Ocean Viruses Hitch a Ride on Sinking Particles Into the Twilight Zone

Far below the sunlit surface of the ocean, in the dim realm scientists call the twilight zone, an enormous and largely invisible traffic system is at work. Organic particles formed in productive surface waters sink steadily through the water column, carrying carbon with them, and a new study published in BMC Biology shows that these particles are also ferries for viruses. A research team led by Yue Zhang, Pudi Wang, Hongbin Liu and Hongmei Jing, working across institutions including the Institute of Deep-Sea Science and Engineering of the Chinese Academy of Sciences and the Hong Kong University of Science and Technology, has mapped how viral communities are distributed across particles of different sizes and depths, and how those communities connect the surface ocean to waters hundreds and even thousands of meters below.

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