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In Vitro Assessment of Organic and Residual Fractions of Nematicidal Culture Filtrates from Thirteen Tropical Trichoderma Strains and Metabolic Profiles of Most-Active

Centro de Investigación Científica de Yucatán, A. C. Calle 43 No. 130, Col. Chuburná de Hidalgo, Mérida 97205, Mexico
Tecnológico Nacional de México, Campus Conkal, Avenida Tecnológico s/n, Conkal 97345, Mexico
Instituto de Ciencias Agrarias, CSIC, Serrano 115-dpdo, 28006 Madrid, Spain
Fundación MEDINA, 18016 Granada, Spain
Authors to whom correspondence should be addressed.
J. Fungi 2022, 8(1), 82;
Received: 23 November 2021 / Revised: 17 December 2021 / Accepted: 12 January 2022 / Published: 15 January 2022
(This article belongs to the Section Fungi in Agriculture and Biotechnology)


The nematicidal properties of Trichoderma species have potential for developing safer biocontrol agents. In the present study, 13 native Trichoderma strains from T. citrinoviride, T. ghanense (2 strains), T. harzianum (4), T. koningiopsis, T. simmonsii, and T. virens (4) with nematicidal activity were selected and cultured in potato dextrose broth to obtain a culture filtrate (CF) for each. Each CF was partitioned with ethyl acetate to obtain organic (EA) and residual filtrate (RF) fractions, which were then tested on second-stage juveniles (J2s) of the nematodes Meloidogyne javanica and M. incognita in a microdilution assay. The most lethal strains were T. harzianum Th43-14, T. koningiopsis Th41-11, T. ghanense Th02-04, and T. virens Th32-09, which caused 51–100% mortality (%M) of J2s of both nematodes, mainly due to their RF fractions. Liquid chromatography–diode array detector-electrospray-high resolution mass spectrometry analysis of the most-active fractions revealed sesquiterpene and polyketide-like metabolites produced by the four active strains. These native Trichoderma strains have a high potential to develop safer natural products for the biocontrol of Meloidogyne species.

1. Introduction

Fungi belonging to the Trichoderma genus are cosmopolitan species, with 488 species identified [1]. Several of these species have been widely studied as biocontrol agents against phytopathogenic fungi [2] and nematodes [3,4], insects [5], and weeds [6], and as plant growth promoters [7,8]. The nematicidal potential of Trichoderma species is increasingly being harnessed to develop new and safer biocontrol agents against parasitic nematodes such as Globodera pallida, Heterodera avenae, Meloidogyne incognita, M. javanica, M. hapla, and Pratylenchus brachyurus [8,9]. In particular, Meloidogyne root-knot nematodes are considered the most harmful because they can affect a wide range of crops, causing production losses between 25% to 50% and millions of dollars. They thus continue to be controlled mainly with synthetic agrochemicals despite recognized problems for the environment and organisms [10,11,12] because of with lack of safer products and eco-friendly and holistic strategies. As harmful synthetic chemicals are withdrawn from the market, the search for alternatives such as crop rotation, resistant plant varieties, and biological control agents or their derivatives to control nematodes has intensified [4,11,13,14] Trichoderma species that have lethal effects against Meloidogyne species include T. harzianum, T. koningii, T. koningiopsis, T. longibrachiatum, T. citrinoviride and T. viride [15,16,17] against M. incognita; T. hamatum, T. harzianum, T. koningii, T. koningiopsis, and T. viridae against M. javanica [15,18,19]; T. asperellum, T. harzianum, T. viride and T. viride on M. hapla [9]; and T. harzianum against M. enterolobii [20].
The main mechanisms of action known for Trichoderma species are antibiosis, competition for space and nutrients, mycoparasitism, and induction of defense mechanisms. The antibiosis involves the production and secretion of secondary and primary metabolites that inhibit the growth and development of root-knot nematodes [19,21,22]. Regarding the production and secretion of metabolites, approximately 390 non-volatile metabolites have been identified from Trichoderma spp. [2,23], but only a few, such as gliotoxin, gliovirin, heptelidic acid, and viridin identified from T. virens [3,24], have been reported to have nematicidal activity. Therefore, a systematic bio-guided screening of Trichoderma species is a promising option to find novel nematicidal products.
During our ongoing bioprospecting studies in search of natural agrochemical products in the Yucatán península (Mexico), our group isolated 56 native Trichoderma species from soils. The foregoing is in response to the need to develop nematicides based on native species adapted to the areas where they are intended to be applied, with the knowledge of the active metabolites produced by fungal strains. These strains were tested for control of M. incognita, and 29 of these strains affected the viability of eggs and second-stage juveniles (J2s) in vitro and acted as plant growth promoters [25,26,27]. Moreover, these active Trichoderma strains decreased the severity of nematode damage on tomato and improved yields in the greenhouse [18,25].
In the present study, 13 Trichoderma strains from Yucatán were selected due to their activity against phytopathogenic fungi, nematodes, and as plant growth promoters. All selected Trichoderma strains were cultured in the liquid media potato dextrose broth. From each fungal strain, the culture filtrate, ethyl acetate fraction, and residual filtrate fraction were obtained and tested against the J2s of M. incognita and M. javanica. The chemical profiles of the most-active filtrates or fractions were analyzed by liquid chromatography– diode array detector-electrospray-high resolution mass spectrometry (LC-DAD-ESI-HRMS).

