Abstract The continental subsurface houses a major portion of life’s abundance and diversity, yet little is known about viruses infecting microbes that reside there. Here, we use a combination of metagenomics and virus-targeted direct-geneFISH (virusFISH) to show that highly abundant carbon-fixing organisms of the uncultivated genus Candidatus Altiarchaeum are frequent targets of previously unrecognized viruses in the deep subsurface. Analysis of CRISPR spacer matches display resistances of Ca . Altiarchaea against eight predicted viral clades, which show genomic relatedness across continents but little similarity to previously identified viruses. Based on metagenomic information, we tag and image a putatively viral genome rich in protospacers using fluorescence microscopy. VirusFISH reveals a lytic lifestyle of the respective virus and challenges previous predictions that lysogeny prevails as the dominant viral lifestyle in the subsurface. CRISPR development over time and imaging of 18 samples from one subsurface ecosystem suggest a sophisticated interplay of viral diversification and adapting CRISPR-mediated resistances of Ca . Altiarchaeum. We conclude that infections of primary producers with lytic viruses followed by cell lysis potentially jump-start heterotrophic carbon cycling in these subsurface ecosystems.
Abstract This paper describes a state-of-the-art research catamaran to investigate processes such as air–sea gas exchange, heat exchange, surface blooms, and photochemistry at the sea surface microlayer (SML) with high-resolution measurements of 0.1-Hz frequency. As the boundary layer between the ocean and the atmosphere, the SML covers 70% of Earth. The remote-controlled Sea Surface Scanner is based on a glass disk sampler to automate the sampling of the thin SML, overcoming the disadvantages of techniques such as low volume sampling and ex situ measurement of the SML. A suite of in situ sensors for seven biogeochemical parameters (temperature, pH, dissolved oxygen, salinity, chromophoric dissolved organic matter, chlorophyll- a , and photosynthetic efficiency) was implemented to characterize the SML in reference to the mixed bulk water. The Sea Surface Scanner has the capability to collect 24 discrete water samples with a volume of 1 L each for further laboratory analysis. Meteorological parameters such as wind speed influence SML properties and are continuously monitored. This paper reports the use of the Sea Surface Scanner to identify and study (i) upwelling regions and associated fronts, (ii) rain events, and (iii) the occurrence of surface blooms. The high patchiness of the SML was detected during the observed sea surface phenomena, and high-resolution mapping of the biogeochemical parameters of the oceanic boundary layer to the atmosphere are presented for the first time. The Sea Surface Scanner is a new technology to map and understand sea surface processes and, ultimately, to fill the gaps in knowledge about ocean–atmosphere interactions relevant to ocean and climate science.
Vast biofilm-like habitats at air–water interfaces of marine and freshwater ecosystems harbor surface-dwelling microorganisms, which are commonly referred to as neuston. Viruses in the microlayer, i.e., the virioneuston, remain the most enigmatic biological entities in boundary surface layers due to their potential ecological impact on the microbial loop and major air–water exchange processes. To provide a broad picture of the viral–bacterial dynamics in surface microlayers, this review compiles insights on the challenges that viruses likely encounter at air–water interfaces. By considering viral abundance and morphology in surface microlayers, as well as dispersal and infection mechanisms as inferred from the relevant literature, this work highlights why studying the virioneuston in addition to the bacterioneuston is a worthwhile task. In this regard, major knowledge gaps and possible future research directions are discussed.
Viruses are the cause of a considerable burden to human, animal and plant health, while on the other hand playing an important role in regulating entire ecosystems. The power of new sequencing technologies combined with new tools for processing "Big Data" offers unprecedented opportunities to answer fundamental questions in virology. Virologists have an urgent need for virus-specific bioinformatics tools. These developments have led to the formation of the European Virus Bioinformatics Center, a network of experts in virology and bioinformatics who are joining forces to enable extensive exchange and collaboration between these research areas. The EVBC strives to provide talented researchers with a supportive environment free of gender bias, but the gender gap in science, especially in math-intensive fields such as computer science, persists. To bring more talented women into research and keep them there, we need to highlight role models to spark their interest, and we need to ensure that female scientists are not kept at lower levels but are given the opportunity to lead the field. Here we showcase the work of the EVBC and highlight the achievements of some outstanding women experts in virology and viral bioinformatics.
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.
