eChapters

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

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

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

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

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

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

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.

Harvesting: “Removal of entire plant or economic parts after maturity from the field" is called harvesting. It includes the operation of cutting, picking, plucking or digging or a combination of these for removing the useful part or economic part from the plants / crops. The portion of the stem that is left in the field after harvest is called as stubble. The economic product may be grain, seed, leaf, root or entire plant.

Harvest Index: (H.I): It is the ratio of the economic yield to the total biological yield expressed as percentage.

H.I = Economic yield / Biological yield x 100

Time of Harvesting: If the crop is harvested early, the produce contains high moisture and more immature ill filled and shriveled grains. High moisture leads to pest attack and reduction in germination percentage and impairs the grain quality.

Late harvesting results in shattering of grains, germination even before harvesting during rainy season and breakage during processing.

Growth is the development of a plant as a whole or of a specific organ. Besides the genetic factors, the environmental factors grouped as climatic factors and soil factors influence plant growth. The supply of mineral nutrient elements to the plants is discussed in this chapter.

A complete analysis of plants detects large number of elements. But only certain elements are essential. An element is said to be essential if the plant cannot complete its life cycle without it, and if the malady (deficiency) that develops in plants in its absence can be remedied only by that element.

Earlier 16 elements were considered as essential for plant growth. They are carbon, hydrogen, oxygen, nitrogen phosphorus, potassium, calcium, magnesium, sulphur, iron, manganese, zinc, copper, molybdenum, boron and chlorine. Recently, sodium, cobalt, vanadium, silica, selenium, gallium, aluminium and iodine are added to the above list. One or the other of these elements (recently added) has been found to be essential for a particular species of plants.

Carbon dioxide, water and molecular oxygen are the forms in which C., H and O are assimilated by plants. Others are taken up by plants from the soil. Nutrient uptake by plants accounts for about 10 percent of total dry weight of crops, the remaining percentage being water. The chemical symbol and the ionic forms in which the essential elements are absorbed by the plants are as follows.

Irrigation

Irrigation is defined as the artificial application of water to the soil for the purpose of crop production in supplement to rainfall and ground water contribution.

Time of Irrigation

The time schedule which indicates when irrigation water is to be applied and the quantity of water to be applied at that time is called irrigation schedule. There are several approaches for scheduling irrigation:

1. Soil moisture depletion approach based on the available soil moisture in the root zone.
2. Climatological approach based on the amount of water lost by evapotranspiration.
3. Combination approach based on soil moisture depletion and climatological approaches.
4. Critical stage approach which indicates the growth stages at which moisture stress leads to yield loss. These stages are known as critical period or moisture sensitive period. In cereals and millets panicle initiation and flowering stages are moisture sensitive stages. In pulses and oilseeds, flowering and pod development stages are critical stages. In sugarcane active tillering or formative stage is critical and in cotton boll development is the critical stage.

Weeds are the plants, which grow where they are not wanted. Jethro Tull (1731) coined the word weed. Weeds can also be referred to as plants out of place.

Definition

Weeds are unwanted and undesirable plant that interfere with utilization of land and water resources and thus, adversely affect crop production and human welfare.

In organic agriculture weeds are treated as childrens of the soil.

In the world 30,000 species of weeds have been listed, of which nearly 18,000 cause serious damage to agricultural production. Eighteen weeds are considered as the most serious in the world and about twenty six species have been listed as principal weeds in crop fields of India, and are listed in annexure V

Crop Stand Establishment

Good crop establishment is one of the most important features in better crop production. The better crop establishment is in turn expressed as optimum plant population in fields.

Plant population is the number of plants per unit area in a cropped field. It indicates the size of the area available for individual plant.

Optimum Plant Population

It is the number of plants required to produce maximum output or biomass per unit area. Any increase beyond this stage results in either no increase or reduction in biomass.

Crop geometry is the pattern of distribution of plant over the ground or the shape of the area available to the individual plant, in a crop field.

Seed is a fertilized ripened ovule consisting of three main parts namely seed coat, endosperm and embryo which in due course gives rise to a new plant. Seed is the nucleus of life. Endosperm is the storage organ for food substance that nourishes the embryo during its development. Seed coat is the outer cover that protects or shields the embryo and endosperm.

