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Soil is the largest terrestrial ecosystem where a wide variety of relationships exists between different types of soil organisms. The associations existing between different soil microorganisms, whether of a symbiotic or antagonistic nature, influence the activities of microorganisms in the soil. Microflora composition of any habitat is governed by the biological equilibrium created by the associations and interactions of all individuals found in the community. In soil, many microorganisms live in close proximity and interact among them-selves in a different ways. Some of the interactions or associations are mutually beneficial, or mutually detrimental or neutral.

Introduction

Microorganisms generally present in all the environments are the most abundant and diverse living organisms present on earth. Microorganisms have great impact on the biosphere due to their inbuilt ability to transform the key elements of life into forms usable by other organisms and plants. Because of heterogeneity in nature of soils from variations in physical, chemical and biological properties the various natural habitat are microbially most diverse environments on the earth maintaining the stability between complex microbial communities and their function (Daniel 2005). One gram of soil contains about 10 billion microorganisms of possibly thousands of different species but microbial diversity in general, and particularly in extreme environments, and its role in ecology is poorly understood (Rossello-Mora and Amann 2001).

Deserts present a unique environment with very little precipitation and large variations in day and night temperatures, making it inhospitable environment for living organisms. Still a number of microbial species do survive in those harsh environments. The populations of aerobic bacteria in deserts across the world are reported to vary from < 10 in Atacama desert to 1.6 × 10⁷ cfu g^–1 in soils of Nevada (Skujnis 1984), and India is not exception to that with the bacterial population in the range of 1.0 × 10³ to 8.35 × 10⁶ cfu g^–1 sediment or ml^–1 water in the samples collected from cold deserts of north western Himalayas (Yadav et al. 2015).

Soil is a living entity having dynamic physico-chemical and biological properties. Besides supporting the growth of various biological communities, it also serves as a medium on which the organic residues, in the form of dead plant and animal or their excretions, are degraded and decomposed. The biological properties to soil are endowed through the interactive activities of plant root, soil microbes and soil animals. The soil organisms live in a constant state of competition and have to struggle hard for their survival. In this struggle some species become dominant and some remain sub-dominant and others perish or remain in very low profile. So a sort of dynamic equilibrium is the net result of wide range of interactions occurring both at organism and population levels amongst different components of soil biota. Many interactions are short-lived and sporadic and others are more stable.

Soil is inhabited by incredibly diverse living microorganisms that are significant to plant growth and development. Soil microorganisms produce a variety of metabolites, probably several thousands, which influence the plant growth either positively or negatively. Therefore, in such a complex situation, identification of any one metabolite or a compound as active phytohormone or phytotoxin is really an uphill task. Appropriate extraction procedure, knowledge about the proper site for its action, appropriate conducive physiological environment and the effective intensity or concentration is of prime importance. Compounds, in general, are inhibitory to growth at higher concentrations but usually stimulatory at lower concentrations. All growth regulators, irrespective of their provenance or structure, may be divided into two groups.

Definition : Soil microbiology is the study of microorganisms living in soil which complete whole or some part of their life cycle in soil. They include both beneficial as well as deleterious microorganisms but as a specialized branch main thrust is laid on their metabolic activities and the role they play in energy flow, cycling of nutrients associated with the primary productivity and soil ecosystem development. Besides, it focuses on environmental impact, whether favourable or unfavourable, on soil microorganisms and the various soil biochemical processes mediated by various microbes. A clear understanding of the interactions between soil microbial communities and elemental soil components is imperative to comprehend total ecosystem function. Atlas and Bartha have defined the soil microbiology as ‘the study of organisms that live in soil; their metabolic activity; their roles in energy flow; their roles in nutrient cycling’. As per Tate soil microbiology involves ‘the study of soil ecosystem which is the product of intricate interactions between physical and chemical matrix of highly variable composition and living communities of all form’.

1. Amoeba are unicellular organisms that feed on

a. Bacteria and algae     b. Bacteria and fungi

c. Fungi and algae        d. Nematode and fungi

Microorganisms being minute and microscopic are ubiquitous. Besides supporting the growth of various biological systems, soil and soil microbes serve as a best medium for plant growth. Soil fauna & flora convert complex organic nutrients into simpler inorganic forms which are readily absorbed by plants.

