Homarine, produced by phytoplankton –microscopic organisms described as “the lungs of the Earth” for their role in producing half of the oxygen we breathe–, is one of the most abundant organic molecules in the sea. However, how bacteria processed it was unknown. This mystery began to clear up when a group of researchers, led by a Puerto Rican scientist, closed a significant knowledge gap about how microorganisms recycle nutrients in the ocean.
Dr. Frank Xavier Ferrer González, lead author and co-first author of the study “Conserved pathway for homarine catabolism in environmental bacteria,” published in March in Nature Microbiology, indicated that they identified a “completely unknown” metabolic pathway that explains how certain marine bacteria degrade homarine. This “has implications for global carbon and nitrogen cycles,” Ferrer González affirmed.
“The environment is full of invisible chemical interactions between microorganisms, and in the ocean as such, microorganisms control many of these interactions, which involves the global recycling of carbon and nitrogen—the cycles that give life to the world. So, although these processes occur on a microscopic scale, collectively they influence the functioning of both marine and global ecosystems, because everything is connected. Many of the molecules involved in these processes are still poorly understood, and understanding how microorganisms use them is important for comprehending the planet's biochemical cycles better,” detailed the marine microbiologist, trained at the University of Puerto Rico (UPR) in Mayagüez.
A metabolic pathway refers to the set of chemical steps that cells use to transform a molecule into energy or other compounds necessary for life, Ferrer González specified.
“The metabolic pathway in this case involves homarine, which is the original compound, and then we will have different genes that will break down this molecule and convert it into glutamic acid. And then, when it reaches glutamic acid, it would be called a compound that cells use to store nitrogen, and from there it travels throughout the cell and is distributed everywhere. The important part is that we discovered how it goes from homarine to glutamic acid,” he added.
The finding allows for a better understanding of how the ocean recycles organic matter and nutrients, which is key given that the saltwater bodies that separate continents absorb large amounts of carbon and help stabilize the planet's climate. Furthermore, the scientist commented that the discovery offers new details on how marine ecosystems respond to climate change.
Regarding the study's value for the Caribbean and Puerto Rico –vulnerable to climate change–, he highlighted that understanding this metabolic pathway allows for studying how it affects the region, better comprehending the health of tropical marine ecosystems, and evaluating how they might be impacted in the future.
“The important thing about all this is that half of the organic matter is produced in the oceans, half of life, of everything that exists in the world, and what also gives life to the oceans comes from these organisms. They are like the primary producers of the ocean. Not only that; one out of every two breaths of oxygen you take is produced by the ocean, and we know very little about the interactions that occur between these organisms that are performing all these processes,” elaborated the researcher from the Department of Chemical Oceanography at the University of Washington, in Seattle.
As part of efforts to understand how bacteria use homarine as an energy and nutrient source, researchers –including another Puerto Rican, student Yarinet Romero Maysonet– combined two methods: laboratory experiments and fieldwork to collect seawater samples. For the latter, they conducted four oceanographic expeditions to different regions of the Pacific Ocean between 2021 and 2023. Ferrer González participated in two of the excursions.
Scientists first identified the genes that bacteria activated when growing using homarine. Then, they used bacterial mutants to confirm which genes were necessary to degrade the organic molecule. The next step included using metabolomics and stable isotopes to track the homarine pathway within cells and in actual marine microbial communities.
“What we discovered is that it's not just a compound found in the sea, at least, the gene pathway. We started to see that it's in sediment, in soil, that it's in plants. We even found it in a cheese, a genome of a microorganism from a cheese that contained it. It's an abundant metabolic pathway in the world. That’s what impacted me the most; this is very important, it's everywhere and nobody knew about it,” Ferrer González highlighted, who dreams of returning to Puerto Rico.