Giant Virus Infection Signatures Are Modulated by Euphotic Zone Depth Strata and Iron Regimes of the Subantarctic Southern Ocean

Abstract

Viruses can alter the abundance, evolution, and metabolism of microorganisms in the ocean, playing a key role in water column biogeochemistry and global carbon cycles. Large efforts to measure the contribution of eukaryotic microorganisms (e.g., protists) to the marine food web have been made, yet the in situ activities of the ecologically relevant viruses that infect these organisms are not well characterized. Viruses within the phylum Nucleocytoviricota ("giant viruses") are known to infect a diverse range of ecologically relevant marine protists, yet how these viruses are influenced by environmental conditions remains under-characterized. By employing metatranscriptomic analyses of in situ microbial communities along a temporal and depth-resolved gradient, we describe the diversity of giant viruses at the Southern Ocean Time Series (SOTS), a site within the subpolar Southern Ocean. Using a phylogeny-guided taxonomic assessment of detected giant virus genomes and metagenome-assembled genomes, we observed depth-dependent structuring of divergent giant virus families mirroring dynamic physicochemical gradients in the stratified euphotic zone. Analyses of transcribed metabolic genes from giant viruses suggest viral metabolic reprogramming of hosts from the surface to a 200-m depth. Lastly, using on-deck incubations reflecting a gradient of iron availability, we show that modulating iron regimes influences the activity of giant viruses in the field. Specifically, we show enhanced infection signatures of giant viruses under both iron-replete and iron-limited conditions. Collectively, these results expand our understanding of how the water column's vertical biogeography and chemical surroundings affect an important group of viruses within the Southern Ocean. IMPORTANCE The biology and ecology of marine microbial eukaryotes is known to be constrained by oceanic conditions. In contrast, how viruses that infect this important group of organisms respond to environmental change is less well known, despite viruses being recognized as key microbial community members. Here, we address this gap in our understanding by characterizing the diversity and activity of "giant" viruses within an important region in the sub-Antarctic Southern Ocean. Giant viruses are double-stranded DNA (dsDNA) viruses of the phylum Nucleocytoviricota and are known to infect a wide range of eukaryotic hosts. By employing a metatranscriptomics approach using both in situ samples and microcosm manipulations, we illuminated both the vertical biogeography and how changing iron availability affects this primarily uncultivated group of protist-infecting viruses. These results serve as a foundation for our understanding of how the open ocean water column structures the viral community, which can be used to guide models of the viral impact on marine and global biogeochemical cycling.

Keywords: Monodnaviria; Nucleocytoviricota; Ribovaria; SOTS; iron availability; marine microbiology; metatranscriptomics; phytoplankton; virocells.

FIG 1

Phylogeny of Nucleocytoviricota genomes and metagenome-assembled-genomes, with detected candidates at the Southern Ocean Time Series (SOTS) shown with their relative transcript abundances (transcripts per million, TPM) in the outermost bar plot. Clades without detected candidates are collapsed. Branches are color-coded by order-level taxonomy. Cultured isolate virus references of interest are labeled in their approximate location along the branches with the following abbreviations: HaV01: Heterosigma akashiwo Virus 01 isolate HaV53 (HaV53), Bathycoccus prasinos Virus 1 (BpV1), Cafeteria roenbergensis Virus (CroV), Aureococcus anophagefferens Virus (AaV), Chrysochromulina ericina Virus (CeV), Phaeocystis globosa Virus (PgV).

FIG 2

Taxon-specific transcript abundance patterns of Nucleocytoviricota across a depth-dependent and temporal scale. (A) Shifts in proportions of normalized transcripts assigned to different Nucleocytoviricota genomes by family. (B) Total Nucleocytoviricota transcript counts with depth, normalized by library size. (C) Heatmap of family-level-summed Nucleocytoviricota transcript abundances across depth profiles sampled on March 5, 7, and 9 with corresponding nutrient and total eukaryotic RPB1 transcript abundance data along the left-hand side. Data for March 17 were omitted due to lack of nutrient data. Family-level color codes have been changed (compared to Fig. 1) for visual purposes. Only the short-hand names of the family-level assignments are shown.

FIG 3

Nucleocytoviricota metabolic gene transcript abundance patterns across a temporal and depth-related scale. (A) Transcript abundances of metabolic genes summed by depth and separated by date sampled. Genes are categorized by broad functional category. (B) Transcript abundances of metabolic genes, summed by functional category and respective genomic phylogenetic assignment to the family level.

FIG 4

Expression patterns of Nucleocytoviricota major capsid proteins (MCPs) across an iron availability gradient within an on-deck incubation of the surface microbial community. Only MCPs with significantly different (Mann-Whitney U test, P < 0.05) normalized transcript values (DESeq2’s variance stabilizing transformation [vst]) between the desferrioxamine-B (DFB) added versus the iron chloride (Fe) added incubations are shown in the heatmap. Variability for normalized expression values (z-scores, [observed vst − mean vst]/standard deviation) are standardized across each row (individual MCPs). Each column is annotated by whether DFB, Fe, or nothing (control) was added. Each row is annotated by the phylogenetic assignment of the MCP. Only MCPs originating from the giant virus genomes/metagenome assembled genomes are annotated with phylogeny following Fig. 1. The dendrograms show similarity in expression patterns by incubation (column) and MCP transcripts (row) using Euclidean distance and hierarchical clustering. Bar plots of the averaged vst values for transcripts across the iron incubation metatranscriptomes and the in situ t = 0 h metatranscriptomes are shown to the right of the heatmap.