Stanford Advisors

All Publications

  • Climate mismatches with ectomycorrhizal fungi contribute to migration lag in North American tree range shifts. Proceedings of the National Academy of Sciences of the United States of America Van Nuland, M. E., Qin, C., Pellitier, P. T., Zhu, K., Peay, K. G. 2024; 121 (23): e2308811121


    Climate change will likely shift plant and microbial distributions, creating geographic mismatches between plant hosts and essential microbial symbionts (e.g., ectomycorrhizal fungi, EMF). The loss of historical interactions, or the gain of novel associations, can have important consequences for biodiversity, ecosystem processes, and plant migration potential, yet few analyses exist that measure where mycorrhizal symbioses could be lost or gained across landscapes. Here, we examine climate change impacts on tree-EMF codistributions at the continent scale. We built species distribution models for 400 EMF species and 50 tree species, integrating fungal sequencing data from North American forest ecosystems with tree species occurrence records and long-term forest inventory data. Our results show the following: 1) tree and EMF climate suitability to shift toward higher latitudes; 2) climate shifts increase the size of shared tree-EMF habitat overall, but 35% of tree-EMF pairs are at risk of declining habitat overlap; 3) climate mismatches between trees and EMF are projected to be greater at northern vs. southern boundaries; and 4) tree migration lag is correlated with lower richness of climatically suitable EMF partners. This work represents a concentrated effort to quantify the spatial extent and location of tree-EMF climate envelope mismatches. Our findings also support a biotic mechanism partially explaining the failure of northward tree species migrations with climate change: reduced diversity of co-occurring and climate-compatible EMF symbionts at higher latitudes. We highlight the conservation implications for identifying areas where tree and EMF responses to climate change may be highly divergent.

    View details for DOI 10.1073/pnas.2308811121

    View details for PubMedID 38805274

  • Ectomycorrhizal fungi alter soil food webs and the functional potential of bacterial communities. mSystems Berrios, L., Bogar, G. D., Bogar, L. M., Venturini, A. M., Willing, C. E., Del Rio, A., Ansell, T. B., Zemaitis, K., Velickovic, M., Velickovic, D., Pellitier, P. T., Yeam, J., Hutchinson, C., Bloodsworth, K., Lipton, M. S., Peay, K. G. 2024: e0036924


    Most of Earth's trees rely on critical soil nutrients that ectomycorrhizal fungi (EcMF) liberate and provide, and all of Earth's land plants associate with bacteria that help them survive in nature. Yet, our understanding of how the presence of EcMF modifies soil bacterial communities, soil food webs, and root chemistry requires direct experimental evidence to comprehend the effects that EcMF may generate in the belowground plant microbiome. To this end, we grew Pinus muricata plants in soils that were either inoculated with EcMF and native forest bacterial communities or only native bacterial communities. We then profiled the soil bacterial communities, applied metabolomics and lipidomics, and linked omics data sets to understand how the presence of EcMF modifies belowground biogeochemistry, bacterial community structure, and their functional potential. We found that the presence of EcMF (i) enriches soil bacteria linked to enhanced plant growth in nature, (ii) alters the quantity and composition of lipid and non-lipid soil metabolites, and (iii) modifies plant root chemistry toward pathogen suppression, enzymatic conservation, and reactive oxygen species scavenging. Using this multi-omic approach, we therefore show that this widespread fungal symbiosis may be a common factor for structuring soil food webs.IMPORTANCEUnderstanding how soil microbes interact with one another and their host plant will help us combat the negative effects that climate change has on terrestrial ecosystems. Unfortunately, we lack a clear understanding of how the presence of ectomycorrhizal fungi (EcMF)-one of the most dominant soil microbial groups on Earth-shapes belowground organic resources and the composition of bacterial communities. To address this knowledge gap, we profiled lipid and non-lipid metabolites in soils and plant roots, characterized soil bacterial communities, and compared soils amended either with or without EcMF. Our results show that the presence of EcMF changes soil organic resource availability, impacts the proliferation of different bacterial communities (in terms of both type and potential function), and primes plant root chemistry for pathogen suppression and energy conservation. Our findings therefore provide much-needed insight into how two of the most dominant soil microbial groups interact with one another and with their host plant.

