Trees in the genus Populus synthesize sticky and fragrant resins to protect dormant leaf buds during winter. These resins contain diverse phenolic metabolites, in particular, hydroxycinnamate esters and methylated flavonoids. Populus trichocarpa leaf bud resin is characterized by methylated dihydrochalcone aglycones. To determine how the resin profile is influenced by seasonal changes, P. trichocarpa lateral leaf bud extracts and secreted surface resin were collected monthly over a 1-year cycle. The dihydrochalcones in both sets of extracts were quantified using ultrahigh pressure liquid chromatography-mass spectrometry (UPLC-MS), and other chemical changes were monitored using nontargeted metabolomics by UPLC-high-resolution MS (UPLC-HRMS). The results indicate that the dihydrochalcone content changes over the seasons and that biosynthesis occurs concomitant with bud development in the summer months. Nontargeted metabolomics data confirmed a pattern of dramatic changes in the summer and further suggested additional periods of substantive biochemical change in the resin. While overall patterns of surface-extracted resin matched those of whole bud extracts, some of the dynamics were shifted in the surface resin samples. This study provides the basis for the use of dihydrochalcones and other identified resin components as metabolic markers for more detailed investigations of resin biosynthesis, secretion, and movement to the bud surface.

Polar, high altitude montane and cold desert environments harbour only sparse plant life and often remain frozen for extended periods. Because of their remoteness, often combined with restricted access, such regions are rarely visited and the fungal biodiversity of the soils is scarcely studied. Despite this, when such studies are undertaken, psychrophilic Penicillium species are often reported and the isolates exhibit a high spectrum of biologically active compounds of biotechnological interest. Small molecule profiling by mass spectrometry (often called 'metabolomics') can supplement phylogenetic species concepts and provide information to characterize variation within species or populations. During large scale fungal isolation surveys exploring new psychrophilic fungi from high altitude alpine and arctic tundra soils, several undescribed Penicillium species were discovered. A polyphasic taxonomic approach was adopted to formally describe ten new species using multigene phylogenetic analyses and phenotypic characterizations including secondary metabolite production, colony characters, and microscopic analysis of morphological structures. Using untargeted metabolomics and molecular networking tools, an emphasis was made to characterize, compare and discuss in depth, the chemical diversity associated with these new Penicillium species. Taxonomic novelties: New species: Penicillium algidum Visagie, Overy, Seifert & Frisvad, Penicillium aquamarinum Visagie, Overy, Seifert & Frisvad, Penicillium discoense Visagie, Overy, Seifert & Frisvad, Penicillium hesseltinei Visagie, Overy, Seifert & Frisvad, Penicillium jugorum Visagie, Overy, Seifert & Frisvad, Penicillium marthae Visagie, Overy, Seifert & Frisvad, Penicillium oreophilum Visagie, Overy, Seifert, Christensen & Frisvad, Penicillium rivulorum Visagie, Overy, Seifert & Frisvad, Penicillium turcosum Visagie, Overy, Seifert & Frisvad, Penicillium wyomingense Visagie, Overy, Seifert & Frisvad. Citation: Overy DP, Frisvad JC, Witte TE, Hicks CL, Hermans A, Sproule A, Louis-Seize G, Seifert KA, Yilmaz N, Price J, van Vuuren NI, Visagie CM (2025). Chemodiversity of Penicillium isolated from alpine and arctic environments, including ten new species. Studies in Mycology 112: 75-116. doi: 10.3114/sim.2025.112.03.

