eChapters

I. FILL UPS

1. _____ are also called ed-worms.
2. _____ nematode causes discolouration in groundnut.
3. _____ in rice is caused by Aphelenchoides besseyi.
4. The ear cockle disease is caused _____.

I. FILL UPS

1. RCA stands for _____.
2. Expert standing committee was set up in _____.
3. In _____year, All India Co-ordinated maize improvement programme was started.
4. First maize hybrid was released in the year _____.
5. All India co-ordinated bajra and sorghum improvement programme was started in _____.
6. First sorghum hybrid was released in the year _____.

I. FILL UPS

1. _____ refers to the actual acquisition and selling packed seeds, intermediate storage delivery and sales promotional activities.
2. _____ entails using marketing information for the purpose of planning.
3. _____ is one of the major channel through which bulk of paddy seeds, pulses seeds and oil seeds are marketed in the state.

Soil is a mass of large variability and thus its sampling is the most challenging problem for any soil analyst. Practically, soil sampling is a two step process which includes (i) collection of soil from homogeneous unit and (ii) processing which in turn includes drying, grinding, sieving, mixing, partitioning and storing.

1.1. Sources of Error in Soil Chemical Analysis

Different sources of error involved starting from soil sampling to chemical analysis of a sample can be divided into three main groups:

1. Sampling error : This error results from variability among the different samples drawn from same soil unit with respect to the objective of sampling.
2. Sub-sampling error : This error is due to variability introduced among sub samples of the same soil sample.
3. Analytical error : This error introduced due to variability from one chemical determination to another on same sub sample.

2.1. Particle Size Distribution Analysis

Soil is composed of particles of varying size and shape. The expression of the proportion of the different size particles is termed as ‘soil texture’. It is one of the most important basic characters being little changed by cultivation or other practices. Particles are arbitrarily distinguished into following groups on the basis of their diameters.

3.1. Determination of Bulk Density of Soil

3.1.1. Determination of Bulk Density of an Undisturbed Soil

Bulk density of soil is expressed as the ratio of the mass (weight) of soil particle to their total volume including the pore space between the soil particles. Alternately, it is the weight of unit volume of dry soil. It is usually expressed in the unit of gram per cubic centimeter (g/cc) or mega gram per cubic meter (Mg/m³). In fine textured soil bulk density varies from 1.00 to 1.60 g/cc, whereas in coarse textured soil from 1.20 to 1.80 g/cc.

In natural condition primary soil particles cohere to each other to form a cluster or an aggregate through the cementing action of various agents like organic matter, oxides of iron and aluminium, carbonates, etc. Aggregate analysis tells one about the structural status, pore geometry which in turn influences the movement of air and water in soil, amount of water stable secondary particles (aggregate) as well as the extent of finer particles aggregated to the coarser particles and the erodibility status of surface soil against wind and water.

Methods of Analysis

Among the several methods of aggregate analysis the commonly used methods practiced in agriculture and related fields are wet sieving and dry sieving method of aggregate analysis.

5.1. Determination of Soil Moisture

5.1.1. Determination of Soil Moisture Content by Gravimetric Method (Direct method)

Traditionally water content in soil is expressed as the ratio of the weight of water present in the soil to the weight of dry soil. When this ratio is multiplied by 100, it becomes the percentage of water in the soil sample on dry weight basis.

6.1. Determination of Hydraulic Conductivity of Saturated Soil: Laboratory Methods

Hydraulic conductivity of a saturated soil indicates the ease with which water is transmitted through the soil pores. If a constant water head (h) is maintained on a saturated soil column of length (L) and the volume of water (V) percolating per unit time (t) through per unit cross sectional area (A) to the other end, then according to Darcy’s Law the rate of flow of liquid or flux (q) is proportional to the hydraulic gradient (ΔH/L) across the length of soil column.

Soil consistency is a term used to designate the manifestation of different physical forces acting within the soil at various moisture levels. The consistency limits, also known as ‘Atterberg Limits’ (Atterberg, 1911; 12) are defined by the water content of the soil to create specified degree of consistency. These limits are – (i) Liquid limit or upper plastic limit, (ii) Plastic limit or lower plastic limit and (iii) Sticky limit.

7.1. Determination of Liquid Limit or Upper Plastic Limit

Equipments and Materials

Liquid limit device (Casagrande, 1932) and accessories, spatula, dish, oven, moisture box, balance, desiccator

8.1. 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’.