    View details for DOI 10.1128/msystems.00369-24

    View details for PubMedID 38717159

  • A risk assessment framework for the future of forest microbiomes in a changing climate NATURE CLIMATE CHANGE Willing, C. E., Pellitier, P. T., Van Nuland, M. E., Alvarez-Manjarrez, J., Berrios, L., Chin, K. N., Villa, L. M., Yeam, J. J., Bourque, S. D., Tripp, W., Leshyk, V. O., Peay, K. G. 2024
  • Potential for functional divergence in ectomycorrhizal fungal communities across a precipitation gradient. ISME communications Pellitier, P. T., Van Nuland, M., Salamov, A., Grigoriev, I. V., Peay, K. G. 2024; 4 (1): ycae031


    Functional traits influence the assembly of microbial communities, but identifying these traits in the environment has remained challenging. We studied ectomycorrhizal fungal (EMF) communities inhabiting Populus trichocarpa roots distributed across a precipitation gradient in the Pacific Northwest, USA. We profiled these communities using taxonomic (meta-barcoding) and functional (metagenomic) approaches. We hypothesized that genes involved in fungal drought-stress tolerance and fungal mediated plant water uptake would be most abundant in drier soils. We were unable to detect support for this hypothesis; instead, the abundance of genes involved in melanin synthesis, hydrophobins, aquaporins, trehalose-synthases, and other gene families exhibited no significant shifts across the gradient. Finally, we studied variation in sequence homology for certain genes, finding that fungal communities in dry soils are composed of distinct aquaporin and hydrophobin gene sequences. Altogether, our results suggest that while EMF communities exhibit significant compositional shifts across this gradient, coupled functional turnover, at least as inferred using community metagenomics is limited. Accordingly, the consequences of these distinct EMF communities on plant water uptake remain critically unknown, and future studies targeting the expression of genes involved in drought stress tolerance are required.

    View details for DOI 10.1093/ismeco/ycae031

    View details for PubMedID 38524763

    View details for PubMedCentralID PMC10960952

  • Positive interactions between mycorrhizal fungi and bacteria are widespread and benefit plant growth. Current biology : CB Berrios, L., Yeam, J., Holm, L., Robinson, W., Pellitier, P. T., Chin, M. L., Henkel, T. W., Peay, K. G. 2023


    Bacteria, ectomycorrhizal (EcM) fungi, and land plants have been coevolving for nearly 200 million years, and their interactions presumably contribute to the function of terrestrial ecosystems. The direction, stability, and strength of bacteria-EcM fungi interactions across landscapes and across a single plant host, however, remains unclear. Moreover, the genetic mechanisms that govern them have not been addressed. To these ends, we collected soil samples from Bishop pine forests across a climate-latitude gradient spanning coastal California, fractionated the soil samples based on their proximity to EcM-colonized roots, characterized the microbial communities using amplicon sequencing, and generated linear regression models showing the impact that select bacterial taxa have on EcM fungal abundance. In addition, we paired greenhouse experiments with transcriptomic analyses to determine the directionality of these relationships and identify which genes EcM-synergist bacteria express during tripartite symbioses. Our data reveal that ectomycorrhizas (i.e., EcM-colonized roots) enrich conserved bacterial taxa across climatically heterogeneous regions. We also show that phylogenetically diverse EcM synergists are positively associated with plant and fungal growth and have unique gene expression profiles compared with EcM-antagonist bacteria. In sum, we identify common mechanisms that facilitate widespread and diverse multipartite symbioses, which inform our understanding of how plants develop in complex environments.

    View details for DOI 10.1016/j.cub.2023.06.010

    View details for PubMedID 37369208

  • Niche modelling predicts that soil fungi occupy a precarious climate in boreal forests GLOBAL ECOLOGY AND BIOGEOGRAPHY Qin, C., Pellitier, P. T., Van Nuland, M. E., Peay, K. G., Zhu, K. 2023

    View details for DOI 10.1111/geb.13684

    View details for Web of Science ID 000970471900001

  • Fungal community composition and genetic potential regulate fine root decay in northern temperate forests. Molecular ecology Argiroff, W. A., Zak, D. R., Upchurch, R. A., Pellitier, P. T., Belke, J. P. 2023


    Understanding how genetic differences among soil microorganisms regulate spatial patterns in litter decay remains a persistent challenge in ecology. Despite fine root litter accounting for ~50% of total litter production in forest ecosystems, far less is known about the microbial decay of fine roots relative to aboveground litter. Here, we evaluated whether fine root decay occurred more rapidly where fungal communities have a greater genetic potential for litter decay. Additionally, we tested if linkages between decay and fungal genes can be adequately captured by delineating saprotrophic and ectomycorrhizal fungal functional groups based on whether they have genes encoding certain ligninolytic class II peroxidase enzymes, which oxidize lignin and polyphenolic compounds. To address these ideas, we used a litterbag study paired with fungal DNA barcoding to characterize fine root decay rates and fungal community composition at the landscape scale in northern temperate forests, and we estimated the genetic potential of fungal communities for litter decay using publicly available genomes. Fine root decay occurred more rapidly where fungal communities had a greater genetic potential for decay, especially of cellulose and hemicellulose. Fine root decay was positively correlated with ligninolytic saprotrophic fungi and negatively correlated with ECM fungi with ligninolytic peroxidases, likely because these saprotrophic and ectomycorrhizal functional groups had the highest and lowest genetic potentials for plant cell wall degradation, respectively. These fungal variables overwhelmed direct environmental controls, suggesting fungal community composition and genetic variation are primary controls over fine root decay in temperate forests at regional scales.

