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Research article
Antagonistic Efficacy of Symbiotic Bacterium Xenorhabdus sp. SCG against Meloidogyne spp.
1Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
2Department of Biotechnology, Pukyong National University, Busan 48513, Republic of Korea
3ECOWIN Co., Ltd., Daegu 42993, Republic of Korea
4Nematode Research Center, Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea
J. Microbiol. Biotechnol. 2024; 34(8): 1627-1635
Published August 28, 2024 https://doi.org/10.4014/jmb.2404.04003
Copyright © The Korean Society for Microbiology and Biotechnology.
Abstract
Keywords
Graphical Abstract
Introduction
Approximately 4,000 species of plant-parasitic nematodes (PPNs), some of which cause significant damage to industries such as agriculture and forestry, are distributed worldwide [1, 2]. These nematodes account for up to approximately 25% of annual losses in agriculture, resulting in economic damage of approximately $157 billion [3, 4]. Based on their feeding mechanisms, PPNs are classified into migratory ectoparasites, migratory endoparasites, and sedentary endoparasites. Among these, root-knot nematodes (RKNs), a major group of sedentary endoparasites, cause the greatest damage to crops [5]. There are 98 known genera of RKNs, among which the
There are various methods for controlling RKNs, including synthetic nematicides, botanical essential oils, biological control, and resistant cultivars, for use alone or in combination for better control [8]. The most commonly used synthetic nematicides are chemical fumigants (
Materials and Methods
Entomopathogenic Nematodes
EPNs were isolated from sandy soil samples collected from forest sites in Pocheon-si, Gyeonggi-do, Republic of Korea using the
To identify species of isolated EPNs, genomic DNA of each isolate was extracted using a standard phenolchloroform extraction method and a partial 28S rDNA gene was amplified by polymerase chain reaction (PCR) using primers 539_F (5'-GGATTTCCTTAGTAACTGCGAGTG-3') and 535_R (5'-TAGTCTTCGCCCCTATACCCTT- 3'). Purified products were sequenced by Macrogen, Inc., (Republic of Korea). The sequence of the 28S rDNA gene was compared with that of the type strains available at the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/GenBank/index.html) to identify closely related species. The molecular phylogeny of 28S rDNA was inferred using the neighbor-joining method in MEGA X software [29].
To determine the insecticidal activity of the seven isolated EPNs, bioassays were performed against 3rd instar larvae of
Isolation and Identification of Symbiotic Bacteria
The last instar larvae of
Genomic DNA was extracted using a standard phenol-chloroform extraction method, and a partial 16S rRNA gene was amplified by PCR for molecular identification of the bacterial isolates. Universal primers 27F (5'-AGAGTTTGATCMTGGCTCA-3') and 1492R (5'-TACGGYTACCTTGTTACGACTT-3') were used. Purified products were sequenced by Macrogen, Inc. The 16S rRNA gene sequence was compared with that of the type strains available in the EzBioCloud database (ChunLab Inc., Republic of Korea) to identify closely related species. The molecular phylogeny of 16S rRNA was inferred using the neighbor-joining method in the MEGA X software.
Nematicidal Activity
The
The egg masses were obtained from infected tomato using a 0.5% NaOCl solution according to the methods reported by Hussey and Barker with minor modifications, and incubated at 28°C for 24 h in distilled water using a modified Baermann funnel to obtain second-stage juveniles (J2s) of
Bacterial isolates were fermented in a 500 ml baffled Erlenmeyer flask containing 100 ml of LB broth (BD Difco, USA) which was incubated on a shaking incubator (200 ×
Isolation and Identification of Nematicidal Compound from Strain SCG Cultures
Strain cultures were prepared as described above and centrifuged at 10,000 rpm for 10 min. The collected supernatant was then sequentially extracted with an equivalent volume of
Pot Experiments under Greenhouse Condition
An experiment was performed in the controllable greenhouse of the Nematode Research Center, Life and Industry Convergence Research Institute, Pusan National University (Republic of Korea) with a temperature range of 25 ± 3°C and 70% relative humidity, and 12 h light/12 h dark cycle. Pots (12 cm in diameter and 10 cm in depth) were filled with 500g of soil from a commercial greenhouse in Seongju-gun, Republic of Korea (35°55'32.2"N 128°17'13.8"E) and inoculated with
Statistical Analysis
One-way ANOVA was performed using SPSS software (version 24; SPSS, Inc., USA). The mean values were compared using Scheffé’s method, and
Results
Insecticidal Activities of Isolated Entomopathogenic Nematodes
In total, seven EPN were isolated from sandy soils of forest sites (Republic of Korea). Based on the 28S rDNA sequence, all isolated EPNs belonged to the
Isolation and Identification of Nematicidal Xenorhabdus Species
On the basis of blue colony morphology, we isolated four strains from
-
Fig. 1. Phylogenetic relationship of the isolated
Xenorhabdus strains based on 16S rRNA gene sequence. Neighbor-joining phylogenetic tree based on 16S rRNA gene sequences and closely related species constructed using MEGA X software. Numbers at each branch indicate the bootstrap percentage of 1,000 replications.
