Please visit our Sponsors

Related FAQs: Biological Filtration, Biofiltration 2, Establishing Cycling 1, Establishing Cycling 2, Establishing Cycling 3, Establishing Cycling 4, Establishing Cycling 5, Establishing Cycling 6Establishing Cycling 7, Marine Cycling 8, Marine Cycling 9, Marine Cycling 10, & FAQs on Biological Cycling: Science/Rationale, Techniques/Methods: Seeding Filter Media, Live Rock/Sand, Using Livestock, Cycling Products: By Manufacturers/Names: Bio-Spira, Cycle...  Chemical Feeding, Anomalies/Fixing 1, Trouble/Fixing 2, & Fluidized Beds, Undergravel Filters/FiltrationDenitrification/Denitrifiers, Ammonia, Nitrites, Nitrates, Phosphates, & Nutrient Export,

Related Articles: Establishing Biological Cycling, Marine Filtration, Mechanical, Physical, DenitrificationLive Rock, Live Sand, Nutrient Control and Export

/The Conscientious Marine Aquarist

 Biological Filtration


By Bob Fenner


Fishes, invertebrates, algae, live rock and the living components of the substrate and water all impart changes to your system's water. Whether you're conscious of it, or try to improve on it, or not, there are multifarious reactions that take place to convert, "cycle", otherwise off-set the accumulation and toxicity of these waste and by-products.

Most celebrated in the hobby literature you'll see aspects of the element nitrogen and it's cycling. What makes nitrogen such a spiffy tool for keeping your eye on your system's water quality? Imagine being able to make an easy measure/test for what's going on in your system metabolically. Nitrogen compound testing gives you that.

Basically, all living things are made up of molecular building blocks called Amino Acids (AA for short). These are structures of carbon chains (some with sulfur), oxygen, hydrogen that are linked to one another by amino bonds to form proteins. Amino bond sounds a lot like ammonia, because it is. The nitrogen cycle is the sum total of processes that convert atmospheric nitrogen (N2) into compounds useful to animals and plants (proteins made up of AA's), that eventually make their way back (cycle) to their original start (atmospheric nitrogen). Please see Figure 1 for a detailed overview of nitrogen cycling.

For marine aquarium keeping the picture is much simpler (Figure 2). Protein Nitrogen enters into the system mainly as livestock and food. Eaten and not most of this material is broken down/converted to (unionized) ammonia (NH3) and (ionized) ammonium (NH4) a less toxic form. Nitrification occurs principally through bacteria (e.g. Nitrosomonas) metabolizing ammonia to nitrites (NO2-) and other groups (e.g. Nitrobacter) in turn converting nitrites to nitrates (NO3-). Let's look at this in another way (refer to Figure 3); an "idealized" time line for establishing nitrogen cycling in a new marine aquarium:

At mark "0" you've just set up your system and placed all new (read that as sterile) marine water (synthetic). In most cases, the hobbyist will shortly thereafter ("1") introduce either A) Some hardy (nitrogenous waste resistant) fishes, such as damsels to help "pop" the system, B) A chemical "feeding" system (source of ammonia, etc. with or without a source of beneficial microbes, C) And/or some "food" as a source of decomposing ammonia to instigate bacterial immobilization.

At point "2" enough ammonia is being converted by bacteria that have been intentionally or accidentally introduced to the system to detect the presence of the nitrification product, nitrite. Point "3" denotes the beginning of Nitrobacter activity with "4" marking the detectable initialization of conversion of nitrites to nitrates. At "5" ammonia concentration has "peaked" and generally declines rapidly. Point "6" shows the same for nitrite. Both ammonia and nitrites are toxic at low levels to most fishes and invertebrates. At the time of "7", generally four to eight weeks into the set-up, both have fallen to acceptably low concentrations to allow further stocking.

Nitrates in our example continue to rise and might build to dangerous levels in a truly closed system (shown by the ascending curve of "9"). Intervention methods by aquarists; water changes, chemical filtrants, sped-up complete biological cycling (wet-dry filtration, algal scrubbers, abundant, vigorous live rock, macro-algae) can be brought into play to successfully limit the "bottle-neck" accumulation of nitrate ("8").

Expediency and Rates of Reaction:

Depending on such factors as the physical format of food/wastes provided, temperature, bacteria population dynamics, and oxygen supply, biological filtration in your system can be a forgotten breeze or an unending nightmare.

Allow me to elaborate briefly on these points; it's important to understanding, indeed, avoiding the most common pitfalls of aquarium keeping: metabolite poisoning.

"Here we go again"; this time it's me, not Ronald Reagan. Don't overfeed; especially flake foods. Why? your livestock won't be able to find and process it all. In fact, the extra ammonia might overwhelm your microbes and your macro-life, either necessitating a minor/major re-establishment of nutrient cycling, or turning the whole system into a bouillabaisse.

Ever see a microbial culture system in a school or hospital laboratory? Notice all the care taken to keep the temperature at a certain point and constant? The good-guy microbes in your system function optimally under the same conditions. Take care to avoid thermal 'drift' (see 3) G) re).

