Aureobasidium pullulans volatile organic compounds as alternative postharvest method to control brown rot of stone fruits

Diversity of spoilage microorganisms associated with fresh fruits and vegetables in French households

Food loss and waste generated throughout the food chain are major concerns in today's society. A high level of food waste occurs at the household's level and fresh fruit and vegetable (FFV) spoilage caused by microbial growth accounts for a large part of these losses. While numerous studies focused on spoilage microorganism diversity from primary production to distribution, little is known about those involved at the household level. In this context, this study aimed at investigating which FFV are usually wasted depending on the season and storage conditions at households, and identifying the microorganisms associated with spoiled FFV. During two periods (summer and autumn), 346 spoiled FFV samples were collected using a citizen science approach in 49 households in the Brest area (Finistère, Brittany, France). About three quarters of spoiled FFV collected originated from room temperature storage and 75 % were collected during summer. Among the studied samples, 75 % showed microbial growth after plating onto agar-based medium, and therefore, were likely spoiled because of microbial spoilage. Overall, 183 molds, 31 yeasts and 96 bacteria were isolated and identified using MALDI-TOF MS and sequencing. Among the 42 different mold species identified, Penicillium spp. were the most common representing more than 50 % of mold isolates followed by Botrytis (12.4 %), Mucor (8.6 %) and Cladosporium (7.6 %) spp. Hanseniaspora uvarum and Aureobasidium pullulans were the most prevalent yeast species while bacterial isolates showed the highest diversity of all identified organisms (49 species) with Pseudomonas spp., enterobacteria and lactic acid bacteria representing the most frequently isolated taxa. This study shows for the first time the microbial diversity associated with spoiled FFV of which a large proportion were stored at room temperature, suggesting that a better usage of FFV refrigeration could help reduce FFV waste in households.

Biocontrol Ability of Strain Bacillus amyloliquefaciens SQ-2 against Table Grape Rot Caused by Aspergillus tubingensis

Bacillus amyloliquefaciens strain SQ-2, isolated from a cured product, has been demonstrated to exhibit a highly efficacious performance against phytopathogens, including Stemphylium solani, Fusarium moniliforme, Fusarium graminearum, and Aspergillus tubingensis. In particular, with regard to A. tubingensis, which causes summer bunch rot, SQ-2 has been observed to suppress the mycelial growth of all tested grape cultivars by over 40%. Especially on Kyoho grapes, it has the highest inhibition rate of 53%. Scanning electron microscopy (SEM) confirms that SQ-2 is an effective agent for suppressing the mycelia proliferation, differentiation, and spore formation of A. tubingensis. Furthermore, an LC/MS analysis revealed that SQ-2 produces two principal lipopeptides, namely, bacillibactin and surfactin, in addition to a polyketide, bacillaene. Further analysis through gas chromatography-mass spectrometry (GC/MS) identified 41 distinct volatile organic compounds secreted by SQ-2. Transcriptomic analysis indicated that exposure to the metabolite of SQ-2 induced substantial gene expression alterations in A. tubingensis. These data suggest that B. amyloliquefaciens strain SQ-2 exhibits promising crop protection potential of inhibiting plant pathogens through the secretion of bacillibactin, surfactin, bacillaene, and VOCs.

Chemical transformation of the multibudding yeast, Aureobasidium pullulans

Aureobasidium pullulans is a ubiquitous polymorphic black yeast with industrial and agricultural applications. It has recently gained attention amongst cell biologists for its unconventional mode of proliferation in which multinucleate yeast cells make multiple buds within a single cell cycle. Here, we combine a chemical transformation method with genome-targeted homologous recombination to yield ∼60 transformants/μg of DNA in just 3 days. This protocol is simple, inexpensive, and requires no specialized equipment. We also describe vectors with codon-optimized green and red fluorescent proteins for A. pullulans and use these tools to explore novel cell biology. Quantitative imaging of a strain expressing cytosolic and nuclear markers showed that although the nuclear number varies considerably among cells of similar volume, total nuclear volume scales with cell volume over an impressive 70-fold size range. The protocols and tools described here expand the toolkit for A. pullulans biologists and will help researchers address the many other puzzles posed by this polyextremotolerant and morphologically plastic organism.

Pseudomonas protegens volatile organic compounds inhibited brown rot of postharvest peach fruit by repressing the pathogenesis-related genes in Monilinia fructicola

Brown rot, caused by Monilinia fructicola, is considered one of the devasting diseases of pre-harvest and post-harvest peach fruits, restricting the yield and quality of peach fruits and causing great economic losses to the peach industry every year. Presently, the management of the disease relies heavily on chemical control. In the study, we demonstrated that the volatile organic compounds (VOCs) of endophyte bacterial Pseudomonas protegens QNF1 inhibited the mycelial growth of M. fructicola by 95.35% compared to the control, thereby reducing the brown rot on postharvest fruits by 98.76%. Additionally, QNF1 VOCs severely damaged the mycelia of M. fructicola. RNA-seq analysis revealed that QNF1 VOCs significantly repressed the expressions of most of the genes related to pathogenesis (GO:0009405) and integral component of plasma membrane (GO:0005887), and further analysis revealed that QNF1 VOCs significantly altered the expressions of the genes involved in various metabolism pathways including Amino acid metabolism, Carbohydrate metabolism, and Lipid metabolism. The findings of the study indicated that QNF1 VOCs displayed substantial control efficacy by disrupting the mycelial morphology of M. fructicola, weakening its pathogenesis, and causing its metabolic disorders. The study provided a potential way and theoretical support for the management of the brown rot of peach fruits.

