Biology subjects

Vilgalys, R.

Publications and source records attributed to Vilgalys, R..

12 recordsLinked to original sources

bioRxiv2026

Not all roads lead to selfing: mating-system stability in an invasive ectomycorrhizal fungus

Baker's rule predicts that selfing is a beneficial trait for colonizers, whose prediction in the kingdom Fungi is reinforced by recent work showing the invasive ectomycorrhizal basidiomycete Amanita phalloides with self-incompatibility (SI) system has evolved unisexual reproduction in its introduced range. Unlike in plants, the multiallelic SI system of basidiomycetes does not fully prevent selfing among the meiotic offspring of a single dikaryotic (diploid) parent. This distinction allows observation of an intermediate state of selection where selfing is preferred in a species with SI system during colonization before a change in self-incompatibility architecture. Here, we analyzed the genomes of 189 isolates of the ectomycorrhizal basidiomycete Suillus luteus collected from both its native European range and five independently introduced regions to test whether selfing rates increase and whether the SI system had degraded after introduction. Unlike the A. phalloides case, we found no evidence of unisexual reproduction or loss of the SI system in the introduced ranges of S. luteus. Rather, all introduced populations maintained outcrossing rates higher than random mating as in the native populations. However, selfing events were detected in three individuals from a single introduced population, representing the first documented case of selfed sporocarps of Boletales fungi. Our works in S. luteus demonstrates that although selfing is possible in this species, it is not favored during colonization, potentially due to inbreeding depression and higher population density, highlighting the complex interaction among the invasion biology, genetics, and the colonizing context.

evolutionary biology↗

bioRxiv2026

Benchmarking Short-Read ITS2 and Full-Length ITS Sequencing Reveals Pipeline-Dependent Biases in Indoor Fungal Community Profiling

Short-read amplicon sequencing is widely used for fungal surveys but can limit taxonomic resolution. Long-read sequencing enables recovery of the full internal transcribed spacer (ITS) region and may improve ecological and taxonomic inference. Here, we conducted a paired comparison of Illumina ITS2 and PacBio HiFi full-length ITS sequencing using identical DNA extracts from built-environmental air and surface samples (n = 68) collected across homes, a dormitory, and laboratories. Both datasets were taxonomically assigned using the same algorithm and reference database. We performed paired statistics, in-silico ITS2 trimming of long-read sequences, and cross-platform mapping at multiple identity thresholds. Full-length ITS provided higher taxonomic resolution, assigning a greater fraction of ASVs at the family (98% vs. 88%) and species (42% vs. 32%) ranks than ITS2 (paired Wilcoxon q = 0.002). Alpha-diversity comparisons showed similar Shannon diversity across pipelines, whereas richness metrics were consistently higher for full-length ITS. Beta-diversity analyses indicated broadly comparable community-level patterns, although full-length ITS revealed stronger sample-type- and location-associated structure (PERMANOVA R{superscript 2} [≥] 0.06, p = 0.0001). In-silico ITS2 trimming reduced these differences, indicating that amplicon length is a major contributor to enhanced taxonomic resolution and ecological inference. Cross-platform mapping further showed extensive one-to-many relationships between ITS2 and full-length ITS ASVs, consistent with increased sequence resolution in long-read data. Together, these results show that ITS2 sequencing provides robust community-level profiling, while full-length ITS enables improved richness estimates and finer ecological and taxonomic resolution. This paired, bias-aware framework provides a practical template for selecting fungal amplicon sequencing strategies in built-environment mycobiome studies. ImportanceFungal communities in built environments influence indoor air quality and human exposure, yet their characterization depends strongly on sequencing strategy. This study provides a controlled, paired comparison of short-read ITS2 and long-read full-length ITS sequencing, showing that differences in amplicon length substantially contribute to variation in taxonomic resolution and ecological inference. While both approaches yield comparable community-level patterns, full-length ITS improves richness estimates, species-level assignment, and environmental discrimination by resolving sequence variation collapsed in ITS2 surveys. By integrating paired diversity analyses, in-silico ITS2 trimming, and cross-platform ASV mapping, this work offers a bias-aware framework for evaluating fungal amplicon pipelines. Importantly, improved species-level resolution enables functional interpretation of indoor fungi, for example the identification of taxa associated with pathogenic traits, allergen production, or toxin synthesis, supporting the development of more informative exposure metrics and targeted assays relevant to human health in built environments.

microbiology↗

bioRxiv2026

Global population structures and demographic history of Suillus luteus, a pine co-introduced ectomycorrhizal fungus associated with exotic forestry and invasion.

