Volatile organic compounds and microorganisms

Changes in Endophyte Communities across the Different Plant Compartments in Response to the Rice Blast Infection

The rice blast disease, caused by the fungal pathogen, Magnaporthe oryzae (syn. Pyricularia oryzae), poses a significant threat to the global rice production. Understanding how this disease impacts the plant's microbial communities is crucial for gaining insights into hostpathogen interactions. In this study, we investigated the changes in communities of bacterial and fungal endophytes inhabiting different compartments in healthy and diseased plants. We found that both alpha and beta diversities of endophytic communities do not change significantly by the pathogen infection. Rather, the type of plant compartment appeared to be the main driver of endophytic community structures. Although the overall structure seemed to be consistent between healthy and diseased plants, our analysis of differentially abundant taxa revealed the specific bacterial and fungal operational taxonomic units that exhibited enrichment in the root and leaf compartments of infected plants. These findings suggest that endophyte communities are robust to the changes at the early stage of pathogen infection, and that some of endophytes enriched in infected plants might have roles in the defense against the pathogen.

Impacts of seasonality, drought, nitrogen fertilization, and litter on soil fluxes of biogenic volatile organic compounds in a Mediterranean forest

Biogenic volatile organic compounds (BVOCs) play critical roles in ecosystems at various scales, influencing above- and below-ground interactions and contributing to the atmospheric environment. Nonetheless, there is a lack of research on soil BVOC fluxes and their response to environmental changes. This study aimed to investigate the impact of drought, nitrogen (N) fertilization, and litter manipulation on soil BVOC fluxes in a Mediterranean forest. We assessed the effects of drought and N fertilization on soil BVOC exchanges and soil CO2 fluxes over two consecutive years using a dynamic chamber method, and solid-phase microextraction was utilized to quantify soil BVOCs in one year. Our findings revealed that the soil acted as an annual net sink for isoprenoids (1.30-10.33 μg m-2 h-1), with the highest uptake rates observed during summers (25.90 ± 9.36 μg m-2 h-1). The increased summer uptake can be attributed to the significant concentration gradient of BVOCs between atmosphere and soil. However, strong seasonal dynamics were observed, as the soil acted as a source of BVOCs in spring and autumn. The uptake rate of isoprenoids exhibited a significant positive correlation with soil temperature and atmospheric isoprenoid concentrations, while displaying a negative correlation with soil moisture and soil CO2 flux. The effects of drought and N fertilization on soil BVOCs were influenced by the type of VOCs, litter layer, and season. Specifically, drought significantly affected the exchange rate and quantities of sesquiterpenes. N fertilization led to increased emissions of specific BVOCs (α-pinene and camphene) due to the stimulation of litter emissions. These findings underscore the importance of the soil as a sink for atmospheric BVOCs in this dry Mediterranean ecosystem. Future drought conditions may significantly impact soil water content, resulting in drier soils throughout the year, which will profoundly affect the exchange of soil BVOCs between the soil and atmosphere.

Fungal Cultivars of Higher Attine Ants Promote Escovopsis Chemotropism

In varied environments, microorganisms search for partners or nutritional resources using chemical signals. Microbes are drawn (chemotaxis) or grow directionally (chemotropism) towards the chemical source, enabling them to establish and maintain symbiosis. The hypocrealean fungi Escovopsis enhance their growth towards the basidiomycete fungus Leucoagaricus gongylophorus, which is cultivated by leaf-cutting attine ants for food. Although directional growth is well documented in this symbiosis, it is unclear whether non-volatile or volatile organic compounds participate in the interaction between cultivar and Escovopsis, and which specific chemical compounds might attract and induce chemotropism. In this study, we examined the growth responses of Escovopsis isolates to non-volatile and volatile organic compounds produced by fungal cultivars of higher attine ants. We also isolated and identified molecules released by the ant-cultivar and assessed the chemotropism of Escovopsis towards them. Our results indicate that the growth of Escovopsis is stimulated in the presence of both non-volatile and volatile compounds from fungal cultivars. We also identified three isomeric diketopiperazines molecules from crude extracts of the ant cultivar, suggesting that these might play a role in Escovopsis chemotropism. Our findings provide insights into the complex chemical interactions that govern the association between Escovopsis and fungal cultivars.

Mechanistic insights into the role of actinobacteria as potential biocontrol candidates against fungal phytopathogens

Worldwide mounting demand for better food production to nurture exasperating population emphasizes on reduced crop losses. The incidence of pathogens into the agricultural fields has tend to dwindle plethora of cereal, vegetable, and other fodder crops. This, in turn, has seriously impacted the economic losses on global scale. Apart from this, it is quite challenging to feed the posterity in the coming decades. To counteract this problem, various agrochemicals have been commercialized in the market that no doubt shows positive results but along with adversely affecting the ecosystem. Therefore, the excessive ill-fated use of agrochemicals to combat the plant pests and diseases highlights that alternatives to chemical pesticides are need of the hour. In recent days, management of plant diseases using plant-beneficial microbes is gaining interest as safer and potent alternatives to replace chemically based pesticides. Among these beneficial microbes, actinobacteria especially streptomycetes play considerable role in combating plant diseases along with promoting the plant growth and development along with their productivity and yield. The mechanisms exhibited by actinobacteria include antibiosis (antimicrobial compounds and hydrolytic enzymes), mycoparasitism, nutrient competition, and induction of resistance in plants. Thus, in cognizance with potential of actinobacteria as potent biocontrol agents, this review summarizes role of actinobacteria and the multifarious mechanisms exhibited by actinobacteria for commercial applications.

Fusaricidins, Polymyxins and Volatiles Produced by Paenibacillus polymyxa Strains DSM 32871 and M1

Paenibacilli are efficient producers of potent agents against bacterial and fungal pathogens, which are of great interest both for therapeutic applications in medicine as well as in agrobiotechnology. Lipopeptides produced by such organisms play a major role in their potential to inactivate pathogens. In this work we investigated two lipopeptide complexes, the fusaricidins and the polymyxins, produced by Paenibacillus polymyxa strains DSM 32871 and M1 by MALDI-TOF mass spectrometry. The fusaricidins show potent antifungal activities and are distinguished by an unusual variability. For strain DSM 32871 we identified numerous yet unknown variants mass spectrometrically. DSM 32871 produces polymyxins of type E (colistins), while M1 forms polymyxins P. For both strains, novel but not yet completely characterized polymyxin species were detected, which possibly are glycosylated. These compounds may be of interest therapeutically, because polymyxins have gained increasing attention as last-resort antibiotics against multiresistant pathogenic Gram-negative bacteria. In addition, the volatilomes of DSM 32781 and M1 were investigated with a GC–MS approach using different cultivation media. Production of volatile organic compounds (VOCs) was strain and medium dependent. In particular, strain M1 manifested as an efficient VOC-producer that exhibited formation of 25 volatiles in total. A characteristic feature of Paenibacilli is the formation of volatile pyrazine derivatives.

