Seasonal changes of bacterial and archaeal communities in the dark ocean: Evidence from the Mediterranean Sea

The study site located in the northwestern Mediterranean Sea was visited nine times in 2005-2006 to collect water samples from the epipelagic (5 m), mesopelagic (200 m, 600 m), and bathypelagic (1000 m, 2000 m) zones. The relative abundance of Bacteria, Crenarchaea, and Euryarchaea was determined by catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH). Apparent richness (total number of phylotypes detected) and community composition (different phylotypes detected) of Bacteria and Archaea were assessed by denaturing gradient gel electrophoresis (DGGE) analysis of polymerase chain reaction (PCR)-amplified fragments of the 16S ribosomal ribonucleic acid (rRNA) gene followed by sequencing and phylogenetic analysis of selected phylotypes. The relative abundance of Crenarchaea and Euryarchaea in the epipelagic zone increased as stratification decreased. Apparent bacterial richness increased with decreasing stratification in the mesopelagic and bathypelagic zones. Deep vertical mixing at the study site represented the beginning of a seasonal succession. The effects of this succession were detectable throughout the water column and led to distinct prokaryotic communities in different depth layers during the stratified period. The seasonal variability in the relative abundance of Bacteria, as well as apparent prokaryotic richness and community composition, was comparable between the different depth layers. This suggests that prokaryotic communities of the dark ocean can be as dynamic as those found at the surface.