به وبلاگ انجینر حسام الدین "حسام " خوش آمدید: Defination of Soil Microbiology & soil in view of Microbiology

Defination of Soil Microbiology & soil in view of Microbiology

Definition:

It is branch of science/microbiology which deals with study of soil microorganisms and their activities in the soil.

Soil:

It is the outer, loose material of earth’s surface which is distinctly different from the underlying bedrock and the region which support plant life. Agriculturally, soil is the region which supports the plant life by providing mechanical support and nutrients required for growth. From the microbiologist view point, soil is one of the most dynamic sites of biological interactions in the nature. It is the region where most of the physical, biological and biochemical reactions related to decomposition of organic weathering of parent rock take place.

Components of Soil:

Soil is an admixture of five major components viz. organic mater, mineral matter, soil-air, soil water and soil microorganisms/living organisms. The amount/ proposition of these components varies with locality and climate.

1. Mineral / Inorganic Matter: It is derived from parent rocks/bed rocks through decomposition, disintegration and weathering process. Different types of inorganic compounds containing various minerals are present in soil. Amongst them the dominant minerals are Silicon, Aluminum and iron and others like Carbon, Calcium Potassium, Manganese, Sodium, Sulphur, Phosphorus etc. are in trace amount. The proportion of mineral matter in soil is slightly less than half of the total volume of the soil.

2. Organic matter/components: Derived from organic residues of plants and animals added in the soil. Organic matter serves not only as a source of food for microorganisms but also supplies energy for the vital processes of metabolism which are characteristics of all living organisms. Organic matter in the soil is the potential source of N, P and S for plant growth. Microbial decomposition of organic matter releases the unavailable nutrients in available from. The proportion of organic matter in the soil ranges from 3-6% of the total volume of soil.

3. Soil Water: The amount of water present in soil varies considerably. Soil water comes from rain, snow, dew or irrigation. Soil water serves as a solvent and carrier of nutrients for the plant growth. The microorganisms inhabiting in the soil also require water for their metabolic activities. Soil water thus, indirectly affects plant growth through its effects on soil and microorganisms. Percentage of soil-water is 25% total volume of soil.

4. Soil air (Soil gases): A part of the soil volume which is not occupied by soil particles i.e. pore spaces are filled partly with soil water and partly with soil air. These two components (water & air) together only accounts for approximately half the soil's volume. Compared with atmospheric air, soil is lower in oxygen and higher in carbon dioxide, because CO2 is continuous recycled by the microorganisms during the process of decomposition of organic matter. Soil air comes from external atmosphere and contains nitrogen, oxygen Co2 and water vapour (CO2 > oxygen). Co2 in soil air (0.3-1.0%) is more than atmospheric air (0.03%). Soil aeration plays important role in plant growth, microbial population, and microbial activities in the soil.

5. Soil microorganisms: Soil is an excellent culture media for the growth and development of various microorganisms. Soil is not an inert static material but a medium pulsating with life. Soil is now believed to be dynamic or living system.

Soil contains several distinct groups of microorganisms and amongst them bacteria, fungi, actinomycetes, algae, protozoa and viruses are the most important. But bacteria are more numerous than any other kinds of microorganisms. Microorganisms form a very small fraction of the soil mass and occupy a volume of less than one percent. In the upper layer of soil (top soil up to 10-30 cm depth i.e. Horizon A), the microbial population is very high which decreases with depth of soil. Each organisms or a group of organisms are responsible for a specific change / transformation in the soil. The final effect of various activities of microorganisms in the soil is to make the soil fit for the growth & development of higher plants.
Living organisms present in the soil are grouped into two categories as follows.

1. Soil flora (micro flora) e.g. Bacteria, fungi, Actinomycetes, Algae and

2. Soil fauna (micro fauna) animal like eg. Protozoa, Nematodes, earthworms, moles, ants, rodents.

Relative proportion / percentage of various soil microorganisms are: Bacteria-aerobic (70%), anaerobic (13 %), Actinomycetes (13%), Fungi /molds (03 %) and others (Algae Protozoa viruses) 0.2-0.8 %. Soil organisms play key role in the nutrient transformations.

Scope and Importance of Soil Microbiology

Living organisms both plant and animal types constitute an important component of soil. Though these organisms form only a fraction (less than one percent) of the total soil mass, but they play important role in supporting plant communities on the earth surface. While studying the scope and importance of soil microbiology, soil-plant-animal ecosystem as such must be taken into account. Therefore, the scope and importance of soil microbiology, can be understood in better way by studying aspects like

1. Soil as a living system

2. Soil microbes and plant growth

3. Soil microorganisms and soil structure

4. Organic matter decomposition

5. Humus formation

6. Biogeochemical cycling of elements

7. Soil microorganisms as bio-control agents

8. Soil microbes and seed germination

9. Biological N2 fixation

10. Degradation of pesticides in soil.

1. Soil as a living system: Soil inhabit diverse group of living organisms, both micro flora (fungi, bacteria, algae and actinomycetes) and micro-fauna (protozoa, nematodes, earthworms, moles, ants). The density of living organisms in soil is very high i.e. as much as billions / gm of soil, usually density of organisms is less in cultivated soil than uncultivated / virgin land and population decreases with soil acidity. Top soil, the surface layer contains greater number of microorganisms because it is well supplied with Oxygen and nutrients. Lower layer / subsoil is depleted with Oxygen and nutrients hence it contains fewer organisms. Soil ecosystem comprises of organisms which are both, autotrophs (Algae, BOA) and heterotrophs (fungi, bacteria). Autotrophs use inorganic carbon from CO2 and are "primary producers" of organic matter, whereas heterotrophs use organic carbon and are decomposers/consumers.

2. Soil microbes and plant growth: Microorganisms being minute and microscopic, they are universally present in soil, water and air. Besides supporting the growth of various biological systems, soil and soil microbes serve as a best medium for plant growth. Soil fauna & flora convert complex organic nutrients into simpler inorganic forms which are readily absorbed by the plant for growth. Further, they produce variety of substances like IAA, gibberellins, antibiotics etc. which directly or indirectly promote the plant growth

3. Soil microbes and soil structure: Soil structure is dependent on stable aggregates of soil particles-Soil organisms play important role in soil aggregation. Constituents of soil are viz. organic matter, polysaccharides, lignins and gums, synthesized by soil microbes plays important role in cementing / binding of soil particles. Further, cells and mycelial strands of fungi and actinomycetes, Vormicasts from earthworm is also found to play important role in soil aggregation. Different soil microorganisms, having soil aggregation / soil binding properties are graded in the order as fungi > actinomycetes > gum producing bacteria > yeasts.
Examples are: Fungi like Rhizopus, Mucor, Chaetomium, Fusarium, Cladasporium, Rhizoctonia, Aspergillus, Trichoderma and Bacteria like Azofobacler, Rhizobium Bacillus and Xanlhomonas.

4. Soil microbes and organic matter decomposition: The organic matter serves not only as a source of food for microorganisms but also supplies energy for the vital processes of metabolism that are characteristics of living beings. Microorganisms such as fungi, actinomycetes, bacteria, protozoa etc. and macro organisms such as earthworms, termites, insects etc. plays important role in the process of decomposition of organic matter and release of plant nutrients in soil. Thus, organic matter added to the soil is converted by oxidative decomposition to simpler nutrients / substances for plant growth and the residue is transformed into humus. Organic matter / substances include cellulose, lignins and proteins (in cell wall of plants), glycogen (animal tissues), proteins and fats (plants, animals). Cellulose is degraded by bacteria, especially those of genus Cytophaga and other genera (Bacillus, Pseudomonas, Cellulomonas, and Vibrio Achromobacter) and fungal genera (Aspergillus, Penicilliun, Trichoderma, Chactomium, Curvularia). Lignins and proteins are partially digested by fungi, protozoa and nematodes. Proteins are degraded to individual amino acids mainly by fungi, actinomycetes and Clostridium. Under unaerobic conditions of waterlogged soils, methane are main carbon containing product which is produced by the bacterial genera (strict anaerobes) Methanococcus, Methanobacterium and Methanosardna.

5. Soil microbes and humus formation: Humus is the organic residue in the soil resulting from decomposition of plant and animal residues in soil, or it is the highly complex organic residual matter in soil which is not readily degraded by microorganism, or it is the soft brown/dark coloured amorphous substance composed of residual organic matter along with dead microorganisms.

6. Soil microbes and cycling of elements: Life on earth is dependent on cycling of elements from their organic / elemental state to inorganic compounds, then to organic compounds and back to their elemental states. The biogeochemical process through which organic compounds are broken down to inorganic compounds or their constituent elements is known “Mineralization”, or microbial conversion of complex organic compounds into simple inorganic compounds & their constituent elements is known as mineralization.

Soil microbes plays important role in the biochemical cycling of elements in the biosphere where the essential elements (C, P, S, N & Iron etc.) undergo chemical transformations. Through the process of mineralization organic carbon, nitrogen, phosphorus, Sulphur, Iron etc. are made available for reuse by plants.

7. Soil microbes and biological N2 fixation: Conversion of atmospheric nitrogen in to ammonia and nitrate by microorganisms is known as biological nitrogen fixation.

Fixation of atmospheric nitrogen is essential because of the reasons:

1. Fixed nitrogen is lost through the process of nitrogen cycle through denitrification.

2. Demand for fixed nitrogen by the biosphere always exceeds its availability.

3. The amount of nitrogen fixed chemically and lightning process is very less (i.e. 0.5%) as compared to biologically fixed nitrogen

4. Nitrogenous fertilizers contribute only 25% of the total world requirement while biological nitrogen fixation contributes about 60% of the earth's fixed nitrogen

5. Manufacture of nitrogenous fertilizers by "Haber" process is costly and time consuming.

The numbers of soil microorganisms carry out the process of biological nitrogen fixation at normal atmospheric pressure (1 atmosphere) and temp (around 20 °C).

Two groups of microorganisms are involved in the process of BNF.
A. Non-symbiotic (free living) and B. Symbiotic (Associative)

Non-symbiotic (free living): Depending upon the presence or absence of oxygen, non symbiotic N2 fixation prokaryotic organisms may be aerobic heterotrophs (Azotobacter, Pseudomonas, Achromobacter) or aerobic autotrophs (Nostoc, Anabena, Calothrix, BGA) and anaerobic heterotrophs (Clostridium, Kelbsiella. Desulfovibrio) or anaerobic Autotrophs (Chlorobium, Chromnatium, Rhodospirillum, Meihanobacterium etc)

Symbiotic (Associative): The organisms involved are Rhizobium, Bratfyrhizobium in legumes (aerobic): Azospirillum (grasses), Actinonycetes frantic(with Casuarinas, Alder).

8. Soil microbes as biocontrol agents: Several ecofriendly bioformulations of microbial origin are used in agriculture for the effective management of plant diseases, insect pests, weeds etc. eg: Trichoderma sp and Gleocladium sp are used for biological control of seed and soil borne diseases. Fungal genera Entomophthora, Beauveria, Metarrhizium and protozoa Maltesia grandis. Malameba locustiae etc are used in the management of insect pests. Nuclear polyhydrosis virus (NPV) is used for the control of Heliothis / American boll worm. Bacteria like Bacillus thuringiensis, Pseudomonas are used in cotton against Angular leaf spot and boll worms.

8. Degradation of pesticides in soil by microorganisms: Soil receives different toxic chemicals in various forms and causes adverse effects on beneficial soil micro flora / micro fauna, plants, animals and human beings. Various microbes present in soil act as the scavengers of these harmful chemicals in soil. The pesticides/chemicals reaching the soil are acted upon by several physical, chemical and biological forces exerted by microbes in the soil and they are degraded into non-toxic substances and thereby minimize the damage caused by the pesticides to the ecosystem. For example, bacterial genera like Pseudomonas, Clostridium, Bacillus, Thiobacillus, Achromobacter etc. and fungal genera like Trichoderma, Penicillium, Aspergillus, Rhizopus, and Fusarium are playing important role in the degradation of the toxic chemicals / pesticides in soil.

9. Biodegradation of hydrocarbons: Natural hydrocarbons in soil like waxes, paraffin’s, oils etc are degraded by fungi, bacteria and actinomycetes. E.g. ethane (C2 H6) a paraffin hydrocarbon is metabolized and degraded by Mycobacteria, Nocardia, Streptomyces Pseudomonas, Flavobacterium and several fungi.

Soil Humus

Humus is the organic residue in the soil resulting from decomposition of plant and animal residues in soil, or it is the highly complex organic residual matter in soil which is not readily degraded by microorganism, or it is the soft brown/dark coloured amorphous substance composed of residual organic matter along with dead microorganisms.

Composition of Humus:

In most soil, percentage of humus ranges from 2-10 percent, whereas it is up to 90 percent in peat bog. On average humus is composed of Carbon (58 %), Nitrogen (3-6 %, Av.5%), acids - humic acid, fulvic acid, humin, apocrenic acid, and C: N ratio 10:1 to 12:1. During the course of their activities, the microorganisms synthesize number of compounds which plays important role in humus formation.

Functions/Role of Humus:

It improves physical condition of soil
Improve water holding capacity of soil
Serve as store house for essential plant nutrients
Plays important role in determining fertility level of soil
It tend to make soils more granular with better aggregation of soil particles
Prevent leaching losses of water soluble plant nutrients
Improve microbial/biological activity in soil and encourage better development of plant-root system in soil
Act as buffering agent i.e. prevent sudden change in soil PH/soil reaction
Serve as source of energy and food for the development of soil organisms
It supplies both basic and acidic nutrients for the growth and development of higher plants
Improves aeration and drainage by making the soil more porous

12. History of Soil Microbiology (1600 - 1920)

13. There is enough evidence in the literature to believe that microorganisms were the earliest of the living things that existed on this planet. Man depends on crop plants for his existence and crop plants in turn depend on soil and soil microorganisms for their nutrition. Scientists form the beginning studied the microorganisms from water, air, soil etc. and recognized the role of microorganisms in natural processes and realized the importance of soil microorganisms in growth and development of plants.

Thus, we see that microorganisms have been playing a significant role long before they were discovered by man. Today, soil is considered to be the main source of scavenging the organic wastes through microbial action and is also a rich store house for industrial micro flora of great economic importance.

Unlike soil science whose origin can be traced back to Roman & Aryan times, soil microbiology is emerged as a distinct branch of soil science during first half of the 19th century. Some of the notable contributions made by several scientists in field of soil microbiology are highlighted in the following paragraphs.

A. V. Leeuwenhock (1673) discovered and described microorganisms through his own made first simple microscope with magnification of 200 to 300 times. He observed minute, moving objects which he called “animalcules" (small animals) which are now known as protozoa, fungi and bacteria. He for the first time made the authentic drawings of microorganisms (protozoa, bacteria, fungi).

Robert Hook (1635-1703) developed a compound microscope with multiple lenses and described the fascinating world of the microbes.

J. B. Boussingault (1838) showed that leguminous plants can fix atmospheric nitrogen and increase nitrogen content in the soil.

