Shedding light on Aspergillus niger volatile exometabolome

Linking Pedobacter lusitanus NL19 volatile exometabolome with growth medium composition: what can we learn using comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry?

Microbial metabolomics allows understanding and to comprehensively analyse metabolites, and their related cellular and metabolic processes, that are produced and released to the extracellular environment under specific conditions. In that regard, the main objective of this research is to understand the impact of culture media changes in the metabolic profile of Pedobacter lusitanus NL19 (NL19) and Pedobacter himalayensis MTCC 6384 (MTCC6384) and respective influence on the production of biotechnologically relevant compounds. Solid-phase microextraction combined with comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry with time-of-flight analyser (GC × GC-ToFMS) was applied to comprehensively study the metabolites produced by NL19 and MTCC6384 both in tryptic soy broth 100% (TSB100) and tryptic soy broth with 25% casein peptone (PC25). A total of 320 metabolites were putatively identified, which belong to different chemical families: alcohols, aldehydes, esters, ethers, hydrocarbons, ketones, nitrogen compounds, sulphur compounds, monoterpenes, and sesquiterpenes. Metabolites that were statistically different from the control (sterile medium) were selected allowing for the construction of the metabolic profile of both strains. A set of 80 metabolites was tentatively associated to the metabolic pathways such as the metabolism of fatty acids, branched-chain aminoacids, phenylalanine, methionine, aromatic compounds, and monoterpene and sesquiterpene biosynthesis. This study allowed to better understand how slight changes of the culture media and thus the composition of nutrients impair the metabolic profile of bacteria, which may be further explored for metabolomics pipeline construction or biotechnological applications.

Mapping Aspergillus niger Metabolite Biomarkers for In Situ and Early Evaluation of Table Grapes Contamination

The Aspergillus niger exometabolome was recently investigated using advanced gas chromatography in tandem with multivariate analysis, which allowed a metabolite biomarker pattern to be proposed. Microbial metabolomics patterns have gained enormous relevance, mainly due to the amount of information made available, which may be useful in countless processes. One of the great challenges in microbial metabolomics is related to applications in more complex systems of metabolomics information obtained from studies carried out in culture media, as complications may occur due to the dynamic nature of biological systems. Thus, the main objective of this research was to evaluate the applicability of the A. niger metabololite biomarkers pattern for in situ and early evaluation of table grapes contamination, used as study model. A. niger is a ubiquitous fungus responsible for food contamination, being reported as one of the main agents of the black mold disease, a serious post-harvest pathology of table grapes. This work included analysis from 1 day of growth time of pure A. niger cultures, A. niger cultures obtained from previously contaminated grapes, and finally, an in situ solid-phase microextraction (SPME) approach directly on previously contaminated table grapes. Supervised multivariate analysis was performed which revealed that after 1 day of inoculation it was possible to detect A. niger biomarkers, which can be extremely useful in making this type of method possible for the rapid detection of food contamination. The results obtained confirm the potential applicability of the pattern of A. niger biomarkers for early detection of the fungi (after 1 day of contamination), and may be further explored for access food susceptibility to fungi contamination, based on direct analysis of the food item.

SubTap, a Versatile 3D Printed Platform for Eavesdropping on Extracellular Interactions

