Category: Research

Saving the Brook Trout by Restoring their Spawning Habitat

Professor Casey Huckins has been studying the ecology of coaster brook trout for nearly 20 years. He started out investigating these migratory fish’s population ecology and life history. His research now focuses on analyzing the movement patterns of coaster brook trout due to human impact on the watershed. He is also focusing on ways to restore them and the habitat they need to spawn. Recently, with funding from the Michigan Departments of Environment, Great Lakes and Energy (EGLE) and the Department of Natural Resources, his lab has been actively restoring its critical habitat. “Human actions have turned these iconic heritage species of Lake Superior into a conservation concern by overharvesting them and disturbing their habitat,” Huckins explains.

Casey using a tool in a stream
Casey Huckins working in the field

His team is actively studying the two coaster brook trout populations still known to exist along the south-central shore of Lake Superior.

These migratory coaster brook trout live in Lake Superior. However, they return to their rivers of origin to breed in the same spots where they were spawned. Due to disturbances in the watersheds, like logging and road use, the spawning habitat of these creatures has been buried. This has altered the critical dynamic of erosion and sedimentation, leading to a buildup of fine sand. The sand present here is responsible for covering larger sediment particles like cobbles and pebbles. Cobbles are small rocks that have been rounded by water flow. These pebbles serve as the spawning habitat and also as the home for the brook trout’s food and aquatic insects.

With his recent state funding, Huckins says his goal is to restore the critical spawning habitat. He will do this by removing excess sand and studying the impacts on the habitat and the brook trout population. His team has installed in-stream sand collectors that passively collect sand as it flows over them. The researchers then routinely operate pumps to move the sand out of the floodplain.

Huckins’ team is now investigating whether the community of stream insects that are necessary food items for the brook trout also increases in abundance, diversity, and community structure. He hopes to see a site similar to the natural, free-flowing cobble-based cold-water habitat found at the site when he started studying it with his graduate students nearly two decades ago.

Huckins’ team is now investigating whether the community of stream insects that are key food items for the brook trout also increases in abundance, diversity, and community structure. He hopes to see a site with natural, free-flowing cobble-based cold-water habitat. Huckins found this at the site when he started studying it with his graduate students nearly two decades ago.

Brook trout
Brook Trout

His next goal is to acquire additional funding to automate the sand collectors to operate independently. Huckins’ goal is to eliminate the need for researchers to manually pump sand at the site, saving them time and fuel expenses. The team is currently expanding their efforts to implement this system in various streams and rivers. Their equipment is being utilized to rehabilitate other waterways that have suffered from erosion due to flooding, land use, or other factors that cause sand to flow downstream. As our climate changes, we expect to see more extreme events that will have outcomes we need to address to restore and maintain these critical aquatic ecosystems.

Paul Goetsch Receives NIH Grant to Study Cell Cycle Regulation

Dr. Goetsch assisting a graduate student in the lab

Assistant Professor Paul Goetsch received a $423,381 grant from the National Institutes of Health. Dr. Goetsch will study how the DREAM transcriptional repressor complex regulates the cell cycle of cellular progression and cellular quiescence.

Cellular division is extremely important as an organism grows to maturity, but just as important are the mechanisms that stop cells from dividing. Dysfunction in cellular quiescence generally leads to the development of cancer cells, Goetsch explains.

Working in the model system Caenorhabditis elegans, a 1 mm-long transparent nematode, the Goetsch lab is using CRISPR/Cas9-mediated genome editing to disrupt how the DREAM complex forms and test how that affects its function. “By exploiting advances in genomic editing and genetic tools in a tractable model system, we will gain new insights into how the DREAM complex protects cellular and organismal health,” says Goetsch.

Another part of the grant supports bringing research directly into the classroom for Biological Sciences students in the second-year genetics lab. Goetsch and his colleagues are implementing Course-based Undergraduate Research Experiences (CUREs). These are used to provide students a glimpse into research opportunities within the department.

In Spring 2021, Goetsch and his student Emily Washeleski developed a unique experiment combining C. elegans genetics with environmental microbiology. “We are continuing to expand upon our CURE approach to provide students equitable access to research experience as a cornerstone of their professional development within the department,” Goetsch says.

