Biophysical Management of Soil

Soil Biology

The dead plants contribute to the formation of soil organic matter, which in turn provides food, energy and nutrients to microorganisms and also higher plants – a process of cycling of plant nutrients. Continuous decay of plant roots adds organic matter to soil, thereby changing the soil properties, viz. Soil aggregation, cation exchange capacity, water and nutrient retention capacity, etc. of soil. If the vegetation is removed, the soil characters change completely. When the roots decay, the vacant space makes room for water and air to move in.

Soil Microflora

Biological nitrogen fixation plays an important role in the economy of crop production. The microbes in this class of microflora are, besides bacteria, fungi, actinomycetes and algae. Of these, bacteria are the most abundant in soil, next in order are actinomyeetes, followed by fungi. Soil microorganisms are divided into two broad groups – heterotrophs and autotrophs.


  • Moisture: - In the presence of excess water, waterlogging, anaerobic condition occur the aerobes become suppressed and inactive. In the absence of adequate moisture in soil, some of the microbes die due to tissue dehydration and some of them change their form into resting stages of spores or cysts.

  • Temperature: - Temperature is the most important environmental factor influencing the biological processes and the microbial activity. When the temperature is low, the number and activity of microorganisms fall. Most of the soil organisms are mesophiles and grow well between 150C and 450C. A temperature of 370C is considered to be optimum for most mesophiles.

  • Aeration: - Microbes consume oxygen from soil air and give out carbon dioxide. In the absence of such gaseous exchange, carbon dioxide accumulates in soil air and becomes toxic to the microbes. Rate of oxygen intake and simultaneous evolution of carbon dioxide are measures of microbial activity. Direct sunlight is injurious to most of the microorganisms except algae.

  • Reaction: - Bacteria prefer near neutral to slightly alkaline reaction between pH 6.5 and 8.0; fungi grow in acidic reaction between pH 4.5 and 6.5; actinomyeetes prefer slightly alkaline conditions.

  • Food: - Well-aerated soil rich in organic matter is an essential prerequisite for maximum number and activity of heterotrophic microorganisms. The microbial cells undergoing senescence serve as a source of food for the organisms.

  • Soil Factor: - A soil in good physical condition has good aeration and moisture supplying capacity, which are so essential for optimum microbial activity.

Soil Bacteria

  • Function: - Through a number of transformations and biochemical reactions in soil and thereby directly or indirectly help nutrition of biological fixation of nitrogen-symbiotic and non-symbiotic; decomposition of carbohydrates and lignins; decomposition of proteins with the liberation of ammonia or ammonification, nitrification and denitrification, the transformation of carbon, nitrogen, phosphorous, sulphur, iron, manganese etc. All these processes play a significant role in plant nutrition. The process of conversion of molecular nitrogen into complex proteins through the agency of biological organisms is known as biological nitrogen fixation. Symbiotic nitrogen fixing bacteria e.g. Rhizobium and Nonsymbiotic nitrogen fixing bacteria e.g. Azotobacter, Clostridium pasteurianum

  • Nitrogen Transforming Bacteria: - nitrogen is utilized by micro-organisms and higher plants in inorganic form as nitrate or ammonium. The complex proteinaceous and nitrogenous organic compounds are broken down to produce ammonia through a microbiological process known as ammonification and the microbes responsible for this are ammonifiers or ammonifying bacteria. In nitrification, first, nitrites are formed by nitrite forming bacteria (Nitrosomonas) and then to nitrate by nitrifying bacteria or nitfifier (Nitrobacter). The immobilized nitrogenous is dead bodies of the organisms is again converted by microbes into inorganic forms, ammonium or nitrate, which can be utilized by plants and micro-organisms.

  • Denitrifying Bacteria or Denitrifiers: - Denitrification is the process by which nitrates are reduced to oxides of nitrogen and even too gaseous nitrogen. The bacteria, which are responsible for this transformation, are known as denitrifying bacteria or denitrifiers. e.g. Pseudomonas, Bacillus and Paracoccus. These microbes are aerobic, but Denitrification mostly takes place under anaerobic condition.

