eChapters

Introduction

Environment pollution is a burning topic of the day. Air, water and soil are being polluted alike. Soil being a “universal sink” bears the greatest burden of environmental pollution. It is getting polluted in a number of ways. There is importance in controlling the soil pollution in order to preserve the soil fertility and increase the productivity. Pollution may be defined as an undesirable change in the physical, chemical and biological characteristics of air, water and soil which affect human life, lives of other useful living plants and animals, industrial progress, living conditions and cultural resources. A pollutant is something which harmfully interferes with health, comfort and environment of the people. Most pollutants are introduced in the environment by waste, accidental discharge, sewage or else. They are by-products or residues from the production of something useful. Due to this our valuable natural resources like air, water and soil are getting polluted. The basis of agriculture is Soil. All crops for human food and animal feed depend upon it. We are losing this important natural resource by the accelerated erosion to some extent. In addition to this the huge quantities of man-made waste products, sludge and other product from new waste treatment plants, and even polluted water are also causing or leading to soil pollution. In order to preserve the fertility and the productivity of the soil.

Submerged soils/Flooded soil

Submerged soils are the type of soils that are saturated with water for a sufficiently long time in a year. This gives the soil the following distinctive gley horizons resulting from oxidation-reduction processes:

The soil is intermittently saturated with water, oxidation of organic matter is slow and it accumulated within the “A” horizon. Fe and Mn are deposited as rusty mottles or streaks if the diffusion of O2 into the soil is slow in the second horizon, whereas if the diffusion is rapid, they are deposited as concretions.

Types of submerged soils

1. Waterlogged soils- Waterlogged soils are saturated with water for a sufficiently long time annually to give the soil the distinctive gley horizons resulting from oxidation-reduction processes. Saturation with water may be due to impermeability of the soil material, or the presence of an impervious layer, or a high water table.

2. Marsh Soils- These types of soils are more or less permanently saturated or submerged. Freshwater marshes can be classified according to their origin into upland, lowland, and transitional. Upland marshes are poor in bases and have pH 3.5-4.5 because they receive mainly rainwater. Lowland marshes are saturated or submerged with water-carrying bases and have pH 5.0-6.0.

Introduction

Soil is one of the crucial natural resources that support life on the earth and controls the economic conditions of the nation. Soil erosion has become a serious problem in both rainfed and irrigated areas of India thus it of vital importance to raise awareness about soil erosion and their reclamation / management methods, so that future land management decisions can lead to more sustainable and resilient agricultural systems. In India almost 130 million hectares of land, i.e., 45 % of total geographical surface area, is affected by serious soil erosion through gorge and gully, shifting cultivation, cultivated wastelands, sandy areas, deserts, and water logging.

In India, the soil is eroded at an average annual rate of 16.35 tonnes per hectare which means 5334 million tonnes per year for the country as a whole. Out of this, about 29 per cent is permanently lost to the sea, while 61% is simply transferred from one place to another, and the remaining 10% is deposited in reservoirs (which mean the storage capacity is reduced by 1-2 per cent annually (Narayana and Ram Babu, 1983)). Singh et al. (1990) estimated that the average annual soil loss is about 15.2 tonnes per hectare and at national level it amounts to about 4978 million tonnes annually. The annual erosion rates vary from region to region. In dense forests covers, snow-clad cold deserts and arid regions of western Rajasthan, the annual erosion rates are less than 5 tonnes per hectare. On the other hand, about 64 per cent of the total soil is contributed by highly to very severely eroded areas, such as the Shiwalik hills (annual rate is more than 80 tonnes per hectare), the Western Ghats, black and red soil regions, ravines and other gully eroded areas and the northeastern region. For the first time, Gurmel Singh prepared map of soil erosion in India (Fig. 7.1), on the basis of iso-erosion lines i.e. line joining the place of same erosion rates.

