Aquarium Biofiltration

Today, the term “bio” is in everybody’s word usage: bio food, bio fuel, bio degradable, etc. The aquatic hobby has not been overlooked and aquarium biofiltration and biofiltration media are mentioned everywhere. Rather than going into the pros and cons of various media or the basic chemistry of the nitrogen cycle, this article is dedicated to the biofilter processes that happen in nature and have implications for our aquariums.

Water biofiltration in nature

Most water in nature is biofiltered by soils it infiltrates or by small filter organisms that live a planktonic lifestyle. Infiltration is the process by which water enters the soil by gravity or capillary forces after it rains or from creeks, rivers, lakes, and other bodies of water. Various soils can have quite different components but always contain a solid phase (minerals and organic materials), while the rest is called pore space that is filled with liquids and gases. The pore space or porosity (not to be confused with PPI for foam) is expressed in percentage and depends on the type of soil. Sandy soil has more pore space than silty or clay soils, because the latter have smaller particles that fill the space more densely. This pore space is where the water is filtered.

Moreover, in nature water filtration is also performed by free swimming and planktonic organisms such as phyto- and bacterioplankton, both in fresh- and saltwater habitats. However, the planktonic component of water filtration is undesirable in our aquariums because it would make the water cloudy. Algae blooms or infusoria explosions are usually the result of excess phosphates in an aquatic system.

Soil biofiltration depends on:

  • Soil components and chemistry
  • Particle size
  • Pore size
  • Specific surface area and biofilms
  • Microbial community and soil biology

Soil components and chemistry

Soil is a very variable mixture of minerals and organic materials that greatly influences the water chemistry when water percolates through it. For example, calcite and dolomite release calcium carbonates and magnesium carbonates that make water “hard”. Consequently, acid rain may be neutralized if it encounters mineral rich soils with high carbonate content. Many metals such as iron or manganese leach from natural deposits into the water. Fine particles of silt or clay are washed out and turn the water cloudy, leading to the term “whitewater”. On the other end of the spectrum, organic matter releases humic acid into the water when it breaks down. In the extreme, this results in “blackwater” found for example in the Amazon basin, on Borneo, or in our peat bogs. Plant litter or peat swamps formed by sphagnum moss and other acid-tolerant plants dominate such habitats. Hence, the pH in soils varies widely  (pH from 3.5-9.5) but it is often between pH 5.5-8.5.  These are all physical and chemical effects created by the dissolving properties of the universal solvent H2O. Many of the dissolved substances influence what types of (micro)organism preferentially grow in the substrate.

Particle size

However, water is not just dissolving substances from the soils it flows through. Particles may be released by rainfall and then trapped further down by soil layers that are denser, thus creating a sieve effect. Gravel rich or sandy soils are more readily penetrated by water flows than clay or silty soils. Thus, sand is a very effective filter for larger particles, while silt captures finer material. Clay maybe so dense that almost no water flows through. However, clays (there are many different types depending on clay minerals, metal oxides, and organic matter) also capture and contain many cations. Hence, they form an ion exchanger for iron, magnesium, alkali metals, alkaline earths, and other cations. Particle sizes are internationally categorized as follows:

Boulder: larger rocks >200 mm.
Cobble: rocks sized 63-200 mm.
Gravel: lose rock fragments. Size: 2-63 mm.
Sand: mostly silica (silicon dioxide, quartz) and biogenic calcium carbonate, such as aragonite, created by coral and shellfish. Size: 0.063-2.0 mm.
Silt: mostly quartz and feldspar. Size:  0.002-0.063 mm (2.0-63 µm).
Clay:  clay minerals with traces of metal oxides and organic matter. Size: <2.0 µm.

Pore size

The pore space or porosity of any given soil is directly dependent on the particle composition and organic matter that make up the soil. Since smaller particles pack more tightly, soils made up of silt and clay have less pore space. However, they also have a smaller pore size and in general a larger specific surface. In soil science, pore space is divided in three size categories: macropores >75 µm; mesopores 30-75 µm; and micropores <30 µm. The pore space is either filled with gases or liquids.

