Fungal volatile organic compounds: A review with emphasis on their biotechnological potential

Endophytic Fungal Volatile Compounds as Solution for Sustainable Agriculture

Endophytic fungi produce various mixtures of carbon-based compounds, which are known as volatile organic compounds (VOCs). Research regarding the use of VOCs as pesticide substitutes has garnered much attention. This review summarizes the recent knowledge about VOCs regarding their origin and chemical properties and emphasizes their antimicrobial potential against a wide variety of agricultural pathogens. Several studies have highlighted the importance of VOCs as antimicrobial agents. Nevertheless, the application of VOCs in biofumigation methods still requires the advanced evaluation of their phytotoxicity.

Comparison of non-volatile and volatile flavor compounds in six Pleurotus mushrooms

BACKGROUND

Non-volatile and volatile flavor compounds of six Pleurotus mushrooms including Pleurotus citrinopileatus, P. cornucopiae, P. djamor, P. floridanus, P. ostreatus and P. sapidus were studied.

RESULTS

The content of total free amino acids ranged from 21.80 to 40.60 g kg^-1 and the content of monosodium glutamate (MSG)-like amino acids ranged from 3.10 to 8.64 g kg^-1 . The content of total 5'-nucleotides ranged from 4.16 to 8.80 g kg^-1 while the content of flavor 5'-nucleotides ranged from 2.00 to 4.51 g kg^-1 . Sixty-three volatile compounds were identified in six Pleurotus mushrooms, including 17 aldehydes, 10 ketones, 14 alcohols, 2 ethers, 5 acids, 5 hydrocarbons, 10 heterocyclic and aromatic compounds. 1-Octen-3-one and 1-octen-3-ol were the key odor compounds in P. citrinopileatus, P. djamor, P. ostreatus, P. floridanus and P. sapidus, while 1-octen-3-one, 1-octen-3-ol and 2-octenal were the key odor compounds in P. cornucopiae.

CONCLUSION

Pleurotus citrinopileatus had highest content of total free amino acids (40.60 g kg^-1 ), total 5'-nucleotides (8.80 g kg^-1 ) and flavor 5'-nucleotides (4.51 g kg^-1 ) than other Pleurotus mushrooms. Moreover, eight-carbon compounds were the most abundant compounds in six Pleurotus mushrooms. Our study should be helpful in promoting the cultivation and consumption of these Pleurotus mushrooms. © 2018 Society of Chemical Industry.

Yeast Smell Like What They Eat: Analysis of Volatile Organic Compounds of Malassezia furfur in Growth Media Supplemented with Different Lipids

Malassezia furfur is part of the human skin microbiota. Its volatile organic compounds (VOCs) possibly contribute to the characteristic odour in humans, as well as to microbiota interaction. The aim of this study was to investigate how the lipid composition of the liquid medium influences the production of VOCs. Growth was performed in four media: (1) mDixon, (2) oleic acid (OA), (3) oleic acid + palmitic acid (OA+PA), and (4) palmitic acid (PA). The profiles of the VOCs were characterized by HS-SPME/GC-MS in the exponential and stationary phases. A total number of 61 VOCs was found in M. furfur, among which alkanes, alcohols, ketones, and furanic compounds were the most abundant. Some compounds previously reported for Malassezia (γ-dodecalactone, 3-methylbutan-1-ol, and hexan-1-ol) were also found. Through our experiments, using univariate and multivariate unsupervised (Hierarchical Cluster Analysis (HCA) and Principal Component Analysis (PCA)) and supervised (Projection to Latent Structures Discriminant Analysis (PLS-DA)) statistical techniques, we have proven that each tested growth medium stimulates the production of a different volatiles profile in M. furfur. Carbon dioxide, hexan-1-ol, pentyl acetate, isomer5 of methyldecane, dimethyl sulphide, undec-5-ene, isomer2 of methylundecane, isomer1 of methyldecane, and 2-methyltetrahydrofuran were established as differentiating compounds among treatments by all the techniques. The significance of our findings deserves future research to investigate if certain volatile profiles could be related to the beneficial or pathogenic role of this yeast.

Volatile organic compounds (VOCs) produced by biocontrol yeasts

The Volatile organic compounds (VOCs) produced by biocontrol yeast strains which belong to the Wickerhamomyces anomalus, Metschnikowia pulcherrima, Aureobasidium pullulans and Saccharomyces cerevisiae species were identified by solid phase microextraction (SPME) coupled with Gas Chromatography-Mass Spectrometry (GC-MS). Alcohols (ethyl alcohol, 3-methyl-1-butanol and phenylethyl alcohol) and esters (ethyl acetate and isoamyl acetate) were found to be the main VOCs emitted by the yeast strains, which had different production rate over a 16-day period. In addition, the tested yeast strains showed a remarkable ability to consume oxygen and to produce high percentages of carbon dioxide over a 5 days incubation period in a model system. The yeast strains, which were proven to very efficiently suppress in vivo the growth of postharvest fungal by VOCs, also quickly produced high percentages of ethyl acetate and carbon dioxide. . For all these reasons, we believe that the level of yeast biocontrol efficacy through the production of volatiles could be the result of a synergistic effect between VOCs and carbon dioxide in the packaging environment.