Yeasts volatile organic compounds (VOCs) as potential growth enhancers and molds biocontrol agents of mushrooms mycelia

Volatile organic compounds (VOCs) produced by yeasts can positively affect crops, acting as antifungals or biostimulants. In this study, Aureobasidium pullulans and Metschnikowia pulcherrima were evaluated as potential antagonists of Trichoderma spp., common fungal pathogen in mushroom cultivation. To assess the biocontrol ability and biostimulant properties of the selected yeast species, in vitro co-culture and VOCs exposure assays were conducted. In both assays, VOCs produced by Aureobasidium spp. showed the stronger antifungal activity with a growth inhibition up to 30 %. This result was further confirmed by the higher volatilome alcohol content revealed by solid phase microextraction-gas chromatography mass spectrometry (SPME/GC-MS). Overall, Aureobasidium strains can be potentially used as biocontrol agent in Pleorotus ostreatus and Cyclocybe cylindracea mycelial growth, without affecting their development as demonstrated by VOCs exposure assay and Fourier-transform infrared spectroscopy (FT-IR). Conversely, M. pulcherrima was characterized by a lower or absent antifungal properties and by a volatilome composition rich in isobutyl acetate, an ester often recognized as plant growth promoter. As confirmed by FT-IR, Lentinula mycelia exposed to M. pulcherrima VOCs showed a higher content of proteins and lipids, suggesting an improvement of some biochemical properties. Our study emphasizes that VOCs produced by specific yeast strains are potentially powerful alternative to synthetic fungicide in the vegetative growth of mushroom-forming fungi and also able to modify their biochemical composition.

Screening of core microorganisms in healthy and diseased peaches and effect evaluation of biocontrol bacteria (Burkholderia sp.)

Biological antagonists serve as the most important green alternatives to chemical fungicides, a class of microorganism that inhibits the growth of pathogenic fungi to reduce fruit incidence. In this paper, healthy and diseased peach fruit was selected for amplicon sequencing of the epiphytic microbiota on their surface to obtain a comprehensive understanding. Community structure, diversity and LefSe analysis were performed to screen Acetobacter, Muribaculaceae and Burkholderia as the core bacteria, Mycosphaerella, Penicillium and Alternaria as the core fungi, they showed significant differences and were highly enriched. Two strains fungi (Penicillium K3 and N1) and one strain antagonistic bacteria (Burkholderia J2) were isolated. The in intro test results indicated the bacterial suspension, fermentation broth and volatile organic compounds of antagonistic bacteria J2 were able to significantly inhibit pathogen growth. In vivo experiments, peach was stored at 28 °C for 6 days after different treatments, and samples were taken every day. It was found that Burkholderia J2 enhanced peach resistance by increasing the activities of antioxidant-related enzymes such as SOD, POD, PAL, PPO, GR, MDHAR, and DHAR. The results improved that Burkholderia J2 has great biocontrol potential and could be used as a candidate strain for green control of blue mold.

Efficacy of Essential Oil Vapours in Reducing Postharvest Rots and Effect on the Fruit Mycobiome of Nectarines

Nectarines can be affected by many diseases, resulting in significant production losses. Natural products, such as essential oils (EOs), are promising alternatives to pesticides to control storage rots. This work aimed to test the efficacy of biofumigation with EOs in the control of nectarine postharvest diseases while also evaluating the effect on the quality parameters (firmness, total soluble solids, and titratable acidity) and on the fruit fungal microbiome. Basil, fennel, lemon, oregano, and thyme EOs were first tested in vitro at 0.1, 0.5, and 1.0% concentrations to evaluate their inhibition activity against Monilinia fructicola. Subsequently, an in vivo screening trial was performed by treating nectarines inoculated with M. fructicola, with the five EOs at 2.0% concentration by biofumigation, performed using slow-release diffusers placed inside the storage cabinets. Fennel, lemon, and basil EOs were the most effective after storage and were selected to be tested in efficacy trials using naturally infected nectarines. After 28 days of storage, all treatments showed a significant rot reduction compared to the untreated control. Additionally, no evident phytotoxic effects were observed on the treated fruits. EO vapors did not affect the overall quality of the fruits but showed a positive effect in reducing firmness loss. Metabarcoding analysis showed a significant impact of tissue, treatment, and sampling time on the fruit microbiome composition. Treatments were able to reduce the abundance of Monilinia spp., but basil EO favored a significant increase in Penicillium spp. Moreover, the abundance of other fungal genera was found to be modified.

