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. 2024 Aug 23;10(9):596.
doi: 10.3390/jof10090596.

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

Feng Huang  1 , Jinfeng Ling  1 , Yiping Cui  1 , Bin Guo  1 , Xiaobing Song  1
Affiliations

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

Feng Huang et al. J Fungi (Basel). .

Abstract

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.

Keywords: citrus; endophyte; fungal community; mycobiota; pathogen.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
A phylogenetic tree constructed based on the ITS sequence of citrus-related fungi.
Figure 2
Figure 2
Profiling and comparison of citrus endophytic fungal communities in lemon, mandarin, orange, and pomelo. (A) The rarefaction curves of observed species versus the number of sequences of all 161 samples; (B) the observed species, and (C) Shannon diversity among samples of lemon, mandarin, orange, and pomelo; (D) principle coordinate plot of samples of, and (E) heatmap comparison of the relative abundance of major genera among lemon, mandarin, orange, and pomelo. The significant differences were marked with “**” (p < 0.01).
Figure 3
Figure 3
The occurrence of reported citrus-related fungi in citrus leaf endophytic communities of lemon, mandarin, orange, and pomelo. (A) An unrooted tree displaying 62 fungal groups occurring in citrus leaf endophytic fungal communities; (B) the relative abundance of the 62 fungal groups in the endophytic fungal community of lemon, mandarin, orange, and pomelo; (C) the average relative abundance of the 62 fungal groups in the citrus leaf endophytic fungal community.
Figure 4
Figure 4
The dominance of pathogens and potential pathogens within their genus. (A) an unrooted tree displaying the genera occurring in citrus leaf endophytic fungal communities; (B) the relative abundance of OTUs of pathogens and potential pathogens in the genera listed in (A); (C) the relative abundance of all OTUS in the genera listed in (A); (D) the ratio of OTUs of pathogens and potential pathogens calculated for each genus.
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