Soil Fungi

Fungi are heterotrophic plants larger than the bacteria. Those that live on the dead tissues of organic substances are saprophytic. Fungi may be regarded as the scavengers who will decompose in soil almost anything of organic nature that bacteria cannot tackle and many of them serve as food for the bacteria.

  • Cellulose and Hemicellulose Decomposing Fungi

In acid soils, the fungi are the main decomposers of cellulose as under acidic conditions, bacteria and actinomycetes become inactive. In acid soils, Penicillium and Trichoderma take part in cellulose decomposition, whereas in other soils the fungi species are Aspergillus, Fusarium, etc.

  • Humus Forming Fungi

Certain species of fungi, Alternaria, Aspergillus, etc. produce substances similar to humic substances in soil and may be important in the synthesis of soil humus. The black or dark brown colour of soil humus may be due to their presence.

Soil Actinomycetes

Actinomycetes have characteristics, which are transitional between bacteria and fungi and are sometimes called fungi-like bacteria. Actinomycetes are more abundant in dry soil than in wet soils and more in grassland and pasture soils than in the cultivated soils. They are responsible for the decomposition of the more resistant organic matter of soil and produce a number of dark black to brown pigments, probably contributing to the dark colour of soil humus.

Soil Algae

Soil algae are microscopic, chlorophyll containing organisms, being the simplest chlorophyllous plants. Moisture and adequate sunlight are the most significant environmental conditions influencing the algal population. One of the important roles of certain strains of blue-green algae is the fixation of nitrogen from air.

Soil Macrofauna

  • Earthworms: - They transform the food so as to be more beneficial for the higher plants. These animals are more abundant in moist soils having high organic matter and undecomposed plant residues. They are more common in fine textured soils than in the coarse sandy soils.

  • Moles: - Molehills, frequently observed in some fields, are composed of subsoil deposited by moles. They need a good reserve of calcium in soil.

  • Ants: - More active in humifying insects than plants.

Soil Microfauna

  • Soil Protozoa

Form only a small part of the soil population. They are more abundant in surface soil. Feeds on decaying organic matter are called saprohytic; those on earthworms, other nematodes, etc. are predatory, and those on roots of higher plants are parasitic. As they feed on the bacteria and actinomycetes, they probably help to maintain a favourable balance of the microflora in soil. Nematodes are the abundant soil microfauna in soil. They cause loss of vigour of the root system and make plants growing in nematode infested soil liable to diseases.

  • Soil Viruses

The viruses in soils are known to parasitize bacteria and are specifically known as bacteriophages. Clay and organic matter in soil adsorb bacteriophages and thus cause their retention and spread in soil.

Beneficial Role of Soil Organisms

The soil organisms play a significant role in the life cycles of plants and animals through a number of processes such as decomposition, synthesis and transformation. The most important reactions which the micro-organisms carry out and have significant bearing on soil properties and plant growth are decomposition of organic matter and synthesis of humic substances in soil, biological fixation of nitrogen, microbial transformation of nutrients and nutrient recycling in soil. From the animal and plant bodies, through processes of decomposition, nitrogen enters into the bodies of soil organisms and organic substances (humus) in soil and is recycled through plants and animals. Carbon and nitrogen cycles are the two major biological processes, which take part in the decomposition of added organic matter to soil and formation of humus substances in soil.

Synthesis of Humus Substances in Soil

The carbon and nitrogen cycles show the probable pathways of breakdown of added organic substances in soil. They ultimately lead to the formation of microbial cells in soil and soil organic matter. The main partners are plants, microorganisms, and soil. The organic residues, which undergo breakdown and transformation, are complex in nature, containing carbohydrates, proteins and other nitrogenous compound lignins, fats, etc. in course of the microbial reactions, the soil is enriched with the dead tissues of organisms forming part of its organic matter. Humus is a complex mixture of amorphous and colloidal organic substances. The whole process of decomposition of organic matter, mainly of plant origins, is due to the microbes.