14. J. Von Liebig (1856) showed that nitrates were formed in soil due to addition of nitrogenous fertilizers in soil.

S. N. Winogradsky discovered the autotrophic mode of life among bacteria and established the microbiological transformation of nitrogen and sulphur. Isolated for the first time nitrifying bacteria and demonstrated role of these bacteria in nitrification (l890), further he demonstrated that free-living Clostridium pasteuriamum could fix atmospheric nitrogen (1893). Therefore, he is considered as "Father of soil microbiology".

W. B. Leismaan (1858) and M. S. Woronin (1866) demonstrated that root nodules in legumes were formed by a specific group of bacteria.

Jodin (1862, France) gave the first experimental evidence of elemental nitrogen fixation by microorganisms.

15. Robert Koch (1882) developed gelatin plate/ streak plate technique for isolation of specific type of bacteria in soil, formulated Koch's postulates to establish causal relationship between host - pathogen and disease.

R. Warington (1878) showed that nitrification in soil was a microbial process.

B. Frank i) discovered (1880) an actinomycetes “Frankia” (Actinorhizal symbiosis) inducing root nodules in non-legumes tress of genera Alnus sp and Casurina growing in temperate forests, ii) coined (1885) the term " Mycorrhiza" to denote association of certain fungal symbionts with plant roots (Mycorrhiza-A symbiotic association between a fungus and roots of higher plants. Renamed the genus Bacillus as Rhizobium (1889).

H. Hellriegel and H. Wilfarth (1886) showed that the growth of non-legume plant was directly proportional to the amount of nitrogen supplied, whereas, in legumes there was no relationship between the quantity of nitrogen supplied and extent of plant growth. They also suggested that bacteria in the root nodules of legumes accumulate atmospheric nitrogen and made it available to plants. Showed that a mutually beneficial association exists between bacteria (Rhizobia) and legume root and legumes could utilize atmospheric nitrogen (1988).

M. W. Beijerinck (1888) isolated root nodule bacteria in pure culture from nodules in legumes and named them as Bacillus radicola Considered as father of "Microbial ecology". He was the first Director of the Delft School of microbiology (Netherland).

Beijerinck and Winogradsky (1890) developed the enrichment culture technique for isolation of soil organisms, proved independently that transformation of nitrogen in nature is largely due to the activities of various groups of soil microorganisms (1891). Therefore, they are considered as "Pioneer's in soil bacteriology”.

S. N. Winogadsky (1891) demonstrated the role of bacteria in nitrification and further in fill 1983 demonstrated that free living Clostridium pasteurianum could fix atmospheric nitrogen.

Omeliansky (1902) found the anaerobic degradation of cellulose by soil bacteria.

J. G. Lipman and P. E. Brown (1903, USA) studied ammonification of organic nitrogenous substances by soil microorganisms and developed the Tumbler or Beaker for studying different types of transformation in soil.

Hiltner (Germany, 1904) coined the term "Rhizosphere" to denote that region of soil which is subjected to the influence of plant roots. Rhizosphere is the region where soil
and plant roots make contact.

Russel and Hutchinson (1909, England), proved the importance of protozoa controlling/ maintaining bacterial population and their activity in soil.

Conn (1918) developed “Direct soil examination” technique for studying soil microorganisms.

Rayner (192I) and Melin (1927) carried out the intensive study on Mycorrhiza.

16. History of Soil Microbiology (1921 – 20th Century)

17. S. A. Waksman published the book “Principles of soil Microbiology" and thereby encouraged the research in soil microbiology (1927). Studied the role of soil as the source of antagonistic organisms with special reference to soil actinomycetes (1942) and discovered the antibiotic "Streptomycin" produced by Streptomyces griseus, a soil actinomycets (1944).

Rossi (1929) and Cholondy (1930) developed "Contact Slide / Buried slide" technique for studying soil micro flora.

Van Niel (1931USA) studied chemoautotrophic bacteria and bacterial photosynthesis.

Bortels (1936) demonstrated the importance of molybdenum in accelerating nitrogen fixation by nodulating legumes.

Garrett (1936) established the school in UK on "Soil fungi and ecological classification".

Kubo (1939, Japan) showed/proved-the role and importance of “leghaemoglobin” (Red pigment) present in root nodules of legumes in nitrogen fixation.

Ruinen (1956) Dutch microbiologist coined the term "Phyllosphere" to denote the region of leaf influenced by microorganisms.

18. Alien et al (1980) (suggested that VAM fungi stimulate plant growth by physiological effects other than by enhancement of nutrient uptake.

Jensen (1942) developed the method of studying nodulation on agar media in test tubes.

Barbara Mosse and J. W. Gerdemann (1944) reported occurrence of VAM (vesicular-arbuscular Mycorrhiza) fungi (Glomus, Aculopora genera) in the roots of agricultural crop plants which helps in the mobilization of phosphate.

Starkey (1945) studied role of bacteria (Bacillus and Clostridium) in the transformation of iron.

Barker (1945) studied anaerobic fermentation by methane bacteria (Methanococcus, Methanosarcina)

Thornton, (1947), studied root nodule bacteria form clovers.

Virtanen (1947) studied chemistry and mechanism of leghaemoglobin in nitrogen fixation.

Nutman (1948 England) studied hereditary mechanism of root nodulation in legumes.

Burris and Wilson (1957) developed the "Isotope technique" to quantify the amount of nitrogen fixed and further isolated and characterized the enzyme "Nitrogenase".

Bergersen (1957 Australia) elaborated the biochemistry of nitrogen fixation in legume root nodules.

Carnham (1960 USA) discovered nitrogen fixation by cell-free extract of Clostridium pasteurianum.

Alexander Fleming started the "School of soil microbiology" at Cornell University to study microbial aspects of pesticides degradation (1961) and developed the antibiotic "Penicillin" from the fungus Penicillium notatum (1929).

Date, Brockwell and Roughley (1962, Australia) developed the technique of bio-inoculants production & seed application.

Hardy & Associates (1968, USA) developed the technique of measurement of nitrogenase activity by acetylene-reduction test coupled with gas chromatography and thereby estimation of biological nitrogen fixation.

R J Swaby (1970, Australia) developed "Biosuper" containing rock phosphate sulphur and Thiobacillus which was used to enhance the phosphorus nutrition of plants.

Foog and Stewart (1970, UK) intensified the work on N2 fixing blue-green algae.

Trinick (1973, Australia) isolated Rhizobia from root nodule of genus Trema (Parasponia) which was an unique association of Rhizobium with non-leguminous plants causing root nodulation.

Dobereiner and associates (1975, Brazil) studied nitrogen fixing potential of Azospirillum in some tropical forage grasses like Digitaria, Panicum and some cereals like maize, sorghum, wheat, rye etc. in their roots. He reported four species of Azospirillum viz. A. lipoferum, A. brasilense, A. amazonense and A. serpedica. He coined the term “Associative Symbiosis” to denote the association between nitrogen fixing Azospirillum and cereal roots. Recently this terminology has been changed and renamed as “Diazotrophic Biocoenocis”.

Challham and Associates (1978) isolated an actinomycetous endophyte Frankia sp from root nodules of Camptonia peregrina which is again an example of non-leguminous root nodulation.

Dommergues & associates (France and Senegal) had discovered / reported nodules on stem of Sesbania rostrata which could fix nitrogen and therefore this legume can be used as an excellent green manure crop in low land rice cultivation. Similarly they also discovered N2 fixing stem nodules on Casurina sp caused by Frankia, an actinomycete.

Louis Pasteur Proved the role of soil microorganisms in biochemical changes of elements. He also showed that decomposition of organic residues in soil was dependent on the nature of organic matter and environmental conditions.

Brefeld Introduced the practice of isolating soil fungi by "Single Cell" technique and cultivating / growing them on solid media. He used gelatin (first solidifying agent) in culture media as solidifying agent.

Gerretsen & Mulder (Holland) studied "Phosphate mobilization" by soil microorganisms and showed the importance of molybdenum in nitrogen metabolism by microorganisms.

Fritch, fogg & Stewart (UK) and lyengar (India) studied fixation by algae in general and micro algae in particular. They also intensified the work on N2 fixing BGA.

James Trappe and Don Marx worked on ectomycorrhiza, colonizing the roots of forest trees.

W. S. Cook, G. C. Papavizas, J. Baker and N.S. Kerr contributed to the field of biological control of plant pathogens using antagonistic organisms from soil. From the beginning of 20th century emphasis was given to the study of microorganisms in soil in relation to their physiology, ecology, interrelationship, role in soil processes and soil fertility. Further role of fungi and actinomycetes in cellulose decomposition was better understood and cellulose decomposing, sulphur oxidizing, iron bacteria etc were isolated from soil and studied in detail.

19. Types of Microorganisms in Soil

20. Living organisms both plants and animals, constitute an important component of soil. The pioneering investigations of a number of early microbiologists showed for the first time that the soil was not an inert static material but a medium pulsating with life. The soil is now believed to be a dynamic or rather a living system, containing a dynamic population of organisms/microorganisms. Cultivated soil has relatively more population of microorganisms than the fallow land, and the soils rich in organic matter contain much more population than sandy and eroded soils. Microbes in the soil are important to us in maintaining soil fertility / productivity, cycling of nutrient elements in the biosphere and sources of industrial products such as enzymes, antibiotics, vitamins, hormones, organic acids etc. At the same time certain soil microbes are the causal agents of human and plant diseases.
The soil organisms are broadly classified in to two groups viz soil flora and soil fauna, the detailed classification of which is as follows.

21. Soil Organisms

22. A. Soil Flora

a) Microflora: 1. Bacteria 2. Fungi, Molds, Yeast, Mushroom 3. Actinomycetes, Stretomyces 4. Algae eg. BGA, Yellow Green Algae, Golden Brown Algae.

23. 1. Bacteria is again classified in I) Heterotrophic eg. symbiotic & non - symbiotic N2 fixers, Ammonifier, Cellulose Decomposers, Denitrifiers II) Autrotrophic eg. Nitrosomonas, Nitrobacter, Sulphur oxidizers, etc.

24. b) Macroflora: Roots of higher plants

25. B. Soil Fauna

26. a) Microfauna: Protozoa, Nematodes

27. b) Macrofauna: Earthworms. moles, ants & others.

28. As soil inhabit several diverse groups of microorganisms, but the most important amongst them are: bacteria, actinomycetes, fungi, algae and protozoa. The characteristics and their functions / role in the soil are described in the next topics.

Soil Microorganism: Bacteria

Amongst the different microorganisms inhabiting in the soil, bacteria are the most abundant and predominant organisms. These are primitive, prokaryotic, microscopic and unicellular microorganisms without chlorophyll. Morphologically, soil bacteria are divided into three groups viz Cocci (round/spherical), (rod-shaped) and Spirilla I Spirllum (cells with long wavy chains). Bacilli are most numerous followed by Cocci and Spirilla in soil.

The most common method used for isolation of soil bacteria is the "dilution plate count" method which allows the enumeration of only viable/living cells in the soil. The size of soil bacteria varies from 0.5 to 1.0 micron in diameter and 1.0 to 10.0 microns in length. They are motile with locomotory organs flagella.
Bacterial population is one-half of the total microbial biomass in the soil ranging from 1,00000 to several hundred millions per gram of soil, depending upon the physical, chemical and biological conditions of the soil.

Winogradsky (1925), on the basis of ecological characteristics classified soil microorganisms in general and bacteria in particular into two broad categories i.e. Autochnotus (Indigenous species) and the Zymogenous (fermentative). Autochnotus bacterial population is uniform and constant in soil, since their nutrition is derived from native soil organic matter (eg. Arthrobacter and Nocardia whereas Zymogenous bacterial population in soil is low, as they require an external source of energy, eg. Pseudomonas & Bacillus. The population of Zymogenous bacteria increases gradually when a specific substrate is added to the soil. To this category belong the cellulose decomposers, nitrogen utilizing bacteria and ammonifiers.

As per the system proposed in the Bergey's Manual of Systematic Bacteriology, most of the bacteria which are predominantly encountered in soil are taxonomically included in the three orders, Pseudomonadales, Eubacteriales and Actinomycetales of the class Schizomycetes. The most common soil bacteria belong to the genera Pseudomonas, Arthrobacter, Clostridium Achromobacter, Sarcina, Enterobacter etc. The another group of bacteria common in soils is the Myxobacteria belonging to the genera Micrococcus, Chondrococcus, Archangium, Polyangium, Cyptophaga.

Bacteria are also classified on the basis of physiological activity or mode of nutrition, especially the manner in which they obtain their carbon, nitrogen, energy and other nutrient requirements. They are broadly divided into two groups i.e. a) Autotrophs and b) Heterotrophs

Autotrophic bacteria are capable synthesizing their food from simple inorganic nutrients, while heterotrophic bacteria depend on pre-formed food for nutrition. All autotrophic bacteria utilize Co2 (from atmosphere) as carbon source and derive energy either from sunlight (photoautotrophs, eg. Chromatrum. Chlorobium. Rhadopseudomonas or from the oxidation of simple inorganic substances present in soil (chemoautotrophs eg. Nitrobacter, Nitrosomonas, Thiaobacillus).
Majority of soil bacteria are heterotrophic in nature and derive their carbon and energy from complex organic substances/organic matter, decaying roots and plant residues. They obtain their nitrogen from nitrates and ammonia compounds (proteins) present in soil and other nutrients from soil or from the decomposing organic matter. Certain bacteria also require amino acids, B- Vitamins, and other growth promoting substances also.

Functions / Role of Bacteria:

Bacteria bring about a number of changes and biochemical transformations in the soil and thereby directly or indirectly help in the nutrition of higher plants growing in the soil. The important transformations and processes in which soil bacteria play vital role are: decomposition of cellulose and other carbohydrates, ammonification (proteins ammonia), nitrification (ammonia-nitrites-nitrates), denitrification (release of free elemental nitrogen), biological fixation of atmospheric nitrogen (symbiotic and non-symbiotic) oxidation and reduction of sulphur and iron compounds. All these processes play a significant role in plant nutrition,

Process/reaction	Bacterial genera
Cellulose decomposition (celluloytic bacteria ) most cellulose decomposers are mesophilic	a. Aerobic : Angiococcus, Cytophaga, Polyangium, Sporocytophyga, Bacillus, Achromobacter, Cellulomonas b. anaerobic: Clostridium Methanosarcina, Methanococcus
Ammonification (Ammonifiers)	Bacillus, Pseudomonas
Nitrification (Nitrifying bacteria)	Nitrosomonas, Nilrobacter Nitrosococcus
Denitrification (Denitrifies)	Achromobacter, Pseudomonas, Bacillus, Micrococcus
Nitrogen fixing bacteria	a Symbiotic- Rhizobium, Bradyrrhizobium b Non-symbiotic: aerobic – Azotobacter Beijerinckia (acidic soils), anaerobic-Clostridium

Bacteria capable of degrading various plant residues in soil are :

*Cellulose*	*Hemicelluloses*	*Lignin*	*Pectin*	*Proteins*
Pseudomonas	Bacillus	Pseudomonas	Erwinia	Clostridium
Cytophaya	Vibrio	Micrococcus		Proteus
Spirillum	Pseudomonas	Flavobacteriumm		Pseudomonas
Actinomycetes	Erwinia	Xanthomonas		Bacillus
Cellulomonas		Streptomyces

Soil Microorganism – Actinomycetes

These are the organisms with characteristics common to both bacteria and fungi but yet possessing distinctive features to delimit them into a distinct category. In the strict taxonomic sense, actinomycetes are clubbed with bacteria the same class of Schizomycetes and confined to the order Actinomycetales.