Mathematical Formulation of the Law of Mass Action

Let us take a simple case of a reversible reaction at constant temperature represented by the equation:

9.1. Balance and Weighing

9.1.1. Principle of Functioning of a Balance

It is one of the important tools used in the laboratory and one should have thorough knowledge about its assembly, use and care, otherwise it may be the initial step for introducing error in any physical or chemical analysis. Every balance has 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.9.1). The both ends of beam have prism edges upon which the balance pans are suspended by means of suitable suspension.

10.1. 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.

11.1. 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).

Carbon may 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.

13.1 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.

14.1. Determination of Total Nitrogen in Soil (Modified Kjeldahl Method)

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

Phosphorus in soil present 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) nucleic acid and other unidentified esters and phosphoproteins.

15.1. 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 H₂PO₄^- and HPO₄^2- ions prevail. At strongly acidic soil H₂PO₄^- ion tends to dominate, while above pH 9.0, the PO₄^3- ion becomes more important than H₂PO₄^-.

16.1. Forms of Soil K

Ignoring potassium (K) in soil organism, total K in soil may be classified as (i) water soluble K, (ii) readily exchangeable K (exchangeable K), (iii) slowly exchangeable K (non- exchangeable or fixed K) and (iv) mineral or lattice K. The different forms are in dynamic equilibrium with one another.

Sulphur (S) occurs in soil in both organic and inorganic forms. Inorganic S fraction may occur 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 carried out in two steps:

18.1. 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 DTPA extractant may result overestimation due to excess dissolution of CaCO_3, thus releases 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 complex 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.

19.1. 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 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.

Crop production broadly depends on the fertility of the soil where a crop is raised. There are several factors like the kind and quality of seed, climate, water supply, and plant protection measures etc. that affect the crop production. Among these factors, the fertility status of the soil largely determines the ultimate yield even if all these factors are optimum for crop production. A clear distinction should be made between soil fertility and soil productivity. Soil fertility deals with the inherent capacity of soil to provide nutrients in adequate amounts and in proper balance, for the growth of specified plants when other growth factors such as light, water and temperature, and the physical condition of the soil are favourable. Soil productivity is concerned with the capability of soil to produce a specified plant or plant parts or a sequence of plants under well defined and specified systems of management inputs and environmental conditions, viz. climatic conditions. It does not mean that a fertile soil is always productive. A fertile soil, under a bad management system, may be unproductive for a crop. In this book, plant nutrient elements and their available forms, functions and deficiency symptoms are briefly described for the better understanding of soil testing and fertilizer recommendation.

Soil testing is a useful tool that can help to ensure the efficient use of applied plant nutrients. Soil tests provide a means for assessing the fertility status of a soil, but soil tests do not provide a direct measure of the actual quantity of plant available nutrients in the soil. Instead, soil tests measure the quantity of a nutrient element that is extractable from a soil by a particular chemical extracting solution. The measured quantity of extractable nutrient in a soil is then used to predict the crop yield response to application of the nutrient as fertilizer, manure, or other amendment. As soil test levels increase for a particular nutrient, the expected crop yield response to additions of that nutrient decreases. A soil-testing programme has four phases as follows:

1.Collection of soil samples,

2.Chemical analysis of soil samples,

3.Calibration and interpretation of the results of chemical analysis, and

4.Nutrient/Fertilizer Recommendation.

3.1 Important Soil Physical Properties

3.1.1 Analysis of Soil Texture

Soil texture refers to the relative proportions of sand, silt, and clay on weight basis. Soil texture was recognized from very early times by experienced farmers from the feel of moist soil placed between the thumb and forefinger. The size groups arbitrarily classified by the International Society of Soil Science (ISSS) into clay (< 0.002 mm), silt (0.002 0.02 mm), fine sand (0.02-0.2 mm), and coarse sand (0.2 2.0 mm). Each soil textural name specifies the weight percent of each fraction falls within certain defined limits. The determination of the percentage of the soil separate present in a sample is called particle-size analysis.

Each type of particle present makes its contribution to the nature of the soil as a whole. Sandy soils are usually quite permeable to air, water, and roots, but they have two important limitations. One is their relatively low water-holding capacity; the second is that they are poor storehouses for plant nutrients. These limitations of sandy soils can, of course, be overcome if both fertilizer and irrigation water are available, but the costs are large.