Introduction

The optimum soil pH for plant production is one that is slightly acidic, at this pH soil microorganisms are most active and plant nutrients are readily available. At extremes of high (alkaline) and low (acidic) pH this delicate balance is disturbed and plant nutrients that were in adequate supply can become either deficient or toxic to plant growth. Some essential nutrients such as phosphorous, calcium, magnesium and molybdenum become unavailable if the soil pH becomes too acidic. Acidic conditions will result in a lowering of plant production in farming systems. This will result in reduced profitability and an increased reliance on fertilizers to sustain any form of productive agriculture. Correcting soil pH to a more favorable pH range will increase the availability of essential nutrients.

Introduction

Soils are formed by weathering of rocks and minerals and all soils contain some amount of soluble salts. Many of these act as a source of essential nutrients for the healthy growth of plants. However, when quantity and quality of salts in the soil near rhizosphere exceeds a particular value, growth, yield and/or quality of most crops is adversely affected. Such a soil is called salt-affected. The degree of adverse effects depends upon the type and quantity of salts, crop and its variety, stage of growth, cultural practices and environmental factors viz. temperature, relative humidity, and rainfall etc. Development of salinity and waterlogging is a serious problem in arid and semi-arid regions of the world and threatening the sustainability of irrigated agriculture.

Soil degradation resulting from salinity and sodicity is a major environmental threat to soil fertility and agricultural productivity in arid and semiarid regions of the world. Saline–sodic soils are degraded due to the simultaneous effect of salinity and sodicity. This causes loss of soil physical structure by clay swelling, and dispersion because of high Na+ concentrations in the soil solution or at the exchange phase. Apart from these physicochemical effects, this leads to biological properties, such as microbial respiration and biomass, becoming worse. On the other hand, salinity affects plant growth by creating osmotic imbalances and specific ion toxicities, which pose limitations to morphological, histological, chemical, biochemical, and metabolic processes. In turn, these reduce stomatal opening and photosynthetic rate, leading to decreased plant growth, crop yield, and quality.

Introduction

Pedology:- Pedology word drive from Greek word pedon, means soil or earth and logos means to study. Pedology is concerned with origin of the soil, its classification, distribution and character (Physical, Chemical and Biological).

Definition:- Soils are natural bodies made from both mineral and organic materials and capable of supporting plants out-of-doors.

Composition of soil on volume basis (Soil components)

i. Mineral matter :- 45%

ii. Organic matter :- 5%

iii. Soil water :- 25%

iv. Soil air :- 25%

Soil formation is a long term process. It takes several million years to form a thin layer of soil. The soil is made up of broken down rock material of varying degree of fineness and changed in varying degrees from the parent rocks by the action of different agencies such that the growth of vegetation is made possible. As soil is a complex mixture of various components, its formation is also more complex. The Formation of a particular type of soil depends upon the physico-chemical properties of the parent rock, intensity and duration of weathering, climatic and other parameters.

Introduction

Soil is a very precious natural resource. It is considered as the epicentre of all the life forms on earth. One cm of soil takes about 1000 years to form but if not used sustainably and managed properly, it may degrade and get converted into a wasteland in just few countable years. The heavy population load, rapid industrialization, unscientific agricultural practices have already put a lot of pressure on soil resulting in reduced soil fertility, degraded wastelands and problematic soils. In India, out of the 329 m ha of geographical area, nearly 50% is subjected to degradation by the various agents like water, wind and biotic interference. In this chapter we will focus on the wastelands and problematic soils, their distribution, cause of formation, management practices mainly in respect to the Indian state of Jharkhand.

Introduction

Over 250 million people are directly affected by land degradation worldwide. Each year 12 million hectares are lost to deserts. Only 11 % of the global land surface can be considered as prime or Class-I land.

India contains 2.4 % of world’s total land. Out of the total geographical area of 329 million ha of the country, land use statistics are available for about 93 % of the total area which comes around 306 million ha. The arable land (net area sown plus the current and other fallow lands) was estimated at 166.14 million ha (54.2%) while the area under forest was accounted at 69.02 million ha (22.6%). Land put to non-agricultural uses was estimated at 22.97 million ha (7.5%) and the barren and uncultivable land at 19.44 million ha (6.4%). Permanent pastures and other grazing lands where estimated 11.04 million ha. (3.6%), land under miscellaneous uses at 3.62 million ha. (1.2%) and the cultivable waste land at 13.08 million ha (4.5%). By summing up these figures, the reporting area comes out 306 million ha.