They are unicellular like bacteria, but produce a mycelium which is non-septate (coenocytic) and more slender, tike true bacteria they do not have distinct cell-wall and their cell wall is without chitin and cellulose (commonly found in the cell wall of fungi). On culture media unlike slimy distinct colonies of true bacteria which grow quickly, actinomycetes colonies grow slowly, show powdery consistency and stick firmly to agar surface. They produce hyphae and conidia / sporangia like fungi. Certain actinomycetes whose hyphae undergo segmentation resemble bacteria, both morphologically and physiologically.

Actinomycetes are numerous and widely distributed in soil and are next to bacteria in abundance. They are widely distributed in the soil, compost etc. Plate count estimates give values ranging from 10^4 to 10^8 per gram of soil. They are sensitive to acidity / low PH (optimum PH range 6.5 to 8.0) and waterlogged soil conditions. The population of actinomycetes increases with depth of soil even up to horizon ‘C’ of a soil profiler They are heterotrophic, aerobic and mesophilic (25-30 ^c) organisms and some species are commonly present in compost and manures are thermophilic growing at 55-65° c temperature (eg. Thermoatinomycetes, Streptomyces).

Actinomycetes belonging to the order of Actinomycetales are grouped under four families viz Mycobacteriaceae, Actinomycetaceae, Streptomycetaceae and Actinoplanaceae. Actinomycetous genera which are agriculturally and industrially important are present in only two families of Actinomycetaceae and Strepotmycetaceae.

In the order of abundance in soils, the common genera of actinomycetes are Streptomyces (nearly 70%), Nocardia and Micromonospora although Actinomycetes, Actinoplanes, Micromonospora and Streptosporangium are also generally encountered.

Functions / Role of actinomycetes:

1. Degrade/decompose all sorts of organic substances like cellulose, polysaccharides, protein fats, organic-acids etc.

2. Organic residues / substances added soil are first attacked by bacteria and fungi and later by actinomycetes, because they are slow in activity and growth than bacteria and fungi.

3. They decompose / degrade the more resistant and indecomposable organic substance/matter and produce a number of dark black to brown pigments which contribute to the dark colour of soil humus.

4. They are also responsible for subsequent further decomposition of humus (resistant material) in soil.

5. They are responsible for earthy / musty odor / smell of freshly ploughed soils.

6. Many genera species and strains (eg. Streptomyces if actinomycetes produce/synthesize number of antibiotics like Streptomycin, Terramycin, Aureomycin etc.

7. One of the species of actinomycetes Streptomyces scabies causes disease "Potato scab" in potato.

Soil Microorganism – Fungi

Fungi in soil are present as mycelial bits, rhizomorph or as different spores. Their number varies from a few thousand to a few -million per gram of soil. Soil fungi possess filamentous mycelium composed of individual hyphae. The fungal hyphae may be aseptate /coenocytic (Mastigomycotina and Zygomycotina) or septate (Ascomycotina, Basidiomycotina & Deuteromycotina).

As observed by C.K. Jackson (1975), most commonly encountered genera of fungi in soil are; Alternaria, Aspergillus, Cladosporium, Cephalosporium Botrytis, Chaetomium, Fusarium, Mucor, Penicillium, Verticillium, Trichoderma, Rhizopus, Gliocladium, Monilia, Pythium, etc. Most of these fungal genera belong to the subdivision Deuteromycotina / Fungi imperfeacta which lacks sexual mode of reproduction.

As these soil fungi are aerobic and heterotrophic, they require abundant supply of oxygen and organic matter in soil. Fungi are dominant in acid soils, because acidic environment is not conducive / suitable for the existence of either bacteria or actinomycetes. The optimum PH range for fungi lies-between 4.5 to 6.5. They are also present in neutral and alkaline soils and some can even tolerate PH beyond 9.0

Functions / Role of Fungi

1. Fungi plays significant role in soils and plant nutrition.

2. They plays important role in the degradation / decomposition of cellulose, hemi cellulose, starch, pectin, lignin in the organic matter added to the soil.

3. Lignin which is resistant to decomposition by bacteria is mainly decomposed by fungi.

4. They also serve as food for bacteria.

5. Certain fungi belonging to sub-division Zygomycotina and Deuteromycotina are predaceous in nature and attack on protozoa & nematodes in soil and thus, maintain biological equilibrium in soil.

6. They also plays important role in soil aggregation and in the formation of humus.

7. Some soil fungi are parasitic and causes number of plant diseases such as wilts, root rots, damping-off and seedling blights eg. Pythium, Phyiophlhora, Fusarium, Verticillium etc.

8. Number of soil fungi forms mycorrhizal association with the roots of higher plants (symbiotic association of a fungus with the roots of a higher plant) and helps in mobilization of soil phosphorus and nitrogen eg. Glomus, Gigaspora, Aculospora, (Endomycorrhiza) and Amanita, Boletus, Entoloma, Lactarius (Ectomycorrhiza).

Soil Microorganism – Algae

Algae are present in most of the soils where moisture and sunlight are available. Their number in soil usually ranges from 100 to 10,000 per gram of soil. They are photoautotrophic, aerobic organisms and obtain CO2 from atmosphere and energy from sunlight and synthesize their own food. They are unicellular, filamentous or colonial. Soil algae are divided in to four main classes or phyla as follows:

1. Cyanophyta (Blue-green algae)
2. Chlorophyta (Grass-green algae)
3. Xanthophyta (Yellow-green algae)
4. Bacillariophyta (diatoms or golden-brown algae)

Out of these four classes / phyla, blue-green algae and grass-green algae are more abundant in soil. The green-grass algae and diatoms are dominant in the soils of temperate region while blue-green algae predominate in tropical soils. Green-algae prefer acid soils while blue green algae are commonly found in neutral and alkaline soils. The most common genera of green algae found in soil are: Chlorella, Chlamydomonas, Chlorococcum, Protosiphon etc. and that of diatoms are Navicula, Pinnularia. Synedra, Frangilaria.

Blue green algae are unicellular, photoautotrophic prokaryotes containing Phycocyanin pigment in addition to chlorophyll. They do not posses flagella and do not reproduce sexually. They are common in neutral to alkaline soils. The dominant genera of BGA in soil are: Chrococcus, Phormidium, Anabaena, Aphanocapra, Oscillatoria etc. Some BGA posses specialized cells know as "Heterocyst" which is the sites of nitrogen fixation. BGA fixes nitrogen (non-symbiotically) in puddle paddy/water logged paddy fields (20-30 kg/ha/season). There are certain BGA which possess the character of symbiotic nitrogen fixation in association with other organisms like fungi, mosses, liverworts and aquatic ferns Azolla, eg Anabaena-Azolla association fix nitrogen symbiotically in rice fields.

Functions / role of algae or BGA:

1. Plays important role in the maintenance of soil fertility especially in tropical soils.

2. Add organic matter to soil when die and thus increase the amount of organic carbon in soil.

3. Most of soil algae (especially BGA) act as cementing agent in binding soil particles and thereby reduce/prevent soil erosion.

4. Mucilage secreted by the BGA is hygroscopic in nature and thus helps in increasing water retention capacity of soil for longer time/period.

5. Soil algae through the process of photosynthesis liberate large quantity of oxygen in the soil environment and thus facilitate the aeration in submerged soils or oxygenate the soil environment.

6. They help in checking the loss of nitrates through leaching and drainage especially in un-cropped soils.

7. They help in weathering of rocks and building up of soil structure.

Soil Microorganism – Protozoa

These are unicellular, eukaryotic, colourless, and animal like organisms (Animal kingdom). They are larger than bacteria and size varying from few microns to a few centimeters. Their population in arable soil ranges from l0,000 to 1,00,000 per gram of soil and are abundant in surface soil. They can withstand adverse soil conditions as they are characterized by "cyst stage" in their life cycle. Except few genera which reproduce sexually by fusion of cells, rest of them reproduces asexually by fission / binary fission. Most of the soil protozoa are motile by flagella or cilia or pseudopodia as locomotors organs. Depending upon the type of appendages provided for locomotion, protozoa are

Rhizopoda (Sarcondia)
Mastigophora
Ciliophora (Ciliata)
Sporophora (not common Inhabitants of soil)

Class-Rhizopoda: Consists protozoa without appendages usually have naked protoplasm without cell-wall, pseudopodia as temporary locomotory organs are present some times. Important genera are Amoeba, Biomyxa, Euglypha, etc.

Class Mastigophora: Belongs flagellated protozoa, which are predominant in soil. Important genera are: Allention, Bodo, Cercobodo, Cercomonas, Entosiphon Spiromonas, Spongomions and Testramitus. Many members are saprophytic and some posses chlorophyll and are autotrophic in nature. In this respect, they resemble unicellular algae and hence are known as "Phytoflagellates".

The soil protozoa belonging to the class ciliate / ciliophora are characterized by the presence of cilia (short hair-like appendages) around their body, which helps in locomotion. The important soil inhabitants of this class are Colpidium, Colpoda, Balantiophorus, Gastrostyla, Halteria, Uroleptus, Vortiicella, Pleurotricha etc.

Protozoa are abundant in the upper layer (15 cm) of soil. Organic manures protozoa. Soil moisture, aeration, temperature and PH are the important factors affecting soil protozoa.

Function / Role of Protozoa

1. Most of protozoans derive their nutrition by feeding or ingesting soil bacteria belonging to the genera Enterobacter, Agrobacterium, Bacillus, Escherichia, Micrococcus, and Pseudomonas and thus, they play important role in maintaining microbial / bacterial equilibrium in the soil.

2. Some protozoa have been recently used as biological control agents against phytopathogens.

3. Species of the bacterial genera viz. Enterobacter and Aerobacter are commonly used as the food base for isolation and enumeration of soil protozoans.

4. Several soil protozoa cause diseases in human beings which are carried through water and other vectors, eg. Amoebic dysentery caused by Entomobea histolytica.

Factors Affecting Distribution, Activity and Population of Soil Microorganisms

Soil microorganisms (Flora & Fauna), just like higher plants depends entirely on soil for their nutrition, growth and activity. The major soil factors which influence the microbial population, distribution and their activity in the soil are

1. Soil fertility 2. Cultural practices 3. Soil moisture 4. Soil temperature
5. Soil aeration 6. Light 7. Soil PH (H-ion Concentration) 8. Organic matter 9. Food and energy supply 10. Nature of soil and 11. Microbial associations.

All these factors play a great role in determining not only the number and type of organism but also their activities. Variations in any one or more of these factors may lead to the changes in the activity of the organisms which ultimately affect the soil fertility level. Brief account of all these factors influencing soil micro flora / organisms and their activities is activities are discussed paragraphs.

1. Cultural practices (Tillage):Cultural practices viz. cultivation, crop rotation, application of manures and fertilizers, liming and gypsum application, pesticide/fungicide and weedicide application have their effect on soil organism. Ploughing and tillage operations facilitate aeration in soil and exposure of soil to sunshine and thereby increase the biological activity of organisms, particularly of bacteria. Crop rotation with legume maintains the favorable microbial population balance, particularly of N2 fixing bacteria and thereby improve soil fertility.

Liming of acid soils increases activity of bacteria and actinomycetes and lowers the fungal population. Fertilizers and manures applied to the soil for increased crop production, supply food and nutrition not only to the crops but also to microorganisms in soil and thereby proliferate the activity of microbes.

Foliar or soil application of different chemicals (pesticides, fungicides, nematicides etc.) in agriculture are either degraded by the soil organisms or are liable to leave toxic residues in soil which are hazardous to cause profound reduction in the normal microbial activity in the soil.

2. Soil fertility: Fertility level of the soil has a great influence on the microbial population and their activity in soil. The availability of N, P and K required for plants as well as microbes in soil determines the fertility level of soil. On the other hand soil micro flora has greater influence on the soil fertility level.

3. Soil moisture: It is one of the important factors influencing the microbial population & their activity in soil. Water (soil moisture) is useful to the microorganisms in two ways i.e. it serve as source of nutrients and supplies hydrogen / oxygen to the organisms and it serve as solvent and carrier of other food nutrients to the microorganisms. Microbial activity & population proliferate best in the moisture range of 20% to 60%. Under excess moisture conditions / water logged conditions due to lack of soil aeration (Oxygen) anaerobic microflora become active and the aerobes get suppressed. While in the absence of adequate moisture in soil, some of microbes die out due to tissue dehydration and some of them change their forms into resting stages spores or cysts and tide over adverse conditions. Therefore optimum soil moisture (range 20 to 60 %) must be there for better population and activity of microbes in soil.

4. Soil temperature: Next to moisture, temperature is the most important environmental factor influencing the biological physical & chemical processes and of microbes, microbial activity and population in soil. Though microorganisms can tolerate extreme temperature (such as - 60 ° or + 60 u) conditions, but the optimum temperature range at which soil microorganisms can grow and function actively is rather narrow.

Depending upon the temperature range at which microorganisms can grow and function, are divided into three groups i.e. psychrophiles (growing at low temperature below 10 °C) Mesophiles (growing well in the temp range of 20 ° C to 45° C) and thermopiles (can tolerate temperature above 45° C and optimum 45-60°C).

Most of the soil microorganisms are mesophilic (25 to 40 °) and optimum temperature for most mesophiles is 37° C. True psychrophiles are almost absent in soil, and thermopiles though present in soil behaves like mesophiles. True thermopiles are more abundant in decaying manure and compost heaps where high temperature prevails.

Seasonal changes in soil temperature affect microbial population and their activity especially in temperate regions. In winter, when temperature is low (below 50° C ), the number and activity of microorganisms falls down, and as the soils warms up in spring, they increases in number as well as activity. In general, population and activities of soil microorganisms are the highest in spring and lowest in winter season.

5. Soil air (Aeration): For the growth of microorganisms better aeration (oxygen and sometimes CO2) in the soil is essential. Microbes consume oxygen from soil air and gives out carbon dioxide. Activities of soil microbes is often measured in terms of the amount of oxygen absorbed or amount of Co2 evolved by the organisms in the soil environment. Under high soil moisture level / water logged conditions, gaseous exchange is hindered and the accumulation of Co4 occurs in soil air which is toxic to microbes. Depending upon oxygen requirements, soil microorganisms are grouped into categories viz aerobic (require oxygen for like processes), anaerobic (do not require oxygen) and microaerophilic (requiring low concentration / level of oxygen).

6. Light: Direct sunlight is highly injurious to most of the microorganisms except algae. Therefore upper portion of the surface soil a centimeter or less is usually sterile or devoid of microorganisms. Effect of sunlight is due to heating and increase in temperature (More than 45°)

7. Soil Reaction / Soil PH: Soil reaction has a definite influence / effect on quantitative and qualitative composite on of soil microbes. Most of the soil bacteria, blue-green algae, diatoms and protozoa prefer a neutral or slightly alkaline reaction between PH 4.5 and 8.0 and fungi grow in acidic reaction between PH 4.5 and 6.5 while actinomycetes prefer slightly alkaline soil reactions. Soil reactions also influence the type of the bacteria present in soil. For example nitrifying bacteria (Nitrosomonas & Nitrobacter) and diazotrophs like Azotobacter are absent totally or inactive in acid soils, while diazotrophs like Beijerinckia, Derxia, and sulphur oxidizing bacteria like Thiobacillus thiooxidans are active in acidic soils.

