Fundamentals of Microbiology

Lesson 26. MICROBIOTA OF SOIL

Module 7. Environmental microbiology

Lesson 26

MICROBIOTA OF SOIL

26.1 Introduction

Soil microbiology is branch of microbiology which deals with study of soil microorganisms and their activities in the soil. Soil is the outer, loose material of earth’s surface which is distinctly different from the underlying bedrock and the region which support plant life. Agriculturally, soil is the region which supports the plant life by providing mechanical support and nutrients required for growth. From the microbiologist view point, soil is one of the most dynamic sites of biological interactions in the nature. It is the region where most of the physical, biological and biochemical reactions related to decomposition of organic weathering of parent rock take place.

26.2 Components of Soil

Soil is an admixture of five major components viz. organic matter, mineral matter, soil-air, soil water and soil microorganisms/living organisms (Fig.26.1). The amount/proposition of these components vary with locality and climate.

Fig. 26.1 Major components of soil

26.2.1 Mineral/Inorganic matter

It is derived from parent rocks/bed rocks through decomposition, disintegration and weathering process. Different types of inorganic compounds containing various minerals are present in soil. Amongst them the dominant minerals are Silicon, Aluminum and iron and others like Carbon, Calcium Potassium, Manganese, Sodium, Sulphur, Phosphorus etc. are in trace amount. The proportion of mineral matter in soil is slightly less than half of the total volume of the soil.

26.2.2 Organic matter (components)

These are derived from organic residues of plants and animals added in the soil. Organic matter serves not only as a source of food for microorganisms but also supplies energy for the vital processes of metabolism which are characteristics of all living organisms. Organic matter in the soil is the potential source of N, P and S for plant growth. Microbial decomposition of organic matter releases the unavailable nutrients in available from. The proportion of organic matter in the soil ranges from 3-6% of the total volume of soil.

26.2.3 Soil water

The amount of water present in soil varies considerably. Soil water comes from rain, snow, dew or irrigation. Soil water serves as a solvent and carrier of nutrients for the plant growth. The microorganisms inhabiting in the soil also require water for their metabolic activities. Soil water thus, indirectly affects plant growth through its effects on soil and microorganisms. Percentage of soil-water is 25% total volume of soil.

26.2.4 Soil air (Soil gases)

A part of the soil volume which is not occupied by soil particles i.e. pore spaces are filled partly with soil water and partly with soil air (Fig.26.2). Most microbes are in micro colonies on soil particle. They may escape predator activities by refuge in these small pores. These two components (water and air) together, accounts for approximately half the soil's volume. Compared with atmospheric air, soil is lower in oxygen and higher in carbon dioxide, because CO2 is continuous recycled by the microorganisms during the process of decomposition of organic matter. Soil air comes from external atmosphere and contains nitrogen, oxygen, CO2 and water vapor (CO2 > oxygen). CO2 in soil air (0.3-1.0%) is more than atmospheric air (0.03%). Soil aeration plays important role in plant growth, microbial population, and microbial activities in the soil.

26.2.5 Soil microorganisms

Soil is an excellent culture media for the growth and development of various microorganisms. Soil is not an inert static material but a medium pulsating with life. Soil is now believed to be dynamic or living system. Soil contains several distinct groups of microorganisms and amongst them bacteria, fungi, actinomycetes, algae, protozoa and viruses are the most important. But bacteria are more numerous than any other kinds of microorganisms. Microorganisms form a very small fraction of the soil mass and occupy a volume of less than one percent. In the upper layer of soil (top soil up to 10-30 cm depth i.e. Horizon A), the microbial population is very high which decreases with depth of soil. Each organisms or a group of organisms are responsible for a specific change transformation in the soil. The final effect of various activities of microorganisms in the soil is to make the soil fit for the growth and development of higher plants.

