Depth-related variability in viral communities in highly stratified sulfidic mine tailings

• Published in: Microbiome Vol. 8; no. 1; pp. 89 - 13
• Main Authors: Gao, Shao-Ming, Schippers, Axel, Chen, Nan, Yuan, Yang, Zhang, Miao-Miao, Li, Qi, Liao, Bin, Shu, Wen-Sheng, Huang, Li-Nan
• Format: Journal Article
• Language: English
• Published: London BioMed Central 09.06.2020; BMC
• Subjects: Acids; Auxiliary metabolic genes; Bacteria - genetics; Bacteria - isolation & purification; Bacteria - metabolism; Bacteria - virology; Bioinformatics; Biomedical and Life Sciences; Biomedicine; Community composition; Deoxyribonucleic acid; Diversity; DNA; Ecology; Environmental conditions; Functions; Genera; Genomes; Geochemistry; Hydrogen-Ion Concentration; Medical Microbiology; Metabolism; Metagenomics; Microbial Ecology; Microbial Genetics and Genomics; Microbiology; Mining; pH effects; Principal components analysis; Prophages; RNA, Ribosomal, 16S - genetics; rRNA 16S; Stratified mine tailings; Sulfate reduction; Sulfides - metabolism; Sulfur; Taxonomy; Virology; Viruses; Viruses - genetics; Viruses - isolation & purification; Viruses - metabolism; Auxiliary metabolic genes; Viruses; Functions; Stratified mine tailings; Diversity
• ISSN: 2049-2618; 2049-2618
• DOI: 10.1186/s40168-020-00848-3

Background Recent 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. Results Here, 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. Conclusions Overall, 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-mJVeghGxVjw1ei Video Abstract