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Academic Appointments


Research & Scholarship

Current Research and Scholarly Interests


Our lab studies the ecological processes that structure natural communities and the links between community structure and the cycling of nutrients and energy through ecosystems. We focus primarily on fungi, as these organisms are incredibly diverse and are the primary agents of carbon and nutrient cycling in terrestrial ecosystems.

Much of our research focuses on plant-fungal root associations, better known as mycorrhizas, which constitute one of the most pervasive mutualisms in terrestrial ecosystems. We work on questions at three scales of this symbiosis, (1) how does environmental variation and functional variation in mycorrhizal fungi affect the symbiosis at the root tip scale, (2) how does dispersal contribute to the predictability of community assembly patterns at the landscape scale, and (3) how does biogeography affect mycorrhizal community structure and ecosystem function? By integrating these three levels of research we hope to build a 'roots-to-biomes' understanding of plant-microbe symbiosis.

Teaching

2013-14 Courses


Graduate and Fellowship Programs


  • Biology (School of Humanities and Sciences) (Phd Program)

Publications

Journal Articles


  • Ectomycorrhizal fungal traits reflect environmental conditions along a coastal California edaphic gradient. FEMS microbiology ecology Moeller, H. V., Peay, K. G., Fukami, T. 2014; 87 (3): 797-806

    Abstract

    Multispecies mutualisms, such as the association between trees and ectomycorrhizal fungi, are often shaped by environmental context. Here, we explored the functional mechanisms underlying this environmental filtering. Using a single population of Pinus muricata (Bishop pine) growing along a strong edaphic gradient, we examined how environmental stress affected ectomycorrhizal fungi. The gradient spans c. 400 000 years of soil age, and reduced nutrient availability and increased water stress dwarf trees on older sites. Fungal community composition shifted with nutrient and water availability and with the stature of the P. muricata host trees. Not only did pygmy trees host a taxonomically different fungal subset as compared to nonpygmy trees, but associated fungal communities also differed in life history strategies: trees in more stressful conditions hosted fungi with more carbon-intensive foraging strategies. Our results indicate a link between environmental controls of host nutritional status and turnover in the ectomycorrhizal fungal community. The transition to more energy-intensive strategies under nutrient stress may allow for close recycling of recalcitrant nutrient pools within the root zone and facilitate transport of nutrients and water over long distances. These results highlight the value of life history data to understanding the mechanistic underpinnings of species distributions.

    View details for DOI 10.1111/1574-6941.12265

    View details for PubMedID 24289145

  • Sequence depth, not PCR replication, improves ecological inference from next generation DNA sequencing. PloS one Smith, D. P., Peay, K. G. 2014; 9 (2)

    Abstract

    Recent advances in molecular approaches and DNA sequencing have greatly progressed the field of ecology and allowed for the study of complex communities in unprecedented detail. Next generation sequencing (NGS) can reveal powerful insights into the diversity, composition, and dynamics of cryptic organisms, but results may be sensitive to a number of technical factors, including molecular practices used to generate amplicons, sequencing technology, and data processing. Despite the popularity of some techniques over others, explicit tests of the relative benefits they convey in molecular ecology studies remain scarce. Here we tested the effects of PCR replication, sequencing depth, and sequencing platform on ecological inference drawn from environmental samples of soil fungi. We sequenced replicates of three soil samples taken from pine biomes in North America represented by pools of either one, two, four, eight, or sixteen PCR replicates with both 454 pyrosequencing and Illumina MiSeq. Increasing the number of pooled PCR replicates had no detectable effect on measures of α- and β-diversity. Pseudo-β-diversity - which we define as dissimilarity between re-sequenced replicates of the same sample - decreased markedly with increasing sampling depth. The total richness recovered with Illumina was significantly higher than with 454, but measures of α- and β-diversity between a larger set of fungal samples sequenced on both platforms were highly correlated. Our results suggest that molecular ecology studies will benefit more from investing in robust sequencing technologies than from replicating PCRs. This study also demonstrates the potential for continuous integration of older datasets with newer technology.