Fig. 26.2 Structure of soil

26.3 Types of Microorganisms in Soil

Living organisms both plants and animals, constitute an important component of soil. The pioneering investigations of a number of early microbiologists showed for the first time that the soil was not an inert static material but a medium pulsating with life. The soil is now believed to be a dynamic or rather a living system, containing a dynamic population of microorganisms. Cultivated soil has relatively more population of microorganisms than the fallow land, and the soils rich in organic matter contain much more population than sandy and eroded soils. Microbes in the soil are important to us in maintaining soil fertility/productivity, cycling of nutrient elements in the biosphere and sources of industrial products such as enzymes, antibiotics, vitamins, hormones, organic acids etc. At the same time certain soil microbes are the causal agents of human and plant diseases.

The soil organisms are broadly classified in to two groups viz. soil flora and soil fauna, the detailed classification of which is as follows.

26.3.1 Soil flora

a) Microflora

• Bacteria
• Fungi, Molds, Yeast, Mushroom
• Actinomycetes, Streptomyces
• Algae e.g. BGA, Yellow Green algae, Golden brown algae.

Bacteria is again classified in

I) Heterotrophic e.g. symbiotic and non - symbiotic N2 fixers, Ammonifier, Cellulose Decomposers, Denitrifiers
II) Autrotrophic e.g. Nitrosomonas, Nitrobacter, Sulphur oxidizers, etc.

b) Macroflora

1. Microfauna: Protozoa, Nematodes
2. Macrofauna: Earthworms, moles, ants and others. As soil inhabit several diverse groups of microorganisms, but the most important amongst them are: bacteria, actinomycetes, fungi, algae and protozoa.

Relative proportion/percentage of various soil microorganisms are: bacteria - aerobic (70%), anaerobic (13 %), actinomycetes (13%), fungi/molds (3%) and others (algae, protozoa, viruses) 0.2-0.8 %.

Major groups of microorganisms are discussed in following sections:

26.4 Bacteria

Amongst the different microorganisms inhabiting in the soil, bacteria are the most abundant and predominant organisms. These are primitive, prokaryotic, microscopic and unicellular microorganisms without chlorophyll. Morphologically, soil bacteria are divided into three groups viz. cocci (round/spherical), bacilli (rod-shaped) and spirilla (cells with long wavy chains). Bacilli are most numerous followed by cocci and spirilla in soil. The most common method used for isolation of soil bacteria is the ‘dilution plate count’ method which allows the enumeration of only living cells in the soil. The size of soil bacteria varies from 0.5 to 1.0 µ in diameter and 1.0 to 10.0 µ in length. They are motile with locomotory organs flagella. Bacterial population is one-half of the total microbial biomass in the soil ranging from 1,00000 to several hundred millions per gram of soil, depending upon the physical, chemical and biological conditions of the soil.

Winogradsky (1925), on the basis of ecological characteristics classified soil microorganisms in general and bacteria in particular into two broad categories i.e. autochnotus (Indigenous species) and the zymogenous (fermentative). Autochnotus bacterial population is uniform and constant in soil, since their nutrition is derived from native soil organic matter (e.g. Arthrobacter and Nocardia, whereas zymogenous bacterial population in soil is low, as they require an external source of energy, e.g. Pseudomonas and bacillus. The population of zymogenous bacteria increases gradually when a specific substrate is added to the soil. To this category belong the cellulose decomposers, nitrogen utilizing bacteria and ammonifiers. As per the system proposed in the ‘Bergey's Manual of Systematic Bacteriology’, most of the bacteria which are predominantly encountered in soil are taxonomically included in the three orders, Pseudomonadales, Eubacteriales and Actinomycetales of the class Schizomycetes. The most common soil bacteria belong to the genera Pseudomonas, Arthrobacter, Clostridium Achromobacter, Sarcina, Enterobacter etc. The another group of bacteria common in soils is the Myxobacteria belonging to the genera Micrococcus, Chondrococcus, Archangium, Polyangium, Cyptophaga.

Bacteria are also classified on the basis of physiological activity or mode of nutrition, especially the manner in which they obtain their carbon, nitrogen, energy and other nutrient requirements.

