Vincent Denef

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Vincent Denef

Assistant Professor

Office Location(s): 1141/1027 Kraus Natural Science Building
Phone: 734.764.6481
Lab Phone: 734.936.5777
Fax: 734.763.0544
Denef Lab
View Curriculum Vitae

  • About

    Academic background
    Postdoc, Earth and Planetary Science, University of California, Berkeley, 2005-2011
    Visiting Scholar, Center for Microbial Ecology, Michigan State University, 2000-2005
    Ph.D., Applied Biological Sciences, Universiteit Gent, Belgium, 2005
    M.Sc., Bio-engineering, KU Leuven, Belgium, 2001
    B.S., Bio-engineering, KU Leuven, Belgium, 1999

    Is global change tuning the invisible engine of the freshwater world?

    “A lake is the landscape's most beautiful and expressive feature. It is the earth's eye.” With these words, Henry David Thoreau expressed his admiration for the aesthetic value of lakes. He was unaware that below their surface, billions of microorganisms act as invisible ‘engines’ to drive crucial cycles of Earth’s essential elements, particularly carbon. As opposed to the oceans, most freshwater systems are net emitters of CO2, in large part due to bacterial respiration of terrestrial organic carbon. Globally, they are estimated to emit a net amount of CO2 to the atmosphere (1.5 Pg) that is similar to the net uptake by the oceans (2.6 Pg).

    Because they are smaller than marine systems, freshwater ecosystem functioning is more vulnerable to the impacts of global change (land use change, invasive species, and climate change). Yet, freshwater carbon cycling is rarely incorporated into global carbon budgets. This exclusion means that we lack proper models to evaluate the responses of freshwater carbon cycling to global change. Existing ecosystem modeling approaches in any system generally make abstraction of the specific composition and activity of microbial communities. In order to explore how specific microbial community metrics (species diversity, genetic diversity underlying specific functions, ...) may improve modeling of freshwater carbon cycling responses to anthropogenic change, we need to first improve our grasp of the relationship between carbon metabolism and the dynamics and functioning of bacteria, archaea, and their viruses—the main drivers of carbon and nutrient cycling.

    Core questions

    Throughout all our projects, we are driven by questions at the interface of evolution and ecology:

    (i) How does human disturbance of the local and global environment drive microbial ecological dynamics (changes in community structure and behavior (through gene expression)?
    (ii) How do these population and community level responses affect ecosystem functioning, particularly the balance between carbon storage and respiration?
    (iii) What is the role of fine-scale evolutionary processes in microbial adaptation to change, and how does it impact ecosystem functioning?

    Study systems and projects
    These questions are universally relevant, and therefore can be addressed in many suitable systems. We address them in the context of the microbial contributions to the carbon cycle in north temperate freshwater lakes, including the Laurentian Great Lakes. See our website for more details.

    Building on my experience with more traditional microbial physiology and genetics methods, I am currently using metagenomic and metaproteomic approaches to gather systems-level understanding of microbial community functioning. Although these techniques have been most successfully applied in systems with low species richness such as the acid mine drainage communities I studied during my post-doctoral work, recent advances in sequencing technology, cell sorting, and mass spectrometry are enabling us to assess the genomic make-up of microbial populations and expression of their genetic potential in ever more complex systems.

    Why UM EEB
    Joining EEB as part of the cross-disciplinary program in microbial ecology allows me to study fundamental concepts regarding the interrelation of evolution and ecology that enhance our understanding of the microbial contributions to ecosystem functioning. New insights from research performed by the members of this research cluster will hopefully contribute to tackling current societal challenges related to climate change, sustainability, bio-energy, and the role of microbes in plant, animal, and human health.


    Microbial Ecology - EEB 446
    A greater focus on the microbial component of the biosphere is warranted, since "microbes run the world." If we are to build comprehensive and predictive models for ecosystems important to environmental and human health, we need a better understanding of how microbial communities assemble and operate. This course will cover the ecology of microbes by highlighting their interactions with each other and the environment, and will present the latest insights into their role in ecosystems ranging from thawing permafrost to the human gastrointestinal tract. Ecological and evolutionary concepts and tools used in microbial research, including novel "omics" techniques, will be introduced. The course also aims at uncovering how concepts developed in plant and animal ecology do and do not translate to the microbial world.

    Life: decoded. Genomics in Society - BIO 144
    Our genome is the blueprint to our existence: it encodes all the information we need to develop from a single cell into a hugely complicated functional organism. But it is more than a static information store: our genome is a dynamic, tightly regulated collection of genes, which switch on and off in many combinations to give the variety of cells from which our bodies are formed. But how is the genome constructed and how do we identify the genes that make up our genome? How do we determine their function? How do organisms differ or match and what does genomics teach us about the evolutionary relationships between different organisms? What does our understanding of genomics mean in terms of our future health and wellbeing?

    “Life: decoded. Genomics in society” aims for students, who will not necessarily focus on a career in science, to acquire an understanding of how the genomics revolution has transformed many facets of our society. From the more obvious impacts on the way we conduct scientific research, to its impacts on the medical practice, which is moving towards human genome-based personalized medicine; from its impacts on agriculture (domestication, genetically modified organisms) to ethical considerations regarding genetic discrimination; and from genomic insights into the microbial inhabitants of our body to genomic insights into the microbes that sustain our planet’s environmental health.

  • Research Areas of Interest
    • Freshwater microbial evolutionary ecology, community and population genomics
  • Graduate students
    • Marian Schmidt
  • Postdoctoral Fellow
    • Masanori (Masa) Fujimoto