Human colonization since the 19th century has resulted in the global spread of pines across the Southern Hemisphere, well beyond their original northern boreal distribution. Such introductions moved not only the pines but also expanded the distribution of their symbiotic partners. Although the introduction of pines is documented through historical records, little is known about the introduction history of their ectomycorrhizal fungi, which are critical symbionts for the survival and invasion of pines. Using Suillus luteus as an example, population genomic analyses of 208 individuals across both native and introduced ranges showed that all introductions originated from Europe, likely mediated by human activities along with pine introductions. With the exception of North America, introduced populations were genetically differentiated from the Europe population, with varying magnitudes of population expansion in different introduced regions, often linked to forestry practices. Genetic variation within the native European population followed isolation by distance, but not in the introduced range, highlighting the disparity in the spatial genetic patterns of native versus exotic habitats. This study provides insight into the population genetics of a globally introduced ectomycorrhizal fungus whose introduction process is likely applicable to other pine-co-introduced ectomycorrhizal fungi.

evolutionary biology↗

bioRxiv2025

Time-series RNA metabarcoding of the active Populus tremuloides root microbiome reveals hidden temporal dynamics and dormant core members

Dormancy is a key life history stage of many microbes that involves existence in a metabolically inactive state. Although dormant taxa may contribute little to community function, most microbial metabarcoding community surveys of microbial systems target DNA which captures dormant and dead taxa in addition to the active and living fraction of the community. RNA metabarcoding offers the potential to delineate the active fraction of microbial communities. Transitions between dormancy and activity may also serve as a rapid response mechanism for communities for communities to alter their function faster than turnover in community composition. Additionally, a focus on active microbiomes may provide further insight into which taxa should be prioritized as part of the core microbiome. We used DNA and RNA metabarcoding in samples collected as a time-series of the quaking aspen (Populus tremuloides) root microbiome across a natural environmental gradient to identify the degree of spatiotemporal dynamism in active and total microbial communities and to document the extent of dormancy in the core microbiome. We found that active bacterial and fungal communities were more temporally dynamic than total communities, while total communities exhibited a stronger response to spatial variability in site conditions. Additionally, we found that core microbiome members are frequently inactive, resulting in a reduced active core microbiome. This study stresses the need to focus on turnover in the active microbial community to detect variation in microbial communities in time-series and to use microbial activity levels as a key determinant of core microbiome membership.

ecology↗

bioRxiv2024

An Experimental Test of Local Adaptation in Native and Introduced Populations of an Ectomycorrhizal Fungus, Suillus luteus

After species introductions and subsequent invasions, organisms often encounter intense selection pressures from biotic and abiotic aspects of novel environments, driving rapid evolutionary changes that potentially lead to local adaptation. This study aimed to investigate how invasion has influenced symbiotic interactions through rapid evolution in exotic isolates of the ectomycorrhizal (EcM) fungus Suillus luteus, which was co-introduced with obligately symbiotic pine trees into the Southern Hemisphere. We conducted a cross-inoculation experiment testing the compatibility of sympatric and allopatric pairings between pines and isolates of S. luteus from native and introduced populations. Our results showed that plant and fungal performance were substantially affected by these pairings, largely supporting a hypothesis of local maladaptation. Several performance metrics indicated stronger outcomes in allopatric pairings compared to sympatric ones. This suggests that fungal isolates may have evolved traits that are less beneficial or even somewhat harmful to their local host plants. These findings highlight the complex dynamics of coevolution and emphasize the necessity of considering both local adaptation and maladaptation in understanding species interactions.

evolutionary biology↗

bioRxiv2024

MicroFisher: Fungal taxonomic classification for metatranscriptomic and metagenomic data using multiple short hypervariable markers

Profiling the taxonomic and functional composition of microbes using metagenomic (MG) and metatranscriptomic (MT) sequencing is advancing our understanding of microbial functions. However, the sensitivity and accuracy of microbial classification using genome- or core protein-based approaches, especially the classification of eukaryotic organisms, is limited by the availability of genomes and the resolution of sequence databases. To address this, we propose the MicroFisher, a novel approach that applies multiple hypervariable marker genes to profile fungal communities from MGs and MTs. This approach utilizes the hypervariable regions of ITS and large subunit (LSU) rRNA genes for fungal identification with high sensitivity and resolution. Simultaneously, we propose a computational pipeline (MicroFisher) to optimize and integrate the results from classifications using multiple hypervariable markers. To test the performance of our method, we applied MicroFisher to the synthetic community profiling and found high performance in fungal prediction and abundance estimation. In addition, we also used MGs from forest soil and MTs of root eukaryotic microbes to test our method and the results showed that MicroFisher provided more accurate profiling of environmental microbiomes compared to other classification tools. Overall, MicroFisher serves as a novel pipeline for classification of fungal communities from MGs and MTs.