Specific surface area and biofilms

Particle and pore size determine the specific or inner surface area. The more particles and pores there are per unit of volume (say a liter), the more surface is created that can be colonized by biofilms. In other words: the specific surface provides the real estate for biofilms. The more, the better.

Biofilms are communities of microorganisms (see below) in which cells are embedded in a self-produced matrix of extracellular polymeric substance (EPS), which is often called “slime”. The cells adhere to each other and/or the surface. Biofilms are a system/network of microorganisms that adapts to environmental conditions. They form on living or non-living surfaces and are prevalent in natural and artificial settings. EPS is a polymeric conglomeration generally composed of extracellular biopolymers in various structural forms. Biofilms are the basis of substrate-bound aquarium biofiltration.

Microbial community & soil biology

The microbial community in soil is diverse in species and highly variable depending on physical, chemical, and animate conditions such as temperature, pH, and the presence of roots for example. In soil, you will find all three domains of live: Archaea, Bacteria, and Eukaryota (animals, algae, fungi, and plants). Archaea and bacteria often co-exist in biofilms and form around particles and in pores of the soil substrate.

Archaea: initially classified with bacteria, they lack a nucleus, but have many features such as enzymes that read genetic information (transcription) and make proteins (translation) that are more closely related to those found in eukaryotes. Unique to archaea is that their cell membranes are dominated by ether lipids. As energy sources they can use organics such as sugars but also sunlight, ammonia, metal ions, etc. Recent research indicates that these organisms are the dominant group found in many natural habitats.

Bacteria: most of us see bacteria as something bad since we usually hear about them being responsible for disease or food spoilage. Nothing could be further from the truth, because without bacteria, life as we know it would simply cease to exist. Together with the archaea, bacteria are the masters of recycling. Anything organic or inorganic that has a little bit of energy left to be used will be consumed by these guys as food. Hence, waste decomposition in nature is done by these two groups in collaboration with higher eukaryotes below.

Eukaryota: the pore space in soils is full of organisms, some are sizeable such as earthworms and various insects, others are very small such as mites. Fungi are somewhere in the middle, since individual hyphae are tiny (in the micron range), while the whole colony can cover several square miles. Many of these organisms are summarized as detritivores, detritus feeders, or saprophages. They start the decomposition of organics by eating leaves, dead animals, excrements, etc. Their waste in turn is eaten by ever smaller organisms until we reach the true saprotrophs, which digest waste and organic matter by extracellular digestion (fungi but also bacteria and archaea). Saprotrophs release enzymes that break down matter and then absorb its components such as amino- and fatty acids, sugars, etc.

What does that mean for aquarium biofiltration?

Water filtration is teamwork by the members of the substrate microbial community from all domains of life. This is an important conclusion, both for freshwater and marine habitats. The different players form a food web, where most organisms cannot exist alone but are interdependent. The microbial community varies greatly depending on the availability of foods, pore sizes, and substrates. Soil biofiltration is therefore very plastic, meaning it can cope with a variety of conditions. However, one feature is common. Natural layers of biofiltration are usually undisturbed for longer periods of time (many weeks and months). In nature, no one squeezes out the debris or rinses the media on a weekly schedule. Occasionally, seasonal floods or rains may “wash” a gravel bed but regular rinsing of the filter media is not happening. The microorganisms eat the debris and the sludge is completely broken down into gases and soluble products that then escape the pore space. Soil biofilters are almost maintenance-free. The released substances are either getting into the atmosphere or are taken up by plants.

For aquarium biofiltration to be most effective, filters should be running undisturbed for as long as possible. Filter media that remain passable and have a variety of pore sizes are best. Given that we like to influence the water parameters depending on the species we keep, and thus make water soft, hard, etc, the filter media should be chemically inert, so that it does not affect the water chemistry by itself.

Author © Stephan M. Tanner, PhD

Last modified: July 20, 2023 at 11:12 pm