The Aquarium Microbiome and Biofilm
Which microbes live in aquarium filters, on surfaces and on fish skin, how biofilm forms and feeds grazing shrimp, and what studies show about how a new tank's community develops and matures.
Biofilm: how aquarium microbes live
Most bacteria in an aquarium do not float freely in the water; they live in biofilms. A biofilm is a community of microorganisms whose cells stick to each other and usually to a surface, held together by a self-produced matrix of extracellular polymeric substances made of polysaccharides, proteins and nucleic acids. Formation runs through recognisable stages: reversible attachment of free cells, irreversible anchoring, growth of embedded micro-colonies as the film matures, and finally dispersal of cells that colonise new surfaces. Cells inside a biofilm can be far more tolerant of antimicrobials than free-floating cells, partly because the dense matrix slows penetration. In streams, biofilms on rocks are an important base of the food chain, while in aquaculture they can also harbour pathogens.
The filter community
An aquarium biofilter is a fixed-film bioreactor: carrier materials such as ceramic beads and sponges give biofilm a surface, and water flow keeps oxygen and nutrients moving into it. Nitrification there converts ammonia to nitrite and then nitrate. Three groups of microbes can oxidise ammonia: ammonia-oxidising bacteria (AOB), ammonia-oxidising archaea (AOA) and complete ammonia-oxidising (comammox) Nitrospira, which carry out both steps to nitrate in one organism. AOA were discovered in 2005 and comammox Nitrospira in 2015; before that, the aquarium industry treated AOB as the dominant ammonia oxidisers.
A 2024 survey of residential and commercial aquaria found comammox Nitrospira in all 38 freshwater biofilter samples and dominant in 30 of them, AOA dominant in 7, and AOB at low abundance except in the tank with the highest ammonia. In saltwater biofilters, no comammox Nitrospira were detected, and AOA or AOB dominated. Network analysis showed positive links between nitrifiers and heterotrophic bacteria, which break down organic waste. A 2025 study found that AOA preferentially colonised ceramic beads over sponge, suggesting that several carrier types offer different niches. Filter maintenance and nitrogen chemistry are covered in the beneficial-bacteria-biofilter-guide and the RAS nitrification-microbiology guide.
Substrate and other surfaces
Gravel, rock, wood, glass and plant leaves all carry biofilm. The first cultivated AOA, Nitrosopumilus maritimus, was isolated from gravel taken from a marine tropical aquarium. Besides nitrifiers, these surfaces support heterotrophs that decompose fish waste, uneaten food and decaying plant matter. In a two-month study of six freshwater exhibits, routine husbandry such as 5–20% partial water changes and vacuuming of sand substrate was associated with short-term increases in microbial richness and evenness and with lower relative abundance of genera linked to opportunistic infections, including Pseudomonas, Edwardsiella and Mycobacterium.
The fish skin mucus microbiome
Fish skin carries its own microbiota, which helps exclude pathogens, primes the immune system and breaks down nutrients. An analysis of 1,922 skin microbiomes from 98 species found Proteobacteria, especially Gammaproteobacteria, on every marine and freshwater fish. In freshwater fish, Acinetobacter, Aeromonas, Ralstonia, Sphingomonas and Flavobacterium were the most abundant genera. Water temperature, pH, dissolved oxygen and salinity were linked to differences in community composition.
The skin community is closely tied to the surrounding water. When Tanakia lanceolata were moved repeatedly between an aquaponic system and a pond, their skin microbiota restructured within one day and came to resemble the destination water more than the water they had left. The change reversed when the fish were moved back, showing that a transfer between tanks also changes the fish's surface microbes.
Biofilm as food for shrimp and other grazers
Biofilm that builds up on surfaces with algae, cyanobacteria, other microbes and detritus is called periphyton. Many invertebrates, tadpoles and some fish feed on it; the rock-dwelling mbuna cichlids of Lake Malawi, for example, have teeth adapted for scraping it from rocks. Neocaridina davidi is an omnivore that feeds on biofilms, algae and detritus, does not eat vascular plants, and eats its own moulted exoskeletons. In a stable-isotope study of a Chinese river, the related Neocaridina denticulata was classed with the scrapers, the feeding group that grazes surfaces. Evidence from aquaculture is mixed: in a trial with giant freshwater prawns (Macrobrachium rosenbergii), a periphyton-based system matched a recirculating system, but feed conversion was the same, so periphyton was not shown to replace part of the feed.
New tank versus mature tank
A new aquarium is colonised from tap water, fish, plants and other sources; nitrifying communities form in biofilters even without added cultures. In three home aquariums followed for 12 weeks, nitrification brought ammonia and nitrite below detection by week 3 in two tanks and by week 8 in the third. The authors suggest that fast-growing AOB may rise first while ammonia is high, then give way to slower-growing comammox Nitrospira and AOA once ammonia stays low, because those groups often bind ammonia more strongly. By week 12, all three filters held similar nitrifiers, dominated by comammox Nitrospira, with several nitrifier types providing functional redundancy.
In seven newly established zoo aquarium systems monitored for a year, total bacterial counts rose and then stabilised. Each system developed its own community that shifted after events such as new fish, maintenance and temperature extremes, yet overall nitrifying capacity was unaffected. In public freshwater exhibits, the most severe imbalance (dysbiosis) involved a transient Pseudomonas bloom reaching 51.4% of the community, loss of the nitrifiers Nitrosomonas and Nitrospira, and fish health problems at the same time.