Clay not only have a large surface area per gram, it also has electrically charged particles. These charges give clay the capacity to attract plant nutrient ions to its surface in forms available to plants, but sand lacks this capacity. Clay holds much more water than sands because they have a large surface area to be coated with water. One important problem with clay soils is their stickiness. When wet, they stick to ploughs, boots, or whatever they contact. Loam and silt loam soils are highly desirable for most uses. They have enough clay to store adequate amount of water and plant nutrients for optimum plant growth but not so much clay as to cause poor aeration or to make working with them difficult.

4.1 Sampling and Preparation for Analysis

The determination of nutritional need of crops is an important aspect of nutrient management of any plant analysis programme. The need of fruit plants for mineral nutrients differ from those of annual crop species in a number of ways, many of which are related to the perennial nature of tree crops. In perennial tree crops, there is a need to supply nutrients both for ultimate fruit production, the fruits and the vegetative organs, which persist from year to year. The need for leaf analysis in perennial horticultural crops and forest trees has proved its superiority over soil diagnostic methods. This is essentially because of their deeper root system and the fact that nutrients supplied in one year may have its effect on both the nutrition and crop production in following years. However, it is largely being used not as an alternative method to soil testing, but as a supplement to soil testing. Results of foliar analysis are usually interpreted using the critical nutrient level (CNL) approach. Accurate interpretation of foliar analysis using the CNL approach is possible only when sampling is restricted to the same growth stage at which standard reference values have been established (Beaufils, 1971, 1973). The general purposes of plant analyses are:

5.1 Sampling

There are different sources of water such as rain, streams, canals, lakes, tanks, ponds, large reservoirs, shallow and deep wells, shallow and deep tube wells, as well as sewage effluents and sea water. The composition of the different sources of water vary with the season, rate of flow, the extent of effluents from the industrial units and sewage effluents from the municipal area during rainy season, the river tank and pond water becomes salty and muddy due to soil erosion. The depth of ground water also varies with the seasons. The sources of water available to the farmer for irrigation of crops are generally few such as canal, shallow and deep wells, pumping sets, tube wells and runoff water collected in excavations along roads, natural drains and adjoining areas under impeded drainage. The composition of water also varies with the season. Whatever may be sources of water, the water sample is taken along with the soil sample to soil testing laboratory for its analysis by way of assessing the suitability of water for irrigation.

For drawing maximum benefit the samples taken be representative of the water in bulk and it should be collected in a clean vessel. One to three litres capacity plastic bottles duly washed with a detergent are satisfactory. However, before filling with water samples the bottles must be rinsed with water samples three times. The information such as farmers name, owner of pumping sets, date and month of sampling depth of ground water, crops and soils being irrigated, any specific agricultural or human problems encountered to be briefly recorded along with the name of village, block, tehsil and district. The water sample should be properly labeled and submitted to soil testing laboratory for its analysis.

India is recovering from the euphoria of the Green Revolution and battling the residual effects of the extensively used chemical fertilizers and pesticides in the country’s soils. The decade from 1980 to 1990 alone saw the area under pesticides in India, increased a whopping 20-fold, from six million hectares to 125 million hectares. After a high annual consumption of nearly 75000 MT reached in the early ’90s, interventions in the form of Integrated Pest Management (IPM) practices have only now started to show a declining trend in the use of pesticides in India. Interestingly, India’s consumption of pesticides per hectare is low (0.288 kg/ha) when compared with world averages—0.5 kg/ha against Korea’s 6.60 kg/ha and Japan’s 12.0 kg/ha. According to the pesticides industry statistics, India spends US $3/ha on pesticides compared with US $24/ha spent by Philippines, US $255/ha spent by South Korea and US $633/ha by Japan. Yet, despite a comparatively low use of pesticides in India, the contamination of food products in the country is alarming. About 20 per cent of Indian food products contain pesticide residues above tolerance level compared to only 2 per cent globally. No detectable residues are found in only 49 per cent Indian food products compared to 80 per cent globally. A pesticide is any substance or mixture of substances intended for preventing, destroying, repelling or mitigating any pest. Though often misunderstood to refer only to insecticides, the term pesticide also applies to herbicides, fungicides and various other substances used to control pests.

