Nicole Dubilier Lab and Matthew Sullivan Lab Master's thesis project Max Planck Institute for Marine Microbiology, Bremen, Germany and Ohio State University, Columbus, Ohio, USA September 18, 2017 until March 28, 2018 (continuing to work on data summer of 2018)
Project aims: 1. Examine the virome associated with the symbiosis between Bathymodiolus mussels (pictured below) and their chemosynthetic bacterial symbionts. 2. Assess the effectiveness of two phage induction approaches: heat shock and UV light exposure on mussel gill tissue
Picture of Bathymodiolus mussels at a deep sea vent.
To subsist in the deep sea, Bathymodiolus mussels have formed a symbiotic relationship with chemosynthetic sulfide and methane oxidizing bacteria, SOX and MOX bacteria, respectively. My project examines the phages associated with this symbiosis through metagenomic sequences of mussel gill tissues. Although viruses are the most abundant biological entities on the planet, their particles are relatively small on average, and they typically have extremely small genomes. Because of these characteristics, their DNA sequence signal is often drowned out by that of organisms with larger genomes, in this case the mussel and bacterial DNA. To enhance the viral sequence signal, samples were filtered to remove mussel cells. One sample was enriched for phages via heat shock, and the other UV light exposure (mytomycin C was unavailable). All samples were then filtered separately to remove bacteria cells.
After some additional filtration, purification, and concentration steps, the samples were then sequenced, and I am currently playing with the viruses detected in these sequences, using tools such as VirSorter and VirFinder, after having assembled the metagenomes with SPAdes (and MEGAHIT for comparison).
During my master's thesis, I examined a preliminary metagenomic data set (the heat shock treated sample with single-end reads) and successfully detected viral sequences, which I explored their potential functions and hosts. Now, I am working on all of the samples' metagenomes (paired-end reads).