Prospective application of melanized fungi for the biofiltration of indoor air in closed bioregenerative systems

Cultures of melanized fungi representative of the black yeast orders Capnodiales (Cladosporium cladosporioides and Neohortaea acidophila) and Chaetothyriales (Cladophialophora psammophila) were confined with indoor air from the laboratory during 48 h. Volatile organic compounds (VOCs) from the headspace were analyzed by thermal desorption gas chromatography time-of-fly mass spectrometry (TD-GC-ToFMS, detection threshold 0.1 μg m^-3) and compared against an abiotic control. A mixture of 71 VOCs were identified and quantified in the indoor air (total concentration 1.4 mg m^-3). Most of these compounds were removed in the presence of fungal biomass, but 40 newly formed putative volatile metabolites were detected, though at comparatively low total concentrations (<50 μg m^-3). The VOCs emission profile of C. cladosporioides, a ubiquitous and well-known species often associated to the sick building syndrome, was consistent with previous literature reports. The specialized C. psammophila and N. acidophila, isolated respectively from gasoline polluted soil and from lignite, displayed rather specific VOCs emission profiles. Mass balances on the fungal uptake and generation of VOCs resulted in overall VOCs removal efficiencies higher than 96% with all tested fungi. Applied aspects and biosafety issues concerning the suitability of black yeasts for the biofiltration of indoor air have been discussed.

The Arabidopsis-Trichoderma interaction reveals that the fungal growth medium is an important factor in plant growth induction

Trichoderma spp colonizes the plant rhizosphere and provides pathogen resistance, abiotic stress tolerance, and enhance growth and development. We evaluated the Arabidopsis-Trichoderma interaction using a split system in which Trichoderma atroviride and Trichoderma virens were grown on PDA or MS medium. Arabidopsis growth was significantly increased at 3 and 5 days post-inoculation with both Trichoderma species, when the fungal strains were grown on PDA in split interaction. The analysis of DR5:uidA reporter line revealed a greater auxin accumulation in root tips when the fungi were grown on PDA in a split interaction. The root hair-defective phenotype of Arabidopsis rhd6 mutant was reverted with both Trichoderma species, even in split interactions. At 12 °C, Trichoderma species in split interactions were able to mitigate the effects of cold stress on the plant, and also Trichoderma induced the AtERD14 expression, a cold related gene. Volatile organic compounds analysis revealed that Trichoderma strains produce mainly sesquiterpenes, and that the type and abundance of these compounds was dependent on the fungal strain and the culture medium. Our results show that fungal nutrition is an important factor in plant growth in a split interaction.

Biosynthetic pathway and optimal conditions for the production of indole-3-acetic acid by an endophytic fungus, Colletotrichum fructicola CMU-A109

Endophytic fungi are known to produce indole-3-acetic acid (IAA), which can stimulate plant growth. Twenty-seven isolates of endophytic fungi were isolated from Coffea arabica in northern Thailand. Only one isolate (CMU-A109) produced IAA in vitro. This isolate was identified as Colletotrichum fructicola based on morphological characteristics and molecular phylogenetic analysis of a combined five loci (internal transcribed spacer of ribosomal DNA, actin, β-tubulin 2, chitin synthase and glyceraldehyde-3-phosphate dehydrogenase genes). Identification of a fungal IAA production obtained from indole 3-acetamide (IAM) and tryptophan 2-monooxygenase activity is suggestive of IAM routed IAA biosynthesis. The highest IAA yield (1205.58±151.89 μg/mL) was obtained after 26 days of cultivation in liquid medium supplemented with 8 mg/mL L-tryptophan at 30°C. Moreover, the crude fungal IAA could stimulate coleoptile elongation of maize, rice and rye. This is the first report of IAA production by C. fructicola and its ability to produce IAA was highest when compared with previous reports on IAA produced by fungi.

Volatile Compounds Emitted by Diverse Verticillium Species Enhance Plant Growth by Manipulating Auxin Signaling

Some volatile compounds (VC) play critical roles in intra- and interspecies interactions. To investigate roles of VC in fungal ecology, we characterized how VC produced by Verticillium spp., a group of broad-host-range soilborne fungal pathogens, affect plant growth and development. VC produced by 19 strains corresponding to 10 species significantly enhanced the growth of Arabidopsis thaliana and Nicotiana benthamiana. Analysis of VC produced by four species revealed the presence of diverse compounds, including those previously shown to affect plant growth. Using A. thaliana, we investigated the mechanism underpinning plant growth enhancement by Verticillium dahliae VC. Allometric analysis indicated that VC caused preferential resource allocation for root growth over shoot growth. Growth responses of A. thaliana mutants defective in auxin or ethylene signaling suggested the involvement of several components of auxin signaling, with TIR3 playing a key role. AUX1, TIR1, and AXR1 were also implicated but appeared to play lesser roles. Inhibition of auxin efflux using 1-naphthylphthalamic acid blocked VC-mediated growth enhancement. Spatial and temporal expression patterns of the auxin-responsive reporter DR5::GUS indicated that the activation of auxin signaling occurred before enhanced plant growth became visible. Results from this study suggest critical yet overlooked roles of VC in Verticillium ecology and pathology.

