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Soil Microorganisms – Types, Examples, Factors, Importance 

Table of Contents

What are Soil Microorganisms or Soil Microflora?

The term “soil microflora” is used to describe the community of microorganisms that make up most of the soil’s organic matter and a smaller, colloidal amount of humus.

  • Soil microflora consists of bacteria, fungus, algae, and protozoa, the five primary classes of microorganisms.
  • Each subpopulation of the microorganisms that make up the soil’s microbial community contributes significantly to the overall health of the soil and the plants it supports.
  • Soil food webs are made up of the communities of microorganisms that live in and on the soil.
  • Soil microorganisms interact with the biotic components of the environment, such as plants, animals, and humans, and together they form a food web.
  • The primary producers or contributors to the first trophic level of the soil food web are the soil’s organic materials, such as plant and animal wastes.
  • The second trophic level consists of primary consumers like decomposers and mutualists like bacteria and fungi.
  • The third trophic level of the soil food chain consists of secondary consumers like shredders and predators (such nematodes, arthropods, and protozoans).
  • The tertiary consumers in the soil food web are preyed upon by larger animals and birds.

What is Soil Microfauna?

  • Size-wise, they’re smaller than 0.1 mm.
  • Soil microfauna, such as nematodes and protozoa, prey upon the soil’s major decomposers and mutualists (bacteria, mycorrhizal fungi and saprophytic fungi).
  • Because of this, they serve as both predators and parasites (cause crop diseases).
  • Some of them eat soil particles and the thin layer of water that covers the ground, but roots are their primary food source.

What is Soil Microflora?

  • Bacteria and fungi make up the bulk of this group.
  • Numerous bacteria are involved in many of the soil’s transformation processes, including rock weathering, organic matter decomposition, and nutrient recycling.
  • In addition to their role in decomposition, fungi contribute to soil aggregation and nutrient restoration.

What is Soil Microbiology?

  • Soil microbiology is the study of soil organisms, including their roles and the ecological effects they have on soil.

Factors Affecting Microbial Community in Soil

Like higher plants, the nourishment, growth, and activity of soil microorganisms (Flora & Fauna) are totally reliant on soil. The primary soil variables that affect the abundance, distribution, and activity of soil microorganisms. The abundance and diversity of life, as well as their behaviours, are profoundly influenced by a number of things. Soil fertility can be affected by shifts in microbial activity, which can be caused by changes in any of the aforementioned variables. All of these elements that have an effect on the micro flora/organisms and their activity in the soil are covered in brief in the following paragraphs.

1. Cultural practices (Tillage)

  • Soil organisms respond to the cultural practises of cultivating the soil, rotating crops, applying manures and fertilisers, liming and gypsum, and spraying for pests and fungi and weeds.
  • Soil aeration and sunlight exposure, brought about by ploughing and tillage, boost the activity of living organisms in the soil, especially bacteria.
  • Soil fertility is increased through crop rotation that includes legumes because they help to preserve a healthy population of microorganisms, especially nitrogen-fixing bacteria.
  • When acid soils are limed, bacteria and actinomycetes become more active while the fungus population decreases.

2. Soil fertility

  • The number and activity of soil microbes is significantly affected by the soil’s overall fertility.
  • Soil fertility is determined by the availability of nutrients like nitrogen, phosphorus, and potassium that are needed by plants and bacteria.
  • However, soil microflora exerts a far more significant effect on soil fertility.

3. Soil moisture

  • The microorganisms can use water (soil moisture) in two ways: first, as a source of nutrients and a supplier of hydrogen and oxygen; and second, as a solvent and transporter of other food ingredients.
  • The ideal wetness for microbial activity and population growth is between 20% and 60%.
  • Lack of oxygen in the soil allows anaerobic microflora to flourish in waterlogged environments, whereas aerobic microbes are repressed.
  • While some bacteria in the soil die from tissue dehydration, others transform into dormant stages like spores or cysts to survive dry circumstances.

4. Soil temperature

  • The rate of physiological activity, such as enzyme activity, is directly affected by temperature, and the rate of other physico-chemical processes, such as the diffusion and solubility of nutrients, mineral weathering and evaporation, is indirectly affected by temperature.
  • There is a general trend toward more biological activity as temperatures rise, within certain bounds.
  • Common soil organisms have an active temperature range of roughly 0°C to about 60 °C. However, it is highly unlikely that any single species will be active across the full range.

