Biology subjects

Kolarik, M.

Publications and source records attributed to Kolarik, M..

6 recordsLinked to original sources

bioRxiv2026

Sister species, shared and divergent responses: early transcriptomic profiling of Bursaphelenchus xylophilus exposed to Esteya spp.

Bursaphelenchus xylophilus (pinewood nematode, PWN) responds transcriptionally to nematophagous fungi, but the earliest events preceding cuticle penetration are poorly characterized, and whether closely related fungal antagonists elicit comparable responses is unknown. Here, we compared PWN transcriptomic responses to Esteya floridanum V14639 (EF) and E. vermicola CCF3117 (EV) at 1 h post-inoculation (hpi), capturing the onset of host-fungus interaction. Despite their phylogenetic proximity, under our exposure conditions the two fungi elicited partly divergent host responses at 1 hpi. EF induced a broad transcriptional response enriched in peptidase activity and lysosomal pathways, accompanied by downregulation of cuticle structural components. In contrast, EV triggered a narrower response, without the proteolytic and lysosomal enrichment observed with EF. Direct comparison of the two treatments revealed no significantly enriched Gene Ontology categories, although pathway analysis identified DNA replication and repair pathways, comprising genes more highly expressed under EF. Enrichment analyses revealed a shared transcriptional signature in both interactions characterized by downregulation of xenobiotic- and central carbon-metabolism pathways, suggesting an early reduction in xenobiotic detoxification capacity rather than induction of detoxification programs. These findings suggest that phylogenetic proximity does not necessarily predict conserved early transcriptional responses, although comparisons of single isolates cannot separate species-level from isolate-level effects.

microbiology↗

bioRxiv2026

Genome reshuffling as a route to specialization? Chromosome-level insights from the bark beetle symbiont genus Geosmithia.

Evolution of genome architecture is increasingly recognized as a major driver of fungal adaptation. However, because most studies have focused on plant and human pathogens, the genomic mechanisms underlying adaptation beyond pathogenic lifestyles remain poorly understood. Here, we establish the bark beetle-associated fungal genus Geosmithia as a model for studying genome evolution during ecological transitions. Geosmithia species occupy diverse ecological niches ranging from generalists, facultative symbionts of multiple beetle vectors and host tree species to more specialized conifer specialists and obligate nutritional symbionts of ambrosia beetles. Using chromosome-level genome assemblies of eleven species representing independently evolved ecological strategies, we investigated how genome architecture, repetitive DNA, and gene family evolution contribute to this ecological diversification. Comparative genomics revealed pervasive intra- and interchromosomal rearrangements, even between recently diverged species, demonstrating that extensive chromosome restructuring can accumulate over short evolutionary timescales. Breakpoints frequently occurred in gene-rich rather than repeat-rich regions, contrasting with the transposable element-associated patterns commonly described in fungi. Hi-C analyses revealed a typical Rabl chromosome organization but highly unusual centromeres that are repeat-poor, gene-rich, transcriptionally active, and conserved as syntenic blocks across species. Further, centromere identity may be determined by a highly divergent CenH3 variant. Despite similar genome sizes, specialists had increased repetitive DNA content and widespread gene family contractions, consistent with metabolic streamlining during ecological specialization. Our results demonstrate that extensive structural genome evolution can occur in gene-dense fungal genomes and establish Geosmithia as a powerful model for studying the interplay between genome evolution and ecological diversification.

genomics↗

bioRxiv2025

Long-term evolution of prokaryotic genomes in a chemolithotrophic cave over 5.5 million years of isolation

Fluctuating conditions drive adaptive evolution, yet understanding how genomes evolve under stable conditions over extended periods remains a major challenge, since most research on microbial evolution relies on short-term experiments or phylogenetic comparisons. The Movile Cave, isolated from external influences 5.5 million years, offers a unique opportunity to explore microbial evolution under prolonged environmental stability. Here, we analyzed metagenome-assembled genomes from this cave, revealing that prokaryotes exhibit lower gene diversity and higher levels of pseudogenization compared to those from non-isolated environments, mainly affecting housekeeping functions involved in translation. Functional redundancy across genomes remained comparable to related habitats. Our results suggest that pseudogenization may serve as a fine-tuning mechanism to reduce excess redundancy. Although horizontal gene transfer is limited overall, the cave virome seems to contribute to microbial adaptation through the transfer of auxiliary metabolic genes. Movile microorganisms harbor fewer phage-defense systems than counterparts in related environments, suggesting a long-term adaptation to a relatively stable virosphere. Our findings indicate that prolonged isolation under stable selective pressures does not necessarily lead to major genomic divergence, but rather promotes adaptive gene loss. This study provides key insights into how long-term stability shapes microbial genome evolution and ecosystem function.

microbiology↗

bioRxiv2024

Resolving phylogenetic relationships within the Trichophyton mentagrophytes complex: a RADseq genomic approach challenges status of "terbinafine-resistant" Trichophyton indotineae as distinct species

