Soil microbial flora - Discover Biotech

In this article, I briefly describe different soil microorganisms that constitute the soil microbial flora.

Table of Contents

Soil

The soil is the land surface of the earth, which provides the substratum for plant and animal life. The soil represents a favorable habitat for microorganisms and is inhabited by many microorganisms, such as bacteria, fungi, algae, viruses, and protozoa (figure 1). The mineral constituents of soil determine the physical structure, aeration, water-holding capacity, and availability of nutrients. The weathering of rock and the degradative metabolic activities of the soil microorganisms form the mineral constituents of soil. Microbes in the soil are important in maintaining soil fertility, cycling of nutrient elements in the biosphere, and sources of industrial products such as enzymes, antibiotics, vitamins, hormones, organic acids, etc. However, certain microbes in the soil are the causal agents of various human and plant diseases.

Bacterial population in soil

Soil bacterial population exceeds the population of other groups of microorganisms. The Bergey’s Manual of Systematic Bacteriology taxonomically includes most of the soil bacteria in three orders, Pseudomonadales, Eubacteriales, and Actinomycetales of the class Schizomycetes. Based on physiological activity bacteria are classified into two groups, i.e., autotrophs and heterotrophs. Autotrophic bacteria are capable of synthesizing their food from simple inorganic nutrients. They are of two types, i.e., photoautotrophs and chemoautotrophs. Photoautotrophs (Chromatrum, Chlorobium) utilize CO₂ as a carbon source and derive energy from sunlight, whereas chemoautotrophs (Nitrobacter, Nitrosomonas) utilize CO₂ as a carbon source and derive energy from the oxidation of simple inorganic substances present in soil.

Most of the bacteria present in soil are heterotrophic. Heterotrophic bacteria derive their carbon and energy from complex organic matter, decaying roots, and plant residues. The majority of beneficial soil-dwelling bacteria need oxygen and are therefore aerobic in nature. Those that do not require air are referred to as anaerobic and tend to cause putrefaction of dead organic matter. It is generally agreed that there are many species of bacteria in soil that are yet to be discovered.

Bacteria perform certain processes in soil

Bacteria brought about several changes and biochemical transformations in the soil. Thus, they directly or indirectly help provide nutrition to higher plants growing in the soil. The important transformations and processes in which soil bacteria play a vital role are the decomposition of cellulose and other carbohydrates, ammonification, nitrification, denitrification, biological fixation of atmospheric nitrogen, oxidation, and reduction of sulfur and iron compounds.

The bacterial genera Nocardia, Streptomyces, and Micromonospora belong to the order Actinomycetes (aerobic and heterotrophic) and are capable of degrading many complex organic substances. These bacterial species thus play an important role in building soil fertility. The actinomycetes are also able to synthesize and excrete antibiotics, e.g., streptomycin is produced by growing soil actinomycetes in pure culture.

Soil bacteria carry out ammonification

The soil bacteria belong to the genera Bacillus and Pseudomonas carry out the process of ammonification. Amino acids are subject to different pathways for microbial decomposition, a process known as ammonification, in which ammonia is produced. Microorganisms convert ammonia to nitrate in a process called nitrification. It is a two-step process and a different group of bacteria performs each step. The first step is ammonia oxidation to nitrite, performed by ammonia-oxidizing bacteria including Nitrosomonas, Nitrosococcus, and Nitrosovibrio. The second step involves the oxidation of nitrite to nitrate, which is done by nitrite-oxidizing bacteria (genera include Nitrobacter and Nitrospina).

Dentrification is a process where the transformation of nitrates to gaseous nitrogen is accomplished by a series of biochemical reactions. Species of several genera of bacteria are capable of transforming NO^3- to N₂, e.g., Agrobacterium, Bacillus, Chromobacterium, Flavobacterium, Achromobacter, Hyphomicrobium, Pseudomonas, Alcaligenes, Thiobacillus and Vibrio.

Many microorganisms can use molecular nitrogen in the atmosphere as their nitrogen source. Nitrogen fixation is the process of conversion of molecular nitrogen into ammonia by soil microorganisms. The process is carried out by both non-symbiotic and symbiotic microorganisms. Non-symbiotic microorganisms live freely and independently in the soil whereas symbiotic microorganisms live in the roots of plants. Non-symbiotic nitrogen fixation is carried out by the bacterial genera Clostridium and Azotobacter. The genus Rhizobium carries out the symbiotic nitrogen fixation. Rhizobium accomplishes the process in association with the plants belonging to the family leguminoceae. This association process is beneficial for both plants and bacteria. The bacteria convert atmospheric nitrogen into fixed nitrogen, which is available to the plant, and in turn, the bacteria derive nutrients from plant tissues.

