Microbes

Microbes are the invisible engine of the aquarium. They are too small to see, but they run the processes that decide whether a tank cycles, stays clear, and recovers from disturbance: nitrification, decomposition, and the microbial loop that recycles dissolved organic matter back into the food web.

This catalog groups the model's microbes into three functional types whose ecology is tightly interlinked:

• Bacteria — chemoautotrophic nitrifiers (ammonium → nitrate), heterotrophic decomposers of DOM and detritus, and the obligate-anaerobe sediment guilds that respire the buried diagenetic ladder.
• Fungi — the specialists of refractory decomposition, converting tough humic substrates into labile DOM that bacteria can then exploit (fungal conditioning).
• Protists — the single-celled grazers (ciliates and heterotrophic nanoflagellates) that eat bacteria and close the loop back to larger consumers.

Bacteria and fungi mineralize organic matter back into the inorganic nutrients that primary producers need; protists graze the bacteria and shuttle that production up the food web. For how these pieces fit together as a system, see the conceptual Microbes overview.

A note on scope. "Microbe" here means the microscopic bacteria, fungi, and protists that form the decomposer–nutrient loop. Microscopic animals such as rotifers are metazoans, not protists, and are catalogued with the invertebrate grazers under Consumers.