eChapters

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

It is well known that organic matter plays a unique role in the binding of pesticides in soil, and that this phenomenon is usually the most important cause for interaction of pesticides in the soil environment. Fulvic or humic acids are most commonly associated with the binding interactions. Binding can take place with either the original pesticide or a transformation product, the reaction being induced by abiotic or biotic agents (microbial or plant enzymes). The reactions or processes involved are apparently the same as those responsible for the formation of humic substances, i.e., for the humification process.

Organic matter is of immense importance in forming good aggregates in a wide range of soil types, particularly those representing Mollisols, Alfisols, Ultisols and Inceptisols. Organic matter is somewhat less important in the Oxisols where hydrous oxides may play apredominant role. These relationships are depicted in Fig. 13.

Fig. 13.1: Relationship between OM and the formation of soil aggregates

Aggregates do not directly influence plant growth, but they alter the physical and chemical environments in which plant roots grow through their effects on porosity, aeration, moisture retention, etc., when well-irrigated, even fine- textured soils permit adequate exchange of gases with the atmosphere. The polysaccharides of soil have received the greatest attention in producing stable aggregates, but other organic substances bonded to clay through association with Fe or Al may also be involved.

Extensive studies have shown that much of the humified material in soil is finely bound to colloidal clay. However, it is uncertain to what proportion of the clay surface in any given soil is coated by organic substances as this will depend on the organic matter content and the type and amount of clay.

The ways in which organic substances are retained in soil are as follows:

1. As insoluble polymeric complexes of humic and fulvic acids.
2. As polymeric complexes of humic and fulvic acids bound together by di- and trivalent cations such as Ca²+, Fe³+ and Al³+.

Understanding the mechanisms controlling the adsorption of organic molecules on clay minerals is of significance in many branches of science and industry. The interaction between clay minerals and organic compounds elicits interest that emanates from the prospect that the adsorption of the organic matter fraction in the soil on the mineral particles would render physical stability to soil aggregates.

Organic compounds tend to interact with clay minerals by:

• adsorption process at the external surfaces
• adsorption process at the external and internal surfaces

The chemistry of humic substances is the least comprehended in the field of Soil Science. The many important functions of humus will remain obscure if the structural chemistry of the humic and fulvic acids is not known. A variety of functional groups have been reported in humic substances. However, considerable disagreement still exists in respect of the exact amounts present and, in some cases, proof of existence is lacking.

Some important structural groups of organic molecules are given below:

Practically every aspect of the chemistry of heavy metals in soil is related to the formation of complexes with organic matter. While monovalent cations (Na+, K+, etc.) are held mainly by simple cation exchange through the formation of salts with COOH groups (RCOONa, RCOOK), multivalent cations (Cu²+, Zn²+, Mn²+, etc.) form coordinate linkages with organic molecules.

A schematic diagram showing organic matter reactions involving metal ions in soils is given in Fig. 9.1. The metals present in the solution phase as charged species and as soluble metal-organic complexes (MChe), are shown to be influenced by the activities of higher plants and microbes, both of which serve as sources of water-soluble ligands for complex formation; some metals are held in insoluble organic complexes and are non-leachable and relatively unavailable to plants.

The synthesis of humic substances is the least understood and the most intriguing aspect of humus chemistry. This has been one of the intensely- researched subjects for a long time. Formation of humic substances takes several pathways during the decay of plant and animal remains in soil and the four important ones are shown in Fig. 8.1.

Fig. 8.1: Mechanisms for the formation of soil humic substances

The classical theory by Waksman advocated humic substances as modified lignins (Pathway 1), but a vast majority of current crop of investigators favour a mechanism involving quinones (Pathways 2 and 3). Including sugar-amine condensation pathway (Pathway 4), all the four pathways must be considered as likely mechanisms for the synthesis of humic and fulvic acids in nature. It is absolutely possible that these four pathways may operate in all soils, though not to the same extent or in the same order of importance. 

Soil is the fundamental resource in the agricultural production systems and monitoring its fertility is critical to the sustainability of agriculture. Plant nutrients undergo different transformation processes through which they are converted from unavailable to available forms. Nutrient cycling thus involves the transformation and availability of nutrients and is mediated by microbial action. Understanding the dynamics of nutrient and soil organic matter transformations requires an understanding of the biological, chemical, and physical processes involved.

7.1. Soil Nitrogen

Soil organic matter is among the most complex materials existing in nature. In addition to the organic constituents present in undecayed plant and animal tissues, soil organic matter contains living and dead microbial cells, microbially synthesized compounds and an endless array of derivatives of these materials produced as the result of microbial activity. Soil organic matter probably contains most of the naturally occurring organic compounds. Some components of soil organic matter are no doubt distinctive to the soil environment, particularly those involving inorganic-organic complexes.

6.1. Composition of Soil Organic Matter

The composition of soil organic fraction is as follows:

1. Components of organic residues undergoing decomposition

Soil is the product of various soil forming factors acting on the parent material over a period of time. The parent material is usually devoid of organic matter and consists of variable quantities of sand, silt, clay and carbonates. High temperatures and adequate moisture promote mineral transformations, but these effects are magnified by living organisms and the organic substances they produce. The biosphere and the organic substances they produce are directly or indirectly responsible for the following:

1. Decay of organic matter by microbes leads to the formation of CO₂ which is quantitatively the most important “aggressive” weathering agent because of its tendency to form carbonic acid with water [CO₂ + H₂O → H₂CO₃].

Carbon is the cornerstone of all life on Earth. Plant tissues and microbial cells contain approximately 40 to 50% of carbon on dry weight basis. Yet, the ultimate source is the CO₂ of the atmosphere. The CO₂ is converted into organic carbon by the action of photoautotrophic organisms (higher plants and green algae). It has been estimated that the vegetation on earth’s surface consume some 1.3 x 10¹⁴ kg of CO₂ per annum which is about V₂₀ of the total CO₂ supply of the atmosphere or ¹/₁₀₀₀ of that in the ocean.