Biology subjects

Yurkov, A. M.

Publications and source records attributed to Yurkov, A. M..

6 recordsLinked to original sources

bioRxiv2026

Old Compound, New Context: Naphthocyclinones Mediate Microbial Competition in Wild Bee Nests

Although thousands of microbial specialized metabolites have been identified, the ecological functions of most remain unknown. Naphthocyclinones are aromatic polyketide antibiotics discovered more than five decades ago, yet their biological role has remained elusive. Investigating the microbial community of the oligolectic ivy bee (Colletes hederae), a bacterial community that included several Streptomyces species and members of the class Bacilli was recovered from fermented nest provisions. One Streptomyces isolate, B-004T (DSM 121525T = LMG 34598T), was identified as representing a novel species based on polyphasic taxonomic studies, for which the name Streptomyces hederae sp. nov. is proposed. This strain showed potent antibacterial activity against co-isolated Gram-positive bacteria as well as Paenibacillus larvae, the causative agent of American foulbrood. Bioassay-guided fractionation coupled with liquid chromatography-mass spectrometry analysis led to the identification of naphthocyclinone congeners as the active metabolites. Whole-genome sequencing and genome mining revealed a type II polyketide synthase biosynthetic gene cluster closely related to that of the characterized naphthocyclinone pathway. Targeted deletion of the cluster-encoded ketosynthase gene (B-004_07360) abolished naphthocyclinone production and resulted in the complete loss of antibacterial activity, whereas heterologous overexpression of the Streptomyces antibiotic regulatory protein gene papR2 significantly increased antibiotic production, confirming the function of the naphthocyclinone biosynthetic gene cluster. Furthermore, naphthocyclinone biosynthesis was found to be induced by sympatric bacterial isolates from bee nests. Together, our findings provide the first evidence for an ecological function of naphthocyclinones as mediators of bacterial competition in wild bee nests and highlight their potential as antimicrobial substances against P. larvae.

microbiology↗

bioRxiv2025

Genomic and phenotypic insights into the expanding phylogenetic landscape of the Cryptococcus genus

The fungal genus Cryptococcus includes several life-threatening human pathogens as well as diverse saprobic species whose genome architecture, ecology, and evolutionary history remain less well characterized. Understanding how some lineages evolved into major pathogens remains a central challenge and may be advanced by comparisons with their nonpathogenic counterparts. Integrative approaches have become essential for delimiting species and reconstructing evolutionary relationships, particularly in lineages with cryptic diversity or extensive chromosomal rearrangements. Here, we formally characterize six Cryptococcus species representing distinct evolutionary lineages, comprising both newly discovered and previously recognized but unnamed taxa, through a combination of phylogenomic analyses, divergence metrics, chromosomal comparisons, mating assays, and phenotypic profiling. Among pathogenic taxa, we formally name Cryptococcus hyracis sp. nov., corresponding to the previously characterized VGV lineage within the C. gattii complex. In parallel, we describe five saprobic, nonpathogenic species isolated from fruit, soil, and bark beetle galleries, spanning four phylogenetic clades. We identify a strong ecological association with bark beetles for Cryptococcus porticicola sp. nov., the only newly described nonpathogenic species with multiple sequenced strains from diverse sites. In this species, we detect strain-level chromosomal variation and evidence of sexual reproduction, along with population-level signatures of recombination. Across the genus, chromosome-level comparisons reveal extensive structural variation, including species- and strain-specific rearrangements that may restrict gene flow. We also identify multiple instances of chromosome number reduction, often accompanied by genomic signatures consistent with centromere inactivation or loss of centromeric identity. Comparative metabolic profiling with Biolog phenotype microarrays reveals clade-level differentiation and distinct substrate preferences, which may reflect metabolic divergence and habitat-specific diversification. Notably, we confirm that thermotolerance is restricted to clinically relevant taxa. These findings refine the species-level taxonomy of Cryptococcus, broaden its known genomic and ecological diversity, and strengthen the framework for investigating speciation, adaptation, and the emergence of pathogenicity within the genus. Author SummaryCryptococcus is a genus of fungi that includes both pathogenic species capable of causing life-threatening infections in humans and many environmental species that inhabit soil, fruit, decaying wood, and insect-associated environments with no known link to disease. Here, we formally describe six previously unnamed species based on genome-wide comparisons, genetic divergence metrics, chromosome structure, reproductive behavior, and metabolic profiling. One of these species belongs to the pathogenic lineage, while the others are distinct environmental taxa, including several recovered from bark beetles or their galleries, indicating repeated occurrence in this ecological niche. For one of these insect-associated species, represented by multiple isolates, we detected signatures of sexual reproduction and genetic exchange in natural populations. This study expands the framework for investigating how certain Cryptococcus lineages adapt to new environments or evolve traits relevant to pathogenicity. It also emphasizes that continuous environmental sampling remains essential for capturing fungal diversity and illustrates the power of combining genomic and phenotypic data to define species boundaries and uncover lineages that may otherwise remain undetected.

