Sponge-Dwelling Archaea Turn Out to Be Dietary Flexitarians, Not Ammonia Specialists

For more than a century, microbiologists have sorted the microbial world into tidy nutritional categories. Some organisms eat light, some eat chemicals, and some eat other living things. Among the most famous specialists in this catalogue are the ammonia-oxidizing archaea, ancient single-celled organisms that make a living by harvesting energy from ammonia, one of the simplest nitrogen-containing molecules in nature. These microbes have long been portrayed as the purists of the microbial realm: strictly chemolithoautotrophic, meaning they draw energy exclusively from inorganic ammonia and build all of their cellular material from carbon dioxide. A new study, however, shows that at least one group of these archaea breaks the rule book in spectacular fashion. Symbiotic ammonia oxidizers living inside marine sponges, researchers report, also consume organic amino acids, revealing a metabolic flexibility that was entirely unexpected for this lineage.

The discovery comes from a team led by microbiologists Bettina Glasl and Katharina Kitzinger at the Centre for Microbiology and Environmental Systems Science at the University of Vienna, working in collaboration with partners at the Australian Institute of Marine Science. Their findings, published in the journal Science Advances, describe how archaea living in partnership with the elephant ear sponge Ianthella basta supplement their ammonia-based diet with branched-chain amino acids, including valine, leucine, and isoleucine. In doing so, the microbes behave less like rigid specialists and more like what the researchers playfully call flexitarians, organisms that prefer one food source but readily incorporate others when the opportunity arises. The result reshapes how scientists think about one of the oldest animal-microbe partnerships on Earth.

Marine sponges are among the most ancient animals still swimming in the oceans, and their bodies are anything but simple. A single sponge can host billions of microorganisms packed into its internal channels, forming a symbiotic community that is essential to the animal’s survival. Among these residents, ammonia-oxidizing archaea hold a place of particular importance. Sponges constantly produce ammonia as a metabolic waste product, and in the confined chemistry of a reef organism this compound would quickly become toxic. The archaea act as a microscopic sanitation crew, oxidizing ammonia and keeping the sponge’s internal environment habitable. This service has long been considered their defining role, and their nutritional identity seemed equally settled.

Until now, the textbook view held that ammonia-oxidizing archaea were strict chemolithoautotrophs. The term describes a demanding lifestyle: the organism must generate all of its energy from inorganic chemical reactions, in this case the oxidation of ammonia to nitrite, while simultaneously fixing carbon dioxide into the organic molecules of life. Free-living ammonia oxidizers studied in soils and oceans have occasionally shown modest flexibility, using simple nitrogenous compounds such as cyanate and urea as additional nitrogen sources, but their carbon metabolism remained firmly anchored to carbon dioxide. The sponge symbionts, the new work demonstrates, have gone considerably further down the path of dietary liberation.

The first hints of this flexibility came not from experiments but from genomes. When researchers sequenced the DNA of symbiotic ammonia-oxidizing archaea from sponges, they noticed something odd: unlike many of their free-living relatives, these symbionts carried genes encoding transporters for branched-chain amino acids. Transporters are membrane proteins that import specific molecules from the environment, and their presence suggested the archaea might be equipped to take up valine, leucine, and isoleucine from their surroundings. Genome predictions, however, are only hypotheses. A transporter gene does not prove that the protein works, that the amino acids are actually available inside the sponge, or that the symbionts use them for growth. Direct experimental evidence was needed.

Providing that evidence required the researchers to watch individual microbial cells at work inside a living animal, a formidable technical challenge. The team studied the bright yellow elephant ear sponge, a species found across coral reefs of the Indo-Pacific, including the Great Barrier Reef, and its archaeal symbiont Nitrosospongia ianthellae. They combined advanced chemical and microscopic imaging techniques, including nanoscale secondary ion mass spectrometry, or NanoSIMS, a method capable of detecting isotopically labeled compounds incorporated into single cells. By offering the symbionts amino acids tagged with heavy isotopes, the researchers could trace exactly which cells absorbed the molecules and incorporated them into their biomass.

The imaging delivered an unambiguous answer. As Kitzinger explained, the labeled amino acids could be seen being incorporated into individual symbiont cells, allowing the team to link a cell’s identity directly to its function rather than relying on genome predictions alone. This single-cell approach matters because sponge tissue is a crowded, mixed community of bacteria, archaea, and host cells. Bulk measurements of labeled material in sponge tissue cannot reveal who ate what. By resolving activity at the level of individual archaeal cells, the study provided the first direct experimental demonstration that symbiotic ammonia oxidizers are genuine mixotrophs, organisms capable of using both carbon dioxide and organic amino acids as carbon sources.

The implications extend well beyond a revised dinner menu. Because the symbionts can both consume and produce branched-chain amino acids, they may actively shape the availability of these essential molecules within their host. Branched-chain amino acids are not merely building blocks for proteins; in animals they also act as signaling compounds. The researchers propose that archaeal metabolism could even influence the mTOR signaling pathway, a conserved regulator of cell growth and metabolism that responds to branched-chain amino acid availability in organisms across the tree of life. If the archaea modulate the supply of these molecules, they could, in principle, participate in chemical conversations with the sponge itself, a possibility that transforms them from passive waste processors into active metabolic partners.

Glasl captured the shift in perspective by noting that these symbionts were previously viewed primarily as a waste disposal service for the sponge. By producing and consuming amino acids that may serve as signaling molecules, she observed, the symbionts could potentially modulate important signals for their host, suggesting a form of communication between microbes and animals with deep evolutionary roots. Sponges and their microbial communities have coexisted for hundreds of millions of years, and the new findings hint that this partnership may involve far richer chemical exchange than the simple removal of toxic waste. Michael Wagner, head of the FWF Cluster of Excellence that supported the work and last author of the study, emphasized that the research depended on tight collaboration between teams in Austria and Australia.

Beyond the sponges, the study raises broader questions about archaeal ecology in the ocean. If symbiotic ammonia oxidizers can tap organic compounds, other members of this ancient lineage may harbor similar capacities that have gone undetected because researchers assumed a purely inorganic diet. The work also underscores how symbiosis can drive metabolic innovation: an organism’s lifestyle inside a host can differ dramatically from that of its free-living cousins. For a group of microbes once considered the strictest of specialists, the sponge archaea offer a reminder that microbial nutrition, like the animals these organisms inhabit, is often stranger, older, and more interconnected than it first appears.

Subject of Research: Mixotrophic amino acid assimilation by ammonia-oxidizing archaeal symbionts of marine sponges

Article Title: Archaea as "flexitarians": ammonia-oxidizing microbes also feed on amino acids

Article References: Archaea as "flexitarians": ammonia-oxidizing microbes also feed on amino acids. (n.d.). Original publication

Image Credits: AI Generated

DOI: Not provided

Keywords: archaea, marine sponges, symbiosis, ammonia oxidation, amino acids, mixotrophy, NanoSIMS, microbiome, coral reefs, mTOR signaling, Nitrosospongia, Science Advances