Communication within the microbiome occurs through an immense diversity of small molecules. Capturing these microbial interactions is a significant challenge due to the complexity of the exometabolome and its sensitivity to environmental stimuli. Traditional methods for acquiring exometabolomic data from interacting microorganisms are limited by their low throughput or lack of sampling depth. To address this challenge, we introduce subtapping (short for substrate tapping), a technique for tapping into extracellular metabolites that are being transferred through the growth substrate during coculture. High-throughput subtapping is made possible by a new coculturing platform, named SubTap, that we engineered to resemble a 96-well plate. The three-dimensional (3D) printed SubTap platform captures the exometabolome in an agar compartment that connects physically separated growth chambers, which permits cell growth without competition for space. We show how SubTap facilitates replicable and quick detection of exometabolites via direct infusion mass spectrometry analysis. Using bacterial isolates from the soil, we apply SubTap to characterize the effects of growth medium, growth duration, and mixed versus unmixed coculturing on the exometabolome. Finally, we demonstrate SubTap's versatility by interrogating microbial interactions in multicultures with up to four strains. IMPORTANCE Improvements in experimental techniques and instrumentation have led to the discovery that the microbiome plays an essential role in human and environmental health. Nevertheless, there remain major impediments to conducting large-scale interrogations of the microbiome in a high-throughput manner, particularly in the field of exometabolomics. Existing methods to coculture microorganisms and interrogate their interactions are labor-intensive and low throughput. This inspired us to develop a solution for coculturing that was (i) open source, (ii) inexpensive, (iii) scalable, (iv) customizable, and (v) compatible with existing mass spectrometry instrumentation. Here, we present SubTap-a 3D printed coculturing platform that permits tapping directly into the growth substrate between physically separated, but interconnected, growth compartments. SubTap allows multiculture (with up to four distinct growth compartments) in spatially mixed or unmixed configurations and enables repeatable results with mass spectrometry, as shown by our validation with known compounds and cultures of one to four organisms.

Soybean Metabolomics Based in Mass Spectrometry: Decoding the Plant's Signaling and Defense Responses under Biotic Stress

Metabolomics is an omics technology that is extremely valuable to analyze all small-molecule metabolites in organisms. Recent advances in analytical instrumentation, such as mass spectrometry combined with data processing tools, chemometrics, and spectral data libraries, allow plant metabolomics studies to play a fundamental role in the agriculture field and food security. Few studies are found in the literature using the metabolomics approach in soybean plants on biotic stress. In this review, we provide a new perspective highlighting the potential of metabolomics-based mass spectrometry for soybean in response to biotic stress. Furthermore, we highlight the response and adaptation mechanisms of soybean on biotic stress about primary and secondary metabolism. Consequently, we provide subsidies for further studies of the resistance and improvement of the crop.

Comprehensive Study of Variety Oenological Potential Using Statistic Tools for the Efficient Use of Non-Renewable Resources

The evaluation of the variety suitability regarding each appellation’s specificities should be a strategy for maximizing the varieties’ oenological potential while contributing to the sustainable production of quality wines, keeping their typicity and rationalizing winemaking costs. Thus, the combination of several grape physicochemical attributes, modulated by climate and vineyard characteristics, providing knowledge for each grape variety’s oenological potential, is a relevant and reliable support for winemakers’ decisions. To prove this hypothesis, six mature grape varieties from three harvests, each one from three vineyard parcels with different topographical conditions from Bairrada Appellation (Portugal), were studied using analysis of variance–simultaneous components analysis (ASCA). The effects of harvest year and parcel on grape berry weight, pH, titratable acidity, total sugars, total phenolics, antiradical activity, and volatile composition in free and glycosidically-linked forms were analyzed. The compositional plasticity of autochthonous varieties (white Arinto and Bical and red Baga, Castelão, and Touriga Nacional) was observed. Sauvignon Blanc grape composition was significantly modulated by harvest. This study represents an important contribution for the maintenance of varieties’ biodiversity while contributing to establishing their peculiarities. Autochthonous varieties, if accurately exploited, can provide higher characteristic diversity than worldwide used varieties, an aspect to be more objectively taken into consideration by winemakers.

Establishment of a New PNA-FISH Method for Aspergillus fumigatus Identification: First Insights for Future Use in Pulmonary Samples