Leaves of Indoor Ornamentals Are Biodiversity and Functional Hotspots for Fungi

Leaf-inhabiting fungi are an important, but often overlooked component of molecular biodiversity studies. To understand their diversity and function in relation to plant species and climate, the phyllospheres of 14 phylogenetically diverse ornamental plant species were analyzed under different controlled greenhouse conditions. We found unexpectedly high fungal diversity (H' = 2.8-6.5), OTU numbers (449-1050) and abundances (103-106 CFU cm-2 leaf surface) associated with all plants studied indoors. Despite experimental limitations, the composition of fungal communities were inclined toward a plant species-dependent pattern compared to the ambient climatic variables. Most detected fungi were patho- and saprotrophs showing a yeast-like growth morphology and were associated to the groups of endophytes and potential plant pathogens in a plant species-specific manner. A representative strain collection showed that 1/3 of the tested fungi (mainly Penicillium, Cladosporium, and Cryptococcus spp.) were able to inhibit mycelial growth and 2/3 inhibit sporulation of the plant pathogen Botrytis cinerea by the production of antifungal volatile organic compounds (VOCs) completely. This study indicates that plant leaves harbor a stable phyllosphere fungal diversity in diverse microclimates and enrich distinctive functional guilds.

Isolation and characterization of plumbagin (5- hydroxyl- 2- methylnaptalene-1,4-dione) producing endophytic fungi Cladosporium delicatulum from endemic medicinal plants: Isolation and characterization of plumbagin producing endophytic fungi from endemic medicinal plants

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Diversity of endophytic fungi from endemic medicinal plants in Eastern Ghats.

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Molecular identification and anti-microbial activity of isolated endophytic cultures.

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GCMS analysis and compound identification of potential crud extract.

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Characterization of purified fraction using FTIR spectroscopy, MS and NMR.

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Potentially inhibition of tested pathogens by identified compound 5-hydroxy-2-methylnaphthalene-1, 4-Dione.

The rationale of the present study was to isolate and identify endophytic fungi from endemic medicinal plants in Eastern Ghats and screened for antimicrobial potential of isolated fungal crude extracts. A total of 329 endophytic strains were isolated from 600 infected leaves and stem cuttings of endemic plants. The diversity and species richness was analyzed statistically and found to be higher in leaf segments than in stem segments. From isolated fungal strains, Cladosporium delicatulum was identified using molecular identification methods and selected as the most potent plumbagin-producing endophytic strain. Further the isolation and structural characterization of endophytic fungal plumbagin (5-hydroxyl-2-methylnaptalene-1,4-dione) was purified and confirmed through spectroscopy analysis. The molecular weight was determined as m/z 188 in positive mode by ESI-MS, which confirmed to be plumbagin which potentially inhibited all tested pathogens, therefore the endophytic fungal plumbagin from the current study possesses important biological activities against pathogens.

Revisiting bacterial volatile-mediated plant growth promotion: lessons from the past and objectives for the future

BACKGROUND

Bacterial volatile compounds (BVCs) are important mediators of beneficial plant-bacteria interactions. BVCs promote above-ground plant growth by stimulating photosynthesis and sugar accumulation and by modulating phytohormone signalling. These compounds also improve below-ground mineral uptake and modify root system architecture.

SCOPE

We review advances in our understanding of the mode of action and practical applications of BVCs since the discovery of BVC-mediated plant growth promotion in 2003. We also discuss unanswered questions about the identity of plant receptors, the effectiveness of combination of two or more BVCs on plant growth, and the potential side effects of these compounds for human and animal health.

CONCLUSION

BVCs have good potential for use as biostimulants and protectants to improve plant health. Further advances in the development of suitable technologies and preparing standards and guidelines will help in the application of BVCs in crop protection and health.

1-Octen-3-ol Is Formed from Its Glycoside during Processing of Soybean [ Glycine max (L.) Merr.] Seeds

Soaking and maceration of dry soybean seeds induce the formation of aliphatic volatile compounds that impact the flavor properties of food products prepared from soybean. Most aliphatic volatile compounds are formed through oxygenation of unsaturated fatty acids by lipoxygenases; however, lipoxygenases are not responsible for the formation of 1-octen-3-ol. 1-Octen-3-ol in soybean products is in general an off-flavor compound; thus, a procedure to manage its formation is required. In this study, we show that the formation of 1-octen-3-ol after hydration of soybean seed powder is independent of oxygen, suggesting that 1-octen-3-ol is not formed de novo from unsaturated fatty acids but instead from its derivative. When crude methanol extract of soybean seeds was reacted with β-glycosidases, 1-octen-3-ol was rather liberated from its glycoside. We purified the parent glycoside from soybean seeds and confirmed it as ( R)-1-octen-3-yl β-primeveroside [( R)-1-octen-3-yl 6- O-β-d-xylopyranosyl-β-d-glucopyranoside]. Green immature soybean fruits (pericarp and seeds) contain a high amount of 1-octen-3-yl β-primeveroside. Its amount decreases after hydration of dry soybean powder. The results indicate that management of 1-octen-3-ol levels in soybean products requires a different strategy than that applied to off-flavor compounds formed de novo.

