Lesson 27. INTERACTION AMONG SOIL MICROFLORA

Module 7. Environmental microbiology

Lesson 27
INTERACTION AMONG SOIL MICROFLORA

27.1 Soil Humus
Humus is the organic residue in the soil resulting from decomposition of plant and animal residues in soil, or it is the highly complex organic residual matter in soil which is not readily degraded by microorganism, or it is the soft brown/dark coloured amorphous substance composed of residual organic matter along with dead microorganisms and comprises B horizon of soil (Fig. 27.1).

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Fig. 27.1 Different horizons of soil

27.1.1 Composition of humus
In most soil, percentage of humus ranges from 2-10%, whereas it is up to 90% in peat bog. On average humus is composed of Carbon (58%), Nitrogen (3-6 %, avg.5%), acids - humic acid, fulvic acid, humin, apocrenic acid, and C:N ratio 10:1 to 12:1. During the course of their activities, the microorganisms synthesize number of compounds which plays important role in humus formation.

27.1.2 Functions of humus
  • It improves physical condition of soil
  • Improve water holding capacity of soil
  • Serve as store house for essential plant nutrients
  • Plays important role in determining fertility level of soil
  • It tend to make soils more granular with better aggregation of soil particles
  • Prevent leaching losses of water soluble plant nutrients
  • Improve microbial/biological activity in soil and encourage better development of plant-root system in soil
  • Act as buffering agent i.e. prevent sudden change in soil pH/soil reaction
  • Serve as source of energy and food for the development of soil organisms
  • It supplies both basic and acidic nutrients for the growth and development of higher plants
  • Improves aeration and drainage by making the soil more porous
27.2 Interactions among Soil Microorganisms
Living organisms both plant and animal types constitute an important component of soil. Though these organisms form only a fraction (less than one percent) of the total soil mass, but they play important role in supporting plant communities on the earth surface. While studying the scope and importance of soil microbiology, soil-plant-animal ecosystem as such must be taken into account. Therefore, the scope and importance of soil microbiology can be understood in better way by studying following aspects:

27.2.1 Soil as a living system
Soil inhabits diverse group of living organisms, both microflora (fungi, bacteria, algae and actinomycetes) and micro-fauna (protozoa, nematodes, earthworms, moles, ants). The density of living organisms in soil is very high i.e. as much as billions/gm of soil, usually density of organisms is less in cultivated soil than uncultivated/virgin land and population decreases with soil acidity. Top soil, the surface layer contains greater number of microorganisms because it is well supplied with oxygen and nutrients. Lower layer/subsoil is depleted with oxygen and nutrients hence it contains fewer organisms. Soil ecosystem comprises of organisms which are both, autotrophs (algae, BGA) and heterotrophs (fungi, bacteria). Autotrophs use inorganic carbon from CO2 and are ‘primary producers’ of organic matter, whereas heterotrophs use organic carbon and are decomposers/consumers.

27.2.2 Soil microbes and plant growth
Microorganisms being minute and microscopic, they are universally present in soil, water and air. Besides supporting the growth of various biological systems, soil and soil microbes serve as a best medium for plant growth. Soil fauna and flora convert complex organic nutrients into simpler inorganic forms which are readily absorbed by the plant for growth. Further, they produce variety of substances like indole acetic acid, gibberellins, antibiotics etc. which directly or indirectly promote the plant growth.

27.2.3 Soil microbes and soil structure
Soil structure is dependent on stable aggregates of soil particles-Soil organisms play important role in soil aggregation. Constituents of soil are viz. organic matter, polysaccharides, lignins and gums, synthesized by soil microbes plays important role in cementing/binding of soil particles. Further, cells and mycelial strands of fungi and actinomycetes, Vormicasts from earthworm is also found to play important role in soil aggregation. Different soil microorganisms, having soil aggregation/soil binding properties are graded in the order as fungi > actinomycetes > gum producing bacteria > yeasts e.g. fungi like Rhizopus, Mucor, Chaetomium, Fusarium, Cladasporium, Rhizoctonia, Aspergillus, Trichoderma and bacteria like Azotobacter, Rhizobium Bacillus and Xanlhomonas.