Four isolated strains were evaluated for nematicidal activity against four
-
Fig. 2. Nematicidal activities of isolated bacteria against the J2s of four
Meloidogyne species. (A) Mortality rate of the J2s of Meloidogyne after 48 h treated with 10% cell-free filtrates of isolated bacteria. Sunchungtan 150EC (150 μg/ml of fosthiazate) were used as the positive control, while LB broth was used as the negative control. (B) Morphological observation of the assessed nematodes with active nematodes (upper) and the dead nematodes with straight form and immobility (below) post-stimulation using a fine needle. All experiments were performed in triplicate wells and repeated three times under the same conditions. Different letters above the error bars indicate significant differences by Scheffé's test (p < 0.05). Scale bar: 20 μm.
Nematicidal Spectrum of SCG Strain
To determine the nematicidal potential of strain SCG, the nematicidal activity spectrum was assessed against J2s of four plant-parasitic nematodes (
-
Fig. 3. Assessments of the nematicidal spectrum of cell-free filtrates of SCG strain against the second-stage juveniles of four plant parasitic nematodes.
Sunchungtan 150EC (150 μg/ml of fos-thiazate) were used as the positive control, while LB broth was used as the negative control. All experiments were performed in triplicate wells and repeated three times under the same conditions. Different letters above the error bars indicate significant differences by Scheffé's test (
p < 0.05).
Purification of Nematicidal Compound from SCG Strain
Based on bioassay-guided monitoring, the ethyl acetate extract of strain SCG was fractionated, and white active compound was obtained. The molecular weight and formula of active compound was determined as C5H6N2O2 by ESI-MS ([M + H]+, m/z 126.8) and 1D NMR spectra (1H and 13C NMR) (Fig. S2 and Table S2). The structure of active compound was readily identified as thymine by comparison with previously reported structures [35, 36]. Thymine isolated from strain SCG showed nematicidal activity in a concentration-dependent manner against
-
Fig. 4. Concentration-dependent nematicidal activity of thymine from strain SCG.
All experiments were performed in triplicate wells and repeated three times under the same conditions.
Effect of Strain SCG on M. incognita under Greenhouse Conditions
The population of
-
Fig. 5. Effects of cell-free filtrates of SCG strain on the number of nematode populations (A) and egg masses (B) per plant in the pot experiment (
n = 5). (C) Root symptoms ofS. lycopersicum . The number of egg masses was determined using phloxine B staining. The red arrows indicate egg masses formed byM. incognita infection. The experiment was performed in triplicate under the same conditions. Different letters above the error bars indicate significant differences according to Scheffé's test (p < 0.05).
The application of 10% cell-free filtrates of strain SCG significantly affected all the plant growth parameters (fresh height and weight of shoots and roots) after 45 days and had a relatively optimized effect on tomato growth compared to positive control (fosthiazate) (Fig. 6). It yielded the highest fresh shoot length (38.4 ± 1.4 cm), fresh root length (21.2 ± 1.9), fresh shoot weight (10.2 ± 0.3), and fresh root weight (3.8 ± 0.4). However, the fresh root length did not differ significantly between 10% cell-free filtrates of SCG and fosthiazate (
-
Fig. 6. Effects of SCG strain cell-free filtrates on the growth of
S. lycopersicum in the pot experiment (A). Fresh height and weight of the testS. lycopersicum was measured after 45 days of transplanting (B) (n = 5). The experiment was performed in triplicate under the same conditions. Different letters above the error bars indicate significant differences based on Scheffé's test (p < 0.05).
Discussion
Over the last several decades, eco-friendly nematicidal agents have been extensively studied to overcome the side effects of synthetic nematicides, such as toxic environmental hazards [37]. Recent studies suggest that the symbiotic bacterium of EPNs,
Despite numerous advances in the laboratory studies of bacterial nematicides, extensive research is needed for their successful application under field conditions because of their lack of field adaptability and activity. Therefore, the discovery of new nematicidal strains from rhizospheric environments with high field activity and adaptability is essential for the sustainable control of RKNs. The results of the pot experiment indicated that the cell-free filtrates of the SCG strain could control
Our study showed that
Supplemental Materials
Acknowledgments
This work was supported by Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry (IPET) through “Crop Viruses and Pests Response Industry Technology Development” Program (No. 321110–4) funded by Ministry of Agriculture, Food and Rural Af-fairs (MAFRA).
Author Contributions
J.-H. Kim: Validation, Formal analysis, Data curation, Visualization, Writing—Original Draft, Writing—Review & Editing; B.-M. Lee: Investigation; H.-C. Lee: Investigation, Methodology; I.-S. Choi: Methodology; K.-B. Koo: Conceptualization, Resources, Supervision; K.-H. Son: Data curation, Funding acquisition.
Conflict of Interest
The authors have no financial conflicts of interest to declare.
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Related articles in JMB
Article
Research article
J. Microbiol. Biotechnol. 2024; 34(8): 1627-1635
Published online August 28, 2024 https://doi.org/10.4014/jmb.2404.04003
Copyright © The Korean Society for Microbiology and Biotechnology.
Antagonistic Efficacy of Symbiotic Bacterium Xenorhabdus sp. SCG against Meloidogyne spp.
Jong-Hoon Kim1,2, Byeong-Min Lee1, Hyung Chul Lee3, In-Soo Choi4, Kyung-Bon Koo3*, and Kwang-Hee Son1*
1Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
2Department of Biotechnology, Pukyong National University, Busan 48513, Republic of Korea
3ECOWIN Co., Ltd., Daegu 42993, Republic of Korea
4Nematode Research Center, Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea
Correspondence to:Kyung-Bon Koo, bon612@daum.net
Kwang-Hee Son, sonkh@kribb.re.kr
Abstract
The inhabitation and parasitism of root-knot nematodes (RKNs) can be difficult to control, as its symptoms can be easily confused with other plant diseases; hence, identifying and controlling the occurrence of RKNs in plants remains an ongoing challenge. Moreover, there are only a few biological agents for controlling these harmful nematodes. In this study, Xenorhabdus sp. SCG isolated from entomopathogenic nematodes of genus Steinernema was evaluated for nematicidal effects under in vitro and greenhouse conditions. The cell-free filtrates of strain SCG showed nematicidal activity against Meloidogyne species J2s, with mortalities of > 88% at a final concentration of 10%, as well as significant nematicidal activity against the three other genera of plant-parasitic nematodes in a dose-dependent manner. Thymine was isolated as active compounds by assay-guided fractionation and showed high nematicidal activity against M. incognita. Greenhouse experiments suggested that cell-free filtrates of strain SCG efficiently controlled the nematode population in M. incognita-infested tomatoes (Solanum lycopersicum L., cv. Rutgers). In addition, a significant increase in host plant growth was observed after 45 days of treatment. To our knowledge, this is the first to demonstrate the nematicidal activity spectrum of isolated Xenorhabdus species and their application to S. lycopersicum L., cv. Rutgers under greenhouse conditions. Xenorhabdus sp. SCG could be a promising biological nematicidal agent with plant growth-enhancing properties.
