Sallie Penny Chisholm - Ocean microbes display a hidden talent: releasing countless tiny lipid-filled sacs

MIT finding could one day lead to new approaches for manufacturing biofuels.
Nancy W. Stauffer | MIT Energy Initiative
July 7, 2014

In the search for a renewable energy source, systems using algae look like a good bet. Algae can grow quickly and in high concentrations in areas unsuitable for agriculture; and as they grow, they accumulate large quantities of lipids, carbon-containing molecules that can be extracted and converted into biodiesel and other energy-rich fuels. However, after three decades of work, commercially viable production of biofuels from algae hasn’t been achieved, in part because the processes needed to break apart the algae and recover the lipids are costly and energy-intensive.

Another option is to use bacteria. For the past 25 years, Sallie (Penny) Chisholm, the Lee and Geraldine Martin Professor of Environmental Studies, has been studying Prochlorococcus, an ocean-dwelling bacterium that she calls “a pretty spectacular organism.” Of all organisms that perform photosynthesis, this single-celled bacterium is both the most abundant and the smallest — less than 1 micron in diameter. It accounts for fully 10 percent of all photosynthesis on Earth and forms the base of the ocean food chain. It also has the smallest genome of any known photosynthetic cell. “Three billion years of evolution has streamlined its genome, and it now contains the least amount of information that can make biomass from solar energy and carbon dioxide,” says Chisholm, who has a joint appointment in civil and environmental engineering (CEE) and biology. “It makes sense that we try to understand it — inspired by its simplicity — and see if we can use this understanding to help us design microorganisms that efficiently produce biofuels directly from sunlight.”

In 2010, Chisholm’s much-studied bacterium delivered a surprise: As it grows, it naturally releases small, spherical, membrane-bound vesicles containing fatty oils related to those that make algae so appealing. This was a serendipitous discovery. In 2008, Chisholm’s group needed some images of Prochlorococcus for a publication. Using a scanning electron microscope, then-graduate-student Anne Thompson PhD ’10 took the images — and they showed small spheres near the surfaces of the Prochlorococcus cells (see image in the slideshow below). The spheres remained a mystery to the ocean biologists until 2010, when Steven Biller joined Chisholm’s group as a postdoctoral associate in CEE. Based on his work with soil bacteria, he proposed — and subsequently confirmed — that the spheres are lipid-bound vesicles.

That finding is remarkable for two reasons. While many species are known to release vesicles, the behavior has never before been observed in a marine organism—and it could significantly change today’s understanding of marine ecosystems, including their influence on the global carbon cycle. “Prochlorococcus is making organic carbon from sunlight and then packaging it up and releasing it into the seawater around it,” says Chisholm. “What we need to figure out now is, Why and how? And what role do these vesicles play in ocean food webs and the ocean carbon cycle?”

Equally surprising, this is the first observation of vesicle release in an organism that performs photosynthesis. The implications for industrial use — including biofuels production — are significant. Given just sunlight, carbon dioxide, and water, Prochlorococcus would continually release lipid-containing vesicles, which could be collected without disturbing the growing bacteria. “With algae, retrieving the lipids requires destroying one batch of cells and starting with a new batch,” says Biller. “With Prochlorococcus, it could be a ‘continuous culture.’”

Technical challenges, new insights

Chisholm stresses that such commercial applications are “way down the road.” For now, research in her lab focuses on developing a fundamental understanding of the newly observed behavior. For example, how often does a Prochlorococcus cell release vesicles? How many does it release? And what’s inside them?

To answer those questions, Biller overcame a series of technical challenges. First he developed improved methods of culturing large quantities of Prochlorococcus cells. Then he designed techniques for filtering off the vesicles and concentrating and purifying them — while keeping them intact. But his biggest problem was how to count the individual vesicles. Standard methods of counting particles don’t provide sufficient resolution to look at the vesicles, which are less than 100 nm in diameter. After some trial and error, Biller was successful in adapting recent advances in nanoparticle analysis techniques to studying these tiny bacterially derived structures.