Ammonia-oxidizing archaea living inside marine sponges are not strict specialists, but rather versatile mixotrophs that consume both carbon dioxide and branched-chain amino acids, according to a study published in Science Advances.
Redefining a Deep-Sea Partnership
For decades, microbiologists categorized ammonia-oxidizing archaea as strict chemolithoautotrophs. According to scientific consensus prior to this research, these microbes relied exclusively on inorganic compounds—primarily extracting energy from toxic ammonia and fixing carbon dioxide—to survive. In marine sponges, which represent some of the oldest animals on Earth, these archaea act as a biological waste disposal system by clearing out metabolic ammonia waste products.
However, genomic analyses previously hinted at a more flexible diet. Researchers noticed that sponge-associated ammonia-oxidizing archaea possess genes for specific transporters capable of absorbing branched-chain amino acids, setting them apart from their free-living relatives. The new study provides direct experimental proof that these symbionts are actually mixotrophs, combining traditional carbon fixation with the direct uptake of organic amino acids.
Tracing Individual Microbe Activity with NanoSIMS
To pinpoint how these microbes feed, the research team focused on the coral reef sponge Ianthella basta, commonly known as the elephant ear sponge, and its specific archaeal symbiont, Nitrosospongia ianthellae.
By tracking labeled amino acids, the researchers watched the molecules integrate directly into individual symbiont cells, linking cellular identity to function rather than relying solely on genomic predictions.
Implications for Microbial Communication
Beyond expanding the dietary profile of these microbes, the findings point toward a sophisticated chemical dialogue between the host sponge and its microbiome. Because the archaea both produce and consume these amino acids, they actively shape the chemical environment inside the animal host.
By regulating amino acid availability, the microbes may influence critical signaling pathways within the sponge, representing an ancient form of cross-kingdom communication.
The researchers hypothesize that this metabolic interaction could influence the mTOR signaling pathway, an evolutionarily conserved regulator of cell growth and metabolism. The research was supported by the Austrian Science Fund (FWF) as part of the “Microbiomes Drive Planetary Health” Cluster of Excellence, uniting institutions across Austria and Australia to investigate fundamental ecological partnerships.
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