Preface Soil is a basic vital component of agriculture. This natural resource has not been fully explored nor exploited with respect to its live components, their enormous biochemical activities and soil processes. The huge hidden world present in soil has yet remained a great mystery although several folds of diversity, versatility, function and biochemical activities of its various components have been explored. These revelations have helped the mankind in improving its standard of living and cultivation practices. Soil microbiology involves wide ranging multidisciplinary fields and in this book information on the fundamental and applied aspects of soil microbiology have been covered in simple comprehensive manner. The book has primarily been aimed at to adequately introduce Soil Microbiology and Biochemistry with thrust on understanding the various microbial processes occurring in soil. The book is expected to be useful to undergraduate and postgraduate students, teachers and researchers dealing with agriculture, horticulture and forestry in general and agricultural microbiology, soil science and environmental sciences in particular. The issues related to soil fertility, microbial ecology and environment, diversity and biochemical activities, soil health, biological nitrogen fixation, phosphorus solubilisation, nutrient cycling, mineral transformations, waste recycling, pesticide-microbe interaction, biofertilizers/ biopesticides, soil protection, plant-soil microbe-continuum and soil biotechnology are some of the aspects dealt comprehensively in this book. Though good knowledge has been accumulated on various processes of mineral transformations occurring in soil, there is urgent need to intensify the efforts to integrate these processes so as to harness maximum dividends from the knowledge generated. These processes have wide role in achieving sustainable crop growth and soil fertility. The book is designed to provide an insight about the current trends and concepts in the field of soil microbiology supported with tables, diagrams and glossary of the terms frequently used in the field. Those desirous to have deep insight in the subject may consult the selected references given in the end of each chapter. I express my sincere thanks to all the colleagues in the S.K. University of Agricultural Sciences & Technology of Kashmir, Shalimar, Srinagar, J&K (SKUAST-K) who one way or the other assisted me in completing this book. I am especially grateful to Dr. Javid A. Wani, Head, Division of Soil Sciences and Dr. M.A. Beig, Dr. Nissar A. Qazi, Dr. Vinay Sagar, Dr. M.D. Shah, Dr. T.A. Shah and Mr. N.A. Ganai of the Division of Plant Pathology, SKUASTK who critically evaluated the manuscript and gave valuable suggestions to improve the manuscript. I am grateful to all Indian expatriate experts serving in the Department of Plant Sciences, Alemaya University, Ethiopia during 1999-2001 whose encouragement prompted my inspiration to proceed ahead with this assignment. Thanks are due to my wife Mrs. Shamima Jahan for endurance and patience and my children, Arbaz Hassan and Andleeb Hassan, for the preparation of neat and beautiful diagrams.

Definition : Soil microbiology is the study of microorganisms living in soil which complete whole or some part of their life cycle in soil. They include both beneficial as well as deleterious microorganisms but as a specialized branch main thrust is laid on their metabolic activities and the role they play in energy flow, cycling of nutrients associated with the primary productivity and soil ecosystem development. Besides, it focuses on environmental impact, whether favourable or unfavourable, on soil microorganisms and the various soil biochemical processes mediated by various microbes. A clear understanding of the interactions between soil microbial communities and elemental soil components is imperative to comprehend total ecosystem function. Atlas and Bartha have defined the soil microbiology as ‘the study of organisms that live in soil; their metabolic activity; their roles in energy flow; their roles in nutrient cycling’. As per Tate soil microbiology involves ‘the study of soil ecosystem which is the product of intricate interactions between physical and chemical matrix of highly variable composition and living communities of all form’.

The plant roots, soil animals and microorganisms make up soil biological communities, accelerate biochemical activities through intra- and extra-cellular enzymes and interact in such a manner that biogeochemical cycling on this earth continues uninterrupted. Without intermeshing vital processes of soil microflora, microfauna and associated mesofauna, the soil would have become a repository of plant residues and animal remains with no facility for recycling the vital nutrients for plant growth, thus halting the whole process of geo-chemical recycling in nature. Though living component rarely makes up more than 4% of the total soil organic carbon, it plays vital role in geochemical recycling, soil development and ecosystem stability.

Soil is the outer loose layer of earth consisting of layers of mineral material (regolith) whose properties differ from one another and these differences are largely due to the variation in biological activities. Soil micro-environment principally comprizes of inorganic particulates (sand, silt and clay) plus certain oxides and hydroxides, plant roots, organic matter, microbial biomass and aqueous and gaseous phases. The uneven distribution of these components provides a great variety of conditions from field to micropores. The interaction of physical and chemical factors contributes to the creation of varied soil habitat and hence determines the composition and activity of soil biota at a particular site and time. Over geological times, microorganisms have had great opportunity to become distributed worldwide. Such growth and development of microorganisms as well as species diversity is of considerable significance. The existing geographic distribution is reflective of long term adaptation of microorganisms to the various environmental conditions. The preferred environment of an organism is usually referred as ‘habitat’.

