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Journal of Fungi (Basel, Switzerland) Jan 2023Most research on the human microbiome focuses on the bacterial component, and this has led to a lack of information about the fungal component (mycobiota) and how this...
Most research on the human microbiome focuses on the bacterial component, and this has led to a lack of information about the fungal component (mycobiota) and how this can influence human health, e.g., by modulation through the diet. The validated, dynamic computer-controlled model of the colon (TIM-2) is an in vitro model to study the microbiome and how this is influenced by interventions such as diet. In this study, it was used to the study the gut fungal-community. This was done in combination with next-generation sequencing of the ITS2 region for fungi and 16S rRNA for bacteria. Different dietary interventions (control diet (SIEM), high-carbohydrate, high-protein, glucose as a carbon source) were performed, to see if diet could shape the mycobiome. The mycobiome was investigated after the adaptation period, and throughout the intervention period which lasted 72 h, and samples were taken every 24 h. The fungal community showed low diversity and a greater variability when compared to bacteria. The mycobiome was affected most in the first hours of the adaptation period. Taxonomic classification showed that at the phylum-level Ascomycota and Basidiomycota dominated, while Agaricus, Aspergillus, Candida, Penicillum, Malassezia, Saccharomyces, Aureobasidium, Mycosphaerella, Mucor and Clavispora were the most abundant genera. During the intervention period, it was shown that the change of diet could influence the diversity. Clustering of samples for different time points was analyzed using Bray−Curtis dissimilarities. Samples of t0 clustered together, and samples of all other time points clustered together. The Bray−Curtis-dissimilarity analysis also showed that for the different dietary interventions, samples treated with glucose clustered together and were different from the other groups (p < 0.05, PERMANOVA). Taxonomic classification showed that the genera Alternaria, Thanatephorus, Candida and Dekkera differentially changed for the various diet groups (p < 0.05, Kruskal−Wallis). These results show that the mycobiota could be modelled in TIM-2; however, the low diversity and high variability make studying fungal, as compared to bacterial, communities, much more challenging. Future research should focus on the optimization of the stability of the fungal community to increase the strength of the results.
PubMed: 36675926
DOI: 10.3390/jof9010104 -
Journal of Fungi (Basel, Switzerland) Oct 2023Intertidal zones comprise diverse habitats and directly suffer from the influences of human activities. Nevertheless, the seasonal fluctuations in fungal diversity and...
Intertidal zones comprise diverse habitats and directly suffer from the influences of human activities. Nevertheless, the seasonal fluctuations in fungal diversity and community structure in these areas are not well comprehended. To address this gap, samples of seawater and sediment were collected seasonally from the estuary and swimming beaches of Qingdao's intertidal areas in China and were analyzed using a metabarcoding approach targeting ITS2 rDNA regions. Compared to the seawater community dominated by and Agaricomycetes, the sediment community was rather dominated by Dothideomycetes and Eurotiomycetes. Furthermore, the seawater community shifted with the seasons but not with the locations, while the sediment community shifted seasonally and spatially, with a specific trend showing that , , and occurred predominantly in the estuarine habitats during winter and in the beach habitats during spring. These spatiotemporal shifts in fungal communities' composition were supported by the PERMANOVA test and could be explained partially by the environmental variables checked, including temperature, salinity, and total organic carbon. Unexpectedly, the lowest fungal richness was observed in the summer sediments from two swimming beaches which were attracting a high influx of tourists during summer, leading to a significant anthropogenic influence. Predicted trophic modes of fungal taxa exhibited a seasonal pattern with an abundance of saprotrophic fungi in the summer sediments, positively correlating to the temperature, while the taxa affiliated with symbiotroph and pathotroph-saprotroph occurred abundantly in the winter and spring sediments, respectively. Our results demonstrate the space-time shifts in terms of the fungal community, as well as the trophic modes in the intertidal region, providing in-depth insights into the potential influence of environmental factors and human activity on intertidal mycobiomes.
