Microbes in petrodiesel and biodiesel products can mean serious problems. They can cause product deterioration, sludge formation, and corrosion of tanks and pipework. The fuel that presents the most serious problems in terms of microbiological growth is diesel fuel, whether it is petrodiesel or worse, biodiesel. Conditions in diesel fuel storage containers are ideal for significant and rapid growth. Biodiesel is subject to even more microbial contamination than petrodiesel.
Characteristics of Diesel
Diesel is a hydrocarbon by-product with a boiling point between 150 °C and 400 °C. It has carbon chain lengths of C15-C22 and a molecular weight of between 212 and 294. A variety of additives such as aliphatic amines, chelating agents, detergents, and corrosion inhibitors are usually added by the refiners, but some of these eventually become a nutrient source for microorganisms. Diesel is the fuel that suffers most from microbial contamination.
Contamination in Storage Tanks
Even in the best maintained tanks, microbial contamination can be a problem. Tanks that hold strategic reserves are particularly vulnerable and large quantities of microbial growth have been reported. One of the essential substances for microbiological growth is water:
- Water that is dissolved in the fuel will condense on tank walls
- Moisture in the air that enters through vents or floating tank lids
- Poorly designed tanks that do not drain properly allow water to remain in the bottom
- High water content of “new” diesel fuel that is delivered
Even the allowable amount of moisture in new diesel is enough to start a microbiological colony growing. The resulting cell metabolism then produces more water and the cycle continues. Since oxygen is usually present, all ingredients needed for rapid microbiological growth are present including the carbon source from diesel.
The equation of life and evolution is:
Bacteria + Water + Oxygen --> More Bacteria + Carbon Dioxide + More water
Even if oxygen were not present, such facultative organisms such as Bacillus and anaerobes such as sulfur-reducing bacteria (SRB) continue to thrive and corrode tank material. It is best to keep the water content of diesel below 50 wppm.
Problems Caused by Microbial Growth
In diesel, microbial contamination will contribute to aging instability of the fuel, but by far the most serious damage is done by microbially induced corrosion of the storage tanks and pipe work as well as the formation of thick microbial mats that will block filters and pipelines and wear out pumps.
The following microorganisms have been isolated from petrodiesel and biodiesel:
- Thirty (30) types of bacteria
- Twelve (12) types of yeasts
- Eighty-three (83) types of filamentous fungi (mat forming)
During a recent hurricane in Florida, emergency generators in five hospitals did not start when they were needed. Their fuel tanks, pipes, and filters were clogged with microorganisms.
Some Uninvited Guests
![]() |
Pseudomonas aeruginosa |
![]() |
Cladosporium |
![]() |
Candida tropicalis |
![]() |
Hormoconis resinae |
Counter Measures
Magnetism
When microorganisms are subjected to a strong magnetic flux field, the ability of the protein channels that maintain the electrical and chemical potential across the cell membrane is torn apart and the microorganism is destroyed. The resulting debris settles to the bottom of the tank or can be filtered out. This is an expensive and often impractical method.
Biocides
Biocides are expensive and highly toxic chemicals that have potential for serious environmental contamination. The fallout of dead cells creates sludge in the bottom of the tank, clogging fuel lines and filters alike. Over time, the microorganisms develop a resistance to any biocide through the process of evolution and other toxins must be brought to bear.

Filtration
Continuous filtration of petrodiesel or biodiesel with filter elements that remove water as well as bio-solids will maintain the fuel at a high degree of cleanliness. One such system is the Allen Continuous Filtration System (ACF).
The Allen ACF system is designed to operate continuously to remove moisture and solids from diesel fuel. It ensures that the fuel is continuously cleaned and that the generator is ready to start when needed.
A special inexpensive filter element removes water and solids from the fuel. The system will have paid for itself the first time the emergency generator starts without a problem.