5. Root Exudates

  • The distribution, density, and activity of soil microorganisms are also influenced by root exudates in plant-growing soil.
  • The quality and quantity of microorganisms in the rhizosphere are affected, either directly or indirectly, by the root exudates and sloughed off material of root surfaces.
  • Soil bacteria respond strongly to the sugars, organic acids, amino acids, sterols, vitamins, and other growth factors found in root exudates.

6. Soil Nature 

  • Microbial population size and composition are affected by the soil’s physical, chemical, and physico-chemical composition as well as its nutrient status.
  • Healthy soils, both chemically and physically, have the ideal balance of air and water for thriving microbes.
  • The presence or absence of particular microbes and their activity is also influenced by the macro and micronutrients and organic humus components.

7. Organic Matter of Soil

  • Given that organic matter is the primary source of both energy and food for the vast majority of soil organisms, it exerts considerable control over the composition of the microbial community.
  • Soil microorganisms and their population and activity are affected by organic matter either immediately or indirectly.
  • In turn, this affects the microorganisms’ ability to function in the soil by changing its structure and texture.

8. Light

  • Most microorganisms, with the exception of algae, are severely damaged by direct sunshine. That’s why the top centimetre or two of soil is typically sterile or free of microorganisms: it never gets exposed to the elements.
  • The result of the sun’s rays is a rise in temperature of more than 45 degrees.

9. Soil air (Aeration)

  • Increased soil aeration (oxygen and, occasionally, carbon monoxide) is crucial for microbial growth.
  • In order to survive, microbes in the soil must take in oxygen from the air and release carbon dioxide.
  • Soil microorganisms are divided into three types based on their oxygen needs: aerobic (need oxygen for similar functions), anaerobic (don’t need oxygen), and microaerophilic (requiring low concentration of oxygen).

10. Soil pH

  • Extreme conditions are not fatal to most organisms, but they do force cells to expend energy keeping their pH levels steady (pH 7.0).
  • The composition of soil microorganisms, both in terms of number and quality, is affected by the soil’s reaction.
  • Fungi grow in acidic reaction between pH 4.5 and 6.5, while actinomycetes prefer slightly alkaline soil reactions. Most soil bacteria, blue-green algae, diatoms, and protozoa require a neutral or slightly alkaline reaction between pH 4.5 and 8.0.
  • The kinds of bacteria that thrive in soil are affected by a number of factors, including human activities.

11. Food and energy supply

  • Added plant residues or organic materials provide sustenance and energy for the vast majority of soil microorganisms.
  • Biological processes in microbes demand energy.
  • Autotrophs obtain their energy needs from either the sun or the oxidation of simple inorganic molecules (chemoautotrophs), while heterotrophs use the energy released by the oxidation of complex organic compounds in soil (Photoautotroph).
  • Therefore, the organic matter provides both food and energy for the soil organisms.

12. Microbial interactions

  • Soil microbial population and activity are profoundly affected by the nature of the associations between different organisms, whether they be symbiotic or hostile.
  • Protozoa and certain mycobacteria, which feed on bacteria, may be able to reduce or even eradicate these microbes due to their predatory nature.
  • Bacteria and other soil organisms benefit from the release of organic acids by fungus, an increase in oxygen from the activity of algae, a shift in soil response, etc.

Types of Soil Microorganisms

  • Soil contains a greater variety of microorganisms than any other environment on Earth, with concentrations of 107 to 1010 cells per gramme.
  • Lively microbial growth in soil facilitates global elemental cycle and nutrition availability to plants.
  • There would be no plants, no herbivores, and so on up the food chain if soil bacteria weren’t present.
  • A wide variety of microhabitats are provided by the complicated physical and chemical factors that sustain soil’s microbial populations.
  • Soil consists of both solid particles and the air and water-filled spaces between them.
  • Soil texture influences the total pore space and, by extension, gas diffusion. For instance, because sandier soils have more open places for water to drain than clayier soils, sandier soils are often preferred.
  • The porous structure is particularly important since it fosters the ideal conditions for microbial growth.
  • Here microorganisms are living in hydrophobic environments, protected by thin water films on particle surfaces, with abundant oxygen readily available for diffusion-based replenishment.

