Endophytic bacteria from strawberry plants control gray mold in fruits via production of antifungal compounds against Botrytis cinerea L

Botrytis fruit rot management: What have we achieved so far?

Botrytis cinerea is a destructive necrotrophic phytopathogen causing overwhelming diseases in more than 1400 plant species, especially fruit crops, resulting in significant economic losses worldwide. The pathogen causes rotting of fruits at both pre-harvest and postharvest stages. Aside from causing gray mold of the mature fruits, the fungus infects leaves, flowers, and seeds, which makes it a notorious phytopathogen. Worldwide, in the majority of fruit crops, B. cinerea causes gray mold. In order to effectively control this pathogen, extensive research has been conducted due to its wide host range and the huge economic losses it causes. It is advantageous to explore detection and diagnosis techniques of B. cinerea to provide the fundamental basis for mitigation strategies. Botrytis cinerea has been identified and quantified in fruit/plant samples at pre- and post-infection levels using various detection techniques including DNA markers, volatile organic compounds, qPCR, chip-digital PCR, and PCR-based nucleic acid sensors. In addition, cultural, physical, chemical, biological, and botanical methods have all been used to combat Botrytis fruit rot. This review discusses research progress made on estimating economic losses, detection and diagnosis, as well as management strategies, including cultural, physical, chemical, and biological studies on B. cinerea along with knowledge gaps and potential areas for future research.

Enhancing the Storage Longevity of Apples: The Potential of Bacillus subtilis and Streptomyces endus as Preventative Bioagents against Post-Harvest Gray Mold Disease, Caused by Botrytis cinerea

Gray mold, caused by Botrytis cinerea Pers. Fr., is one of the most vital plant diseases, causing extensive pre- and post-harvest losses in apple fruits. In the current study, we isolated and identified two potential endophytic bioagents, Bacillus subtilis and Streptomyces endus. Both bioagents exhibited a potent fungistatic effect against B. cinerea under both in vitro and in planta conditions. Moreover, two experiments were carried out; (i) the first experiment was conducted at room temperature after artificial inoculation with B. cinerea to monitor the progression of the infection and the corresponding biochemical responses of the apples. Our in vivo findings showed that the treated B. cinerea-infected apple fruits with the cell-free bacterial filtrate of B. subtilis and S. endus (dipping or wrapping) significantly reduced the rotten area of the treated apple at room temperature. Additionally, B. subtilis and S. endus enhanced the enzymatic (POX and PPO) and non-enzymatic (phenolics and flavonoids) antioxidant defense machinery in treated apples. (ii) The second experiment focused on the preventive effects of both bioagents over a 90-day storage period at 1 °C of healthy apples (no artificial inoculation). The application of both bacterial filtrates prolonged the storage period, reduced the relative weight loss, and maintained high-quality parameters including titratable acidity, firmness, and total soluble solids of apple fruits under cold storage at 1 °C. The Kaplan-Meier analysis of rotten apples over 90 days during cold storage showed that the treated apples lasted longer than the non-treated apples. Moreover, the lifespan of apple fruits dipped in the culture filtrate of B. subtilis, or a fungicide, was increased, with no significant differences, compared with the non-treated apples. The current results showed the possibility of using both bioagents as a safe and eco-friendly alternative to chemical fungicides to control gray mold disease in apples.

Application of plasma-activated hydrogen peroxide solution synergized with Ag@SiO2 modified polyvinyl alcohol coating for strawberry preservation

To extend the postharvest storage time of strawberries, this study aims to prepare a composite coating using plasma-activated hydrogen peroxide solution (PAH) synergized with nano-Ag@SiO2 by blending method to modify polyvinyl alcohol (PVA) solution. Results showed that the viscosity and the swelling rate of PVA significantly decreased with the addition of Ag@SiO2 at 0.18 %. Meanwhile, the elongation at break and the tensile strength of PVA increased to 0.87 MPa and 214 %. When the addition of Ag@SiO2 was 0.18 % and the composite ratio of PAH to PVA was 1:1, the composites could inactivate the pathogenic bacteria at 2 h. During the storage of strawberries, the initial colony counts on the surface of strawberries could be reduced by about 1 lg CFU/g after coating with the composite film. Moreover, with the extension of the storage time to 7 d, the respiratory intensity, colony counts, and rot index in the strawberries were 65.7 mg/(kg•h), 4.05 log CFU/g, and 38.7 %. Meanwhile, the superoxide dismutase activity and Vc content were 944 U/g and 690 μg/g, respectively. Overall, this study provides ideas and the theoretical basis for applying composite films in fruit preservation.