Analysis of Environmental Variables and Carbon Input on Soil Microbiome, Metabolome and Disease Control Efficacy in Strawberry Attributable to Anaerobic Soil Disinfestation

Charcoal rot and Fusarium wilt, caused by Macrophomina phaseolina and Fusarium oxysporum f. sp. fragariae, respectively, are major soil-borne diseases of strawberry that have caused significant crop losses in California. Anaerobic soil disinfestation has been studied as an industry-level option to replace soil fumigants to manage these serious diseases. Studies were conducted to discern whether Gramineae carbon input type, incubation temperature, or incubation duration influences the efficacy of this disease control tactic. In experiments conducted using 'low rate' amendment applications at moderate day/night temperatures (24/18 °C), and carbon inputs (orchard grass, wheat, and rice bran) induced an initial proliferation and subsequent decline in soil density of the Fusarium wilt pathogen. This trend coincided with the onset of anaerobic conditions and a corresponding generation of various anti-fungal compounds, including volatile organic acids, hydrocarbons, and sulfur compounds. Generation of these metabolites was associated with increases in populations of Clostridium spp. Overall, carbon input and incubation temperature, but not incubation duration, significantly influenced disease suppression. All Gramineae carbon inputs altered the soil microbiome and metabolome in a similar fashion, though the timing and maximum yield of specific metabolites varied with input type. Fusarium wilt and charcoal rot suppression were superior when anaerobic soil disinfestation was conducted using standard amendment rates of 20 t ha-1 at elevated temperatures combined with a 3-week incubation period. Findings indicate that anaerobic soil disinfestation can be further optimized by modulating carbon source and incubation temperature, allowing the maximum generation of antifungal toxic volatile compounds. Outcomes also indicate that carbon input and environmental variables may influence treatment efficacy in a target pathogen-dependent manner which will require pathogen-specific optimization of treatment protocols.

Measurement of Volatile Compounds for Real-Time Analysis of Soil Microbial Metabolic Response to Simulated Snowmelt

Snowmelt dynamics are a significant determinant of microbial metabolism in soil and regulate global biogeochemical cycles of carbon and nutrients by creating seasonal variations in soil redox and nutrient pools. With an increasing concern that climate change accelerates both snowmelt timing and rate, obtaining an accurate characterization of microbial response to snowmelt is important for understanding biogeochemical cycles intertwined with soil. However, observing microbial metabolism and its dynamics non-destructively remains a major challenge for systems such as soil. Microbial volatile compounds (mVCs) emitted from soil represent information-dense signatures and when assayed non-destructively using state-of-the-art instrumentation such as Proton Transfer Reaction-Time of Flight-Mass Spectrometry (PTR-TOF-MS) provide time resolved insights into the metabolism of active microbiomes. In this study, we used PTR-TOF-MS to investigate the metabolic trajectory of microbiomes from a subalpine forest soil, and their response to a simulated wet-up event akin to snowmelt. Using an information theory approach based on the partitioning of mutual information, we identified mVC metabolite pairs with robust interactions, including those that were non-linear and with time lags. The biological context for these mVC interactions was evaluated by projecting the connections onto the Kyoto Encyclopedia of Genes and Genomes (KEGG) network of known metabolic pathways. Simulated snowmelt resulted in a rapid increase in the production of trimethylamine (TMA) suggesting that anaerobic degradation of quaternary amine osmo/cryoprotectants, such as glycine betaine, may be important contributors to this resource pulse. Unique and synergistic connections between intermediates of methylotrophic pathways such as dimethylamine, formaldehyde and methanol were observed upon wet-up and indicate that the initial pulse of TMA was likely transformed into these intermediates by methylotrophs. Increases in ammonia oxidation signatures (transformation of hydroxylamine to nitrite) were observed in parallel, and while the relative role of nitrifiers or methylotrophs cannot be confirmed, the inferred connection to TMA oxidation suggests either a direct or indirect coupling between these processes. Overall, it appears that such mVC time-series from PTR-TOF-MS combined with causal inference represents an attractive approach to non-destructively observe soil microbial metabolism and its response to environmental perturbation.

Volatilome of Aleppo Pine litter over decomposition process

Biogenic Volatile Organic Compounds (BVOC) are largely accepted to contribute to both atmospheric chemistry and ecosystem functioning. While the forest canopy is recognized as a major source of BVOC, emissions from plant litter have scarcely been explored with just a couple of studies being focused on emission patterns over litter decomposition process. The aim of this study was to quantitatively and qualitatively characterize BVOC emissions (C1-C15) from Pinus halepensis litter, one of the major Mediterranean conifer species, over a 15-month litter decomposition experiment. Senescent needles of P. halepensis were collected and placed in 42 litterbags where they underwent in situ decomposition. Litterbags were collected every 3 months and litter BVOC emissions were studied in vitro using both online (PTR-ToF-MS) and offline analyses (GC-MS). Results showed a large diversity of BVOC (58 compounds detected), with a strong variation over time. Maximum total BVOC emissions were observed after 3 months of decomposition with 9.18 µg gDM -1 hr-1 mainly composed by terpene emissions (e.g., α-pinene, terpinolene, β-caryophyllene). At this stage, methanol, acetone, and acetic acid were the most important nonterpenic volatiles representing, respectively, up to 26%, 10%, and 26% of total emissions. This study gives an overview of the evolution of BVOC emissions from litter along with decomposition process and will thus contribute to better understand the dynamics and sources of BVOC emission in Mediterranean pine forests.