Soil fungi

More than hundreds of different species of fungi inhabit the soil. They prefer to live in the soil in an aerobic condition. Fungi perform important functions within the soil like nutrient cycling, disease suppression, and water dynamics. These make plants healthier and more vigorous. Fungi exist in both the mycelial and spore stages.

Soil fungi are microscopic plant-like cells that grow in long threadlike structures or hyphae that make a mass called mycelium. The mycelium absorbs nutrients from the roots it has colonized, surface organic matter, or the soil. The fungi throw up their fruiting bodies from the mycelia. The fruiting bodies, e.g., mushrooms, the visible part above the soil contain millions of spores. When the fruiting body bursts, these spores are dispersed through the air to settle in fresh environments and can lie dormant for up to years. They wait for the favorable conditions to get activated.

The soil improves its physical structure by accumulating mycelium mold within it. Fungi actively decompose the major constituents of plant tissues namely cellulose, lignin, and pectin. Saprophytic fungi convert dead organic matter into fungal biomass, carbon dioxide, and organic acids. These fungi have enzymes that work to digest the cellulose and lignin found in the organic matter, with the lignin being an important carbon source for many organisms. If this digestion didn’t happen, organic material would accumulate until the forest became a huge rubbish dump of dead leaves and trees. Fungi consume organic matter and thus play an important role in immobilizing and retaining nutrients in the soil.

Fungi in a symbiotic association

Mycorrhizal fungi are the best-known mutualists as they live in a mutually beneficial relationship with plants. They mainly make trees as their partners. However, they form a partnership with some plants. Their presence significantly increases the roots’ effectiveness. In a mycorrhizal association, the fungus colonizes the host plant’s roots, either intracellularly as in arbuscular mycorrhizal fungi (AMF), or extracellularly as in ectomycorrhizal fungi.

Arbuscular mycorrhiza (VAM) is the most common form of mycorrhiza, especially in agricultural plant associations. The fungus gets relatively constant and direct access to carbohydrates, such as glucose and sucrose. The carbohydrates are translocated from the leaves to the root tissue. From the root, they are transferred to the plant’s fungal partners. Plant roots can’t receive phosphate ions demineralized in soils with a basic pH. However, the mycelium of the mycorrhizal fungus accesses these phosphorus sources to the plants they colonize.

Parasitic fungi

A group of fungi also known as pathogenic fungi (parasitic fungi), is the second largest group present in the soil. This group includes the genera Verticillium, Phytophthora, Rhizoctonia, and Pythium. These fungi being parasitic on plants, draw all the nutrients from the plant and finally cause its death.

Fungi can tolerate a wide range of pH and tend to dominate over bacteria and actinomycetes in acid soils. They can survive in the soil for long periods even through periods of water deficit by living in dead plant roots and as spores or fragments of hyphae.

Soil algae

The population of algae in soil is usually smaller than bacteria and fungi. They are photoautotrophic, aerobic organisms, and obtain CO₂ from the atmosphere and energy from sunlight. They are predominantly present on the soil surface or just below it. The accumulation of organic matter begins on bare and fretted land because of their ability to carry out photosynthesis and other metabolic activities.

The green algae and diatoms are the major types of algae present in the soil. Soil algae are divided into four major classes, i.e., Cyanophyta (blue-green algae), Chlorophyta (grass-green algae), Xanthophyta (Yellow-green algae), and Bacillariophyta (diatoms). Cyanophyta (blue-green algae) and Chlorophyta (grass-green algae) are more abundant in soil. Algae of the class Chlorophyta and Bacillariophyta are dominant in the temperate region of soil. Blue-green algae are dominant in tropical soils.

The blue-green algae

Cyanobacteria, also known as blue-green algae are unicellular, oxygenic photosynthetic prokaryotes that grow on the surface of freshly exposed rocks. The accumulation of their cells on the surface of rocks results in the simultaneous deposition of organic matter. This gives a nutrient base that will support the growth of other bacterial species. Cyanobacteria are not heterotrophic decomposers like bacteria, rather they trap the energy of sunlight with the help of the green pigment chlorophyll and help organisms to carry on photosynthesis. Thus, cyanobacteria are autotrophic producers of their food from simple raw materials.