Introduction

Intensive production of agricultural crops has contributed to decline in soil quality, leading to lower crop productivity and farm profitability. Major causes of this decline are soil compaction, surface crusting, low organic matter, increased pressure and damage from diseases, weeds, insects, and other pests, as well as a lower density and diversity of beneficial soil organisms. These constraints have increased the interest of farmers in assessing the health status of their soils and in implementing sustainable soil management practices. Soil health is critically important to sustainable agricultural productivity and environmental well being. Healthy soils provide a range of environmental services including water infiltration, habitat provision and profitable and sustainable agriculture.

A laboratory is essential for research work in science and development. Most of the research institutes have dedicated laboratories for researchers and students to conduct experiments, perform research work, as well as to provide hands-on learning/training to students. There are certain rules and regulations laid down by the laboratory in-charge which need to be followed strictly for safety purposes. Some of the laboratories keep ‘safety manual’ for researchers to read before entering into the laboratory to conduct experiments. Whenever safety is compromised in a laboratory, there is increase in risk of unwanted incidents in the laboratory. Storing food/beverages in the same refrigerator where laboratory chemicals are kept may lead to disastrous effects on health. This chapter aims to provide instructions in brief on the things to be performed (Do’s) before and after entering onto a laboratory as well as the things never to be done (Don’ts) in a laboratory for the safety reasons.

Good Laboratory Practices (Do’s)

• P Wear apron/labcoat while working in the laboratory.
• P Use gloves/respiratory mask/fumehood while handling toxic/volatile/inflammable chemicals/reagents.
• P Use pippet or pippetor for safety in transfer of solutions.
• P Protect eyes, face and naked parts of the body from UV radiations. Use safety goggles or face mask/apron.
• P Keep your eyes away from Liquid Nitrogen and use cryogloves while handling it.
• P Arrange all the necessary materials/solutions before starting the experiment.
• P Periodically fumigate/ozonize culture and inoculation rooms.
• P Autoclave all contaminated materials before discarding.
• P Pre-treat gel or solution containing Ethidium Bromide (EtBr) before discarding into laboratory waste-disposal bin, and use gloves while handling them.
• P Burn all the transgenic plant materials in an incinerator after taking necessary observations.
• P Make entry in the designated log-book and clean the instrument after using it properly.
• P Switch-off the instrument after use or when not in use.
• P Wash hands with soap and remove the labcoat before leaving/going out of the laboratory7.
• P Ensure that switches for fans/lights, and water taps are off while leaving the laboratory.
• P Follow the biosafety guidelines suggested for handling and disposal of the hazardous chemical.

Introduction

Several hazardous chemicals, microbes, and techniques like recombinant DNA technology are used for research and development work in research Institutes and universities. Therefore, the researchers, technical, helping and supporting staffs as well as the laboratory outputs must be kept free from contaminations. Thus, biosafety is necessary to prevent unintentional exposure/ release of hazardous chemicals, microbes/pathogens, and toxins to the laboratory staff and environment. Following the biosafety guidelines and ethical considerations are essential to maintain safety standards for the researchers as well as the environment. This chapter deals with various biosafety measures and ethical issues to be strictly followed while working in a research laboratory. The required safety level needs to be determined as per the chemical/biological materials are used in the laboratory to keep the researcher/environment safe for sustainable research and developmental activities.

Biosafety

The term biosafety is used to describe the procedure and policies needed to ensure environmental and personal safety. Biosafety refers to the containment principles, technologies and practices that are implemented to prevent unintentional exposure to pathogens, toxins, or their accidental release into the environment. A fundamental objective of any biosafety program is the containment of potentially harmful chemical/biological agents as precautionary safety measures.

Why Biosafety?

