Substrate

There is a lot of biological activity happening in the substrate that goes way beyond nitrification. Macro and microorganisms help break down detritus and chemicals, making them available as plant nutrients. Microbes in the substrate produce organic molecules that directly assist plant growth, plant immunity development, and outcompete plant pathogens.

Heterotrophic bacteria live in aerobic (oxygen-rich) and anoxic (oxygen-poor) environments and help process detritus in the system to bio-available nutrients. Autotrophic bacteria also live in aerobic and anoxic environments and process chemicals and metals into nutrients.

Heterotrophic microorganisms mainly feed upon dead plants and animals and are known as decomposers. Some animals also specialize in feeding on dead organic matter and are known as detritivores^[34].

Heterotrophic bacteria are largely responsible for organic matter decomposition. The recycling of minerals in aquatic ecosystems is made possible by heterotrophic bacteria. Heterotrophic bacteria also process fine particulate food too small for larger animals to eat.

Autotrophic bacteria synthesize their food. They derive energy from light or chemical reactions. They utilize simple inorganic compounds like carbon dioxide, water, hydrogen sulfide, etc., and convert them into organic compounds like carbohydrates, proteins, etc., to supplement their energy requirements^[35]. A common example of autotrophic bacteria in aquatic ecosystems that hobbyists often see is cyanobacteria (blue-green algae). Autotrophic bacteria are also responsible for the nitrogen cycle in aquatic ecosystems.

Substrate gain size and depth matter. The substrate is graded by mesh (or grit) size. The higher the mesh number, the finer the substrate. Rooted aquatic plants will do very well in 30 to 60-mesh sand. It is recommended that you have at least 1½ to 2 inches (3 to 5 cm) of fine sand. Sand substrate keeps most detritus on top so it can easily filter out.

Pea gravel, 1½-inch landscape drain gravel, and river cobblestone rock can provide a natural river look, but it makes a poor substrate for rooted plants. The advantage of using larger gravel or rock in part of the aquascape is that it does repel plants with runners (Vallisneria spp., Sagittaria spp.) to some extent. In systems with sand and larger gravel or rock, plants with runners will colonize the sand much quicker.

Some macro and microorganisms may be better adapted to thrive in larger substrates than sand. Larger gravel or rock provides space in between where microorganisms can live, and if the rock is large enough, for fish, shrimp, and gastropods to hide. Piles of larger rocks can provide a refuge for smaller organisms from predators.

Including a deep substrate bed in a system will help create an anoxic zone where anaerobic bacteria can reduce nitrate to nitrogen gas.

The aquarium hobby has a common myth about the toxic levels of hydrogen sulfide (H₂S) developing in the deep substrate. Hydrogen sulfide does develop in substrates when multiple conditions are met. Still, it never reaches a high enough concentration in closed systems (aquariums and ponds) with good surface agitation or aeration to cause health issues with fish.

Only slightly denser than air, hydrogen sulfide is a gas that can be quickly driven out of the water by surface agitation or aeration. Therefore a toxic level of hydrogen sulfide in an aquarium is impossible in a system with even moderate surface agitation (air-driven sponge filter).

Sulfide has three forms (H₂S [hydrogen sulfide], HS- [hydrosulfide] and S₂- [sulfide]), and the ratio is affected by pH and temperature^[36]. As pH increases, the ratio of hydrogen sulfide declines, and hydrosulfide rises until the two forms have equal proportions at a pH of 7 at a temperature of 77°F (25°C). Above a pH of 7, the greater the ratio is hydrosulfide.

Hydrogen sulfide build-up in the substrate is more common in gravel substrate than sand. Heterotrophic bacteria in the Desulfosporosinus genus live in anoxic areas of the substrate^[37]. Desulfosporosinus spp. need detritus (dissolved organic carbon) to create hydrogen sulfide. Sand tends to keep the detritus on top, where it can be removed from an aquarium via mechanical filtration. Because of this, it is not common to have areas in the sand where hydrogen sulfide is produced in significant quantities to be detectable by a rotten egg smell (above 0.5 ppb).

Aerobic and anaerobic oxidation of hydrogen sulfide (H₂S) by Thiobacillus denitrificans and other species of Thiobacillus genus are chemoautotrophs that carry out this process in substrates^[38][39]. Under aerobic conditions, 85% oxidation to sulfate (SO₄²-) was achieved in controlled conditions in 40 seconds^[40][41].

Evidence of sulfide oxidizing bacteria and archaea can often be seen as black areas where sulfide has oxidized metals (i.e., iron, manganese, copper, silver) in the substrate. This forms insoluble metallic sulfides that precipitate. The process lessens the hydrogen sulfide concentration in the substrate.

Chemolithoautotrophic sulfur-oxidizing bacteria (Thiomicrospira spp.) in the freshwater and marine substrate oxidizes hydrogen sulfide H₂S to sulfate (SO₄²-), which is a plant macronutrient^[42].

Moving substrate around while doing aquatic gardening can sometimes disturb areas where hydrogen sulfide gas may have been trapped. The classic rotten egg smell will be noticeable. A water change and strong surface or aeration will quickly dissipate the gas from the water, but the smell can linger in the air since it is heavier than air.

Anoxic conditions in the substrate provide an environment for anaerobic bacteria to metabolize detritus into ethanol, acetic acid, fatty acids, and hydrogen gas. Ethanol and acetic acid can be used by anaerobic bacteria to reduce nitrate to nitrogen gas.

Methanogenesis (biomethanation) occurs in the anaerobic areas of the substrate. Methanogenesis respiration generates methane (CH₄) as the final product of metabolism. Science has identified multiple species of methanogenic anaerobic bacteria in the genus' of Methanobacterium, Methanobrevibacter, Methanomicrobium, Methanogenium, Methanospirillum, Methanosarcina, and Methanococcus. Methanogenic anaerobic bacteria using acetic acid, hydrogen gas, and carbon dioxide formed during fermentation and can produce methane, carbon dioxide, and water^[43].

Methanogenic bacteria are found in all-natural aquatic ecosystems. The release of bubbles from sediment is typically an indicator of the presence of methanogenic activity. Methane is a gas that will bubble out of the aquarium. CO₂ generated by methanogenesis can be used by aquatic plants as a nutrient and is often a major source of carbon dioxide in natural aquatic ecosystems.

Methane oxidation can occur in the oxygen-rich layer of the substrate by methane-oxidizing bacteria. Pseudomonas methanica, Methanomonas methanooxidans, and other species of bacteria are known to carry out this process in sediments^[44].

The substrate is responsible for diverse biological processes essential to maintaining healthy aquatic systems. Ensuring the substrate is deep enough to support anaerobic bacteria is vital to aquarium and plant health. The following is a list of biological processes that take place in the substrate and detritus on the bottom of the aquarium:

Under gravel filtration (UGF) was commonly used in the 1970s and 80s. The UGF necessitated the invention of the gravel vacuum to clean the detritus out of the gravel substrate. The gravel vacuum is a piece of essential equipment for hobbyists still using UGF, but in modern systems, it is not a necessity.

Vacuuming the substrate in a system that does not use UGF destroys aerobic and anoxic environments, removes organic fertilizer, and it can take months for the aerobic and anaerobic biome to stabilize. Systems set up for a year or longer with a substrate that is never vacuumed are very healthy and require little to no fertilizer. Aerobic and anaerobic bacteria that live in the substrate process detritus and chemicals to make them available as nutrients for plants.

The gravel vacuum can still be used for water changes, but it must not be allowed to sink into the substrate. One method to prevent the gravel vacuum from sinking into the substrate is to wrap the polyester fiber around the intake.