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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 #403433

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: Metagenomic analysis of a root sample affected by plum leaf scald disease caused by Xylella fastidiosa subsp. multiplex in Georgia, the United States

item JOHNSON, KENDALL - University Of Georgia
item BRANNEN, PHILLIP - University Of Georgia
item Chen, Jianchi
item Bock, Clive

Submitted to: Journal of Plant Health
Publication Type: Abstract Only
Publication Acceptance Date: 7/1/2023
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Plum leaf scald disease (PLSD) occurs in the southeastern United States (US). The disease is caused by infection of plum (Prunus domestica) with a strain of Xylella fastidiosa subsp. multiplex (Xfm), a Gram-negative, nutritionally fastidious bacterium. Symptoms include characteristic leaf marginal necrosis. Xfm is widespread in host plant Xylem systems, and in peach (P. persica) reaches the highest titer in roots. Recent advances in metagenomics have revealed that along with Xfm, other microbes may also be present in diseased tissues as part of the host microbiome. Knowledge of microbiome adds a new perspective to PLSD research and potential control of Xfm. In this study, a root sample (PLS-5) from a plum tree showing typical leaf scald symptoms was collected in Fort Valley, Georgia, US in 2020. DNA was extracted and presence of Xfm confirmed by a PCR test. Next-generation sequencing was performed using an Illumina NovaSeq 6000 PE150 format. The PLSD DNA sample yielded a total of 42,254,521,468 bp sequence data (279,831,268 reads, each read = 151 bp). Sequence reads were binned using the Kaiju metagenomic classifier against the nr database that includes all published bacterial and fungal DNA sequences in GenBank. Based on the number of matched reads, the top five most abundant bacterial genera were: Xylella (22.1%), Pseudomonas (0.12%), Staphylococcus (0.06%), Paenarthrobacter (0.06%), and Lactobacillus (0.03%). The high titer of Xfm and the significant association of Pseudomonas in the PLSD root sample are of particular interests and deserve further research.