Spatial propagation of temperate phages within and among biofilms.

Bacteria form groups comprised of cells and secreted adhesive matrix that controls their spatial organization. These groups - termed biofilms - can act as refuges from environmental disturbance and from biotic threats, including phages. Despite the ubiquity of temperate phages and bacterial biofilms, temperate phage propagation within biofilms has never been characterized on multicellular spatial scales. Here, we leverage several approaches to track temperate phages and distinguish between lytic and lysogenic infections. We determine that lysogeny within E. coli biofilms most often occurs within a predictable region of cell group architecture. Because lysogens are generally found on the periphery of large groups, where lytic viral activity also reduces local structural integrity, lysogens are predisposed to disperse and are over-represented in biofilms formed downstream of the original biofilm-phage system. Comparing our results with those for virulent phages reveals that the temperate phages possess previously unknown advantages for propagation in architecturally heterogeneous biofilm communities.

Viruses of sulfur oxidizing phototrophs encode genes for pigment, carbon, and sulfur metabolisms.

Viral infections modulate bacterial metabolism and ecology. Here, we investigated the hypothesis that viruses influence the ecology of purple and green sulfur bacteria in anoxic and sulfidic lakes, analogs of euxinic oceans in the geologic past. By screening metagenomes from lake sediments and water column, in addition to publicly-available genomes of cultured purple and green sulfur bacteria, we identified almost 300 high and medium-quality viral genomes. Viruses carrying the gene psbA, encoding the small subunit of photosystem II protein D1, were ubiquitous, suggesting viral interference with the light reactions of sulfur oxidizing autotrophs. Viruses predicted to infect these autotrophs also encoded auxiliary metabolic genes for reductive sulfur assimilation as cysteine, pigment production, and carbon fixation. These observations show that viruses have the genomic potential to modulate the production of metabolic markers of phototrophic sulfur bacteria that are used to identify photic zone euxinia in the geologic past.