Poseidoniales, the archaeal hosts of these viruses, are abundant in surface oceans and play a significant role in the natural functioning of marine ecosystems. These single-celled organisms contribute to organic-matter degradation and carbon cycling, processes that sit at the heart of how the ocean stores and transforms carbon. Because archaeal viruses can influence the metabolism, population dynamics, and evolutionary trajectory of their hosts, understanding the viruses that infect Poseidoniales is essential to building a complete picture of this ecologically significant group. Until now, however, Aoguangviridae had been represented by only a small number of genomes, leaving its true diversity, evolutionary structure, functional potential, and global distribution poorly characterized.

“Marine archaea of the order Poseidoniales are abundant in surface oceans and contribute to organic-matter processing, yet the viruses associated with them remain poorly characterized,” said Changyue Zhao, a researcher at the Ocean University of China in Qingdao, China, and lead author of the study. “Aoguangviridae had been represented by only a small number of genomes, leaving its true diversity, evolutionary structure, functional potential, and global distribution largely unresolved. We therefore integrated public marine metagenomic and metatranscriptomic datasets to build a broader genomic framework for this archaeal virus family and to examine where its members occur and are active.”

The methodological foundation of the study rested on metagenomics, the study of genetic material recovered directly from environmental samples rather than from organisms grown in the laboratory. This approach is particularly valuable for viruses, many of which cannot be cultured independently of their hosts. To construct their reference dataset, the researchers began with five high-confidence Aoguangviridae genomes that had served as seed genomes, representing the first identified and best-characterized members of the family. They then incorporated 54 additional Aoguangviridae-related genomes that had been assembled during previous metagenomic studies. After removing redundancies, this curated starting set of 59 genomes provided the benchmark against which the team could identify new members of the family hiding in publicly available ocean sequencing data.

With that framework in place, the researchers turned to comparative genomic analyses to understand how the family is organized evolutionarily. They identified eight single-copy core genes, genes present exactly once in each genome and inherited vertically, which provided a reliable basis for inferring evolutionary relationships within Aoguangviridae. Single-copy core genes are a standard tool in viral phylogenetics because their conserved presence across related genomes allows researchers to align sequences, build phylogenetic trees, and define taxonomic boundaries with confidence. Applying this framework to the expanded dataset revealed substantially greater diversity than previously recognized: the family now encompasses 22 subfamilies, 157 genera, and 167 species, a dramatic increase over what the original 59 genomes had suggested.

“Aoguangviridae is far more diverse and widespread than previously recognized,” Zhao said. “We expanded the non-redundant genome set from 59 to 227 and resolved extensive diversity at the subfamily, genus, and species levels. These viruses occur across the global ocean, are particularly abundant in epipelagic and Arctic waters, and show transcriptional activity in the deep chlorophyll maximum. Their genomes also encode auxiliary metabolic genes, suggesting the capacity to influence host metabolism during infection.” The deep chlorophyll maximum is the subsurface layer of the ocean where chlorophyll concentrations peak, often marking a zone of intense photosynthetic activity and nutrient gradients. Transcriptional activity there, detected through metatranscriptomic data, indicates that the viruses are not merely present but actively expressing their genes, a sign of ongoing infection and replication.

The global survey showed that Aoguangviridae is found in marine and coastal habitats worldwide, but the researchers also found that different lineages within the family occupy different environments. Some lineages were enriched in epipelagic waters, the sunlit upper layer of the ocean, and in polar waters, whereas others were more frequently detected at greater depths. These contrasting distribution patterns suggest ecological differentiation within the family, with different lineages occupying distinct niches across the global ocean. Such ecological specialization may also be associated with differences in how each lineage interacts with its Poseidoniales hosts and with the roles the viruses play in marine biogeochemical processes, the chemical cycles that move elements such as carbon and nitrogen through the ocean system.

One of the most intriguing findings concerns auxiliary metabolic genes, host-like metabolic genes carried in viral genomes that can supplement or redirect host metabolism during infection. In marine systems, such genes are known to modulate processes central to energy and carbon flow, and their presence in Aoguangviridae genomes suggests that these viruses may have the capacity to influence the metabolism of Poseidoniales during infection. Because Poseidoniales contribute to organic-matter processing and carbon cycling in the surface ocean, viruses capable of altering their hosts’ metabolic activity could, in principle, ripple outward to affect how organic carbon is degraded and transformed in marine waters. Establishing whether such effects are measurable in the real ocean is precisely what the team hopes to test next.

