Biology subjects

Demina, T.

Publications and source records attributed to Demina, T..

5 recordsLinked to original sources

bioRxiv2026

Metatranscriptomic Profiling of Viral Diversity in Aquatic Environments with a Focus on Microalgal Viruses

Freshwater microeukaryotes contribute to aquatic productivity, yet the RNA viruses associated with these communities remain incompletely characterized compared with their marine counterparts. Here, we used metatranscriptomics to profile viral diversity across five Finnish freshwater sites (one river and four lakes) and one coastal marine sample from Hiroshima Bay in the Seto Inland Sea, Japan. We recovered 399 viral operational taxonomic units (vOTUs), of which 285 (71.4%) represented RNA viruses distributed across five viral phyla and putatively associated with fungal, plant or algal, metazoan and bacterial hosts. DNA viruses formed a smaller component of the dataset, including bacteriophage-like vOTUs with transcripts encoding replication, structural, packaging, and lysis proteins. Two vOTUs, which were detected in the Vantaanjoki river sample, were putatively classified within the family Marnaviridae, which comprises RNA viruses that infect protists in marine and freshwater environments. Both vOTUs encoded conserved replication and picornavirus-like capsid domains, and one represented a near-complete dicistronic genome. RNA-dependent RNA polymerase (RdRp) -based phylogeny placed these vOTUs in a strongly supported lineage outside the currently recognized genera within the family Marnaviridae, supporting their provisional assignment to the candidate genus Vandarnavirus proposed here within Marnaviridae. Whole-genome comparisons using the IMG/VR v4 database revealed genetic similarities between the vOTUs representing the candidate Vandarnavirus genus and picorna-like virus sequences from freshwater, wetland, saltmarsh, and estuarine metatranscriptomes. These findings expand the known ecological range of marnavirus-like RNA viruses and identify freshwater habitats as under-sampled reservoirs of microalgae-associated viral sequences.

microbiology↗

bioRxiv2026

Viral diversity and activity in Arctic tundra soils in wintertime

Arctic soils store vast amounts of carbon and are warming faster than the rest of the globe. Still, little is known about microbe-mediated feedback responses to the ongoing environmental changes in the warming Arctic. Specifically, viral diversity, functions, and virus-host interactions remain largely unknown in northern soils outside the growing season. Here, we analyzed the diversity and activity of viruses in oroarctic tundra soils during wintertime using metatranscriptomics. Through de novo virus prediction as well as targeted searches, we identified 995 viral operational taxonomic units (vOTUs) in total. Most of these vOTUs, 93%, represented RNA viruses, part of which were presumably segments of multipartite genomes. RNA vOTUs were classified mainly within the phyla Lenarviricota (259), Kitrinoviricota (198), Pisuviricota (135), Ambiviricota (103), Negarnaviricota (79), and Duplornaviricota (42). Thirty-seven DNA vOTUs (mostly Caudoviricetes) were also detected, suggesting active viral infections. In total, 81% of all vOTUs were assigned with a putative host organism, mostly fungi (515 vOTUs). Viral communities were distinct across vegetation types, and pH and moisture contributed to the differences. Putative novel clades within Ambiviricota and Orpoviricetes were identified, expanding their known diversity. The study contributes to uncovering diverse RNA viruses and viroid-like elements in Arctic tundra soils and highlights that soil viruses remain active in wintertime.

microbiology↗

bioRxiv2025

Viral genetic diversity and functional potential in polar and subarctic sea ice

Sea ice plays a critical role in regulating the global climate and serves as a unique habitat for diverse microbial communities. Still, our understanding of viruses in these communities remains limited. To further uncover the diversity and functional potential of viruses in polar and subarctic sea ice, we explored the viral component of Arctic, Baltic Sea, and Antarctic sea ice metagenomes. Altogether, 550 viral operational taxonomic units (vOTUs) were recovered, most of which were putatively classified within the class Caudoviricetes, which comprises bacterial and archaeal tailed double-stranded DNA viruses. Hosts were predicted for 187 vOTUs, with Gammaproteobacteria and Bacteroidia being the most prevalent viral host groups. Potential functions were assigned for 56% of predicted viral gene products, including putative auxiliary metabolic genes (AMGs) involved in oxidative metabolism, photosynthesis, and metabolism regulation under stress conditions. Related viral genomes carrying similar AMGs were detected in other Arctic and more geographically distant freshwater, marine, and ice environments. Genus- and/or family-level links between the studied vOTUs were detected across samples. Our results suggest diverse and complex virus-host interactions in sea ice and highlight the essential roles viruses may play in sea ice ecosystem dynamics across polar and subpolar environments.

