Diversity and ecological functions of viruses inhabiting the oil reservoirs

Abstract

Oil reservoirs, being one of the most significant subsurface repositories of energy and carbon, have long hosted diverse microorganisms affecting energy production and carbon emissions. Viruses play crucial roles in the ecology of microbiomes, however, their distribution and ecological significance in oil reservoirs remain undetermined. Here, we assembled an extensive catalogue encompassing viral and prokaryotic genomes sourced from oil reservoirs. The catalogue comprises 7,229 prokaryotic genomes and 6,218 viral genomes from 182 oil reservoir metagenomes, respectively. Based on sequence clustering we identified 3,886 Operational Taxonomic Units (vOTUs) approximately at species level, 94.80% of which were not found in any other environments. The results showed that viruses were widely distributed in oil reservoirs, and oil reservoirs contain a significant number of unique and unexplored viruses. We also constructed a catalogue of 322,060 viral gene clusters including 105 virus-encoded putative auxiliary metabolic genes (AMGs) that participate in host metabolism and adaptation to the environment. Furthermore, our investigation has yielded a total of 7,197 putative virus-host pairs based on CRISPR and tRNA profiles. Viruses within oil reservoirs profoundly infected bacterial Actinobacteriota, Desulfobacterota, as well as archaeal Halobacteriota and Methanobacteriota. Combined microcosm enrichment experiments and bioinformatics analysis, we validated the ecological roles of viruses in regulating the community structure of sulfate reduction microorganisms, primarily through the predation of virulent viruses. Collectively, these findings have unveiled a rich diversity of novel viruses and their ecological functions within oil reservoirs. This study provides a comprehensive understanding of the role of viral communities in the biogeochemical cycle of the deep biosphere. It also facilitates microbial applications aimed at addressing challenges related to fossil-fuel production and carbon emissions in the petroleum industry.