With the increasing number of countries adopting molecular biology tools and techniques in life science research and development activities, especially in the areas of agriculture and medicine, the biosafety issues are gaining importance to ensure biological safety for the public and the environment. Conducting research in safe and sustainable manner is not only a personal requirement but essential collective efforts to ensure biological safety for a clean and safe environment. This requires rules, regulations, monitoring bodies, and awareness among the workers as well as the public. Therefore, biosafety per se is an integral part of laboratory research and requires awareness among the researchers so that biological safety can be well taken care from the grassroot level.

For a researcher, laboratory is another home where he/she spends much time every day. As we take care of cleanliness, safety, and design of our home, we must take care on these aspects of laboratory too. It is the responsibility of the laboratory personnel to ensure cleanliness/safety of the laboratory. Since every laboratory chemical and equipment have the potential to cause harms if not used with appropriate precautions. Hence, as a laboratory user, it is our responsibility to follow the basic safety/biosafety rules and regulations set up by the Principal Investigator of the laboratory, Institutional Biosafety Committee, as well as by other regulatory authorities, if any. We must be aware of the general/personal protective measures, cleanliness and laboratory waste disposal prior to joining a research laboratory. In this chapter we will briefly discuss about personal safety, chemical safety, cleanliness, waste disposal, etc.

A. Personal Safety

1. Personal Protective Equipment (PPE)

Personal protective equipment (PPE) is special arrangement to protect the worker from specific hazards because of using a hazardous substance. PPE does not reduce or eliminate the hazard, but protects the wearer from exposure to hazardous material. PPE should not be reused or brought outside the laboratory as these might increase the risk of spread hazardous material or contamination. Used PPE must be kept inside the laboratory in a designated waste storage area adjacent to the work area.

Introduction

Proper electrical wiring and earthing are crucial for laboratory safety and functionality. A laboratory houses several installations/equipment that demand stable/continuous power supply. Inappropriate or faulty wiring and earthing may lead to significant risks, including electrical shocks, damage to equipment, and even incidence of fire. Therefore, understanding the requirements of electrical wiring and earthing is essential for designing, construction, and maintenance of laboratory. This chapter aims to provide a basic knowledge of electrical wiring and earthing necessary for a laboratory. Importance of earthing in mitigating electrical hazards and ensuring integrity of electrical installations are also described.

Basics of Electrical Wiring

Basic understanding of electrical wiring is necessary for laboratory safety and efficient electrical functioning. The potential difference between two electrical points (negative and positive) is known as Voltage, which drives the flow of electric current. This is measured as volt (V). The rate of flow of electricity in a circuit is known as Current (I), which is measured as ampere (A). Current can be either direct (DC) or alternating (AC). Opposition/resistance experienced in the flow of current in circuit is known as Resistance (R) and it is measured in ohms (Ω). Higher the resistance means lesser the current flows at a given voltage. The rate at which electrical energy is transferred/utilized in an electric circuit is known as Power (P), which is measured in watt (W). The Power can be calculated as the product of voltage and current (P = V × I).

Introduction

We come across a variety of chemicals every day in a laboratory. While some of them are relatively safer, others are extremely hazardous. Thus, it is very important to know the potential hazards that can be caused by the chemicals present in the laboratory and the safety measures needed to be followed to avoid the hazards. Additionally, we should also be aware of the steps necessary to be taken on such hazardous situations. According to IUPAC, a hazardous chemical mean the chemical which has the potential to cause damage in various ways. In a laboratory, there are chemicals that might be irritant, carcinogen, respiratory fibrogen, systemic poison, asphyxiant, flammable, etc. which have the potential to cause hazard to the workers or environment. Therefore, it is important to use appropriate procedure to reduce the risk and protect the health/safety of laboratory personnel, the public and the environment.

Types of Hazards Associated with Chemicals

Chemical hazards: The hazards caused by chemicals can be broadly classified into three categories.

1. Health hazard: This is also known as toxic effects of chemical. The risk associated with a chemical in laboratory depends on the extent of exposure and the inherent toxicity of the chemical. Many chemical reactions form the product that might be much more toxic than the reacting chemicals. For example, inadvertent mixing of formaldehyde (a common tissue fixative) and hydrogen chloride results in the generation of bis(chloromethyl) ether, a potent human carcinogen. For most of the chemicals, the route of exposure (through skin, eyes, gastrointestinal tract, or respiratory tract) is more important (Figure 17.1) that must be considered during risk assessment.