    View details for DOI 10.1371/journal.pone.0090234

    View details for PubMedID 24587293

  • Strong coupling of plant and fungal community structure across western Amazonian rainforests ISME JOURNAL Peay, K. G., Baraloto, C., Fine, P. V. 2013; 7 (9): 1852-1861

    Abstract

    The Amazon basin harbors a diverse ecological community that has a critical role in the maintenance of the biosphere. Although plant and animal communities have received much attention, basic information is lacking for fungal or prokaryotic communities. This is despite the fact that recent ecological studies have suggested a prominent role for interactions with soil fungi in structuring the diversity and abundance of tropical rainforest trees. In this study, we characterize soil fungal communities across three major tropical forest types in the western Amazon basin (terra firme, seasonally flooded and white sand) using 454 pyrosequencing. Using these data, we examine the relationship between fungal diversity and tree species richness, and between fungal community composition and tree species composition, soil environment and spatial proximity. We find that the fungal community in these ecosystems is diverse, with high degrees of spatial variability related to forest type. We also find strong correlations between α- and β-diversity of soil fungi and trees. Both fungal and plant community β-diversity were also correlated with differences in environmental conditions. The correlation between plant and fungal richness was stronger in fungal lineages known for biotrophic strategies (for example, pathogens, mycorrhizas) compared with a lineage known primarily for saprotrophy (yeasts), suggesting that this coupling is, at least in part, due to direct plant-fungal interactions. These data provide a much-needed look at an understudied dimension of the biota in an important ecosystem and supports the hypothesis that fungal communities are involved in the regulation of tropical tree diversity.

    View details for DOI 10.1038/ismej.2013.66

    View details for Web of Science ID 000323385600015

    View details for PubMedID 23598789

  • Host plant genus-level diversity is the best predictor of ectomycorrhizal fungal diversity in a Chinese subtropical forest MOLECULAR ECOLOGY Gao, C., Shi, N., Liu, Y., Peay, K. G., Zheng, Y., Ding, Q., Mi, X., Ma, K., Wubet, T., Buscot, F., Guo, L. 2013; 22 (12): 3403-3414

    View details for DOI 10.1111/mec.12297

    View details for Web of Science ID 000320396100018

  • Independent roles of ectomycorrhizal and saprotrophic communities in soil organic matter decomposition SOIL BIOLOGY & BIOCHEMISTRY Talbot, J. M., Bruns, T. D., Smith, D. P., Branco, S., Glassman, S. I., Erlandson, S., Vilgalys, R., Peay, K. G. 2013; 57: 282-291
  • Rat invasion of islands alters fungal community structure, but not wood decomposition rates OIKOS Peay, K. G., Dickie, I. A., Wardle, D. A., Bellingham, P. J., Fukami, T. 2013; 122 (2): 258-264
  • Towards global patterns in the diversity and community structure of ectomycorrhizal fungi MOLECULAR ECOLOGY Tedersoo, L., Bahram, M., Toots, M., Diedhiou, A. G., Henkel, T. W., Kjoller, R., Morris, M. H., Nara, K., Nouhra, E., Peay, K. G., Polme, S., Ryberg, M., Smith, M. E., Koljalg, U. 2012; 21 (17): 4160-4170

    Abstract

    Global species richness patterns of soil micro-organisms remain poorly understood compared to macro-organisms. We use a global analysis to disentangle the global determinants of diversity and community composition for ectomycorrhizal (EcM) fungi-microbial symbionts that play key roles in plant nutrition in most temperate and many tropical forest ecosystems. Host plant family has the strongest effect on the phylogenetic community composition of fungi, whereas temperature and precipitation mostly affect EcM fungal richness that peaks in the temperate and boreal forest biomes, contrasting with latitudinal patterns of macro-organisms. Tropical ecosystems experience rapid turnover of organic material and have weak soil stratification, suggesting that poor habitat conditions may contribute to the relatively low richness of EcM fungi, and perhaps other soil biota, in most tropical ecosystems. For EcM fungi, greater evolutionary age and larger total area of EcM host vegetation may also contribute to the higher diversity in temperate ecosystems. Our results provide useful biogeographic and ecological hypotheses for explaining the distribution of fungi that remain to be tested by involving next-generation sequencing techniques and relevant soil metadata.

