rhizosphère, génomique, http://aims.fao.org/aos/agrovoc/c_1637, http://aims.fao.org/aos/agrovoc/c_6569, http://aims.fao.org/aos/agrovoc/c_92382,
Online Access:http://agritrop.cirad.fr/590608/
http://agritrop.cirad.fr/590608/1/Xu%202018%2C%20Nature%20Com-The%20citrus%20rhizosphere%20microbiome.pdf
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spelling dig-cirad-fr-5906082024-01-29T01:32:08Z http://agritrop.cirad.fr/590608/ http://agritrop.cirad.fr/590608/ The structure and function of the global citrus rhizosphere microbiome. Xu Jin, Zhang Yunzeng, Zhang Pengfan, Trivedi Pankaj, Riera Nadia, Wang Yayu, Liu Xin, Fan Guangyi, Tang Jiliang, Coletta-Filho Helvécio D, Cubero Jaime, Deng Xiaoling, Ancona Veronica, Lu Zhanjun, Zhong Balian, Roper Caroline, Capote Nieves, Catara Vittoria, Pietersen Gerhard, Vernière Christian, Al-Sadi Abdullah M., Li Lei, Yang Fan, Xu Xun, Wang Jian, Yang Huanming, Jin Tao, Wang Nian. 2018. Nature Communications, 9:4894, 10 p.https://doi.org/10.1038/s41467-018-07343-2 <https://doi.org/10.1038/s41467-018-07343-2> The structure and function of the global citrus rhizosphere microbiome Xu, Jin Zhang, Yunzeng Zhang, Pengfan Trivedi, Pankaj Riera, Nadia Wang, Yayu Liu, Xin Fan, Guangyi Tang, Jiliang Coletta-Filho, Helvécio D Cubero, Jaime Deng, Xiaoling Ancona, Veronica Lu, Zhanjun Zhong, Balian Roper, Caroline Capote, Nieves Catara, Vittoria Pietersen, Gerhard Vernière, Christian Al-Sadi, Abdullah M. Li, Lei Yang, Fan Xu, Xun Wang, Jian Yang, Huanming Jin, Tao Wang, Nian eng 2018 Nature Communications F61 - Physiologie végétale - Nutrition F62 - Physiologie végétale - Croissance et développement Citrus rhizosphère génomique http://aims.fao.org/aos/agrovoc/c_1637 http://aims.fao.org/aos/agrovoc/c_6569 http://aims.fao.org/aos/agrovoc/c_92382 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. article info:eu-repo/semantics/article Journal Article info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/590608/1/Xu%202018%2C%20Nature%20Com-The%20citrus%20rhizosphere%20microbiome.pdf text Cirad license info:eu-repo/semantics/openAccess https://agritrop.cirad.fr/mention_legale.html https://doi.org/10.1038/s41467-018-07343-2 10.1038/s41467-018-07343-2 info:eu-repo/semantics/altIdentifier/doi/10.1038/s41467-018-07343-2 info:eu-repo/semantics/altIdentifier/purl/https://doi.org/10.1038/s41467-018-07343-2
institution CIRAD FR
collection DSpace
country Francia
countrycode FR
component Bibliográfico
access En linea
databasecode dig-cirad-fr
tag biblioteca
region Europa del Oeste
libraryname Biblioteca del CIRAD Francia
language eng
topic F61 - Physiologie végétale - Nutrition
F62 - Physiologie végétale - Croissance et développement
Citrus
rhizosphère
génomique
http://aims.fao.org/aos/agrovoc/c_1637
http://aims.fao.org/aos/agrovoc/c_6569
http://aims.fao.org/aos/agrovoc/c_92382
F61 - Physiologie végétale - Nutrition
F62 - Physiologie végétale - Croissance et développement
Citrus
