Biology subjects

Oksanen, H. M.

Publications and source records attributed to Oksanen, H. M..

9 recordsLinked to original sources

bioRxiv2026

A Bactericidal Phospholipase from Archaea

Archaea kill bacteria, at least on occasion. The molecular underpinnings of these lethal interactions are barely understood. Here, we describe cinquedea, an /{beta} hydrolase secreted by the halophilic archaeon Haloferax larsenii s5a-1. Cinquedea exhibits bactericidal activity in the nanomolar range, killing halophilic Pontibacillus bacteria. Bacterial death is accompanied by gross morphological abnormalities, indicative of severe damage to the cell envelope. We predict, and confirm in vitro, that cinquedea is a phospholipase, with structural similarities to a phospholipase A1 enzyme isolated from hornet venom. Exposing lipids extracted from a cinquedea-sensitive Pontibacillus strain to the enzyme leads to accumulation of lysophosphatidylglycerol, a cleavage product of phospholipase A activity. This is consistent with direct activity of cinquedea against the Pontibacillus membrane, which we show is chiefly composed of phosphatidylglycerol. Considered alongside recent findings that some archaea encode bactericidal peptidoglycan hydrolases, these results suggest that archaea can kill bacteria in mechanistically diverse ways. Our work provides a template for future experimental discovery and characterization of bactericidal proteins of archaeal origin and reinforces an emerging view that archaea represent a substantial reservoir for the discovery of new antibacterial compounds.

microbiology↗

bioRxiv2026

Boreal and subarctic freshwaters harbour a diversity of jumbophages

Bacteriophages (phages) are major drivers of microbial evolution and ecology, yet their diversity and functional roles remain poorly characterised in many natural environments, such as in freshwater systems. In boreal and subarctic freshwater habitats, where bacteria are typically slow-growing and nutrient-limited, phages are predicted to have a critical role in host regulation and horizontal gene exchange. However, only a few isolates have been obtained from such environments, leaving the genetic and functional diversity of these phages largely unexplored. Here, we present a collection of 40 bacteriophages isolated from boreal lakes and rivers using a set of diverse freshwater bacterial hosts. Despite using conventional isolation methods, eight of the isolates possess genomes larger than 200 kilobases and are classified as jumbophages. All jumbophages exhibited myovirus morphology and comparatively slow infection dynamics. These jumbophages include the first known representatives infecting members of Janthinobacterium and Herbaspirillum. Comparative genomic and phylogenetic analyses show that nearly all genomes are distinct from previously described phages, indicating substantial novelty. Diverse auxiliary metabolic and anti-defence systems were identified, including putative NAD+ salvage and acyl carrier protein modules, along with predicted Anti-Thoeris and Anti-CBASS elements. The Pseudomonas-infecting jumbophage Ahti encoded homologues of all 21 core genes that define the nucleus-forming family Chimalliviridae. Additionally, Ahti displayed compartmentalisation of DNA during infection, establishing it as the first freshwater nucleus-forming phage. These findings expand our understanding of the ecological, genomic, and functional diversity of phages in boreal environments, and highlight the role of freshwater ecosystems as significant reservoirs of novel viral lineages. ImportanceBacteriophages are viruses that infect bacteria and play important roles in shaping microbial communities and nutrient cycling in natural waters. However, much of what is known about their diversity comes from sequencing data alone, without environmental isolates that allow direct studies on their biology. In this study, we described 40 bacteriophages from boreal and subarctic lakes and rivers using freshwater bacterial hosts, including species of Flavobacterium, Pseudomonas, Janthinobacterium and other lesser-known phage hosts. Eight of these viruses had exceptionally large genomes, categorising them as jumbophages. These isolates included the first known jumbophages infecting Janthinobacterium and Herbaspirillum, as well as the first freshwater jumbophage shown to form a nucleus-like structure during infection. Together, these findings reveal boreal freshwaters as an important source of previously unknown virus diversity and provide new model systems for exploring phage biology in environmentally relevant contexts.

