The bacteria and Archaea which are responsible for dealing with the nitrogen complex in our tanks live in a biofim which attaches them to hard surfaces. They are both photophobic with the Archaea being moreso. There are bacteria which process ammonia to nitrite or directly to nitrate and which also process nitrite to nitrate. So far, only ammonia oxidizing Archaea have been discovered/identified.
Also, live aquatic plants will host the mitrifying bacteria on their stems or leaves where there is enough lack of light. The micororganisms prefer ammonia while the plants use ammonium.
Both types of the microorganisms make their own energy and both require oxygen to do so. Because they are mostly inside the attaching biofilm, everything they need must be delivered to them. They both need oxygen to do their thing. This is why the ones in the substrate are normally lmited to less than the first 1 inch depth of substrate. But, in planted tanks where one has plants that will transport O down to their roots amd release it in the anaerobic zones of substrate do so to facilitate nitrifcation where it would otherwise not happen. When this does occur, there will also usually be zones both above and below the deeper nitrification ccreated where there is denitrification happening.
Petersen, N.R. and Jensen, K., 1997. Nitrification and denitrification in the rhizosphere of the aquatic macrophyte Lobelia dortmanna L.
Limnology and Oceanography,
42(3), pp.529-537.
Abstract
Nitrogen and O2 transformations were studied in sediments covered by
Lobelia dortmanna L.; a combination of 15N isotope pairing and microsensor (O2, NO3−, and NH4+) techniques were used. Transformation rates and microprofiles were compared with data obtained in bare sediments. The two types of sediment were incubated in doublecompartment chambers connected to a continuous flow-through system.
The presence of
L. dortmanna profoundly influenced both the nitrification-denitrification activity and porewater profiles of O2, NO3−, and NH4+ within the sediment. The rate of coupled nitrification-denitrification was greater than sixfold higher in
L. dortmnanna-vegetated sediment than in bare sediment throughout the light–dark cycle. Illumination of the
Lobelia sediment reduced denitrification activity by ∼30%. In contrast, this process was unaffected by light–dark shifts in the bare sediment. Oxygen microprofiles showed that O2 was released from the
L. dortmanna roots to the surrounding sediment both during illumination and in darkness. This release of O2 expanded the oxic sediment volume and stimulated nitrification, shown by the high concentrations of NO3− (∼30 µM) that accumulated within the rhizosphere. Both 15N2 isotope and microsensor data showed that the root-associated nitrification site was surrounded by two sites of denitrification above and below, and this led to a more efficient coupling between nitrification and denitrification in the
Lobelia sediment than in the bare sediment.
A component of mulm may be bacteria and archaea since some of it can be a surface wher the nitrifyier might attach. If you use Dr. Time One and Only nitrifying bacteria what you will see when you pour it into a tank is a white cloud in the water. That is due to the particles on which it is attached. Bear in mind all of this is on a microscopic level. That cloud dissipates pretty fast.
Here is what Dr. Tanner writes about aquarium biofiltration:
"Natural layers of biofiltration are usually undisturbed for longer periods of time (many weeks and months). In nature, no one squeezes out the debris or rinses the media on a weekly schedule. Occasionally, seasonal floods or rains may “wash” a gravel bed but regular rinsing of the filter media is not happening. The microorganisms eat the debris and the sludge is completely broken down into gases and soluble products that then escape the pore space. Soil biofilters are almost maintenance-free. The released substances are either getting into the atmosphere or are taken up by plants.
For aquarium biofiltration to be most effective, filters should be running undisturbed for as long as possible. Filter media that remain passable and have a variety of pore sizes are best."
from
https://www.swisstropicals.com/library/aquarium-biofiltration/
