Abstract
BackgroundRecent studies have significantly expanded our knowledge of viral diversity and functions in the environment. Exploring the ecological relationships between viruses, hosts, and the environment is a crucial first step towards a deeper understanding of the complex and dynamic interplays among them.ResultsHere, we obtained extensive 16S rRNA gene amplicon, metagenomics sequencing, and geochemical datasets from different depths of two highly stratified sulfidic mine tailings cores with steep geochemical gradients especially pH, and explored how variations in viral community composition and functions were coupled to the co-existing prokaryotic assemblages and the varying environmental conditions. Our data showed that many viruses in the mine tailings represented novel genera, based on gene-sharing networks. Siphoviridae, Podoviridae, and Myoviridae dominated the classified viruses in the surface tailings and deeper layers. Both viral richness and normalized coverage increased with depth in the tailings cores and were significantly correlated with geochemical properties, for example, pH. Viral richness was also coupled to prokaryotic richness (Pearson’s r = 0.65, P = 0.032). The enrichment of prophages in the surface mine tailings suggested a preference of lysogenic viral lifestyle in more acidic conditions. Community-wide comparative analyses clearly showed that viruses in the surface tailings encoded genes mostly with unknown functions while viruses in the deeper layers contained genes mainly annotated as conventional functions related to metabolism and structure. Notably, significantly abundant assimilatory sulfate reduction genes were identified from the deeper tailings layers and they were widespread in viruses predicted to infect diverse bacterial phyla.ConclusionsOverall, our results revealed a depth-related distribution of viral populations in the extreme and heterogeneous tailings system. The viruses may interact with diverse hosts and dynamic environmental conditions and likely play a role in the functioning of microbial community and modulate sulfur cycles in situ.6mWQNmd-mJVeghGxVjw1eiVideo
Highlights
Recent studies have significantly expanded our knowledge of viral diversity and functions in the environment
We found seven predicted viral scaffolds that harbored genes participating in assimilatory sulfate reduction (ASR) (COG0175) (Fig. 6a and Additional file 1: Table S9), which are important for the reduction of
Given that the reticulate classification method of viral sequences uses shared gene content information [2, 34] and that currently the isolated archaeal viruses are largely outnumbered by bacteriophages [35, 36], it is likely that archaeal viruses may account for a substantial fraction of the unclassified viral scaffolds in our study, especially in the archaea-predominating surface tailings
Summary
Recent studies have significantly expanded our knowledge of viral diversity and functions in the environment. (2020) 8:89 to the absence of a phylogenetically informative universal marker owing to the mosaic nature of viral genome organization [3] To tackle these problems, recent works have employed metagenomic sequencing to discover viral sequences from a wide variety of habitats including marine and freshwater environments [3,4,5], soils [6, 7], and extreme environments [8,9,10]. Recent works have employed metagenomic sequencing to discover viral sequences from a wide variety of habitats including marine and freshwater environments [3,4,5], soils [6, 7], and extreme environments [8,9,10] These studies often reveal the existence of diverse viral assemblages in nature, whose members remain largely uncharacterized (unknown virosphere), and significantly improve our understanding of the ecological roles of viruses in Earth’s major ecosystems [4, 11]. All these aspects imply a complicated interaction between viruses, hosts, and environments
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