2. Materials and Methods

2.1. Trichoderma Strains

The 13 Trichoderma spp. strains, obtained from cultivated and non-cultivated soil in Yucatán state in Mexico [25,26] and supplied by the Phytopathology Laboratory of Tecnológico Nacional de México, Campus Conkal (Table 1), belonged to six Trichoderma species: T. citrinoviride (Th33-58), T. ghanense (Th02-04, Th26-52), T. harzianum (Th02-01, Th20-07, Th43-14 and Th33-59), T. koningiopsis Th41-11, T. simmonsii Th09-06; and T. virens (Th05-02, Th27-08, Th32-09, and Th43-13). The 5.8S-ITS regions of each strain were sequenced previously and are available in the GenBank database [27,28]. The fungal strains were reactivated in Petri dishes with potato dextrose agar (PDA, Dibico, Edo. Mex., MX) and incubated at 25 ± 2 °C, 12/12 h of light/dark for 8 days (Table 1, Figure 1).

Liquid Culture of Trichoderma Strains

The strains were grown in potato dextrose broth (PDB), which was made by adding 200 g of potato fragmented in distilled water at the boiling point (1000 mL) for 15 min, then filtered and 20 g of dextrose (Difco, Baltimore, MD, USA) added. A volume of 200 mL of the medium was deposited in Roux bottles and sterilized in an autoclave at 121 °C, 15 lb pressure, for 15 min. For each Trichoderma strain, cultured in PDA (8 days), a mycelial disk (7 mm diameter) was added to the medium in each of three Roux bottles. PDB without a Trichoderma strain was used as a control (blank). Three replicates of these cultures were incubated at 25 ± 2 °C, 12/12 h light/dark for 31 days. The mycelium was then removed from the culture broth by filtration through a double layer of cheesecloth. Each culture filtrate (CF), designated as 100% concentration, was then diluted with distilled water to 50% and 25% concentrations. The pH of 5 mL of the 100% CF was measured, then stored at 4 ± 2 °C until organic extraction (1–3 days).

2.2. Preparation of Fractions from Culture Filtrates

Each CF was liquid–liquid extracted with ethyl acetate three times (2:1, 1:1, 1:1 v/v), obtaining an ethyl acetate (EA) and residual filtrate (RF) fractions. The EA fraction was dried over sodium sulfate (Merck, New Jersey, USA), and the solvent was vacuum-evaporated at 40 °C in a rotary evaporator (IKA model RV-10, Staufen, Germany). The residual solvent in the RFs was also removed by evaporation, and the residue was designated as 100% concentration. The PDB control was processed the same way. All EAs were stored at 4 °C, and the RF fractions were frozen.

2.3. Nematicidal Bioassay

2.3.1. Nematode Inoculum

The population of M. incognita was obtained from the Tecnológico Nacional de México/ campus Conkal, Yucatán, México (30 ± 2 °C, 90% relative humidity) and M. javanica from the Instituto de Ciencias Agrarias, CSIC in Madrid, Spain (25 ± 1 °C, 70% relative humidity). Both nematodes were maintained on tomato plants (variety Marmanded) growing in pots in a greenhouse. Egg masses were collected from infested tomato roots and incubated for 72 h in sterile distilled water at 25 ± 2 °C for M. javanica and 30 ± 2 °C for M. incognita. The hatched J2s of Meloidogyne were adjusted to a final concentration of 100 J2 nematodes/100 μL distilled water to test CFs and RFs fractions (aqueous samples) and to 100 J2 nematodes/95 μL of distilled water solution to test EA samples [29,30].

2.3.2. Sample Preparation and Nematicidal Bioassay

Aqueous samples (100 µL) of a serial dilution (100, 50, or 25%) of either the CF or RF samples of a Trichoderma strain or a blank were deposited in wells of 96-well plates with U-bottom (BD Falcon, San Jose, CA, USA). The J2s suspended in distilled water (100 μL) that had been filtered through a 25 µm mesh screen were then transferred into each well. The negative controls consisted of CF or RF blanks, distilled water (DW), and 100 J2s. EA samples (5 µL) dissolved in DMSO:0.6%-Tween 20 (DT) were transferred to each well containing nematode suspension (95 µL), with a final concentration of 1 µg/µL. In this case, the negative control consisted of blank extracts, a mixture of water-DT 95:5 (WDT), and 100 J2s. Four replicates for each treatment were performed. The experimental plates were sealed with parafilm to prevent evaporation and maintained at the same conditions described above for egg masses in the dark [29,31].
After 72 h, immobile and rigid J2s that lacked intestinal contents were counted as dead, using a binocular microscope, and expressed as the percentage of juvenile mortality (%M). The nematicidal activity data were corrected using Schneider–Orelli’s formula [32]. A completely randomized design was used, and means were compared using the Scott-Knott test (p ≤ 0.05) in the statistical package Infostat Ver. 2018 [33].

