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Plant microbiomes are critical components to plant health and can influence disease outcomes. We provide empirical data describing disease-induced shifts within the citrus microbiome at different levels of huanglongbing (HLB) disease severity. HLB is associated with an invasive phloem-limited bacterium, ‘Candidatus Liberibacter asiaticus’, that is introduced into the aerial portions of the tree by an insect vector. Disease manifests as aboveground foliar and fruit symptoms and significant root decline belowground. During the early phase of disease, there were depletions of putative keystone taxa in leaves and roots, followed by enrichments of putative beneficial taxa, suggesting a microbially derived immune response involved in plant protection that is ancillary to immune components encoded in the plant’s genome. In the late phase of disease, we observed enrichments of parasitic and saprophytic microorganisms, particularly in the roots. The community shifts within the root compartment are emblematic of a disease-induced dysbiosis where pathogens other than ‘Ca. L. asiaticus’ begin to dominate the community. Furthermore, we define key taxa enriched in trees with a slower rate of disease development, referred to as survivor trees, that are hallmarks of those found in trees in the early phase of disease that may be drivers of the survivor tree phenotype. We propose a disease ecology model that illustrates the relationship between the pathogen, the microbiome, and the host plant that highlights microorganisms that may serve as disease facilitators or antagonists.

Citrus production throughout the world is being severely threatened by Huanglongbing (HLB), which is a disease associated with the bacteria ‘Candidatus Liberibacter asiaticus’ (CLas), africanus, and americanus. This Resource Announcement provides amplicon-based next generation sequencing (NGS) datasets of the bacterial and fungal rRNA internal transcribed spacer (ITS) region from CLas-infected citrus budwood, leaves, and roots from five orchards located in different geographical regions in Florida (USA). To our knowledge, this is the first amplicon-based NGS study (i) that describes the fungal taxa associated with citrus and (ii) that provides comparative analyses of the bacterial and fungal taxa associated with budwood, leaves, and roots from the same citrus trees. This report also provides the sample metadata linked to these sequence datasets including HLB severity rating, tissue type, citrus rootstock, citrus scion, geographical region, and year trees were planted. When analyzed with other similar datasets, we anticipate that researchers will be able to obtain a greater understanding of the factors that shape the citrus microbiome as well as identify individual microorganisms or consortia of microorganisms that play a role in HLB suppression or exacerbation.