8. Soil Organic Matter: The organic matter in soil being the chief source of energy and food for most of the soil organisms, it has great influence on the microbial population. Organic matter influence directly or indirectly on the population and activity of soil microorganisms. It influences the structure and texture of soil and thereby activity of the microorganisms.

9. Food and energy supply: Almost all microorganisms obtain their food and energy from the plant residues or organic matter / substances added to the soil. Energy is required for the metabolic activities of microorganisms. The heterotrophs utilize the energy liberated during the oxidation of complex organic compounds in soil, while autotrophs meet their energy requirement form oxidation of simple inorganic compounds (chemoautotroph) or from solar radiation (Photoautotroph). Thus, the source of food and energy rich material is essential for the microbial activity in soil. The organic matter, therefore serves both as a source of food nutrients as well as energy required by the soil organisms.

10. Nature of Soil: The physical, chemical and physico-chemical nature of soil and its nutrient status influence the microbial population both quantitatively and qualitatively. The chemical nature of soil has considerable effect on microbial population in soil. The soils in good physical condition have better aeration and moisture content which is essential for optimum microbial activity. Similarly nutrients (macro and micro) and organic constituents of humus are responsible for absence or presence of certain type of microorganisms and their activity. For example activity and presence of nitrogen fixing bacteria is greatly influenced by the availability of molybdenum and absence of available phosphate restricts the growth of Azotobacter.

11. Microbial associations / interactions: Microorganisms interact with each other giving rise to antagonistic or symbiotic interactions. The association existing between one organism and another whether of symbiotic or antagonistic influences the population and activity of soil microbes to a great extent. The predatory habit of protozoa and some mycobacteria which feed on bacteria may suppress or eliminate certain bacteria. On the other hand, the activities of some of the microorganisms are beneficial to each other. For instance organic acids liberated by fungi, increase in oxygen by the activity of algae, change in soil reaction etc. favors the activity or bacteria and other organisms in soil.

12. Root Exudates: In the soil where plants are growing the root exudates also affects the distribution, density and activity of soil microorganism. Root exudates and sloughed off material of root surfaces provide an abundant source of energy and nutrients and thus directly or indirectly influence the quality as well as quantity of microorganisms in the rhizosphere region. Root exudates contain sugars, organic acids, amino acids, sterols, vitamins and other growth factors which have the profound effect on soil microbes.

Rhizosphere Concept and It’s Historical Background

The root system of higher plants is associated not only with soil environment composed of inorganic and organic matter, but also with a vast community of metabolically active microorganisms. As living plants create a unique habitat around the roots, the microbial population on and around the roots is considerably higher than that of root free soil environment and the differences may be both quantitative and qualitative.

1. Rhizosphere: It is the zone/region of soil immediately surrounding the plant roots together with root surfaces, or it is the region where soil and plant roots make contact, or it is the soil region subjected to influence of plant roots and characterized by increased microbial.

2. Rhizoplane: Root surface along with the closely adhering soil particles is termed as rhizoplane.

Historical Background:

Term "Rhizosphere" was introduced for the first time by the German scientist Hiltner (1904) to denote that region of soil which is subjected to the influence of plant roots. The concept of "Rhizosphere Phenomenon" which shows the mutual interaction of roots and microorganisms was came into existence with the work of Starkey et al (1929), Clark (1939) and Rauath and Katznelson (1957).

N. V. Krassinikov (1934) found that free living nitrogen-fixing bacteria, Azotobacter were unable to grow in the wheat rhizosphere.

Starkey (1938) examined the rhizosphere region of some plant species and demonstrated the effect of root exudates on the predominance of bacterial population in particular and other soil microorganisms in general in the rhizosphere region. Thus, he put forth the concept of "Rhizosphere effect / phenomenon" for the first time.

F E Clark (1949) introduced / coined the term "Rhizoplane” to denote the root surface together with the closely adhering soil particles.

R. I. Perotti (1925) suggested the boundaries of the rhizosphere region and showed that it was bounded on one side by the general soil region (called as Edaphosphere) and on the other side by the root tissues (called Histosphere).

G. Graf and S. Poschenrieder (1930) divided the rhizosphere region into two general areas i.e. outer rhizosphere and inner rhizosphere for the purpose of describing the same site of microbial action.

H. Katznelson (1946) suggested the R:S ratio i.e. the ratio between the microbial population in the rhizosphere (R) and in the soil (S) to find out the degree or extent of plant roots effect on soil microorganisms. R: S ratio gives a good picture of the relative stimulation of the microorganisms in the rhizosphere of different plant species.

R: S ratio is defined as the ratio of microbial population per unit weight of rhizosphere soil (R), to the microbial population per unit weight of the adjacent non-rhizosphere soil (S)

A. G. Lochhead and H. Katznelson (1940) examined in detail the qualitative differences between the microflora of the rhizosphere and microflora of the non-rhizosphere region and reported that gram-negative, rod shaped and non-spore forming bacteria are abundant in the rhizosphere than in the non-rhizosphere soil

C. Thom and H. Humfeld (1932) found that corn roots in acidic soils yielded predominantly Trichoderma while roots from alkaline soils mainly contained Penicillium.

M J. Timonin (1940) reported some differences in the fungal types and population in the rhizosphere of cereals and legumes. R: S ratio of fungal population was believed to be narrow in most of the plant species, usually not exceeding 10.

E. A. Peterson and others (1958) reported that the plant age and soil type influence the nature of fungal flora in the rhizosphere, and the number of fungal population gradually increases with the age of plant.

M. Adati (1932) studied many crops and found that though actinomycetes were relatively less stimulated than bacteria, but in some cases the R: S ratio of actinomycetes was as high as 62.

R. Venkatesan and G. Rangaswami (1965) studied the rhizosphere effect in rice plant on bacteria, actinomycetes and fungi and reported that (i) for actinornycetes R: S was more (ranging from 0 to 25) depending on the age of plant roots and the dominant genera reported were Nocardia, (ii) R:S ratio reduced with the depth of soil.

E. A. Gonsalves and V. S. Yalavigi (1960) reported the presence of greater number of algae in the rhizosphere

J. W. Rouatt et al reported positive rhizosphere effect on protozoa, but a negative effect on algae in wheat plants.

Microorganisms in the Rhizosphere and Rhizosphere Effect

The rhizosphere region is a highly favorable habitat for the proliferation, activity and metabolism of numerous microorganisms. The rhizosphere microflora can be enumerated intensively by microscopic, cultural and biochemical techniques. Microscopic techniques reveal the types of organisms present and their physical association with the outer root tissue surface / root hairs. The cultural technique most commonly followed is "serial dilution and plate count method" which reveal the quantitative and qualitative population of microflora. At the same time, a cultural method shows the selective enhancement of certain categories of bacteria. The biochemical techniques used are designed to measure a specific change brought about by the plant or by the microflora. The rhizosphere effect on most commonly found microorganisms viz. bacteria, actinomycetes, fungi, algae and protozoa is being discussed herewith in the following paragraphs.

A. Bacteria:
The greater rhizosphere effect is observed with bacteria (R: S values ranging from 10-20 or more) than with actinomycetes and fungi. Gram-negative, rod shaped, non-sporulating bacteria which respond to root exudates are predominant in the rhizosphere (Pseudomonas, Agrobacterium). While Gram-positive, rods, Cocci and aerobic spore forming (Bacillus, Clostridium) are comparatively rare in the rhizosphere. The most common genera of bacteria are: Pseudomonas, Arthrobacter, Agrobacterium, Alcaligenes, Azotobacter, Mycobacterium, Flavobacter, Cellulomonas, Micrococcus and others have been reported to be either abundant or sparse in the rhizosphere. From the agronomic point of view, the abundance of nitrogen fixing and phosphate solubilizing bacteria in the rhizosphere assumes a great importance. The aerobic bacteria are relatively less in the rhizosphere because of the reduced oxygen levels due to root respiration. The bacterial population in the rhizosphere is enormous in the ranging form 10^8 to 10^9 per gram of rhizosphere soil. They cover about 4-10% of the total root area occurring profusely on the root hair region and rarely in the root tips. There is predominance of amino acids and growth factors required by bacteria, are readily provided by the root exudates in the region of rhizosphere.

B. Fungi:
In contrast to their effects on bacteria, plant roots do not alter / enhance the total count of fungi in the rhizosphere. However, rhizosphere effect is selective and significant on specific fungal genera (Fusarium, Verticillium, Aspergillus and Penicillium) which are stimulated. The R:S ratio of fungal population is believed to be narrow in most of the plants, usually not exceeding to 10. The soil / serial dilution and plating technique used for the enumeration of rhizosphere fungi may often give erratic results as most of the spore formers produce abundant colonies in culture media giving a wrong picture / estimate (eg Aspergilli and Penicillia). In fact the mycelial forms are more dominant in the field. The zoospore / forming lower fungi such as Phytophthora, Pythium, Aphanomyces are strongly attracted to the roots in response to particular chemical compounds excreted by the roots and cause diseases under favorable conditions. Several fungi eg Gibberella and fujikurio produces phytohormones and influence the plant growth.

C. Actinomycetes, Protozoa and Algae:
Stimulation of actinomycetes in the rhizosphere has not been studied in much detail so far. It is generally understood that the actinomycetes are less stimulated in the rhizosphere than bacteria. However, when antagonistic actinomycetes increase in number they suppress bacteria. Actinomycetes may also increase in number when antibacterial agents are sprayed on the crop. Among the actinomycete, the phosphate solublizers (eg. Nocardia, Streptomyces) have a dominant role to play.

As rule actinomycetes, protozoa and algae are not significantly influenced by their proximity to the plant roots and their R: S ratios rarely exceed 2 to 3: 1 and around roots of plants, R: S ratio for these microorganisms may go to high. Because of large bacterial community, an increase in the number or activity of protozoa is expected in the rhizosphere. Flagellates and amoebae are dominant and ciliates are rare in the region.

Alterations in Rhizosphere Microflora

Foliar application of various chemicals leads to alterations in the rhizosphere microflora by changing the pattern of root exudates. The pattern of the rhizosphere microflora i.e. numbers and species composition can be changed / altered by various factors, such as: (i) Soil amendments, (ii) Foliar application of fertilizers / nutrients, fungicides, insecticides and hormones and (iii) Bacterization / microbial seed inoculants.

A. Soil amendments:

Soil amendments with inorganic and organic fertilizers can alter the rhizosphere microflora and an understanding of the type of changes in the microflora can be useful in the indirect control of pathogens. Dwivedi and Chaube (1985) showed that amendment of soil with neem-cake can stimulate the activity of actinomycetes which results into the reduction of propagules of Macrophomina phaseolina. It is also known to control phytopathogenic nematodes in soil by stimulating nematode trapping fungi. Amendment of soil with castor and bean leaves stimulate the activity of Trichoderma viride and Penicillium in the rhizosphere leading to the control of Sclerotium rolfsii.

B. Foliar application of fertilizers and agrochemicals:

Translocation of photosynthete from leaves to roots takes place as a part of the normal metabolic activity in plants. Therefore, organic substances, including plant protection chemicals (fungicides, insecticides), growth regulators and plant nutrients applied to foliage / leaves get absorbed into the leaf tissue and further get translocated to roots along with photosynthates. Many workers have reported that foliar application with various chemicals cause marked alterations in the number and kind / qualities of microorganisms in the rhizosphere of several cereals and leguminous crop plants. Thus, such an approach can be used as a new tool in the biological control of root diseases, stimulation of activity of nitrogen-fixing bacteria and other beneficial microorganisms in the soil.

C. Seed treatment with bio inoculants:

Bio inoculants such as Azotobacter, Beijerinckia, Azospirillum, Rhizobium or P -solubilizing microorganisms (eg. Bcillus, plymyxa, Azotobacter croococcum, Aspergillus niger, Penicillium digitatum etc.) When applied to the seed / soil helps in the establishment of beneficial microorganisms in the rhizosphere region which will further benefit in plant growth, encourage inhibition of plant pathogenic organisms in the root vicinity and enrich the soil with added microbial bio-mass.

Factors affecting microbial flora of the Rhizosphere / Rhizosphere Effect

The most important factors which affect / influence the microbial flora of the rhizosphere or rhizosphere effect are: soil type & its moisture, soil amendments, soil PH, proximity of root with soil, plant species, and age of plant and root exudates.

A. Soil type and its moisture: In general, microbial activity and population is high in the rhizosphere region of the plants grown in sandy soils and least in the high humus soils, and rhizosphere organisms are more when the soil moisture is low. Thus, the rhizosphere effect is more in the sandy soils with low moisture content.

B. Soil amendments and fertilizers: Crop residues, animal manure and chemical fertilizers applied to the soil cause no appreciable effect on the quantitative or qualitative differences in the microflora of rhizosphere. In general, the character of vegetation is more important than the fertility level of the soil.

C. Soil PH/ Rhizosphere PH: Respiration by the rhizosphere microflora may lead to the change in soil rhizosphere PH. If the activity and population of the rhizosphere microflora is more, then the PH of rhizosphere region is lower than that of surrounding soil or non-rhizosphere soil. Rhizosphere effect for bacteria and protozoa is more in slightly alkaline soil and for that of fungi is more in acidic soils.

D. Proximity of root with Soil: Soil samples taken progressively closer to the root system have increasingly greater population of bacteria, and actinomycetes and decreases with the distance and depth from the root system. Rhizosphere effect decline sharply with increasing distance between plant root and soil.

E. Plant Species: Different plant species inhabit often some what variable microflora in the rhizosphere region. The qualitative and quantitative differences are attributed to variations in the rooting habits, tissue composition and excretion products. In general, legumes show / produce a more pronounced rhizosphere effect than grasses or cereals. Biennials, due to their long growth period exert more prolonged stimulation on rhizosphere effect than annuals.

F. Age of Plant: The age of plant also alter the rhizosphere microflora and the stage of plant maturity controls the magnitude of rhizosphere effect and degree of response to specific microorganisms. The rhizosphere microflora increases in number with the age of the plant and reaching at peak during flowering which is the most active period of plant growth and metabolism. Hence, the rhizosphere effect was found to be more at the time of flowering than in the seedling or full maturity stage of the plants. The fungal flora (especially, Cellulolytic and Amylolytic) of the rhizosphere usually increases even after fruiting and the onset of senescence due to accumulation of moribund tissue and sloughed off root parts / tissues: whereas, bacterial flora of the rhizosphere decreases after the flowering period and fruit setting.

G. Root / exudates /excretion: One of the most important factors responsible for rhizosphere effect is the availability of a great variety of organic substances at the root region by way of root exudates/excretions. The quantitative and qualitative differences in the microflora of the rhizosphere from that of general soil are mainly due to influences of root exudates. The spectrum of chemical composition root exudates varies widely, and hence their influence on the microflora also varies widely.