2.4. Liquid Chromatography-Diode Array Detector-Electrospray-High Resolution Mass Spectrometry

The active EA and RF fractions were freeze-dried (Labconco FreeZone 2.5, model 7670520, Houston, TX, USA) and dissolved to 1% w/v with methanol, then 3 µL was injected onto a C8 column (Zorbax SB, 2.1 × 30 mm) in an Agilent 1200 liquid chromatograph (LC, Santa Clara, CA, USA) coupled to an Agilent diode array detector and a Bruker Maxis HR-QTOF mass detector (HRMS Bruker GmbH, Bremen, Germany). The samples were separated at 40 °C with a flow of 300 μL/min. The mobile phase was a mixture of water–acetonitrile 90:10 v/v 0.01% trifluoroacetic acid and 1.3 mM ammonium formate (solvent A) and 10:90 v/v 0.01% trifluoroacetic acid and 1.3 mM ammonium formate (solvent B). The gradient was from 10% to 100% of solvent B in 6 min, maintained in 100% B for 2 min, then returned to 10% B for 2 min [34]. Mass spectra (50 to 2000 m/z) in the positive mode were acquired, and components detected were compared against the MEDINA Microbial Dereplication Databases (with approximately 900 known bioactive molecules), the Chapman & Hall Dictionary of Natural Products (v25.1, CRC Press, Boca Raton, FL, USA), and a database available in the literature.

3. Results

3.1. Nematicidal Activity

The lethality of the CFs of the 13 species of Trichoderma against M. incognita differed (p ≤ 0.05) from that of the negative controls at the 100% concentration (Figure 2, Table 2). All the CFs were mortal to M. incognita at 100% concentration, except for that of T. citrinoviride (M = 62%) after 72 h. The most mortal CFs at 50% concentration against M. incognita after 72 h were from T. ghanense Th02-04 (M = 100%), T. virens Th27-08 (M = 71%), and T. harzianum Th43-14 (M = 66%). The activity of the CFs decreased to M < 50%) at 25% dilution, so they were considered non-nematicidal at this dilution. Against J2s of M. javanica, however, only CFs from T. ghanense Th02-04, T. harzianum Th20-07, and T. virens Th27-08 (M values of 85–99%) were effective at 100% concentration after 72 h (Table 2). The nematicidal activity of the CFs at 50% and 25% dilution against M. javanica did not differ from the DW. Therefore, the 100% concentration CF from T. ghanense Th02-04 was the most effective against both nematodes (M = 99–100%).
After the ethyl acetate extraction of the CFs, the activity of all the RF fractions differed greatly (p ≤ 0.05) from that of the negative control. All the residual filtrates generated from the ethyl acetate extraction of the CFs of the 13 strains were mortal against M. incognita, and all but those from T. harzianum Th20-07 and T. simmonsii Th09-06 were mortal against M. javanica (Table 2). The highest mortality against J2s of M. incognita at 25% dilution of the RFs after 72 h was caused by T. koningiopsis Th41-11 (M = 82%) and T. virens Th32-09 (M = 83%). Against J2s of M. javanica, the highest mortality was achieved with 50% dilutions of the RFs from T. ghanense Th26-52 (M = 63%), T. koningiopsis Th41-11 (M = 51%) and T. virens Th27-08 (M = 94%). After a 72 h exposure to EA fractions, the most active against M. incognita were from T. harzianum Th43-14 (M = 51%), T. koningiopsis Th41-11 (M = 54%), and T. virens Th32-09 (M = 100%) at 1 µg/µL; the EA fraction from T. harzianum Th43-14 strain was the only EA fraction active (M = 66%) against M. javanica at 1 µg/µL (Table 2).
In general, against both nematodes, the CFs and their RF and EA fractions from T. harzianum Th43-14 and T. virens Th27-08 were the most active. In addition, the RF fraction from CF of T. koningiopsis induced J2s mortality of both nematodes at the lowest dilution tested.

3.2. Identification of Components in Active Fractions from Trichoderma Strains by LC-DAD-ESI-HRMS

The results obtained from analyses of the liquid chromatograms and ultraviolet and high-resolution mass spectrometry data of the RF fraction from T. harzianum Th43-14, T. ghanense Th26-52, and T. virens Th27-08 and the EA fraction of T. koningiopsis are shown in Table 3, Table 4, Table 5 and Table 6 No significant differences were observed between the chromatograms from the active strains T. ghanense Th02-04 and the T. virens Th32-09 and negative control unfermented culture medium.
The compounds were tentatively identified by taking into account the species of the producing strain, the UV spectrum, and the molecular formula assigned through analysis of the protonated and ammonium adducts of each molecule, helped in some cases by the presence of dimers and dehydration products, and through searches of in the internal MEDINA database of HRMS spectra, dictionary of natural products and other natural product databases.

