Virus-Host Dynamics in Archaeal Groundwater Biofilms and the Associated Bacterial Community Composition

Abstract

Spatial and temporal distribution of lytic viruses in deep groundwater remains unexplored so far. Here, we tackle this gap of knowledge by studying viral infections of Altivir_1_MSI in biofilms dominated by the uncultivated host Candidatus Altiarchaeum hamiconexum sampled from deep anoxic groundwater over a period of four years. Using virus-targeted direct-geneFISH (virusFISH) whose detection efficiency for individual viral particles was 15%, we show a significant and steady increase of virus infections from 2019 to 2022. Based on fluorescence micrographs of individual biofilm flocks, we determined different stages of viral infections in biofilms for single sampling events, demonstrating the progression of infection of biofilms in deep groundwater. Biofilms associated with many host cells undergoing lysis showed a substantial accumulation of filamentous microbes around infected cells probably feeding off host cell debris. Using 16S rRNA gene sequencing across ten individual biofilm flocks from one sampling event, we determined that the associated bacterial community remains relatively constant and was dominated by sulfate-reducing members affiliated with Desulfobacterota. Given the stability of the virus-host interaction in these deep groundwater samples, we postulate that the uncultivated virus-host system described herein represents a suitable model system for studying deep biosphere virus-host interactions in future research endeavors.

Spatio-functional organization in virocells of small uncultivated archaea from the deep biosphere

“…Recently, advances in fluorescence in situ hybridization (FISH) enabled researchers to detect an uncultivated virus via tagging the viral genome [ 8 , 9 ] and Schaible et al to correlated FISH imaging with scanning electron microscopy (SEM) for identification of specific prokaryotes using 16S rRNA tagging [ 10 ]. However, the combination of virusFISH (i.e., virus-targeted direct-geneFISH) with SEM has been proposed [ 11 ] but not been established, as virusFISH protocols necessitate 300 base pairs double-stranded (ds) probes to enter target cells and thus a harsh temperature treatment of cells, which results in disintegration of the cellular ultrastructure (Supplementary Fig. S1 ).…”

“…Altiarchaeal cells infected with uncultivated viruses (infection rate 5% [ 11 ]) were 10–20% larger and slightly more spherical than their ribocell counterparts (Fig. 2b ; 30 infected and 145 non-infected cells; Wilcoxon test, two-sided, p value < 0.001; Supplementary Table S2 , Supplementary Figs.…”