Research projects

The lab's research program combines aspects of community ecology, ecosystem ecology, and evolutionary biology. All projects contribute to two core questions, which are:

(1) what is the relative importance of community compositional shifts, phenotypic plasticity, and evolution in microbial responses to anthropogenic change.

(2) what are the feedbacks between these responses and ecosystem processes that microbial communities mediate, in particular those affecting emissions of climate-active gases from natural systems.

We pursue these questions using freshwater microbial communities as a study system. For this we combine in situ survey and experimental work, laboratory experiments, and both traditional microbiology approaches as well as state-of-the-art molecular and bioinformatic methods. Why should we care about freshwater bacteria? Bacterial communities play key roles in nutrient cycling and contribute significantly to biomass and energy fluxes. For example, bacterial respiration of terrestrial carbon subsidies contributes to global net freshwater CO2 emissions (2 Pg / yr) that rival net uptake by the oceans (2.6 Pg / yr) despite the relatively small footprint of freshwater systems. Anthropogenic disturbances can alter bacterial communities, which can either mitigate the predicted direct effects of these disturbances, or lead to major shifts in bacterially mediated fluxes. As such, understanding the links between global change and microbial communities is essential for predicting what our future biosphere will look like.


Study systems and projects

1. Species invasion as a tractable system to advance our understanding of microbial disturbance ecology
Project focus: Species invasion, which is one of the main components of global change, is a particularly useful system to help address knowledge gaps in microbial disturbance ecology as we can readily determine (1) the initial response to species introduction in laboratory or field experiments, (2) the in situ long-term response to this long-term disturbance by comparing systems that are and are not invaded. System-wise, we focus on one of the most deleterious aquatic invaders, filter-feeding dreissenid mussels (IDMs; Dreissena polymorpha (zebra mussel) and D. bugensis (quagga mussel)), which have radically changed the freshwater food web by altering the biomass and community composition of phytoplankton and zooplankton, thus shifting biomass and energy fluxes from the water column to the lake floor environment. IDMs are compelling because they (1) continue to spread to over 30 US states and throughout large parts of Eurasia, and (2) have large impacts on freshwater systems. Their effects on bacterial community composition and function have not been broadly investigated, though our preliminary data indicates they can significantly alter bacterial community composition (Denef et al., 2017; Props et al., in review). This research theme has been funded by a grant from the Erb Family Foundation through the UM Water Center (2015-2016), and an NSF EAGER award (2017-2019), which focuses on the question whether phenotypic plasticity are part of the response to long-term ecological disturbance.

Study system: We focus on inland lakes in Southern Michigan, Lake Michigan, and Lake Erie and for field experiments, we work at the UM Biological Station.

Lab researchers: Marian Schmidt, Nikesh Dahal, Cassandra Huerta

2. Feedbacks between ecological, evolutionary, and ecosystem process dynamics.
Project focus: The realization that evolution can happen on ecological time scales, thus can alter system dynamics so that they cannot be predicted based on ecological principles alone, has led to increased attention to studies towards eco-evolutionary feedbacks. We have worked with Jay Lennon (Indiana University) to write a book chapter to highlight the particular importance of eco-evolutionary feedbacks in microbial systems (Lennon and Denef, 2015). In addition, eco-evolutionary dynamics may also be driven by and drive changes in ecosystem properties (e.g. primary productivity). These interactions are the focus of an NSF preproposal (DEB Population and Community Ecology) in collaboration with Bradley Cardinale (Co-PI, UM SNRE).
We will examine the forces that shape algal-bacterial associations, and whether these interactions impact competitive interactions between algae. As phytoplankton communities are responsible for half of Earth’s net primary productivity, and since phytoplankton species differ in their requirements and uptake of essential elements (e.g, C, N, P), phytoplankton community composition can regulate many biogeochemical cycles. Therefore, it is important to understand the factors controlling phytoplankton composition. While it is known bacterial populations can inhibit or facilitate algal populations, it is currently unresolved whether bacteria can impact algal competitive interactions. In addition, it is not known whether genotype, environmental conditions, or bacterial source populations control the identities of bacteria associated with phytoplankton species.