3.2.1. Metabolites from Residual Filtrate Fraction of Trichoderma harzianum Th43-14

The chromatogram of the RF fraction from T. harzianum Th43-14 showed eight main components (Figure 3, Table 3). Five of these were tentatively identified as sesquiterpenes according to their UV and HRMS data. Component 5 (Rt = 2.86 min) presented in its HRMS an ammonium adduct (m/z 300.1807), a protonated molecular ion at m/z 283.1541, indicative of a molecular formula C15H22O5 (calc. for C15H23O5+, 283.1540), which was tentatively assigned as 3,4,15-scirpenetriol. The HRMS of component 2 (Rt = 1.35 min) exhibited an ammonium adduct (m/z 316.1758), and a protonated molecular ion at m/z 299.1492 consistent with the molecular formula C15H22O6 (calc. C15H23O6+, 299.1489) and was putatively identified as 3,7,8,15-scirpenetetrol. All compounds tentatively identified (2, 5, and 8) have the same structural skeleton.
The HRMS spectrum of the minor component 3 (Rt = 2.05 min) displayed several protonated fragments (m/z, 231.1383, 221.1544, 213.1272) and a protonated molecular ion at m/z 249.1488 in agreement with the molecular formula C15H22O6 (calc. for C15H23O6+, 249.1489) and was putatively identified as illudin M. The HRMS spectrum of another minor component (6, Rt = 3.09 min) revealed a protonated molecular ion at m/z 249.1488 and was given a molecular formula C15H20O3 (calc. for C15H21O3+, 249.1485) and tentatively identified as naematolin.
The largest peaks were from two unknown molecules (1 and 4), which according to their protonated molecular adducts (m/z 317.1599 and 255.1591, respectively), ammonium (m/z 334.1866 and 272.186, respectively), and [2M+ H]+ (m/z 650.3387 and 509.3114, respectively) ions, have molecular formulae of C15H24O7 (Rt = 0.88 min) and C14H22O4 (Rt = 2.69 min). In addition, another non-identified minor component (7, Rt = 2.16 min) was assigned a molecular formula of C29H44O10 (Rt = 3.66 min) based on the analysis of its protonated (m/z 553.3000) and ammonium adducts (m/z 570.3270).
Table 3. Dereplicated metabolites from residual filtrate fraction of Trichoderma harzianum Th43-14.
Table 3. Dereplicated metabolites from residual filtrate fraction of Trichoderma harzianum Th43-14.
[M + H]+ m/zMolecular FormulaPutative Metabolite
10.88200, 215317.1599317.1595C15H24O7unknown
21.35205, 210299.1492299.1489C15H22O63,7,8,15-Scirpenetetrol
32.05200, 220249.1488249.1485C15H20O3Illudin M
42.69200, 220255.1591255.1591C14H22O4unknown
52.86200, 220283.1541283.1540C15H22O53,4,15-Scirpenetriol
63.09200, 218, 270309.1692309.1697C17H24O5Naematolin
73.66200, 220553.3000553.3007C29H44O10unknown
83.84200, 220251.1644251.1642C15H22O3Trichodermol
No.: Component number; Rt: Retention time; UV: Ultraviolet.

3.2.2. Metabolites from Residual Filtrate Fraction of Trichoderma ghanense Th26-52

Seven components were detected in the chromatogram of the residual fraction of T. ghanense Th26-52 (Figure 4, Table 4). The most abundant component, 1 (Rt = 0.63 min) displayed in its HRMS spectrum an ammonium adduct (m/z 278.1233) and a protonated molecular ion at m/z 261.0966, indicative of a molecular formula of C11H16O7 (calc. C11H16O7+, 261. 0973); this polar metabolite could not be identified. The HRMS of component 4 (Rt = 2.16 min) with a protonated molecular ion at m/z 169.0493 has a molecular formula C8H8O4 (calc. C8H9O4+, 169.0500) and was putatively identified as atrichodermone D. The analysis of the HRMS data of the minor component 7 (Rt = 2.89 min) displayed an ammonium adduct (m/z 212.1640), and a molecular protonated ion at m/z 195.1379 supporting the molecular formula C12H18O2 (calc. C12H19O2+, 195.1384) and tentatively assignment as the unsaturated lactone 6-heptyl-2H-pyron-2one. The other four unknown components included small metabolites with the molecular formulae of C8H9NO3 (Rt = 0.86 min), C8H10O3 (Rt = 1.22 min), C11H12O5 Rt = 2.40 min), and C14H18O3 (Rt = 2.64 min) according to their UV and HRMS data (Table 4).
Table 4. Dereplication metabolites from ethyl acetate fraction of Trichoderma ghanense Th26-52.
Table 4. Dereplication metabolites from ethyl acetate fraction of Trichoderma ghanense Th26-52.
[M + H]+ m/zMolecular FormulaPutative Metabolite
10.63200, 218261.0966261.0969C11H16O7unknown
20.86218, 230, 300168.0656168.0655C8H9NO3unknown
31.22205, 290155.0700155.0703C8H10O3Unknown
42.16200, 220, 310169.0493169.0495C8H8O4atrichodermone D
52.40200, 210, 240225.0756225.0758C11H12O5Unknown
62.64200, 230, 270235.1328235.1329C14H18O3Unknown
72.89200, 220, 280195.1379195.1380C12H18O26-heptyl-2H-pyron-2-one
No.: Component number; Rt: Retention time; UV: Ultraviolet.

3.2.3. Metabolites from Ethyl Acetate Fraction of Trichoderma koningiopsis Th41-11

The chromatogram of the ethyl acetate extract from T. koningiopsis Th41-11 (Figure 5) showed three components, which tentatively were assigned as koninginin isomers. The HRMS of component 1 (Rt = 2.81 min) and 2 (Rt = 3.04 min) exhibited similar dehydration adducts (m/z 263.1642 245.1535) and protonated adducts (m/z 281.1750 and 281.1749, respectively), indicative of a molecular formula of C16H24O4 (calc. for C16H25O4+, 281.1752) for both molecules. Component 3 (Rt = 3.68 min) in its HRMS data showed dehydrated species (m/z 265.1796, 247.1668, 237.1847), a dimer adduct ([2M+H]+, m/z 565.3759), and a protonated molecular ion at m/z 283.1906 in accordance with a molecular formula of C16H26O4 (calc. for C16H27O4+, 283.1908). An extensive search of the literature based on spectral data and previous reports led to their tentatively identification as koninginin L (1), T (2), and B (3) (Table 5).
Table 5. Dereplicated metabolites from ethyl acetate fraction of Trichoderma koningiopsis Th41-11.
Table 5. Dereplicated metabolites from ethyl acetate fraction of Trichoderma koningiopsis Th41-11.
[M + H]+ m/zMolecular FormulaPutative Metabolite
12.81200, 255281.1750281.1747C16H24O4Koninginin L
23.04200, 255281.1749281.1747C16H24O4Koninginin T
33.68200, 260283.1906283.1904C16H26O4Koninginin B
No.: Component number; Rt: Retention time; UV: Ultraviolet.

