Developing a Method for Detecting and Counting Marine Bacteriophages Using a Solid State Nanopore

Abstract:

UCSC GEOPATHS is an NSF-supported initiative to improve student success in the geosciences, driven by a desire to broaden participation. One component of the program is undergraduate student internships that provide authentic, career-relevant experiences – across all employment sectors – to increase student engagement in the geoscience pipeline.

My GEOPATHS internship involves working with Dr. Deamer and at Ontera Inc. where we analyzed seawater samples for marine bacteriophages using a NanoCounter. The focus is on marine viruses called bacteriophages that specialize in parasitizing prokaryotic hosts. Marine phages make up the most abundant biomass in the ocean with up to 250 million phages per milliliter of seawater, outnumbering their bacterial hosts nearly ten to one. As many of these phages attack photosynthetic cyanobacteria, they represent a large uncounted part of our global carbon cycling.

Literature on marine bacteriophages is extremely limited because it is difficult to isolate them from solution. The purpose of our study is to test a new solid-state nanopore device called a NanoCounter to see if it can detect and count different bacteriophages in seawater. The NanoCounter, designed and manufactured by biotech company Ontera Inc., counts macromolecules like DNA, RNA, and other polymers and characterizes them by size. We are using a NanoCounter to quantify and describe bacteriophages from both seawater and fresh water. To our knowledge, this is the first time that a nanopore device has been used to monitor the phage content of water samples.