About

Rytas J. Vilgalys is a Professor of Biology at Duke University, with a focus on mycology, including systematics, evolution, medical mycology, plant pathology, genetics/genomics, and ecology. He is best known for his involvement in transitioning fungal systematics from a non-quantitative, morphologically based science to a rigorous genome-based discipline. Over the past 20 years, his lab has increasingly studied fungal 'ecogenomics' using targeted and shotgun metagenomics, linking molecular function with fungal diversity. In collaboration with medical mycologists and basic scientists at Duke Medical Center, he has contributed to integrating an evolutionary biology perspective into the study of human mycoses. His academic appointments include being a Professor of Biology since 2000 and a Professor in Molecular Genetics and Microbiology since 2024. Vilgalys holds a Ph.D. from Virginia Polytech Institute and State University, earned in 1985, and has a background in genetics and mycology, with earlier degrees from the State University of New York, Geneseo.

Research topics

• Biology
• Genetics
• Computational biology
• Evolutionary biology
• Botany
• Horticulture
• Zoology
• Ecology
• Agronomy

Selected publications

• Comparative genomics provides insights into the cold adaptation of endophytic fungi associated with Deschampsia antarctica

  Fungal Genetics and Biology · 2026-03-31

  articleOpen access

  Endophytic fungi from Deschampsia antarctica, the southernmost flowering plant, provide insights into the cold adaptation mechanisms of plant-associated fungi in extreme environments. This study presents the genome sequences and comparative analysis of eight fungal isolates from D. antarctica leaves. These Antarctic fungal isolates were analyzed alongside 121 plant-associated fungal genomes to uncover signatures of adaptation and endophytic specialization. Antarctic endophytes show striking patterns, including reduced genome size (∼26.3 Mb on average), streamlined gene content (∼8844 genes), and notably small secretomes (∼288 proteins). Despite this reduced gene repertoire, they maintain a robust set of genes encoding carbohydrate-active enzymes (CAZymes) but lack those for lignin and bacterial cell wall degradation, indicating a symbiotic lifestyle that avoids host damage and predation. One isolate, Alternaria sp. UNIPAMPA017 stood out, with 26% of its genome occupied by transposable elements. Lifestyle, rather than phylogeny, was the main driver of CAZyme and secretome profiles, underscoring ecological convergence. Compared to endophytes from Arabidopsis and Populus, D. antarctica endophytes harbor fewer pectin-degrading enzymes, reflecting their adaptation to the cell wall structure of their monocot host. Together, these fungi reveal a pattern of genomic reduction and functional fine-tuning, hallmarks of life adapted to persist in cold, nutrient-scarce niches.

  PublisherDOI

• Multiple hypervariable markers improve mycobiome classification in metatranscriptome and metagenome data

  Communications Biology · 2026-04-08

  articleOpen access

  Profiling the taxonomic and functional composition of mycobiome using metagenomic and metatranscriptomic sequencing is advancing our understanding of fungal functions in ecosystems. However, the sensitivity and accuracy of mycobiome classification using genome- or core protein-based approaches, is limited by the availability of reference genomes and the resolution of sequence databases. To address this, we propose the MicroFisher, a novel tool to identify taxonomically useful reads from metagenomic or metatranscriptomic data, enabling taxonomic identification of community members based on multiple hypervariable markers. We applied MicroFisher to profile the simulated fungal communities to assess the performance of the developed tool, and found higher performance in fungal prediction and abundance estimation compared to existing tools. In addition, we also used metagenomes from forest soil and metatranscriptomes of root eukaryotic microbes to test our method and found that MicroFisher provided more accurate profiling of environmental microbiomes compared to other classification tools. MicroFisher leverages high-resolution hypervariable marker gene databases and weighted integration algorithms to deliver more accurate fungal community classification compared to existing state-of-the-art tools. Additionally, it enables the detection of rare taxa, which is challenging with other available tools. Thus, MicroFisher serves as a novel pipeline for classification of fungal communities from metagenomes and metatranscriptomes.

  PublisherDOI

• Scattered far and wide: A broadly distributed temperate dune grass finds familiar fungal root associates in its invasive range

  UNC Libraries · 2025-11-05

  articleOpen access
  PublisherDOI

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

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-02-24 · 3 citations

  preprintOpen accessSenior author

  Abstract 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.

