To adapt to the Earth’s daily light-dark (diel) cycle, the diurnal rhythms of gene expression, metabolism, and behavior have been shown in all three domains of life, including cyanobacteria, but how the diel cycles influence cyanophages, which are viruses infecting cyanobacteria, remains unclear. The diurnal transcriptional rhythms of cyanophages have been characterized in both laboratory cultures and field populations. In the field study, the aggregate transcripts mapped to assembled cyanophage contigs showed diurnal rhythms, which could be driven by the synchronized diurnal infections of cyanophages or the lowered cyanophage transcription level caused by the inhibition of photosynthesis in the dark. In addition to the diurnal transcriptional rhythms, the life history traits of cyanoph...[ Read more ]

To adapt to the Earth’s daily light-dark (diel) cycle, the diurnal rhythms of gene expression, metabolism, and behavior have been shown in all three domains of life, including cyanobacteria, but how the diel cycles influence cyanophages, which are viruses infecting cyanobacteria, remains unclear. The diurnal transcriptional rhythms of cyanophages have been characterized in both laboratory cultures and field populations. In the field study, the aggregate transcripts mapped to assembled cyanophage contigs showed diurnal rhythms, which could be driven by the synchronized diurnal infections of cyanophages or the lowered cyanophage transcription level caused by the inhibition of photosynthesis in the dark. In addition to the diurnal transcriptional rhythms, the life history traits of cyanophages were also found to be affected by the diel cycles in this study using laboratory cultures. Based on the extent of light dependency, three different diel-dependent life history traits (diel traits) were characterized: 1) P-HM2, with light-dependent adsorption; 2) P-SSM2, with adsorption but no replication in the dark; and 3) P-SSP7, which could complete the infection cycle in the dark. However, the mechanism controlling different diel traits remains unclear.

In this thesis, I first questioned whether cyanophage infections were synchronized to diel cycles in the field. Similar to other bacteriophages, cyanophage infection relies on robust temporal gene expression programs. Based on the peak expression time of cyanophage genes after infection, cyanophage genes could be divided into three temporal expression classes: early, middle and late. I reanalyzed previously published time-series meta-transcriptomic data to study the temporal expression pattern of cyanophage genes in the field populations. Among the periodically expressed cyanophage genes, the late genes showed significantly later peak expression times compared to the early and middle genes, indicating synchronized infection by cyanophages in the ocean.

After the verification of the diurnal infection rhythms of cyanophage populations in the ocean, I conducted a comprehensive study to reveal the mechanisms controlling the diurnal infection rhythm. Three different diel traits have been characterized in three cyanophages, describing the effect of diel cycles on cyanophages, but our knowledge of cyanophage diel traits is limited to the three studied cyanophages and the molecular mechanisms remain unknown.

Thus, I extended the investigation of diel traits to 77 cyanophage strains against two host cyanobacterial strains and studied their genomes to identify the phage factors controlling different diel traits. I acquired the genome sequences and characterized the diel traits of 77 cyanophage strains, including 3 known cyanophages and 74 novel cyanophages isolated from the South China Sea. The gene content comparison among cyanophages with different diel traits suggested that the lack of DNApol might explain the light-dependent replication leading to the P-SSM2 diel traits exhibited by 21 cyanopodoviruses.

Cyanobacterial genes involved in the infection process might also be important for the exhibited diel traits. To identify the important host factors, the genomes of 52 resistant cyanobacterial substrains selected against 18 cyanophages and 6 wild-type substrains were sequenced. Through comparison of the resistance-conferring genes among cyanobacteria substrains selected against cyanophages exhibiting different diel traits, a potential receptor gene (PMM1124) was suggested to be responsible for the light-dependent adsorption resulting in the P-HM2-like diel trait in one cyanopodovirus.

In summary, the diurnal infection rhythm of cyanophage populations in the ocean was verified through a reanalysis of previously published metatranscriptomic data. Subsequently, I worked on the molecular mechanisms underlying the diurnal infection rhythms of cyanophages and identified two candidate genes for P-HM2-like and P-SSM2-like diel traits in several cyanophages, with the mechanisms for other cyanophages remaining unknown. The identification of the candidate genes provides future directions for the study of diel traits, and the lack of generalized rules controlling diel traits suggests that complex and diverse mechanisms take part in shaping the diurnal rhythms of cyanophages.