    View details for DOI 10.1111/j.1365-294X.2012.05602.x

    View details for Web of Science ID 000308047100004

    View details for PubMedID 22568722

  • Measuring ectomycorrhizal fungal dispersal: macroecological patterns driven by microscopic propagules MOLECULAR ECOLOGY Peay, K. G., Schubert, M. G., Nguyen, N. H., Bruns, T. D. 2012; 21 (16): 4122-4136

    Abstract

    Dispersal plays a prominent role in most conceptual models of community assembly. However, direct measurement of dispersal across a whole community is difficult at ecologically relevant spatial scales. For cryptic organisms, such as fungi and bacteria, the scale and importance of dispersal limitation has become a major point of debate. We use an experimental island biogeographic approach to measure the effects of dispersal limitation on the ecological dynamics of an important group of plant symbionts, ectomycorrhizal fungi. We manipulated the isolation of uncolonized host seedlings across a natural landscape and used a range of molecular techniques to measure the dispersal rates of ectomycorrhizal propagules and host colonization. Some species were prolific dispersers, producing annual spore loads on the order of trillions of spores per km(2). However, fungal propagules reaching host seedlings decreased rapidly with increasing distance from potential spore sources, causing a concomitant reduction in ectomycorrhizal species richness, host colonization and host biomass. There were also strong differences in dispersal ability across species, which correlated well with the predictable composition of ectomycorrhizal communities associated with establishing pine forest. The use of molecular tools to measure whole community dispersal provides a direct confirmation for a key mechanism underlying island biogeography theory and has the potential to make microbial systems a model for understanding the role of dispersal in ecological theory.

    View details for DOI 10.1111/j.1365-294X.2012.05666.x

    View details for Web of Science ID 000306897500019

    View details for PubMedID 22703050

  • Flowers as Islands: Spatial Distribution of Nectar-Inhabiting Microfungi among Plants of Mimulus aurantiacus, a Hummingbird-Pollinated Shrub MICROBIAL ECOLOGY Belisle, M., Peay, K. G., Fukami, T. 2012; 63 (4): 711-718

    Abstract

    Microfungi that inhabit floral nectar offer unique opportunities for the study of microbial distribution and the role that dispersal limitation may play in generating distribution patterns. Flowers are well-replicated habitat islands, among which the microbes disperse via pollinators. This metapopulation system allows for investigation of microbial distribution at multiple spatial scales. We examined the distribution of the yeast, Metschnikowia reukaufii, and other fungal species found in the floral nectar of the sticky monkey flower, Mimulus aurantiacus, a hummingbird-pollinated shrub, at a California site. We found that the frequency of nectar-inhabiting microfungi on a given host plant was not significantly correlated with light availability, nectar volume, or the percent cover of M. aurantiacus around the plant, but was significantly correlated with the location of the host plant and loosely correlated with the density of flowers on the plant. These results suggest that dispersal limitation caused by spatially nonrandom foraging by pollinators may be a primary factor driving the observed distribution pattern.

    View details for DOI 10.1007/s00248-011-9975-8

    View details for Web of Science ID 000306127300001

    View details for PubMedID 22080257

  • Phylogenetic relatedness predicts priority effects in nectar yeast communities PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES Peay, K. G., Belisle, M., Fukami, T. 2012; 279 (1729): 749-758

    Abstract

    Priority effects, in which the outcome of species interactions depends on the order of their arrival, are a key component of many models of community assembly. Yet, much remains unknown about how priority effects vary in strength among species in a community and what factors explain this variation. We experimented with a model natural community in laboratory microcosms that allowed us to quantify the strength of priority effects for most of the yeast species found in the floral nectar of a hummingbird-pollinated shrub at a biological preserve in northern California. We found that priority effects were widespread, with late-arriving species experiencing strong negative effects from early-arriving species. However, the magnitude of priority effects varied across species pairs. This variation was phylogenetically non-random, with priority effects stronger between closer relatives. Analysis of carbon and amino acid consumption profiles indicated that competition between closer relatives was more intense owing to higher ecological similarity, consistent with Darwin's naturalization hypothesis. These results suggest that phylogenetic relatedness between potential colonists may explain the strength of priority effects and, as a consequence, the degree to which community assembly is historically contingent.

