Plant Pathol J > Volume 40(3); 2024 > Article
Kim, Jeon, and Kwak: Antifungal Properties of Streptomyces bacillaris S8 for Biological Control Applications

Abstract

Soybean (Glycine max), a crucial global crop, experiences yearly yield reduction due to diseases such as anthracnose (Colletotrichum truncatum) and root rot (Fusarium spp.). The use of fungicides, which have traditionally been employed to control these phytopathogens, is now facing challenges due to the emergence of fungicide-resistant strains. Streptomyces bacillaris S8 strain S8 is previously known to produce valinomycin t through a nonribosomal peptide synthetase (NRPS) pathway. The objective of this study was to evaluate the antifungal activity of S. bacillaris S8 against C. truncatum and Fusarium sp., assessing its efficacy against soybean pathogens. The results indicate that strain S8 effectively controlled both above-ground and underground soybean diseases, using the NRPS and NRPS-related compound, suggesting its potential as a biological control in plant-microbe interactions. These findings underscore the pivotal role of the stain S8 in fostering healthy soybean microbial communities and emphasize the significance of microbiota structure studies in unveiling potent biocontrol agents.

Streptomyces strains have been recognized for their ability to produce diverse secondary metabolites with significant roles in plant defense against pathogens (Bentley et al., 2002; Deshpande et al., 1988; Lee et al., 2020). Apart from their well-established role in suppressing plant diseases, Streptomyces is increasingly gaining attention as a potential abiotic stress controller through the production of various secondary metabolites (Durán et al., 2018; Harir et al., 2018; Yagüe et al., 2012) The importance on biological control approaches in sustainable agriculture, particularly involving the Streptomyces genus have been underscored (Cha et al., 2016; Genilloud, 2017; Kim and Kwak, 2023; Kim et al., 2019; Oskay, 2009). Given the broad spectrum of Streptomyces interactions with host plants, these bacteria emerge as an excellent model system for studying plant-microbe interactions (Lindow and Brandl, 2003; Redford et al., 2010). Building upon our previous findings that Streptomyces bacillaris S8 exhibits noteworthy antifungal and antibacterial activities while demonstrating suppressive effects on various plant diseases (Jeon et al., 2019, 2021; Kim et al., 2022), the present study aims to elucidate the feasibility of employing these strains as a biological control agent in the intricate dynamics of plant-microbe interactions.
To achieve sterilization of 3 g of soybean seeds (Glycine max cv. Daewon), the seeds were aseptically transferred into 50-ml tubes. Subsequently, they underwent a 30-s exposure to 70% ethanol. After, the ethanol supernatant was decanted, and a 1% NaOCl solution was added to the seeds. The seed-NaOCl mixture was vigorously vortexed for 1 min. Following this, the seeds underwent thorough washing with ddH2O for 1 min, and this rinsing process was repeated three or more times. Once the rinsing sequence was completed, the seeds were carefully placed within sterilized cotton paper in a Petri dish. The dishes were then incubated for 3 days at 28°C under dark conditions. After germination, the sprouted seeds were transferred to individual plastic square pots (18 cm × 18 cm), ensuring a distance of more than 20 cm between each pot to prevent cross-contamination. The plants were cultivated in a controlled glass greenhouse with a light exposure of 14 h at a temperature of 28 ± 3°C, followed by a dark period of 10 hours at a temperature of 15 ± 3°C. This growth schedule was maintained for a duration of 28 days.