bioinformatics↗

bioRxiv2023

Decoding the chemical language of Suillus fungi: genome mining and untargeted metabolomics uncover terpene chemical diversity

Ectomycorrhizal fungi establish mutually beneficial relationships with trees, trading nutrients for carbon. Suillus are ectomycorrhizal fungi that are critical to the health of boreal and temperate forest ecosystems. Comparative genomics has identified a high number of non-ribosomal peptide synthetase and terpene biosynthetic gene clusters (BGC) potentially involved in fungal competition and communication. However, the functionality of these BGCs is not known. This study employed co-culture techniques to activate BGC expression and then used metabolomics to investigate the diversity of metabolic products produced by three Suillus species (S. hirtellus EM16, S. decipiens EM49, and S. cothurnatus VC1858), core members of the Pine microbiome. After 28 days of growth on solid media, liquid chromatography-tandem mass spectrometry identified a diverse range of extracellular metabolites (exometabolites) along the interaction zone between Suillus co-cultures. Prenol lipids were among the most abundant chemical classes. Out of the 62 unique terpene BGCs predicted by genome mining, 116 putative terpenes were identified across the three Suillus species using metabolomics. Notably, some terpenes were significantly more abundant in co-culture conditions. For example, we identified a metabolite matching to isomers isopimaric acid, sandaracopimaric acid, and abietic acid, which can be found in pine resin and play important roles in host defense mechanisms and Suillus spore germination. This research highlights the importance of combining genomics and metabolomics to advance our understanding of the chemical diversity underpinning fungal signaling and communication. ImportanceUsing a combination of genomics and metabolomics, this studys findings offer new insights into the signaling and communication of Suillus fungi, which serve a critical role in forest ecosystems.

microbiology↗

bioRxiv2022

The establishment of Populus x Laccaria bicolor ectomycorrhiza requires the inactivation of MYC2 coordinated defense response with a key role for root terpene synthases

The jasmonic acid (JA) signaling pathway plays an important role in the establishment of the ectomycorrhizal symbiosis (ECM) between Laccaria bicolor and poplar. We previously showed that the L. bicolor effector MiSSP7 induces the stabilization of the poplar JAZ6, a JA co-repressor protein that binds to Populus MYC2.1 and MYC2.2, orthologs of the Arabidopsis MYC2 transcription factor (TF), blocking their activity. Here we showed that both TFs play a central role in root colonization by L. bicolor mycelium, since their overexpression decreased the formation of the Hartig net, the hyphal network involved in symbiotic nutrient exchanges. By combining RNA sequencing and DNA Affinity Purification sequencing (DAP-seq) analysis, we identified a core set of JA-responsive genes directly activated by poplar MYC2.1 and MYC2.2, that need to be bypassed by the fungi to colonize root apoplastic spaces. These genes encode for other TFs, receptor-like kinases and many defense-related proteins, including terpene synthases (TPS). Monoterpenes produced by some of these TPS impact L. bicolor growth and ECM formation, suggesting a role for poplar root monoterpenes as negative regulators of in planta fungal growth and ECM symbiosis. Significance statementThe ectomycorrhizal symbiosis is a predominant mutualistic plant-fungus interaction occurring in forests, sustaining tree health. Ectomycorrhizal fungi colonize the root intercellularly establishing the symbiotic interface required for bidirectional nutrients exchanges, the Hartig net. During root colonization, the fungus L. bicolor produces the effector protein MiSSP7 that binds to the jasmonate co-receptor PtJAZ6, maintaining the repression of MYC2-targeted genes. Here we showed that defensive genes are major targets of MYC2, suggesting that their strict control is required to allow fungal colonization, with special emphasis on the host root monoterpene synthesis. Future research will focus on how root terpene defenses mediate belowground mutualistic interactions and how they can be manipulated to engineer plants with enhanced disease resistance but stable mutualistic interactions.

plant biology↗

bioRxiv2020

Vegetation and Microbes Interact to Preserve Organic Matter in Wooded Peatlands

Peatlands have persisted as massive carbon sinks over millennia, even during past periods of climate change. The commonly accepted theory of abiotic controls (mainly anoxia and low temperature) over carbon decomposition cannot explain how vast low-latitude wooded peatlands consistently accrete peat under warm and seasonally unsaturated conditions. Similarly, that theory cannot accurately project the decomposition rate in boreal peatlands where warming and drought have decreased Sphagnum and increased shrub expansion. Here, by comparing composition and ecological traits of microbes between Sphagnum- and shrub-dominated peatlands, we present a previously unrecognized natural course that curbs carbon loss against climate change. Slow-growing microbes decisively dominate the studied wooded peatlands, concomitant with plant-induced, high recalcitrant carbon and phenolics. The slow-growing microbes inherently metabolize organic matter slowly. However, the fast-growing microbes that dominate our Sphagnum site (most boreal peatlands as well) decomposed labile carbon >30 times faster than the slow-growing microbes. We show that the high-phenolic shrub/tree induced shifts in microbial composition may compensate for positive effects of temperature and/or drought on metabolism over time in peatlands. This biotic self-sustaining process that modulates abiotic controls on carbon cycling may help better project long-term climate-carbon feedbacks in peatlands.

