Ocean on a Tabletop: "Gravity Machine" Bridges Vast Scales, from Cells to Climate Change

Manu Prakash of Stanford University, left, and MBL Physiology course students collected seawater samples every day to use in lab experiments with the "Gravity Machine." Photo courtesy of Manu Prakash

By Diana Kenney and Alex Megerle August 29, 2024

Every day and night, the biggest migration on Earth takes place in the ocean. Trillions and trillions of small marine organisms – and the bigger ones that eat them -- descend to the ocean depths by day and rise to the surface layer at night, where they can graze and feed under cover of darkness.

Accompanying this enormous vertical migration is the fixation of carbon from the atmosphere by phytoplankton, the single-celled organisms that form the very base of the entire marine food chain. As organisms sink to the bottom of the ocean, some of this carbon ends up buried under the seafloor, where it stays sequestered for hundreds of thousands of years.

“It’s the world’s largest, most successful carbon sequestration technology that we don’t understand,” said Manu Prakash, associate professor of bioengineering at Stanford University. “And we don’t know how long it will continue,” he said, as the ocean changes with global warming, affecting the organisms that perform this giant migration.

Prakash joined the MBL Physiology course as a faculty member this summer to engage students in climate-change focused solutions using an ingenious device his lab invented, called the “Gravity Machine.”

This “app” for light microscopes allows scientists to measure, for the first time, single cells as they travel vertically over hundreds of meters, rising or falling in the ocean’s water column.

The "Gravity Machine" is an app for light microscopes that allows us, for the first time, to observe and measure marine microbes traveling hundreds of meters up or down in the ocean's water column. Bioengineer Manu Prakash of Stanford University, whose lab invented the Gravity Machine, joined the faculty of the MBL Physiology course this summer. He and course participants used the Gravity Machine to observe how "marine snow" forms and descends to the bottom of the ocean, carrying carbon along with it. Marine snow is tiny clumps of living and dead microorganisms and inorganic particles stuck together, which sink like little snowballs in the ocean. Credit: Sam Cummis

Prakash demonstrated the Gravity Machine, which looks like a transparent wheel, in the bustling Physiology course lab, wearing dark jeans and a T-shirt that proclaimed “Experiment Fail Learn Repeat.”

“The idea is, if you take a long tube and join the two ends together, it creates an infinite loop of water” to simulate ocean-scale distances, Prakash said. Inside the machine’s circular fluidic chamber was Woods Hole seawater, sampled from a boat that morning, carrying all kinds of marine microbes that displayed on the microscope’s video monitor.

“Now here’s a special cell, a dinoflagellate,” he said, pointing at the screen at a descending cell. He locked it into the microscope’s field of view. As the cell moved down, the wheel spun up, and as the cell moved up, the wheel spun down, powered by a machine-learning code tracking an individual organism.

“In the frame of reference of the lab, the cell is stationary. In its own frame of reference, it's sinking forever or rising forever,” Prakash said. “So we've been able to essentially create an ‘ocean on a tabletop’ using this framework.”

Linking Cell Physiology, Behavior, and Ecology

The only constant in the ocean is gravity, while all other conditions – light, temperature, pressure, etc. –shift as organisms move up or down in the water column. Accordingly, they constantly read cues from their environment to make behavioral decisions, such as diving or feeding.

The latest version of the Gravity Machine includes a “virtual reality arena” where environmental parameters can be adjusted, such as light to dark, specific temperature and pressure - to gauge how organisms integrate these environmental cues to pattern their behaviors.

With the Physiology course students, Prakash used the Gravity Machine to perturb seawater and create “marine snow”: tiny clumps of living and dead microorganisms and other particles stuck together, which sink like little snowballs in the ocean. The students adjusted various parameters, such as water temperature and acidity (which are rising as the climate warms) and observed how the marine snow first forms and its final fate as it sinks to the bottom, capturing carbon.

“The rate at which the snow goes down gives us, directly, the carbon sequestration rate,” Prakash said. “And that's the worry that we don't understand. How would biology react to environmental change to change this carbon sequestration process? And what is the tipping point? If this sequestration process stops any moment, it is estimated that the CO₂ in the atmosphere will instantaneously jump from 400 parts per million to 600 parts per million. But we have no understanding of this, from the perspective of cellular physiology. We know the process works, but we don't know why or how it works and how it would react to climate change. So the big thing we're trying to do is build a map of that.”

Prakash much appreciates the “living lab” that the MBL provides. “We are studying a real ecosystem as close to possible,” he said. “We go out on an MBL boat every day at 10:30 a.m. and bring fresh samples to the lab from a nearby bloom we spotted on satellites in the morning. Then we organize all the samples by lunch time, so we can do the perturbations that are naturally happening -- temperature, pH, adding microplastics, anything literally that we care about studying.”

“That gives you a sense of why we are at MBL: physically having this infrastructure and a boat ready to go any time,” he said. “We sample at different time points, even at night.”

In other collaborations, the Prakash lab has brought the Gravity Machine aboard seagoing research vessels, participating in 17 expeditions so far in regions from the Arctic to Antarctica, the Pacific and Atlantic Oceans.

“In a lot of cell biology and biology and general, we’ve forgotten about ecology in some sense,” Prakash said. “Molecular biology and ecology sort of split apart, 50 or 60 years ago. That was a big mistake. We cannot understand either of them in isolation.”

Tracking Marine Larvae

The Gravity Machine isn’t limited to observing single cells. It can also track the multicellular planktonic phase of larval marine invertebrates, when they are too weak to swim and are just carried by tides and currents.

The Prakash lab has measured larval shape, posture, orientation, and feeding and swimming behaviors for numerous marine species, including the purple sea urchin (S. purpuratus), acorn worm (S. californicum), bat star (P. miniata), and sea snails (Credidula sp.) (See Krishnamurthy et al., Nature Methods, 2020). The lab has run expeditions across the world since 2020, and the current behavioral database includes roughly 600 species collected across the planet.

In the future, by adding various modules to the microscope using the Gravity Machine, “we foresee measurements that directly link any planktonic cell’s physiological state, such as the phase of cell cycle, to its virtual depth in the water column,” the team writes.

Very much in line with the Physiology course ethos, Prakash reaffirmed the need to build new tools to tackle the big unknowns.

“Tools are an incredibly important aspect of thinking about what is possible and what you can actually do,” he said. “If you don’t make new tools, you can’t ask new questions.”

Learn More About the MBL Physiology Course