Now comes the twist that can lead to some confusion. When we look under a microscope, we look at microbial appearance. The growth pattern or appearance of the microbe is called phenotype. For example, all human DNA sequences as species Homo sapiens. However we appear quite different which is due to phenotype.
Bacteria like humans can have the same genetic makeup but appear very different. Some examples here include an organisms going from floc forming to filamentous when D.O. drops. Others such as Thauera and Zooglea are important floc forming microbes in activated sludge but under certain conditions their growth can cause non-filamentous bulking. Other bacteria such as Nocardia are not always the foaming mess that stresses many operators.
Molecular testing needs to be coupled with other monitoring techniques such as SV30, F/M, MCRT, Respiration Rates, and microscopic exam to fully system microbial dynamics and make predictions on system performance.