1. Introduction
Vegetable crops are vital sources of essential nutrients, such as vitamins and minerals, for the human diet [
1]. Ranked after food and sugar crops, vegetables are among the most significant crops worldwide. Given the constraints of limited arable land and the escalating demands of a growing global population, ensuring a food supply is a formidable challenge [
2]. Consequently, producing high-quality food without excessive chemical residues has become an urgent necessity [
3].
In vegetable production, diseases caused by plant pathogens persistently result in significant reduction in harvestable yields. Among these, fungal pathogens can cause a wide range of diseases in vegetables, leading to direct damage to plant tissues and significant yield losses [
4,
5,
6]. In addition, pathogenic fungi can dimmish the aesthetic appeal of agricultural crops and also reduce their storage lifespan, causing significant economic setbacks for producers [
7]. The economic impact of fungal diseases in vegetable production is therefore considerable, emphasizing the need for effective management strategies to mitigate these diseases.
One of the most detrimental fungal diseases to plants including vegetables is the Fusarium wilt caused by the fungal pathogen
Fusarium oxysporum [
8]. This pathogen is notorious for its persistence in soil and its ability to cause severe wilt symptoms in a variety of vegetable crops [
9]. Among various vegetable crops,
F. oxysporum f. sp.
conglutinans presents a significant challenge for cabbage cultivation, profoundly affecting both yield and quality [
10]. This pathogen’s impact is particularly severe, leading to substantial economic losses for cabbage producers. Similarly,
F. oxysporum f. sp.
lycopersici is a critical threat to tomato production, causing severe wilt symptoms that jeopardize tomato yields in many regions [
11]. The widespread nature of this pathogen makes it a significant concern for tomato growers, necessitating vigilant management practices to mitigate its effects. Additionally,
F. oxysporum f. sp.
cucumerinum is recognized as one of the most destructive diseases for cucumber crops, inflicting serious damage that can severely reduce both the quantity and the quality of the harvest [
12,
13]. In addition to vegetables, Fusarium wilt also poses a significant threat to ornamental plants. Chrysanthemum Fusarium wilt, a common soil-borne disease affecting chrysanthemums throughout their growth period, can lead to considerable economic losses for producers [
14]. Overall, the pervasive threat of Fusarium wilt to both vegetable and ornamental crops indicates the critical need for innovative and effective management strategies to mitigate its widespread and economically devastating effects.
Given the challenges posed by Fusarium wilt, effective disease management strategies are essential. However, only a limited number of fungicides on the market have proven efficacious against this pathogen [
15]. The prolonged and excessive application of these chemical-based fertilizers and fungicides not only leads to air and groundwater contamination, particularly through the eutrophication of water bodies [
16], but also contributes to soil acidification [
17,
18]. As environmental awareness grows, biological materials have emerged as viable alternatives to chemical pesticides and fertilizers, offering a sustainable approach to enhance crop yield and mitigate crop diseases [
3].
One promising solution is the use of beneficial micro-organisms, particularly those from the genus
Bacillus. The Bacillus genus encompasses a diverse group of aerobic or facultatively anaerobic, rod-shaped bacteria known for their ability to form endospores. These bacteria are prevalent across various environments [
19]. Notably, species such as
B. subtilis,
B. cereus,
B. pumilus,
B. amyloliquefaciens,
B. firmus,
B. megaterium,
B. safensis, and
B. velezensis have demonstrated antagonistic properties against a range of plant pathogens, including bacteria, fungi, and nematodes [
20,
21,
22]. In particular,
Bacillus has been found to inhibit important
F. oxysporium of various hosts including but not limited to
F. oxysporum f. sp.
cubense and
F. oxysporum f. sp.
cucumerinum [
13,
23,
24,
25,
26]. Within the different
Bacillus spp.,
B. velezensis has recently been identified to offer plant growth benefits in addition to its phytopathogen-inhibiting characteristics [
13,
27,
28].
Plant growth-promoting rhizobacteria (PGPR), such as
B. velezensis, exhibit multiple beneficial properties that enhance plant growth and health. These properties include nitrogen fixation, phosphate solubilization, and the production of phytohormones, which collectively contribute to improved nutrient availability and stress tolerance in plants [
29].
