1. Role of microbes in soil fertility
Soil fertility is determined by biological factors, mainly by microorganisms. The development of life in soil endows it with the property of fertility. The notion of soil is inseparable from the notion of the development of living organisms in it. Soil is created by microorganisms.

2. Microorganisms derives its energy by oxidizing organic residues left behind by the plants growing on the soil or by the animals feeding on these plants. In the final analysis, the plants growing on the soil subsist on the products of microbial activity, for the microorganisms are continually oxidizing the dead plant remains and leaving behind, in a form available to the plant, the nitrogenous and mineral compounds needed by the plants for their growth.

3. Fertile and infertile soil
On this concept, a fertile soil is one, which contains either an adequate supply of plant food in an available form, or a microbial population, which is releasing nutrients fast enough to maintain rapid plant growth; an infertile soil is one in which this does not happen, as for example, if the microorganisms are removing and locking up available plant nutrients from the soil. The soil microorganisms can be classified into major divisions, such as the bacteria, actinomycetes, fungi and algae and the protozoa, worms and arthropods.

4. Bacteria:
Bacteria live mainly on the surface of the soil and humus particles. Their numbers in soil as have been reported to be 109 bacteria per gram of soil, which is reported from a soil containing sufficient and of farmyard manure. In the soil, the bacteria seem to be concentrated on clumps of humus particles rather than on mineral particles

5. Symbiotic N2-fixing bacteria
 For nodulating legumes, nitrogen is provided through symbiotic fixation of atmospheric N2 by nitrogenase in rhizobial bacteroids. This process of biological nitrogen fixation (BNF) accounts for 65% of the nitrogen currently utilized in agriculture, and will continue to be important in future sustainable crop production systems .
Rhizobia (species of  Rhizobium, Mesorhizobium, Bradyrhizobium, Azorhizobium, Allorhizobium and Sino-rhizobium) form intimate symbiotic relationships with legumes by responding chemotactically to flavonoid molecules released as signals by the legume host. These plant compounds induce the expression of nodulation (nod) genes in Rhizobia , which in turn produce lipochitooligosaccharide(LCO) signals that trigger mitotic cell division in roots, leading to nodule formation.

6. Rhizobium
Sometimes, no nodulation occurs in spite of inoculation with certain rhizobial cultures, because the strains used in such cases become exopolysaccharide-deficient due to mutation or any unspecified reason .

7. In many low input grassland systems, the grasses depend on the N2 fixed by the legume counterparts for their N nutrition and protein synthesis. In addition to N2-fixation in legumes, Rhizobia such as species of Rhizobium and Bradyrhizobium Produce molecules (auxins, cytokinins, abscicic acids, lumichrome,rhiboflavin, lipochitooligosaccharides and vitamins) that  promote plant growth. Their colonization and infection of roots would also be expected to increase plant development and grain yield.

8. Other PGPR traits of  Rhizobia and Bradyrhizobia include phytohormone production, siderophore release , solubilization of inorganic phosphorus and antagonism against   plant pathogenic microorganisms . Applying  Bradyrhizobium japonicum to radish significantly increased plant dry matter, by 15% (Antoun et al.1998). Naturally-occurring Rhizobia, isolated from nodules of some tropical legumes, have also been shown to infect roots of many agricultural species such as rice, wheat and maize via cr

9. Non-symbiotic N2-fixing bacteria
A range of plant growth promoting rhizobacteria (PGPR) participate in interaction with C3 and C4 plants (e.g., rice, wheat, maize, sugarcane and cotton), and significantly increase their vegetative growth and grain yield (Kennedyet al.2004).
Strains of  Azospirillum, a nitrogen-fixing organism living in close association with plants in the rhizosphere. Azospirillum species are aerobic heterotrophs that fix N2 under microaerobic conditions (Roper and Ladha 1995) and grow extensively in the rhizosphere of gramineous plants (Kennedy and Tchan1992; Kennedyet al.2004). The