Soil microbes as nitogen fixers-Symbiotic (Associative): The organisms involved are Rhizobium, Bradyrhizobium in legumes(aerobic): Azospirillum, Azotobacter (grasses), Actinonycetes- Frantkia (with Casuarinas, Alder).

Soil microbes as biocontrol agents: Several ecofriendly bioformulations of microbial origin are used in agriculture for the effective management of plant diseases, insect pests, weeds etc. eg: Trichoderma sp and Gleocladium sp are used for biological control of seed and soil borne diseases. Fungal genera Entomophthora, Beauveria, Metarrhizium and protozoa- Maltesia grandis. Malameba locustiae etc.- are used in the management of insect pests. Nuclear polyhydrosis virus (NPV) is used for the control of Heliothis/American boll worm. Bacteria like Bacillus thuringiensis, Pseudomonas are used in cotton against Angular leaf spot and bollworms.

Degradation of pesticides in soil: Soil receives different toxic chemicals in various forms and causes adverse effects on beneficial soil micro flora / micro fauna, plants, animals and human beings. Various microbes present in soil act as the scavengers of these harmful chemicals in soil. The pesticides/chemicals reaching the soil are acted upon by several physical, chemical and biological forces exerted by microbes in the soil and they are degraded into non-toxic substances and thereby minimize the damage caused by the pesticides to the ecosystem. For example, bacterial genera like Pseudomonas, Clostridium, Bacillus, Thiobacillus, Achromobacter etc. and fungal genera like Trichoderma, Penicillium, Aspergillus, Rhizopus, and Fusarium play important role in the degradation of the toxic chemicals / pesticides in soil.

Biodegradation of hydrocarbons: Natural hydrocarbons in soil like waxes, paraffins, oils etc are degraded by fungi, bacteria and actinomycetes. E.g. ethane (C2 H6) is metabolized and degraded by Mycobacteria, Nocardia, Streptomyces Pseudomonas, Flavobacterium and several fungi.

4.1. Role of soil microorganisms

Soil N utilization by plants.

Dead organic matters decomposed.

Nutrient transformation.

Physical and chemical properties of soil.

CO₂ content.

Soil formation.

Soil minerals are naturally formed inorganic compounds with definite chemical composition and characteristic geometric (crystalline) form. They are classified as primary and secondary minerals, silicates and non-silicates minerals, and crystalline and non-crystalline minerals. Primary minerals have not been significantly altered chemically since deposition or crystallization from molten magma and are usually found in the sand and coarse silt fractions. Secondary minerals form as a result of the alteration of primary minerals by weathering and are found in the clay and fine silt fractions.

ALLIC: soil family class term used in Oxisols as a calcareous and reaction class category. Soils placed in the allic class are acid and have low CEC with high amounts of KCl-extractable aluminum in a layer at least 30 cm thick within the control section. If used for agriculture, these Oxisols require large inputs of lime to displace the aluminum and raise pH.

The soil water plays an important role in the physical, chemical and biological activities taken place in the soil which directly or indirectly affects the crop growth. The water content of the soil can be measured by different methods. These methods are gravimetric method, neutron scattering method and electrical resistance method.

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 Soil Moisture

6.1.1 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.

Equipments and Materials

Soil auger, aluminium moisture box with air tight lid, balance, oven and desiccator

Soil moisture is the water retained within soil pores and represents a critical link between precipitation, evapotranspiration, runoff, infiltration and groundwater recharge. It provides the principal water supply for plant growth and strongly influences crop establishment, nutrient availability and yield. This chapter discusses soil-moisture storage, field capacity, permanent wilting point, available water, infiltration, percolation and root-zone dynamics. It examines methods of measurement, estimation and monitoring and explains how soil texture, structure, organic matter, vegetation and weather influence moisture conditions. Effective soil-moisture management supports irrigation scheduling, drought mitigation, water-use efficiency and prevention of waterlogging, thereby strengthening agricultural productivity and environmental sustainability.

