The versatile nature of environmental genomic surveys can be seen in two separate papers from Oded Béjà and collaborators, in which their bacterial artificial chromosome (BAC) libraries from the Mediterranean and Red seas have been interrogated for two very different purposes.

In a study that is due to be published in the October issue of Environmental Microbiology and is currently available online, Zeidner et al. provide evidence that the phages that infect Synechococcus and Prochlorococcus could influence the evolution of the genes involved in photosynthesis in these phototrophic cyanobacteria.

In a survey of the BAC libraries using degenerate primers based on psbA, which encodes D1, one of the two protein components of the reaction centre of photosystem II, the authors found that the psbA genes present belonged to two distinct clades — a bacterial clade and a phage clade. Codon and nucleotide evolution models showed that psbA in the phage clade was evolving faster than in the bacterial clade, and that both clades are under similar levels of strong purifying selection. Analyses of the GC content revealed that the phage psbA genes are mosaics that represent intermediates between the psbA genes present in Synechococcus and Prochlorococcus. Collectively, these results suggest that the psbA genes in cyanophage can be shuffled between phages and the two cyanobacterial genera, and this accessible phage gene pool could therefore have a crucial role in the evolution of photosynthetic gene diversity.

In a separate paper in a recent issue of PLoS Biology, Sabehi, Lay and others publish the results of another analysis of the same BAC libraries, this one designed to obtain a more detailed picture of the distribution of proteorhodopsin-encoding genes in the ocean photic zones.

Using new degenerate proteorhodopsin primers, the authors assessed 55 BAC clones and calculated that 13% of microorganisms in the photic zone contain proteorhodopsin genes. They went on to look for clues to other metabolic properties of proteorhodopsin-containing bacteria, and discovered that in some clones, a reverse sulphite reductase operon is present. In chemotrophs and anaerobic phototrophs, the proteins encoded by this operon are involved in using reduced sulphur compounds as energy sources, and the authors speculate that the presence of this operon in proteorhodopsin-containing bacteria indicates that these bacteria could have a role in sulphur cycling by degrading dimethyl sulphide. Additionally, the presence of a carotenoid biosynthesis gene cluster suggests that some proteorhodopsin-containing bacteria can also synthesize retinal. The proteorhodopsin-containing bacteria are therefore more metabolically diverse than was previously suspected.

So, by interrogating the same BAC libraries with two different sets of gene primers, Béjà and collaborators have obtained a wealth of new information on what's going on beneath the waves.