Annual Report 2020

Otto X. Cordero Explores the Relationships Within Microbial Communities

Life Sciences

When microbial ecologist Otto X. Cordero describes his approach to understanding complex societies of microbes, he pivots to talking about cars. 

“If I ask you how a car works, and you give me a list of parts, I can’t do anything with that,” says Cordero, an associate professor at the Massachusetts Institute of Technology. “But if you tell me there’s an engine that produces movement, and a wheel that can steer, then that makes more sense.” 

Likewise, when it comes to microbial communities, biologists understand the parts — the individual species. But Cordero wants to identify the engine and the wheels, to build a more functional description of how the species work together to create microscopic guilds that break down organic matter — a job vital to life on Earth.

“The interconnection between the Earth and microbes is just amazing,” he says. “But we understand very little about how these diverse communities of organisms work.”

To that end, Cordero co-leads the Simons Collaboration on Principles of Microbial Ecosystems, or PriME. Now entering its fifth year, PriME brings together researchers across many disciplines to understand how microbes assume their well-defined roles — with no ‘chief microbe’ telling them what to do — and how multispecies microbial communities respond to and influence Earth’s ever-changing environment.

Doing so has required breaking from business as usual in microbiology, to approach the problem with an eye to the big picture rather than individual microbes. And although the collaboration employs many researchers worldwide to make that change happen, much of the vision trickles down from Cordero, whose eclectic background helps him approach microbiology from atypical angles.

Marine bacteria colonizing and consuming polysaccharide particles. The microbes are stained with a fluorescent dye. Credit: Otto X. Cordero

“He brings a really unique flavor to the research,” says PriME co-director Roman Stocker of ETH Zürich. “He’s very good at distilling [complex problems] into simplified questions and approaches.”

Cordero is a long way from where he started. Growing up in Ecuador in the 1980s and ’90s, he had no scientific role models. “I didn’t have any idea about what a scientist does or what a scientist looks like,” he says. But his grandfather — “a writer, a poet and a bohemian” — had a huge library in his home. “That sparked my interest in knowledge, learning and science.”

As an undergrad at the Polytechnic University of Ecuador, Cordero became fascinated with ‘artificial life’: computer simulations built on simple rules out of which complex collective behaviors emerge. He took this passion with him to graduate school at Utrecht University in the Netherlands. There he met Paulien Hogeweg, a pioneer of artificial life who was using the simulations to study everything from social behaviors to evolution. Under her tutelage, Cordero pivoted to biology. 

“He had this eagerness of doing science, of understanding things and using whatever means are available for doing it, and really getting into the subject,” Hogeweg recalls.

With Hogeweg as his dissertation adviser, Cordero became interested in the evolution of gene regulatory networks in microorganisms — the web of biochemical signals that allow microorganisms to sense the environment and alter behavior by turning genes on or off. But by the end of his Ph.D., he realized that if he wanted to understand evolution, he needed to understand ecology. 

So he once again crossed the ocean, to MIT for postdoctoral work, experimenting in the lab to better understand the microbes themselves. It was here that the seeds for PriME took root. His Ph.D. had been focused on mathematically modeling biological processes. But as an experimentalist, “I learned a lot more about what is actually happening with the lives of microbes,” he says. “I learned in more concrete terms how interconnected the planet is with microorganisms.”

Microbes en masse wield enormous influence. They produce more than half of Earth’s oxygen, form the marine food web’s base, and play a key role in recycling carbon throughout the environment. In the ocean, much of this recycling happens on motes of organic matter known as marine snow. When carbon-consuming critters such as phytoplankton die, they tend to stick together and form small, whitish flecks, which then sink. If that were the whole story, much of the ocean’s carbon would end up on the seafloor. But these ‘snowflakes’ are a buffet for microbes, who colonize the particles and scarf up the carbon, eventually returning it to the sea or atmosphere.

“That’s what we’ve been studying in our lab for the last five or so years,” says Cordero. “How the microbes assemble into complex communities on these tiny particles, and how their interactions mediate the degradation of organic matter.” The rate of that degradation is one of the tuning knobs influencing how much carbon is freely available on Earth.

Marine microbes growing on nutrient patches. All the microbes originated from the same liter of seawater, yet the patterns that emerge as they grow vary across the different micro-ecosystems. Credit: Rachel Szabo and Otto X. Cordero

Though the pandemic slowed things down, it didn’t stop the team from making discoveries. One thing they’ve learned in the past year is that although turnover among microbes on these particles is high, the basic jobs available stay the same. “You can see hundreds of different species coming and going,” he says. “The next day, you may see different species coming and going. And the next day, slightly different species.” But all those different species assume similar functional roles, depending on how they obtain food. “Degraders” harvest their food from the marine snow, “cheaters” steal from the degraders’ hard work, and “waste scavengers” munch on everyone else’s excrement. Identifying those roles has been a major achievement. “This to me is one of the main problems in the field,” he says. “How to go from this shopping list of species to a functional description of the system.”

The discoveries haven’t been limited to Cordero’s lab at MIT. The PriME collaboration encompasses nine labs worldwide, each focused on different aspects of marine microbial communities. At the University of Southern California, for example, biologist Naomi Levine and others recently reported on how marine microbes leverage competing evolutionary strategies. And Roman Stocker and colleagues have shown how the fluid flow created by sinking marine snow affects consumption rates.

“We have done a pretty bold experiment with this collaboration,” says Stocker. “We’ve brought in people from a variety of disciplines, including a number of people who have never before worked on the oceans.” 

Through the efforts of physicists, chemists, mathematicians and microbiologists, the team has established a new research platform by turning marine snow communities into a ‘model system,’ an archetype for further exploration, much the way that fruit flies are the classic staging ground for genetics research. 

“Now we have a platform to do really exciting things,” says Cordero. “We’re at a stage now where we can actually ask much better questions.”

Getting to this stage has required about 40 researchers across disciplines and around the globe to work together and try something new. But some of the success undoubtedly comes from Otto X. Cordero’s character — from his being someone who enjoys life and enjoys connecting with people from backgrounds as varied as his own. 

“Not everybody having the same background as Otto would be as good,” says Hogeweg. “I would more say it’s just … Otto.”