Antifungal Activity of Novel Indole Derivatives Containing 1,3,4-Thiadiazole

In this study, 24 indole derivatives containing 1,3,4-thiadiazole were discovered and synthesized. The target compounds' antifungal efficacy against 14 plant pathogenic fungal pathogens was then determined in vitro. With an EC50 value of 2.7 μg/mL, Z2 demonstrated the highest level of bioactivity among them against Botrytis cinerea (B.c.), exceeding the concentrations of the control prescription drugs azoxystrobin (Az) (EC50 = 14.5 μg/mL) and fluopyram (Fl) (EC50 = 10.1 μg/mL). Z2 underwent in vivo testing on blueberry leaves in order to evaluate its usefulness in real-world settings. A reasonable protective effect was obtained with a control effectiveness of 93.0% at 200 μg/mL, which was superior to those of Az (83.0%) and Fl (52.0%). At 200 μg/mL, this chemical had an efficacy of 84.0% in terms of curative efficacy. These figures outperformed those of Az (69.0%) and Fl (48.0%). Scanning electron microscopy (SEM) experiments and light microscopy experiments showed that Z2 altered the integrity of the cell wall and cell membrane of the pathogenic fungus B.c., which led to an increase in the content of malondialdehyde (MDA), cellular leakage, and cellular permeability. Enzyme activity assays and molecular docking studies indicated that Z2 could act as a potential succinate dehydrogenase inhibitor (SDHI). It was hypothesized that Z2 could cause disruption of mycelial cell membranes, which in turn leads to mycelial death. According to the research, indole derivatives containing 1,3,4-thiadiazole were expected to evolve into new fungicides due to their significant antifungal effects on plant fungi.

Insights into additional lactone-based signaling circuits in Streptomyces: existence of acyl-homoserine lactones and LuxI/LuxR homologs in six Streptomyces species

Acyl-homoserine lactones (AHLs), mediating pivotal physiological activities through quorum sensing (QS), have conventionally been considered limited to Gram-negative bacteria. However, few reports on the existence of AHLs in Gram-positive bacteria have questioned this conception. Streptomyces, as Gram-positive bacteria already utilizing a lactone-based QS molecule (i.e., gamma-butyrolactones), are yet to be explored for producing AHLs, considering their metabolic capacity and physiological distinction. In this regard, our study examined the potential production of AHLs within Streptomyces by deploying HPLC-MS/MS methods, which resulted in the discovery of multiple AHL productions by S. griseus, S. lavendulae FRI-5, S. clavuligerus, S. nodosus, S. lividans, and S. coelicolor A3(2). Each of these Streptomyces species possesses a combination of AHLs of different size ranges, possibly due to their distinct properties and regulatory roles. In light of additional lactone molecules, we further confirm that AHL- and GBL-synthases (i.e., LuxI and AfsA enzyme families, respectively) and their receptors (i.e., LuxR and ArpA) are evolutionarily distinct. To this end, we searched for the components of the AHL signaling circuit, i.e., AHL synthases and receptors, in the Streptomyces genus, and we have identified multiple potential LuxI and LuxR homologs in all 2,336 Streptomyces species included in this study. The 6 Streptomyces of interest in this study also had at least 4 LuxI homologs and 97 LuxR homologs. In conclusion, AHLs and associated gene regulatory systems could be more widespread within the prokaryotic realm than previously believed, potentially contributing to the control of secondary metabolites (e.g., antibiotics) and their complex life cycle, which leads to substantial industrial and clinical applications.

