Brazilian sponges of the genus Metania (phylum Porifera) are filter-feeding organisms from freshwater ecosystems. Here, we explored viral communities of Metania sp., their functional role in the sponge and how they differ from those in surrounding water. We identified 1163 viral operational taxonomic units (vOTUs) from sponge tissue and adjacent water, with 555 vOTUs shared across habitats. Viral diversity was higher in sponges than in water, and community composition differed significantly (PERMANOVA, p = 0.037). Sponge-associated vOTUs exhibited broad phylogenetic diversity, including deep-branching and unclassified clades, and several exclusively sponge-associated Caudoviricetes. Virus-host predictions revealed 173 interactions, largely with sponge-associated bacteria, supported by CRISPR spacer matches, variant formation in multiple vOTUs across sponge individuals, and a high prevalence of microbial defence systems, particularly restriction-modification, abortive infection, and CRISPR-Cas pathways. Functionally, viral communities carried diverse auxiliary viral genes, including those involved in amino acid and central carbon metabolism, carbohydrate degradation, fatty acid biosynthesis, stress responses (e.g., metacaspase-1), and sulphur cycling. Nine sponge-associated vOTUs encoded carbonic anhydrase (CA), and phylogenomic as well as structural analyses showed strong conservation of CA active sites between sponge viruses, bacterial symbionts, and the sponge host. Protein-level homology searches revealed broad biogeographic distribution of viral CA homologs across global ocean microbiomes, despite limited nucleotide similarity, highlighting deep functional conservation. These findings reveal a phylogenetically diverse and functionally rich viral community associated with freshwater Metania sp., characterized by extensive host interactions, diverse defence mechanisms, and auxiliary metabolic capacities. The structural conservation and widespread distribution of viral carbonic anhydrase genes further suggest ecologically significant roles in carbon transformation within freshwater sponges and potentially across aquatic ecosystems. ### Competing Interest Statement The authors have declared no competing interest. Swedish Research Council, 2023-03310_VR, 2022-06725 Coordination for the Improvement of Higher Education Personnel (CAPES) the National Council for Scientific and Technological Development (CNPq) Foundation for Research Support of the Federal District (FAP-DF)

The sea-surface microlayer (hereafter microlayer), which forms the interface between the ocean and atmosphere, plays a key role in nutrient cycling and microbial dynamics. Coastal slicks, which are viscous and biogenic surface films, often serve as hotspots for microbial activity, yet their structure and interactions remain incompletely understood. Here, we investigated viral and microbial abundance, surfactants, dissolved organic carbon, and total dissolved nitrogen in slick microlayer and their corresponding underlying water in the coastal Baltic Sea. Dissolved organic carbon and total dissolved nitrogen showed minor enrichment in the microlayer, while surfactants were elevated in several slicks. Some microbial abundances were significantly higher in the slick microlayer, including prokaryotes and different phytoplankton size classes. Co-occurrence network analysis revealed clusters in the slick: surfactant-associated groups (nanophytoplankton groups, viruses) and surfactant-independent groups (cyanobacteria, picophytoplankton). Cyanobacteria were enriched in the slick microlayer relative to the slick underlying water, and their abundance in the microlayer was negatively correlated with total dissolved nitrogen and dissolved organic carbon. Viruses were positively correlated with prokaryotes in both the slick microlayer and slick underlying water, and additionally with microphytoplankton in the slick underlying water. Microscopic analysis of the > 100 mu m slick fraction revealed a detritus-dominated matrix containing juvenile sporophytes, pennate diatoms, filamentous cyanobacteria, and a ciliate-dominated microzooplankton community. Overall, the microlayer within slicks in this eutrophic coastal system contained elevated microbial and viral densities, along with distinct patterns of correlations among community members, indicating that it can locally influence surface-layer biogeochemistry and ecology.

