The Skeptical Fishkeeper: Nitrifying Bacteria

Author: Laura Muha

One of my greatest fears—at least as far as this column is concerned—is that someday a deadline will be looming, my editor will be lobbing terse emails my way (“Are you planning to turn in your column any time this century, Laura? Please advise.”), and I’ll be panicking at my computer because I have run out of ideas.

Like most columnists, I do keep a list of potential topics, and I’m in no danger of scratching off the last item anytime soon. But that nagging fear persists, which was why I was so happy to get an email from Eric Linthicum, a cichlid keeper from Tucson, Arizona.

Inconsistent Rules

Linthicum asked whether I would consider doing a column on establishing and caring for the nitrifying bacteria that make up an aquarium’s biological filter. “I’ve noticed as I read magazines, books, and websites that the advice and rules given by experts and novices alike are inconsistent,” he wrote. “Some folks feel these bacteria are almost indestructible (rinsing in chlorinated water is okay, will live for several hours out of water), while others treat them as most delicate (never rinse in anything but old tank water, can only live for minutes outside of water). Also, how long they actually live and how quickly they migrate to new objects and colonize seems to be a matter of much speculation.”

Linthicum didn’t have to convince me the topic was worth exploring. How many times had I been told that I should only vacuum half the gravel in my tank gravel at a time to prevent sucking up too many nitrifying bacteria? And what about antibiotics? Could they wipe out a biofilter, or are they—as the package inserts that come with aquarium medications insist—harmless to nitrifying bacteria?

“Sometimes one article even contradicts the next in [the same] major periodical,” Linthicum pointed out. “And there is a reason for this, I think: most of the information is anecdotal. You just don’t see a lot of references to scientific, objective studies of the life cycle of these bacteria, at least as they pertain to pet fish…I’m sure you’re talking to some real scientists, so I’ll be interested in getting some concrete answers!”

He wasn’t the only one. Like Linthicum, I’ve long been fascinated by the microscopic organisms that make up an aquarium’s biofilter. They process organic debris that would otherwise build up in the water and sicken or kill the fish, so our success as aquarists depends on them. Yet we can’t see them, can’t count them (at least not without the high-powered microscopes few of us have access to), and even the people who study them for a living can’t agree on what they are.

Nitrifying Bacteria

For years, scientists assumed Nitrosomonas (sometimes referred to as “Nitrosomas”) were the bacteria responsible for breaking down ammonia in aquatic systems and Nitrobacter were responsible for oxidizing nitrite. That’s because when aquarium bacteria were cultured in the laboratory, those two species tended to predominate.

But the lab environment tends to select for particular bacteria, says Dr. Peter Strom, a professor of environmental sciences at Cook College in New Jersey. Strom has been studying nitrifying bacteria in wastewater treatment for more than 30 years. That’s because the lab environment selects for particular bacteria. So while Nitrosomonas and Nitrobacter grow quickly in the lab, that doesn’t mean they’re doing most of the nitrification in the natural environment, he said.

Indeed, in recent years studies published in academic journals have suggested that other bacteria, most notably a species known as Nitrospira, may actually be handling much of the nitrification in fish tanks. “Bottom line is this: there are a lot of species of bacteria that will feed on nitrogen compounds,” said Thom Demas, curator of fishes at the Tennessee Aquarium in Chattanooga, the world’s largest freshwater aquarium. “It’s most probable that there are many bacteria responsible for the nitrogen cycle in any given place at any given time.”

Self-Contained Ecosystems

Regardless of which bacteria are involved, it’s important to realize that they, all living things, evolve and adapt to their environment. And because each tank represents a self-contained ecosystem, ever so slightly different than that of any other tank (and that includes the one sitting next to it), the microorganisms within it are likely to evolve with the slightest difference as well. “If you have a tank that has been established for a few months, some of us feel it will have evolved its own unique organisms that have become very well adapted to that environment,” Strom explained. “If any one of them has a slight advantage, it will outcompete the others. After one year are they different species? You could have arguments about that.”

Arguments aside, the two things every aquarist has to worry about when it comes to nitrifying bacteria are establishing them and maintaining them.

I discussed the former at length in earlier columns on cycling an aquarium (TFH, June and July 2005), so for the purposes of this article, suffice to say that nitrifying bacteria seem to be present in all aquatic environments, including new aquarium setups. But in such tanks, there won’t be enough of them to process the waste produced by a full load of fish; asking them to do so would be the fish-tank equivalent of asking a small-town wastewater treatment plant to suddenly take on all the sewage produced by New York City.


