Two Stanford Microscopes. 31 New Species. One Deep Sea.
What does it take to find 31 new species in just two weeks? According to a recent expedition aboard Schmidt Ocean Institute's research vessel Falkor (too), the answer lies in new bioengineering tools, new collaborations, and lots of passion for the deep-sea.
Stanford Bioengineering's Manu Prakash and a team of 20 midwater specialists from around the globe spent 2 weeks exploring the tropical South Atlantic off the coast of Brazil. The international team focused on probing the ocean's "midwater" — the largest biosphere on our planet, covering everything between the sunlit ocean surface and the seafloor. Using a combination of advanced imaging and onboard sequencing, the team confirmed more than two dozen new species in a fraction of the time this normally takes. Among the new species identified were gossamer worms, siphonophores, comb jellies, and giant single-celled rhizarians.
The Prakash Lab has been building imaging instruments that operate on research vessels for almost a decade - bringing capabilities previously only possible in the lab to the middle of the ocean. These custom tools, known as "The Squid" and "The Gravity Machine", paired with important collaborations with researchers and the Schmidt Ocean Institute, were central to the expedition's success.
The Squid is an open-source confocal microscope developed in the Prakash Lab, now licensed to a new company, Cephla, to bring it to market. Aboard the ship, Squid achieved something that had never been done before in seagoing research: imaging the living, three-dimensional internal cellular structure of a deep-sea organism in real time. The team used it to observe a large single-celled protist and watch how its internal architecture interacted with its glass skeleton — a feat that, until now, was not possible. Some of these rare deep-sea organisms have never been imaged alive before. The second tool is a specialized "virtual reality" microscope - often described by Prakash as a hydrodynamic treadmill for microbes called 'The Gravity Machine'. This microscope allows scientists to observe free-swimming organisms behaving naturally as if in an infinite tall water column.
Dr. Prakash says the work "opens a new door for researching deep-sea physiology, linking cellular architectures to organism function." Understanding how these organisms adapt to the depths of the ocean is only possible if we can keep them alive under the pressure and darkness they call home. Real-life observation turns biology that used to be inferred into biology you can directly observe.
This expedition demonstrates how contemporary bioengineering technologies are setting the terms of what could be discovered. The research and instruments our bioengineers design on campus could set the standards for understanding Earth's largest, least-explored habitat. In addition, tools developed by the Prakash Lab, like The Squid, are all open-source, meaning any lab, anywhere, can build one and use these imaging tools to ask their own questions.
This expedition is a reminder of what bioengineering looks like when it leaves the building: not a device borrowed for a field trip, but a specialized instrument that can determine what is possible to see and study in the first place. The Squid and the Gravity Machine were built to answer questions in the open ocean — and they ended up rewriting what scientists can learn about life in the largest, least-explored habitat on Earth.
Read the full press release from Schmidt Ocean Institute here.