Pesticides and their metabolites have received particular attention in the last few years in environmental trace organic analysis because they are regularly detected in food products, surface/ground waters and soil strata throughout the world as consequence of their widespread use for agricultural and nonagricultural purposes. So it is the need of the hour to study the levels of pesticides residues in plants, water and soil and their fate in environment after its degradation.

It would be necessary to work out tolerance limits of pesticides residues in/on crops, soil and water and the efforts, therefore, are directed towards various residue analytical methods like TLC, GLC and HPLC etc. which are suitable for the purpose.

Soil testing kit is developed to determine the available nutrient status of soil by rapid test methods. With this system of soil testing, a farmer can test his own soil as often and, in as many places as he feels necessary, and after gauging the need of his soil, he can apply the fertilizers as required. The present mode of soil testing in laboratories usually takes few days and sometime weeks and the farmers may have to travel long distances to submit the soil sample.

To set up a soil-testing laboratory the minimum requirements are as follows:

8.1 Laboratory floor area

Minimum four rooms are needed. They are as follows:

1. Office room, floor size: 18’x 12’

This room is used for registration of the soil samples received, recording recommendations along with soil test results in laboratory book and in report sheet, their dispatch, accounts etc.

The analytical work in a soil-testing laboratory mainly involves standard chemical methods, suitably modified to permit handling of a large number of soil samples with the required degree of accuracy and speed. Many of the analytical operations are carried out more conveniently with help of common as well as sophisticated instruments.

The various instrumental measurements followed in soil and water-testing work in the laboratory can be broadly divided into two groups:

1) Determination of pH and electrical conductivity

2) Colorimetric, spectrophotometric

Abstract

Based on oxygen requirement, microorganisms have been classified into different groups, like facultative anaerobes, micro-aerophilic, aerotolerant and strict/obligate anaerobes. Obligate or strict anaerobes are the key components of anoxic environments and provide valuable ecosystem services like methanogenesis, sulphate reduction, metal reduction, degradation of pollutants etc. Apart from being valuable for the ecosystem, they are causative agents of human infections. They are the key players of human-gut microbiology, and can be used in bio-toilets, solid waste management, anaerobic digestion of waste, wastewater treatment processes and generation of waste to energy etc. Only few anaerobic microorganisms are pathogenic in nature. A mechanistic understanding about physiology and metabolism of anaerobic microorganisms is imperative for their industrial applications. Cultivation of these organisms is the first and very important step for the basic and applied study of anaerobes. Unlike cultivation of aerobic microorganisms anaerobic cultivation needs special care and facilities for successful handling of anaerobes. In the current chapter, We tried to incorporate the components and technicalities of anaerobic pre-reduced media preparation, cultivation and successful isolation of strict anaerobes. In addition, we also tried to discuss the different tools used for cultivation of anaerobes.

Abstract

Microbes are key ingredients of various ecosystems and backbone of modern biotechnology and industry. In addition to their cultivation, purification and characterization, preservation of microorganisms is equally important. Different preservation methods and protocols have been developed for long term preservation of microbes. Microbial Resource Centers (MRCs) are providing active services in the field of life sciences. National Centre for Microbial Resource (NCMR) at National center for Cell Science (NCCS), Pune is one of the MRCs. Unlike aerobes little work has been done in the area of cultivation and preservation of anaerobic microbes. In the previous chapter we have discussed the technicalities and problems of anaerobic cultivation. The aim of current chapter is to provide the recent overview of preservation of anaerobic microorganisms like methanogens, sulfate and metal reducers and the obligate anaerobes of clinical and industrial importance with fermentative mode of life style.