Pseudomonas synxantha volatile organic compounds: efficacy against Cadophora luteo-olivacea and Botrytis cinerea of kiwifruit

Volatile organic compounds (VOCs) are responsible for the antagonistic activity exerted by different biological control agents (BCAs). In this study, VOCs produced by Pseudomonas synxantha strain 117-2b were tested against two kiwifruit fungal postharvest pathogens: Cadophora luteo-olivacea and Botrytis cinerea, through in vitro and in vivo assays. In vitro results demonstrated that P. synxantha 117-2b VOCs inhibit mycelial growth of C. luteo-olivacea and B. cinerea by 56% and 42.8% after 14 and 5 days of exposition, respectively. In vivo assay demonstrated significant inhibitory effects. VOCs used as a biofumigant treatment reduced skin-pitting symptoms disease severity by 28.5% and gray mold incidence by 66.6%, with respect to the untreated control. BCA volatiles were analyzed by solid-phase microextraction coupled with gas chromatography-mass spectrometry (SPME-GC/MS), and among the detected compounds, 1-butanol, 3-methyl and 1-nonene resulted as the most produced. Their efficacy as pure synthetic compounds was assayed against mycelial growth of fungal pathogens by different concentrations (0.34, 0.56, and 1.12 µL mL-1 headspace). The effect of the application of VOCs as a biofumigant was also investigated as the expression level of seven defense-related genes of kiwifruit at different exposition times. The results indicated an enhancement of the expression of almost all the genes starting from 3 h of treatment. These results described P. synxantha VOCs characteristics and their potential as a promising method to adopt for protecting kiwifruit from postharvest diseases caused by C. luteo-olivacea and B. cinerea.

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.

6-Pentyl-2H-pyran-2-one from Trichoderma erinaceum Is Fungicidal against Litchi Downy Blight Pathogen Peronophythora litchii and Preservation of Litchi

The postharvest losses of litchi caused by litchi downy blight are considerably high. We identified a natural antifungal volatile pyrone, 6-pentyl-2H-pyran-2-one (6PP), synthesized by Trichoderma erinaceum LS019-2 and investigated as biocontrol for litchi downy blight and preservation. 6PP significantly inhibited the growth and sporangial germination of Peronophythora litchii, the causal agent of litchi downy blight, and caused severe cellular and intracellular destructions, as evidenced by electron microscopic analysis. Furthermore, in the treatment, the fruit kept better color, higher weight, and antioxidant activity, so it can maintain freshness and prolong shelf life. Metabolome analysis confirmed the decline of lipids and the accumulation of organic acids in litchi fruits in response to 6PP treatment. These effects from 6PP could alleviate disease effects and prolong the shelf life of litchi fruits. These findings suggested that 6PP could be a useful natural product to control downy blight disease and a new preservative of litchi fruits.

Diversity of Culture Microorganisms from Portuguese Sweet Cherries

Consumers today seek safe functional foods with proven health-promoting properties. Current evidence shows that a healthy diet can effectively alleviate oxidative stress levels and reduce inflammatory markers, thereby preventing the occurrence of many types of cancer, hypertension, and cardiovascular and neurological pathologies. Nevertheless, as fruits and vegetables are mainly consumed fresh, they can serve as vectors for the transmission of pathogenic microorganisms associated with various disease outbreaks. As a result, there has been a surge in interest in the microbiome of fruits and vegetables. Therefore, given the growing interest in sweet cherries, and since their microbial communities have been largely ignored, the primary purpose of this study is to investigate their culturome at various maturity stages for the first time. A total of 55 microorganisms were isolated from sweet cherry fruit, comprising 23 bacteria and 32 fungi species. Subsequently, the selected isolates were molecularly identified by amplifying the 16S rRNA gene and ITS region. Furthermore, it was observed that the communities became more diverse as the fruit matured. The most abundant taxa included Pseudomonas and Ralstonia among the bacteria, and Metschnikowia, Aureobasidium, and Hanseniaspora among the fungi.

Volatile Organic Compounds of Scheffersomyces spartinae W9 Have Antifungal Effect against Botrytis cinerea on Strawberry Fruit

This study aims to evaluate the antifungal effects of volatile organic compounds (VOCs) produced by a marine biocontrol yeast, Scheffersomyces spartinae W9. The results showed that the VOCs from the yeast inhibited the growth of Botrytis cinerea mycelium and spore germination by 77.8% and 58.3%, respectively. Additionally, it reduced the disease incidence and lesion diameter of gray mold on the strawberry fruit surface by 20.7% and 67.4%, respectively. Electronic micrographs showed that VOCs caused damage to the morphology and ultrastructure of the hyphae. Based on headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME/GC-MS), S. spartinae W9 emitted 18 main VOCs, and the pure substance of VOCs, such as 3-methyl-1-butanol, 2-methyl-1-butanol, 2-phenylethanol, and isoamyl acetate, showed antifungal effects against B. cinerea mycelium growth. Among them, 2-phenylethanol exhibited the strongest antifungal activity. It has been concluded that VOCs are the key antifungal mechanism of S. spartinae W9, and a promising strategy for controlling gray mold on strawberry fruit.

