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  • 1
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    Supplementary material 7 from: Laciny A, Zettel H, Kopchinskiy A, Pretzer C, Pal A, Salim KA, Rahimi MJ, Hoenigsberger M, Lim L, Jaitrong W, Druzhinina IS (2018) Colobopsis explodens sp. n., model species for studies on “exploding ants” (Hymenoptera, Formicidae), with biological notes and first illustrations of males of the Colobopsis cylindrica group. ZooKeys 751: 1-40. https://doi.org/10.3897/zookeys.751.22661
    Pensoft Publishers ; 2018
    In:  ZooKeys Vol. 751 ( 2018-04-19), p. 1-40
    Details
    In: ZooKeys, Pensoft Publishers, Vol. 751 ( 2018-04-19), p. 1-40
    Abstract: A taxonomic description of all castes of Colobopsisexplodens Laciny & amp; Zettel, sp. n. from Borneo, Thailand, and Malaysia is provided, which serves as a model species for biological studies on “exploding ants” in Southeast Asia. The new species is a member of the Colobopsiscylindrica (COCY) group and falls into a species complex that has been repeatedly summarized under the name Colobopsissaundersi (Emery, 1889) (formerly Camponotussaundersi ). The COCY species group is known under its vernacular name “exploding ants” for a unique behaviour: during territorial combat, workers of some species sacrifice themselves by rupturing their gaster and releasing sticky and irritant contents of their hypertrophied mandibular gland reservoirs to kill or repel rivals. This study includes first illustrations and morphometric characterizations of males of the COCY group: Colobopsisexplodens Laciny & amp; Zettel, sp. n. and Colobopsisbadia (Smith, 1857). Characters of male genitalia and external morphology are compared with other selected taxa of Camponotini. Preliminary notes on the biology of C.explodens Laciny & amp; Zettel, sp. n. are provided. To fix the species identity of the closely related C.badia , a lectotype from Singapore is designated. The following taxonomic changes within the C.saundersi complex are proposed: Colobopsissolenobia (Menozzi, 1926), syn. n. and Colobopsistrieterica (Menozzi, 1926), syn. n. are synonymized with Colobopsiscorallina Roger, 1863, a common endemic species of the Philippines. Colobopsissaginata Stitz, 1925, stat. n ., hitherto a subspecies of C.badia , is raised to species level.
    Type of Medium: Online Resource
    ISSN: 1313-2970 , 1313-2989
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    DOI: 10.3897/zookeys.751.22661
    DOI: 10.3897/zookeys.751.22661.figure1
    DOI: 10.3897/zookeys.751.22661.figure10
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    DOI: 10.3897/zookeys.751.22661.suppl1
    DOI: 10.3897/zookeys.751.22661.suppl2
    DOI: 10.3897/zookeys.751.22661.suppl3
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    DOI: 10.3897/zookeys.751.22661.suppl6
    DOI: 10.3897/zookeys.751.22661.suppl7
    Language: Unknown
    Publisher: Pensoft Publishers
    Publication Date: 2018
    detail.hit.zdb_id: 2445640-8
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  • 2
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    Forecasting the number of species of asexually reproducing fungi (Ascomycota and Basidiomycota)
    Springer Science and Business Media LLC ; 2022
    In:  Fungal Diversity Vol. 114, No. 1 ( 2022-05), p. 463-490
    Details
    In: Fungal Diversity, Springer Science and Business Media LLC, Vol. 114, No. 1 ( 2022-05), p. 463-490
    Type of Medium: Online Resource
    ISSN: 1560-2745 , 1878-9129
    URL: Article
    DOI: 10.1007/s13225-022-00500-5
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2424484-3
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  • 3
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    Horizontal Gene Transfer as an Indispensable Driver for Evolution of Neocallimastigomycota into a Distinct Gut-Dwelling Fungal Lineage
    American Society for Microbiology ; 2019
    In:  Applied and Environmental Microbiology Vol. 85, No. 15 ( 2019-08)
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 85, No. 15 ( 2019-08)
    Abstract: Survival and growth of the anaerobic gut fungi (AGF; Neocallimastigomycota) in the herbivorous gut necessitate the possession of multiple abilities absent in other fungal lineages. We hypothesized that horizontal gene transfer (HGT) was instrumental in forging the evolution of AGF into a phylogenetically distinct gut-dwelling fungal lineage. The patterns of HGT were evaluated in the transcriptomes of 27 AGF strains, 22 of which were isolated and sequenced in this study, and 4 AGF genomes broadly covering the breadth of AGF diversity. We identified 277 distinct incidents of HGT in AGF transcriptomes, with subsequent gene duplication resulting in an HGT frequency of 2 to 3.5% in AGF genomes. The majority of HGT events were AGF specific (91.7%) and wide (70.8%), indicating their occurrence at early stages of AGF evolution. The acquired genes allowed AGF to expand their substrate utilization range, provided new venues for electron disposal, augmented their biosynthetic capabilities, and facilitated their adaptation to anaerobiosis. The majority of donors were anaerobic fermentative bacteria prevalent in the herbivorous gut. This study strongly indicates that HGT indispensably forged the evolution of AGF as a distinct fungal phylum and provides a unique example of the role of HGT in shaping the evolution of a high-rank taxonomic eukaryotic lineage. IMPORTANCE The anaerobic gut fungi (AGF) represent