eChapters

Industrial Microbiology is the discipline that uses micro organisms, usually grown on large scale, to produce commercial products or carry out important chemical transformations.

The products derived from such processes are

1 Alcohols and alcoholic beverages.
2 Production of pharmaceutical agents like antibiotics, vaccines etc.
3 Food additives
4 Enzymes
5 Chemicals
6 Single cell proteins

Genetics is the study of what genes are, how they carry information, how their information is expressed, and how they are replicated and passed to subsequent generations or other organisms.

DNA in cells exists as a double-stranded helix; the two strands are held together by hydrogen bonds between specific nitrogenous base pairs: A-T and C-G.

A gene is a segment of DNA, a sequence of nucleotides, that code for a functional product, usually a protein.

When a gene is expressed, DNA is transcribed to produce RNA; mRNA is then translated into proteins. This is also referred as Central Dogma of Life. The DNA in a cell is replicated before the cell divides, so each daughter cell receives the same genetic information.

Sterilization refers the complete removal or elimination of microorganisms from an environment. Physical and chemical agents are available to remove the microorganisms from the environment. Heat, irradiation and filtration are the three physical agents and various chemicals are available for sterilization.

Terms related to control of microorganisms

Cide or cidal means to kill the microorganism (Ex. Bactericidal refers the killing of bacteria).

Static or stasis means inactivation or inhibition, but not killing. They prevent multiplication of the organism. (Ex. Fungistatic refers the inhibition of growth of fungi.).

Sepsis refers break down of a living tissue by organisms and is accompanied by inflammation and pus formation.

Antispetic is an agent applied externally on living tissues to kill or inhibit the growth of the organisms.

Disinfectant is an agent applied externally on inanimate objects (not living tissues) to destroy harmful pathogens in their vegetative stage.

(Antiseptics are milder than disinfectants because to avoid the side effects)

Sanitation refers removal of organisms from a location by cleaning but not by sterilization.

The essential nutrients and their function in microbial cells

Virus can be defined as a genetic element containing either DNA or RNA that replicates in host cells as intracellular parasites but is characterized by having an extracellular state.

Virus can use the metabolic machinery of the host cell and can modify the genetics of the host cell. Virus has both extracellular and intracellular state.

Extracellular State

Outside the host cell, the virus is a minute particle containing nucleic acid surrounded by protein, which is referred as virions or virus particles. Virions are inert and have no biosynthetic and metabolic functions. Extracellular state or virus particle is the perfect stage of virus to study the morphology and chemistry.

Intracellular State

The active state in which the virus replicate in the host cell. When the virus nucleic acid is introduced to host cell and replication starts, the process is referred as infection. The cell in which infection of virus and replication takes place is referred as host cell.

Proto – first; Zoon – animal

Protozoa are single celled eukaryotic organisms, which lack cell wall and ability to move at some stage of their life cycle.

They are referred as the first animals.

There are about 65000 described species grouped into 7 phyla. Among them, 50 per cent are not available as living forms (as fossils) and out of remaining 50%, 22,000 species are free-living and 10,000 species are parasitic forms.

The protozoa are distinguished from other organisms by following characters

Algae are a large and diverse group of eukaryotic organisms that contain chlorophyll and carry out the oxygenic photosynthesis.

Study of algae is referred as phycology or algalogy

They vary from cyanobacteria or blue green algae by their eukaryotic nature.

Eukaryotic, spore – producing, achlorophyllous organisms with absorptive nutrition that generally reproduce both sexually and asexually and whose thallus is usually filamentous, branched somatic structures known as hyphae, typically surrounded with cell wall.

Mycology – Study of fungi

The fungi can be divided into two groups namely

True fungi: Chytridiomycota, Zygomycota, Ascomycota, Basidiomycota

Additional phyla: Myxomycota, Dictyosteliomycota, Acrasiomycota, Plasmodiophoromycota, Oomycota, Labyrinthulomycota, Hypochitridomycoya.

Size – Shapes - Arrangements – Morphology

Bacteria are very small, most being approximately 0.5 to 1.0 mm diameter. Smallest bacteria are Mycoplasmas, as small as 0.2 micrometers (almost as small as largest poxviruses).

Accepted wisdom is that bacteria are smaller than eukaryotes. But certain cyanobacteria are quite large; Oscillatoria cells are 7 micrometers diameter, size of red blood cells. And certain eukaryotes (e.g. Nanochlorum eukaryotum) are very small, only 1 to 2 micrometers, but true eukaryotes (nucleus, chloroplast, mitochondrion are present). So size difference is, like many generalizations, only a useful yardstick, not an absolute truth.

Epulopiscium fishelsoni, discovered in 1985 in intestinal tract of sturgeonfish, is an enormous, cigar-shaped cell, as large as 80 x 600 micrometers (that’s 0.6 mm, large enough to be seen by the naked eye). Amazingly, this cell is prokaryotic! Initial evidence by EM was hard to believe, but confirmed rRNA comparisons with other organisms, a cousin of Gram-positive Clostridium genus.

The relative size of the bacteria are as follows :

Place of Microorganisms in Living World

Haeckel’s kingdom Protista

E.H. Haeckel, 1866 proposed this concept. Apart from plant and animal kingdom, the third kingdom “Protista” was developed by him. The protista includes unicellular organisms that are typically neither plant nor animal. These organisms, the protists, include bacteria, algae, fungi and protozoa. Bacteria are referred as lower protists and others are called as higher protists.