There are seven main classes of microorganisms in soil. In other words, they are

  1. Bacteria
  2. Fungi
  3. Actinomycetes
  4. Protozoa 
  5. Blue-green algae (cyanobacteria)
  6. Viruses
  7. Nematodes

Bacteria as a Soil Microorganisms

  • Bacteria far outnumber and outtype all other soil microorganisms.
  • There are more than a few million, and potentially even a few billion, of them in only a single gramme of soil.
  • The amount and types of soil bacteria are often counted using direct microscopic methods or plate counts.
  • Prokaryotic species, such as bacteria and archaea, are the smallest in the soil after viruses.
  • Soil microorganisms play a crucial role in the environment, especially in nitrogen fixation, and are the most numerous of all soil creatures.
  • Soil minerals can be colonised by certain bacteria, which can then affect their weathering and decomposition.
  • The variety of bacteria in the soil is influenced by its general chemical make-up. The greater the concentration of minerals, the greater the potential for bacterial growth in that location.
  • The aggregates that these bacteria generate are beneficial to the soil as a whole.

Types and Examples of Bacteria found in Soil

Variations in soil pH, temperature, moisture content, and nutrient availability all have an effect on the bacterial population. Bacteria in the soil can be roughly divided up into the following categories based on their function.

1. Decomposers

  • They help turn dead plants and animals into usable nutrients. Before fungi can get to work, bacteria must first break down the dead organic matter.
  • Some common examples include Bacillus subtilis and Pseudomonas fluorescens.

2. Nitrogen Fixers or Nitrifying Bacteria

  • These microbes convert nitrogen from the air into a form that plants can use.
  • Nitrite-forming bacteria (Nitrosomonas spp. ), first, convert ammonia to nitrites (NO2-), and nitrate-forming bacteria (Nitrobacter spp. ), second, convert nitrites to nitrates (NO3-).
  • The soil’s fertility is increased, and they favour an alkaline environment.

3. Denitrifiers

  • They convert nitrates back into atmospheric nitrogen, hence lowering the soil’s nitrogen content.

4. Mutualists

  • Mutualistic bacteria called Rhizobium associate with the roots of legumes to produce root nodules, which are responsible for fixing atmospheric nitrogen in the soil.
  • Nitrogen fixing bacteria that are not restricted to a particular environment include the Azotobacter, Azospirillum, and Clostridium species.

5. Pathogenic Bacteria

  • Plant diseases like bacterial blight, bacterial canker, and black rot are caused by only a handful of bacterial species. They can spread rapidly and inflict extensive damage to many different kinds of crops, from the leaves all the way to the ground.
  • Bacterial speck of tomato is caused by Pseudomonas syringae, and citrus canker is caused by Xanthomonas axonopodis pv. citri.

6. Disease suppressors

  • Some species of the soil bacterial population produce antibiotics that protect plants from disease-causing or pathogenic organisms or plant diseases.
  • Diverse bacterial populations compete for the same nutrients, minerals, and water to preserve the homeostasis of the soil environment.

7. Sulfur oxidizers

  • Some bacteria (such as Thermothrix, Thiobacillus, etc.) convert soil-based sulphides into sulphates.
  • Sulfides cannot be utilised by plants, hence they must be transformed into a form that plants can utilise.

8. Actinomycetes or Actinobacteria

  • They are a type of filamentous bacteria that gives soil its distinctive odour, shape, and texture by secreting the chemical geosmin.
  • As with fungus, they breakdown organic leftovers such as chitin, lignin, etc.

Positive effects of Bacteria in Soil

  • Numerous ecosystem services are provided by soil bacterial populations that have direct and indirect effects on the health and productivity of soil.
  • Many soil bacteria secrete polysaccharides or glycoproteins that coat the soil particle’s outside. As cementing agents, these compounds strengthen the soil.
  • Bacteria participate in several biogeochemical cycles, including the nitrogen cycle and the carbon cycle, where they provide a wide variety of nutrients for the ground and the plants that grow there.
  • Natural succession is aided by microorganisms that boost soil quality, ensuring the continued viability of emerging plant groups.
  • In addition, bacteria play a crucial role in the release of nutrients and trace Enzymes elements from the mineral soil fraction, as well as in the enzymatic decomposition of complex organic and Soil compounds to nutrients.
  • Soil bacterial populations are good barometers of soil health.

Negative effects of Bacteria in Soil

  • The presence of pathogenic bacteria in the soil has the potential to negatively impact crop health, which in turn reduces agricultural yields and ultimately leads to crop loss.
  • There are certain bacteria that are known to disrupt the delicate ecological balance of soil, leading to lower fertility and overall soil health.
  • Soil-dwelling pathogens are another potential source of plant illness.
  • Soil’s pH, cation exchange capacity, and nutrient content are only some of the chemical qualities that could shift as a result of the discharge of various byproducts.