PubMed: 37888271
DOI: 10.3390/jof9101015 -
World Journal of Microbiology &... Jun 2023Malic acid is mainly produced by chemical methods which lead to various environmental sustainability concerns associated with CO emissions and resulting global warming.... (Review)
Review
Malic acid is mainly produced by chemical methods which lead to various environmental sustainability concerns associated with CO emissions and resulting global warming. Since malic acid is naturally synthesized, microorganisms offer an eco-friendly and cost-effective alternative for its production. An additional advantage of microbial production is the synthesis of pure L-form of malic acid. Due to its numerous applications, biotechnologically- produced L-malic acid is a much sought-after platform chemical. Malic acid can be produced by microbial fermentation via oxidative/reductive TCA and glyoxylate pathways. This article elaborates the potential and limitations of high malic acid producing native fungi belonging to Aspergillus, Penicillium, Ustilago and Aureobasidium spp. The utilization of industrial side streams and low value renewable substrates such as crude glycerol and lignocellulosic biomass is also discussed with a view to develop a competitive bio-based production process. The major impediments present in the form of toxic compounds from lignocellulosic residues or synthesized during fermentation along with their remedial measures are also described. The article also focuses on production of polymalic acid from renewable substrates which opens up a cost-cutting dimension in production of this biodegradable polymer. Finally, the recent strategies being employed for its production in recombinant organisms have also been covered.
Topics: Malates; Fermentation; Fungi; Glycerol
PubMed: 37269376
DOI: 10.1007/s11274-023-03666-5 -
FEMS Yeast Research Sep 2020Aureobasidium pullulans is the most abundant and ubiquitous species within the genus and is also considered a core component of the grape juice microflora. So far, a...
Aureobasidium pullulans is the most abundant and ubiquitous species within the genus and is also considered a core component of the grape juice microflora. So far, a small number of other Aureobasidium species have been reported, that in contrast to A. pullulans, appear far more constrained to specific habitats. It is unknown whether grape juice is a reservoir of novel Aureobasidium species, overlooked in the course of conventional morphological and meta-barcoding analyses. In this study, eight isolates from grape juice taxonomically classified as Aureobasidium through ITS sequencing were subjected to whole-genome phylogenetic, synteny and nucleotide identity analyses, which revealed three isolates to likely represent newly discovered Aureobasidium species. Analyses of ITS and metagenomic sequencing datasets show that these species can be present in grape juice samples from different locations and vintages. Functional annotation revealed the Aureobasidium isolates possess the genetic potential to support growth on the surface of plants and grapes. However, the loss of several genes associated with tolerance to diverse environmental stresses suggest a more constrained ecological range than A. pullulans.
Topics: Aureobasidium; Comparative Genomic Hybridization; DNA, Fungal; DNA, Ribosomal Spacer; Fruit and Vegetable Juices; Genome, Fungal; Phylogeny; Sequence Analysis, DNA; South Australia; Vitis
PubMed: 32897317
DOI: 10.1093/femsyr/foaa052 -
Yeast (Chichester, England) Jan 2022Insects interact with a wide variety of yeasts, often providing a suitable substrate for their growth. Some yeast-insect interactions are tractable models for... (Review)
Review
Insects interact with a wide variety of yeasts, often providing a suitable substrate for their growth. Some yeast-insect interactions are tractable models for understanding the relationships between the symbionts. Attine ants are prominent insects in the Neotropics and have performed an ancient fungiculture of mutualistic basidiomycete fungi for more than 55-65 million years. Yeasts gain access to this sophisticated mutualism, prompting diversity, ecological, and biotechnological studies in this environment. We review half a century research in this field, surveying for recurrent yeast taxa and their putative ecological roles in this environment. We found that previous studies mainly covered the yeast diversity from a small fraction of attine ants, being Saccharomycetales, Tremellales, and Trichosporonales as the most frequent yeast or yeast-like orders found. Apiotrichum, Aureobasidium, Candida, Cutaneotrichosporon, Debaryomyces, Meyerozyma, Papiliotrema, Rhodotorula, Trichomonascus, and Trichosporon are the most frequent recovered genera. On the other hand, studies of yeasts' ecological roles on attine ant-fungus mutualism only tapped the tip of the iceberg. Previous established hypotheses in the literature cover the production of lignocellulosic enzymes, chemical detoxification, and fungus garden protection. Some of these roles have parallels in biotechnological processes. In conclusion, the attine ant environment has a hidden potential for studying yeast biodiversity, ecology, and biotechnology, which has been particularly unexplored considering the vast diversity of fungus-growing ants.
