The microbiome in the aquarium – explained in detail
In aquariums or aquaculture, the chemistry of the water is not the only factor determining success or failure; the world of microorganisms is also crucial. We use the term microbiome to refer to all bacteria and other microorganisms that live in water, biofilm, and substrate. On this page, we explain how this invisible ecosystem works – and why it is worth taking a closer look.
Observe, understand, act in a targeted manner
Those who understand their microbiome can identify problems much earlier and plan measures more effectively. Instead of just reacting when animals get sick or water values tip, microbial data provides information on how resilient a system really is – and whether imbalances are gradually building up.
What we mean by the microbiome
The microbiome includes all microorganisms in a system – not just individual “good” or “bad” bacteria. The interaction of the entire community is decisive. In a stable aquarium, many different groups of bacteria work together: in the degradation of organic pollutants, in nitrification, and in numerous other processes that take place in the background.
Classic water values such as pH, nitrite, or nitrate only provide information about what substances are present in the water. The microbiome, on the other hand, shows who is behind it: Which bacteria dominate? How diverse is the community? And is there any evidence that certain groups are gaining the upper hand or that important partners are missing?
A balanced microbiome is usually more flexible and can better buffer peak loads. A microbiome that is strongly one-sided, on the other hand, reacts more sensitively to changes – for example, in feeding, stocking, water changes, or the use of medication.
Water, biofilm, and substrate – where the microbiome lives
In the aquarium, the microbiome is distributed across various habitats:
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Free water – here we find mainly free-floating bacteria that react quickly to changes.
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Biofilm on surfaces – bacteria form stable communities on glass, decorations, plants, stones, and especially in the filter material.
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Bodengrund und poröse Materialien – in Sand, Kies oder anderen Substraten entstehen Sauerstoff- und Nährstoffgradienten, in denen sich jeweils spezialisierte Mikroorganismen ansiedeln.
To assess a system, it is important to know from which of these areas a sample comes. The microbiome in the free water can look very different from that in the filter – only together do they give the overall picture.
How we make the microbiome measurable
From sample to bacterial profile
To make the microbiome visible, a simple swab is not enough. In a laboratory procedure, the genetic material of the microorganisms is extracted from the sample and broken down into many small pieces. From these DNA signatures, it is then possible to deduce which bacterial groups are represented and how strongly they occur in relation to each other.
Sampling
Samples are taken specifically from water, biofilm, or substrate so that the result matches the respective question.
DNA analysis
In the laboratory, the bacterial DNA is isolated from the sample and evaluated using modern sequencing or profiling methods.
Bacterial profile & evaluation
The data is used to create a bacterial profile: Which groups dominate, how diverse is the microbiome, and are there any abnormalities?
A microbiome report does not replace the classic water analysis – it complements it. Only the combination of chemistry and microbiology shows how stable a system really is.
Note from Panta Germ practice
Putting microbiome knowledge into practice
You now know the basics of the microbiome and how important the bacterial community is for a stable system. If you want to control your own aquarium, breeding facility, or institute not only by feeling, but on the basis of concrete data, you can have the microbiome analyzed specifically with Panta Germ.
