University of Michigan
Department of Ecology and Evolutionary Biology

In the spring of 2012, Professor Vincent Denef set sail with Great Lakes Environmental Research Laboratory (GLERL) scientists who initiated an intensive research effort in Lake Huron. They are partnering with the U.S. Geological Survey Great Lakes Science Center, the U.S. Environmental Protection Agency Great Lakes National Program Office, the Michigan Department of Natural Resources, the University of Michigan, and Environment Canada.

The field campaign, entitled “2012 Lake Huron Coordinated Science and Monitoring Initiative (CSMI),” is sponsored by EPA and the National Oceanic and Atmospheric Administrationin part through the Great Lakes Restoration Initiative. The research will help scientists understand the structure and function of the Lake Huron ecosystem - from bacteria to fish – and clarify the impacts of stressors such as invasive species, climate change, nutrient loading, and overfishing, according to a GLERL press release.

As part of this broad effort, Denef is participating in research cruises coordinated by the NOAA GLERL. His area of research involves the structure and function of the open water food web and more specifically, the investigation of the microbial and viral components of the microbial loop. He and his colleagues will collect samples in the spring, summer and fall 2012 along a transect that begins in Alpena, Mich. These cruises are part of a multiagency study to understand the structure and function of the Lake Huron food web. Researchers will obtain a highly genetically resolved view of the bacterioplankton and virus communities in a Laurentian Great Lake and interpret their dynamics in the context of geochemical and biological (phytoplankton, zooplankton, larval and adult fish) data.

“Very few such studies have been performed in any system, terrestrial or aquatic,” said Denef. “This is the first major project in Lake Huron that would incorporate a detailed sequencing-based analysis of the microbial food web, and will form a point of reference to identify the effects of climate change, land use change, and invasive species on the Laurentian Great Lakes.

“While the role of bacterio- and virioplankton communities as part of the marine and freshwater microbial loop is well appreciated, the resolution at which these communities are incorporated into food web models is very coarse. Efforts to increase this resolution by employing novel DNA sequencing-based technologies are being performed at rapidly increasing rates in marine environments yet lag significantly behind in freshwater environments. The bacterial, archaeal, and viral components of the microbial food web are important recyclers of nutrients and carbon, and feed into higher tropic levels primarily through heterotrophic nanoflagellate (the "hidden" flora of phytoplankton populations) grazing. They also have important interactions with dissolved organic carbon(DOC), the major regulator of UV penetration in lake water. Most ecosystem models have a component for detritus and nutrient recycling, but they are black box approaches that do not take into account the underlying spatial and seasonal variability in species composition and activity. The sampling across seasons, day and night, along the depth profile, and along a transect from the shore to the deep, open waters allows us to generate a more integrated view of the microbial food web structure. By including metatransciptomics (a branch of the study of the messenger RNA molecules, or transcripts, produced in a cell or a population of cells,that correlates the transcriptomesof a group of interacting organisms or species) and metaproteomics (the study of all protein samples recovered directly from environmental sources) we can make inferences regarding microbial activity levels, in particular regarding the role of different populations in the carbon cycle and how environmental constraints control these activities.”

Caption: Vincent Denef sampling water on a spring research cruise on Lake Huron. Credit: Joann Cavaletto, NOAA-GLERL