10. N2-fixation (Okon and Labandera-Gonzalez1994; Okon and Itzigsohn1995)
N2-fixation (Okon and Labandera-Gonzalez1994; Okon and Itzigsohn1995). Phytohormones synthesized by Azospirillum influence the host root respiration rate, metabolism and root proliferation and hence improve mineral and water uptake in inoculated plants (Okon and Itzigsohn1995). Azospirillum lipoferum and Azospirillum brasilense have been isolated from roots and stems of rice and sugar cane plants (Ladha et al.1982;James et al.2000) Balandreau (2002) found in a field experiment  that estimated yield increased was around 1.8 t ha −1due to inoculation with Azospirillum lipoferum

11. Wheat grain yield was increased by up to 30% (Okon and Labandera-Gonzalez1994) by inoculation with Azospirillum brasilense. Plant inoculation with Azospirillum brasilense
promoted greater uptake of NO3-, K +and H2PO4 in corn, sorghum and wheat (Zavalin et al.1998; Saubidet et al.2000). Inoculation with  Azospirillum brasilense
significantly increases cotton plant height and dry matter under greenhouse conditions (Bashan1998).Soil applications with Azospirillum can significantly increase cane yield in both plant and ratoon crops in the field (Shankariah and Hunsigi2001). The PGPR effects also increase N and P uptake in field trials (Galal et al.2000; Panwar and Singh2000), presumably by stimulating greater plant root growth. Substantial increases in N uptake by wheat plants and grain were observed in greenhousetrials with inoculation of  Azospirillum brasilense (Islam et al.2002).  N tracer techniques showed that  Azospirillum brasilense and Azospirillum lipoferum contributed  – 12%of wheat plant N by BNF (Malik et al.2002). Inoculation with Azospirillum brasilense significantly increases Ncontents of cotton up to 0.91 mg plant −1 (Fayez and Daw1987). Inoculation with

12. Azospirillum also significantly increased N content of sugarcane leaves in greenhouse experiments (Muthukumarasamy et al.1999).
Azospirillum is also capable of producing antifungal and antibacterial compounds, growth regulators and siderophores (Pandeyand Kumar 1989).
Acetobacter (Gluconacetobacter ) diazotrophicus is another acid-tolerant endophyte which grows best on sucrose-rich medium (James et al.1994; Kennedyet al.2004). Studies confirmed that up to 60 –80% of sugarcane plant N (equivalent to over 200 kg N ha−1 year −1) was derived from BNF and Azospirillum diazotrophicus Is apparently responsible for much of this BNF (Boddey et al.1991). The Acetobacter -sugarcane system has now become an effective experimental model and the diazotrophiccharacter (nif +) is important component of this system(Lee et al.2002). Reinhold-Hurek et al. (1993) studied a  strain of the endophytic Gram-negative N2-fixing bacterium.

13. Herbaspirillum is an endophyte which colonises sugarcane, rice,maize, sorghum and other cereals (James et al.2000). It canfix 31 – 
45% of total plant N in rice (30-day-old riceseedling) N from the atmosphere (Baldani et al.2000).The estimated N fixation by Herbaspirillum was 33 –58 mgtube−1
under aseptic conditions (Reis et al.2000). In a greenhouse study, inoculation with

14. Herbaspirillum increased rice yield significantly up to 7
Herbaspirillum increased rice yield significantly up to 7.5 g plant −1 (Mirza et al.2000). These authors quantified BNF by different strains of  Herbaspirillum
in both basmati and super basmatirice. The %N (N derived from the atmosphere) values were19.5 – 38.7, and 38.1– 58.2 in basmati and super basmati,respectively.
Herbaspirillum seropedicae also acts as anendophytic diazotroph of wheat plants (Kennedy and Islam2001), colonizing wheat roots internally between the cells.
 Herbaspirillum seropedicae is also found in roots and stems of sugarcane plant while Herbaspirillum rubrisubal-bicans
is an obligate endophyte of roots, stems and leaves (Reis et al., 2000). Herbaspirilla can also colonize maize plants endophytically and fix N2, in addition to sugarcane and wheat (James et al.2000).