27.2.4 Soil microbes and organic matter decomposition
The organic matter serves not only as a source of food for microorganisms but also supplies energy for the vital processes of metabolism that are characteristics of living beings. Microorganisms such as fungi, actinomycetes, bacteria, protozoa etc. and macro organisms such as earthworms, termites, insects etc. plays important role in the process of decomposition of organic matter and release of plant nutrients in soil. Thus, organic matter added to the soil is converted by oxidative decomposition to simpler nutrients/substances for plant growth and the residue is transformed into humus. Organic matter/substances include cellulose, lignins and proteins (in cell wall of plants), glycogen (animal tissues), proteins and fats (plants, animals). Cellulose is degraded by bacteria, especially those of genus Cytophaga and other genera (Bacillus, Pseudomonas, Cellulomonas, Vibrio, Achromobacter) and fungal genera (Aspergillus, Penicillium, Trichoderma, Chactomium, Curvularia). Lignins and proteins are partially digested by fungi, protozoa and nematodes. Proteins are degraded to individual amino acids mainly by fungi, actinomycetes and Clostridium. Under anaerobic conditions of waterlogged soils, methane are main carbon containing product which is produced by the bacterial genera (strict anaerobes) Methanococcus, Methanobacterium and Methanosarcina.

27.2.5 Soil microbes and humus formation
Humus is the organic residue in the soil resulting from decomposition of plant and animal residues in soil, or it is the highly complex organic residual matter in soil which is not readily degraded by microorganism, or it is the soft brown/dark coloured amorphous substance composed of residual organic matter along with dead microorganisms.

27.2.6 Soil microbes and cycling of elements
Life on earth is dependent on cycling of elements from their organic/elemental state to inorganic compounds, then to organic compounds and back to their elemental states. The biogeochemical process through which organic compounds are broken down to inorganic compounds or their constituent elements is known as ‘Mineralization’, or microbial conversion of complex organic compounds into simple inorganic compounds and their constituent elements is known as mineralization. Soil microbes plays important role in the biochemical cycling of elements in the biosphere where the essential elements (C, P, S, N and Iron etc.) undergo chemical transformations (Fig. 27.2 – 27.4). Through the process of mineralization organic carbon, nitrogen, phosphorus, sulphur, iron etc. are made available for reuse by plants.

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Fig. 27.2 Carbon cycle
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Fig. 27.3 Phosphorous cycle

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Fig. 27.4 Sulphur cycle

27.2.7 Soil microbes and biological N2 fixation

Conversion of atmospheric nitrogen in to ammonia and nitrate by microorganisms is known as biological nitrogen fixation (Fig. 27.5). Fixation of atmospheric nitrogen is essential because of the reasons:
  • Fixed nitrogen is lost through the process of nitrogen cycle through denitrification.
  • Demand for fixed nitrogen by the biosphere always exceeds its availability.
  • The amount of nitrogen fixed chemically and lightning process is very less (i.e. 0.5%) as compared to biologically fixed nitrogen
  • Nitrogenous fertilizers contribute only 25% of the total world requirement while biological nitrogen fixation contributes about 60% of the earth's fixed nitrogen
  • Manufacture of nitrogenous fertilizers by ‘Haber’ process is costly and time consuming. The numbers of soil microorganisms carry out the process of biological nitrogen fixation at normal atmospheric pressure (1 atmosphere) and temp (around 20°C).
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Fig. 27.5 Nitrogen cycle

Two groups of microorganisms are involved in the process of biological nitrogen fixation.

27.2.7.1 Non-symbiotic (free living)
Depending upon the presence or absence of oxygen, non symbiotic N2 fixation prokaryotic organisms may be aerobic heterotrophs (Azotobacter, Pseudomonas, Achromobacter) or aerobic autotrophs (Nostoc, Anabena, Calothrix, BGA) and anaerobic heterotrophs (Clostridium, Kelbsiella, Desulfovibrio) or anaerobic Autotrophs (Chlorobium, Chromnatium, Rhodospirillum, Meihanobacterium etc.

27.2.7.2 Symbiotic (Associative)

The organisms involved are Rhizobium, Bradyrhizobium in legumes, Azospirillum non legumes, Actinonycetes.
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Fig.27.6 Nodulated roots
Root nodules (Fig. 27.6) occur on the roots of plants (primarily Fabaceae) that associate with symbiotic nitrogen-fixing bacteria. Under nitrogen-limiting conditions, capable plants form a symbiotic relationship with a host-specific strain of rhizobia.

