In this article we will discuss about the biogeochemical cycling of carbon, nitrogen, phosphorus and sulfur.
1. The Carbon Cycle:
In nature carbon exists in the form of inorganic and complex organic compounds. In atmosphere the concentration of CO2 is only 0.32% which is less than what is required by plants for photosynthesis. The CO2 is the main source of carbon required to build the organic world.
The CO2 returns back into the atmosphere through the respiration process by all groups of organisms. The other method of returning carbon is through degradation (decomposition) of organic matter by microorganisms (see organic matter dynamics). A simplified carbon cycle is given in Fig. 30.6.
2. The Nitrogen Cycle:
Nitrogen is found in the atmosphere in the highest concentration (79%). It is an essential constituent of proteins and chlorophyll found in organisms. In spite of being in such a high amount, nitrogen is not directly taken by the animals or plants from the atmosphere. In soil it remains in limited amount, and whatever concentration is found, that is governed by microbial activities.
Therefore, concentration of nitrogen made available in soil directly governs soil fertility.
3. The Phosphorus Cycle:
Phosphorus is an important constituent of protoplasm and required for metabolism of all living organisms. However, the major store house of phosphorus is the rock deposits. Agricultural crops contain 0.05 to 0.5% of phosphorus in their tissues in the form of several compounds such as phytin, phospholipids, nucleic acids, phosphorylated sugars, coenzymes and related compounds.
Several transformation processes are done by the microorganisms:
(a) alteration of solubility of inorganic compounds of phosphorus,
(b) mineralization of organic compounds with the release of inorganic phosphate,
(c) immobilization of phosphorus i.e. conversion of inorganic, available ions into cell components, and
(d) oxidation/reduction reaction of inorganic phosphorus compounds (Fig. 30.8).
However, microbiologically only two processes (mineralization and immobilization) are important.
The bulk of phosphorus present in bacterial cell accounts for 1/3 to 1/2 of all phosphorus. In soil, 15 to 85% of total phosphorus is organic. Soil rich in organic matter contains abundant organic phosphorus. Therefore, a good correlation exists between the concentrations of organic phosphorus, organic carbon and total nitrogen. The C:N:P ratio in carrington silt loam soil at soil depth 0-15 cm is found 98 : 8.3 : 1.
The inorganic phosphorus, which is unavailable to plants, is solubilized by many microorganisms into solution. Such bacteria are abundant on root surfaces of plants and account for 105– 107 per gram soil, Phosphate solubilization commonly requires acid production, but liberation of hydrogen sulfide (a product that reacts with ferric phosphate to yield ferrous sulfide) by some bacteria also made phosphorus more available to plants. Species of Pseudomonas, Bacillus, Flavobacterium, Mycobacterium, Micrococcus, Penicillium, Fusarium, Aspergillus, etc. are associated with phosphorus conversion.
Soil contains a large amount of organic phosphorus which is unavailable to plants unless it is microbiologically converted into inorganic forms. This process is known as mineralization, which is achieved by decomposition. The cleavage of phosphorus from organic matter is done by enzymes which are collectively known as phosphatases.
The mycorrhizal fungi play a key role in making the phosphorus available to host plants by extracting it from unavailable fraction of soil reservoir.
Phosphorus exists in several oxidation forms such as -3 form of phosphine (PH3) to the oxidized +5 form of orthophosphate.
4. The Sulfur Cycle:
Sulfur is an essential nutrient of plants and animals. It is most abundant in earth crust in low concentration and is unavailable to plants. In soil sulfur enters in the form of plant residues, animal wastes, chemical fertilizers and rain water.
It is taken up by the plant roots as the sulfate ions (SO4-2) which is required for their growth and development. It occurs in plant, animal and microbial proteins in the amino acids, cystine and methionine, and in B vitamins e.g. thiamine, biotin and lipoic acid. Also it is found in excretory products of animals as free sulfate, thiosulfate, thiocyanate, and taurine.
Organic and inorganic forms of sulfur is microbiologically metabolised in soil through different transformation processes (Fig. 30.9) as given below:
(a) Decomposition of organic sulfur compounds by microorganisms into smaller units and finally into inorganic compounds (i.e. mineralization).
(b) Assimilation/immobilization of simple sulfur compounds and their incorporation into bacterial, fungal and actinomycete cells,
(c) Oxidation of inorganic ions and compounds such as sulfides, thiosulfate, polythionates and elemental sulfur, and
(d) Reduction of sulfate and other anions to sulfide.
