Volatiles produced by the mycophagous soil bacteriumCollimonas

Enhanced surface colonisation and competition during bacterial adaptation to a fungus

Bacterial-fungal interactions influence microbial community performance of most ecosystems and elicit specific microbial behaviours, including stimulating specialised metabolite production. Here, we use a co-culture experimental evolution approach to investigate bacterial adaptation to the presence of a fungus, using a simple model of bacterial-fungal interactions encompassing the bacterium Bacillus subtilis and the fungus Aspergillus niger. We find in one evolving population that B. subtilis was selected for enhanced production of the lipopeptide surfactin and accelerated surface spreading ability, leading to inhibition of fungal expansion and acidification of the environment. These phenotypes were explained by specific mutations in the DegS-DegU two-component system. In the presence of surfactin, fungal hyphae exhibited bulging cells with delocalised secretory vesicles possibly provoking an RlmA-dependent cell wall stress. Thus, our results indicate that the presence of the fungus selects for increased surfactin production, which inhibits fungal growth and facilitates the competitive success of the bacterium.

Novel Pseudomonas Species Prevent the Growth of the Phytopathogenic Fungus Aspergillus flavus

In response to the escalating demand for sustainable agricultural methodologies, the utilization of microbial volatile organic compounds (VOCs) as antagonists against phytopathogens has emerged as a viable eco-friendly alternative. Microbial volatiles exhibit rapid diffusion rates, facilitating prompt chemical interactions. Moreover, microorganisms possess the capacity to emit volatiles constitutively, as well as in response to biological interactions and environmental stimuli. In addition to volatile compounds, these bacteria demonstrate the ability to produce soluble metabolites with antifungal properties, such as APE Vf, pyoverdin, and fragin. In this study, we identified two Pseudomonas strains (BJa3 and MCal1) capable of inhibiting the in vitro mycelial growth of the phytopathogenic fungus Aspergillus flavus, which serves as the causal agent of diseases in sugarcane and maize. Utilizing GC/MS analysis, we detected 47 distinct VOCs which were produced by these bacterial strains. Notably, certain volatile compounds, including 1-heptoxydecane and tridecan-2-one, emerged as primary candidates for inhibiting fungal growth. These compounds belong to essential chemical classes previously documented for their antifungal activity, while others represent novel molecules. Furthermore, examination via confocal microscopy unveiled significant morphological alterations, particularly in the cell wall, of mycelia exposed to VOCs emitted by both Pseudomonas species. These findings underscore the potential of the identified BJa3 and MCal1 Pseudomonas strains as promising agents for fungal biocontrol in agricultural crops.

Role of Microbial Volatile Organic Compounds in Promoting Plant Growth and Disease Resistance in Horticultural Production

Microbial volatile organic compounds (MVOCs) are a diverse group of volatile organic compounds that microorganisms may produce and release into the environment. These compounds have both positive and negative effects on plants, as they have been shown to be effective at mitigating stresses and functioning as immune stimulants. Furthermore, MVOCs modulate plant growth and systemic plant resistance, while also serving as attractants or repellents for insects and other stressors that pose threats to plants. Considering the economic value of strawberries as one of the most popular and consumed fruits worldwide, harnessing the benefits of MVOCs becomes particularly significant. MVOCs offer cost-effective and efficient solutions for disease control and pest management in horticultural production, as they can be utilized at low concentrations. This paper provides a comprehensive review of the current knowledge on microorganisms that contribute to the production of beneficial volatile organic compounds for enhancing disease resistance in fruit products, with a specific emphasis on broad horticultural production. The review also identifies research gaps and highlights the functions of MVOCs in horticulture, along with the different types of MVOCs that impact plant disease resistance in strawberry production. By offering a novel perspective on the application and utilization of volatile organic compounds in sustainable horticulture, this review presents an innovative approach to maximizing the efficiency of horticultural production through the use of natural products.

Bacterial volatiles elicit differential olfactory responses in insect species from the same and different trophic levels

Insect communities consist of species from several trophic levels that have to forage for suitable resources among and within larger patches of nonresources. To locate their resources, insects use diverse stimuli, including olfactory, visual, acoustic, tactile and gustatory cues. While most research has focused on cues derived from plants and other insects, there is mounting evidence that insects also respond to volatile organic compounds (VOCs) emitted by microorganisms. However, to date little is known about how the olfactory response of insects within and across different trophic levels is affected by bacterial VOCs. In this study, we used Y-tube bioassays and chemical analysis of VOCs to assess how VOCs emitted by bacteria affect the olfactory response of insects of the same and different trophic levels. Experiments were performed using two aphid species (Amphorophora idaei Börner and Myzus persicae var. nicotianae Blackman), three primary parasitoid species (Aphidius colemani Viereck, A. ervi Haliday, and A. matricariae Viereck), and two hyperparasitoid species (Asaphes suspensus Nees and Dendrocerus aphidum Rondani). Olfactory responses were evaluated for three bacterial strains (Bacillus pumilus ST18.16/133, Curtobacterium sp. ST18.16/085, and Staphylococcus saprophyticus ST18.16/160) that were isolated from the habitat of the insects. Results revealed that insects from all trophic levels responded to bacterial volatiles, but olfactory responses varied between and within trophic levels. All bacteria produced the same set of volatile compounds, but often in different relative concentrations. For 11 of these volatiles we found contrasting correlations between their concentration and the behavior of the primary parasitoids and hyperparasitoids. Furthermore, olfactometer experiments on three of these compounds confirmed the contrasting olfactory responses of primary parasitoids and hyperparasitoids. The potential of these findings for the development of novel semiochemical-based strategies to improve biological aphid control has been discussed.

Biocontrol of fungal phytopathogens by Bacillus pumilus

Plant growth-promoting bacteria are one of the most interesting methods of controlling fungal phytopathogens. These bacteria can participate in biocontrol via a variety of mechanisms including lipopeptide production, hydrolytic enzymes (e.g., chitinase, cellulases, glucanase) production, microbial volatile organic compounds (mVOCs) production, and induced systemic resistance (ISR) triggering. Among the bacterial genera most frequently studied in this aspect are Bacillus spp. including Bacillus pumilus. Due to the range of biocontrol traits, B. pumilus is one of the most interesting members of Bacillus spp. that can be used in the biocontrol of fungal phytopathogens. So far, a number of B. pumilus strains that exhibit biocontrol properties against fungal phytopathogens have been described, e.g., B. pumilus HR10, PTB180, B. pumilus SS-10.7, B. pumilus MCB-7, B. pumilus INR7, B. pumilus SE52, SE34, SE49, B. pumilus RST25, B. pumilus JK-SX001, and B. pumilus KUDC1732. B. pumilus strains are capable of suppressing phytopathogens such as Arthrobotrys conoides, Fusarium solani, Fusarium oxysporum, Sclerotinia sclerotiorum, Rhizoctonia solani, and Fagopyrum esculentum. Importantly, B. pumilus can promote plant growth regardless of whether it alters the native microbiota or not. However, in order to increase its efficacy, research is still needed to clarify the relationship between the native microbiota and B. pumilus. Despite that, it can already be concluded that B. pumilus strains are good candidates to be environmentally friendly and commercially effective biocontrol agents.

Long-term fertilization suppresses rice pathogens by microbial volatile compounds

Microbial volatile organic compounds (VOCs) can suppress plant pathogens. Although fertilization strongly affects soil microbial communities, the influence of fertilization on microbial VOC-mediated suppression of pathogens has not been elucidated. Soil was sampled from a paddy field that had been subjected to the following treatments for 30 years: a no-fertilizer control, mineral fertilization (NPK), NPK combined with rice straw (NPK + S), NPK combined with chicken manure (70% NPK + 30% M). Then, within a laboratory experiment, pathogens were exposed to VOCs without physical contact to assess the impact of VOCs emitted from paddy soils on in vitro growth of the fungal rice pathogens: Pyricularia oryzae and Rhizoctonia solani. The VOCs emitted from soil reduced the mycelial biomass of P. oryzae and R. solani by 36-51% and 10-30%, respectively, compared to that of the control (no soil; no VOCs emission). Overall, the highest suppression of P. oryzae and R. solani was in the NPK and NPK + S soils, which emitted more quinones, phenols, and low alcohols than NPK + M soils. The abundances of quinones and phenols in the soil air were maximal in the NPK-fertilized soil because the low ratio of dissolved organic carbon and Olsen-P increased the population of key species such as Acidobacteriae, Anaerolineae, and Entorrhizomycetes. The abundance of alcohols was minimum in the NPK + S fertilized soil because the high SOC content decreased the population of Sordariomycetes. In conclusion, mineral fertilization affects bacterial and fungal VOC emissions, thereby suppressing the growth of R. solani and P. oryzae.

