One of the historic debates in molecular evolution concerns the strong variation in the genomic guanine-cytosine (GC) content of prokaryotes, which ranges from approximately 20-75%: Is this factor selectively neutral, or is it the result of natural selection? In a previous article published by our group, we showed that inside well-defined taxonomic groups of prokaryotes, strictly aerobic organisms tend to display higher genomic GC levels than strictly anaerobic species. In the present study, we examined the GC content of fragments of DNA obtained from microbial communities along a well-defined environmental gradient: a 4,000-m vertical profile in the North Pacific subtropical gyre. The patterns of GC distribution might be associated with oxygen concentrations in the seawater column. These results give further support to the link between a physiologic trait (aerobic respiration) and genomic GC content.