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 at the E.S. Geaorge Reserve in Southern Michigan for experiments and as a source of freshly isolated algae.

Lab researchers: Kathryn Schmidt, Sara Jackrel

3. Critical evaluation of ecological and evolutionary concepts in microbial ecology and evolution.
Project focus: At a conceptual level, determining what consists of an ecologically and evolutionary cohesive population remains a major challenge within our field. Recently, a series of studies have promoted the use of ‘oligotypes’, based on subtle sequence variation (down to 1 nucleotide) in a commonly used marker gene (16S rRNA gene). We leveraged a collection of Microcystis isolates and field survey data from a harmful algal bloom season in Lake Erie to evaluate whether these oligotypes are indeed meaningful ecological and evolutionary units, as various recent authors have purported. Our data casts significant doubt on these assertions, as ecological traits are not reliably predicted based on oligotype, nor are oligotypes forming monophyletic groups (Berry et al., 2017b). This research has been funded by a grant from the Erb Family Foundation through the UM Water Center and was performed in collaboration with researchers at Michigan State University (Orlando Sarnelle), NOAA GLERL (Tim Davis), and UM (Tom Johengen, Greg Dick).
Another concept we have critically reflected upon is the concept of microbial dormancy. In a recently published paper (Denef et al., 2016), we raised questions regarding the operational definition based on RNA:DNA ratios previously proposed and provided support for the notion that these ratios are driven in large part by cell size rather than activity. Funding for this work came in part from the DOE Community Science Program and through a generous collaboration with NOAA GLERL (Henry Vanderploeg).

Study system: We focus on inland lakes in Southern Michigan, Lake Michigan, Muskegon Lake, and Lake Erie and for field experiments, we work at the UM Biological Station.

Lab researchers: Kyle Buffin, Marian Schmidt

4. Advancing understanding of forces that shape freshwater microbial community assembly
Project focus: We are carrying out a series of projects in inland Michigan lakes and the Great Lakes that contribute to our understanding of what drives the population and community dynamics in freshwater microbial communities and what are the roles of key populations in these systems. While ranging in focus, these contributions aim to strengthen the understanding of freshwater microbial community ecology, which is essential for the pursuit of our (and the wider community’s) core questions. Our published work revealed the surprising class- to phylum level conservation of habitat preferences among freshwater bacteria (Schmidt et al., 2016), deconvoluted disturbance effects (specifically eutrophication and resulting harmful algal blooms) and seasonal dynamics in community composition (Fujimoto et al., 2016; Berry et al., 2017a), and contributed to the understanding of why a certain bacterial taxon is able to contribute up to 20% of all cells in the deep water layers of large lakes worldwide (Denef et al., 2016). We are further building on this work with studies focused on (a) understanding how algal-bacterial interactions may shape bacterial community dynamics (led by undergraduate students in collaboration with Hunter Carrick, Central Michigan University and Henry Vanderploeg, NOAA GLERL)), (b) how taxa that are abundantly present across widely varying temperatures and nutrient levels may maintain themselves through phenotypic plasticity and/or evolutionary fine-tuning (Props et al., in prep), and (c) what mechanism underpin differential diversity-productivity relationships in free-living and particle-associated bacteria (Schmidt et al., in prep; in collaboration with Bopaiah Biddanda, Grand Valley State University). Work on this theme has been funded by the DOE Community Science Program, the Erb Family Foundation through the UM Water Center, and an NSF DDIG to Marian.

Study system: We focus on inland lakes in Southern Michigan, Lake Michigan, Muskegon Lake, and Lake Erie and for field experiments, we work at the UM Biological Station.

Lab researchers: Marian Schmidt


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.