  PublisherOA PDFDOI

• Dual-mycorrhizal colonization is determined by plant age and host identity in two species of Populus

  Mycorrhiza · 2025-06-01 · 3 citations

  articleSenior author
  PublisherDOI

• Fungal endophytes

  Current Biology · 2025-10-01 · 4 citations

  review
  PublisherDOI

• Inorganic nitrogen and organic matter jointly regulate ectomycorrhizal fungi‐mediated iron acquisition

  New Phytologist · 2025-01-22 · 7 citations

  articleOpen access

  Summary Ectomycorrhizal fungi (EMF) play a crucial role in facilitating plant nutrient uptake from the soil although inorganic nitrogen (N) can potentially diminish this role. However, the effect of inorganic N availability and organic matter on shaping EMF‐mediated plant iron (Fe) uptake remains unclear. To explore this, we performed a microcosm study on Pinus taeda roots inoculated with Suillus cothurnatus treated with +/−Fe‐coated sand, +/−organic matter, and a gradient of NH 4 NO 3 concentrations. Mycorrhiza formation was most favorable under conditions with organic matter, without inorganic N. Synchrotron X‐ray microfluorescence imaging on ectomycorrhizal cross‐sections suggested that the effect of inorganic N on mycorrhizal Fe acquisition largely depended on organic matter supply. With organic matter, mycorrhizal Fe concentration was significantly decreased as inorganic N levels increased. Conversely, an opposite trend was observed when organic matter was absent. Spatial distribution analysis showed that Fe, zinc, calcium, and copper predominantly accumulated in the fungal mantle across all conditions, highlighting the mantle's critical role in nutrient accumulation and regulation of nutrient transfer to internal compartments. Our work illustrated that the liberation of soil mineral Fe and the EMF‐mediated plant Fe acquisition are jointly regulated by inorganic N and organic matter in the soil.

  PublisherDOI

• Dual-mycorrhizal colonization is determined by plant age and host identity in two species of Populus

  Research Square · 2025-04-29

  preprintOpen accessSenior author
  PublisherOA PDFDOI

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

  mSystems · 2025-11-07 · 2 citations

  articleOpen accessSenior author

  ABSTRACT The rhizosphere is a critical interface between plant roots and soil, harboring diverse microbial communities that are essential to plant and ecosystem health. Although these communities exhibit stark temporal dynamics, their dormancy/activity transitions remain poorly understood. Such transitions may enable microbes to rapidly adjust functional contributions faster than community turnover alone would allow. Here, we used RNA metabarcoding to characterize the active fraction of microbial communities on the roots of quaking aspen ( Populus tremuloides ) in a time-series study across a natural environmental gradient. We explore cryptic temporal microbial community dynamics of rhizosphere communities at the ecosystem scale. The active rhizosphere bacterial and fungal communities were more temporally dynamic than total communities, while total communities exhibited a stronger response to site-specific conditions. Notably, some core microbiome members were often inactive, yielding a smaller “active core” subset. The fungal endophyte Hyaloscypha finlandica was the only microbe that was both present and active in all plots across all timepoints. Soil temperature strongly influenced both total and active community composition, with the fungal class Eurotiomycetes showing a temperature-dependent seasonal decline in abundance. Together, these results reveal that modulation of microbial activity levels is a key mechanism by which the plant root holobiont responds to environmental variation, and that even dominant symbionts may frequently persist in dormancy within the rhizosphere. IMPORTANCE Members of the rhizosphere exhibit dynamic patterns of activity and dormancy. This study stresses the need to focus on active microbial communities to detect temporal changes in plant microbiomes. Additionally, the metabolic activity of microbes should be considered a key determinant of core microbiome membership. Parallel patterns in active community dynamics between fungal and bacterial communities provide a potentially generalizable rule of microbial community temporal dynamics in plant rhizospheres.

  PublisherDOI

• A native and an invasive dune grass share similar, patchily distributed, root-associated fungal communities

  UNC Libraries · 2025-11-05

  articleOpen access
  PublisherDOI

Recent grants

• Phylogenetic Systematics and Diversity of the Agaricales Fungi

  NSF · $226k · 2000–2003

• DISSERTATION RESEARCH: Coevolutionary Diversification in Septobasidium, a Fungal Symbiont of Scale Insects

  NSF · $12k · 2004–2006

• The Agaricales: Molecular Systematics and Evolution of Mushrooms

  NSF · $218k · 1997–2001

• Collaborative Research: Ectomycorrhizal fungal diversity of the central Guiana Shield

  NSF · $260k · 2009–2013

• Dissertation Research: Systematics and Phylogeography of Truffles (Tuber)

  NSF · $12k · 2007–2010

Frequent coauthors

• Hui-ling Liao

  264 shared

• Colin Averill

  Lawrence Livermore National Laboratory

  247 shared

• Ryan Tappero

  Brookhaven National Laboratory

  220 shared

• Jennifer Bhatnagar

  Boston University

  219 shared

• Haihua Wang

  218 shared

• Edward Brzostek

  West Virginia University

  217 shared

• Nahuel Policelli

  Centro Científico Tecnológico Patagónico

  197 shared

• Thomas G. Mitchell

  78 shared

Education

• Ph.D., Biology

  Virginia Polytechnic Institute and State University

• B.A., Biology

  SUNY Geneseo