15. Phosphorus-solubilizing bacteria
To convert insoluble phosphates (both organic and inorganic) compounds in a form accessible to the plant is an important trait for a PGPR in increasing plant yields(Igual et al.2001; Rodríguez et al.2006). Bacterial strains belonging to genera  Pseudomonas, Bacillus, Rhizobium, Burkholderia, Achromobacter, Agrobacterium, Microccocus, Aerobacter, Flavobacterium and Erwinia have the ability to solubilize insoluble inorganic phosphate (mineral phosphate) compounds such as tricalcium phosphate, dicalcium phosphate, hydroxyl apatite and rock phosphate(Goldstein1986; Rodríguez and Fraga 1999; Rodríguez et  al.2006). Strains from genera 

16. Pseudomonas, Bacillus and  Rhizobium are among the most powerful phosphate solubilizers, while tricalcium phosphate and hydroxyl apatite seem to be more degradable substrates than rock phosphate (Arora and Gaur 1979; Illmer and Schinner 1992; Halder and Chakrabarty1993; Rodríguez and Fraga 1999; Banerjee et  al.2006). The production of organic acids especially gluconic acid seems to be the most frequent agent of mineral phosphate solubilization by bacteria such as
Pseudomonas sp., Erwinia herbicola, Pseudomonas cepacia and Burkhol-deria cepacia
(Rodríguez and Fraga 1999). Another organic acid identified in strains with phosphate-solubilizing abilityis 2-ketogluconic acid, which is present in Rhizobium leguminosarum (Halder et al.1990), Rhizobium meliloti (Halder and Chakrabarty1993),

17. Bacillus firmus (Banik andDey1982), and other unidentified soil bacteria (Duff andWebley1959). Strains of Bacillus licheniformis and B.amyloliquefaciens were found to produce mixtures of lactic, isovaleric, isobutyric, and acetic acids. Other organic acids, such as glycolic acid, oxalic acid, malonic acid, succinicacid, citric acid and propionic acid, have also been identified among phosphate solubilizers (Illmer and Schinner 1992;(Banik and Dey1982; Chen et al.2006).

18. The Carbon Cycle

19. The Nitrogen Cycle

20. The Nitrogen Cycle Amino acids Amino acids (–NH2) Ammonia (NH3)
Microbial decomposition
Amino acids
Microbial ammonification
Amino acids (–NH2)
Ammonia (NH3)
Nitrosomonas
Ammonium ion (NH4+)
Nitrite ion (NO2- )
Nitrobacter
Nitrite ion (NO2-)
Nitrate ion (NO3- )
Pseudomonas
Nitrate ion (NO3-) N2

21. Nitrogen Fixation In rhizosphere Azotobacter Beijerinckia
Clostridium pasteurianum
Cyanobacteria: heterocysts

22. Nitrogen Fixation
In root nodules
Rhizobium
Bradyrhizobium
Frankia

23. The Formation of a Root Nodule

24. The Sulfur Cycle

25. The Sulfur Cycle Proteins and waste products Amino acids
Microbial decomposition
Amino acids
Microbial dissimilation
Amino acids (–SH)
H2S
Thiobacillus
H2S
SO42– (for energy)
Microbial & plant assimilation
SO42–
Amino acids

26. Phosphorous cycle
PO43- in rocks and in cells
Acid from Thiobacillus

27. The Degradation of Synthetic Chemicals
Natural organic matter is easily degraded by microbes
Xenobiotics are resistant to degradation

29. Bioremediation: Use of microbes to detoxify or degrade pollutants; enhanced by nitrogen and phosphorus fertilizer
Bioaugmentation: Addition of specific microbes to degrade of pollutant
Composting: Arranging organic waste to promote microbial degradation by thermophiles

