About

Kabir Peay is a Senior Associate Dean for Education, Director of the Earth Systems Program, and a Professor of Biology and Earth System Science at Stanford University. He holds a PhD from UC Berkeley's Department of Environmental Science, Policy and Management, obtained in 2008, a Master of Environmental Science from Yale School of Forestry in 2003, and a BA from UC Santa Barbara in 1997. His academic and research background includes postdoctoral training at UC Berkeley in the Department of Plant & Microbial Biology with Tom Bruns, and at Stanford in the Department of Biology with Tadashi Fukami. Peay's research focuses on ecology, community structure, and ecosystem function of plant-microbial symbiosis, with primary affiliation in Ecology and Environmental Science. His contributions include advancing understanding of plant-microbial interactions and their role in ecosystem processes.

Research topics

• Biology
• Ecology
• Computer Science
• Genetics
• Computational biology
• Evolutionary biology
• Environmental science
• Data science
• Botany
• Library science
• Astronomy
• World Wide Web
• Atmospheric sciences

Selected publications

• Cryogenic electron tomography by the numbers: Charting underexplored lineages in structural cell biology

  Proceedings of the National Academy of Sciences · 2026-02-18

  articleOpen access

  Imaging 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 collate cryo-ET data from hundreds of cells and tissues across the biosphere to i) identify emerging methodological trends, ii) pinpoint strategies to reduce imaging time and costs, iii) quantitatively compare methods for cell freezing and sectioning, and iv) census cryo-ET species coverage across all domains of life. Comparing the fraction of cellular material within a single lamella across all domains of life reveals an order of magnitude difference between eukaryotes (1%) compared to bacteria (9%) and archaea (14%). 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 approach for obtaining more complete cellular depictions. Finally, we show that the biodiversity of current cryo-ET studies is 2 to 3 orders of magnitude lower than in sequence libraries and 4 to 5 lower than the total predicted on Earth. Our analyses reveal major evolutionary lineages which remain critically understudied and highlight where future cryo-ET research would be most impactful.

  PublisherOA PDFDOI

• BPS2026 – Nanoscale architecture of field-derived fungal-bacterial symbiosis revealed by cryogenic electron tomography

  Biophysical Journal · 2026-02-01

  article
  PublisherDOI

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

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-03-12

  articleOpen access

  Abstract 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.

  PublisherOA PDFDOI

• Symbiotic fungi underlie the regeneration potential of island rainforests

  Current Biology · 2026-04-30 · 1 citations

  articleOpen access

  Symbioses can be vital on islands, where low species diversity leaves few alternative partners and the failure of associations can cascade into broader community collapse. Key to the functioning of many island ecosystems is the rainforest tree, Pisonia grandis (pisonia). Pisonia attracts nesting seabirds whose guano delivers intense nutrient pulses that fuel coral reef ecosystems. Symbiotic mycorrhizal fungi have been hypothesized to be crucial for capturing and distributing these nutrients to pisonia trees. However, little is known about the factors that influence the distribution of mycorrhizal fungi on islands. Here, we map the diversity and distribution of mycorrhizal fungi in relation to pisonia and other tree species across Palmyra Atoll, the most remote island on Earth that is a US territory in the Northern Line Islands. We found that pisonia is obligately associated with specific Tomentella fungi that are able to survive in the extreme nutrient environments created by seabird feces (guano). Tomentella was widespread in soils across different habitats, and its abundance was predicted by distance to pisonia. In addition, burrowing by crabs, the dominant group of land animals on Palmyra Atoll, was associated with increased fungal diversity, including new or globally rare fungal species. These findings support the hypothesized critical role of mycorrhizal fungi for key atoll tree species, indicating that fungal distributions may affect the success of restoration projects. More broadly, this work highlights the importance of specific interactions between species in isolated island ecosystems. VIDEO ABSTRACT.