Aspergillus fumigatus is the main causative agent of Invasive Aspergillosis. This mold produces conidia that when inhaled by immunocompromized hosts can be deposited in the lungs and germinate, triggering disease. In this paper, the development of a method using peptide nucleic acid-fluorescence in situ hybridization (PNA-FISH) is described. The PNA-FISH probe was tested in several strains and a specificity and sensitivity of 100% was obtained. Detection of A. fumigatussensu stricto was then achieved in artificial sputum medium (ASM) pre-inoculated with 1 × 10² conidia·mL^-1-1 × 10³ conidia·mL^-1, after a germination step of 24 h. The PNA-FISH method was evaluated in 24 clinical samples (10 sputum, 8 bronchoalveolar lavage (BAL), and 6 bronchial lavage (BL)) that were inoculated with 1 × 10⁴ conidia·mL^-1 in sputum; 1 × 10³ conidia·mL^-1 in BL and BAL, for 24 h. Despite a specificity of 100%, the sensitivity was 79%. This relatively low sensitivity can be explained by the fact that hyphae can yield "fungal ball" clusters, hindering pipetting procedures and subsequent detection, leading to false negative results. Nonetheless, this study showed the potential of the PNA-FISH method for A. fumigatussensu stricto detection since it takes only 1 h 30 m to perform the procedure with a pre-enrichment step of 6 h (pure cultures) and 24 h (clinical samples), and might provide a suitable alternative to the existing methods for studies in pure cultures and in clinical settings.

Analysis of volatile emissions from grape berries infected with Aspergillus carbonarius using hyphenated and portable mass spectrometry

Mycotoxins represent a serious risk for human and animal health. Οchratoxin A (OTA) is a carcinogenic mycotoxin produced by A. carbonarius that constitutes a severe problem for viticulture. In this study, we investigate the development of novel detection and on-line monitoring approaches for the detection of OTA in the field (i.e. out of the chemical laboratory) using advanced molecular sensing. Both stand-alone and hyphenated mass spectrometry (MS) based systems (e.g. Time-of-Flight ToF-MS and gas chromatography GC combined with MS) and compact portable membrane inlet MS (MIMS) have been employed for the first time to detect and monitor volatile emissions of grape berries infected by the fungus Aspergillus carbonarius. In vacuo (electron impact-EI) and ambient ionisation (electrospray ionisation-ESI) techniques were also examined. On-line measurements of the volatile emissions of grape berries, infected by various strains of A. carbonarius with different toxicity levels, were performed resulting in different olfactory chemical profiles with a common core of characteristic mass fragments, which could be eventually used for on-site detection and monitoring allowing consequent improvement in food security.

Candida Species (Volatile) Metabotyping through Advanced Comprehensive Two-Dimensional Gas Chromatography

Microbial metabolomics is a challenge strategy that allows a comprehensive analysis of metabolites within a microorganism and may support a new approach in microbial research, including the microbial diagnosis. Thus, the aim of this research was to in-depth explore a metabolomics strategy based on the use of an advanced multidimensional gas chromatography for the comprehensive mapping of cellular metabolites of C. albicans and non-C. albicans (C. glabrata and C. tropicalis) and therefore contributing for the development of a comprehensive platform for fungal detection management and for species distinction in early growth times (6 h). The volatile fraction comprises 126 putatively identified metabolites distributed over several chemical families: acids, alcohols, aldehydes, hydrocarbons, esters, ketones, monoterpenic and sesquiterpenic compounds, norisoprenoids, phenols and sulphur compounds. These metabolites may be related with different metabolic pathways, such as amino acid metabolism and biosynthesis, fatty acids metabolism, aromatic compounds degradation, mono and sesquiterpenoid synthesis and carotenoid cleavage. These results represent an enlargement of ca. 70% of metabolites not previously reported for C. albicans, 91% for C. glabrata and 90% for C. tropicalis. This study represents the most detailed study about Candida species exometabolome, allowing a metabolomic signature of each species, which signifies an improvement towards the construction of a Candida metabolomics platform whose application in clinical diagnostics can be crucial to guide therapeutic interventions.