B. velezensis enriches the soil with a variety of macro- and micro-nutrients through processes such as nitrogen fixation, phosphate and potassium solubilization or mineralization, and the release of plant growth regulators [
30,
31]. Additionally, it produces antibiotics and facilitates the biodegradation of organic matter in the soil, thereby improving soil health and fertility [
32]. Some strains of
B. velezensis can directly enhance plant growth by secreting compounds like indole-3-acetic acid (IAA) [
33]. These multifaceted activities of
B. velezensis not only promote plant growth but also protect against pathogens, making it a potential tool in sustainable agriculture.
B. velezensis has been utilized as a bio-fertilizer to enhance the growth of a variety of vegetables, fruit trees, and seedlings. Previous studies have shown that various
B. velezensis strains significantly improve plant growth parameters across different crops. Meng et al. [
34] observed that
B. velezensis BAC03 significantly increased the fresh weight of leaves and tubers in root vegetables, including radishes, carrots, turnips, and beets. Similarly, Zhang et al. [
35] noted a substantial increase in pepper seedling production with the use of
B. velezensis NJAU-Z9. Additionally, Balderas-Ruíz et al. [
36] found an increase in root weight for maize and Arabidopsis seedlings treated with
B. velezensis 83. Myo et al. [
37] reported that
B. velezensis NKG-2 enhanced the seed germination rate, fresh weight, and dry weight in tomatoes. These findings highlight the potential of
B. velezensis as a powerful bio-fertilizer to enhance agricultural productivity and sustainability.
In view of the potential of Bacillus spp. and B. velezensis to promote crop growth and control plant diseases, this study collected organic rice field soil in southern Taiwan, in order to isolate indigenous Bacillus strains. The isolated strains were analyzed for their potential to promote plant growth in various vegetables at both the plant and seed stages within a greenhouse setting. The objectives of this study were to screen plant growth promoting microorganisms and evaluate their ability to counteract phytopathogens. Additionally, we aimed to investigate the efficacy of the isolated strains as biocontrol agents for vegetable seedlings against phytopathogens.
2. Materials and Methods
2.1. Bacteria Isolation and Identification
In this study, organic soils were collected in Qishan District of Kaohsiung (22.8583417° N, 120.5170298° E), Neipu Township (22.610881° N, 120.561626° E), and Wandan Township (22.5477969° N, 120.4843653° E) in Pingtung County, Taiwan. Samples were taken from the top 30 cm of soil [
38] and the bacterial were isolated according to the method previously described [
39]. The isolated bacteria were first identified at the genus level based on colony morphology. Subsequently, isolates exhibiting antibiotic activity were sent to the Food Industry Research and Development Institute of Taiwan for further identification using 16S ribosomal DNA (rDNA) and gyrase subunit B (gyrB) gene sequencing (
Figures S1 and S2) [
40]. Sequence alignment of 16S rDNA and gyrB gene regions was conducted using the maximum parsimony (MP) and maximum likelihood (ML) in MEGA 10.0 (Molecular Evolutionary Genetics Analysis) as described by Tamura et al. [
41] and subsequently analyzed by Bayesian inference, based on a Markov Chain Monte Carlo (MCMC) approach, was performed in MrBayes v.3.1.2 [
42], with 1,000,000 generations, sampled every 100 generations. FigTree version 1.4 [
43] was used to view the phylogenetic trees and data files. Reference sequences were sourced from the National Center for Biotechnology Information (NCBI) as published by Wang et al. [
44]. For long-term storage, isolated bacteria were stored in 50% sterile glycerin at −20 °C and −80 °C.
2.2. Evaluation of Various Hydrolytic Enzymes
2.2.1. Protease Activity Assay
The test bacteria were cultured for 2 days and then sub-cultured on protease-specific media containing gelatin following the method described by Abdel Galil et al. [
45]. After 48 h incubation at 30 °C in the dark, the diameter of the zone of hydrolysis was measured. Each test was replicated three times.
