Microbiome and Metagenome Analysis Reveals Huanglongbing Affects the Abundance of Citrus Rhizosphere Bacteria Associated with Resistance and Energy Metabolism

Abstract

The plant rhizosphere microbiome is known to play a vital role in plant health by competing with pathogens or inducing plant resistance. This study aims to investigate rhizosphere microorganisms responsive to a devastating citrus disease caused by ‘Candidatus Liberibacter asiaticus’ (CLas) infection, by using 16S rRNA sequencing and metagenome technologies. The results show that 30 rhizosphere and 14 root bacterial genera were significantly affected by CLas infection, including 9 plant resistance-associated bacterial genera. Among these, Amycolatopsis, Sphingopyxis, Chryseobacterium, Flavobacterium, Ralstonia, Stenotrophomonas, Duganella, and Streptacidiphilus were considerably enriched in CLas-infected roots, while Rhizobium was significantly decreased. Metagenome analysis revealed that the abundance of genes involved in carbohydrate metabolism, such as glycolysis, starch and sucrose metabolism, amino sugar and nucleotide sugar metabolism, was significantly reduced in the CLas-infected citrus rhizosphere microbial community. Likewise, the abundance of genes involved in phosphoinositide signaling and phosphoinositide metabolism, which play important roles in energy metabolism (such as carbohydrate metabolism and lipid metabolism), was also decreased in the CLas-infected samples. Taken together, our results indicate that CLas infection could affect the resistance potential and energy metabolism of the citrus rhizosphere microbial community, which may help us to understand the rhizosphere responses to plant disease and thus facilitate the development and application of antagonistic microorganism products in citrus industry.

Bioprospecting Microbiome for Soil and Plant Health Management Amidst Huanglongbing Threat in Citrus: A Review

“…Some bacterial genera like Bacillus, Methylobacterium, Halomonas , etc. were observed abundantly in citrus leaves and fruits following the infection with canker and melanosis diseases ( Li et al, 2021 ).…”

“…Application of 16SrRNA sequencing and metagenomics provided a comprehensive analysis of the citrus microbiome and its response during C Las infection ( Li et al, 2021 ). A total of 30 rhizosphere and 14 root bacterial genera were affected by C Las infection, of which 9 were plant resistance-associated bacterial genera ( Chryseobacterium , Amycolatopsis , Sphingopyxis , Duganella , Flavobacterium , Ralstonia , Streptacidiphilus , and Stenotrophomonas ) loaded in C Las-infected roots, while Rhizobium population depleted.…”

“…The abundance of genes involved in carbohydrate metabolism, glycolysis, starch and sucrose metabolism, amino sugar, and nucleotide sugar metabolism was reduced in the citrus rhizosphere microbial community of citrus rhizosphere during the process of HLB-infection. These results were highly effective in understanding the rhizosphere responses to HLB disease and the possible development of microbial antagonists-based products against HLB ( Li et al, 2021 ).…”

Co-Occurrence Analysis of Citrus Root Bacterial Microbiota under Citrus Greening Disease

“…In this survey, we confirmed that ~10% of the trees subjected to the survey remained disease-free during the entire two-year-long survey conducted by qPCR using DNA fractions prepared from leaves and fibrous roots. It has been shown that HLB compromised the recruitment and/or the composition of certain microbes in the citrus root system [ 12 , 42 ], and an attempt has been made to use bacteria with antibacterial activity isolated from the rhizosphere of the escape trees as a tool to mitigate the damage caused by HLB [ 10 ]. These data prompted us to investigate and compare the microbe population associated with the fibrous root system of trees with different HLB disease histories to investigate the potential involvement of rhizosphere microbe(s) for the tolerance against HLB as seen in the escape trees.…”

A host‐derived chimeric peptide protects citrus against Huanglongbing without threatening the native microbial community of the phyllosphere

“…On the other hand, if peptides are selective against the pathogen, their application can restore the microbiome that can benefit plant growth. HLB is known to have significant impacts on both the structure and functions of plant‐associated microbiome (Hu et al, 2022; Li et al, 2021; Liu et al, 2023; Trivedi et al, 2016). The HLB‐mediated changes in the plant‐associated microbiome is postulated to have a detrimental influence in overall citrus health (Trivedi et al, 2012).…”