Molecular advances in mycoremediation of polycyclic aromatic hydrocarbons: Exploring fungal bacterial interactions

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous high global concern environmental pollutants and tend to bioaccumulate due to hydrophobic properties. These xenobiotics, having variable concentrations along different matrices, gradually undergo various physical, chemical, and biological transformation processes. Myco-remediation aids accelerated degradation by effectively transforming complex ring structures to oxidized/hydroxylated intermediates, which can further funnel to bacterial degradation pathways. Exploitation of such complementing fungal-bacterial enzymatic activity can overcome certain limitations of incomplete bioremediation process. Furthermore, high-throughput molecular methods can be employed to unveil community structure, taxon abundance, coexisting community interactions, and metabolic pathways under stressed conditions. The present review critically discusses the role of different fungal phyla in PAHs biotransformation and application of fungal-bacterial cocultures for enhanced mineralization. Moreover, recent advances in bioassays for PAH residue detection, monitoring, developing xenobiotics stress-tolerant strains, and application of fungal catabolic enzymes are highlighted. Application of next-generation sequencing methods to reveal complex ecological networks based on microbial community interactions and data analysis bias in performing such studies is further discussed in detail. Conclusively, the review underscores the application of mixed-culture approach by critically highlighting in situ fungal-bacterial community nexus and its role in complete mineralization of PAHs for the management of contaminated sites.

Microbes-mediated sulphur cycling in soil: Impact on soil fertility, crop production and environmental sustainability

Reduction in soil fertility and depletion of natural resources due to current intensive agricultural practices along with climate changes are the major constraints for crop productivity and global food security. Diverse microbial populations' inhabiting the soil and rhizosphere participate in biogeochemical cycling of nutrients and thereby, improve soil fertility and plant health, and reduce the adverse impact of synthetic fertilizers on the environment. Sulphur is 4th most common crucial macronutrient required by all organisms including plants, animals, humans and microorganisms. Effective strategies are required to enhance sulphur content in crops for minimizing adverse effects of sulphur deficiency on plants and humans. Various microorganisms are involved in sulphur cycling in soil through oxidation, reduction, mineralization, and immobilization, and volatalization processes of diverse sulphur compounds. Some microorganisms possess the unique ability to oxidize sulphur compounds into plant utilizable sulphate (SO₄^2-) form. Considering the importance of sulphur as a nutrient for crops, many bacteria and fungi involved in sulphur cycling have been characterized from soil and rhizosphere. Some of these microbes have been found to positively affect plant growth and crop yield through multiple mechanisms including the enhanced mobilization of nutrients in soils (i.e., sulphate, phosphorus and nitrogen), production of growth-promoting hormones, inhibition of phytopathogens, protection against oxidative damage and mitigation of abiotic stresses. Application of these beneficial microbes as biofertilizers may reduce the conventional fertilizer application in soils. However, large-scale, well-designed, and long-term field trials are necessary to recommend the use of these microbes for increasing nutrient availability for growth and yield of crop plants. This review discusses the current knowledge regarding sulphur deficiency symptoms in plants, biogeochemical cycling of sulphur and inoculation effects of sulphur oxidizing microbes in improving plant biomass and crop yield in different crops.

Exploring the Interspecific Interactions and the Metabolome of the Soil Isolate Hylemonella gracilis

Microbial community analysis of aquatic environments showed that an important component of its microbial diversity consists of bacteria with cell sizes of ~0.1 μm. Such small bacteria can show genomic reductions and metabolic dependencies with other bacteria. However, so far, no study has investigated if such bacteria exist in terrestrial environments like soil. Here, we isolated soil bacteria that passed through a 0.1-μm filter. The complete genome of one of the isolates was sequenced and the bacterium was identified as Hylemonella gracilis. A set of coculture assays with phylogenetically distant soil bacteria with different cell and genome sizes was performed. The coculture assays revealed that H. gracilis grows better when interacting with other soil bacteria like Paenibacillus sp. AD87 and Serratia plymuthica. Transcriptomics and metabolomics showed that H. gracilis was able to change gene expression, behavior, and biochemistry of the interacting bacteria without direct cell-cell contact. Our study indicates that in soil there are bacteria that can pass through a 0.1-μm filter. These bacteria may have been overlooked in previous research on soil microbial communities. Such small bacteria, exemplified here by H. gracilis, can induce transcriptional and metabolomic changes in other bacteria upon their interactions in soil. In vitro, the studied interspecific interactions allowed utilization of growth substrates that could not be utilized by monocultures, suggesting that biochemical interactions between substantially different sized soil bacteria may contribute to the symbiosis of soil bacterial communities. IMPORTANCE Analysis of aquatic microbial communities revealed that parts of its diversity consist of bacteria with cell sizes of ~0.1 μm. Such bacteria can show genomic reductions and metabolic dependencies with other bacteria. So far, no study investigated if such bacteria exist in terrestrial environments such as soil. Here, we show that such bacteria also exist in soil. The isolated bacteria were identified as Hylemonella gracilis. Coculture assays with phylogenetically different soil bacteria revealed that H. gracilis grows better when cocultured with other soil bacteria. Transcriptomics and metabolomics showed that H. gracilis was able to change gene expression, behavior, and biochemistry of the interacting bacteria without direct contact. Our study revealed that bacteria are present in soil that can pass through 0.1-μm filters. Such bacteria may have been overlooked in previous research on soil microbial communities and may contribute to the symbiosis of soil bacterial communities.

Volatiles of the Apicomplexan Alga Chromera velia and Associated Bacteria

Volatiles released by the apicomplexan alga Chromera velia CCAP1602/1 and their associated bacteria have been investigated. A metagenome analysis allowed the identification of the most abundant heterotrophic bacteria of the phycosphere, but the isolation of additional strains showed that metagenomics underestimated the complexity of the algal microbiome, However, a culture-independent approach revealed the presence of a planctomycete that likely represents a novel bacterial family. We analysed algal and bacterial volatiles by open-system-stripping analysis (OSSA) on Tenax TA desorption tubes, followed by thermodesorption, cryofocusing and GC-MS-analysis. The analyses of the alga and the abundant bacterial strains Sphingopyxis litoris A01A-101, Algihabitans albus A01A-324, "Coraliitalea coralii" A01A-333 and Litoreibacter sp. A01A-347 revealed sulfur- and nitrogen-containing compounds, ketones, alcohols, aldehydes, aromatic compounds, amides and one lactone, as well as the typical algal products, apocarotenoids. The compounds were identified by gas chromatographic retention indices, comparison of mass spectra and syntheses of reference compounds. A major algal metabolite was 3,4,4-trimethylcyclopent-2-en-1-one, an apocarotenoid indicating the presence of carotenoids related to capsanthin, not reported from algae so far. A low overlap in volatiles bouquets between C. velia and the bacteria was found, and the xenic algal culture almost exclusively released algal components.

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.

Do Volatiles Affect Bacteria and Plants in the Same Way? Growth and Biochemical Response of Non-Stressed and Cd-Stressed Arabidopsis thaliana and Rhizobium E20-8

Plant roots are colonized by rhizobacteria, and these soil microorganisms can not only stimulate plant growth but also increase tolerance to stress through the production of volatile organic compounds. However, little is known about the effect that these plant beneficial volatiles may have on bacteria. In this study, the effects on growth and oxidative status of different concentrations of three volatiles already reported to have a positive influence on plant growth (2-butanone, 3-methyl-1-butanol, and 2,3-butanediol) were determined in A. thaliana and Rhizobium sp. strain E20-8 via airborne exposure in the presence and absence of Cd. It was expected to ascertain if the plant and the bacterium are influenced in the same way by the volatiles, and if exposure to stress (Cd) shifts the effects of volatiles on plants and bacteria. Results showed the antioxidant activity of the volatiles protecting the plant cell metabolism from Cd toxicity and increasing plant tolerance to Cd. Effects on bacteria were less positive. The two alcohols (3-methyl-1-butanol and 2,3-butanediol) increased Cd toxicity, and the ketone (2-butanone) was able to protect Rhizobium from Cd stress, constituting an alternative way to protect soil bacterial communities from stress. The application of 2-butanone thus emerges as an alternative way to increase crop production and crop resilience to stress in a more sustainable way, either directly or through the enhancement of PGPR activity.

