Virulence Traits and Population Genomics of the Black Yeast Aureobasidium melanogenum

The Impact of Environmental Gaseous Pollutants on the Cultivable Bacterial and Fungal Communities of the Aerobiome

Understanding air microbial content, especially in highly polluted urban areas, is crucial for assessing its effect on human health and ecosystems. In this context, the impact of gaseous pollutants on the aerobiome remains inconclusive due to a lack of studies separating this factor from other contaminants or environmental factors. In this study, we aimed to experimentally assess the influence of contrasting concentrations of atmospheric gaseous pollutants as isolated variables on the composition of the aerobiome. Our study sites were contrasting Air Quality Index (AQI) sites of the Metropolitan Region of Chile, where nitric oxide (NO) was significantly lower at the low-AQI site than at the high-AQI site, while ozone (O3) was significantly higher. Cultivable aerobiome communities from the low-AQI site were exposed to their own pollutants or those from the high-AQI site and characterized using high-throughput sequencing (HTS), which allowed comparisons between the entire cultivable communities. The results showed increased alpha diversity in bacterial and fungal communities exposed to the high-AQI site compared to the low-AQI site. Beta diversity and compositional hierarchical clustering analyses revealed a clear separation based on NO and O3 concentrations. At the phylum level, four bacterial and three fungal phyla were identified, revealing an over-representation of Actinobacteriota and Basidiomycota in the samples transferred to the high-AQI site, while Proteobacteria were more abundant in the community maintained at the low-AQI site. At the functional level, bacterial imputed functions were over-represented only in samples maintained at the low-AQI site, while fungal functions were affected in both conditions. Overall, our results highlight the impact of NO and/or O3 on both taxonomic and functional compositions of the cultivable aerobiome. This study provides, for the first time, insights into the influence of contrasting pollutant gases on entire bacterial and fungal cultivable communities through a controlled environmental intervention.

Use of Aureobasidium in a sustainable economy

Aureobasidium is omnipresent and can be isolated from air, water bodies, soil, wood, and other plant materials, as well as inorganic materials such as rocks and marble. A total of 32 species of this fungal genus have been identified at the level of DNA, of which Aureobasidium pullulans is best known. Aureobasidium is of interest for a sustainable economy because it can be used to produce a wide variety of compounds, including enzymes, polysaccharides, and biosurfactants. Moreover, it can be used to promote plant growth and protect wood and crops. To this end, Aureobasidium cells adhere to wood or plants by producing extracellular polysaccharides, thereby forming a biofilm. This biofilm provides a sustainable alternative to petrol-based coatings and toxic chemicals. This and the fact that Aureobasidium biofilms have the potential of self-repair make them a potential engineered living material avant la lettre. KEY POINTS: •Aureobasidium produces products of interest to the industry •Aureobasidium can stimulate plant growth and protect crops •Biofinish of A. pullulans is a sustainable alternative to petrol-based coatings •Aureobasidium biofilms have the potential to function as engineered living materials.

Clinical Aureobasidium Isolates Are More Fungicide Sensitive than Many Agricultural Isolates

Fungicide applications in agriculture and medicine can promote the evolution of resistant, pathogenic fungi, which is a growing problem for disease management in both settings. Nonpathogenic mycobiota are also exposed to fungicides, may become tolerant, and could turn into agricultural or medical problems, for example, due to climate change or in immunocompromised individuals. However, quantitative data about fungicide sensitivity of environmental fungi is mostly lacking. Aureobasidium species are widely distributed and frequently isolated yeast-like fungi. One species, A. pullulans, is used as a biocontrol agent, but is also encountered in clinical samples, regularly. Here, we compared 16 clinical and 30 agricultural Aureobasidium isolates based on whole-genome data and by sensitivity testing with the 3 fungicides captan, cyprodinil, and difenoconazole. Our phylogenetic analyses determined that 7 of the 16 clinical isolates did not belong to the species A. pullulans. These isolates clustered with other Aureobasidium species, including A. melanogenum, a recently separated species that expresses virulence traits that are mostly lacking in A. pullulans. Interestingly, the clinical Aureobasidium isolates were significantly more fungicide sensitive than many isolates from agricultural samples, which implies selection for fungicide tolerance of non-target fungi in agricultural ecosystems. IMPORTANCE Environmental microbiota are regularly found in clinical samples and can cause disease, in particular, in immunocompromised individuals. Organisms of the genus Aureobasidium belonging to this group are highly abundant, and some species are even described as pathogens. Many A. pullulans isolates from agricultural samples are tolerant to different fungicides, and it seems inevitable that such strains will eventually appear in the clinics. Selection for fungicide tolerance would be particularly worrisome for species A. melanogenum, which is also found in the environment and exhibits virulence traits. Based on our observation and the strains tested here, clinical Aureobasidium isolates are still fungicide sensitive. We, therefore, suggest monitoring fungicide sensitivity in species, such as A. pullulans and A. melanogenum, and to consider the development of fungicide tolerance in the evaluation process of fungicides.