Fusarium avenaceum is an important root rot pathogen of pulses and a causative agent of Fusarium head blight of cereals. Studies have shown higher abundance of F. avenaceum in the field as a result of pulse-cereal rotations. It is not known whether this rotation can have an influence on the aggressiveness or pathogenicity of the F. avenaceum isolates, as they interact among different host species. In the present work, F. avenaceum isolates collected from common rotation crops, pea, wheat, and lentil, were assessed for root rot in pea and lentil and for head blight in durum wheat. Based on the least squares mean of root rot severity in pea and lentil, the isolate aggressiveness was categorized into low, moderate, and high. The majority of the isolates collected from pea, wheat, and lentil, respectively, were highly aggressive, moderately to highly aggressive, and less aggressive on pea and lentil. In point-inoculated durum wheat, there was no significant difference in aggressiveness between pea- and wheat-derived isolates; a direct comparison with lentil-derived isolates could not be made, as they were screened separately. When comparing the overall isolate aggressiveness, isolates recovered from pea were more aggressive on all three hosts. These data suggest that inclusion of pea in a cereal-based rotation may lead to increased incidence and severity of F. avenaceum-associated head blight in the subsequent wheat crop in the rotation.

Ergot is a fungal disease of many plants but is perhaps most commonly associated with domesticated grasses or cereals, such as rye, wheat, barley, oat, sorghum, millet, maize and rice. Ergot is of historical significance, having been reported for several millennia, but is also of concern in modern agricultural production systems. Caused by many different species within the genus Claviceps , the fungi cause the production of sclerotia, which are typically dark in colour, in place of healthy grain. The sclerotia contain toxins that can make the grain unsafe for consumption by humans or livestock. Ergot can be managed both preharvest as well as postharvest to minimize the presence of sclerotia and their associated toxins in food and feed systems. In this review, we provide a detailed update on our current knowledge of ergot on cereals, with a focus on recent advances in our understanding of fungal toxins and their regulation, pathogen biology and disease management.

Microbial plant pathogens deploy amphipathic cyclic lipopeptides to reduce surface tension in their environment. While plants can detect these molecules to activate cellular stress responses, the role of these lipopeptides or associated host responses in pathogenesis are not fully clear. The gramillin cyclic lipopeptide is produced by the Fusarium graminearum fungus and is a virulence factor and toxin in maize. Here, we show that gramillin promotes virulence and necrosis in both monocots and dicots by disrupting ion balance across membranes. Gramillin is a cation-conducting ionophore and causes plasma membrane depolarization. This disruption triggers cellular signaling, including a burst of reactive oxygen species (ROS), transcriptional reprogramming, and callose production. Gramillin-induced ROS depends on expression of host ILK1 and RBOHD genes, which promote fungal induction of virulence genes during infection and host susceptibility. We conclude that gramillin's ionophore activity targets plant membranes to coordinate attack by the F. graminearum fungus.

Fusarium avenaceum is an aggressive pathogen of pulse crops and a causal agent in root rot disease that negatively impacts Canadian agriculture. This study reports the results of a targeted metabolomics-based profiling of secondary metabolism in an 18-strain panel of Fusarium avenaceum cultured axenically in multiple media conditions, in addition to an in planta infection assay involving four strains inoculated on two pea cultivars. Multiple secondary metabolites with known roles as virulence factors were detected which have not been previously associated with F. avenaceum, including fungal decalin-containing diterpenoid pyrones (FDDPs), fusaoctaxins, sambutoxin and fusahexin, in addition to confirmation of previously reported secondary metabolites including enniatins, fusarins, chlamydosporols, JM-47 and others. Targeted genomic analysis of secondary metabolite biosynthetic gene clusters was used to confirm the presence/absence of the profiled secondary metabolites. The detection of secondary metabolites with diverse bioactivities is discussed in the context of virulence factor networks potentially coordinating the disruption of plant defenses during disease onset by this generalist plant pathogen.