Root-Associated Microbiomes of Panax notoginseng under the Combined Effect of Plant Development and Alpinia officinarum Hance Essential Oil

Essential oils (EOs) have been proposed as an alternative to conventional pesticides to inhibit fungal pathogens. However, the application of EOs is considerably limited due to their highly volatile nature and unpredictable effects on other microbes. In our study, the composition of bacterial and fungal communities from the rhizosphere soil of P. notoginseng under four treatment levels of Alpinia officinarum Hance EO was characterized over several growth stages. Leaf weight varied dramatically among the four EO treatment levels after four months of growth, and the disease index at a low concentration (0.14 mg/g) of EO addition was the lowest among the P. notoginseng growth stages. The content of monomeric saponins was elevated when EO was added. Bacterial and fungal diversity in the absence of plants showed a decreasing trend with increasing levels of EO. Bacterial diversity recovery was more correlated with plant growth than was fungal diversity recovery. Compared with the control (no EO addition), a low concentration of EO significantly accumulated Actinomycota, including Acidothermus, Blastococcus, Catenulispora, Conexibacter, Rhodococcus, and Sinomonas, after one month of plant-microbial interaction. Overall, the results showed that both the plant growth stage and EOs drive changes in the microbial community composition in the rhizosphere of P. notoginseng. Plant development status had a stronger influence on bacterial diversity than on fungal diversity. EO had a more significant effect on fungal community composition, increasing the dominance of Ascomycota when EO concentration was increased. Under the interaction of P. notoginseng growth and EO, a large number of bacterial genera that have been described as plant growth-promoting rhizobacteria (PGPR) responded positively to low concentrations of EO application, suggesting that EO may recruit beneficial microbes in the root zone to cope with pathogens and reduce root rot disease. These results offer novel insights into the relationship between EO application, altered microbial communities in the plant roots, plant growth stage, and disease occurrence.

Profiling of Volatile Organic Compounds from Four Plant Growth-Promoting Rhizobacteria by SPME–GC–MS: A Metabolomics Study

The rhizosphere microbiome is a major determinant of plant health. Plant-beneficial or plant growth-promoting rhizobacteria (PGPR) influence plant growth, plant development and adaptive responses, such as induced resistance/priming. These new eco-friendly choices have highlighted volatile organic compounds (biogenic VOCs) as a potentially inexpensive, effective and efficient substitute for the use of agrochemicals. Secreted bacterial VOCs are low molecular weight lipophilic compounds with a low boiling point and high vapor pressures. As such, they can act as short- or long-distance signals in the rhizosphere, affecting competing microorganisms and impacting plant health. In this study, secreted VOCs from four PGPR strains (Pseudomonas koreensis (N19), Ps. fluorescens (N04), Lysinibacillus sphaericus (T19) and Paenibacillus alvei (T22)) were profiled by solid-phase micro-extraction gas chromatography mass spectrometry (SPME–GC–MS) combined with a multivariate data analysis. Metabolomic profiling with chemometric analyses revealed novel data on the composition of the secreted VOC blends of the four PGPR strains. Of the 121 annotated metabolites, most are known as bioactives which are able to affect metabolism in plant hosts. These VOCs belong to the following classes: alcohols, aldehydes, ketones, alkanes, alkenes, acids, amines, salicylic acid derivatives, pyrazines, furans, sulfides and terpenoids. The results further demonstrated the presence of species-specific and strain-specific VOCs, characterized by either the absence or presence of specific VOCs in the different strains. These molecules could be further investigated as biomarkers for the classification of an organism as a PGPR and selection for agricultural use.

Elicitation of Innate Immunity by a Bacterial Volatile 2-Nonanone at Levels below Detection Limit in Tomato Rhizosphere

Bacterial volatile compounds (BVCs) exert beneficial effects on plant protection both directly and indirectly. Although BVCs have been detected in vitro, their detection in situ remains challenging. The purpose of this study was to investigate the possibility of BVCs detection under in situ condition and estimate the potentials of in situ BVC to plants at below detection limit. We developed a method for detecting BVCs released by the soil bacteria Bacillus velezensis strain GB03 and Streptomyces griseus strain S4-7 in situ using solid-phase microextraction coupled with gas chromatography-mass spectrometry (SPME-GC-MS). Additionally, we evaluated the BVC detection limit in the rhizosphere and induction of systemic immune response in tomato plants grown in the greenhouse. Two signature BVCs, 2-nonanone and caryolan-1-ol, of GB03 and S4-7 respectively were successfully detected using the soil-vial system. However, these BVCs could not be detected in the rhizosphere pretreated with strains GB03 and S4-7. The detection limit of 2-nonanone in the tomato rhizosphere was 1 µM. Unexpectedly, drench application of 2-nonanone at 10 nM concentration, which is below its detection limit, protected tomato seedlings against Pseudomonas syringae pv. tomato. Our finding highlights that BVCs, including 2-nonanone, released by a soil bacterium are functional even when present at a concentration below the detection limit of SPME-GC-MS.

Bacterial Volatiles Known to Inhibit Phytophthora infestans Are Emitted on Potato Leaves by Pseudomonas Strains

Bacterial volatiles play important roles in mediating beneficial interactions between plants and their associated microbiota. Despite their relevance, bacterial volatiles are mostly studied under laboratory conditions, although these strongly differ from the natural environment bacteria encounter when colonizing plant roots or shoots. In this work, we ask the question whether plant-associated bacteria also emit bioactive volatiles when growing on plant leaves rather than on artificial media. Using four potato-associated Pseudomonas, we demonstrate that potato leaves offer sufficient nutrients for the four strains to grow and emit volatiles, among which 1-undecene and Sulfur compounds have previously demonstrated the ability to inhibit the development of the oomycete Phytophthora infestans, the causative agent of potato late blight. Our results bring the proof of concept that bacterial volatiles with known plant health-promoting properties can be emitted on the surface of leaves and warrant further studies to test the bacterial emission of bioactive volatiles in greenhouse and field-grown plants.

Plant growth-promoting and non-promoting rhizobacteria from avocado trees differentially emit volatiles that influence growth of Arabidopsis thaliana

Microbial volatile organic compounds (mVOCs) play important roles in inter- and intra-kingdom interactions, and they are also important as signal molecules in physiological processes acting either as plant growth-promoting or negatively modulating plant development. We investigated the effects of mVOCs emitted by PGPR vs non-PGPR from avocado trees (Persea americana) on growth of Arabidopsis thaliana seedlings. Chemical diversity of mVOCs was determined by SPME-GC-MS; selected compounds were screened in dose-response experiments in A. thaliana transgenic lines. We found that plant growth parameters were affected depending on inoculum concentration. Twenty-six compounds were identified in PGPR and non-PGPR with eight of them not previously reported. The VOCs signatures were differential between those groups. 4-methyl-2-pentanone, 1-nonanol, 2-phenyl-2-propanol and ethyl isovalerate modified primary root architecture influencing the expression of auxin- and JA-responsive genes, and cell division. Lateral root formation was regulated by 4-methyl-2-pentanone, 3-methyl-1-butanol, 1-nonanol and ethyl isovalerate suggesting a participation via JA signalling. Our study revealed the differential emission of volatiles by PGPR vs non-PGPR from avocado trees and provides a general view about the mechanisms by which those volatiles influence plant growth and development. Rhizobacteria strains and mVOCs here reported are promising for improvement the growth and productivity of avocado crop.