Plants derive sulfur from soil in the form of sulfate (some directly from atmosphere). Animals get sulfur by feeding plants, or animals. The dead parts of plants, animals and also microorganisms upon incorporation into soil are decomposed by microorganisms.
Proteins are hydrolysed into amino acids and other sulfur-containing molecules. These in turn are attacked by microorganisms resulting in release and accumulation of sulfate and sulfide. Moreover, in anaerobic conditions H2S accumulates, whereas in aerobic environment the combined sulfur is metabolized to sulfate. However, in nature the concentration of sulfate and sulfide is low.
Oxidation states of sulfur varies from -2 of sulfite to +6 of sulfate. The reaction is catalysed by enzymes. The soil inhabitants that utilize inorganic sulfur are autotrophs or heterotrophs, for example Thiobacillus thiooxidans, T. thioparus, T. ferrooxidans, T. novellas, T. denitrificans. The heterotrophic bacteria, actinomycetes and fungi also oxidized inorganic sulfur compounds.
The examples of these microbes are species of Arthrobacter, Bacillus, Flavobacterium and Pseudomonas that generate thiosulfate from elemental sulfur. The filamentous fungi (e.g. species of Aspergillus, Penicillium and Microsporum) produce sulfate from organic substrates such as methionine, cystine, thiourea, taurine, etc.
T. thiooxidans and T. novellus carry out the following reaction:
Na2S2O3 + 2O2 + H2O → 2NaHSO4
T. thiooxidans oxidizes sulfur as below:
S + 1 ½ O2 + H2O → H2SO4
Due to flooding, increase in temperature and addition of organic material when O2 level decreases, the level of sulfide increases considerably and sometime exceeds above 150 ppm.
Consequently, the number of sulfate reducing microorganisms increases with increase in sulfide. The predominant bacteria of two categories: are Desulfovibrio desulfuricans, Desulfotomaculum. There is evidence for the presence of Bacillus, Pseudomonas and Saccharomyces species that liberate H2S from sulfate.
Mixed cultures of Desulfuromonas acetooxidans with Chlorobium also reduce elemental sulphur to H2S. The photosynthetic Chlorobium utilizes CO2 and H2S gives rise sulphur. It is D. acetooxidans which utilizes only sulphur as an electron acceptor.
Reduction of sulphur is also, observed in some archaebacteria such as Pyrodictium occultum and P. buckii. Species of Acidianus can also reduce sulphur to H2S with molecular H2 and H donor (sulphur-respiration).
Certain bacteria reduce sulphur by dissimilatory process, in which elemental sulphur is reduced to sulphide but are unable to reduce sulphate to sulphide as in case of Desulphuromonas, Desulfurella and Campylobacter.
Direct reduction of sulphate can be carried out by two groups of bacteria.
Non-acetate oxidizing bacteria – Acetate oxidizing bacteria
Desulfovibrio, Desulfomicrobium – Desulfobacter, Desulfobacterium,
Desulfobotulus, Desulfotomaculum, – Desulfococcus, Desulfonema,
Desulfomonile, Desulfobacula, – Desulfosarcina, Desulfoarculus,
Archaeoglobus, Desulfobulbus, – Desulfacinum, Desulforhabdus,
Thermodesulfobacterium – Thermosulforhabdus
The mechanism of H2S formation from sulfate is not fully understood. However, possible pathways of sulfate reduction by Desulfovibrio is given in Fig. 30.10.
Fig. 30.10 shows the three hypothetical pathways for sulfur metabolisms:
(a) Direct reduction of sulfate to sulfite without forming free sulfur products,
(b) Formation of thiosulfate from sulfite which in turn is cleaved to form sulfide and sulfite, and
(c) An initial production of trithionate which is subsequently converted to a mixture of thiosulfate and sulfite.
Phylogenetically, Desulfotomaculum (endospore forming Gram-positive bacterium), placed with the Clostridium subdivision, whereas other sulfate reducing bacteria (Gramnegative) are in the delta subdivision of the purple bacterial group.
Few are related to Bdellovibrio and gliding myxobacteria genera Desulfovibrio, Desulfobacter. Most of them are able to grow chemolithotrophically with H2 as an electron donor, sulphate as electron acceptor, and CO2 as sole C source. Many bacteria use nitrate instead of sulfate. This is the reason that some sulphate reducing bacteria are able to fix nitrogen e.g. Desulfovibrio, Desulfobacter.