Root exudates are composed of the chemical substances like:

Sr. No	Root Executes	Chemical Substances
1	Amino Acids	All naturally occurring amino acids.
2	Organic acids	Acetic, butyric, citric, fumaric, lactic, malic, propionic, succinic etc.
3	Carbohydrates / sugars	Arabinose, fructose, galactose, glucose, maltose, mannose, oligosaccharides, raffinose, ribose, sucrose, xylose etc.
4	Nucleic acid derivatives	Adenine, cystidine, guanine, undine
5	Growth factors (phytohormones)	Biotin, choline, inositol, pyridoxine etc
6	Vitamins	Thiamine, nicotinic acid, biotin etc
7	Enzymes	Amylase, invertase, protease, phosphatase etc.
8	Other compounds	Auxins, glutamine, glycosides, hydrocyanic acid peptides, Uv-absorbing compounds, nematode attracting factors, spore germination stimulators, spore inhibitors etc.

The nature and amount of chemical substances thus exuded are dependent on the species of plant, plant age, inorganic nutrients, and temperature, light intercity, O2 / CO2 level, root injury etc. Another source of nutrients for the microorganisms in the rhizosphere region is the sloughed off root epidermis which exert selective stimulation effect on some specific groups of microorganisms. For instance, glucose and amino acids in the exudates readily attract Gram-negative rods which predominantly colonize the roots. Sugars and amino acids in the root exudates stimulate the germination of chlamydospores and other resting spores of fungi; stimulation effect of root exudates on plant pathogenic fungi, nematodes is also well known.

Alterations in Rhizosphere Microflora

Associative and Antagonistic activities in the Rhizosphere

In natural environments (eg. Soil, Air, Water etc.) a number of relationships exist between individual microbes, microbial species and between individual cells. The composition of microflora of any habitat (soil / rhizosphere) is governed by the biological equilibrium created by the associations and interactions of all individuals found in the community. In soil and rhizosphere region, many microorganisms live in close proximity and their interactions with each other may be associative or antagonistic.

A. Associative interactions / activities in rhizosphere: The dependence of one microorganism upon another for extra-cellular products (eg. amino acids & growth promoting substances) can be regarded as an associative activity / effect in rhizosphere. There is an increase in the exudation of amino acids, organic acids and monosaccharide by plant roots in the presence of microorganisms. Gibberellins and gibberellin- like substances are known to be produced by bacterial genera viz Azotobacter, Arthrobacter, Pseudomonas, and Agrobacterium which are commonly found in the rhizosphere. Microorganisms also influence root hair development, mucilage secretion and lateral root development. Fungi inhabiting the root surface facilitate the absorption of nutrient by the roots.

Mycorrhiza is one of the best known associative / symbiotic interactions which exist between the roots of higher plants and fungi. This mycorrhizal association has been found to improve plant growth through better uptake of phosphorus and zinc from soil, suppression of root pathogenic fungi and nematodes. Another example is association between the bacterium Rhizobium and roots of legumes and Azospirillum with cereal crops (wheat, rye, bajara, maize etc).

B. Antagonistic interactions / activities in rhizosphere: The biochemical qualities of root exudates and the presence of antagonistic microorganisms, plays important role in encouraging or inhibiting the soil borne plant pathogens in the rhizosphere region. Several mutualistic, communalistic, competitive and antagonistic interactions exist in the rhizosphere. The number and qualities of antagonistic microorganisms in the rhizosphere could be increased through artificial means such as fertilizer application, organic amendments, foliar spraying of chemicals etc.

Antagonistic microorganisms in the rhizosphere play an important role in controlling some of the soil borne plant pathogens. Stanier et al (1966) discovered the bacterial strain Pseudomonas fluorescens and the fluorescent pigments of this species in biological control of root pathogens. Strains of P. fluorescence are collectively called as "Fluorescent Pseudomonads". They produce variety of biologically active compounds such as plant growth substances, cyanides, antibiotics and iron chelating substances called "Siderophores" Rovira and Campbell (1975) , showed that bacterial strains of P fluorescens could lyse the hyphae of Gaumannomyces graminis var. Tritici, the causative agent of take-all disease of wheat. Fluorescent pseudomonads (P. fluorescens, P. putida) are known to produce iron chelating substances called Siderophores. These are low molecular weight, extra cellular, iron-binding agents produced by pseudomonads in response to low iron stress or when Fe3 is in short supply. Thus, iron stress triggers the formation of iron-binding ligands called siderophores. Siderophores contains the pigments Pyovirdin (Fluorescent) and Pyocyanin (non-Fluorescent) having iron chelating properties. Another pigment "Pseudobactin" is a fluorescent chelator of iron which is known to promote plant growth and inhibition of pathogenic bacteria in the rhizosphere. An antibiotic called "Pyrrolnitrin" reduces damping-off disease in cotton caused by Rhizoctonia solani. Several species of Bacillus are known to cause mycolysis in the rhizosphere. eg. Fusarium oxysporum hyphae are known to undergo lysis in soil due to these bacterial metabolites.

The successful antagonists among fungi are Trichoderma sp (T. viride and T. harzianum, T. hamatum) and Gliocladium virens which parasitize, lyse or kill the phytopathogenic fungi in the soil. Antifungal and antibacterial actinomycetes in the rhizosphere play an important role in controlling pathogenic fungi and bacteria, for example Micromonospora globosa is a potent antagonist of Fusarium udum causing wilt of pigeon pea. Amoebae are also known to play an antagonistic role in controlling soil fungi, eg. control of take-all disease of wheat caused by Gaumannomyces graminis through the use of Myxamoebae. There can also occur antagonisms between two fungi producing metabolite and interfering the growth of the other fungus as in case of Peniophora antagonizing Heterobasidium.

Rhizosphere in relation to Plant Pathogens

Plant root exudates influence pathogenic fungi, bacteria and nematodes in various ways. The effect may be in the form of attraction of fungal zoospores, or bacterial cells towards the roots; stimulation of germination of dormant spores and hatching of cysts of nematodes. Root exudates may contain inhibitory substances preventing the establishment of pathogens. The balance between the rhizosphere microflora and plant pathogens and soil microflora and plant pathogens is important in host-pathogenic relationship. In this context, the biochemical qualities of root exudates and the presence of antagonistic micro-organisms plays an important role in the proliferation and survival of root infecting pathogens in soil either through soil fungi stasis, inhibition or antibiosis of pathogens in the rhizosphere.

Some of the most common interactions between plant roots and plant pathogenic microorganisms in the rhizosphere are discussed herewith.

A. Zoospore attraction: Amino acids, organic acids and sugars in the root exudates stimulate the movement and attraction of zoospores towards root of the plants. For example attraction of zoospores has been reported in Phytophthora citrophthora (Citrus roots), P. parasitica (tobacco roots) and Pythium aphanidermatum (pea root).

B. Spore germination: The spores or conidia of many pathogenic fungi such as Rhizoctonia, Fusarium, Sclerotium, Pythium, Phytophthora etc. have been stimulated to germinate by the root exudates of susceptible cultivars of the host plants. There are some reports on the selective stimulation of Fusarium, Pseudomonas and root infecting nematodes in the rhizosphere region of the respective susceptible hosts. This stimulus to germination is especially important to those plant pathogens which are not vigorous competitors and remain in resting stage due to shortage of nutrients or fungistasis. As a rule, germination and subsequent hyphal development are promoted by non host species and also by both susceptible and resistant cultivars of the host plants. The quantity and quality of microorganisms present in the rhizosphere of disease resistant crop varieties are significantly different from those of susceptible varieties.

C. Changes in morphology and physiology of host plant: Changes in the physiology and morphology of host plant influence the rhizosphere microflora through root exudations. Hence, significant changes in the rhizosphere microflora of diseased plants were reported which are attributed to the nature and severity of the disease. Systemic virus diseases cause marked changes in the plant morphology and physiology to drastically alter the rhizosphere microflora.

D. Increase in antagonists activity: Root exudates provide a food base for the growth of antagonistic organisms which plays an important role in controlling / suppressing some of the soil borne plant pathogens. Generally, rhizosphere of the resistant plant varieties harboure moer number of Streptomyces and Trichoderma than that of susceptible varieties. For example in the rhizosphere of pigeon pea varieties resistant to Fusarium udum, the population of Streptomyces was found more which inhibited the growth of the pathogen. High density of Trichoderma viride in the rhizosphere of Tomato varieties resistant to Verticillium wilt has been reported with its ability to reduce the severity of wilt in susceptible plants.

E. Inhibition of pathogen: Root exudates containing toxic substances such as glycosides and hydrocyanic acid may inhibit the growth of pathogens in the rhizosphere. It has been reported that root exudates from resistant varieties of Flax (eg. Bison) excrete a glucoside which on hydrolysis produces hydrocyanic acid that inhibits Fusarium oxysporum, the flax root pathogen. Exudates of resistant pea reduce the germination of spores of Fusarium oxysporum.

In this light, the rhizosphere may be considered as a microbiological buffer zone in which the microflora serves to protect the plants against the attack of the pathogens.

F. Attraction of bacteria and nematodes: Root exudates attracts phytopathogenic bacteria and fungi in the rhizosphere for example Agrobacterium tumefaciens have been reported to be attracted to the roots of the host plants like peas, maize, onion, tobacco, tomato and cucumber.

Host root exudates also influence phytopathogenic nematodes in two ways: (i) though stimulation of egg-hatching process and (ii) attraction of larvae towards plant roots.

Soil Microorganisms in Cycling of Elements or Plant Nutrient

Soil microorganisms are the most important agents in the cycling / transformation of various elements (N, P, K, S, Iron etc.) in the biosphere; where the essential elements undergo cyclic alterations between the inorganic state as free elements in nature and the combined state in living organisms. Life on earth is dependent on the cycling of nutrient elements from their elemental states to inorganic compounds to organic compounds and back into their elemental states.

The microbes through the process of biochemical reactions convert / breakdown complex organic compounds into simple inorganic compounds and finally into their constituent elements. This process is known as "Mineralization".

Mineralization of organic carbon, nitrogen, phosphorus, sulphur and iron by soil microorganisms makes these elements available for reuse by plants. In the following paragraphs the cycling / transformations of some of the important elements are discussed.

The four most important cycles are mention below

Nitrogen Cycle
Sulphur Cycle / Sulphur Transformation
Phosphorus Cycle / Transformation
Iron Cycle / Transformation

Nitrogen Cycle

Although molecular nitrogen (N2) is abundant (i.e 78-80 % by volume) in the earth's atmosphere, but it is chemically inert and therefore, can not be utilized by most living organisms and plants. Plants, animals and most microorganisms, depend - on a source of combined or fixed nitrogen (eg. ammonia, nitrate) or organic nitrogen compounds for their nutrition and growth. Plants require fixed nitrogen (ammonia, nitrate) provided by microorganisms, but about 95 to 98 % soil nitrogen is in organic form (unavailable) which restrict the development of living organisms including plants and microorganisms. Therefore, cycling/transformation of nitrogen and nitrogenous compounds mediated by soil microorganisms is of paramount importance in supplying required forms of nitrogen to the plants and various nutritional classes of organisms in the biosphere. In nature, nitrogen exists in three different forms viz. gaseous / gas (78 to 80 % in atmosphere), organic (proteins and amino acids, chitins, nucleic acids and amino sugars) and inorganic (ammonia and nitrates).

Biological N2 Fixation:

A. Symbiotic: Eg. Rhizobium (Eubacteria) legumes, Frankia (Actinomycete) and Anabaena (cyanobacteria) non - legumes

B. Non Symbiotic:

1. Free Living: eg. Azobacter, Derxia, Bejerinkia, Rhodospirillum and BGA.

2. Associative: eg. Azospirillum, Acetobacter, Herbaspirillim.

Nutritional categories of N2 fixing Bacteria

A. Heterotrops

B. Photoautotrophs

Nitrogen cycle is the sequence of biochemical changes form free atmospheric N2 to complex organic compounds in plant and animal tissues and further to simple inorganic compounds (ammonia, nitrate) and eventual release of molecular nitrogen (N2) back to the atmosphere is called "nitrogen cycle".

In this cycle a part of atmospheric nitrogen (N2) is converted into ammonia and then to amino acids (by soil microorganisms and plant-microbe associations) which are used for the biosynthesis of complex nitrogen-containing organic compound such as proteins, nucleic acids, amino sugars etc. The proteins are then degraded to simpler organic compounds viz. peptones and peptides into amino acids which are further degraded to inorganic nitrogen compounds like ammonia, nitrites and nitrates. The nitrate form of nitrogen is mostly used by plants or may be lost through leaching or reduced to gaseous nitrogen and subsequently goes into the atmosphere, thus completing the nitrogen cycle. Thus, the process of mineralization (conversion of organic form of nutrients to its mineral /inorganic form) and immobilization (process of conversion of mineral / inorganic form of nutrient elements into organic form) are continuously and simultaneously going on in the soil.

Several biochemical steps involved in the nitrogen cycle are:
1. Proteolysis
2. Ammonification
3. Nitrification
4. Nitrate reduction and
5. Denitrification.

Nitrogen Cycle: Proteolysis & Ammonification

Several biochemical steps involved in the nitrogen cycle are:

1. Proteolysis
2. Ammonification
3. Nitrification
4. Nitrate reduction and
5. Denitrification.

1. Proteolysis:
Plants use the ammonia produced by symbiotic and non-symbiotic Nitrogen fixation to make their amino acids & eventually plant proteins. Animals eat the plants and convert plant proteins into animal proteins. Upon death, plant and animals undergo microbial decay in the soil and the nitrogen contained in their proteins is released. Thus, the process of enzymatic breakdown of proteins by the microorganisms with the help of proteolysis enzymes is known as “proteolysis".

The breakdown of proteins is completed in two stages. In first stage proteins are converted into peptides or polypeptides by enzyme "proteinases" and in the second stage polypeptides / peptides are further broken down into amino acids by the enzyme "peptidases".

Proteins ------------------------> Peptides ------------------------> Amino Acids
Proteinases Peptidases

The amino acids produced may be utilized by other microorganisms for the synthesis of cellular components, absorbed by the plants through mycorrhiza or may be de animated to yield ammonia.

The most active microorganisms responsible for elaborating the proteolytic enzymes (Proteinases and Peptidases) are Pseudomonas, Bacillus, Proteus, Clostridium Histolyticum, Micrococcus, Alternaria, Penicillium etc.

2. Ammonification (Ammo acid degradation):
Amino acids released during proteolysis undergo deamination in which nitrogen containing amino (-NH2) group is removed. Thus, process of deamination which leads to the production of ammonia is termed as "ammonification". The process of ammonification is mediated by several soil microorganisms. Ammonification usually occurs under aerobic conditions (known as oxidative deamination) with the liberation of ammonia (NH3) or ammonium ions (NH4) which are either released to the atmosphere or utilized by plants ( paddy) and microorganisms or still under favorable soil conditions oxidized to form nitrites and then to nitrates.

The processes of ammonification are commonly brought about by Clostridium sp, Micrococcus sp, Proteus sp. etc. and it is represented as follows.