Gene expression of indoor fungal communities under damp building conditions: Implications for human health

Dampness and visible mold growth in homes are associated with negative human health outcomes, but causal relationships between fungal exposure and health are not well established. The purpose of this study was to determine whether dampness in buildings impacts fungal community gene expression and how, in turn, gene expression may modulate human health impacts. A metatranscriptomic study was performed on house dust fungal communities to investigate the expression of genes and metabolic processes in chamber experiments at water activity levels of 0.5, 0.85, and 1.0. Fungi at water activities as low as 0.5 were metabolically active, focusing their transcriptional resources on primary processes essential for cell maintenance. Metabolic complexity increased with water activity where communities at 1.0 displayed more diverse secondary metabolic processes. Greater gene expression at increasing water activity has important implications for human health: Fungal communities at 1.0 a_w upregulated a greater number of allergen-, mycotoxin-, and pathogenicity-encoding genes versus communities at 0.85 and 0.5 a_w . In damp buildings, fungi may display increases in secondary metabolic processes with the potential for greater per-cell production of allergens, toxins, and pathogenicity. Assessments in wet versus dry buildings that do not account for this elevated health impact may not accurately reflect exposure.

Comparison of volatile compounds released by entomopathogenic fungi

Entomopathogenic fungi are fungal species which are used as a potential source of biopesticides. These fungi produce secondary metabolites which in insects can cause disruption in the normal functioning of their bodies, disease or even death. In order to fully characterize the physiology of entomopathogenic fungi we should identify the volatile organic compounds which are involved in this process. Therefore, we conducted a qualitative and quantitative analysis of volatile compounds produced by entomopathogenic fungi. Seven different species of fungi were analyzed: Metarhizium anisopliae, Metarhizium flavoviride, Pandora sp., Isaria fumosorosea, Hirsutella danubiensis, Batkoa sp. and Beauveria bassiana. The analyses were performed using the HS-SPME/GCMS technique. In the analyzed fungi, 63 volatile compounds were identified and classified into the following groups: aldehydes, ketones, alcohols, esters, acids, terpenes and others. The results show that entomopathogenic fungi produce a wide profile of secondary metabolites. Principal Components Analysis was used to determine whether separate classes of fungi can be distinguished from one another based on their metabolite profiles.

Micro-organisms growing on rapeseed during storage affect the profile of volatile compounds of virgin rapeseed oil

BACKGROUND

Micro-organisms populate on rapeseed after harvest during storage depending on the growing conditions. The composition of the bacterial colonization is unknown, although its contribution to the profile of volatile aroma-active compounds determines the sensory quality of virgin cold-pressed rapeseed oil.

RESULTS

From four rapeseed samples, 46 bacterial strains were isolated. By DNA-sequencing, the identification of four bacteria species and 17 bacteria genera was possible. In total, 22 strains were selected, based on their typical off-flavors resembling those of virgin sensory bad cold-pressed rapeseed oils. The cultivation of these strains on rapeseed meal agar and examination of volatile compounds by solid phase microextraction-gas chromatography-mass spectrometry allowed the identification of 29 different compounds, mainly degradation products of fatty acids such as alkanes, alkenes, aldehydes, ketones and alcohols and, in addition, sulfur-containing compounds, including one terpene and three pyrazines. From these compounds, 19 are described as aroma-active in the literature.

CONCLUSION

Micro-organisms populating on rapeseed during storage may strongly influence the sensory quality of virgin rapeseed oil as a result of the development of volatile aroma-active metabolic products. It can be assumed that occurrence of off-flavor of virgin rapeseed oils on the market are the result of metabolic degradation products produced by micro-organisms populating on rapeseed during storage. © 2017 Society of Chemical Industry.

Screening and Evaluation of Yeast Antagonists for Biological Control of Botrytis cinerea on Strawberry Fruits

Gray mold (Botrytis cinerea) is one of the most common diseases of strawberries (Fragaria × ananassa Duchesne) worldwide. Although many chemical fungicides are used for controlling the growth of B. cinerea, the risk of the fungus developing chemical resistance together with consumer demand for reducing the use of chemical fungicides have necessitated an alternative method to control this pathogen. Various naturally occurring microbes aggressively attack plant pathogens and benefit plants by suppressing diseases; these microbes are referred to as biocontrol agents. However, screening of potent biocontrol agents is essential for their further development and commercialization. In this study, 24 strains of yeast with antagonistic ability against gray mold were isolated, and the antifungal activity of the volatile and diffusible metabolites was evaluated. Putative mechanisms of action associated with the biocontrol capacity of yeast strains against B. cinerea were studied through in vitro and in vivo assays. The volatile organic compounds produced by the Galactomyces candidum JYC1146 could be useful in the biological control of plant pathogens and therefore are potential alternative fungicides with low environmental impact.

