Unraveling Qu-aroma variation between inner and outer layers of medium-temperature Daqu: A multi-omics and sensory approach.

Malodorous gases production from food wastes decomposition by indigenous microorganisms

Microbial communities in trickle bed air biofilters (TBABs) were evaluated under conditions of interchanging the feed volatile organic compounds (VOCs) and VOC mixtures. Three independent TBABs (Biofilter “A,” “B,” and “C”) were run under interchanging VOCs conditions with different initial VOCs. Two aromatic compounds (toluene and styrene) and two oxygenated compounds (methyl ethyl ketone (MEK) and methyl isobutyl ketone (MIBK)) were interchanged as single solutes. Two other TBABs “D” and “E” were run for two VOC mixtures. Biofilter “D” had a VOC mixture with equal molar ratio of the four components and Biofilter “E” received a VOC mixture with its composition based on EPA 2003 emission report. Denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA genes was used to assess the microbial richness in TBABs for treating the VOC mixtures and the impact of interchanging VOCs on the bacterial community structure in the biofilters. The results from DGGE indicated that the microbial community structure in the biofilter was different after each interchange of VOCs. Some bands of microbial species faded and some bands were strengthened. For the two TBABs treating VOC mixtures, the microbial species did not show significant difference, but the richness among these species was different from each other.

Volatile organic compounds (VOCs) produced by plant-associated microorganisms could serve as natural biocontrol compounds. In this work, we investigate the potential of wheat rhizosphere Microbacterium and Arthrobacter actinomycetes to inhibit the growth of major wheat phytopathogenic fungi, Fusarium graminearum and Zymoseptoria tritici via production of antifungal VOCs. A correlative analysis between fungal-growth inhibition versus bacterial volatilomic profiles identified four dimethylpolysulfide (DMPS) VOCs as the main active compounds behind their biocontrol potential. Subsequent inhibition assays reveal that DMTriS (dimethyltrisulfide) exhibits the strongest inhibition effects, then dimethyldisulfide (DMDiS). Further investigation focuses on the mechanisms behind F. graminearum-growth inhibition by the most active strain Microbacterium JM188 in dual culture. Surprisingly, nine interaction-induced VOCs, including two fungal sesquiterpenes, were exclusively detected in dual cultures, suggesting a complex interplay between microbial VOC production and sensing. More importantly, all JM188 VOCs, including antifungal DMPS, were less abundant in dual cultures, suggesting an uptake of bacterial VOCs by the fungus. Quantification of pure DMPS after confrontation with F. graminearum confirmed complete and partial uptake by the fungus of DMTriS and DMDiS VOCs, respectively, suggesting a potential link between the fungal uptake level of bacterial VOCs and their toxicity. Finally, we demonstrated that F. graminearum growth inhibition leads to a complete depletion of DON (deoxynivalenol) carcinogenic mycotoxins, highlighting a significant modulation of fungal metabolism. Collectively, these results pinpoint DMPS as broad-range fungal-inhibiting VOCs produced by rhizosphere Microbacterium and Arthrobacter, and emphasize the extensive VOC-mediated interplay between bacterial biocontrol agents and fungal pathogens.IMPORTANCEAs the management of wheat fungal diseases becomes increasingly challenging, the use of bacterial agents with biocontrol potential against the two major wheat phytopathogens, Fusarium graminearum and Zymoseptoria tritici, may prove to be an interesting alternative to conventional pest management. Here, we have shown that dimethylpolysulfide volatiles are ubiquitously and predominantly produced by wheat-associated Microbacterium and Arthrobacter actinomycetes, displaying antifungal activity against both pathogens. By limiting pathogen growth and DON virulence factor production, the use of such DMPS-producing strains as soil biocontrol inoculants could limit the supply of pathogen inocula in soil and plant residues, providing an attractive alternative to dimethyldisulfide fumigant, which has many non-targeted toxicities. Notably, this study demonstrates the importance of bacterial volatile organic compound uptake by inhibited F. graminearum, providing new insights for the study of volatiles-mediated toxicity mechanisms within bacteria-fungus signaling crosstalk.

