Bacteriophage morphotype and genome diversity in Seine River sediment

1. We investigated a sediment sample of the Seine River downstream of Paris for morphotype and genome diversity of bacteriophages using electron microscopy, pulsed-field gel electrophoresis and a metagenomic analysis. 2. Short-term incubations of the sediment in bacterial culture media, with or without addition of mitomycin C, were used to study the influence of pseudolysogens and induced lysis of lysogenic cells. 3. Electron microscopy of phages from the sediment revealed five morphotypes, whereas 13 morphotypes were observed after sediment incubation both with and without mitomycin C added. Pulsed-field gel electrophoresis yielded seven size-classes of double-stranded DNA genomes. 4. Representatives of the three common families of tailed bacteriophages (Myoviridae, Siphoviridae or Podoviridae) were observed. Capsid sizes ranged from 85 to 200 nm in diameter and tail sizes from < 50 nm to 265 nm in length. 5. PCR amplification of eubacterial 16S rDNA sequences from the incubated sediment revealed that the predominant bacteria were members of the Proteobacteria. In line with this result, sample analysis of metagenomic phage DNA libraries showed that phage-homologous sequences were most similar to temperate phages infecting Proteobacteria. This correspondence supports the idea that temperate phages may play an important role in influencing the dynamics of bacterial hosts in river sediments.