They are broadly divided into two groups i.e. a) Autotrophs and b) Heterotrophs

• Autotrophic bacteria are capable synthesizing their food from simple inorganic nutrients, while heterotrophic bacteria depend on pre-formed food for nutrition. All autotrophic bacteria utilize CO2 (from atmosphere) as carbon source and derive energy either from sunlight (photoautotrophs, e.g. Chromatrum. Chlorobium. Rhadopseudomonas or from the oxidation of simple inorganic substances present in soil (chemoautotrophs e.g. Nitrobacter, Nitrosomonas, Thiaobacillus).
• Majority of soil bacteria are heterotrophic in nature and derive their carbon and energy from complex organic substances/organic matter, decaying roots and plant residues. They obtain their nitrogen from nitrates and ammonia compounds (proteins) present in soil and other nutrients from soil or from the decomposing organic matter. Certain bacteria also require amino acids, B-vitamins, and other growth promoting substances also.

26.4.1 Functions/role of bacteria

Bacteria bring about a number of changes and biochemical transformations in the soil and thereby directly or indirectly help in the nutrition of higher plants growing in the soil. The important transformations and processes in which soil bacteria play vital role are: decomposition of cellulose and other carbohydrates, ammonification (proteins ammonia), nitrification (ammonia-nitrites-nitrates), denitrification (release of free elemental nitrogen), biological fixation of atmospheric nitrogen (symbiotic and non-symbiotic) oxidation and reduction of sulphur and iron compounds. All these processes play a significant role in plant nutrition.

26.5 Actinomycetes

These are the organisms with characteristics common to both bacteria and fungi but yet possessing distinctive features to delimit them into a distinct category. In the strict taxonomic sense, actinomycetes are clubbed with bacteria the same class of Schizomycetes and confined to the order Actinomycetales. They are unicellular like bacteria, but produce a mycelium which is non-septate (coenocytic) and more slender, tike true bacteria they do not have distinct cell-wall and their cell wall is without chitin and cellulose (commonly found in the cell wall of fungi). On culture media unlike slimy distinct colonies of true bacteria which grow quickly, actinomycetes colonies grow slowly, show powdery consistency and stick firmly to agar surface. They produce hyphae and conidia/sporangia like fungi. Certain actinomycetes whose hyphae undergo segmentation resemble bacteria, both morphologically and physiologically.

Actinomycetes are numerous and widely distributed in soil and are next to bacteria in abundance. They are widely distributed in the soil, compost etc. Plate count estimates give values ranging from 104 to 108 per gram of soil. They are sensitive to acidity/low pH (optimum pH range 6.5 to 8.0) and waterlogged soil conditions. The population of actinomycetes increases with depth of soil even up to horizon ‘C’ of a soil profiler They are heterotrophic, aerobic and mesophilic (25-30°C) organisms and some species are commonly present in compost and manures are thermophilic growing at 55-65°C temperature (e.g. Thermoatinomycetes, Streptomyces). Actinomycetes belonging to the order of Actinomycetales are grouped under four families viz. Mycobacteriaceae, Actinomycetaceae, Streptomycetaceae and Actinoplanaceae. Actinomycetous genera, which are agriculturally and industrially important, are present in only two families of Actinomycetaceae and Strepotmycetaceae. In the order of abundance in soils, the common genera of actinomycetes are Streptomyces (nearly 70%), Nocardia and Micromonospora although Actinomycetes, Actinoplanes, Micromonospora and Streptosporangium are also generally encountered.