Whittaker’s five kingdom concept

R.H.Whittaker (1969) proposed the concept of five kingdom. He divided the living things in to 5 kingdoms.

Microscope is an instrument to magnify and enable to see the microorganisms by us.

Microscopes are of two types. Light and Electron microscope.

Basic Principles of light microscope

The light is the primary source on which magnification is performed. The magnification is obtained by a system of optical lenses using light waves. These light microscopes can be further classified into

Obviously human have had to deal with microbes even before the recorded history. The first record of human using microorganisms comes from ancient tablets from mid east.

Babylonians were using yeast to make beer over 8000 years ago and acetic acid bacteria to make vinegar over 6000 years ago. About 5000 years ago, Persia (Now Iran) region recorded the wine making.

The Romans had God for specific microorganisms. The roman God of mold and mildew were “Robigus” and “Robigo” which mean crop rust. (Rust is one of the plant disease caused by fungus). God Robigus was very much feared because of crop lost. About 2000 years ago, Romans proposed that diseases were caused by tiny animals. But, fundamentalist religions had a strong hold over the progress. The real microbiology history starts from 1600s, when people began to make crude lenses and microscopes.

The following are the scientists and their role in the development of microbiology:

Microbiology

Study of microorganisms, a large and diverse group of microscopic organisms, that exist as single cell or cluster. It also includes virus, which are microscopic, but not cellular.

Development of Agriculture in the World and in India

Agricultural ecosystems will increasingly be called on to deliver food and fiber for a demanding and expanding global population. Until recently, increased production relied on expansion of the amount of land under cultivation and irrigation. Since World War II, production advances have relied on genetics and plant breeding, advances in fertilizer and pesticide use and improved cultural management (Matson et al., 1997). Since 1950, agriculture worldwide has expanded cereal production by an average of 2% per annum while population has increased by 1.9% per year (Borlaug and Dowswell, 1994).

Modern science-based agriculture had its beginnings in the late 19^th century with improved traction and tillage equipments. However, it was not until after World War II that the research findings that led to the modern-day productive systems in the United States and later in European and other developed countries. The expansion was directly related to the great demand for food to support the Allied war effort. Knowledge bases developed in plant genetics, physiology and pathology, along with a ten-fold increase in fertilizer use, advances in seed technology, weed control, irrigation and cultural methods allowed the development of the systems that dominate agriculture in many of the countries today. Corn or maize responded dramatically to the advances in production technology. Maize yield in the United States has increased more than 300 per cent over the past 50 years and continues to rise. Maize production technology has been delivered worldwide (Borlaug and Dowswell, 1994).

Agroecology : Agroecology can be defined broadly or narrowly. “Loosely defined, agroecology often incorporates ideas about a more environmentally and socially sensitive approach to agriculture, one that focuses not only on production, but also on the ecological sustainability of the productive system.

or

The science of applying ecological concepts and principles to the design and management of sustainable agroecosystems.

Alternative Farming/Alternative Agriculture : These are essentially synonymous terms encompassing a vast array of practices and enterprises, all of which are considered different from prevailing or conventional agricultural activities. “They include:

Agricultural practices in India remained virtually unchanged for over 2000 years till 1950-60. With technological advancement in medicine and improvement in health care services, population in India substantially increased in the post independence period. The result was that there was acute shortage of food during 1960s and India had to import massive quantities of wheat from USA to avert famine. Most of these food shipments were in the form of aid. It was then that Government of India realised the gravity of situation and invested heavily in agricultural research. Fortunately, during this period food research laboratories in the West developed hybrid varieties of seeds to suit various types of soil and climatic conditions. At the same time new types of fertilizers and pesticides were introduced which showed dramatic increase in the yield. The agricultural research laboratories in India were able to build on this research and provided extension services to adopt new agricultural techniques to farms in India. This led to dramatic improvement in agricultural production which was hailed as “Green Revolution”. Within two decades a country perennially deficient in food and subject to cyclic famines became a food surplus country in spite of the fact that there was a continuous rise in population which doubled in 30 years after independence. This trend continued into 1980’s when Government built huge buffer stocks of wheat and rice to meet the needs during lean production years.

However the momentum of Green Revolution could not be maintained and certain disturbing trends were noticed in 1990s. The growth rate in productivity declined from 2.99 per cent per annum to 1.21 per cent This was not because we had come to a technical plateau our yields of various products are still quite low as compared to those achieved by developed countries and even some of the developing countries.

Leisa

Sustainable agriculture is an important element of the overall effort to make human activities compatible with the demands of the earth’s eco-system. Thus, an understanding of the different approaches to ecological agriculture is necessary if we want to utilise the planet’s resources wisely.

While sustainable agriculture is based on long-term goals but not a specific set of farming practices, it is usually accompanied by a reduction of purchased inputs in favor of managing on-farm resources. A good example is reliance on biologically-fixed nitrogen from legumes versus manufactured nitrogen fertilizers. Low-input agriculture is one of several alternative farming systems whose methods are adaptable to sustainable agriculture.

Low-input farming is based on a reduction—but not necessarily elimination—of chemical fertilizers, insecticides, and herbicides. Farmers are adopting these practices primarily to reduce costs, but also because they want to minimize impact on the environment or because they perceive future pesticide regulations.

In a search for information on how to farm with fewer chemicals, it is helpful to examine alternative farming systems in existence that largely exclude chemicals in favor of biological farming practices. Experiences of producers who have successfully practiced these methods are valuable to farmers considering a transition to low-input sustainable agriculture.