Amy Marcarelli Receives NSF Grant to Explore How Microbes Process Organic Matter in Streams

Professor Amy Marcarelli and a multi-disciplinary team have received a two-year, $300,000 NSF grant. The grant from the National Science Foundation is to study the relationships between organic matter and micro-organisms in streams. 

Marcarelli and colleague in stream with five gallon bucket collecting a water sample
Marcarelli and colleague collecting water samples

An ecosystems ecologist, Marcarelli is leading a team of Michigan Tech ecosystem scientists, microbiologists, environmental chemists, and data scientists. The researchers are conducting detailed laboratory experiments to gather data on how microbial communities work together to process complex mixtures of dissolved organic matter in streams.  Steve Techtmann, associate professor of Biological Sciences and an environmental microbiologist, is doing all the microbial work on the project in his lab at Michigan Tech. 

Dissolved organic matter comprises many different kinds of molecules that come from terrestrial and aquatic plants and microbes.  The researchers expect different microbes that live in streams to be specialized to break down these different molecules. 

“We expect the relationships to be extremely complicated,” Marcarelli says. 

They are looking at rates of respiration, carbon breakdown, and energy release. They hope to discover how the characteristics of dissolved organic matter and stream microbes can explain rates of carbon dioxide emission from streams. 

The researchers will use the data to develop machine-learning models. “The relationships between the organic matter and micro-organisms might not be evident in simpler analysis methods,” Marcarelli explains. 

The current work is the start of a much larger project. “We hope to build on the results of this project with a much bigger proposal for a large field project,” she says. 

And why is this work important?  “Although we, as a field, have studied carbon dioxide production and emission across many different streams, we can only predict a small amount of the variation we see based on environmental characteristics like temperature,” Marcarelli explains. “We think there is an important role of both microbes and organic matter structure that contributes to this variability, and understanding that is important for predicting these emissions in the future and response to global changes like climate and land use change.”

Marcarelli is the director of the Ecosystem Science Center at Michigan Tech.

In Print: Trista Vick-Majors

Congratulations to Trista Vick-Majors and colleagues who recently published a paper titled “Constraints on the Timing and Extent of Deglacial Grounding Line Retreat in West Antarctica” in AGU Adventures.

Graph indicating the subglacial core locations along with filling and draining amounts
(a) Southern Ross Sea sector ice streams with previous subglacial core locations (Whillans Subglacial Lake (SLW; Tulaczyk et al., 2014), Whillans Grounding Zone (WGZ; Venturelli et al., 2020), the upstream site at of Whillans Ice Stream (UpB; Engelhardt & Kamb, 1997), and Crary Ice Rise (CIR; Bindschadler et al., 1988) marked with gray circles, Mercer Subglacial Lake (SLM) indicated with a purple circle, and the lake directly upstream Conway Subglacial Lake (SLC) labeled. Ice velocity (Mouginot et al., 2019) is overlain on an imagery mosaic (Scambos et al., 2007), with active subglacial lake areas (blue polygons; Siegfried & Fricker, 2018), hydropotential flow paths (blue lines; Siegfried & Fricker, 2018), and grounding line (black; Depoorter et al., 2013) indicated. (b) Volume changes in Mercer Subglacial Lake inferred from CryoSat-2 radar altimetry (Siegfried et al., 2023) with a yellow star marking the timing of sampling.

Abstract

Projections of Antarctica’s contribution to future sea level rise are associated with significant uncertainty, in part because the observational record is too short to capture long-term processes necessary to estimate ice mass changes over societally relevant timescales. Records of grounding line retreat from the geologic past offer an opportunity to extend our observations of these processes beyond the modern record and to gain a more comprehensive understanding of ice-sheet change. Here, we present constraints on the timing and inland extent of deglacial grounding line retreat in the southern Ross Sea, Antarctica, obtained via direct sampling of a subglacial lake located 150 km inland from the modern grounding line and beneath >1 km of ice. Isotopic measurements of water and sediment from the lake enabled us to evaluate how the subglacial microbial community accessed radiocarbon-bearing organic carbon for energy, as well as where it transferred carbon metabolically. Using radiocarbon as a natural tracer, we found that sedimentary organic carbon was microbially translocated to dissolved carbon pools in the subglacial hydrologic system during the 4.5-year period of water accumulation prior to our sampling. This finding indicates that the grounding line along the Siple Coast of West Antarctica retreated more than 250 km inland during the mid-Holocene (6.3 ± 1.0 ka), prior to re-advancing to its modern position.

