Illuminated sugars show how microbes eat the ocean's carbon

A team of chemists, microbiologists and ecologists designed a molecular probe (a molecule designed to detect e.g. proteins or DNA inside an organism) that lights up when a sugar is consumed. In the journal JACS they now describe how the probe helps studying the microscopic tug-of-war between algae and microbial degraders in the ocean.

“Sugars are ubiquitous in marine ecosystems, yet it's still unclear whether or how microbes can degrade them all,” says Jan-Hendrik Hehemann from the Max Planck Institute for Marine Microbiology and the MARUM – Center for Marine Environmental Sciences, both located in Bremen. “The new probe allows us to watch it happen live”, Peter Seeberger from the Max Planck Institute of Colloids and Interfaces adds.

Sugars capture carbon

Algae capture carbon dioxide and convert it into oxygen and organic matter. Sugars are a key part of this. However, not all sugars are easily broken down. Some are so complex that most microbes struggle to digest them. This allows carbon to sink to the ocean floor, where it stays for centuries until the right enzymes come along. Identifying which microbes digest which sugars has been a long-standing challenge, especially in complex microbiomes.

Lighting up sugar breakdown

To address this issue, the team employed automated glycan assembly to create a sugar labelled with two fluorescent dyes. These dyes interact via a process called Förster resonance energy transfer (FRET). Together, they function like a molecular switch. When the probe is intact, it remains dark. However, as soon as an enzyme breaks the sugar’s backbone, the probe lights up. Thus, the researchers can see where and when the sugar is degraded. In their experiments, the team tracked α-mannan turnover, a polysaccharide (long sugar chain) found in algal blooms. The glycan probe worked in purified enzymes, bacterial cell lysates, live cultures and even microbial communities.

“This research is a wonderful example of interdisciplinary collaboration between Max Planck Institutes. With our FRET glycans, we now have a new tool for researching phytoplankton-bacterioplankton interactions in the ocean”, says Rudolf Amann from the Max Planck Institute for Marine Microbiology.

Revealing hidden degraders 

By enabling the tracking of α-mannan turnover, this glycan probe opens up new avenues for studying microbial metabolism without the need for prior genomic knowledge. Researchers can now pinpoint active degraders in situ, map the progression of glycan breakdown through space and time, and quantify turnover rates in complex communities. This tool paves the way for deeper insights into glycan cycling across ecosystems, from ocean algal blooms to the human gut. By observing which microbes are activated and under what conditions, scientists can link specific enzymatic activities to environmental processes and ultimately gain a better understanding of carbon flux in the ocean.

“Sugars are central to the marine carbon cycle,” concludes first author Conor Crawford from the Max Planck Institute of Colloids and Interfaces. “With this FRET probe, we can ask: Who's eating what, where, and when?”