Fungi and other microorganisms can survive and multiply in diesel fuel if water is present. The fungi can be present in any part of the fuel handling system. These fungi grow into long strings and will form into large globules. The growths appear slimy and are usually black, green, or brown. The fungi may grow anywhere in the fuel but are most plentiful where diesel fuel and water meet. As the fuel is agitated (when service station tanks are being filled), fungi are distributed throughout the tank and may be pumped into a vehicle.

Fungi use the fuel as their main energy supply and need only trace amounts of water and minerals. As they grow and multiply, they change fuel into water, sludge, acids, and products of metabolism. The most common symptom is fuel filter plugging; however, various metal components (fuel tank, pipes, and injection pump) can corrode.

Caution: Avoid physical contact with the biocides in order to avoid personal injury.

If fungi have caused fuel system contamination, use a diesel fuel biocide to sterilize the fuel system. Do not exceed the dosage recommended on the label. Discontinue the use of a biocide when towing a trailer. It is permissible to have biocide in the fuel when starting to tow, but do not add any biocide while towing.

Steam cleaning may be necessary if most of the fungus growth cannot be removed with biocides.

The presence of water or gasoline in diesel fuel may also cause injection pump and nozzle damage.

This procedure checks for the presence of water and gasoline in diesel fuel that may cause injection pump and nozzle damage.

Remove the fuel filter element and inspect it.

1. Disconnect the batteries.
2. Drain the fuel tank.
3. Remove the fuel tank (Refer to Fuel Tank Replacement).
4. Remove the fuel sender unit (Refer to Fuel Sender Assembly Replacement ).
5. Inspect the fuel tank and the fuel sender for rust, fungi or bacteria.
6. Clean the inside of the fuel tank and the fuel sender with hot water.
7. Use compressed air in order to dry the fuel tank and the fuel sender.
8. Disconnect the ends of the following lines:

•	The lift pump suction line

•	The lift pump feed line

•	The fuel filter outlet line

•	The fuel filter drain line

•	The fuel return line

9. Inspect each of the pipes.
10. Replace any rusted pipes.
11. Clean the inside of the fuel filter housing.
12. Dry the fuel filter housing with compressed air.
13. Dry the inside of each line with low pressure air.
14. Remove the ECM 1 fuse from the underhood relay center.
15. Install a new fuel filter element.
16. Install the fuel sender and the fuel tank (add clean diesel fuel to ¼ full).
17. Reconnect the following lines:

•	The lift pump suction (both ends) lines.

•	The lift pump feed (both ends) lines.

•	The fuel filter drain line.

•	The fuel return (at the injection pump) line.

18. Connect the fuel filter outlet and the fuel return line at the fuel sender to the hoses that flow to the metal containers.
19. Connect the batteries.
20. Use the scan tool in order to command the lift pump ON.
21. Operate the lift pump until clean fuel flows from the fuel filter outlet into a metal container.
22. Connect the hose from the fuel filter outlet to the injection pump inlet.
23. Open each injection line at its nozzle end and crank the engine until clean fuel flows from it.

•	Use two wrenches when loosening the injection line fittings.

•	Allow a maximum of 15 seconds cranking time, followed by 1 minute of cranking motor cooling time.

24. Tighten each injection line fitting at its nozzle. Use two wrenches when tightening the injection line fittings.
25. Install the ECM 1 fuse in the underhood relay center.
26. Start and run the engine for 1 minute while the fuel flows from the fuel return line into a metal container.
27. Stop the engine.
28. Connect the fuel return hose to the fuel sender.
29. Clean any fuel spillage from the engine.
30. Fill the fuel tank and add a biocide, if needed.

1. Drain the fuel tank.
2. Fill the fuel tank.
3. Remove the ECM 1 fuse from the underhood relay center.
4. Remove the fuel filter outlet and connect it to a hose that flows to a metal container.
5. Use a scan tool and command the lift pump ON until clean fuel flows from the fuel filter outlet into a metal container.
6. Connect the hose from the fuel filter outlet to the injection pump inlet.
7. Install the ECM 1 fuse into the underhood relay center.
8. Attempt to start and run the engine for 15 minutes (If engine does not start, purge the injection system).
9. Stop the engine.
10. Clean any fuel spillage from the engine.
11. Clear the engine of any DTCs.