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Nitrifying bacteria and the biofilter

4 months ago

6 min read

Chapter 2 discussed the vital role of nitrifying bacteria in regard to the overall aquaponic process. The nitrifying bacteria convert the fish waste, which enters the system mainly as ammonia, into nitrate, which is fertilizer for the plants (Figure 5.1). This is a two- step process, and two separate groups of nitrifying bacteria are involved. The first step is converting ammonia to nitrite, which is done by the ammonia-oxidizing bacteria (AOB). These bacteria are often referred to by the genus name of the most common group, the Nitrosomonas. The second step is converting nitrite to nitrate is done by the nitrite-oxidizing bacteria (NOB). These are commonly referred to by the genus name of the most common group, the Nitrobacter. There are many species within these groups, but for the purposes of this publication, the individual differences are not important, and it is more useful to consider the group as a whole. The nitrification process occurs as follows:

  1. AOB bacteria convert ammonia (NH₃) into nitrite (NO₂-)

  2. NOB bacteria then convert nitrite (NO₂-) into nitrate (NO₃-)

Nitrification and, therefore, a healthy bacterial colony is essential to a functioning aquaponic system. Nitrifying bacteria are relatively slow to reproduce and establish colonies, requiring days and sometimes weeks, and therefore the patience of the farmer is one of the most important management parameters when establishing a new aquaponic system. Many aquariums and aquaponic systems have failed because too many fish were added before the colony of bacteria was fully developed. There are several other key parameters to support nitrifying bacteria. Generally, bacteria require a large, dark location to colonize with good water quality, adequate food and oxygen. Often, nitrifying bacteria form a slimy, light brown or beige matrix on the biofilter, and have a distinctive odour that is difficult to describe, but does not smell particularly foul which could indicate other micro-organisms.

High surface area

Biofiltration material with a high specific surface area (SSA) is optimal to develop extensive colonies of nitrifying bacteria. SSA is a ratio defining the surface area exposed from a given volume of media, and is expressed in square metres per cubic metres (m2/m3). In general, the smaller and more porous the particles of the media, the greater is the surface available for bacteria to colonize. This results in more efficient biofiltration. There are many such materials used in aquaponics, either as growing media or for biofiltration, e.g. volcanic gravel, expanded clay, commercial plastic biofilter balls, and plant roots. The volcanic tuff and Bioballs® considered in this manual have, respectively, 300 m2/m3 and 600 m2/m3, which is an adequate SSA to enable bacteria to thrive. Further characteristics and SSA of the different media used in aquaponics are summarized in Table 4.1 and Appendix 4. If the biofilter material is not ideal and has a lower surface area to volume ratio, then the biofilter should be larger. An oversized biofilter cannot harm an aquaponic system, and although overly large biofilters would add unnecessary expense, excess biofiltration capacity has saved many systems from collapse.

Water pH

Nitrifying bacteria function adequately through a pH range of 6-8.5. Generally, these bacteria work better at higher pH, with the Nitrosomonas group preferring a pH of 7.2-7.8, and the Nitrobacter group preferring a pH of 7.2-8.2. However, the target pH for aquaponics is 6-7, which is a compromise between all of the organisms within this ecosystem. Nitrifying bacteria function adequately within this range, and any decrease in bacterial activity can be offset with a larger biofilter.

Water temperature

The optimal temperature range for nitrifying bacteria is 17-34 °C. This range encourages growth and productivity. If the water temperature drops below this range, the productivity of the bacteria will tend to decrease. In particular, the Nitrobacter group is less tolerant of lower temperature than is the Nitrosomonas group, and as such, during colder periods nitrite should be more carefully monitored to avoid harmful accumulations.

Dissolved oxygen

Nitrifying bacteria need adequate levels of DO in the water at all times to grow healthily and maintain high levels of productivity. Nitrification is a reduction/oxidation (redox) reaction, where the bacteria derive the energy to live when oxygen is combined with the nitrogen. Optimum levels of DO are 4-8 mg/litre, which is also the level required for the fish and the plants. Nitrification does not occur if the DO concentration drops below 2 mg/litre. Ensure adequate biofiltration by dedicating aeration to the biofilter, either through flood-and-drain cycles in media beds, air stones in external biofilters, or cascading water return lines to the canals and sump tanks.

UV light

Nitrifying bacteria are photosensitive until they fully establish a colony, and sunlight can cause considerable harm to the biofilter. Media beds already protect the bacteria from sunlight; but if using an external biofilter, be sure to keep it shaded from direct sunlight.

Monitoring bacterial activity

If all of these five parameters are respected, it is safe to assume that the bacteria are present and functioning properly. That said, bacteria are so important to aquaponics that it is worth knowing the overall health of the bacteria at any given time. However, bacteria are microscopic organisms, and it is impossible to see them without a microscope. There is a simple method to monitor the bacterial function; testing for ammonia, nitrite and nitrate provides information on the health of the bacterial colony. Ammonia and nitrite should always be 0-1 mg/litre in a functioning and balanced aquaponic unit. If either is detectable, it indicates a problem with the nitrifying bacteria. There are two possible, common reasons for this to occur. First, the biofilter is too small for the amount of fish and fish feed. Therefore, there is an imbalance and there are too many fish. To rectify, either increase the biofilter size or reduce the number of fish, or the fish feeding regime. Sometimes, this problem can occur when the system started out balanced when the fish were smaller, but gradually became unbalanced as the fish grew and were fed more with the same size biofilter. Second, if the system is balanced in size, then the bacteria themselves may not be functioning properly. This could indicate a problem with the water quality, and each parameter listed above should be checked. Often, this can occur during winter seasons as the water temperature begins to fall and bacterial activity slows.

Source: Food and Agriculture Organization of the United Nations, 2014, Christopher Somerville, Moti Cohen, Edoardo Pantanella, Austin Stankus and Alessandro Lovatelli, Small-scale aquaponic food production, http://www.fao.org/3/a-i4021e.pdf. Reproduced with permission.

Food and Agriculture Organization of the United Nations


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