IntroductionHumans have used wood as a construction material throughout history. Currently, mass timber products, such as cross-laminated timber (CLT), are becoming more popular as a structural material, since they are renewable and have a lower carbon footprint than concrete or steel. Nonetheless, some building types, such as healthcare, veterinary, and food manufacturing, avoid using structural mass timber due to concerns about microbial growth in the event of wetting. One solution is to use protective coatings on mass timber products to increase moisture resistance, although the coatings themselves may generate concerns about volatile organic compound (VOC) emissions. Natural uncoated wood also produces VOCs, some of which may have intrinsic antimicrobial effects.MethodsIn this study, we inoculated coated and uncoated cross- laminated timber (CLT) blocks with a mock microbial community and isolated each block within individual sealed microcosms. We characterized VOCs and surface microbial communities from the CLT blocks before, during, and after wetting periods of varying durations. VOC concentration and emission rate were analyzed with chromatography-mass spectrometry (GC-MS), while microbial community abundance, diversity, and composition were analyzed through qPCR and shotgun metagenomics.ResultsVOC emissions were elevated immediately after inoculation, then decreased through the remainder of the experiment, except for a plateau during the wetting period. VOCs from uncoated CLT blocks were primarily terpenes, while coated blocks emitted VOCs associated with coatings, plastics, and industrial solvents, as well as terpenes. One VOC—acetoin (3-hydroxy, 2-butanone)—was present at high levels across all samples immediately after microbial inoculation. Bacteria comprised 99.54% of the identified microbial sequences. The plastic control microcosm (not containing a CLT block) had higher abundance of viable bacteria for the majority of the study, but there was no difference in abundance between coated and uncoated blocks. Prior to wetting periods, microbial composition was driven primarily by sampling day, whereas surface type played a larger role during and after wetting periods.

Volatile organic compounds (VOCs) are emitted by plants and microorganisms and have significant impacts on atmospheric chemistry. Soil systems are sources of VOCs driven by abiotic and biotic factors. We investigated the emissions of VOCs by soils and their plant cover from three contrasted biotopes: meadow, heathland and oak forest, during 24-h in summer. We hypothesized that the spatial and temporal dynamics of VOC fluxes are reflected in soil properties, soil microbial communities, vegetation covers, and litter composition that differed in the three biotopes VOC fluxes were measured after direct on-field sampling at four sampling times (two at night and two at day) using a proton transfer reaction mass spectrometer, and results were linked to some climatic, edaphic and biotic parameters simultaneously monitored in each biotope. While differences in the composition of the soil bacterial communities, in the richness of the plant cover and in some soil physicochemical properties between the three biotopes were observed, the total VOC fluxes from the soil to the atmosphere did not present spatial patterns. However, differences in the mass composition of the VOC spectra were detected; for example, the soil from the forest that was covered with oak leaf litter had specific bacterial communities and emitted distinct VOC spectra than the two other biotopes. The total VOC fluxes responded to rainfall and were significantly driven by soil temperature. While we observed changes in the structure of soil bacterial communities between day and night in all biotopes using fingerprinting analysis, a diurnal dynamic of VOC fluxes was only observed in the forest biotope where the soil was protected from rainfall due to the canopy. This soil presented higher fluxes in day time up to 10.8 µg VOCs h−1 m−2 and lower fluxes in night time down to 3.8 µg VOCs h−1 m−2. Overall, the present study supplies data regarding VOC emissions by soils which are scare compared to plant sources. The results highlighted the complex interconnections existing between abiotic and biotic parameters that could directly or indirectly drive VOC emissions by soil systems.

Kitchen waste (KW) generates odors comprising complex volatile organic compounds (VOCs). We used gas chromatography-mass spectrometry to analyze VOCs, and 16S gene sequencing was used to analyze the microbial community composition and microbial metabolic mechanism. The results showed that the major odor-causing VOCs were hydrogen sulfide, methanethiol, methyl sulfide, dimethyl disulfide, and ethyl acetate. As the temperature increased, the VOCs and microbial community composition became more complex, and the microbial community related to VOC production included Leuconostoc, Pediococcus, Acetobacter, and Weissella. Based on PICRUSt2 analysis, the possibility of typical VOC interconversion by microbial metabolism was low. It was more likely that precursor substances were catalyzed by enzymes to generate the corresponding VOCs. Attention should be given to trichloromethane and 1,2-dichloroethane, which may cause adverse health effects through long-term inhalation. The study results provide guidance for controlling VOCs from KW.

This thesis aimed to contribute to a more profound understanding of the microbial communities present in the airways of adult cystic fibrosis (CF) patients. Additionally, a breath analytical method was developed to detect microbial biomarkers (volatile organic compounds; VOCs) in exhaled air of the infected host and the feasibility of the method was tested in a CF outpatient clinic. Only culture-independent methods, such as single-strand conformation polymorphism (SSCP) fingerprinting and Illumina sequencing, revealed the broad spectrum of microorganisms associated with sputum from CF patients. Profiling of bacterial communities was performed and revealed no strong correlation between lung function and individual relative abundances of single species. In a polymicrobial perspective, however, distinct and persistent subgroups of bacterial communities could be defined by the individual compositions of species. In contrast to bacteria, an unexpected high richness of fungi was detected. Likewise, high fluctuation rates in species numbers were observed over time and between different patients, suggesting rather low colonization abilities of fungi in CF airways. For the breath analytical diagnostic approach, it was at first demonstrated that VOCs released by microorganism allowed discrimination of pathogens in vitro. The individual VOCs compositions monitored in exhaled breath of infected patients in vivo allowed distinction between CF patients and controls. Overall, this thesis supports the hypothesis of polymicrobial consortia being involved in pulmonary infections and provides for the first time an overview of the entire microbiome in a broader CF cohort, including fungi and bacteria. Furthermore, the potential of exhaled VOCs analysis to identify patients with certain pulmonary infections was demonstrated which may facilitate rapid and highly accurate diagnosis in the future.