a distinct basal phylum lineage (Neocallimastigomycota) commonly encountered in the rumen and alimentary tracts of herbivores. Survival and growth of anaerobic gut fungi in these anaerobic, eutrophic, and prokaryote-dominated habitats necessitates the acquisition of several traits absent in other fungal lineages. We assess here the role of horizontal gene transfer as a relatively fast mechanism for trait acquisition by the Neocallimastigomycota postsequestration in the herbivorous gut. Analysis of 27 transcriptomes that represent the broad diversity of Neocallimastigomycota identified 277 distinct HGT events, with subsequent gene duplication resulting in an HGT frequency of 2 to 3.5% in AGF genomes. These HGT events have allowed AGF to survive in the herbivorous gut by expanding their substrate utilization range, augmenting their biosynthetic pathway, providing new routes for electron disposal by expanding fermentative capacities, and facilitating their adaptation to anaerobiosis. HGT in the AGF is also shown to be mainly a cross-kingdom affair, with the majority of donors belonging to the bacteria. This study represents a unique example of the role of HGT in shaping the evolution of a high-rank taxonomic eukaryotic lineage.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.00988-19
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2019
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  • 4
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    Industrially Applicable De Novo Lager Yeast Hybrids with a Unique Genomic Architecture: Creation and Characterization
    American Society for Microbiology ; 2021
    In:  Applied and Environmental Microbiology Vol. 87, No. 3 ( 2021-01-15)
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 87, No. 3 ( 2021-01-15)
    Abstract: Lager beer is produced by Saccharomyces pastorianus , which is a natural allopolyploid hybrid between Saccharomyces cerevisiae and Saccharomyces eubayanus . Lager strains are classified into two major groups based largely on genomic composition: group I and group II. Group I strains are allotriploid, whereas group II strains are allotetraploid. A lack of phenotypic diversity in commercial lager strains has led to substantial interest in the reconstitution of de novo allotetraploid lager strains by hybridization of S. cerevisiae and S. eubayanus strains. Such strategies rely on the hybridization of wild S. eubayanus isolates, which carry unacceptable traits for commercial lager beer such as phenolic off flavors and incomplete utilization of carbohydrates. Using an alternative breeding strategy, we have created de novo lager hybrids containing the domesticated S. eubayanus subgenome from an industrial S. pastorianus strain by hybridizing diploid meiotic segregants of this strain to a variety of S. cerevisiae ale strains. Five de novo hybrids were isolated which had fermentation characteristics similar to those of prototypical commercial lager strains but with unique phenotypic variation due to the contributions of the S. cerevisiae parents. Genomic analysis of these de novo lager hybrids identified novel allotetraploid genomes carrying three copies of the S. cerevisiae genome and one copy of the S. eubayanus genome. Most importantly, these hybrids do not possess the negative traits which result from breeding wild S. eubayanus . The de novo lager strains produced using industrial S. pastorianus in this study are immediately suitable for industrial lager beer production. IMPORTANCE All lager beer is produced using two related lager yeast types: group I and group II, which are highly similar, resulting in a lack of strain diversity for lager beer production. To date, approaches for generating new lager yeasts have generated strains possessing undesirable brewing characteristics which render them commercially inviable. We have used an alternative approach that circumvents this issue and created new lager strains that are directly suitable for lager beer production. These novel lager strains also possess a unique genomic architecture, which may lead to a better understanding of industrial yeast hybrids. We propose that strains created using our approach be classified as a third group of lager strains (group III). We anticipate that these novel lager strains will be of great industrial relevance and that this technique will be applicable to the creation of additional novel lager strains that will help broaden the diversity in commercial lager beer strains.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.02434-20
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2021
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  • 5
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    Orchard Management and Landscape Context Mediate the Pear Floral Microbiome
    American Society for Microbiology ; 2021
    In:  Applied and Environmental Microbiology Vol. 87, No. 15 ( 2021-07-13)
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 87, No. 15 ( 2021-07-13)