Fungi as a Soil Microorganisms

  • In the soil, you can find both fungi and bacteria.
  • Beneficial symbiotic relationships between plants and other species, as well as the nutritional value that fungi add to the soil, highlight the importance of fungi to the ecosystem.
  • The size, shape, and colour of the reproductive spores that are utilised to spread the fungus from generation to generation are the primary criteria for classifying fungi into different species.
  • Environmental factors that affect the spread and abundance of bacteria and actinomycetes also have a significant impact on fungal populations.
  • Most fungi require organic matter as a source of nutrition, hence the quality and amount of organic matter in the soil is directly related to the growth of fungi.
  • Fungi gain more from acidic soils than bacteria do.
  • Since fungi are aerobic, or dependent on oxygen, and the higher the moisture content in the soil, the less oxygen there is for them, fungus do best in dry, desert soils.

Types and Examples of Fungi Found in Soil

1. Decomposers

  • Active decomposers such as fungi are necessary for the breakdown of bacterially resistant organic compounds such as cellulose, chitin, lignin, and pectin, all of which are found in woody or complex organic debris.
  • Also, they are crucial in nutrient security because they immobilise soil nutrients.

2. Mycelial fungi

  • They are multicellular and extend their hyphae deep into the earth to generate mycelium, a thick network.
  • The mycelium entangles soil particles to facilitate their binding or aggregation.
  • They create aggregates of water-resistant soil.

3. Disease suppressors

  • They generate fungal enzymes and antibiotic-like compounds that inhibit the growth of other fungus, soil microbes, and diseases.

4. Mutualists

  • Arbuscular mycorrhiza (VAM) are arbuscule-bearing fungus. These growths are created within the root’s cortical cells, which have numerous tiny projections into root cells.
  • Their hyphae extend beyond the root, which strengthens the connection between the soil and plant. In addition to increasing the availability of water and nutrients, they shield the roots from pests and diseases.

5. Pathogens

  • Some spores of Phytophthora, Rhizoctonia, and Pythium species destroy live tissue by causing sores, blisters, wilting, and other apparent signs.
  • Pathogenic fungus spores remain latent in the soil.

Positive effects of fungi in Soil

Fungi are a vital component of soil biodiversity, and this diverse group of organisms can assist in addressing global issues such as climate change and famine. The relationship between fungi and vegetation, as well as carbon and nutrient cycle, is intimate. As a result, among other ecosystem activities, they are key drivers of soil health and carbon sequestration. Let’s look at the benefits of fungus.

1. Nutrient Cycling

  • Fungi are capable of transforming nutrients into forms that are used for plants.
  • Some fungi are decomposers, which means they decompose plant and animal matter, hence cycling nutrients and increasing their soil availability.
  • They can also promote nitrogen fixation and phosphorus mobilisation, two of the most essential elements for plant growth and yield.

2. Carbon Cycling and Climate regulation

  • Important contributors to the soil carbon supply include fungi. They contribute significantly to the carbon cycle via the soil food web.
  • Other species, such as mycorrhizal fungi, which live in symbiotic relationship with plant roots, provide more stable carbon supplies than decomposers.
  • Fungi are heterotrophic creatures; hence, they rely on photosynthetic carbon to generate energy, with certain species obtaining this carbon through plant root exudates.
  • Together, plants and fungi engage in a process known as soil carbon sequestration, which involves absorbing carbon from the atmosphere and storing it in the soil for decades or even centuries.
  • This essential activity not only enhances soil fertility, but it can also assist in reducing the extra carbon that human activities have added to the environment. According to a study, biodiverse soils can absorb up to 10 tonnes of CO2 per hectare every year.

3. Nutrition and food security 

  • Mushrooms are a staple in the diets of many people throughout the world. These edible mushrooms are rich in vitamins B, C, and D, fibre, minerals such as potassium, phosphorus, and calcium, and a good source of protein.
  • In terms of protein content, mushrooms actually rank above vegetables for a number of varieties. As a result, edible mushrooms are seen as a suitable substitute for meat in vegetarian/vegan diets and in the diets of individuals who lack access to meat.
  • In addition, edible mushrooms can be grown using agricultural waste, do not require fertile soil, and do not compete with other food crops for available resources.
  • Consequently, mushroom growing can reduce agro-waste while simultaneously enhancing food supply, farmer income, and job possibilities.

4. Human Health

  • In addition to their environmental benefits, fungus can provide health benefits for humans. In fact, six percent of edible mushrooms include therapeutic compounds that can aid in illness prevention and immune system enhancement.
  • Shiitake, for example, exhibit antiviral characteristics and can lower serum cholesterol. Other species are known to possess a variety of additional benefits, including tumour and AIDS development inhibition, anti-oxidant properties, and anti-diabetic effects.

