Fig. 3: Visualization and quantification of Ca. Altiarchaeum virus Altivir_1_MSI-infected and noninfected Altiarchaeota biofilm (BF) cells from MSI site.

For all virusFISH experiments shown here, an Altivir_1_MSI probe was used for detecting viral infections. BF material was visualized with filter sets for DAPI (blue, cells), ATTO 488 (purple, 16S rRNA signal), and Alexa 594 (yellow, viral genomes), and merged for analysis and display purposes. a VirusFISH displays the interactions between Altiarchaeota cells and their virus shown as yellow dots. For unmerged imaging data, see Supplementary Fig. 11. Scale bar: 10 µm. b Different infection stages with Altivir_1_MSI. The enumeration performed with a regular epifluorescence microscope was based on 18,411 archaeal cells and categorized into three infection stages. For the categorization we used in total 18 Altiarchaeota biofilms, whereby 17 biofilms were treated with the Altivir_1_MSI probe (n = 17) and one biofilm was treated with a Metallosphaera sp. virus probe (n = 1). Purple arrows indicate exemplary viruses that attach to host’s cell surface, white arrows show advanced infections, and orange arrows bursting cells with free viruses. Scale bars: 2 µm. c Coupling virusFISH with structured illumination microscopy showed extracellular signals of tiny fluorescently labeled viral particles attaching to Altiarchaeota’s cell surface but also in a free state as presumably released virions (n = 1). Scale bar: 2 µm. d Transmission electron microscopy revealed intracellular virus-like particles (n = 3). Scale bar: 100 nm.