Using signature genes as tools to assess environmental viral ecology and diversity

Abstract

Viruses (including bacteriophages) are the most abundant biological entities on the planet. As such, they are thought to have a major impact on all aspects of microbial community structure and function. Despite this critical role in ecosystem processes, the study of virus/phage diversity has lagged far behind parallel studies of the Bacterial and Eukaryotic kingdoms, largely due to the absence of any ‘universal phylogenetic marker’. Here we review the development and use of signature genes to investigate viral diversity, as a viable strategy for datasets of specific virus groups. Genes that have been used include those encoding structural proteins, portal protein, major capsid protein and tail sheath protein, auxiliary metabolism genes such as psbA, psbB and phoH, and several polymerase genes. These marker genes have been used in combination with PCR-based fingerprinting and/or sequencing strategies to investigate spatial, temporal and seasonal variation and diversity in a wide range of habitats.