5. Environmental protection

  • Various environmental pollutants, such as plastic and other petroleum-based products, pharmaceuticals and personal care products, and oil, are degraded by fungi.
  • Some of these compounds are persistent poisons, which means that they take a long time to break down in the environment and accumulate in humans and other organisms, causing harmful effects. Consequently, fungi are a potent tool for reducing environmental pollution.
  • In addition, research indicates that certain fungal species can aid in ecosystem restoration by promoting reforestation in degraded soils, as well as serve as pesticides as pathogens of arthropods and nematodes.

6. Sustainable materials

  • Mycelium, the root structure of mushrooms, is currently being used in substitution of non-renewable materials such as plastic, synthetic, and animal-based items.
  • Mycelium-derived products are biodegradable and require less water and land to produce.
  • Currently available mycelium-based items include packaging, clothing, footwear, sustainable leather, and skin care products, among others.

Negative effects of fungi in Soil

  • Pathogenic fungi in the soil are responsible for a wide variety of plant illnesses by attacking plant tissue and leaving the host plant weak and malnourished.
  • Fungi not only have direct effects on plants, but also alter the relationships between them, shifting the competitive balance between species.
  • Seedlings are vulnerable to attack by mycorrhiza and fungal diseases, which can have negative effects on plant population dynamics.

Algae as a Soil Microorganisms

  • Algae tend to make up a lesser percentage of the soil population than either bacteria or fungi.
  • Green algae and diatoms are the most common forms seen here.
  • Because of their photosynthetic makeup, they are typically found on or near the soil’s surface.
  • Algae’s metabolic activities in healthy soil are overshadowed by those of bacteria and fungi.
  • However, algae can conduct noticeable and helpful alterations under some conditions. For instance, because of their capacity for photosynthesis and other metabolic activities, they may kickstart the accumulation of organic matter on barren and degraded areas. Some desert soils have been found to exhibit this property.
  • There is evidence that cyanobacteria, a type of oxygenic photosynthetic bacteria, colonises newly exposed rock surfaces, where their cells accumulate and cause the concomitant deposition of organic materials. This creates a nutritional foundation upon which more bacterial species can flourish.
  • Initial algal growth and bacterial activity clear the path for subsequent microbial development.
  • Acids produced by microbial metabolism progressively degrade the rock’s mineral contents. As organic matter and dissolved minerals continue to accumulate, the environment becomes conducive to the development of lichens, followed by mosses, and finally, higher plants.
  • It is the cyanobacteria that initiate the initial stage of rock plant succession, the breakdown of rock into soil.

Types and Examples of Algae Found in Soil

1. Cyanophyceae

  • They are often blue-green to violet in hue, as they contain chlorophyll and pigments.

2. Chlorophyceae

  • They possess solely chlorophyll and appear green.

3. Bacillariaceae

  • They are brown and contain both chlorophyll and pigments.

Positive effects of Algae

  • The deposition of cyanobacteria over the bare rock surface supplies the organic matter or nutrient base for the growth of bacterial and fungal species.
  • By continually depositing organic matter and dissolved minerals across the rocks, they perform a crucial role in changing rock into soil, allowing for the growth of lichens, mosses, and eventually the higher plants.
  • Especially in tropical regions, they help to keep the soil fertile. In addition to increasing the amount of organic carbon in soil, the decomposition of algae also provides the organic matter needed by bacteria and fungi to thrive. As a cementing agent, they help soil aggregate, which keeps more water and nutrients in the ground.
  • Through the process of photosynthesis, algae produce oxygen by dividing carbon dioxide from the air and release it into the water, so enhancing the circulation of oxygen in the subsoil. They also aid in the breakdown of rocks through weathering and the development of soil structure.

Negative effects of Blue-green algae in Soil

  • Blue-green algae can cause algal blooms, which then decompose and release toxins into the soil, which can have a negative effect on plants either immediately or later.
  • When the soil’s cyanobacteria population drops dramatically, oxygen levels drop and certain microorganisms die off.

Protozoa as a Soil Microorganism

  • Flagellates and amoebas make up the bulk of soil protozoa, with populations ranging from tens to hundreds of thousands per gramme in wet soils high in organic matter. Since consuming bacteria is their primary source of sustenance, they are of interest to microbiologists.
  • The fact that they show a preference for particular microbial species is of scholarly significance.
  • Protozoa may have a role in keeping the microbial community in soil in some sort of balance, as not all bacteria can serve as a food source for them.