Introduction

Flowering plants (Angiosperms) are identified by their morphological characteristics like flower, fruit and seeds that help their taxonomic characterization into different species, genera, families and orders. The floral characters which are used for taxonomic characterization of plants include the type of inflorescences, perianth structure, floral symmetry, arrangement of floral leaves, type of androecium, stamens, gynoecium, carpel, ovule, etc. The type of fruit and seed also play important roles in taxonomic classification. In this chapter we will briefly discuss about various morphological features of flowering plants (in botanical terms) that are useful in taxonomy.

Nomenclature of Plant

Nomenclature of plant is the formal and scientific naming of plants. It is related to but distinct from taxonomy for grouping and classifying plants and provide botanical name.

The scientific/botanical nomenclature started with Species Plantarum by Carolus Linnaeus in 1753. Botanical nomenclature is governed by the International Code of Nomenclature for algae, fungi, and plants (ICN), which replaces the International Code of Botanical Nomenclature (ICBN).

ICBN and ICN

International Code of Botanical Nomenclature, (ICBN) was adopted by the VIIth International Botanical Congress held in Stockholm, July1950. While the International Code of Nomenclature for algae, fungi, and plants (ICN) was adopted by the XVIIIth International Botanical Congress held in Melbourne, Australia in July 2011.

Introduction

Test of pollen viability (extent of pollen viability) is important in pollination experiments to ensure fertility/seed setting. It is also important in monitoring state of pollens during storage in ecological/ taxonomic studies as well as during research on pollen biochemistry, genetics, stigma interactions, and incompatibility studies. Pollen viability refers to the ability of pollen to accomplish post-pollination events to achieve fertilization. Pollen viability test has gained importance particularly in plant breeding and hybrid seed production experiments/ practices. In this chapter, you will be acquainted with the basics of pollen viability test. However, for more professional knowledge on the topic readers are suggested to refer specialized books.

Pollen Viability Test

It is important to know the extent of viability of pollens used in pollination experiment, in finding fertility of a plant of interest, to monitor state of pollen on storage, in ecological/taxonomic studies, as well as in research on biochemistry, genetics, stigma interaction, incompatibility assay, etc. of pollen. Several pollen viability tests have been developed time-to-time. It is recommended to initially use different tests for a given pollen type to find out the most appropriate method that provides reliable result on pollen viability. It is important to note that every procedure requires standardization of protocol according to the sample used. Following different tests are used for assessing pollen viability.

1. In-vitro Pollen Germination Test

It is a simple, speedy, and quantitative test for assessing pollen viability. In this method, a collection/sample of pollen is germinated in vitro and observed under microscope. The percentage of germinating pollens (producing pollen tube) after appropriate treatment and a given period of time is determined. The percentage provides an index of viability of the pollen sample.

Introduction

Seed is a living entity (mature ovule) consisting of a tiny plant in embryonic stage along with the stored food protected by an outer layer known as seed coat. Seed is an important biological input in agriculture, which is economically important for successful crop husbandry. Cotyledons serve as the source of nutrients (proteins, carbohydrates, and oils) that not only nurture the plant at the early developmental (seedling) stages of plant but also the vegetarian (heterotroph) organisms. Being one of the important inputs in agriculture, viability of seed needs to be assessed to know the germination percentage of seeds used to raise a crop. Since viability of seeds may deteriorate on storage depending on the storage conditions. Therefore, often it becomes important to test viability/germinability and vigour of seeds before being used for raising a crop or conducting an experiment. In this chapter, we briefly discuss about the different methods which can be used for testing the viability of seeds.

Seed Viability

Seed viability can be defined as the capability of the seed to germinate and produce a normal seedling within a specified period. In other words, seed viability indicates how many seeds in a lot are alive and could develop into plants under appropriate field conditions. It is very important that most of the stored seeds are capable of germinating when sown in a field. They must possess higher viability at the beginning of storage and maintain it over the storage. A seed with high initial viability survives longer in storage; however, the viability deteriorates slowly at first and then rapidly as the storage prolongs. It is important to know the duration of storage after which a considerable decline in viability occurs under given storage conditions so that to take necessary action to revive the seeds. Excessive deterioration in vianility of seeds may lead to loss of the seed/material/ germplasm.