Barley is the third most important cereal crop in terms of production in Canada, and Fusarium head blight (FHB) is one of the main fungal diseases of barley. FHB is caused by a species complex of Fusaria, of which Fusarium graminearum Schwabe is the main causal species of FHB epidemics in Canada. Field surveys show that two or more Fusarium species often co-exist within the same field or grain sample, and F. poae is reported as another important species in barley. This study aimed to determine the pathogenicity of F. graminearum, F. poae, and a co-inoculation of both species causing FHB in barley. Two susceptible barley cultivars were spray-inoculated at 10 to 14 days after heading. Phenotypic disease severity was rated on a scale of 0–9 at 4, 7, 14, 21, and 28 days after inoculation. There was a significant difference in FHB severity between F. graminearum and F. poae, where infection with F. graminearum produced more severe disease ratings. F. poae generated lower disease ratings and was not statistically different from the control. When heads were co-inoculated with both Fusarium species, the resulting FHB severity was unchanged relative to heads inoculated with F. graminearum only. The ratio of F. graminearum to F. poae genomic DNA was also no different than when heads were inoculated with F. graminearum alone, as quantified with ddPCR using markers specific to each species. The metabolomic analysis of sample extracts showed that F. graminearum-associated metabolites dominated the mycotoxin profile of co-inoculated samples, which corroborated our other findings where F. graminearum appeared to outcompete F. poae in barley. No significant effect on visual FHB disease ratings or fungal DNA detection was observed between the cultivars tested. However, there were some metabolome differences between cultivars in response to the challenge by both F. graminearum and F. poae.

The need for therapeutics to treat a plethora of medical conditions and diseases is on the rise and the demand for alternative approaches to mammalian-based production systems is increasing. Plant-based strategies provide a safe and effective alternative to produce biological drugs but have yet to enter mainstream manufacturing at a competitive level. Limitations associated with batch consistency and target protein production levels are present; however, strategies to overcome these challenges are underway. In this study, we apply state-of-the-art mass spectrometry-based proteomics to define proteome remodelling of the plant following agroinfiltration with bacteria grown under shake flask or bioreactor conditions. We observed distinct signatures of bacterial protein production corresponding to the different growth conditions that directly influence the plant defence responses and target protein production on a temporal axis. Our integration of proteomic profiling with small molecule detection and quantification reveals the fluctuation of secondary metabolite production over time to provide new insight into the complexities of dual system modulation in molecular pharming. Our findings suggest that bioreactor bacterial growth may promote evasion of early plant defence responses towards Agrobacterium tumefaciens (updated nomenclature to Rhizobium radiobacter). Furthermore, we uncover and explore specific targets for genetic manipulation to suppress host defences and increase recombinant protein production in molecular pharming.

Fusarium poae is commonly detected in field surveys of Fusarium head blight (FHB) of cereal crops and can produce a range of trichothecene mycotoxins. Although experimentally validated reports of F. poae strains producing T-2/HT-2 trichothecenes are rare, F. poae is frequently generalized in the literature as a producer of T-2/HT-2 toxins due to a single study from 2004 in which T-2/HT-2 toxins were detected at low levels from six out of forty-nine F. poae strains examined. To validate/substantiate the observations reported from the 2004 study, the producing strains were acquired and phylogenetically confirmed to be correctly assigned as F. poae; however, no evidence of T-2/HT-2 toxin production was observed from axenic cultures. Moreover, no evidence for a TRI16 ortholog, encoding a key acyltransferase shown to be necessary for T-2 toxin production in other Fusarium species, was observed in any of the de novo assembled genomes of the F. poae strains. Our findings corroborate multiple field-based and in vitro studies on FHB-associated Fusarium populations which also do not support the production of T-2/HT-2 toxins with F. poae and therefore conclude that F. poae should not be generalized as a T-2/HT-2 toxin producing species of Fusarium.

During a survey of culturable microfungi from the bark of sugar maple (Acer saccharum), Atrocalyx glutinosus and Nigrograna rubescens, two novel species of Pleosporales (Dothideomycetes) were isolated from several locations in eastern Ontario, Canada. Formal species descriptions are presented based on unique colony phenotypes and micromorphological characteristics and supported using multi-locus molecular phylogenetic comparisons with similar species. Both A. glutinosus and N. rubescens produce pycnidial asexual morphs in culture. As their names imply, under specific culture conditions, A. glutinosus excretes large amounts of the glutinous polysaccharide pullulan and N. rubescens produces a dark red naphthoquinone pigment that diffuses in the culture medium. Citation: Mack JN, Sproule A, Shields SW, Seifert KA, Smith M, Overy DP (2024). Two novel Pleosporales species isolated from the bark of Acer saccharum . Fungal Systematics and Evolution 13: 1-14. doi: 10.3114/fuse.2024.13.01.