Importance

Plants reproduce sexually by seeds and asexually by vegetative parts. Grains which are used for multiplication are called seeds while those used for human or animal consumption are called grains. Good stalks of planting materials are basic to profitable crop production. The seed or planting material largely determines the quality and quantity of the produce. A good seed or stalk of planting material is genetically satisfactory and true to type, fully developed and free from contamination, deformities, diseases and pests.

Tillage operations in various forms have been practiced from the very inception of growing plants. Primitive man used tools to disturb the soils for placing seeds. The word tillage is derived from the Anglo-Saxon words tilian and teolian, meaning to plough and prepare soil for seed to sow, to cultivate and to raise crops. Jethro Tull, who is considered as father of tillage suggested that thorough ploughing is necessary so as to make the soil into fine particles.

For better understanding of different systems of farming it is essential to study certain terminologies.

Farm is a piece of land with specific boundaries, where crop and livestock enterprises are taken up under a common management.

Farming is the process of harnessing solar energy in the form of economic plant and animal products or it is the business of cultivating land, raising livestock etc.

System refers to an orderly set of interdependent and interacting components none of which can be modified without causing a related change elsewhere in the system.

There are three district systems of farming as wetland system of farming, garden land (irrigated dry land) system of farming and dryland system of farming.

Wetland: Pertaining to soils flooded or copiously irrigated through lake or pond or tank for a least several weeks in each year (or) to crop growth in such soils. The water is not entirely under the control of the farmer.

Agricultural Seasons

Season is defined as “part of the year during which a distinguished type of weather prevails”.

A) Seasons of Temperate region

1. Spring (March – May) is the first season of the year in which plants being to grow and leaves emerge.
2. Summer (June – August) is the second and warmest season of the year out side the tropics during which plants flourish
3. Fall or Autumn (September – November) is the third season of the year in which leaves turn brown.
4. Winter (December – February) is the last and the coldest season of the year. Many trees loose their leaves.

Soil is defined as the thin layer of earth’s crust made up of disintegrated and decomposed rocks, complex mineral compound, organic matter, water/air and living organism like bacteria, fungi, insects and worms and serves as the natural medium of growth of plants.

• It provides nutrients, moisture, anchorage (support) and provides air to root system.
• There are different soil groups found in varied regions of India.
• Each group differs from other in physical and chemical properties.
• The variation in behaviour is mainly due to the nature of the parent material from which the soils are formed.
• Parent materials are Igneous rocks, sedimentary rocks and metamorphic rocks.
• Physical properties like structure, texture, colour, water holding capacity, depth etc. are to be noted. Chemical properties like the presence of various plant elements, pH, EC, CEC, acidic or alkaline, etc. are considered.

Internal Factors

The increased yield and other desirable characters are related to the genetic make up of the plant. They are :

• High yields under given environmental conditions.
• Early maturity (in some cases late maturity).
• Resistance to lodging.
• Drought, flood and salinity tolerance.
• Tolerance to insects and diseases.
• Chemical composition of grains (high percentage of oil, increase in protein quantity or quality, etc.)
• Quality of grains (fineness, coarseness, etc.)
• Quality of straw (sweetness, juiciness, etc.)

In general crop is an organism grown or harvested for obtaining yield. Agronomically crop is a plants cultivated for economic purpose.

Classification of Crops

Classification is done to generalize similar crop plants as a class for attaining better understanding of them. Field crops are classified in the following ways.

1. According to range of cultivation
2. According to the place of origin
3. Botanical classification
4. Commercial classification
5. Economic / Agricultural / Agrarian classification
6. Seasonal classification
7. Classification based on ontogeny

The word agronomy has been derived from two Greek words, agros and nomos having the meaning of field and to manage, respectively. Literally, agronomy means the “art of managing field”. Technically, it means the “Science and economics of crop production by management of farm land”.

Definitions

Agronomy is the art and underlying science in production and improvement of field crops with the efficient use of soil fertility, water, labour and other factors related to crop production.

Agronomy is defined as “a branch of agricultural science which deals with principles and practices of field crop production and management of soil for higher productivity.