Identification and application of an endophytic fungus Arcopilus aureus from Panax notoginseng against crop fungal disease

Endophytic fungi are important microbial resources for developing novel antibacterial and antifungal drugs to prevent and control crop diseases. Panax notoginseng has been used as a Chinese medicinal herb for a long time, as it has various bioactivities. However, information on endophytic fungi isolated from Panax notoginseng is rare. In this study, an endophytic fungus known as SQGX-6, which was later identified as the golden hair fungus Arcopilus aureus, was isolated from Panax notoginseng. SQGX-6 was extracted using ethyl acetate, and the active components of the fungus were identified using ultra-performance liquid chromatography-mass spectrometry (UHPLC-MS). The antifungal and antioxidant activities of the extract were determined and evaluated in vitro and in vivo. SQGX-6 and its extract inhibited the growth of Corn stalk rot (Fusarium graminearum), Corn southern leaf blight (Helminthosporium maydis), and Tomato gray mold (Botrytis cinerea) in vitro. The free radical scavenging rates for 2,2-Diphenyl-1-pyridinyl hydrazide (DPPH) radical scavenging activity, 3-Ethylbenzothiazoline-6-Sulfonic Acid Radical scavenging (ABTS) activity were also downregulated by the SQGX-6 extract. In vivo, the SQGX-6 extract inhibited the mycelial growth rates of the three aforementioned fungi and downregulated malondialdehyde (MDA) content and upregulated peroxidase (POD) and phenylalanine ammonia-lyase (PAL) content in fruits, leading to significant reduction in damage to cherry tomatoes caused by Botrytis cinerea. UHPLC-MS was performed to identify various active substances, including Alkaloids, Azoles, Benzofurans, Coumarins, Flavonoids, Organic acids, Phenols, and plant growth regulators contained in the extract. These results suggested that the endophytic fungus SQGX-6 of Panax notoginseng and its extract have excellent antifungal and antioxidant activities, and thus, it is an important microbial resource for the developing novel drugs against plant fungal infections.

Efficacy of rhizobacteria Paenibacillus polymyxa SY42 for the biological control of Atractylodes chinensis root rot

Atractylodes chinensis is one of the most commonly used bulk herbs in East Asia; however, root rot can seriously affect its quality and yields. In contrast to chemical pesticides, biological control strategies are environmentally compatible and safe. For this study, 68 antagonistic bacterial strains were isolated from the rhizospheres of healthy Atractylodes chinensis. Strain SY42 exhibited the most potent fungicidal activities, with inhibition rates against F. oxysporum, F. solani, and F. redolens of 67.07 %, 63.40 % and 68.45 %, respectively. Through morphological observation and molecular characterization, strain SY42 was identified as Paenibacillus polymyxa. The volatile organic components (VOCs) produced by SY42 effectively inhibited the mycelial growth of pathogenic fungi through diffusion. SY42 significantly inhibited the germination of pathogenic fungal spores. Following co-culturing with SY42, the mycelium of the pathogenic fungus was deformed, folded, and even ruptured. SY42 could produce cellulases and proteases to degrade fungal cell walls. Pot experiments demonstrated the excellent biocontrol efficacy of SY42. This study revealed that P. polymyxa SY42 inhibited pathogenic fungi through multiple mechanisms, which verified its utility as a biocontrol agent for the control of A. chinensis root rot.

Molecular Identification of Juglans Regia Endophyte LTL-G3, Its Antifungal Potential and Bioactive Substances

Background

Endophyte is one of the potential biocontrol agents for inhibiting plant pathogens. However, the mechanisms and characteristics involved in the inhibition of different phytopathogenic fungi by endophytes, especially walnut endophytes, are still largely unknown.

Objectives

The present study aimed to identify the walnut endophytic fungus LTL-G3 from a genetic point of view, assess the strain's antifungal activity, and determine the bioactivities of the substances it produces against plant pathogens.

Materials and Methods

The homologous sequence of strain LTL-G3 was examined, and typical strains of the Trichoderma virens group were used to build NJ phylogenetic trees and analyze the taxonomic position of the strain. The biocontrol agent's antagonistic potential for many plant pathogenic fungi. By using silica gel G chromatography, the active components of the strain were separated and purified. The active components were identified using GC-MS and NMR.