Abstract

Anoxygenic phototrophic bacteria (APB) are having the genetic potential of converting radiant energy into chemical energy useful for growth and metabolic activities without evolving oxygen. They are physiologically, metabolically and phylogenetically versatile group of organism spread in five distinct phyla; Proteobacteria (purple bacteria), Chlorobi (green-sulfur bacteria), Chloroflexi (green non-sulfur bacteria), Fir micutes (heliobacteria) and Acidobacteria. Different group of APB harbors distinct photosynthetic pigments, carotenoids, and a photosynthetic reaction center. These group of bacteria succeeds in a natural environment with light availability and presence of anoxic conditions as the pigment, and the molecular oxygen inhibits bacteriochlorophyll synthesis whereas few APB can grow in hypooxic as well as in aerobic conditions. Calvin-Benson-Bassham (CBB) pathway, reverse tricarboxylic acid (rTCA) cycle, and hydroxypropionate cycle are reported pathways for carbon assimilation in APB to fix carbon dioxide. Photosynthesis occurs in either intracytoplasmic membrane (ICM) or membrane bound chlorosomes and in the cytoplasm for few APB. APB have a wide range of potential applications including removal of H₂S from wastewater and gas streams, hydrogen production, degradation of xenobiotic, toxic metals and radioisotopes, work as host for the production of challenging membrane proteins, source of carotenoids and terpenoids, single cell protein, extensive applications in agriculture and production of bioactive compounds with antimicrobial, antioxidant and anticancer activity. The chapter is focused on the diversity of different types of APB, habitats, their growth requirements, photosynthetic machinery and biotechnological applications of APB.

Abstract

The anaerobic fungi are one of the early organisms in evolution which are commonly found in the digestive tract of ruminating and non-ruminating animals, (including herbivores) deep sea and earth, dumping sites, etc. In animals, these are considered the primary colonizers of the plant biomass ingested by them. Still their taxonomy was unclear for a long period of time. However, with the help molecular techniques, they are now classified under a separate phylum Neocallimastigomycota. There are 38 species known so far belonging to 11 genera. These have been identified based on both morphological data (like thallus, rhizoids, flagella per zoospore, etc.) and phylogenetic analysis. There is a need to explore the undiscovered anaerobic fungi and look for their potential in industrial applications and solutions to the present environmental problems. It can be achieved by improving techniques of sampling, isolation, maintenance and long term preservation. Animals like herbivores do not have the ability to produce enzymes for degrading the plant biomass and anaerobic fungi help them by producing a range of extracellular enzymes. This ability of anaerobic fungi are of use to humans in bioenergy (biogas production) and biomass degradation (by producing cellulases). Recent advances in metagenomics coupled with new methods of cultivation are helping immensely to know the uncultivated anaerobic fungal populations from the animal gut. The present book chapter discusses the past and present of anaerobic fungi, lacunaes and need for more work on this group of fungi, It focuses on the progress in sampling, isolation and preservation techniques, simultaneously discussing the advances in the application these fungi in biotechnology.

Abstract

Microorganisms that produce methane as their metabolic end product are known as methanogens. Methanogens are prokaryotic, unicellular, obligate anaerobes having fastidious growth requirements making them difficult to isolate and preserve. They catalyse the terminal step in anaerobic breakdown of organic substances. Even though methanogenic archaea or methanogens show very limited metabolic diversity, they are one of the most phylogenetically and ecologically diverse group of Archaea. Methanogenic community varies greatly with respect to temperature. Methanogens have been reported from permanently frozen habitats like permafrost to hyperthermophilic environments such as hydrothermal vents. However, the metabolic and phylogenetic diversity of methanogens in these habitats vary greatly. Methanogens are the biocatalysts, having the ability to provide a solution to help solve energy crisis by producing methane as storable energy carrier. Methane being a flammable gas, can act as a clean and renewable source of energy. The biogenic methane gas thus produced may serve as an efficient alternative for fossil fuels in the future.

Abstract

Methane is the second most important green-house gas and has a major role in global warming. Aerobic oxidation of methane is known for more than 100 years. Anaerobic methane oxidation (AOM) was recently discovered before ~25 years, first in marine sediments. The first discovered AOM was found to be mediated by anaerobic methanotrophic archaea (ANME) in association with sulphate reducing bacteria (SRB) and termed as sulphate dependent anaerobic methane oxidation (S-DAMO). Three main groups of ANME are present which perform methane oxidation by reverse methanogenesis pathway. Later on, methane oxidation by using nitrate or nitrite as the electron acceptor was discovered from a freshwater sediment. N-DAMO or nitrate/ nitrite dependent AMO can be carried out by an archaeal or a bacterial member, respectively. Members of Ca. Methylomirabilis oxyfera are bacteria, and use nitrite as the electron acceptor and methane monooxygenase to carry out methane oxidation. Whereas, members of Ca. Methanoperedens nitroreducens are archaea, and use reverse methanogenesis coupled to nitrate reduction. Metals like FeIII or Mn IV can also be used as electron acceptors for AOM, a process recently discovered (M-DAMO). In this case, one archaeal partner and one bacterial partner could be involved, although more research is going in this area. S-DAMO is the main methane oxidation process in the marine sediments and accounts for the major methane oxidation in the marine sediments. In fresh water sediments, aerobic methane oxidation and processes like N-DAMO seem to play an important role.