Introduction

Nitrogen constitutes 78% of the atmospheric gases and there is about 75,000 Mg N on each hectare of land. However, 99% of the atmospheric N is as N₂ and is inert and non-reactive, while the rest 1% or even less is the reactive-N. Reactive-N is linked with H, O and C and is responsible for the creation and sustenance of all life on the planet Earth. Nitrogen is the key nutrient that separates proteins from carbohydrates and fats, the three major macronutrients for humans. As a component of proteins, N is present in DNA and RNA, which carry the hereditary characters and then as the major constitute of the body muscles of humans (and animals). Plant growth and crop production are also very much dependent on the adequate availability of N in soil.

Introduction

Organic matter in soil is the key to soil health. SOM improves many physical, chemical, and biological characteristics of the soil, including water holding capacity, cation exchange capacity, pH, buffering capacity, and chelating of micronutrients. Furthermore, well decomposed SOM improves soil structure by increasing aggregation, enhances biological activities in the soil, slowly releases nutrients, and suppresses some diseases. A loss of SOM can lead to soil erosion, loss of fertility, compaction, and general land degradation.

Introduction

The soil is the largest terrestrial pool of organic carbon, about 1150 Pg (1Pg = 10¹⁵ g) compared with about 700 Pg in the atmosphere and 600 Pg in land biota (Lal and Kimble,1997). Organic carbon level of soils reaches a fixed equilibrium that is determined by a number of interacting factors such as precipitation, temperature, soil type, tillage, cropping systems, fertilizers, the type and quantity of crop residues returned to soil, and the method of residues management. In the temperate climate, it may take about 50 years for the organic carbon of soils to reach a new equilibrium level following a change in management. However, this period is much shorter in a semiarid and arid climate and also in tropical climate like India.

5.1. What is soil organic matter?

Plant and animal residues which are not yet added to the soil are considered as organic materials. However, once they are added to soil, they become soil organic matter. Therefore, organic materials contributing to the soil matrix are referred as Soil Organic Matter (SOM). Sometimes SOM is also used to highlight only the non-living organic materials produced by living organisms. But SOM should be regarded as a broad term that includes biomass, partially decayed residue, and highly decomposed and transformed organic substances, humus. Agricultural soil contains nearly 1-5% of SOM, which is regarded as least amount in soil as compared to other three soil components, minerals (45%), air (25%) and water (25%). However, it contributes enormously to soil productivity. Soil productivity and fertility exhibit direct positive relationship with SOM content in soil. Plants and animals are considered as primary and secondary sources of soil organic matter, respectively. Plant residues and application of organic manures e.g., farmyard manure, compost or green manuring help to build up organic matter in soil and thus, enrich the soil with organic carbon and other plant nutrients. Under natural conditions, roots of grasses in grasslands, the leaves including shoot portion of the large trees in forest lands and after harvesting the crop remnants in agricultural field provide enough incorporation of organic materials in soil. SOM plays a vital role to maintain sustainability in agricultural production through producing healthy soils and thus, healthy crops.

Soil organic matter makes up only a few per cent of most soils, but it has a great deal of influence on soil properties and on agricultural productivity.

2.1. Quantity of Organic Matter

Based on the content of organic matter, soils are identified as mineral or organic. Mineral soils dominate most of the world’s cultivated land and may contain anything from a trace to 30 per cent of organic matter. Organic soils are naturally rich in organic matter, chiefly due to climatic reasons. Although they contain more than 30 per cent organic matter, it is precisely for this reason that they are not vital cropping soils.

Plants are the generators or the primary source of organic matter while animals are the transformers- secondary source of organic matter. In agriculture, plants add 10–30 percent of organic matter through their roots stubbles and leaf fall and exudations. The excreta of livestock, the organic wastes of urban and rural residential areas include the garbage and sewage and sludge. The by products of agro based industries viz. bagasse, vinasse, pressmud from sugar industries, the coir dust from the coir industries, dust of cotton from ginning industries, the fruit and food processing industries wastes.