Antimicrobial Volatiles of the Insect Pathogen Metarhizium brunneum

Fungal volatile organic compounds (VOCs) represent promising candidates for biopesticide fumigants to control crop pests and pathogens. Herein, VOCs produced using three strains of the entomopathogenic fungus Metarhizium brunneum were identified via GC-MS and screened for antimicrobial activity. The VOC profiles varied with fungal strain, development state (mycelium, spores) and culture conditions. Selected VOCs were screened against a range of rhizosphere and non-rhizosphere microbes, including three Gram-negative bacteria (Escherichia coli, Pantoea agglomerans, Pseudomonas aeruginosa), five Gram-positive bacteria (Micrococcus luteus, Staphylococcus aureus, Bacillus subtilis, B. megaterium, B. thuringiensis), two yeasts (Candida albicans, Candida glabrata) and three plant pathogenic fungi (Pythium ultimum, Botrytis cinerea, Fusarium graminearum). Microbes differed in their sensitivity to the test compounds, with 1-octen-3-ol and isovaleric acid showing broad-spectrum antimicrobial activity. Yeasts and bacteria were inhibited by the same VOCs. Cryo-SEM showed that both yeasts and bacteria underwent some form of “autolysis”, where all components of the cell, including the cell wall, disintegrated with little evidence of their presence in the clear, inhibition zone. The oomycete (P. ultimum) and ascomycete fungi (F. graminearum, B. cinerea) were sensitive to a wider range of VOCs than the bacteria, suggesting that eukaryotic microbes are the main competitors to M. brunneum in the rhizosphere. The ability to alter the VOC profile in response to nutritional cues may assist M. brunneum to survive among the roots of a wide range of plant species. Our VOC studies provided new insights as to how M. brunneum may protect plants from pathogenic microbes and correspondingly promote healthy growth.

Air Ambulance: Antimicrobial Power of Bacterial Volatiles

We are currently facing an antimicrobial resistance crisis, which means that a lot of bacterial pathogens have developed resistance to common antibiotics. Hence, novel and innovative solutions are urgently needed to combat resistant human pathogens. A new source of antimicrobial compounds could be bacterial volatiles. Volatiles are ubiquitous produced, chemically divers and playing essential roles in intra- and interspecies interactions like communication and antimicrobial defense. In the last years, an increasing number of studies showed bioactivities of bacterial volatiles, including antibacterial, antifungal and anti-oomycete activities, indicating bacterial volatiles as an exciting source for novel antimicrobial compounds. In this review we introduce the chemical diversity of bacterial volatiles, their antimicrobial activities and methods for testing this activity. Concluding, we discuss the possibility of using antimicrobial volatiles to antagonize the antimicrobial resistance crisis.

Impact of bacterial volatiles on phytopathogenic fungi: an in vitro study on microbial competition and interaction

Microorganisms in the rhizosphere are abundant and exist in very high taxonomic diversity. The major players are bacteria and fungi, and bacteria have evolved many strategies to prevail over fungi, among them harmful enzyme activities and noxious secondary metabolites. Interactions between plant growth promoting rhizobacteria and phytopathogenic fungi are potentially valuable since the plant would benefit from fungal growth repression. In this respect, the role of volatile bacterial metabolites in fungistasis has been demonstrated, but the mechanisms of action are less understood. We used three phytopathogenic fungal species (Sclerotinia sclerotiorum, Rhizoctonia solani, and Juxtiphoma eupyrena) as well as one non-phytopathogenic species (Neurospora crassa) and the plant growth promoting rhizobacterium Serratia plymuthica 4Rx13 in co-cultivation assays to investigate the influence of bacterial volatile metabolites on fungi on a cellular level. As a response to the treatment, we found elevated lipid peroxidation, which indirectly reflected the loss of fungal cell membrane integrity. An increase in superoxide dismutase, catalase, and laccase activities indicated oxidative stress. Acclimation to these adverse growth conditions completely restored fungal growth. One of the bioactive bacterial volatile compounds seemed to be ammonia, which was a component of the bacterial volatile mixture. Applied as a single compound in biogenic concentrations ammonia also caused an increase in lipid peroxidation and enzyme activities, but the extent and pattern did not fully match the effect of the entire bacterial volatile mixture.

Bacterial volatile organic compounds induce adverse ultrastructural changes and DNA damage to the sugarcane pathogenic fungus Thielaviopsis ethacetica

Due to an increasing demand for sustainable agricultural practices, the adoption of microbial volatile organic compounds (VOCs) as antagonists against phytopathogens has emerged as an eco-friendly alternative to the use of agrochemicals. Here, we identified three Pseudomonas strains that were able to inhibit, in vitro, up to 80% of mycelial growth of the phytopathogenic fungus Thielaviopsis ethacetica, the causal agent of pineapple sett rot disease in sugarcane. Using GC/MS, we found that these bacteria produced 62 different VOCs, and further functional validation revealed compounds with high antagonistic activity to T. ethacetica. Transcriptomic analysis of the fungal response to VOCs indicated that these metabolites downregulated genes related to fungal central metabolism, such as those involved in carbohydrate metabolism. Interestingly, genes related to the DNA damage response were upregulated, and micro-FTIR analysis corroborated our hypothesis that VOCs triggered DNA damage. Electron microscopy analysis showed critical morphological changes in mycelia treated with VOCs. Altogether, these results indicated that VOCs hampered fungal growth and could lead to cell death. This study represents the first demonstration of the molecular mechanisms involved in the antagonism of sugarcane phytopathogens by VOCs and reinforces that VOCs can be a sustainable alternative for use in phytopathogen biocontrol.

Volatile Organic Compounds from Bacillus aryabhattai MCCC 1K02966 with Multiple Modes against Meloidogyne incognita

Plant-parasitic nematodes cause severe losses to crop production and economies all over the world. Bacillus aryabhattai MCCC 1K02966, a deep-sea bacterium, was obtained from the Southwest Indian Ocean and showed nematicidal and fumigant activities against Meloidogyne incognita in vitro. The nematicidal volatile organic compounds (VOCs) from the fermentation broth of B. aryabhattai MCCC 1K02966 were investigated further using solid-phase microextraction gas chromatography-mass spectrometry. Four VOCs, namely, pentane, 1-butanol, methyl thioacetate, and dimethyl disulfide, were identified in the fermentation broth. Among these VOCs, methyl thioacetate exhibited multiple nematicidal activities, including contact nematicidal, fumigant, and repellent activities against M. incognita. Methyl thioacetate showed a significant contact nematicidal activity with 87.90% mortality at 0.01 mg/mL by 72 h, fumigant activity in mortality 91.10% at 1 mg/mL by 48 h, and repellent activity at 0.01-10 mg/mL. In addition, methyl thioacetate exhibited 80-100% egg-hatching inhibition on the 7th day over the range of 0.5 mg/mL to 5 mg/mL. These results showed that methyl thioacetate from MCCC 1K02966 control M. incognita with multiple nematicidal modes and can be used as a potential biological control agent.

Effects of volatile sulfur compounds on growth and oxidative stress of Rhizobium leguminosarum E20-8 exposed to cadmium

Volatile sulfur compounds (VSCs) have been reported to be produced by many bacterial species. Depending on the compound, they can negatively influence some organisms (fungi, nematodes and insects) or promote plant growth. Some of these compounds have also been hypothesized to play a role in bacterial response to cadmium (Cd) induced stress. This study aimed to assess the potential effects of four VSCs (dimethyl sulfide - DMS, dimethyl disulfide - DMDS, dimethyl trisulfide - DMTS and methyl thioacetate - MTA) on the growth and oxidative status of Rhizobium sp. strain E20-8 via airborne exposure, in order to test the hypothesis that these volatile compounds can influence growth and tolerance to cadmium. Our results show that, overall, the tested compounds triggered similar antioxidant mechanisms in Rhizobium in the presence of Cd. The protective effect at the membrane level by DMDS and DMTS particularly demonstrates the antioxidant effect of these volatiles, with reductions of up to 50% (DMS) and 80% (DMTS) in lipid peroxidation levels. Due to the volatile nature of these compounds, the low concentrations tested (1 nM to 100 mM), and considering that they are released by bacteria and other organisms such as plants, it is possible that these effects also occur in the soil ecosystem.