Influence of indoor chemistry on the emission of mVOCs from Aspergillus niger molds

People spend 80% of their time indoors exposed to poor air quality due to mold growth in humid air as well as human activities (painting, cooking, cleaning, smoking…). To better understand the impact of molds on indoor air quality, we studied the emission of microbial Volatile Organic Compounds (mVOCs) from Aspergillus niger, cultivated on malt agar extract, using a high-resolution proton transfer reaction- time of flight- mass spectrometer (PTR-TOF-MS). These emissions were studied for different cultivation time and indoor relative humidities. Our results show that the concentration of the known C₄-C₉ mVOCs tracers of the microbial activity (like 1-octen-3-ol, 3-methylfuran, 2-pentanone, dimethyl sulfide, dimethyl disulfide, nitromethane, 1,3-octadiene…) was the highest in the early stage of growth. However, these emissions decreased substantially after a cultivation time of 10-14 days and were highly affected by the relative humidity. In addition, the emissions of certain mVOCs were sensitive to indoor light, suggesting an impact of photochemistry on the relative amounts of indoor mVOCs. Based on this study, an estimation of the mVOC concentration for a standard living room was established at different air exchange rates and their indoor lifetimes toward hydroxyl radicals and ozone were also estimated. These findings give insights on possible mVOCs levels in moisture-damaged buildings for an early detection of microbial activity and new evidences about the effect of indoor light on their emission.

Critical thresholds of 1-Octen-3-ol shape inter-species Aspergillus interactions modulating the growth and secondary metabolism

In fungi, contactless interactions are mediated via the exchange of volatile organic compounds (VOCs). As these pair-wise interactions are fundamental to complex ecosystem, we examined the effects of inter-species VOCs trade-offs in Aspergillus flavus development. First, we exposed A. flavus to the A. oryzae volatilome (Treatment-1) with highest relative abundance of 1-Octen-3-ol (~ 4.53 folds) among the C-8 VOCs. Further, we examined the effects of gradient titers of 1-Octen-3-ol (Treatment-2: 100–400 ppm/day) in a range that elicits natural interactions. On 7-day, VOC-treated A. flavus displayed significantly reduced growth and sclerotial counts (p < 0.01) coupled with higher conidial density (T2_{100-200 ppm/day}, p < 0.01) and α-amylase secretion (T2_200 ppm/day, p < 0.01), compared to the untreated sets. Similar phenotypic trends except for α-amylases were evident for 9-day incubated A. flavus in T2. The corresponding metabolomics data displayed a clustered pattern of secondary metabolite profiles for VOC-treated A. flavus (PC1-18.03%; PC2-10.67%). Notably, a higher relative abundance of aflatoxin B1 with lower levels of most anthraquinones, indole-terpenoids, and oxylipins was evident in VOC-treated A. flavus. The observed correlations among the VOC-treatments, phenotypes, and altered metabolomes altogether suggest that the distant exposure to the gradient titers of 1-Octen-3-ol elicits an attenuated developmental response in A. flavus characterized by heightened virulence.

Characterization of volatile metabolites formed by molds on barley by mass and ion mobility spectrometry

The contamination of barley by molds on the field or in storage leads to the spoilage of grain and the production of mycotoxins, which causes major economic losses in malting facilities and breweries. Therefore, on-site detection of hidden fungus contaminations in grain storages based on the detection of volatile marker compounds is of high interest. In this work, the volatile metabolites of 10 different fungus species are identified by gas chromatography (GC) combined with two complementary mass spectrometric methods, namely, electron impact (EI) and chemical ionization at atmospheric pressure (APCI)-mass spectrometry (MS). The APCI source utilizes soft X-radiation, which enables the selective protonation of the volatile metabolites largely without side reactions. Nearly 80 volatile or semivolatile compounds from different substance classes, namely, alcohols, aldehydes, ketones, carboxylic acids, esters, substituted aromatic compounds, alkenes, terpenes, oxidized terpenes, sesquiterpenes, and oxidized sesquiterpenes, could be identified. The profiles of volatile and semivolatile metabolites of the different fungus species are characteristic of them and allow their safe differentiation. The application of the same GC parameters and APCI source allows a simple method transfer from MS to ion mobility spectrometry (IMS), which permits on-site analyses of grain stores. Characterization of IMS yields limits of detection very similar to those of APCI-MS. Accordingly, more than 90% of the volatile metabolites found by APCI-MS were also detected in IMS. In addition to different fungus genera, different species of one fungus genus could also be differentiated by GC-IMS.