2.2.2. Cellulase Activity Assay
The cellulose medium containing was prepared and adjusted to pH 5.0 according to previously established protocol [
46], and the medium was covered with a polycarbonate membrane and filter paper disks with bacterial solutions. After 5 days of incubation at 30 °C in the dark, the medium plate was stained with 1% Congo red solution and incubated for 20 min at 30 °C, followed by a 15 min rinse in 1 M NaCl, and the hydrolysis zone measured. This assay was conducted in triplicate.
2.2.3. Lecithinase Activity Assay
The lecithinase activity assay was based on egg yok agar method previously described [
47]. Bacterial cultures were cultured on the medium for 5 days at 30 °C in darkness. The diameter of the permeabilization circle was measured, with each assay replicated three times.
2.2.4. Amylase Activity Assay
Amylase activity was assessed using starch medium previously reported [
46]. After incubation, the agar plates were submerged in 1% iodine solution to visualize amylase activity, indicated by clear zones. The diameter of these zones was measured, with each assay conducted in triplicate.
2.3. Analysis of Plant Growth-Promoting Compounds
2.3.1. Siderophore Production Assessment
Siderophore production was carried out using the overlay-chrome azurol S (O-CAS) method [
48]. The test bacteria were cultured in International Streptomyces Project 2 (ISP2) medium and incubated at 30 °C in darkness for a duration of 7 days. Then, the ISP2 medium was overlaid with chrome azurol S (CAS) medium and incubated at 28 °C for 2 days. The formation of orange or yellow halo zones around the bacterial colonies indicated siderophore production, with each test performed in triplicate.
2.3.2. Phosphate Solubilization Activity Assay
Phosphate solubilization was assessed using a phosphorus-dissolving medium as per the methodology previously described [
49]. Following incubation at 30 °C for 4 days in medium containing sucrose (10 g L
−1), NH
4NO
3 (0.27 g L
−1), KCl (0.20 g L
−1), MgSO
4·7H
2O (0.10 g L
−1), FeSO
4·7H
2O (1 mg L
−1), MnSO
4·4H
2O (1 mg L
−1), and Ca
3(PO
4)
2 (5 g L
−1), the bacterial suspension was centrifuged, and the supernatant filtered. The filtered supernatant was analyzed using a spectrophotometer (IMPLEN Inc., Westlake Village, CA, USA) at 420 nm wavelength, and quantification was carried out utilizing phosphorus standard curve. Each test was conducted in triplicate.
2.3.3. Indole-3-Acetic Acid (IAA) Production Assessment
Indole-3-acetic acid (IAA) production was assessed by culturing the test bacteria in nutrient broth (NB) medium. The medium contained D(+)-glucose (1 g L
−1), peptone (15 g L
−1), sodium chloride (6 g L
−1), and yeast extract (3 g L
−1), with a pH adjusted to 7.5. Culturing was conducted at 30 °C in darkness at 120 rpm. After the optical density reached 0.3 at 620 nm, tryptophan (500 μg mL
−1) was added, and the culture was incubated with shaking. Sample were taken at various intervals, centrifuged at 10,000×
g for 10 min, and mixed with 1.6 mL of Salkowaki reaction solution [
50]. The absorbance was measured at 530 nm, and IAA concentration was determined using a standard curve. Each assay was performed in triplicate.
2.4. Preparation of Test Plants
The impact of microbes on the growth of nine crops was evaluated, including tomato (Solanum lycopersicum L. cv. Known You 301), spoon cabbage (Brassica chinensis cv. Fang Rong), red lettuce (Lactuca sativa cv. LS-006), black-leaf cabbage (L. sativa cv. Known You 2), celery (L. sativa cv. V-025), rapeseed (B. chinensis var. oleifera Makino), cucumber (Cucumis sativus cv. Ashin), Chinese cabbage (B. chinensis cv.), and chrysanthemum (Chrysanthemum coronarium). All seeds, sourced from KNOWN-YOU SEED Co., Ltd., Kaohsiung, Taiwan were planted in 45-hole circular seedling trays containing peat soil (DAYI AGRITECH Co., Ltd., Pingtung, Taiwan) and cultivated in a growth chamber at 25 °C with a 12 h photoperiod.