Effects of temporal and spatial scales on soil yeast communities in the peach orchard

Shihezi Reclamation Area is located at the southern edge of the Junggar Basin, with natural, soil, and climatic conditions unique to the production of peaches. In turn, peach orchards have accumulated rich microbial resources. As an important taxon of soil fungi, the diversity and community structure changes of yeast in the soil of peach orchards on spatial and temporal scales are still unknown. Here, we aimed to investigate the changes in yeast diversity and community structure in non-rhizosphere and rhizosphere soils of peach trees of different ages in the peach orchard and the factors affecting them, as well as the changes in the yeast co-occurrence network in the peach orchard at spatial and temporal scales. High-through put sequencing results showed that a total of 114 yeast genera were detected in all soil samples, belonging to Ascomycota (60 genera) and Basidiomycota (54 genera). The most dominant genus, Cryptococcus, was present in greater than 10% abundance in each sample. Overall, the differences in yeast diversity between non-rhizosphere and rhizosphere soil of peach trees at 3, 8 and 15 years were not significant. Principal coordinate analysis (PCoA) showed that differences in yeast community structure were more pronounced at the temporal scale compared to the spatial scale. The results of soil physical and chemical analysis showed that the 15-year-old peach rhizosphere soil had the lowest pH, while the OM, TN, and TP contents increased significantly. Redundancy analysis showed that soil pH and CO were key factors contributing to changes in soil yeast community structure in the peach orchard at both spatial and temporal scales. The results of co-occurrence network analysis showed that the peach orchard soil yeast network showed synergistic effects as a whole, and the degree of interactions and connection tightness of the 15-year-old peach orchard soil yeast network were significantly higher than the 3- and 8-year-old ones on the time scale. The results reveal the distribution pattern and mechanism of action of yeast communities in peach orchard soils, which can help to develop effective soil management strategies and improve the stability of soil microecology, thus promoting crop growth.

Biocontrol Potential of Antagonistic Yeasts on In Vitro and In Vivo Aspergillus Growth and Its AFB1 Production

Aspergillus flavus is a major aflatoxin B₁, posing significant health concerns to humans, crops, and producer fungi. Due to the undesirable consequences of the usage of synthetic fungicides, biological control using yeasts has gained more attention. In this study, eight isolates of epiphytic yeasts belonging to Moesziomyces sp., Meyerozyma sp. and Metschnikowia sp., which have been identified as antagonists, were isolated from different plants, including grapes, blueberries, hawthorns, hoşkıran, beans and grape leaf. While volatile organic compounds (VOCs) produced by Moesziomyces bullatus DN-FY, Metschnikowia aff. pulcherrima DN-MP and Metschnikowia aff. pulcherrima 32-AMM reduced in vitro A. flavus mycelial growth and sporulation, only VOCs produced by Metschnikowia aff. fructicola 1-UDM were found to be effective at reducing in vitro AFB₁ production. All yeasts reduced the mycelial growth of A. flavus by 76-91%, while AFB₁ production reduced to 1.26-10.15 ng/g and the control plates' growth was 1773 ng/g. The most effective yeast, Metschnikowia aff. Pulcherrima DN-HS, reduced Aspergillus flavus growth and aflatoxin B₁ production on hazelnuts. The AFB₁ content on hazelnuts reduced to 333.01 ng/g from 536.74 ng/g. To our knowledge, this is the first report of yeasts isolated from plants being tested as potential biological control agents to reduce AFB₁ production on hazelnuts.

The power of the smallest: The inhibitory activity of microbial volatile organic compounds against phytopathogens

Plant diseases caused by phytopathogens result in huge economic losses in agriculture. In addition, the use of chemical products to control such diseases causes many problems to the environment and to human health. However, some bacteria and fungi have a mutualistic relationship with plants in nature, mainly exchanging nutrients and protection. Thus, exploring those beneficial microorganisms has been an interesting and promising alternative for mitigating the use of agrochemicals and, consequently, achieving a more sustainable agriculture. Microorganisms are able to produce and excrete several metabolites, but volatile organic compounds (VOCs) have huge biotechnology potential. Microbial VOCs are small molecules from different chemical classes, such as alkenes, alcohols, ketones, organic acids, terpenes, benzenoids and pyrazines. Interestingly, volatilomes are species-specific and also change according to microbial growth conditions. The interaction of VOCs with other organisms, such as plants, insects, and other bacteria and fungi, can cause a wide range of effects. In this review, we show that a large variety of plant pathogens are inhibited by microbial VOCs with a focus on the in vitro and in vivo inhibition of phytopathogens of greater scientific and economic importance in agriculture, such as Ralstonia solanacearum, Botrytis cinerea, Xanthomonas and Fusarium species. In this scenario, some genera of VOC-producing microorganisms stand out as antagonists, including Bacillus, Pseudomonas, Serratia and Streptomyces. We also highlight the known molecular and physiological mechanisms by which VOCs inhibit the growth of phytopathogens. Microbial VOCs can provoke many changes in these microorganisms, such as vacuolization, fungal hyphal rupture, loss of intracellular components, regulation of metabolism and pathogenicity genes, plus the expression of proteins important in the host response. Furthermore, we demonstrate that there are aspects to investigate by discussing questions that are still not very clear in this research area, especially those that are essential for the future use of such beneficial microorganisms as biocontrol products in field crops. Therefore, we bring to light the great biotechnological potential of VOCs to help make agriculture more sustainable.