C4 Bacterial Volatiles Improve Plant Health

Plant growth-promoting rhizobacteria (PGPR) associated with plant roots can trigger plant growth promotion and induced systemic resistance. Several bacterial determinants including cell-wall components and secreted compounds have been identified to date. Here, we review a group of low-molecular-weight volatile compounds released by PGPR, which improve plant health, mostly by protecting plants against pathogen attack under greenhouse and field conditions. We particularly focus on C4 bacterial volatile compounds (BVCs), such as 2,3-butanediol and acetoin, which have been shown to activate the plant immune response and to promote plant growth at the molecular level as well as in large-scale field applications. We also disc/ uss the potential applications, metabolic engineering, and large-scale fermentation of C4 BVCs. The C4 bacterial volatiles act as airborne signals and therefore represent a new type of biocontrol agent. Further advances in the encapsulation procedure, together with the development of standards and guidelines, will promote the application of C4 volatiles in the field.

The Malaria Metabolite HMBPP Does Not Trigger Erythrocyte Terpene Release

Infection with malarial parasites renders hosts more mosquito-attractive than their uninfected, healthy counterparts. One volatile organic compound, α-pinene, is associated with Plasmodium spp. infection in multiple studies and is a known mosquito attractant. However, how malarial infection results in elevated levels of host-associated α-pinene remains unclear. One study suggested that exposure of erythrocytes to the malarial metabolite (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBPP) results in increased levels of α-pinene. Here we establish that endogenous levels of α-pinene are present in human erythrocytes, that these levels vary widely by erythrocyte donor, and that α-pinene levels are not altered by HMBPP treatment.

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.

Sniffing fungi - phenotyping of volatile chemical diversity in Trichoderma species

Volatile organic compounds (VOCs) play vital roles in the interaction of fungi with plants and other organisms. A systematic study of the global fungal VOC profiles is still lacking, though it is a prerequisite for elucidating the mechanisms of VOC-mediated interactions. Here we present a versatile system enabling a high-throughput screening of fungal VOCs under controlled temperature. In a proof-of-principle experiment, we characterized the volatile metabolic fingerprints of four Trichoderma spp. over a 48 h growth period. The developed platform allows automated and fast detection of VOCs from up to 14 simultaneously growing fungal cultures in real time. The comprehensive analysis of fungal odors is achieved by employing proton transfer reaction-time of flight-MS and GC-MS. The data-mining strategy based on multivariate data analysis and machine learning allows the volatile metabolic fingerprints to be uncovered. Our data revealed dynamic, development-dependent and extremely species-specific VOC profiles from the biocontrol genus Trichoderma. The two mass spectrometric approaches were highly complementary to each other, together revealing a novel, dynamic view to the fungal VOC release. This analytical system could be used for VOC-based chemotyping of diverse small organisms, or more generally, for any in vivo and in vitro real-time headspace analysis.

Mass Spectrometry: A Rosetta Stone to Learn How Fungi Interact and Talk

Fungi are a highly diverse group of heterotrophic organisms that play an important role in diverse ecological interactions, many of which are chemically mediated. Fungi have a very versatile metabolism, which allows them to synthesize a large number of still little-known chemical compounds, such as soluble compounds that are secreted into the medium and volatile compounds that are chemical mediators over short and long distances. Mass spectrometry (MS) is currently playing a dominant role in mycological studies, mainly due to its inherent sensitivity and rapid identification capabilities of different metabolites. Furthermore, MS has also been used as a reliable and accurate tool for fungi identification (i.e., biotyping). Here, we introduce the readers about fungal specialized metabolites, their role in ecological interactions and provide an overview on the MS-based techniques used in fungal studies. We particularly present the importance of sampling techniques, strategies to reduce false-positive identification and new MS-based analytical strategies that can be used in mycological studies, further expanding the use of MS in broader applications. Therefore, we foresee a bright future for mass spectrometry-based research in the field of mycology.

Inhibition of Fungal Growth and Induction of a Novel Volatilome in Response to Chromobacterium vaccinii Volatile Organic Compounds

The study of chemical bioactivity in the rhizosphere has recently broadened to include microbial metabolites, and their roles in niche construction and competition via growth promotion, growth inhibition, and toxicity. Several prior studies have identified bacteria that produce volatile organic compounds (VOCs) with antifungal activities, indicating their potential use as biocontrol organisms to suppress phytopathogenic fungi and reduce agricultural losses. We sought to expand the roster of soil bacteria with known antifungal VOCs by testing bacterial isolates from wild and cultivated cranberry bog soils for VOCs that inhibit the growth of four common fungal and oomycete plant pathogens, and Trichoderma sp. Twenty one of the screened isolates inhibited the growth of at least one fungus by the production of VOCs, and isolates of Chromobacterium vaccinii had broad antifungal VOC activity, with growth inhibition over 90% for some fungi. Fungi exposed to C. vaccinii VOCs had extensive morphological abnormalities such as swollen hyphal cells, vacuolar depositions, and cell wall alterations. Quorum-insensitive cviR⁻ mutants of C. vaccinii were significantly less fungistatic, indicating a role for quorum regulation in the production of antifungal VOCs. We collected and characterized VOCs from co-cultivation assays of Phoma sp. exposed to wild-type C. vaccinii MWU328, and its cviR⁻ mutant using stir bar sorptive extraction and comprehensive two-dimensional gas chromatography—time-of-flight mass spectrometry (SBSE-GC × GC-TOFMS). We detected 53 VOCs that differ significantly in abundance between microbial cultures and media controls, including four candidate quorum-regulated fungistatic VOCs produced by C. vaccinii. Importantly, the metabolomes of the bacterial-fungal co-cultures were not the sum of the monoculture VOCs, an emergent property of their VOC-mediated interactions. These data suggest semiochemical feedback loops between microbes that have co-evolved for sensing and responding to exogenous VOCs.

Reduced microbial diversity induces larger volatile organic compound emissions from soils

Microorganisms in soil are known to be a source and a sink of volatile organic compounds (VOCs). The role of the microbial VOCs on soil ecosystem regulation has been increasingly demonstrated in the recent years. Nevertheless, little is known about the influence of the microbial soil community structure and diversity on VOC emissions. This novel study analyzed the effect of reduced microbial diversity in soil on VOC emissions. We found that reduced levels of microbial diversity in soil increased VOC emissions from soils, while the number of different VOCs emitted decreased. Furthermore, we found that Proteobacteria, Bacteroidetes and fungi phyla were positively correlated to VOC emissions, and other prokaryotic phyla were either negatively correlated or very slightly positively correlated to VOCs emissions. Our interpretation is that Proteobacteria, Bacteroidetes and fungi were VOC producers while the other prokaryotic phyla were consumers. Finally, we discussed the possible role of VOCs as mediators of microbial interactions in soil.

