Metagenomic analysis reveals the interaction between cyanobacteria and their phages in a freshwater lake

Author(s):  Shang Shen
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Institution or organization of origin: Kyoto University
Country: Japan


Cyanobacteria is a crucial driver of carbon cycling or may cause a harmful bloom. Although cyanophages are an essential factor in controlling the abundance of cyanobacteria, diversity and seasonal variation of cyanophages are still known, mainly because viral genomes lack a universal gene. However, the recent metagenomic sequencing method, which is cultivation-independent, made it possible to clarify the phage diversity. Here we describe the diversity and seasonal variation of cyanophage in Lake Biwa using the metagenomic technique. In this study, we collected lake water samples monthly from the surface euphotic layer (5m) and deep aphotic layer (60 m) for 14 months. We obtained 33 complete (circular) viral genomes, and 66 viral contigs (fragments) predicted to infect cyanobacteria in Lake Biwa. Their genome or contig size was ranged from 11.0 to 355.9 kbp. Of the 99 phages, 31 were predicted as the Myoviridae family, 17 as the Podoviridae family, and 17 as the Siphoviridae family. The abundance of these 99 phases increased at the surface layer in the summer season (around July to September) when the relative abundance of cyanobacteria increased. Moreover, we identified 14 cyanophages that may infect a cyanobacterial species predominated in Lake Biwa (7% in September) using co-occurrence and association analysis. These results suggest that the activity of cyanophages in Lake Biwa is closely linked to the activity of cyanobacteria and is an essential factor in controlling the abundance of cyanobacteria.

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