Biome cycling is the health, diversity, and balance of seen and unseen micro and macro organisms, biofilm, crustaceans, and gastropods. Developing a mature, healthy biome cycle can take months and even over a year in new systems.
New systems lack biodiversity. It is the lack of biodiversity that leads to ammonia and nitrite spikes, as well as diatom algae, cyanobacteria, poor aquatic plant growth, and other plague algae outbreaks.
Some beneficial macroorganisms you can find in well-established systems include isopods (pillbug, sowbug), amphipods (Gammarus spp., scud), cladocerans (daphnia, water fleas), Planaria spp., copepods, rotifers, tubificid worms, and ostracods.
Some beneficial microorganisms include vorticella, stentor, paramecium, amoebas, and euglena.
The substrate contains beneficial bacteria that process nitrogen, fish waste, decaying fish food and plants, and houses rhizobacteria which make nutrients available for plants.
One of the best ways to seed a new system with a diversity of macro and micro-organisms is by taking a deep scoop of substrate out of a system that has been set up for years and placing it on the bottom of a new system taking care not to mix up the layers. A good tool for this is a large specimen container or a dustpan. Moving over a filter, plants, and decor from a system with a mature biome cycle is another method of introducing diversity.
Technically all life, including fish, crustaceans, gastropods (snails), plants, and algae in the system, is part of the biome cycle. Fish, crustaceans, and gastropods you add to the system can cause disruptions to the biome cycle. These disruptions can cause algae outbreaks because they prey on organisms that keep algae at low levels.
The fish or snails hobbyists add that consume algae-eating snails could result in a plague algae outbreak a few months later. Adding a seemingly harmless shrimp to the system may feed on macro or microorganisms that help filter the water. Removing those filter feeders may result in a phytoplankton (green water) outbreak.
Any change made to the biome cycle could have both desirable and undesirable effects. Hobbyists cannot be sure that any change they make will have a positive outcome a few months later.
Water chemistry also plays an integral part in the freshwater biome cycle. All organisms kept in freshwater aquariums have evolved to thrive in a limited range of water chemistry. The natural freshwater biome has a limited range of variability. Rivers, creeks, and streams can change water chemistry and temperature during heavy rain events. Lake water chemistry tends to stay more stable, but the surface water temperature and water chemistry can change temporarily during heavy rain events.
The hardscape hobbyists use within the system can also affect the biome cycle. Rocks, wood, gravel, and sand can affect which microbes and larger animals will thrive. The fish-feeding behavior must be considered when selecting the hardscape for the system.
Many fish are algae scrapers and would appreciate large smooth rocks to graze on. Some plecostomus species (Peckoltia spp.) appreciate wood to rasp on. Corydoras spp. catfish, and Geophagus spp. cichlids are sand sifters. Stacked large cobblestone rocks can provide a hiding place for Synodontis lucipinnis (dwarf petricola catfish), juvenile fish, snails, and shrimp.