Fragrant and sticky allergens from the pinewood: Cohabiting and coreacting

BACKGROUND

Tree moss (Pseudevernia furfuracea [L.] Zopf.), a lichen growing on conifers, is a frequent fragrance sensitizer. Previous studies have shown two subgroups of tree moss-allergic patients: a group sensitized to common allergens of tree and oak moss (Evernia prunastri), and another group sensitized to colophonium-derived allergens, which may contaminate tree moss extract.

OBJECTIVES

To report the results of including tree moss extract in the baseline series and discuss the clinical implications.

METHODS

Tree moss extract was included in the baseline series and sensitized patients were assessed for concomitant allergy to colophonium and oak moss, and the relevance of these reactions was analyzed.

RESULTS

Altogether, 22 of 632 patients (3.5%) had positive reactions to tree moss. Eight patients were sensitized to tree moss only (among fragrance allergens) and 75% had relevant reactions to colophonium. Fourteen patients were sensitized to other fragrance allergens as well and 28.5% had relevant colophonium reactions.

CONCLUSIONS

The prevalence of positive tree moss reactions is high enough to justify its inclusion in the baseline series. If tree moss is not included, patients with positive colophonium reactions should be informed of possible (false) cross-reactivity to tree moss to avoid this labeled fragrance allergen.

Fathoming Aspergillus oryzae metabolomes in formulated growth matrices

The stochasticity of Aspergillus oryzae (Trivially: the koji mold) pan-metabolomes commensurate with its ubiquitously distributed landscapes, i.e. growth matrices have been seemed uncharted since its food fermentative systems are mostly being investigated. In this review, we explicitly have discussed the likely tendencies of A. oryzae metabolomes pertaining to its growth milieu formulated with substrate matrices of varying nature, composition, texture, and associated physicochemical parameters. We envisaged typical food matrices, namely, meju, koji, and moromi as the semi-natural cultivation models toward delineating the metabolomic patterns of the koji mold, which synergistically influences the organoleptic and functional properties of the end products. Further, we highlighted how tailored conditions in sub-natural growth matrices, i.e. synthetic cultivation media blends, inducers, and growth surfaces, may influence A. oryzae metabolomes and targeted phenotypes. In general, the sequential or synchronous growth of A. oryzae on formulated matrices results in a number of metabolic tradeoffs with its immediate microenvironment influencing its adaptive and regulatory metabolomes. In broader context, evaluating the metabolic plasticity of A. oryzae relative to the tractable variables in formulated growth matrices might help approximate its growth and metabolism in the more complex natural matrices and environs. These approaches may considerably help in the design and manipulation of hybrid cultivation systems towards the efficient harnessing of commercial molds.

A comprehensive look into the volatile exometabolome of enteroxic and non-enterotoxic Staphylococcus aureus strains

Staphylococcal food poisoning is a disease that originates significant health and economic losses and is caused by Staphylococcus aureus strains able to produce enterotoxins. The aim of this work is to go further on the study of the volatile exometabolome of S. aureus using an advanced gas chromatographic technique. Enterotoxic and non-enterotoxic strains were assessed. The volatile exometabolome profile comprised 240 volatiles belonging to ten chemical families. This volatiles were mainly by-products of branched-chain amino acids and methionine degradation, pyruvate metabolism, diacetyl pathway, oxidative stress and carotenoid cleavage. Metabolites released by the first two pathways were produced in higher contents by the enterotoxic strains. This study add further insights to S. aureus volatile exometabolome, and also shows that by applying it, it is possible to distinguish strains of S. aureus by the number of produced enterotoxins, which is especially important from the food safety point of view.

