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

Marine sponges are notoriously difficult to identify. Many species lack fixed, easily readable external characteristics, and their morphological traits can be ambiguous, variable with environment, or shared misleadingly among unrelated lineages. This has produced a long history of taxonomic confusion, misidentifications and inconsistent classification, particularly among so-called cryptic species that look nearly identical but differ genetically. In recent years, sponge systematics has been transformed by integrative approaches that pair careful morphological description with molecular tools, allowing researchers to delimit species and reconstruct evolutionary relationships with far greater confidence than morphology alone permits.

The new study focuses on the order Scopalinida, a group erected and redefined only in the last decade using both morphological and molecular evidence. Scopalinida contains a single family, Scopalinidae, which in turn holds just three genera: Scopalina, Stylissa and Svenzea. The genus Svenzea, named in honor of the Colombian spongiologist Sven Zea, was established in 2002 for reef-associated sponges whose classification had long bounced between the former order Halichondrida and the family Dictyonellidae. Its defining features include distinctive microanatomy, the arrangement of skeletal elements, the composition and shape of spicules, and the presence of granular cells observed in both adults and larvae, along with a larva of extraordinary size. The larvae of Svenzea zeai, at up to six millimeters long, are regarded as the largest documented for the entire phylum Porifera.

Despite decades of study, only seven species of Svenzea had ever been described, and none had been recorded anywhere along the Eastern Tropical Pacific. That gap made the Mexican Pacific an intriguing frontier. Between July and November 2024, a team led by Eric Bautista-Guerrero of the Universidad de Guadalajara collected samples by SCUBA diving at depths of three to eight meters in the coral community known as Plataforma Pavonas, within Islas Marietas National Park in Bahía de Banderas. The site, where live pocilloporid coral cover is roughly eleven percent and sponges account for only about one percent, proved to host an abundant, widely distributed sponge growing over semi-shaded substrates, cave walls and vertical rock formations.

Underwater, the sponge is unmistakable: a thickly encrusting, irregularly massive animal ten to twenty-five centimeters across and two to three centimeters high, glowing bright orange in life and fading to beige in alcohol preservation. Its surface is smooth but microscopically hispid, densely pierced with incurrent pores and marked by bifurcated exhalant channels that lead to elevated, translucent chimney-like oscula. Under the microscope, the internal architecture revealed a cavernous choanosomal skeleton of disorganized, multispicular tracts, bundles of three to six needle-like spicules cemented by spongin fibers, ascending toward the surface. The spicules themselves, slender styles in two size categories measuring roughly 413 to 551 micrometers long, proved to be significantly larger than those of any previously known Svenzea species, and the complete absence of oxea, a second spicule type common in relatives, provided another decisive clue.

The team did not stop at adults. Using plankton nets towed by a diver around the coral community, they captured free-swimming larvae in full planktonic condition and raised them for observation. The larvae are bright orange, elongated to ovoid, and slightly flattened at the posterior pole, giving them a pyriform, or pear-shaped, appearance. Measuring 710 to 766 micrometers in length, they are uniformly covered in fine cilia about 24 micrometers long and swim in counterclockwise spirals, sometimes pausing or sinking before resuming their corkscrew journey. Their clear anterior-posterior polarity and cylindro-conical body plan echo the unusual parenchymella larvae documented in other scopalinid sponges, although the new species’ larvae are far smaller than the giant larvae of the Caribbean Svenzea zeai, which reach over six millimeters in length.

To place the new species on the sponge tree of life, the researchers extracted DNA from three adults and two larvae and amplified two independent genetic markers: the mitochondrial cytochrome c oxidase subunit I gene, COI, and the nuclear small-subunit ribosomal RNA gene, 18S. Sequences were aligned against a comprehensive set of Scopalinidae sequences from public databases, and phylogenetic trees were reconstructed using both maximum likelihood and Bayesian inference methods. The two approaches produced congruent topologies, and both markers placed Svenzea marialmae firmly within a well-supported clade containing Svenzea, Scopalina and Stylissa, confirming its membership in the family Scopalinidae and its distinction from the family Dictyonellidae, to which some of its relatives were once assigned.