Cochlodiniinecator piscidefendens gen. nov., sp. nov., an algicidal bacterium against the ichthyotoxic dinoflagellate Cochlodinium polykrikoides

Harmful algal blooms caused by Cochlodinium polykrikoides result in enormous economic damage to the aquaculture industry. Biological control methods have attracted wide attention due to their environmental-friendliness. In this study, a novel algicidal bacterium, designated strain M26A2M^T, was determined for its taxonomic position and was evaluated for its potential to mitigate C. polykrikoides blooms. Strain M26A2M^T exhibited the highest 16S rRNA gene sequence similarity to the type strains of Planktotalea lamellibrachiae (97.3%), Halocynthiibacter namhaensis (97.2%), Pseudohalocynthiibacter aestuariivivens (96.8%) and Halocynthiibacter arcticus (96.4%) in the family Rhodobacteraceae. The predominant fatty acids were C_{10 : 0} 3-OH and summed feature 8 (comprising C_{18 : 1} ω7c and/or C_{18 : 1} ω6c). The major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid and three unidentified lipids. Q-10 was the respiratory quinone. Strain M26A2M^T exerted significant algicidal activity against C. polykrikoides cells by destroying the membrane integrity and the photosynthetic system. Our findings suggest that strain M26A2M^T shows a high potential to control outbreaks of C. polykrikoides. Based on the polyphasic characterization, strain M26A2M^T is considered to represent a novel species within a novel genus of the family Rhodobacteraceae, for which the name Cochlodiniinecator piscidefendens gen. nov., sp. nov. is proposed. The type strain is M26A2M^T (=KCTC 82083^T=JCM 34119^T).

It Takes Two to Tango: A Bacterial Biofilm Provides Protection against a Fungus-Feeding Bacterial Predator

Fungus-bacterium interactions are widespread, encompass multiple interaction types from mutualism to parasitism, and have been frequent targets for microbial inoculant development. In this study, using in vitro systems combined with confocal laser scanning microscopy and real-time quantitative PCR, we test whether the nitrogen-fixing bacterium Kosakonia radicincitans can provide protection to the plant-beneficial fungus Serendipita indica, which inhabits the rhizosphere and colonizes plants as an endophyte, from the fungus-feeding bacterium Collimonas fungivorans. We show that K. radicincitans can protect fungal hyphae from bacterial feeding on solid agar medium, with probable mechanisms being quick hyphal colonization and biofilm formation. We furthermore find evidence for different feeding modes of K. radicincitans and C. fungivorans, namely “metabolite” and “hyphal feeding”, respectively. Overall, we demonstrate, to our knowledge, the first evidence for a bacterial, biofilm-based protection of fungal hyphae against attack by a fungus-feeding, bacterial predator on solid agar medium. Besides highlighting the importance of tripartite microbial interactions, we discuss implications of our results for the development and application of microbial consortium-based bioprotectants and biostimulants.

The Rhizobacterium Pseudomonas alcaligenes AVO110 Induces the Expression of Biofilm-Related Genes in Response to Rosellinia necatrix Exudates

The rhizobacterium Pseudomonas alcaligenes AVO110 exhibits antagonism toward the phytopathogenic fungus Rosellinia necatrix. This strain efficiently colonizes R. necatrix hyphae and is able to feed on their exudates. Here, we report the complete genome sequence of P. alcaligenes AVO110. The phylogeny of all available P. alcaligenes genomes separates environmental isolates, including AVO110, from those obtained from infected human blood and oyster tissues, which cluster together with Pseudomonas otitidis. Core and pan-genome analyses showed that P. alcaligenes strains encode highly heterogenic gene pools, with the AVO110 genome encoding the largest and most exclusive variable region (~1.6 Mb, 1795 genes). The AVO110 singletons include a wide repertoire of genes related to biofilm formation, several of which are transcriptionally modulated by R. necatrix exudates. One of these genes (cmpA) encodes a GGDEF/EAL domain protein specific to Pseudomonas spp. strains isolated primarily from the rhizosphere of diverse plants, but also from soil and water samples. We also show that CmpA has a role in biofilm formation and that the integrity of its EAL domain is involved in this function. This study contributes to a better understanding of the niche-specific adaptations and lifestyles of P. alcaligenes, including the mycophagous behavior of strain AVO110.

Tulbaghia violacea (Harv) Exerts its Antifungal Activity by Reducing Ergosterol Production in Aspergillus flavus

Opportunistic infections in immunosuppressed patients have led to an increase in fungal infections, with Aspergillus being one of the main causative agents. Medicinal plants exhibiting antifungal activity have the potential to be used as chemotherapeutic agents. However, often their mechanisms of action are not fully researched. Tulbaghia violacea exhibits antifungal activity towards Candida, Aspergillus flavus and Aspergillus parasiticus but its mode of action has only recently begun to be investigated. This study aimed to ascertain the effect of T. violacea rhizome extracts on ergosterol production in A. flavus and the mechanism of inhibition. The MIC of a T. violacea rhizome extract against A. flavus was first determined, using a broth dilution assay, to be 15 mg/ml. Thereafter, the culture was subjected to sub-inhibitory concentrations of the extract before sterol intermediates of the ergosterol biosynthetic pathway were isolated and analysed for dose-dependent accumulation. Analysis by reverse-phase HPLC displayed a decline in ergosterol production in a dose-dependent manner when exposed to increasing concentrations of T. violacea extract. Quantification of the sterol intermediates of the ergosterol pathway indicated a definite accumulation of 2,3-oxidosqualene. The results prove that the plant extract affected ergosterol synthesis by inhibiting oxidosqualene cyclase. This prevented the formation of downstream intermediates of the ergosterol pathway ultimately resulting in inhibition of ergosterol production.

Diffusible Compounds Produced by Hanseniaspora osmophila and Gluconobacter cerinus Help to Control the Causal Agents of Gray Rot and Summer Bunch Rot of Table Grapes

Gray and summer bunch rot are important diseases of table grapes due to the high economic and environmental cost of their control with synthetic fungicides. The ability to produce antifungal compounds against the causal agents Botrytis, Aspergillus, Penicillium, and Rhizopus of two microorganisms isolated from table grapes and identified as Hanseniaspora osmophila and Gluconobacter cerinus was evaluated. In dual cultures, both biocontrol agents (together and separately) inhibited in vitro mycelial growth of these pathogens. To identify the compounds responsible for the inhibitory effect, extractions were carried out with organic solvents from biocontrol agents separately. Through dual cultures with pathogens and pure extracts, only the hexane extract from H. osmophila showed an inhibitory effect against Botrytis cinerea. To further identify these compounds, the direct bioautography technique was used. This technique made it possible to determine the band displaying antifungal activity at Rf = 0.05–0.2. The compounds present in this band were identified by GC-MS and compared to the NIST library. The most abundant compounds, not previously reported, corresponded to alkanes, ketones, alcohols, and terpenoids. H. osmophila and G. cerinus have the potential to control the causal agents of gray and summer bunch rot of table grapes.

Microbial volatile organic compounds in intra-kingdom and inter-kingdom interactions

Microorganisms produce and excrete a versatile array of metabolites with different physico-chemical properties and biological activities. However, the ability of microorganisms to release volatile compounds has only attracted research attention in the past decade. Recent research has revealed that microbial volatiles are chemically very diverse and have important roles in distant interactions and communication. Microbial volatiles can diffuse fast in both gas and water phases, and thus can mediate swift chemical interactions. As well as constitutively emitted volatiles, microorganisms can emit induced volatiles that are triggered by biological interactions or environmental cues. In this Review, we highlight recent discoveries concerning microbial volatile compounds and their roles in intra-kingdom microbial interactions and inter-kingdom interactions with plants and insects. Furthermore, we indicate the potential biotechnological applications of microbial volatiles and discuss challenges and perspectives in this emerging research field.

Volatile organic compounds profile synthesized and released by endophytes of tomato (Solanum lycopersici L.) and their antagonistic role

The endophytic microbiome uses mechanisms such as the secretion of diffusible antibiotic molecules, synthesis and release of volatile organic compounds, and/or toxins to protect plants. The aim of this research was to study the volatile organic compounds (VOCs) profile as well as the diffusible secondary metabolites produced and released by endophytic bacteria isolated from tomato plants that in in-vitro assays prevented growth of pathogenic fungi. Bacteria belonging to seven genera (Acinetobacter, Arthrobacter, Bacillus, Microbacterium, Pantoea, Pseudomonas, and Stenotrophomonas) were isolated from different tissues of tomato plants with and without symptoms of Gray leaf spot, a disease provoked by Stemphylium lycopersici. In vitro, antagonistic assays were performed and the effect of volatile and soluble compounds released by endophytic bacteria on the growth of pathogenic fungi was determined. The VOCs synthesized by the endophytes were extracted, identified and quantified. These isolates representatives of seven bacterial genera inhibited the growth of three fungal pathogens of tomato S. lycopersici, Alternaria alternata and Corynespora cassiicola, which was related to the synthesis of soluble compounds as well as VOCs. Endophytes synthesize and release different VOCs, probably due to the different type of interaction that each bacterium establishes with the fungus, presenting a range of fungal growth inhibition.

