Ocean microbe’s unusual pair of enzymes may boost carbon storage, study suggests

Stanford scientists have discovered multiple forms of a ubiquitous enzyme in microbes that thrive in low-oxygen zones off the coasts of Central and South America

 News Release 17-Dec-2024
Stanford University

Stanford researchers have found a surprising genetic twist in a lineage of microbes that may play an important role in ocean carbon storage. The microbes, known as blue-green algae or cyanobacteria, have two different forms of a ubiquitous enzyme that rarely appear together in the same organism. 

“This is one of those great examples of science where you go out looking for one thing, but you end up finding something else that’s even better,” said Anne Dekas, an assistant professor of Earth system science at the Stanford Doerr School of Sustainability and senior author of the Nov. 25 study in Proceedings of the National Academy of Sciences. 

Billions of years ago, long before plants arrived on the scene, cyanobacteria invented oxygenic photosynthesis. In the process of producing food from carbon dioxide and sunlight, the widespread microbes released oxygen into the air, making our planet’s atmosphere hospitable to the array of life on Earth today. “Cyanobacteria are arguably the most important life form on Earth,” said Dekas. “They oxygenated the atmosphere of Earth and created a biological revolution.”

Special cyanobacteria

Like plants, cyanobacteria use an enzyme called ribulose bisphosphate carboxylase, or RuBisCo, to convert carbon dioxide into biomass. One of the most abundant proteins in nature, RuBisCo comes in several forms: The most common type, known as form I RuBisCo, often uses a structure called a carboxysome to selectively react with carbon dioxide but not oxygen, allowing photosynthesis to proceed efficiently. Organisms with a less common type of the enzyme, known as form II, lack a carboxysome and can effectively build biomass from carbon dioxide in environments where oxygen is scarce. 

Usually, organisms have only one form of RuBisCo, said lead author Alex Jaffe, a postdoctoral scholar in Earth system science. So he was surprised when he happened upon an exception to that rule while studying carbon fixation in ocean microbes. Jaffe was analyzing DNA from seawater samples collected from deep waters off the coasts of Central and South America when he noticed that some shallow water DNA samples had accidentally slipped in. He discovered that cyanobacteria in these samples seemed to have genes for both RuBisCo forms. “My initial reaction was this is probably wrong,” said Jaffe. 

Further research confirmed that both forms of the enzyme were present and actively used for photosynthesis in the cyanobacteria from shallow water, although additional testing will be required to understand how cyanobacteria use the two forms. “By having two versions,” said Jaffe, “it might allow you to remove more carbon dioxide from the water than if you only had one of them, or potentially to do it a little bit more efficiently.”  

Efficiency might be key to survival where the samples originated, in an oxygen minimum zone about 50 to 150 meters below the surface, where oxygen and light are both in short supply. “It’s very hard to live there,” said Dekas. “For a photosynthetic organism, when you have low light, you have little energy.”

Carbon storage and extra-efficient crops

The findings could help scientists anticipate how the ocean’s capacity to sequester carbon may shift as climate change expands low-oxygen zones. The revelation that some cyanobacteria have both forms of RuBisCo suggests they may store carbon more efficiently than previously understood and could proliferate along with expanding oxygen minimum zones. 

If two RuBisCos are in fact better than one, the finding could also lead to more efficient crop production. For decades, researchers have tried to engineer form I RuBisCo to enable crops that grow more with less fertilizer and water. “We’re looking forward to continuing to think about this with people who work on the plant engineering side to see whether it might yield some fruit, literally and metaphorically,” said Jaffe.

The findings gave Jaffe a new appreciation for life’s ability to adapt to challenging environments. “These genes, despite being central to organisms’ metabolism, can actually be quite flexible and can be reconfigured and shuffled in ways that we didn’t expect,” he said.

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Co-authors include Navami Jain, MS ’24, who worked on the research as a graduate student in biomedical informatics in the Stanford School of Medicine. Additional co-authors are affiliated with University of Washington; University of California, Berkeley; the Joint BioEnergy Institute; and Lawrence Berkeley National Laboratory. 

This research was funded by the Stanford Science Fellows program, the National Science Foundation, and the Simons Foundation.

 

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Journal

Proceedings of the National Academy of Sciences

DOI

10.1073/pnas.2418345121 

Article Title

Cyanobacteria from marine oxygen-deficient zones encode both form I and form II Rubiscos

Researchers explore carbon capture in fish farms to address climate change

Tons of carbon dioxide could be captured from the environment while removing toxic sulfide from fish farms

University of Connecticut

Scientists are exploring a new model for carbon capture in low-oxygen aquatic environments, such as fisheries, that will help address rising global temperatures and could potentially be cost-effective, a recent study published in Nature Food said.  

Lead researcher Mojtaba Fakhraee, an assistant professor of Earth sciences who will begin his appointment in August 2025, says traditional methods of reducing emissions are no longer sufficient to keep global temperature increases below 2 degrees Celcius, a goal set by the Paris Agreement.    

In recent years, scientists have turned to carbon capture — the process of capturing CO2 emissions from industrial sources — as a possible solution to address climate change alongside traditional efforts to reduce carbon emissions.   

Fakhraee, working with Noah Planavsky, professor of Earth and planetary sciences at Yale University, developed a model to explore how alkalinity production through enhanced iron sulfide formation in fish farms and other low-oxygen aquatic environments could offer a low-cost and efficient way to capture at least 100 million metric tons of CO2 annually. 

“We are in the situation right now that to be able to sustain that 1.5 degree threshold, we should be removing carbon from the atmosphere,” Fakhraee says. “There is no way around this point.” 

Fakhraee says the study focuses on fish farms because they are directly influenced by human activities and can be an ideal place for capturing carbon while reducing toxic sulfide concentrations. 

The researchers’ model found that adding iron, which reacts with accumulated hydrogen sulfide, increases alkalinity. This, in turn, raises carbonate saturation levels, enhancing the capture of CO2 from the environment. 

This model would be most effective in countries like China and Indonesia, which have abundant fish farms, the authors note. Fakhraee and Planavsky estimate that China alone could remove nearly 100 million metric tons of CO2 per year from the atmosphere. 

Fakhraee says this finding will also positively impact the success of fish farms, as the buildup of hydrogen sulfide can be toxic to fish, leading to increased mortality rates or fish becoming too sick to sell. The proposed model would reduce this toxicity, leading to larger fish populations and more sustainable, profitable operations. 

He added that this approach could be more effective than other methods of carbon capture because it would essentially permanently store the carbon.  

“It’s going to be stored on a time scale of thousands of years, which is much longer than the lifetime of CO2 in the atmosphere,” he says.  

Fakhraee says this is only one approach to carbon capture. However, if put into practice, it could make a significant impact on carbon emissions from fish farms.  

“This is just one possible pathway for carbon capture at a significant scale,” he says. “The co-benefit for this specific pathway is that it would help with neutralizing the carbon emissions from fish farms resulting in a more sustainable fish industry.” 

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Journal

Nature Food

DOI

10.1038/s43016-024-01077-9 

Method of Research

Experimental study

Subject of Research

Not applicable

Article Title

Enhanced sulfide burial in low-oxygen aquatic environments could offset the carbon footprint of aquaculture production