Temporal transcriptional patterns of cyanophage genes suggest synchronized infection of cyanobacteria in the oceans

Abstract

Background: Based on the peak expression times during infection, early, middle, and late genes have been characterized in viruses (cyanophages) that infect the unicellular cyanobacterium Prochlorococcus. Laboratory experiments show that some cyanophages can only replicate in the light and thus exhibit diurnal infection rhythms under light-dark cycles. Field evidence also suggests synchronized infection of Prochlorococcus by cyanophages in the oceans, which should result in progressive expression of cyanophage early, middle, and late genes. However, distinct temporal expression patterns have not been observed in cyanophage field populations.

Results: In this study, we reanalyzed a previous metatranscriptomic dataset collected in the North Pacific Subtropical Gyre. In this dataset, it was previously shown that aggregate transcripts from cyanophage scaffolds display diurnal transcriptional rhythms with transcript abundances decreasing at night. By mapping metatranscriptomic reads to individual viral genes, we identified periodically expressed genes from putative viruses infecting the cyanobacteria Prochlorococcus and Synechococcus, heterotrophic bacteria, and algae. Of the 41 cyanophage genes, 35 were from cyanomyoviruses. We grouped the periodically expressed cyanomyovirus genes into early, middle, and late genes based on the conserved temporal expression patterns of their orthologs in cyanomyovirus laboratory cultures. We found that the peak expression times of late genes in cyanophage field populations were significantly later than those of early and middle genes, which were similar to the temporal expression patterns of synchronized cyanophage laboratory cultures.

Conclusions: The significantly later peak expression times of late genes in cyanomyovirus field populations suggest that cyanophage infection of Prochlorococcus is synchronized in the North Pacific Subtropical Gyre. The night-time peak expression of late genes also suggests synchronized lysis of Prochlorococcus at night, which might result in synchronized release of dissolved organic matter to the marine food web. Video abstract.

Keywords: Cyanobacterium; Cyanophage; Diurnal rhythm; Light-dark cycle; Metatranscriptomics.

Fig. 1

Diel transcript abundances of viral genes in the North Pacific Subtropical Gyre. a Every 4 h over 8 days (July 27–31 and August 1–3, 2015), the transcript abundances of viral genes at each sampling time point were normalized to the total non-rRNA transcripts that were aligned to an in-house microbial protein database. The transcript proportions of the five most abundant virus groups are shown. Grey bars indicate night periods. The pie chart on the right shows the average transcript proportions of cyanomyovirus, cyanopodovirus, and cyanosiphovirus relative to the total cyanophage transcripts. b Numbers of total genes and genes with diurnal transcriptional rhythms are shown for cyanophages, phages infecting heterotrophic bacteria, and algal viruses (see Supplementary Table 1 for details)

Fig. 2

Peak expression times of periodically expressed cyanophage genes. The jackknife distributions of the estimated peak expression times of each gene are shown in violin plots. The red vertical line in each violin plot shows the peak expression time of each gene estimated from all data points and the two black vertical lines indicate the 90% confidence interval of the peak expression times estimated using the jackknife method from partial data points (Supplementary Figure 2). The color of the ortholog name denotes different cyanophage groups: blue for cyanomyovirus, green for cyanopodovirus, and orange for cyanosiphovirus. On the right of each ortholog name, E, M, L indicates early, middle, and late temporal expression classes, respectively. The double helix symbol indicates genes involve in nucleic acid metabolism and the hexagon symbol indicates genes involved in phage capsid assembly

Fig. 3

Comparison of the peak expression times of early, middle, and late genes in cyanomyovirus field populations. As shown in Fig. 2, the periodically expressed cyanomyovirus genes are classified as early (3 genes), middle (11 genes), and late genes (7 genes) according to the temporal expression patterns of their orthologs in cultured cyanophages. The peak expression times of early, middle, and late genes in cyanomyovirus field populations are shown in box and whisker plots. The bottom and top of a box indicate the first and third quartiles, respectively. The band inside a box indicates the median and the ends of a whisker represent the upper and lower extremes. Black dots indicate the estimated peak expression times of cyanomyovirus genes. The peak expression times of early, middle, and late genes are compared using the two-tailed Student’s test and the p values are indicated on top of the plots (*indicates p < 0.05 and ns indicates no significance)