Wildfire effects on BVOC emissions from boreal forest floor on permafrost soil in Siberia

One of the effects of climate change on boreal forest will be more frequent forest wildfires and permafrost thawing. These will increase the availability of soil organic matter (SOM) for microorganisms, change the ground vegetation composition and ultimately affect the emissions of biogenic volatile organic compounds (BVOCs), which impact atmospheric chemistry and climate. BVOC emissions from boreal forest floor have been little characterized in southern boreal region, and even less so in permafrost soil, which underlies most of the northern boreal region. Here, we report the long-term effects of wildfire on forest floor BVOC emission rates along a wildfire chronosequence in a Larix gmelinii forest in central Siberia. We determined forest floor BVOC emissions from forests exposed to wildfire 1, 23 and > 100 years ago. We studied how forest wildfires and the subsequent succession of ground vegetation, as well as changes in the availability of SOM along with the deepened and recovered active layer, influence BVOC emission rates. The forest floor acted as source of a large number of BVOCs in all forest age classes. Monoterpenes were the most abundant BVOC group in all age classes. The total BVOC emission rates measured from the 23- and >100-year-old areas were ca. 2.6 times higher than the emissions from the 1-year-old area. Lower emissions were related to a decrease in plant coverage and microbial decomposition of SOM after wildfire. Our results showed that forest wildfires play an important indirect role in regulating the amount and composition of BVOC emissions from post-fire originated boreal forest floor. This could have a substantial effect on BVOC emissions if the frequency of forest wildfires increases in the future as a result of climate warming.

Temporal Dynamics of the Soil Metabolome and Microbiome During Simulated Anaerobic Soil Disinfestation

Significant interest exists in engineering the soil microbiome to attain suppression of soil-borne plant diseases. Anaerobic soil disinfestation (ASD) has potential as a biologically regulated disease control method; however, the role of specific metabolites and microbial community dynamics contributing to ASD mediated disease control is mostly uncharacterized. Understanding the trajectory of co-evolutionary processes leading to syntrophic generation of functional metabolites during ASD is a necessary prelude to the predictive utilization of this disease management approach. Consequently, metabolic and microbial community profiling were used to generate highly dimensional datasets and network analysis to identify sequential transformations through aerobic, facultatively anaerobic, and anaerobic soil phases of the ASD process and distinct groups of metabolites and microorganisms linked with those stages. Transient alterations in abundance of specific microbial groups, not consistently accounted for in previous studies of the ASD process, were documented in this time-course study. Such events initially were associated with increases and subsequent diminution in highly labile metabolites conferred by the carbon input. Proliferation and dynamic compositional changes in the Firmicutes community continued throughout the anaerobic phase and was linked to temporal changes in metabolite abundance including accumulation of small chain organic acids, methyl sulfide compounds, hydrocarbons, and p-cresol with antimicrobial properties. Novel potential modes of disease control during ASD were identified and the importance of the amendment and "community metabolism" for temporally supplying specific classes of labile compounds were revealed.

The Role of Volatile Organic Compounds and Rhizosphere Competence in Mode of Action of the Non-pathogenic Fusarium oxysporum FO12 Toward Verticillium Wilt

Verticillium wilts caused by Verticillium spp. are among the most challenging plant diseases to control and affect numerous hosts worldwide. Due to the lack of effective, conventional control methods, integrated control strategies provide a promising approach to manage these diseases. The non-pathogenic Fusarium oxysporum strain FO12 was reported in previous studies to be an effective biocontrol agent against Verticillium dahliae, however, its mode of action remains to be elucidated. In this study, complementary in vitro and in vivo experiments were conducted in order to explore the implications of inhibitory substances and rhizosphere competence in antagonistic effects of FO12 against V. dahliae and V. longisporum. Volatile organic compounds and soluble substances produced by FO12, which caused significant inhibition of mycelial growth and microsclerotia viability in the two tested Verticillium species, were identified by means of gas and liquid chromatography-mass spectrometry. We showed that the antagonistic effect of F. oxysporum FO12 is partially due to the production of bioactive compounds such as 3-methyl-1-butanol and 2-methyl-1-butanol, among others. Several metabolic pathways of FO12 were altered upon contact with V. dahliae ELV22 volatiles. The reduced production of alpha, alpha-trehalose, a metabolite used in starch and sucrose metabolism, suggests that the biocontrol agent activates its stress response in the presence of the phytopathogen. Microscopic analysis using sGFP-tagged FO12 on oil seed rape as a model plant suggests that the biocontrol strain is an efficient root colonizer, which could compete with V. dahliae in the same ecological niche. The findings obtained in this study provide new insights into the mode of action of this potential biocontrol agent, which are relevant for controlling Verticillium wilt through an ecologically friendly approach.

Volatile emissions from thawing permafrost soils are influenced by meltwater drainage conditions

Vast amounts of carbon are bound in both active layer and permafrost soils in the Arctic. As a consequence of climate warming, the depth of the active layer is increasing in size and permafrost soils are thawing. We hypothesize that pulses of biogenic volatile organic compounds are released from the near-surface active layer during spring, and during late summer season from thawing permafrost, while the subsequent biogeochemical processes occurring in thawed soils also lead to emissions. Biogenic volatile organic compounds are reactive gases that have both negative and positive climate forcing impacts when introduced to the Arctic atmosphere, and the knowledge of their emission magnitude and pattern is necessary to construct reliable climate models. However, it is unclear how different ecosystems and environmental factors such as drainage conditions upon permafrost thaw affect the emission and compound composition. Here we show that incubations of frozen B horizon of the active layer and permafrost soils collected from a High Arctic heath and fen release a range of biogenic volatile organic compounds upon thaw and during subsequent incubation experiments at temperatures of 10°C and 20°C. Meltwater drainage in the fen soils increased emission rates nine times, while having no effect in the drier heath soils. Emissions generally increased with temperature, and emission profiles for the fen soils were dominated by benzenoids and alkanes, while benzenoids, ketones, and alcohols dominated in heath soils. Our results emphasize that future changes affecting the drainage conditions of the Arctic tundra will have a large influence on volatile emissions from thawing permafrost soils - particularly in wetland/fen areas.