The study of soil microorganisms involves various complicacies when compared with those of plants or animals aboveground. The complicated heterogeneous environment existing in soil and the varied growth behaviour of microbial populations in soil have necessitated the development of special techniques to study the microbes and their metabolic diversity, individually and holistically without disturbing their natural habitat. With the gradual improvement in microscopy since its discovery in 1667 and also with the greater understanding of the nature of soil microbes and their properties in relation to total ecosystem function, the concept of studying microbes in isolation has enormously changed. Microscopes have helped in magnifying these, otherwise invisible, minute creatures within the limits of naked eyes.

Soil microorganisms in true sense are one of natural safety valves that regulate biogeochemical transformations in soil ecosystem. They act as natural agents for the disposal of organic matter. The various essential biological elements such as C, N, S and P, apart from H and O, form the primary building blocks of cells and their constituent elements are recycled through tiny microorganisms present in soil. More they are in quality and quantity, better recycling is expected by them. The organically bound materials are converted to simpler inorganic forms to complete biological cycle initiated during photosynthesis and other anabolic processes.

Nitrogen ranks fourth element in cell composition after C, H and O. It forms main components of amino acids, the building blocks of peptides and proteins. Besides, it is present in the genetic material of cell as well as in the chlorophyll and cell wall in the form of chitin and mucopeptides. Plant growth in soil is often limited by less supply of nitrogen, therefore a major nutrient limiting factor in crop production. About 26 x 106 Mg N is globally applied to soil each year to enhance crop productivity.

Phosphorus, an essential element, plays a central role in cell metabolism and reproduction. It is a structural component of energy transferring molecules (ATP, ADP and AMP), nucleic acids, coenzymes, phosphoproteins, phospholipids and sugar phosphates. In soils, the phosphorus does not occur as abundantly as nitrogen or potassium. The total phosphorus in an average arable soil is estimated to be about 0.05% (by weight) with an average of approximately 1100 kg P ha-1 (range 200-2000 kg P ha-1). But only a meager proportion (only ~0.1-1.0%) of it is available for use by plants and microorganisms because phosphorus has poor solubility and gets fixed in soil. Not only the native inorganic phosphates but even the added soluble phosphates of fertilizers and manure readily combine with the cations present in soil solution to form low solubility products. Fixation reactions in soils allow only a small fraction (10-15%) of phosphorus fertilizer to be taken up by the plants in the year of its application.

Sulphur in nature follows similar cycle as that of nitrogen and shares many common features with it. In soils, decomposition of organic matter releases major portion of nitrogen and sulphur bound in proteins, as cystine or methionine amino acids, or vitamins, etc. In proteins, on an average, for every 36 atoms of nitrogen one atom of sulphur is present. Mineralization supplies a large fraction of nitrogen and sulphur to the plants. Secondly, both nitrogen and sulphur have several chemical forms under different soil conditions (Table 8.1) and both are subject to microbial reduction. Thirdly, both can enter or leave soil in gaseous form and both are subject to some degree of leaching in the anionic form.

Soil microorganisms immobilize and mineralize various elements to satisfy their growth requirements. The subsequent turnover of microbial biomass also releases several mineral elements. The elements may be released as a result of organic matter decomposition (e.g. during the process of mineralization, ammonification, etc.) or through biological weathering. Other transformations may involve oxidation and reduction of various inorganic ions and compounds which are mostly catalyzed by chemoautotrophic bacteria during oxidation of ammonium, nitrite, sulphur, iron, etc. Such oxidations may also release energy for microbial growth.

Mycorrhizae denote the symbiotic associations between plant roots and fungal mycelia. Literally it means fungal root. In 1840, Vittandini proposed that ‘tree rootlets are nourished by certain fungal mycelia which mantle them’. The first illustrations of mycorrhiza were published in the same year by Robert Hartig. However, in 1885 A.B. Frank coined the term “mykorrhizen” to the mutualistic symbiotic fungal association of roots (‘mykos’ fungus ‘rhizen’ roots). He characterized the sheath-forming fungi on tree as ‘ectotropisch’ (ectotrophic) and those without such compact sheath as ‘endotropisch’ (endotrophic). Fossil records reveal that mycorrhizae are as old as terrestrial plants.

Soil is a living entity having dynamic physico-chemical and biological properties. Besides supporting the growth of various biological communities, it also serves as a medium on which the organic residues, in the form of dead plant and animal or their excretions, are degraded and decomposed. The biological properties to soil are endowed through the interactive activities of plant root, soil microbes and soil animals. The soil organisms live in a constant state of competition and have to struggle hard for their survival. In this struggle some species become dominant and some remain sub-dominant and others perish or remain in very low profile. So a sort of dynamic equilibrium is the net result of wide range of interactions occurring both at organism and population levels amongst different components of soil biota. Many interactions are short-lived and sporadic and others are more stable.

