Prevalence of Viral Photosynthetic and Capsid Protein Genes from Cyanophages in Two Large and Deep Perialpine Lakes

Abstract

Cyanophages are important components of aquatic ecosystems, but their genetic diversity has been little investigated in freshwaters. A yearlong survey was conducted in surface waters of the two largest natural perialpine lakes in France (Lake Annecy and Lake Bourget) to investigate part of this cyanophage diversity through the analysis of both structural (e.g., g20) and functional (e.g., psbA) genes. We found that these cyanophage signature genes were prevalent throughout the year but that the community compositions of g20 cyanomyoviruses were significantly different between the two lakes. In contrast, psbA-containing cyanophages seemed to be more similar between the two ecosystems. We also found that a large proportion of g20 sequences grouped with cyanomyophage isolates. psbA sequences, belonging to phages of Synechococcus spp., were characterized by distinct triplet motifs (with a novel viral triplet motif, EFE). Thus, our results show that cyanophages (i) are a diverse viral community in alpine lakes and (ii) are clearly distinct from some other freshwater and marine environments, suggesting the influence of unique biogeographic factors.

Metabolic Genes within Cyanophage Genomes: Implications for Diversity and Evolution

“…Currently, a range of host-derived metabolic genes have been used as signature biomarkers to investigate the genetic diversity and the evolutionary relationship of cyanophages from cultured and environmental samples (Table 1). The cyanophage-encoded photosynthesis genes psbA and psbD have been used as additional marker molecules to investigate the genetic diversity and evolution of phage populations in natural aquatic environments [100,101,102,103,104]. Phylogenetic analyses, based on the psbA gene, indicated that cyanophages from freshwater environments possess an evolutionary history different from their marine counterparts.…”

Structure and diversity of ssDNA Microviridae viruses in two peri-alpine lakes (Annecy and Bourget, France)

“…It is now recognized that the ssDNA viral community has been largely underestimated (because of technical constraints, such as insufficient staining in fluorescence-based methods such as flow cytometry and epifluorescence microscopy, or insufficient material when using PFGE). Its importance (both in terms of diversity and/or abundance) has been highlighted in lakes [23,38], desert ponds of the Mauritanian Sahara desert [10], reclaimed water [37], aquifers [45], stromatolithes [9], corals [55], ground and marine sediments [18,20,60], coastal estuaries [21,22,27] and the ocean in general [1,4,53].…”

Genetic diversity of cyanophages of the myoviridae family as a constituent of the associated community of the Baikal sponge Lubomirskia baicalensis

“…For this purpose, the g20 gene fragment was used as a genetic marker [14,15]. The marker is widely used in the analysis of cyanophages associated with a variety of water ecosystems [14][15][16][17][18][19][20].…”