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

Abstract

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

Viral challenges and adaptations between Central Arctic Ocean and atmosphere

“…In contrast, results from Baltic Sea SML showed, that an inducible phage occurred in one of the most abundant bacterial strains, Alishewanella sp. being additionally hunted by lytic phages [108]. Flavobacteria were previously found in the SML from different oceans [109,110], represent frequent hosts for lytic and temperate phages in the SML [108], and were important predicted viral hosts in the Arctic in this study.…”

“…being additionally hunted by lytic phages [108]. Flavobacteria were previously found in the SML from different oceans [109,110], represent frequent hosts for lytic and temperate phages in the SML [108], and were important predicted viral hosts in the Arctic in this study. Lysogeny is often prevalent or dominant in polar environments [82,111,112].…”

Scratching the ocean surface

“…Since phages are usually specific to their host, they can be used as a surrogate for studying bacterial diversity. For example, work led by Janina Rahlff-a postdoctoral researcher specializing in bacterial/viral interactions in the SML at Linnaeus University, Kalmar, Sweden-has revealed that viral compositions in thick SML biofilms known as slicks (often found in coastal waters) differ from those in non-slick surface water and samples from below the surface (preprint: Rahlff et al, 2023). The study concluded that lytic viral activity in slicks contributes to biogeochemical cycling in coastal ecosystems, which is important Rahlff's work has also found that viral communities in the SML differ by latitude, and she says that ongoing studies have even identified phage-encoded antifreeze proteins in phages isolated from surface microlayers in the Baltic Sea.…”