The viruses in the oil reservoirs and their roles in the alkane degradation
Soil Sciences
Final Report Abstract
We developed two bioinformatic pipelines to analyze viral sequences and identify Hydrocarbon - degrading Genes (HYDGs) in sequencing data - ViroProfiler, for viral metagenomic analysis, and HYDGscan, for rapid detection of viral-encoded HYDGs. We found no direct evidence of HYDEG-encoding viruses in the virome from oil reservoirs. However, analysis of metabolic pathways suggested several pathways contribute to hydrocarbon degradation, indicating the potential roles of viruses in the process. In addition, we analyzed 5.6 million viral genomes/contigs from public databases and found that less than 0.1% of them encoded at least one HYDEG. We identified 57 high-quality vHYDEGs, which were classified into six functional groups. Six protein families involved in the initial alkane hydroxylation steps were identified. Phylogenetic analyses revealed the diverse evolutionary trajectories of vHYDEGs across habitats revealing previously unknown biodegraders linked evolutionarily with vHYDEGs. Our findings suggest phage may contribute to alkane and aromatic hydrocarbon degradation, participating in the initial, rate -limiting hydroxylation steps, thereby aiding hydrocarbon pollution bioremediation and promoting their propagation. To support future research, we developed vHyDeg, a database containing identified vHYDEGs with comprehensive annotations, facilitating the screening of viral encoded hydrocarbon degradation genes and encouraging their bioremediation applications. In addition, we also isolated eight phages infecting two strains of alkane-degradation bacteria from the genus Dietzia. We found that one of the isolated phages encodes the formate acetyltransferase gene (PflD), indicating its potential role in anaerobic alkane degradation. Our results shed some light on the previously unknown role of viruses on hydrocarbon degradation. In addition, we have developed two bioinformatics pipelines and a comprehensive database of vHYDEGs identified in this study with detailed annotations. These resources will simplify the screening of viral sequences for identifying hydrocarbon degradation-associated genes and promote their potential applications in bioremediation. Further researches focusing on unravelling the mechanism and kinetics of those phage-encoded vHYDEGs have the potential to increase overall degradation activities, thus opening new doors for more efficient bioremediation in the future.
Publications
-
Unveiling the hidden role of aquatic viruses in hydrocarbon pollution bioremediation. Journal of Hazardous Materials, 459, 132299.
Ru, Jinlong; Xue, Jinling; Sun, Jianfeng; Cova, Linda & Deng, Li
-
ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis. Gut Microbes, 15(1).
Ru, Jinlong; Khan, Mirzaei Mohammadali; Xue, Jinling; Peng, Xue & Deng, Li