                                                     Alanine
CH3 CHNH2 COOH + 1/2 O2 -----------------> C H3COCOOH      +      NH3
   Alanine                                    deaminase         Pyruvic acid               ammonia

Nitrogen Cycle: Proteolysis & Ammonification

Several biochemical steps involved in the nitrogen cycle are:

1. Proteolysis
2. Ammonification
3. Nitrification
4. Nitrate reduction and
5. Denitrification.

Proteins ------------------------> Peptides ------------------------> Amino Acids
Proteinases Peptidases

The amino acids produced may be utilized by other microorganisms for the synthesis of cellular components, absorbed by the plants through mycorrhiza or may be de animated to yield ammonia.

The processes of ammonification are commonly brought about by Clostridium sp, Micrococcus sp, Proteus sp. etc. and it is represented as follows.

                                                     Alanine
CH3 CHNH2 COOH + 1/2 O2 -----------------> C H3COCOOH      +      NH3
   Alanine                                    deaminase         Pyruvic acid               ammonia

Nitrogen Cycle: Denitrification

Several biochemical steps involved in the nitrogen cycle are:
1. Proteolysis
2. Ammonification
3. Nitrification
4. Nitrate reduction and
5. Denitrification.

5. Denitrification:

This is the reverse process of nitrification. During denitrification nitrates are reduced to nitrites and then to nitrogen gas and ammonia. Thus, reduction of nitrates to gaseous nitrogen by microorganisms in a series of biochemical reactions is called “denitrification". The process is wasteful as available nitrogen in soil is lost to atmosphere. The overall process of denitrification is as follows:
NaR NiR NoR NoR
Nitrate -----> Nitrite ----> Nitric Oxide ----> Nitrous Oxide ------> Nitrogen gas

This process also called dissimilatory nitrate reduction as nitrate nitrogen is completely lost into atmospheric air. In the soils with high organic matter and anaerobic soil conditions (waterlogged or ill-drained) rate of denitrification is more. Thus, rice / paddy fields are more prone to denitrification.

The most important denitrifying bacteria are Thiobacillus denitrificans, Micrococcus denitrificans, and species of Pseudomonas, Bacillus, Achromobacter, Serrtatia paracoccus etc.

Denitrification leads to the loss of nitrogen (nitrate nitrogen) from the soil which results into the depletion of an essential nutrient for plant growth and therefore, it is an undesirable process / reaction from the soil fertility and agricultural productivity. Although, denitrification is an undesirable reaction from agricultural productivity, but it is of major ecological importance since, without denitrification the supply of nitrogen including N2 of the atmosphere, would have not got depleted and No3 (which are toxic) would have accumulated in the soil and water.

Sulphur Cycle / Sulphur Transformations

Sulphur is the most abundant and widely distributed element in the nature and found both in free as well as combined states. Sulphur, like nitrogen is an essential element for all living systems. In the soil, sulphur is in the organic form (sulphur containing amino acids-cystine, methionine, proteins, polypeptides, biotin, thiamine etc) which is metabolized by soil microorganisms to make it available in an inorganic form (sulphur, sulphates, sulphite, thiosulphale, etc) for plant nutrition. Of the total sulphur present is soil only 10-15% is in the inorganic form (sulphate) and about 75-90 % is in organic form.

Cycling of sulphur is similar to that of nitrogen. Transformation / cycling of sulphur between organic and elemental states and between oxidized and reduced states is brought about by various microorganisms, specially bacteria- Thus “the conversion of organically bound sulphur to the inorganic state by microorganisms is termed as mineralization of sulphur". The sulphur / sulphate, thus released are either absorbed by the plants or escapes to the atmosphere in the form of oxides.

Various transformations of the sulphur in soil results mainly due to microbial activity, although some chemical transformations are also possible (eg. oxidation of iron sulphide) the major types of transformations involved in the cycling of sulphur are:
1. Mineralization 2. Immobilization 3. Oxidation and 4. Reduction

1. Mineralization: The breakdown / decomposition of large organic sulphur compounds to smaller units and their conversion into inorganic compounds (sulphates) by the microorganisms. The rate of sulphur mineralization is about 1.0 to 10.0 percent / year.

2. Immobilization: Microbial conversion of inorganic sulphur compounds to organic sulphur compounds.

3. Oxidation: Oxidation of elemental sulphur and inorganic sulphur compounds (such as h2S, sulphite and thiosulphale) to sulphate (SO4) is brought about by chemoautotrophic and photosynthetic bacteria.

When plant and animal proteins are degraded, the sulphur is released from the amino acids and accumulates in the soil which is then oxidized to sulphates in the presence of oxygen and under anaerobic condition (water logged soils) organic sulphur is decomposed to produce hydrogen sulphide (H2S). H2S can also accumulate during the reduction of sulphates under anaerobic conditions which can be further oxidized to sulphates under aerobic conditions,
                                                             Ionization
a) 2 S + 3O2 + 2 H2 O --------> 2H2SO4 --------------> 2H (+) + SO4 (Aerobic)
                                Light
b) CO2 + 2H2S--------------> (CH2 O) + H2 O + 2 S
                                             Light
OR H2 + S + 2 CO2 + H2 O ---------> H2 SO4 + 2 (CH2 O) (anaerobic)

The members of genus Thiobacillus (obligate chemolithotrophic, non photosynthetic) eg, T. ferrooxidans and T. thiooxidans are the main organisms involved in the oxidation of elemental sulphur to sulphates. These are aerobic, non-filamentous, chemosynthetic autotrophs. Other than Thiobacillus, heterotrophic bacteria (Bacillus, Pseudomonas, and Arthrobacter) and fungi (Aspergillus, Penicillium) and some actinomycetes are also reported to oxidize sulphur compounds. Green and purple bacteria (Photolithotrophs) of genera Chlorbium, Chromatium. Rhodopseudomonas are also reported to oxidize sulphur in aquatic environment.

Sulphuric acid produced during oxidation of sulphur and H: S is of great significance in reducing the PH of alkaline soils and in controlling potato scab and rot diseases caused by Streptomyces bacteria. The formation of sulphate / Sulphuric acid is beneficial in agriculture in different ways : i) as it is the anion of strong mineral acid (H2 SO4) can render alkali soils fit for cultivation by correcting soil PH. ii) solubilize inorganic salts containing plant nutrients and thereby increase the level of soluble phosphate, potassium, calcium, magnesium etc. for plant nutrition.

4. Reduction of Sulphate: Sulphate in the soil is assimilated by plants and microorganisms and incorporated into proteins. This is known as "assimilatory sulphate reduction". Sulphate can be reduced to hydrogen sulphide (H2S) by sulphate reducing bacteria (eg. Desulfovibrio and Desulfatomaculum) and may diminish the availability of sulphur for plant nutrition. This is “dissimilatory sulphate reduction” which is not at all desirable from soil fertility and agricultural productivity view point.

Dissimilatory sulphate-reduction is favored by the alkaline and anaerobic conditions of soil and sulphates are reduced to hydrogen sulphide. For example, calcium sulphate is attacked under anaerobic condition by the members of the genus Desulfovibrio and Desulfatomaculum to release H2 S.

CaSO4 + 4H2 -----------> Ca (OH)2 + H2 S + H2 O.

Hydrogen sulphide produced by the reduction of sulphate and sulphur containing amino acids decomposition is further oxidized by some species of green and purple phototrophic bacteria (eg. Chlorobium, Chromatium) to release elemental sulphur.
                                 Light
CO2 + 2H2 + H2S -----------> (CH2O)       +      H2O     +     2 S.
                                 Enzyme   Carbohydrate                        Sulphur

The predominant sulphate-reducing bacterial genera in soil are Desulfovibrio, Desulfatomaculum and Desulfomonas. (All obligate anaerobes). Amongst these species Desulfovibrio desulfuricans are most ubiquitous, non-spore forming, obligate anaerobes that reduce sulphates at rapid rate in waterlogged / flooded soils. While species of Desulfatomaculum are spore forming, thermophilic obligate anaerobes that reduce sulphates in dry land soils. All sulphate-reducing bacteria excrete an enzyme called “desulfurases” or "bisulphate Reductase". Rate of sulphate reduction in nature is enhanced by increasing water levels (flooding), high organic matter content and increased temperature.

Phosphorus Cycle or Transformation

Phosphorus is only second to nitrogen as a mineral nutrient required for plants, animals and microorganisms. It is a major constituent of nucleic acids in all living systems essential in the accumulation and release of energy during cellular metabolism. This element is added to the soil in the form of chemical fertilizers, or in the form of organic phosphates present in plant and animal residues. In cultivated soils it is present in abundance (i.e. 1100 kg/ha), but most of which is not available to plants, only 15 % of total soil phosphorus is in available form. Both inorganic and organic phosphates exist in soil and occupy a critical position both in plant growth and in the biology of soil.

Microorganisms are known to bring a number of transformations of phosphorus, these include:

(i) Altering the solubility of inorganic compounds of phosphorus,
(ii) Mineralization of organic phosphate compounds into inorganic phosphates,
(iii) Conversion of inorganic, available anion into cell components i.e. an immobilization process and
(iv) Oxidation or reduction of inorganic phosphorus compounds. Of these mineralization and immobilization are the most important reactions / processes in phosphorus cycle.

Insoluble inorganic compounds of phosphorus are unavailable to plants, but many microorganisms can bring the phosphate into solution. Soil phosphates are rendered available either by plant roots or by soil microorganisms through secretion of organic acids (eg. lactic, acetic, formic, fumaric, succinic acids etc). Thus, phosphate-dissolving / solubilizing soil microorganisms (eg. species of Pseudomonas, Bacillus, Micrococcus, Mycobacterium, Flavobacterium, Penicillium, Aspergillus, Fusarium etc.) plays important role in correcting phosphorus deficiency of crop plants. They may also release soluble inorganic phosphate (H2PO4), into soil through decomposition of phosphate-rich organic compounds.

Solubilization of phosphate by plant roots and soil microorganisms is substantially influenced by various soil factors, such as PH, moisture and aeration.

In neutral or alkaline soils solubilization of phosphate is more as compared to acidic soils. Many phosphates solubilizing microorganisms are found in close proximity of root surfaces and may appreciably enhance phosphate assimilation by higher plants.

By their action, fungi bacteria and actinomycetes make available the organically bound phosphorus in soil and organic matter and the process is known as mineralization. On the other hand, certain microorganisms especially bacteria assimilate soluble phosphate and use for cell synthesis and on the death of bacteria, the phosphate is made available to plants. A fraction of phosphate is also lost in soil due to leaching. One of the ways to correct deficiency of phosphorus in plants is to inoculate seed or soil with commercial preparations (eg. Phosphobacterin) containing phosphate - solubilizing microorganisms along with phosphatic fertilizers.

Mineralization of phosphate is generally rapid and more in virgin soils than cultivated land. Mineralization is favored by high temperatures (thermophilic range) and more in acidic to neutral soils with high organic phosphorus content. The enzyme involved in mineralization (cleavage) of phosphate from organic phosphorus compound is collectively called as “Phospatases".

The commercially used species of phosphate solubilizing bacteria and fungi are: Bacillus polymyxa, Bacillus megatherium. Pseudomonas strita, Aspergillus, Penicllium avamori and Mycorrhiza

Iron Cycle or Transformation

Iron exists in nature either as ferrous (Fe++) or ferric (Fe+++) ions. Ferrous iron is oxidized spontaneously to ferric state, forming highly insoluble ferric hydroxide. Plants as well as microorganisms require traces of iron, manganese copper, zinc, molybdenum, calcium boron, cobalt etc. Iron is always abundant in terrestrial habitats, and it is oftenly in an unavailable form for utilization by plants and leads to the serious deficiency in] plants.

Soil microorganisms play important role in the transformations of iron in al number of distinctly different ways such as:

Certain bacteria oxidize ferrous iron to ferric state which precipitate as ferric hydroxide around cells
Many heterotrophic species attack on in soluble organic iron salts and convert into inorganic salts
Oxidation-reduction potential decreases with microbial growth and which leads to the formation of more soluble ferrous iron from highly insoluble ferric ions
Number of bacteria and fungi produce acids such as carbonic, nitric, Sulphuric and organic acids which brings iron into solution
Under anaerobic conditions, the sulfides formed from sulphate and organic sulphur compounds remove the iron from solution as ferrous sulfide
As microbes liberate organic acids and other carbonaceous products of metabolism which results in the formation of soluble organic iron complex. Thus, iron may be precipitated in nature and immobilized by iron oxidizing bacteria under alkaline soil reaction and on the other hand solubilization of iron may occur through acid] formation.

Some bacteria are capable of reducing ferric iron to ferrous which lowers the oxidation-reduction potential of the environment (eg. Bacillus, Clostridium, Klebsiella etc). However, some chemoautotrophic iron and sulphur bacteria such as Thiobacillus ferroxldans and Ferrobacitlus ferrooxidans can oxidize ferrous iron to ferric hydroxide which accumulates around the cells.

Most of the aerobic microorganisms live in an environment where iron exists in the oxidized, insoluble ferric hydroxide form. They produce iron-binding compounds in order to take up ferric iron. The iron-binding or chelating compounds / ligands produced by microorganisms are called "Siderophores". Bacterial siderophores may act as virulence factors in pathogenic bacteria and thus, bacteria that secrete siderophores are more virulent than non- siderophores producers. Therefore, siderophore producing bacteria can be used as biocontrol agents eg. Fluorescent pseudomonads used to control Pythium, causing damping-off diseases in seedlings. Recently Vascular - Arbusecular – Mycorrhiza (VAM) has been reported to increase uptake of iron.

Composition of Organic Matter

Soil organic matter plays important role in the maintenance and improvement of soil properties. It is a dynamic material and is one of the major sources of nutrient elements for plants. Soil organic matter is derived to a large extent from residues and remains of the plants together with the small quantities of animal remains, excreta, and microbial tissues. Soil organic matter is composed of three major components i.e. plants residues, animal remain and dead remains of microorganisms. Various organic compounds are made up of complex carbohydrates, ( Cellulose, hemicellulose, starch) simple sugars, lignins, pectins, gums, mucilages, proteins, fats, oils, waxes, resins, alcohols, organic acids, phenols etc. and other products. All these compounds constituting the soil organic matter can be categorized in the following way.

Organic Matter (Undecomposed)

Organic:

Nitrogenous:

Water Soluble eg. Nitrates, ammonical compounds, amides, amino acids etc.
Insoluble eg. Proteins nucleoproteins, peptides, alkaloids purines, pyridines chitin etc.

Non Nitrogenous:

Carbohydrates eg. Sugars, starch, hemicellulose, gums, mucilage, pectins, etc.
Micellaneous: eg. Lignin, tannins, organic acid, etc.
Ether Solube: eg. Fats, oils, wax etc.

Inorganic

The organic complex / matter in the soil is, therefore made up of a large number of substances of widely different chemical composition and the amount of each substance varies with the type, nature and age of plants. For example cellulose in a young plant is only half of the mature plants; water-soluble organic substances in young plants are nearly double to that of older plants. Among the plant residues, leguminous plants are rich in proteins than the non-leguminous plants. Grasses and cereal straws contain greater amount of cellulose, lignin, hemicelluloses than the legumes and as the plant gets older the proportion of cellulose, hemicelluloses and lignin gets increased. Plant residues contain 15-60% cellulose, 10-30 % hemicelluslose, 5-30% lignin, 2-15 % protein and 10% sugars, amino acids and organic acids. These differences in composition of various plant and animal residues have great significance on the rate of organic matter decomposition in general and of nitrification and humification (humus formation) in particular. The end products of decomposition are CO2, H2O, NO3, SO4, CH4, NH4, and H2S depending on the availability of air.