Transmission of fungal partners to incipient Cecropia-tree ant colonies

Ascomycete fungi in the nests of ants inhabiting plants (= myrmecophytes) are very often cultivated by the ants in small patches and used as food source. Where these fungi come from is not known yet. Two scenarios of fungus recruitment are possible: (1) random infection through spores or hyphal fragments from the environment, or (2) transmission from mother to daughter colonies by the foundress queen. It is also not known at which stage of the colony life cycle fungiculture is initiated, and whether the- symbiont fungi serve as food for the ant queen. To clarify these questions, we investigated four Azteca ant species inhabiting three different Cecropia species (C. insignis, C. obtusifolia, and C. peltata). We analysed an rRNA gene fragment from 52 fungal patches produced by founding queens and compared them with those from established Azteca colonies (n = 54). The infrabuccal pockets of winged queens were dissected to investigate whether young queens carry fungi from their mother colony. Additionally, 15N labelling experiments were done to verify whether the queen feeds on the patches until she is nourished by her first worker offspring. We infer from the results that the fungi cultivated in hollow plant structures are transferred from the parental colony of the young queen. First, fungal genotypes/OTU diversity was not significantly different between foundress queen patches and established colonies, and second, hyphal parts were discovered in the infrabuccal pockets of female alates. We could show that fungiculture already starts before queens lay their eggs, and that the queens do not feed on fungal patch material but feed it to the larvae. Our findings suggest that fungiculture may be crucial for successful colony founding of arboreal ants in the tropics.

Development of an adaptable headspace sampling method for metabolic profiling of the fungal volatome

Culture headspace sampling and analysis of aspergillus fumigatus volatile metabolites by TD-GC-MS.

Volatile organic compounds from Wickerhamomyces anomalus, Metschnikowia pulcherrima and Saccharomyces cerevisiae inhibit growth of decay causing fungi and control postharvest diseases of strawberries

The effectiveness of Wickerhamomyces anomalus, Metschnikowia pulcherrima and Saccharomyces cerevisiae as biocontrol agents on postharvest decay of strawberry (Fragaria x ananassa, cv. 'Alba') fruit, and their inhibitory activities on some decay-causing fungi were evaluated. Volatile organic compounds from these yeasts decreased mycelial growth of Botrytis cinerea by 69%, and by less for Monilinia fructicola, Alternaria alternata, Aspergillus carbonarius, Penicillium digitatum, Cladosporium spp., and Colletotrichum spp. Strawberry fruit exposed to 6-day-old liquid cultures of W. anomalus, M. pulcherrima and S. cerevisiae for 48h showed 89%, 40%, and 32% reductions, respectively, in gray mold McKinney Index. Vapours of ethyl acetate, the main volatile organic compound of these yeasts, completely inhibited B. cinerea growth at 8.97mg/cm³, and suppressed gray mold on strawberry fruit at 0.718mg/cm³. The biocontrol activities of these yeasts can be ascribed to ethyl acetate, which can be used for control of postharvest gray mold of strawberry fruit.

Plant Phenotypic and Transcriptional Changes Induced by Volatiles from the Fungal Root Pathogen Rhizoctonia solani

Beneficial soil microorganisms can affect plant growth and resistance by the production of volatile organic compounds (VOCs). Yet, little is known on how VOCs from soil-borne plant pathogens affect plant growth and resistance. Here we show that VOCs released from mycelium and sclerotia of the fungal root pathogen Rhizoctonia solani enhance growth and accelerate development of Arabidopsis thaliana. Seedlings briefly exposed to the fungal VOCs showed similar phenotypes, suggesting that enhanced biomass and accelerated development are primed already at early developmental stages. Fungal VOCs did not affect plant resistance to infection by the VOC-producing pathogen itself but reduced aboveground resistance to the herbivore Mamestra brassicae. Transcriptomics of A. thaliana revealed that genes involved in auxin signaling were up-regulated, whereas ethylene and jasmonic acid signaling pathways were down-regulated by fungal VOCs. Mutants disrupted in these pathways showed similar VOC-mediated growth responses as the wild-type A. thaliana, suggesting that other yet unknown pathways play a more prominent role. We postulate that R. solani uses VOCs to predispose plants for infection from a distance by altering root architecture and enhancing root biomass. Alternatively, plants may use enhanced root growth upon fungal VOC perception to sacrifice part of the root biomass and accelerate development and reproduction to survive infection.

