Stanford University 

Resupinate fungi
                              collected during first NSF Dimensions of
                              Biodiversity sampling trip at Duke
                              Experimental Forest







Long leaf pine
                            forest in the southeastern U.S. as part of
                            the NSF DOB project

Long leaf pine forest in Texas where soils were sampled for the NSF Dimensions of Biodiversity project (photo credit: Rytas Vilgalys)

Sporocarp diversity at DOB field site
                              in Alberta, Canada

Sporocarp diversity at DOB field site in Alberta, Canada (photo credit: Kabir Peay)

Soil core illustrating the changes
                              in soil quality with increasing depth. The
                              fruiting body from a Leccinum species is
                              connected to microscopic filaments
                              (hyphae) which make up the active fungal
                              body and spread throughout the soil.
                              (Kabir Peay)

Soil core with
Leccinum fruiting body connected to microscopic filaments (hyphae) which make up the active fungal body and spread throughout the soil. (photo credit: Kabir Peay)

Our culture collection, including
                              fully-functional species of
                              ectomycorrhizal, brown rot, white rot, and
                              pathogenic fungi with sequenced genomes

Our culture collection, including fully-functional species of ectomycorrhizal, brown rot, white rot, and pathogenic fungi with sequenced genomes

Arabidopsis thaliana
Left to right: Columbia wild type, low lignin mutant, low cellulose mutant


Partial HSQC of lignocellulose in wild type, high guaiacyl, and high aldehyde Arabidopsis, intact and decomposed

Microbial communities can exhibit spatial and geographic patterns of distribution, but our knowledge of what drives these patterns for microbes lags behind our understanding of other organisms like plants and animals. One distribution pattern that has emerged repeatedly in soil communities is that saprotrophic fungi dominate the upper layers of soil, while mycorrhizal fungi dominate lower layers. In my postdoctoral
research, I am testing the hypothesis that niche partitioning of soil resources among these fungal groups is an important mechanism driving this pattern. For this test, I am exploring relationships between resource availability, fungal community structure, and enzyme activity along the soil profile in Pinus-dominated ecosystems across North America. This NSF Dimensions of Biodiversity project is a multi-institution collaboration between fungal biologists at Stanford University,University of California, Berkeley, and Duke University. Using a spatially-explicit sampling design, we are combining next-generation sequencing, population genomics, transcriptomics, and functional enzyme assays to characterize different biochemical aspects of soil fungal communities in forest ecosystems across North America.

See photos and a map of our field collection sites on Rytas Vilgalys' lab website!

Related papers

Liao, H-L, Y Chen, TD Bruns, KG Peay, JW Taylor, S Branco, JM Talbot, and R Vilgalys. In review. Metatranscriptomic analysis of ectomycorrhizal roots reveals genes associated with Piloderma-Pinus symbiosis. Environmental Microbiology.

Talbot JM, TD Bruns, JW Taylor, DP Smith, S Branco, SI Glassman, S Erlandson, R Vilgalys, H-L Liao, ME Smith, and KG Peay. 2014. Endemism and functional convergence across the North American soil mycobiome. Proceedings of the National Academy of Sciences doi:10.1073/pnas.1402584111.

Talbot JM, S Erlandson, D Smith, S Glassman, R Vilgalys, T Bruns, J Taylor, M Smith, KG Peay. In press. Independent roles of ectomycorrhizal and saprotrophic fungi in soil organic matter decay. Soil Biology and Biochemistry. 57: 282-291. (PDF)

Fungi regulate critical ecosystem functions that control the major pools and fluxes of carbon (C) between the atmosphere and the biosphere. Conventional models of atmosphere-biosphere C cycling lump all microbial decomposition processes into a single “black box”, through which easily degradable litter C is converted into either atmospheric CO2 or recalcitrant soil C via single trajectories that are defined by a single decay rate coefficient. However, fungal diversity can affect the rates of decomposition and CO2 release, because fungal species often differ in characteristics like substrate preferences and extracellular enzyme production. Nevertheless, we still do not understand the mechanisms by which different fungi transform the chemical and physical properties of soil particles, or how this affects the subsequent stabilization or loss of the remaining soil C. This issue is important to address, because soils contain 3.3 times the amount of C found in the atmosphere . Therefore, shifts in the activity or diversity of fungi that cause even small changes in soil C stabilization could have large consequences for atmospheric CO2 concentrations and the stability of the global climate system.

Identifying how individual fungal species transform the chemical and physical structure of soil organic matter via complex belowground biochemical pathways is one of the greatest challenges in ecology research. As a NOAA Climate and Global Change Postdoctoral Fellow with Dr. Kabir Peay at Stanford University, I am overcoming this challenge by leveraging genomic and transcriptomic characteristics of these model fungi with the detailed analysis of their extracellular biochemistry to create a statistical model of how genetic diversity is linked to functional diversity in soil microbial communities. The model is being validated with field data collected in the collaborative NSF Dimensions of Biodiversity project described above.

Related papers

Talbot JM
, KG Peay. In review. Functional guild predicts the role of fungi in fast and slow soil biogeochemical cycles. Fungal Ecology.

Talbot JM
, KK Treseder. 2011. Dishing the dirt on carbon cycling. Nature Climate Change 1:
144-146 (PDF).

Talbot JM, KK Treseder. 2010. Controls over mycorrhizal uptake of organic N. Pedobiologia 53: 169-179. (PDF)

Talbot JM, SD Allison, KK Treseder. 2008. Decomposers in disguise: Mycorrhizal fungi as regulators of soil carbon dynamics in ecosystems under global change. Functional Ecology 22: 955-963. (PDF)


Decomposition is a critical step in the cycling of carbon and nutrients within ecosystems.  One of the most common observations in ecosystem ecology is that litter with low initial ratios of lignin:N or lignin:cellulose decomposes more quickly than does litter with higher ratios.  Understanding the relationships between carbon chemistry, N availability, and the activity of decomposer microbes may improve our predictive models of how decomposition will be altered by global changes such as anthropogenic N, species invasions, and elevated CO2.  However, it is challenging to isolate the impact of lignin, cellulose or N on decomposition rates.  In naturally-produced litter, these traits tend to co-vary with one another and with other aspects of litter chemistry.  As a result, we currently lack a detailed understanding of the chemical and microbial mechanisms by which these factors limit decomposition rates. 

I address this challenge by using the model plant system, Arabidopsis thaliana.
Arabidopsis has been used as a model in plant genetics and biochemistry, and now we have borrowed it to serve as a model to study ecosystem processes. To understand litter chemistry controls over decomposition, I use Arabidopsis mutants that have been manipulated to vary in concentrations of lignin, cellulose, and N, and in specific aspects of lignin chemical composition. In my research, I use Arabidopsis mutants in field-based and laboratory-based decomposition studies to test long-standing hypotheses of how lignin, cellulose, N, and the decomposer community interact to control rates of litter decomposition.

Related papers

Talbot JM, KK Treseder. 2012. Interactions between lignin, cellulose, and N drive litter chemistry-decay relationships. Ecology. 93: 345-354 (Featured on journal cover). (PDF)

Talbot JM, DJ Yelle, JS Nowick, KK Treseder. 2012. Litter decay rates are determined by lignin chemistry. Biogeochemistry 108: 279-295.

Todd-Brown KEO, FM Hopkins, SN Kivlin, JM Talbot, SD Allison. 2012. A framework for representing microbial decomposition in coupled climate models. Biogeochemistry 109: 19-33 (Invited). (PDF)

For a full list of publications and presentations, click