Types of Protozoa Found in Soil

1. Flagellates

  • There is a lot riding on these protozoa, as they are the most common and have a major impact on the cycle of nutrients. Soil ammonium, the form of nitrogen available to plants, is produced in large quantities as a result of their feeding on bacteria.
  • They are able to traverse the water coating on soil particles by agitating a whip-like device called a flagellum.
  • They feed on bacteria by entering pore holes that larger protozoa can’t access due to their small size and pliability.
  • Flagellates are real aerobes, and finding them in soil means there is at least 6 parts per million of oxygen there.

2. Amoebae

  • Amoebae are the ultimate “shape-shifters” that we’ve all seen or read about. Protozoan amoeba come in two forms: those that are nude and those that have testes.
  • They go where they need to go by erecting “pseudopods,” which are like feet and help them travel toward the nearest cluster of bacteria.
  • The naked can easily shift their form and investigate microscopic areas where there is bacterial activity. This feature greatly increases their value in nutrient cycling.
  • Clay is one type of soil that is easily recognisable due to its porous texture. Naked amoebae are crucial to the wellbeing of plants and soil in these environments.
  • Those amoebae that generate a testate, or tough outer shell, are called testate amoebae. The bigger soil pores found in sand and silt are ideal for their proliferation.

3. Ciliates

  • The cilia, which are essentially tiny hairs, move around the cell like oars, allowing the cell to move.
  • Often used as a precursor to or diagnostic of anaerobic conditions, these organisms are facultative, meaning they can survive in low oxygen (below 6 ppm Oxygen) environments.
  • The cilia create tiny water currents that transport bacteria to the ciliate’s feeding area, the cytostome.
  • Like other protozoa, they can hibernate in protective cysts until soil conditions improve.

Positive effects of Protozoa in Soil

  • Mineralization of nutrients by protozoa makes them accessible to plants and other soil organisms.
  • Cellular nitrogen is less abundant in protozoa (and nematodes) than in the bacteria they consume. (Protozoans have a carbon-to-nitrogen ratio of 10:1 or higher, while bacteria have a range of 3:1-10:1). Protozoa can’t get enough carbon from the bacteria they eat because bacteria have too much nitrogen. Ammonium (NH4+) is the byproduct when too much nitrogen is present. This most often manifests itself close to the plant’s roots. While most of the ammonium is quickly taken up by bacteria and other organisms, the plant is able to use a small amount. (For a visual description of mineralization and immobilisation, see the accompanying figure.)
  • Protozoa play a part in controlling bacterial abundances. Protozoa, through their grazing behaviour, promote the expansion of bacterial populations (and, in turn, decomposition rates and soil aggregation.) While the reasons for this are still up for debate, we can liken grazing to trimming a tree: just the right amount encourages development, while too much stunts it or alters the composition of the bacterial population.
  • Protozoa not only help to decrease disease by competing with or feeding on pathogens, but they are also a vital food source for other soil organisms.

Negative effects of Protozoa in Soil

  • Since most protozoan diets consist of soil bacteria, protozoa presence in soil can have an impact on the diversity of soil bacteria.
  • It’s possible that certain protozoa are detrimental to plants and thus reduce crop health and agricultural productivity.

Actinomycetes as a Soil Microorganism

  • As many as millions of actinomycetes are present per gramme of soil.
  • Nocardia, Streptomyces, and Micromonosporium are the major genera inside the soil.
  • Actinomycetes are capable of decomposing a wide array of complex organic compounds and, as a result, serve a crucial role in enhancing soil fertility.
  • Antibiotic production is one of the actinomycetes’ most distinguishing traits.
  • Streptomycin, neomycin, erythromycin, and tetracycline are among examples.

Positive effects of Actinomycetes in Soil

  • Contribute to organic acid synthesis.
  • Facilitate Nitrogen fixation.
  • The breakdown of organic substance.
  • Actinomycetes are bacteria that promote plant growth.
  • Production of growth regulators for plants.
  • Siderophores development.
  • Actinomycetes as growth-promoting agents for plants.
  • Actinomycetes as agents of biocontrol.
  • Actinomycetes as a source of plant growth hormone synthesis (indole3-acetic acid).
  • Actinomycetes contribute to biocorrosion.
  • Actinomycetes produce numerous enzymes that degrade complex organic compounds in soil and sediments, including protease, cellulase, amylase, gelatinase, lectinase, catalase, chitinase, and ureases.
  • Actinomycetes are responsible for the breakdown of pesticides with diverse chemical structures, such as organochlorines, s-triazines, triazinones, carbamates, organophosphates, organophosphonates, acetanilides, and sulfonylureas.
  • Organic phosphate is mineralized and released by the phosphatase enzyme, which is excreted by certain microbes. Actinobacteria that are closely related to the genera Saccharopolyspora, Thermobifida, and Thermonospora. 

