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This textbook is a undergraduate standard Agricultural Microbiology for agricultural students. Microbes may be the most significant life form sharing this planet with plants and animals because of their pervasive presence and their utilization of any available food sources and in other important forms. Beneficial roles of microbes include recycling of organic matter through microbe-induced decay and through digestion and nutrition for the soils helps to the plants. The definition of microbiology, or the study of microorganisms, is frequently given as the study of organisms and agents that are too small to be seen clearly with the unaided eye. Microbiology is primarily concerned with organisms and agents this size and smaller since items less than around one millimetre in diameter cannot be seen properly and must be inspected under a microscope. 

ntroduction Millions of living organisms present in soil make it a living and a dynamic system. Under a microscope, it reveals a complex array of soil particles and pore spaces filled with air and water. In these pore spaces that plant roots and millions of organisms develop, which are ranging from sub-microscopic to macroscopic in size. The physical and chemical characteristics of soil determine the nature of the environment in which vast number of soil microorganisms especially soil microorganisms are found. Living organisms in soils include both macro (earthworms, rodents, termites etc.) and microorganisms (bacteria, fungi, actinomycetes, algae and protozoa). These organisms not only help in the development of soils but also carry out a number of transformations, facilitating the availability of nutrients to the plants.

Introduction The microorganisms exist as single cell or cluster of cells capable of orderly growth, metabolism and reproduction in two identical daughter cells. These includes cellular organisms {protozoa, algae and fungi (Eukaryotes), bacteria and archaea (Prokaryotes)} and viruses (non cellular entities). The study of microorganisms contribute to understanding of : Basic biological sciences - It acts as a tool for providing the basic information for life processes. The discovery of DNA, RNA, proteins and enzyme functions all came from microbial study. Applied biological sciences - Medicine, agriculture, industry, plant and animal pathology, immunology, plant and animal nutrition, biotechnology all have origin from the understanding of the cell function and metabolism of microorganisms.

Introduction The term actinomycetes, coined in the late 1800s (actins, meaning ‘ray’ and myces, meaning ‘fungus’) is a misnomer. Because actinomycetes have a considerably smaller aerial mycelium than fungi and can produce a large number of asexual spores called conidia, which give the colonies a ‘powdery or chalky’ look. The actinomycetes constitute a specialized group of soil bacteria that occur in soils throughout the world. The actinomycetes are prokaryotes confirming cellular structures and functions of true bacteria and their morphological similarity to the fungi (Eukaryotes). Between bacteria and fungi, actinomycetes are a transitional category. On their hyphae, most actinomycetes produce single, pairs, or chains of asexual spores.The diameter of the hyphae varies from 0.5 to 1.0 µm. 

Fungi are a diverse group of multicellular eukaryotic organisms with wide variation in vegetative and reproductive morphologies and diverse life cycles. They are more abundant, on a mass basis, in soils than any other group of microorganisms; their biomass ranges from 500 to 5000 wet kg ha-1 (Metting, 1993). Fungi inhabit almost any niche containing organic substrates, so that they are active participants in ecosystems as - degraders of organic matter agents of disease as well as beneficial symbionts - lichen (algae and fungi), mycorrhizal association

Introduction Soil algae are not as numerous as bacteria, actinomycetes and fungi. Furthermore, these are photosynthetic microorganisms. Recent work has led to a more complete knowledge of the ecology and importance of terrestrial algae. These algae are found abundant in the habitats in which moisture is adequate and light is accessible. Classification Soil algae are classified into four major classes: Cyanophyceae (Blue green algae) Chlorophyceae (Green algae)

Introduction The soil protozoa are unicellular and the simplest forms of animal life. Most of the protozoa are devoid of chlorophyll but transitional genera resemble the algae and possess chloroplasts containing chlorophyll pigments. The active life stage is commonly known as trophozoite phase where they feed and multiply but under adverse climatic conditions, they form resting stage or cyst, which develop a thick coating on the cell surface. Mostly, the protozoa multiply by longitudinal or transverse fission but some species reproduce sexually by fusion of two cells followed by exchange of genetic material between their nuclei and cell division.

Introduction The microbial cells of bacteria, actinomycetes, fungi, algae and protozoa are visible by light microscopy. Beyond the resolution of light microscope are the unique organisms that are sub microscopic and intracellular parasites known as viruses. The term virus is a Latin word means poisonous substance. The viruses are functionally and metabolically different from the cellular organisms as (i) they are infectious agents and contain only one type of nucleic acid encapsulated in a protein coat. Some may possess membranes but do not have any cytoplasm or metabolism of their own. (ii) They are much smaller in size than the smallest bacteria and can pass through bacteriological filters. 

