Near-term Ecological Forecasting Initiative (NEFI): soil microbes


Humans have studied microorganisms since the 19th century (and probably earlier), yet we still struggle to articulate how microbes will fare in the future, when exposed to increasing pressure and environmental shifts from human activities, including climate change. This project asks the question, “Do we have enough information – and the right type of information – to forecast the future of ecological communities the same way we forecast the weather?” To do this, we have teamed with the Dietze Lab in BU’s Department of Earth & Enviroment to develop predictive models of soil microbial communities, based on high-throughput DNA sequence data collected from soils at the NEON sites.

Co-PIs: Michael Dietze (Boston University), Shannon La Deau (Cary Institute), Kathleen Weathers (Cary Institute)

Molecular mechanisms and biogeochemical consequences of decomposer interactions

Culture collection1

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

Fungi regulate critical ecosystem functions that control the major pools and fluxes of carbon (C) between the atmosphere and the biosphere. A widely observed pattern of fungal species interactions occurs during decay of dead organic matter (i.e. litter), where communities of decomposer fungi succeed one another over time and track changes in the abundance of litter chemicals. However, the mechanisms by which individual species consistently become dominant during decay, and how their interactions with other species influence the biogeochemistry of the system, are poorly understood. The objective of this project is to identify the molecular-level factors that regulate decomposer species interactions during decay using a combination of -omics, modeling, and community ecology approaches. To do this, we are placing the fungi in our culture collection into “cage matches”, monitoring the biochemical response of each species to different molecular stimuli produced by competitor fungi, and measuring the effects of combat on soil and litter biogeochemistry.

Co-PIs: Daniel Segre (Boston University), Daniel Cullen (University of Wisconsin, Madison)

Resistance and resilience of microbial guilds and biogeochemical functions to rapid climate change in the cold biome

Waxy cap mushroom in the White Mountains of New Hampshire

Waxy cap mushroom in the White Mountains of New Hampshire

We have joined the CCASE project at Hubbard Brook Experimental Forest to link ecosystem changes to the microbial communities that may drive them. We will be working in collaboration with Pamela Templer at BU (lead PI, NSF-funded project) and the Joint Genome Institute (JGI) to investigate interacting effects of climate warming and increased frequency of soil freeze/thaw on ecosystem functioning ( At its core, this project is examining the responses of both plant growth and soil biogeochemistry to these climate-induced changes through measurements of plant physiology, nitrogen cycling, microbial biomass, and extracellular enzyme activity in soil.  We are characterizing the microbial community drivers of these ecosystem responses through identification of total microbial community composition, active microbial communities, and genomic relationships between microbial stress tolerance and biogeochemical function in soil samples across seasons.

Co-PIs: Pamela Templer (BU), Peter Groffman (Cary Institute), Lindsey Rustad (USFS), John Campbell (USFS),

Collaborators: Maria Garcia (BU), Adrien Finzi (BU), Pat Sorenson (BU)

Integrated genomic/transcriptomic/secretomic study of interactions between pines and their symbiotic ectomycorrhizal fungi in the mushroom genus Suillus

Amanita sp at Great Brook State Farm, Carlisle, MA

Amanita sp in Great Brook State Farm

Ectomycorrhizal fungi (EMF) are emerging as a model system for understanding microbial community dynamics and the linkages between microbial communities and ecosystem function. Despite the importance of EMF and other soil fungi for global nutrient cycles, we still know little about the molecular basis of functional diversity among different EMF species. In this collaborative project, we are aiming to identify transcripts/metabolites/proteins associated with host-specificity, adaptation, and ecology of mycorrhizae in soils. Our lab’s specific role in the project is to collaborate with the Environmental Molecular Sciences Laboratory (EMSL) at the Pacific Northwest Laboratory to create digital images of the the extracellular biochemistry of these fungi directly in soil.

Co-PIs: Rytas Vilgalys (Duke University), Kabir G. Peay (Stanford University), Thomas Bruns (UC Berkeley), John Taylor (UC Berkeley), Sunny Liao (Duke University)

Collaborators: Joint Genome Institute (JGI), EMSL (Pacific Northwest Laboratory)

The role of microbial diversity in biogeochemical cycles

Fungal diversity often affects 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.

Lentinula edodes

Lentinula edodes decomposing Populus tremuloides litter in the lab

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 at UMN and Stanford University, we began leveraging genomic and transcriptomic characteristics of 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. This model is being validated with field data collected in a collaborative project on the Dimensions of Biodiversity of soil fungi.

Collaborator: Kabir G. Peay (Stanford University)

Functional geography of microorganisms (Postdoctoral research)

Mississippi site1

DOB sampling site in Mississippi

Microbial communities can exhibit geographic patterns of distribution and activity, but our knowledge of what drives these patterns for microbes lags behind our understanding of other organisms like plants and animals. To remedy this issue, we are 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, the project combines 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. As a postdoc on this project, Jenny has been responsible for the functional assays of soil fungi collected directly from the field.

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

Recent Posts

  1. Colin’s paper on ectomycorrhizal and soil C responses to N deposition is published! Leave a reply
  2. Sasha wins Biogeoscience Travel Award Leave a reply
  3. Sasha wins MSA Graduate Fellowship! Leave a reply