Results

The strain LTL-G3 was identified as Trichoderma virens. Its fermentation and secondary metabolite extracts had a broad spectrum and strong inhibitory effect on the spread of six plant pathogens (Botrytis cinerea, Fusarium graminearum, Gloeosporium fructigenum, Phytophthora capsici, Rhizoctonia solani, and Valsa mali) evaluated, of which, its inhibition rate against Valsa mali reached 76.6% (fermentation extract) and 100% (ethyl acetate and n-butanol extracts). On silica gel G chromatography, bioactive compounds were divided into 6 fractions and 7 sub-fractions. Fr.2-2 was the sub-fraction that showed the greatest inhibitory against V. mali, as an inhibition percentage of 89.36% in 1 mg. mL-1. Fifteen key inhibitory chemicals identified using GC-MS. By examining the NMR data, the chemical make-up of the precipitated white solid was identified. The inhibition rate against V. mali increased by over 95% at a dosage of 1 mg. mL-1, indicating a significant linear association between compound A and that rate.

Conclusions

The strain LTL-G3 can be applied as an efficient biological control agent against V. mali, and its highly inhibitive secondary metabolites provide the mechanism for this action.

Biocontrol Potential of Beneficial Fungus Aureobasidium pullulans Against Botrytis cinerea and Colletotrichum acutatum

Biological control is a promising approach to reduce plant diseases caused by fungal pathogens and ensure high productivity in horticultural production. In the present study, we evaluated the biocontrol potential and underlying mechanisms of the beneficial fungus Aureobasidium pullulans against Botrytis cinerea and Colletotrichum acutatum, casual agents of gray mold and anthracnose diseases in strawberry. Notably, this is the first time that A. pullulans has been tested against C. acutatum in strawberry. A. pullulans strains (AP-30044, AP-30273, AP-53383, and AP-SLU6) showed significant variation in terms of growth and conidia production. An inverse relationship was found between the growth and conidiation rate, suggesting a trade-off between resource allocation for growth and conidial production. Dual plate co-culturing assays showed that mycelial growth of B. cinerea and C. acutatum was reduced by up to 35 and 18%, respectively, when challenged with A. pullulans compared with control treatments. Likewise, culture filtrates of A. pullulans showed varying levels of antifungal activity against B. cinerea and C. acutatum, reducing the mycelial biomass by up to 90 and 72%, respectively. Furthermore, milk powder plate assays showed that A. pullulans produced substantial amounts of extracellular proteases, which are known to degrade fungal cuticle. Ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS) analyses revealed that A. pullulans produced exophilins, liamocins, and free fatty acids known to have antifungal properties. A. pullulans shows high potential for successful biological control of strawberry diseases and discuss opportunities for further optimization of this beneficial fungus.

Identification and localization of morphological feature-specific metabolites in Reynoutria multiflora roots

Reynoutria multiflora roots are a classical herbal medicine with unique nourishing therapeutic effects. Anomalous vascular bundle (AVB) forming "cloudy brocade patterns" is a typical morphological feature of R. multiflora roots and has been empirically linked to its quality classification. However, scientific evidence, especially for AVB-specific specialised metabolites, has not been comprehensively revealed thus far. Herein, desorption electrospray ionization-mass spectrometry imaging (DESI-MSI) analysis was applied to carry out an in situ analysis of specialised metabolites distributed specifically at the AVB and cork of R. multiflora roots. To enlarge the scope of compounds by DESI detection, various solvent systems including acetone, acetonitrile, methanol, and water were used to assist in the discoveries of 40 specialised metabolites with determined localization. A series of bioactive constituents including stilbenes, flavonoids, anthraquinones, alkaloids, and naphthalenes were found specifically around the brocade patterns. Notably, phospholipids were detected from R. multiflora roots by in situ analysis for the first time and were found mainly in the phloem of AVB (PAB). This is the first study to use gradient solvent systems in DESI-MSI analysis to locate the specialised metabolites distribution. The discovery of feature-specific compounds will bridge the empirical identification to precision quality control of R. multiflora roots.