To a soil microorganism, the rhizosphere is like a lush oasis in the desert. In comparison to near-starvation conditions of the bulk soil, the rhizosphere is the place where nutrients are plentiful and microorganisms flourish. The term rhizosphere was first used by Hiltner in 1904 to describe the zone of soil under the influence of roots. The rhizosphere can extend more than 5 mm from the root and is the area of increased microbial activity due to exudation of low molecular weight compounds from root cells. The rhizoplane is the surface of plant root and any strongly adhering soil particles. The microbial populations that colonize the interior of the root and from intimate associations with the root are considered endophytes.

There are two mini-cycles in the soil nitrogen cycle: Soil-based processes such as mineralization, ammonification, nitrification, and immobilisation include the conversion of organic nitrogenous molecules to plant-useable mineral forms, and subsequently back to biomass (microbial, plant and indirectly animal biomass). The process of converting atmospheric nitrogen into forms available to the living components of the ecosystem, i.e. nitrogen fixation and the transformations within the soil, as well as the return of the fixed nitrogen to atmospheric inert forms of nitrogen through denitrification, are all soil and biosphere resident processes.

At the point where ammonium is produced, the reactions involved in organic nitrogen mineralization come to a halt. This most reduced form of inorganic nitrogen is the starting point for the nitrification process, which involves the biological synthesis of nitrate or nitrite from reduced nitrogen molecules. The ability of nitrifying bacteria to create nitrate, which is the primary nitrogen source ingested by higher plants, determines their relevance. Nitrate is formed in a variety of places, including soil, marine environments, manure piles, and sewage treatment, where it is the result of the final stage of turning organic nitrogen inoffensive.

Introduction The various reactions of nitrogen (N2) cycle, transform one form of the element to another. Mineralization liberates nitrogen in inorganic form, immobilization converts its back to an unavailable state, while nitrification changes the nitrogen from a reduced to oxidized state. Certain transformations of nitrogen lead to a net loss of element from the soil through volatilization. For the purpose of crop production, nitrogen volatilization has a deleterious influence because it depletes part of soils reserve of an essential nutrient. The sequence of steps that results in gaseous loss is called denitrification. So denitrification refers to the reduction of nitrates and nitrites to gaseous nitrogen products, principally di-nitrogen and nitrous oxide, coupled to energy production through oxidative phosphorylation.

The excessive and imbalanced use of nitrogenous fertilizers in the last few decades to meet the challenges of growing food demand of Worlds population has led to serious consequences of soil and water pollution, leaching of toxic nitrate into ground water and volatilization of nitrogen oxides into the environment. Therefore, judicious management of nitrogen in the environment is very much essential in the development of more productive and sustainable agriculture. Rapid declining of non-renewable energy sources viz. petroleum products, natural gas as well as energy crisis in the recent days, release of several pollutants during production of fertilizer N has also necessitated the development of alternative and/or supplemental technologies to obtain the fertilizer N for crop production.

Introduction 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. Phosphorus is found in soil, plants and microorganisms in number of organic and inorganic compounds. It is the second major inorganic nutrient after nitrogen in term of quantitative requirement for both crop plants and microorganisms. This element may be added to soil in the form of chemical fertilizers, or it may be incorporated as leaf litter, plant residues or animal remains. 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. Thus, phosphorus occupies a critical position both in plant growth and in the biology of soil.

Introduction In soil, microorganisms influence not only the availability of carbon and nitrogen, which are important constituents of plants, but also of sulfur (S), phosphorus and many other trace elements for plant absorption. Sulphur is found widely distributed and considered as tenth most abundant element in the nature. Sulfur is considered as an essential element for survival of plant and animals and found as gypsum (CaSO4.2H2O), pyrite (FeS2) and other combined form and also in elemental form (S0) in the nature. The requirement of sulphur by plant is comparatively less than the primary nutrients, hence sulfur is recognised as ‘secondary’ nutrient. 

Unlike root-free soil, the rhizosphere around growing plants is a very dynamic environment that hosts a much higher number of microbes, in particular bacteria. Microbes interact with each other and with plants in symbiotic, associative, neutral or antagonistic ways. A plant colonized or penetrated by a microorganism can either result in asymptomatic or disease or form an association or symbiosis, depending on the cells’ perception of each other and how the environment affects that interaction. Microbes that penetrate and colonize plants have developed elaborate strategies to subvert plant defenses.