The genetic evidence was strikingly specific. Based on COI sequences, the new species is closest to the Caribbean sponge Svenzea cristinae, with a genetic distance of just 0.052, followed by an undescribed Svenzea and Svenzea zeai, while showing much larger distances from all species of Scopalina and Stylissa. The 18S data told the same story, yielding the lowest interspecies distance, a mere 0.005, between Svenzea marialmae and Svenzea cristinae. Intriguingly, the two markers disagreed on one point: COI recovered Svenzea as monophyletic while 18S suggested it is paraphyletic, a discrepancy the authors attribute to the scarcity of Scopalinida sequences in public databases and to the possibility that some Scopalina species, such as S. goletensis and S. kuyamu, may have been misidentified. Resolving this will require additional genetic markers, but the congruence of the adult and larval sequences within a single clade provides strong evidence that both life stages belong to the same new species.

Morphologically, the new sponge walks a fascinating line between its named relatives. Its skeletal architecture, prominent dendritic spongin fibers cored by long styles over a basal spongin plate, resembles that of Scopalina species, and its thin cushions, conulose surface and bright orange color closely recall the Caribbean Scopalina ruetzleri. Yet it lacks the oxeas and other spicule modifications seen in that species, and it differs sharply from the erect, flabellate Stylissa, whose choanosome is supported by confusedly plumoreticulate spicule tracts. Against its congeners, the comparisons are equally decisive: Svenzea tubulosa is tubular with smaller styles, Svenzea flava bears blunt-ended styloids, Svenzea germanyanezi is a tiny cave-dweller with two categories of oxea, and Svenzea zeai carries short styles and a purple-brown, volcano-like form. Only the combination found in the Mexican specimens, giant styles, no oxeas and vivid orange pigmentation, defines the new species.

Beyond its taxonomic significance, the discovery carries a dedication with deep personal meaning. The species epithet marialmae honors María del Rocío Troncoso González, mother of co-author Dr. Alma Paola Rodríguez-Troncoso, a marine biologist who has spent two decades conserving and restoring the coral communities of Islas Marietas National Park and strengthening biodiversity management in this Marine Protected Area. The type specimens are deposited in the Colección de Esponjas del Pacífico Mexicano at the Institute of Marine Sciences of the National Autonomous University of Mexico, and all genetic sequences have been archived in GenBank, making the data freely available for future studies.

The broader implications reach well beyond one sponge. By raising the global count of Svenzea species to eight and establishing the first documented record of the genus in the Eastern Tropical Pacific, the study fills a conspicuous biogeographic gap and hints at unrecognized evolutionary connections across ocean basins, the new species’ closest relative after all lives on the far side of the American continent in the Caribbean. It also validates the combined use of mitochondrial and ribosomal markers alongside morphological and reproductive characters as a robust framework for testing phylogenetic hypotheses in Demospongiae, reducing the uncertainty of misidentifications that has long plagued sponge taxonomy. For the coral reefs of the Mexican Pacific, the message is clear: even in a marine protected area studied for decades, an abundant, brightly colored animal can remain formally unknown to science. As integrative taxonomy spreads to underexplored regions, researchers expect many more such surprises, each one refining our understanding of how sponge diversity evolved and how these ecologically important filter feeders are distributed across the world’s tropical seas.

Subject of Research: Taxonomic and molecular description of a new marine sponge species of the genus Svenzea from coral communities in the Eastern Tropical Pacific

Article Title: New insights into the diversity of Scopalinida (Porifera: Demospongiae) in the Eastern Tropical Pacific

Article References: Bautista-Guerrero, E., Marin-Ramirez, M. F., Carballo, J. L., Rodríguez-Troncoso, A. P., & Santiago-Valentín, J. D. (2026). New insights into the diversity of Scopalinida (Porifera: Demospongiae) in the Eastern Tropical Pacific. Discover Ecology, 2(1), Article 13. https://doi.org/10.1007/s44396-026-00031-2

Image Credits: AI Generated

DOI: 10.1007/s44396-026-00031-2

Keywords: marine sponges, Svenzea marialmae, Scopalinidae, Eastern Tropical Pacific, new species, integrative taxonomy, phylogenetics, COI, 18S rRNA, coral reefs, Islas Marietas, biodiversity

Colistin, also called polymyxin E, occupies a special and precarious position in modern medicine. It is a cationic polypeptide that attacks the outer membrane of Gram-negative bacteria, and after decades of limited use because of kidney toxicity, it was reintroduced in recent years as a final defense against multidrug-resistant infections. With few new antibiotics in the development pipeline, clinicians increasingly depend on colistin when carbapenem-resistant pathogens strike hospital patients. The emergence of bacteria that resist this drug is therefore not a routine scientific concern but a genuine emergency in global public health, and the new study demonstrates that the ocean may be serving as an unexpected reservoir and highway for the genes responsible.