A study was conducted to evaluate the use of volatile organic microbial metabolites, particularly geosmin and 2‐methylisoborneol, as indicators of activity of specific groups of microorganisms (actinomycetes, bacteria, or fungi) in soil. Substrates and selective antibiotics were added to soil microcosms to establish different soil microbial communities; volatile organic compounds (VOCs) in the headspace atmosphere of the microcosms were collected by purge‐and‐trap methods and analyzed by gas chromatography‐mass spectrometry. Treatments differed in total amount of VOCs produced, numbers and kinds of VOCs detected, and in temporal patterns of VOC production. The greatest total amount of VOCs and largest number of different VOCs were produced in the treatment with greatest actinomycetal and bacterial activity, followed by the treatment dominated by fungal activity. Geosmin was occasionally detected in small amounts but only in microcosms with substantial activity of all three groups of microorganisms (actinomycetes, bacteria, and fungi). 2‐Methylisoborneol was regularly detected in significant amounts but only in the treatment dominated by actinomycetes and bacteria. Terpenes were the VOCs produced in greatest quantity in the treatment with the most fungal activity. Results indicate that VOCs from soil may provide information as to the nature of the soil microbial community; however, relating the structure of the microbial community to soil VOC emissions is complicated because VOCs present in natural soils may be derived from a variety of sources and their production is strongly influenced by environmental conditions.

All over the world, Microbial systems are used to clean soils, waters and air streams that have been contaminated with volatile organic compounds (VOC). Information about the structure and function of the microbes that metabolize these contaminants can be gained by studying these microbial systems. Here we describe the spatial patterns of respiratory activity in Pseudomonas putida 54G aerobic biofilms degrading two VOC, toluene and ethanol. Oxygen concentration profiles within the biofilm were measured using microsensors. These profiles are thought to be most accurate reflection of the structure and function of aerobic microbial biofilms. The degrading process certainly imposed a structural and functional patterns on the microbial biofilm community growing at the expense of the VOC substrate. Cryosectioning coupled with the staining of biofilm samples confirmed a high respiratory activity near the substratum, that decreased towards the biofilm/fluid interface. The accumulation of inactive cells in the outer biofilm layer protects the inner biofilm from high concentrations of toxic compounds and also limits the degradation rate. This stratification phenomenon appeared to be a general pattern for P. putida 54G biofilms degrading VOC.

Soil microbes produce an immense diversity of metabolites, including volatile organic compounds (VOCs), which can shape the structure and function of microbial communities. VOCs mediate a multitude of microbe-microbe interactions, including antagonism. Despite their importance, the diversity and functional relevance of most microbial volatiles remain uncharacterized. We assembled a taxonomically diverse collection of 48 Actinobacteria isolated from soil and airborne dust and surveyed the VOCs produced by these strains on two different medium types in vitro using gas chromatography-mass spectrometry (GC-MS). We detected 126 distinct VOCs and structurally identified approximately 20% of these compounds, which were predominately C1 to C5 hetero-VOCs, including (oxygenated) alcohols, ketones, esters, and nitrogen- and sulfur-containing compounds. Each strain produced a unique VOC profile. While the most common VOCs were likely by-products of primary metabolism, most of the VOCs were strain specific. We observed a strong taxonomic and phylogenetic signal for VOC profiles, suggesting their role in finer-scale patterns of ecological diversity. Finally, we investigated the functional potential of these VOCs by assessing their effects on growth rates of both pathogenic and nonpathogenic pseudomonad strains. We identified sets of VOCs that correlated with growth inhibition and stimulation, information that may facilitate the development of microbial VOC-based pathogen control strategies. IMPORTANCE Soil microbes produce a diverse array of natural products, including volatile organic compounds (VOCs). Volatile compounds are important molecules in soil habitats, where they mediate interactions between bacteria, fungi, insects, plants, and animals. We measured the VOCs produced by a broad diversity of soil- and dust-dwelling Actinobacteria in vitro. We detected a total of 126 unique volatile compounds, and each strain produced a unique combination of VOCs. While some of the compounds were produced by many strains, most were strain specific. Importantly, VOC profiles were more similar between closely related strains, indicating that evolutionary and ecological processes generate predictable patterns of VOC production. Finally, we observed that actinobacterial VOCs had both stimulatory and inhibitory effects on the growth of bacteria that represent a plant-beneficial symbiont and a plant-pathogenic strain, information that may lead to the development of novel strategies for plant disease prevention.

