Core endophyte communities of different citrus varieties from citrus growing regions in China

Yixin Wu,Min Huang,Wenyan Cui,Pengfei He,Pengbo He,Shahzad Munir,Yongmei Li,Yueqiu He,Pengjie He

doi:10.1038/s41598-020-60350-6

Yixin Wu, Min Huang + Show 7 more

Open Access

https://doi.org/10.1038/s41598-020-60350-6

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Abstract

The native microbiomes of citrus trees play important roles in plant health, with good communication between the native microbiome and the host plant. Here, we report on the native endophytes in 24 citrus varieties in nine citrus growing regions in China; some of the trees were healthy and others had asymptomatic or symptomatic huanglongbing, which is caused by the pathogen Candidatus Liberibacter asiaticus (CLas). We used culture-dependent analysis and characterized the isolates by partial 16S rRNA gene sequencing. The endophytes were compared between different citrus varieties, regions, and disease states (healthy, asymptomatic, and symptomatic). The total number of endophytes isolated from most of the citrus varieties was 104–106 CFU/g of leaves, but it differed significantly by disease state, with the highest numbers in the healthy leaves and the lowest in the symptomatic leaves (p < 0.05). Among the citrus varieties, the Valencia variety had the maximum number of endophyte species (22). The most dominant endophytes were Bacillus subtilis, B. velezensis, Curtobacterium luteum, and Microbacterium testaceum. The higher frequency of B. subtilis in the healthy/asymptomatic plants compared to the symptomatic plants suggests that it has a role in huanglongbing resistance. Native endophyte communities in various citrus varieties could be used to improve citrus growth and combat CLas.

Highlights

The native microbiomes of citrus trees play important roles in plant health, with good communication between the native microbiome and the host plant
Similar trends has been reported regarding the devastating citrus disease, huanglongbing (HLB), which is caused by Candidatus Liberibacter asiaticus (CLas), Candidatus Liberibacter americanus, and Candidatus Liberibacter africanus[32], resulting in severe losses to the citrus industry worldwide[33]
The native bacterial endophytic communities of healthy, symptomatic, and asymptomatic citrus leaves in nine citrus growing regions was assessed in 2016–2018, and Fig. 2 show the endophytic microbial diversity of different citrus varieties from different citrus growing regions in China

Summary

Introduction

The native microbiomes of citrus trees play important roles in plant health, with good communication between the native microbiome and the host plant. We report on the native endophytes in 24 citrus varieties in nine citrus growing regions in China; some of the trees were healthy and others had asymptomatic or symptomatic huanglongbing, which is caused by the pathogen Candidatus Liberibacter asiaticus (CLas). Native endophyte communities in various citrus varieties could be used to improve citrus growth and combat CLas. Most plants are hosts to a diverse group of bacteria, known as endophytes, that do not harm the host and colonizing the internal tissues of plants without causing any immediate and overt negative symptoms[1]. Plant microbiomes comprise hundreds to thousands of operational taxonomic units (OTUs), with a small number of taxa representing a small proportion of the overall abundance of bacteria having dominant roles[16,17,18]. It has previously been shown that the restructuring of the citrus microbiome caused by HLB disease development could be overcome using native bacteria to manage the pathogen titer[34,35]

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