30. mobilize soil nutrients from the reserves;
transform fertilizer nutrients into easily available forms;
store water-soluble nutrients in easily available forms, thus preventing leaching;
offer the plants a balanced nutrient supply due to its self-regulating system;
store and supply sufficient water;
maintain good soil aeration for the oxygen requirements of roots;
not 'fix' nutrients, i.e. convert them into unavailable form;
Improve crop use efficiency of nutrients and resources such as water and light; and
Provide nutrients throughout the growing season and especially during critical peak periods of plant development

31. Microorganisms can bring about changes in plant growth which may be stimulatory or inhibitory. These may be due to: -
1. Use of microbial metabolites as major nutrients.
2. The effect of growth regulators produced by microorganism 3. Suppression of plant pathogens 4. The production of plant phototoxic substances by saprophytes and parasites 5. The production of enzymes 6. Competition of microorganisms with plants for essential nutrients

32. Use of microbial metabolites as major nutrients
Almost any substance produced by microorganisms and released into the soil might serve as a nutrient for plant growth. Among these, nitrogen is particularly important to plants because it contributes to the formation of proteins but heavily cropped soils lose nitrogen readily through leaching and volatilization and may become nitrogen deficient unless positive steps are taken to avoid this

33. . Nitrogen is abundant in the earth’s atmosphere where it constitutes about 80% of the gases present. Unfortunately, atmospheric nitrogen is not metabolized by most plants, but many microorganismsm are able to fix it and convert it to ammonium compounds, which are available to plants, These organism include *The symbiotic root-nodule bacteria of legumes *nodule organismsm associated with ceratin other trees and shrubs *Free-living bacteria such as Azotobacter, Beijrinckia, Clostriditm, Derxia, Nocardia, Pseudomonas and Rhodospirlum, many blue-green algae(especially those forming heterocyst) and some yeasts. Other nitrogen conversions in soil that provide nutrients for plants include nitrification and the deamination of proteins.

34. The effect of growth regulators produced by microorganisms
Many mycorrhizal fungi affect plants growth by accumulation soluble nutrients from the soil and transferring them to the plant, and by synthesizing growth substances of various sorts. Mycorrhizal fungi assist in the uptake of phosphate by plant roots. Phosphate from the soil is absorbed into the fungal sheath where much of it is accumulated. Only a small is passed to the root if the external supply is plentiful, but if the external supply is low, a good deal of accumulated phosphate is transferred. Uptake of other minerals is also enhanced by the mycorrhiza, for e.g mycorrhiza vigorously absorb potassium ions and can provide the plant. It has been shown that the plants growth is increased by mycorrhizal apple roots in sterile soil possible through the increased uptake of K, Ca,Cu and Fe.
Microorganisms break down organic matters and release inorganic nutrients which may be then used for plant growth. The whole of the saprophytic soil microflora participates in this process of nutrient release, e.g; Rhizoctonia release sugars from cellulose degradation and pass them to host plant.

35. In raw soils, phosphates and silicates are generally present in insoluble form, often combined with iron and aluminium. It has been estimated that the average phosphate content of many soils is about 0.04%. Plants need approximately kg of phosprorus (P2O5/hectare/annum), most of which must be derived from the phosphate reserve and insoluble phosphate fertilizers. Silicates are also highly insoluble, but their break down by microbial action can lead to the liberation of potassium ions and other nutrients.

36. In order to dissolve these minerals, microbes produce organic acids e
In order to dissolve these minerals, microbes produce organic acids e.g;2-keto gluconic acid (bacteria) and citric acid and oxalic acids (fungi). Phosphates are resistant to these acids e.g: Iron and aluminium phosphate, may be dissolved by the microbially produced H2S.

37. The greatest numbers of silicate and phosphate decomposers are found in soil with good supply of organic matters. Not surprisingly, increased numbers of phosphate dissovers are found in the rhizosphere and on the root surface. Organic phosphorus compounds such as phenolphthalein diphosphate , glycerophosphate and sodium phytate are attacked most frequently by microbes, where lecithin and deoxyribonucliec acids are less frequently.
Some organic phosphates are often resistant to decomposition in the soil because they are adsorbed by clay minerals and sesquioxides.