Transect Magazine: From Satellites to Single Cells

This story originally appeared in the Summer 2025 edition of Transect.

Early on a mid-April morning, a group of scientists headed down the dock at Bigelow Laboratory onto the institute’s research vessel, loaded to the gills with equipment. It was that time of year in Maine when it could still be cold and blustery or balmy with bright skies. Fortunately, this day was the latter — and not just because it would make the long day on the boat more pleasant.

The team was out on the water for the Gulf of Maine North Atlantic Time Series, which provides an unparalleled view of changing conditions and biological communities in the Gulf of Maine. Funded by NASA, GNATS is used by the agency to validate its satellite observations of ocean color with on-the-water measurements (hence, the need for a clear day to ensure an unobstructed satellite overpass!).

After several years of uncertainty, GNATS is back this year under the leadership of Senior Research Scientist Catherine Mitchell, using the R/V Bowditch to collect data on the Gulf ’s optical properties, temperature, nutrient levels, and more. Timed with last year’s launch of PACE, NASA’s newest and most advanced ocean color satellite, the next era of GNATS will enable significant advances in scientists’ understanding of how the Gulf of Maine is changing and how satellites can be used to study the ocean.

Mitchell has partnered with Senior Research Scientist Julia Brown to make sure of that.

A collaborative project proposed by Brown and Mitchell was recently funded by NASA. They aim to link remote sensing, and satellite-based measurements of ocean color, with in-situ measurements of the diversity and activity of microbes. It’s the perfect marriage of two of Bigelow Laboratory’s most established areas of expertise.

The ultimate goal is to develop oceanographic models that incorporate information on what microbes live in the Gulf of Maine and what they’re actively doing. With that information, researchers could use satellites to better understand — and potentially even predict — how those communities, and the biogeochemical processes they drive, are changing. In the process, the team will advance computational tools to link data collected at wildly different temporal and spatial scales, creating new ways of studying even the most dynamic and remote parts of the ocean.

“Microbes drive ocean biogeochemistry,” Brown says. “With this project, we’ll be able to use satellites to look into the past, and even project into the future, to see how those essential microbial communities and the services they provide are changing.”

“I think this reflects one of the best parts of being at Bigelow,” Mitchell adds. “My background is in physics, and Julia is a microbial biologist. There are not many institutions where we’d be able to find each other and do this kind of work together.”

AN INTERDISCIPLINARY LEADER

Since its earliest days, Bigelow Laboratory has been a leader in the field of satellite oceanography, using satellite-observable qualities like color to understand the abundance and type of organic matter in the ocean. Likewise, the institute has been a leader in advancing genetic sequencing tools to characterize microbial communities down to the level of DNA within a single cell. And interdisciplinarity is even baked into the institute’s guiding principles. But combining those areas of research has remained a challenge.

So, scientists got together for regular “Café Code” sessions to brainstorm how to leverage their similar computational approaches to bring together different areas of expertise. Out of those discussions, Brown and Mitchell wrote a white paper on how remotely-sensed satellite information could potentially be used to predict the diversity of microbial communities at a global scale.

Then, everything fell into place.

Just as the researchers finished their white paper, the institute began offering kickstarter funds to support early-stage projects. At the same time, data began pouring in from the revolutionary Tara Oceans Expedition — an almost-three-year, 125,000-kilometer sailing trip around the world in the early 2010s where an international team collected both optics data and microbial samples.

“It’s become more common, but at the time, it was really rare for people to be measuring both those things on the same ship,” Mitchell says. “It’s opened up the door for all sorts of possibilities.”

Using the seed money, Brown and Mitchell began digging into how to pair ocean color and microbial information from Tara Oceans, asking whether that unique combination revealed any interesting patterns. For the most part, the answer was no.

“But there was this one sample on the Patagonian Shelf off South America that looked completely different from everything else,” Brown says. “It made us think that, maybe, in these dynamic shelf environments where everything is heterogenous and constantly changing, we might be able to see something. It was the seed of an idea within the seed of a project.”

A BOLD PROPOSAL

Late last year, leveraging those preliminary findings, Mitchell and Brown secured NASA funding to undertake their own sampling and continue exploring ways to link these different data sources.

Senior Research Associate Tim D’Angelo joined Mitchell and her team aboard the first GNATS cruise in April to kick off the sampling component of the project, and he and Brown will continue to join the expeditions for the rest of the year. At each stop along the transect, they’ll gather water samples to sequence for microbial DNA, which will tell them what microbes are there, and RNA, which will suggest what those microbes are doing. They’ll use a database of around 7,000 microbial genomes from the Gulf of Maine, already sequenced by researchers at Bigelow Laboratory, as reference to map out which microbes are present and active.

The next step will be to combine that biological information with optical data collected by instruments on the Bowditch that measure how much, and at what wavelength, light is reflected and absorbed by different kinds of organic matter. That will enable the researchers to understand the relationship between the microbial community and the abundance and type of organic matter in the water. Using those direct measurements from the boat will also help the team develop methods to accurately match the datasets, which can then be scaled up to use color data from satellites.

The final step will be to build models that use this relationship to understand and predict how the diversity and function of the microbial community is changing over time and space.

“We’re trying to match something collected from a satellite on a kilometer scale to an in-situ measurement from a single point in the ocean so, even with our modeling experience, there’s lots of exciting challenges we need to work through,” Mitchell says. “It’s definitely going to push our teams to learn new things.”

That bold approach is exactly what Bigelow Laboratory aimed to foster with its kickstarter projects, and that preliminary work was invaluable for getting this larger effort funded. Otherwise, Mitchell says, their plans may have seemed “impossible.” Brown adds that being able to leverage the GNATS cruises that were already planned and funded was another huge bonus for their proposal.

But both say that the real key to making this work happen is the institution itself.

“At Bigelow Laboratory, we’re all on the same team,” Brown says. “The expertise and reputation we have in these two separate areas helped. But really, it’s the collaborative environment that allowed this project to come together.”

Photo Captions:

Photo 1: A circle shows the Patagonian Shelf off the coast of Argentina where researchers identified interesting patterns in the potential relationship between ocean color and microbes during a seed project (Credit: NASA Ocean Biology Processing Group).

Photo 2: NASA satellite imagery shows how the presence of phytoplankton and other organic matter alters the color of seawater in coastal shelf environments like the Gulf of Maine (Credit: NASA PACE).

Photo 3: The Schooner Tara is pictured after completing its epic, multi-year journey across the global ocean, providing scientists with unprecedented data combining measurements on seawater optics and microbes (Credit: Yohann Cordelle).

Photo 4: Senior Research Associate Tim D’Angelo collects water samples during a GNATS research cruise while other scientists on board gather ocean color data (Credit: Catherine Mitchell).

Photo 5: Senior Research Scientist Julia Brown (right) begins to sequence the genetic information of microbial samples (Credit: Schmidt Ocean Institute).