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We use genomic and molecular tools to examine microbial diversity in soils. We seek to understand the ecological and evolutionary mechanisms that regulate microbial diversity and its impacts on soil processes.

Why study soil microorganisms?

Microorganisms are the Earth’s firstborn. They were teeming on the land and in the seas for billions of years before the evolution of plants and animals, and their diversity is staggering. Every pinch of soil contains billions of microbes whose activities regulate terrestrial nutrient cycles and influence the evolution of our biosphere. Despite their importance many aspects of soil microbial communities are still a mystery and soil remains a fertile habitat for discovery. In the broadest terms our research program focuses on soil microbial diversity: its extent, its regulation, and its impact on biogeochemical cycles in soils.

Our research has two main foci:
i) exploring the ecological and evolutionary factors that govern microbial diversity in soils
ii) exploring the impact of microbial diversity on soil processes.

List of Publications

Research Topics

Evolutionary Ecology of Streptomyces
We are using population genomics to explore microbial evolution and ecology in soil systems. Streptomycetes are common soil organisms and the source of many clinically useful antibiotics. We are using Streptomyces as a model system to explore the ecological and evolutionary mechanisms that drive microbial diversification and microbial biogeography in soil systems.

Soil and Plant Microbiomes
We are investigating the mechanisms controlling the structure and function of soil microbiomes to characterize their impact on both natural and managed ecosystems. We use multiple approaches to explore relationships between microbial diversity and soil processes associated with cycles of carbon and nitrogen. A current project explores the microbial microbial basis of soil health to describe the microbial mechanisms that underlie soil health and to determine how this knowledge can be used in agricultural management. We are also exploring plant microbiomes to determine how plants alter microbial community composition in the rhizosphere and how these microbes in turn impact plant growth.

Microbial Food Web Mapping
We have developed an approach, high throughput sequencing enabled stable isotope probing (HTS-SIP), that makes it possible to trackĀ  carbon metabolism within microbial communities. HTS-SIP allows us to track the movement of 13C-labeled substrates over time into thousands of microbes as they occur in soils. We are using HTS-SIP to explore the ecological basis of carbon metabolism within soils and to describe the ecological and genomic characteristics of uncultivated microorganisms.

Free-living Diazotrophs in Soils
Free-living nitrogen fixing bacteria provide an important source of nitrogen in many ecosystems and in the roots of certain plants. We have explored the characteristics of these diazotrophic bacteria in a range of systems. Through this work we developed a nitrogenase nifH sequence database for use in microbial ecology.



We would like to express our gratitude to the following sponsors for their past and continuing support:

  • The National Science Foundation

-Phylogenetic Systematics Program
-Faculty Early Career Development Program (NSF CAREER)
-Microbial Observatories Program

  • The Department of Energy

-Genomic Science Program

  • The USDA National Institute of Food and Agriculture

Bioenergy, Natural Resources, and Environment Program
Cornell Center for Comparative and Population Genomics
Cornell University Agricultural Experiment Station



School of Integrative Plant Science
Cornell University
Ithaca, NY 14853
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