Lytic archaeal viruses infect abundant primary producers in Earth’s crust

Abstract

The continental subsurface houses a major portion of life’s abundance and diversity, yet little is known about viruses infecting microbes that reside there. Here, we use a combination of metagenomics and virus-targeted direct-geneFISH (virusFISH) to show that highly abundant carbon-fixing organisms of the uncultivated genus Candidatus Altiarchaeum are frequent targets of previously unrecognized viruses in the deep subsurface. Analysis of CRISPR spacer matches display resistances of Ca. Altiarchaea against eight predicted viral clades, which show genomic relatedness across continents but little similarity to previously identified viruses. Based on metagenomic information, we tag and image a putatively viral genome rich in protospacers using fluorescence microscopy. VirusFISH reveals a lytic lifestyle of the respective virus and challenges previous predictions that lysogeny prevails as the dominant viral lifestyle in the subsurface. CRISPR development over time and imaging of 18 samples from one subsurface ecosystem suggest a sophisticated interplay of viral diversification and adapting CRISPR-mediated resistances of Ca. Altiarchaeum. We conclude that infections of primary producers with lytic viruses followed by cell lysis potentially jump-start heterotrophic carbon cycling in these subsurface ecosystems.

Patterns and ecological drivers of viral communities in acid mine drainage sediments across Southern China

“…The relatively low species richness, broad range and steep gradients of geochemical variables promise more straight-forward establishment of ecological patterns and underlying mechanisms. The diversity and community dynamics of viruses in extreme environments such as the Atacama Desert 17 , cryosphere 18 , 19 , acid mine drainage (AMD) environment 20 , 21 , and Earth’s subsurface 7 , 22 , 23 have recently been investigated through meta-omics approaches; yet, extensive sampling and analysis of viral communities across large geographic scales to resolve their ecological distribution patterns and drivers have not been conducted. Here we strive to address this knowledge gap by utilizing a massive metagenomic data set generated from 90 AMD sediments sampled across Southern China (Fig.…”

New Microviridae isolated from Sulfitobacter reveals two cosmopolitan subfamilies of ssDNA phages infecting marine and terrestrial Alphaproteobacteria

“…Here, we have applied the relatively new direct-geneFISH method (Barrero-Canosa et al 2017; Barrero-Canosa and Moraru 2021b), which uses multiple probes directly labeled with fluorochromes and thus avoids signal amplification steps. This method was used recently for intracellular virus detection of dsDNA archaeal and picoeukaryotic viruses in environmental samples and pure cultures (Castillo et al 2020; Castillo et al 2021; Rahlff et al 2021). In our study, using phage-targeted genome-wide probes, we were able to characterize the lytic cycle of an ssDNA phage.…”

Host-associated phages disperse across the extraterrestrial analogue Antarctica

“…PGFs were identified from metagenome assemblies using a combination of bioinformatic tools, namely Virsorter v1 (33), VirFinder (97), CircMG (98), renamed to VRCA (https://github.com/alexcritschristoph/VRCA), VOGdb (version VOG93) (99), and Endmatcher (https://github.com/ProbstLab/viromics/tree/master/Endmatcher). The classification of predicted PGFs as “putative viruses” and “viruses” was done as previously described in the Supplementary Figure 3 of (100). VIBRANT v.1.2.1 (30) with default settings was used to find additional PGFs.…”