Volatile-Mediated Inhibitory Activity of Rhizobacteria as a Result of Multiple Factors Interaction: The Case of Lysobacter capsici AZ78

Plant beneficial rhizobacteria may antagonize soilborne plant pathogens by producing a vast array of volatile organic compounds (VOCs). The production of these compounds depends on the medium composition used for bacterial cell growth. Accordingly, Lysobacter capsici AZ78 (AZ78) grown on a protein-rich medium was previously found to emit volatile pyrazines with toxic activity against soilborne phypathogenic fungi and oomycetes. However, the discrepancy between the quantity of pyrazines in the gaseous phase and the minimum quantity needed to achieve inhibition of plant pathogens observed, lead us to further investigate the volatile-mediated inhibitory activity of AZ78. Here, we show that, besides VOCs, AZ78 cells produce ammonia in increased amounts when a protein-rich medium is used for bacterial growth. The production of this volatile compound caused the alkalinization of the physically separated culture medium where Rhizoctonia solani was inoculated subsequently. Results achieved in this work clearly demonstrate that VOC, ammonia and the growth medium alkalinization contribute to the overall inhibitory activity of AZ78 against R. solani. Thus, our findings suggest that the volatile-mediated inhibitory activity of rhizobacteria in protein-rich substrates can be regarded as a result of multiple factors interaction, rather than exclusively VOCs production.

Fungal volatiles mediate cheese rind microbiome assembly

In vitro studies in plant, soil, and human systems have shown that microbial volatiles can mediate microbe-microbe or microbe-host interactions. These previous studies have often used artificially high concentrations of volatiles compared to in situ systems and have not demonstrated the roles volatiles play in mediating community-level dynamics. We used the notoriously volatile cheese rind microbiome to identify bacteria responsive to volatiles produced by five widespread cheese fungi. Vibrio casei had the strongest growth stimulation when exposed to all fungi. In multispecies community experiments, fungal volatiles caused a shift to a Vibrio-dominated community, potentially explaining the widespread occurrence of Vibrio in surface-ripened cheeses. RNA sequencing identified activation of the glyoxylate shunt as a possible mechanism underlying volatile-mediated growth promotion and community assembly. Our study demonstrates how airborne chemicals could be used to control the composition of microbiomes and illustrates how volatiles may impact the development of cheese rinds.

Chemical Compositions and In Vitro Antiphytopathogenic Fungi Activities of the Leaf and Cones Essential Oils ofCunninghamia lanceolataFrom Taiwan

In this study, antiphytopathogenic fungi activities of the leaf and cones essential oils and its constituents from Cunninghamia lanceolata were evaluated in vitro against 6 plant pathogenic fungi. The main compounds responsible for the antiphytopathogenic fungi activities were isolated and identified. The essential oil from the fresh leaves and cones of C. lanceolata was isolated using hydrodistillation in a Clevenger-type apparatus, and characterized by GC-FID and GC-MS, respectively. The leaf oil consisted primarily of ferruginol (10%), τ-cadinol (8.2%), and α-cadinol (6.6%); the cones oil’s main constituents were abietadiene (42.5%), abietatriene (13.1%), and α-pinene (9.6%). Comparing the antiphytopathogenic fungi activities of the oils suggested that leaf oil was the most effective one. Further fractionation of the leaf oil produced ferruginol, τ-cadinol, and α-cadinol. The 3 compounds exhibited very strong antiphytopathogenic fungi activities. For the antiphytopathogenic fungi activities of the leaf oil, the active source compounds were determined to be ferruginol, τ-cadinol, and α-cadinol.

Non-rhizobial endophytic (NRE) yeasts assist nodulation of Rhizobium in root nodules of blackgram (Vigna mungo L.)

The signal orchestration between legumes and the rhizobia attribute to symbiotic nitrogen fixation through nodule formation. Root nodules serve as a nutrient-rich reservoir and harbor diverse microbial communities. However, the existence of non-rhizobial endophytes (NRE) and their role inside the root nodules are being explored; there is no evidence on yeast microflora inhabiting nodule niche. This study focused on unraveling the presence of yeast in the root nodules and their possible function in either nodulation or signal exchange. From the root nodules of blackgram, two yeast strains were isolated and identified as Candida glabrata VYP1 and Candida tropicalis VYW1 based on 18S rRNA gene sequencing and phylogeny. These strains possessed plant growth-promoting traits viz., IAA, ACC deaminase, siderophore, ammonia, and polyamine production. The functional capacity of endophytic yeast strains, and their interaction with Rhizobium sp. was further unveiled via profiling volatile organic compounds (VOC). Among the VOCs, α-glucopyranoside and pyrroloquinoline pitches a pivotal role in activating lectin pathways and phosphorous metabolism. Further, lectin pathways are crucial for nodulating bacterium, and our study showed that these endophytic yeasts assist nodulation by Rhizobium sp. via activating the nod factors. The plant growth-promoting traits of NRE yeast strains coupled with their metabolite production, could recruit them as potential drivers in the plant-microbe interaction.

A non-invasive soil-based setup to study tomato root volatiles released by healthy and infected roots

The role of root exudates in mediating plant–microbe interactions has been well documented. However, the function of volatile organic compounds (VOCs) emitted by plant roots has only recently begun to attract attention. This newly recognized relevance of belowground VOCs has so far mostly been tested using systems limited to a two-compartment Petri-dish design. Furthermore, many of the plant–microbe interaction studies have only investigated the effects of microbial VOCs on plant growth. Here, we go two steps further. First we investigated the volatile profile of healthy and pathogen (Fusarium oxysporum) infected tomato roots grown in soil. We then used a unique soil-based olfactometer-choice assay to compare the migration pattern of four beneficial bacteria (Bacillus spp.) towards the roots of the tomato plants. We demonstrate that the blend of root-emitted VOCs differs between healthy and diseased plants. Our results show that VOCs are involved in attracting bacteria to plant roots.

Pathogen suppression by microbial volatile organic compounds in soils

There is increasing evidence that microbial volatile organic compounds (mVOCs) play an important role in interactions between microbes in soils. In this minireview, we zoom in on the possible role of mVOCs in the suppression of plant-pathogenic soil fungi. In particular, we have screened the literature to see what the actual evidence is that mVOCs in soil atmospheres can contribute to pathogen suppression. Furthermore, we discuss biotic and abiotic factors that influence the production of suppressive mVOCs in soils. Since microbes producing mVOCs in soils are part of microbial communities, community ecological aspects such as diversity and assembly play an important role in the composition of produced mVOC blends. These aspects have not received much attention so far. In addition, the fluctuating abiotic conditions in soils, such as changing moisture contents, influence mVOC production and activity. The biotic and abiotic complexity of the soil environment hampers the extrapolation of the production and suppressing activity of mVOCs by microbial isolates on artificial growth media. Yet, several pathogen suppressive mVOCs produced by pure cultures do also occur in soil atmospheres. Therefore, an integration of lab and field studies on the production of mVOCs is needed to understand and predict the composition and dynamics of mVOCs in soil atmospheres. This knowledge, together with the knowledge of the chemistry and physical behaviour of mVOCs in soils, forms the basis for the development of sustainable management strategies to enhance the natural control of soil-borne pathogens with mVOCs. Possibilities for the mVOC-based control of soil-borne pathogens are discussed.