    View details for DOI 10.1111/mec.16852

    View details for PubMedID 36650921

  • Embracing climate emotions to advance higher education Nature Climate Change Pellitier, P., Ng, M., Castaneda, S., Moser, S., Wray, B. 2023
  • Microbes modify soil nutrient availability and mediate plant responses to elevated CO2 PLANT AND SOIL Pellitier, P. T., Jackson, R. B. 2022
  • Ectomycorrhizal root tips harbor distinctive fungal associates along a soil nitrogen gradient FUNGAL ECOLOGY Pellitier, P. T., Zak, D. R. 2021; 54
  • Decay by ectomycorrhizal fungi couples soil organic matter to nitrogen availability ECOLOGY LETTERS Argiroff, W. A., Zak, D. R., Pellitier, P. T., Upchurch, R. A., Belke, J. P. 2022; 25 (2): 391-404


    Interactions between soil nitrogen (N) availability, fungal community composition, and soil organic matter (SOM) regulate soil carbon (C) dynamics in many forest ecosystems, but context dependency in these relationships has precluded general predictive theory. We found that ectomycorrhizal (ECM) fungi with peroxidases decreased with increasing inorganic N availability across a natural inorganic N gradient in northern temperate forests, whereas ligninolytic fungal saprotrophs exhibited no response. Lignin-derived SOM and soil C were negatively correlated with ECM fungi with peroxidases and were positively correlated with inorganic N availability, suggesting decay of lignin-derived SOM by these ECM fungi reduced soil C storage. The correlations we observed link SOM decay in temperate forests to tradeoffs in tree N nutrition and ECM composition, and we propose SOM varies along a single continuum across temperate and boreal ecosystems depending upon how tree allocation to functionally distinct ECM taxa and environmental stress covary with soil N availability.

    View details for DOI 10.1111/ele.13923

    View details for Web of Science ID 000719401800001

    View details for PubMedID 34787356

  • From DNA sequences to microbial ecology: Wrangling NEON soil microbe data with the neonMicrobe R package ECOSPHERE Qin, C., Bartelme, R., Chung, Y., Fairbanks, D., Lin, Y., Liptzin, D., Muscarella, C., Naithani, K., Peay, K., Pellitier, P., St Rose, A., Stanish, L., Werbin, Z., Zhu, K. 2021; 12 (11)

    View details for DOI 10.1002/ecs2.3842

    View details for Web of Science ID 000723142700042

  • Ectomycorrhizal access to organic nitrogen mediates CO2 fertilization response in a dominant temperate tree. Nature communications Pellitier, P. T., Ibanez, I., Zak, D. R., Argiroff, W. A., Acharya, K. 2021; 12 (1): 5403


    Plant-mycorrhizal interactions mediate plant nitrogen (N) limitation and can inform model projections of the duration and strength of the effect of increasing CO2 on plant growth. We present dendrochronological evidence of a positive, but context-dependent fertilization response of Quercus rubra L. to increasing ambient CO2 (iCO2) along a natural soil nutrient gradient in a mature temperate forest. We investigated this heterogeneous response by linking metagenomic measurements of ectomycorrhizal (ECM) fungal N-foraging traits and dendrochronological models of plant uptake of inorganic N and N bound in soil organic matter (N-SOM). N-SOM putatively enhanced tree growth under conditions of low inorganic N availability, soilconditions where ECM fungal communities possessed greater genomic potential to decay SOM and obtain N-SOM. These trees were fertilized by 38 years of iCO2. In contrast, trees occupying inorganic N rich soils hosted ECM fungal communities with reduced SOM decay capacity and exhibited neutral growth responses to iCO2. This study elucidates how the distribution of N-foraging traits among ECM fungal communities govern tree access to N-SOM and subsequent growth responses to iCO2.

    View details for DOI 10.1038/s41467-021-25652-x

    View details for PubMedID 34518539

  • Coupled Shifts in Ectomycorrhizal Communities and Plant Uptake of Organic Nitrogen Along a Soil Gradient: An Isotopic Perspective ECOSYSTEMS Pellitier, P. T., Zak, D. R., Argiroff, W. A., Upchurch, R. A. 2021
  • Variation in the Size-Structure of Dominant Branching Coral Taxa (Acroporidae: Acropora) and (Pocilloporidae: Pocillopora) in New Ireland Province, Papua New Guinea PACIFIC SCIENCE Pellitier, P. T. 2020; 74 (3): 283–96

    View details for DOI 10.2984/74.3.6

    View details for Web of Science ID 000618963900006