Long-term genomic coevolution of host-parasite interaction in the natural environment

Abstract

Antagonistic coevolution of parasite infectivity and host resistance may alter the biological functionality of species, yet these dynamics in nature are still poorly understood. Here we show the molecular details of a long-term phage-bacterium arms race in the environment. Bacteria (Flavobacterium columnare) are generally resistant to phages from the past and susceptible to phages isolated in years after bacterial isolation. Bacterial resistance selects for increased phage infectivity and host range, which is also associated with expansion of phage genome size. We identified two CRISPR loci in the bacterial host: a type II-C locus and a type VI-B locus. While maintaining a core set of conserved spacers, phage-matching spacers appear in the variable ends of both loci over time. The spacers mostly target the terminal end of the phage genomes, which also exhibit the most variation across time, resulting in arms-race-like changes in the protospacers of the coevolving phage population.Arms races between phage and bacteria are well known from lab experiments, but insight from field systems is limited. Here, the authors show changes in the resistance and CRISPR loci of bacteria and the infectivity, host range and genome size of phage over multiple years in an aquaculture environment.

Fig. 1

Time shift of phage–bacterium coevolution in the fish farming environment. Phage–bacterium coevolution measured as mean proportion (± S.E.) of resistant host population, described as annual relative change in host resistance when exposed to phages from the past (−4 to −1 years), contemporary (0), and future (+1 to +5 years). The bacteria are in general resistant against phages from the past but susceptible to infection by phages from contemporary and future time points (24% and 18% resistant, respectively; GLMM, F _{(2, 507)} = 15.099, p < 0.001)

Fig. 2

Arms race coevolution of phage infectivity and host resistance at genetic level. The effect of long-term genomic coevolution on phage infectivity and genome, and on host bacterium CRISPR content. a Spacer diversity in the variable ends of both CRISPR loci (C1 and C2) is indicated by numbered and colored rectangles above each bacterial strain (each number and color referring to a specific spacer within a locus). C1 spacers are marked with solid lines (left spacer column) and C2 spacers with dotted lines (right spacer column). Numbers and colors are locus-specific and only variable spacers are shown. All spacers except C1s32, C1s38, and C2s15 are targeting the phages. b Host range of phages (rows) infecting Flavobacterium columnare isolates (columns). Gray rectangles indicate infection (presence of plaques) and white rectangles indicate resistance. The first number within these rectangles indicates the number of CRISPR spacers with an identical match in the phage genome and the second number the maximum number of phage-targeting spacers the bacterium has. c Close-up: CRISPR protospacer regions mapped to a ~11 kb portion of the multiple sequence alignment, where the four highlighted protospacers indicate specific, possibly CRISPR-driven, changes in these areas. d Patterns of molecular evolution in the phage genomes in response to host range. Each sequenced phage genome follows the corresponding host range row from b. Green color in the consensus sequence (above) indicates identical sequence, yellow 30%, and red < 30% identity. Note that also the bar height changes accordingly. Black indicates nucleotide differences and insertion elements