O-fish-ally Fin-tastic Research!

Tessa Tormoen is a fourth-year student majoring in ecology and evolutionary biology with a minor in fish biology. She is one of the most adventurous people you’ll ever meet. You can often find her cross-country skiing on the Swedetown and Tech Trails. Not only is she a fan of heart-racing adventures, but her curiosity has also led to her getting involved in undergraduate research. Throughout Tessa’s classes, she learned the basic skills and processes needed in the lab. Her confidence grew. She was ready to put these skills into practice and take on an independent project. In the fall of 2021, she discussed her interest with Dr. Kristin Brzeski, assistant professor at Michigan Tech.

A picture of Tessa in the lab using a pipette to transfer a sample.
Tessa in the lab

Fishing for DNA

Dr. Brzeski put Tessa to work observing Golden and Blueline Tilefish. She extracted DNA from the digestive tracts of predator fish and constructed what the taxonomic group looks like by using a method called Metabarcoding, which is a process of DNA sequencing and identification. Using this technique she was able to characterize the dietary composition of the two different tilefish species to better determine the species’ niche breadth (or use of food resources in this case) and degree of similarity. This is one factor showing how the two species co-exist.

Like any craft, it’s a continual learning process. Working alongside graduate students and mentors, she developed her independent problem-solving and management technique. Learning the ins and outs of research was a steep learning curve, but Tessa was able to gain valuable skills and knowledge during her time as a researcher. “It’s a joy to have an undergraduate like Tessa in the lab. She brings passion, intelligence, and a genuine interest in research and natural resource conservation to every interaction,” said Dr. Brzeski.

Tessa exhibited her research at the 2023 Undergraduate Research Symposium, winning the third place GLRC award. She also won a merit award at the Ecosystem Science Center poster session. And she presented her findings at the Wildlife Society National Conference in Spokane, Washington with others in her lab.

Tessa is presenting her research to an audience by referring to a poster. The audience is pictured from behind.
Tessa presents her research “Using DNA Metabarcoding to Evaluate Dietary Resource Partitioning Between Two Sympatric Tilefish” at the 2023 Undergraduate Research Symposium

A Close-Net-Bunch

Tessa believes that her experiences in research have helped shape the future for the better. “I’m a lucky person. I’ve had an incredible four years. Jill Olin and Kristin Brzeski [have] built me into an independent scientist. They taught me how to solve problems, how to be independent and confident in my abilities,” she says. She credits both graduate and undergraduate colleagues in the lab with perpetuating the culture Drs Brzeski and Olin cultivated. “It was a welcoming and hopeful atmosphere.”

That feeling extends to the department. “Everyone is extremely kind, no matter who you talk to! All of my professors throughout my coursework have been very approachable and extremely passionate about what they study. I love that the biological sciences department is so personal and you can build relationships with the faculty. It truly makes the department’s environment so incredible. The support I have received from my advisor and my professors has been a valuable part of my education. I also love how the biological sciences department is a bit smaller compared to other departments like engineering. Each semester I recognize many familiar faces. I’ve been able to create great relationships with my peers through this,” Tessa said.

The Water is Just Right at Michigan Tech

Like many before her, Tessa chose to study ecology and evolutionary biology at Michigan Tech because she fell in love with this area. “I realized that I have a passion for understanding the world around me and this is a beautiful place to do that,” she said. “Plus, the experiences you’re able to have in this degree are fantastic, and I was compelled by the sheer amount of opportunities available to me.”

Tessa appreciated the flexibility the ecology and evolutionary biology degree program offered. “A lot of the coursework is electives that you get to choose from, so you can tailor your education to what you are most interested in. Thus, I was able to take courses like Mammalogy, Tropical Island Biology, Valuing the Great Lakes, Botany, and more!” Tessa said. “Sometimes you get to go outside for classes; one of my biggest memories from my degree is my Tropical Island Biology course, where we stayed in the Bahamas over Spring Break. This degree program has given me such a strong foundation and a whole list of interests that I can build upon with secondary education and post-education work experience.”