What could you say about microbiological population dynamics? They are as vigorous and dynamic as the larger life on the reef. Even chemical self-feeders (chemo-autotrophs if you're going on Jeopardy) like the bacteria we want have to look out for competitors, predators, lack of oxygen, too much carbon dioxide, and other sources of poisoning like fish medications. As I've written before Cleanliness is not sterility. Cleaning, vacuuming, bleaching ornaments too much, too soon disrupts/destroys needed bacterial cultures. Don't be too fastidious about cleaning all your system at once; you want good, strong beneficial microbe populations living in and on the "hard" surfaces in your system.

Wherefore Art Thou, Beneficial Microbes?

So it can be seen that one measure of a system's viability, it's capacity to support fish and other life, is the presence, abundance and vitality of "magical" "mystery" microbes. Well, actually, these bacteria are to be found most everywhere; in fact, they will "fall" into your system from the air, ornaments, etc. without purposefully introducing them. Because the job of these microscopic helpers is so critical, all manner of contraptions have been invented for their life support. The various filter materials; sponge, filter fiber, substrate, double-layer (DLS, DLF), ceramic and glass beads, "sand", and more, in all types of containers; wet-dry/trickle, canister, outside/inside power, air-lift... all are for the primary benefit of keeping these beneficial microbes healthy and metabolically active. But what can you do to bring them on-board faster? A lot.

There are stock inoculations of bacteria cultures for sale in spades for the purpose of initially establishing biological cycling. Sometimes they work; too often they don't. The reasons for this are many. Most cultures are feeble, too dilute, and/or made up of inappropriate species of microbes. Way too many times, the hobbyist is to blame. They put the "bugs" in a chemically hostile, non-nutritive medium; or alternatively over-poison the water with an ammonia feeding stock. Watch out for these chemical solutions to "feed" your system; read and follow the directions provided to the "T"; the ammonia provided is concentrated.

The saddest thing about utilizing these commercially prepared cultures is not that as modern marvels instead of waiting thirty-sixty days, now it only takes one or two months; but that there are other safer, faster and inexpensive methods. What I'm hinting at is simply transplanting the beneficial microbes from an established system to the new one. In actual practice, some of a stabilized, pollutant and parasite free source's gravel, rock, filter media is carefully placed in a sterile new-one of close temperature, specific gravity and pH. Voila! Instant bacteria benefits. A "conditioning period" of time with careful feeding, testing and sparse livestock population must still be observed of course.

How Do It Know?

How can you tell how much ammonia, nitrite, nitrate you have, and why should you care? The easy answers are A) test kits and B) because at sufficient concentrations they're deadly to your livestock. Do you really need to be aware of and measure for these parameters in order to be successful? No; you're tank will "cycle" either way. But a conscientious marine aquarist will be conscious of what is going on in there system, and understand the basics of why it's so.

Some water chemistry parameters you want to keep in mind and maintain your system at:

1) Ammonia (un-ionized ammonia) (NH3), less than 0.01 ppm

2) Ammonium (ionized ammonia) (NH4+), less than 0.25 ppm

(the relative concentration of both types of ammonia can be determined from separate test kits, or a table showing the relationship between pH, temperature, and total ammonia as ammonium)

3) Nitrite ions (NO2-), less than 0.1 ppm as nitrite ion.

4) Nitrate ions (NO3-), less than 25 ppm.

(there is no clear dividing line in which nitrate is absolutely harmful; conditioned fishes and invertebrates have been cultured in water of several hundred (even thousands) ppm. All that can be agreed is less is better.)

5) pH, within a range of 8.0 to 8.5 ideally.

6) Temperature, 72-80 degrees Fahrenheit. (Periodically higher, not generally a problem for tropical systems. Stability more important than any given point.)

Ancient History; Undergravel Filters:

All closed systems need a biological filter as large and efficient as possible/practical to mineralize wastes into non-toxic nutrients, while providing for a minimal changing of water composition, in particular pH. All other gear, ultraviolet sterilizers, redox meters and dosimeters, infusers... are superfluous to proper biological filtration.

One approach to finding out how we now know all this is historical. Just how, when did aquarists figure out the nuts and bolts of biological cycling? Well, it's sort of like the question of "Did people really evolve from apes?". The answer to both is, "Not yet".

Original marine systems were "semi-open" (versus closed) with their administrators constantly pouring in new water, taking out the old, and hoping and praying their thinly stocked charges would survive another day.

Starting in the 1950's in the United States, Robert P.L. Straughan and others popularized the use of undergravel plates, along with calcareous gravel. Their reasons? They worked. Not much was commonly known as to why. Now we "know" that the aforementioned beneficial bacteria thrive in such settings with their chemical food (ammonia, nitrite, oxygen, and CO2 as a source of carbon) flowing oh-so conveniently by the nooks and crannies living space provided by the "holey" substrate.

Even today, with the advent of macro-algae, reef, "Berlin" and other "live-rock" systems in use providing the same habitat, circulation and buffering advantages, undergravel filtration remains the predominant method of "boosting" biological filtration, especially for fish-only systems (see 5) A) i).

