Globally, citrus is threatened by huanglongbing (HLB), and the lack of effective control measures is a major concern of farmers, markets, and consumers. There is compelling evidence that plant health is a function of the activities of the plant's associated microbiome. Using
Liberibacter crescens
, a culturable surrogate for the unculturable HLB-associated bacterium “
Candidatus
Liberibacter asiaticus,” we tested the hypothesis that members of the citrus microbiome produce potential anti-“
Ca
. Liberibacter asiaticus” natural products with potential anti-“
Ca
. Liberibacter asiaticus” activity. A subset of isolates obtained from the microbiome inhibited
L. crescens
growth in an agar diffusion inhibition assay. Further fractionation experiments linked the inhibitory activity of the fungus
Cladosporium cladosporioides
to the fungus-produced natural products cladosporols A, C, and D, demonstrating dose-dependent antagonism to
L. crescens
.
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.