Agriculturally important microbial biofilms: Present status and future prospects

Microbial biofilms are a fascinating subject, due to their significant roles in the environment, industry, and health. Advances in biochemical and molecular techniques have helped in enhancing our understanding of biofilm structure and development. In the past, research on biofilms primarily focussed on health and industrial sectors; however, lately, biofilms in agriculture are gaining attention due to their immense potential in crop production, protection, and improvement. Biofilms play an important role in colonization of surfaces - soil, roots, or shoots of plants and enable proliferation in the desired niche, besides enhancing soil fertility. Although reports are available on microbial biofilms in general; scanty information is published on biofilm formation by agriculturally important microorganisms (bacteria, fungi, bacterial-fungal) and their interactions in the ecosystem. Better understanding of agriculturally important bacterial-fungal communities and their interactions can have several implications on climate change, soil quality, plant nutrition, plant protection, bioremediation, etc. Understanding the factors and genes involved in biofilm formation will help to develop more effective strategies for sustainable and environment-friendly agriculture. The present review brings together fundamental aspects of biofilms, in relation to their formation, regulatory mechanisms, genes involved, and their application in different fields, with special emphasis on agriculturally important microbial biofilms.

Fungal volatile compounds induce production of the secondary metabolite Sodorifen in Serratia plymuthica PRI-2C

The ability of bacteria and fungi to communicate with each other is a remarkable aspect of the microbial world. It is recognized that volatile organic compounds (VOCs) act as communication signals, however the molecular responses by bacteria to fungal VOCs remain unknown. Here we perform transcriptomics and proteomics analyses of Serratia plymuthica PRI-2C exposed to VOCs emitted by the fungal pathogen Fusarium culmorum. We find that the bacterium responds to fungal VOCs with changes in gene and protein expression related to motility, signal transduction, energy metabolism, cell envelope biogenesis, and secondary metabolite production. Metabolomic analysis of the bacterium exposed to the fungal VOCs, gene cluster comparison, and heterologous co-expression of a terpene synthase and a methyltransferase revealed the production of the unusual terpene sodorifen in response to fungal VOCs. These results strongly suggest that VOCs are not only a metabolic waste but important compounds in the long-distance communication between fungi and bacteria.

Characterization of Morphology, Volatile Profiles, and Molecular Markers in Edible Desert Truffles from the Negev Desert

Desert truffles are mycorrhizal, hypogeous fungi considered a delicacy. On the basis of morphological characters, we identified three desert truffle species that grow in the same habitat in the Negev desert. These include Picoa lefebvrei (Pat.), Tirmania nivea (Desf.) Trappe, and Terfezia boudieri (Chatain), all associated with Helianthemum sessiliflorum. Their taxonomy was confirmed by PCR-RFLP. The main volatiles of fruit bodies of T. boudieri and T. nivea were 1-octen-3-ol and hexanal; however, volatiles of the latter species further included branched-chain amino acid derivatives such as 2-methylbutanal and 3-methylbutanal, phenylalanine derivatives such as benzaldehyde and benzenacetaldehyde, and methionine derivatives such as methional and dimethyl disulfide. The least aromatic truffle, P. lefebvrei, contained low levels of 1-octen-3-ol as the main volatile. Axenic mycelia cultures of T. boudieri displayed a simpler volatile profile compared to its fruit bodies. This work highlights differences in the volatile profiles of desert truffles and could hence be of interest for selecting and cultivating genotypes with the most likable aroma.

Chemical and canine analysis as complimentary techniques for the identification of active odors of the invasive fungus, Raffaelea lauricola

Raffaelea lauricola, a fungus causing a vascular wilt (laurel wilt) in Lauraceae trees, was introduced into the United States in the early 2000s. It has devastated forests in the Southeast and has now moved into the commercial avocado groves in southern Florida. Trained detection canines are currently one of the few successful methods for early detection of pre-symptomatic diseased trees. In order to achieve the universal and frequent training required to have successful detection canines, it is desirable to create accessible, safe, and long-lasting training aids. However, identification of odorants and compounds is limited by several factors, including both the availability of chemicals and the need to present chemicals individually and in combination to detection canines. A method for the separation and identification of volatile organic compounds (VOCs) from environmental substances for the creation of such a canine training aid is presented here. Headspace solid phase microextraction-gas chromatography-mass spectrometry (HS-SPME-GC-MS) was used to identify the odors present in avocado trees infected with the R. lauricola phytopathogen. Twenty-eight compounds were detected using this method, with nine present in greater than 80% of samples. The majority of these compounds were not commercially available as standard reference materials, and a canine trial was designed to identify the active odors without the need of pure chemical compounds. To facilitate the creation of a canine training aid, the VOCs above R. lauricola were separated by venting a 0.53mm ID solgel-wax gas chromatography column to the atmosphere. Ten minute fractions of the odor profile were collected on cotton gauze in glass vials and presented to the detection canines in a series of field trials. The canines alerted to the VOCs from the vials that correspond to a portion of the chromatogram containing the most volatile species from R. lauricola. This innovative fractionation and collection method can be used to develop reliable and cost effective canine training aids.