Factors Influencing rate of Organic Matter Decomposition

In addition to the composition of organic matter, nature and abundance of microorganisms in soil, the extent of C, N, P and K., moisture content of the soil and its temperature, PH, aeration, C: N ratio of plant residues and presence/absence of inhibitory substances (e.g. tannins) etc. are some of the major factors which influence the rate of organic matter decomposition.

As soon as plant and animal residues are added to the soil, there is a rapid increase in the activity of microorganisms. These are not true soil organisms, but they continue their activity by taking part in the decomposition of organic matter and thereby release of plant nutrients in the soil. Bacteria are the most abundant organisms playing important role in the decomposition of organic matter. Majority of bacteria involved in decomposition of organic matter are heterotrophs and autotrophs are least in proportion which are not directly involved in organic matter decomposition. Actinomycetes and fungi are also found to play important role in the decomposition of organic matter. Soil algae may contribute a small amount of organic matter through their biomass but they do not have any active role in organic matter decomposition. The various microorganisms involved in the decomposition of organic matter are listed in the following table.

Constituents	Microorganisms
Constituents	Bacteria	Fungi	Actinomycetes
Cellulose	Achromobacter, Bacillus, Cellulomonas, Cellvibrio, Clostridium, Cytophaga, Vibrio Pseudomonas, Sporocytophaga etc.	Aspergillus, Chaetomium, Fusarium, Pencillium Rhizoctonia, Rhizopus, Trichoderma, Verticilltttm.	Micromonospora, Nocardia Streptomyces, Thermonospora
Hemicellulose	Bacillus, Achromobacter, Cytophaga Pseudomonas, Erwinia, Vibrio, Lactobacillus	Aspergillus, Fusarium, Chaetomium, Penicillium, Trichoderma, Humicola	Streptomyces, Actinomycetes
Lignin	Flavobacterium, Pseudomonas, Micrococcus, Arthorbacter, Xanthomonas	Humicola, Fusarium Fames, Pencillium, Aspergillus, Ganoderma	Streptomyces, Nocardia
Starch	Achromobacter, Bacillus, Clostridium	Fusarium, Fomes, Aspergillus, Rhizopus	Micromonospora, Nocardia, Streptomyces,
Pectin	Bacillus, Clostridium, Pseudomonas	Ftisarium, Verticillum
Chitin	Bacillus, Achromobacter, Cytophaga, Pseudomonas	Mucor, Fusarium, Aspergillus, Trichoderma	Streptomyces, Nocardia, Micromanospora
Proteins & Nucleic acids	Bacillus, Pseudomonas, Clostriddum, Serratia, Micrococcus	Penicillium, Rhodotorula,	Streptomyces

a) Aeration: Good aeration is necessary for the proper activity of the microorganisms involved in the decomposition of organic matter. Under anaerobic conditions fungi and actinomycetes are almost suppressed and only a few bacteria (Clostridium) take part in anaerobic decomposition. The rate of decomposition is markedly retarded. It was found that under aerobic conditions 65 percent of the total organic matter decomposes during six months, while under anaerobic conditions only 47 percent organic matter can be decomposed during the same period. Anaerobic decomposition of organic matter results into the production of large quantity of organic acids and evolution of gases like methane (CH 4) hydrogen (H2) and carbon dioxide (CO2).

b) Temperature: The rate of decomposition is more rapid in the temperature range of 30° to 40°' At temperatures below or above this range, the rate of decomposition is markedly retarded. Appreciable organic mater decomposition occurs at 25° C and further fluctuation in the soil temperature has little effect on decomposition.

c) Moisture: Adequate soil moisture i.e. about 60 to 80 percent of the water-holding capacity of the soil is must for the proper decomposition of organic matter. Too much moisture leads to insufficient aeration which results in the reduced activity of microorganisms and there by checks the rate of decomposition.

d) Soil PH/soil reaction: Soil PH affects directly the kind, density and the activity of fungi, bacteria & actinomycetes involved in the process of decomposition and thereby rate of decomposition of organic matter. The rate of decomposition is more in neutral soils than that of acidic soils. Therefore, treatment of acid soils with lime can accelerate the rate of organic matter decomposition.

e) C: N ratio: C: N ration of organic matter has great influence on the rate of decomposition. Organic matter from diverse plant-tissues varies widely in their C: N ratio (app. 8-10 %). The optimum C: N ratio in the range of 20-25 is ideal for maximum decomposition, since a favorable soil environment is created to bring about equilibrium between mineralization and immobilization processes. Thus, a low nitrogen content or wide C'.N ratio results into the slow decomposition. Protein rich, young and succulent plant tissues are decomposed more rapidly than die protein-poor, mature and hard plant tissues. Therefore, C:N ratio of organic matter as well as soil should be narrow/less for better and rapid decomposition. Thus, high aeration, mesophilic temperature range, optimum moisture, neutral/alkaline soil reaction and narrow C: N ratio of soil and organic matter are required for rapid and better decomposition of organic matter.

Microbiology of decomposition of various constituents in organic matter

When plant and animal residues are added to the soil, the various constituents of the soil organic matter are decomposed simultaneously by the activity of microorganisms and carbon is released as CO2, and nitrogen as NH4 —>NO3 for the use by plants. Other nutrients are also converted into plant usable forms. This process of release of nutrients from organic matter is called mineralization. The insoluble plant residues constitute the part of humus and soil organic matter complex. The final product of aerobic decomposition is CO2 and that of anaerobic decomposition are Hydrogen, ethyl alcohol (CH4), various organic acids and carbon dioxide (CO2). Soil organisms use organic matter as a source of energy and food.

The process of decomposition is initially fast, but slows down considerably as the supply of readily decomposable organic matter gets exhausted. Sugars, water-soluble nitrogenous compounds, amino acids, lipids, starches and some of the hemicellulases are decomposed first at rapid rate, while insoluble compounds such as cellulose, hemicellulose, lignin, proteins etc. which forms the major portion of organic matter are decomposed later slowly. Thus, the organic matter added to the soil is converted by oxidative decomposition to simpler substances which are made available in stages for plant growth and the residue is transformed into humus.

The microbiology of decomposition/degradation of some of the major constituents (viz. Cellulose, Hemicellulose, Lignin, Proteins etc.) of soil organic matter/plant residues are discussed in brief in the following paragraphs.

a) Decomposition of Cellulose: Cellulose is the most abundant carbohydrate present in plant residues/organic matter in nature. When cellulose is associated with pentosans (eg. xylans & mannans) it undergoes rapid decomposition, but when associated with lignin, the rate of decomposition is very slow. The decomposition of cellulose occurs in two stages: (i) in the first stage the long chain of cellulase is broken down into cellobiase and then into glucose by the process of hydrolysis in the presence of enzymes cellulase and cellobiase, and (ii) in second stage glucose is oxidized and converted CO2 and water.

Cellulase Cellobiase
1. Cellulose ----------------> Cellobiose ------------------> Glucose
Hydrolysis hydrolysis

Oxidation Oxidation
2. Glucose ---------------> Organic Acids --------------> CO2 + H2O

The intermediate products formed/released during enzymatic hydrolysis of cellulose (eg. cellobiose and glucose) are utilized by the cellulose-decomposing organisms or by other organisms as source of energy for biosynthetic processes. The cellulolytic microorganisms responsible for degradation of cellulose through the excretion of enzymes (cellulase & Cellobiase) are fungi, bacteria and actinomycetes.

b) Decomposition of Hemicelluloses: Hemicelluloses are water-soluble polysaccharides and consists of hexoses, pentoses, and uronic acids and are the major plant constituents second only in quantity of cellulose, and sources of energy and nutrients for soil microflora.

When subjected to microbial decomposition, hemicelluloses degrade initially at faster rate and are first hydrolyzed to their component sugars and uronic acids. The hydrolysis is brought about by number of hemicellulolytic enzymes known as "hemicellulases" excreted by the microorganisms. On hydrolysis hemicelluloses are converted into soluble monosaccharide/sugars (eg. xylose, arabinose, galactose and mannose) which are further convened to organic acids, alcohols, CO2 and H2O and uronic acids are broken down to pentoses and CO2. Various microorganisms including fungi, bacteria and actinomycetes both aerobic and anaerobic are involved in the decomposition of hemicelluloses.

c) Lignin Decomposition: Lignin is the third most abundant constituent of plant tissues, and accounts about 10-30 percent of the dry matter of mature plant materials. Lignin content of young plants is low and gradually increases as the plant grows old. It is one of the most resistant organic substances for the microorganisms to degrade however certain Basidiomycetous fungi are known to degrade lignin at slow rates. Complete oxidation of lignin result in the formation of aromatic compounds such as syringaldehydes, vanillin and ferulic acid. The final cleavages of these aromatic compounds yield organic acids, carbon dioxide, methane and water.

d) Protein Decomposition: Proteins are complex organic substances containing nitrogen, sulphur, and sometimes phosphorus in addition to carbon, hydrogen and oxygen. During the course of decomposition of organic matter, proteins are first hydrolyzed to a number of intermediate products eg. Proteases, peptides etc. collectively known as polypeptides

The intermediate products so formed are then hydrolyzed and broken down ultimately to individual amino acids, or ammonia and amides. The process of hydrolysis of proteins to amino acids is known as “aminization or ammonification”, which is brought about by certain enzymes, collectively known as “proteases” or “proteolytic” enzymes secreted by various microorganisms. Amino acids and amines are further decomposed and converted into ammonia. During the course of ammonification, various organic acids, alcohols, aldehydes etc. are produced which are further decomposed finally to produce carbon dioxide and water.

All types of microorganisms, bacteria, fungi, and actinomycetes are able to bring about decomposition of proteins. In acid soils, fungi are pre-dominant, while in neutral and alkaline soils bacteria are dominant decomposers of proteins.

Ecological Association/Interactions among Soil Microorganisms

Soil is the largest terrestrial ecosystem where a wide variety of relationships exists between different types of soil organisms. The associations existing between different soil microorganisms, whether of a symbiotic or antagonistic nature, influence the activities of microorganisms in the soil. Microflora composition of any habitat is governed by the biological equilibrium created by the associations and interactions of all individuals found in the community. In soil, many microorganisms live in close proximity and interact among them-selves in a different ways. Some of the interactions or associations are mutually beneficial, or mutually detrimental or neutral. The various types of possible interactions/associations occurring among the microorganisms in soil can be: a) beneficial i) mutualism ii) commensalisms and iii) proto-cooperation or b) detrimental / harmful - i) amensalism, ii) antagonism, iii) competition iv) Parasitism and v) predation

a) Beneficial Association/Interactions:

Mutualism (Symbiosis): It is a relationship or a type of symbiosis in which both the interacting organisms/partners are benefited from each other. The way/manner in which benefit is derived depends on the type of interactions. When the benefit is in the term of exchange of nutrients, then the relationship is termed as "syntrophism" (Greek meaning: Syn -mutual and trophe = nourishment), for example, Lichen (association of algae or BGA with fungus) in which algae benefits by protection afforded to it by the fungal hyphae from environmental stresses, while the fungus obtain and use CO2 released by the algae during photosynthesis. Where the blue green algae are the partners in the lichen association, the heterotrophs (Fungus), benefit from the fixed nitrogen by the blue green algae.

Microorganisms may also form mutualistic relationships with plants, for example nitrogen fixing bacteria i.e. Rhizobium growing in the roots of legumes. In this Rhizobium-legume association, Rhizobium bacteria are benefited by protection from the environmental stresses while in turn plant is benefited by getting readily available nitrate nitrogen released by the bacterial partner.

The Anabaena-Azolla is an association between the water fern Azolla and the cyanobacterium Amabaena. This association is of great importance in paddy fields, where nitrogen is frequently a limiting nutrient.

An actinorrhizal symbiosis of actinomycetes, Frankia with the roots of Alnus and Casurina (non-legumes) is common in temperate forest ecosystem for soil nitrogen economy. Another type of symbiotic association which exists between the roots of higher plants and fungus is Mycorrhiza. In this association fungus gets essential organic nutrients and protection form roots of the plants and allows them to multiply and in turn plants uptake phosphorus, nitrogen and other inorganic nutrients made available by the fungus.

2. Commensalisms: In this association one organism/partner in association is benefited by other partner without affecting it. For example, many fungi can degrade cellulose to glucose, which is utilized by many bacteria. Lignin which is major constituent of woody plants and is usually resistant to degradation by most of the microorganisms but in forest soils, lignin is readily degraded by a group of Basidiomycetous fungi and the degraded products are used by several other fungi and bacteria which can not utilize lignin directly. This type of association is also found in organic matter decomposition process.

3. Proto-cooperation: It is mutually beneficial association between two species / partners. Unlike symbiosis, proto-cooperation is not obligatory for their existence or performance of a particular activity. In this type of association one organism favor its associate by removing toxic substances from the habitat and simultaneously obtain carbon products made by the another associate/partner. Nutritional proto-cooperation between bacteria and fungi has been reported for various vitamins, amino and purines in terrestrial ecosystem and are very useful in agriculture. Proto-cooperative associations found beneficial in agriculture are : i) synergism between VAM fungus-legume plants and Rhizobium in which nitrogen fixation and phosphorus availability / uptake is much higher resulting in higher crop yields and improved soil fertility, ii) synergism between PSM-legume plants and Rhizobium and iii) synergism between plant roots and PGPR in rhizosphere where rhizobacteria restrict the growth of phytopathogens on plant roots and secrets growth promoting substances.

b) Detrimental (Harmful) Associations/Interactions:

1. Antagonism: It is the relationship in which one species of an organism is inhibited or adversely affected by another species in the same environment. In such antagonism, one organism may directly or indirectly inhibit the activities of the other. Antagonistic relations are most common in nature and are also important for the production of antibiotics. The phenomenon of antagonism may be categorized into three i.e. antibiosis, competition and exploitation.

In the process of antibiosis, the antibiotics or metabolites produced by one organism inhibits another organism. An antibiotic is a microbial inhibitor of biological origin. Innumerable examples of antibiosis are found in soil. For example, Bacillus Species from soil produces an antifungal agent which inhibits growth of several soil fungi. Several species of Streptomyces from soil produces antibacterial and antifungal antibiotics. Most of the commercial antibiotics such as streptomycin, chloramphenicol, Terramycin and cyclohexamide have been produced from the mass culture of Streptomyces. Thus, species of Streptomyces are the largest group of antibiotic producer’s in soil. Another example of antibiosis is inhibition of Verticillium by Trichoderma, inhibition of Rhizoctonia by a bacterium Bacillus subtilis, inhibition of soil fungus Aspergillus terreus by a bacterium Staphylococcus aureus.

2. Ammensalism: In this interaction /association one partner suppress the growth of other partner by producing toxins like antibiotics and harmful gases like ethylene, HCN, Nitrite etc.

