Analyzing microbiomes and water quality, Indigenous Students Learn the Love for Sciences

Now in its third year, Monitoring Environmental Microbiome program participants dive into complex computational analysis of environmental justice issues.

DURANGO, COLO.— It’s mid-May, and while most college students are out for the summer, a handful are at Fort Lewis College analyzing the metal composition of sediment samples using computational methods.

“Did everyone generate the plot for their metal of interest?” asks Joslynn Lee, Ph.D., an assistant professor of chemistry at FLC. “What are you all seeing on the X-axis for yours as the max? It looks like lead is just over 100,” she says as students discuss their results, moving between screens and query pages to analyze different metals. 

The class is the capstone of a weeklong course called “Monitoring Environmental Microbiome,” or MEM, a program designed to provide Native American and underrepresented students with hands-on experience in data science and scientific computing.

Lee, an enrolled member of the K’awaika (Laguna Pueblo), Haak’u (Acoma Pueblo), and Diné (Navajo Nation) says the program utilizes microbiome research to study the impacts on the San Juan Watershed through environmental and social justice lenses, incorporating Indigenous values and approaches in scientific research.

“Science can and should integrate the cultural and environmental knowledge that Indigenous communities hold,” said Lee. "Our program is built on this principle."

Lee says Indigenous students often face disproportionate barriers to undergraduate research in part because of the inequitable or exclusive approaches often used by higher education institutions.

It takes a scientific village

Lee was a Data Science Educator at Cold Spring Harbor Laboratory’s DNA Learning Center in Long Island, NY, when she first learned about a collaboration between researcher Dave Jackson and Little Big Horn Tribal College, a tribal college located in the Crow Reservation in Montana.

The program, funded by the National Science Foundation, brought together scientists from several institutions to provide hands-on research for underrepresented students.

In addition to Lee, Jackson’s collaborators included Agnes Chan (J. Craig Venter Institute in Rockville, Maryland), Ann Sylvester (University of Wyoming), Mari Eggers (Montana State University), and John Doyle (Little Big Horn College).

Lee, who has a broad background in bioinformatics and specific training and expertise in next-generation sequencing data, said her mind was racing with ideas about how to grow the program.=

“Coming from a computational background, I was excited: Could we train the students to think about what's in the sample and identify unique genes of interest (in microbes)? What sequence of DNA were they extracting? Who does it belong to?”

She also thought the Animas River presented a great opportunity for this research because of its connection with the Navajo Nation and the environmental disaster of 2015. That year, Environmental Protection Agency (EPA) personnel and contractors at the Gold King Mine near Silverton, Colorado, accidentally released three million gallons of mine wastewater and tailings, including heavy metals such as cadmium and lead, and other toxic elements, such as arsenic, beryllium, zinc, iron, and copper into Cement Creek, a tributary of the Animas River. The Animas River is part of the San Juan and Colorado River watersheds near the Navajo Nation.

The program expanded to include FLC students, and as Lee transitioned to a different role at Howard Hughes Medical Institute (HHMI), she presented the project at a conference.

“Larry Hunter from CU Anschutz came to talk to me afterward. He approached me and was like, I can see this going into the computational sciences, so let's chat about this.”

Coming home

In 2019, Lee came back to FLC as a professor. After a break due to the pandemic, Lee and her collaborators resumed the program with a training grant through the National Institutes of Health, supplemented by funding from CU Anschutz.

The team now includes Jennifer Lowell from the Department of Public Health at FLC and Brooklyn Sant'Angelo from CU Anschutz. Navajo Nation Tribal Elder Clyde Benally serves as a cultural resource expert and photographer. 

The weeklong program starts with a trip to Silverton, where participants see the wastewater station where the spill initially occurred. They also stop at key sites where water and sediment samples have been taken.

“We have people who aren't from this area, so it's a nice way to get them to understand the scale of the mountains and watershed,” Lee says. “We talk about the mining history, the communities affected by it, where the water samples they will be analyzing come from.”

The next day, they dive into data analysis.

“This workshop is an exposure to interdisciplinary sciences. We could focus just on computing methods, but I think that's too abstract. That's why we say, let's look at an environmental problem and see how this can be answered using computational techniques.

“For me, it's more of an exposure and having them see themselves being able to use this and learn and then be comfortable taking a class if this interests them.”

From reluctant researcher to TA

Averlee Lander, from Shiprock, New Mexico, and a rising junior at FLC, first learned about the program from Lee, her research advisor.

As a first-year student, learning about coding wasn’t the first thing on her mind when she considered how to boost her research credentials for grad school, said Lander, who aspires to become a veterinarian.