Concept of Agro-ecology

Ecology and environment

The word environment is derived from the French verb environner, which means “encircle” or “surround”. Thus, our environment can be defined as the physical, chemical and biological world that surrounds us, as well as the complex of social and cultural conditions affecting an individual or community. This broad definition includes the natural world and the technological environment, as well as the cultural and social contexts that shape human lives.

The earth is the only known planet habited by man and other life forms, plants and vegetation. Man and nature have lived together and so long as man’s wants were in conformity with nature, there was no problem. But unfortunately, man’s ambition for limitless enjoyment and comfort has led him towards the exploitation of nature’s wealth so indiscriminately and so shamelessly as to reduce nature’s capacity for self stabilization. The indiscriminate exploitation of nature over centuries has created numerous environmental problems. Man’s voracious appetite for resources and his desire to conquer nature has put him on collision course with environment. The demands of his explosive technological society impose intense stress on the state of equilibrium with the environment.

Ecology is the branch of biological science concerned with the relationships and interactions between living organisms and their physical surroundings or environment. Living organisms and the environment with which they exchange materials and energy together make up an ecosystem, which is the basic unit of ecology. An ecosystem includes biotic components – the living plants and animals and abiotic components the air, water, minerals and soil that constitute the environment. A third and essential component of most natural ecosystems is energy, usually in the form of sunlight.

Familiar examples of land based or terrestrial ecosystems include forests, deserts, jungles and medows. Water based or aquatic ecosystems include streams, rivers, lakes, marshes and estuaries. There is no specific limitation on the size or boundaries of an ecosystem. A small pond can be studied as a separate ecosystem, as can a desert comprising hundreds of square kilometers. Even the entire surface of earth can be viewed as an ecosystem; the term biosphere is often used in this context.

Sustainable agriculture can be defined as a tool of using the natural resources for meeting the present needs without jeopardizing the future potential, increasing per capita productivity without causing degradation of soil and water resources, enhancing profitability without reducing total production and reducing excessive dependence on off farm inputs. Thus the holistic view of sustainability is an approach which is ecologically sound, economically profitable and socially equitable. Theoretically this is an ideal concept and of recent origin. But the real danger to sustainable agriculture stem from the compelling needs of increasing population for food, fuel, fodder on one hand and limited natural resource base of land and water on the other.

Characterisation of Natural Resources

The objective of food security can be met by promoting sustainable agricultural production systems. Increasing agricultural production should not be at the cost of degrading soil and depicting the water bodies. If the basic needs of people are to be met on a sustainable basis, the earth’s natural resource base must be conserved and enhanced. In other words, for food security and sustainable livelihoods, ecological security is necessary. Areas under ecological stress need attention, pressure on natural resources increases with population increase in order to fulfill the demand.

A systems perspective is essential in understanding sustainability. The system is envisioned in its broadest sense i.e., from the individual farm to the local ecosystem and to communities affected by this farming system both locally and globally. An emphasis on the system allows a longer and thorough view of the consequences of farming practices on both human communities and the environment. A systems approach gives us the tools to explore the interconnections between farming and other aspects of our environment.

Towards Sustainability

Sustainability means preserving human life on Earth. Meeting human needs is thus vital in creating a sustainable society. It follows that one of The Natural Step’s principles of sustainability is to meet human needs worldwide.

The concept of multiple dimensions of a sustainable agriculture is more broad which has to be viewed with awareness of potential technologies, fragile ecosystem and human interference to disrupt with limited resource availability. All these aspects have to be taken into account for proper understanding of sustainable agriculture.

The major aspects are,

1. Agriculture must be increasingly productive and efficient in resource use.
2. Biological processes within agriculture systems must be controlled from within (rather than by external inputs of pesticides) and
3. Nutrient cycles within the farm must be closed.

Within this frame work a sustainable model has to be developed. The proposed concept of sustainable agriculture which is best suited for developing and developed countries and is a viable model for the present and future is depicted schematically (Fig. 1).

In its purest form sustainable agriculture would be a complete reversion to subsistence agriculture relying on organic wastes and manures within farms without applying

Preserving the productivity of agricultural land over a long term requires sustainable food production. Sustainability is achieved through alternative agricultural practices informed by in-depth knowledge of the ecological processes occurring in farm fields and the larger landscape of which they are a part. From this foundation, we can move towards the social and economic changes that promote sustainability of all sectors of the food system. Sustainability means different things to different people, but there is a general agreement that it has an ecological basis.

In recent years, all eyes seem to be focused on visions of the future. High-tech, bio-tech, and info-tech are the key words most frequently used among those who are concerned with future agriculture development. Many also forecast increasing vertical integration of production, processing distribution functions-including activities from molecular level to consumer preference i.e. from seed to table, thus increasing dependence on biotechnology and information technology at all levels in world agriculture.

Conventional farming systems vary from farm to farm and from country to country. However, they share many common characteristics viz.,rapid technological innovation; large capital investments in order to apply production and management technology; large-scale farms; single crops/ row crops grown continuously over many seasons; uniform high-yielding hybrid crops; extensive use of pesticides, fertilizers, and external energy inputs; high labour efficiency; and dependency on agribusiness. In the case of livestock, most production comes from confined, concentrated systems.

