The invention is directed towards methods and compositions for identifying the specific microorganisms present in a particular portion of a papermaking processes. The method involves obtaining and comparing a diversity index of a sample from the process. Because no system is completely free from biological infestation, utilizing information taken from the changes in the populations provides information useful in protecting the system from unwanted effects. Not only does the diversity index allow for the distinguishing between biological and non-biological events, it even allows for the prediction of problems without previously knowing that a particular organism will cause a particular problem.