Abstract

Anaerobic sulfur compound reduction processes make use of sulfur, thiosulfate, trithionate, tetrathionate, and sulfite during the reduction process. Complete reduction of these sulfur compounds leads to production of H₂S. Isolation of sulfur compound reducers requires a suitable electron donor and one of the sulfur compound as a sole electron acceptor during the reduction process carried out in anaerobic conditions. Anaerobic sulfur, thiosulfate and tetrathionate reductases identified to date are molybdopterin binding oxidoreductases that extract out electron during the reduction process. The electron transport chain during the reduction process involves cytochromes and menaquinones. Dissimilatory sulfite reductases include conventional siroheme dissimilatory sulfite reductase and the nonconventional sulfite reductases including ASR sulfite reductase, F₄₂₀ dependent sulfite reductase and the MccA sulfite reductase. Anaerobic sulfur compound reduction process are almost ubiquitous in nature and are important part of the biogeochemical cycle. They occurs in aquatic systems, are found in extreme environments such as hydrothermal vents, acid mine drainage sites and are also found in important human and animal pathogens.

Abstract

Grazing animals have developed symbiotic relationship with anaerobic microorganisms, which survive in their rumen and help in the oxidation of complex molecules of feed containing lignocellulosic materials into volatile fatty acids. The consortium comprises anaerobic bacteria, fungi and protozoans. The rich microbial diversity of rumen remains constant after its establishment and does not get affected by intruding contaminants along with feed or water. The rumen contains a wide range of microbes such as Fibrobacter spp., Ruminococcus spp., Clostridium spp., Prevotella spp., Eubacterium spp., Methanobacterium spp., Treponema sp. Lachnospira sp., Bacterioides s pp., fungi: Anaeromyces s pp., Neocallimastix spp., and protozoa: Enoplastron sp., Eudiplodinium spp., Ostracodinium sp. They often have a variety of enzymes, glucanases, xylanase, glucuronidase, pectinase and amylase, etc. These enzymes inhabit the microbes and even break down complex molecules into simpler forms like; glucose and volatile fatty acids. The present chapter discusses on the role of microorganisms of rumen.

Abstract

Hydrogen synthesis from bioprocesses a good approach for generation clean of fuel for world's development. Throughout the ancient and current periods, most of the developmental activities are completed by consumption of non-renewable fossil fuel energy that which has resulted in multiple environmental issues or challenges (Climate change and pollution by toxic gases or byproducts formation) at global level. Biohydrogen synthesis from anaerobic bacterial fermentation could be a good effort for sustainable energy production without any toxic byproduct formation. For production of hydrogen, lignocellulosic material can be utilized as cheap raw substrates. This would help the farmers in providing surplus benefits to farmer for their agriculture residues that normally burnt and cause the serious air pollution. Utilization of agro-waste residues can help in development of sustainable biofuels for world energy need. Burning of agrowaste residues by farmer's can be discouraged via utilization as raw carbon substrates thereby reducing air pollution.

Abstract

Rise in global energy demand has led to an increase in consumption of fossil fuels. In recent years, there has been an increasing awareness about the consequences of pollution and global warming caused by burning of fossil fuels. This has led to an increased interest in the search for sustainable energy. Transportation sector is a major consumer of world’s energy resources. n-Butanol is one of the most promising alternative bio-fuels which has various advantages over other biofuels. The microbial n-butanol is produced by anaerobic conversion of the substrate to n-butyric acid and subsequently utilized to form n-butanol. The present chapter explores the scope of bacterial butanol production as need of the hour and its use as an alternative biofuel.