Screening of endophytic bacteria from potato tubers and their antagonistic activity against soil-borne potato pathogens

In order to appraise the bacterial endophyte communities that help resist disease in potato tuber, the separation, the population density, biodiversity and the antagonistic activity of endophytic bacteria, from the tuber peel of potato cultivars (Fontan90, Agria, Sante’a and Jeli89), were examined in the Fars province in Iran. In this study, the bacterial endophyte Colony Forming Units (CFU) were counted based on the most suitable dilution in petri dishes and expressed per g of wet weight of tuber tissue. The presence of bacteria was found mostly in the outer layer. A wide variety of endophyte species biodiversity was in Agria cultivar. To estimate the antagonistic effect of potato associated endophytic bacteria, 115 bacterial isolates were evaluated by dual culture method against main soil-borne potato pathogens Fusarium oxysporum, Rhizoctonia solani, Verticillium dahliae, Streptomyces scabies and Ralstonia solanacearum. Endophyte strains were identified based on physiological, morphological and chemical characteristics and the 16S rRNA gene sequence analysis. The highest degree of the inhibitory activity in all layers of potato cultivars was related to Bacillus subtilis, Bacillus mojavensis and Klebsiella variicola. Antagonistic activity of endophytic bacteria against the pathogens was significantly higher (p<0.01) in the examined strains from the outermost layer of tuber peel and decreased progressively toward the center of the tuber. In this research, Klebsiella variicola was reported as endophyte bacteria in the four commercial potatocultivars mentioned above, for the first time.

Biocontrol of strawberry gray mold caused by Botrytis cinerea with the termite associated Streptomyces sp. sdu1201 and actinomycin D

Strawberry gray mold caused by Botrytis cinerea is one of the most severe diseases in pre- and post-harvest periods. Although fungicides have been an effective way to control this disease, they can cause serious “3R” problems (Resistance, Resurgence and Residue). In this study, Streptomyces sp. sdu1201 isolated from the hindgut of the fungus-growing termite Odontotermes formosanus revealed significant antifungal activity against B. cinerea. Four compounds (1–4) were isolated from Streptomyces sp. sdu1201 and further identified as actinomycins by the HRMS and 1D NMR data. Among them, actinomycin D had the strongest inhibitory activity against B. cinerea with the EC₅₀ value of 7.65 μg mL⁻¹. The control effect of actinomycin D on strawberry gray mold was also tested on fruits and leaves in vitro, and its control efficiency on leaves was 78.77% at 3 d. Moreover, actinomycin D can also inhibit the polarized growth of germ tubes of B. cinerea. Therefore, Streptomyces sp. sdu1201 and actinomycin D have great potential to gray mold as biocontrol agents.

Novel Approaches for Sustainable Horticultural Crop Production: Advances and Prospects

Reduction of plant growth, yield and quality due to diverse environmental constrains along with climate change significantly limit the sustainable production of horticultural crops. In this review, we highlight the prospective impacts that are positive challenges for the application of beneficial microbial endophytes, nanomaterials (NMs), exogenous phytohormones strigolactones (SLs) and new breeding techniques (CRISPR), as well as controlled environment horticulture (CEH) using artificial light in sustainable production of horticultural crops. The benefits of such applications are often evaluated by measuring their impact on the metabolic, morphological and biochemical parameters of a variety of cultures, which typically results in higher yields with efficient use of resources when applied in greenhouse or field conditions. Endophytic microbes that promote plant growth play a key role in the adapting of plants to habitat, thereby improving their yield and prolonging their protection from biotic and abiotic stresses. Focusing on quality control, we considered the effects of the applications of microbial endophytes, a novel class of phytohormones SLs, as well as NMs and CEH using artificial light on horticultural commodities. In addition, the genomic editing of plants using CRISPR, including its role in modulating gene expression/transcription factors in improving crop production and tolerance, was also reviewed.

Contrasting genome patterns of two pseudomonas strains isolated from the date palm rhizosphere to assess survival in a hot arid environment

The plant growth-promoting rhizobacteria (PGPRs) improve plant growth and fitness by multiple direct (nitrogen fixation and phosphate solubilization) and indirect (inducing systematic resistance against phytopathogens, soil nutrient stabilization, and maintenance) mechanisms. Nevertheless, the mechanisms by which PGPRs promote plant growth in hot and arid environments remain poorly recorded. In this study, a comparative genome analysis of two phosphate solubilizing bacteria, Pseudomonas atacamensis SM1 and Pseudomonas toyotomiensis SM2, isolated from the rhizosphere of date palm was performed. The abundance of genes conferring stress tolerance (chaperones, heat shock genes, and chemotaxis) and supporting plant growth (plant growth hormone, root colonization, nitrogen fixation, and phosphate solubilization) were compared among the two isolates. This study further evaluated their functions, metabolic pathways, and evolutionary relationship. Results show that both bacterial strains have gene clusters required for plant growth promotion (phosphate solubilization and root colonization), but it is more abundant in P. atacamensis SM1 than in P. toyotomiensis SM2. Genes involved in stress tolerance (mcp, rbs, wsp, and mot), heat shock, and chaperones (hslJ and hslR) were also more common in P. atacamensis SM1. These findings suggest that P. atacamensis SM1could have better adaptability to the hot and arid environment owing to a higher abundance of chaperone genes and heat shock proteins. It may promote plant growth owing to a higher load of root colonization and phosphate solubilization genes and warrants further in vitro study.