microbiology↗

bioRxiv2025

Draft genome sequence of a predatory bacterium from northern peatland soil

Predatory bacteria are abundant in soil, but their diversity and functions remain not fully understood, especially in subarctic regions. Here, we report strain 1-FT3.2, a predatory bacterium obtained from peatland soil in Northern Finland (Pallas, 68 {degrees}N). The bacterium was cultivated on Mucilaginibacter cryoferens FT3.2 as prey. Although a pure culture of strain 1-FT3.2 was not obtained, its draft genome was assembled from sequencing reads derived from the co-culture with its prey. The draft genome of 1-FT3.2 is 7.2 Mb in length and 81% complete. Genome analyses suggested that 1-FT3.2 belongs to the family Polyangiaceae (phylum Myxococcota), which comprises predatory bacteria. The genome annotation revealed (near-)complete metabolic modules of central carbon metabolism and aerobic respiration. Two proviral regions were predicted in the draft genome, both putatively representing tailed phages of the class Caudoviricetes. Several CRISPR-Cas system proteins were also identified. The draft genome sequence could be used in future comparative studies assessing the diversity of predatory bacteria in northern soils or other environments.

microbiology↗

bioRxiv2024

Tunturi virus isolates and metagenome-assembled viral genomes provide insights into the virome of Acidobacteriota in Arctic tundra soils

BackgroundArctic soils are climate-critical areas, where microorganisms play crucial roles in nutrient cycling processes. Acidobacteriota are phylogenetically and physiologically diverse bacteria that are abundant and active in Arctic tundra soils. Still, surprisingly little is known about acidobacterial viruses in general and those residing in the Arctic in particular. Here, we applied both culture-dependent and -independent methods to study the virome of Acidobacteriota in Arctic soils. ResultsFive virus isolates, Tunturi 1-5, were obtained from Arctic tundra soils, Kilpisjarvi, Finland (69{degrees}N), using Tunturibacter spp. strains originating from the same area as hosts. The new virus isolates have tailed particles with podo-(Tunturi 1, 2, 3), sipho-(Tunturi 4), or myovirus-like (Tunturi 5) morphologies. The dsDNA genomes of the viral isolates are 63-98 kbp long, except Tunturi 5, which is a jumbo phage with a 309-kbp genome. Tunturi 1 and Tunturi 2 share 88% overall nucleotide identity, while the other three are not related to one another. For over half of the open reading frames in Tunturi genomes, no functions could be predicted. To further assess the Acidobacteriota-associated viral diversity in Kilpisjarvi soils, bulk metagenomes from the same soils were explored and a total of 1881 viral operational taxonomic units (vOTUs) were bioinformatically predicted. Almost all vOTUs (98%) were assigned to the class Caudoviricetes. For 125 vOTUs, including five (near-)complete ones, Acidobacteriota hosts were predicted. Acidobacteriota-linked vOTUs were abundant across sites, especially in fens. Terriglobia-associated proviruses were observed in Kilpisjarvi soils, being related to proviruses from distant soils and other biomes. Approximately genus- or higher-level similarities were found between Tunturi viruses, Kilpisjarvi vOTUs, and other soil vOTUs, suggesting some shared groups of Acidobacteriota viruses across soils. ConclusionsThis study provides acidobacterial virus isolates as laboratory models for future research and adds insights into the diversity of viral communities associated with Acidobacteriota in tundra soils. Predicted virus-host links and viral gene functions suggest various interactions between viruses and their host microorganisms. Largely unknown sequences in the isolates and metagenome-assembled viral genomes highlight a need for more extensive sampling of Arctic soils to better understand viral functions and contributions to ecosystem-wide cycling processes in the Arctic.

microbiology↗