In order to avoid major problems, the facility—in this case the bacterial colonies—must first be expanded, and you do that by providing them with their favorite energy source, ammonia. As they oxidize it, two things happen: they begin to multiply, and they also produce nitrites, which provide an energy source for the second key group of bacteria, the nitrite oxidizers, which also multiply. When both colonies are large enough to handle all the waste produced in the tank, it is considered “cycled,” meaning the biofilter has been established.

How long this takes to occur varies considerably, from as little as 21 days to as long as six weeks, but under any circumstances, nitrifiers are slow growers as compared to many other bacteria. For instance, E. coli bacteria double in number every 20 minutes, but the fastest growing nitrifiers take eight hours to do the same, said Strom.

In my earlier columns I explored the variables that impact this, among them water temperature, oxygen levels, the presence of stressors such as heavy metals or pollutants, and the amount of food available.

The reason those variables are worth bringing up again here is because they also affect the long-term well-being of the bacteria in the biofilter. In addition, nitrifying bacteria are sensitive to ammonia. So ironically, even though they require it to grow and multiply, too much will have the inverse effect, said Demas.


Each species also has a temperature range within which it grows best. If the temperature strays outside that range, bacterial growth slows down. Fish ponds are a case in point; in colder climates, most of the nitrifying bacteria die off over the winter, so the biofilter must be re-established each spring.

Likewise, a drop in oxygen—which can occur if the water becomes too warm or a power outage disrupts its circulation—can destroy some of the bacteria. And even a buildup of debris in the filter can cause problems, because it increases the tank’s bioload and also slows the turnover of water in the tank. “The reduced flow [means] less water through the bio-filter, which means less ammonia/food for the bacteria, resulting in a decrease in the bacterial count,” Demas explained.

Poor tank maintenance can affect bacteria in another way, as well, because the acids that are a byproduct of nitrification build up in the water. At first they’re neutralized by the buffering capacity of the water. But over time this is depleted, and if not replenished through a water change, the pH of the water begins to drop, which stresses not only the fish, but the bacteria. “A pH of 6 is really quite inhibitory to nitrifying bacteria, and 5.5 would be the absolute cutoff,” Strom said. “There wouldn’t be any of the traditional nitrification below that. Even 6.5 slows them down.”

Tank Maintenance

But what about the impact of tank maintenance itself on aquarium bacteria? Bacteria grow on surfaces such as aquarium glass and gravel, so what happens when we scour the sides of a tank with an algae magnet, or clean the bottom with a gravel vacuum? I’ve been told on a number of occasions that vacuuming more than half the tank bottom at a time could remove so many bacteria that the system could go into a secondary cycle.

Nonsense, says Strom. He explained that within hours of the time the bacteria begin growing, they lay down what’s known as a biofilm (“we used to call it a slime, but ‘biofilm’ sounds much more scientific!” Strom jokes) essentially gluing themselves to whatever surface they’re growing on. Over time, this biofilm can get quite thick, and in streams and other fast-moving bodies of water, its outer layers are sometimes peeled away by the force of water passing over them. But the tug of water through an aquarium siphon is too weak to have that effect, and even if it did, there would still be plenty of bacteria left behind to handle the tank waste. “Powerwashing wouldn’t get them all off!” Strom assured me.


One of the last subjects I wanted to tackle in relation to aquarium bacteria is antibiotics, but before I do, I want to stress that I’m not a proponent of their use—at least not without an extremely good reason and an extremely good diagnosis. As I explained in an earlier column (TFH, December 2004) adding any drug to a tank can set off a complex series of chain reactions that can have unintended consequences for fish, partly because of the fish’s unique physiology, and partly because of the way most of the drugs are delivered.

While most drugs for humans and animals are typically delivered orally, topically, or via an injection, nearly all over-the-counter fish drugs are added to the tank itself. That not only affects the osmoregulatory processes of the fish, but also the bacteria in the biofilter. “An antimicrobial by definition is a substance that is against microbial organisms—and what are the bacteria in your filtration system? Microbial organisms,” Dr. John Pitts, a veterinary consultant and former aquaculture veterinarian for Washington State, told me when I interviewed him for the earlier column. But, he added, “it does depend on the product…not every product does kill [nitrifying] microbes.”

A Newfound Respect

Before I started this column, I felt mystified and perhaps even a little intimidated by the invisible microorganisms on which my tanks depend. As I wrap it up, I realize I’ve gained a new respect for them. They don’t ask much from us fishkeepers—just a place to live, food to eat, and a stable environment. But think of what they give us in return: healthy tanks for our fish to live in and for us fishkeepers to enjoy.