Discovering Viruses of Thermophilic Ammonia-Oxidizing Archaea Using de novo Analysis of Terrestrial Hot Spring Metagenomes
By: Marwin Fernandez
Department: Biology
Faculty Advisor: Dr. José R. De La Torre
Viruses are ubiquitous parasites that infect all domains of life. They play a key role in driving microbial ecology and evolution and have a profound effect on biogeochemical cycles. These effects can be seen from viruses of Nitrosophaeria, a lineage of ammonia-oxidizing archaea (AOA) that play a major role in the global nitrogen cycle, particularly in marine and soil environments. However, little is known about the viruses of thermophilic Nitrososphaeria, the earliest diverging branch of this lineage. Using metagenomics, the cultivation-independent sequencing of entire microbial communities, it is possible to characterize organisms and viruses in environmental samples. In this study, we explored the diversity of viruses in terrestrial hot springs where thermophilic AOA (ThAOA) are known to be abundant. Using GeNomad, viral contigs were extracted from metagenomic assemblies and characterized through genome annotation and assessing its completeness and contamination. On average, we found more than 100 viral contigs from each metagenome with 2% being closed genomes and proviruses. Through annotation, we found that the viral contigs contain genes encoding proteins used in nucleic acid processing and metabolism, with majority of predicted genes encoding hypothetical proteins with no known function. The viral contigs were then assigned hosts using iPHoP and manual CRISPR matching and found that a small amount of contigs are assigned to ThAOA hosts. After close inspection of the CRISPR match, the hosts are targeting hypothetical genes in the viral contig. Further analysis into these genes will be required to understand what the virus is encoding that harm ThAOA.