Research Program

Human activities are altering global carbon (C) and nitrogen (N) cycles at an unprecedented rate.  It is unclear how significant changes in global elemental cycles will affect ecosystem functions, such as primary productivity or C storage over the long-term.  My research aims to understand how plant-microbe interactions mediate ecosystem-specific responses to global climate change.  This research connects microbial processes to ecosystem functions to yield new insights into microbial ecology and elemental cycling.  Research in my laboratory focuses on three main questions:

  1. What are the mechanisms structuring soil microbial communities?
  2. How do functional groups of microorganisms respond to changing environmental conditions (e.g. elevated atmospheric N deposition, warming, altered precipitation, restoration)?
  3. How does variation in specific microbial communities relate to decomposition and N cycling?


This research aims to reveal the microbial mechanisms that regulate carbon (C) stabilization in soils dedicated to biofuel crops, and test identified mechanisms in ecosystem-scale field experiments. Emerging evidence suggests that dead microbial biomass, or necromass, constitutes a significant fraction of soil organic matter. Although microbial necromass stabilization is frequently invoked as a mechanisms for long-term soil C storage, there remains limited empirical data illustrating the complement of molecules that comprise microbially derived soil organic C. I aim to evaluate the effect of bioenergy crops on the production of microbial necromass and the selective preservation of microbial necromass in two distinct bioenergy soils. I will quantify the microbial contribution to soil organic C accumulation under perennial (switchgrass) and annual (corn) biofuels in long-term experimental plots of the Great Lakes Bioenergy Research Center. Using a combination of model informed lab and field experiments, I will apply molecular approaches to identify dominant microbial metabolic pathways and quantify the extent to which their stable end products influence C cycling in bioenergy feedstock agroecosystems.

co-PIs Sarah Hobbie and Melanie Mayes

The overarching goal of this research is to use a continental-scale network of replicated, long-term grassland nutrient addition experiments, the Nutrient Network, to enhance the Microbial ENzyme Decomposition (MEND) model towards determining how N inputs affect: (1) biochemical stabilization of soil organic matter (SOM) by altering the quantity and quality of plant inputs to soils, and soil microbial community structure, stoichiometry, and functional potential; and (2) physicochemical stabilization of SOM by altering soil aggregate formation and SOM-mineral interactions. At ten Central Great Plains Nutrient Network experiments that span soil texture and water balance gradients, the project will examine N enrichment effects on SOM dynamics, and the mechanisms underpinning such effects, by measuring the stoichiometry and quantities of plant inputs; the stoichiometry, composition, and activity of soil microbes; and the formation of micro- and macroaggregates. Empirical work on C-N interactions will be integrated into a modeling framework, via parameterization, model development, and model evaluation of the MEND model. MEND will be used to explore the combined effects of N enrichment on SOM dynamics via altered litter inputs and stoichiometry, microbial communities, microbial biomass, and hydrolytic vs. oxidative enzyme activity, to determine whether the proposed model structure captures the variation in soil C responses to N additions observed across the Central Great Plains.

Co-PI: Adina Howe, Folker Meyer, Galya Orr

Understanding and accurately predicting the microbial cycling of carbon in soil environments has been challenged by our ability to associate microbial community dynamics into ecosystem-scale biogeochemical models. Soil fractionation techniques provide an opportunity to examine intact microbial communities in a context that is relevant to both microbial community metabolism and ecosystem processes. We propose to develop approaches that target metabolically active microorganisms and functions that drive carbon cycling in soils from bioenergy cropping systems. With the combined expertise and support of the Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory Cell Isolation and Systems Analysis group and the Argonne National Laboratory Computational Biology Cluster, we aim to employ transcriptomics, genome sequencing, carbon metabolite labeling, cell sorting, and cell isolation methods to access the key organisms involved in soil carbon cycling (e.g. cellulose decomposition) in soil aggregate fractions.

Can Microbial Ecology and Mycorrhizal Functioning Inform Climate Change Models?

Co-PI Erik Hobbie, University of New Hampshire

This research aims to validate predictive C cycling models with field experiments that test the relative contribution of fungal and bacterial functional guilds to the decomposition of organic N. Using archived samples from forest Free Air CO2 Enrichment (FACE) experiments, field measurements from the Marcell Experimental Forest (MEF) and the Spruce and Peatland Response Under Climatic and Environmental Change (SPRUCE) experiment, and the Mycorrhizal Status, Carbon and Nutrient cycling (MySCaN) model, we will identify how the microbial regulation of organic nitrogen (N) availability influences forest responses to climate change.