A morphological, enzymatic and metabolic approach to elucidate apoptotic-like cell death in fungi exposed to h- and α-molybdenum trioxide nanoparticles

The present study compares for the first time the effects of h-MoO3 and α-MoO3 against two fungal strains: Aspergillus niger and Aspergillus flavus. The h-MoO3 nanoparticles were more toxic to both fungi than α-MoO3. The toxic effects of h-MoO3 were more pronounced toward A. flavus, which presented a growth inhibition of 67.4% at 200 mg L-1. The presence of the nanoparticles affected drastically the hyphae morphology by triggering nuclear condensation and compromising the hyphae membrane. Further analysis of the volatile organic compounds (VOCs) produced by both fungi in the presence of the nanomaterials indicated important metabolic changes related to programmed cell death. These nanomaterials induced the production of specific antifungal VOCs, such as β-Elemene and t-Cadinol, by the fungi. The production of essential enzymes involved in fungal metabolism, such as acid phosphatase, naphthol-As-BI-phosphohydrolase, β-galactosidase, β-glucosidase and N-acetyl-β-glucosaminidase, reduced significantly in the presence of the nanomaterials. The changes in enzymatic production and VOCs corroborate the fact that these nanoparticles, especially h-MoO3, exert changes in the fungal metabolism, triggering apoptotic-like cell death responses in these fungi.

Safety of the fungal workhorses of industrial biotechnology: update on the mycotoxin and secondary metabolite potential of Aspergillus niger, Aspergillus oryzae, and Trichoderma reesei

This review presents an update on the current knowledge of the secondary metabolite potential of the major fungal species used in industrial biotechnology, i.e., Aspergillus niger, Aspergillus oryzae, and Trichoderma reesei. These species have a long history of safe use for enzyme production. Like most microorganisms that exist in a challenging environment in nature, these fungi can produce a large variety and number of secondary metabolites. Many of these compounds present several properties that make them attractive for different industrial and medical applications. A description of all known secondary metabolites produced by these species is presented here. Mycotoxins are a very limited group of secondary metabolites that can be produced by fungi and that pose health hazards in humans and other vertebrates when ingested in small amounts. Some mycotoxins are species-specific. Here, we present scientific basis for (1) the definition of mycotoxins including an update on their toxicity and (2) the clarity on misclassification of species and their mycotoxin potential reported in literature, e.g., A. oryzae has been wrongly reported as an aflatoxin producer, due to misclassification of Aspergillus flavus strains. It is therefore of paramount importance to accurately describe the mycotoxins that can potentially be produced by a fungal species that is to be used as a production organism and to ensure that production strains are not capable of producing mycotoxins during enzyme production. This review is intended as a reference paper for authorities, companies, and researchers dealing with secondary metabolite assessment, risk evaluation for food or feed enzyme production, or considerations on the use of these species as production hosts.

Detection of volatile organic compounds in the headspace above mold fungi by GC-soft X-radiation-based APCI-MS

Mold fungi on malting barley grains cause major economic loss in malting and brewery facilities. Possible proxies for their detection are volatile and semivolatile metabolites. Among those substances, characteristic marker compounds have to be identified for a confident detection of mold fungi in varying surroundings. The analytical determination is usually performed through passive sampling with solid phase microextraction, gas chromatographic separation, and detection by electron ionization mass spectrometry (EI-MS), which often does not allow a confident determination due to the absence of molecular ions. An alternative is GC-APCI-MS, generally, allowing the determination of protonated molecular ions. Commercial atmospheric pressure chemical ionization (APCI) sources are based on corona discharges, which are often unspecific due to the occurrence of several side reactions and produce complex product ion spectra. To overcome this issue, an APCI source based on soft X-radiation is used here. This source facilitates a more specific ionization by proton transfer reactions only. In the first part, the APCI source is characterized with representative volatile fungus metabolites. Depending on the proton affinity of the metabolites, the limits of detection are up to 2 orders of magnitude below those of EI-MS. In the second part, the volatile metabolites of the mold fungus species Aspergillus, Alternaria, Fusarium, and Penicillium are investigated. In total, 86 compounds were found with GC-EI/APCI-MS. The metabolites identified belong to the substance classes of alcohols, aldehydes, ketones, carboxylic acids, esters, substituted aromatic compounds, terpenes, and sesquiterpenes. In addition to substances unspecific for the individual fungus species, characteristic patterns of metabolites, allowing their confident discrimination, were found for each of the 4 fungus species. Sixty-seven of the 86 metabolites are detected by X-ray-based APCI-MS alone. The discrimination of the fungus species based on these metabolites alone was possible. Therefore, APCI-MS in combination with collision induced dissociation alone could be used as a supervision method for the detection of mold fungi.

