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. 2024 Dec 6:15:1422360.
doi: 10.3389/fmicb.2024.1422360. eCollection 2024.

Mycobiome analysis of leaf, root, and soil of symptomatic oil palm trees (Elaeis guineensis Jacq.) affected by leaf spot disease

Abiodun Abeeb Azeez  1   2 , Daniel Ofeoritse Esiegbuya  3 , Adebola Azeez Lateef  1   4 , Fred O Asiegbu  1
Affiliations

Mycobiome analysis of leaf, root, and soil of symptomatic oil palm trees (Elaeis guineensis Jacq.) affected by leaf spot disease

Abiodun Abeeb Azeez et al. Front Microbiol. .

Abstract

Recently, attention has been shifting toward the perspective of the existence of plants and microbes as a functioning ecological unit. However, studies highlighting the impacts of the microbial community on plant health are still limited. In this study, fungal community (mycobiome) of leaf, root, and soil of symptomatic leaf-spot diseased (SS) oil palm were compared against asymptomatic (AS) trees using ITS2 rRNA gene metabarcoding. A total of 3,435,417 high-quality sequences were obtained from 29 samples investigated. Out of the 14 phyla identified, Ascomycota and Basidiomycota were the most dominant accounting for 94.2 and 4.7% of the total counts in AS, and 75 and 21.2% in SS, respectively. Neopestalotiopsis is the most abundant genus for AS representing 8.0% of the identified amplicons compared to 2.0% in SS while Peniophora is the most abundant with 8.6% of the identified amplicons for SS compared to 0.1% in AS. The biomarker discovery algorithm LEfSe revealed different taxa signatures for the sample categories, particularly soil samples from asymptomatic trees, which were the most enriched. Network analysis revealed high modularity across all groups, except in root samples. Additionally, a large proportion of the identified keystone species consisted of rare taxa, suggesting potential role in ecosystem functions. Surprisingly both AS and SS leaf samples shared taxa previously associated with oil palm leaf spot disease. The significant abundance of Trichoderma asperellum in the asymptomatic root samples could be further explored as a potential biocontrol agent against oil palm disease.

Keywords: asymptomatic; fungal community; leaf spot disease; mycobiome; oil palm; symptomatic.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision.

Figures

FIGURE 1
FIGURE 1
Oil palm fronds (leaves) from healthy asymptomatic tree (A) and symptomatic leaf-spot diseased tree (B).
FIGURE 2
FIGURE 2
Relative abundance of fungal phyla from the annotated ASVs based on sample type. OLA, Okomu asymptomatic leaf samples; OLS, Okomu symptomatic leaf samples; ORA, Okomu asymptomatic root samples; ORS, Okomu symptomatic root samples; OSA, Okomu asymptomatic soil samples; OSS, Okomu symptomatic soil samples; RLA, Ore asymptomatic leaf samples; RLS, Ore symptomatic leaf samples; RRA, Ore asymptomatic root samples; RRS, Ore symptomatic root samples; RSA, Ore asymptomatic soil samples; RSS, Ore symptomatic soil samples.
FIGURE 3
FIGURE 3
Relative abundance of fungal genera from the annotated ASVs based on sample type. OLA, Okomu asymptomatic leaf samples; OLS, Okomu symptomatic leaf samples; ORA, Okomu asymptomatic root samples; ORS, Okomu symptomatic root samples; OSA, Okomu asymptomatic soil samples; OSS, Okomu symptomatic soil samples. RLA, Ore asymptomatic leaf samples; RLS, Ore symptomatic leaf samples; RRA, Ore asymptomatic root samples; RRS, Ore symptomatic root samples; RSA, Ore asymptomatic soil samples; RSS, Ore symptomatic soil samples.
FIGURE 4
FIGURE 4
Relative abundance of fungal genera from annotated ASVs based on group. ORLA, Okomu/Ore asymptomatic leaf samples; ORLS, Okomu/Ore symptomatic leaf samples; ORRA, Okomu/Ore asymptomatic root samples; ORRS, Okomu/Ore symptomatic root samples; ORSA, Okomu/Ore asymptomatic soil samples; ORSS, Okomu/Ore symptomatic soil samples. OLA, Okomu asymptomatic leaf samples; OLS, Okomu symptomatic leaf samples; ORA, Okomu asymptomatic root samples; ORS, okomu symptomatic root samples; OSA, Okomu asymptomatic soil samples; OSS, Okomu symptomatic soil samples; RLA, Ore asymptomatic leaf samples; RLS, Ore symptomatic leaf samples; RRA, Ore asymptomatic root samples; RRS, Ore symptomatic root samples; RSA, Ore asymptomatic soil samples; RSS, Ore symptomatic soil samples.
FIGURE 5
FIGURE 5
Venn diagrams showing the shared and unique number of genus (A) between the sample types (B) across the group. ORLA, Okomu/Ore asymptomatic leaf samples; ORLS, Okomu/Ore symptomatic leaf samples; ORRA, Okomu/Ore asymptomatic Root samples; ORRS, Okomu/Ore symptomatic root samples; ORSA, Okomu/Ore asymptomatic soil samples; ORSS, Okomu/Ore symptomatic soil samples.
FIGURE 6
FIGURE 6
LEfSe bar plot based on significantly enriched genera across groups. ORLA, Okomu/Ore asymptomatic leaf samples; ORLS, Okomu/Ore symptomatic leaf samples; ORRA, Okomu/Ore asymptomatic root samples; ORRS, Okomu/Ore symptomatic root samples; ORSA, Okomu/Ore asymptomatic soil samples; ORSS, Okomu/Ore symptomatic soil samples.
FIGURE 7
FIGURE 7
Alpha diversity of the fungal communities based on (A) sample type and (B) group. ORLA, Okomu/Ore asymptomatic leaf samples; ORLS, Okomu/Ore symptomatic leaf samples; ORRA, Okomu/Ore asymptomatic root samples; ORRS, Okomu/Ore symptomatic root samples; ORSA, Okomu/Ore asymptomatic soil samples; ORSS, Okomu/Ore symptomatic soil samples.
FIGURE 8
FIGURE 8
Association network maps of oil palm tissue and soil fungal communities generated according to relative abundance correlation data for sample type: (a) asymptomatic (b) symptomatic, and group: (c) ORLA (d) ORLS (e) ORRA (f) ORRS (g) ORSA (h) ORSS. ORLA, Okomu/Ore asymptomatic leaf samples; ORLS, Okomu/Ore symptomatic leaf samples; ORRA, Okomu/Ore asymptomatic root samples; ORRS, Okomu/Ore symptomatic root samples; ORSA, Okomu/Ore asymptomatic soil samples; ORSS, Okomu/Ore symptomatic soil samples.
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