Studying airborne viruses in remote environments like the sub-Antarctic island of South Georgia offers key insights into viral ecology, diversity, and their role in shaping ecosystems through microbial and nutrient interactions. We analyzed airborne viral community composition at two sites in South Georgia. Sampling took place using multiple methodologies, with the data produced subjected to viral metagenomics. The Coriolis μ device (wet collection) was the most effective, yielding 30 viral scaffolds. Two-thirds of the scaffolds were only obtained from the coastal location, indicating that location influences airborne viral diversity. Protein-based clustering of 39 viral operational taxonomic units (vOTUs) revealed similarities of 15 with known marine viruses, suggesting oceanic influence on the airborne viral community. Protein homologs related to UV damage protection and photosynthesis from two airborne vOTUs were widely distributed across major oceans, suggesting their potential role in supporting the resilience of marine microorganisms under changing climate conditions. Some vOTUs had protein similarities to viruses infecting extremophiles, indicating viral adaptations to harsh environments. This study provides a baseline for understanding the complexity and sustainability of airborne viral communities in remote ecosystems. It underscores the need for continued monitoring to assess how these communities respond to shifting atmospheric and ecological conditions.

The sea-surface microlayer (SML) is a crucial ocean-atmosphere interface involved in gas exchange and nutrient cycling. Slicks, i.e., viscous surface layers, common in coastal regions serve as microbial hotspots. We studied microbial abundance, surfactants, dissolved organic carbon (DOC), and net community production (NCP) of O2 in slick and non-slick SMLs and underlying water (ULW) in the coastal Baltic Sea. Slicks often showed higher surfactant levels compared to the ULW. Microbial respiration often exceeded production, resulting in net O2 consumption, although some ULW sites exhibited net O2 production. The SML was enriched with pico- and nanophytoplankton, with cyanobacteria being negatively correlated with total dissolved nitrogen. In contrast, microphytoplankton accumulated in the ULW, indicating niche separation with depth. Microscopy revealed ciliates and juvenile sporophytes dominating a slick’s >100 µm fraction. In eutrophic coastal systems, slicks influence plankton communities and O2 dynamics, supporting their role in surface biogeochemical cycling and climate-driven changes. ### Competing Interest Statement The authors have declared no competing interest. Swedish Research Council, https://ror.org/03zttf063, 2023-03310_VR German Research Foundation, 460129525

Outdoor viruses from atmospheric ecosystems have rarely been investigated, and thus only a few viral genomes from the air can be found in public databases. Viruses and their hosts have positively correlating guanine-cytosine (GC) contents in their DNA1. High GC content was previously found in actinobacterial and betaproteobacterial isolates from the stratosphere2 as well as in aerosol and rainwater viruses3. This is proposed as an adaptation to harsh environmental conditions, primarily as protection against ultraviolet radiation. Here, we combine metagenomically derived viral operational taxonomic units (vOTUs) collected from aerosols and precipitation samples from the Swedish coast3, along with time-series data collected in Antarctica using different sampling devices. Additionally, cloud water samples from the Puy de Dôme in France4 were included. A total of 80 assembled vOTUs, of which 37 were predicted phages, across all samples, had a GC content between 55.2% and 70.3%, considered 'high GC.' Antarctic air vOTUs were found after sampling with the Coriolis µ (wet) but not with the Coriolis Compact (dry) air sampler. The time series indicates overlapping vOTUs between days and sampling height (sea-level or altitude). In Antarctic air, high GC vOTUs (mean GC = 59.6% ± 4.0) were detected on one of the seven days, while low GC viruses were absent in this sample. On other days, the GC of vOTUs was

Clouds are aqueous atmospheric systems hosting diverse and active microorganisms. Viruses may also persist despite harsh conditions, support active viral infections, and contribute to microbial dynamics during aerial transport. However, assessing viruses, and even more, virus-bacteria interactions in the atmospheric environment is highly challenging, and knowledge remains very limited. Here, based on current knowledge in cloud microbiology, we estimate the cloud virome at ∼1021 virus particles globally. One out of a million of cloud droplets is susceptible to host virus-bacteria interactions, which represents considerable volume at global scale, and we discuss potential implications for microbial ecology. We finally propose future research directions to explore further the cloud virosphere and its ecological roles.

