Phenotypic Characterization and Comparative Genomics of the Melanin-Producing Yeast Exophiala lecanii-corni Reveals a Distinct Stress Tolerance Profile and Reduced Ribosomal Genetic Content

The black yeast Exophiala lecanii-corni of the order Chaetothyriales is notable for its ability to produce abundant quantities of DHN-melanin. While many other Exophiala species are frequent causal agents of human infection, E. lecanii-corni CBS 102400 lacks the thermotolerance requirements that enable pathogenicity, making it appealing for use in targeted functional studies and biotechnological applications. Here, we report the stress tolerance characteristics of E. lecanii-corni, with an emphasis on the influence of melanin on its resistance to various forms of stress. We find that E. lecanii-corni has a distinct stress tolerance profile that includes variation in resistance to temperature, osmotic, and oxidative stress relative to the extremophilic and pathogenic black yeast Exophiala dermatitidis. Notably, the presence of melanin substantially impacts stress resistance in E. lecanii-corni, while this was not found to be the case in E. dermatitidis. The cellular context, therefore, influences the role of melanin in stress protection. In addition, we present a detailed analysis of the E. lecanii-corni genome, revealing key differences in functional genetic content relative to other ascomycetous species, including a significant decrease in abundance of genes encoding ribosomal proteins. In all, this study provides insight into how genetics and physiology may underlie stress tolerance and enhances understanding of the genetic diversity of black yeasts.

Productivity of quails for use in fodder of polyphenol carbon complex from antarctic black yeast Nadsoniella nigra

In the article, results of researches on an establishment of an optimum level of polyphenolic carbon complex from Antarctic black yeast Nadsoniella nigra are resulted. Experimental studies conducted in terms of problem research laboratory of feed additives National University of Life and Environmental Sciences of Ukraine. Independent experiment was conducted with growing quails. We conducted a randomized block experiment with 4 treatments, each with 4 replicates of 30 growing birds (1 to 42 d of age). It was experimentally established that feeding quails polyphenolcarbonate complex from antarctic black yeast Nadsoniella nigra, the basis of which is melanin, in the compound feed at 1.0 mg/kg increased body weight at 42 days of age by 3.2 % (P < 0.001). Feeding the complex at the level of 0.5 mg/kg contributed to a probable increase in body weight of animals by 2.9 % (P < 0.001). The difference between animals of groups 3 and 4 was 0.3 %. This indicates an already effective dose of the complex at the level of 0.5 mg/kg of feed. Adding to the feed complex at the level of 0.1–1.0 mg/1 kg of feed helps to reduce feed costs by 0.6–1.6 %. The most effective feed conversion for the 1–42-day period is set at 3,345 kg per 1 kg of body weight gain of quails.

Deciphering the potential niche of novel black yeast fungal isolates in a biological soil crust based on genomes, phenotyping, and melanin regulation

Black yeasts are polyextremotolerant fungi that contain high amounts of melanin in their cell wall and maintain a primarily yeast form. These fungi grow in xeric, nutrient deplete environments which implies that they require highly flexible metabolisms and the ability to form lichen-like mutualisms with nearby algae and bacteria. However, the exact ecological niche and interactions between these fungi and their surrounding community is not well understood. We have isolated two novel black yeast fungi of the genus Exophiala: JF 03-3F “Goopy” E. viscosium and JF 03-4F “Slimy” E. limosus, which are from dryland biological soil crusts. A combination of whole genome sequencing and various phenotyping experiments have been performed on these isolates to determine their fundamental niches within the biological soil crust consortium. Our results reveal that these Exophiala spp. are capable of utilizing a wide variety of carbon and nitrogen sources potentially from symbiotic microbes, they can withstand many abiotic stresses, and can potentially provide UV resistance to the crust community in the form of secreted melanin. Besides the identification of two novel species within the genus Exophiala, our study also provides new insight into the production and regulation of melanin in extremotolerant fungi.

