The Modern Manager's 2025 Guide to Diesel Algae, Bacteria & Sludge

As the years stretch out since ultra-low sulfur diesel (ULSD) became our reality between 2007 and 2010, more and more professionals are learning what fuel handling personnel have known for years - the likelihood of having the problem of microbes and "algae" contamination in diesel fuel is a matter of 'when', not 'if'. They're also learning that finding a real solution to solve this problem is easier said than done.

Is It Really Algae Growing in My Diesel Fuel?

The first thing to clear up is that, while many of us call the problem 'algae', it's not actually algae. Algae is what the average Joe calls diesel fuel microbes, probably because they're easy to visualize. But algae is a microscopic plant, and since plants need light to grow, there's no algae in diesel fuel. What there are is bacteria and fungi that grow and thrive in stored fuels that have even a little bit of water in them. Those are the microbes that cause all the problems. It's not a huge deal breaker to call it that, since many people will know what you mean. We're just putting it out there in the interests of accuracy.

Why Are Fuel Microbe Problems Getting Worse?

We made an inference that fuel microbes are a growing problem, and there's a reason we did that. Ultra-low sulfur diesel fuel ("ULSD") behaves differently when it's stored than the higher sulfur diesel fuels of years past.

ULSD is better for the environment because most of the sulfur has been taken out at the refinery (from 5000 parts per million in 1992 down to just 15 ppm in 2007). For those keeping score, that's a 99.7% reduction in 15 years. This prevents sulfur from going into the air and causing acid rain. That's a good thing - we all like healthy trees in our environment.

But the unforeseen consequence is that now the fuel is a much more hospitable place for microbes to grow and thrive. Microbes don't like high sulfur levels - it keeps them away (many of them, anyway). The hydrotreating process used to create ULSD also removes and changes the structure of specific aromatic molecules that microbes dislike. And on top of that, the same regulations dictating the removal of sulfur also lowered the limit of aromatic content in the fuel (burning aromatic molecules in fuel helps cause smog and ground-level ozone). All of these changes come together to make today's diesel fuel far more hospitable to bacterial and fungal growth than the fuel of years past.

If you look back in the historical archives (most people won't, so that's our job), Prior to 2006, in most cases, keeping stored diesel free of microbes required only controlling water buildup. That's not the case anymore, and many of the old-standard solutions that used to work for keeping microbes and algae away just don't cut it. It's not their fault. They're water-controllers for fuel, not biocides.

What Makes ULSD Even More Prone to Water and Microbial Problems?

Today's ULSD is also more hygroscopic than older diesel formulations, meaning it absorbs water more readily from the surrounding environment. This increased water absorption is due not only to changes in its composition from processing, but also to trace biodiesel blends (even as low as B2 or B5) that are commonly mixed with conventional diesel to improve lubricity and meet environmental standards.

More water absorption means more opportunities for microbes to establish themselves and multiply in your fuel system.

Do Ethanol and Biodiesel Blends Have the Same Microbial Issues?

Those storing fuels have traditionally focused their efforts on diesel fuel with respect to keeping it free of microbes like bacteria and fungi. Not because other fuels like ethanol (E10 or E15) or biodiesel are resistant to them, but because of diesel fuel's more widespread use in applications that store fuel for extended periods.

Storage time is a key factor in whether microbial problems will occur - longer storage times equal more prolonged exposure to conditions favorable to microbial growth. All other things being equal, ethanol blends and biodiesel blends are just as likely to wind up with microbial contamination as conventional diesel fuel.

Many businesses now use low-percentage biodiesel blends like B5 to enhance the lubricity of their ultra-low sulfur diesel while helping them meet green fuel standards. Biodiesel blends provide excellent sources of nutrients for bacteria and fungi in stored fuel tanks, even at low concentrations.

The Only Real Solution for Killing Microbes in Fuel

We said the magic word. Biocide.

We know better than anyone that the diesel fuel additive industry is, shall we say, "competitive". Every joker and their brother seems to be coming up with magic solutions to dump in fuel and fix every fuel problem known or imagined.

But when you're talking about infected fuel tanks, it's nothing to play around with. The consequences for users in terms of time and money are huge and expensive. Nobody has time to waste on snake oil garbage that claims to do things like "controls microbial growth" when it doesn't do a thing about that.

The only effective method for eliminating microbes and "algae" in stored fuel is the use of a biocide—a pesticide for fuel. You can have fuel treatments that make fuzzy claims about "controlling water to help prevent or control bacterial growth in fuel". But what they're really saying is: "This is the kind of stuff that used to work in high sulfur diesel fuels. And if you keep water buildup out, you might keep microbes from growing. However, since ULSD fuels are easily susceptible to bacterial contamination, there's no guarantee. Meanwhile, we've got your money, so if you have a problem despite using this, better luck next time."

Hardly a satisfying claim if they were sincere.

How to Identify Real Biocides vs Marketing Hype

There aren't that many true biocides on the market, and for good reason. We called them "pesticides for fuel" because they're poisonous and hazardous. But that's the kind of chemical you need to kill microbial living organisms in the fuel.

Because there are few real biocides available, maybe it's a good idea to point out what you need to look for and what separates an honest-to-goodness biocide that's going to kill your microbe problem and make it go away, vs. a non-biocide water controller or other fuel additive that's just making fuzzy claims in their marketing to try and fool consumers.