ecology↗

bioRxiv2020

Phylogenetic diversity of 200+ isolates of the ectomycorrhizal fungus Cenococcum geophilum associated with Populus trichocarpa soils in the Pacific Northwest, USA and comparison to globally distributed representatives

The ectomycorrhizal fungal symbiont Cenococcum geophilum is of great interest as it is globally distributed, associates with many plant species, and has resistance to multiple environmental stressors. C. geophilum is only known from asexual states but is often considered a cryptic species complex, since extreme phylogenetic divergence is often observed within morphologically identical strains. Alternatively, C. geophilum may represent a highly diverse single species, which would suggest cryptic but frequent recombination. Here we describe a new isolate collection of 229 C. geophilum isolates from soils under Populus trichocarpa at 123 collection sites spanning a ~283 mile north-south transect in Washington and Oregon, USA (PNW). To further understanding of the phylogenetic relationships within C. geophilum, we performed maximum likelihood phylogenetic analyses to assess divergence within the PNW isolate collection, as well as a global GAPDH phylogenetic analysis of 789 isolates with publicly available data from the United States, Europe, Japan, and other countries. Phylogenetic analyses of the PNW isolates revealed three distinct phylogenetic groups, with 15 clades that strongly resolved at >80% bootstrap support based on a GAPDH phylogeny and one clade segregating strongly in two principle component analyses. The abundance and representation of PNW isolate clades varied greatly across the North-South range, including a monophyletic group of isolates that spanned nearly the entire gradient at ~250 miles. A direct comparison between the GAPDH and ITS phylogenies combined with additional analyses revealed stark incongruence between the ITS and GAPDH gene regions, implicating probable intra-species recombination between PNW isolates. In the global isolate collection phylogeny, 34 clades were strongly resolved at >80% bootstrap support, with some clades having intra- and intercontinental distributions. These data are highly suggestive of divergence within multiple cryptic species, however additional analyses such as higher resolution genotype-by-sequencing approaches are needed to distinguish potential species boundaries and recombination patterns.

ecology↗

bioRxiv2019

Incipient local adaptation in a fungus: evolution of heavy metal tolerance through allelic and copy-number variation

Human-altered environments can shape the evolution of organisms. Fungi are no exception, though little is known about how they withstand anthropogenic pollution. Here, we document incipient polygenic local adaptation in the mycorrhizal fungus Suillus luteus driven by recent soil heavy metal contamination. Genome scans across individuals from recently polluted and nearby unpolluted soils in Belgium revealed no evidence of population structure but detected allelic divergence and gene copy number variation in genes involved in metal exclusion, storage, immobilization, and reactive oxygen species detoxification. Standing genetic variation included multiple alleles of small effects contributing to heavy metal tolerance, suggesting the existence of different strategies to withstand contamination. These variants were shared across the whole population but under selection in isolates exposed to pollution. Together, our results point to S. luteus undergoing the initial steps of adaptive divergence and contribute to understanding the processes underlying local adaptation under strong environmental selection.

evolutionary biology↗

bioRxiv2018

Global climate changes will lead to regionally divergent trajectories for ectomycorrhizal communities in North American Pinaceae forests

Ectomycorrhizal fungi (ECMF) are partners in a globally distributed tree symbiosis that enhanced ecosystem carbon (C)-sequestration and storage. However, resilience of ECMF to future climates is uncertain. We sampled ECMF across a broad climatic gradient in North America, modeled climatic drivers of diversity and community composition, and then forecast ECMF response to climate changes over the next 50 years. We predict ECMF richness will decline over nearly half of North American Pinaceae forests, with median species losses as high as 21%. Mitigation of greenhouse gas emissions can reduce these declines, but not prevent them. Warming of forests along the boreal-temperate ecotone results in projected ECMF species loss and declines in the relative abundance of C demanding, long-distance foraging ECMF species, but warming of eastern temperate forests has the opposite effect. Sites with more ECMF species had higher activities of nitrogen-mineralizing enzymes, suggesting that ECMF species-losses will compromise their associated ecosystem functions.

ecology↗