26.5.1 Functions of actinomycetes

• Degrade all sorts of organic substances like cellulose, polysaccharides, protein fats, organic-acids etc.
• Soil, added with organic residues/substances, is first attacked by bacteria and fungi and later by actinomycetes, because they are slow in activity and growth than bacteria and fungi.
• They decompose/degrade the more resistant and indecomposable organic substance/matter and produce a number of dark black to brown pigments which contribute to the dark color of soil humus.
• They are also responsible for subsequent further decomposition of humus (resistant material) in soil.
• They are responsible for earthy/musty odor/smell of freshly ploughed soils.
• Many genera species and strains (e.g. Streptomyces, if actinomycetes synthesize number of antibiotics like Streptomycin, Terramycin, Aureomycin etc.
• One of the species of actinomycetes, Streptomyces scabies causes disease ‘potato scab’ in potato.

26.6 Fungi

Fungi in soil are present as mycelial bits, rhizomorph or as different spores. Their number varies from a few thousand to a few million per gram of soil. Soil fungi possess filamentous mycelium composed of individual hyphae. The fungal hyphae may be aseptate/coenocytic (Mastigomycotina and Zygomycotina) or septate (Ascomycotina, Basidiomycotina and Deuteromycotina). As observed by C. K. Jackson (1975), most commonly encountered genera of fungi in soil are; Alternaria, Aspergillus, Cladosporium, Cephalosporium Botrytis, Chaetomium, Fusarium, Mucor, Penicillium, Verticillium, Trichoderma, Rhizopus, Gliocladium, Monilia, Pythium, etc. Most of these fungal genera belong to the subdivision deuteromycotina/fungi imperfeacta which lacks sexual mode of reproduction. As these soil fungi are aerobic and heterotrophic, they require abundant supply of oxygen and organic matter in soil. Fungi are dominant in acid soils, because acidic environment is not suitable for the existence of either bacteria or actinomycetes. The optimum pH range for fungi lies-between 4.5 to 6.5. They are also present in neutral and alkaline soils and some can even tolerate pH beyond 9.0

26.6.1 Functions/role of fungi

• Fungi plays significant role in soils and plant nutrition.
• They plays important role in the degradation/decomposition of cellulose, hemi cellulose, starch, pectin, lignin in the organic
• Matter added to the soil.
• Lignin which is resistant to decomposition by bacteria is mainly decomposed by fungi.
• They also serve as food for bacteria.
• Certain fungi belonging to sub-division Zygomycotina and Deuteromycotina are predaceous in nature and attack on protozoa and nematodes in soil and thus, maintain biological equilibrium in soil.
• They also plays important role in soil aggregation and in the formation of humus.
• Some soil fungi are parasitic and causes number of plant diseases such as wilts, root rots, damping-off and seedling blights e.g. Pythium, Phyiophlhora, Fusarium, Verticillium etc.
• Number of soil fungi forms mycorrhizal association with the roots of higher plants (symbiotic association of a fungus with the roots of a higher plant) and helps in mobilization of soil phosphorus and nitrogen e.g. Glomus, Gigaspora, Aculospora, (Endomycorrhiza) and Amanita, Boletus, Entoloma, Lactarius (Ectomycorrhiza).

26.7 Algae

Algae are present in most of the soils where moisture and sunlight are available. Their number in soil usually ranges from 100 to 10,000 per gram of soil. They are photoautotrophic, aerobic organisms and obtain CO₂ from atmosphere and energy from sunlight and synthesize their own food. They are unicellular, filamentous or colonial. Soil algae are divided in to four main classes or phyla as follows:

• Cyanophyta (Blue-green algae)
• Chlorophyta (Grass-green algae)
• Xanthophyta (Yellow-green algae)
• Bacillariophyta (diatoms or golden-brown algae)