EPA and State Registration Requirements

Real biocides have to be registered and approved by two different entities - the EPA's Office of Pesticides and by each individual state they're sold in. These processes are expensive and time-consuming, both to start and to keep up with. These state and national authorities require this so they can make sure the public's safety is protected, and they know what's out there. A fly-by-night company trying to make a quick buck will not have gone through these registrations. So, as a consumer, it should make you wonder about how good their "biocide" product really is.

Proper Hazard Labeling

This, too, is to protect the public's safety. Biocides are potent and hazardous, and anyone applying them needs to know everything about the risks. Therefore, the labels for real biocides tend to have lots of "fine print" on them to detail all the potential risks and what to do about them. They may even be "accordion" labels with multiple pages that unfold. If you go to Home Depot or Lowe's, grab a bottle of Roundup and look at the back label. You'll see what we're talking about.

A product that isn't a "real biocide" will probably have a brief label with generic risk phrases. Keep out of reach of children. Don't drink this stuff. This is not enough to satisfy the legal requirements. And that shouldn't be enough for a potential user to feel at ease about how safe or effective it is.

EPA and Fulfillment Numbers

They're also required to have two specific numbers on their label - the EPA Registration Number and the Fulfillment Number. The Registration Number helps the authorities trace the origin of the biocide quickly if there's a problem, like if someone dumps a drum of biocide into a lake and the local authorities have to know, quickly, what they're really dealing with. The Fulfillment Number helps trace where it was packaged. Again, in case there's an emergency problem.

"Non-biocides" won't list these numbers even though any product claiming to kill microbes in fuel MUST have them. They won't, because they're skirting the law, which should be another red flag for consumers.

Testing for Microbes in Your Fuel Tank

Regular microbial monitoring is your first line of defense against costly fuel contamination. The good news is that testing has become more accessible and affordable than ever before.

ATP-By-Filtration Testing

This provides rapid, semi-quantitative results on total microbial activity and can be performed on-site with immediate feedback. ATP testing measures the energy that living cells use to function - if there's ATP present, there are living microbes in your fuel.

You should conduct ATP testing on both a fuel sample (taken about 18 inches from the tank bottom) and a water bottom sample from your stored fuel tank. These tests should be done before and after any biocide treatment to confirm effectiveness.

When to Test Your Fuel

Testing should be part of your regular fuel maintenance routine, especially if you store fuel for extended periods. Consider testing before seasonal storage periods, if you notice filter plugging or fuel quality issues, every 6-12 months for long-term storage tanks (helps build trend information for your specific system), after any water contamination events, and before and after biocide treatments (to verify that they worked).

Warning Signs of Microbial Contamination

Watch for these telltale signs that microbes have taken hold in your fuel system: dark, slimy growths at the fuel/water interface, plugged fuel filters that need frequent replacement, fuel that smells sour or rotten, visible sediment or "stringy" material in fuel samples, corrosion around tank fittings or fuel lines, and equipment that runs rough or stalls unexpectedly.

Speed of Microbial Growth

Under the right conditions - adequate water, nutrients from the fuel, and moderate temperatures - the kind of microbial populations that like to live in fuel systems can double (reproduce) every 20 minutes to 2 hours. Granted, they have to reach the billions in order to visibly detect them, but the point is that what starts as a minor contamination can become a serious infestation in just weeks.

Biocide Effectiveness and Treatment

Quality biocides like Bellicide can eliminate microbial counts within hours of application. They're also cost-effective, with typical treatment rates around 1 ounce per 40 gallons of fuel.

However, one-size treatment doesn't always fit all situations. If after-treatment testing reveals a significant presence of microbes, this can usually be resolved with a second application of biocide. This is why testing before and after treatment is so necessary - it gives you peace of mind that the problem is truly eradicated.

Prevention vs Treatment

Prevention involves using fuel stabilizers and water control measures to create conditions that discourage microbial growth. Treatment requires biocides to kill existing microbial populations.

Preventive measures include fuel stabilizers like Dee-Zol Life for diesel and Bio Dee-Zol Life for biodiesel blends, water separation and removal systems, regular tank maintenance and cleaning, and proper fuel rotation (first in, first out).

Treatment requires EPA-registered biocides to kill existing microbes, possible fuel polishing to remove dead biomass and sediment, and tank cleaning in severe cases.

Biocide Compatibility Across Fuel Types

Most quality biocides work across different fuel types - diesel, biodiesel blends, heating oil, and even some gasoline applications. However, always check the product label and EPA registration to confirm the specific fuels and applications it's approved for.

The key is using a properly registered biocide at the correct concentration for your specific situation.

Don't Play Games - Stick With What Works

For fuel handlers, companies, and large-scale users with stored fuel tanks, they will eventually face infected fuel. Not if, but when. When that happens to you, remembering these guidelines should increase your chances of finding an efficient solution that will solve your problem and help you get back to work.

Stored diesel represents a significant investment for operators and fleet managers. Proactively maintaining fuel quality avoids the logistical and financial headache of managing thousands of gallons of degraded fuel - and supports better operational and economic outcomes.

You may be interested in these other posts about diesel fuel:

• Generator Owners: How to Tell if You Have a Diesel Fuel Fungus Problem
• Diesel Fuel Additives: Top 5 Things You Never Knew You Didn't Know
• Diesel Cetane Improver: Busting Myths