Tessa Tormoen
Tessa Tormoen enjoys the views of Portage Lake from the Biological Sciences Lounge

In addition to research and the degree program, Tessa took advantage of other opportunities on campus. She served as vice president of the Ski and Snowboard Club. Tessa also coordinated activities as part of the Women’s Leadership Council.

Leaving the School: Tessa’s Post-Graduation Plan

Following commencement this month, Tessa plans to “go with the flow.” This summer, you’ll find her on Isle Royale working as a fisheries technician, performing limnological assessments and fish surveys on their inland lakes. “I’m excited about this opportunity as it honestly feels like a dream job,” she said.

After taking one year to work in the field and gain more experience, Tessa wants to return to school for her master’s degree and potentially a Ph.D. “I think my experience at Michigan Tech has helped me greatly in understanding the opportunities available to me after graduation. I think that my education, research experience, and relationships at Tech have set me up for success once I leave,” she said.

We are certain her future will go swimmingly well!

Biological Sciences in the Undergraduate Research and Scholarship Symposium

Thank you to all of the Biological Sciences students that presented and shared their research at the 2023 Undergraduate Research and Scholarship Symposium!

Overall Awards

First Place – Leah Harazin and Nathan Ostlund: “Stability of Terephthalate Degrading Microbial Consortia for Plastic Upcycling”

Second Place – Haley Marchese: “Sympathetic Activity to the Heart is Increased in a Mouse Model of Hypertrophic Cardiomyopathy”

Third Place – Grace Gonzalez: “The Gut Microbiome of Fish and Its Relevance to Antimicrobial Resistance”

Special awards for research affiliated with the Great Lakes Research Center

First Place — Leah Harazin and Nathan Ostlund: “Stability of Terephthalate Degrading Microbial Consortia for Plastic Upcycling”

Second Place Grace Gonzalez: “The Gut Microbiome of Fish and Its Relevance to Antimicrobial Resistance”

Third Place — Tessa Tormoen: “Using DNA Metabarcoding to Evaluate Dietary Resource Partitioning Between Two Sympatric Tilefish”

Congratulations to all participants!

In Print: Jill Olin

Congratulations to Jill Olin and her postdoctoral fellow, Jim Junker, who recently published a paper titled “Can biodiversity of preexisting and created salt marshes match across scales? An assessment from microbes to predators” in the Ecosphere Journal. You can learn more about the research on the LSU website.

Jill Olin
Jill Olin
Jim Junker

Abstract: Coastal wetlands are rapidly disappearing worldwide due to a variety of processes, including climate change and flood control. The rate of loss in the Mississippi River Delta is among the highest in the world and billions of dollars have been allocated to build and restore coastal wetlands. A key question guiding assessment is whether created coastal salt marshes have similar biodiversity to preexisting, reference marshes. However, the numerous biodiversity metrics used to make these determinations are typically scale dependent and often conflicting. Here, we applied ecological theory to compare the diversity of different assemblages (surface and below-surface soil microbes, plants, macroinfauna, spiders, and on-marsh and off-marsh nekton) between two created marshes (4–6 years old) and four reference marshes. We also quantified the scale-dependent effects of species abundance distribution, aggregation, and density on richness differences and explored differences in species composition. Total, between-sample, and within-sample diversity (γ, β, and α, respectively) were not consistently lower at created marshes. Richness decomposition varied greatly among assemblages and marshes (e.g., soil microbes showed high equitability and α diversity, but plant diversity was restricted to a few dominant species with high aggregation). However, species abundance distribution, aggregation, and density patterns were not directly associated with differences between created and reference marshes. One exception was considerably lower density for macroinfauna at one of the created marshes, which was drier because of being at a higher elevation and having coarser substrate compared with the other marshes. The community compositions of created marshes were more dissimilar than reference marshes for microbe and macroinfauna assemblages. However, differences were small, particularly for microbes. Together, our results suggest generally similar taxonomic diversity and composition between created and reference marshes. This provides support for the creation of marsh habitat as tools for the maintenance and restoration of coastal biodiversity. However, caution is needed when creating marshes because specific building and restoration plans may lead to different colonization patterns.