Sedimentomics methods offer insight into the physiological parameters that influence freshwater sediment organic matter (sedOM). To date, most sedimentomics studies characterized variations across large spatial and environmental gradients; here we examine whether sedimentomics methods capture subtle sedOM variations within a relatively homogeneous study area in southwestern Nova Scotia, Canada. Additionally, we explore the lake sedimentome for candidate biomarkers related to ongoing carnivorous animal farming in the region. Sediment cores were recovered from seven lakes across a trophic (oligo- to eu- trophic) and anthropogenic land use gradient (carnivorous animal farming in catchment, downstream of farming, no farming nearby). Subsamples that dated prior to 1910 (pre-carnivorous animal farming) and later than 2010 (during carnivorous animal farming) were analyzed using UHPLC-HRMS in both negative (ESI-) and positive (ESI+) electrospray ionization modes. Cluster analysis (k-means) showed replicate samples from a given lake clustered distinctly from one another in both ESI modes, indicating sedOM captured subtle variations between lake systems. PCA combined with multiple linear regression indicated carnivorous animal farming and OM source explained most of the observed variation in lake sedOM. Principal component analysis (PCA) and Partial Least Squares Discriminant Analysis (PLS-DA) of ESI- and ESI+ data sets identified 103 unique candidate biomarkers. Ten strong candidate biomarkers were identified using graphical methods; more research is required for biomarker verification and molecular characterization. Our results indicate sedimentomics could be used in environmentally homogeneous areas, offering insight into the controls of sedOM cycling. Additionally, we identified prospective biomarkers related to carnivorous animal farming that could be used to understand relative contributions of farming to ongoing eutrophication issues in southwestern Nova Scotia.

The whole genomes of three Claviceps purpurea strains were sequenced using Oxford Nanopore Technologies' MinION and assembled into complete, chromosome-level assemblies. The C. purpurea genome consists of eight conserved chromosomes, with evidence of inter-chromosomal structural rearrangements between strains.

Fusarium graminearum is a causal organism of Fusarium head blight in cereals and maize. Although a few secondary metabolites produced by F. graminearum are considered disease virulence factors, many molecular products of biosynthetic gene clusters expressed by F. graminearum during infection and their associated role in the disease are unknown. In particular, the predicted meroterpenoid products of the biosynthetic gene cluster historically designated as "C16" are likely associated with pathogenicity. Presented here are the results of CRISPR-Cas9 gene-editing experiments disrupting the polyketide synthase and terpene synthase genes associated with the C16 biosynthetic gene cluster in F. graminearum. Culture medium screening experiments using transformant strains were profiled by UHPLC-HRMS and targeted MS2 experiments to confirm the associated secondary metabolite products of the C16 biosynthetic gene cluster as the decalin-containing diterpenoid pyrones, FDDP-D and FDDP-E. Both decalin-containing diterpenoid pyrones were confirmed to be produced in wheat heads challenged with F. graminearum in growth chamber trials. The extent to which the F. graminearum C16 biosynthetic gene cluster is dispersed within the genus Fusarium is discussed along with a proposed role of the FDDPs as pathogen virulence factors.

Genetic studies have shown that the MAP kinase MGV1 and the transcriptional regulator TRI6 regulate many of the same biosynthetic gene clusters (BGCs) in Fusarium graminearum. This study sought to investigate the relationship between MGV1 and TRI6 in the regulatory hierarchy. Transgenic F. graminearum strains constitutively expressing MGV1 and TRI6 were generated to address both independent and epistatic regulation of BGCs by MGV1 and TRI6. We performed a comparative transcriptome analysis between axenic cultures grown in nutrient-rich and secondary metabolite-inducing conditions. The results indicated that BGCs regulated independently by Mgv1 included genes of BGC52, whereas genes uniquely regulated by TRI6 included the gene cluster (BGC49) that produces gramillin. To understand the epistatic relationship between MGV1 and TRI6, CRISPR/Cas9 was used to insert a constitutive promoter to drive TRI6 expression in the Δmgv1 strain. The results indicate that BGCs that produce deoxynivalenol and fusaoctaxin are co-regulated, with TRI6 being partially regulated by MGV1. Overall, the findings from this study indicate that MGV1 provides an articulation point to differentially regulate various BGCs. Moreover, TRI6, embedded in one of the BGCs provides specificity to regulate the expression of the genes in the BGC.