The Trichophyton (T.) mentagrophytes complex encompasses common dermatophytes causing superficial mycoses in humans and animals. The taxonomy of the complex is unstable, with conflicting views on the species status of some taxa, particularly T. indotineae and T. interdigitale. Due to presence of intermediate genotypes, MALDI-TOF MS and ITS rRNA sequencing cannot accurately distinguish all taxa in the complex, potentially contributing to clinical misdiagnoses. In order to resolve the phylogenetic relationship of T. mentagrophytes complex, we employed Restriction Site Associated DNA Sequencing (RADseq) to produce a high-resolution single nucleotide polymorphism (SNP) dataset from 95 isolates. The SNP-based analyses indicated the presence of two major genetic clusters, corresponding to T. mentagrophytes (including T. indotineae) and T. interdigitale. Our results challenge the species status of T. indotineae, because of insufficient genetic divergence from T. mentagrophytes. Therefore, we propose designating T. indotineae as T. mentagrophytes var. indotineae (or T. mentagrophytes ITS genotype VIII) to avoid further splitting of the complex and taxonomic inflation. Although T. interdigitale shows clearer genetic differentiation, its separation is incomplete and identification of some isolates is ambiguous when using routine methods, leading us to consider it a variety as well: T. mentagrophytes var. interdigitale. We recommend using T. mentagrophytes as the overarching species name for all complex isolates. Where precise molecular identification is possible, the use of variety ranks is encouraged. Since identical resistance mechanisms are not specific to any genotype or dermatophytes species, identifying antifungal resistance is more important than differentiating closely related genotypes or populations. ImportanceAccurate identification of the causal agent is essential for managing dermatophytosis. However, the taxonomy of the T. mentagrophytes complex has been plagued by inconsistencies and misidentifications. Our high-resolution SNP analysis revealed that T. indotineae, often associated with terbinafine resistance, is not genetically distinct enough from T. mentagrophytes to warrant species status. This finding has significant implications for both taxonomy and clinical practice. We suggest consolidating the taxonomy under T. mentagrophytes, with variety ranks for T. indotineae and T. interdigitale. This simplified system will reduce confusion and ensure the comparability of historical and emerging epidemiological data under the umbrella name of T. mentagrophytes. By shifting the focus to antifungal resistance detection rather than complex taxonomic distinctions, this reclassification will streamline clinical decision-making. Notably, identical resistance mechanisms are not exclusive to ITS genotype VIII (T. indotineae) but also occur in other genotypes and dermatophyte species, albeit with varying prevalence.

microbiology↗

bioRxiv2024

Secondary metabolites and their impact on symbiotic interactions in the ambrosia fungus Geosmithia eupagioceri

Ambrosia fungi colonize freshly dead trees, sequester nutrients, and serve as nutritional source for ambrosia beetles in exchange for dispersal. A key aspect of this symbiosis is the ability of fungi to colonize and dominate the wood around the beetle tunnels, forming a monospecific nutritional mycelium in the beetle gallery. Hypotheses for these dynamics include active beetle management, fungal inoculation priority, and the funguss chemical ecology facilitating resource capture and competition. The ecological role of allelochemicals produced by ambrosia fungi is unknown, although they may suppress microbes while being harmless to beetles, which has potential medical or food technology applications. This study presents a comprehensive analysis of secondary metabolites from the ambrosia fungus Geosmithia eupagioceri (Ascomycota: Hypocreales). Eight extracellular compounds were identified in vitro: 5-hydroxymethyl-2-furancarboxylic acid, 4-hydroxybenzoic acid, 2,3-dihydroxybenzoic acid, 3,4-dihydroxybenzoic acid, 4-hydroxyphenylacetic acid (4-HPA), 4-HPA methyl ester, tyrosol, and thymine. Most compounds show cross-taxon activity, suppressing the growth of bacteria, fungi, a nematode, and a mite. We have shown that often overlooked chemically simple compounds may have activities leading to increased fitness of beetle hosts, including previously unconsidered activity against mites and nematodes. For the first time, we point out that these compounds also have the previously unconsidered potential to modulate the physiology of their producer (by inducing symbiotic morphology by quorum sensing mechanisms), the beetle host and associated microbes through synergism. Furthermore, we have shown that the ambrosia fungi have biotechnological potential in the search for growth suppressors of microorganisms and invertebrates, not toxic to humans. IMPORTANCEBark and ambrosia beetles and their microbial symbionts play crucial roles in forest ecosystems by aiding in the decomposition of dead trees, nutrient cycling, and habitat creation. However, they can cause extensive damage to both natural and planted forests by killing trees. Our study has led to a fundamental shift in the understanding of interactions between beetle symbiotic fungi and the environment, mediated by secondary metabolites. Newly, we show that these substances can not only be antimicrobial but also suppress the growth of mites, nematodes, but also can modulate the physiology of the producer fungus and potentially the host beetle and associated microbes. Our study, although conducted on a relatively artificial system with the need for validation on other lineages of ambrosia fungi, suggests entirely new research directions in the understanding of bark beetle holobiont and ambrosia beetles.

microbiology↗

bioRxiv2020

GlobalFungi: Global database of fungal records from high-throughput-sequencing metabarcoding studies

Fungi are key players in vital ecosystem services, spanning carbon cycling, decomposition, symbiotic associations with cultural and wild plants and pathogenicity. The high importance of fungi in the ecosystem processes contrasts with the incompleteness of understanding of the patterns of fungal biogeography and the environmental factors that drive it. To close this gap of knowledge, we have here collected and validated data published on the composition of soil fungal communities in terrestrial environments including soil and plant-associated habitats and made them publicly accessible through a user interface at http://globalfungi.com. The GlobalFungi database contains over 650 million observations of fungal sequences across >20 000 samples with geographical locations and additional metadata contained in 207 original studies with millions of unique sequence variants of the fungal internal transcribed spacers (ITS) 1 and 2 representing fungal species and genera. As it is, the study represents the most comprehensive atlas of fungal distribution on the global scale open to further additions.

ecology↗