In the News

Ebenezer Tumban portriat
Ebenezer Tumban

Ebenezer Tumban (BioSci) was quoted in the story “MTU virologist discusses virus differences,” in the Daily Mining Gazette:

MTU virologist discusses virus differences

Joshua Vissers, Associate Editor, Daily Mining Gazette, March 27, 2020

HOUGHTON — Influenza and coronaviruses both travel between the infected wrapped in a stolen bit of the previous host cell’s outer, lipid-based layer called an envelope. That layer protects the viruses from harsh environments, and works as a kind of disguise to help them inject themselves into the next cell. The difference that makes an outbreak of coronavirus so much more dangerous is the difference in that envelope.

“Normally, envelope viruses are not stable in the environment,” Ebenezer Tumban said.

Tumban is a molecular virologist and vaccinologist at Michigan Technological University. He’s been studying viruses in an effort to learn how to vaccinate against them.

Envelopes dry out and deteriorate fairly quickly outside the body, and the virus inside is rendered helpless to infect another cell, he said.

This image shows the lipid envelope of coronavirus, taken from an infected cell, and the crown-like proteins added by the virus that are its namesake.
Provided image This image shows the lipid envelope of coronavirus, taken from an infected cell, and the crown-like proteins added by the virus that are its namesake.

However, coronaviruses have hollow proteins embedded in their envelope. Scientists thought this structure looked like a crown, and so called it corona (Latin for crown).

“The crown basically makes them more stable compared to the regular flu,” Tumban said.

This extra stability allows it to last longer in the air and on surfaces compared to influenza viruses. So a coronavirus-infected person coughing in an area can infect people passing though that area for much longer than someone with influenza.

Despite having symptoms quite similar to a flu, fighting a coronavirus is more difficult for the body than fighting a flu virus for a few reasons. 

“There’s a lot of things, some of it has to do with the virus and some of it has to do with us,” Tumban said.

A more stable envelope means the virus can exist in more parts of the human body. The flu virus is typically destroyed by fluid in the gastrointestinal tract, but COVID-19’s corona protects them from that, according to Tumban.

The virus also seems to be able to suppress immune system response in some people.

“People that were infected with coronavirus had a low level of lymphocytes,” he said.

This suggests that the coronavirus is also infecting those types of cells, which are part of the body’s defense system. The influenza virus doesn’t do that. 

Tumban said there’s also evidence that the virus can trigger a reaction in the body similar to an allergic reaction.

“My body might overreact and produce a lot of cytokines,” he said.

These cytokines can trigger sepsis and organ failure in severe cases.

And medical professionals have fewer tools to fight coronavirus, too.

“We don’t have a vaccine for corona, we have a vaccine for influenza,” Tumban said.

Influenza vaccines have been in use for a long time, training our immune systems in how to make antibodies that fight that particular virus and creating a group immunity that protects even those without the vaccine. While the flu virus does mutate regularly, it’s rarely enough to render a vaccine entirely ineffective.

“Vaccinations from the past might help to make the disease less severe compared to coronavirus which is new,” Tumban said. “You don’t have a single antibody against it in your body.”

People hospitalized with the flu can receive certain treatments like Tamiflu, but Tumban said with coronavirus, doctors right now mostly give “supportive care” – using tools like ventilators to support the patient’s body while it fights or endures the infection on its own.

These factors together create a much more deadly virus than the flu.

“The mortality rate is about 10 times that of influenza,” Tumban said on Tuesday.

Tumban’s calculations, based on numbers from the Centers for Disease Control, show that a high estimate of influenza’s mortality this year is about 0.1% in the United States, but coronavirus is showing to be about 1.27%. 

Worldwide, the mortality rate for coronavirus is about 4.3% according to Tumban.

The increased mortality and lack of treatment and defense are what is leading countries and organizations around the world to implement social distancing and quarantine measures as healthcare providers ramp up capacity and researches search for vaccines.

However, while coronavirus can be far more infectious and harmful than the influenza virus, many of the same precautions work to prevent infection. The No. 1 recommendation, hand washing and sanitizing, destroys the all-important envelope protecting the virus, rendering it virtually harmless.

“There’s no way they can cause the disease,” Tumban said.

Editor’s Note: This story has been changed to more accurately portray Dr. Tumban’s work. While he has worked directly with Zika, dengue, HPV and other viruses, he has not worked directly with coronaviruses.