Temporal variation and detection limit of an estuarine bacterioplankton community analyzed by denaturing gradient gel electrophoresis (DGGE)

Abstract

To understand how the composition of estuarine bacterioplankton changes on a monthly basis, microbial communities in the Baltimore Inner Harbor were investigated using denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene. As revealed by DGGE fingerprints, the composition of bacterioplankton populations in the harbor varied from month to month, and 3 major seasonal patterns were identified: winter (December and January), spring (February to May) and summer-fall (June to November). Sequencing of DGGE bands showed that Planctomycetes and uncultured α-Proteobacteria were detected in all seasons. Roseobacter spp. and Rhodobacter sp. were only present in winter and spring. Marine α-Proteobacteria and Cyanobacteria exhibited similar seasonal patterns and appeared to be more dominant from late summer to fall. β-Proteobacteria were present in most months, but different phylotypes were present from spring to summer-fall. γ-Proteobacteria and Bacteroidetes were only present in winter and early spring. In addition to DGGE analysis, 48 bacterial isolates from summer and winter were cultured and characterized. Few of these bacterial isolates matched with phylotypes determined by sequencing DGGE bands, which suggested that the density of 'easy-to-culture' bacteria in the natural environment may be too low to be detected by PCR-DGGE. Bacterial seeding experiments showed that detection thresholds for PCR-DGGE ranged from 2.5 × 103 to 1 × 104 cells ml-1 (0.1 to 0.4% of total cell counts), depending on the copy number of rRNA operons in the genome of individual species. © Inter-Research 2006.