Phosphorus: - microbial grown a requires available and utilizable forms of phosphorus. Immobilization of available soil phosphate may occur when large amounts of available carbon and nitrogen are present in the decomposing material. Thus addition of straw and similar materials causes biological phosphorus depletion and immobilization.

Sulphur: - Sulphur ion in soil is the major source of sulphur for plants, which can also utilize a small amount of sulphur dioxide from air. When plant and animal residues are incorporated in soil, organically bound sulphur is mineralized by micro-organisms into sulphate ions. Part of the mineralized sulphur is immobilized by the microflora and part is available to the plants for their nutrition. The autotrophic bacteria, chiefly members of the genus Thiobacillus, are capable of oxidizing inorganic sulphur compounds. Hydrogen sulphide, it should be noted, is toxic to plants even in small concentration.

Other Elements: -Other plant nutrient elements that undergo microbial transformations and influence their availability for plant growth are potassium, calcium, magnesium, iron, manganese, copper, zinc, molybdenum, boron, etc. certain bacteria and fungi are capable of decomposing alumina silicate minerals in soil, thus releasing a portion of the potassium contained therein. The potassium thus liberated to satisfy the demand of the microbial nutrition becomes ultimately available to plants due to the release of soluble potassium ion during decomposition of microbial cells. Iron transformation in soil depends on the activity of the microorganisms which, in turn, depend upon the compounds of iron. The iron bacteria may be performing the function of oxidation and reduction, and iron precipitation. Bacteria are more dominant in these transformations. Deficiency of manganese is closely related to the number of manganese oxidizing bacteria in soil.


Biofertilizers are the cultures of micro-organisms used for inoculating seed or soil or both under ideal conditions to increase the availability of plant nutrients. Their purpose is to supplement chemical fertilizers and not to replace them. Some of the microorganisms have the beneficial role of biological nitrogen fixation to supply nitrogen to crops, solubilizing insoluble phosphates to soluble forms to make them available to crops, synthesizing biomass for manuring crops, particularly rice, and hasten the process of decomposition of cellulose in composts and farmyard manures through cellulolytic organisms.

Soil Aggregation

Some organisms may play a beneficial role indirectly be creating better soil physical condition, e.g. by improving soil aggregation. Soil microorganisms cause soil aggregation probably by the gum or polysaccharides produced by them. Azotobacter, Beijerinckia and Rhizobium are examples of gum producing bacteria.

Effects of cultural practices on soil organisms

Cultural practices, viz. Cultivation, crop rotation, application of manures and fertilizers, liming and gypsum application, application of pesticides for crop production have their effect on the soil organisms. Ploughing and tilling operations facilitate air movement in soil and expose soil surface to sunshine, and thereby increase biological activity, particularly of bacteria. Cultivation of a single crop causes accumulation of a particular group of microbes, which dominate over the others. Crop rotation disturbs the unfavourable population balance. Crop rotation with a legume is the common practice. Irrigation of soil brings about a significant proliferation of soil microbes.

Soil Amendments: - Liming of acid soil increases activity of bacteria and actinomycetes and lowers the fungal population. Gypsum application of sodic soil is favourable for bacterial activity. Application of fertilizers and manures increases crop production supply food and nutrition not only to the crops but also to the microbial population in the soil. Phosphatic fertilizers applied to berseem (Trifolium alexandrimum) increase significantly the activity of nitrogen fixing bacteria. Organic manures provide a readily available source of carbon for the heterotrophs. Repeated heavy fertilization with nitrogenous fertilizer alone promotes rapid growth of fungi. Oilcakes, viz. Neem, karanj and groundnut encourage the growth of nematode-trapping fungi. Application of chemicals (pesticides) to control damage to crops by insects, fungi, nematodes and weeds is imperative. The pesticide molecules may interact with soil constituents and get adsorbed on the soil particles or they may move with water to find their way into ground water, rivers and stems. The pesticides are systemic in nature, they persist in soil and may be taken up by plants and ultimately by animals. Some pesticides are biodegradable by soil organisms, other are liable to leave toxic residues, which are likely to be hazardous. The usual dosage is not high enough to cause any profound change in the normal microbial activity of soil.