Topics: Animals; Ants; Biotechnology; Fungi; Phylogeny; Symbiosis; Yeasts
PubMed: 34473375
DOI: 10.1002/yea.3667 -
Scientific Reports Jun 2023Saccharomyces cerevisiae, an essential player in alcoholic fermentation during winemaking, is rarely found in intact grapes. Although grape-skin environment is...
Saccharomyces cerevisiae, an essential player in alcoholic fermentation during winemaking, is rarely found in intact grapes. Although grape-skin environment is unsuitable for S. cerevisiae's stable residence, Saccharomycetaceae-family fermentative yeasts can increase population on grape berries after colonization during raisin production. Here, we addressed adaptation of S. cerevisiae to grape-skin ecosystem. The yeast-like fungus Aureobasidium pullulans, a major grape-skin resident, exhibited broad spectrum assimilation of plant-derived carbon sources, including ω-hydroxy fatty acid, arising from degradation of plant cuticles. In fact, A. pullulans encoded and secreted possible cutinase-like esterase for cuticle degradation. When intact grape berries were used as a sole carbon source, such grape-skin associated fungi increased the accessibility to fermentable sugars by degrading and assimilating the plant cell wall and cuticle compounds. Their ability seems also helpful for S. cerevisiae to obtain energy through alcoholic fermentation. Thus, degradation and utilization of grape-skin materials by resident microbiota may account for their residence on grape-skin and S. cerevisiae's possible commensal behaviors. Conclusively, this study focused on the symbiosis between grape-skin microbiota and S. cerevisiae from the perspective of winemaking origin. Such plant-microbe symbiotic interaction may be a prerequisite for triggering spontaneous food fermentation.
Topics: Saccharomyces cerevisiae; Vitis; Ecosystem; Wine; Fungi
PubMed: 37340058
DOI: 10.1038/s41598-023-35734-z -
The Science of the Total Environment Sep 2021Different types of pots and growing and casing media, including biodegradable materials, are used for plant and mushroom production. The fungus Peziza ostracoderma has... (Review)
Review
Different types of pots and growing and casing media, including biodegradable materials, are used for plant and mushroom production. The fungus Peziza ostracoderma has gained attention for its visible growth on growing media for plants and casing media for mushrooms. Through a review of the literature we aim to evaluate whether exposure to fungi from recyclable pots and different growing and casing media occurs and causes occupational health effects. Based on the published papers, specific fungal species were not related to a specific medium. Thus P. ostracoderma has been found on paper pots, peat, sterilized soil, vermiculite, and rockwool with plants, and on peat, pumice, and paper casing for mushrooms. It has been found in high concentrations in the air in mushroom farms. Also Acremonium spp., Aspergillus niger, A. fumigatus, Athelia turficola, Aureobasidium pullulans, Chaetomium globosum, Chrysonilia sitophila, Cladosporium spp., Cryptostroma corticale, Lecanicillium aphanocladii, Sporothrix schenckii, Stachybotrys chartarum, and Trichoderma spp. have been found on different types of growing or casing media. Most of the fungi have also been found in the air in greenhouses, but the knowledge about airborne fungal species in mushroom farms is very limited. Eight publications describe cases of health effects associated directly with exposure to fungi from pots or growing or casing media. These include cases of hypersensitivity pneumonitis caused by exposure to: A. fumigatus, A. niger, Au. pullulans, Cr. corticale, P. ostracoderma, and a mixture of fungi growing on different media. Different approaches have been used to avoid growth of saprophytes including: chemical fungicides, the formulation of biodegradable pots and growing media and types of peat. To increase the sustainability of growing media different types of media are tested for their use and with the present study we highlight the importance of also considering the occupational health of the growers who may be exposed to fungi from the media and pots.