A major focus of my research is to understand not only how the relationship between plant and microbial communities vary among ecosystems, but also to understand how these relationships are altered by global change. Specifically, my research has focused on how increased elevated atmospheric O3 and CO2 affect plant-microbe interactions. The significance of global change for biogeochemical cycling is well recognized at broad scales, but the microbial mechanisms that regulate ecosystem responses to global change are not well understood. Integrating microorganisms into our understanding of ecosystem ecology is a critical next step for accurately predicting ecosystem responses to global change and appropriately managing terrestrial ecosystems. Climate change affects the composition and function of microbial communities indirectly through alterations in plant community composition or the physical environment. It is also possible that climate change can have a direct effect on the physiology of some microorganisms. Changes in the composition and function of soil microbial communities, in turn, affect the biogeochemical cycling of elements, resulting in positive and negative feedbacks to aboveground communities as well as C storage and trace gas fluxes. Ongoing research at the Duke and Rhinelander Free Air CO2 enrichment sites investigates how soil C and N cycling is altered by global change. This research examines how microbial metabolism and soil C sequestration is affected by elevated atmospheric CO2. A second branch of this research aims to understand how chitin-degrading microorganisms are affected by elevated atmospheric CO2 and O3 and the implications this has for N cycling.

A critical gap in making progress toward ecologically beneficial farming practices is an explicit understanding of how soils store carbon (C) and nitrogen (N) over the long term. Farmers are facing new challenges that require management practices for improving soil quality, increasing both belowground (live roots) and aboveground (live cover) biomass, increasing soil organic matter, and reducing greenhouse gas emissions. To identify optimal man¬agement strategies, an understanding of microbial processes that regulate C and N cycling is essential. It is known that microbial activity is strongly influenced by both soil moisture and vegetation, and that microbial metabolism regulates the production of greenhouse gases, such as CO2, as well as the transfor¬mation of plant material into soil organic matter. Therefore, landscape position and cropping system are important factors determining the availability of water, N and C, which are the substrates for microbial metabolism.

This research aims to develop a new under¬standing of which cropping systems favor soil organic matter formation and reduce greenhouse gas emissions by developing a mechanistic understanding of the soil microbial processes that regulate soil C and N cycling. This research is being conducted at the Uthe Farm in collaboration with Lisa Schulte Moore, Tom Isenhart, Emily Heaton, Rick Hall, Arne Hallam, Matt Helmers, Ken Moore and Randy Kolka.

Across broad spatial scales we know that the structure and function of plant and soil microbial communities influence each other. This is because the availability of growth-limiting resources shapes the composition of biotic communities. Resource availability for soil microorganisms is constrained by organic compounds in dead leaves and roots that can be used to generate cellular energy. The pool of available substrates (plant inputs) influences which microorganisms are most competitive in the soil environment and that is reflected in the soil microbial community structure, which is the assembly of organisms present in a microbial community, and the microbial community function, which is the capacity to produce enzymes that catalyze biogeochemical reactions. Microbial community structure and function feeds back to impact the availability and cycling of growth limiting nutrients, and ultimately the success of plant communities. Although this conceptual model of plant-microbe interactions is well accepted, the strength and directionality of such interactions is not well understood. To investigate such interactions, I have established six experimental plots at the Chichaqua Wildlife Area in collaboration with Stan Harpole. At these sites we will manipulate nutrient additions to alter plant productivity and resource allocation, thereby creating conditions that will likely alter the structure and function of the plant and soil microbial communities. These prairie sites are part of the Nutrient Network (NutNet), a larger network of sites designed to address questions about the general impacts of nutrient additions on ecological systems.

Denitrification is a crucial aspect of the N cycle, transforming terrestrial N into atmospheric N.  While this can reduce eutrophication of aquatic systems, it can also product N2O, a potent greenhouse gas.  At present there is a critical need to understand the underlying microbiology that drives denitrification so land managers can maximize the benefits of denitrification and minimize greenhouse gas emissions. Our research consists of both field measurements and laboratory manipulations aimed at linking microbiology to ecosystem denitrification rates. We aim to identify the microbial mechanisms controlling denitrification by examining native prairie potholes and adjacent agricultural plots. 
Prairie potholes are depressions connected by shallow drainage ways.  In Iowa, prairie potholes were created apporximately 12,000 years ago whten the Des Moines Lobe of the Wisconsinan Glacial Event retreated.  Today few prairie potholes remain, as most of the landscape has been transformed into agricultural land.  Prairie potholes provide an important native landscape to study biogeochemical processes.  In this research we compare the denitrification potential in various pothole landscape positions at Kalsow prairie and from adjacent agricultural fields.  Compared to the prairie sites, cropped soils have lower total N and C contents, lower water contents and increased pools of inorganic N.  In addition this landscape provides a natural pH gradient to investigate the influence of environmental factors on the microbial mechanisms driving denitrification.

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