Modern filter plates, commercial and custom-made utilize chemically inert materials to provide continuous, even flow through the whole systems base. The best incorporate large (one inch plus) air-lift, powerhead and pump driven mechanisms. (photograph).

There is nothing wrong with airstone-only driven systems. These move a goodly volume of water, with the added benefit of increased gaseous diffusion; while not adding extra waste heat. Air pumps are the "lowest-cost" provider of water movement.

Sponge and Box Types:

Laugh if you will, you old-timer freshwater aquarists. These filter types still rank high as "bacteria homes" for newly-overcrowded systems and quarantine/hospital tanks. They weather changes (such as moving) and won't change your water chemistry during treatments.

Power Filters:

Hang on the back, inside the tank, pressurized and not canister models are all good ideas. In addition to speeding and stabilizing "cycling", these workhorses are great mechanical filters and water circulators. They can be easily outfitted with chemical filtrants as well. I strongly encourage the use of at least a power filter in conjunction with undergravel and a protein skimmer for the simplest of marine systems.

A note regarding their "biological" filter function; take care to not change all the media in power filters at once. Rotating the floss, etc., back to front in the unit's water flow will allow for bacterial transference.

Wet-Dry/Trickle Filters:

Are strongly suggested for all serious marine aquarists with medium to larger systems; and definitely for all wanting to try their hand at keeping corals, live-rock and other reef invertebrates.

A giant step in biologically improved water quality was taken with the introduction of wet-dry (aka reef, trickle) filters. Fishes and invertebrates live longer, healthier lives and maintenance is greatly reduced with their use.

Properly constructed and operated wet-dry filters perform several important functions (the same one's as all other biological filters) better than all other filter modes. They provide adequate circulation and exchange of water; harbor beneficial aerobic (and often anaerobic) microbes, promote gaseous exchange; mechanically filter out large solid wastes (generally in a pre-filter arrangement) and their sumps are often equipped with contactors, dosers, meters, and skimmers.

These units do have their shortcomings; improperly engineered they can be a flood or electrical hazard; their pumps and other gear can be energy hogs, compounded with heat and water losses. It is easy to fall into the "black-hole" of purchasing more and more gear with them, without concomitant understanding of how you're (mal)affecting other aspects of the system's well-being.

The bottom line is that wet-dry filters "speed-up" the same biological reactions better than any other mode of filtration, thereby supremely improving and stabilizing water quality; to the extent that a multitude of organisms that would otherwise die are able to sustain the other vagaries of aquarium captivity.

Brave New World Technology:

Fluidized bed, algal (turf) scrubbers, anaerobic denitraters, and oh, so much more are on the cutting-edge of new ways to biologically filter water.

Fluidized bed filters are additional borrowed technology from the sewage treatment industry (along with novel "out-gassing" rings, etc. for wet-dry filters). These towers employ a media and circulation in an attempt to optimize filter surface area, and per-unit circulation/conversion efficiency. They work; and are especially useful in Large, crowded (as in wholesale) systems with widely vacillating bio-loads.

Other filter's focus on the removal of the "end-product" of crowded closed marine systems, nitrates. Macro-algae and other nitrate-using live-rock constituents can only do so much in using up this hotly-debated metabolite. Algal scrubbers of different sorts, with intense light, shallow water and specialized attachment media can do amazing amounts of nitrate (et al. nutrient) elimination. I eagerly await the commercialization of these units.

My respect is not so great for anaerobic denitrators. Denitrification is just what it appears to be; a reverse of the biological processes we've gone over called nitrification, with nitrate being converted back to nitrite, ammonia and finally nitrogen gas. This feat is accomplished by other bacteria species that thrive in the absence of oxygen (hence anaerobic). Some anaerobic denitrification does occur in every system; but not enough to offset the forward accumulation of nitrate. There are filter module products that portend to promote these microbes and their beneficial activities. Like dating, I urge you to be careful in their selection and use. Many (dates and denitrators) are "high-maintenance" units requiring daily fooling-with. All have the potential defect of other anaerobic production toxifying your system. Finally, in my opinion, they're just not worth the hassle, cost and possible chemical downside; compared with water changes, chemical filtrants, and other biological intervention (i.e. photosynthesis).


There are several other filtering "efforts" that secondarily, tertiarily serve as adjuncts to biological filtration. You'll get a glimpse of most of them in the nest two sections on physical/mechanical, and chemical filtration methods.

Bibliography/Further Reading:

Cunningham, Gregory. 1993. A thank-you, apology and warning to FAMA readers concerning algal turf scrubbers and model ecosystems. (an advertisement for EcoActivity (tm)) FAMA 11/93.

Fenner, Robert, 1992. Marine filtration: A retailer's view. The Pet Dealer 5/92.

Fruland, Robert M. & Harold W. Miller. 1979. Nitrogen in the marine aquarium, parts 1 & 2. FAMA 10,11/79.

Smit, George, 1989. The water quality factor in marine aquariums, pts. 1 & 2. FAMA 1,3/89.


Become a Sponsor Features:
Daily FAQs FW Daily FAQs SW Pix of the Day FW Pix of the Day New On WWM
Helpful Links Hobbyist Forum Calendars Admin Index Cover Images
Featured Sponsors: