Widespread genetic exchange among terrestrial bacteriophages

Abstract

Bacteriophages are the most numerous entities in the biosphere. Despite this numerical dominance, the genetic structure of bacteriophage populations is poorly understood. Here, we present a biogeography study involving 25 previously undescribed bacteriophages from the Cystoviridae clade, a group characterized by a dsRNA genome divided into three segments. Previous laboratory manipulation has shown that, when multiple Cystoviruses infect a single host cell, they undergo (i) rare intrasegment recombination events and (ii) frequent genetic reassortment between segments. Analyzing linkage disequilibrium (LD) within segments, we find no significant evidence of intrasegment recombination in wild populations, consistent with (i). An extensive analysis of LD between segments supports frequent reassortment, on a time scale similar to the genomic mutation rate. The absence of LD within this group of phages is consistent with expectations for a completely sexual population, despite the fact that some segments have >50% nucleotide divergence at 4-fold degenerate sites. This extraordinary rate of genetic exchange between highly unrelated individuals is unprecedented in any taxa. We discuss our results in light of the biological species concept applied to viruses.

Fig. 1.

The 50%-majority-rule consensus trees of the S, M, and L segments. Trees were constructed in mrbayes by using the general time-reversible model, with γ distributed rate variation across sites. Posterior probabilities are indicated above each branch. The nomenclature of the isolates is as follows: state of origin, collector, and order of sample isolation; clones taken from a single clover are identified with an alphabetical suffix that is serially assigned. Gray shading indicates phylogenetic grouping based on clades within the small segment; previously isolated Cystoviridae are two-tone. The scale bar indicates 0.1 substitutions per site.

Fig. 2.

Distributions of tree similarity metrics. (A) Number of resolved, shared identical triplets. Bars indicate the random expectation of identical triplets for 20,000 tree-to-tree comparisons. Arrows indicate the median number of identical triplets found between segment phylogenies, none of which showed statistical significance (see text). (B) Number of resolved different triplets. Bars indicate the random expectation of different triplets for 25,000 tree-to-tree comparisons. Arrows indicate the median number of different triplets between 500 segment phylogenies (25,000 comparisons); only the median S-M segment comparison was found to be statistically significant (see text).