3.2.4. Metabolites from Residual Filtrate Fraction of Trichoderma virens Th27-08

The chromatogram of RF fraction of T. virens Th27-08 displayed four components not present in the blank sample (Figure 6, Table 6). Component 3, eluting at Rt of 1.00 min exhibited an ammonium adduct (m/z 242.1020), dehydration fragments (m/z 207.0652, 191.1424), and a protonated ion at m/z 225.0757 indicative of a molecular formula of C11H12O5 (calc. for C11H13O5+, 225.0762). Based on HRMS and UV data, compound 1 was tentatively identified as sepedonin. The major (1) and two minor components (2 and 4) were not identified, and molecular formulae were assigned as C11H10O4 (Rt = 0.78 and 1.57 min) and C16H20O4 (Rt = 3.35) based on their protonated HRMS ion [M+H]+ and additionally supported by its ammonium and dimer adducts.
Table 6. Dereplicated metabolites from residual fractions of Trichoderma virens Th27-08.
Table 6. Dereplicated metabolites from residual fractions of Trichoderma virens Th27-08.
No. Rt
[M + H]+ m/zMolecular FormulaPutative Metabolite
10.78205, 240, 290207.0653207.0657C11H10O4unknown
21.00210, 225, 295,225.0757225.0762C11H12O5sepedonin
31.57205, 240, 290207.0652207.0657C11H10O4unknown
43.35215, 255, 300277.1435277.1438C16H20O4unknown
No.: Component number; Rt: Retention time; UV: Ultraviolet.