Introduction

Tissue culture refers to the technique of growing cells, tissues, or organs under controlled, artificial conditions. This allows propagation of tissues from a small sample of cells/tissues under sterile conditions. Plant tissue culture is widely used for various purposes, including the production of disease-free plants, rapid multiplication of plants with desirable traits, genetic modification, conservation of rare or endangered species, etc. Tissue culture is a valuable technique because it enables consistent and large-scale production of plants, ensures genetic uniformity, and allows manipulation of plant biology at cellular level. In this chapter, we will discuss about the major types of tissue culture techniques and their advantages, disadvantages, as well as applications in brief.

Different Types of Tissue Culture

Callus culture involves induction and growing of unorganized, undifferentiated cell masses from an explant on a nutrient/culture medium. The part of plant used to induce callus is called explant which can be tissue, organ or part of a plant.

Organ culture is used to maintain or grow an entire organ or a part of organ in vitro. It preserves the structure and function of the organ for studies or transplantation.

Embryo culture involves isolating and growing embryos from seeds or ovules in a nutrient medium. It is used to bypass seed dormancy or rescue embryos from hybrid crosses that may not develop naturally.

Cell suspension culture involves growing dispersed cells or small cell clusters in a liquid medium under continuous shaking. This is used for large-scale production of cells, secondary metabolites, and studying cell biology..

Introduction

Different types of culture media are used for culturing microbes and plant tissues. Preparing as well as sterilizing them properly following appropriate method with safety for the desired purpose are important parts of research work. In this chapter, we will discuss briefly about different types of media, their composition, preparation and sterilization in laboratory for microbial or plant tissue culture.

Culture Medium

Ingredients mixed to prepare solid, liquid or semi-solid substance to support the growth of microorganism or plant tissue in vitro (outside the body) is called culture medium. Frequently, it becomes important to grow microorganism or plant/animal tissue in vitro for any or all of the following purposes:

• To study characteristic features or properties of microorganisms.

• To identify the causal organism(s) of infection in a clinical sample, so that appropriate remedy can be determined.

• To culture/multiply microorganism or plant/animal tissues in vitro for research or commercial purposes.

• To prepare/produce biological molecules, vaccines, antigens, proteins, metabolites, etc. in vitro for research or industrial purposes.

Introduction

Use of acid/base is common in laboratories for experiments like titration and proper safety in their handling laboratory is necessary. In this chapter we will briefly discuss about the safety measures necessary to be adopted while using acids/bases in laboratory for any experiment.

Handling of Strong Acid/Base

There are four major points that need to be taken care of while working with strong acids or bases that might be quite harmful if any accident happens.

1. Protect Yourself

Wear a lab-coat and acid-resistant gloves: Always use lab-coat/apron and make it sure that the sleeves properly cover your arms. More importantly, use gloves made of acid-resistant materials and also wear shoes to protect your feet while wearing long-pants/jeans. Female with long hair, must tie her hair properly (with rubber band) to avoid any disturbance caused by appearance in between.

Wear safety goggles: It is important to wear safety goggles to protect your eyes using larger and fitting goggles that cover front as well as sides of your eyes. Always use properly fitting and adjustable goggles because smaller/ loose goggles may not protect the areas around your eyes against accidental acid spills and it may fall down from your face, if it is too loose.

Locate emergency wash area: There must be an emergency washing area nearby the work place or laboratory containing lab spill management kits. All the workers in the laboratory must be aware of using the kits and emergency plans.

Neutralize acid: Don’t panic even if an acid or chemical spill happens. Stay calm and act as quickly as possible. In case an acid spills, neutralize it by using sodium bicarbonate so that they can be cleaned and disposed safely. If acid comes in contact of skin, wash it off under running tap water but do not use/ apply sodium bicarbonate on skin.