    View details for DOI 10.1098/rspb.2011.1230

    View details for Web of Science ID 000299114100017

    View details for PubMedID 21775330

  • Spongiforma squarepantsii, a new species of gasteroid bolete from Borneo MYCOLOGIA Desjardin, D. E., Peay, K. G., Bruns, T. D. 2011; 103 (5): 1119-1123

    Abstract

    A gasteroid bolete collected recently in Sarawak on the island of Borneo is described as the new species Spongiforma squarepantsii. A comprehensive description, illustrations, phylogenetic placement and a comparison with a closely allied species are provided.

    View details for DOI 10.3852/10-433

    View details for Web of Science ID 000294529400017

    View details for PubMedID 21558499

  • Rethinking ectomycorrhizal succession: are root density and hyphal exploration types drivers of spatial and temporal zonation? FUNGAL ECOLOGY Peay, K. G., Kennedy, P. G., Bruns, T. D. 2011; 4 (3): 233-240
  • Evidence of dispersal limitation in soil microorganisms: Isolation reduces species richness on mycorrhizal tree islands ECOLOGY Peay, K. G., Garbelotto, M., Bruns, T. D. 2010; 91 (12): 3631-3640

    Abstract

    Dispersal limitation plays an important role in a number of equilibrium and nonequilibrium theories about community ecology. In this study we use the framework of island biogeography to look for evidence of dispersal limitation in ectomycorrhizal fungal assemblages on "tree islands," patches of host trees located in a non-host vegetation matrix. Because of the potentially strong effects of island area on species richness and immigration, we chose to control island size by sampling tree islands consisting of a single host individual. Richness on tree islands was high, with estimates ranging up to 42 species of ectomycorrhizal fungi associating with a single host individual. Species richness decreased significantly with increasing isolation of tree islands, with our regression predicting a 50% decrease in species richness when tree islands are located distances of approximately 1 km from large patches of contiguous forests. Despite the fact that fungal fruit bodies produce large numbers of spores with high potential for long-distance travel, these results suggest that dispersal limitation is significant in ectomycorrhizal assemblages. There were no discernible effects of isolation or environment on the species identity of tree island fungal colonists. In contrast to the highly predictable patterns of tree island colonization we observed in a previous study on early successional forests, we suggest that over longer time periods the community assembly process becomes more dominated by stochastic immigration and local extinction events.

    View details for Web of Science ID 000285635100024

    View details for PubMedID 21302834

  • Testing the ecological stability of ectomycorrhizal symbiosis: effects of heat, ash and mycorrhizal colonization on Pinus muricata seedling performance PLANT AND SOIL Peay, K. G., Bruns, T. D., Garbelotto, M. 2010; 330 (1-2): 291-302
  • Potential link between plant and fungal distributions in a dipterocarp rainforest: community and phylogenetic structure of tropical ectomycorrhizal fungi across a plant and soil ecotone NEW PHYTOLOGIST Peay, K. G., Kennedy, P. G., Davies, S. J., Tan, S., Bruns, T. D. 2010; 185 (2): 529-542

    Abstract

    *Relatively little is known about diversity or structure of tropical ectomycorrhizal communities or their roles in tropical ecosystem dynamics. In this study, we present one of the largest molecular studies to date of an ectomycorrhizal community in lowland dipterocarp rainforest. *We sampled roots from two 0.4 ha sites located across an ecotone within a 52 ha forest dynamics plot. Our plots contained > 500 tree species and > 40 species of ectomycorrhizal host plants. Fungi were identified by sequencing ribosomal RNA genes. *The community was dominated by the Russulales (30 species), Boletales (17), Agaricales (18), Thelephorales (13) and Cantharellales (12). Total species richness appeared comparable to molecular studies of temperate forests. Community structure changed across the ecotone, although it was not possible to separate the role of environmental factors vs host plant preferences. Phylogenetic analyses were consistent with a model of community assembly where habitat associations are influenced by evolutionary conservatism of functional traits within ectomycorrhizal lineages. *Because changes in the ectomycorrhizal fungal community parallel those of the tree community at this site, this study demonstrates the potential link between the distribution of tropical tree diversity and the distribution of tropical ectomycorrhizal diversity in relation to local-scale edaphic variation.