Bacteriophages, the ubiquitous bacterial viruses, are the most abundant biological entities on Earth. However, information regarding the impact of environmental factors on the genetic makeup of phages is scarce. Based on the analysis of genomes of 45 phage isolates from different ecosystems we demonstrate a significant ( p < 0.0001) positive correlation of the number of structural genes and their placement in above-average guanine-cytosine (GC) content of the genome. This feature appears to be more evident in isolates from deep-sea and sea-ice environments compared to desert and Baltic Sea slick, indicating a potential ecosystem-based factor (although insignificant due to low sample size). Additionally, the percentage of structural genes in above-average GC regions was found to be significantly ( p = 0.0038) negatively correlated with the genome size of the phages and significantly ( p = 0.0266) positively correlated with the overall GC for phage genomes > 50 kb, but not for genomes < 50 kb ( p = 0.556). We therefore propose a relationship of structural genes and GC content, a property that may influence the adaptation and evolution of phages in various environmental niches. ### Competing Interest Statement The authors have declared no competing interest.

Aquatic viruses act as key players in shaping microbial communities. In polar environments, they face significant challenges like limited host availability and harsh conditions. However, due to restricted ecosystem accessibility, our understanding of viral diversity, abundance, adaptations, and host interactions remains limited. To fill this knowledge gap, we studied viruses from atmosphere-close aquatic ecosystems in the Central Arctic and Northern Greenland. Aquatic samples for virus-host analysis were collected from ~60 cm depth and the submillimeter surface microlayer (SML) during the Synoptic Arctic Survey 2021 on icebreaker Oden in Arctic summer. Water was sampled from a melt pond and open water before undergoing size-fractioned filtration and followed by genome-resolved metagenomic and cultivation investigations. The prokaryotic diversity in the melt pond was considerably lower compared to open water. The melt pond was dominated by a Flavobacterium sp. and Aquiluna sp., the latter having a relatively small genome size of 1.2 Mb and the metabolic potential to generate ATP using the phosphate acetyltransferase-acetate kinase pathway. Viral diversity on the host fraction (0.2 – 5 µm) of the melt pond was strikingly limited compared to open water. From 1154 dereplicated viral operational taxonomic units (vOTUs), of which two-thirds were predicted bacteriophages, 17.2% encoded for auxiliary metabolic genes (AMGs) with metabolic functions. Some AMGs like glycerol-3-phosphate cytidylyltransferase and ice-binding like proteins might serve cryoprotection of the host. Prophages were often associated with SML genomes, and two active prophages of a new viral genera from the Arctic SML strain Leeuwenhoekiella aequorea Arc30 were induced. We found evidence that vOTU abundance in the SML compared to ~60 cm depth was more positively correlated to the distribution of a vOTU across five different Arctic stations. The results indicate that viruses employ elaborated strategies to endure in extreme and host-limited environments. Moreover, our observations suggest that the immediate air-sea interface serves as a platform for viral distribution in the Central Arctic. ### Competing Interest Statement The authors have declared no competing interest. * AMG : Auxiliary metabolic gene CRISPR : Clustered Regularly Interspaced Short Palindromic Repeat EPS : Extracellular polymeric substances IBP : Ice-binding protein iRep : Index of replication KEGG : Kyoto Encyclopedia of Genes and Genomes MAG : Metagenome-assembled genomes SML : Sea-surface microlayer SSW : Subsurface water TEM : Transmission electron microscopy vOTU : Viral operational taxonomic unit