Out of these four classes/phyla, blue-green algae and grass-green algae are more abundant in soil. The green-grass algae and diatoms are dominant in the soils of temperate region while blue-green algae predominate in tropical soils. Green-algae prefer acid soils while blue green algae are commonly found in neutral and alkaline soils. The most common genera of green algae found in soil are: Chlorella, Chlamydomonas, Chlorococcum, Protosiphon etc. and that of diatoms are Navicula, Pinnularia. Synedra, Frangilaria. Blue green algae are unicellular, photoautotrophic prokaryotes containing Phycocyanin pigment in addition to chlorophyll. They do not posses flagella and do not reproduce sexually. They are common in neutral to alkaline soils. The dominant genera of BGA in soil are: Chrococcus, Phormidium, Anabaena, Aphanocapra, Oscillatoria etc. Some BGA posses specialized cells known as ‘Heterocyst’ which is the sites of nitrogen fixation. BGA fixes nitrogen (non-symbiotically) in puddle paddy/water logged paddy fields (20-30 kg/ha/season). There are certain BGA which possess the character of symbiotic nitrogen fixation in association with other organisms like fungi, mosses, liverworts and aquatic ferns Azolla, e.g. Anabaena-Azolla association fix nitrogen symbiotically in rice fields.

26.7.1 Functions/role of algae or BGA

• Plays important role in the maintenance of soil fertility especially in tropical soils.
• Add organic matter to soil when die and thus increase the amount of organic carbon in soil.
• Most of soil algae (especially BGA) act as cementing agent in binding soil particles and thereby reduce/prevent soil erosion.
• Mucilage secreted by the BGA is hygroscopic in nature and thus helps in increasing water retention capacity of soil for longer time/period.
• Soil algae through the process of photosynthesis liberate large quantity of oxygen in the soil environment and thus facilitate the aeration in submerged soils or oxygenate the soil environment.
• They help in checking the loss of nitrates through leaching and drainage especially in un-cropped soils.
• They help in weathering of rocks and building up of soil structure.

26.8 Protozoa

These are unicellular, eukaryotic, colorless, and animal like organisms (Animal kingdom). They are larger than bacteria and size varying from few microns to a few centimeters. Their population in arable soil ranges from l0,000 to 1,00,000 per gram of soil and are abundant in surface soil. They can withstand adverse soil conditions as they are characterized by ‘cyst stage’ in their life cycle. Except few genera which reproduce sexually by fusion of cells, rest of them reproduces asexually by fission/binary fission. Most of the soil protozoa are motile by flagella or cilia or pseudopodia as locomotors organs. Depending upon the type of appendages provided for locomotion, protozoa are

• Rhizopoda (Sarcondia)
• Mastigophora
• Ciliophora (Ciliata)
• Sporophora (not common inhabitants of soil)

Rhizopoda consists protozoa without appendages usually have naked protoplasm without cell-wall, pseudopodia as temporary locomotory organs are present some times. Important genera are Amoeba, Biomyxa, Euglypha, etc.

Mastigophora Belongs flagellated protozoa, which are predominant in soil. Important genera are: Allention, Bodo, Cercobodo, Cercomonas, Entosiphon Spiromonas, Spongomions and Testramitus. Many members are saprophytic and some posses chlorophyll and are autotrophic in nature. In this respect, they resemble unicellular algae and hence are known as ‘Phytoflagellates’.

Ciliophora are characterized by the presence of cilia (short hair-like appendages) around their body, which helps in locomotion. The important soil inhabitants of this class are Colpidium, Colpoda, Balantiophorus, Gastrostyla, Halteria, Uroleptus, Vortiicella, Pleurotricha etc.

Protozoa are abundant in the upper layer (15 cm) of soil. Organic manures protozoa. Soil moisture, aeration, temperature and pH are the important factors affecting soil protozoa.

26.8.1 Function/role of protozoa

• Most of protozoans derive their nutrition by feeding or ingesting soil bacteria belonging to the genera Enterobacter, Agrobacterium, Bacillus, Escherichia, Micrococcus, and Pseudomonas and thus, they play important role in maintaining microbial/bacterial equilibrium in the soil.
• Some protozoa have been recently used as biological control agents against phytopathogens.
• Species of the bacterial genera viz. Enterobacter and Aerobacter are commonly used as the food base for isolation and enumeration of soil protozoans.
• Several soil protozoa cause diseases in human beings which are carried through water and other vectors, e.g. Amoebic dysentery caused by Entomobea histolytica.