Abstract
Viruses provide top-down control on microbial communities, yet their direct study in natural environments was hindered by culture limitations. The advance of bioinformatics enables cultivation-independent study of viruses. Many studies assemble new viral genomes and study viral diversity using marker genes from free viruses. Here we use cellular metatranscriptomics to study active community-wide viral infections. Recruitment to viral contigs allows tracking infection dynamics over time and space. Our assemblies represent viral populations, but appear biased towards low diversity viral taxa. Tracking relatives of published T4-like cyanophages and pelagiphages reveals high genomic continuity. We determine potential hosts by matching dynamics of infection with abundance of particular microbial taxa. Finally, we quantify the relative contribution of cyanobacteria and viruses to photosystem-II psbA (reaction center) expression in our study sites. We show sometimes >50% of all cyanobacterial+viral psbA expression is of viral origin, highlighting the contribution of viruses to photosynthesis and oxygen production.
Highlights
Viruses provide top-down control on microbial communities, yet their direct study in natural environments was hindered by culture limitations
Some regional patterns were evident, e.g. some viral contigs were unique to the Port of LA (Fig. 1), and Port of Los Angeles (POLA) always differed from the other sites in expression of viral contigs more than SPOT and Catalina Island Two Harbors (CAT) differed from each other (Supplementary Figure 2B)
This pattern corresponds to the difference in microbial abundance and heterotrophic production between the port and the other sites (Supplementary Figure 1), and to patterns of microbial community composition and activity by amplicon single variants of 16SrRNA (ASV, Supplementary Figure 2C, D)
Summary
Viruses provide top-down control on microbial communities, yet their direct study in natural environments was hindered by culture limitations. Because viruses generally shut down synthesis of new mRNA coded by the host genome, expression of the viral version of this gene is required to maintain photosynthesis, and it is expressed almost throughout the cyanophage latent period[8,40]. Active viral infections in mixed natural communities could be tracked by assembling and characterizing multigene transcripts from cellular microbial metatranscriptomes. While some such transcripts may represent host operons or other vectors, recently developed methods can reasonably well identify sequences of viral origin[50,51]. We use that approach to characterize active viral infections via marine metatranscriptomic and metagenomic analyses and show temporal and spatial patterns in the diversity and activity of such infections
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