eChapters

Introduction

The term actinomycetes, coined in the late 1800s (actins, meaning ‘ray’ and myces, meaning ‘fungus’) is a misnomer. Because actinomycetes have a considerably smaller aerial mycelium than fungi and can produce a large number of asexual spores called conidia, which give the colonies a ‘powdery or chalky’ look.

The actinomycetes constitute a specialized group of soil bacteria that occur in soils throughout the world. The actinomycetes are prokaryotes confirming cellular structures and functions of true bacteria and their morphological similarity to the fungi (Eukaryotes). Between bacteria and fungi, actinomycetes are a transitional category. On their hyphae, most actinomycetes produce single, pairs, or chains of asexual spores.The diameter of the hyphae varies from 0.5 to 1.0 µm. 

Unlike root-free soil, the rhizosphere around growing plants is a very dynamic environment that hosts a much higher number of microbes, in particular bacteria. Microbes interact with each other and with plants in symbiotic, associative, neutral or antagonistic ways. A plant colonized or penetrated by a microorganism can either result in asymptomatic or disease or form an association or symbiosis, depending on the cells’ perception of each other and how the environment affects that interaction. Microbes that penetrate and colonize plants have developed elaborate strategies to subvert plant defenses.

Introduction

In soil, microorganisms influence not only the availability of carbon and nitrogen, which are important constituents of plants, but also of sulfur (S), phosphorus and many other trace elements for plant absorption. Sulphur is found widely distributed and considered as tenth most abundant element in the nature. Sulfur is considered as an essential element for survival of plant and animals and found as gypsum (CaSO₄.2H₂O), pyrite (FeS₂) and other combined form and also in elemental form (S⁰) in the nature. The requirement of sulphur by plant is comparatively less than the primary nutrients, hence sulfur is recognised as ‘secondary’ nutrient. 

Introduction

Phosphorus is only second to nitrogen as a mineral nutrient required for plants, animals and microorganisms. It is a major constituent of nucleic acids in all living systems essential in the accumulation and release of energy during cellular metabolism. Phosphorus is found in soil, plants and microorganisms in number of organic and inorganic compounds. It is the second major inorganic nutrient after nitrogen in term of quantitative requirement for both crop plants and microorganisms. This element may be added to soil in the form of chemical fertilizers, or it may be incorporated as leaf litter, plant residues or animal remains. In cultivated soils it is present in abundance (i.e. 1100 kg/ha), but most of which is not available to plants, only 15% of total soil phosphorus is in available form. Thus, phosphorus occupies a critical position both in plant growth and in the biology of soil.

The excessive and imbalanced use of nitrogenous fertilizers in the last few decades to meet the challenges of growing food demand of Worlds population has led to serious consequences of soil and water pollution, leaching of toxic nitrate into ground water and volatilization of nitrogen oxides into the environment. Therefore, judicious management of nitrogen in the environment is very much essential in the development of more productive and sustainable agriculture. Rapid declining of non-renewable energy sources viz. petroleum products, natural gas as well as energy crisis in the recent days, release of several pollutants during production of fertilizer N has also necessitated the development of alternative and/or supplemental technologies to obtain the fertilizer N for crop production.

Introduction

The various reactions of nitrogen (N₂) cycle, transform one form of the element to another. Mineralization liberates nitrogen in inorganic form, immobilization converts its back to an unavailable state, while nitrification changes the nitrogen from a reduced to oxidized state. Certain transformations of nitrogen lead to a net loss of element from the soil through volatilization. For the purpose of crop production, nitrogen volatilization has a deleterious influence because it depletes part of soils reserve of an essential nutrient. The sequence of steps that results in gaseous loss is called denitrification. So denitrification refers to the reduction of nitrates and nitrites to gaseous nitrogen products, principally di-nitrogen and nitrous oxide, coupled to energy production through oxidative phosphorylation.

At the point where ammonium is produced, the reactions involved in organic nitrogen mineralization come to a halt. This most reduced form of inorganic nitrogen is the starting point for the nitrification process, which involves the biological synthesis of nitrate or nitrite from reduced nitrogen molecules. The ability of nitrifying bacteria to create nitrate, which is the primary nitrogen source ingested by higher plants, determines their relevance. Nitrate is formed in a variety of places, including soil, marine environments, manure piles, and sewage treatment, where it is the result of the final stage of turning organic nitrogen inoffensive.

There are two mini-cycles in the soil nitrogen cycle:

1. Soil-based processes such as mineralization, ammonification, nitrification, and immobilisation include the conversion of organic nitrogenous molecules to plant-useable mineral forms, and subsequently back to biomass (microbial, plant and indirectly animal biomass).
2. The process of converting atmospheric nitrogen into forms available to the living components of the ecosystem, i.e. nitrogen fixation and the transformations within the soil, as well as the return of the fixed nitrogen to atmospheric inert forms of nitrogen through denitrification, are all soil and biosphere resident processes.

To a soil microorganism, the rhizosphere is like a lush oasis in the desert. In comparison to near-starvation conditions of the bulk soil, the rhizosphere is the place where nutrients are plentiful and microorganisms flourish. The term rhizosphere was first used by Hiltner in 1904 to describe the zone of soil under the influence of roots. The rhizosphere can extend more than 5 mm from the root and is the area of increased microbial activity due to exudation of low molecular weight compounds from root cells. The rhizoplane is the surface of plant root and any strongly adhering soil particles. The microbial populations that colonize the interior of the root and from intimate associations with the root are considered endophytes.