Volatiles Mediated Interactions Between Aspergillus oryzae Strains Modulate Morphological Transition and Exometabolomes

Notwithstanding its mitosporic nature, an improbable morpho-transformation state i. e., sclerotial development (SD), is vaguely known in Aspergillus oryzae. Nevertheless an intriguing phenomenon governing mold's development and stress response, the effects of exogenous factors engendering SD, especially the volatile organic compounds (VOCs) mediated interactions (VMI) pervasive in microbial niches have largely remained unexplored. Herein, we examined the effects of intra-species VMI on SD in A. oryzae RIB 40, followed by comprehensive analyses of associated growth rates, pH alterations, biochemical phenotypes, and exometabolomes. We cultivated A. oryzae RIB 40 (S1_VMI: KACC 44967) opposite a non-SD partner strain, A. oryzae (S2: KCCM 60345), conditioning VMI in a specially designed “twin plate assembly.” Notably, SD in S1_VMI was delayed relative to its non-conditioned control (S1) cultivated without partner strain (S2) in twin plate. Selectively evaluating A. oryzae RIB 40 (S1_VMI vs. S1) for altered phenotypes concomitant to SD, we observed a marked disparity for corresponding growth rates (S1_VMI < S1)_7days, media pH (S1_VMI > S1)_7days, and biochemical characteristics viz., protease (S1_VMI > S1)_7days, amylase (S1_VMI > nS1)_3–7days, and antioxidants (S1_VMI > S1)_7days levels. The partial least squares—discriminant analysis (PLS-DA) of gas chromatography—time of flight—mass spectrometry (GC-TOF-MS) datasets for primary metabolites exhibited a clustered pattern (PLS1, 22.04%; PLS2, 11.36%), with 7 days incubated S1_VMI extracts showed higher abundance of amino acids, sugars, and sugar alcohols with lower organic acids and fatty acids levels, relative to S1. Intriguingly, the higher amino acid and sugar alcohol levels were positively correlated with antioxidant activity, likely impeding SD in S1_VMI. Further, the PLS-DA (PLS1, 18.11%; PLS2, 15.02%) based on liquid chromatography—mass spectrometry (LC-MS) datasets exhibited a notable disparity for post-SD (9–11 days) sample extracts with higher oxylipins and 13-desoxypaxilline levels in S1_VMI relative to S1, intertwining Aspergillus morphogenesis and secondary metabolism. The analysis of VOCs for the 7 days incubated samples displayed considerably higher accumulation of C-8 compounds in the headspace of twin-plate experimental sets (S1_VMI:S2) compared to those in non-conditioned controls (S1 and S2—without respective partner strains), potentially triggering altered morpho-transformation and concurring biochemical as well as metabolic states in molds.

Comprehensive volatile metabolic fingerprinting of bacterial and fungal pathogen groups