Antifungal volatile organic compounds from Streptomyces setonii WY228 control black spot disease of sweet potato

Volatile organic compounds (VOCs) produced by microorganisms are considered as promising environmental-safety fumigants for controlling postharvest diseases. Ceratocystis fimbriata, the pathogen of black spot disease, seriously affects the quality and yield of sweet potato in the field and postharvest. This study tested the effects of VOCs produced by Streptomyces setonii WY228 on the control of C. fimbriata in vitro and in vivo. The VOCs exhibited strong antifungal activity and significantly inhibited the growth of C. fimbriata. During the 20-days storage, VOCs fumigation significantly controlled the occurrence of pathogen, increased the content of antioxidant and defense-related enzymes and flavonoids, and boosted the starch content so as to maintain the quality of sweet potato. Headspace analysis showed that volatiles 2-ethyl-5-methylpyrazine and dimethyl disulfide significantly inhibited the mycelial growth and spore germination of C. fimbriata in a dose dependent manner. Fumigation with 100 μL/L 2-ethyl-5-methylpyrazine completely controlled the pathogen in vivo after 10-days storage. Transcriptome analysis showed that volatiles mainly downregulated the ribosomal synthesis genes and activated the proteasome system of pathogen in response to VOCs stress, while the genes related to spore development, cell membrane synthesis, mitochondrial function, as well as hydrolase and toxin synthesis were also downregulated, indicating that WY228-produced VOCs act diverse modes of action for pathogen control. Our study demonstrates that fumigation of sweet potato tuberous roots with S. setonii WY228 or use of formulations based on the VOCs is a promising new strategy to control sweet potato and other food and fruit pathogens during storage and shipment. Importance Black spot disease caused by Ceratocystis fimbriata has caused huge economic losses to worldwide sweet potato production. At present, the control of C. fimbriata mainly depends on toxic fungicides, and there is a lack of effective alternative strategies. The research on biological control of sweet potato black spot disease is also very limited. The development of efficient biocontrol technique against pathogens using microbial volatile organic compounds could be an alternative method to control this disease. Our study revealed the significant biological control effect of volatile organic compounds of Streptomyces setonii WY228 on black spot disease of postharvest sweet potato and the complex antifungal mechanism against C. fimbriata. Our data demonstrated that Streptomyces setonii WY228 and its volatile 2-ethyl-5-methylpyrazine could be candidate strain and compound for the creation of fumigants, and showed the important potential of biotechnology application in the field of food and agriculture.

Mechanisms of Action of Microbial Biocontrol Agents against Botrytis cinerea

Botrytis cinerea is a phytopathogenic fungus responsible for economic losses from USD 10 to 100 billion worldwide. It affects more than 1400 plant species, thus becoming one of the main threats to the agriculture systems. The application of fungicides has for years been an efficient way to control this disease. However, fungicides have negative environmental consequences that have changed popular opinion and clarified the need for more sustainable solutions. Biopesticides are products formulated based on microorganisms (bacteria or fungi) with antifungal activity through various mechanisms. This review gathers the most important mechanisms of antifungal activities and the microorganisms that possess them. Among the different modes of action, there are included the production of diffusible molecules, both antimicrobial molecules and siderophores; production of volatile organic compounds; production of hydrolytic enzymes; and other mechanisms, such as the competition and induction of systemic resistance, triggering an interaction at different levels and inhibition based on complex systems for the production of molecules and regulation of crop biology. Such a variety of mechanisms results in a powerful weapon against B. cinerea; some of them have been tested and are already used in the agricultural production with satisfactory results.