Agricultural development in independent India can be divided into 3 distinct phases. The phase I started during 1950, wherein local cultivars, indigenous technology, green manuring being the inputs and the expected output was quite low. Alarming rise in the population rate forced the scientists to think of alternatives to the local cultivars with higher response to fertilizers & jump in yield levels. This marked the beginning of phase-II (1965), wherein high yielding varieties, fertilizers, mechanistion & irrigation were used as the inputs and production increase was lucrative. And this phase was popularly called as ‘Green Revolution’ phase in the History of Indian Agriculture. But after 20-25 years the impact of high input technology was reflected in the degradation of agro-ecosystem & once again forced the scientists to think of a viable option to keep intact the resource base & to harvest more/sustain yield levels to feed the burgeoning population. This being the third phase is popularly called as phase of sustainable agriculture organic farming phase started from 1980’s onwards. This gave an impetus to environmentalists, to think seriously regarding protection of the ecosystem.

Multipurpose trees and shrubs are defined as all woody perennials that are purposefully grown to provide more than one significant contribution to the production and/or service functions of a land-use system that they occupy. In agroforestry systems, different species of trees and shrubs can be planted with many types of crops in a variety of patterns. Thus, it is required to know about the methods of propagation and nursery raising, planting and other silvicultural management practices along with the diverse uses of multipurpose trees and shrubs of tropical and subtropical areas before their selection for forestry and agroforestry activities. It is important to select the most suitable tree species since it is not easy to replace them once they have been planted.

Mangium (Acacia Mangium)

Acacia mangium is a single-stemmed evergreen tree that grows to 25-35 m in height and up to 60 cm in diameter. The bole is usually straight, often fluted near the base, free of branches for up to half its height. Mangium is native to Australia, Indonesia and Papua New Guinea. However, it tolerates varied site conditions and has adaptability to different planting objectives. Mangium shows most vigorous growth on well-drained, fertile soils in high rainfall areas in the humid tropics. It is valued for its rapid growth and has been planted throughout the humid tropics and is a major plantation species in the Asia Pacific. Provenances from Papua New Guinea consistently show better growth in height and diameter.

Trees have been used in cropping systems since the beginning of agriculture. Throughout the world, at one period or another in its history, it has been the practice to cultivate tree species and agricultural crops in intimate combination. In the tropics, human beings underwent a transition from hunting/gathering to the use of domesticated plants and livestock. As a part of the process they cut down trees, cleared the debris by burning and sowed crops in the ash- enriched soil. It was the ‘slash-and-burn’ agriculture, a primary forerunner of the present day agroforestry and a practice that might have originated in the Neolithic period, around 7000 BC.

There are innumerable examples of traditional land-use practices involving combined production of trees and agricultural species on the same piece of land in many parts of the world. Trees were an integral part of these farming systems and they were deliberately retained on farmlands to support agriculture. These practices are now known as agroforestry. However, the ultimate objective of these practices was not tree production but food production.

In agroforestry systems the various components like tree, crop and pasture exist in different proportions and orientations. It is difficult to find out which agroforestry system is the best suited for a given land situation. Similarly, it is to be decided which technologies are required for refinement and improvement of the existing agroforestry practices. But without sufficient knowledge of the existing system in a particular land situation, it is very difficult to set the research priorities for modification and development of this system.

Diagnosis and Design (D & D) is a systematic and objective methodology developed by International Centre for Research in Agroforestry (ICRAF) to initiate, monitor and evaluate agroforestry programmes. D & D is based on the philosophy that knowledge of the existing situation (diagnosis) is essential to plan and evaluate (design) meaningful and effective programmes in agroforestry research for development. The methodology plays a strategic role in all the phases of the agroforestry research process. D & D in agroforestry is unique and it has been specially developed for the following purposes.

Agroforestry is a land use system that involves two or more plant species at least one of which must be a woody perennial. When perennial woody and herbaceous components are grown together on the same piece of land their performance would largely depend on their ability to share various growth resources in a given environmental situation. Due to difference in growth pattern and resource requirement of the components in agroforestry situation, a close interactive relation is obvious. Thus, careful management practices for the components are required to establish a successful agroforestry system. The characteristics of the trees and crops, and their interactions, can be modified with good management practices in order to take advantage of the positive characteristics and minimize the effects of the negative ones. Effective and efficient agroforestry management may be divided into two groups - tree management and agricultural crop management.

Factors Affecting The Selection Of Tree Species

Trees in an agroforestry system contribute significantly to the total output of the system and therefore, success of the system depends on the selection of the tree species. The following factors are to be considered to choose the best tree species for the agroforestry systems in a particular site.

Farmers have been growing trees for different purposes for thousands of years. Tree species that are grown to provide more than one significant function are called multipurpose trees. These functions may be productive such as producing fuelwood, timber, fibre, fodder, food, medicine, etc. and/ or protective such as soil conservation, shade, shelterbelt, microclimate amelioration, land sustainability, biodiversity preservation, etc. All trees are multipurpose; some, however, are more multipurpose than others. Tree species can be multipurpose in two ways.

1. A single tree can provide more than one function. For example, Gliricidia sepium is grown as living fences that provide fuel, fodder and green manure for agricultural crops - all at the same time.
2. Trees of the same species, when managed differently, can provide different functions. For example, Leucaena leucocephala is managed so that some trees will mainly yield wood while others mainly produce leaf fodder.

Farmers can grow multipurpose trees (MPT) in various combinations with other crops, as in agroforestry, in block plantations of trees or in naturally regenerating tree farms. In certain cases, multipurpose trees are grown and managed for only one purpose. For example, Gliricida sepium is grown only to provide shade in coffee plantations. The same species may be planted in some other places and is managed differently for a very different use.