Microbial Volatile Organic Compounds: An Alternative for Chemical Fertilizers in Sustainable Agriculture Development

Microorganisms are exceptional at producing several volatile substances called microbial volatile organic compounds (mVOCs). The mVOCs allow the microorganism to communicate with other organisms via both inter and intracellular signaling pathways. Recent investigation has revealed that mVOCs are chemically very diverse and play vital roles in plant interactions and microbial communication. The mVOCs can also modify the plant's physiological and hormonal pathways to augment plant growth and production. Moreover, mVOCs have been affirmed for effective alleviation of stresses, and also act as an elicitor of plant immunity. Thus, mVOCs act as an effective alternative to various chemical fertilizers and pesticides. The present review summarizes the recent findings about mVOCs and their roles in inter and intra-kingdoms interactions. Prospects for improving soil fertility, food safety, and security are affirmed for mVOCs application for sustainable agriculture.

Antifungal activity of the volatile organic compounds produced by Ceratocystis fimbriata strains WSJK-1 and Mby

Microorganism-produced volatile organic compounds (VOCs) are considered promising environmental-safety fumigants in food preservation. In this study, the VOCs from fungal Ceratocystis fimbriata strains (WSJK-1, Mby) were tested against postharvest fungi Monilinia laxa, Fusarium oxysporum, Monilinia fructicola, Botrytis cinerea, Alternaria solani, and Aspergillus flavus in vitro. The mycelial growth was significantly inhibited, in particular M. fructicola and B. cinerea (76.95, 76.00%), respectively. VOCs were identified by headspace solid-phase microextraction coupled with Gas Chromatography-Mass Spectrometry (HS-SPME-GC-MS); 40 compounds were identified. The antifungal activity of 21 compounds was tested by the minimum inhibitory concentrations (MIC) value. Benzaldehyde, 2-Phenylethanol, and 1-Octen-3-ol showed strong antifungal activity with the MIC in vitro ranging from 0.094 to 0.284 ml L-1 depending on the pathogen tested. The optical microscope showed serious morphological damage, including cell deformation, curling, collapse, and deficiency in mycelial or conidia cell structures treated with C. fimbriata VOCs and pure compounds. In vivo tests, C. fimbriata VOCs decreased brown rot severity in peaches, and compounds Benzaldehyde and 2-Phenylethanol could reduce peach brown rot in peaches at 60 μl L-1. The VOCs produced by C. fimbriata strain have good antifungal effects; low concentration fumigation could control peach brown rot. Its fragrance is fresh, safe, and harmless, and it is possible to replace chemical fumigants. It could be used as a potential biofumigant to control fruit postharvest transportation, storage, and food preservation. To the best of our knowledge, this is the first report on the antifungal activity and biocontrol mechanism of VOCs produced by C. fimbriata.

Volatile organic compounds produced by Bacillus velezensis L1 as a potential biocontrol agent against postharvest diseases of wolfberry

Volatile organic compounds (VOCs) produced by antagonistic microorganisms have good biocontrol prospects against postharvest diseases. Infection caused by Alternaria iridiaustralis and 10 other significant fungal diseases can be successfully inhibited by VOCs produced by an identified and screened endophytic strain L1 (Bacillus velezensis). This study revealed the in vivo and in vitro biocontrol effects of VOCs released by B. velezensis L1 on A. iridiaustralis, a pathogenic fungus responsible for rot of wolfberry fruit. The inhibition rates of VOCs of B. velezensis L1 on the mycelial growth of A. iridiaustralis in vitro were 92.86 and 90.30%, respectively, when the initial inoculum concentration on the plate was 1 × 10⁹ colony forming unit (CFU)/ml. Spore germination and sporulation were 66.89 and 87.96%, respectively. VOCs considerably decreased the wolfberry’s disease index and decay incidence in vivo. Scanning electron microscopy revealed that the morphological and structural characteristics of A. iridiaustralis could be altered by VOCs. Ten VOCs were identified through headspace-gas chromatography-ion mobility spectrometry. Pure chemical tests revealed that 2.3-butanedione had the strongest antifungal effects, totally inhibiting A. iridiaustralis in wolfberry fruit at a 60 μl/L concentration. The theory underpinning the potential application of VOCs from B. velezensis is provided herein. This is also the first study to document the antifungal capabilities of the B. velezensis strain on postharvest wolfberry fruit.