3. Competition: As soil, is inhabited by many different species of microorganisms, there exists an active competition among them for available nutrients and space. The limiting substrate may result in favoring one species over another. Thus, competition can be defined as “the injurious effect of one organism on another because of the removal of some resource of the environment”. This phenomenon can result in major fluctuations in the composition of the microbial population in the soil.

For example, chlamydospores of Fusarium, Oospores of Aphanomyces and conidia of Verticillium dahlae require exogenous nutrients to germinate in soil. But other fungi and soil bacteria deplete these critical nutrients required for spore germination and thereby hinder the spore germination resulting into the decrease in population. Competition for free space has been, reported to suppress the fungal population by soil bacteria. Therefore, organisms with inherent ability to grow fast are better competitors.

4. Parasitism: It is an association, in which one organism lives in or on the body of another. The parasite is dependent upon the host and lives in intimate physical contact and forms metabolic association with the host. So this is a host -parasite relationship in which one (parasite) is benefited while other (host) is adversely affected, although not necessarily killed. Parasitism is widely spread in soil communities, for example, bacteriophages (viruses which attack bacteria) are strict intracellular parasites Chytrid fungi, which parasitize algae, as well as other fungi and plants; there are many strains of fungi which are parasitic on algae, plants, animals parasitized by different organisms, earthworms are parasitized by fungi, bacteria, viruses etc.

5. Predation: Predation is an association / exploitation in which predator organism directly feed on and kills the pray organism. It is one of the most dramatic inter relationship among microorganisms in nature, for example, the nematophagous fungi are the best examples of predatory soil fungi. Species of Arthrobotrytis and Dactylella are known as nematode trapping fungi. Other examples of microbial predators are the protozoa and slime mold fungi which feed on the bacteria and reduce their population. The bacteriophages may also be considered as predators of bacteria.

Soil Microorganisms in Biodegradation of Pesticides and Herbicides

Pesticides are the chemical substances that kill pests and herbicides are the chemicals that kill weeds. In the context of soil, pests are fungi, bacteria insects, worms, and nematodes etc. that cause damage to field crops. Thus, in broad sense pesticides are insecticides, fungicides, bactericides, herbicides and nematicides that are used to control or inhibit plant diseases and insect pests. Although wide-scale application of pesticides and herbicides is an essential part of augmenting crop yields; excessive use of these chemicals leads to the microbial imbalance, environmental pollution and health hazards. An ideal pesticide should have the ability to destroy target pest quickly and should be able to degrade non-toxic substances as quickly as possible.

The ultimate “sink” of the pesticides applied in agriculture and public health care is soil. Soil being the storehouse of multitudes of microbes, in quantity and quality, receives the chemicals in various forms and acts as a scavenger of harmful substances. The efficiency and the competence to handle the chemicals vary with the soil and its physical, chemical and biological characteristics.

1. Effects of pesticides: Pesticides reaching the soil in significant quantities have direct effect on soil microbiological aspects, which in turn influence plant growth. Some of the most important effects caused by pesticides are : (1) alterations hi ecological balance of the soil microflora, (2) continued application of large quantities of pesticides may cause ever lasting changes in the soil microflora, (3) adverse effect on soil fertility and crop productivity, (4) inhibition of N2 fixing soil microorganisms such as Rhizobium, Azotobacter, Azospirillum etc. and cellulolytic and phosphate solubilizing microorganisms, (5) suppression of nitrifying bacteria, Nitrosomonas and Nitrobacter by soil fumigants ethylene bromide, Telone, and vapam have also been reported, (6) alterations in nitrogen balance of the soil, (7) interference with ammonification in soil, (8) adverse effect on mycorrhizal symbioses in plants and nodulation in legumes, and (9) alterations in the rhizosphere microflora, both quantitatively and qualitatively.

2. Persistence of pesticides in soil: How long an insecticide, fungicide, or herbicide persists in soil is of great importance in relation to pest management and environmental pollution. Persistence of pesticides in soil for longer period is undesirable because of the reasons: a) accumulation of the chemicals in soil to highly toxic levels, b) may be assimilated by the plants and get accumulated in edible plant products, c) accumulation in the edible portions of the root crops, d) to be get eroded with soil particles and may enter into the water streams, and finally leading to the soil, water and air pollutions. The effective persistence of pesticides in soil varies from a week to several years depending upon structure and properties of the constituents in the pesticide and availability of moisture in soil. For instance, the highly toxic phosphates do not persist for more than three months while chlorinated hydrocarbon insecticides (eg. DOT, aldrin, chlordane etc) are known to persist at least for 4-5 years and some times more than 15 years.

From the agricultural point of view, longer persistence of pesticides leading to accumulation of residues in soil may result into the increased absorption of such toxic chemicals by plants to the level at which the consumption of plant products may prove deleterious / hazardous to human beings as well as livestock's. There is a chronic problem of agricultural chemicals, having entered in food chain at highly inadmissible levels in India, Pakistan, Bangladesh and several other developing countries in the world. For example, intensive use of DDT to control insect pests and mercurial fungicides to control diseases in agriculture had been known to persist for longer period and thereby got accumulated in the food chain leading to food contamination and health hazards. Therefore, DDT and mercurial fungicides has been, banned to use in agriculture as well as in public health department.

3. Biodegradation of Pesticides in Soil: Pesticides reaching to the soil are acted upon by several physical, chemical, and biological forces. However, physical and chemical forces are acting upon/degrading the pesticides to some extent, microorganism’s plays major role in the degradation of pesticides. Many soil microorganisms have the ability to act upon pesticides and convert them into simpler non-toxic compounds. This process of degradation of pesticides and conversion into non-toxic compounds by microorganisms is known as “biodegradation”. Not all pesticides reaching to the soil are biodegradable and such chemicals that show complete resistance to biodegradation are called “recalcitrant”.

The chemical reactions leading to biodegradation of pesticides fall into several broad categories which are discussed in brief in the following paragraphs.

a) Detoxification: Conversion of the pesticide molecule to a non-toxic compound. Detoxification is not synonymous with degradation. Since a single chance in the side chain of a complex molecule may render the chemical non-toxic.
b) Degradation: The breaking down / transformation of a complex substrate into simpler products leading finally to mineralization. Degradation is often considered to be synonymous with mineralization, e.g. Thirum (fungicide) is degraded by a strain of Pseudomonas and the degradation products are dimethlamine, proteins, sulpholipaids, etc.
C. Conjugation (complex formation or addition reaction): In which an organism make the substrate more complex or combines the pesticide with cell metabolites. Conjugation or the formation of addition product is accomplished by those organisms catalyzing the reaction of addition of an amino acid, organic acid or methyl crown to the substrate, for e.g., in the microbial metabolism of sodium dimethly dithiocarbamate, the organism combines the fungicide with an amino acid molecule normally present in the cell and thereby inactivate the pesticides/chemical.
d) Activation: It is the conversion of non-toxic substrate into a toxic molecule, for eg. Herbicide, 4-butyric acid (2, 4-D B) and the insecticide Phorate are transformed and activated microbiologically in soil to give metabolites that are toxic to weeds and insects.
e) Changing the spectrum of toxicity: Some fungicides/pesticides are designed to control one particular group of organisms / pests, but they are metabolized to yield products inhibitory to entirely dissimilar groups of organisms, for e.g. the fungicide PCNB fungicide is converted in soil to chlorinated benzoic acids that kill plants.

Biodegradation of pesticides / herbicides is greatly influenced by the soil factors like moisture, temperature, PH and organic matter content, in addition to microbial population and pesticide solubility. Optimum temperature, moisture and organic matter in soil provide congenial environment for the break down or retention of any pesticide added in the soil. Most of the organic pesticides degrade within a short period (3-6 months) under tropical conditions. Metabolic activities of bacteria, fungi and actinomycetes have the significant role in the degradation of pesticides.

4. Criteria for Bioremediation / Biodegradation: For successful biodegradation of pesticide in soil, following aspects must be taken into consideration. i) Organisms must have necessary catabolic activity required for degradation of contaminant at fast rate to bring down the concentration of contaminant, ii) the target contaminant must be bioavailability, iii) soil conditions must be congenial for microbial /plant growth and enzymatic activity and iv) cost of bioremediation must be less than other technologies of removal of contaminants.

According to Gales (1952) principal of microbial infallibility, for every naturally occurring organic compound there is a microbe / enzyme system capable its degradation.

5. Strategies for Bioremediation: For the successful biodegradation / bioremediation of a given contaminant following strategies are needed.

a) Passive/ intrinsic Bioremediation: It is the natural bioremediation of contaminant by tile indigenous microorganisms and the rate of degradation is very slow.
b) Biostimulation: Practice of addition of nitrogen and phosphorus to stimulate indigenous microorganisms in soil.
c) Bioventing: Process/way of Biostimulation by which gases stimulants like oxygen and methane are added or forced into soil to stimulate microbial activity.
d) Bioaugmentation: It is the inoculation/introduction of microorganisms in the contaminated site/soil to facilitate biodegradation.
e) Composting: Piles of contaminated soils are constructed and treated with aerobic thermophilic microorganisms to degrade contaminants. Periodic physical mixing and moistening of piles are done to promote microbial activity.
f) Phytoremediation: Can be achieved directly by planting plants which hyperaccumulate heavy metals or indirectly by plants stimulating microorganisms in the rhizosphere.
g) Bioremediation:Process of detoxification of toxic/unwanted chemicals / contaminants in the soil and other environment by using microorganisms.
h) Mineralization: Complete conversion of an organic contaminant to its inorganic constituent by a species or group of microorganisms.

Introduction to Biofertilizers

Biofertilizers are microbial inoculants or carrier based preparations containing living or latent cells of efficient strains of nitrogen fixing, phosphate is solublizing and cellulose decomposing microorganisms intended for seed or soil application and designed to improve soil fertility and plant growth by increasing the number and biological activity of beneficial microorganisms in the soil.

The objects behind the application of Biofertilizers /microbial inoculants to seed, soil or compost pit is to increase the number and biological / metabolic activity of useful microorganisms that accelerate certain microbial processes to augment the extent of availability of nutrients in the available forms which can be easily assimilated by plants. The need for the use of Biofertilizers has arisen primarily due to two reasons i.e. though chemical fertilizers increase soil fertility, crop productivity and production, but increased / intensive use of chemical fertilizers has caused serious concern of soil texture, soil fertility and other environmental problems, use of Biofertilizers is both economical as well as environment friendly. Therefore, an integrated approach of applying both chemical fertilizers and Biofertilizers is the best way of integrated nutrient supply in agriculture.

Organic fertilizers (manure, compost, vermicompost) are also considered as Biofertilizers, which are rendered in available forms due to the interactions of microorganisms or their association with plants. Biofertilizers, thus include i) Symbiotic nitrogen fixers Rhizobium sp. ii) Non-symbiotic, free living nitrogen fixers Azotobacter, Azospirillum etc. iii) BGA-inoculants Azolla-Anabaena, iv) Phosphate solubilizing microorganisms (PSM) Bacillus Pseudomonas, Penicillium Aspergillus etc. v) Mycorrhiza vi) Cellulolytic microorganisms and vii) Organic fertilizers.

Nobbe and Hiltner (1895, USA) produced the first Rhizobium biofertilizer under the brand name “Nitragin” for 17 different legumes.

Role of Biofertilizers in soil fertility and Agriculture

Biofertilizers are known to play a number of vital roles in soil fertility, crop productivity and production in agriculture as they are eco friendly and can not at any cost replace chemical fertilizers that are indispensable for getting maximum crop yields. Some of the important functions or roles of Biofertilizers in agriculture are:

1. They supplement chemical fertilizers for meeting the integrated nutrient demand of the crops.

2. They can add 20-200 kg N/ha year (eg. Rhizobium sp 50-100 kg N/ha year ; Azospirillum , Azotobacter : 20-40 kg N/ha /yr; Azolla : 40-80 kg N/ha; BGA :20-30 kg N/ha) under optimum soil conditions and thereby increases 15-25 percent of total crop yield.

3. They can at best minimize the use of chemical fertilizers not exceeding 40-50 kg N/ha under ideal agronomic and pest-free conditions.

4. Application of Biofertilizers results in increased mineral and water uptake, root development, vegetative growth and nitrogen fixation.

5. Some Biofertilizers (eg, Rhizobium BGA, Azotobacter sp) stimulate production of growth promoting substance like vitamin-B complex, Indole acetic acid (IAA) and Gibberellic acids etc.

6. Phosphate mobilizing or phosphorus solubilizing Biofertilizers / microorganisms (bacteria, fungi, mycorrhiza etc.) converts insoluble soil phosphate into soluble forms by secreting several organic acids and under optimum conditions they can solubilize / mobilize about 30-50 kg P2O5/ha due to which crop yield may increase by 10 to 20%.

7. Mycorrhiza or VA-mycorrhiza (VAM fungi) when used as Biofertilizers enhance uptake of P, Zn, S and water, leading to uniform crop growth and increased yield and also enhance resistance to root diseases and improve hardiness of transplant stock.

8. They liberate growth promoting substances and vitamins and help to maintain soil fertility.

9. They act as antagonists and suppress the incidence of soil borne plant pathogens and thus, help in the bio-control of diseases.

10. Nitrogen fixing, phosphate mobilizing and cellulolytic microorganisms in bio-fertilizer enhance the availability of plant nutrients in the soil and thus, sustain the agricultural production and farming system.

11. They are cheaper, pollution free and renewable energy sources

12. They improve physical properties of soil, soil tilth and soil health in general.

13. They improve soil fertility and soil productivity.

14. Blue green algae like Nostoc, Anabaena, and Scytonema are often employed in the reclamation of alkaline soils.

15. Bio-inoculants containing cellulolytic and lignolytic microorganisms enhance the degradation/ decomposition of organic matter in soil, as well as enhance the rate of decomposition in compost pit.

16. BGA plays a vital role in the nitrogen economy of rice fields in tropical regions.

17. Azotobacter inoculants when applied to many non-leguminous crop plants, promote seed germination and initial vigor of plants by producing growth promoting substances.

18. Azolla-Anabaena grows profusely as a floating plant in the flooded rice fields and can fix 100-150 kg N/ha /year in approximately 40-60 tones of biomass produced,

19. Plays important role in the recycling of plant nutrients.

Quality Control Measures (as per ISI Specifications)

1. Since, Biofertilizers contains live cells, care should be taken during their transportation and storage.

2. They should be kept in a cold place and not exposed to sunlight.

3. Biofertilizers for legumes are crop-specific; therefore, they must be used for the crop for which they are meant.

4. Biofertilizers when used under adverse soil conditions, appropriate remedial measures (liming and use of Gypsum) should be followed.

5. Biofertilizers must be carrier-based

6. Carrier material used should be in form of powder (75-106 micron size.

7. It should contain minimum of 10^8 viable cells of microorganisms /gram of the carrier material on dry weight basis.

8. It should have a minimum period of six months expiry from date of its

9. It should be tree from any contaminant /contamination with other microorganisms.

10. PH should be in the range of 6.0-7.5.

11. It should induce desired beneficial effects on all those crops, species /cultivars listed on the packet before the expiry date.

12. It should be packed in 50-75 micron low density polythene packets

Monday, May 21, 2012

Defination of Soil Microbiology & soil in view of Microbiology

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