“We aim to recover additional complete genomes, improve host assignments, and combine time-series meta-omics with laboratory cultivation and infection experiments,” Zhao said. “Ultimately, we want to determine how Aoguangviridae interacts with Poseidoniales cells and whether these infections measurably alter organic-carbon processing and other biogeochemical functions in the ocean.” Time-series meta-omics, in which genetic and transcriptomic data are sampled repeatedly at the same location over time, can reveal seasonal patterns of viral activity, while laboratory infection experiments would provide the direct biological evidence needed to confirm what the genome-based predictions imply. Cultivating Poseidoniales and their viruses remains challenging, but pairing observational data with controlled experiments is the standard path from genomic inference to demonstrated ecological function.

The study, titled Global Distribution, Genomic Diversity, and Phylogeny of Aoguangviridae, was a collaborative effort involving Kaiyang Zhang, Haolin Jia, Hongbing Shao, Andrew McMinn, Min Wang, and Yantao Liang of the Ocean University of China, together with Yeong Yik Sung, Wen Jye Mok, and Li Lian Wong of the UMT-OUC Joint Center for Marine Studies. The research was supported by the Laoshan Laboratory, the Natural Science Foundation of China, a 2024 Graduate Self-Directed Research Project, and the Fundamental Research Funds for the Central Universities. By transforming a sparse genomic record into a rich, globally distributed catalogue, the work provides the reference framework that future studies of archaeal viruses in the ocean will build upon, and it underscores how much of the viral diversity shaping marine microbial life remains to be discovered in the sequence data already collected from the world’s oceans.

Subject of Research: Genomic diversity and global distribution of Aoguangviridae, viruses infecting Poseidoniales marine archaea

Article Title: Virus that infects some plankton more widespread than previously suspected

Article References: Virus that infects some plankton more widespread than previously suspected. (n.d.). Original publication

Image Credits: AI Generated

DOI: Not provided

Keywords: Aoguangviridae, marine viruses, Poseidoniales, marine archaea, metagenomics, metatranscriptomics, carbon cycling, auxiliary metabolic genes, ocean biogeochemistry, deep chlorophyll maximum, Arctic waters, viral diversity

The twilight zone, formally known as the mesopelagic zone, occupies the depth range between the base of the euphotic layer and roughly one thousand meters. It is a critical waypoint in the biological carbon pump, the suite of processes by which carbon fixed by photosynthesis in the surface ocean is transported to depth, where a portion of it can be sequestered away from the atmosphere for decades to centuries. Most of that vertical transport happens on aggregates of particulate organic matter, flakes and pellets and colloidal clusters that vary enormously in size, density and composition. Microbes colonize these particles and remineralize their carbon, and viruses, by infecting and lysing those microbes, can accelerate the breakdown and reshape which carbon makes it to the deep ocean. Yet the viral ecology of sinking particles has remained one of the least charted corners of marine microbiology, because particles are hard to sample intact and viruses are hard to assign to hosts.

To overcome these obstacles, the team collected seawater from three oceanic regions and separated the particulate matter into multiple size fractions, then sequenced the metagenomes of samples taken at different depths from the surface down through the twilight zone and into deeper waters. From this material they recovered a total of 5,016 viral operational taxonomic units, or vOTUs, a level of diversity that underscores how rich and poorly described the particle-associated virosphere really is. By analyzing how these viral populations were distributed across particle sizes and water layers, the researchers could ask a question that has rarely been addressed at this scale: do viruses simply float passively in the water, or do they travel with the particles that sink out of the sunlit zone?

The answer turned out to depend strongly on both depth and particle size. Small particles near the surface harbored proportionally more lytic viruses, the kind that replicate aggressively inside a host cell and then burst it open, releasing new virions and dissolved organic matter in the process. Large particles at greater depths, by contrast, were enriched in lysogenic viruses, which integrate their genomes into those of their hosts and ride along with the dividing cells, replicating only when triggered. This pattern fits ecological theory: in productive surface waters, where microbial hosts are abundant and fast-growing, the kill-the-winner dynamics of lytic infection pay off, while in the resource-poor twilight zone, a dormant, integrated lifestyle is a safer bet for a virus whose potential hosts are scarce and scattered.