GRAPHICAL ABSTRACT

Microbial volatile organic compounds: Antifungal mechanisms, applications, and challenges

The fungal decay of fresh fruits and vegetables annually generates substantial global economic losses. The utilization of conventional synthetic fungicides is damaging to the environment and human health. Recently, the biological control of post-harvest fruit and vegetable diseases via antagonistic microorganisms has become an attractive possible substitution for synthetic fungicides. Numerous studies have confirmed the potential of volatile organic compounds (VOCs) for post-harvest disease management. Moreover, VOC emission is a predominant antifungal mechanism of antagonistic microorganisms. As such, it is of great significance to discuss and explore the antifungal mechanisms of microbial VOCs for commercial application. This review summarizes the main sources of microbial VOCs in the post-harvest treatment and control of fruit and vegetable diseases. Recent advances in the elucidation of antifungal VOC mechanisms are emphasized, and the applications of VOCs produced from antagonistic microorganisms are described. Finally, the current prospects and challenges associated with microbial VOCs are considered.

Antibiotic Effects of Volatiles Produced by Bacillus tequilensis XK29 against the Black Spot Disease Caused by Ceratocystis fimbriata in Postharvest Sweet Potato

Black spot disease caused by Ceratocystis fimbriata is destructive to the production, transportation, and storage of sweet potato. The antifungal effects of Bacillus tequilensis XK29 against C. fimbriata through volatile organic compounds (VOCs) were evaluated in this study. The activated carbon assay proved that XK29 could exert antibiotic effects through volatiles. By optimizing the wheat seed weight, inoculation method, concentration, volume, and time, the antifungal activity of XK29 was significantly improved. XK29 fumigation inhibited spore formation and germination and changed the cell morphology of C. fimbriata. During the storage of sweet potato tuber roots, XK29 effectively controlled black spot disease and reduced the weight loss and malondialdehyde content. Metabolomic analysis revealed that 21 volatile compounds were released from XK29. Isovaleric acid, isobutyric acid, and 2-methylbutanoic acid effectively inhibited the growth of C. fimbriata. These results indicate that B. tequilensis XK29 has a good potential to be developed as a microbial fumigation agent.

Fungal Community Analyses of Endophytic Fungi from Two Oak Species, Quercus mongolica and Quercus serrata, in Korea

Fungal endophytes have been recorded in various plant species with a richness of diversity, and their presence plays an essential role in host plant protection against biotic and abiotic stresses. This study applied the Illumina MiSeq sequencing platform based on the amplification of fungal ribosomal ITS2 region to analyze fungal endophytic communities of two oak species (Quercus mongolica and Q. serrata) with different oak wilt disease susceptibilities in Korea. The results showed a total of 230,768 sequencing reads were obtained and clustered at a 97% similarity threshold into 709 operational taxonomic units (OTUs). The OTUs of Q. serrata were higher than that of Q. mongolica with the number of 617 OTUs and 512 OTUs, respectively. Shannon index also showed that Q. serrata had a significantly higher level of fungal diversity than Q. mongolica. Total of OTUs were assigned into 5 fungal phyla, 17 classes, 60 orders, 133 families, 195 genera, and 280 species. Ascomycota was the dominant phylum with 75.11% relative abundance, followed by Basidiomycota with 5.28%. Leptosillia, Aureobasidium and Acanthostigma were the most abundant genera detected in Q. serrata with the average relative abundance of 2.85, 2.76, and 2.19%, respectively. On the other hand, Peltaster, Cladosporium and Monochaetia were the most common genera detected in Q. mongolica with the average relative abundance of 4.83, 3.03, and 2.87%, respectively. Our results indicated that fungal endophytic communities were significantly different between two oak species and these differences could influence responses of host trees to oak wilt disease caused by Raffaelea quercus-mongolicae.

Elucidating the interaction of carbon, nitrogen, and temperature on the biosynthesis of Aureobasidium pullulans antifungal volatiles

The combined biochemical impact of carbon, nitrogen and temperature on the biosynthesis of the antifungal volatile organic compounds (VOCs): ethanol, 2-methyl-1-propanol, 3-methyl-1-butanol and 2-phenylethanol produced by Aureobasidium pullulans A1 and A3 was investigated using a Box-Behnken experimental design and response surface methodology (RSM). Normalized peak areas derived from solid phase micro extraction-gas chromatography-mass spectrometry (SPME-GC-MS) analysis, indicated that initial carbon content had a significant influence on the biosynthesis of ethanol and alcohols with greater than three carbon atoms. This result suggests a dominant activity of the A. pullulans anabolic pathway to biosynthesize three higher alcohols via de novo biosynthesis of amino acids from sugar metabolism. Low concentrations of carbon (3-13 g l^-1 ) with nitrogen as both ammonium and amino acids in the growth medium resulted in a higher number of significant linear and quadratic relationships. Nitrogen availability and growth temperature had significant negative linear and quadratic correlations with VOCs biosynthesis in most instances. Isolate-dependant metabolic response was evident for all abiotic parameters tested on alcohol production. The findings of this study offer new perspectives to improve the production of key antifungal compounds by antagonists in biological control systems.

Post-Harvest Non-Conventional and Traditional Methods to Control Cadophora luteo-olivacea: Skin Pitting Agent of Actinidia chinensis var. deliciosa (A. Chev.)