4. Discussion

The results of this study complement our previous discoveries on native Trichoderma strains with nematicidal properties against two Meloidogyne species as part of our continuing work to find and develop safer biocontrol agents. Herein, we demonstrated that 92% of the screened tropical Trichoderma strains (all 13 except T. simmonsii) are mortal to J2s of Meloidogyne javanica and confirmed that the CFs and the EA or RF fractions of all strains were highly mortal to M. incognita. T. koningiopsis UFSMQ40 [12], T. harzianum Th6, JX1614550 [18,19,35], and Trichoderma sp. EF1671 [5] have been shown to have nematicidal effects against J2s of M. javanica, but our report is the first to demonstrate the nematicidal activity of T. citrinoviride, T. ghanense, and T. virens against M. javanica.
The mortality data revealed that M. javanica was less sensitive than M. incognita to the CFs and EA fraction from Trichoderma strains. This differential sensitivity behavior of both Meloidogyne species against extracts, compounds, or fungal strains has been previously reported. For example, fungus Arthobortys sp. MVD18 caused less mortality against M. javanica (92.9%) than against M. incognita (99.0%) after a 48 h exposure. However, two Trichoderma sp. strains (KAV2 and KAV3) were more active against M. javanica than M. incognita [36]. Acetic acid and hexanoic acid yielded an EC50 of 162.4 and 339.3 µg/mL, respectively, against M. javanica but EC50 of 38.3 and 41.1 µg/mL against M. incognita, respectively, after 1 day [37,38]. Sensitivity differences between different species and even different populations of the same species have been attributed to the habitat and environmental conditions to which the organisms are exposed. Other saprophytic fungi have been reported to have low nematicidal effects against J2s of M. javanica; for example, a CF of Arthrobotrys oligospora, A. conoides, and Hypocrea lixii (sexual state of T. harzianum) at 100% concentration [16,39] caused from 16.14 to 64.5% mortality. An EA extract from Trichoderma sp. EFI 671, however, was not active [5].
The present study is also the first nematicidal bio-guided fractionation of the CFs from Trichoderma species and screening the organic and residual aqueous fractions against J2s. After the fractionation, 69% of the RF fractions from the non-nematicidal CFs had a higher mortal effect on M. javanica. This effect could be attributed to antagonistic action between metabolites and the concentration of the metabolites in the RFs of the strains. By contrast, the nematicidal effect of the CF from T. harzianum strain Th20-07 was not confirmed, suggesting that enzymes were mainly involved in the nematicidal activity of strain Th20-07 and were subsequently denatured by the solvent during the fractionation. The antibiosis produced by chitinase and protease action from Trichoderma species has been widely described. For example, an enzymatic filtrate obtained from T. koningiopsis UFSMQ40 is mortal to J2s of M. incognita (90.4% mortality) and M. javanica (63.2%) after 24 h of exposure [15]. Chitinase (51.42 U/mL) and protease (4.27 U/mL) from T. harzianum ITCC 6888 caused high mortality (93%) against M. incognita [40].
On the other hand, in our study, the highest lethal activity against both Meloidogyne species was found for T. koningiopsis Th41-11, T. harzianum Th43-14, T. virens Th27-08, and the two T. ghanense strains tested. The most investigated of these species has been T. harzianum for its properties as a biological control agent and its metabolites [2,4,14]. Other in vitro studies of CFs from T. harzianum strains grown in PDB have shown a significant mortal effect on the J2s of M. incognita. For example, CFs from T. harzianum strains ThU, JX1614550 and Th.6 caused a mortality of 33, 64.5 and 75%, respectively, at 100% concentrations after 72 h [19,41,42].
The residual fraction of T. harzianum Th43-14 revealed a mixture of illudin, naematolin, 4β-scirpenol (syn. trichodermol and roridin C), 3,4,15-scirpenetriol, and 3,7,8,15-scirpenetetrol were tentatively identified based on UV and MS data. Scirpenes have a trichothecene skeleton with a characteristic 9-double-bond and C12-C13 epoxide in their structure and are potent inhibitors of protein synthesis [43,44]. Semisynthetic derivatives of trichodermol have potent cytotoxic and antifungal activity against the fungus Ceratocystiopsis crassivaginata [45,46]. This metabolite has been isolated from several Trichoderma species, and 3,4,15-scirpenetriol has been isolated from Fusarium equiseti, F. roseum, and F. sporotrichiella, whereas 3,7,8,15-scirpenetetrol has only been isolated from F. graminearum [47]. Illudin M, isolated from several Omphalatus species and from Granulobasidium vellereum, has no activity against M. incognita or Caenorhabditis elegans at 100 µg/mL, but it has high antitumor and antimicrobial activities [48,49,50]. Naematolin was isolated from Hypholoma fasciculare (syn. Naematoloma fasciculare), a poisonous basidiomycete [51]. This caryophyllenediol derivative has antitumor, antiviral, and weak antibacterial properties [52,53] and reduced 97% of bloodstream forms of Trypanosoma cruzi at 250 µL/mL [54].
The two studied strains of T. ghanense (Th02-04 and Th26-52) were active on both Meloidogyne species. The data obtained from the UV and ESIMS spectra of its RF fraction allowed us to tentatively identify atrichodermone D and 6-heptyl-2H-pyron-2-one in the RF fraction of T. ghanense Th26-52. To date, metabolites detected from T. ghanense include the phenolics catechin, ferulic acid, and cinnamic acid from the CF of two strains from different areas in India [55]. Atrichodermone D is a cyclopentenone previously reported only from T. atroviride and has no known biological activity [56]. 6-Heptyl-2H-pyran-2-one is an alkyl pyrone isolated from T. koningii strain IMI-308475 and from T. asperellum and T. viride, but no nematicidal activity was reported [57,58]. Related lactones from Trichoderma species include 6-(1-heptenyl)-2-pyran-2-one, 6-(3-hydroxypent-1-en-1-yl)-2H-pyran-2-one and 6-pentyl-2H-pyran-2-one. 6-(3-Hydroxypent-1-en-1-yl)-2H-pyran-2-one was isolated from T. koningiopsis QA3 and has strong antibacterial activity against Micrococcus luteus [59]. 6-Pentyl-2H-pyran-2-one is a recognized plant growth promoter and produced by several Trichoderma species [60].
From the results of the present study, T. koningiopsis Th41-11 is another promising strain that produces nematicidal metabolites. The LC chromatogram of its EA fraction revealed small amounts of koninginins B, L, and T, tentatively identified based on UV, ESIHRMS data analyses, and comparisons with the literature. Koninginin B is a bicyclic polyketide that has also been reported from T. koningii [61], T. neokoningin [62], and T. applanatum [63]. Koninginin L and T are tricyclic polyketides with an oxygen bridge (C7 and C9) at C2 and an alcohol group at C4. Koninginins B, L, and T from T. koningiopsis QA3 and YIM PH30002 were recently reported to be weakly antibacterial [64,65,66].
Among the four T. virens strains studies, only Th27-08 had activity against both nematodes, with the RF fraction achieving the highest mortality. In the LC chromatogram of the RF fraction, we detected sepedonin, a tropolone first isolated from Sepedonium chrysospermum Fries (teleomorph Hyphomyces chrysospermus Tul.) and later from S. ampullosporum, S. chalcipori, S. microspermum, and S. chrysospermum and having antimicrobial activity against several bacterial and fungal pathogens [67]. The artifact anhydrosepedonin (C11H10O4) is produced during the isolation process due to the instability of sepedonin [68,69]. We additionally detected three unknown metabolites in the RF fraction of T. virens Th27-08. Other metabolites previously reported from T. virens include cathequin, caffeic acid, ferulic acid, and 33 other non-volatile metabolites [2,55,70,71]. Our report of sepedonin is thus a new contribution to the chemical composition of this species.
Except for illudin M, the metabolites reported from our native Trichoderma species were not previously tested on nematodes [48]. The nematicidal efficacy of the metabolites tentatively identified from Trichoderma species herein studied are likely due to the alcohol or carboxylic acid groups in their structure. Ntalli et al. [38] reported that acetic acid and hexanoic acid, furfurol (syn. furfuryl alcohol), and furfural paralyzed J2s an EC50/1 h of 1–100 µg/mL or less after 24 h, and the alcohols and aldehyde were more effective than the organic acids. They also demonstrated that acetic acid damages the cuticle and, the nuclei of pseudocoel cells and vacuolizes the cytoplasm of M. incognita, while (E)-2-decenal, and undecanone induced malformation of somatic muscles of the nematodes [72].
In general, few metabolites with nematicidal properties have been isolated from Trichoderma species; some of these are acetic acid, gliotoxin, trichorzianine, viridin [3], trichodermin [73], and cyclonerodiol [65,74]. Therefore, more studies should focus on bioassay-guided isolation and characterization of metabolites responsible for nematicidal activity in the fractions from Trichoderma strains. In addition, studies to optimize the production of the extracts with the most promising active compounds, evaluate their efficacy in greenhouses, and assess their toxicity on plants and beneficial organisms must be carried out before the compounds can be evaluated in the field and further developed as safe bionematicide products.