Host assignment revealed the players behind these interactions. More than 1,000 of the recovered vOTUs could be linked to prokaryotic hosts, and the dominant hosts belonged to the phylum Pseudomonadota, a group that includes many of the most abundant heterotrophic bacteria in the ocean. Using co-occurrence patterns between viral and host genomes, together with metagenome-assembled genomes recovered from the same samples, the researchers built a network of putative virus-host relationships spanning the particle size spectrum. The virus-to-microbe ratios and correlation analyses further suggested that the abundance of hosts shapes not only how many viruses are present but also the balance between lytic and lysogenic strategies in the community.

One of the most striking findings concerns what these viruses can actually do. Metabolic annotation of the viral genomes identified 178 auxiliary metabolic genes, or AMGs, which are host-like genes carried by viruses that can augment the metabolism of the cells they infect. The study also detected 12 families of carbohydrate-active enzymes, known as CAZymes, including glycoside hydrolases, glycosyltransferases and polysaccharide lyases. These enzymes are capable of degrading or remodeling the complex polysaccharides that make up the structural scaffolding of marine particles. Notably, the AMGs and CAZymes were found primarily in lysogenic members of the class Caudoviricetes, the tailed viruses that dominate marine viral communities. In practical terms, this means that viruses integrated into particle-dwelling bacteria may be supplying their hosts with extra tools to break down particulate organic carbon, thereby influencing how fast sinking particles are degraded and how much carbon escapes remineralization on the way down.

The functional complementation implied by these genes has direct consequences for carbon cycling. If a lysogenic virus equips its host with a glycoside hydrolase that can cleave a polysaccharide the host could not otherwise digest, the host gains access to a new energy source, and the particle loses structural material more quickly. Multiply that interaction across thousands of viral types and the countless particles sinking through the water column, and viral genomes emerge as a significant, previously underappreciated lever on the efficiency of the biological carbon pump. The study’s authors frame their results as new insight into the roles of viruses in carbon cycling and vertical connectivity in the ocean, and the metabolic evidence gives that framing concrete biochemical substance.

Equally important is the study’s evidence for connectivity between water layers. Co-occurrence analysis revealed extensive overlap of vOTUs across depths, and marker viruses identified with statistical comparisons of community composition showed that viruses originating in the surface ocean are transported via particles into the twilight zone and beyond, even reaching bathypelagic depths. In other words, the sinking particle highway does not carry carbon alone; it carries an entire mobile virome. Some viral types were significantly enriched at the upper or lower boundaries of the twilight zone in the different study regions, suggesting that particle-associated viruses can serve as biological tracers of vertical export, linking the ecology of the euphotic zone to the microbial processing of carbon far below.

The three-region comparative design strengthens these conclusions. By sampling across distinct oceanographic settings, the researchers could distinguish region-specific patterns from general ones, and the consistency of the size-dependent shift from lytic to lysogenic dominance suggests a robust ecological rule rather than a local curiosity. The use of tools such as vConTACT2 for viral clustering, non-metric multidimensional scaling for community ordination, and STAMP for statistical profiling of marker viruses reflects the maturing analytical toolkit of viral metagenomics, which now allows oceanographers to treat viruses as quantifiable components of biogeochemical models rather than as an unstructured background of biological noise.

The broader implications reach into climate science. Models of the biological carbon pump currently struggle to predict how efficiently carbon is transferred from the surface to the deep ocean, and microbial degradation on sinking particles is one of the largest sources of uncertainty. If particle-associated viruses systematically accelerate the solubilization and remineralization of particulate organic carbon, and if their lytic versus lysogenic balance shifts predictably with depth and particle size, then viral activity belongs explicitly in carbon export models. This study provides the first large-scale, size-resolved baseline for doing exactly that, cataloguing thousands of viral populations, their hosts and their metabolic genes along the particle size spectrum. As sequencing of twilight-zone particles continues, the viral ferry system described here is likely to prove a fundamental feature of ocean biogeochemistry, one that quietly shapes how much carbon the sea sends to the deep and how long it stays there.