Topics: Ascomycota; Chaetomium; Fungi; Hypocreales; Neurospora; Occupational Exposure; Sporothrix; Stachybotrys
PubMed: 34034170
DOI: 10.1016/j.scitotenv.2021.147832 -
Frontiers in Microbiology 2022Endophytic fungi are microorganisms with the ability to colonize plants for the entire or at least a significant part of their life cycle asymptomatically, establishing...
Endophytic fungi are microorganisms with the ability to colonize plants for the entire or at least a significant part of their life cycle asymptomatically, establishing a plant-fungus association. They play an important role in balancing ecosystems, as well as benefiting host through increasing plant growth, and protecting the host plants from abiotic and biotic stresses using various strategies. In the present study, endophytic fungi were isolated from wild and endemic apple cultivars, followed by characterizing their antifungal effect against . To characterize the endophytic fungi, 417 fungal strains were separated from 210 healthy fruit, leaf, and branch samples collected from the north of Iran. Among the purified fungal isolates, 33 fungal genera were identified based on the morphological characteristics, of which 38 species were detected according to the morphological features and molecular data of ITS, , and genomic regions (related to the genus). The results represented that most of the endophytic fungi belonged to Ascomycota (67.8%), 31.4% of isolates were mycelia sterilia, while the others were Basidiomycota (0.48%) and Mucoromycota (0.24%). Additionally, , , and were determined as the dominant genera. The antifungal properties of the identified isolates were evaluated against to determine the release of media-permeable metabolites, Volatile Organic Compounds (VOCs), chitinase, and cellulase as antifungal mechanisms, as well as producing phosphate solubilisation as growth-promoting effect. Based on the results of metabolite and VOC tests, the six isolates of GO13S1, 55S2, 61S2, 7F2, 2S1 and 3 L2 were selected for greenhouse tests. Further, 55S2 and 61S2 could solubilize inorganic phosphate. All isolates except 3 L2 exhibited cellulase activity, while chitinase activity was observed in 2S1, 3 L2, and 61S2. Finally, 55S2 and 2S1 completely controlled the disease on the apple seedling leaves under greenhouse conditions.
PubMed: 36419433
DOI: 10.3389/fmicb.2022.1024001 -
Persoonia Aug 2021Novel species of fungi described in this study include those from various countries as follows: , from coastal sea sand. , on soil, on dead wood, from roots and...