Agroforestry systems are not simply systems where trees and crops or animals give useful products to the farmers, rather systems where trees and crops and/or animals interact. Interaction literally means influence or mutual or reciprocal action. So component interaction refers to the influence of one component of a system on the performance of other component as well as the system as a whole.

In agroforestry systems, trees are grown in close proximity to crops and pasture. Their performance would largely depend on their ability to share various growth resources in a given environmental situation. Various interactions take place between the woody trees and herbaceous plants (crops or pastures) which is referred to as tree-crop interface. These interactions take place through the media of soil and microclimate and may exert favourable or adverse effects on the crop. Study of interaction helps to know how the components of agroforestry utilize and share the resources of the environment, and how the growth and development of any of the components will influence the others. Interaction occurs both above and below the ground and includes a complex set of interactions relating to radiation exchange, the water balance, nutrient budget and cycling, shelter and other microclimatic modifications.

The success of an agroforestry system relies heavily on exploitation of the component interactions. In an ideal relationship, production of trees as well as crops or grasses in combination could be comparable to their sole performance. Agroforestry could be even more advantageous if the production of associated components is increased due to influence of trees. This is possible because trees are capable of improving productivity of soil in many ways. A large number of trees are known to fix nitrogen symbiotically. Nevertheless, instances of crop inhibition in association of trees are not uncommon. Such inhibitions are primarily caused by shade effect as well as competition for below-ground resources such as nutrients and water. In some cases inhibitory effect may also result from allelochemicals secreted by some of the tree species.

The words ‘system’, ‘sub-system’ and ‘practice’ are commonly used in agroforestry literature. In a broad sense, a system is defined as a group of associated elements forming a unified whole and working together in a well defined regular relation for a common goal. An agroforestry system refers to a type of agroforestry land-use that extends over a locality to the extent of forming a land utilization type of the locality. Sub-system and practice are lower-order terms in the hierarchy with lesser magnitudes of role, content and complexity. However, these terms are used loosely, and almost synonymously.

Classification of agroforestry systems is necessary in order to understand and provide a practical framework for evaluating systems and developing action plans for their improvement. Any classification scheme should satisfy the following criteria (Nair, 2008).

A forest is a large area dominated by trees. Many definitions of forest are used throughout the world, incorporating factors such as tree density, tree height, land use, legal standing and ecological function. Although a forest is usually defined by the presence of trees, under many definitions an area completely lacking trees may still be considered a forest if it grew trees in the past, will grow trees in the future, or was legally designated as a forest regardless of vegetation type. According to the Food and Agriculture Organization, forests covered 4 billion hectares or approximately 30% of the world’s land area in 2006. Forests are the dominant terrestrial ecosystem of earth, and are distributed around the globe. Forests account for 75% of the gross primary production of the earth’s biosphere, and contain 80% of the earth’s plant biomass

Classification Of Forest

Forests have been classified in different ways. Forests can be classified on the basis of method of regeneration, age, composition, object of management, ownership, canopy density, stand density or growing stock.

The word ‘social forestry’ was coined by J. C. Westoby and used in the ninth Commonwealth Forestry Conference at New Delhi in 1968. In India the term was first used by the National Commission on Agriculture, Government of India in 1976, to denote tree raising programmes to supply firewood, small timber and minor forest products to rural population. Prasad (1985) defined social forestry as forestry outside the conventional forests which primarily aims at providing continuous flow of goods and services for the benefit of people. This implies that the production of forest goods for fulfilling the needs of the local people is social forestry. Thus, conceptually it deals with the people to produce goods such as fuel, fodder, small timber, etc. to meet the needs of local community particularly the underprivileged section (Shah, 1988).

Agroforestry is a new name for a set of old practices. The farmers have been practicing agroforestry since ancient times. The general concept of agroforestry is to integrate trees and agriculture so as to create a more diversified landscape, while providing the producers with new environmental and economic benefits. In other words, agroforestry is a method of farming that allows trees and shrubs to grow along with crops and/or livestock, therefore blending agriculture and forestry in the same production system. In fact, man’s association with forest is much older than with agriculture. First man was a food gatherer and hunter in forests. Then he realized that the seeds of the fruits he collected germinated, grew into plants and bore the fruits again and thus man started to cultivate foods. Man’s desire to live in a community created settled agriculture.

Since then, the pressure on the agricultural lands has increased manifolds due to the increasing population, expansion of urban area and the industrialization process. The environment has also been disturbed. Soil is losing its productivity and the biodiversity is threatened. Farming community is trying all means to increase the land productivity. Chemical fertilizers and pesticides are applied in higher proportion, causing environmental pollution hazards. Under all these circumstances agroforestry has shown that besides sustainable agriculture it can also help promote a better environment. This relatively young science known as agroforestry was brought from the realm of indigenous knowledge into the forefront of agricultural research four decades ago and was promoted widely as a sustainability-enhancing practice that combines the best attributes of forestry and agriculture.

Different diagnostic tools are designed to avert nutrient deficiency or sufficiency and if properly used both loss of yield and quality of crop can be minimized. Among several diagnostic tools, nutrient analysis of standing crop seems to be an efficient method in arriving at the need-based fertilizer scheduling for various crops.

Nutrient uptake by plants indicates the actual accessibility of nutrients in soil to the plants. Also, concentration of certain heavy metals in plant indicates their solubility in soil which leads to poor crop quality.Although, different plant species and even different varieties of same species may differ in their nutrient requirements, the concentration of nutrient element in plant can act as guide to support the soil test result in assessing nutrient supplying capacity of a soil and as a tool for correcting any deficiency if carried out early enough to prevent yield loss. However, analysis of harvested or mature crop is like a post mortem as this information only can help in nutrient management planning in subsequent years.