A field experimental study on non-methane hydrocarbon (NMHC) emissions from a straw-returned maize cropping system

Non-methane hydrocarbons (NMHCs) play an important role in the atmospheric environment. However, NMHC emissions from agricultural fields, especially their variations with straw return, are poorly understood. Therefore, a field study comprising two treatments, i.e., (1) S0 (straw removal) and (2) S1 (incorporation of maize straw at a rate of 9000 kg ha^-1), was conducted in a straw-returned maize cropping system to characterize NMHC emissions as well as to estimate the effect of straw return on those emissions. Using a Gas Chromatography-Mass Spectrometer (GC-MS) method, 28 types of NMHCs were identified. The total NMHC emission from S0 was 2018 g ha^-1, where 1-methyl-3-propyl-benzene, (1-methylethyl)-benzene, and toluene were obviously predominant, whereas the total NMHC emission from S1 was 1903 g ha^-1, where 1-methyl-3-propyl-benzene, 2-methyl-pentane, and (1-methylethyl)-benzene were the main species. The results showed that straw return had opposing effects on NMHC emissions, ranging from -55.4% to 478.6%. Overall, the total NMHC emission with returned straw alone decreased by 2963 ng kg straw^-1 h^-1. Furthermore, NMHC fluxes had higher correlations with soil temperature than with soil moisture or pH. Notably, the higher correlations of NMHC fluxes with 10 cm soil temperature than with 5 cm soil temperature indicate that soil in the deeper layer might play a more important role in NMHC fluxes. The results also suggest that more field study is needed to accurately estimate the effect of straw return on NMHC emissions from agroecosystems and fully understand its underlying mechanism.

Prodigiosin, Violacein, and Volatile Organic Compounds Produced by Widespread Cutaneous Bacteria of Amphibians Can Inhibit Two Batrachochytrium Fungal Pathogens

Symbiotic bacteria can produce secondary metabolites and volatile compounds that contribute to amphibian skin defense. Some of these symbionts have been used as probiotics to treat or prevent the emerging disease chytridiomycosis. We examined 20 amphibian cutaneous bacteria for the production of prodigiosin or violacein, brightly colored defense compounds that pigment the bacteria and have characteristic spectroscopic properties making them readily detectable, and evaluated the antifungal activity of these compounds. We detected violacein from all six isolates of Janthinobacterium lividum on frogs from the USA, Switzerland, and on captive frogs originally from Panama. We detected prodigiosin from five isolates of Serratia plymuthica or S. marcescens, but not from four isolates of S. fonticola or S. liquefaciens. All J. lividum isolates produced violacein when visibly purple, while prodigiosin was only detected on visibly red Serratia isolates. When applied to cultures of chytrid fungi Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal), prodigiosin caused significant growth inhibition, with minimal inhibitory concentrations (MIC) of 10 and 50 μM, respectively. Violacein showed a MIC of 15 μM against both fungi and was slightly more active against Bsal than Bd at lower concentrations. Although neither violacein nor prodigiosin showed aerosol activity and is not considered a volatile organic compound (VOC), J. lividum and several Serratia isolates did produce antifungal VOCs. White Serratia isolates with undetectable prodigiosin levels could still inhibit Bd growth indicating additional antifungal compounds in their chemical arsenals. Similarly, J. lividum can produce antifungal compounds such as indole-3-carboxaldehyde in addition to violacein, and isolates are not always purple, or turn purple under certain growth conditions. When Serratia isolates were grown in the presence of cell-free supernatant (CFS) from the fungi, CFS from Bd inhibited growth of the prodigiosin-producing isolates, perhaps indicative of an evolutionary arms race; Bsal CFS did not inhibit bacterial growth. In contrast, growth of one J. lividum isolate was facilitated by CFS from both fungi. Isolates that grow and continue to produce antifungal compounds in the presence of pathogens may represent promising probiotics for amphibians infected or at risk of chytridiomycosis. In a global analysis, 89% of tested Serratia isolates and 82% of J. lividum isolates were capable of inhibiting Bd and these have been reported from anurans and caudates from five continents, indicating their widespread distribution and potential for host benefit.

Enhanced performance of the microalga Chlorella sorokiniana remotely induced by the plant growth-promoting bacteria Azospirillum brasilense and Bacillus pumilus

Remote effects (occurring without physical contact) of two plant growth-promoting bacteria (PGPB) Azospirillum brasilense Cd and Bacilus pumilus ES4 on growth of the green microalga Chlorella sorokiniana UTEX 2714 were studied. The two PGPB remotely enhanced the growth of the microalga, up to six-fold, and its cell volume by about three-fold. In addition to phenotypic changes, both bacteria remotely induced increases in the amounts of total lipids, total carbohydrates, and chlorophyll a in the cells of the microalga, indicating an alteration of the microalga’s physiology. The two bacteria produced large amounts of volatile compounds, including CO₂, and the known plant growth-promoting volatile 2,3-butanediol and acetoin. Several other volatiles having biological functions in other organisms, as well as numerous volatile compounds with undefined biological roles, were detected. Together, these bacteria-derived volatiles can positively affect growth and metabolic parameters in green microalgae without physical attachment of the bacteria to the microalgae. This is a new paradigm on how PGPB promote growth of microalgae which may serve to improve performance of Chlorella spp. for biotechnological applications.

Aerial Warfare: A Volatile Dialogue between the Plant Pathogen Verticillium longisporum and Its Antagonist Paenibacillus polymyxa

Verticillium wilt caused by Verticillium spp. results in severe yield losses in a broad range of crops. Verticillium outbreaks are challenging to control, and exacerbated by increases in soil temperatures and drought associated with global warming. Employing natural antagonists as biocontrol agents offers a promising approach to addressing this challenge. Paenibacillus polymyxa Sb3-1 was proven to reduce the growth of Verticillium longisporum during in vitro experiments and was shown to promote the growth of oilseed rape seedlings infested with V. longisporum. Our novel approach combined in vitro and in planta methods with the study of the mode of interaction between Sb3-1 and V. longisporum EVL43 via their volatile organic compounds (VOCs). Volatile and soluble substances, produced by both microorganisms as a reaction to one another's VOCs, were detected by using both gas and liquid chromatography-mass spectrometry. P. polymyxa Sb3-1 continually produced antimicrobial and plant growth promoting VOCs, such as 2-nonanone and 3-hydroxy-2-butanone. Several other antimicrobial volatile substances, such as isoamyl acetate and durenol, were downregulated. The general metabolic activity of Sb3-1, including protein and DNA biotransformations, was upregulated upon contact with EVL43 VOCs. V. longisporum increased its production of antimicrobial substances, such as 1-butanol, and downregulated its metabolic activities upon exposure to Sb3-1 VOCs. Additionally, several stress response substances such as arabitol and protein breakdown products (e.g., L-Isoleucyl-L-glutamic acid), were increased in the co-incubated samples. The results obtained depict an ongoing dialog between these microorganisms resulting in growth inhibition, the slowing down of metabolism, and the cell death of V. longisporum due to contact with the P. polymyxa Sb3-1 VOCs. Moreover, the results indicate that VOCs make a substantial contribution to the interaction between pathogens and their natural antagonists and have the potential to control pathogens in a novel, environmentally friendly manner.