Negative effects of Actinomycetes in Soil

  • Actinomycetes products may reduce soil microbial diversity.
  • Actinomycetes cause plant diseases and crop loss.

Viruses as a Soil Microorganism

  • Plant and animal wastes contribute to the periodic introduction of bacterial viruses (bacteriophages) and plant and animal viruses into soils.
  • Additionally, soil microbes may carry viruses.
  • It has been estimated that the concentration of viruses in soil is 109 viral particles per gramme of dry weight.
  • Small spherical virus particles comparable in size to single-stranded (ss) RNA containing bacteriophages of the Leviviridae family or to certain plant viruses inhabit soil, as do larger spherical viruses comparable to the double-stranded (ds) DNA containing viruses of the Partitiviridae, Chrysoviridae, and Totiviridae families.

Positive effects of Viruses in Soil

  • Soil viruses perform their beneficial roles mostly by horizontal gene transfer, moving genes from one group of microbes to another. Gene transfer paves the way for the sharing of advantageous traits between populations.
  • Plants may also benefit from the viruses present in soils because they may help control plant-pathogenic organisms.
  • Pathogens, such as viruses, play a crucial role in controlling host microbial populations in the soil.
  • Populations of viruses may store genes essential for the proper functioning of their microbial hosts, and new gene variants may be produced by recombination among virus populations during coinfections.

Negative effects of Viruses in Soil

  • Soil is home to a diverse variety of viruses, but a significant fraction of them are plant diseases that infect crops through intermediaries like insects, nematodes, and fungi.
  • Soil microbes including bacteria, fungus, and protozoa are also impacted by viruses, which can lead to an unbalanced biotic environment.
  • Even the biotic and abiotic components of soil could be impacted by viruses, leading to a change in the soil’s physical and chemical properties.

Nematodes as a Soil Microorganism

  • Nematodes are clustered in close proximity to their prey. Bacterial-feeding organisms are abundant around roots where bacteria congregate; fungal-feeding organisms are found near fungal biomass; and root-feeding organisms are prevalent near the roots of stressed or vulnerable plants.
  • In soils with a high number of nematodes, predatory nematodes are more likely to be prevalent.
  • Nematodes tend to be more prevalent in coarser-textured soils due to their size.
  • Nematodes migrate via enormous (>1/500 inch or 50 m) pore gaps in aqueous films.
  • Agricultural soils often contain fewer than 100 nematodes per teaspoon (dry gramme). Per teaspoon, grasslands may have 50 to 500 nematodes, while forest soils typically contain several hundred.
  • The proportion of nematodes that feed on bacteria and fungi is proportional to the amount of bacteria and fungi in the soil.
  • Typically, less disturbed soils contain a greater number of predatory nematodes, indicating that predatory nematodes are extremely sensitive to a wide variety of disturbances.

Positive effects of Nematodes in Soil

  • Nutrient cycling: Similar to protozoa, nematodes play a crucial role in mineralizing or releasing nutrients in plant-accessible forms. Ammonium (NH4+) is produced when nematodes consume bacteria or fungi because bacteria and fungi contain far more nitrogen than the nematodes require.
  • Grazing:  At low worm concentrations, nematode feeding increases the growth rate of prey populations. In other words, bacterial feeders promote bacterial growth, plant feeders promote plant development, etc. Nematodes will diminish the population of their prey at higher densities. This may lower plant productivity, have a detrimental effect on mycorrhizal fungi, and reduce the rates of breakdown and immobilisation by bacteria and fungi. Predatory nematodes may manage populations of nematodes that feed on bacteria and fungi, so limiting overgrazing by these species. The balance between bacteria and fungus and the species composition of the microbial community may be governed by nematode grazing.
  • Dispersal of microbes: Nematodes aid in the distribution of bacteria and fungus across the soil and along the roots by transporting living and dormant microorganisms on their surfaces and in their digestive tracts.
  • Food source: Nematodes are a food source for predators of higher levels, such as predatory nematodes, soil microarthropods, and soil insects. In addition, they are parasitized by bacteria and fungus.
  • Disease suppression and development: Some nematodes cause disease. Others, such as root-feeding nematodes, devour disease-causing organisms or limit their access to roots. These may be potential agents of biocontrol.

