Masters of Microbes

Team of UM Scientists Brings Ocean Research Techniques to Flathead Lake

By Heather Fraley
UM Environmental Science and Natural Resource Journalism Intern

FLATHEAD LAKE — John Ranieri remembers standing in the back of a 200-foot-long ship one night and feeling a kind of solitude he had never felt before. As the sea breeze brushed his face, he realized that if he fell off the ship, he would never be found. He was spending a month at sea on the Pacific Ocean, on his first ever research cruise. There were no other ships for miles, and over 30 days the only land animal he saw was one forlorn bird.

Ranieri is a member of a research team based at the University of Montana’s Flathead Lake Biological Station near Polson, Montana. He works for Associate Professor Matt Church, an oceanographer and aquatic scientist who studies microscopic life. Church came to UM’s bio station from the University of Hawaii two years ago.

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The remotely operated vehicle is prepared for a month-long sampling trip on an ocean research cruise that Matt Church and Emma Wear went on this past June. Photo by Dr. Emma Wear

His Church Lab for Microbial Biogeochemistry and Ecology brings knowledge learned on the open ocean to Flathead Lake.

Church is among the leading researchers in ocean microbial ecology. His work is unique because he runs an oceanography lab that also does work on lakes. Most aquatic scientists work either on lakes or on oceans, creating two distinct camps of people, with little crossover.

“Ironically, many of the techniques or methodologies are directly transferable,” Church says.

Some people in Church’s lab have lake backgrounds and some have ocean backgrounds. They are finding that the “lake people” and the “ocean people” can learn a lot from one another.

Just as a ship in a bottle is a scaled-down version of a sea-going vessel, microbial research on the lake is somewhat like a scaled-down version of research on the ocean.

The lab’s ocean sampling sites can be over three miles deep, vastly outstripping Flathead Lake’s maximum depth of just under 400 feet. On the lake researchers use smaller boats, smaller research tools and far less cable.

One of the ocean research tools that the team is adapting for use in Flathead Lake will help them more efficiently collect water samples. The device, called a rosette, looks a little like a giant pack of dynamite. Several different cylindrical water collection tubes are positioned around a circular frame, and the computer in the device is programmed to close each tube at different depths. These tubes collect an important piece of data from the water: microbes.

Why Study Microbes?

Church studies microbes from the clear, cold water of Flathead Lake that can’t be seen by the naked eye. These include bacteria and single-celled organisms from several other taxonomic groups. The microscopic community in a lake is vital to how a lake functions as a whole, but it hasn’t been extensively studied in Flathead Lake.

Microbes are tiny but mighty. They are like invisible maintenance elves that keep the world running smoothly. They are found everywhere on the planet, including under the earth’s crust, on human bodies and in the atmosphere. Microbes are biologically old, on Earth for over 3 billion years. They can persist in dark, pressure-filled environments, can recycle nutrients and form the very bottom of the food chain.

Microbes are responsible for making the Earth a place that can sustain life, and ocean microbes produce half the oxygen in the atmosphere.

“We would not be here if it weren’t for microorganisms,” Church says.

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Lab Technician John Ranieri prepares a sampling bottle to drop to depth on the Flathead Lake Monitoring Program. Photo by Heather Fraley.

Ranieri, who is a research associate and functions as a jack-of-all-trades for the Church Lab, performs much of the lake fieldwork. He says that people historically have viewed zooplankton as the bottom of the food chain, but microbes are even further down the rungs of the ladder.

“Microbes are even smaller, and even less people care about them,” Ranieri jokes. “But the zooplankton are eating those microbes. If we can understand what changes the microbial community and what nutrients they’re able to recycle at different times of the year, then that is ultimately going to affect the zooplankton communities, and that’s going to affect the fish communities.”

Flathead Lake is a well-known recreational fishery, so anything affecting the fish is of broad interest to the residents and visitors, as well as to agency managers and scientists.

The Church Lab is looking at how the microbial communities in the lake work. To do this, researchers are using genetic techniques similar to those commonly used in ocean research. By analyzing the DNA in the water samples they collect, they look at which microbes are present where in the lake and how many there are at different depths during changing seasons.

Soon the researchers plan to start using metagenomics. Where genetic techniques look at specific genes of an organism, genomics look at the entire genetic profile of an organism — the compilation of all the genes — to decode what ecological functions that organism might perform.

Church’s graduate student Kate Evans will be helping with this project. She loves using math and computer modeling. She also will work with a lot of long-term time series data.

Time Matters

One of the team’s goals is to start tracking changes in the lake’s microbial communities over time. The scientists will add their genetic and genomic data to the long-term Flathead Lake Monitoring Program ongoing since the late 70s. Evans is looking forward to modeling some of the long-term data to find out what’s controlling certain patterns.

“There are a lot of really rigorous math ways that you can get into it that are often untapped,” she says.

Long-term projects are particularly attractive to Church because they put new data into context and can generate future research questions. Church has been involved in another long-term monitoring project, the Hawaii Ocean Time-series (HOT) program, where he served as the principal investigator, and his lab continues to conduct research as part of a project called Simons Collaboration on Ocean Processes and Ecology (SCOPE) at a time-series field site located 62 miles north of the island of Oahu in Hawaii.

What Does it Take to be an Ocean and Lake Researcher?

Joining Church’s Lab is not for the faint of heart. All of the members are stress-tested on research adventures like ocean research cruises. Church calculates that he’s spent a combined one year of his life on the open ocean, and he even met his wife, Holly, on an ocean research cruise. His longest research cruise — 48 days — was in the Antarctic.

