Biology subjects

Peay, K. G.

Publications and source records attributed to Peay, K. G..

7 recordsLinked to original sources

bioRxiv2026

A novel pipeline for the rapid expansion of ecological trait databases using LLMs

This paper presents a novel workflow leveraging Large Language Models (LLMs) to rapidly extract trait data from fungal species descriptions, addressing a significant bottleneck in ecological research. We developed and evaluated an LLM pipeline to extract morphological trait data from arbuscular mycorrhizal fungi, comparing performance against a manually curated dataset (TraitAM). Results demonstrate the potential of LLMs for automated trait data acquisition, though accuracy varies by trait and model, with systematic biases observed. This framework offers a blueprint for building trait databases across diverse taxa and domains, significantly accelerating ecological research and conservation efforts.

ecology↗

bioRxiv2025

Cryogenic Electron Tomography by the Numbers: Charting Underexplored Lineages in Structural Cell Biology

Imaging of cells and their interactions across the whole biosphere, with molecular-scale resolution, is key for understanding structure-function relations. Cryogenic electron tomography (cryo-ET) is a powerful method for obtaining this critical information. However, cryo-ET studies are challenging and often limited to a small number of cell types per study. Here, we bring together cryo-ET data from hundreds of cells and tissues across the biosphere to (i) identify emerging methodological trends, (ii) reduce imaging time and costs, (iii) quantitively compare methods for cell freezing and sectioning and (iv) census cryo-ET species coverage across all domains of life. Comparison of the fraction of cellular material within lamellae across all domains of life reveals an order of magnitude difference between bacteria (9%) and archaea (15%) compared to eukaryotes (1%). We calculate the fraction of cellular material which can be imaged using distinct sectioning methods on multicellular communities and tissues - identifying serial lift-out as a powerful new approach for obtaining more complete cellular depictions. Finally, we show that the biodiversity of current cryo-ET studies is 2-3 order of magnitude lower than in sequence libraries and 4-5 lower than the total predicted on Earth. Our analyses reveal major evolutionary lineages which remain critically understudied and where future cryo-ET research would be most impactful. Significance StatementCryogenic electron tomography (cryo-ET) is a powerful method for imaging inside cells, but it is challenging and typically limited to a few cells per study. We consolidate and quantify data from hundreds of cellular cryo-ET studies across the biosphere. The methodological trends we identify will enhance cryo-ET throughput and heighten biological insight from underexplored lineages of life on Earth.

biophysics↗

bioRxiv2024

Fungal spore seasons advanced across the US over two decades of climate change

Phenological shifts due to climate change have been extensively studied in plants and animals. Yet, the responses of fungal spores--crucial organisms that play important roles in ecosystems and act as airborne allergens--remain understudied. This knowledge gap in global change biology hinders our understanding of its ecological and public health implications. To bridge this gap, we acquired a long-term (2003 [~] 2022), large-scale (the continental US) dataset of airborne fungal spores collected by the US National Allergy Bureau. We first pre-processed the spore data by gap-filling and smoothing. Afterward, we extracted ten metrics describing the phenology (e.g., start and end of season) and intensity (e.g., peak concentration and integral) of fungal spore seasons. These metrics were derived using two complementary but not mutually exclusive approaches--ecological and public health approaches, defined as percentiles of total spore concentration and allergenic thresholds of spore concentration, respectively. Using linear mixed effects models, we quantified annual temporal shifts in these metrics across the continental US. We revealed a significant advancement in the onset of the spore seasons defined in both ecological (11 days, 95% confidence interval: 0.4 [~] 23 days) and public health (22 days, 6 [~] 38 days) approaches over two decades. Nevertheless, the total spore concentration in an annual cycle and in a spore allergy season tended to decrease over time. The earlier start of the spore season was significantly correlated with climatic variables, such as warmer temperatures and altered precipitations. Overall, our findings suggest possible climate-driven advanced fungal spore seasons, highlighting the importance of climate change mitigation and adaptation in public health decision-making.

ecology↗

bioRxiv2021

Different mycorrhizal nutrient acquisition strategies shape tree species competition and coexistence dynamics

Mycorrhizal fungi with different nutrient acquisition strategies influence the functional separation among plant species. This might drive resource competition dynamics that cumulatively impact tree species coexistence, but few manipulative experiments have directly tested this. Combining surveys and experiments in a modern coexistence theory framework, we tested how variation in mycorrhizal strategies and nutrient conditions affect competitive outcomes between co-occurring ectomycorrhizal (EM) and arbuscular mycorrhizal (AM) tree species. The dependency on EM symbioses increased with latitude and nitrogen (N) limitation, matching global trends. Host-specific soil microbiome conditioning and N fertilization combined to qualitatively affect coexistence outcomes. Lower N conditions favored EM over AM trees, but N fertilization reversed this outcome for southern species, consistent with regional-scale forest mycorrhizal transitions. As the magnitude and outcome of microbially-mediated competition depends on mycorrhizal differentiation and soil nutrient availability, this strongly supports the importance of mycorrhizal symbioses in driving large-scale biogeographic patterns of tree species.

ecology↗

bioRxiv2020

Ericoid mycorrhizal diversity increases with soil age and progressive phosphorus limitation across a 4.1 million-year chronosequence

Ericaceous plants rely on ericoid mycorrhizal fungi for nutrient acquisition. However, the factors that affect the composition and structure of these fungal communities remain largely unknown. Here, we use a 4.1-myr soil chronosequence in Hawaii to test the hypothesis that changes in nutrient availability with soil age determine the diversity and species composition of fungi associated with ericoid roots. We sampled roots of a native Hawaiian plant, Vaccinium calycinum, and used DNA metabarcoding to quantify changes in fungal diversity and species composition. We also used a fertilization experiment at the youngest and oldest sites to assess the importance of nutrient limitation. We found an increase in diversity and a clear pattern of species turnover across the chronosequence, driven largely by putative ericoid mycorrhizal fungi. Fertilization with nitrogen at the youngest site and phosphorus at the oldest site reduced total fungal diversity, suggesting a direct role of nutrient limitation. Our results also reveal the presence of novel fungal species associated with Hawaiian Ericaceae and suggest a greater importance of phosphorus availability for communities of ericoid mycorrhizal fungi than is generally assumed.

ecology↗

bioRxiv2020

Decadal changes in fire frequencies shift tree communities and functional traits

Global change has resulted in chronic shifts in fire regimes, increasing fire frequency in some regions and decreasing it in others. Predicting the response of ecosystems to changing fire frequencies is challenging because of the multi-decadal timescales over which fire effects emerge and the variability in environmental conditions, fire types, and plant composition across biomes. Here, we address these challenges using surveys of tree communities across 29 sites that experienced multi-decadal alterations in fire frequencies spanning ecosystems and environmental conditions. Relative to unburned plots, more frequently burned plots had lower tree basal area and stem densities that compounded over multiple decades: average fire frequencies reduced basal area by only 4% after 16 years but 57% after 64 years, relative to unburned plots. Fire frequency had the largest effects on basal area in savanna ecosystems and in sites with strong wet seasons. Analyses of tree functional-trait data across North American sites revealed that frequently burned plots had tree communities dominated by species with low biomass nitrogen and phosphorus content and with more efficient nitrogen acquisition through ectomycorrhizal symbioses (rising from 85% to nearly 100%). Our data elucidate the impact of long-term fire regimes on tree community structure and composition, with the magnitude of change depending on climate, vegetation type, and fire history. The effects of widespread changes in fire regimes underway today will manifest in decades to come and have long-term consequences for carbon storage and nutrient cycling.

ecology↗

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↗