The dominance of MAT alpha among cryptococcal strains has been ascribed to MATa strains being more sensitive to certain environmental factors; however no study has attempted to identify these factors. During the present study we determined whether the chemical composition of woody debris may influence the occurrence of Cryptococcus gattii MATa. We observed a positive correlation between the numbers of C. gattii MATa and the ammonium-nitrogen (NH4-N) concentration in woody debris samples. Subsequent growth studies conducted in woody debris microcosms indicated that this positive correlation is likely not due to additional NH4Cl improving the growth of selected MATa strains. Instead, it might be due to the MATa strains competing better with the MATa strains in the presence of a high NH4Cl concentration compared to a low NH4Cl concentration. This exploratory study paves the way for future studies focused on the interactions of MATa and MAT alpha strains with environmental factors. (C) 2020 Elsevier Ltd and British Mycological Society. All rights reserved.

ABSTRACT Environmental stress often causes phenotypic changes among pathogenic cryptococci, such as altered antifungal susceptibility, changes in capsule and melanin formation, as well as altered levels of the membrane sterol and antifungal target, ergosterol. We therefore hypothesised that nitrogen limitation, a prevalent environmental stress in the natural habitat of these yeasts, might affect virulence and antifungal susceptibility. We tested the effect of different nitrogen concentrations on capsule, melanin and ergosterol biosynthesis, as well as amphotericin B (AmB) and fluconazole (FLU) susceptibility. This was achieved by culturing cryptococcal strains representing Cryptococcus neoformans and Cryptococcus gattii in media with high (0.53 g/l), control (0.42 g/l) and low (0.21 g/l) NH4Cl concentrations. India ink staining was used to determine capsule thickness microscopically, while melanin and ergosterol content were determined spectrophotometrically. We found that lower nitrogen concentrations enhanced both ergosterol and capsule biosynthesis, while a variable effect was observed on melanisation. Evaluation of drug tolerance using time-kill methodology, as well as tests for FLU heteroresistance, revealed that the low nitrogen cultures had the highest survival percentages in the presence of both AmB and FLU, and showed the highest frequency of FLU heteroresistance, suggesting that nitrogen concentration may indeed influence drug tolerance.

Cryptococcus neoformans var. grubii is the causative agent of cryptococcal meningitis, a significant source of mortality in immunocompromised individuals, typically HIV/AIDS patients from developing countries. Despite the worldwide emergence of this ubiquitous infection, little is known about the global molecular epidemiology of this fungal pathogen. Here we sequence the genomes of 188 diverse isolates and characterized the major subdivisions, their relative diversity and the level of genetic exchange between them. While most isolates of C. neoformans var. grubii belong to one of three major lineages (VNI, VNII, and VNB), some haploid isolates show hybrid ancestry including some that appear to have recently interbred, based on the detection of large blocks of each ancestry across each chromosome. Many isolates display evidence of aneuploidy, which was detected for all chromosomes. In diploid isolates of C. neoformans var. grubii ( serotype A/A) and of hybrids with C. neoformans var. neoformans (serotype A/D) such aneuploidies have resulted in loss of heterozygosity, where a chromosomal region is represented by the genotype of only one parental isolate. Phylogenetic and population genomic analyses of isolates from Brazil revealed that the previously ‘African’ VNB lineage occurs naturally in the South American environment. This suggests migration of the VNB lineage between Africa and South America prior to its diversification, supported by finding ancestral recombination events between isolates from different lineages and regions. The results provide evidence of substantial population structure, with all lineages showing multi-continental distributions demonstrating the highly dispersive nature of this pathogen. Author Summary Cryptococcus neoformans var. grubii is a human fungal pathogen of immunocompromised individuals that has global clinical impact, causing half a million deaths per year. Substantial genetic substructure exists for this pathogen, with two lineages found globally (VNI, VNII) whereas a third has appeared confined to sub-Saharan Africa (VNB). Here, we utilized genome sequencing of a large set of global isolates to examine the genetic diversity, hybridization, and biogeography of these lineages. We found that while the three major lineages are well separated, recombination between the lineages has occurred, notably resulting in hybrid isolates with segmented ancestry across the genome. In addition, we showed that isolates from South America are placed within the VNB lineage, formerly thought to be confined to Africa, and that there is phylogenetic separation between these geographies that substantially expands the diversity of these lineages. Our findings provide a new framework for further studies of the dynamics of natural populations of C. neoformans var. grubii .

