During a recent Pacific Ocean scientific cruise, temperature-controlled and light-shaded blue incubators house experiments on the deck of the ship. (image: Daniel Muratore/SFI)

If it werent for the oceans, our planet would be warming far faster. Oceans take up about 30 percent of the carbon dioxide emitted into the atmosphere each year, thanks in large part to marine microorganisms. Now, the results of a new study published on March 15 in the journal mSystems may lead researchers to rethink the role of these microorganisms in the oceanic carbon cycle.

The work holds implications for climate modeling. Scientists have long assumed that marine microorganisms have a certain universal average ratio of carbon to nitrogen. Those assumptions underlie computer models of how the climate is changing. 

In the study, researchers measured the carbon-to-nitrogen ratio in marine microorganisms living in a "dead zone" off of Mexicos northwest coast. The authors found that the ratio can vary in DNA and proteins within the microorganisms depending on nitrogen levels in the surrounding environment. 

Our current way of doing Earth system climate modeling makes simplifying assumptions about the elemental contents of life, particularly marine microorganisms,” says Daniel Muratore, an Omidyar Postdoctoral Fellow at the Santa Fe Institute, who led the study. Our results suggest that a better model would take into account the supply of nitrogen and adjust cellular carbon-to-nitrogen accordingly, which would potentially have profound influences on the movement and efficiency with which carbon is removed from the atmosphere to the deep ocean in these model simulations” such as the simulations the Intergovernmental Panel on Climate Change uses in its assessments. 

The study involved sequencing the genomes of marine bacteria, archaea, and viruses found in the water samples the team collected in the area, called the Eastern Tropical Northern Pacific Oxygen Minimum Zone. The researchers found that the makeup of these microorganisms is influenced by the amount of nitrogen in their habitat. In the upper part of the water column, where nitrogen concentrations were low, bacteria contained genes that had less nitrogen, while at slightly deeper levels, where nitrogen levels were higher, the bacteria contained more nitrogen.  

This is possible because of how nitrogen shows up in DNA. The four types of bases found in a DNA molecule — adenine (A), cytosine (C), guanine (G), and thymine (T) — form pairs. The GC pair has one more nitrogen atom than the AT pair. Consequently, the more GC pairs there are, the more nitrogen that genome has. Similarly, different amino acid combinations can make proteins with varied nitrogen content. For a small cell, these subtle atom-here-and-there changes add up to have a significant effect on the total nitrogen quota to keep the cell running,” Muratore explains. 

The team* also reconstructed the genomes of viruses that infect the bacteria. To their surprise, they found that the viruses, which they assumed would get enough resources from their host alone to thrive, were also influenced by the availability of nitrogen in the environment. Viruses at depths where nitrogen was more abundant used more nitrogen-rich nucleotides and amino acids for the proteins that make up the viral particle, the team found. 

Since viruses have no independent metabolism or nutrient uptake mechanism, we didn’t expect there to be the same environmental correlation” as there was with the bacteria, Muratore says.

The study “shows us that the environmental conditions can have really sophisticated yet mechanistically intuitive influences on evolution and host–virus ecology,” which allows for a better understanding of the makeup of genomes in different marine environments, says Muratore.

The findings also serve as an important reminder that information in cells influences the organisms physiology, they added. In the sequencing era, I think we've implicitly adopted an understanding that genomes are simply information that appears on our computer screens instead of actual molecules that need to be synthesized from resources [such as nitrogen] that cells have to gather in order to persist.” 

Muratore is now back out at sea, sampling microorganisms across a broader swath of ocean with varying nitrogen content. The research trip, conducted in tandem with researchers from the University of Hawaii and the University of Washington, will travel from the nitrogen-poor North Pacific Subtropical Gyre, near the site of the previous study, to the nitrogen-rich Equatorial Upwelling Region. The project will build on the previous work, this time focusing on whether patterns in protein and genomic nitrogen content predicted from DNA sequencing can be seen in the nucleotides and amino acids present in marine ecosystems with different nitrogen concentrations. 

*Study co-authors include Anthony Bertagnolli, Laura Bristow, Bo Thamdrup, Joshua S. Weitz, and Frank Stewart.

Read the paper, “Microbial and Viral Genome and Proteome Nitrogen Demand Varies Across Multiple Spatial Scales Within a Marine Oxygen Minimum Zone,” in mSystems (March 15, 2023) 


Photo Essay

SFI Postdoctoral Fellow Daniel Muratore documented the scientific cruise that they went on from January 22 to February 18, 2023, with fellow researchers to measure the carbon-to-nitrogen ratio in marine microorganisms living across several key currents in the Pacific Ocean. Here’s a selection of images from their time on board the R/V Thomas G. Thompson. (images: Daniel Muratore/SFI)