Discovery of Viruses of Thermophilic Ammonia-Oxidizing Archaea from Terrestrial Hot Spring Metagenomes
By: Marwin Fernandez
Department: Cellular & Molecular Biology
Faculty Advisor: Dr. José R. de la Torre
Viruses are obligate intracellular parasites that infect all domains of life; however, little is known about the viruses of thermophilic ammonia-oxidizing archaea (ThAOA), a contributor to the nitrogen cycle. This is due to the challenges of host cultivation. We will be discovering ThAOA viruses in order to understand how ThAOA evolved and how viral stressors affect nitrogen flux in the terrestrial hot spring ecosystem. Our goal is to discover viruses using de novo analysis of metagenomes from hot springs. Metagenomes from terrestrial hot springs with abundant populations of ThAOAs were selected and run through pipelines that identify viral sequences. The sequences will be annotated, binned, and assigned hosts using a variety of community-developed virus detection programs. Through annotation, we expect to find that the viral contigs contain some genes encoding proteins used in nucleic acid processing and metabolism. However, the majority of the putative viral genes will encode hypothetical proteins with no known function. We expect most viral contigs will belong to Caudovirales with few belonging to a variety of archeal virus. Similar to the binning results, we expect host assignments will show most viral contigs infecting bacteria, few contigs infecting unknown organisms, and very few infecting ThAOA. Our expected results indicate a bias towards assigning to bacteria, which we were aware of due to the small reference database of ThAOA for the host assignment training model. We will retrain the model to include metagenome-assembled genomes of ThAOA discovered from the metagenomes to expand the model’s ability and to reassign contigs. Despite the limitation, we hope to discover ThAOA viruses from metagenomes.