Biological Filtration and Microbial Ecology

Uneaten food, fish poop and dead tissue are broken down by decomposers, bacteria and other microbes that feed on organic matter. As they break it down, they release ammonia. This step is called ammonification. A second group, the ammonia-oxidizers, turns ammonia into nitrite. A third group, the nitrite-oxidizers, turns nitrite into nitrate. Together, turning ammonia into nitrate is called nitrification, and the bacteria that do it are nitrifiers.

Nitrate isn't the end of the chain. In deep sand beds and other places with no oxygen, anaerobic bacteria break nitrate down into nitrogen gas, which leaves the water (section 6). Algae, corals and other organisms use nitrate as food. Water changes take it out too.

Ammonia, nitrite and nitrate aren't simply "bad": what matters is how much. At the right level, nitrate is food. But it shouldn't be allowed to build up too far: ideally, no more than 30 ppm. Above that, report it and find what's adding it.

More food in means more waste to process. Every feeding, every new animal and every dead animal adds to the work these microbes have to do.

Decomposers are heterotrophic bacteria: bacteria that eat organic matter, the same way animals do. They live in the water, on every surface and inside detritus. They grow quickly when there's food for them, and as they eat, they use oxygen and release ammonia.

They can also do the opposite. When they have plenty of carbon to eat but little nitrogen, they take ammonia up out of the water to build their own cells instead of releasing it. Carbon dosing uses this (section 15).

Because they use oxygen, a sudden heap of rotting food or a dead animal can pull oxygen down as well as push ammonia up. Temperature and oxygen are the main things that set how fast decomposition happens.

Nitrifiers live in biofilm, a thin living layer on every wet surface: rock, sand, glass, pipes and especially filter media. They need oxygen, so they do best where water moves past them. Their food is the ammonia and nitrite in the water.

Which nitrifiers do the work in aquariums isn't always what the bottle labels say. In freshwater aquariums, studies found the nitrite-oxidizers were mostly Nitrospira-type bacteria, not the Nitrobacter that many products name. Much is still being learned about which microbes do this work.

Nitrifiers get very little energy from their food, so they grow much more slowly than decomposers. One source puts their cell growth at only a few percent of what a decomposer makes from the same energy. That slowness shapes everything in the next section.

Add a lot of waste at once (ten new fish, a big feeding, a dead animal hidden in the rock) and the bacteria need time to grow. During that gap, ammonia and nitrite rise. That's why new animals go in a few at a time, and why one hidden dead animal can upset a stable system.

It works the other way too. When the load drops (animals removed, a system left nearly empty, feeding cut back for weeks), the bacteria have less food and the population shrinks. Some nitrifiers can survive long periods without food and recover, but the longer they go without, the longer they take to recover. Then the full load comes back at once, and there aren't enough of them. After a quiet spell, add animals and feeding back slowly.

The order is always the same. Ammonia rises first, because nothing is eating it yet. Then the ammonia-oxidizers grow: ammonia falls and nitrite rises. Then the nitrite-oxidizers grow: nitrite falls and nitrate rises. How long it takes varies a lot, from weeks to, in some reported cases, months.

A system is cycled when ammonia and nitrite both read zero and nitrate is being made. Animals then go in slowly, so the bacteria can grow to match each new load.

Not every new system has to cycle from scratch. A new system set up with established rock or sand from a healthy system, or with new live rock, may already have enough helpful bacteria to skip the cycle. Test ammonia and nitrite before and after animals go in to confirm it. New live rock has a catch: if a lot of the life on it dies off, the rotting material can cause water quality problems.

Mature media or rock from an established, healthy system carries living bacteria, so it can seed a new one. It can also carry pests and disease, so the biosecurity rules from Module 2 still apply. Bottled bacteria are covered in section 13.

Water carries oxygen into the outer layers, where aerobic bacteria (bacteria that need oxygen) do nitrification. Deeper in, the oxygen gets used up. There, anaerobic bacteria (bacteria that live without oxygen) turn nitrate into nitrogen gas, which leaves the water: denitrification (Module 6).

The same zones can cause trouble. A low-oxygen zone that fills with detritus (a dirty sand bed, a filter stuffed with waste, a sponge that hasn't been cleaned) becomes a place where waste rots and releases nutrients back into the water.

Porous rock works for the same reason porous media does: lots of surface outside, and low-oxygen zones deep inside.

Bio media only works if oxygen-rich water reaches the bacteria. Keep it in moving water, spread out or as flow-through blocks, with mechanical filtration (a sock, roller or floss) before it so detritus is caught first. Media that traps detritus becomes a place where waste rots into nitrate and phosphate. The problem is the trapped waste, not the media.