The genome of S. bacillaris S8 was previously characterized by Kim and Kwak (2023), underscoring its importance in the synthesis of antifungal metabolites effective against large patch disease (Jeon et al., 2021). To identify potential secondary metabolite gene clusters within this strain, we utilized the antiSMASH 7.0 version tool (https://docs.antismash.secondarymetabolites.org) (Blin et al., 2023). The left flanking and right flanking regions for each deleted gene were amplified using 1 μg of strain S8 genomic DNA and gene-specific primers. The PCR amplification for each gene’s left flanking and right flanking regions followed a protocol comprising an initial denaturation at 98°C for 10 min, 30 cycles of denaturation at 98°C for 1 min, annealing at 52-58°C for 30 s (according to the respective primer melting temperature) (Supplementary Table 1), elongation at 72°C for 30 s, and a final extension at 72°C for 5 min. Subsequently, the left flanking and right flanking regions were fused through PCR, involving an initial denaturation at 98°C for 30 s, followed by five cycles of denaturation at 98°C for 8 s, annealing at 50°C for 30 s, elongation at 72°C for 30 s, and a final extension at 72°C for 5 min. Finally, the target homologous regions, including left flanking and right flanking, were amplified, and the last PCR step adhered to conditions similar to the earlier left flanking and right flanking region PCR, with the annealing temperature set at 60°C. The PCR procedures were executed using the MJ Research RTC-200 Thermal Cycler (Bio-Rad, Hercules, CA, USA).
The purified molecules were ligated to the pGEM-T easy vector (Promega, Madison, WI, USA) using T4 ligase (Promega) and incubated at 16°C for over 20 h. The ligated constructs were transformed into Escherichia coli DH5α via bacterial transformation. Subsequently, the vector and pCRISPomyces-gRNA were digested using XbaI (NEB, Ipswich, MA, USA), followed by elution into 30 μl of EB buffer. A 3:1 molar ratio ligation was performed using 400,000 units (400 units/μl) of T4 ligase. The gRNA was cloned into pBHA (2,002 bp), and pCRISPomyces-2 (Cobb et al., 2015) was digested using BbsI (NEB). The resulting fragments were ligated using T4 ligase, connecting the two fragments and subsequently linking them with the gRNA (guide RNA). The resultant plasmids were then transformed into E. coli ET12567 containing pUZ802 (Bierman et al., 1992).
The transformed cells cultured and underwent centrifugation (1,914 ×g, 15 min), followed by two gentle washes with 10 ml of Luria-Bertani (LB) solution. Each wash was accompanied by centrifugation. The resulting pellet was resuspended in 500 μl of LB broth medium. In a separate E-tube, 500 μl of 2× YT broth medium (10 g yeast extract, 16 g tryptone, 5 g NaCl per liter) was heated at 50°C for 10 min. Subsequently, 10 μl of strain S8 spore stock (109 cfu/ml) containing 20% glycerol was mixed with the heated 2× YT broth. The washed E. coli (ET12567/pUZ8002) cells were gently mixed with the strain S8 spore stock using a pipette and spread onto mannitol soya agar (SFM; 20 g mannitol, 20 g soya flour per 1 liter) medium (Kieser et al., 2000). After 12 h, the agar plates were supplemented with apramycin (50 μg/ml) and nalidixic acid (25 μg/ml). After 7 days, colonies were transferred twice onto SFM agar containing apramycin (50 μg/ml).
C. truncatum and Fusarium sp. were grown onto potato dextrose agar (PDA; 24 g of potato dextrose, 20 g of agar per liter). C. truncatum underwent cultivation at 25°C for 10 days, while Fusarium sp. was cultured at 27°C for 7 days. The production of the Fusarium sp. inoculum as mixture of 99 g of sand and 1 g of oatmeal within a 1-liter plastic bottle, subjected to three cycles of sterilization. Subsequently, this sterilized mixture was inoculated with Fusarium sp., previously cultured on PDA medium for 7 days. The inoculated mixture was cultivated at a temperature of 28°C for 3 weeks to facilitate chlamydospore preparation. To assess the biological control efficacy of wild-type strain S8 and mutant strains, each was streaked on mannitol soya agar (SFM; 20 g mannitol, 20 g soya flour per liter), and cultured at 28°C for 5 days. A single colony from each strain was sub-cultured in 5 mL PDK (10 g potato dextrose broth, 10 g peptone per liter) broth at 28°C for 3 days. The cultured cells were then transferred to 200 ml of PDK broth and incubated at 28°C for 7 days, after which cell densities were adjusted to 106 cfu/ml.
A greenhouse measuring 5 m in length was utilized to establish distinct zones for both infected and non-infected control groups. Subsequently, a suspension containing the wild-type strain S8 and mutant strains was prepared with a final concentration of 0.1% carboxymethyl cellulose. This suspension was applied to the proximity of soybean roots and leaves in both groups. Five days post-inoculation, C. truncatum was administered to each plant at a rate of 10 ml per plant using a spray method. Conversely, for Fusarium sp., a drenching method was employed, administering 10 ml (105 spores) of the suspension per plant. Disease severity assessments were conducted at weekly intervals following pathogen inoculation, utilizing a 5-level index. For C. truncatum, the severity scale encompassed the following categories: 0 = no significant damage, 1 = spots covering <1-10% of the plant, 2 = spots covering 10.1-15% of the plant, 3 = spots covering 15.1-25% of the plant, 4 = complete plant death (Agam et al., 2019). In the case of Fusarium sp., the severity scale was defined as follows: 0 = no symptoms, 1 = mild symptoms (discoloration without visible lesions), 2 = obvious lesions (severe discoloration with lateral root reduction), 3 = severe lesions on the primary and lateral roots and diminished plant vigor, and 4 = stem rotten, plant dead (Chang et al., 2020).
Streptomyces bacillaris S8 has previously been acknowledged for its potent biocontrol capabilities against large patch disease in turfgrass, with the identification of the valinomycin biosynthetic gene cluster (Jeon et al., 2019). Building upon this, our investigation aimed to explore its potential as a biocontrol agent in soybeans, motivated by its relevance to plant health (Kim and Kwak, 2023). The identified gene clusters within the bacteria were found to include genes associated with the production of nonribosomal peptide synthetase (NRPS) or polyketide synthase (PKS) compounds, as detailed in Table 1. Various biosynthesis knockout mutants targeting these clusters were generated using the CRISPR/Cas9 system, to assess their antifungal activities against two soybean phytopathogenic fungi (Table 2).
In the present study, we generated three mutant strains in which nrps/pks2, nrps3, or nrps4 genes were abolished from the wild-type S8 strain (Fig. 1). Notably, the mutants of strain S8 in the nrps3 and nrps/pks2 clusters exhibited reduced efficacy against root rot disease, as evidenced by diminished activity in biocontrol assays (Fig. 2, Supplementary Figs. 1 and 2). Conversely, two distinct mutants showed no significant suppression of the two pathogens, with a statistical significance of P = 1.180e-10 (*** on C. truncatum) and P = 7.770e-13 (*** on Fusarium sp.) (Fig. 3). These observations lend support to the hypothesis that the NRPS and PKS serves as of antibiotics crucial for protecting the plant.
The biosynthesis genes were identified in Streptomyces spp., specifically in Streptomyces albus strain BK 3-25, which is known for salinomycin production, and in the deep-sea-derived S. atratus SCSIO ZH16NS-80S known to produce atratumycin (Almeida-Paes et al., 2021; Yang et al., 2019). Salinomycin has been reported for its anticancer and antifungal properties against Paracoccidioides brasiliensis (Zhou et al., 2013). While information regarding the antifungal effect of atratumycin is limited, its expression level was observed to increase in a co-culture system the fungus Nigrospora oryzae roseF7 and Streptomyces sp. MW-W600-10 (Siupka et al., 2021). This suggests that two distinct NRPS or PKS related compounds play a role in the antifungal effect against plant pathogens. Furthermore, atratumycin exhibited specific activity against C. tuncatum and Fusarium sp., suggesting its promise as a strain-specific biocontrol agent for the S8 strain.
The diminished biocontrol activity of specific mutants underscores the importance of these antibiotic clusters in combatting plant diseases. This study contributes valuable insights into the potential use of Streptomyces strains for sustainable crop disease management, with far-reaching implications for agricultural practices. Additionally, the findings provide a foundation for basic research in environmental biological control, offering potential strategies for controlling soybean diseases and enhancing overall plant health.

Notes

Conflicts of Interest

No potential conflict of interest relevant to this article was reported.

Acknowledgments

This research was supported by an agenda research program funded by the Rural Development Administration (RS-2021-RD009876).

Electronic Supplementary Material

Supplementary materials are available at The Plant Pathology Journal website (http://www.ppjonline.org/).

Fig. 1
Schematic depiction of the targeted deletion of a gene utilizing the CRISPR/Cas9 system. The diagram illustrates the distribution of gene functions within the nrps-like biosynthesis genes, alongside the specific sites targeted for deletion by the CRISPR/Cas9 system (triangles). The cluster was analyzed using antiSMASH version 7.0 (https://antismash.secondarymetabolites.org/). Mutants were generated through the CRISPR/Cas9 system, employing a plasmid containing a codon-optimized Cas9 from Streptococcus pyogenes, as well as BbsI (guide RNA) and XbaI (homologous) sites for the incorporation of editing templates.
ppj-nt-01-2024-0021f1.jpg
Fig. 2
Antibiotic activity and associated gene clusters in strain S8. The agar plates were incubated at 28°C for 7 days, during which the inhibition zones were carefully measured. Statistical analysis of the test data was conducted using the Kruskal-Wallis rank sum test, followed by the Tukey honestly significant difference (HSD) post-hoc test. A significance level of P < 0.05 indicates a significant difference in the size of inhibition zones between strain S8 and mutants. The tested pathogens included Fusarium sp. (A) and Collectotruchum truncatum (B).
ppj-nt-01-2024-0021f2.jpg
Fig. 3
Effectiveness of biocontrol measures against fungal diseases. Collectotrichum truncatum and Fusarium sp. were inoculated in soybean plants during the vegetative stage at 28 days. Plants were treated with a 10 ml drench of bacterial stocks (106 cfu/ml: strain S8, Δnrps3 and Δnrps4, Δnrps/pks2) in 0.1% carboxymethyl cellulose solution (v/v). (A) Fusarium sp. was inoculated with a chlamydospore stock at 105 spores/g. (B) C. truncatum with a conidia stock at 105 spores/g. Each spore stock was applied in a 10-ml volume. The disease index was assessed on a scale of 0 to 5 after 4 weeks (n = 12), and statistical analysis was performed using linear regression ANOVA.
ppj-nt-01-2024-0021f3.jpg
Table 1
Putative antibiotic gene clusters in strain S8 predicted by antiSMASH
AntiSMASH Prediction Cluster similarity

Most similar known cluster Percentage
nrps1 Hypothetical protein Lactazole 33
t3pks Hypothetical protein Alkylresorcinol 100
nrps2 Synthetase gene (vlm1, vlm2) Valinimycin 100
pks1 Transferase Bafilomycin 94
nrps3 Nrps Salinomycin 14
nrps4 Peptide synthetase Bottromycin A2 36
pks2 Pks Herboxidiene 6
nrps5 Siderophore Tylactone 10
nrps6 Siderophore Coelichelin 81
nrps7 Siderophore Streptobactin 88
nrps/pks1 Pks-malonyl-CoA Cosmomycin D 31
nrps/pks2 Line whiE Atratumycin 34
Table 2
Bacteria and plasmids used in this study
Strains/Plasmids Description
Escherichia coli
 DH5α F, Φ80dlacZDM15, (lacZYA-argF)U169, deoR, recA1, endA1, hsdR17 (rk−, mk+), phoA, supE44, λ-, thi-1, gyrA96, relA1
 ET12567/pUZ8002 dam-13::Tn9 dcm-6 hsdM, carries RK2 derivative with defective oriT for plasmid mobilization, Kanr
Streptomyces bacillaris S8
 Strain S8. nrps3 Strain S8 Δnrps3 :: Aprar
 Strain S8. nrps4 Strain S8 Δnrps4 :: Aprar
 Strain S8. nrps/pks2 Strain S8 Δnrps/pks2:: Aprar
Plasmid/Cosmid
 pCRISPomyces-2 Amr, oriT, reppSG5(ts), oriColE1, sSpcas9, sgRNA cassette
 pBHA Amr, pUC ori, gRNA clone
 pCRISP. nrps3 pCRISPomyces-2 + Δnrps3 editing templated, nrps3 sgRNA - sSpcas9
 pCRISP. nrps4 pCRISPomyces-2 + Δnrps4 editing templated, nrps4 sgRNA - sSpcas9
 pCRISP. nrps/pks2 pCRISPomyces-2 + Δnrps/pks2 editing templated, nrps/pks2 sgRNA - sSpcas9

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