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ARS Home » Pacific West Area » Parlier, California » San Joaquin Valley Agricultural Sciences Center » Crop Diseases, Pests and Genetics Research » Research » Publications at this Location » Publication #405440

Research Project: Identifying Vulnerabilities in Vector-host-pathogen Interactions of Grapevine and Citrus Pathosystems to Advance Sustainable Management Strategies

Location: Crop Diseases, Pests and Genetics Research

Title: Microbiome comparison between leaf and root samples within the same citrus tree infected by “Candidatus Liberibacter asiaticus” in Texas, USA

item MADHURABABU, KUNTA - Texas A&M University
item Chen, Jianchi

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 7/1/2023
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Citrus Huanglongbing (HLB) is endemic in commercial citrus orchards and residential sites in the Lower Rio Grande Valley (LRGV) of South Texas. Our previous studies showed that the causal agent associated with HLB, “Candidatus Liberibacter asiaticus” (CLas), was detected in both leaf and root system. Recent research has shown that microbiome is essential for plant health and disease development. To acquire more biological information about HLB in Texas, we investigated the microbiomes of leaf and root samples from the same grapefruit tree showing HLB symptoms. A leaf sample A12-L and a root sample A12-R were collected and used for DNA extraction. PCR with HLBaspr-PCR (targeting 16S rRNA gene) showed Ct of 26.15 for A12-L and 26.54 for A12-R. Both samples were subject to next generation sequencing (Illumina HiSeq paired-end 100 x 2) with a total of 199,330,474 reads for A12-L and 194,539,589 reads for A12-R. Read mapping using Bowtie2 (version 2.4.5) with CLas psy62 genome (NC_012985.3) as a reference identified the overall alignment rate of 0.01% for A12-L and <0.01% for A12-R. Analyses using Kaiju classifier identified significant microbiome difference between A12-L and A12-R. The top-three bacterial list was Pseudomonas (9.3%), Acinetobacter (6.1%), and Dickeya (1.1%) for A12-L and Niastella (0.24%), Acinetobacter (0.17%), and Streptomyces (0.08%) for A12-R. CLas was ranked beyond top-50 in both A12-L (0.001808%) and A12-R (0.000263%). Results from this study provide baseline information for future research in CLas-microbes interactions new perspective in HLB biology.