Like soil testingplant analysis also suffers from some limitations. Amongthem, the most important are the risk of sampling error as well as the chances of incorrect interpretation of test report in recommending fertilizers. Selection of right plant part and right stage of crop growth are very crucial for successful plant analysis.

26.1 Plant Available Fraction of Nickel, Cadmium, Lead and Chromium

The DTPA method was originally developed to extract Mn, Cu, Fe and Zn from slightly acidic to alkaline soils (Lindsay and Norvell, 1978), but in some cases it can be used for other metals also, such as Nickel (Ni), Cadmium (Cd), Lead (Pb) and Chromium (Cr). Among them Ni is considered as an essential micronutrient. The DTPA is used to extract soil metals by forming chelates with free metals in solution, which lowers their ionic activities so that additional quantities of metal are released from the soil colloids until equilibrium is attained. Triehanolamine (TEA) is used to buffer the extracting solution at pH 7.3 in an attempt to optimize the extraction of various metals. Calcium chloride is included in the extracting solution to minimize dissolution of CaCO₃.

25.1 Determination of Available Micronutrient cations (Zn, Cu, Fe and Mn) in Soil

The available micronutrient cations (Zn, Cu, Fe and Mn) can be estimated in a single extraction with diethylene triamine pentaacetic acid (DTPA) as proposed by Lindsay and Norvell (1978). DTPA has the excellent property to combine with free metal ions in the solution forming soluble complexes. The stability constants of metal-DTPA complexes make DTPA as a most suitable extractant for simultaneous complex formation with Zn, Cu, Fe and Mn. In calcareous soil DTPAextractant may result overestimation due to excess dissolution of CaCO₃, causingrelease of occluded micronutrient cations which are not plant available. To avoid this excessive dissolution of CaCO₃, DTPA is buffered at pH 7.3 using triethanol amine (TEA). At this pH major part (3/4^th) of TEA is present as HTEA⁺ (protonation) and exchanges for Ca and Mg ion from the soil exchange site. This increases concentration of Ca and Mg in the solution phase and suppresses dissolution of CaCO₃. The DTPA has the capacity to form complex with each of the micronutrient cations 10 times of its atomic weight and it ranges from 550 to 650 ppm depending on the micronutrient cation.

The amount of cation in the extract is determined on an atomic absorption spectrophotometer (AAS). The experimental condition such as shaking time, DTPA concentration, pH and temperature during shaking influence the amount of Zn, Cu, Fe and Mn extracted. Increase in shaking time and temperature markedly influence the extractability of these cations.

Sulphur (S) occurs in soil in both organic and inorganic forms. Inorganic S fraction may occurs as sulphate (SO₄^2-) and compounds of lower oxidation state such as sulphide (S^2-), polysulphide (S_n^2-), thiosulphate (S₂O₃^2-) and elemental sulphur (S⁰). In well drained soils inorganic S usually present as sulphate. Under anaerobic condition (reduced or waterlogged soil) inorganic S mainly occur as sulphide and under extreme condition as elemental S form. Estimation of S is carried out in two steps:

1. Extraction of different forms of S from soil by suitable extractant.
2. The filtrate is then analysed for S by the turbidimetric method.

The turbidimetric method is the most widely used one because of its simplicity and rapidity.

23.1 Forms of Soil K

Ignoring potassium (K) in soilorganism, total K in soilmaybe classified as (i) water soluble K, (ii) readily exchangeable K (exchangeable K), (iii) slowly exchangeable K (non- exchangeable or fixedK) and (iv) mineral or lattice K. Thedifferentforms are in dynamic equilibrium with one another.

Phosphorus is present in soil both in inorganic form and organic form. The inorganic P can be divided into different pools. The major active inorganic forms are: P bound to aluminium (Al-P), iron (Fe-P), calcium (Ca-P) and silicate minerals and relatively less active forms are occluded and reductant soluble forms of P. On the other hand, the principal organic P compounds present in soil are (i) inositol phosphate, (ii)phospholipids, (iii)nucleicacid and other unidentified esters and phosphoproteins.

22.1 Determination of Available Soil P

The availability of soil P to plant varies greatly depending upon the reaction, minerological composition and amount of the soil colloid. Very little P is present in the soil solution except in recently fertilized or sodic soils. The type of phosphate ions present in the soil solution depends on the soil pH. In soils of neutral to slightly alkaline pH, HPO₄^2-ion is the dominant form. In slightly or moderately acidic soils, both HPO^-and HPO^2-ions prevail. At strongly acidic soil HPO 244 24 ion tends to dominate, while above pH 9.0, the PO₄^3-ion becomes more important - than H₂PO₄ .

As the P is drawn from soil solution largely through diffusion by the plant, it is replenished from solid phase pool of available P. P fertilizer is added to recharge this pool.

21.1 Determination of Total Nitrogen in Soil (Modified Kjeldahl Method)

Nitrogen mostly present in soil in organic form. Relatively small amount of nitrogen usually occurs in ammonium and nitrate form, the available form. The Kjeldahl method of total N determination includes both organic and ammonium forms and with modification nitrate form of N can also be included.

