Using flow cytometry for counting natural planktonic bacteria and understanding the structure of planktonic bacterial communities

Flow cytometry is rapidly becoming a routine methodology in aquatic microbi al ecology. The combination of simple to use bench-top flow cytometers and highly fluorescent nucleic acid stains allows fast and easy determination o f microbe abundance in the plankton of lakes and oceans. The different dyes and protocols used to stain and count planktonic bacteria as well as the e quipment in use are reviewed, with special attention to some of the problem s encountered in daily routine practice such as Fixation, staining and abso lute counting. One of the main advantages of flow cytometry over epifluores cence microscopy is the ability to obtain cell-specific measurements in lar ge numbers of cells with limited effort. We discuss how this characteristic has been used for differentiating photosynthetic from non-photosynthetic p rokaryotes, for measuring bacterial cell size and nucleic acid content, and for estimating the relative activity and physiological state of each cell. We also describe how some of the flow cytometrically obtained data can be used to characterize the role of microbes on carbon cycling in the aquatic environment and we prospect the likely avenues of progress in the study of planktonic prokaryotes through the use of flow cytometry.