Associate Professor
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
Research.
Core question and its importance. The Denef Lab contributes to answering a core question in ecology: how do within- and between-species interactions shape microbial community diversity, composition, and functioning? It is important to focus on between-species interactions as they determine the makeup of communities, which in turn shapes ecosystem functioning, from agricultural crop biomass production to the magnitude of soil greenhouse gas emissions. It is important to consider within-species interactions, particularly between genetically dissimilar individuals of the same species, as recent insights, including from our own work, have shown important ecological consequences of within-species genetic diversity. The small genome sizes and short generation time compared to macroscopic life make microbial systems, particularly interesting model systems for ecological theory development regarding this aspect of within-species interactions.
Study system and its relevance. We use freshwater phytoplankton and bacterioplankton communities as a study system. Understanding how within- and between-species interactions influence phytoplankton composition is important as phytoplankton provide half of Earth’s net primary productivity and their community composition regulates productivity and nutrient cycling. In addition, when phytoplankton composition shifts to harmful bloom-forming species, it negatively affects water quality and mass transfer up the food web, both of which are critical to environmental and human health and economic well-being. Understanding the forces that shape bacterioplankton communities is important as their diversity and composition can exert strong controls on carbon cycling. This is important as freshwater systems are hotspots for carbon emissions to the atmosphere with net emissions of carbon dioxide rivaling the net uptake by the oceans.
Why UM EEB? For much of the history of ecology, microbial life too small to morphologically identify has been excluded. However, methodological advances, primarily based on sequencing technology, have opened our eyes to this unseen majority of life so that we can now broaden ecological theory to include the microbial world. Our work at the interface between microbiology and ecology benefits from being in a great EEB department while also being connected to the campus-wide cross-disciplinary program in microbial ecology. Interactions with microbial ecology groups across campus allow us to study fundamental concepts regarding the interrelation of evolution and ecology that enhance our understanding of microbial contributions to ecosystem functioning. New insights will contribute to tackling current societal challenges related to climate change, bio-energy, and the role of microbes in plant, animal, and human health.
Teaching.
BIO 207 - Microbiology. The lectures describe the basic biology of microbial life, with emphasis on bacteria (Domain Bacteria and Domain Archaea) and information on eukaryotic microbes (protists, fungi, and unicellular algae) of Domain Eukarya. The first section examines the historical origins of microbiology as a science with a reflection on who is engaged in our field and who is served by it historically and now. The second section examines bacterial and eukaryal cell structure and function, and bacterial nutrition and cultivation. The third section addresses the molecular biology of bacteria, including DNA replication, transcription and translation, regulation of gene expression, genomics, and bacterial viruses. The fourth section of the course covers microbial evolution, metabolic and ecological diversity, nutrient cycles, and symbiotic interactions. The final section of the course describes medically related topics, including host-pathogen interactions, epidemiology, immunology, and bacterial, viral, protozoan, and fungal pathogenesis.
EEB 446 - Microbial Ecology. 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.
BIO 144 - Decoding your DNA: Implications for you and society. Our DNA contains all the information we need to develop from a single cell into a hugely complicated human being. But how much of your “you-ness” is pre-determined by your DNA, the set of genes you received from your parents? How much do your experiences matter? Can we change our genes? And what are the implications if we do?
Research Areas(s)
- Freshwater microbial evolutionary ecology, host-microbiome interactions, community and population genomics
Graduate students
- Kathryn Schmidt, Nikesh Dahal, Jinny Yang
Technician
