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Citrus greening (aka Huanglongbing, HLB) caused by the phloem-limited, fastidious α-proteobacteria 'Candidatus Liberibacter' spp. is the most devastating citrus disease in the world. Harnessing the beneficial potential of native microbiota may be one of the few logistically and economically potential solutions for controlling HLB. We investigated the effect of management practices on HLB control via changes in soil microbiota, and used this information to develop a synthetic microbial community (SynCom) with a stable and predictable outcome in the field. Overall, we have developed a microbial toolbox for microbiota-mediated pathogen protection in real world conditions. Further understanding the mechanisms of the SynCom that contribute to the suppression of HLB progression and plant damage will be instrumental for developing better management strategies for grove health and sustainability.