    Abstract: Crop-associated microbiota are a key factor affecting host health and productivity. Most crops are grown within heterogeneous landscapes, and interactions between management practices and landscape context often affect plant and animal biodiversity in agroecosystems. However, whether these same factors typically affect crop-associated microbiota is less clear. Here, we assessed whether orchard management strategies and landscape context affected bacterial and fungal communities in pear ( Pyrus communis ) flowers. We found that bacteria and fungi responded differently to management schemes. Organically certified orchards had higher fungal diversity in flowers than conventional or bio-based integrated pest management (IPM) orchards, but organic orchards had the lowest bacterial diversity. Orchard management scheme also best predicted the distribution of several important bacterial and fungal genera that either cause or suppress disease; organic and bio-based IPM best explained the distributions of bacterial and fungal genera, respectively. Moreover, patterns of bacterial and fungal diversity were affected by interactions between management, landscape context, and climate. When examining the similarity of bacterial and fungal communities across sites, both abundance- and taxon-related turnovers were mediated primarily by orchard management scheme and landscape context and, specifically, the amount of land in cultivation. Our study reveals local- and landscape-level drivers of floral microbiome structure in a major fruit crop, providing insights that can inform microbiome management to promote host health and high-yielding quality fruit. IMPORTANCE Proper crop management during bloom is essential for producing disease-free tree fruit. Tree fruits are often grown in heterogeneous landscapes; however, few studies have assessed whether landscape context and crop management affect the floral microbiome, which plays a critical role in shaping plant health and disease tolerance. Such work is key for identification of tactics and/or contexts where beneficial microbes proliferate and pathogenic microbes are limited. Here, we characterize the floral microbiome of pear crops in Washington State, where major production occurs in intermountain valleys and basins with variable elevation and microclimates. Our results show that both local-level (crop management) and landscape-level (habitat types and climate) factors affect floral microbiota but in disparate ways for each kingdom. More broadly, these findings can potentially inform microbiome management in orchards for promotion of host health and high-quality yields.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.00048-21
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2021
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  • 6
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    Capturing an Early Gene Induction Event during Wood Decay by the Brown Rot Fungus Rhodonia placenta
    American Society for Microbiology ; 2022
    In:  Applied and Environmental Microbiology Vol. 88, No. 8 ( 2022-04-26)
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 88, No. 8 ( 2022-04-26)
    Abstract: Brown rot fungi dominate wood decomposition in coniferous forests, and their carbohydrate-selective mechanisms are of commercial interest. Brown rot was recently described as a two-step, sequential mechanism orchestrated by fungi using differentially expressed genes (DEGs) and consisting of oxidation via reactive oxygen species (ROS) followed by enzymatic saccharification. There have been indications, however, that the initial oxidation step itself might require induction. To capture this early gene regulation event, here, we integrated fine-scale cryosectioning with whole-transcriptome sequencing to dissect gene expression at the single-hyphal-cell scale (tens of micrometers). This improved the spatial resolution 50-fold, relative to previous work, and we were able to capture the activity of the first 100 μm of hyphal front growth by Rhodonia placenta in aspen wood. This early decay period was dominated by delayed gene expression patterns as the fungus ramped up its mechanism. These delayed DEGs included many genes implicated in ROS pathways (lignocellulose oxidation [LOX]) that were previously and incorrectly assumed to be constitutively expressed. These delayed DEGs, which include those with and without predicted functions, also create a focused subset of target genes for functional genomics. However, this delayed pattern was not universal, with a few genes being upregulated immediately at the hyphal front. Most notably, this included a gene commonly implicated in hydroquinone and iron redox cycling: benzoquinone reductase. IMPORTANCE Earth’s aboveground terrestrial biomass is primarily wood, and fungi dominate wood decomposition. Here, we studied these fungal pathways in a common “brown rot”-type fungus, Rhodonia placenta , that selectively extracts sugars from carbohydrates embedded within wood lignin. Using a space-for-time design to map fungal gene expression at the extreme hyphal front in wood, we made two discoveries. First, we found that many genes long assumed to be “on” (constitutively expressed) from the very beginning of decay were instead “off” before being upregulated, when mapped (via transcriptome sequencing [RNA-seq]) at a high resolution. Second, we found that the gene encoding benzoquinone reductase was “on” in incipient decay and quickly downregulated, implying a key role in “kick-starting” brown rot.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/aem.00188-22
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2022
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  • 7
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    A Cross-Inoculation Experiment Reveals that Ophidiomyces ophiodiicola and Nannizziopsis guarroi Can Each Infect Both Snakes and Lizards
    American Society for Microbiology ; 2023