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

Genomic insights into antiviral defense systems in haloarchaea and their impact on virus susceptibility

The ongoing evolutionary arm race between archaea and their viruses has led to the development of diverse defense systems against viruses. While recent computational approaches have uncovered many bacterial antiviral defense systems, the viral infection strategies and antiviral responses of archaea remain poorly explored. In this study, we identified antiviral defense systems encoded in the genomes of 20 recently sequenced haloarchaeal strains. These systems were found to be representative of the broader repertoire of defense systems present across all 253 complete sequenced Halobacteria (class) genomes in the RefSeq database. Detailed analysis showed that these haloarchaea usually harbor multiple different defense systems, with a particularly high abundance of uncharacterized predicted defense systems against viruses (Phage Defense Candidates (PDCs)). To further explore the impact of anti-viral defense mechanisms on host range, an extensive virus-host pair screening was performed using a panel of known virulent viruses. By correlating the genomic defense profiles with observed viral infectivity and adsorption profiles, a weak correlation between the number of encoded defense systems and viral susceptibility was detected. Specifically, hosts infected by fewer viruses tended to encode a broader repertoire of antiviral defense systems, whereas those with fewer defense systems were frequently infected. It was found that the host range of haloarchaeal viruses is majorly determined by the availability of viral receptors, whereas the presence of anti-viral defense systems plays a smaller but significant role. These findings offer valuable insights into the evolutionary pressure shaping archaeal antiviral strategies and lay the groundwork for future functional studies of archaeal defense systems. ImportanceArchaeal viruses are understudied, compared to viruses infecting bacteria and eukaryotes. Haloarchaea have evolved as model organisms for the study of virus-host interaction in archaea, as they harbor the highest number of isolated archaeal viruses. Salt-loving haloarchaea dominate microbial communities in hypersaline environments, where they face constant viral threats. To survive, they have evolved a diverse array of antiviral defense systems. Until now, the relevance of these defense systems for susceptibility to viruses had not been tested in archaea. The findings of this study show that strains with a broader repertoire of defense systems tend to be less susceptible to viral infection, while those with fewer systems are more frequently targeted, suggesting an advantage for the accumulation of different defense systems. In addition, it was found that the major determinant of host range is the availability of viral receptors on the host cell. These insights provide a foundation for future research into the molecular mechanisms and ecological roles of archaeal defense systems.

microbiology↗

bioRxiv2025

Curated high-quality genomes of 39 diverse halophilic archaea

Archaea are widespread and ecologically important microorganisms, yet our understanding of their physiology and evolution is constrained by the limited number of complete genome assemblies available. Haloarchaea have emerged as model organisms for archaeal cell biology, virus-host interactions, and biotechnology. Despite their prominence in hypersaline environments and their potential for industrial applications, high-quality reference genomes remain scarce. Here, we present chromosome-level assemblies for 39 cultivable haloarchaeal strains for which no complete genomes were previously available. Using Oxford Nanopore sequencing, we obtained near-complete assemblies, with 38 strains resolving into single closed chromosomes and additional replicons such as plasmids captured largely in full. These genomes expand the available genomic resources for five haloarchaeal genera and provide a framework for comparative analyses of archaeal metabolism, genome organization, and mobile genetic elements. Given that many of these strains are natural hosts to diverse archaeal viruses, the genomes also represent a critical resource for advancing studies of virus-host interactions in archaea. Beyond fundamental insights into archaeal cell biology and evolution, this dataset will support the development of haloarchaeal model systems and facilitate the exploration of their biomolecules for biotechnological applications.

microbiology↗

bioRxiv2024

Cryo-EM resolves the structure of the archaeal dsDNA virus HFTV1 from head to tail