Introduction

The soil protozoa are unicellular and the simplest forms of animal life. Most of the protozoa are devoid of chlorophyll but transitional genera resemble the algae and possess chloroplasts containing chlorophyll pigments. The active life stage is commonly known as trophozoite phase where they feed and multiply but under adverse climatic conditions, they form resting stage or cyst, which develop a thick coating on the cell surface. Mostly, the protozoa multiply by longitudinal or transverse fission but some species reproduce sexually by fusion of two cells followed by exchange of genetic material between their nuclei and cell division.

Introduction

Soil algae are not as numerous as bacteria, actinomycetes and fungi. Furthermore, these are photosynthetic microorganisms. Recent work has led to a more complete knowledge of the ecology and importance of terrestrial algae. These algae are found abundant in the habitats in which moisture is adequate and light is accessible.

Classification

Soil algae are classified into four major classes:

1. Cyanophyceae (Blue green algae)
2. Chlorophyceae (Green algae)

Fungi are a diverse group of multicellular eukaryotic organisms with wide variation in vegetative and reproductive morphologies and diverse life cycles. They are more abundant, on a mass basis, in soils than any other group of microorganisms; their biomass ranges from 500 to 5000 wet kg ha^-1 (Metting, 1993). Fungi inhabit almost any niche containing organic substrates, so that they are active participants in ecosystems as -

• degraders of organic matter
• agents of disease as well as beneficial symbionts - lichen (algae and fungi), mycorrhizal association

Introduction

The microorganisms exist as single cell or cluster of cells capable of orderly growth, metabolism and reproduction in two identical daughter cells. These includes cellular organisms {protozoa, algae and fungi (Eukaryotes), bacteria and archaea (Prokaryotes)} and viruses (non cellular entities). The study of microorganisms contribute to understanding of :

1. Basic biological sciences - It acts as a tool for providing the basic information for life processes. The discovery of DNA, RNA, proteins and enzyme functions all came from microbial study.
2. Applied biological sciences - Medicine, agriculture, industry, plant and animal pathology, immunology, plant and animal nutrition, biotechnology all have origin from the understanding of the cell function and metabolism of microorganisms.

ntroduction

Millions of living organisms present in soil make it a living and a dynamic system. Under a microscope, it reveals a complex array of soil particles and pore spaces filled with air and water. In these pore spaces that plant roots and millions of organisms develop, which are ranging from sub-microscopic to macroscopic in size. The physical and chemical characteristics of soil determine the nature of the environment in which vast number of soil microorganisms especially soil microorganisms are found. Living organisms in soils include both macro (earthworms, rodents, termites etc.) and microorganisms (bacteria, fungi, actinomycetes, algae and protozoa). These organisms not only help in the development of soils but also carry out a number of transformations, facilitating the availability of nutrients to the plants.

Methods and procedures for the qualitative characterization and quantitative analysis of different constituents of soil organic matter are presented in this Chapter.

20.1. Moisture

The soil sample should be in an air-dry condition after mixing, sieving and grinding. When stored in a moisture-tight container, the free H₂O content should not vary appreciably during storage. While most determinations can be done on air-dry samples, for certain purposes such as obtaining summation values, a moisture content value is required.

Managing soil organic matter is of paramount importance in sustainable crop production. Human interventions always lead to a decrease in soil organic matter content and biological activity. Therefore, even for maintaining moderate levels of organic matter in soils, sustained efforts should be in place. Such sustained efforts should include adopting high-residue crops in rotation and ensuring regular return of residues to soils.

It is all the more difficult to maintain the organic matter content in well aerated soils and soils of hot and arid regions, because in these soils added materials decompose rapidly. However, in comparison, it may not be so difficult to maintain the organic matter levels in fine-textured soils with restricted aeration and in soils of cold temperate regions.

19.1. Measures that Decrease Soil Organic Matter Content

The study of soil organic matter is becoming increasingly important by the day as world agriculture attempts to ensure sustainability of soils, while at the same time striving to enhance food production to feed an ever-burgeoning population. The use of green manures and pasture leys, the return of residues and additions of organic amendments to the soil are often resorted to in an attempt to increase soil organic matter which immensely benefit the physical, chemical and biological make-up of the soil.

The nuclear magnetic resonance spectroscopy (NMR) has led to major advances in the studies on the nature and chemical composition of soil organic matter. The technique has the potential for characterizing organic matter in the intact soil and its size fractions without the need for extraction and fractionation. Furthermore, it can provide information on the compositional changes in crop residues, peat and litter of the forest soils during biodegradation and humification.

Humic substances, the natural organic materials, represent a mixture of relatively small organic components, which form supramolecular structures held together by dispersive forces such as n - n and van der Waals’ interactions. Identification of the best analytical method for complete characterization of humic substances is still being discussed. Humic substances differ in molecular weight, elemental composition, acidity and cation exchange capacity and often are classified into three major fractions according to their solubility as humic acids, fulvic acids and humins.

Humic substances are the most widely-present, natural, complexing ligands occurring in nature. They are found not only in soils, but in natural waters, sewage, compost heaps, marine and lake sediments, peat bogs, carbonaceous shales, coals and other miscellaneous deposits.

The fate of natural organic matter, especially humic substances, has over recent decades attracted increasing attention of scientists representing various disciplines. Humic substances constitute about 25% of the total organic carbon on the earth. These are a group of naturally occurring complex molecular structures into which biomolecules derived from plant and animal residues are transformed progressively through biotic and abiotic pathways, by aggregation and accumulation processes