rhizosphère
génomique
http://aims.fao.org/aos/agrovoc/c_1637
http://aims.fao.org/aos/agrovoc/c_6569
http://aims.fao.org/aos/agrovoc/c_92382
spellingShingle F61 - Physiologie végétale - Nutrition
F62 - Physiologie végétale - Croissance et développement
Citrus
rhizosphère
génomique
http://aims.fao.org/aos/agrovoc/c_1637
http://aims.fao.org/aos/agrovoc/c_6569
http://aims.fao.org/aos/agrovoc/c_92382
F61 - Physiologie végétale - Nutrition
F62 - Physiologie végétale - Croissance et développement
Citrus
rhizosphère
génomique
http://aims.fao.org/aos/agrovoc/c_1637
http://aims.fao.org/aos/agrovoc/c_6569
http://aims.fao.org/aos/agrovoc/c_92382
Xu, Jin
Zhang, Yunzeng
Zhang, Pengfan
Trivedi, Pankaj
Riera, Nadia
Wang, Yayu
Liu, Xin
Fan, Guangyi
Tang, Jiliang
Coletta-Filho, Helvécio D
Cubero, Jaime
Deng, Xiaoling
Ancona, Veronica
Lu, Zhanjun
Zhong, Balian
Roper, Caroline
Capote, Nieves
Catara, Vittoria
Pietersen, Gerhard
Vernière, Christian
Al-Sadi, Abdullah M.
Li, Lei
Yang, Fan
Xu, Xun
Wang, Jian
Yang, Huanming
Jin, Tao
Wang, Nian
The structure and function of the global citrus rhizosphere microbiome
description 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.
format article
topic_facet F61 - Physiologie végétale - Nutrition
F62 - Physiologie végétale - Croissance et développement
Citrus
rhizosphère
génomique
http://aims.fao.org/aos/agrovoc/c_1637
http://aims.fao.org/aos/agrovoc/c_6569
http://aims.fao.org/aos/agrovoc/c_92382
author Xu, Jin
Zhang, Yunzeng
Zhang, Pengfan
Trivedi, Pankaj
Riera, Nadia
Wang, Yayu
Liu, Xin
Fan, Guangyi
Tang, Jiliang
Coletta-Filho, Helvécio D
Cubero, Jaime
Deng, Xiaoling
Ancona, Veronica
Lu, Zhanjun
Zhong, Balian
Roper, Caroline
Capote, Nieves
Catara, Vittoria
Pietersen, Gerhard
Vernière, Christian
Al-Sadi, Abdullah M.
Li, Lei
Yang, Fan
Xu, Xun
Wang, Jian
Yang, Huanming
Jin, Tao
Wang, Nian
author_facet Xu, Jin
Zhang, Yunzeng
Zhang, Pengfan
Trivedi, Pankaj
Riera, Nadia
Wang, Yayu
Liu, Xin
Fan, Guangyi
Tang, Jiliang
Coletta-Filho, Helvécio D
Cubero, Jaime
Deng, Xiaoling
Ancona, Veronica
Lu, Zhanjun
Zhong, Balian
Roper, Caroline
Capote, Nieves
Catara, Vittoria
Pietersen, Gerhard
Vernière, Christian
Al-Sadi, Abdullah M.
Li, Lei
Yang, Fan
Xu, Xun
Wang, Jian
Yang, Huanming
Jin, Tao
Wang, Nian
author_sort Xu, Jin
title The structure and function of the global citrus rhizosphere microbiome
title_short The structure and function of the global citrus rhizosphere microbiome
title_full The structure and function of the global citrus rhizosphere microbiome
title_fullStr The structure and function of the global citrus rhizosphere microbiome
title_full_unstemmed The structure and function of the global citrus rhizosphere microbiome
title_sort structure and function of the global citrus rhizosphere microbiome
url http://agritrop.cirad.fr/590608/
http://agritrop.cirad.fr/590608/1/Xu%202018%2C%20Nature%20Com-The%20citrus%20rhizosphere%20microbiome.pdf
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