Cyanophage diversity, inferred from g20 gene analyses, in the largest natural lake in France, Lake Bourget

Abstract

The genetic diversity of the natural freshwater community of cyanophages and its variations over time have been investigated for the first time in the surface waters of the largest natural lake in France. This was done by random screening of clone libraries for the g20 gene and by denaturing gradient gel electrophoresis (DGGE). Nucleotide sequence analysis revealed 35 distinct cyanomyovirus g20 genotypes among the 47 sequences analyzed. Phylogenetic analyses showed that these sequences fell into seven genetically distinct operational taxonomic units (OTUs). The distances between these OTUs were comparable to those reported between marine clusters. Moreover, some of these freshwater cyanophage sequences were genetically more closely related to marine cyanophage sequences than to other freshwater sequences. Both approaches for the g20 gene (sequencing and DGGE analysis) showed that there was a clear seasonal pattern of variation in the composition of the cyanophage community that could reflect changes in its biological, chemical, and/or physical environment.

FIG. 1.

Temporal changes in the dynamics of viral (A), heterotrophic bacterial (B), picocyanobacterial (C), and P. rubescens (D) communities in Lake Bourget.

FIG. 2.

Phylogenetic relationships among the partial g20 gene sequences from the cyanophage community of Lake Bourget. The unrooted tree was constructed from pairwise Jukes and Cantor distances by using the neighbor-joining method. Marine cyanophage sequences, identified by their GenBank accession numbers, were also added. Only bootstrap values of >80% are indicated at the nodes of the tree.

FIG. 3.

Temporal changes in the abundance of the six clusters defined by the phylogenetic analysis of the g20 gene sequences from the cyanophage community of Lake Bourget.

FIG. 4.

Temporal changes in the DGGE band patterns obtained for PCR products resulting from the amplification of a 592-bp fragment of the g20 gene in the cyanophage community of Lake Bourget. Arrows indicate the principal differences between the September-October and November band patterns. Lanes: A and G, mix of September-October samples; B, September sample; C, October sample; D, November sample; E, December sample; F, January sample.