5. Conclusions

The present contribution enriches our knowledge of the nematicidal potential of 13 tropical Trichoderma species isolated from the soils of Yucatán state. The most effective species against M. incognita and M. javanica were T. ghanense strains Th02-04 and Th26-52, T. harzianum Th43-14, T. koningiopsis Th41-11, and T. virens Th27-08. The LC-DAD-ESIMS chemical profiles of the residual filtrate fractions and ethyl acetate fractions of culture filtrate from Trichoderma spp. revealed the presence of novel metabolites for the genus and others with molecular formulas not found in natural products databases. These results highlight the ability of Trichoderma strains to produce bioactive secondary metabolites that could be developed to manage M. incognita and M. javanica. However, more studies are needed to determine activity and potential phytotoxicity in plant applications and doses for effective, efficient biocontrol effect.

Author Contributions

Design and supervision of the study, J.C.-A. and M.G.-A.; fungal cultures, organic extraction and nematicidal bioassays, F.A.M.-K.; academic support and supervision of the nematicidal bioassays, M.F.A. and J.C.-A.; LC-DAD-ESI-HRMS data acquisition, analyses, interpretation, J.M., F.R. and M.G.-A.; financial support of the project, J.M.T.-S. and M.G.-A.; project coordination, J.C.-A.; writing and review of the manuscript, all authors. All authors have read and agreed to the published version of the manuscript.


Consejo Nacional de Ciencia y Tecnología (CONACYT)- International Development Research Centre (IDRC) financed project No. CEAR2019-01; Ministerio de Ciencia e innovación/ Agencia Estatal de Investigación (MCIN/AEI) financed project 10.13039/501100011033, and Tecnológico Nacional de México (TECNM) financed project 10759.21P.

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

Not applicable.


The authors thank Irma L. Medina-Baizabal and library technical personal for technical support. This research was supported by the projects CONACyT-IDRC-CIESAS No. CEAR2019-01, TECNM 10759.21P, and PID2019-106222RB-C31 project of Spanish MCIN/AEI/10.13039/501100011033.

Conflicts of Interest

The authors declare no conflict of interest.


