LB 18-166 - CANCELLED - Enhancing viral ecology: direct enumeration of viral particles with low-cost, high-throughput microfluidic devices

Microbes have long-served as tractable, malleable models for the study of large-scale ecological and evolutionary phenomena. Throughout the last century, researchers have leveraged host-virus interactions to characterize critically influential phenomena including predator-prey dynamics (i.e. Escherichia coli and T7 or T4), the role of nutrient flow in population ecology (i.e. Chlorella and chloroviruses; diatoms and their viruses), and coevolution (cyanobacteria and cyanophage; Pseudomonas fluorescens and T7-like podoviruses). Despite the role of viruses in modeling important ecological concepts, viral ecology within itself remains under-characterized. While the revolution of metagenomic sequencing cracked open the genomic diversity of environmental viruses, the phenotypes and ecological roles of ubiquitous viral populations remain a mystery. A remaining challenge to characterizing viral populations is the difficulty to accurately and cheaply count and observe free viruses. For example, while lytic infections are widely studied in culture-based experiments, counting plaque-forming units only reveals the number of infective viruses, not the total number of viruses released from a lytic burst event. Current standards of direct viral enumeration require expensive technology (i.e. flow cytometry) or consumable reagents (Anodisc filters). Thus, for the majority of microbial ecology labs worldwide, the task of counting viruses directly remains unaffordable and unattainable. To track viruses accurately, efficiently and affordably, we need new approaches that pair high accuracy with low cost. An interdisciplinary team of virologists, ecologists and bioengineers at the University of Delaware has developed a customizable microfluidic device (the “virometer”) to enumerate viruses from both well-known model systems (E. coli and T7 bacteriophage) and from ecologically important environments such as soybean roots (Bradyrhizobium and their bacteriophage), ponds (Chlorella and chlorovirus), and seawater (cyanobacteria and cyanophage). We’ve paired this novel approach with a customized MATLAB script to automate enumeration. The virometer leverages the naturally occurring net charges on viral capsids to attract and adhere viruses to polymer-coated glass surfaces of the virometer for more reliable and cheaper epifluorescent imaging. Here, we demonstrate the virometer’s utility in direct counting compared to other quantitative methods (i.e. Anodiscs, digital droplet PCR) and integration into classic virology workflows for new insights into host-virus dynamics. Since the virometer is customizable, it has the potential to democratize viral phenotyping, just as PhageHunter democratized viral genomics. Furthermore, we are eager to collaborate with other microbial ecologists to further explore viral phenotypes and ecology.