Physical Properties

Soil is a heterogeneous mixture of silicate particles, humus, and a variety of insoluble salts and oxides of metals called the solid phase, a liquid phase and a gaseous phase. Depending on the relative proportions of the various size groups we can define soil texture. Depending on the size and shape of the aggregates we can define soil structure.

  • Texture

Many of the important soil properties are related to texture. Clayey soils show high water holding capacity, high plasticity, stickiness and swelling whereas sandy soils are conspicuous by the absence of these properties. The most important way in which soil texture affects plant growth is water and with it the nutrient supply. The available water capacity of soil is related to soil texture.

  • Soil Structure

This kind of arrangement and organization of secondary and primary particles under natural condition brings about what has been termed as soil structure. Under natural soil conditions, the primary particles (clay, silt and sand) are mostly bonded together by cementing agents into secondary aggregates of varying sizes.

  • Bulk and Particle Density and Pore Space

Bulk density of a soil is defined as the mass per unit volume of soil consisting of solid and gas phases. Particle density of a soil is the mass per unit volume occupied by the soil particles alone. Bulk density of soil is influenced by soil texture, organic matter content and cultivation practices. The constituents of soil organic matter contribute significantly to aggregation of soil particles. The humus portion in the aggregation is susceptible to biodegradation. To maintain soil aggregation status of cultivates soils, renewed addition of organic matter is essential.

Management Practices

The management practices for crop production have a profound effect on the formation and stability of soil aggregates

  • Cultivation: - Continuous cultivation of arable land year after year, without incorporation of organic matter, deteriorates soil structure, lowering the level of soil structure, lowering the level of soil organic matter. Addition of organic matter helps in improving the structural status of soil. The tillage operation affects the size distribution of peds, density and packing of soil particles, amount of organic matter and moisture content of soil. Tillage is to loosen the surface soil, to facilitate water infiltration and aeration. Friable conditions of soil are the optimum soil condition for tillage operation to produce aggregates of suitable size.

  • Crops and Cropping Practices: - Crops affect soil structure through their vegetative canopy above the ground and their roots below the ground. Grasses are conducive to well structured soil. The vegetative canopy protects the soil from the beating action of raindrops and destruction of the structure of the surface soil and prevents crusting, improve soil structure. The role of legumes in building up soil fertility is well known and legumes have, therefore, their place in sound crop rotation practices. The beneficial effect is usually attributed to nitrogen added to the soil by legumes. The structure is built up with the advancement of stages of crop growth. Legumes treated with phosphatic fertilizers significantly improve soil structure.

  • Manures and Fertilizers

Organic matter level and structural improvement of soil can be built up, to a varying degree, and maintained by continuous judicious application of manures. The degree of improvement depends upon the quantity and length of application of manure, the climatic conditions, and nature of soil. Phosphatic fertilizers used in conjunction with nitrogenous fertilizers improve and maintain soil structure.

Management of Soil Structure

The objective of soil structure management is the improvement and maintenance of soil structure. Inclusion of a suitable legume in a crop rotation is the most effective way of improving and maintaining soil structure. Coupled with phosphatic fertilizers, legumes improve soil structure still further. Use of balanced fertilizers for raising crops is the other means. Judicious application of adequate quantities of well-decomposed manures, as frequently as possible, improves soil structure. In coarse-textured soils, use of organic manures is the only way of improving structure. Application of pond sediments or clay soil brought from another locality is helpful in this respect. In the case of very fine-textured soils, organic manure is no doubt helpful, but the quantity required well be high. Crop rotation and use of phosphatic fertilizers are better methods for such soils. Structural management of acid soils involves liming followed by organic manuring. Highly alkali soil application of gypsum or other amendments in combination with green manuring or manures or incorporation of crop residues has been successful in improving structure and helps in reclamation of such soils.