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 <39%. Thirteen high GC vOTUs from Sweden and Antarctica clustered in a proteomic tree analysis with known high GC phage isolates infecting Microbacterium radiodurans and Arthrobacter sp. (both phylum Actinomycetota). Host predictions using iPHoP revealed that only 11 of the 80 vOTUs could be assigned to bacterial hosts with good confidence, namely to genera Mycobacterium, Ralstonia, Sphingomonas, and Bradyrhizobium. Our results suggest that high GC is a feature in air viruses from different atmospheric sources and latitudes. While these vOTUs occur irregularly at near-ground sampling heights, a high GC content could favor the survival of airborne viruses higher in the troposphere and thus enable infections of extremophilic hosts within air ecosystems.References:1 Simón, D., Cristina, J., & Musto, H. (2021). Nucleotide composition and codon usage across viruses and their respective hosts. Frontiers in Microbiology, 12, 646300.2 Ellington, A. J., Bryan, N. C., Christner, B. C., & Reisch, C. R. (2021). Draft Genome Sequences of Actinobacterial and Betaproteobacterial Strains Isolated from the Stratosphere. Microbiology Resource Announcements, 10(50), e01009-21.3 Rahlff, J., Esser, S.P., Plewka, J., Heinrichs, M.E., Soares, A., Scarchilli, C., Grigioni, P., Wex, H., Giebel, H.A. and Probst, A.J., 2023. Marine viruses disperse bidirectionally along the natural water cycle. Nature Communications, 14(1), p.6354.4 Dillon, K. P., Correa, F., Judon, C., Sancelme, M., Fennell, D. E., Delort, A. M., & Amato, P. (2020). Cyanobacteria and Algae in Clouds and Rain in the Area of puy de Dôme, Central France. Applied and Environmental Microbiology, 87(1), e01850-20.
Abstract The occurrence of foams at oceans’ surfaces is patchy and generally short-lived but a detailed understanding of bacterial communities inhabiting sea foams is lacking. Here we investigated how marine foams differ from the sea-surface microlayer (SML), a <1 mm thick layer at the air-sea interface and underlying water from 1 m depth. Samples of sea foams, SML and underlying water collected from the North Sea and Timor Sea indicated that foams were often characterized by a high abundance of small eukaryotic phototrophic and prokaryotic cells as well as a high concentration of surface-active substances (SAS). Amplicon sequencing of 16S rRNA (gene) revealed a distinctive foam bacterial community compared to SML and underlying water, with high abundance of Gammaproteobacteria . Especially Pseudoalteromonas and Vibrio , typical SML dwellers, were highly abundant, active foam inhabitants and thus might enhance foam formation and stability by producing SAS. Despite a clear difference in the overall bacterial community composition between foam and SML, the presence of SML bacteria in foams supports previous assumptions that foam is strongly influenced by the SML. We conclude that active and abundant bacteria from interfacial habitats potentially contribute to foam formation and stability, carbon cycling and air-sea exchange processes in the ocean. One-sentence summary Floating foams at the oceans’ surface have a unique bacterial community signature in contrast to sea-surface microlayer and underlying water but receive and select for bacterial inhabitants from surface habitats.
Abstract 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. Sustainability Statement Antarctic microbes have potentially unique adaptations to extreme cold and harsh conditions. Viruses that infect these microbes may play a pivotal role in shaping these adaptations and thus understanding virus-host interactions is vital for preserving the unique microbial biodiversity of Antarctica. Moreover, investigating the dynamics of viral aerosolization in and around Antarctica is important for understanding the global dispersal of viruses and their potential impacts on distant ecosystems. Monitoring microbial viruses in Antarctica is essential for tracking community changes over time. Since Antarctica is often considered one of the last pristine environments on Earth, understanding the role of microbial viruses is relevant for developing conservation strategies to protect this ecosystem from potential anthropogenic impacts, including unintentional introduction of foreign microorganisms and viruses. Our research aligns with Sustainable Development Goals Life below water (SDG14) and Life on land (SDG15).
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. are globally distributed and, like other picoplankton species, play an important role in coastal ecosystems at certain times of the year. Further, Ostreococcus sp. are model organisms, 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 the timing of virus-host co-existence, was driver of infection patterns as well. In combination, these findings prove that host-virus co-evolution can be rapid in natural systems.
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