2.5. Preparation of Bacillus velezensis KHH13 Rermentation Broth
A medium modified by Chou [
51] was prepared in a 10 L fermentation tank (model FS-V-D10P, Major Science Co., Ltd., Taoyuan, Taiwan). The medium, comprised of 0.75% molasses, 0.5% soy protein, 0.5% yeast powder, 0.1% K
2HPO
4, 0.1% KH
2PO
4, and 7 L of distilled water. 100 mL of
Bacillus velezensis KHH13 culture (OD600 of 0.3) was introduced. The fermentation was conducted at 28 °C with shaking at 150 rpm for 48 h, then adjusted to 30 °C and 200 rpm until the culture reached a density of 10
8 CFU/mL.
2.6. Oral and Pulmonary Acute Toxicity Analysis in Mice
For toxicity assessment, the
B. velezensis KHH13 fermentation broth was submitted to the Agricultural Chemicals and Toxic Substances Research Institute (Ministry of Agriculture, Taiwan) for testing [
52]. Mice were administered 10
7 CFU/mL of KHH13 via forced tracheal perfusion and gastric tube forced feeding [
53,
54]. Mortality rate and body weights were recorded over 21 days. The forced tracheal perfusion experiment involved a total of 46 mice, while the gastric tube forced feeding experiment included 36 mice. Each of these experiments was replicated six times.
2.7. Effect of B. velezensis KHH13 on Plant Growth
Nine different vegetable seeds were sown and cultivated following the aforementioned method and transplanted into 6-inch pots in a greenhouse at 30 °C ± 2. The seedlings were treated bi-weekly with a 400-fold diluted solution of B. velezensis KHH13 fermentation broth (initial concentration 5 × 108 CFU/mL). The control group was irrigated with an equal amount of sterilized fermentation medium broth. After 35 days, the fresh weight and root length of the plants were measured, with each vegetable type represented by 5 pots per test, replicated thrice.
2.8. Effect on Germination Rate of Vegetable Seeds
The effect of B. velezensis KHH13 on the germination was assessed for chrysanthemum, tomato, cucumber, and Chinese cabbage seeds. The seeds were first surface-sterilized, soaked in a 50-fold diluted solution of B. velezensis KHH13 fermented liquid for 30 s, and sown in water agar (WA) medium. After 7 days, seed germination rate, seedling root length, and fresh weight were recorded, with each test conducted in triplicate.
2.9. Antifungal Activity Assay
The antifungal activity assay was adapted from Boughalleb-M’Hamdi et al. [
55]. Briefly,
B. velezensis KHH13 was streaked linearly on one side of the potato dextrose agar (PDA) plate with a 5 mm mycelial plug of various fungal strains on the opposing end. The test fungi included
Fusarium oxysporum f. sp.
cattleyae,
F. oxysporum f. sp.
cubense,
Botryodiplodia theobromae,
F. oxysporum f. sp.
cucumerinum,
Colletotrichum gloeosporioides,
Phytophthora palmivora,
Pyricularia oryzae, and
Bipolaris oryzae. The plates were then incubated for 5 days at 30 °C. The inhibition rate of hyphal growth was calculated using the following formula: the inhibition rate of hyphal growth (%) = ((the hyphal length of the blank control − the hyphal length of the treatment)/the hyphal length of the blank control) × 100 [
55]. Each test was carried out with three dishes as one replicate and tested thrice.
2.10. Greenhouse Experiment for Controlling Cucumber Fusarium Wilt with KHH13
The experimental design for controlling cucumber Fusarium wilt with
B. velezensis KHH13 was adapted from the methodology described by Abro et al. [
15]. Cucumber seeds (cv. Ashin) were sown in peat-based growing medium (Greenterra Peat Substrate, Greenterra, Latvia) for 14 days prior to immersion in a suspension of