Biogenic volatile organic compound emissions along a high arctic soil moisture gradient

Emissions of biogenic volatile organic compounds (BVOCs) from terrestrial ecosystems are important for the atmospheric chemistry and the formation of secondary organic aerosols, and may therefore influence the climate. Global warming is predicted to change patterns in precipitation and plant species compositions, especially in arctic regions where the temperature increase will be most pronounced. These changes are potentially highly important for the BVOC emissions but studies investigating the effects are lacking. The aim of this study was to investigate the quality and quantity of BVOC emissions from a high arctic soil moisture gradient extending from dry tundra to a wet fen. Ecosystem BVOC emissions were sampled five times in the July-August period using a push-pull enclosure technique, and BVOCs trapped in absorbent cartridges were analyzed using gas chromatography-mass spectrometry. Plant species compositions were estimated using the point intercept method. In order to take into account important underlying ecosystem processes, gross ecosystem production, ecosystem respiration and net ecosystem production were measured in connection with chamber-based BVOC measurements. Highest emissions of BVOCs were found from vegetation communities dominated by Salix arctica and Cassiope tetragona, which had emission profiles dominated by isoprene and monoterpenes, respectively. These results show that emissions of BVOCs are highly dependent on the plant cover supported by the varying soil moisture, suggesting that high arctic BVOC emissions may affect the climate differently if soil water content and plant cover change.

Volatiles released by endophytic Pseudomonas fluorescens promoting the growth and volatile oil accumulation in Atractylodes lancea

Atractylodes lancea is a well-known, but endangered, Chinese medicinal plant whose volatile oils are its main active components. As the volatile oil content in cultivated A. lancea is much lower than that in the wild herb, the application of microbes or related elicitors to promote growth and volatile oil accumulation in the cultivated herb is an important area of research. This study demonstrates that the endophytic bacterium Pseudomonas fluorescens ALEB7B isolated from the geo-authentic A. lancea can release several nitrogenous volatiles, such as formamide and N,N-dimethyl-formamide, which significantly promote the growth of non-infected A. lancea. Moreover, the main bacterial volatile benzaldehyde significantly promotes volatile oil accumulation in non-infected A. lancea via activating plant defense responses. Notably, the bacterial nitrogenous volatiles cannot be detected in the A. lancea - Pseudomonas fluorescens symbiont while the benzaldehyde can be detected, indicating the nitrogenous volatiles or their precursors may have been consumed by the host plant. This study firstly demonstrates that the interaction between plant and endophytic bacterium is not limited to the commonly known physical contact, extending the ecological functions of endophyte in the phytosphere and deepening the understandings about the symbiotic interaction.

Diversity and functions of volatile organic compounds produced by Streptomyces from a disease-suppressive soil

In disease-suppressive soils, plants are protected from infections by specific root pathogens due to the antagonistic activities of soil and rhizosphere microorganisms. For most disease-suppressive soils, however, the microorganisms and mechanisms involved in pathogen control are largely unknown. Our recent studies identified Actinobacteria as the most dynamic phylum in a soil suppressive to the fungal root pathogen Rhizoctonia solani. Here we isolated and characterized 300 isolates of rhizospheric Actinobacteria from the Rhizoctonia-suppressive soil. Streptomyces species were the most abundant, representing approximately 70% of the isolates. Streptomyces are renowned for the production of an exceptionally large number of secondary metabolites, including volatile organic compounds (VOCs). VOC profiling of 12 representative Streptomyces isolates by SPME-GC-MS allowed a more refined phylogenetic delineation of the Streptomyces isolates than the sequencing of 16S rRNA and the house-keeping genes atpD and recA only. VOCs of several Streptomyces isolates inhibited hyphal growth of R. solani and significantly enhanced plant shoot and root biomass. Coupling of Streptomyces VOC profiles with their effects on fungal growth, pointed to VOCs potentially involved in antifungal activity. Subsequent assays with five synthetic analogs of the identified VOCs showed that methyl 2-methylpentanoate, 1,3,5-trichloro-2-methoxy benzene and the VOCs mixture have antifungal activity. In conclusion, our results point to a potential role of VOC-producing Streptomyces in disease suppressive soils and show that VOC profiling of rhizospheric Streptomyces can be used as a complementary identification tool to construct strain-specific metabolic signatures.

A review: what is the spermosphere and how can it be studied?

The spermosphere is the zone surrounding seeds where interactions between the soil, microbial communities and germinating seeds take place. The concept of the spermosphere is usually only applied during germination sensu stricto. Despite the transient nature of this very small zone of soil around the germinating seed, the microbial activities which occur there may have long-lasting impacts on plants. The spermosphere is indirectly characterized by either (i) seed exudates, which could be inhibitors or stimulators of micro-organism growth or (ii) the composition of the microbiome on and around the germinating seeds. The microbial communities present in the spermosphere directly reflect that of the germination medium or are host-dependent and influenced quantitatively and qualitatively by host exudates. Despite its strong impact on the future development of plants, the spermosphere remains little studied. This can be explained by the technical difficulties related to characterizing this concept due to its short duration, small size and biomass, and the number and complexity of the interactions that take place. However, recent technical methods, such as metabolite profiling, combining phenotypic methods with DNA- and RNA-based methods, could be used to investigate seed exudates, microbial communities and their interactions with the soil environment.

Volatile organic compounds in truffle (Tuber magnatum Pico): comparison of samples from different regions of Italy and from different seasons

In this paper volatile organic compounds (VOCs) from Tuber magnatum fruiting bodies were analyzed using a PTR-TOF-MS instrument. The aim was to characterize the VOC's profile of the fruiting bodies and identify if any VOCs were specific to a season and geographical areas. Multiple factorial analysis (MFA) was carried out on the signals obtained by MS. Experiments using ITS region sequencing proved that the T. magnatum life cycle includes the formation of fruiting bodies at two different times of the year. The VOCs profiles diverge when different seasonal and geographical productions are considered. Using PTR-TOF-MS, compounds present at levels as low pptv were detected. This made it possible to determine both the origin of fruiting bodies (Alba and San Miniato) and the two biological phases of fruiting bodies formation in San Miniato truffles.