Keywords: Entomopathogenic nematode, Xenorhabdus, nematicidal activity, root-knot nematode, biological control
Introduction
Approximately 4,000 species of plant-parasitic nematodes (PPNs), some of which cause significant damage to industries such as agriculture and forestry, are distributed worldwide [1, 2]. These nematodes account for up to approximately 25% of annual losses in agriculture, resulting in economic damage of approximately $157 billion [3, 4]. Based on their feeding mechanisms, PPNs are classified into migratory ectoparasites, migratory endoparasites, and sedentary endoparasites. Among these, root-knot nematodes (RKNs), a major group of sedentary endoparasites, cause the greatest damage to crops [5]. There are 98 known genera of RKNs, among which the
There are various methods for controlling RKNs, including synthetic nematicides, botanical essential oils, biological control, and resistant cultivars, for use alone or in combination for better control [8]. The most commonly used synthetic nematicides are chemical fumigants (
Materials and Methods
Entomopathogenic Nematodes
EPNs were isolated from sandy soil samples collected from forest sites in Pocheon-si, Gyeonggi-do, Republic of Korea using the
To identify species of isolated EPNs, genomic DNA of each isolate was extracted using a standard phenolchloroform extraction method and a partial 28S rDNA gene was amplified by polymerase chain reaction (PCR) using primers 539_F (5'-GGATTTCCTTAGTAACTGCGAGTG-3') and 535_R (5'-TAGTCTTCGCCCCTATACCCTT- 3'). Purified products were sequenced by Macrogen, Inc., (Republic of Korea). The sequence of the 28S rDNA gene was compared with that of the type strains available at the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/GenBank/index.html) to identify closely related species. The molecular phylogeny of 28S rDNA was inferred using the neighbor-joining method in MEGA X software [29].
To determine the insecticidal activity of the seven isolated EPNs, bioassays were performed against 3rd instar larvae of
Isolation and Identification of Symbiotic Bacteria
The last instar larvae of
Genomic DNA was extracted using a standard phenol-chloroform extraction method, and a partial 16S rRNA gene was amplified by PCR for molecular identification of the bacterial isolates. Universal primers 27F (5'-AGAGTTTGATCMTGGCTCA-3') and 1492R (5'-TACGGYTACCTTGTTACGACTT-3') were used. Purified products were sequenced by Macrogen, Inc. The 16S rRNA gene sequence was compared with that of the type strains available in the EzBioCloud database (ChunLab Inc., Republic of Korea) to identify closely related species. The molecular phylogeny of 16S rRNA was inferred using the neighbor-joining method in the MEGA X software.
Nematicidal Activity
The
The egg masses were obtained from infected tomato using a 0.5% NaOCl solution according to the methods reported by Hussey and Barker with minor modifications, and incubated at 28°C for 24 h in distilled water using a modified Baermann funnel to obtain second-stage juveniles (J2s) of
Bacterial isolates were fermented in a 500 ml baffled Erlenmeyer flask containing 100 ml of LB broth (BD Difco, USA) which was incubated on a shaking incubator (200 ×
Isolation and Identification of Nematicidal Compound from Strain SCG Cultures
Strain cultures were prepared as described above and centrifuged at 10,000 rpm for 10 min. The collected supernatant was then sequentially extracted with an equivalent volume of
Pot Experiments under Greenhouse Condition
An experiment was performed in the controllable greenhouse of the Nematode Research Center, Life and Industry Convergence Research Institute, Pusan National University (Republic of Korea) with a temperature range of 25 ± 3°C and 70% relative humidity, and 12 h light/12 h dark cycle. Pots (12 cm in diameter and 10 cm in depth) were filled with 500g of soil from a commercial greenhouse in Seongju-gun, Republic of Korea (35°55'32.2"N 128°17'13.8"E) and inoculated with
Statistical Analysis
One-way ANOVA was performed using SPSS software (version 24; SPSS, Inc., USA). The mean values were compared using Scheffé’s method, and
Results
Insecticidal Activities of Isolated Entomopathogenic Nematodes
In total, seven EPN were isolated from sandy soils of forest sites (Republic of Korea). Based on the 28S rDNA sequence, all isolated EPNs belonged to the
Isolation and Identification of Nematicidal Xenorhabdus Species
On the basis of blue colony morphology, we isolated four strains from
-
Figure 1. Phylogenetic relationship of the isolated
Xenorhabdus strains based on 16S rRNA gene sequence. Neighbor-joining phylogenetic tree based on 16S rRNA gene sequences and closely related species constructed using MEGA X software. Numbers at each branch indicate the bootstrap percentage of 1,000 replications.
Four isolated strains were evaluated for nematicidal activity against four
-
Figure 2. Nematicidal activities of isolated bacteria against the J2s of four
Meloidogyne species. (A) Mortality rate of the J2s of Meloidogyne after 48 h treated with 10% cell-free filtrates of isolated bacteria. Sunchungtan 150EC (150 μg/ml of fosthiazate) were used as the positive control, while LB broth was used as the negative control. (B) Morphological observation of the assessed nematodes with active nematodes (upper) and the dead nematodes with straight form and immobility (below) post-stimulation using a fine needle. All experiments were performed in triplicate wells and repeated three times under the same conditions. Different letters above the error bars indicate significant differences by Scheffé's test (p < 0.05). Scale bar: 20 μm.