genomics↗

bioRxiv2025

Tracing the evolution and genomic dynamics of mating-type loci in Cryptococcus pathogens and closely related species

Sexual reproduction in basidiomycete fungi is governed by MAT loci (P/R and HD), which exhibit remarkable evolutionary plasticity, characterized by expansions, rearrangements, and gene losses often associated with mating system transitions. The sister genera Cryptococcus and Kwoniella provide a powerful framework for studying MAT loci evolution owing to their diverse reproductive strategies and distinct architectures, spanning bipolar and tetrapolar systems with either linked or unlinked MAT loci. Building on recent comparative genomic analyses, we generated additional chromosome-level assemblies, uncovering distinct trajectories shaping MAT loci organization. Contrasting with the small-scale expansions and gene acquisitions observed in Kwoniella, our analyses revealed independent expansions of the P/R locus in tetrapolar Cryptococcus, possibly driven by pheromone gene duplications. Notably, these expansions coincided with a pronounced GC-content reduction best explained by reduced GC-biased gene conversion following recombination suppression, rather than relaxed codon usage selection. Diverse modes of MAT locus linkage were also identified, including three previously unrecognized transitions: one resulting in a pseudobipolar arrangement and two leading to bipolarity. All three transitions involved translocations. In the pseudobipolar configuration, the P/R and HD loci remained on the same chromosome but genetically unlinked, whereas the bipolar transitions additionally featured rearrangements that fused the two loci into a nonrecombining region. Mating assays confirmed a sexual cycle in C. decagattii, demonstrating its ability to undergo mating and sporulation. Progeny analysis in K. mangrovensis revealed substantial ploidy variation and aneuploidy, likely stemming from haploid-diploid mating, yet evidence of recombination and loss of heterozygosity indicates that meiotic exchange occurs despite irregular chromosome segregation. Our findings underscore the importance of continued diversity sampling and provide further evidence for convergent evolution of fused MAT loci in basidiomycetes, offering new insights into the genetic and chromosomal changes driving reproductive transitions.

genetics↗

bioRxiv2023

Comparative genomics of Cryptococcus and Kwoniella reveals pathogenesis evolution and contrasting modes of karyotype evolution via chromosome fusion or intercentromeric recombination

A large-scale comparative genomic analysis was conducted for the global human fungal pathogens within the Cryptococcus genus, compared to non-pathogenic Cryptococcus species, and related species from the sister genus Kwoniella. Chromosome-level genome assemblies were generated for multiple species of both genera, resulting in a dataset encompassing virtually all of their known diversity. Although Cryptococcus and Kwoniella have comparable genome sizes (about 19.2 and 22.9 Mb) and similar gene content, hinting at pre-adaptive pathogenic potential, our analysis found evidence in pathogenic Cryptococcus species of specific examples of gene gain (via horizontal gene transfer) and gene loss, which might represent evolutionary signatures of pathogenic development. Genome analysis also revealed a significant variation in chromosome number and structure between the two genera. By combining synteny analysis and experimental centromere validation, we found that most Cryptococcus species have 14 chromosomes, whereas most Kwoniella species have fewer (11, 8, 5 or even as few as 3). Reduced chromosome number in Kwoniella is associated with formation of giant chromosomes (up to 18 Mb) through repeated chromosome fusion events, each marked by a pericentric inversion and centromere loss. While similar chromosome inversion-fusion patterns were observed in all Kwoniella species with fewer than 14 chromosomes, no such pattern was detected in Cryptococcus. Instead, Cryptococcus species with less than 14 chromosomes, underwent chromosome reductions primarily through rearrangements associated with the loss of repeat-rich centromeres. Additionally, Cryptococcus genomes exhibited frequent interchromosomal translocations, including intercentromeric recombination facilitated by transposons shared between centromeres. Taken together, our findings advance our understanding of genomic changes possibly associated with pathogenicity in Cryptococcus and provide a foundation to elucidate mechanisms of centromere loss and chromosome fusion driving distinct karyotypes in closely related fungal species, including prominent global human pathogens.

genomics↗

bioRxiv2019

Genetic and genomic analyses reveal boundaries between species closely related to Cryptococcus pathogens