Mycofumigation through production of the volatile DNA-methylating agent N-methyl-N-nitrosoisobutyramide by fungi in the genus Muscodor

Antagonistic microorganisms produce antimicrobials to inhibit the growth of competitors. Although water-soluble antimicrobials are limited to proximal interactions via aqueous diffusion, volatile antimicrobials are able to act at a distance and diffuse through heterogeneous environments. Here, we identify the mechanism of action of Muscodor albus, an endophytic fungus known for its volatile antimicrobial activity toward a wide range of human and plant pathogens and its potential use in mycofumigation. Proposed uses of the Muscodor species include protecting crops, produce, and building materials from undesired fungal or bacterial growth. By analyzing a collection of Muscodor isolates with varying toxicity, we demonstrate that the volatile mycotoxin, N-methyl-N-nitrosoisobutyramide, is the dominant factor in Muscodor toxicity and acts primarily through DNA methylation. Additionally, Muscodor isolates exhibit higher resistance to DNA methylation compared with other fungi. This work contributes to the evaluation of Muscodor isolates as potential mycofumigants, provides insight into chemical strategies that organisms use to manipulate their environment, and provokes questions regarding the mechanisms of resistance used to tolerate constitutive, long-term exposure to DNA methylation.

Antimicrobial activity of endophytic fungi from olive tree leaves

In this study, the antimicrobial potential of three fungal endophytes from leaves of Olea europaea L. was evaluated and the host plant extract effect in the antimicrobial activity was examined. The volatile compounds produced by endophytes were identified by GC/MS and further correlated with the antimicrobial activity. In potato dextrose agar, both Penicillium commune and Penicillium canescens were the most effective inhibiting Gram-positive and -negative bacteria (up to 2.7-fold compared to 30 µg/mL chloramphenicol), whereas Alternaria alternata was most effective inhibiting yeasts (up to 8.0-fold compared to 25 μg/mL fluconazole). The presence of aqueous leaf extract in culture medium showed to induce or repress the antimicrobial activity, depending on the endophytic species. In the next step, various organic extracts from both A. alternata mycelium and cultured broth were prepared; being ethyl acetate extracts displayed the widest spectrum of anti-microorganisms at a minimum inhibitory concentration ≤0.095 mg/mL. The volatile composition of the fungi that displayed the highest (A. alternata) and the lowest (P. canescens) antimicrobial activity against yeasts revealed the presence of six volatiles, being the most abundant components (3-methyl-1-butanol and phenylethyl alcohol) ascribed with antimicrobial potentialities. Overall the results highlighted for the first time the antimicrobial potential of endophytic fungi from O. europaea and the possibility to be exploited for their antimicrobial agents.

Chemotyping the temporal volatile organic compounds of an invasive fungus to the United States, Raffaelea lauricola

Volatile organic compounds (VOCs) in the headspace of the fungus Raffaelea lauricola have been monitored and identified over a twenty-eight day growth period. R. lauricola is an invasive and phytopathogenic fungus that was first identified in the United States in the mid-2000s. It is believed to be spread by a host beetle, Xyleborus glabratus, and is detrimental both to wild members of the Lauraceae family and to commercial avocado groves particularly in the Southeastern region of the country. The fungus causes the fatal laurel wilt disease, a result of the host tree shutting down its vascular system in order to halt the spread of the fungus. The current study identified the VOCs present in the headspace of R. lauricola over the initial growth stage using headspace solid phase microextracion-gas chromatography-mass spectrometry (HS-SPME-GC-MS). Results revealed the VOC dynamics of the fungus in culture, indicating that the initial growth period of the fungus may coincide with potential responses from the host trees that may recognize and respond to the pathogen when the fungal VOCs are produced as a result of primary metabolic processes. As fungal growth progresses past initial growth phases, the predominant compounds seen in the odor profile are hydrocarbons and terpenes, produced from secondary metabolic processes. The odor profile pattern for the twenty-eight day growth period did change with the stages of growth. Based on the information learned from this pilot study, a discussion is presented of possible host tree reactions to R. lauricola and implications for future experiments.

Harnessing Insect-Microbe Chemical Communications To Control Insect Pests of Agricultural Systems

Insect pests cause serious economic, yield, and food safety problems to managed crops worldwide. Compounding these problems, insect pests often vector pathogenic or toxigenic microbes to plants. Previous work has considered plant-insect and plant-microbe interactions separately. Although insects are well-understood to use plant volatiles to locate hosts, microorganisms can produce distinct and abundant volatile compounds that in some cases strongly attract insects. In this paper, we focus on the microbial contribution to plant volatile blends, highlighting the compounds emitted and the potential for variation in microbial emission. We suggest that these aspects of microbial volatile emission may make these compounds ideal for use in agricultural applications, as they may be more specific or enhance methods currently used in insect control or monitoring. Our survey of microbial volatiles in insect-plant interactions suggests that these emissions not only signal host suitability but may indicate a distinctive time frame for optimal conditions for both insect and microbe. Exploitation of these host-specific microbe semiochemicals may provide important microbe- and host-based attractants and a basis for future plant-insect-microbe chemical ecology investigations.