  PublisherDOI

• One hundred unanswered questions on the dispersal ecology of fungi

  The ISME Journal · 2026-01-01 · 2 citations

  articleOpen access

  Fungi comprise millions of species that play numerous varied roles in Earth's natural and managed ecosystems, engaging in a multitude of positive and negative ecological interactions. The dispersal ecology of fungi is central to global biodiversity patterns, maintenance of terrestrial and aquatic ecosystem functions, and tracking human disease and plant pathogen outbreaks. Mycologists have been studying dispersal mechanisms for over a hundred years, but new technology as well as interdisciplinary approaches have reinvigorated research in the field. Here we present 100 research questions in fungal dispersal organized into ten themes: 1) dispersal traits and mechanisms, 2) effects of phenology and lifestyle, 3) spore liberation and transport mechanisms, 4) colonization and establishment, 5) ecosystem-level consequences of dispersal, 6) dispersal in symbiotic and host-associated fungi, 7) dispersal in anthropogenic and changing environments, 8) evolution and tradeoffs in dispersal, 9) role of dispersal in invasion and disease spread, and 10) methodology and techniques. The questions reflect a diversity of new research avenues from fundamental fungal biology to applied ecosystem management and conservation across spatial and temporal scales. They potentially enable integrating fungi and their unique life-history traits and dispersal strategies into existing dispersal frameworks developed around plant and animal systems. We aim to invigorate fungal dispersal research, sparking conversations and providing a focused agenda to widen the tent by illuminating unanswered questions and new research avenues in ecology and evolutionary biology.

  PublisherDOI

• Impacts of Nutrient Availability on Multiple Mutualisms in the Common Bean

  Stanford Digital Repository · 2026-04-30

  articleOpen access

  In farming systems, soil management practices, such as fertilizer use, greatly influence the growth of plants and their interactions with soil microbes. In agriculture systems like the Milpa or Three Sisters, nutrient availability plays a fundamental role in shaping the ecological interactions these systems depend on; bean plants form beneficial relationships with nitrogen fixing bacteria, and this benefits the corn and squash they’re grown with. High fertilization practices suppress the abundance and activity of nitrogen- fixing bacteria and arbuscular mycorrhizal fungi (AMF), resulting in fewer mutualistic relationships with the beans. These relationships are really important for the plants’ fitness and reproductive success, and the presence of multiple mutualisms doubles the benefits. However, there isn’t a clear understanding of how differing fertilization practices will affect the interactions between the two microbes and resultantly their interactions with the common bean. Furthermore, few studies have been done on polyculture systems, where these microbial interactions not only affect the bean, but also the corn and squash. This study follows the growth of beans from the species Phaseolus vulgaris from seed to 6 weeks old in a growth chamber, capturing plant traits and characterizing the beans’ microbial relationships using root staining and microscopy. The fertilizer treatments differ in amounts of nitrogen and phosphorus because bean plants primarily depend on N-fixing bacteria and AMF for these two nutrients, respectively. The microbes are introduced alone and together for each fertilizer treatment to determine if they influence one another, and if having multiple mutualisms impacts the beans differently. The study found AMF significantly influenced plant biomass allocation, leading to more aboveground biomass relative to absence of AMF. This indicates that beneficial microbes are key to overcoming nutrient limitation and achieving desired yields, while also maintaining the health of the soil and land. The global food system depends on thriving soil ecosystems. In order to feed people generations into the future, it’s imperative that soil microbes be better understood and protected.

  PublisherDOI

• Fungal impacts on Earth’s ecosystems

  Nature · 2025-02-05 · 79 citations

  reviewOpen access
  PublisherOA PDFDOI

• Climate and Land‐Use Changes Predicted to Jointly Drive Soil Fungal Diversity Losses in One‐Third of North American Coniferous Forests

