Profiling of the Citrus Leaf Endophytic Mycobiota Reveals Abundant Pathogen-Related Fungal Groups

Plant endophytic microbial communities consist of many latent plant pathogens and, also, many pathogen-related species with reduced virulence. Though with a long history of co-evolution, the diversity and composition of the endophytic mycobiota, especially the pathogen-related fungal groups, has been under-investigated in Citrus (C.). Based on the amplicon sequencing of fungal internal transcribed spacer (ITS), the leaf endophytic mycobiota were profiled on citrus varieties from different citrus-producing regions. The pomelo variety shared significantly distinctive leaf mycobiota when compared to the mandarin and sweet orange; these conform to their host genetic relationships. In addition, a data set of 241 citrus-related fungi, including 171 (71%) pathogens and potential pathogens, was summarized from previous studies. Under the criteria of local BLAST (covered ITS nucleotide ≥ 150 bp, sequence identity ≥ 99%), a total of 935 fungal operational taxonomic units (OTUs) were assigned to 62 pathogen-related fungal groups, representing 14.9% of the relative abundance in the whole community. Of which, the top groups consisted of Colletotrichum gloeosporioides (mean relative abundance, 4.3%), Co. citricola and Co. karstii (2.7%), Zasmidium citri-griseum (2.4%), and Z. fructigenum (1.4%). At the genus level, the ratio of the pathogen-related fungal groups in 64% of fungal genera (16 out of 25) exceeded 50%, which are the solely or mainly occurring fungi of their genus in citrus. Our study suggests that the leaf endophytic compartment may be an important place for the growth of latent pathogens.