    In:  Applied and Environmental Microbiology Vol. 89, No. 5 ( 2023-05-31)
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 89, No. 5 ( 2023-05-31)
    Abstract: Host range and specificity are key concepts in the study of infectious diseases. However, both concepts remain largely undefined for many influential pathogens, including many fungi within the Onygenales order. This order encompasses reptile-infecting genera ( Nannizziopsis , Ophidiomyces , and Paranannizziopsis ) formerly classified as the Chrysosporium anamorph of Nannizziopsis vriesii (CANV). The reported hosts of many of these fungi represent a narrow range of phylogenetically related animals, suggesting that many of these disease-causing fungi are host specific, but the true number of species affected by these pathogens is unknown. For example, to date, Nannizziopsis guarroi (the causative agent of yellow fungus disease) and Ophidiomyces ophiodiicola (the causative agent of snake fungal disease) have been documented only in lizards and snakes, respectively. In a 52-day reciprocal-infection experiment, we tested the ability of these two pathogens to infect currently unreported hosts, inoculating central bearded dragons ( Pogona vitticeps ) with O. ophiodiicola and corn snakes ( Pantherophis guttatus ) with N. guarroi . We confirmed infection by documenting both clinical signs and histopathological evidence of fungal infection. Our reciprocity experiment resulted in 100% of corn snakes and 60% of bearded dragons developing infections with N. guarroi and O. ophiodiicola , respectively, demonstrating that these fungal pathogens have a broader host range than previously thought and that hosts with cryptic infections may play a role in pathogen translocation and transmission. IMPORTANCE Our experiment using Ophidiomyces ophiodiicola and Nannizziopsis guarroi is the first to look more critically at these pathogens’ host range. We are the first to identify that both fungal pathogens can infect both corn snakes and bearded dragons. Our findings illustrate that both fungal pathogens have a more general host range than previously known. Additionally, there are significant implications concerning the spread of snake fungal disease and yellow fungus disease in popular companion animals and the increased chance of disease spillover into other wild and naive populations.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/aem.02168-22
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2023
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  • 8
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    Amycolatopsis from Desert Specialist Fungus-Growing Ants Suppresses Contaminant Fungi Using the Antibiotic ECO-0501
    American Society for Microbiology ; 2023
    In:  Applied and Environmental Microbiology Vol. 89, No. 2 ( 2023-02-28)
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 89, No. 2 ( 2023-02-28)
    Abstract: Symbiotic Actinobacteria help fungus-growing ants suppress fungal pathogens through the production of antifungal compounds. Trachymyrmex ants of the southwest desert of the United States inhabit a unique niche far from the tropical rainforests in which most fungus-growing ant species are found. These ants may not encounter the specialist fungal pathogen Escovopsis known to threaten colonies of other fungus-growing ants. It is unknown whether Actinobacteria associated with these ants antagonize contaminant fungi and, if so, what the chemical basis of such antagonism is. We find that Pseudonocardia and Amycolatopsis strains isolated from three desert specialist Trachymyrmex species do antagonize diverse contaminant fungi isolated from field-collected ant colonies. We did not isolate the specialist fungal pathogen Escovopsis in our sampling. We trace strong antifungal activity from Amycolatopsis isolates to the molecule ECO-0501, an antibiotic that was previously under preclinical development as an antibacterial agent. In addition to suppression of contaminant fungi, we find that this molecule has strong activity against ant-associated Actinobacteria and may also play a role in bacterial competition in this niche. By studying interspecies interactions in a previously unexplored niche, we have uncovered novel bioactivity for a structurally unique antibiotic. IMPORTANCE Animal hosts often benefit from chemical defenses provided by microbes. These molecular defenses are a potential source of novel antibiotics and offer opportunities for understanding how antibiotics are used in ecological contexts with defined interspecies interactions. Here, we recover contaminant fungi from nests of Trachymyrmex fungus-growing ants of the southwest desert of the United States and find that they are suppressed by Actinobacteria isolated from these ants. The antibiotic ECO-0501 is an antifungal agent used by some of these Amycolatopsis bacterial isolates. This antibiotic was previously investigated in preclinical studies and known only for antibacterial activity.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/aem.01838-22
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2023
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  • 9
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    Discovery of a Novel Glucuronan Lyase System in Trichoderma parareesei
    American Society for Microbiology ; 2022
    In:  Applied and Environmental Microbiology Vol. 88, No. 1 ( 2022-01-11)
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 88, No. 1 ( 2022-01-11)