F. oxysporum f. sp.
cucumerinum (Focu) (1 × 10
6 spores mL
−1) for 30 min, then transplanted into 4-inch pots. The KHH13 treatment group consisted of irrigation with a 400-fold diluted solution of KHH13 powder (initial concentration of 5 × 10
8 CFU mL
−1). Control groups included the pathogen control group (CK), which did not receive any KHH13 treatment, and the blank control group (Mock), consisting of plants that were not subjected to root immersion with Focu fungus but were only irrigated with the KHH13 solution. Each treatment contained 15 pots, replicated thrice. The grading method for plant symptoms was adapted from the study by Killebrew et al. [
56], categorizing root rot severity into six levels of disease severity: Level 0 indicates no symptoms; Level 1 shows browning of the embryonic roots; Level 2 involves browning of all embryonic roots; Level 3 indicates browning of the sub-embryonic axis; Level 4 reveals browning of the entire sub-embryonic axis; and Level 5 corresponds to plant death. Disease incidence and disease index were calculated using the following formulas: Disease incidence (%) = (Number of diseased plants/total number of test plants) × 100 [
57]; Disease index (%) = [Σ (Disease severity × number of plants)/(highest grade of disease severity × total number of tested plants)] × 100 [
58].
2.11. Statistical Analysis
Data were analyzed using SPSS Statistics 22.0 software (SPSS Inc., Chicago, IL, USA). with one-way analysis of variance (one-way ANOVA) and Least Significant Difference Procedure (LSD). Results were considered statistically significant at p < 0.05.
4. Discussion
The current study highlights the biofertilization and biocontrol potential of B. velezensis KHH13, which was isolated from organic soils in southern Taiwan. This strain was evaluated for its ability to promote plant growth and control soil-borne diseases in a variety of vegetable crops. The findings suggest that B. velezensis KHH13 could serve as a valuable agent for sustainable agriculture, offering an eco-friendly alternative to chemical fertilizers and pesticides.
In recent years, the application of biological pesticides and fertilizers in the cultivation of vegetables and fruit trees has gained considerable attention [
3]. These bio-based products represent a safe, effective, and sustainable approach to the cultivation and management of vegetable crops. The
Bacillus genus has been recognized for its ability to enhance soil fertility and crop resilience by mobilizing nutrients, suppressing diseases, and providing stress resilience [
59]. In our greenhouse experiments,
B. velezensis KHH13 significantly enhances the growth of various vegetable crops (
Figure 3,
Figure 4 and
Figure S3), particularly red lettuce (
Figure 3), as compared to other strains such as
B. velezensis KHC2 and
B. amyloliquefaciens KHH5. The superior growth-promoting effect of KHH13 is attributed to its high phosphorus-dissolving activity (2186.1 µg mL
−1 day
−1) and IAA production (63.067 ± 0.595 ppm mL
−1), which facilitate better nutrient availability and root development. These results are consistent with previous studies by Zaidi et al. [
60], which highlighted the role of phosphate-solubilizing micro-organisms (PSMs) in promoting the growth of a wide range of vegetable crops, including tomatoes, potatoes, eggplants, and cucumbers. Indeed,
Bacillus species are known to produce organic acids to solubilize phosphate [
61,
62,
63]. Hence, one potential explanation for this enhanced growth-promoting effect is KHH13’s high phosphorus-dissolving activity (
Table 1), which enables the decomposition of tricalcium phosphate in the soil, thereby facilitating better growth of vegetables.
IAA is another factor that has a crucial role in promoting root development, which, in turn, facilitates overall plant growth [
60]. IAA-producing
Bacillus species have been shown to improve nutrient and water uptake in plants by enhancing water use efficiency and altering root system architecture, such as by increasing the number of root tips and the root surface area [
64]. In our study, we found that among the three
Bacillus isolates,
B. velezensis KHH13 produced the highest IAA level (
Figure 2). Similarly, in a screening of seven bacterial isolates from the rhizosphere for highest IAA producer, the researchers also found a
B. velezensis strain to produce the highest [
65]. Our study revealed that different vegetable crops exhibit varying sensitivities to the microbial inputs provided by
B. velezensis strains. While red lettuce showed significant growth enhancement with KHH13 treatment, other crops such as tomato and cucumber did not exhibit similar responses. This differential sensitivity highlights the need for tailored approaches in utilizing
Bacillus species for crop growth enhancement, as different crops may require varying levels of IAA and phosphorus.
