Metagenome analyses reveal microbiota changes in Citrus sinensis affected by citrus decline disease in Iran

Citrus decline disease was recently reported in Iran, affecting several citrus species grafted on Bakraee a local rootstock. Preliminary studies identified ‘Candidatus Phytoplasma aurantifoliae’ and ‘Candidatus Liberibacter asiaticus’ as putative etiological agents, but were not ultimately able to determine which one, or if an association of both pathogens, were causing the disease. The current study had the aim of characterizing the microbiota of citrus plants that were either asymptomatic, or showed either early or late symptoms, through the amplification of the V1-V3 region of the 16S rRNA gene, using an Illumina sequencer in order to: (i) clarify the etiology of the disease, (ii) describe the microbiota associated with different symptom stages. Our results suggest that liberibacter may be the main pathogen causing citrus decline disease, but cannot entirely rule out the possibility that a phytoplasma be involved as well. The characterization of microbiota described very different situations in the aerial part of the plants and in the roots, or between rootstock and scion: the leaves showed only two kinds of communities, either symptomatic or asymptomatic, while the roots showed a clear distinction between early and late symptoms. These results could lead to the identification of bacteria that are related to successful plant defense response and, therefore, to immunity to citrus decline disease.