Novel species of fungi described in this study include those from various countries as follows: , from coastal sea sand. , on soil, on dead wood, from roots and leaves of and from capsules of , (incl. gen. nov.) from , on soil, from leaf spots on from hypertrophied floral and vegetative branches of and from living leaves of , from a grassland. , from a rotten trunk. , on calcareous soil. , from wood of symptomatic , on pieces of wood and herbaceous debris. , among grass on a lawn. , on wet ground. , on decayed branch of unknown angiosperm tree and on decayed log of unknown angiosperm tree. , (incl. gen. nov.) on dead stems of , from the gut of a sp. termite, on soil and on branches of . , from soil under , on twigs of broadleaved trees on the ground. , on leaves of f. , from healthy roots of , (incl. gen. nov.) from stems of an sp. , (incl. gen. nov.), and (incl. gen. nov.), from dead culms of and from and from and from dead culms of from from dead culms of and from leaves of from sp., (incl. gen. nov.) from dead leaves of from (incl. gen. nov.) from leaves of from from needles of and (incl. gen. nov. and fam. nov.) from . , from twigs of sp., from dead leaves of from fallen leaves and from dead leaves , from permafrost and from driftwood of , from a biofilm covering a deteriorated limestone wall. , from needles of on soil in grasslands, on soil in grasslands, on a dry dead branch of sp., on litter in a mixed forest, from , (incl. gen. nov.) from leaves of and from leaves of , from leaf litter of ssp. from , from bark of from leaf litter of and from twigs of . , on sandy soil, on on from dung, from a blackened metal railing of an industrial warehouse and in soil under , associated with , on corticated wood. , from , from indoor air in a hospital, (incl. gen. nov.) from office dust, (incl. gen. nov.) from a tombstone, from air in a store, from air sample in house, from air in a brick room, from air in a classroom, from air in men's locker room and from sludge in a water reservoir. , on rotten wood, inside seed of , on soil in tropical evergreen mixed forests and from soil and roots of Morphological and culture characteristics are supported by DNA barcodes. : Crous PW, Osieck ER, Jurjević Ž, et al. 2021. Fungal Planet description sheets: 1284-1382. Persoonia 47: 178-374. https://doi.org/10.3767/persoonia.2021.47.06.
PubMed: 38352974
DOI: 10.3767/persoonia.2023.47.06 -
Persoonia Dec 2021Novel species of fungi described in this study include those from various countries as follows: , from coastal sea sand. , on soil, on dead wood, from roots and...
Novel species of fungi described in this study include those from various countries as follows: , from coastal sea sand. , on soil, on dead wood, from roots and leaves of and from capsules of , (incl. gen. nov.) from , on soil, from leaf spots on from hypertrophied floral and vegetative branches of and from living leaves of , from a grassland. , from a rotten trunk. , on calcareous soil. , from wood of symptomatic , on pieces of wood and herbaceous debris. , among grass on a lawn. , on wet ground. , on decayed branch of unknown angiosperm tree and on decayed log of unknown angiosperm tree. , (incl. gen. nov.) on dead stems of , from the gut of a sp. termite, on soil and on branches of . , from soil under , on twigs of broadleaved trees on the ground. , on leaves of f. , from healthy roots of , (incl. gen. nov.) from stems of an sp. , (incl. gen. nov.), and (incl. gen. nov.), from dead culms of and from and from and from dead culms of from from dead culms of and from leaves of from sp., (incl. gen. nov.) from dead leaves of from (incl. gen. nov.) from leaves of from from needles of and (incl. gen. nov. and fam. nov.) from . , from twigs of sp., from dead leaves of from fallen leaves and from dead leaves , from permafrost and from driftwood of , from a biofilm covering a deteriorated limestone wall. , from needles of on soil in grasslands, on soil in grasslands, on a dry dead branch of sp., on litter in a mixed forest, from , (incl. gen. nov.) from leaves of and from leaves of , from leaf litter of ssp. from , from bark of from leaf litter of and from twigs of . , on sandy soil, on on from dung, from a blackened metal railing of an industrial warehouse and in soil under , associated with , on corticated wood. , from , from indoor air in a hospital, (incl. gen. nov.) from office dust, (incl. gen. nov.) from a tombstone, from air in a store, from air sample in house, from air in a brick room, from air in a classroom, from air in men's locker room and from sludge in a water reservoir. , on rotten wood, inside seed of , on soil in tropical evergreen mixed forests and from soil and roots of Morphological and culture characteristics are supported by DNA barcodes. : Crous PW, Osieck ER, Jurjević Ž, et al. 2021. Fungal Planet description sheets: 1284-1382. Persoonia 47: 178-374. https://doi.org/10.3767/persoonia.2021.47.06.
PubMed: 37693795
DOI: 10.3767/persoonia.2021.47.06