Plant microbial community associated with infection of Xylella fastidiosa revealed by next-generation-sequencing analyses

Authors: Van Horn, Christopher; Chen, Jianchi; Sisterson, Mark; DAI, ZEHAN - South China Agricultural University

Submitted to: CDFA Pierce's Disease Control Program Research Symposium
Publication Type: Abstract Only
Publication Acceptance Date: 12/18/2018
Publication Date: 12/18/2018
Citation: Van Horn, C.R., Chen, J., Sisterson, M.S., Dai, Z. 2018. Plant microbial community associated with infection of Xylella fastidiosa revealed by next-generation-sequencing analyses. CDFA Pierce's Disease Control Program Research Symposium. p. 141.

Interpretive Summary:

Technical Abstract: Xylella fastidiosa (Xf) causing Pierce’s Disease (PD) of grapevine is known to interact with microorganisms in the plant endosphere during the course of infection and pathogenicity development. Yet, in planta study of Xf has been highly challenging due to the lack of efficient technology. The increase of Xf genetic resources in online databases, along with improved sequencing and genetic analysis technology, has provided a framework to study this economically important bacterium within the host plant endosphere. A particular interest in study was the composition and variation of microbial community in planta. DNA was extracted from three samples: 1) PD symptomatic grapevine inoculated with Xf strain Stag’s Leap in greenhouse (Greenhouse Grape - GG); 2) a non-symptomatic ragweed (Ambrosia trifida) inoculated with Xf strain Temecula in greenhouse (Greenhouse Ragweed – GR); and 3) PD symptomatic grapevine from a vineyard in Bakersfield, California in July of 2017 (Field Grape - FG). All three samples were subjected to next generation sequencing (NGS). Illumina HiSeq was used on samples GG and FG and generated 190M and 316 M 100-bp short sequence reads, respectively. Illumina MiSeq was used on sample GR and generated 39 M 250 bp short sequence reads. Percentages of Xf reads were 1.7 for GG, 0.5 for FG, and 4.0 for GR. These in planta Xf genome data were analyzed for similarities to the available sequenced Xf genomes as well as for plasmids and other unique genetic content. Genomic variations of Xf under different conditions (field, greenhouse, sampling time, plant host) were studied. Additionally, the microbial community of each plant sample was analyzed to determine the major taxonomic groups of bacteria and fungi through metagenomic approach with the help of Kaiju software. The most abundant bacterial genera present in the greenhouse plant samples were Xylella, followed by Enterococcus and Staphylococcus for both GG and GR. The most abundant bacterial genera present in the field plant sample was Paenarthrobacter, with Xylella ranking the third. The most abundant fungal genera present in all three plant samples was Rhizophagus. These results provide new information on the microbial community of plants associated with Xf infection under different environments.