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 data sets of specific virus groups. Genes that have been used include those encoding structural proteins, such as 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 variations and diversity in a wide range of habitats.

FIG 1

Phylogenetic tree (PhyML) of g23 marker sequences generated by MetaVir. Metagenomic sequence reads (Lake Pavin, El Berbera, Indian Ocean, and Pacific Ocean) were aligned with reference marker sequences from selected isolated T4-like phages by using MUSCLE (at least 35 bp; 98% identity). The tree was visualized using FigTree v1.4.0 and rooted at Rhodothermus phage RM378. Bootstrap support (on 100 bootstraps) of the nodes is indicated by the circles on each node, from white (low support) to black (high support). The scale bar represents the number of substitutions per site. Distinct clades are colored according to their origin: green, environmental sequences from all investigated environments; light blue, marine; purple, freshwater; dark blue, sequences clustering with isolated cyanophages; brown, isolated non-cyano-T4-like phage signatures.