Mycotoxins, derived from toxigenic fungi such as Fusarium, Aspergillus, and Penicillium species have impacted the human food chain for thousands of years. Deoxynivalenol (DON), is a tetracyclic sesquiterpenoid type B trichothecene mycotoxin predominantly produced by F. culmorum and F. graminearum during the infection of corn, wheat, oats, barley, and rice. Glycosylation of DON is a protective detoxification mechanism employed by plants. More recently, DON glycosylating activity has also been detected in fungal microparasitic (biocontrol) fungal organisms. Here we follow up on the reported conversion of 15-acetyl-DON (15-ADON) into 15-ADON-3-O-glycoside (15-ADON-3G) in Clonostachys rosea. Based on the hypothesis that the reaction is likely being carried out by a uridine diphosphate glycosyl transferase (UDP-GTase), we applied a protein structural comparison strategy, leveraging the availability of the crystal structure of rice Os70 to identify a subset of potential C. rosea UDP-GTases that might have activity against 15-ADON. Using CRISPR/Cas9 technology, we knocked out several of the selected UDP-GTases in the C. rosea strain ACM941. Evaluation of the impact of knockouts on the production of 15-ADON-3G in confrontation assays with F. graminearum revealed multiple UDP-GTase enzymes, each contributing partial activities. The relationship between these positive hits and other UDP-GTases in fungal and plant species is discussed.

