Summary: the bacteria and nanotech attack each other, constantly struggling for control and interfering with each other's functions.

While no ship or base would expect to be infiltrated by a hostile microscopic xenoform, in the age of nanotech people are very paranoid about dangerous microscopic threats – biological or mechanical dangers designed by enemies, or their own technology, run amok. The bacteria slips under this screen at first because it is utterly unlike any human organic compound – but once it reaches high enough concentration alarms are triggered and anti-contamination countermeasures kick in. The countermeasures attempt to contain and sterilize the bacteria, and the bacteria responds by trying to corrode and destroy all nanotech.

By the time marines arrive, this battle is well underway, with both sides gridlocked, interfering with each other. See nano-gridlock to learn how this effects marine functions.

The most important consequence of this gridlock is it prevents the bacteria from attempting to infect or attack humans. It is our belief that it views us (humans) as existing for the same reason its own species do – host lifeforms created by a different bacterial lifeform to fight for control of an area's resources. If it can't win the microscopic battle, it starves the competitor to death, and outgrows it by destroying its hosts - stopping the competition from reproducing or controlling resources. This implies a past filled with conflict, and explains why it is so ready, and able, to deal with humans in an aggressive and deadly fashion.

There are more practical effects of the gridlock. It also prevents the bacteria from instantly sensing and transmitting the location of every marine and marine structure onto Kharaa hive sight. Unless a Kharaa can see you, or you've been parasited, they should not know where you are.