New Study Traces how Cells Learned to Live Without Oxygen

A version of this story originally appeared on ASU News.

Mitochondria are among the most important biological structures. These tiny compartments help generate the energy that powers the cells of all eukaryotes — all the organisms with a complex cell containing a nucleus — from humans to microscopic amoebae.

The origin of mitochondria was one of the most dramatic events in the history of life. More than a billion years ago, a bacterium took up residence inside another cell, eventually becoming part of the cell itself and giving rise to a partnership that persists in nearly every eukaryote today. Some of the organisms that thrive in oxygen-free environments, though, have radically altered mitochondrial genomes. In some cases, they’ve lost the entire organelle itself, an evolutionary process that scientists still don’t fully understand.

In a new study in the journal Current Biology, a team featuring researchers from Bigelow Laboratory for Ocean Sciences sequenced tiny amounts of DNA from single isolated cells sampled from one of these low-oxygen environments: Edgecomb Eddy, a mudflat in coastal Maine.

By analyzing the genomes of unusual single-celled eukaryotes, the scientists discovered a previously unknown lineage estimated to be about a billion years old, closely related to an oxygen-independent group called Breviatea. Interestingly, Breviatea lack mitochondrial genomes and have highly reduced mitochondrial functions; in contrast, the newly discovered microbes possess some of the most complex mitochondrial genomes ever observed. This mix of cellular designs in two related lineages provides scientists with a valuable opportunity to study how cellular structures like mitochondria evolve over time.

The findings highlight an important lesson about evolution: even features that seem universal can sometimes be lost if organisms find alternative ways to perform the same tasks. Instead of relying on mitochondria, these microbes appear to have reorganized their metabolism so that key chemical reactions happen elsewhere in the cell. In effect, they have rewired their internal systems to cope in this extreme environment.

“While intertidal mudflats are a familiar sight on the Maine coast, the dark sediments of places like Edgecomb Eddy harbor microbial communities that remain largely unexplored,” said Bigelow Laboratory Senior Research Scientist John Burns, a co-author on the study. “Discoveries from these overlooked environments reveal unexpected ways life can evolve and thrive.”

“While the likelihood of discovering a new major lineage of animal is near-zero, much of microbial diversity remains unknown and therefore major discoveries in diversity are still possible in our field,” added corresponding author Jeremy Wideman, a professor at Arizona State University. “In this case, we have identified a major lineage representing a missing link in evolution. By looking at their genomes, we can begin to understand how a particular lineage adapted to a low-oxygen environment.”

Because mitochondria typically generate energy using oxygen, they become less useful in environments where oxygen is limited. In environments where oxygen is scarce, some microbes have evolved these adapted versions of mitochondria that no longer function as typical energy producers and carry out only a small subset of mitochondria’s usual tasks. In even rarer cases, organisms like Breviatea appear to have evolved without mitochondria entirely.

Single-cell sequencing techniques, like those revolutionized by Bigelow Laboratory’s own Single Cell Genomics Center, are providing scientists new ways to understand these changes and illuminating just how adaptable cells can be. By examining how mitochondria can be reduced, transformed, or lost, researchers gain clues about the original partnership between ancient cells and the bacteria that eventually became mitochondria.

“By overcoming the limitations of earlier research methods, single-cell genomics provides unprecedented insights into the remarkably complex and largely unexplored microbial life that hides in plain sight — in every drop of mud lining Maine’s coast,” said co-author Ramunas Stepanauskas, Bigelow Laboratory senior research scientist and director of the Single Cell Genomics Center.

While the microbes uncovered in the new study are tiny and obscure, their biology carries important implications. Although mitochondria are nearly universal among modern cells, these rare exceptions reveal how evolution can rework cellular machinery in unexpected ways, helping shed light on early evolutionary events that shaped complex life.

The study is led by ASU Postdoctoral Research Scholar Anna Cho and co-authored by Bigelow Laboratory Senior Research Scientist Nicole Poulton and researchers from the U.S. Department of Energy Joint Genome Institute at Lawrence Berkeley National Laboratory and University of California, Merced. Funding for this research was provided by the National Science Foundation, the Department of Energy, and Bigelow Laboratory. Work was done by the Joint Genome Institute, a DOE Office of Science User Facility.

Photo: Edgecomb Eddy in July 2021 (Credit: John Burns).