Speciation is a central mechanism of biological diversification. While speciation is well studied in plants and animals, in comparison, relatively little is known about speciation in fungi. One fungal model is the Cryptococcus genus, which is best known for the pathogenic Cryptococcus neoformans/Cryptococcus gattii species complex that causes over 200,000 new infections in humans annually. The closest non-human pathogenic relatives are the sibling species, Cryptococcus amylolentus and Tsuchiyaea wingfieldii. However, because relatively few isolates of each species are available, it is unclear whether they represent divergent lineages of the same species or different biological species. The recent isolation of an additional strain, preliminarily identified as T. wingfieldii, prompted us to reexamine this group as it may inform about the evolutionary processes underlying the diversification of both non-pathogenic and pathogenic Cryptococcus lineages. Using genomic data, we reappraised the phylogenetic relationship of the four available strains and confirmed the genetic separation of C. amylolentus and T. wingfieldii (now Cryptococcus wingfieldii), and revealed an additional cryptic species, for which the name Cryptococcus floricola is proposed. Comparison of full-length chromosome assemblies revealed approximately 6% pairwise sequence divergence between the three species, and identified significant genomic changes, including inversions as well as a reciprocal translocation that involved inter-centromeric ectopic recombination, which together likely impose significant barriers to genetic exchange. Using genetic crosses, we show that while C. wingfieldii cannot interbreed with any of the other strains, C. floricola can undergo sexual reproduction with C. amylolentus. However, most of the spores resulting from this cross were inviable, and many were sterile, indicating that the two species are genetically isolated through intrinsic post-zygotic barriers and possibly due to niche differentiation. Genome sequencing and analysis of the progeny demonstrated decreased recombination frequency during meiosis in heterospecific crosses compared to C. amylolentus conspecific crosses. This study advances our understanding of speciation in fungi and highlights the power of genomics in assisting our ability to correctly identify and discriminate fungal species. Author SummaryThe idea of species as discrete natural units seems rather intuitive for most people, just as cells are the basic units of life. However, when observing variation across a species range, boundaries can become blurred making it less than obvious when different populations evolve into separate species. Additionally, separate species can still interbreed, such as lions breeding with tigers to produce a liger or a tigon (depending on the paternal and maternal species of origin), but the resulting offspring is usually inviable or sterile, which in turn is evidence that the parents involved are distinct species. Therefore, what species are and how they originate is still an open question in evolutionary biology. While recent advances have been made in the fields of animal and plant speciation, many other important components of biological diversity, such as fungi, are still understudied. Genome sequencing is now providing new tools to address the genetic mechanisms that drive divergence and reproductive isolation between populations, including genetic incompatibilities, sequence divergence, and chromosomal rearrangements. Here we focus on the Cryptococcus amylolentus species complex, a non-pathogenic fungal lineage closely related to the human pathogenic Cryptococcus neoformans/Cryptococcus gattii complex. Using genetic and genomic analysis we reexamined the species boundaries of four available isolates within the C. amylolentus complex and revealed three genetically isolated species. The genomes of these species are ~6% divergent and exhibit chromosome rearrangements, including translocations and small-scale inversions. Although two of the species (C. amylolentus and newly described C. floricola) are still able to interbreed, the resulting hybrid progeny were mostly inviable, and many were sterile, indicating that barriers to reproduction have already been established. Our results will foster additional studies addressing the transitions between non-pathogenic and pathogenic Cryptococcus lineages.

evolutionary biology↗

bioRxiv2016

Adaptive anonymity: Crypsis as an evolutionary trait of floral yeasts?

Nectar-dwelling yeast and bacteria are common inhabitants of flowers and evidently involved in pollination. The limited number of floral plant-pollinator models studied to date reveal inconsistent conclusions on microbial effects, but coincide with respect to high microbial specificity: while bacteria reduce visitation frequencies of pollinators, nectar-borne specialist yeasts (in contrast to allochthonous or transient species) impose none or even a beneficial effect on flower visitation. However, these findings are in conflict with the strong impact of these predominantly fermenting organisms on the nectar environment. In order to cope with the ultimate dependency of nectar-dwellers on repeated transportation by foragers as a result of early floral senescence, the modifications of nectar associated with specialist growth have been interpreted as adaptations that suit foragers preferences. But, the development of foraging preferences to either axenic flowers or flowers colonized by specialist microorganisms would lead to a dead-end for nectar-dwellers, as the probability of inoculation into new suitable habitats would be reduced.\n\nBased on a critical survey of the available literature and an additional pollinator experiment where we find that the allochthonous species Cryptococcus victoriae negatively affects attraction and rewarding of floral visitors, while the specialist yeast Metschnikowia reukaufii does not, we propose the hypothesis that nectar-borne yeasts may have evolved to blend into their environment avoiding detection by pollinators, following the ecological concept of crypsis. Although, neither chemical nor olfactory crypsis has been reported for nectar-borne microorganisms, the attention to this mechanism in yeast dispersal needs to be directed in future studies.

ecology↗