Bioactive Volatiles from an Endophytic Daldinia cf. concentrica Isolate Affect the Viability of the Plant Parasitic Nematode Meloidogyne javanica

Plant-parasitic nematodes form one of the largest sources of biotic stress imposed on plants, and are very difficult to control; among them are the obligate parasites, the sedentary root-knot nematodes (RKNs)-Meloidogyne spp.-which are extremely polyphagous and exploit a very wide range of hosts. Endophytic fungi are organisms that spend most of their life cycle within plant tissue without causing visible damage to the host plant. Many endophytes secrete specialized metabolites and/or emit volatile organic compounds (VOCs) that exhibit biological activity. Recently, we demonstrated that the endophytic fungus Daldinia cf. concentrica secrets biologically active VOCs. Here we examined the ability of the fungus and its VOCs to control the RKN M. javanica both in vitro and greenhouse experiments. The D. cf. concentrica VOCs showed bionematicidal activity against the second-stage juveniles (J2s) of M. javanica. We found that exposure of J2s to fungal volatiles caused 67% reduction in viability, and that application of a synthetic volatile mixture (SVM), comprising 3-methyl-1-butanol, (±)-2-methyl-1-butanol, 4-heptanone, and isoamyl acetate, in volumetric ratio of 1:1:2:1 further reduced J2s viability by 99%. We demonstrated that, although each of the four VOCs significantly reduced the viability of J2s relative to the control, only 4-heptanone elicited the same effect as the whole mixture, with nematicidal activity of 90% reduction in viability of the J2s. Study of the effect of the SVM on egg hatching demonstrated that it decreased eggs hatching by 87%. Finally, application of the SVM to soil inoculated with M. javanica eggs or J2s prior to planting susceptible tomato plants resulted in a significantly reduced galling index and fewer eggs produced on each root system, with no effect on root weight. Thus, D. cf. concentrica and/or SVM based on fungal VOCs may be considered as a novel alternative approach to controlling the RKN M. javanica.

Use of the Endophytic Fungus Daldinia cf. concentrica and Its Volatiles as Bio-Control Agents

Endophytic fungi are organisms that spend most of their life cycle within plant tissues without causing any visible damage to the host plant. Many endophytes were found to secrete specialized metabolites and/or emit volatile organic compounds (VOCs), which may be biologically active and assist fungal survival inside the plant as well as benefit their hosts. We report on the isolation and characterization of a VOCs-emitting endophytic fungus, isolated from an olive tree (Olea europaea L.) growing in Israel; the isolate was identified as Daldinia cf. concentrica. We found that the emitted VOCs were active against various fungi from diverse phyla. Results from postharvest experiments demonstrated that D. cf. concentrica prevented development of molds on organic dried fruits, and eliminated Aspergillus niger infection in peanuts. Gas chromatography-mass spectrometry analysis of the volatiles led to identification of 27 VOCs. On the basis of these VOCs we prepared two mixtures that displayed a broad spectrum of antifungal activity. In postharvest experiments these mixtures prevented development of molds on wheat grains, and fully eliminated A. niger infection in peanuts. In light of these findings, we suggest use of D. cf. concentrica and/or its volatiles as an alternative approach to controlling phytopathogenic fungi in the food industry and in agriculture.

Current knowledge and perspectives of Paenibacillus: a review

Isolated from a wide range of sources, the genus Paenibacillus comprises bacterial species relevant to humans, animals, plants, and the environment. Many Paenibacillus species can promote crop growth directly via biological nitrogen fixation, phosphate solubilization, production of the phytohormone indole-3-acetic acid (IAA), and release of siderophores that enable iron acquisition. They can also offer protection against insect herbivores and phytopathogens, including bacteria, fungi, nematodes, and viruses. This is accomplished by the production of a variety of antimicrobials and insecticides, and by triggering a hypersensitive defensive response of the plant, known as induced systemic resistance (ISR). Paenibacillus-derived antimicrobials also have applications in medicine, including polymyxins and fusaricidins, which are nonribosomal lipopeptides first isolated from strains of Paenibacillus polymyxa. Other useful molecules include exo-polysaccharides (EPS) and enzymes such as amylases, cellulases, hemicellulases, lipases, pectinases, oxygenases, dehydrogenases, lignin-modifying enzymes, and mutanases, which may have applications for detergents, food and feed, textiles, paper, biofuel, and healthcare. On the negative side, Paenibacillus larvae is the causative agent of American Foulbrood, a lethal disease of honeybees, while a variety of species are opportunistic infectors of humans, and others cause spoilage of pasteurized dairy products. This broad review summarizes the major positive and negative impacts of Paenibacillus: its realised and prospective contributions to agriculture, medicine, process manufacturing, and bioremediation, as well as its impacts due to pathogenicity and food spoilage. This review also includes detailed information in Additional files 1, 2, 3 for major known Paenibacillus species with their locations of isolation, genome sequencing projects, patents, and industrially significant compounds and enzymes. Paenibacillus will, over time, play increasingly important roles in sustainable agriculture and industrial biotechnology.