Can you picture Lake Erie’s food web?
On top, you might imagine some of the 130 species of fish, like walleye or bass, that live in the lake. Big fish prey on smaller fish, who eat invertebrates including mussels, mollusks and larval insects.
What’s on the bottom of the web? Microbes.
These microscopic organisms, the various types of algae and bacteria living in Lake Erie, are tiny. Many are less than a micron — one-millionth of a meter — in size.
Yet while small, these organisms play a big role in the health of the Great Lakes. For Lake Erie researcher Trisha Spanbauer, aquatic microbes are the backbone of the food web that can provide insight into the resilience of ecosystems.
“There’s this tension between microbes being the foundation of a healthy ecosystem but also potentially something that can cause issues for humans and other organisms,” said Spanbauer, assistant professor of environmental sciences at The University of Toledo. “So better understanding the players, how they’re connected to each other and their functions within the lower food web is really vital to understanding the health of that ecosystem and the resilience overall.”
To improve this understanding, Spanbauer is leading research funded by Ohio Sea Grant to explore how human shoreline activity impacts communities of microbes on the coast of Lake Erie’s Western Basin.
Researchers at The University of Toledo spent the past two summers collecting microbes — specifically prokaryotes, photosynthetic algae and microbial eukaryotes — at sites across the region’s shoreline. The tiny organisms carry out different functions like primary production, meaning they use photosynthesis to produce energy.
“Energy sort of flows into aquatic food webs through primary productivity that ends up cascading through the food web,” Spanbauer explained. “So the lower food web is very important for sustaining the health of the ecosystem.”
Spanbauer’s team collected aquatic microbes from nine sample sites representing different nearby land uses and shoreline management techniques, such as jetties and seawalls built to control erosion. Sites ranged from areas with agricultural and industrial impact near Toledo to intact wetlands farther east such as Old Woman Creek.
“We really run the gamut,” Spanbauer said. “Having that variety of landscape and land use allows us to test some hypotheses about how different environments might impact the lower food web.”
To understand the diversity of the microbiome, or the groups of microorganisms in the environment, researchers extracted DNA from environmental samples to distinguish them by species, genus or family. The first step in this process involved collecting water and running it through a filter or screen to separate organic matter.
This step also created an opportunity for community members to get involved in the research process. Through the project, Spanbauer’s team started a community science initiative called ERIeDNA and held several “BioBlitzes” where residents collected water from nearby sources, filtered it and then returned the filter to the researchers. University of Toledo researchers Alyssa Armstrong and Megan Ginther helped reach out to student groups and local volunteer firefighter groups to participate in the program.
“This gives people the opportunity to know a little bit more about the water they’re interacting with in the environment,” Spanbauer said.
Next, the researchers extract and purify DNA from the filtered organic material. The filters are first stored in a freezer set at minus 80 degrees Celsius. Later, the team works to open up the cells, remove the DNA and then purify it to remove any non-DNA substances.
“Then you have a little tube filled with all the effort you put forward, and in that tube is the DNA,” Spanbauer explained. “You still need to find out what organisms are there, and there are many different ways to do that.”
One way used in the study is the DNA analysis technique called metabarcoding. Researchers use polymerase chain reactions, or PCR, to focus on a fragment of DNA that is useful for the identification of target organisms. That fragment or “barcode” is then amplified to make thousands of copies that can be studied in greater detail.
“It’s an opportunity for everyone to better understand these microscopic organisms that really sustain and enable healthy fisheries.”
The copies — called amplicons — are sequenced, allowing researchers to identify the microbes. Specifically, the study used an efficient process called high-throughput sequencing, in which many amplicons can be sequenced at the same time. Now, the team is beginning to analyze all the data they collected.
“We’re just starting to crunch through it,” Spanbauer said.
Once that process is finished, she expects the data will provide a wealth of information about ecological resilience and implications for the larger food chain in Lake Erie. Understanding resilience lets researchers know whether an ecosystem will return to baseline conditions if perturbations — such as nutrient loading or erosion — occur.
“If you have minimal resilience, it’s easier for that perturbation to the system to really reverberate and cascade,” she said. “When ecosystems change their underlying structure and function, and we’re relying on it, or lots of organisms are relying on it, that can be a massive issue.”
Accordingly, results from the study will help identify environments on the lake that are resilient or vulnerable to such disturbances. Information will be provided to partner agencies, including the Ohio Department of Natural Resources Coastal Management Office and the Old Woman Creek National Estuarine Research Reserve.
“I think everybody is very interested in finding those predictors that help us understand how a community is changing before it moves into a state that no longer provides the ecosystem services we depend on,” Spanbauer said. “So potentially there’s some ecological indicators that might come of the data.”
For example, data about microbiome diversity could inform natural resource managers that a particular community has low resilience, suggesting that it should be a priority for ecological restoration projects.
Spanbauer also plans to work with her colleagues at The University of Toledo to compare her microbiome data with existing fish abundance data. The goal is to find out if biodiversity is correlated between consumers and producers in the food web.
“Moving up the food chain is wild to me,” Spanbauer explained. “When I came to the university, I was really excited about getting to work with folks that were locally looking at fish abundances and fish population dynamics,” she said. “I’m excited to start talking about how this might relate to fish — or maybe it’s not as simple of a relationship as one might think.”
While no results from the study are final, preliminary data suggests that silica may influence competition among algae. Silica is a compound of silicon and oxygen that makes up minerals like quartz and sandstone and has a high prevalence in the Great Lakes.
Cyanobacteria, or blue-green algae, can dominate communities due to factors like temperature and stratification. Interestingly, Spanbauer found that this dominance also occurred when levels of dissolved silica in the water were low.
“I’ve been very interested in the interplay between competition between algal strains. I started to see some amount of silica depletion around the time that cyanobacteria are abundant,” she said. “But we don’t yet know that it’s a causal relationship.”
To that end, Spanbauer is collaborating on another higher resolution study to better understand how resource competition might impact plankton community dynamics.
Meanwhile, the ERIeDNA community science effort is already showing great results, and the team hopes to keep growing it in the future, Spanbauer said. One plan is to make kits that people can use to collect and filter water samples.
“I think this technique might be interesting to managers and the public,” she said. “This system of collection is really easy, and sequencing has become much less expensive.”
The program offers value to both undergraduate students and local residents. For one, the students get to interface with the public and explain to the community what they’ve learned about the environment.
“It gets students into the community, and then the benefit for the community is that they get to understand a little bit more about a group of organisms that, until they’re harmful, are not at the forefront of everyone’s mind,” Spanbauer said. “It’s an opportunity for everyone to better understand these microscopic organisms that really sustain and enable healthy fisheries in the Western Basin.”
For more about this Ohio Sea Grant-funded research, email Dr. Spanbauer at email@example.com.