Bacteriophages, or phages, are viruses that infect and replicate within bacterial hosts, playing a significant role in regulating microbial populations and ecosystem dynamics. However, phages from extreme environments such as polar regions remain relatively understudied due to challenges such as restricted ecosystem access and low biomass. Understanding the diversity, structure, and functions of polar phages is crucial for advancing our knowledge of the microbial ecology and biogeochemistry of these environments. In this review, we will explore the current state of knowledge on phages from the Arctic and Antarctic, focusing on insights gained from -omic studies, phage isolation, and virus-like particle abundance data. Metagenomic studies of polar environments have revealed a high diversity of phages with unique genetic characteristics, providing insights into their evolutionary and ecological roles. Phage isolation studies have identified novel phage-host interactions and contributed to the discovery of new phage species. Virus-like particle abundance and lysis rate data, on the other hand, have highlighted the importance of phages in regulating bacterial populations and nutrient cycling in polar environments. Overall, this review aims to provide a comprehensive overview of the current state of knowledge about polar phages, and by synthesizing these different sources of information, we can better understand the diversity, dynamics, and functions of polar phages in the context of ongoing climate change, which will help to predict how polar ecosystems and residing phages may respond to future environmental perturbations.

Studying airborne viral diversity in pristine, remote environments like the sub-Antarctic island South Georgia provides crucial insights into viral ecology and their role in sustaining unique ecosystems. Viruses influence microbial dynamics and nutrient cycles, which are vital for ecological balance and long-term ecosystem sustainability. We explored the community composition of airborne viral operational taxonomic units (vOTUs) of two sites in South Georgia, using various sampling devices and viral metagenomics. The Coriolis µ device (wet collection) was the most effective, yielding 30 viral scaffolds. Two-thirds of the scaffolds were from sea-level samples, indicating that location impacts viral diversity. Protein-based clustering of 39 vOTUs revealed similarities of 15 with known marine viruses, suggesting oceanic influence on the island's airborne viral community. Genes related to UV damage protection and photosynthesis from two airborne vOTUs were widely distributed in the major oceans, emphasizing the potential resilience in changing climates. Host predictions indicated associations with bacterial genera like Rickettsia , Myroides , and Bacteroidota. Some vOTUs matched viruses from extremophiles, indicating adaptations to harsh environments. This study provides a baseline for understanding the complexity and sustainability of airborne viral communities in remote ecosystems, underscoring the need for continued monitoring in the face of environmental change. ### Competing Interest Statement The authors have declared no competing interest.

Aquatic viruses act as key players in shaping microbial communities. In polar environments, they face significant challenges such as limited host availability and harsh conditions. However, due to the restricted accessibility of these ecosystems, our understanding of viral diversity, abundance, adaptations, and host interactions remains limited. To fill this knowledge gap, we studied viruses from atmosphere-close aquatic ecosystems in the Central Arctic and Northern Greenland. Aquatic samples for virus-host analysis were collected from 60 cm depth and the submillimeter surface microlayer (SML) during the Synoptic Arctic Survey 2021 on icebreaker Oden in the Arctic summer. Water was sampled from a melt pond and open water before undergoing size-fractioned filtration, followed by genome-resolved metagenomic and cultivation investigations. The prokaryotic diversity in the melt pond was considerably lower compared to that of open water. The melt pond was dominated by a Flavobacterium sp. and Aquiluna sp., the latter having a relatively small genome size of 1.2 Mb and the metabolic potential to generate ATP using the phosphate acetyltransferase-acetate kinase pathway. Viral diversity on the host fraction (0.2–5 µm) of the melt pond was strikingly limited compared to that of open water. From the 1154 viral operational taxonomic units (vOTUs), of which two-thirds were predicted bacteriophages, 17.2