Thermoresistance in black yeasts is associated with halosensitivity and HPP tolerance, but not with UV tolerance or sanitizer tolerance

Black yeasts can survive extreme conditions in food production owing to their polyextremotolerant character. However, significant strain-to-strain variation in black yeast thermoresistance has been observed. In this study, we assessed the variability in tolerance to nonthermal interventions among a collection of food-related black yeast strains. Variation in tolerance to UV light treatment, high pressure processing, sanitizers, and osmotic pressure was observed within each species. The two strains previously shown to possess high thermotolerance, Exophiala phaeomuriformis FSL-E2-0572 and Exophiala dermatitidis YB-734, were also the most HPP tolerant, but were the least halotolerant. Meanwhile, Aureobasidium pullulans FSL-E2-0290 was the most UV and sanitizer tolerant, but had been shown to have relatively low thermoresistance. Fisher’s exact tests showed that thermoresistance in black yeasts was associated with HPP tolerance and inversely with halotolerance, but no association was found with UV tolerance or sanitizer tolerance. Collectively, the relative stress tolerance among strains varied across interventions. Given this variation, a broad range of different food products are susceptible to black yeast spoilage. Additionally, different strains should be selected in challenge studies specific to the intervention. (1312/2000 characters)

Seven Years at High Salinity—Experimental Evolution of the Extremely Halotolerant Black Yeast Hortaea werneckii

The experimental evolution of microorganisms exposed to extreme conditions can provide insight into cellular adaptation to stress. Typically, stress-sensitive species are exposed to stress over many generations and then examined for improvements in their stress tolerance. In contrast, when starting with an already stress-tolerant progenitor there may be less room for further improvement, it may still be able to tweak its cellular machinery to increase extremotolerance, perhaps at the cost of poorer performance under non-extreme conditions. To investigate these possibilities, a strain of extremely halotolerant black yeast Hortaea werneckii was grown for over seven years through at least 800 generations in a medium containing 4.3 M NaCl. Although this salinity is well above the optimum (0.8–1.7 M) for the species, the growth rate of the evolved H. werneckii did not change in the absence of salt or at high concentrations of NaCl, KCl, sorbitol, or glycerol. Other phenotypic traits did change during the course of the experimental evolution, including fewer multicellular chains in the evolved strains, significantly narrower cells, increased resistance to caspofungin, and altered melanisation. Whole-genome sequencing revealed the occurrence of multiple aneuploidies during the experimental evolution of the otherwise diploid H. werneckii. A significant overrepresentation of several gene groups was observed in aneuploid regions. Taken together, these changes suggest that long-term growth at extreme salinity led to alterations in cell wall and morphology, signalling pathways, and the pentose phosphate cycle. Although there is currently limited evidence for the adaptive value of these changes, they offer promising starting points for future studies of fungal halotolerance.

Virulence Traits and Population Genomics of the Black Yeast Aureobasidium melanogenum

The black yeast-like fungus Aureobasidium melanogenum is an opportunistic human pathogen frequently found indoors. Its traits, potentially linked to pathogenesis, have never been systematically studied. Here, we examine 49 A. melanogenum strains for growth at 37 °C, siderophore production, hemolytic activity, and assimilation of hydrocarbons and human neurotransmitters and report within-species variability. All but one strain grew at 37 °C. All strains produced siderophores and showed some hemolytic activity. The largest differences between strains were observed in the assimilation of hydrocarbons and human neurotransmitters. We show for the first time that fungi from the order Dothideales can assimilate aromatic hydrocarbons. To explain the background, we sequenced the genomes of all 49 strains and identified genes putatively involved in siderophore production and hemolysis. Genomic analysis revealed a fairly structured population of A. melanogenum, raising the possibility that some phylogenetic lineages have higher virulence potential than others. Population genomics indicated that the species is strictly clonal, although more than half of the genomes were diploid. The existence of relatively heterozygous diploids in an otherwise clonal species is described for only the second time in fungi. The genomic and phenotypic data from this study should help to resolve the non-trivial taxonomy of the genus Aureobasidium and reduce the medical hazards of exploiting the biotechnological potential of other, non-pathogenic species of this genus.