Principle

When soil is digested with concentrated sulphuric acid organic nitrogen is converted to ammonium sulphate. To speed up the reaction a digestion mixture composed of sodium (or potassium) sulphate (to raise the boiling point of H₂SO₄) and cupric sulphate (CuSO₄) - selenium powder (catalyst) is used.

20.1 Exchange Capacity

Soil colloidal particles carry both negative and positive charges on their surface which attract and hold equivalent amount of oppositely charged ions to their surface. The total number of negative charges present on a given mass of soil or capacity of a given mass of soil to exchange cations or total number of cation held by a given mass of soil is termed as cation exchange capacity (CEC). Similarly, the capacity of a soil to retain anions is known as anion exchange capacity (AEC). The ion exchange capacity of a soil depends upon the type and amount of colloidal particle (clay and organic matter) present in the soil. Ion exchange capacity (CEC/AEC) is expressed as milliequivalent ion (cation/ anion, respectively) per 100 g of soil (meq/100g). It is also expressed as centimoles of charge (positive/negative) per kg of soil [cmol (±) / kg]. Meq/ 100g = cmol (±) / kg of soil.

20.1.1 Determination of Cation Exchange Capacity of Soil Principle

Soil is first saturated with normal ammonium acetate (pH 7.0). Excess ammonium (NH₄⁺) ions and displaced cations are then removed by washing with alcohol. The amount of NH₄⁺ ions retained by the soil is measured by steam distillation of NH₄-saturated soil with MgO. During distillation evolved ammonia is absorbed in a boric acid solution as ammonium borate and the amount ammonium borate formed is determined by titration with standard sulphuric acid in presence of mixed indicator.

Carbon may be present in soil in four different forms:

1. Carbonates: Mainly as CaCO₃ and MgCO₃, active CO₃ ^2- and HCO₃ ^- ions and gaseous CO₂.
2. Highly condensed elemental organic form: Charcoal, graphite.
3. Completely decomposed resistant organic residues: Humus.
4. Undecomposed and partially decomposed organic residues.

The latter three fractions constitute the total organic carbon of which last two are chemically active form.

18.1 Determination of Electrical Conductivity of Soil Solution

The conductivity or more precisely the specific conductance of a soil at a given soil-water ratio is the reciprocal of the specific resistance offered by the solution at 25ºC between the electrodes of 1 sq cm cross section kept 1 cm apart. Thus, the electrical conductivity of any solution depends on the amount of soluble salt present in it. Knowledge on the extent of salinity is important for management of saline soil including the choice of the crop suitable for that soil. Soluble salt content in saturation extract is more reliable index of salinity level than in soil: water ratio of 1: 2 or 1: 2.5, because it simulates the extent of salinity experienced by crop in field moisture condition.

Salinity class of soil is based on the electrical conductivity (EC) of saturation extract at 25ºC. However, EC of water extract from 1:2 soil-water suspension can be transformed into the EC of saturation extract following the formula (except for soil containing gypsum).

17.1 Determination of Soil pH

The soil pH value is the measure of hydrogen or hydroxyl ion activity in the soil solution and it indicates whether the soil is acidic, neutral or alkaline in reaction. The pH is the most important property of soil as it controls the availability of plant nutrients, microbial activity and physical condition of soil. Since crop growth is affected both under very low (strongly acidic) and very high (strongly alkaline) soil pH, reclamation of these soils are necessary. Soil pH in fact indicates the extent of active acidity (activity of hydrogen ion in soil solution) of soil. Depending upon the purpose of measurement and soil condition, soil pH is measured in several soil-water or soil-salt solution ratios. The saturated paste is used for identifying specific soil problems like degree of acidity or alkalinity. For making fertilizer recommendation, 1: 2 soil-water suspension is generally adopted. To mask the variability in salt content of the soil, the pH is measured in soil-CaCl₂ suspension (1:2 soil-0.1 M CaCl₂ solution). The soil pH value is independent of dilution over a wide range of soil-salt solution ratio, thus more reproducible than those obtained with soil-water suspension.

16.1 Balance and Weighing

16.1.1 Principle of Functioning of a Balance

It is one of the important tools used in the laboratory and one should have thorough knowledge aboutitsassembly, use and care,otherwise it may be the initialstep for introducing error in any physical or chemical analysis. Every balancehas its maximum load limit and sensitivity depending upon its construction.

Essentially balance may be regarded as a rigid beam, BC having a central fulcrum, O and two arms of equal length, d₁, d₂ (Fig.16.1). Theboth ends of beam have prism edges upon which the balance pans are suspendedby means of suitable suspension.

15.1 Law of Mass Action

Gulberg and Waage, the two Norwegian chemists in the year 1864 stated the law of mass action in this form: ‘The velocity of any chemical reaction at any instant at a given temperature is proportional to the active mass of each of the reactants at that instant present in the system, the active mass in a homogeneous system is defined as the number of gram molecule of the substance present per unit volume i.e., the molar volume’.

14.1 Principles of X-ray Diffraction

Any crystalline structure is characterized by a regular and systematic arrangement of atoms (or ions) in a three-dimensional array. Since crystals are composed of regularly spaced atoms or ions, each crystal contains planes of atoms or ions separated by a constant distance which is the characteristic of that crystalline species.