Clean media only when it's visibly clogged, and only in water taken from the system: swish it gently and put it straight back. Never clean or replace all of it at once, and never let it dry out. More media isn't always better: bacteria grow to match their food, so extra media in a lightly stocked system just sits there.

When ammonia or nitrite shows up, a matched water change lowers it straight away. But if the cause is still there, a dead fish still rotting in the rock or a pump still clogged, the numbers come back. Always ask: what caused this, and is it still happening?

A bacterial bloom happens when fast-growing bacteria get a sudden surplus of food: an overdose of carbon (section 15), a dead animal, a big disturbance of detritus, or a new system with lots of organic matter. They multiply in the water itself, and the water looks milky.

The bloom isn't just ugly. Those bacteria use oxygen, so oxygen can drop at the same time, and the animals feel it. Find what fed the bloom and stop it: stop or cut back carbon dosing, remove anything dead, and check flow and oxygen. Report it.

New systems often go through an ugly stage. Diatoms, a brown dusty film, show up in nearly every new system, often fed by silicon from new salt, new rock or source water; they usually fade within a few weeks. Other nuisance growth, like cyanobacteria (red or dark slime) or dinoflagellates, can also appear while the community is still unbalanced. Detritus collecting in dead spots, rock with dying material on it, and very low nitrate and phosphate have all been linked to them.

Rushing in with big changes during this stage usually makes things worse. What helps is the basics: good flow without dead spots, removing detritus, steady water changes, and patience. A mature system has a more varied, more settled community, and that's what makes it more stable.

Every surface, every animal and the water itself carry many kinds of microbes. Some break down waste. Some live on and in the animals. Some can cause disease. A varied, crowded community leaves less room and less food for harmful bacteria to take over.

Anything that wipes out a large part of the community (heavy medication, sterilizing everything, a crash) leaves empty space, and whatever grows fastest fills it. That isn't always what you want. This is another reason not to change things suddenly.

DNA-based tests can now show which kinds of bacteria are in a water sample and how varied the community is. Some can also flag known disease organisms. These tests are new, and the people using them say the meaning of the results isn't fully understood: in one trial, healthy, successful tanks didn't score perfectly. Treat them as one more piece of evidence, not a final answer.

Bottled bacteria products are sold to start or speed up cycling and to support the biological filter. The evidence is mixed. In one peer-reviewed study of products sold to speed up cycling, only one product sped it up; four others did no better than adding nothing, at least over the first two weeks. In another study, one nitrifying product kept ammonia and nitrite much lower than in untreated saltwater tanks over four weeks. Each result applies to the product tested, not to every bottle.

Living bacteria in a bottle can die before they reach your tank. Researchers suspect freshness and temperature-controlled storage matter. A product full of decomposers can't replace nitrifiers, and decomposers can even make test results look better for a short time without real nitrification happening.

Judge a product by four things: what's actually in it, whether there's evidence beyond the label, whether it's fresh and stored as the maker says, and whether your own tests show a change. A product added by guessing gives you no way to know what it did.

A probiotic is a live microbe that gives a health benefit to an animal when given in the right amount. In fish and shrimp farming, probiotics, often Bacillus types, are used to try to crowd out harmful bacteria, support immunity and improve water quality. The ideas behind them include taking the space and food harmful bacteria would use, and making substances that hold harmful bacteria back.

The evidence is real but patchy. Results depend on the species, the exact bacterial strain and the conditions, and much of it comes from farms, not reef aquariums. A probiotic that worked for one kind of shrimp may do little for clownfish.

Photosynthetic bacteria (PSB) products usually contain purple non-sulfur bacteria such as Rhodopseudomonas palustris. These can photosynthesize, use organic waste as food and live with or without oxygen, and they've been used in fish and shrimp farming for decades. Claims for reef use include taking up nutrients, feeding filter feeders and suppressing harmful bacteria. Most of these benefits are still described as potential, not proven in reef systems, and PSB isn't a replacement for mechanical or chemical filtration.

Like any additive, probiotics and PSB are dosed by a written plan: which product, how much, how often, on which system. Then the results are watched and logged.

Decomposers that get extra carbon (from vodka, vinegar or a commercial product) grow fast and take up nitrate and phosphate to build their cells. A protein skimmer then removes those bacteria, and the nutrients leave with them (Module 16). Without a skimmer, the bacteria stay in the system and can fuel blooms.

Too much, too fast causes problems: a white-out bacterial bloom, a drop in oxygen, and nitrate and phosphate stripped toward zero, which isn't normal or safe (Module 6). Vinegar can also lower alkalinity and pH over time. Carbon dosing starts low, rises slowly, and is checked with regular nitrate, phosphate, alkalinity and pH tests. It's one of several ways to control phosphate; Module 17 compares them.