Flow cytometry (FCM) is rapidly becoming an essential tool in the field of aquatic microbiology. It provides opportunities for microbial analysis at both the community and single-cell levels. Compared with other techniques, FCM facilitates rapid data acquisition and multi-parameter analysis, leading to increased popularity and widespread applications. Here, we briefly review the current status of FCM in the field of microbiology, focusing on its recent applications in aquatic microbiology. These developments range from straightforward total cell counts to community structure analysis, and further extend to physiological analysis at a single-cell level. Exciting future prospects for the applications of FCM in aquatic microbiology are also discussed based on current scientific and practical needs.
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