Water Infiltration into Soil

Water infiltration is the process of water entry into soil through the surface and the direction of entry may be either downward or lateral or both. Water infiltration characteristics of soil are of practical significance in soil and water conservation, irrigation and watershed management. Factors influencing infiltration- texture, structure and initial moisture content of soil control infiltration rate. Coarse textured and well aggregated soils have usually high infiltration rate. Dry soil condition is conducive to rapid infiltration. Vegetative covers help infiltration while the presence of a somewhat impervious subsoil layer reduces it. The volume of water that enters into soil and the depth to which water moves and wets the soil below the surface are of utmost importance in the soil water plant relationship as this is one of the main sources of water supply to plants.

Importance of Soil Water Studies

Infiltration studies are important for soil and water conservation. The design of furrows or basins for ensuring even distribution of irrigation water will, therefore, depend upon the infiltration rate. Plants meet their water requirement from water stored in soil. Microbes and plants require, besides water, an adequate level of oxygen in soil for their growth and activity. Low porosity and hydraulic conductivity of soil cause inadequate aeration. Proper drainage ensures adequate aeration and removal of salts and other toxic substances from the root zone. Recharge of groundwater is often necessary where excess of rainfall is lost as surface runoff, due to low infiltration capacity of the soil. The soil air and soil temperatures are closely related to water content of soil.

Soil Aeration and Plant Growth

Oxygen is required by microbes and plants for respiration. Oxygen taken up and carbon dioxide evolved are stoichiometric. Root elongation is particularly sensitive to aeration conditions. Oxygen deficiency disturbs metabolic processes in plants, resulting in the accumulation of toxic substances in plants and low uptake of nutrients. Certain plants such as rice are adapted to grow under submerged conditions. These plants have large internal air spaces, which facilitate oxygen transport to the roots.

Soil Temperature and Management

Soil micro-organisms show maximum growth and activity at optimum soil temperature range. Soil temperature has a profound influence on seed germination, root and shoot growth, and nutrient uptake and crop growth. Seeds do not germinate below or above a certain range of temperature. Root elongation is very much dependent on soil temperature. Each crop plant has a specific optimum range of soil temperature for its rapid growth and maximum yield.

Soil temperature under field conditions can be altered by suitable cultural practices such as mulching, irrigation, drainage, and tillage. Tillage loosens the surface soil, increases its porosity and decreases its thermal conductivity. Soil compaction has the reverse effect on porosity and soil temperature. Mulching the surface soil with plastic cover or crop residues may increase or decrease surface soil temperature, depending upon environmental conditions. Mulches conserve soil moisture also. In tropical areas, irrigation generally causes rapid and substantial reduction in maximum temperature in summer and increase in minimum soil temperature in winter. In the cold season, the higher temperature of irrigation water relative to soil, and high heat capacity of irrigation water check lowering of minimum soil temperature.

Soil Compaction

Soil compaction is the process of increasing dry bulk density of soil, reducing the pore space by expulsion of air through applied pressure on a soil body. Initially, when water content is low, the soil is stiff and difficult to compress, low density is the result. Compaction of coarse-extured soil, sometimes desirable, for better seed germination, reducing hydraulic conductivity of soil, and enhancing moisture conservation. Continued compaction will practically remove all air. As the water content of soil increases, the water acts as a lubricant, and the soil becomes workable with the expulsion of soil air. Compacting creating problems for seed germination water transmission and aeration.

Soil Crusting

Crusting of soil is a form of soil compaction. The crusts present a serious barrier for seedling emergence, high exchangeable sodium percentage, poor structure, low organic matter content of soil and also puddling during tillage operations are some of the factors responsible for crust formation. Lowering the exchangeable sodium percentage and incorporation of organic matter prevent crust formation.

(Soil Magt.)