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The secret lives of plankton

Tiny plankton play a huge role in regulating natural systems, but they remain poorly understood. Stanford bioengineer Manu Prakash leads an international effort to develop innovative, low-cost tools that could help enable citizen scientists to monitor oceans and contribute to climate change solutions.
Plankton under a microscope.
Tiny plankton play a huge role in regulating natural systems, but they remain poorly understood. | tonaquatic / iStock

As many as 100 billion lifeforms – about the number of people who have ever lived on Earth  – can be found in a liter of seawater. These microscopic organisms, known collectively as plankton, are the foundation of a global food chain, producers of about half the oxygen we breathe, and climate change superheroes capable of sequestering massive amounts of atmospheric carbon for thousands of years. They are also scientific mysteries, poorly understood due to high costs and erratic funding for research at sea.

Stanford bioengineer Manu Prakash dreams of revealing the secret lives of plankton, and harnessing their outsized powers. He leads an international team of researchers developing innovative, low-cost tools, such as a rotating microscope and an easy-to-use plankton sampling process, that empower citizen scientists to contribute to our understanding of ocean health and biodiversity.

“The ocean is a life-saving technology – Earth’s heart and lungs – but our perception of what it does is so primitive,” said Prakash, an associate professor of bioengineering in the Stanford School of Engineering. “You cannot fix what you don’t understand. Observation is the most fundamental tool scientists have for understanding.”

Video by Madison Pobis, Rob Jordan, and Alexandra May Smith

For Prakash, who grew up in India and first saw the ocean at age 25, the effort is powered by a sense of wonder and existential imperative. His first time on a boat, about eight years ago, Prakash and his fellow researchers came upon a swath of bioluminescent plankton glowing in the silent darkness of the open ocean. “You kind of realize how small you are compared to this planet,” Prakash said. “Completely untethered, and far away from any other civilization – in that loneliness is beauty. It was a spark that made me think this is the next challenge. I really have to understand this.”

To realize Prakash’s visions for new observation tools, he has brought into his lab researchers that span disciplines, such as machine learning, computer science, fluid mechanics, cell biology, biochemistry, architecture, optics, physics, oceanography, and even visual arts and traditional tool making. The aim is to build long-term data sets of plankton migrations, and map future behavior based on predicted ocean conditions. This, in turn, could help us understand what organisms are present where in a dynamic ocean. Perhaps most  importantly, it could unveil these organisms’ behaviors in current ocean conditions and their potential behaviors in altered ocean conditions of the future.

In the years and many observations since Prakash’s first ocean expedition, his sense of our wonder has only grown. “I've seen organisms that are smaller than one-tenth the size of a grain of rice chase each other, like the whole African savannah play out in a tiny little drop of water,” he said. “When you multiply that by the size of the ocean, you start realizing we don't have methodologies to understand the complexity at these scales.”

A plankton world

Little is known about plankton’s distribution and variation. At the same time, about 40 percent of people on Earth live on or near a coastline, and many make their living or find recreation on the sea. Prakash and a team of scientists, engineers, makers, and sailors from France, the U.S., and New Zealand - wondered how to harness this human capital. So they created Planktoscope, an international initiative to engage people in designing and deploying low cost instruments to study plankton, and put their findings in public databases.

In partnership with PlanktonPlanet, another gathering of plankton enthusiasts, the team tested simple, low-cost sampling process, including a net to gather plankton, and a manual pump to transfer them onto a filter. Citizen scientists then dry out the membranes in their boats’ gas-cookers, and mail them to a lab for analysis. Using this protocol, 20 crews of citizen sailors – ‘planktonauts,’ as the researchers called them – were able to build a “planetary dataset of plankton biodiversity” showing scientists which organisms are where.

The researchers acknowledge that planktonauts will not be able to gather the sort of comprehensive data that oceanographic vessels routinely collect, and frame the citizen science effort as a complement to, not a substitute for intensive expert research. Deployment of the first kits on key navigation loops and routes started in 2023, and an ongoing citizen science survey of global surface plankton is set to launch by the end of this year, according to Prakash.

