There is a paper that just was published that possibly will be of interest to those interested in studying microbial ecology of drinking water (or other water systems for that matter): Methodological approaches for studying the microbial ecology of drinking water distribution systems. Unfortunately the paper is not freely or openly available. The paper covers many topics of interest including both culture based and culture independent and a diversity of methods within these categories. It has a focus on methods as they would be applied to studies of microbes in drinking water distribution systems but much of the information would be of value to people studying microbes in other locations. It would be much more useful of a paper to many if it were freely and openly available, but alas, it is not. Still useful mind you and worth a look if you can get access.