Legacy effects of anaerobic soil disinfestation on soil bacterial community composition and production of pathogen-suppressing volatiles

There is increasing evidence that microbial volatiles (VOCs) play an important role in natural suppression of soil-borne diseases, but little is known on the factors that influence production of suppressing VOCs. In the current study we examined whether a stress-induced change in soil microbial community composition would affect the production by soils of VOCs suppressing the plant-pathogenic oomycete Pythium. Using pyrosequencing of 16S ribosomal gene fragments we compared the composition of bacterial communities in sandy soils that had been exposed to anaerobic disinfestation (AD), a treatment used to kill harmful soil organisms, with the composition in untreated soils. Three months after the AD treatment had been finished, there was still a clear legacy effect of the former anaerobic stress on bacterial community composition with a strong increase in relative abundance of the phylum Bacteroidetes and a significant decrease of the phyla Acidobacteria, Planctomycetes, Nitrospirae, Chloroflexi, and Chlorobi. This change in bacterial community composition coincided with loss of production of Pythium suppressing soil volatiles (VOCs) and of suppression of Pythium impacts on Hyacinth root development. One year later, the composition of the bacterial community in the AD soils was reflecting that of the untreated soils. In addition, both production of Pythium-suppressing VOCs and suppression of Pythium in Hyacinth bioassays had returned to the levels of the untreated soil. GC/MS analysis identified several VOCs, among which compounds known to be antifungal, that were produced in the untreated soils but not in the AD soils. These compounds were again produced 15 months after the AD treatment. Our data indicate that soils exposed to a drastic stress can temporarily lose pathogen suppressive characteristics and that both loss and return of these suppressive characteristics coincides with shifts in the soil bacterial community composition. Our data are supporting the suggested importance of microbial VOCs in the natural buffer of soils against diseases caused by soil-borne pathogens.

Biosynthesis of hydrocarbons and volatile organic compounds by fungi: bioengineering potential

Recent advances in the biological production of fuels have relied on the optimization of pathways involving genes from diverse organisms. Several recent articles have highlighted the potential to expand the pool of useful genes by looking to filamentous fungi. This review highlights the enzymes and organisms used for the production of a variety of fuel types and commodity chemicals with a focus on the usefulness and promise of those from filamentous fungi.

Proton transfer reaction-mass spectrometry: online and rapid determination of volatile organic compounds of microbial origin

Analytical tools for the identification and quantification of volatile organic compounds (VOCs) produced by microbial cultures have countless applications in an industrial and research context which are still not fully exploited. The various techniques for VOC analysis generally arise from the application of different scientific and technological philosophies, favoring either sample throughput or chemical information. Proton transfer reaction-mass spectrometry (PTR-MS) represents a valid compromise between the two aforementioned approaches, providing rapid and direct measurements along with highly informative analytical output. The present paper reviews the main applications of PTR-MS in the microbiological field, comprising food, environmental, and medical applications.

Nematicidal activities of bacterial volatiles and components from two marine bacteria, Pseudoalteromonas marina strain H-42 and Vibrio atlanticus strain S-16, against the pine wood nematode, Bursaphelenchus xylophilus

Bacterial volatiles represent an important source for new natural nematicidal compounds that may be developed as novel nematicidal agents to control plant-parasitic nematodes. In this study, two marine bacteria,Pseudoalteromonas marinastrain H-42 andVibrio atlanticusstrain S-16, were isolated from seawater and the bay scallop (Argopecten irradians), respectively, collected from the subtidal beds at Qingdao, China.In vitrobioassays indicated that culture supernatants of the two bacteria displayed strong nematicidal activities with corrected mortalities of more than 93% after 24 h exposure against the pine wood nematode (PWN),Bursaphelenchus xylophilus. Maximal nematicidal activity was exhibited by culture supernatants of the two marine bacteria incubated at 15-20°C for 3 days in Zobell 2216E medium prepared with 100% seawater and initial pH 6.0-7.0, inoculating 19-h-old cultures. Through analysis using solid-phase microextraction-gas chromatography/mass spectrometry, the volatiles produced by the two bacteria were shown to contain mainly dimethyl disulphide, benzaldehyde, dimethyl trisulphide,tert-butylamine, acetone and dimethylamine, N-(diisopropylphosphino)methyl-. Results from nematicidal assay using pure commercial compounds instead of the candidate volatiles demonstrated that the four volatile compounds, dimethyl trisulphide (LC90 = 0.060 mmol l−1), benzaldehyde (LC90 = 0.309 mmol l−1), dimethyl disulphide (LC90 = 0.162 mmol l−1) andtert-butylamine (LC90 = 0.366 mmol l−1), showed strong nematicidal activities against PWN. This is the first report on the nematicidal activity of volatile organic compounds (VOC) from marine microorganisms. This study indicates that the nematicidal VOC produced by marine bacteria are potential substitutes for current chemical control options of pine wilt disease caused by PWN which greatly threatens global forest resources.

Biogenic volatile emissions from the soil

Volatile compounds are usually associated with an appearance/presence in the atmosphere. Recent advances, however, indicated that the soil is a huge reservoir and source of biogenic volatile organic compounds (bVOCs), which are formed from decomposing litter and dead organic material or are synthesized by underground living organism or organs and tissues of plants. This review summarizes the scarce available data on the exchange of VOCs between soil and atmosphere and the features of the soil and particle structure allowing diffusion of volatiles in the soil, which is the prerequisite for biological VOC-based interactions. In fact, soil may function either as a sink or as a source of bVOCs. Soil VOC emissions to the atmosphere are often 1-2 (0-3) orders of magnitude lower than those from aboveground vegetation. Microorganisms and the plant root system are the major sources for bVOCs. The current methodology to detect belowground volatiles is described as well as the metabolic capabilities resulting in the wealth of microbial and root VOC emissions. Furthermore, VOC profiles are discussed as non-destructive fingerprints for the detection of organisms. In the last chapter, belowground volatile-based bi- and multi-trophic interactions between microorganisms, plants and invertebrates in the soil are discussed.