Despite important ecological roles posited for virocells (i.e., cells infected with viruses), studying individual cells in situ is technically challenging. We introduce here a novel correlative microscopic approach to study the ecophysiology of virocells. By conducting concerted virusFISH, 16S rRNA FISH, and scanning electron microscopy interrogations of uncultivated archaea, we linked morphologies of various altiarchaeal cells to corresponding phylogenetic signals and indigenous virus infections. While uninfected cells exhibited moderate separation between fluorescence signals of ribosomes and DNA, virocells displayed complete cellular segregation of chromosomal DNA from viral DNA, the latter co-localizing with host ribosome signals. A similar spatial separation was observed in dividing cells, with viral signals congregating near ribosomes at the septum. These observations suggest that replication of these uncultivated viruses occurs alongside host ribosomes, which are used to generate the required proteins for virion assembly. Heavily infected cells sometimes displayed virus-like particles attached to their surface, which agree with virus structures in cells observed via transmission electron microscopy. Consequently, this approach is the first to link genomes of uncultivated viruses to their respective structures and host cells. Our findings shed new light on the complex ecophysiology of archaeal virocells in deep subsurface biofilms and provide a solid framework for future in situ studies of virocells.

Marine viruses are a major driver of phytoplankton mortality and thereby influence biogeochemical cycling of carbon and other nutrients. In recent years, an understanding of the potential importance of phytoplankton-targeting viruses on ecosystem dynamics has emerged, but experimental investigations of host-virus interactions on a broad spatial and temporal scale are still missing. Here, we investigated in detail a phytoplankton host’s responses reacting to infections by species-specific viruses from i) distinct geographical regions and ii) different sampling seasons. Specifically, we used two species of picophytoplankton (1 µm) Ostreococcus tauri and O. mediterraneus and their viruses (size ca. 100 nm), which represent systems well-known in marine biology, but almost entirely ignored in evolutionary biology. The strains stem from different regions of the Southwestern Baltic Sea that vary in salinity and temperature. Using an experimental cross-infection set-up, we show that in this natural system evolutionary history, and thus the timing of when hosts and their associated viruses coexisted, was the main driver of infection patterns. In addition species and strain specificity underline the present understanding of rapid host-virus co-evolution.

Spatial and temporal distribution of lytic viruses in deep groundwater remains unexplored so far. Here, we tackle this gap of knowledge by studying viral infections of Altivir_1_MSI in biofilms dominated by the uncultivated host Candidatus Altiarchaeum hamiconexum sampled from deep anoxic groundwater over a period of four years. Using virus-targeted direct-geneFISH (virusFISH) whose detection efficiency for individual viral particles was 15%, we show a significant and steady increase of virus infections from 2019 to 2022. Based on fluorescence micrographs of individual biofilm flocks, we determined different stages of viral infections in biofilms for single sampling events, demonstrating the progression of infection of biofilms in deep groundwater. Biofilms associated with many host cells undergoing lysis showed a substantial accumulation of filamentous microbes around infected cells probably feeding off host cell debris. Using 16S rRNA gene sequencing across ten individual biofilm flocks from one sampling event, we determined that the associated bacterial community remains relatively constant and was dominated by sulfate-reducing members affiliated with Desulfobacterota. Given the stability of the virus-host interaction in these deep groundwater samples, we postulate that the uncultivated virus-host system described herein represents a suitable model system for studying deep biosphere virus-host interactions in future research endeavors.

Marine viruses are a major driver of phytoplankton mortality and thereby influence biogeochemical cycling of carbon and other nutrients. Phytoplankton-targeting viruses are important components of ecosystem dynamics, but broad-scale experimental investigations of host-virus interactions remain scarce. Here, we investigated in detail a picophytoplankton (size 1 µm) host’s responses to infections by species-specific viruses from distinct geographical regions and different sampling seasons. Specifically, we used Ostreococcus tauri and O. mediterraneus and their viruses (size ca. 100 nm). Ostreococcus sp. is globally distributed and, like other picoplankton species, play an important role in coastal ecosystems at certain times of the year. Further, Ostreococcus sp. is a model organism, and the Ostreococcus -virus system is well-known in marine biology. However, only few studies have researched its evolutionary biology and the implications thereof for ecosystem dynamics. The Ostreococcus strains used here stem from different regions of the Southwestern Baltic Sea that vary in salinity and temperature and were obtained during several cruises spanning different sampling seasons. Using an experimental cross-infection set-up, we explicitly confirm species and strain specificity in Ostreococcus sp. from the Baltic Sea. Moreover, we found that the timing of virus-host co-existence was a driver of infection patterns as well. In combination, these findings prove that host-virus co-evolution can be rapid in natural systems.