The identification of pathogen-specific volatile metabolic 'fingerprints' could lead to the rapid identification of disease-causing organisms either directly from ex vivo patient bio-specimens or from in vitro cultures. In the present study, we have evaluated the volatile metabolites produced by 100 clinical isolates belonging to ten distinct pathogen groups that, in aggregate, account for 90% of bloodstream infections, 90% of urinary tract infections, and 80% of infections encountered in the intensive care unit setting. Headspace volatile metabolites produced in vitro were concentrated using headspace solid-phase microextraction and analyzed via two-dimensional gas chromatography time-of-flight mass spectrometry (HS-SPME-GC×GC-TOFMS). A total of 811 volatile metabolites were detected across all samples, of which 203 were: (1) detected in 9 or 10 (of 10) isolates belonging to one or more pathogen groups, and (2) significantly more abundant in cultures relative to sterile media. Network analysis revealed a distinct metabolic fingerprint associated with each pathogen group, and analysis via Random Forest using leave-one-out cross-validation resulted in a 95% accuracy for the differentiation between groups. The present findings support the results of prior studies that have reported on the differential production of volatile metabolites across pathogenic bacteria and fungi, and provide additional insight through the inclusion of pathogen groups that have seldom been studied previously, including Acinetobacter spp., coagulase-negative Staphylococcus, and Proteus mirabilis, as well as the utilization of HS-SPME-GC×GC-TOFMS for improved sensitivity and resolution relative to traditional gas chromatography-based techniques.

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

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

Response of Rhizobium to Cd exposure: A volatile perspective

The volatile metabolome of Rhizobium sp. strain E20-8 exposed to three concentrations of cadmium (2.5, 5.0 and 7.5 μM) was screened using comprehensive two-dimensional gas chromatography coupled to time of flight mass spectrometry (GC × GC-ToFMS), combined with headspace solid phase microextraction (HS-SPME). Cd exposure induced a global increase in the concentration of volatile organic compounds (VOCs) both intra and extracellularly. Peak areas of several linear alkanes, ketones, aldehydes, alcohols, terpenic and volatile sulfur compounds, and one ester (ethyl acetate), were especially increased when compared with the control condition (no Cd). These compounds might originate from the metabolization of toxic membrane peroxidation products, the proteolysis of oxidized proteins or the alteration of metabolic pathways, resulting from the oxidative stress imposed by Cd. Several VOCs are related to oxidative damage, but the production of VOCs involved in antioxidant response (menthol, α-pinene, dimethyl sulfide, disulfide and trisulfide, 1-butanol and 2-butanone) and in cell aggregation (2,3-butanedione, 3-methyl-1-butanol and 2-butanone) is also observed. These results bring new information that highlights the role of VOCs on bacteria response to Cd stress, identify a novel set of biomarkers related with metal stress and provide information to be applied in biotechnological and remediation contexts.

Sniffing out the hypoxia volatile metabolic signature of Aspergillus fumigatus

Invasive aspergillosis (IA) is a life-threatening infectious disease caused by fungi from the genus Aspergillus, with an associated mortality as high as 90% in certain populations. IA-associated pulmonary lesions are characteristically depleted in oxygen relative to normal lung tissue, and it has been shown that the most common causal agent of IA, Aspergillus fumigatus, must respond to low-oxygen environments for pathogenesis and disease progression. Previous studies have demonstrated marked alterations to the Aspergillus fumigatus transcriptome in response to low-oxygen environments that induce a 'hypoxia response'. Consequently, we hypothesized that these transcriptomic changes would alter the volatile metabolome and generate a volatile hypoxia signature. In the present study, we analyzed the volatile molecules produced by A. fumigatus in both oxygen replete (normoxia) and depleted (hypoxia) environments via headspace solid-phase micro-extraction coupled to two-dimensional gas chromatography-time-of-flight mass spectrometry. Using the machine learning algorithm random forest, we identified 19 volatile molecules that were discriminatory between the four growth conditions assessed in this study (i.e., early hypoxia (1 h), late hypoxia (8 h), early normoxia (1 h), and late normoxia (8 h)), as well as a set of 19 that were discriminatory between late hypoxia cultures and all other growth conditions in aggregate. Nine molecules were common to both comparisons, while the remaining 20 were specific to only one of two. We assigned putative identifications to 13 molecules, of which six were most highly abundant in late hypoxia cultures. Previously acquired transcriptomic data identified putative biochemical pathways induced in hypoxia conditions that plausibly account for the production of a subset of these molecules, including 2,3-butanedione and 3-hydroxy-2-butanone. These two molecules may represent a novel hypoxia fitness pathway in A. fumigatus, and could be useful in the detection of hypoxia-associated A. fumigatus lesions that develop in established IA infections.