    View details for DOI 10.1111/j.1469-8137.2009.03075.x

    View details for Web of Science ID 000272893800017

    View details for PubMedID 19878464

  • Root tip competition among ectomycorrhizal fungi: Are priority effects a rule or an exception? ECOLOGY Kennedy, P. G., Peay, K. G., Bruns, T. D. 2009; 90 (8): 2098-2107

    Abstract

    Competition for root colonization among ectomycorrhizal fungi is well documented, but the mechanisms determining competitive outcomes are not clearly understood. In a previous study, we observed that timing of colonization (i.e., a priority effect) had a significant effect on the outcome of competition between two ectomycorrhizal (EM) fungi in the genus Rhizopogon. In this study, we explicitly tested the role of priority effects in competition among EM fungi by experimentally manipulating the timing of colonization of four Rhizopogon species on Pinus muricata seedlings. In a first experiment, we set up 12 two-species combinations, in which seedlings were first inoculated from spores with one species, grown for three months, and then inoculated with an equal density of spores of a second species and grown for an additional three months. Root tip occupation in the two-species treatments was determined by polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) analysis of internal transcribed spacer region (ITS) of rDNA. In a second experiment, we further examined competitive interactions between two Rhizopogon species using split-root P. muricata seedlings. One side of the root system was pre-colonized by one species, and spores of the second species were added to the other side of the root system in all same and different species pair-wise combinations. We found that for three of the four species (R. occidentalis, R. salebrosus, R. vulgaris), the outcome of competition in the first experiment depended strongly on the timing of colonization, with the first colonizing species always being the competitive dominant. For R. evadens, however, initial colonization did not prevent significant subsequent colonization by R. occidentalis and R. vulgaris. This appeared to be caused by the lower colonization of R. evadens compared to the three other species. In the second experiment, we observed that the portion of the split root system that was initially uncolonized remained receptive to colonization when spores were added. The amount of colonization of R. occidentalis and R. salebrosus on the side of the root system to which they were added was not significantly influenced by species identity on the other side of the seedling. In combination, these results confirm that priority effects do play a major role in dynamics of EM root tip colonization, at least in the early colonization of seedlings, and that the proportion of the root system occupied by a species appears to be a key factor determining competitive success.

    View details for Web of Science ID 000268293000009

    View details for PubMedID 19739372

  • Spore heat resistance plays an important role in disturbance-mediated assemblage shift of ectomycorrhizal fungi colonizing Pinus muricata seedlings JOURNAL OF ECOLOGY Peay, K. G., Garbelotto, M., Bruns, T. D. 2009; 97 (3): 537-547
  • Fungal Community Ecology: A Hybrid Beast with a Molecular Master BIOSCIENCE Peay, K. G., Kennedy, P. G., Bruns, T. D. 2008; 58 (9): 799-810

    View details for DOI 10.1641/B580907

    View details for Web of Science ID 000259886500006

  • A strong species-area relationship for eukaryotic soil microbes: island size matters for ectomycorrhizal fungi ECOLOGY LETTERS Peay, K. G., Bruns, T. D., Kennedy, P. G., Bergemann, S. E., Garbelotto, M. 2007; 10 (6): 470-480

    Abstract

    While the effects of habitat size and isolation have been successfully studied for macro-organisms, there is currently debate about their relative importance in explaining patterns of microbial species richness. In this study, we examine the species richness of a dominant group of eukaryotic soil microbes, ectomycorrhizal fungi, on 'tree islands' of constant age and host composition that range in size from < 10 to > 10,000 m(2). Our results show that ectomycorrhizal species richness is significantly reduced on smaller and more isolated tree islands, and the species-area slope that we observe (0.20-0.23) is similar to average slopes reported for macro-organisms. Additionally, species' occurrence patterns across tree islands and investment trends in fungal fruit bodies suggest that a trade-off between competition and dispersal could play an important role in structuring ectomycorrhizal assemblages.

    View details for DOI 10.1111/j.1461-0248.2007.01035.x

    View details for Web of Science ID 000246364500004

    View details for PubMedID 17498146

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