Host-Associated Phages Disperse across the Extraterrestrial Analogue Antarctica

Rahlff, Janina; Bornemann, Till L. V.; Lopatina, Anna; Severinov, Konstantin; Probst, Alexander J.

doi:10.1128/aem.00315-22

Cited by 10 publications

(11 citation statements)

References 129 publications

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“…This workflow resulted in 428 representative viral scaffolds (further referred to as viral operational taxonomic units = vOTUs) as the final output. Viral relative abundance (depth of coverage) and breadth of coverage for vOTUs and phage isolates (see below) was calculated with scripts and settings as done previously [82] after read-mapping with Bowtie2 and following conventions of [83]. Viral genes in vOTUs and phage isolates were predicted using Prodigal v.2.6.3 in meta mode [84] and functionally annotated using DRAM-v v.1.2.4 [57].…”

Section: Metagenomic Analyses Of Dsdna Virusesmentioning

confidence: 99%

Ecogenomics reveals distinctive viral-bacterial communities in the surface microlayer of a natural surface slick

Rahlff

Wietz

Giebel

et al. 2023

Preprint

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Visible surface films, termed slicks, can extensively cover the sea surface, particularly in coastal regions. The sea-surface microlayer (SML), the upper 1-mm at the air-water interface in slicks (slick SML) harbors a distinctive bacterial community, but little is known about SML viruses. Using flow cytometry, metagenomics, and cultivation, we investigated viruses and the bacterial community from a brackish slick SML in comparison to non-slick SML as well as the seawater below (SSW). We conducted size-fractionated filtration of all samples to distinguish 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. The distinctness was underlined by specific metabolic profiles of bacterial metagenome assembled genomes and isolates, which revealed prevalence of motility genes and diversity of CAZymes in the slick SML. Despite overall lower diversity, several vOTUs were enriched in slick SML over slick SSW. Nine vOTUs were only found in slick SML and six of them were targeted by slick SML-specific CRISPR spacers likely originating from Gammaproteobacteria. Moreover, isolation of three previously unknown lytic phages forAlishewanellasp. andPseudoalteromonas tunicata, representing abundant and actively replicating slick SML bacteria, suggests that viral activity in slicks can contribute to biogeochemical cycling in coastal ecosystems

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Section: Metagenomic Analyses Of Dsdna Virusesmentioning

confidence: 99%

Ecogenomics reveals distinctive viral-bacterial communities in the surface microlayer of a natural surface slick

Rahlff

Wietz

Giebel

et al. 2023

Preprint

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“…The atmosphere is known to mediate rapid transport of prokaryotes and viruses from marine and terrestrial sources over thousands of kilometers 62,63 . Aerosol and rain samples contained MAGs and genetic signatures from marine microbes, suggesting that aerosolization from the sea surface generally took place.…”

Section: Discussionmentioning

confidence: 99%

Heads in the clouds: marine viruses disperse bidirectionally along the natural water cycle

Rahlff

Esser

Plewka

et al. 2022

Preprint

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Marine viruses have thoroughly been studied in seawater, 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 and rain. Viruses detected in rain and aerosols showed a significantly higher percent G/C base content compared to marine viruses, and a genetically distinct rain virome supports that those viruses could inhabit higher air masses. 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 and long-range atmospheric dispersal implicate virus-mediated carbon turnover in remote areas, viral dispersal mechanisms relevant to human health, and involvement of viruses in atmospheric processes like ice-nucleation.

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“…Mean depth and breadth of the resulting viral operational taxonomic units (vOTUs) coverage were calculated after mapping reads to vOTUs using Bowtie2 v.2.4.5 with settings --mp 1,1 --np 1 --rdg 0,1 --rfg 0,1 --score-min L,0,-0.1 [57] for mapping of ≥90 % identical reads and following conventions of [58]. A coverage of ≥75 % (read breadth) of the viral genome was achieved by running the calcopo.rb script [59]. Coverages were analyzed using the 04_01calc_coverage_v3.rb script [45] and subsequently normalized to read depths.…”

Section: Methodsmentioning

confidence: 99%

Viral challenges and adaptations between Central Arctic Ocean and atmosphere

Rahlff,

Westmeijer,

Weissenbach

et al. 2024

Preprint

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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 aFlavobacteriumsp. andAquilunasp., 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 strainLeeuwenhoekiella aequoreaArc30 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.

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Host-Associated Phages Disperse across the Extraterrestrial Analogue Antarctica

Cited by 10 publications

References 129 publications

Ecogenomics reveals distinctive viral-bacterial communities in the surface microlayer of a natural surface slick

Ecogenomics reveals distinctive viral-bacterial communities in the surface microlayer of a natural surface slick

Heads in the clouds: marine viruses disperse bidirectionally along the natural water cycle

Viral challenges and adaptations between Central Arctic Ocean and atmosphere

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