Spores of several
Bacillus species have long history of consumption and safe use as probiotics and a variety of formulations containing these organisms is available in the global market [
66]. To date, a total of 13 probiotic
Bacillus species are considered as a Generally Recognized as Safe organism (GRAS) approved by the US Federal Food, Drug, and Cosmetic Act (FDCA), and these species are used for food and feed additives [
67]. However,
B. velezensis has not yet been considered. Furthermore, in the acute toxicity tests conducted orally and pulmonarily in rats,
B. velezensis KHH13 did not affect the body weight of the rats or cause mortality (
Table 2,
Table 3,
Table 4 and
Table S1). These findings align with those reported by Hayes and Kruger [
52], confirming the non-toxic nature of
B. velezensis metabolites to mammals. Consequently, KHH13 can be considered safe for agricultural practices, with no significant safety concerns for humans.
Interestingly,
B. velezensis has also been recognized for its ability to effectively controlling various plant diseases.
B. velezensis SDTB038 reduces the severity of potato late blight, as reported by Yan et al. [
38], while
B. velezensis NH-1 mitigates the severity of cucumber Fusarium wilt, as observed by Luo et al. [
13]. More recently, Abdel-Moghies et al. [
68] showed that
B. velezensis effectively protected potato against
F. oxysporum and
Ralstonia solanacearum. Our study demonstrated the efficacy of
B. velezensis KHH13 in controlling cucumber Fusarium wilt, significantly reducing the disease index from 74.33% to 41.67%. This reduction aligns with findings by Luo et al. [
13], who reported the effectiveness of
B. velezensis NH-1 in mitigating the severity of cucumber Fusarium wilt. Current research [
6] has demonstrated that
Bacillus species producing enzymes such as protease, glucanase, and chitinase exhibit strong inhibitory effects on pathogens like
F. verticillioides. Additionally,
B. velezensis, known for producing a range of hydrolases (protease, glucanase, chitinase, cellulase), has been found effective against gray mold disease caused by
Botrytis cinereal. Similarly,
B. amyloliquefaciens, producing protease, has shown efficacy in preventing
F. oxysporum infections. These data suggest a correlation between the activities of hydrolytic enzymes (protease, glucanase, chitinase, and cellulase) produced by
Bacillus species and their ability to prevent crop diseases.
Bacillus velezensis KHH13 has potential as a safe, effective, and sustainable biological agent in agricultural practices. This study underlines its multifaceted utility in promoting the growth of both leafy and fruiting vegetables, while also showcasing its efficacy in reducing the incidence of soil-borne diseases, notably, Fusarium wilt in cucumber. The use of B. velezensis KHH13 in microbial seedling substrates has been particularly effective in disease prevention. However, the potential applications of this beneficial microorganism extend beyond soil treatment. Alternative application methods, such as foliar spraying, offer avenues for further exploration to determine whether B. velezensis KHH13 can enhance vegetable yields or provide protection against other plant diseases.
5. Conclusions
This study has demonstrated the substantial biofertilizer and biocontrol potential of Bacillus velezensis KHH13, isolated from organic soils, which offers a promising solution for sustainable agriculture. The significant findings of this research highlight KHH13’s ability to enhance plant growth and suppress disease incidence effectively. The superior phosphate solubilization and IAA production capabilities of KHH13 significantly promoted the growth and health of various vegetables, notably, red lettuce, tomatoes, and cucumbers, in a controlled greenhouse setting. Furthermore, KHH13’s biocontrol efficacy was particularly notable in reducing Fusarium wilt in cucumbers, showcasing its potential as a biological control agent.
Moreover, the safety profile of KHH13, as confirmed through acute oral and pulmonary toxicity tests in mammals, underscores its suitability for use in agriculture without adverse effects on human and animal health. These attributes make B. velezensis KHH13 a valuable resource for developing eco-friendly agricultural practices that reduce dependency on chemical fertilizers and pesticides, thereby promoting environmental sustainability and enhancing food security.
The outcomes of this research provide a strong foundation for the application of B. velezensis KHH13 in agriculture, offering insights into its mechanisms of action and potential integration into crop management systems. Future studies should explore the scalability of utilizing KHH13 in diverse agricultural settings and its long-term impacts on soil health and crop productivity.