2-Furoic acid associated with the infection of nematodes by Dactylellina haptotyla and its biocontrol potential on plant root-knot nematodes

Abstract

Dactylellina haptotyla is a typical nematode-trapping fungus that has garnered the attention of many scholars for its highly effective lethal potential for nematodes. Secondary metabolites play an important role in D. haptotyla-nematode interactions, but which metabolites perform which function remains unclear. We report the metabolic functions based on high-quality, chromosome-level genome assembly of wild D. haptotyla YMF1.03409. The results indicate that a large variety of secondary metabolites and their biosynthetic genes were significantly upregulated during the nematode-trapping stage. In parallel, we identified that 2-furoic acid was specifically produced during nematode trapping by D. haptotyla YMF1.03409 and isolated it from fermentation production. 2-Furoic acid demonstrated strong nematicidal activity with an LD₅₀ value of 55.05 µg/mL against Meloidogyne incognita at 48 h. Furthermore, the pot experiment showed that the number of galls of tomato root was significantly reduced in the experimental group treated with 2-furoic acid. The considerable increase in the 2-furoic acid content during the infection process and its virulent nematicidal activity revealed an essential synergistic effect during the process of nematode-trapping fungal infection. IMPORTANCE Dactylellina haptotyla have significant application potential in nematode biocontrol. In this study, we determined the chromosome-level genome sequence of D. haptotyla YMF1.03409 by long-read sequencing technology. Comparative genomic analysis identified a series of pathogenesis-related genes and revealed significant gene family contraction events during the evolution of D. haptotyla YMF1.03409. Combining transcriptomic and metabolomic data as well as in vitro activity test results, a compound with important application potential in nematode biocontrol, 2-furoic acid, was identified. Our result expanded the genetic resource of D. haptotyla and identified a previously unreported nematicidal small molecule, which provides new options for the development of plant biocontrol agents.

Keywords: 2-furoic acid; Dactylellina haptotyla; genomics; infection; metabolomic; nematode-trapping fungi.

Fig 1

The characterizations of D. haptotyla YMF1.03409. (A) The growth status of D. haptotyla YMF1.03409 on PDA. (B) and (C) The conidiophores of D. haptotyla YMF1.03409, which are marked by red arrows. (D) and (E) The knobs of D. haptotyla YMF1.03409, which are marked by blue arrows.

Fig 2

The new chromosome genome assembly of D. haptotyla YMF1.03409. (A) Circos plot of D. haptotyla YMF1.03409. The outer to inner circles represent the mapping identity with MHA_v2, repetitive region density, and gene density, respectively. (B) The Hi-C heatmap of D. haptotyla YMF1.03409 indicates the satisfactory quality of the assembly. (C) The dotplot for genome-wide alignment between MHA_v2 and D. haptotyla YMF1.03409.

Fig 3

Comparative genomics of D. haptotyla YMF1.03409. (A) Statistics of genes in orthogroups among the 12 fungi. (B) The expanded and contracted gene families among the 12 fungi. (C) The overlapped and species-specific genes among D. haptotyla YMF1.03409 and three other nematode-trapping fungi. (D) Synteny map of D. haptotyla YMF1.03409 and two other nematode-predator fungi.

Fig 4

Analysis of BGCs of D. haptotyla YMF1.03409. (A) Statistics of BGCs among the 12 fungi. (B) Comparative BGCs between D. haptotyla YMF1.03409 and D. haptotyla CBS 200.50.

Fig 5

The transcriptome analysis of D. haptotyla YMF1.03409 gene transcription dynamics of the nematodes-infection assay. (A) The volcano plot of DEGs. The red color represents DEGs with significance (P < 0.05). The x-axis represents the expression change level of PD group relative to D group, and y-axis represents the significant level. (B) The heatmap of the expression levels of 1,087 DEGs. (C) The KEGG pathway enrichment results of upregulated (left) and downregulated (right) genes. The heatmaps of (D) 23 secondary metabolite biosynthetic gene clusters, (E) core genes of gene clusters, and (F) post-modification genes of gene clusters.

Fig 6

The metabolome analysis during P. redivivus infection by D. haptotyla YMF1.03409 and that of the metabolites obtained from the fermentation of D. haptotyla YMF 1.03409. (A) PCA of all extracts. (B) The volcano plot of PD48 vs D48 group. Significance cutoffs were P = 0.01 (Bayes moderated t-tests) and fold change (FC) = 1. Each dot represents an individual compound (within ±10 ppm in mass), and the probability of that quantitative observation being statistically significant is indicated by a P value on the y-axis (determined using the standard linear model within the SIEVE software). (C) The structures of metabolites from the fermentation of D. haptotyla YMF1.03409.

Fig 7

Nematicidal and anti-infestation ability of 2-furoic acid. (A) Lethality of different concentrations of 2-furoic acid on M. incognita. (B) Tomato growth status in the experimental and control groups after 20 days; control represents the negative control and avermectin represents the positive control. (C) State of infestation of the roots of the experimental and control groups after 20 days. (D) Statistics on the number of galls in the root system of experimental and control groups after 20 days. (E) Tomato growth status in the experimental and control groups after 35 days; control represents the negative control, avermectin represents the positive control. (F) State of infestation of the roots of the experimental and control groups after 35 days. (G) Statistics on the number of galls in the root system of experimental and control groups after 35 days.