    Abstract: Glucuronan lyases (EC 4.2.2.14) catalyze depolymerization of linear β-(1,4)-polyglucuronic acid (glucuronan). Only a few glucuronan lyases have been characterized until now, most of them originating from bacteria. Here we report the discovery, recombinant production, and functional characterization of the full complement of six glucuronan specific polysaccharide lyases in the necrotic mycoparasite Trichoderma parareesei . The enzymes belong to four different polysaccharide lyase families and have different reaction optima and glucuronan degradation profiles. Four of them showed endo-lytic action and two, TpPL8A and TpPL38A, displayed exo-lytic action. Nuclear magnetic resonance revealed that the monomeric end product from TpPL8A and TpPL38A underwent spontaneous rearrangements to tautomeric forms. Proteomic analysis of the secretomes from T. parareesei growing on pure glucuronan and lyophilized A. bisporus fruiting bodies, respectively, showed secretion of five of the glucuronan lyases and high-performance anion-exchange chromatography with pulsed amperometric detection analysis confirmed the presence of glucuronic acid in the A. bisporus fruiting bodies. By systematic genome annotation of more than 100 fungal genomes and subsequent phylogenetic analysis of the putative glucuronan lyases, we show that glucuronan lyases occur in several ecological and taxonomic groups in the fungal kingdom. Our findings suggest that a diverse repertoire of glucuronan lyases is a common trait among Hypocreales species with mycoparasitic and entomopathogenic lifestyles. IMPORTANCE This paper reports the discovery of a set of six complementary glucuronan lyase enzymes in the mycoparasite Trichoderma parareseei . Apart from the novelty of the discovery of these enzymes in T. parareesei , the key importance of the study is the finding that the majority of these lyases are induced when T. parareesei is inoculated on Basidiomycete cell walls that contain glucuronan. The study also reveals putative glucuronan lyase encoding genes in a wealth of other fungi that furthermore points at fungal cell wall glucuronan being a target C-source for many types of fungi. In a technical context, the findings may lead to controlled production of glucuronan oligomers for advanced pharmaceutical applications and pave the way for development of new fungal biocontrol agents.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.01819-21
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2022
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    Lipid Composition Analysis Reveals Mechanisms of Ethanol Tolerance in the Model Yeast Saccharomyces cerevisiae
    American Society for Microbiology ; 2021
    In:  Applied and Environmental Microbiology Vol. 87, No. 12 ( 2021-05-26)
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 87, No. 12 ( 2021-05-26)
    Abstract: Saccharomyces cerevisiae is an important unicellular yeast species within the biotechnological and the food and beverage industries. A significant application of this species is the production of ethanol, where concentrations are limited by cellular toxicity, often at the level of the cell membrane. Here, we characterize 61 S. cerevisiae strains for ethanol tolerance and further analyze five representatives with various ethanol tolerances. The most tolerant strain, AJ4, was dominant in coculture at 0 and 10% ethanol. Unexpectedly, although it does not have the highest noninhibitory concentration or MIC, MY29 was the dominant strain in coculture at 6% ethanol, which may be linked to differences in its basal lipidome. Although relatively few lipidomic differences were observed between strains, a significantly higher phosphatidylethanolamine concentration was observed in the least tolerant strain, MY26, at 0 and 6% ethanol compared to the other strains that became more similar at 10%, indicating potential involvement of this lipid with ethanol sensitivity. Our findings reveal that AJ4 is best able to adapt its membrane to become more fluid in the presence of ethanol and that lipid extracts from AJ4 also form the most permeable membranes. Furthermore, MY26 is least able to modulate fluidity in response to ethanol, and membranes formed from extracted lipids are least leaky at physiological ethanol concentrations. Overall, these results reveal a potential mechanism of ethanol tolerance and suggest a limited set of membrane compositions that diverse yeast species use to achieve this. IMPORTANCE Many microbial processes are not implemented at the industrial level because the product yield is poorer and more expensive than can be achieved by chemical synthesis. It is well established that microbes show stress responses during bioprocessing, and one reason for poor product output from cell factories is production conditions that are ultimately toxic to the cells. During fermentative processes, yeast cells encounter culture media with a high sugar content, which is later transformed into high ethanol concentrations. Thus, ethanol toxicity is one of the major stresses in traditional and more recent biotechnological processes. We have performed a multilayer phenotypic and lipidomic characterization of a large number of industrial and environmental strains of Saccharomyces to identify key resistant and nonresistant isolates for future applications.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.00440-21
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2021
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