The mechanics of colistin resistance matter for understanding why the new results are so significant. Resistance can arise in two ways. Intrinsic resistance develops through chromosomal mutations that alter lipid A, the lipopolysaccharide component of the bacterial outer membrane that colistin targets, reducing the drug’s ability to bind. Acquired resistance, by contrast, depends on the horizontal transfer of mcr genes, usually carried on plasmids, which are mobile DNA elements that can shuttle between bacterial cells. Since the discovery of the mcr-1 gene in Escherichia coli plasmids a decade ago, researchers have identified ten mcr variants, from mcr-1 through mcr-10, and watched them disperse across continents, animal populations, and clinical settings. What remained poorly understood was how extensively these genes had colonized marine ecosystems.

To answer that question, the Brazilian team designed a natural experiment spanning roughly 330 kilometers of the Rio de Janeiro coastline plus the Fernando de Noronha Archipelago, a volcanic island group about 360 kilometers offshore in the Western Atlantic. Their sampling sites deliberately covered a gradient of human influence. At one extreme sat Bom Jesus Cove in Guanabara Bay, a tropical urban estuary receiving raw sewage, oils, and industrial contaminants from Rio de Janeiro city. At the other extreme lay the submarine caves of Fernando de Noronha, protected within a national marine park and accessible only by SCUBA diving. Between those poles, the researchers sampled the Cagarras Archipelago, a no-take marine protected area unfortunately positioned near the Ipanema submarine sewage outfall; the biodiverse waters of Arraial do Cabo, including the Gruta Azul submarine cave; and Ilha Grande Bay, one of the world’s largest tropical bays, which faces growing pressure from coastal settlements and maritime traffic.

The laboratory work was methodical and technically demanding. From 1,550 total bacterial isolates, the team focused on 308 Gram-negative bacilli identified as potential hosts of acquired colistin resistance determinants. Bacteria were cultured on Luria Bertani and MacConkey agar from water samples, washed and swabbed from pieces of floating plastic, and extracted from sponge tissue through serial dilution across four growth media. Identification proceeded by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry on a Bruker Microflex LT platform, and DNA was extracted using a thermal lysis protocol with Chelex 100 resin. Polymerase chain reaction screening then probed each strain for eight mcr variants, and any positive strains were tested further for beta-lactamase genes, quinolone resistance genes, aminoglycoside resistance genes, sulfonamide resistance genes, and class 1, 2, and 3 integron-integrase genes.

The results were striking in both breadth and detail. Of the 308 potential host strains, 101 carried at least one mcr variant, generating 128 total gene occurrences. Water samples contributed 59.4 percent of the positive strains, plastic litter 35.6 percent, and marine sponges 5.0 percent. The mcr-9 variant dominated with 33 occurrences, followed by mcr-3 with 23, mcr-2 with 18, and mcr-1 with 17. That mcr-9 topped the list is noteworthy because global metagenomic surveys have often ranked mcr-1 as the most dispersed variant. The mcr-9 gene is known to circulate on IncHI2 plasmids that interconnect human, animal, and environmental isolates, suggesting an efficient dissemination network that the ocean may now be extending.

The bacterial hosts carrying these genes were equally concerning. Among ten identified genera, Enterobacter, Acinetobacter, Vibrio, and Klebsiella predominated. Enterobacter species alone accounted for 31 strains and harbored the greatest mcr diversity, with every variant except mcr-5 and mcr-7 detected in the genus. More alarming still, mcr-positive Enterobacter was not confined to polluted Bom Jesus Cove but turned up in marine sponges and cave waters in Fernando de Noronha, an area with restricted human access. One Enterobacter hormaechei strain, isolated from a sponge in Sapata Cave, simultaneously carried mcr-2, mcr-9, and the sulfonamide resistance gene sul1. Four strains carried three mcr variants at once, including Klebsiella pneumoniae isolates from pristine sponges and from floating plastic, and an Enterobacter cloacae from Noronha water. Both K. pneumoniae and E. cloacae belong to the notorious ESKAPE group of pathogens, and their carriage of multiple resistance genes in aquatic matrices highlights the risk of waterborne transmission to humans.