Nematicidal Spectrum of SCG Strain
To determine the nematicidal potential of strain SCG, the nematicidal activity spectrum was assessed against J2s of four plant-parasitic nematodes (
-
Figure 3. Assessments of the nematicidal spectrum of cell-free filtrates of SCG strain against the second-stage juveniles of four plant parasitic nematodes.
Sunchungtan 150EC (150 μg/ml of fos-thiazate) were used as the positive control, while LB broth was used as the negative control. All experiments were performed in triplicate wells and repeated three times under the same conditions. Different letters above the error bars indicate significant differences by Scheffé's test (
p < 0.05).
Purification of Nematicidal Compound from SCG Strain
Based on bioassay-guided monitoring, the ethyl acetate extract of strain SCG was fractionated, and white active compound was obtained. The molecular weight and formula of active compound was determined as C5H6N2O2 by ESI-MS ([M + H]+, m/z 126.8) and 1D NMR spectra (1H and 13C NMR) (Fig. S2 and Table S2). The structure of active compound was readily identified as thymine by comparison with previously reported structures [35, 36]. Thymine isolated from strain SCG showed nematicidal activity in a concentration-dependent manner against
-
Figure 4. Concentration-dependent nematicidal activity of thymine from strain SCG.
All experiments were performed in triplicate wells and repeated three times under the same conditions.
Effect of Strain SCG on M. incognita under Greenhouse Conditions
The population of
-
Figure 5. Effects of cell-free filtrates of SCG strain on the number of nematode populations (A) and egg masses (B) per plant in the pot experiment (
n = 5). (C) Root symptoms ofS. lycopersicum . The number of egg masses was determined using phloxine B staining. The red arrows indicate egg masses formed byM. incognita infection. The experiment was performed in triplicate under the same conditions. Different letters above the error bars indicate significant differences according to Scheffé's test (p < 0.05).
The application of 10% cell-free filtrates of strain SCG significantly affected all the plant growth parameters (fresh height and weight of shoots and roots) after 45 days and had a relatively optimized effect on tomato growth compared to positive control (fosthiazate) (Fig. 6). It yielded the highest fresh shoot length (38.4 ± 1.4 cm), fresh root length (21.2 ± 1.9), fresh shoot weight (10.2 ± 0.3), and fresh root weight (3.8 ± 0.4). However, the fresh root length did not differ significantly between 10% cell-free filtrates of SCG and fosthiazate (
-
Figure 6. Effects of SCG strain cell-free filtrates on the growth of
S. lycopersicum in the pot experiment (A). Fresh height and weight of the testS. lycopersicum was measured after 45 days of transplanting (B) (n = 5). The experiment was performed in triplicate under the same conditions. Different letters above the error bars indicate significant differences based on Scheffé's test (p < 0.05).
Discussion
Over the last several decades, eco-friendly nematicidal agents have been extensively studied to overcome the side effects of synthetic nematicides, such as toxic environmental hazards [37]. Recent studies suggest that the symbiotic bacterium of EPNs,
Despite numerous advances in the laboratory studies of bacterial nematicides, extensive research is needed for their successful application under field conditions because of their lack of field adaptability and activity. Therefore, the discovery of new nematicidal strains from rhizospheric environments with high field activity and adaptability is essential for the sustainable control of RKNs. The results of the pot experiment indicated that the cell-free filtrates of the SCG strain could control
Our study showed that
Supplemental Materials
Acknowledgments
This work was supported by Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry (IPET) through “Crop Viruses and Pests Response Industry Technology Development” Program (No. 321110–4) funded by Ministry of Agriculture, Food and Rural Af-fairs (MAFRA).
Author Contributions
J.-H. Kim: Validation, Formal analysis, Data curation, Visualization, Writing—Original Draft, Writing—Review & Editing; B.-M. Lee: Investigation; H.-C. Lee: Investigation, Methodology; I.-S. Choi: Methodology; K.-B. Koo: Conceptualization, Resources, Supervision; K.-H. Son: Data curation, Funding acquisition.
Conflict of Interest
The authors have no financial conflicts of interest to declare.
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