Novel species of fungi described in this study include those from various countries as follows: Australia , Aschersonia mackerrasiae on whitefly, Cladosporium corticola on bark of Melaleuca quinquenervia , Penicillium nudgee from soil under Melaleuca quinquenervia , Pseudocercospora blackwoodiae on leaf spot of Persoonia falcata , and Pseudocercospora dalyelliae on leaf spot of Senna alata . Bolivia , Aspicilia lutzoniana on fully submersed siliceous schist in high-mountain streams, and Niesslia parviseta on the lower part and apothecial discs of Erioderma barbellatum onatwig. Brazil , Cyathus bonsai on decaying wood, Geastrum albofibrosum from moist soil with leaf litter, Laetiporus pratigiensis on a trunk of a living unknown hardwood tree species, and Scytalidium synnematicum on dead twigs of unidentified plant. Bulgaria , Amanita abscondita on sandy soil in a plantation of Quercus suber . Canada , Penicillium acericola on dead bark of Acer saccharum , and Penicillium corticola on dead bark of Acer saccharum . China , Colletotrichum qingyuanense on fruit lesion of Capsicum annuum . Denmark , Helminthosphaeria leptospora on corticioid Neohypochnicium cremicolor. Ecuador (Galapagos) , Phaeosphaeria scalesiae on Scalesia sp. Finland , Inocybe jacobssonii on calcareouss oils in dry forests and park habitats. France , Cortinarius rufomyrrheus on sandy soil under Pinus pinaster , and Periconia neominutissima on leaves of Poaceae . India , Coprinopsis fragilis on decaying bark of logs, Filoboletus keralensis on unidentified woody substrate, Penicillium sankaranii from soil, Physisporinus tamilnaduensis on the trunk of Azadirachta indica , and Poronia nagaraholensis on elephant dung. Iran , Neosetophoma fic on infected leaves of Ficus elastica . Israel , Cnidariophoma eilatica (incl. Cnidariophoma gen. nov.) from Stylophora pistillata . Italy , Lyophyllum obscurum on acidic soil. Namibia , Aureobasidium faidherbiae on dead leaf of Faidherbia albida , and Aureobasidium welwitschiae on dead leaves of Welwitschia mirabilis . Netherlands , Gaeumannomycella caricigena on dead culms of Carex elongata , Houtenomyces caricicola (incl. Houtenomyces gen. nov.) on culms of Carex disticha , Neodacampia ulmea (incl. Neodacampia gen. nov.) on branch of Ulmus laevis , Niesslia phragmiticola on dead standing culms of Phragmites australis , Pseudopyricularia caricicola on culms of Carex disticha , and Rhodoveronaea nieuwwulvenica on dead bamboo sticks. Norway , Arrhenia similis half-buried and moss-covered pieces of rotting wood in grass-grownpath. Pakistan , Mallocybe ahmadii on soil. Poland , Beskidomyces laricis (incl. Beskidomyces gen. nov.) from resin of Larix decidua ssp. polonica , Lapidomyces epipinicola from sooty mould community on Pinus nigra , and Leptographium granulatum from a gallery of Dendroctonus micans on Picea abies . Portugal , Geoglossum azoricum on mossy areas of laurel forest areas planted with Cryptomeria japonica , and Lunasporangiospora lusitanica from a biofilm covering a bio deteriorated limestone wall. Qatar , Alternaria halotolerans from hypersaline sea water, and Alternaria qatarensis from water sample collected from hypersaline lagoon. South Africa , Alfaria thamnochorti on culm of Thamnochortus fraternus , Knufia aloeicola on Aloe gariepensis , Muriseptatomyces restionacearum (incl. Muriseptatomyces gen. nov.) on culms of Restionaceae , Neocladosporium arctotis on nest of cases of bagworm moths( Lepidoptera, Psychidae ) on Arctotis auriculata , Neodevriesia scadoxi on leaves of Scadoxus puniceus , Paraloratospora schoenoplecti on stems of Schoenoplectus lacustris , Tulasnella epidendrea from the roots of Epidendrum × obrienianum , and Xenoidriella cinnamomi (incl. Xenoidriella gen. nov.) on leaf of Cinnamomum camphora . South Korea , Lemonniera fraxinea on decaying leaves of Fraxinus sp. frompond. Spain , Atheniella lauri on the bark of fallen trees of Laurus nobilis , Halocryptovalsa endophytica from surface-sterilised, asymptomatic roots of Salicornia patula , Inocybe amygdaliolens on soil in mixed forest, Inocybe pityusarum on calcareous soil in mixed forest, Inocybe roseobulbipes on acidic soils, Neonectria borealis from roots of Vitis berlandieri × Vitis rupestris , Sympoventuria eucalyptorum on leaves of Eucalyptus sp., and Tuber conchae fromsoil. Sweden , Inocybe bidumensis on calcareous soil. Thailand , Cordyceps sandindaengensis on Lepidoptera pupa, buried in soil, Ophiocordyceps kuchinaraiensis on Coleoptera larva, buried in soil, and Samsoniella winandae on Lepidoptera pupa, buriedinsoil. Taiwan region (China) , Neophaeosphaeria livistonae on dead leaf of Livistona rotundifolia . Türkiye , Melanogaster anatolicus on clay loamy soils. UK , Basingstokeomyces allii (incl. Basingstokeomyces gen. nov.) on leaves of Allium schoenoprasum . Ukraine , Xenosphaeropsis corni on recently dead stem of Cornus alba. USA , Nothotrichosporon aquaticum (incl. Nothotrichosporon gen. nov.) from water, and Periconia philadelphiana from swab of coil surface. Morphological and culture characteristics for these new taxa are supported by DNA barcodes.