Bioaerosols and VOC emissions from landfill leachate treatment processes: Regional differences and health risks

<p>The ability of an agricultural soil to function and sustainably provide an increasing food supply for a rapidly increasing global population has become of vital worldwide importance. Traditionally, soil health has been determined on a physico-chemical basis with biological characteristics often being ignored. Although several biological methods have been proposed, to date, none of these methods adequately indicate soil health. One method proposed to correct these circumstances is profiling or fingerprinting the volatile organic compounds (VOCs) from soil. VOCs in soils originate from a large variety of biological sources; microbial, fungal, animal- and plant-derived. These volatilomes are vital to plant/fungi-microbe and animal/human-microbe interactions and therefore offer a potential reactive, functional diagnostic tool to determine soil health by investigating the intra and interspecies interactions.</p><p>The standard methodology for VOC profiling has been solid phase microextraction (SPME). This automated VOC extraction method allows the monitoring of the community structure, physiological state, and activity of any microbial community in a soil without the need of manual extraction or cultivation procedures. Other common techniques that could be used to monitor the VOC fingerprints from soils include high capacity sorptive extraction (HCSE) or thermal desorption using sorbent-packed tubes for passive, in-situ sampling of soil gas.</p><p>Combining each of these techniques with an innovative cryogen-free focussing and pre-concentration trap has two main advantages:</p><ol><li>All extraction techniques can run on a single platform without the need to change the hardware.</li> <li>Single (SPME-trap) and multiple extractions (SPME-trap with enrichment) can be carried out automatically on a single sample to increase the analytical sensitivity, thus achieving a comprehensive VOC profile.</li> </ol><p>In this microcosm study, soils were treated in three different ways and their VOC profiles investigated. A ‘good’ soil comprised of brown earth and compost, a ‘medium’ soil of unaltered brown earth and a ‘bad’ soil of brown earth held under eutrophic anaerobic conditions. 2 g of each soil was analysed with SPME-trap, SPME-trap with enrichment, HCSE and sorbent tubes. Both a targeted (phenol, p-cresol, isophorone, indole and trans-β-ionone) and untargeted approach indicates that there are significant differences between the different soil types. By increasing the sensitivity of the untargeted approach with SPME-trap enrichment, this study was able to extend the number of VOCs identified, allowing a much more comprehensive VOC profile and possibility to determine the actual functions of specific VOC produced by the soil microbial community.</p>

Raman system for sensitive and selective identification of volatile organic compounds

Effect of inoculation with different Eurotium cristatum strains on the microbial communities and volatile organic compounds of Fu brick tea

In the porous network of soil, microbes are unevenly distributed. Interactions between soil (micro-) organisms that are physically separated could be mediated by volatile organic compounds (VOCs). VOCs are small, partially very smelly, molecules that can diffuse through air- and water-filled soil pores. Microbes, similar to plants, produce a diverse set of VOCs. The importance of these compounds in communication and competitiveness between microbes and plants in soil is increasingly recognized. However, our understanding on the relevance of VOCs-mediated interactions belowground is still limited. The aim of this thesis was to reveal novel insights into the ecological role of VOCs in microbial interactions and community dynamics in soil. A soil model system which more closely reflects conditions of soil environment in and around the rhizosphere was designed to study VOCs-mediated interactions between bacteria-bacteria, bacteria-fungi and plant-bacteria. Furthermore, novel aspects on the ecological role of VOCs in interactions of soil microorganisms such as protists were examined. Results of this thesis revealed that microbial interactions and shifts in the community composition strongly affect the volatile emission in soil. In this context, bacteria associated to the fungus can significantly influence the VOCs production and fitness of the fungal host. Moreover, within this thesis it was demonstrated that VOCs produced by microbes in the rhizosphere or plant roots can have a significant long distance effect on microorganisms in the surrounding nutrient-depleted bulk soil. For instance, VOCs released by bacterial interactions in the rhizosphere could stimulate the activity of distant starved bacteria. Furthermore, it was shown that plants can attract (beneficial) bacteria by root-VOCs. These results suggest that the rhizosphere effect might not be restricted to narrow zone – the few millimeters around the roots – but is further expanded by VOCs-mediated interactions. Interestingly, VOCs can also play a role as long-distance messenger in interactions between bacteria and protists. It was shown that bacterial VOCs such as terpenes affect protist activity and motility. This was mostly correlated to responses in direct feeding-interactions. Accordingly, bacterial VOCs could serve as signals for protists to find suitable prey. Overall, findings of this thesis provide novel information on the complexity of VOCs-mediated interactions in soil and contribute to our knowledge on the importance of VOCs-mediated (chemical) communication in ecosystem functioning belowground.