Cryptococcus a significant source of mortality in immunocompromised individuals, typically HIV/AIDS 65 patients from developing countries. Despite the worldwide emergence of this ubiquitous infection, little is known about the global molecular epidemiology of this fungal pathogen. Here we sequence the genomes of 188 diverse isolates and characterized the major 68 subdivisions, their relative diversity and the level of genetic exchange between them. While 69 most isolates of C. neoformans var. grubii belong to one of three major lineages (VNI, VNII, 70 and VNB), some haploid isolates show hybrid ancestry including some that appear to have 71 recently interbred, based on the detection of large blocks of each ancestry across each 72 chromosome. Many isolates display evidence of aneuploidy, which was detected for all 73 chromosomes. In diploid isolates of C. neoformans var. grubii ( serotype A/A) and of hybrids 74 with C. neoformans var. neoformans (serotype A/D) such aneuploidies have resulted in loss 75 of heterozygosity, where a chromosomal region is represented by the genotype of only one 76 parental isolate. Phylogenetic and population genomic analyses of isolates from Brazil 77 reveal that the previously ‘African’ VNB lineage occurs naturally in the South American environment. This suggests migration of the VNB lineage between Africa and South America 79 prior to its diversification, supported by finding ancestral recombination events between 80 isolates from different lineages and regions. The results provide evidence of substantial 81 population structure, with all lineages showing multi-continental distributions demonstrating 82 the highly dispersive nature of this pathogen.

Knowledge of the environmental prevalence of members of the Ctyptococcus neoformans/Cryptococcus gattii species complex is important, since cryptococcal infection is acquired from the environment. We determined whether trees located in two South African recreational areas harboured pathogenic cryptococci and compared the isolates to clinical isolates obtained from Western Cape hospitals with molecular typing techniques. The majority of isolates originating from trees in a public park in Cape Town (PPCT) were C. gattii sensu stricto, followed by C neoformans sensu stricto genotype AFLP1/VNI. The PPCT trees might be a source of infection, since all genotype AFLP1/VNI isolates from these trees and one clinical isolate belonged to the same sequence type (ST), i.e. ST23. Recombination and basidiospore production might be occurring in PPCT trees that contained C gattii s.s. isolates belonging to both mating types. The presence of C gattii s.s. in PPCT trees might therefore pose a risk to human health. (C) 2017 Elsevier Ltd and British Mycological Society. All rights reserved.

Cryptococcus neoformans var. grubii is the causative agent of cryptococcal meningitis, a significant source of mortality in immunocompromised individuals, typically human immunodeficiency virus/AIDS patients from developing countries. Despite the worldwide emergence of this ubiquitous infection, little is known about the global molecular epidemiology of this fungal pathogen. Here we sequence the genomes of 188 diverse isolates and characterize the major subdivisions, their relative diversity, and the level of genetic exchange between them. While most isolates of C. neoformans var. grubii belong to one of three major lineages (VNI, VNII, and VNB), some haploid isolates show hybrid ancestry including some that appear to have recently interbred, based on the detection of large blocks of each ancestry across each chromosome. Many isolates display evidence of aneuploidy, which was detected for all chromosomes. In diploid isolates of C. neoformans var. grubii (serotype AA) and of hybrids with C. neoformans var. neoformans (serotype AD) such aneuploidies have resulted in loss of heterozygosity, where a chromosomal region is represented by the genotype of only one parental isolate. Phylogenetic and population genomic analyses of isolates from Brazil reveal that the previously “African” VNB lineage occurs naturally in the South American environment. This suggests migration of the VNB lineage between Africa and South America prior to its diversification, supported by finding ancestral recombination events between isolates from different lineages and regions. The results provide evidence of substantial population structure, with all lineages showing multi-continental distributions; demonstrating the highly dispersive nature of this pathogen.

AIMS:Investigating the effect of perturbations, with relatively low Cu concentrations, on yeast community composition in low-nutrient virgin soil.METHODS AND RESULTS:Culturable soil yeast populations were monitored at an experimental site treated with the fungicide copper oxychloride (10 mg Cu per kg soil). Yeast numbers were unaffected by additional Cu; however, a shift in yeast community composition from Hymenomycetes to Urediniomycetes species occurred. Subsequent growth experiments conducted with a synthetic liquid medium revealed that hymenomycetous and urediniomycetous yeasts were affected differently by 1 and 10 mg l(-1) Cu. Soil microcosm experiments then indicated that additional 10 mg kg(-1) Cu may improve the competitive ability of urediniomycetous yeasts in the presence of hymenomycetous yeasts.CONCLUSIONS:The shift from hymenomycetous to urediniomycetous yeasts, as a result of slightly increased soil Cu levels, may be because of hymenomycetous yeasts being more sensitive to elevated Cu levels and urediniomycetous yeasts having an improved competitive ability in the presence of elevated Cu levels.SIGNIFICANCE AND IMPACT OF THE STUDY:Yeast community composition of pristine low-nutrient soils may change as a result of perturbations with relatively low concentrations of Cu. Urediniomycetous yeasts should be studied as potential bio-indicators of Cu perturbations.

To explore the beneficial qualities or detrimental consequences of cultureable soil yeasts, it is important to understand which physicochemical soil properties most impact populations of these unicellular fungi in their natural habitat. The goal of this study was to determine which soil properties dictate yeast numbers in pristine sandy, low nutrient soils within a semi-arid region. A correlation matrix of the data obtained for 19 different environmental variables indicated a negative correlation between soil pH and yeast numbers. Using general regression models, it was demonstrated that soil pH and copper concentration were the 2 variables that correlated best with soil yeast counts in these soils. However, soil moisture content was found to be the environmental factor with the most impact on cultureable actinomycetes and heterotrophic microbes. The study also demonstrated that divalent cation availability might impact the size of both yeast and prokaryote populations in these soils.