Widespread Ocean Viruses Infecting Plankton-Like Archaea Are Far More Diverse Than Thought

A family of marine viruses that infects some of the most abundant microorganisms in the surface ocean turns out to be far more widespread and genetically diverse than scientists had realized. In a study published on 2 September in the journal Ocean-Land-Atmosphere Research, researchers at the Ocean University of China presented the first comprehensive characterization of Aoguangviridae, a recently established family of viruses associated with Poseidoniales, a widespread and ecologically important group of marine archaea. By mining public marine metagenomic and metatranscriptomic datasets from across the world’s oceans, the team expanded the family’s non-redundant genomic catalogue from just 59 genomes to 227, revealing a level of taxonomic richness and global distribution that previous work had left largely unresolved.

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