Subject of Research: Viral communities associated with particles of different sizes in the ocean twilight zone and their roles in carbon cycling and vertical connectivity

Article Title: Connectivity and potential functions of viral communities along the particle size spectrum in the twilight zone

Article References: Zhang, Y., Wang, P., Liu, H., & Jing, H. (2026). Connectivity and potential functions of viral communities along the particle size spectrum in the twilight zone. BMC Biology. https://doi.org/10.1186/s12915-026-02750-0

Image Credits: AI Generated

DOI: 10.1186/s12915-026-02750-0

Keywords: ocean twilight zone, marine viruses, viral metagenomics, particle-associated viruses, biological carbon pump, auxiliary metabolic genes, carbohydrate-active enzymes, lysogeny, Pseudomonadota, carbon export, vOTUs, vertical connectivity

A new laboratory study, published in MicrobiologyOpen, suggests that a solution may lie in one of the most abundant molecules inside every living cell: ribosomal RNA. Previous work on prokaryotes demonstrated that when viruses lyse bacterial cells, substantial amounts of rRNA are released into the extracellular medium, where it can be detected and quantified. Building on that observation, researchers developed an approach called Mortality by Ribosomal Sequencing, or MoRS, which compares ribosomal RNA sequences in cellular and dissolved fractions of seawater to estimate taxon-specific cell lysis. What remained untested was whether the concept could be extended to eukaryotic microalgae, whose complex internal organization and diverse viral enemies make such an extrapolation far from trivial.

To test the idea, a research team led by investigators working with marine algal virus systems conducted controlled infection experiments with two contrasting host-virus pairs. The first was the diatom Chaetoceros tenuissimus, a small coastal phytoplankton species less than ten micrometers across that is susceptible to Chaetoceros tenuissimus RNA virus type II, a small single-stranded RNA virus with particles roughly 22 to 38 nanometers in diameter. The second was the raphidophyte Heterosigma akashiwo, a globally distributed, flagellated species notorious for forming harmful algal blooms, which was challenged with HaV strain 120, a large double-stranded DNA virus with strain-specific infectivity. Together, these systems span different host physiologies and viral genome types, providing a rigorous framework for testing whether cell-free rRNA behaves as a general lysis marker in eukaryotes.

The experimental design was carefully controlled. Host cultures were grown at 22 degrees Celsius under a 12-hour light and 12-hour dark cycle in sterile artificial seawater media and acclimated for multiple generations before infection. For each host-virus system, triplicate flasks received virus at a multiplicity of infection of ten, while triplicate control flasks received none. The cultures were incubated for six days and sampled daily. To track viral proliferation, the team used the most probable number method to determine infectious virus titers at the beginning and end of the incubation. Critically, they also added purified Escherichia coli ribosomes to every flask as spike-in controls, at a concentration of approximately 2.9 times ten to the seventh copies per milliliter, allowing them to measure how quickly free rRNA degrades in the medium.

Separating the cellular from the dissolved fraction was achieved by gentle filtration through 0.22-micrometer polycarbonate filters under low vacuum. RNA retained on the filter was operationally defined as the cellular fraction, while RNA passing through was defined as cell-free. Cellular RNA was extracted with a silica-column kit enhanced by bead-beating, whereas cell-free RNA was concentrated from twenty-milliliter filtrates using a column-based vacuum system optimized for large water volumes. After genomic DNA removal and complementary DNA synthesis, absolute quantification was performed with a digital PCR system, using newly designed primers targeting the V4 region of the algal 18S rRNA gene and primers specific to the major capsid protein genes of each virus. Extraction efficiencies of 21.9 percent for the cellular fraction and 83.1 percent for the cell-free fraction were used to correct the measured concentrations.

The growth dynamics of the two hosts diverged sharply. In the Chaetoceros experiment, cells in the virus-added treatment grew at rates comparable to controls until day three but then grew significantly more slowly, while cell density, chlorophyll a, and cellular rRNA all continued to rise until day three or four. In striking contrast, Heterosigma cultures declined immediately after viral addition, with most cells losing motility within 24 hours, echoing earlier reports on this host-virus system. Infectious virus particles increased dramatically in both systems, from 5.8 times ten to the fifth to 1.9 times ten to the eighth most probable number units per milliliter for the diatom RNA virus, and from 7.6 times ten to the fifth to 1.4 times ten to the seventh for the Heterosigma DNA virus, confirming active viral replication.

