The core microbiome of citrus rhizosphere


The paper in Nature Communications is here:

Now our manuscript on the structure and function of the global citrus rhizosphere microbiome is finally online. It has been an exciting journey for my colleagues from worldwide and I. 

We initiated this project because of the profound effect of citrus Huanglongbing (HLB) on microbial community and our hope to restore the microbial community affected by HLB to improve citrus health. Our initial thought was to conduct a survey type of study to know more about the microbes associated with the healthy citrus by conducting a citrus microbiome study across the globe. We hope to understand what they are, what they do and how they do regarding the citrus root microbial community and to help isolate the beneficial microbes for application purpose. 

We have invited many colleagues from the citrus production areas worldwide. We were excited that more than 20 colleagues worldwide joined us from USA, China, Brazil, Spain, Australia, South Africa, Italy, Oman, and France. Looking back, we were so lucky to have the wonderful colleagues joined us with some of them we never met even today except email exchanges. They put their trust, resources, and effort into our hands without any conditions and without knowing the fate of the future manuscript. I appreciate their being excellent collaborators and cherish their friendship formed during working together. 

I personally collected samples from Jiangxi, Guangdong, and Guangxi provinces in China with assistance from our collaborators in China. In this process, we founded the International Citrus Microbiome (Phytobiome) Consortium to facilitate the collaboration. It took us about half a year from July to the end of 2015 to collect the DNA samples and related soil sample information. The metagenomic sequencing and sequencing of the 16S and ITS amplicons took about five months. 

The most difficult part is the sequence analysis which took us around one and a half years, and we formed a strong team including more than six bioinformaticans from UF and BGI, and used a lot of computing resource from UF hipergator and BGI, for this project. It is not surprising since our dataset is much larger any previously published similar dataset. The citrus rhizosphere gene catalog is four and eighteen times larger than the tara ocean and human gut microbiome gene catalog, respectively. 

The large dataset gave us not only a lot of headaches during the analysis, but also rich information regarding the microbial community. For our manuscript, we have received many constructive and critical instructions from several reviewers. We were really impressed with the quality of the reviews. Importantly, my formal advisor Dr. Steven E. Lindow during my postdoc at UC Berkeley and Dr. Frank White at University of Florida helped us a lot with revision of the manuscript. 

At the end, we are happy that this collaborative effort has provided a comprehensive taxonomic and functional biogeographical analysis of the citrus rhizosphere microbiome and the core citrus rhizosphere microbiome is proposed. We hope our study will provide valuable information to guide microbial isolation and culturing and, potentially, to harness the power of the microbiome to improve plant production and health.

Geographic distribution of sampling sites across the world’s citrus producing regions. Purple stars, the sampling sites; orange, major citrus producing countries. Asterisk: only rhizosphere soil samples were collected.

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