Mapping the inner life of a mysterious ocean microbe

Diplonemids are among the most abundant and diverse single-celled organisms in the world’s oceans. They are commonly found in plankton communities and steadily become more abundant in the depths of oceanic environments, yet they remain some of the least understood forms of life on the planet.

In a new study, researchers at Arizona State University and international collaborators have produced the most detailed picture yet of how the model organism of this group is organized, and how it feeds, creating a foundational resource for studying a major but overlooked branch of life.

The study, published in PLOS Biology, was led by Jeremy Wideman, a researcher within ASU's Biodesign Center for Mechanisms of Evolution and the School of Life Sciences. He is joined by co-lead author Michael Hammond of the Czech Academy of Sciences and other U.S. and international collaborators.

As part of the study, the research team focused on Paradiplonema papillatum, a free-living marine protist — currently the only diplonemid species that can be genetically manipulated in the laboratory. Using advanced fractionation techniques to analyze the cell’s internal structure, the researchers identified nearly 5,000 proteins and traced them to 22 distinct compartments inside the cell, including the nucleus and mitochondria, revealing how its molecular machinery is organized and coordinated.

One of the study’s most striking findings involved digestion. The researchers discovered enzymes that can break down complex carbohydrates, such as those found in plants and algae, positioned on the cell’s outer membrane. This suggests that P. papillatum may partially digest food outside its body before internalizing the released products, a strategy that differs from the classic "engulfment" view of how certain single-celled organisms feed. Additional carbohydrate-degrading enzymes were found inside specialized compartments, indicating that digestion continues inside the cell after the material is taken in.

Together, these findings support the idea that diplonemids may specialize in consuming plant- and algae-derived material, making use of a varied diet of both carbohydrate as well as protein sources. Direct observations of diplonemid feeding in natural environments remain limited considering that the majority of diplonemids remain difficult to observe within the depths of the ocean. As such, molecular studies like this remain the most accessible solution to clarify the ecological roles played by these enigmatic single-celled organisms. 

Beyond digestion, the study also revealed unexpected flexibility in how the cell organizes its metabolism. The researchers found that metabolic pathways related to sugar processing and energy production are compartmentalized differently in diplonemids than in their closest relatives. These differences offer clues about how metabolic systems evolved early in eukaryoticEukaryotes are complex cells that include plants, animals and fungi. history. 

Evolutionary biologists are particularly interested in diplonemids because they retain many ancient genetic features thought to resemble those of the earliest complex cells. By clarifying how proteins are distributed across cellular compartments, the new dataset helps researchers identify which traits are ancestral and which evolved later.

The research provides a reference framework that other scientists can use to explore diplonemid biology, marine ecology and the evolution of complex cells.