27.2.8 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. e.g.: 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 is used for the control of Heliothis/American boll worm. Bacteria like Bacillus thuringiensis, Pseudomonas are used in cotton against angular leaf spot and boll worms.

27.2.9 Biodegradation of hydrocarbons

Natural hydrocarbons in soil like waxes, paraffin’s, oils etc are degraded by fungi, bacteria and actinomycetes e.g. ethane (C2H6) a paraffin hydrocarbon is metabolized and degraded by Mycobacteria, Nocardia, Streptomyces Pseudomonas, Flavobacterium and several fungi.

27.3 Bioremediation

Pesticides are the chemical substances that kill pests and herbicides are the chemicals that kill weeds. In the context of soil, pests are fungi, bacteria insects, worms, and nematodes etc. that cause damage to field crops. Thus, in broad sense pesticides are insecticides, fungicides, bactericides, herbicides and nematicides that are used to control or inhibit plant diseases and insect pests. Although wide-scale application of pesticides and herbicides is an essential part of augmenting crop yields; excessive use of these chemicals leads to the microbial imbalance, environmental pollution and health hazards. An ideal pesticide should have the ability to destroy target pest quickly and should be able to degrade non-toxic substances as quickly as possible. The ultimate ‘sink’ of the pesticides applied in agriculture and public health care is soil. Soil being the storehouse of multitudes of microbes, in quantity and quality, receives the chemicals in various forms and acts as a scavenger of harmful substances. The efficiency and the competence to handle the chemicals vary with the soil and its physical, chemical and biological characteristics.

27.4 Effects of Pesticides
Pesticides reaching the soil in significant quantities have direct effect on soil microbiological aspects, which in turn influence plant growth. Some of the most important effects caused by pesticides are: (1) alterations hi ecological balance of the soil microflora, (2) continued application of large quantities of pesticides may cause everlasting changes in the soil microflora, (3) adverse effect on soil fertility and crop productivity, (4) inhibition of N2 fixing soil microorganisms such as Rhizobium, Azotobacter, Azospirillum etc. and cellulolytic and phosphate solubilizing microorganisms, (5) suppression of nitrifying bacteria, Nitrosomonas and Nitrobacter by soil fumigants ethylene bromide, telone, and vapam have also been reported, (6) alterations in nitrogen balance of the soil, (7) interference with ammonification in soil, (8) adverse effect on mycorrhizal symbioses in plants and nodulation in legumes, and (9) alterations in the rhizosphere microflora, both quantitatively and qualitatively.

27.5 Persistence of Pesticides in Soil
How long an insecticide, fungicide, or herbicide persists in soil is of great importance in relation to pest management and environmental pollution. Persistence of pesticides in soil for longer period is undesirable because of the reasons: a) accumulation of the chemicals in soil to highly toxic levels, b) may be assimilated by the plants and get accumulated in edible plant products, c) accumulation in the edible portions of the root crops, d) to be get eroded with soil particles and may enter into the water streams, and finally leading to the soil, water and air pollutions. The effective persistence of pesticides in soil varies from a week to several years depending upon structure and properties of the constituents in the pesticide and availability of moisture in soil. For instance, the highly toxic phosphates do not persist for more than three months while chlorinated hydrocarbon insecticides (e.g. DOT, aldrin, chlordane etc.) are known to persist at least for 4-5 years and some times more than 15 years. From the agricultural point of view, longer persistence of pesticides leading to accumulation of residues in soil may result into the increased absorption of such toxic chemicals by plants to the level at which the consumption of plant products may prove deleterious/hazardous to human beings as well as livestock's. There is a chronic problem of agricultural chemicals, having entered in food chain at highly inadmissible levels in India, Pakistan, Bangladesh and several other developing countries in the world. For example, intensive use of DDT to control insect pests and mercurial fungicides to control diseases in agriculture had been known to persist for longer period and thereby got accumulated in the food chain leading to food contamination and health hazards. Therefore, DDT and mercurial fungicides has been, banned to use in agriculture as well as in public health department.