Abstract

Solid Waste Management (SWM) has become a significant global concern, specifically for developing countries like India because of increasing population, rapid urbanization and high rate of municipal solid waste generation. Bio-composting and anaerobic digestion are the methods majorly used for solid waste management. Present chapter comprises detailed information on methods, microbiology involved and pros and cons of these methods to provide the detail information of solid waste management processes to the readers. Variable nature of substrates are available for bio-composting process. It includes sludge from effluent treatment plant (ETP), sewage treatment plant (STP) and bio-toilets, municipal solid waste, food waste and garden waste etc. Nutritional content, carbon /nitrogen (C/N) ratio of the substrate, available space and cost of the process are the main factors that affect selection method for waste management. Anaerobic digestion is the preferred method of solid waste management in comparison to other processes of composting due to methane generation as biogas and bioconversion of organic compounds to manure.

Abstract

Anaerobes are a diverse groups of microorganisms which do not require oxygen or energy for respiration/metabolism and are one of the important components of nitrogen cycle. They are capable of using various other organic and even inorganic materials as electron acceptors during respiration. Anaerobic based wastewater treatment is a biological approach where microorganisms degrade organic contaminants (i.e. rich in carbon and nitrogen) in the absence of oxygen. In this chapter, the role of anaerobes in wastewater treatment has been discussed as it offers an alternative, cheap and eco friendly treatment technology among different biological treatment methods. Anaerobic biological treatment of wastewater is well developed, understood, and frequently used in anaerobic digesters to treat complex organic carbon and nitrogen compounds such as primary and secondary wastewater sludge. The anaerobic sludge contains diverse groups of anaerobic microorganisms that work together in association via a multistage processe consisting of the following biochemical reactions like hydrolysis, acidification, acetogenesis, and methanogenesis thereby converting the organic matter to biogas. The composition of biogas includes 70% methane (CH₄) and 30% carbon dioxide (CO₂) in addition to traces of other gases (e.g., H₂ and H₂S). The methane produced as a by-product can be used as an energy source. The potentiality of anaerobes in anaerobic based bioreactors for its maximum efficiency can be implemented in a variety of ways. The chapter discusses about the working principle, performance, treatment potential, and cost implication in the application of anaerobic treatment technology. The main bioprocess parameters such as pH, temperature, mixing, organic loading rate (OLR), and hydraulic retention time (HRT) have also been discussed in brief. Anaerobic treatment offers several benefits over aerobic treatment, including lower energy requirements, less chemicals, low capital, operation, and maintenance costs, and less sludge production. Hence, it saves money and the environment and overall simplifies the whole process.

Abstract

The normal human microbial flora comprises of both aerobes and anaerobes at various sites. Anaerobes are recognised as pathogens causing simple abscesses to life threatening human infections like gas gangrene. They are also incriminated in a large number of mixed bacterial infections and their diagnosis and specific therapy is important for better patient outcomes. The emergence of Clostridioides difficile as an important pathogen causing antibiotic associated diarrhoeas and its emerging resistance to antimicrobial agents has brought anaerobic microbiology into the forefront. Unfortunately, anaerobic clinical microbiology is difficult to practice with long turnaround time, difficult to grow pathogens, new genera and species being discovered based on 16S rRNA sequencing methods and increasing incidence of antimicrobial resistance being reported in anaerobes. This chapter delves into the important aspects required to improve utilization of anaerobic microbiology services and the variety of human infections we encounter in clinical practice due to anaerobic bacteria.

Abstract

Gastrointestinal tract (GIT) harbors mixed microbial community, these are highly diversified, as revealed by molecular and phylogenetic studies. It is also estimated that microbiota of the GIT is composed of over 35,000 species and play a crucial role in human health and diseases. Thus are now of great interest to both the industrial and scientific communities. The microbes exhibit health benefits are known as probiotics. Anaerobic bacteria dominate in the GIT environment and genera like Bifidobacterium, Clostridium, are strict anaerobes while Lactobacillus, Lactococcus, is facultative anaerobes implicated in the probiotic effects.

For developing anaerobic bacterial based bio-products, it is necessary to cultivate large-scale biomass production that could be done using a modern manufacturing practice. Information on detailed understanding of the perfect growth medium and other bioprocessing parameters for the growth and viability is must. Also high cell viability is a prerequisite during downstream processing and storage of probiotic formulation. In this work we review the latest information about the history, mechanism of action, benefits of probiotic, selection criteria, sources of anaerobic probiotic bacteria, industrial cultivation medium along with biomass production, downstream processing.