Soil is inhabited by incredibly diverse living microorganisms that are significant to plant growth and development. Soil microorganisms produce a variety of metabolites, probably several thousands, which influence the plant growth either positively or negatively. Therefore, in such a complex situation, identification of any one metabolite or a compound as active phytohormone or phytotoxin is really an uphill task. Appropriate extraction procedure, knowledge about the proper site for its action, appropriate conducive physiological environment and the effective intensity or concentration is of prime importance. Compounds, in general, are inhibitory to growth at higher concentrations but usually stimulatory at lower concentrations. All growth regulators, irrespective of their provenance or structure, may be divided into two groups.

The soil microorganisms thrive on organic matter in soil by feeding readily on soluble substrates and rather slowly on insoluble substrates. Organisms derive carbon and energy during the process of organic matter decomposition and release organically-bound carbon, thereby decrease C :N ratio and utilize nutrients. Any decrease in organic matter content in soil is likely to affect the microbial biomass and their activities thereby influence the soil fertility and productivity. It is, therefore, imperative to recycle the organic matter in soil in whatsoever form it may be. The raw organic matter requires appropriate treatment to boost decomposition process.

In agricultural practices pesticide application is an inevitable factor for maintaining high crop productivity and is currently an integral part of modern farming. Pests (insects, microbes and weeds) cause approximately 20-30% loss in crop production so making pesticide use indispensable for crop protection.   Pesticide : A pesticide may be defined as ‘any agent or chemical or a mixture of chemicals/ substances intended to prevent, destroy, repel or irritate one or more pest populations causing economic loss in crop production’. Worldwide more than 450 active pesticide chemicals formulated into more than 10,000 commercial products are currently used by farmers. The most worrying aspect is that about two-third of the 800 chemicals tested so far have been found involved in causing or promoting tumor in rodents. Yet more than 50,000 synthetic chemicals/formulations remain untested so far.

Boost to crop production has been the ultimate goal of researchers involved in agriculture so as to feed the ever-increasing human and domestic herbivorous animal populations. Crop production is not only constrained by the limited inherent potential of available varieties currently in use, but is also largely affected by the limitations of soil nutrient availability and damages by diseases, insects and weeds. To counter later challenges, augmentation of soil nutrients through use of biofertilizers in integrated nutrient management programmes and restricting the use of chemical pesticide by integrating biopesticides in plant protection programmes has received much attention in recent years because of consumer’s preference for organic food.

Biotechnological research started in early seventies with some impressive discoveries in the field of genetics, microbiology, biochemistry, biology and chemical bioengineering. The amalgamation of these sciences particularly integration of their basic principles and applied aspects gave rise to a new field, completely diverse and versatile in nature, what we call today ‘biotechnology’. Originating from research laboratories in universities, biotechnology rapidly captured the attention of industries as the number of its potential products increased. This newly developed frontier science later found broad application in medical science, pharmaceutical industry, agriculture, veterinary sciences and chemical industry for the welfare of mankind. Biotechnology by definition means ‘any technique that uses living organism or a part thereof to make or modify a product, to improve plant or animal or to develop microorganisms for specific purposes’.

Glossary A A horizon : The surface horizon of a mineral soil having maximum organic matter accumulation, maximum biological activity, and/or eluviation of materials such as iron and aluminum oxides and silicate clays. ABA : Abscisic acid, a terpenoid growth inhibitor synthesized from mevalonate as well as from the fragmentation of carotenoids. Abiogenesis : Spontaneously generation of living organisms from non-living matter. Absorption, active : Movement of ions and water into the plant root as a result of metabolic processes by the roots, frequently against an activity gradient. Absorption, passive : Movement of ions and water into the plant roots as a result of diffusion along a gradient. Acetylene-block method : Estimates denitrification by determining release of nitrous oxide (N2O) from acetylene-treated soil. Acetylene-reduction assay : Estimates nitrogenase activity by measuring the rate of acetylene reduced to ethylene Acid phosphatase : An ectoenzyme involved in phosphorus solubilization Acid rain : Atmospheric precipitation with pH values less than 5.6; the acidity being due to inorganic acids such as nitric and sulphuric acids that are formed when oxides of nitrogen and sulphur are emitted into the atmosphere. Acid soil : A soil with a pH values <6.6; usually applied to surface layer or root zone, but may be used to characterize any horizon. Acidity, active : The activity of hydrogen ion in the aqueous phase of a soil; measured and expressed as a pH value. Acidophile : The microorganisms active in acidic soils with optimum pH range 2.0 to 3.0.