Bacterioplankton community in Chesapeake Bay: Predictable or random assemblages

We monitored bacterioplankton communities from Chesapeake Bay over 2 years (2002–2004) by use of denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA gene. Chesapeake Bay bacterioplankton exhibited a repeatable annual pattern and strong seasonal shifts. In winter, the bacterial communities were dominated by Alphaproteobacteria and Actinobacteria, whereas in summer, the predominant bacteria were members of Alphaproteobacteria, Gammaproteobacteria, Cyanobacteria, Actinobacteria, Planctomycetes, and Bacteroidetes. Phylotypes of Alphaproteobacteria and Actinobacteria present in warm seasons were different from those in cold seasons. Relatively stable communities were present in summer–fall across the sampling years, whereas winter communities were highly variable interannually. Temporal variations in bacterial communities were best explained by changes of chlorophyll a (Chl a) and water temperature, but dissolved oxygen, ammonia, nitrite and nitrate, and viral abundance also contributed significantly to the bacterial seasonal variations. Over the past 2 decades, our view of aquatic bacterial communities has changed considerably because of the application of molecular techniques. With the advantages of cultivation independence, molecular techniques determine the structure of bacterial communities by characterization of indicative macromolecules, generally rRNA genes, directly isolated from the environments (Giovannoni et al. 1990; Ward et al. 1990). Community fingerprinting approaches, such as denaturing gradient gel electrophoresis (DGGE), provide powerful tools for comparison of bacterial communities (Muyzer et al. 1993). DGGE is a quick-fingerprint technique, and it can separate different PCR fragments, even with single base-pair difference on a denaturant gradient gel (Muyzer et al. 1993). Diversity profiles from different microbial communities can be compared according to their gel patterns and the sequences of representative bands. Simultaneous comparisons of DGGE fingerprint patterns allow rapid assessment of changes in bacterial-community structures over time and