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The microbiome associated with crop plants has a strong impact on their health and productivity.  Candidatus  Liberibacter asiaticus (Las), the bacterial pathogen responsible for Huanglongbing (HLB) disease, lives inside the phloem of citrus plants including the root system. It has been suggested that Las negatively affects citrus microbiome. On the other hand, members of citrus microbiome also influence the interaction between Las and citrus. Here, we report the isolation and characterization of multiple putative beneficial bacteria from healthy citrus rhizosphere. Firstly, six bacterial strains showing antibacterial activity against two bacteria closely related to Las:  Agrobacterium tumefaciens  and  Sinorhizobium meliloti  were selected. Among them,  Burkholderia metallica  strain A53 and  Burkholderia territorii  strain A63 are within the β-proteobacteria class, whereas  Pseudomonas granadensis  strain 100 and  Pseudomonas geniculata  strain 95 are within the γ-proteobacteria class. Additionally, two gram-positive bacteria  Rhodococcus jialingiae  strain 108 and  Bacillus pumilus  strain 104 were also identified. Secondly, antimicrobial activity against three fungal pathogens:  Alternaria alternata ,  Colletotrichum acutatum ,  Phyllosticta citricarpa , and two oomycetes:  Phytophthora nicotianae  and  Phytophthora palmivora.  Four bacterial strains  Burkholderia territorii  A63,  Burkholderia metallica  A53,  Pseudomonas geniculata  95, and  Bacillus pumilus  104 were shown to have antagonistic activity against the citrus root pathogen  Phytophthora nicotianae  based on dual culture antagonist assays and compartmentalized petri dish assays. The four selected bacteria were sequenced. Genes involved in phosphate solubilization, siderophore production and iron acquisition, volatile organic compound production, osmoprotection and osmotic tolerance, phytohormone production, antagonism, and nutrient competition were predicted and discussed related to the beneficial traits.

Characterization of Antimicrobial-Producing Beneficial Bacteria Isolated from Huanglongbing Escape Citrus Trees