Prochlorococcus marinus, a tiny, emerald-colored microbe, is the most abundant photosynthesizing organism on Earth. It is found in large numbers throughout the ocean’s surface waters. These small, single-celled microbes play a vital role in carbon fixation, contributing as much as all the crops on land combined.
New research by MIT scientists has revealed an additional ocean-regulating function of Prochlorococcus: they release DNA building blocks into the water, which are then “cross-fed” to other organisms. These compounds serve as nutrients and energy or help regulate metabolism in other ocean microbes, turning Prochlorococcus’ byproducts into valuable resources.
Prochlorococcus marinus releases DNA building blocks into the ocean on a regular cycle, typically at night. During this time, other microbes, such as SAR11, the most abundant bacteria in the ocean, consume these byproducts.
For SAR11, these nighttime “snacks” help slow its metabolism, allowing it to recharge for the next day. This cross-feeding interaction may support the sustainable growth of many microbial communities, as Prochlorococcus provides what it no longer needs. Through this process, Prochlorococcus could help regulate the daily rhythms of microbes across the globe.
Co-author and MIT Institute Professor Sallie “Penny” Chisholm said, “The relationship between the two most abundant groups of microbes in ocean ecosystems has intrigued oceanographers for years. Now we have a glimpse of the finely tuned choreography that contributes to their growth and stability across vast regions of the oceans.”
Since Prochlorococcus and SAR11 dominate the surface oceans, researchers believe that the exchange of molecules between these microbes could be a significant cross-feeding relationship, significantly regulating the ocean’s carbon cycle.
Rogier Braakman, the study’s lead author and a research scientist at MIT’s Department of Earth, Atmospheric, and Planetary Sciences (EAPS), emphasizes that exploring the details of these cross-feeding processes will help uncover key forces that influence the carbon cycle.
Cross-feeding, where microbes exchange resources, is common in microbial communities, such as the human gut, where microbes are closely clustered. In contrast, Prochlorococcus are free-floating microbes that move throughout the ocean’s surface layers. While scientists have suspected that these microbes engage in cross-feeding, studying this process has been challenging due to the low concentrations of materials Prochlorococcus release, making them difficult to measure.
In their study, the researchers closely examined how Prochlorococcus engages in cross-feeding and its effects on other ocean microbes. They focused on how Prochlorococcus uses purine and pyridine before releasing them into the environment. By analyzing the microbes’ genomes, they identified genes involved in purine and pyridine metabolism.
The team found that these compounds create DNA and replicate the microbial genome. Any surplus is recycled, but a portion is eventually expelled into the surroundings. Prochlorococcus efficiently uses these compounds, discarding only what it doesn’t need.
The team also analyzed gene expression data and found that genes responsible for recycling purine and pyrimidine peaked a few hours after the known genome replication peak at dusk. This raised the question: which organisms benefit from this nightly release?
To answer this question, the researchers examined the genomes of over 300 heterotrophic microbes—organisms that consume organic carbon rather than produce it through photosynthesis. They hypothesized that these carbon-feeders might be the recipients of Prochlorococcus’ organic byproducts. Their findings revealed that most of the heterotrophs possessed genes to uptake purine or pyridine, indicating that these microbes have evolved different mechanisms for cross-feeding.
The researchers focused on SAR11, the most abundant heterotrophic microbe in the ocean, which is known for preferring purines. By comparing genes across different strains of SAR11, they discovered that these microbes use purines in various ways—either by directly taking them up or breaking them down for energy, carbon, or nitrogen.
Braakman and his team conducted a metagenome analysis to understand this diversity, comparing the genomes of all microbes in over 600 seawater samples worldwide, specifically focusing on SAR11. The analysis, which also considered environmental conditions and geographic locations, revealed that SAR11 uses purine for nitrogen when it is scarce in seawater and for carbon or energy when nitrogen is abundant.
This highlights how local environmental factors shape the microbial communities in different ocean regions.
Co-author Kujawinski said, “The work here suggests that microbes in the ocean have developed relationships that advance their growth potential in unexpected ways.”
The team then conducted a lab experiment to observe how purine affects SAR11. They cultured the bacteria and exposed them to varying purine concentrations. Surprisingly, purine slowed the bacteria’s normal metabolic activities and growth.
However, when the cells were exposed to stressful environmental conditions, they continued to grow healthily, as if the metabolic slowdown induced by purine had prepared them for the stress. This suggests that purine may help SAR11 prime itself for growth, allowing it to better withstand challenging conditions.
Journal Reference:
- Rogier Braakman et al. Global niche partitioning of purine and pyrimidine cross-feeding among ocean microbes. Science Advances. DOI: 10.1126/sciadv.adp1949