Carbon Cycle: Fixation and Return
Carbon is the foundation of all organic matter. Its global cycle begins with fixation, when plants, algae, and cyanobacteria capture carbon dioxide ($CO_2$) from the atmosphere through photosynthesis.
When living organisms die, microbes step in to return carbon by decomposing organic residues. The rate and products of this breakdown depend on oxygen availability:
- Aerobic decomposition: occurs in the presence of oxygen. Organic molecules are fully oxidized, yielding carbon dioxide ($CO_2$) and water ($H_2O$).
- Anaerobic fermentation: occurs in an oxygen-free environment. Organic matter is incompletely broken down, producing various organic acids and alcohols alongside $CO_2$.
Types of Anaerobic Fermentation
Depending on the enzymatic machinery of specific microorganisms, several carbohydrate fermentation pathways exist.
| Fermentation Type | Main Microorganisms | End Products |
|---|---|---|
| Alcoholic | Yeasts | Ethanol and $CO_2$ |
| Lactic acid | Lactic acid bacteria | Lactic acid, acetic acid, $CO_2$ |
| Propionic acid | Propionibacterium species | Propionic and other acids, $CO_2$ |
| Butyric acid | Clostridium species (acetone-butanol fermentation) | Butyric acid and corresponding acids, $CO_2$ |
Nitrogen Cycle: Fixation and Protein Breakdown
The nitrogen cycle is more complex than the carbon cycle and critically depends on bacterial activity at all stages. First, atmospheric nitrogen must be "fixed" into a bioavailable form. This is performed by free-living soil microorganisms and symbiotic root nodule bacteria.
Another crucial stage is ammonification, or nitrogen mineralization. This is the conversion of complex organic nitrogen (stored in dead tissues, plant debris, and microbial biomass) into simple ammonium compounds. Protein degradation is carried out by pseudomonads, bacilli, clostridia, and Proteus species.
Protein breakdown also follows two pathways:
- Aerobic: yields ammonia, sulfates, water, and $CO_2$.
- Anaerobic (putrefaction): produces ammonia, amines, organic acids, and $CO_2$. This process releases toxic and foul-smelling compounds: hydrogen sulfide ($H_2S$), indole, and skatole.
Note: Ureolytic bacteria (urea-splitting bacteria) form a distinct group specialized in breaking down urea into ammonia, carbon dioxide, and water.
Nitrification and Denitrification
Plants can utilize ammonium salts produced during fermentation, but nitrates are their preferred and most readily assimilated nitrogen source. The conversion of ammonia to nitrates is called nitrification. It increases soil fertility and proceeds in two distinct phases:
- First phase: Nitrosomonas bacteria oxidize ammonia to nitrous acid (forming nitrites).
- Second phase: Nitrobacter bacteria continue the oxidation, converting nitrous acid to nitric acid (forming nitrates).
Concurrently, the reverse process—denitrification—occurs in the soil. Here, microorganisms reduce beneficial nitrates back into free molecular nitrogen gas, which escapes into the atmosphere. This depletes soil nitrogen reserves and progressively reduces soil fertility.