Visible surface films, termed slicks, can extensively cover freshwater and marine ecosystems, with coastal regions being particularly susceptible to their presence. The sea-surface microlayer (SML), the upper 1-mm at the air-water interface in slicks (herein slick SML) harbors a distinctive bacterial community, but generally little is known about SML viruses. Using flow cytometry, metagenomics, and cultivation, we characterized viruses and bacteria in a brackish slick SML in comparison to non-slick SML as well as seawater below slick and non-slick areas (subsurface water = SSW). Size-fractionated filtration of all samples distinguished viral attachment to hosts and particles. The slick SML contained higher abundances of virus-like particles, prokaryotic cells, and dissolved organic carbon compared to non-slick SML and SSW. The community of 428 viral operational taxonomic units (vOTUs), 426 predicted as lytic, distinctly differed across all size fractions in the slick SML compared to non-slick SML and SSW. Specific metabolic profiles of bacterial metagenome-assembled genomes and isolates in the slick SML included a prevalence of genes encoding motility and carbohydrate-active enzymes (CAZymes). Several vOTUs were enriched in slick SML, and many virus variants were associated with particles. Nine vOTUs were only found in slick SML, six of them being targeted by slick SML-specific clustered-regularly interspaced short palindromic repeats (CRISPR) spacers likely originating from Gammaproteobacteria. Moreover, isolation of three previously unknown lytic phages for Alishewanella sp. and Pseudoalteromonas tunicata, abundant and actively replicating slick SML bacteria, suggests that viral activity in slicks contributes to biogeochemical cycling in coastal ecosystems.

CRISPR–Cas systems defend prokaryotic cells from invasive DNA of viruses, plasmids and other mobile genetic elements. Here, we show using metagenomics, metatranscriptomics and single-cell genomics that CRISPR systems of widespread, uncultivated archaea can also target chromosomal DNA of archaeal episymbionts of the DPANN superphylum. Using meta-omics datasets from Crystal Geyser and Horonobe Underground Research Laboratory, we find that CRISPR spacers of the hosts Candidatus Altiarchaeum crystalense and Ca. A. horonobense, respectively, match putative essential genes in their episymbionts’ genomes of the genus Ca. Huberiarchaeum and that some of these spacers are expressed in situ. Metabolic interaction modelling also reveals complementation between host–episymbiont systems, on the basis of which we propose that episymbionts are either parasitic or mutualistic depending on the genotype of the host. By expanding our analysis to 7,012 archaeal genomes, we suggest that CRISPR–Cas targeting of genomes associated with symbiotic archaea evolved independently in various archaeal lineages. CRISPR spacers in DPANN archaea target putative essential genes in their episymbionts and could be a widespread occurrence across diverse archaeal lineages.

Marine viruses in seawater have frequently been studied, yet their dispersal from neuston ecosystems at the air-sea interface towards the atmosphere remains a knowledge gap. Here, we show that 6.2% of the studied virus population were shared between air-sea interface ecosystems and rainwater. Virus enrichment in the 1-mm thin surface microlayer and sea foams happened selectively, and variant analysis proved virus transfer to aerosols collected at ~2 m height above sea level and rain. Viruses detected in rain and these aerosols showed a significantly higher percent G/C base content compared to marine viruses. CRISPR spacer matches of marine prokaryotes to foreign viruses from rainwater prove regular virus-host encounters at the air-sea interface. Our findings on aerosolization, adaptations, and dispersal support transmission of viruses along the natural water cycle.