Cadophora luteo-olivacea represents a critical problem for kiwifruit in the post-harvest phase, mainly for its little note epidemiology. The study presented some results about the possibility of preserving kiwifruit from skin pitting symptoms using alternative methods to fungicides. By in vitro assays, antagonist mechanisms of action against pathogen isolates were tested. Trichoderma harzianum (Th1) showed the highest inhibitory activity against C. luteo-olivacea isolates by volatile, non-volatile, and by dual culture assay, displaying an inhibition respectively by 90%, 70.6%, and 78.8%, and with respect to Aureobasidium pullulans (L1 and L8) by 23.3% and 25.8%, 50% and 34.7%, and 22.5% and 23.6%, respectively. Further, the sensitivity on CFU and mycelial growth of C. luteo-olivacea isolates to fludioxonil, and CaCl2 was tested, displaying interesting EC50 values (0.36 and 0.92 g L−1, 22.5 g L−1, respectively). The effect of Brassica nigra defatted meal was tested as biofumigation assays and through FT-IR (Fourier-Transform Infrared) spectroscopy. The above-mentioned treatments were applied in vivo to evaluate their efficacy on kiwifruits. Our data demonstrated that alternative solutions could be considered to control postharvest pathogens such as C. luteo-olivacea.

Genome, transcriptome and secretome analyses of the antagonistic, yeast-like fungus Aureobasidium pullulans to identify potential biocontrol genes

Aureobasidium pullulans is an extremotolerant, cosmopolitan yeast-like fungus that successfully colonises vastly different ecological niches. The species is widely used in biotechnology and successfully applied as a commercial biocontrol agent against postharvest diseases and fireblight. However, the exact mechanisms that are responsible for its antagonistic activity against diverse plant pathogens are not known at the molecular level. Thus, it is difficult to optimise and improve the biocontrol applications of this species. As a foundation for elucidating biocontrol mechanisms, we have de novo assembled a high-quality reference genome of a strongly antagonistic A. pullulans strain, performed dual RNA-seq experiments, and analysed proteins secreted during the interaction with the plant pathogen Fusarium oxysporum. Based on the genome annotation, potential biocontrol genes were predicted to encode secreted hydrolases or to be part of secondary metabolite clusters (e.g., NRPS-like, NRPS, T1PKS, terpene, and β-lactone clusters). Transcriptome and secretome analyses defined a subset of 79 A. pullulans genes (among the 10,925 annotated genes) that were transcriptionally upregulated or exclusively detected at the protein level during the competition with F. oxysporum. These potential biocontrol genes comprised predicted secreted hydrolases such as glycosylases, esterases, and proteases, as well as genes encoding enzymes, which are predicted to be involved in the synthesis of secondary metabolites. This study highlights the value of a sequential approach starting with genome mining and consecutive transcriptome and secretome analyses in order to identify a limited number of potential target genes for detailed, functional analyses.

Potential of Volatile Organic Compounds Emitted by Pseudomonas fluorescens ZX as Biological Fumigants to Control Citrus Green Mold Decay at Postharvest

In this study, volatile organic compounds (VOCs) were generated by Pseudomonas fluorescens ZX with incubation in nutrient broth (NB), on NA (NB with agar), and on healthy orange fruits, and pure individual components of VOCs were used to manage citrus green mold infected by Penicillium digitatum. At a concentration of 1 × 10¹⁰ cfu/mL, the VOCs from antagonist-containing NA plates inhibited P. digitatum conidial germination and mycelial growth by about 60%, while the VOCs from bacterial fluid exhibited approximately 75% inhibitory effect. Biofumigation by VOCs significantly reduced the disease index, with a higher biocontrol efficacy by VOCs from bacterial fluid (about 51%) than from antagonist-containing NA plates (around 40%) or from antagonist-infested fruit (approximately 24%). Exposure to VOCs led to morphological abnormalities of P. digitatum conidia and hyphae. However, VOCs exhibited poor preventative and curative action against P. digitatum. The storage test showed that biofumigation had no negative effects on fruit quality. Antifungal assays suggested that dimethyl disulfide and dimethyl trisulfide exhibited the highest inhibitory effects, which afforded complete inhibition at the lowest concentrations. In addition, organic acids were also promising in controlling green mold, but only at suitable low concentrations to avoid eliciting fruit's physiological diseases.

Dynamics of the Apple Fruit Microbiome after Harvest and Implications for Fruit Quality

The contribution of the apple microbiome to the production chain of apple was so far largely unknown. Here, we describe the apple fruit microbiome and influences on its composition by parameters such as storage season, storage duration, storage technology, apple variety, and plant protection schemes. A combined culturing and metabarcoding approach revealed significant differences in the abundance, composition, and diversity of the apple fruit microbiome. We showed that relatively few genera contribute a large portion of the microbiome on fruit and that the fruit microbiome changes during the storage season depending on the storage conditions. In addition, we show that the plant protection regime has an influence on the diversity of the fruit microbiome and on the dynamics of pathogenic fungal genera during the storage season. For the genus Neofabraea, the quantitative results from the metabarcoding approach were validated with real-time PCR. In conclusion, we identified key parameters determining the composition and temporal changes of the apple fruit microbiome, and the main abiotic driving factors of microbiome diversity on apple fruit were characterized.

