Bacteriomic analyses of Asian citrus psyllid and citrus samples infected with “Candidatus Liberibacter asiaticus” in southern California and Huanglongbing management implications

Authors: HUANG, J - South China Agricultural Univerisity; DAI, Z - South China Agricultural Univerisity; ZHENG, Z - South China Agricultural Univerisity; DA SILVA, P - Fundecitrus - Brazil; KUMAGAI, L - California Department Of Food And Agriculture; XIANG, Q - Citrus Research Board; Chen, Jianchi; DENG, X - South China Agricultural Univerisity

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/17/2021
Publication Date: 7/2/2021
Citation: Huang, J., Dai, Z., Zheng, Z., da Silva, P., Kumagai, L., Xiang, Q., Chen, J., Deng, X. 2021. Bacteriomic analyses of Asian citrus psyllid and citrus samples infected with “Candidatus Liberibacter asiaticus” in southern California and Huanglongbing management implications. Frontiers in Microbiology. 12. Article 683481. https://doi.org/10.3389/fmicb.2021.683481.
DOI: https://doi.org/10.3389/fmicb.2021.683481

Interpretive Summary: Citrus Huanglongbing (HLB, yellow shoot disease) is associated with an unculturable bacterial pathogen called “Candidatus Liberibacter asiaticus” (CLas) and was found in southern California in 2012. Current HLB management in California is based on eradication requiring extensive knowledge of the disease. HLB pathogen is transmitted by an insect vector, Asian citrus psyllid (ACP). Both ACP and citrus plant are known to harbor non-CLas bacteria that may influence HLB development and management. In this study, the bacterial community in ACP and citrus samples collected from southern California were analyzed using a DNA sequencing-based technique called metagenomics. Ten bacteria were identified and validated. Analyses on these bacteria revealed information useful for future HLB biological control and provided explanation on how some non-CLas bacteria influenced the current PCR detection method. The CLas strain recently found in San Bernardino County of California was similar to other known Californian strains. This new bacterial information will directly contribute to current efforts on HLB management in California and around the world.

Technical Abstract: Citrus Huanglongbing (HLB, yellow shoot disease) is associated with an unculturable proteobacterium “Candidatus Liberibacter asiaticus” (CLas). HLB was found in southern California in 2012 and current management strategy is based on eradication. The HLB patho-system can be described as the interactions among CLas, insect vector Asian citrus psyllid (ACP, Diaphorina citri), and citrus host. Little is known about the roles of non-CLas ACP associated bacteria (AABacts) and citrus associated bacteria (CABacts). Recent advancement in next generation sequencing (NGS) technology provides a new venue to study all bacteria (CLas, AABacts and CABacts) or bacteriome through genomic DNA sequence analyses (metagenomics). In this study, the bacteriomes of ACP and citrus (represented by leaf midrib tissues) samples from southern California were studied. A metagenomic pipeline was developed that included NGS in Illumina platform, using Kaiju tool to classify and acquire bacterial draft genome sequences and taxonomic validations based on average nucleotide identity (ANI). Ten bacteria at genus or species levels from ACP and citrus were identified. The significant bacteriomic discoveries are summarized as: 1) Burkholderia, Paraburkholderia and Pseudomonads were common in ACP and citrus that could serve as candidates for future HLB biocontrol research; 2) The presence of Bradyrhizobium and Mesorhizobium could interfere with the TaqMan PCR (HLBas/HLBp/HLBr) detection of CLas, particularly at low or zero CLas titer situation; 3) A Buchnera bacterium was first found in ACP; and 4) The recently reported CLas strains in San Bernardino County of California were similar to other known Californian strains.