Soil organic matter (SOM) is the largest carbon pool in terrestrial ecosystems and underpins the health and productivity of soil. Accurate characterization of its chemical composition will improve our understanding of biotic and abiotic processes regulating its stabilization. Our purpose in this study was to estimate the loss of SOM by microbial and exoenzymatic activity that might occur when soil is extracted for analysis of representative low molecular weight mass features using untargeted metabolomics. Two mined clays (kaolinite, montmorillonite) and three diverse soils (varying in texture, specific surface area and cation exchange capacity) were used to assess the extraction efficiency and loss of three enzymatic activity indicators (2,6-dichloroindophenol sodium salt hydrate [DCIP], 4-methylumbelliferyl phosphate [MUBph] and 3,4-dihydroxy-L-phenylalanine [LDOPA]) during extraction with two different solvents (water and methanol). Losses of the indicators were attributed to extraction method (ultrasonication, shaking, or shaking following chloroform fumigation), physical properties associated with the soil/clay type, and microbial activity. Soil/clay type strongly influenced indicator recovery and hence, SOM recovery. Choice of extraction method strongly influenced the composition and recovery of representative SOM mass features, while the choice of solvent determined whether the soil type or extraction method had a greater influence of compositional differences in the SOM mass features extracted. Extraction following chloroform fumigation had the greatest loss of the indicators, due to enzymatic activity and/or adsorption onto the soil matrix. Minimal variation in composition and loss of SOM mass features occurred during extraction by shaking for the soils tested; we therefore recommend it as the method of choice for untargeted SOM extraction studies.

This chapter describes protocols for the development of consensus chemical phenotypes or "metabolomes" of fungal populations using ultra-high pressure liquid chromatography coupled to high resolution mass spectrometry (UPLC-HRMS). Isolates are cultured using multiple media conditions to elicit the expression of diverse secondary metabolite biosynthetic gene clusters. The mycelium and spent culture media are extracted using organic solvents and profiled by ultra-high pressure chromatography coupled with a high resolution Thermo Orbitrap XL mass spectrometer with the ability to trap and fragment ions to general MS2 spectra. MS data preprocessing is explained and illustrated using the freely available software MZMine 2. Through data processing, binary matrices of mass features can be generated and then combined into a consensus secondary metabolite phenotype of all isolates grown in all media conditions. The production of consensus chemical phenotypes is useful for screening large fungal populations (both inter and intra-species populations) for isolates potentially expressing novel secondary metabolites or analogs of known secondary metabolites.

Gas-fermenting acetogens can upgrade one-carbon (C1) compounds (such as CO 2 and CO) to the two-carbon (C2) metabolite acetyl coenzyme A (CoA) and convert sugar feedstocks to acetyl-CoA with minimal CO 2 emissions. Fulfilling the biosynthetic potential of these microbes requires overcoming challenges in pathway engineering. Here we design a synthetic acetyl-CoA bi-cycle—in addition to the natural carbon-fixing pathways—for C2 metabolite synthesis. This pathway produces an acetyl-CoA by fixation of two CO 2 equivalents via three functional modules acting in sequence: carbon fixation, gluconeogenesis and non-oxidative glycolysis. The pathway was examined by in silico thermodynamic and kinetic analyses. The prototypic pathway was implemented in a syngas-fermenting organism, Clostridium ljungdahlii DSM 13528, by expressing a heterologous phosphoketolase that can work with other native enzymes in the host acetogen. The carbon conversion pathway is possible under various growth conditions and is independent of the Wood–Ljungdahl pathway for the valorization of H 2 and CO 2 . This study reports the improvement of carbon conversion using a reductive acetyl-CoA bi-cycle and the potential impact of redox homoeostasis in the acetogenic host for industrial applications of gas fermentation.

Alternaria section Alternaria is comprised of many species that infect a broad diversity of important crop plants and cause post-harvest spoilage. Alternaria section Alternaria species, such as A. alternata and A. arborescens, are prolific producers of secondary metabolites that act as virulence factors of disease and are mycotoxins that accumulate in infected tissues—metabolites that can vary in their spectrum of production between individuals from the same fungal species. Untargeted metabolomics profiling of secondary metabolite production using mass spectrometry is an effective means to detect phenotypic anomalies in secondary metabolism within a species. Secondary metabolite phenotypes from 36 Alternaria section Alternaria isolates were constructed to observe frequency of production patterns. A clear and unique mass feature pattern was observed for three of the strains that were linked with the production of the dehydrocurvularin family of toxins and associated detoxification products. Examination of corresponding genomes revealed the presence of the dehydrocurvularin biosynthesis gene cluster associated with a sub-telomeric accessory region. A comparison of sequence similarity and occurrences of the dehydrocurvularin biosynthetic gene cluster within Pleosporalean fungi is presented and discussed.