Volatile Organic Compounds of Endophytic Burkholderia pyrrocinia Strain JK-SH007 Promote Disease Resistance in Poplar

Volatile organic compounds (VOCs) play important roles in the regulation of plant growth and pathogen resistance. However, little is known about the influence of VOCs released from endophytic strains (Burkholderia pyrrocinia strain JK-SH007) on controlling pathogens or inducing systemic resistance in poplar. In this study, we found that VOCs produced by strain JK-SH007 inhibit three poplar canker pathogens (Cytospora chrysosperma, Phomopsis macrospora, and Fusicoccum aesculi) and promote defense enzyme activity and malondialdehyde (MDA) and total phenol (TP) accumulation. Thirteen kinds of VOC components were identified using the solid-phase microextraction combined with gas chromatography-mass spectrometry method. Dimethyl disulfide (DMDS) accounted for the largest proportion of these VOCs. Treatments of poplar seedlings with different volumes of VOC standards (DMDS, benzothiazole, dimethylthiomethane, and phenylacetone) showed that DMDS had the greatest effects on various defense enzyme activities and MDA and TP accumulation. We also found that the inhibitory effect of the VOCs on the three pathogens was gradually enhanced with increasing standard volume. Moreover, the treatment of samples with DMDS significantly reduced the severity and development of the disease caused by three poplar canker pathogens. Comparative transcriptomics analysis of poplar seedlings treated with DMDS showed that there were 1,586 differentially expressed genes in the leaves and stems, and quantitative PCR showed that the gene expression trends were highly consistent with the transcriptome sequencing results. The most significant transcriptomic changes induced by VOCs were related to hormone signal transduction, transcriptional regulation of plant-pathogen interactions, and energy metabolism. Moreover, 137 transcription factors, including members of the ethylene response factor, NAC, WRKY, G2-like, and basic helix-loop-helix protein families, were identified to be involved in the VOC-induced process. This study elucidates the resistance induced by Burkholderia pyrrocinia strain JK-SH007 to poplar canker at the molecular level and can make possible a new method for the comprehensive prevention and control of poplar disease.

Airborne medicine: bacterial volatiles and their influence on plant health

Like most other eukaryotes, plants do not live alone but in close association with a diverse microflora. These plant-associated microbes contribute to plant health in many different ways, ranging from modulation of hormonal pathways to direct antibiosis of plant pathogens. Over the last 15 yr, the importance of volatile organic compounds as mediators of mutualistic interactions between plant-associated bacteria and their hosts has become evident. This review summarizes current knowledge concerning bacterial volatile-mediated plant protection against abiotic and biotic stresses. It then discusses the translational potential of such metabolites or of their emitters for sustainable crop protection, the possible ways to harness this potential, and the major challenges still preventing us from doing so. Finally, the review concludes with highlighting the most pressing scientific gaps that need to be filled in order to enable a better understanding of: the molecular mechanisms underlying the biosynthesis of bacterial volatiles; the complex regulation of bacterial volatile emission in natural communities; the perception of bacterial volatiles by plants; and the modes of actions of bacterial volatiles on their host.

Exhaled volatile organic compounds as markers for medication use in asthma

INTRODUCTION

Asthma is a heterogeneous condition, characterised by chronic inflammation of the airways, typically managed with inhaled bronchodilators and corticosteroids. In the case of uncontrolled asthma, oral corticosteroids (OCSs) are often prescribed. Good adherence and inhalation technique are associated with improved outcomes; however, it is difficult to monitor appropriate drug intake and effectiveness in individual patients. Exhaled breath contains thousands of volatile organic compounds (VOCs) that reflect changes in the body's chemistry and may be useful for monitoring drug pharmacokinetics/pharmacodynamics. We aimed to investigate the association of exhaled VOCs in severe asthma patients from the U-BIOPRED cohort (by gas chromatography coupled with time-of-flight mass spectrometry) with urinary levels of salbutamol and OCSs (by liquid chromatography coupled with high-resolution mass spectrometry).

METHODS

Samples were collected at baseline and after 12-18 months of follow-up. Statistical analysis was based on univariate and multivariate modelling, followed by area under the receiver operating characteristic curve (AUC) calculation. Results were verified through longitudinal replication and independent validation.

RESULTS

Data were available for 78 patients (baseline n=48, replication n=30 and validation n=30). Baseline AUC values were 82.1% (95% CI 70.4-93.9%) for salbutamol and 78.8% (95% CI 65.8-91.8%) for OCS. These outcomes could be adequately replicated and validated. Additional regression analysis between qualified exhaled VOCs and urinary concentrations of salbutamol and prednisone showed statistically significant correlations (p<0.01).

CONCLUSION

We have linked exhaled VOCs to urinary detection of salbutamol and OCSs. This merits further development of breathomics into a point-of-care tool for therapeutic drug monitoring.

Microbial and volatile profiling of soils suppressive to Fusarium culmorum of wheat

In disease-suppressive soils, microbiota protect plants from root infections. Bacterial members of this microbiota have been shown to produce specific molecules that mediate this phenotype. To date, however, studies have focused on individual suppressive soils and the degree of natural variability of soil suppressiveness remains unclear. Here, we screened a large collection of field soils for suppressiveness to Fusarium culmorum using wheat (Triticum aestivum) as a model host plant. A high variation of disease suppressiveness was observed, with 14% showing a clear suppressive phenotype. The microbiological basis of suppressiveness to F. culmorum was confirmed by gamma sterilization and soil transplantation. Amplicon sequencing revealed diverse bacterial taxonomic compositions and no specific taxa were found exclusively enriched in all suppressive soils. Nonetheless, co-occurrence network analysis revealed that two suppressive soils shared an overrepresented bacterial guild dominated by various Acidobacteria. In addition, our study revealed that volatile emission may contribute to suppression, but not for all suppressive soils. Our study raises new questions regarding the possible mechanistic variability of disease-suppressive phenotypes across physico-chemically different soils. Accordingly, we anticipate that larger-scale soil profiling, along with functional studies, will enable a deeper understanding of disease-suppressive microbiomes.

Scent of a Killer: Microbial Volatilome and Its Role in the Biological Control of Plant Pathogens

The use of synthetic fungicides represents the most common strategy to control plant pathogens. Excessive and/or long-term distribution of chemicals is responsible for increased levels of environmental pollution, as well as adverse health consequence to humans and animals. These issues are deeply influencing public perception, as reflected by the increasing demand for safer and eco-friendly agricultural commodities and their by-products. A steadily increasing number of research efforts is now devoted to explore the use of safer and innovative approaches to control plant pathogens. The use of microorganisms as biological control agents (BCAs) represents one of the most durable and promising strategies. Among the panoply of microbial mechanisms exerted by BCAs, the production of volatile organic compounds (VOCs) represents an intriguing issue, mostly exploitable in circumstances where a direct contact between the pathogen and its antagonist is not practicable. VOCs are potentially produced by all living microorganisms, and may be active in the biocontrol of phytopathogenic oomycetes, fungi, and bacteria by means of antimicrobial activity and/or other cross-talk interactions. Their biological effects, the reduced residuals in the environment and on agricultural commodities, and the ease of application in different agricultural systems make the use of VOCs a promising and sustainable approach to replace synthetic fungicides in the control of plant pathogens. In this review, we focus on VOCs produced by bacteria and fungi and on their role in the cross-talk existing between the plant pathogens and their host. Biologic systemic effect of the microbial volatile blends on both pathogen and host plant cells is also briefly reviewed.

Isolation and Identification of Endophytic Bacteria from Mycorrhizal Tissues of Terrestrial Orchids from Southern Chile

Endophytic bacteria are relevant symbionts that contribute to plant growth and development. However, the diversity of bacteria associated with the roots of terrestrial orchids colonizing Andean ecosystems is limited. This study identifies and examines the capabilities of endophytic bacteria associated with peloton-containing roots of six terrestrial orchid species from southern Chile. To achieve our goals, we placed superficially disinfected root fragments harboring pelotons on oatmeal agar (OMA) with no antibiotic addition and cultured them until the bacteria appeared. Subsequently, they were purified and identified using molecular tools and examined for plant growth metabolites production and antifungal activity. In total, 168 bacterial strains were isolated and assigned to 8 OTUs. The orders Pseudomonadales, Burkholderiales, and Xanthomonadales of phylum Proteobacteria were the most frequent. The orders Bacillales and Flavobacteriales of the phylla Firmicutes and Bacteroidetes were also obtained. Phosphate solubilization was detected in majority of isolates; however, it was significantly higher in Collimonas pratensis and Chryseobacterium sp. (PSI = 1.505 ± 0.09 and 1.405 ± 0.24, respectively). Siderophore production was recorded only for C. pratensis (0.657 ± 0.14 mm day−1), Dyella marensis (0.131 ± 0.02 mm day−1), and Luteibacter rhizovicinus (0.343 ± 0.12 mm day−1). Indole acetic acid production was highly influenced by the isolate identity; however, the significantly higher activity was recorded for Pseudomonas spp. (ranging from 5.507 ± 1.57 µg mL−1 to 7.437 ± 0.99 µg mL−1). Additionally, six bacterial isolates were able to inhibit the growth of some potential plant pathogenic fungi. Our findings demonstrate the potential for plant growth promoting capabilities and some antifungal activities of endophytic bacteria inhabiting the mycorrhizal tissue of terrestrial orchids, which may contribute especially at early developmental stages of orchid seedlings.