Chrococcus, Phormidium, Anabaena, Aphanocapra, Oscillatoria, etc. are some of the dominant genera of blue-green algae in soil. Cyanobacteria are abundant in neutral to alkaline soil. They secrete a substance known as mucilage, which helps in increasing the water retention capacity of the soil. Cyanobacteria convert rock to soil. This conversion is the first step in rock-plant succession.

The blue-green algae helps to bind soil particles and thus prevent soil erosion. In un-cropped soil, soil algae check the loss of nitrates through leaching and drainage. They liberate large quantities of oxygen through photosynthesis in the soil environment and thus facilitate aeration in submerged soils. In tropical soils, soil algae maintain soil fertility.

Soil protozoa

These are larger than bacteria and found in abundance on the soil surface. Most soil protozoa are flagellates or amoebas. Their dominant mode of nutrition involves the ingestion of bacteria. They can withstand adverse soil conditions characterized by the “cyst stage” in their life cycle. They mostly reproduce asexually by binary fission. Most soil protozoa possess flagella, cilia, or pseudopodia as their locomotive organ. The type of locomotion classified protozoa into four different classes: Rhizopoda, Mastigophora, Ciliophora, and Sporophora.

Amoeba, Biomyxa, Euglypha, etc. are some of the important genera that belong to the class Rhizopoda. Class Rhizopoda includes protozoa without appendages, having naked protoplasm without cell walls. Class Mastigophora includes the flagellated protozoa, which are predominant in soil. This class includes both saprophytic and autotrophic protozoa. The class Ciliophora, as the name suggests includes members having cilia around their bodies. Cilia are short, hair-like appendages, which help in locomotion.

Protozoa ingest bacteria and thus they play an important role in maintaining bacterial equilibrium in soil. They depend upon the soil bacterial genera Agrobacterium, Bacillus, Enterobacter, Escherichia, Micrococcus, and Pseudomonas. Some protozoa can be used as biological control agents against phytopathogens.

Presence of viruses in soil

The addition of plant and animal wastes places bacterial viruses, and plant and animal viruses in the soil. Viruses in soil are of great importance as they may influence the ecology of soil biological communities through an ability to transfer genes from host to host and as a potential cause of microbial mortality. Soils probably harbor many novel viral species that may represent a large reservoir of genetic diversity. Different forms of viruses, such as tailed, spherical, rod-shaped, filamentous, and bacilliform particles are detected in the soil samples.

Soil-borne wheat mosaic virus (SBWMV) can cause severe stunting and mosaic in susceptible wheat, barley, and rye cultivars. This virus affects autumn-sown small grains. Soil-borne viral infection may include irregular, chlorotic patches in the field. However, several other viruses or other biotic and abiotic factors cause similar symptoms.

Conclusion

Microbes in the soil are important to us in maintaining soil fertility, cycling of nutrient elements in the biosphere, and sources of industrial products such as enzymes, antibiotics, vitamins, hormones, organic acids, etc.

Soil bacterial population exceeds the population of other groups of microorganisms. The majority of the beneficial soil-dwelling bacteria are aerobic. The soil bacteria belong to the genera Bacillus and Pseudomonas carry out the process of ammonification. Nitrogen fixation is the process of conversion of molecular nitrogen into ammonia by soil microorganisms. Both non-symbiotic and symbiotic microorganisms carry out the process.

Soil fungi are microscopic plant-like cells that grow in long threadlike structures or hyphae that make a mass called mycelium. The mycelium absorbs nutrients from the roots it has colonized, surface organic matter, or the soil. Mycorrhizal fungi are the best-known mutualists as they live in a mutually beneficial relationship with plants. A group of fungi also known as pathogenic fungi (parasitic fungi), is the second largest group present in the soil. Fungi can tolerate a wide range of pH and therefore tend to dominate over bacteria and actinomycetes in acid soils.

The population of algae in soil is usually smaller than bacteria and fungi. They are photoautotrophic, aerobic organisms and obtain CO₂ from the atmosphere and energy from sunlight. They are predominantly present on the soil surface or just below it due to their photosynthetic nature. Most soil protozoa are flagellates or amoebas. These are larger than bacteria and found in abundance on the soil surface. They mostly reproduce asexually by binary fission. Most of the soil protozoa possess flagella, cilia, or pseudopodia as their locomotive organ. As protozoa ingest bacteria and thus they play an important role in maintaining bacterial equilibrium in soil.