The central result concerned the redistribution of rRNA between particulate and dissolved pools. In the Chaetoceros experiment, cell-free 18S rRNA remained low in controls, below about 4 times ten to the eighth copies per milliliter, but rose sharply in infected flasks to a maximum of 3.7 times ten to the ninth copies per milliliter on day four. Per-cell rRNA content varied up to 2.8-fold within each condition but showed no significant treatment effect, and cellular rRNA correlated strongly with cell density in both species, with Pearson correlation coefficients of 0.72 and 0.94. These findings established that rRNA abundance tracks plankton biomass at the population scale, while its release into the dissolved phase signals cell rupture.

To convert rRNA dynamics into lysis rates, the team built a rate-based model describing daily changes in cell-free rRNA concentration. The model rests on first-order degradation kinetics, an assumption validated by the spike-in ribosomes, which decayed exponentially with rate constants of roughly 1.78 to 2.16 per day in the Chaetoceros experiment, corresponding to half-lives of 7.7 to 9.3 hours. By rearranging a simple mass-balance equation, the researchers solved for the cell-free rRNA production rate, a direct proxy for cell lysis. Normalizing this production rate by host cell abundance yielded a metric they call cell-free rRNA production per cell. In the Chaetoceros system, this metric was 46.1-fold higher in infected treatments than controls between days two and three, and in the Heterosigma system it reached 302.1-fold higher between days three and four, with maximum per-cell release rates up to 46.1- and 302.1-fold above controls across the experiments.

The two host-virus systems also revealed fundamentally different infection strategies. In Chaetoceros, viral marker genes accumulated progressively in the cellular fraction over days one to four, and lysis peaked between days two and three even as the population was still growing, demonstrating that active viral lysis can occur during the apparent growth phase of a bloom. In Heterosigma, elevated per-cell rRNA release appeared both early, during days zero to one, and late, during days three to five. The early mortality could not be explained by canonical viral lysis, since viral capsid gene expression peaked only on day two. The authors suggest several possible mechanisms, including abortive infection, membrane destabilization during viral entry, a phenomenon analogous to lysis from without described in bacteriophage systems, or damage caused by bacteria introduced with the nonaxenic viral lysate, which flow cytometry confirmed had proliferated to high densities in infected treatments.

The implications reach well beyond the laboratory. Unlike dilution assays, which are labor-intensive and lack taxonomic resolution, cell-free rRNA quantification combined with high-throughput sequencing could simultaneously assess lysis across diverse taxa in natural communities, offering a taxon-resolved measure of lytic mortality that plankton ecologists have long sought. Because viral lysis is estimated to contribute up to roughly 45 percent of the labile dissolved organic carbon pool in marine systems, better quantification of who is being lysed, and when, could sharpen models of carbon cycling and microbial loop dynamics. The authors caution that the approach has limits: ribosome content per cell varies several-fold, infected bacteria can actively reduce their ribosome pools, degradation constants differ among seawater samples and must be measured for each one, and nonviral processes such as sloppy feeding, parasitism, and algicidal bacteria can also release intracellular rRNA. They also note that the degradation kinetics of E. coli 16S rRNA may not perfectly match those of eukaryotic 18S rRNA, calling for spike-in standards derived from representative plankton. Even with these caveats, the study provides a mechanistic foundation for reading cell death directly from the RNA dissolved in seawater, turning a ubiquitous molecule into a quantitative witness of the viral shunt at work.

Subject of Research: Quantifying viral lysis of eukaryotic microalgae using cell-free ribosomal RNA as a molecular marker

Article Title: Quantifying Viral Lysis in Microalgae Using Cell‐Free rRNA

Article References: Kikuya, S., Tomaru, Y., Nagasaki, K., Morimoto, D., Yamagishi, Y., Ogata, H., & Endo, H. (2026). Quantifying Viral Lysis in Microalgae Using Cell‐Free rRNA. MicrobiologyOpen, 15(5), Article e70402. https://doi.org/10.1002/mbo3.70402

Image Credits: AI Generated

DOI: 10.1002/mbo3.70402

Keywords: viral lysis, microalgae, ribosomal RNA, phytoplankton, viral shunt, marine viruses, Chaetoceros tenuissimus, Heterosigma akashiwo, MoRS, digital PCR, plankton mortality, biogeochemistry