The co-occurrence of resistance genes painted an even darker picture. Nearly half of the mcr-positive strains, 46.5 percent, also carried other antimicrobial resistance genes or integron-integrases, with sulfonamide resistance genes, particularly sul1, the most frequent companions, followed by the beta-lactamase genes blaTEM and blaSHV. In Bom Jesus Cove, the team detected the carbapenemase gene blaKPC alongside mcr-3 in Enterobacter bugandensis and Raoultella ornithinolytica strains, a combination that effectively eliminates two of the last therapeutic options for infections caused by these organisms. Integron-integrases, genetic platforms that capture and shuffle gene cassettes, co-occurred with mcr exclusively in the polluted cove, suggesting bacterial adaptation to intense anthropogenic selective pressure. Because changes in membrane permeability in mcr-positive bacteria can reduce sensitivity to multiple drugs, these combinations can compound into true multidrug resistance, complicating treatment of hospital-associated infections.

The gradient of pollution left a measurable fingerprint on the data. In Bom Jesus Cove, 27 of 104 water-isolated strains tested positive for mcr, and 36 of 82 strains from floating plastic litter carried the genes, a prevalence of roughly 44 percent that represents the highest in the study. The finding positions plastic debris as both a reservoir and a vector for antimicrobial resistance, offering microbes a stable, drifting substrate on which biofilms can form, exchange genes, and travel with currents. At the Cagarras Archipelago, 40 percent of water-isolated strains were positive despite formal protection, a legacy of the nearby sewage outfall. Arraial do Cabo showed 36.5 percent prevalence among water isolates and Ilha Grande Bay 36.3 percent. In Fernando de Noronha, prevalence dropped to about 5 percent of candidate host strains, with two of 17 water isolates and five of 15 sponge isolates positive, proving that resistance persists even where human pressure is minimal.

What emerges from the study is a warning that antimicrobial surveillance cannot remain confined to clinics and farms. Marine sponges, submarine caves, and drifting plastic are now documented hotspots of colistin resistance, and the genes involved sit on mobile elements capable of jumping into human pathogens. The Brazilian coastline, with its juxtaposition of dense urban pollution and remote protected archipelagos, offered an ideal natural laboratory, but the pattern it revealed is almost certainly global. The researchers argue for integrated monitoring programs that treat the ocean as a critical node in the antimicrobial resistance network, alongside conservation strategies that reduce sewage discharge and plastic pollution. As colistin remains a last resort for patients out of options, every mcr gene circulating in seawater, attached to plastic, or sheltering inside a sponge represents a card stacked against future medicine, and the ocean, it turns out, is dealing them freely.

Subject of Research: Distribution of mobile colistin resistance (mcr) genes in bacteria from Brazilian marine environments

Article Title: Widespread occurrence of mobile colistin resistance genes in Brazilian marine environments

Article References: Brunelli, R. C., de Jesus Carvalho Baptista, T. V., de Oliveira Nithack Marques, M., da Silva Oliveira Alves, G., Abdon, B. B., Mello, M. P., Paranhos, R., Gallo, M. N., Vinzon, S. B., Lage, A., Sandes, J., Muricy, G., Klautau, M., Lopes, M. V., Dias, G. R., Canellas, A. L. B., & Laport, M. S. (2025). Widespread occurrence of mobile colistin resistance genes in Brazilian marine environments. Ocean Microbiology, 1(1), Article 3. https://doi.org/10.1186/s44375-025-00003-z

Image Credits: AI Generated

DOI: 10.1186/s44375-025-00003-z

Keywords: antimicrobial resistance, colistin, mcr genes, marine microbiology, plastic pollution, Guanabara Bay, Fernando de Noronha, Enterobacter, Klebsiella pneumoniae, integrons, marine sponges, One Health