Outnumbering their hosts by at least a factor of 10, viruses are the most common biological entity on Earth, are major drivers of evolution, and greatly impact on the dynamics of our planets ecosystems. While viruses infecting bacteria and eukaryotes have been extensively studied, the viruses roaming the archaeal domain remain largely unexplored. In recent years, a growing number of archaeal viruses have been described, revealing a stunningly diverse range of morphologies that appear unique to archaea. Detailed structural studies are paramount to fully understand how archaeal viruses infect their hosts. However, no complete atomic models of archaeal viruses are available to date. Using electron cryo-microscopy, we investigated the structure of the archaeal virus Haloferax tailed virus 1 (HFTV1), which infects the halophile Haloferax gibbonsii LR2-5 originating from the Senegalese salt lake Retba. Through single particle analysis, we achieved near-atomic resolution for the entire set of HFTV1s structural proteins, enabling the building of a full atomic model of the virion. Comparing the structures of DNA filled and empty capsids, we visualise structural changes occurring upon DNA ejection. By investigating the double-stranded DNA inside the capsid, we elucidate how the genome is spooled upon loading. Furthermore, our structure reveals putative cell-surface receptor-binding and catalytic roles of capsid turret, baseplate, and tail fibre proteins. Together, our data provide new insights into the mechanisms of HFTV1 assembly and infection, unveiling new perspectives on general rules of host-virus interactions in archaea and their evolutionary links to bacterial and eukaryotic viruses.

microbiology↗

bioRxiv2021

Diversity, taxonomy and evolution of archaeal viruses of the class Caudoviricetes

The archaeal tailed viruses (arTV), evolutionarily related to tailed double-stranded DNA bacteriophages of the class Caudoviricetes, represent the most common isolates infecting halophilic archaea. Only a handful of these viruses have been genomically characterized, limiting our appreciation of their ecological impacts and evolution. Here, we present 37 new genomes of haloarchaeal tailed virus isolates, more than doubling the current number of sequenced arTVs. Analysis of all 63 available complete genomes of arTVs, which we propose to classify into 14 new families, suggests ancient divergence of archaeal and bacterial tailed viruses and points to an extensive sharing of genes involved in DNA metabolism and counter defense mechanisms, illuminating common strategies of virus-host interactions with tailed bacteriophages. Coupling of the comparative genomics with the host range analysis on a broad panel of haloarchaeal species uncovered four distinct groups of viral tail fiber adhesins controlling the host range expansion. The survey of metagenomes using viral hallmark genes suggests that the global architecture of the arTV community is shaped through recurrent transfers between different biomes, including hypersaline, marine and anoxic environments.

microbiology↗

bioRxiv2020

Cellular and genomic properties of Haloferax gibbonsii LR2-5, the host of euryarchaeal virus HFTV1

Hypersaline environments are the source of many viruses infecting different species of halophilic euryarchaea. Information on infection mechanisms of archaeal viruses is scarce, due to the lack of genetically accessible virus-host models. Recently a new archaeal siphovirus, Haloferax tailed virus 1 (HFTV1), was isolated together with its host belonging to the genus Haloferax, but it is not infectious on the widely used model euryarcheon Hfx. volcanii. To gain more insight into the biology of HFTV1 host strain LR2-5, we studied characteristics that might play a role in its virus susceptibility: growth-dependent motility, surface layer, filamentous surface structures and cell shape. Its genome sequence showed that LR2-5 is a new strain of Hfx. gibbonsii. LR2-5 lacks obvious viral defense systems, such as CRISPR-Cas, and the composition of its cell surface is different from Hfx. volcanii, which might explain the different viral host range. This work provides first deep insights into the relationship between the host of halovirus HFTV1 and other members of the genus Haloferax. Given the close relationship to the genetically accessible Hfx. volcanii, LR2-5 has high potential as a new model for virus-host studies in euryarchaea.

microbiology↗

bioRxiv2017

Genomic, proteomic, and phylogenetic analysis of spounaviruses indicates paraphyly of the order Caudovirales

It is almost a cliche that tailed bacteriophages of the order Caudovirales are the most abundant and diverse viruses in the world. Yet, their taxonomy still consists of a single order with just three families: Myoviridae, Siphoviridae, and Podoviridae. Thousands of newly discovered phage genomes have recently challenged this morphology-based classification, revealing that tailed bacteriophages are genomically even more diverse than once thought. Here, we evaluate a range of methods for bacteriophage taxonomy by using a particularly challenging group as an example, the Bacillus phage SPO1-related viruses of the myovirid subfamily Spounavirinae. Exhaustive phylogenetic and phylogenomic analyses indicate that the spounavirins are consistent with the taxonomic rank of family and should be divided into at least five subfamilies. This work is a case study for virus genomic taxonomy and the first step in an impending massive reorganization of the tailed bacteriophage taxonomy.

microbiology↗