Research projects

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. Currently we focus on three interconnected projects:

1. Invasive species (in collaboration with Dr. Ace Sarnelle at Michigan State University)
Project focus: Zebra mussels are native to the Ponto-Caspian basin. Human activity has dispersed them to freshwater systems around the world. Their invasion has been linked to significant shifts in composition and functioning of phytoplankton (including Cyanobacteria) and zooplankton communities. Little is known regarding impacts on heterotrophic bacterioplankton. If bacterial production and abundance in the water column are maintained, as previous studies have suggested, a shift towards populations that process carbon of terrestrial origin is likely. The central hypothesis of this project is that zebra mussel invasion affects both heterotrophic bacterioplankton community composition and bacterial respiration of terrestrial carbon, leading to an increased flux from terrestrial organic carbon to atmospheric CO2.

Study system: We focus on inland lakes in Southern Michigan, half of which are invaded. The two groups do not significantly differ in nutrient concentrations and morphometries, which allows us to asses the long-term impacts of invasion. We also use experimental lake enclosures and mesocosm to tease apart the mechanism by which zebra mussels affect microbial community ecology, evolution, and processes.

Lab researchers: Marian Schmidt

2. Land use and climate change (with collaborators at UM, GVSU Annis Water Resources Institute, and NOAA Great Lakes Environmental Research Laboratory).
Project focus: Carbon cycling has been poorly characterized in Earth’s large lake systems, despite their more rapid response to change compared to the oceans and their biodiversity and economic values. The Laurentian Great Lakes are the largest contiguous freshwater system in the world. They drain > 200,000 square miles of land via ~3,000 tributaries, resulting in significant terrestrial loadings. The freshwater estuaries at the juncture of the tributaries and the lakes are critical geochemical hotspots for primary production, respiration of terrestrial C loadings, and cycling of N and P loadings, but their study lags far behind their marine counterparts. We focus on land-water linkages in a major Great Lakes watershed and estuary in the context of shifts in C, N, and P loadings induced by land use and climate change.

We are also establishing a long term ecological research study of the Lake Michigan microbial food web by complementing NOAA GLERL's transect study from Muskegon, which is focused on the higher trophic levels of the food web. This effort aims to chronicle how climate-affected environmental factors constrain the structure and function of the North American Great Lakes microbial food web and insights will be key towards predicting how climate change will impact carbon emissions from the world’s largest freshwater system.

Study system: We focus on the Muskegon River watershed and estuary, particularly Muskegon Lake, a large drowned river mouth lake that connects the river to Lake Michigan. The Muskegon River drains one of the largest watersheds in the Great Lakes region. Land development in the catchment results in sediment loads equal to that of a typical watershed five times its size. Agricultural development along the river tributaries and urban runoff around Muskegon Lake result in heightened nutrient loads as well. Muskegon Lake is attractive as a field site as long term monitoring data are available from the NOAA long-term transect on Lake Michigan, and from seasonal and continuous monitoring by our GVSU collaborators.

Lab researchers: Ann McCarthy, Edna Chiang

3. Interactions between phytoplankton and heterotrophic bacterioplankton (in collaboration with Dr. Bradley Cardinale)
Project focus: Whereas the previous projects focus more on the processing of terrestrial carbon, a main source of carbon available to heterotrophic bacterioplankton originates from freshwater algae. This projects focuses on how interactions between these two groups of organisms affects community dynamics. Findings from this study will assist in interpreting data from the terrestrial carbon focused projects. We aim to determine how bacteria living in the phycosphere – the aquatic analog of land plants’ rhizo- and phyllosphere – influence the ability of phytoplanktonic algae to compete successfully with other algal species. We are also interested in determining whether associations between bacterial genotypes and their host algae are evolutionarily conserved, and how, consequently, heterotrophic bacterial composition is partly driven by the phytoplankton composition.

Study system: We take advantage of a culture collection of the 60 most prevalent freshwater green algae in North America - a collection that has been assembled for an ongoing DIMENSIONS of Biodiversity project led by Dr. Cardinale. We also use inland lakes in Southern Michigan for experiments and as a source of freshly isolated algae.

Lab researchers: Ann McCarthy, Natalie Imirzian


We use both traditional microbial physiology and genetics methods as well as metagenomic, metatranscriptomic, 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, recent advances in sequencing technology, cell sorting, mass spectrometry, and bio-informatics are enabling us to assess the genomic make-up of microbial populations and expression of their genetic potential in ever more complex systems.


We are part of the 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 the 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.