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Figure 1. Cultures of the 13 study strains of Trichoderma on potato dextrose agar incubated at 25 ± 2 °C, 12 h light/12 h dark for 8 days.
Figure 1. Cultures of the 13 study strains of Trichoderma on potato dextrose agar incubated at 25 ± 2 °C, 12 h light/12 h dark for 8 days.
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Figure 2. Second-stage juveniles (J2s) of Meloidogyne incognita in (A) control in distilled water, (B) dead and living in culture filtrate of Trichoderma virens Th27-08.
Figure 2. Second-stage juveniles (J2s) of Meloidogyne incognita in (A) control in distilled water, (B) dead and living in culture filtrate of Trichoderma virens Th27-08.
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Figure 3. UV210 nm chromatograms of residual filtrate fraction from Trichoderma harzianum Th43-14 and unfermented culture medium. 1: Not identified (C15H24O7), 2: 3,7,8,15-scirpenetetrol, 3: illudin M, 4: not identified (C14H22O4), 5: 3,4,15-scirpenetriol, 6: naematolin, 7: not identified (C29H44O10), 8: trichodermol.
Figure 3. UV210 nm chromatograms of residual filtrate fraction from Trichoderma harzianum Th43-14 and unfermented culture medium. 1: Not identified (C15H24O7), 2: 3,7,8,15-scirpenetetrol, 3: illudin M, 4: not identified (C14H22O4), 5: 3,4,15-scirpenetriol, 6: naematolin, 7: not identified (C29H44O10), 8: trichodermol.
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Figure 4. UV210 nm chromatograms of residual filtrate fraction from Trichoderma ghanense Th26-52 and the unfermented culture medium. 1: Not identified (C11H16O7), 2: not identified C8H9NO3, 3: not identified C8H10O3, 4: atrichodermone D, 5: Not identified (C11H12O5), 6: not identified (C14H18O3). 7: 6-heptyl-2H-pyron-2-one.
Figure 4. UV210 nm chromatograms of residual filtrate fraction from Trichoderma ghanense Th26-52 and the unfermented culture medium. 1: Not identified (C11H16O7), 2: not identified C8H9NO3, 3: not identified C8H10O3, 4: atrichodermone D, 5: Not identified (C11H12O5), 6: not identified (C14H18O3). 7: 6-heptyl-2H-pyron-2-one.
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Figure 5. UV210 nm chromatogram of residual filtrate fraction from Trichoderma koningiopsis Th41-11 and the unfermented culture medium. 1: Koninginin T, 2: koninginin L, 3: koninginin B.
Figure 5. UV210 nm chromatogram of residual filtrate fraction from Trichoderma koningiopsis Th41-11 and the unfermented culture medium. 1: Koninginin T, 2: koninginin L, 3: koninginin B.
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Figure 6. UV210 nm chromatogram of residual filtrate fraction from Trichoderma virens Th27-08 and the unfermented culture medium. 1: Not identified (C11H10O4), 2: sepedonin, 3: not identified (C11H10O4), 4: not identified (C16H20O4).
Figure 6. UV210 nm chromatogram of residual filtrate fraction from Trichoderma virens Th27-08 and the unfermented culture medium. 1: Not identified (C11H10O4), 2: sepedonin, 3: not identified (C11H10O4), 4: not identified (C16H20O4).
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Table 1. Trichoderma strains selected and their biological activity.
Table 1. Trichoderma strains selected and their biological activity.
Trichoderma SpeciesKeyGenBank
ActivityPlace of Collection
T. citrinoviride Bissett 1984Th33-58MF078653A/BTicul
T. ghanense Yoshim. Doi, Y. Abe & Sugiy 1987Th02-04MF078652A/BTizimín
T. harzianum Rifai 1969Th02-01MF952887A/BTizimín
Th43-14MF078649ASan Felipe
T. koningiopsis Samuels, Carm. Suárez & H.C. Evans 2006Th41-11MF952888A/BSanahcat
T. simmonsii P. Chaverri, F.B. Rocha, Samuels, Degenkolb & Jaklitsch 2015Th09-06MF078647A/BDzidzantun
T. virens (J.H. Mill., Giddens & A.A. Foster) Arx 1987Th05-02MF952889A/BDzilam González
Th43-13MF078644ASan Felipe
A: Meloidogyne incognita antagonist; B: plant growth promoter.
Table 2. Mortality of second-stage juveniles of Meloidogyne spp. after 72 h exposure to culture filtrate (CF), ethyl acetate (EA), or residual filtrate (RF) fractions from tropical Trichoderma strains.
Table 2. Mortality of second-stage juveniles of Meloidogyne spp. after 72 h exposure to culture filtrate (CF), ethyl acetate (EA), or residual filtrate (RF) fractions from tropical Trichoderma strains.
Trichoderma SpeciesStrainsMean Percentage Mortality
Meloidogyne incognitaMeloidogyne javanica
100%50%1 µg/µL100%50%25%100%1 µg/µL100%50%
T. citrinovirideTh33-5862 b21 c30 c100 a66 c13 c15 d8 b100 a1 h
T. ghanenseTh02-04100 a100 a20 d100 a63 c24 c99 a0 c100 a16 e
Th26-52100 a23 c22 d100 a100 a20 c3 f11 b100 a63 b
T. harzianumTh02-01100 a42 c0 e100 a23 d15 c4 f0 c98 a34 d
Th20-07100 a6 d0 e98 a66 c13 c97 a0 c7 e0 h
Th43-14100 a66 b51 b100 a100 a57 b45 c66 a93 b4 g
Th33-59100 a21 c30 c100 a72 b22 c9 e9 b10 a0 h
T. koningiopsisTh41-11100 a38 c54 b100 a100 a82 a7 e1 c93 b51 c
T. simmonsiiTh09-06100 a6 d37 c100 a96 a53 b6 e0 c14 d0 h
T. virensTh05-02100 a22 c18 d100 a19 d18 c8 e0 c100 a10 f
Th27-08100 a71 b0 e100 a100 a64 b85 b9 b100 a94 a
Th32-09100 a20 c100 a100 a100 a83 a7 e3 c86 c5 g
Th43-13100 a23 c31 c100 a86 b49 c7 e8 b95 b0 h
ControlPDB0 c0 d0 e0 b0 d0 c0 f0 c0 f0 h
DW/WDT *0 c0 d0 e*0 b0 d0 c0 f0 c*0 f0 h
Blank0 c0 d0 e0 b0 d0 c0 f0 c0 f0 h
PDB: potato dextrose broth, DW: distilled water, WDT *: water-DMSO–0.6% Tween 20 (95:5); Blank: unfermented medium. SD: standard deviation, calculated from the analysis of variance for treatments (CFs, EA, RFs from each strain). Values with different letters within a column differed significantly in Scott–Knott test (p ≤ 0.05).
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Moo-Koh, F.A.; Cristóbal-Alejo, J.; Andrés, M.F.; Martín, J.; Reyes, F.; Tun-Suárez, J.M.; Gamboa-Angulo, M. In Vitro Assessment of Organic and Residual Fractions of Nematicidal Culture Filtrates from Thirteen Tropical Trichoderma Strains and Metabolic Profiles of Most-Active. J. Fungi 2022, 8, 82.

AMA Style

Moo-Koh FA, Cristóbal-Alejo J, Andrés MF, Martín J, Reyes F, Tun-Suárez JM, Gamboa-Angulo M. In Vitro Assessment of Organic and Residual Fractions of Nematicidal Culture Filtrates from Thirteen Tropical Trichoderma Strains and Metabolic Profiles of Most-Active. Journal of Fungi. 2022; 8(1):82.

Chicago/Turabian Style

Moo-Koh, Felicia Amalia, Jairo Cristóbal-Alejo, María Fé Andrés, Jesús Martín, Fernando Reyes, Jose María Tun-Suárez, and Marcela Gamboa-Angulo. 2022. "In Vitro Assessment of Organic and Residual Fractions of Nematicidal Culture Filtrates from Thirteen Tropical Trichoderma Strains and Metabolic Profiles of Most-Active" Journal of Fungi 8, no. 1: 82.

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