Microbial monoterpene transformations-a review

Isoprene and monoterpenes constitute a significant fraction of new plant biomass. Emission rates into the atmosphere alone are estimated to be over 500 Tg per year. These natural hydrocarbons are mineralized annually in similar quantities. In the atmosphere, abiotic photochemical processes cause lifetimes of minutes to hours. Microorganisms encounter isoprene, monoterpenes, and other volatiles of plant origin while living in and on plants, in the soil and in aquatic habitats. Below toxic concentrations, the compounds can serve as carbon and energy source for aerobic and anaerobic microorganisms. Besides these catabolic reactions, transformations may occur as part of detoxification processes. Initial transformations of monoterpenes involve the introduction of functional groups, oxidation reactions, and molecular rearrangements catalyzed by various enzymes. Pseudomonas and Rhodococcus strains and members of the genera Castellaniella and Thauera have become model organisms for the elucidation of biochemical pathways. We review here the enzymes and their genes together with microorganisms known for a monoterpene metabolism, with a strong focus on microorganisms that are taxonomically validly described and currently available from culture collections. Metagenomes of microbiomes with a monoterpene-rich diet confirmed the ecological relevance of monoterpene metabolism and raised concerns on the quality of our insights based on the limited biochemical knowledge.

Clinical application of volatile organic compound analysis for detecting infectious diseases

This review article introduces the significance of testing of volatile organic compounds (VOCs) in clinical samples and summarizes important features of some of the technologies. Compared to other human diseases such as cancer, studies on VOC analysis in cases of infectious diseases are limited. Here, we have described results of studies which have used some of the appropriate technologies to evaluate VOC biomarkers and biomarker profiles associated with infections. The publications reviewed include important infections of the respiratory tract, gastrointestinal tract, urinary tract, and nasal cavity. The results highlight the use of VOC biomarker profiles resulting from certain infectious diseases in discriminating between infected and healthy subjects. Infection-related VOC profiles measured in exhaled breath as well as from headspaces of feces or urine samples are a source of information with respect to disease detection. The volatiles emitted in clinical matrices may on the one hand represent metabolites of the infecting pathogen or on the other hand reflect pathogen-induced host responses or, indeed, a combination of both. Because exhaled-breath samples are easy to collect and online instruments are commercially available, VOC analysis in exhaled breath appears to be a promising tool for noninvasive detection and monitoring of infectious diseases.

Production of onion fly attractants and ovipositional stimulants by bacterial isolates cultured on onion

Decomposing onions at certain microbial successional stages produce potent volatile attractants and ovipositional stimulants of the onion fly,Delia antiqua (Diptera: Anthomyiidae). A reproducible source of these compounds was obtained by culturingErwinia carotovora var.carotovora (EC) on sterile onion tissue. In laboratory choice tests, EC-inoculated onion was more attractive thanKlebsiella pneumoniae (KP) cultured on onion, EC cultured on potato (a nonhost of onion fly), or the chemical synthetic baits dipropyl disulfide and an aqueous solution of 2-phenylethanol and pentanoic acid. Onion flies were mildly attracted to potato after inoculation with EC, but females did not accept EC-inoculated potato for oviposition. This work emphasizes that sources of semiochemicals may need to be defined microbiologically as well as physically and chemically.

Acetaldehyde exchange above a managed temperate mountain grassland

An overview of acetaldehyde exchange above a managed temperate mountain grassland in Austria over four growing seasons is presented. The meadow acted as a net source of acetaldehyde in all four years, emitting between 7 and 28 mg C m-2 over the whole growing period. The cutting of the meadow resulted in huge acetaldehyde emission bursts on the day of harvesting or one day later. During undisturbed conditions, both uptake and emission fluxes were recorded. The bidirectional nature of acetaldehyde fluxes was also reflected by clear diurnal cycles during certain time periods, indicating strong deposition processes before the 1st cut and emission towards the end of the growing season. The analysis of acetaldehyde compensation points revealed a complex relationship between ambient acetaldehyde mixing ratios and respective fluxes, significantly influenced by multiple environmental parameters and variable throughout the year. As a major finding of this study, we identified both a positive and negative correlation between concentration and flux on a daily scale, where soil temperature and soil water content were the most significant factors in determining the direction of the slope. In turn, this bidirectional relationship on a daily scale resulted in compensation points between 0.40 ppbv and 0.54 ppbv, which could be well explained by collected ancillary data. We conclude that in order to model acetaldehyde fluxes at the site in Neustift on a daily scale over longer time periods, it is crucial to know the type of relationship, i.e. the direction of the slope, between mixing ratios and fluxes on a given day.

Bacterial and fungal community composition over time in chicken litter with high or low moisture content

1. Changes in bacterial and fungal communities in chicken litter with high and low moisture content over a five week period during a single chicken grow out cycle in a poultry shed in subtropical Australia were investigated to study the association between specific microbes and odour production. 2. Microbial biomass, as indicated by DNA yields, was higher and community composition was more dynamic over time in moist compared with dry chicken litter. 3. Bacillus, Atopostipes and Aspergillus species increased in relative abundance in moist chicken litter samples over time reflecting the relatively high fitness and hence activity of these specific bacteria and this specific fungus in this environment.

Detection and validation of volatile metabolic patterns over different strains of two human pathogenic bacteria during their growth in a complex medium using multi-capillary column-ion mobility spectrometry (MCC-IMS)

Headspace analyses over microbial cultures using multi-capillary column-ion mobility spectrometry (MCC-IMS) could lead to a faster, safe and cost-effective method for the identification of pathogens. Recent studies have shown that MCC-IMS allows identification of bacteria and fungi, but no information is available from when on during their growth a differentiation between bacteria is possible. Therefore, we analysed the headspace over human pathogenic reference strains of Escherichia coli and Pseudomonas aeruginosa at four time points during their growth in a complex fluid medium. In order to validate our findings and to answer the question if the results of one bacterial strain can be transferred to other strains of the same species, we also analysed the headspace over cultures from isolates of random clinical origin. We detected 19 different volatile organic compounds (VOCs) that appeared or changed their signal intensity during bacterial growth. These included six VOCs exclusively changing over E. coli cultures and seven exclusively changing over P. aeruginosa cultures. Most changes occurred in the late logarithmic or static growth phases. We did not find differences in timing or trends in signal intensity between VOC patterns of different strains of one species. Our results show that differentiation of human pathogenic bacteria by headspace analyses using MCC-IMS technology is best possible during the late phases of bacterial growth. Our findings also show that VOC patterns of a bacterial strain can be transferred to other strains of the same species.