27.6 Biodegradation of Pesticides in Soil
Pesticides reaching to the soil are acted upon by several physical, chemical, and biological forces. However, physical and chemical forces are acting upon/degrading the pesticides to some extent, microorganism’s plays major role in the degradation of pesticides. Many soil microorganisms have the ability to act upon pesticides and convert them into simpler non-toxic compounds. This process of degradation of pesticides and conversion into non-toxic compounds by microorganisms is known as ‘biodegradation’. Not all pesticides reaching to the soil are biodegradable and such chemicals that show complete resistance to biodegradation are called ‘recalcitrant’. The chemical reactions leading to biodegradation of pesticides fall into several broad categories which are discussed in brief in the following paragraphs.

27.6.1 Detoxification

Conversion of the pesticide molecule to a non-toxic compound. Detoxification is not synonymous with degradation. Since a single chance in the side chain of a complex molecule may render the chemical non-toxic.

27.6.2 Degradation

The breaking down/transformation of a complex substrate into simpler products leading finally to mineralization. Degradation is often considered to be synonymous with mineralization, e.g. Thirum (fungicide) is degraded by a strain of Pseudomonas and the degradation products are dimethlamine, proteins, sulpholipaids, etc.

27.6.3 Conjugation (complex formation or addition reaction)

In which an organism make the substrate more complex or combines the pesticide with cell metabolites. Conjugation or the formation of addition product is accomplished by those organisms catalyzing the reaction of addition of an amino acid, organic acid or methyl crown to the substrate, for e.g. in the microbial metabolism of sodium dimethyl dithiocarbamate, the organism combines the fungicide with an amino acid molecule normally present in the cell and thereby inactivate the pesticides/chemical.

27.6.4 Activation

It is the conversion of non-toxic substrate into a toxic molecule, for e.g. Herbicide, 4-butyric acid (2, 4-D B) and the insecticide Phorate are transformed and activated microbiologically in soil to give metabolites that are toxic to weeds and insects.

27.6.5 Changing the spectrum of toxicity

Some fungicides/pesticides are designed to control one particular group of organisms/pests, but they are metabolized to yield products inhibitory to entirely dissimilar groups of organisms, for e.g. the fungicide PCNB fungicide is converted in soil to chlorinated benzoic acids that kill plants. Biodegradation of pesticides/herbicides is greatly influenced by the soil factors like moisture, temperature, pH and organic matter content, in addition to microbial population and pesticide solubility. Optimum temperature, moisture and organic matter in soil provide congenial environment for the break down or retention of any pesticide added in the soil. Most of the organic pesticides degrade within a short period (3-6 months) under tropical conditions. Metabolic activities of bacteria, fungi and actinomycetes have the significant role in the degradation of pesticides.

27.7 Criteria for Bioremediation/Biodegradation

For successful biodegradation of pesticide in soil, following aspects must be taken into consideration.
  • Organisms must have necessary catabolic activity required for degradation of contaminant at fast rate to bring down the concentration of contaminant,
  • The target contaminant must be bioavailability,
  • Soil conditions must be congenial for microbial/plant growth and enzymatic activity and
  • Cost of bioremediation must be less than other technologies of removal of contaminants.
According to Gales (1952) principal of microbial infallibility, for every naturally occurring organic compound there is a microbe/enzyme system capable its degradation.

27.8 Strategies for Bioremediation

For the successful biodegradation/bioremediation of a given contaminant following strategies are needed.

27.8.1 Passive/intrinsic Bioremediation

It is the natural bioremediation of contaminant by tile indigenous microorganisms and the rate of degradation is very slow.

27.8.2 Biostimulation

Practice of addition of nitrogen and phosphorus to stimulate indigenous microorganisms in soil.

27.8.3 Bioventing

Process/way of Biostimulation by which gases stimulants like oxygen and methane are added or forced into soil to stimulate microbial activity.

27.8.4 Bioaugmentation

It is the inoculation/introduction of microorganisms in the contaminated site/soil to facilitate biodegradation.

27.8.5 Composting

Piles of contaminated soils are constructed and treated with aerobic thermophilic microorganisms to degrade contaminants. Periodic physical mixing and moistening of piles are done to promote microbial activity.

27.8.6 Phytoremediation

It can be achieved directly by planting plants which hyper accumulate heavy metals or indirectly by plants stimulating microorganisms in the rhizosphere.

27.8.7 Bioremediation

Process of detoxification of toxic/unwanted chemicals/contaminants in the soil and other environment by using microorganisms.

27.8.8 Mineralization

Complete conversion of an organic contaminant to its inorganic constituent by a species or group of microorganisms.
Last modified: Monday, 5 November 2012, 10:13 AM