The ecological role of bacterial seed endophytes associated with wild cabbage in the United Kingdom

Endophytic bacteria are known for their ability in promoting plant growth and defense against biotic and abiotic stress. However, very little is known about the microbial endophytes living in the spermosphere. Here, we isolated bacteria from the seeds of five different populations of wild cabbage (Brassica oleracea L) that grow within 15 km of each other along the Dorset coast in the UK. The seeds of each plant population contained a unique microbiome. Sequencing of the 16S rRNA genes revealed that these bacteria belong to three different phyla (Actinobacteria, Firmicutes, and Proteobacteria). Isolated endophytic bacteria were grown in monocultures or mixtures and the effects of bacterial volatile organic compounds (VOCs) on the growth and development on B. oleracea and on resistance against a insect herbivore was evaluated. Our results reveal that the VOCs emitted by the endophytic bacteria had a profound effect on plant development but only a minor effect on resistance against an herbivore of B. oleracea. Plants exposed to bacterial VOCs showed faster seed germination and seedling development. Furthermore, seed endophytic bacteria exhibited activity via volatiles against the plant pathogen F. culmorum. Hence, our results illustrate the ecological importance of the bacterial seed microbiome for host plant health and development.

Volatile-mediated antagonism of soil bacterial communities against fungi

Competition is a major type of interaction between fungi and bacteria in soil and is also an important factor in suppression of plant diseases caused by soil‐borne fungal pathogens. There is increasing attention for the possible role of volatiles in competitive interactions between bacteria and fungi. However, knowledge on the actual role of bacterial volatiles in interactions with fungi within soil microbial communities is lacking. Here, we examined colonization of sterile agricultural soils by fungi and bacteria from non‐sterile soil inoculums during exposure to volatiles emitted by soil‐derived bacterial communities. We found that colonization of soil by fungi was negatively affected by exposure to volatiles emitted by bacterial communities whereas that of bacteria was barely changed. Furthermore, there were strong effects of bacterial community volatiles on the assembly of fungal soil colonizers. Identification of volatile composition produced by bacterial communities revealed several compounds with known fungistatic activity. Our results are the first to reveal a collective volatile‐mediated antagonism of soil bacteria against fungi. Given the better exploration abilities of filamentous fungi in unsaturated soils, this may be an important strategy for bacteria to defend occupied nutrient patches against invading fungi. Another implication of our research is that bacterial volatiles in soil atmospheres can have a major contribution to soil fungistasis.

Biological activities associated with the volatile compound 2,5-bis(1-methylethyl)-pyrazine

Pyrazines are 1,4-diazabenzene-based volatile organic compounds and known for their broad-spectrum antimicrobial activity. In the present study, we assessed the antimicrobial activity of 2,5-bis(1-methylethyl)-pyrazine, produced by Paenibacillus sp. AD87 during co-culture with Burkholderia sp. AD24. In addition, we were using transcriptional reporter assays in E. coli and mammalian cells to decipher the possible mode of action. Bacterial and mammalian luciferase reporter strains were deployed to elucidate antimicrobial and toxicological effects of 2,5-bis(1-methylethyl)-pyrazine. At high levels of exposure, 2,5-bis(1-methylethyl)-pyrazine exerted strong DNA damage response. At lower concentrations, cell-wall damage response was observed. The activity was corroborated by a general toxicity reporter assay in E. coli ΔampD, defective in peptidoglycan turnover. The maximum E. coli cell-wall stress activity was measured at a concentration close to the onset of the mammalian cytotoxicity, while other adverse outcome pathways, such as the activation of aryl hydrocarbon and estrogenic receptor, the p53 tumour suppressor and the oxidative stress-related Nrf2 transcription factor, were induced at elevated concentrations compared to the response of mammalian cells. Because of its broad-spectrum antimicrobial activity at lower concentrations and the relatively low mammalian toxicity, 2,5-bis(1-methylethyl)-pyrazine is a potential bio-based fumigant with possible applications in food industry, agriculture or logistics.

Development of a Robust and Quantitative High-Throughput Screening Method for Antibiotic Production in Bacterial Libraries

Over the past 30 years, there has been a dramatic rise in the number of infections caused by multidrug-resistant bacteria, which have proliferated due to the misuse and overuse of antibiotics. Over this same time period, however, there has also been a decline in the number of antibiotics with novel mechanisms of action coming to market. Therefore, there is a growing need for an increase in the speed at which new antibiotics are discovered and developed. Natural products produced by bacteria have been and continue to be a robust source of novel antibiotics; however, new and complementary methods for screening large bacterial libraries for novel antibiotic production are needed due to the current agar methods being limited in scope, time consuming, and prone to error. Herein, we describe a rapid, robust, and quantitative high-throughput liquid culture screening method for antibiotic production by bacteria. This method has the ability to screen both mono- and coculture mixtures of bacteria in vitro and be adapted to other phenotypic natural product analyses. Over 260 bacterial species were screened in monoculture, and 38 and 34% were found to produce antibiotics capable of inhibition of Staphylococcus aureus or Escherichia coli, respectively, with 8 and 4% being classified as strong producers (≥30% growth inhibition), respectively. Bacteria found to not produce antibiotics in monoculture were also screened in coculture using an adaptation of this method. Of the more than 270 cocultures screened, 14 and 30% were found to produce antibiotics capable of inhibition of S. aureus or E. coli, respectively. Of those bacteria found to produce antibiotics in monoculture, 43 bacteria were subjected to 16S rRNA sequencing and found to be majority Pseudomonas (37%), Serratia (19%), and Bacillus (14%) bacteria, but two novel producers, Herbaspirillum and Kluyvera, were also found.

Linking soil's volatilome to microbes and plant roots highlights the importance of microbes as emitters of belowground volatile signals

Plants and microbes release a plethora of volatiles that act as signals in plant-microbe interactions. Characterizing soil's volatilome and microbiome might shed light on the nature of relevant volatile signals and on their emitters. This hypothesis was tested by characterizing plant cover, soil's volatilome, nutrient content and microbiomes in three grasslands of the Swiss Jura Mountains. The fingerprints of soil's volatiles were generated by solid-phase micro-extraction gas chromatography/mass spectrometry, whereas high-throughput sequencing was used to create a snapshot of soil's microbial communities. A high similarity was observed in plant communities of two out of three sites, which was mirrored by the soil's volatilome. Multiple factor analysis evidenced a strong association among soil's volatilome, plant and microbial communities. The proportion of volatiles correlated to single bacterial and fungal taxa was higher than for plants. This suggests that those organisms might be major contributors to the volatilome of grassland soils. These findings illustrate that key volatiles in grassland soils might be emitted by a handful of organisms that include specific plants and microbes. Further work will be needed to unravel the structure of belowground volatiles and understand their implications for plant health and development.

Volatiles of pathogenic and non-pathogenic soil-borne fungi affect plant development and resistance to insects

Plants are ubiquitously exposed to a wide diversity of (micro)organisms, including mutualists and antagonists. Prior to direct contact, plants can perceive microbial organic and inorganic volatile compounds (hereafter: volatiles) from a distance that, in turn, may affect plant development and resistance. To date, however, the specificity of plant responses to volatiles emitted by pathogenic and non-pathogenic fungi and the ecological consequences of such responses remain largely elusive. We investigated whether Arabidopsis thaliana plants can differentiate between volatiles of pathogenic and non-pathogenic soil-borne fungi. We profiled volatile organic compounds (VOCs) and measured CO₂ emission of 11 fungi. We assessed the main effects of fungal volatiles on plant development and insect resistance. Despite distinct differences in VOC profiles between the pathogenic and non-pathogenic fungi, plants did not discriminate, based on plant phenotypic responses, between pathogenic and non-pathogenic fungi. Overall, plant growth was promoted and flowering was accelerated upon exposure to fungal volatiles, irrespectively of fungal CO₂ emission levels. In addition, plants became significantly more susceptible to a generalist insect leaf-chewing herbivore upon exposure to the volatiles of some of the fungi, demonstrating that a prior fungal volatile exposure can negatively affect plant resistance. These data indicate that plant development and resistance can be modulated in response to exposure to fungal volatiles.