In any system, you are most likely to find microbes living on physical surfaces (like tank walls) and at interfaces between fuel and free water. When on surfaces, microbes live in and behind biofilm formations - slimy growths that house entire living ecosystems of microbes. It is this slimy growth that may also turn into particulate that is suspended in fuel and blocks filters.
Microbes are a primary causal factor in instances of “MIC” - microbially induced corrosion. They do this by a variety of mechanisms - some simple, some more complex. Aluminum structures in aircraft wings become corroded through the action of acids produced by microbes that live in these biofilm formations.
MIC damage in aircraft and aviation systems can be recognized by signs of pitting or etching on surfaces. It may also develop at a surprisingly fast rate. So monitoring is an essential element of staying ahead of this problem. Yet, metal structures in aircraft aren’t so easily accessible.
That’s why it’s so important to monitor the microbiological contamination levels of the fuel itself, through regular fuel testing as with ATP-By-Filtration. The industry itself seems to concur - IATA recommends routine microbial testing, as do the AMMs for many leading aircraft manufacturers - Airbus, Boeing, Gulfstream, and others, both noncommercial and commercial.