The PlanktoScope

Rather than send samples to a lab for analysis, citizen scientists could do it themselves, Prakash reasoned. So, together with participants from around the world, his lab developed an open source imaging platform that matches the quality of much larger and more expensive commercial instruments. Called the PlanktoScope, it is portable and easy to operate from any Wi-Fi enabled device. Its components are off the shelf, easy to find, and the necessary materials cost less than $800 in total. The designs use a laser-cut framework, and can be made with materials ranging from acrylic and recycled plastic to wood, metal, and fiberboard. An open-source single board computer controls the electronics and processes the images.

Over the course of more than 20 oceanic voyages in a short period of time, the PlanktoScope has demonstrated its capacity to analyze plankton in field conditions. During a 45-day scientific expedition to the Arctic, the Planktoscope collected data from more than 200 field stations and continuously monitored plankton in open waters and under ice cover. On a two-month ocean journey from France to Chile, the device brought back results that matched up with previous observations showing that surface plankton compositions are essentially controlled by nutrient limitations. Prakash’s passion for making scientific observation accessible led him to post detailed Planktoscope manufacturing instructions on the project’s website. Hundreds of people around the world have built and replicated the tool since then.

Prakash and researchers in his lab have distributed more than 150 Planktoscopes for citizen science applications ranging from monitoring coastal aquaculture in California to finding harmful algal blooms in Indonesia. Thibaut Pollina, a former researcher in Prakash’s lab and co-inventor of the Planktoscope, currently manufactures the device for sale to people who don’t want to build it themselves.

“It’s a joy to see this tool in the hands of people I have never met,” Prakash said.

The "gravity machine”

Perhaps the most revolutionary of Prakash’s plankton-observation tools is something he jokingly calls the "gravity machine." Because plankton’s daily migration between the ocean depths and surface can span tens of thousands of feet and many days, there is no effective way to watch it unfold. To capture this journey, Prakash and researchers in his lab developed a vertical tracking microscope based on what they call a “hydrodynamic treadmill.” The idea involves a simple yet elegant insight: a circular geometry provides an infinite water column ring that can be used to simulate ocean depths. Organisms injected into this fluid-filled circular chamber move about freely as the device tracks them and rotates to accommodate their motion. A camera feeds full-resolution color images of the plankton and other microscopic marine critters into a computer for closed-loop feedback control.

Researchers using a rotating microscope.
Stanford researchers Manu Prakash and Deepak Krishnamurthy use a rotating microscope that they developed to observe a single-cell diatom, a type of plankton, as it changes its density to move through water. | Hongquan Li

With funding from the Big Ideas for Oceans program of the Stanford Doerr School of Sustainability’s Oceans Department and the Stanford Woods Institute for the Environment, Prakash is developing ways for the rotating microscope to recreate changing ocean characteristics, such as light intensity, pressure, and water temperature, creating what the researchers call a “virtual reality environment” for single cells.

“We will create and emulate every single parameter that plankton can perceive,” Prakash said. “That's really the magic of technology. I could program the machine to be emulating the Mediterranean or Chukchi Sea.”

Perpetual innovation

Prakash and his fellow researchers in the lab envision making versions of all of their tools that are autonomous and portable, able to take measurements onboard any boat, and available – via satellite – so students and others around the world can control them and analyze resulting data. The researchers are expanding a library of parts that allows people to reconfigure the instruments in many different ways. They are also putting together an online data set of plankton behavior video footage for more than a thousand different species, the largest behavioral data set for aquatic species.

“There’s a lot of anxiety around the collapse of ecosystems," Prakash said. “Every time I’m depressed I think about the aesthetic and the beauty of the microscopic world. It brings me out every single time. It’s brutal. It’s very unorthodox. It’s very non-intuitive. But there’s a lot of hope because you just see the abundance, you see how powerful these tiny creatures really are."

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