Understanding the ocean ecosystem starting with its smallest members: improving genome to phenome approaches for studying unknown viral populations
Date
2021
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Publisher
University of Delaware
Abstract
Viruses that infect bacteria (bacteriophages) are the most abundant and diverse biological entities on the planet. These tiny but mighty replication machines will impact their hosts and ecosystem in many ways causing changes to global nutrient cycling, namely in the pelagic oceans. Accurate enumeration and the availability of phenotypic information on bacteriophages are some of the largest rate-limiting steps to understanding the ecosystem-level impact of environmental viruses. This study used a two-prong approach to the study of environmental viruses. First, the development of a more accurate and high-throughput method for epifluorescent enumeration of viruses in natural water samples. This method is shown to be accurate and precise in comparison to established microscopy counting and digital PCR used to quantify absolute abundance. Second, the development of helicase enzymes as marker genes for environmental viruses to categorize viral sequences and relate to phenotypic traits. Helicases were shown to occur in close association with other marker genes of interest, namely DNA polymerase A. The T7-like gp4 helicase most often occurs in conjunction with fast tyrosine-type polymerases in both environmental and database sequences. This work builds the proverbial toolbox for both wet-lab and bioinformatic based analyses of environmental viruses.
Description
Keywords
Bacteriophages, Helicase enzymes, Epifluorescent enumeration