“I encourage people who are working with me to go out to sea, and I think it’s sort of a once-in-a-lifetime kind of opportunity,” he says.

Church encouraged Ranieri to experience ocean research, and he has the perfect personality for it. Ranieri gives the sense that not much fazes him. He also possesses an important trait for surviving ocean cruises: a good sense of humor. (One of his running jokes is to steal one decoration per holiday from the office door of a particularly holiday-minded co-worker. His office nameplate now sports a shiny green shamrock and sparkling red heart).

Every member of the lab also has jaw-dropping amounts of research experience at the cutting edge of their fields.

Emma Wear is a postdoctoral researcher in Church’s lab. Wear met Church at the University of Hawaii when she was working on her Ph.D. and took his microbial oceanography summer class. When Church moved from Hawaii to the Biological Station and advertised for postdocs, she immediately applied.

Wear just finished her first month-long ocean cruise with Church in June, funded by the Gordon and Betty Moore Foundation, a private foundation interested in biological conservation.

This most recent cruise focused on the ecosystem at the very bottom of the ocean, known as the abyssal sea floor. Other than surface fishing, this ecosystem is virtually undisturbed by human activity. It’s escaped dramatic alteration because it’s so deep under the surface.

The goal of the research cruise was to catalogue the organisms present in the ecosystem before the start of some planned deep-sea mining. Wear catalogued manganese nodules. These are mysterious slow-forming growths of manganese and other metals packed together that grow at the rate of millimeters per millions of years.

Wear says that the thrill of discovery was part of what made the cruise so alluring for her. She’s interested in how dissolved carbon like proteins and detritus from dead animals cycles in the water. Carbon cycling at the surface of the ocean is well-known because it’s all based on sunlight, but what’s less-known is what drives microbes in the deep ocean sediments where the sun doesn’t reach.

While Wear usually samples surface water, this time she worked with sea-floor sediments.

The particular area the crew reached is remote in distance, as well as in depth. It took Church and Wear four days of continuous boat travel just to reach the sampling site.

“That’s why it’s a month-long cruise,” says Wear. “By the time you get out there, you might as well stay there for a while.”

Being on this ocean cruise presented some striking challenges for Wear.

For example, the frustrating part of sediment collection was that the sediments sometimes were too sandy to stay in the collection tube on the remotely operated unmanned underwater vehicle.

Wear would stay up at all hours collecting samples. Watching her precious sample fall out of the collection tube in the wee morning hours was frustrating.

“It’s less funny at 3 o’clock in the morning,” she says.

Another challenge that took some getting used to on a long-term cruise was the lack of space to walk. She usually walks her dog every day. On the boat there was really nowhere to go.

She also missed the color green.

“You don’t see green things for a full month other than the salad bar,” she says. “Then eventually the salad bar starts rotting and goes away. It’s great being back here in the summer, because I get to see all the green stuff that I missed.”

She agrees that there are parallels between ocean and lake research, and that an ocean background can make her that much more qualified to study lakes.

She says researchers are asking similar questions in both environments about microbial metabolism, and they are using some of the same techniques. Wear, who is an “ocean person,” will be involved in the genomics research on Flathead Lake, while she continues to do work on the ocean following the cruise.

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Lab Technician John Ranieri prepares a sampling bottle to drop to depth on the Flathead Lake Monitoring Program. Photo by Heather Fraley.

Trista Vick-Majors is another postdoc in Church’s lab. She also met Church through his summer microbial oceanography class in Hawaii. She’s overcome motion sickness to go on a two-week ocean cruise, but as a “lake person,” the majority of her background lies in studying microbes in ice-covered Antarctic lakes.

During her Ph.D. research, she was part of a crew that did some of the first sampling of subglacial lake water. Her team used a giant hot water drill to put a hole through the Antarctic ice sheet and drop sampling gear 800 meters down to the water. Vick-Majors was among the first to definitively show that there were microbes in Antarctic subglacial lake water.

“There are plenty of them,” she says with a smile, as she pours liquid into a graduated cylinder in the Bio Station lab.

Vick-Majors currently investigates if microbes are responsible for producing extra methane found in the water of Flathead Lake.

The lab’s theory is that certain microbes in the lake can separate methyl groups from organic compounds to produce extra methane. Church has done research on this phenomenon in the ocean, and now he’s finding it may apply in Flathead Lake as well. Vick-Majors is feeding lake microbes a compound called methylphosphonate and looking for production of methane.

Methane is thought to be produced exclusively by microbes growing without oxygen, but Flathead Lake is well-oxygenated. The possibility that methane is produced in well-oxygenated lake water is exciting. It opens up a whole new pathway of methane production.

Since methane is a powerful greenhouse gas, this research is important in the face of changing climate.

For Ranieri, working for Church has been a great experience. The ocean cruise made him feel like a real scientist straight off the Discovery Channel that he watched as a kid.

Part of the reason he came to the Flathead Lake Biological Station was to join a place full of opportunities for collaboration and innovation. His previous experience working on wildlife biology projects showed him how easy it can be to focus on one thing and not look at the other pieces of ecosystem. He enjoys the crossover between lake and ocean work.

“It’s cool how much overlap there is,” he says, “and how when you bring those two knowledge bases together, you can really understand a lot more about the lake in a faster time.”

For further updates on the research conducted at the Church Lab, or for more information about the recent deep-sea research expedition in the Pacific Ocean, visit the Biological Station website at


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