X-rays are essentially electrostatic and electromagnetic fields oscillating in planes perpendicular to each other and to the direction of propagation in periodic cycles. X-rays having wavelengths in the order of 10^-3 to 10¹ nm, are produced within a vacuum x-ray tube by bombardment of a metal anode with high-velocity electrons. High-velocity electrons transfer their energy to the electrons of metal anode causing their elevation to higher energy level (excited state). Excited electrons of metal atom soon come back to the vacant shell and each electron transfer from higher to lower energy state results release of a quantum of energy (x-ray photon) equivalent to the difference in energy between these two levels. The energy and the wavelength of emitted x-ray photons are finite and characteristic of the particular atoms of the metal anode used in x-ray tube. Usually, photons generated due to electron transfer from L-shell to K-shell are used for x-ray diffraction analysis.

Diffraction of x-ray involves scattering of x-rays by planes of atoms of the crystal separated by definite distance and reinforcement of scattered rays in definite direction away from the crystal. Reinforcement of scattered rays is quantitatively related to the distance of atomic planes in a crystal as defined by Bragg’s equation:

The total energy of a molecule consists of translation, vibrational, rotational and electronic energies. Transition among different types of energy levels occurs in different regions of electromagnetic spectrum. Transitions between rotational and vibrational energy levels of the ground state molecules give rise to absorption bands throughout the infrared region of the electromagnetic spectrum. Organic molecules are characterized by possessing bonds and groups that vibrate independently of each other. Thus, initially infrared spectrometry was used for identification of functional groups of organic molecules. There is lot of ambiguity in the interpretation of infrared spectra of organic matter preparations due to complexity and diversity of the components of soil organic matter. But if used carefully it can provide information on: (i) nature, reactivity and structural arrangement of oxygen-containing functional groups, (ii) presence of protein and carbohydrate constituents, (iii) presence or absence of inorganic impurities (metallic ions, clays, etc in humic fractions), (iv) the amount of different soil organic matter components, and (v) interaction of organic components with pesticides, herbicides, fertilizers, etc.

On the contrary to organic molecules, minerals tend to have few isolated vibrating groups. It can be used for mineralogical analysis when used in conjunction with x-ray diffraction and other similar techniques.

Infrared spectrometry is used in the identification of inorganic compounds including minerals which have well-defined absorption bands in determining- (i) whetherlayer silicate isdioctahedral or trioctahedral in composition, (ii) in studying isomorphous substitution, (iii) hydration of minerals, and (iv) in quantitative analysis. Infrared spectrometer provides information about nature and identify of inorganic compounds that are amorphous in x-ray diffraction analysis.

Thermal Analysis

Physical and chemical properties of any soil are governed largely by the mineralogical make up of the soil, and more specifically by the clay fraction. Identification, characterization and an understanding of properties of different minerals are important in evaluating soils in relation to classification, agronomic practices and engineering purposes.

Clay fractions of soils are usually composed of mixture of one or more secondary phyllosilicate minerals along with primary minerals inherited from the parent materials. Identification of minerals species as well as their quantitative estimation in such polycomponent system require application of several qualitative and quantitative analysis.

The methods used for identification and quantification have steadily been improved over the last 50 years. Among the several methods often used for this purpose three are very common, e.g. (i) differential thermal analysis (DTA), (ii) x-ray diffraction analysis (XRD), and (iii) infrared spectroscopy (IR).

Thermal analysis is a term covering a group of analyses that determine the changes of some physical parameters, such as weight, energy, dimension and evolved volatile substances with change in temperature. Many soil constituents undergo various thermal reactions upon heating, which can be utilized as a diagnostic tool for qualitative identification and quantitative estimation of the substances. These reactions may be exothermic or endothermic, and phase change or crystal change may take place during reactions. Whatever be the reactions, if properly measured, they give some valuable information to identify the substance under consideration.

Among the several methods available for thermal analysis, three methods are frequently used in soil research: differential thermal analysis (DTA), differential scan calorimetry (DSC), and thermogravimetry (TG). Among these, DTA and TG will be discussed here.

11.1 Determination of Penetrability of Soil

Penetrability of a soil is usually assessed by the penetration resistance, which a measure of soil strength and thereby the soil compaction. Penetration resistance is the capacity of the soil in its confined state to resist penetration by a rigid object. Besides soil strength, the penetration resistance also depends on the size, shape and orientation of the axis of the penetrating probe. The penetrating probe may be a finger, pencil, stick, root or any specially designed object having a specified geometric shape and a device to measure the resistance as it is pushed into the soil.

Soil penetrability is intimately related to agriculture because of its adverse impact on draught requirement during ploughing, root development and crop yield, to civil engineering due to its relation to settlement, stability and ground water flow.

Soil penetrability is a measure of the ease with which an object can be pushed or driven into the soil. Any device designed to measure the resistance to penetration may be called penetrometer. There are several types of penetrometers: (i) pocket penetrometer, (ii) proctor penetrometer, (iii) cone penetrometer, and (iv) split-spoon penetrometer. Here, we will discuss about two most commonly used penetrometers viz. pocket penetrometer and cone penetrometer used for agricultural purposes.

Temperature is a fundamental property of usually used to characterize the thermal condition of a system. The growth of any biological system is optimal within certain ranges of temperature and inhibited or ceased beyond this boundary. In addition to plant growth, the significance of temperature on agriculture can be ascertained by its role on physical, chemical and biological processes occurring in soil. Therefore, to study these soil properties intensively measurement of soil temperature is essential.

10.1 Measurement of Soil Temperature

Temperature of any system cannot be directly measured. It can only be estimated by its influence on some properties (thermometric properties) which respond to the variation in the intensity of heat of that system. These thermometric properties include volume, pressure, length, electrical resistance, thermal emf of the matter. Instruments built to take the advantage of any of these thermometric properties of the matter are called thermometer.