  Global Change Biology · 2025-11-01 · 1 citations

  articleOpen access

  Soil fungi underpin key ecosystem functions but face increasing threats from climate and land-use changes, with their future impacts remaining unclear. This uncertainty is exacerbated by limited large-scale data and the challenge of quantifying and comparing both factors at comparable spatial scales. By leveraging two continental-scale sampling networks in North America and applying stacked species distribution models combined with countryside species-area relationship frameworks, we assessed the impacts of climate and land-use change on soil fungal diversity and identified regions affected by both factors across four biomes. We projected climate and land-use change by incorporating shared socioeconomic pathways (SSPs) and associated greenhouse gas-induced radiative forcing, focusing on moderate- (SSP2-4.5) and high-emission (SSP5-8.5) scenarios. Climate change typically led to both diversity losses and gains, particularly in coniferous forests and among arbuscular mycorrhizal (AM) fungi. Land-use change predominantly caused diversity losses under SSP2-4.5, especially in broadleaf-mixed forests and for ectomycorrhizal (EM) fungi, with these effects diminished under SSP5-8.5 due to minimal land-use changes. Across emission scenarios, both factors were predicted to cause widespread diversity losses in coniferous forests (whole-community, EM fungi, and soil saprotrophs) and grasslands (AM fungi and plant pathogens) while promoting gains in broadleaf-mixed forests (whole-community, EM fungi, and saprotrophs) and coniferous forests (AM fungi and pathogens). These results support the need for biome- and guild-specific fungal conservation planning under global change.

  PublisherOA PDFDOI

• Global hotspots of mycorrhizal fungal richness are poorly protected

  Nature · 2025-07-23 · 33 citations

  articleOpen access

  Mycorrhizal fungi are ecosystem engineers that sustain plant life and help regulate Earth’s biogeochemical cycles1–3. However, in contrast to plants and animals, the global distribution of mycorrhizal fungal biodiversity is largely unknown, which limits our ability to monitor and protect key underground ecosystems4,5. Here we trained machine-learning algorithms on a global dataset of 25,000 geolocated soil samples comprising >2.8 billion fungal DNA sequences. We predicted arbuscular mycorrhizal and ectomycorrhizal fungal richness and rarity across terrestrial ecosystems. On the basis of these predictions, we generated high-resolution, global-scale maps and identified key reservoirs of highly diverse and endemic mycorrhizal communities. Intersecting protected areas with mycorrhizal hotspots indicated that less than 10% of predicted mycorrhizal richness hotspots currently exist in protected areas. Our results describe a largely hidden component of Earth’s underground ecosystems and can help identify conservation priorities, set monitoring benchmarks and create specific restoration plans and land-management strategies. Machine-learning algorithms trained on 25,000 geolocated soil samples are used to create high-resolution global maps of mycorrhizal fungi, revealing that less than 10% of their biodiversity hotspots are in protected areas.

  PublisherOA PDFDOI

• BPS2025 - Cryogenic electron tomography and fluorescence light microscopy of multispecies communities within the soil microbiome

  Biophysical Journal · 2025-02-01

  article
  PublisherDOI

Recent grants

• DISSERTATION RESEARCH: Mechanisms of host preference in the ectomycorrhizal symbiosis

  NSF · $21k · 2016–2019

• Collaborative research: Defining the scope and consequences of ectomycorrhizal fungal control on forest organic matter decomposition

  NSF · $157k · 2020–2024

• Collaborative Proposal: MRA: Macroecology of microorganisms: Scaling fungal biodiversity from soil cores to the North American continent

  NSF · $370k · 2019–2024

• Dimensions: Collaborative Research: Deconstructing diversity and ecosystem function at multiple spatial and genetic scales in a keystone plant-microbe symbiosis

  NSF · $710k · 2010–2012

• RAPID: Collaborative Research: Do negative plant-soil feedbacks outweigh positive ectomycorrhizal mutualisms in dipterocarp rainforest?

  NSF · $128k · 2013–2015

Frequent coauthors

• Laura Bogar

  University of California, Davis

  1058 shared

• Glade Dlott

  Stanford University

  1051 shared

• Thomas D. Bruns

  Physikalisch-Technische Bundesanstalt

  34 shared

• Peter G. Kennedy

  University of Minnesota

  26 shared

• Nhu H. Nguyen

  University of California, Davis

  16 shared

• Sara Branco

  University of Évora

  15 shared

• Peter B. Reich

  University of Minnesota

  14 shared

• Gabriel Reuben Smith

  12 shared

Labs

• Peay LabPI

  Not provided

Education

• M.S.

  Yale School of Forestry and Environment Science (F&ES)

  2003

• Ph.D.

  UC Berkeley’s Dept. of Environmental Science, Policy and Management (ESPM)

  2008

• Other

  UC Berkeley’s Dept. of Plant & Microbial Biology

• Other

  Stanford’s Dept. of Biology