Phylogenetic diversity of sequences of cyanophage photosynthetic gene psbA in marine and freshwaters

Abstract

Many cyanophage isolates which infect the marine cyanobacteria Synechococcus spp. and Prochlorococcus spp. contain a gene homologous to psbA, which codes for the D1 protein involved in photosynthesis. In the present study, cyanophage psbA gene fragments were readily amplified from freshwater and marine samples, confirming their widespread occurrence in aquatic communities. Phylogenetic analyses demonstrated that sequences from freshwaters have an evolutionary history that is distinct from that of their marine counterparts. Similarly, sequences from cyanophages infecting Prochlorococcus and Synechococcus spp. were readily discriminated, as were sequences from podoviruses and myoviruses. Viral psbA sequences from the same geographic origins clustered within different clades. For example, cyanophage psbA sequences from the Arctic Ocean fell within the Synechococcus as well as Prochlorococcus phage groups. Moreover, as psbA sequences are not confined to a single family of phages, they provide an additional genetic marker that can be used to explore the diversity and evolutionary history of cyanophages in aquatic environments.

FIG. 1.

Phylogenetic tree of psbA determined by MP using PAUP version 4.0b8. The percent bootstrap support (n = 100) is indicated by the color of the filled circles at the nodes: black, >85%; gray, 75 to 84%, light blue, 74 to 65%; white, 64 to 50%. The colored text indicates isolates of Prochlorococcus (blue) or Synechococcus (green) spp., myoviruses isolated using either Synechococcus (red) or Prochlorococcus (teal) spp. as hosts, and podoviruses isolated using Synechococcus (orange) or Prochlorococcus (purple) spp. as hosts. The filled bars designate the sampling locations from which the viral environmental sequences were derived (see key).

FIG. 2.

Phylogenetic relationship, percent GC content, and the triplet sequences from the D1 protein motifs of partial psbA genes from environmental samples clustering in the three unknown marine groups (Mar3, Mar5, and Mar7). The MP tree was constructed with PAUP version 4.0b8. The percent GC content and the triplet sequences of the D1 protein motif are listed to the right of the phylogenetic reconstruction. Triplet sequences in bold represent those that are “virus-like,” while triplet sequences with asterisks represent those found only in viruses.