Genome characteristics of bacteriophages infecting the abundant freshwater bacterioplankton acI lineage

초록

Studies on bacteriophages infecting abundant bacterial groups are important, but have been hampered by the scarcity of cultured isolates of ecologically relevant bacterial groups, on which the isolation of their phages depend. Recently, one of the most abundant bacterial groups in freshwater, the actinobacterial acI lineage, was successfully cultured. Here, we report three lytic phages infecting acI bacterial strains ‘Ca. Planktophila rubra’ IMCC25003 and ‘Ca. Planktophila aquatilis’ IMCC26103. These phages were isolated from Lake Soyang, a freshwater reservoir where the host strains had been isolated, through enrichment culture followed by purification using dilution-to-extinction. Transmission electron microscopy demonstrated that all three phages belong to the Siphoviridae family. Complete genome sequences were obtained for all three phages. The IMCC26103 phage genome had a very small size of 14,210 bp. The two IMCC25003 phage genomes were assembled into the exactly same size of 39,578 bp. Genomic comparison revealed that the two IMCC25003 phage genomes were identical to each other, except for mostly-nonsynonymous differences in ~60 bases found in only one gene encoding a putative tail-fiber protein, which might implicate recombination between two very similar phages in their natural habitat or during enrichment. The relative abundances of the IMCC25003 phages, investigated by recruitment of the viral metagenomes of Lake Soyang, showed seasonal fluctuation. This study reports the first isolation of bacteriophages infecting the acI lineage, providing potential model systems for a more in-depth study of interaction between abundant freshwater bacteria and their phages.