Abstract

Hundreds of bacterial taxa makes up human gut microbiota and it is comprised primarily of anaerobes belonging to four main phyla which are Firmicutes, Bacteriodetes, Actinobacteria, and Proteobacteria. Anaerobes colonizes the human body, including oral cavity, small intestine, vagina, skin but the majority of them are housed in the colon. The composition and distribution anaerobes varies along the length of gastrointestinal tract because of variation in oxygen gradient, anatomy of intestinal tract and other host physiological factors. Human gets colonized by anaerobes during the birth and these initial colonizers have impact on infant’s health status. The colonization and development of the gut microbiome is responsive to variety of factors including the mode of delivery, feeding methods, environment etc. The human gut microbiota plays an important role in healthy status of host. It plays an important role in nutrient metabolism and absorption, synthesis of vitamins and production of short-chain fatty acids (SCFAs). In turn these metabolites have positive effect on host immunity and overall host fitness. Studying, the anaerobes using culturing method remains critical in microbiology. However, culturomics approach, combined with sequencing technology, provides new insights in studying anaerobes of human gut microbiota. In this chapter we have discussed that, how human gut is an ideal habitat for the colonization and growth of anaerobes and their impact on host health. We also tried to shed light on latest technical advancement in sequencing culturing technology and their application in studying gut anaerobes.

Abstract

Anaerobic microorganisms occur in oxygen-free environments as they possess biomolecules and metabolic processes that have adapted to sustain them in the stressed environments. These biomolecules and metabolic processes are harnessed and employed in various biotechnological applications. Anaerobes are abundant in various ecological niches such as freshwater or marine sediments, subsurface aquifers, deep thermal vents etc. where, in the absence or limitation of oxygen, they utilise reduced ions such as nitrate, sulphate, ferric, carbonate and certain organic compounds like degrading organic matter, fatty acids or alcohols as electron acceptors during respiration/fermentation to produce more or fewer reduced products such as, alcohols, ammonia, organic acids, hydrogen and carbon dioxide as the oxidised product. Diversity of substrates that can be fermented and the wide range of products that can be formed make anaerobic processes useful in biotechnological applications. Their substrate versatility and flexibility, for example, they can utilize simple sugars as well as many of them can utilise complex renewable biomass make their biotechnological applications sustainable and environment friendly. Anaerobes have been employed in food, chemical and material industries for the production of food items, preservative, additives, chemical intermediates, solvents, catalysts and polymers. They find widespread usage in energy sector for generation of various kinds of biofuels that can mitigate our reliance on non-renewable sources for fuel production. An emerging aspect of anaerobic biotechnology is waste valorization that involves treatment of any kind of waste (industrial, municipal, agricultural, pharmaceutical), where organic fraction of the waste is converted into valuable products. Anaerobes play key role in maintaining the global cycles of carbon, nitrogen, and sulfur, and also facilitate bioremediation by breakdown of persistent compounds. Lately, role of anaerobes in medicine and health care sector is widely explored as they are found to produce several bacteriocins, antibiotics, immunomodulators, vitamins and anti-tumor compounds. Some of the anaerobes have also been employed as probiotics. In the present chapter, we discussed these and many more biotechnological applications of anaerobes in white, green, red and blue biotechnology.

1.1 General

The term “biomass” generally refers to renewable organic matter generated by plants through photosynthesis. Materials having organic combustible matter is also referred under biomass.Biomass is an important fuel source in our overall energy scenario. Biomass is produced through chemical storage of solar energy in plants and other organic matter as a result of photosynthesis. During this process conversion of solar energy in sugar and starch, which are energy rich compounds takes place. The chemical reaction of photosynthesis can be written as:

6CO₂ + 6H₂O + sunlight → C₆H₁₂O₆ + 6O₂ + 636kcal

It indicates that the storage of 636 kcal is associated with the transfer of 72 gm carbon into organic matter. Biomass can be directly utilized as fuel or can be converted through different routes into useful forms of fuel. In fact, biomass is a source of five useful agents, which start with ‘F’ like food, fodder, fuel, fiber and fertilizer. Further, biomass has many advantages like.

(1) It is widely available

(2) Its technology for production and conversion is well understood.

(3) It is suitable for small or large applications

(4) Its production and utilisation requires only low light intensity and low temperature (5 to 35°C)

(5) It incorporates advantage of storage and transportation

(6) Comparatively, it is associated with low or negligible pollution.