An important query in marine microbial ecology is at what temporal and spatial scales variations in the structure of natural bacterial communities occur. Samples of different volumes were collected at different spatial (vertical and horizontal) and temporal (from hours to seasons) scales along a transect between a coastal station (26 m depth) and an offshore Microbial Observatory (1000 m depth) in the NW Mediterranean Sea. The structure of the bacterial communities was determined by capillary electrophoresis–single strand conformation polymorphism (CE–SSCP) fingerprinting of polymerase chain reaction (PCR)-amplified 16S rDNA. This technique is a powerful tool to compare natural microbial assemblages at different spatial or temporal scales. Similar bacterial assemblages were found up to 3.7 km from the coastal station, whereas significant changes were found over greater distances (from 9.3 to 33.3 km). Although the bacterial community structure did not change with depth at coastal and shallow stations, vertical changes were found at deeper stations, most likely due to vertical variations in physico-chemical and biogeochemical parameters. Temporal changes were mainly related to environmental variations that occurred at a seasonal scale and during phytoplankton blooms. Finally, we suggest that long-term studies, at least in the NW Mediterranean Sea, should involve a minimum sampling time scale of 2 wk and a shorter time-scale when environmental changes are detected by the real-time monitoring of a few basic parameters (i.e. fluorescence, temperature, salinity). Sampling strategies should also include different depths depending on the vertical structure of the water column, based on the same basic parameters.
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