Trichoderma asperellum T76-14 Released Volatile Organic Compounds against Postharvest Fruit Rot in Muskmelons (Cucumis melo) Caused by Fusarium incarnatum

Postharvest fruit rot caused by Fusarium incarnatum is a destructive postharvest disease of muskmelon (Cucumis melo). Biocontrol by antagonistic microorganisms is considered an alternative to synthetic fungicide application. The aim of this study was to investigate the mechanisms of action involved in the biocontrol of postharvest fruit rot in muskmelons by Trichoderma species. Seven Trichoderma spp. isolates were selected for in vitro testing against F. incarnatum in potato dextrose agar (PDA) by dual culture assay. In other relevant works, Trichoderma asperellum T76-14 showed a significantly higher percentage of inhibition (81%) than other isolates. Through the sealed plate method, volatile organic compounds (VOCs) emitted from T. asperellum T76-14 proved effective at inhibiting the fungal growth of F. incarnatum by 62.5%. Solid-phase microextraction GC/MS analysis revealed several VOCs emitted from T. asperellum T76-14, whereas the dominant compound was tentatively identified as phenylethyl alcohol (PEA). We have tested commercial volatile (PEA) against in vitro growth of F. incarnatum; the result showed PEA at a concentration of 1.5 mg mL⁻¹ suppressed fungal growth with 56% inhibition. Both VOCs and PEA caused abnormal changes in the fungal mycelia. In vivo testing showed that the lesion size of muskmelons exposed to VOCs from T. asperellum T76-14 was significantly smaller than that of the control. Muskmelons exposed to VOCs from T. asperellum T76-14 showed no fruit rot after incubation at seven days compared to fruit rot in the control. This study demonstrated the ability of T. asperellum T76-14 to produce volatile antifungal compounds, showing that it can be a major mechanism involved in and responsible for the successful inhibition of F. incarnatum and control of postharvest fruit rot in muskmelons.

Bioactivity of volatile organic compounds by Aureobasidium species against gray mold of tomato and table grape

Aureobasidium strains isolated from diverse unconventional environments belonging to the species A. pullulans, A. melanogenum, and A. subglaciale were evaluated for Volatile Organic Compounds (VOCs) production as a part of their modes of action against Botrytis cinerea of tomato and table grape. By in vitro assay, VOCs generated by the antagonists belonging to the species A. subglaciale showed the highest inhibition percentage of the pathogen mycelial growth (65.4%). In vivo tests were conducted with tomatoes and grapes artificially inoculated with B. cinerea conidial suspension, and exposed to VOCs emitted by the most efficient antagonists of each species (AP1, AM10, AS14) showing that VOCs of AP1 (A. pullulans) reduced the incidence by 67%, partially confirmed by the in vitro results. Conversely, on table grape, VOCs produced by all the strains did not control the fungal incidence but were only reducing the infection severity (< 44.4% by A. pullulans; < 30.5% by A. melanogenum, and A. subglaciale). Solid-phase microextraction (SPME) and subsequent gas chromatography coupled to mass spectrometry identified ethanol, 3-methyl-1-butanol, 2-methyl-1-propanol as the most produced VOCs. However, there were differences in the amounts of produced VOCs as well as in their repertoire. The EC50 values of VOCs for reduction of mycelial growth of B. cinerea uncovered 3-methyl-1-butanol as the most effective compound. The study demonstrated that the production and the efficacy of VOCs by Aureobasidium could be directly related to the specific species and pathosystem and uncovers new possibilities for searching more efficient VOCs producing strains in unconventional habitats other than plants.

Volatile organic compounds produced by Aureobasidium pullulans induce electrolyte loss and oxidative stress in Botrytis cinerea and Alternaria alternata

Aureobasidium pullulans is a yeast-like fungus that produces volatile organic compounds (VOCs) with antifungal properties. VOCs have the potential to trigger the production of intracellular reactive oxygen species (ROS), lipid peroxidation and electrolyte loss in microorganisms. The relationship among A. pullulans VOCs, induced ROS accumulation and electrolyte leakage was investigated in Botrytis cinerea and Alternaria alternata in vitro. Exposure to a mixture of A. pullulans VOCs: ethanol, 2-methyl-1-propanol, 3-methyl-1-butanol and 2-phenylethanol, resulted in electrolyte leakage in both B. cinerea and A. alternata. Fluorescence microscopy using 2',7'-dichlorofluorescein diacetate indicated triggered ROS accumulation in exposed fungal mycelia and the presence of the superoxide radical was evident by intense red fluorescence with dihydroethidium. Partial inhibition of enzymes of the mitochondrial respiratory chain complex I of B. cinerea and A. alternata by pre-treatment with rotenone reduced ROS accumulation in hypha exposed to A. pullulans VOCs and reversed the VOCs inhibition of fungal growth. Scanning electron micrographs revealed that B. cinerea and A. alternata hypha exposed to A. pullulans VOCs had altered cell wall structures. Our findings give insights into the potential mechanisms involved in the antifungal properties of A. pullulans in the suppression of B. cinerea and A. alternata growth in vitro.