First case of neonatal fungemia caused by Aureobasidium melanogenum

Aureobasidium melanogenum is a saprophytic, dematiaceous, yeast-like fungus rarely implicated in human infections. Here, we report the first case of A. melanogenum fungemia in a 30-week-old preterm, very low birth weight neonate born to a primigravida with history of gestational diabetes, pregnancy induced hypertension and oligohydramnios. The baby developed respiratory distress, hypotension, bradycardia, coagulopathy and septic shock shortly after birth, and eventually succumbed to multiple organ dysfunction syndrome on day 9 of life. Paired blood culture showed growth of a dematiaceous yeast-like fungus which was identified as A. melanogenum by rDNA internal transcribed spacer (ITS) sequencing. Antifungal susceptibility testing of the isolate showed high minimum inhibitory concentration of fluconazole (32 µg/mL), indicating resistance. Diagnosis of A. melanogenum fungemia is difficult as it is easily confused with Candida species in Gram stained smears and similar colony morphology during the initial stages of growth. Also, the conventional diagnostic methods, such as VITEK 2 and MALDI-TOF MS are unreliable for identification of this pathogen. Accurate identification using molecular techniques is crucial for making treatment decisions as A. melanogenum shows substantial antifungal resistance. Clinicians should be aware that yeast-like cells in blood culture are not only indicative of Candida species, but also rare pathogens like A. melanogenum and should exercise caution while starting fluconazole therapy. At present, there are no established susceptibility breakpoints for Aureobasidium spp. Further studies are needed to determine the optimal treatment for such infections.

Genomic characterization of polyextremotolerant black yeasts isolated from food and food production environments

Black yeasts have been isolated from acidic, low water activity, and thermally processed foods as well as from surfaces in food manufacturing plants. The genomic basis for their relative tolerance to food-relevant environmental stresses has not been well defined. In this study, we performed whole genome sequencing (WGS) on seven black yeast strains including Aureobasidium (n=5) and Exophiala (n=2) which were isolated from food or food production environments. These strains were previously characterized for their tolerance to heat, hyperosmotic pressure, high pressure processing, hypochlorite sanitizers, and ultraviolet light. Based on the WGS data, three of the strains previously identified as A. pullulans were reassigned as A. melanogenum. Both haploid and diploid A. melanogenum strains were identified in this collection. Single-locus phylogenies based on beta tubulin, RNA polymerase II, or translation elongation factor protein sequences were compared to the phylogeny produced through SNP analysis, revealing that duplication of the fungal genome in diploid strains complicates the use of single-locus phylogenetics. There was not a strong association between phylogeny and either environmental source or stress tolerance phenotype, nor were trends in the copy numbers of stress-related genes associated with extremotolerance within this collection. While there were obvious differences between the genera, the heterogenous distribution of stress tolerance phenotypes and genotypes suggests that food-relevant black yeasts may be ubiquitous rather than specialists associated with particular ecological niches. However, further evaluation of additional strains and the potential impact of gene sequence modification is necessary to confirm these findings.

From Glaciers to Refrigerators: the Population Genomics and Biocontrol Potential of the Black Yeast Aureobasidium subglaciale

Apples are affected by numerous fungi known as storage rots, which cause significant losses before and after harvest. Concerns about increasing antimicrobial resistance, bans on various fungicides, and changing consumer preferences are motivating the search for safer means to prevent fruit rot. The use of antagonistic microbes has been shown to be an efficient and environmentally friendly alternative to conventional phytopharmaceuticals. Here, we investigate the potential of Aureobasidium subglaciale for postharvest rot control. We tested the antagonistic activity of 9 strains of A. subglaciale and 7 closely related strains against relevant phytopathogenic fungi under conditions simulating low-temperature storage: Botrytis cinerea, Penicillium expansum, and Colletotrichum acutatum. We also investigated a selection of phenotypic traits of all strains and sequenced their whole genomes. The tested strains significantly reduced postharvest rot of apples at low temperatures caused by B. cinerea, C. acutatum (over 60%), and P. expansum (about 40%). Several phenotypic traits were observed that may contribute to this biocontrol capacity: growth at low temperatures, tolerance to high temperatures and elevated solute concentrations, and strong production of several extracellular enzymes and siderophores. Population genomics revealed that 7 of the 15 strains originally identified as A. subglaciale most likely belong to other, possibly undescribed species of the same genus. In addition, the population structure and linkage disequilibrium of the species suggest that A. subglaciale is strictly clonal and therefore particularly well suited for use in biocontrol. Overall, these data suggest substantial biological control potential for A. subglaciale, which represents another promising biological agent for disease control in fresh fruit.

IMPORTANCE After harvest, fruits are often stored at low temperatures to prolong their life. However, despite the low temperatures, much of the fruit is lost to rot caused by a variety of fungi, resulting in major economic losses and food safety risks. An increasingly important environmentally friendly alternative to conventional methods of mitigating the effects of plant diseases is the use of microorganisms that act similarly to probiotics—occupying the available space, producing antimicrobial compounds, and consuming the nutrients needed by the rot-causing species. To find a new microorganism for biological control that is particularly suitable for cold storage of fruit, we tested different isolates of the cold-loving yeast Aureobasidium subglaciale and studied their phenotypic characteristics and genomes. We demonstrated that A. subglaciale can significantly reduce rotting of apples caused by three rot-causing molds at low temperatures and thus has great potential for preventing fruit rot during cold storage.

Identification of fungi found on desiccated human remains in an arid outdoor environment

Three fungi not previously reported on desiccated human remains were identified on cadavers at the Forensic Investigation Research Station (FIRS) in Whitewater, Colorado. The location of the FIRS provides the unique opportunity to observe the stages of decomposition in a high desert environment. The two cadavers used in the study were in the late stages of decomposition (PMI of approximately 1520 and 1820 days) to the point of desiccation and had developed an extensive black crust on the skin that remained. Skin samples of the two cadavers were taken and plated onto potato dextrose agar to determine whether fungi were present on the desiccated tissues. Three different fungi consistently dominated cultures grown from numerous samples taken from each cadaver. Based on morphological observations, nuclear rDNA sequence data, and phylogenetic analyses, two fungi were identified to species (Aureobasidium melanogenum and Didymella glomerata) and one fungus was identified to the genus level (Alternaria). These results will contribute to the understanding of the role that fungi might play in late-stage decomposition and the extended postmortem period.