Growth and division mode plasticity by cell density in marine-derived black yeasts

The diversity and ecological contribution of the fungus kingdom in the marine environment remain under-studied. A recent survey in the Atlantic (Woods Hole, MA, USA) brought to light the diversity and unique biological features of marine fungi. The study revealed that black yeast species undergo an unconventional cell division cycle, which has not been documented in conventional model yeast species such as Saccharomyces cerevisiae (budding yeast) and Schizosaccharomyces pombe (fission yeast). The prevalence of this unusual property is unknown. Inspired by the findings in Woods Hole, I collected and identified >50 marine fungi species across 40 genera from the ocean surface, sediment, and macroalgal surface in the Pacific (Sugashima, Toba, Japan). The Sugashima collection largely did not overlap with the Woods Hole collection and included several unidentifiable species, further illustrating the diversity of marine fungi. Three black yeast species were isolated, two of which were commonly found in Woods Hole (Aureobasidium pullulans, Hortaea werneckii). Surprisingly, I observed that their cell division mode was dependent on cell density, and the previously reported unconventional division mode was reproduced only at a certain cell density. For all three black yeast species, cells underwent filamentous growth with septations at low cell density and immediately formed buds at high cell density. At intermediate cell density, two black yeasts showed rod cells undergoing septation at the cell equator, in a manner similar to S. pombe. In contrast, all eight budding yeast species showed a consistent division pattern regardless of cell density. In five budding yeast species, the mother cell formed a single bud at a time at an apparently random site, similar to S. cerevisiae. The other three budding yeast species possessed a fixed budding site. This study illustrates the plastic nature of the growth/division mode of marine-derived black yeast.

Intermediate thermoresistance in black yeast asexual cells variably increases with culture age, promoting survival and spoilage in thermally processed shelf-stable foods

Black yeasts are a functional group that has caused spoilage in cold-filled and hot-filled beverages as well as other water activity (a w )-controlled food products. We established quantitative thermoresistance parameters for the inactivation of 12 Aureobasidium and Exophiala isolates through isothermal experiments and a challenge study. Culture age (2-day vs. 28-day) variably affected the thermoresisitance among the black yeast strains. Variation in thermoresistance exists within each genus, but the two most resistant strains were the Exophiala isolates. The two most heat resistant isolates were E. phaeomuriformis FSL-E2-0572 with a D 60 -value of 7.69±0.63 min in 28-day culture and E. dermatitidis YB-734 with a D 60 -value of 16.32±2.13 min in 28-day culture. While these thermoresistance levels were, in some cases, greater than those for conidia and vegetative cells from other common food spoilage fungi, they were much more sensitive than the ascospores of heat resistant molds most associated with spoilage of hot-filled products. However, given that black yeasts have caused spoilage in hot-filled products, we hypothesized that this intermediate degree of thermoresistance may support survival following introduction during active cooling before package seals have formed. A challenge study was performed in an acidic (apple cider) and a w -controlled (maple syrup) product to evaluate survival. When apple cider was hot-filled at 82C, black yeast counts were reduced by 4.1-log CFU/ml 24 h after the heat treatment, but the survivors increased up to 6.7-log CFU/ml after two weeks. In comparison, the counts were below the detection limit after both 24 h and 14 days of shelf-life in both products when filled at their boiling points. This suggests that ensuring water microbial quality in cooling tunnels and nozzle sanitation may be essential in mitigating the introduction of these fungi.

Black Yeast Genomes Assembled from Plastic Fabric Metagenomes Reveal an Abundance of Hydrocarbon Degradation Genes

ABSTRACT We report the assembly and annotation of 10 different black yeast genomes from microbiome metagenomic data derived from biofouled plastic fabrics. The draft genomes are estimated to be 9 to 33.2 Mb, with 357 to 5,108 contigs and G+C contents of 43.9% to 57.4%, and they harbor multiple genes for hydrocarbon adaptation and degradation.