“Dr. Lee explained what she does with the water and the microbiomes and how to take DNA out, and I was like, ‘Oh, that's a little researchy,’” Lander recalled. “I was not into that.”

Despite her initial hesitation, Lander joined the program a year ago and returned this year as a teaching assistant. A panel presentation of her work was recently accepted for the next SACNAS (Society for Advancement of Chicanos/Hispanics & Native Americans in Science) Conference in Phoenix, Arizona.

“This workshop really helps. It opened my mind to how other people might understand my research and how to explain my research with graphs and everything,” she said.

Replicating success­­

Eric Castro, from Hardin, Montana, said he was encouraged by Sara Plaggemeyer, a science instructor at Little Big Horn College, to attend the workshop. A graduate student at Montana State University, he said his work focuses on addressing environmental issues on the Crow Reservation.

“What I hope to gain from this workshop is a lot of information about how they collect samples and how Dr. Lee runs her labs,” he said, adding that eventually, they would like to replicate the workshop at LBHC.

“There are several sites throughout the Crow Reservation with old landfills that have just been covered up. They were not treated right, and several of them have little creeks that flow through the area,” he said.

“We’ll be testing water wells at residences in the reservation and finding out how we can address the problem and what we can do,” he said. “This knowledge will only benefit the health of my community.”

Health and community

Jennifer Lowell, Ph.D., a professor with the Department of Public Health at FLC and co-investigator in the project, said she enjoys helping students build connections between the environment and how it can affect people’s health. 

She says that by utilizing bioinformatics techniques, students learn how environments impacted by metals shift these microbial communities to have less diversity, possibly limiting their capabilities to perform important ecosystem services, which can impact water quality.

"It's fun to see students make those connections during the workshop and begin recognizing how our impacts on the environment can have far-reaching effects on our health. I love showing students how human health is inextricably linked to the environment and how even though we can’t see microbes, they are there by the millions in these environments impacted by metals.”

Data sovereignty

As part of the workshop, researchers also emphasize research ethics, the importance of including marginalized communities in the research process, and the concept of data sovereignty.

“The scientific community has a complicated and often oppressive history with research that has sown distrust among many people of color. We try to bring some examples to the workshop and discuss ways to incorporate community involvement and the importance of data sovereignty in previously marginalized populations,” Lowell said. “The students have amazing ideas and experiences that will really make an impact in the future. It's great to show the students all the different ways bioinformatics can be used.”

That's something that Lander, the FLC student, has taken to heart. Lander comes from a long line of farmers, and as the older generation passes away, she is committed to helping new Diné farmers and ranchers keep their animals healthy.

Her research includes studying the microbiome of animals like horses and cows. She works closely with community members in the Navajo Nation before taking soil samples that she will analyze and then share her findings with the community. As she plans to communicate these results, she is planning to seek help translating her work to Navajo, as many of the elders do not speak English.

“Elders who only speak Navajo think science is bad,” says Lander. "And I'm like, Okay, I need to figure out how to explain this, that this is good. I just want to see how the water is. But I'm like, Okay, so how do I say that in Navajo?

Growing the community of Indigenous researchers

Lee said that, as a young researcher, she was often the only female and person of color who presented at computational chemistry conferences.

“I have been wanting to shift that dynamic. We can empower some of these students early on to consider becoming computationally adept or develop these computational thinking skills or know that they are accessible,” said Lee, who SACNAS has recognized or her efforts with the 2023 SACNAS Outstanding Mentor Award.

Last fall, Lee and her collaborators published their findings as an open-access article in the peer-reviewed journal Molecular Ecology Resources. In it, the researchers discuss how they developed the flexible undergraduate curriculum to leverage place-based research on environmental microbiomes and increase the number of Indigenous researchers in microbiology, data science, and scientific computing.

In the first iteration, MEM had 83 percent Indigenous students, representing 17 federally recognized tribes. Of them, 71 percent were female students, and 70 percent came from primarily undergraduate institutions, community colleges, and tribal colleges and universities.

“Some of these students might never encounter a computational course in their institution,” Lee said. "That's why this program is so important: Let's have fun and learn together in an environment without getting graded. It's more just like a research experience.”

She added that it is also fun for those coming from a research university.­­­­

“We've had some people from R1 institutions like CU Boulder come. After chatting with them, they're like, I'm at predominantly institution. It's fun to come here and be in a cohort of a lot of people of color.’”

Study: Monitoring environmental microbiomes: Alignment of microbiology and computational biology competencies within a culturally integrated curriculum and research framework