Negative effects of Nematodes in Soil

  • Predatory nematodes reduce soil health by eliminating beneficial microorganisms.
  • Nematodes are a type of plant parasite that can cause significant damage to crops by feasting on young seedlings and roots.

What is Rhizosphere?

  • The rhizosphere is the limited zone of soil or substrate that is directly influenced by root secretions and the root microbiome, which consists of related soil microorganisms.
  • Numerous bacteria and other microbes feed on shed plant cells, termed rhizodeposition, and the proteins and sugars released by roots, dubbed root exudates, in the rhizosphere comprising soil pores.
  • This symbiosis results in increasingly complicated interactions, which influence plant development and resource competition.
  • Due to root exudates and metabolic products of symbiotic and pathogenic microbial communities, the majority of nutrient cycling and disease suppression by antibiotics required by plants takes place immediately next to roots.
  • Additionally, the rhizosphere provides area for the production of allelochemicals used to control neighbours and relatives.
  • The rhizoplane refers to the root surface, including the soil particles connected with it. The plant-soil feedback loop and other physical processes occurring at the plant-root soil interface are significant selective forces in rhizosphere and rhizoplane communities and growth.

Importance of Soil Microflora/Soil Microbes

  • Microorganisms serve a crucial role in crop and soil health, yet they can be either useful or destructive.
  • Current research has not yet maximised the contribution of microorganisms to soil systems.
  • The influence of soil microorganisms on crop and soil health is contingent upon the composition and activities of existing soil microorganisms, as well as other soil properties.
  • Farmers are asked to use discretion when employing time- or money-intensive management approaches.
  • Some items or techniques can be evaluated on a farm-by-farm basis, while others should be evaluated in small trials.
  • It is possible to introduce infections or other microorganisms with detrimental effects when introducing beneficials.
  • On farms, soil building methods are encouraged because they can have positive effects on soil biological communities and improve soil health.


What are soil microorganisms?

Soil microorganisms are tiny living organisms that reside in the soil and play a crucial role in maintaining soil fertility and ecosystem functioning.

What types of microorganisms are found in soil?

Soil is home to a wide variety of microorganisms, including bacteria, fungi, protozoa, nematodes, and archaea.

What is the role of soil microorganisms in soil health?

Soil microorganisms play a critical role in maintaining soil health by decomposing organic matter, cycling nutrients, enhancing soil structure, and suppressing plant diseases.

How do soil microorganisms affect plant growth?

Soil microorganisms can affect plant growth in many ways, including by providing nutrients, promoting root growth, and protecting plants from disease.

How do soil microorganisms respond to changes in soil management practices?

Soil microorganisms are highly responsive to changes in soil management practices, such as tillage, fertilizer application, and crop rotation. Changes in management can affect the abundance and diversity of soil microorganisms, which can impact soil health and crop productivity.

Can soil microorganisms be harmful to humans?

While most soil microorganisms are harmless or even beneficial, some can be pathogenic to humans. For example, soil-borne bacteria like Salmonella and E. coli can cause foodborne illness.

How do soil microorganisms interact with other soil components?

Soil microorganisms interact with other soil components, such as organic matter and minerals, in complex ways. For example, some microorganisms can break down complex organic molecules into simpler forms that plants can use for growth.

How do scientists study soil microorganisms?

Scientists use a variety of methods to study soil microorganisms, including DNA sequencing, microscopy, and culturing techniques.

How can farmers and gardeners support soil microorganisms?

Farmers and gardeners can support soil microorganisms by practicing soil conservation techniques, like reducing tillage, planting cover crops, and applying organic amendments like compost.

What are some of the challenges associated with studying soil microorganisms?

Studying soil microorganisms can be challenging because they are often difficult to isolate and identify, and their activities can be influenced by a wide range of environmental factors. Additionally, soil microorganisms are highly diverse, making it difficult to draw general conclusions about their behavior and function.


  • Bhatti, A. A., Haq, S., & Bhat, R. A. (2017). Actinomycetes benefaction role in soil and plant health. Microbial Pathogenesis, 111, 458–467. doi:10.1016/j.micpath.2017.09.036
  • Talwar, HarleenKaur & Chatli, Anshu. (2018). MICROFLORA OF SOIL: A REVIEW.. International Journal of Advanced Research. 6. 1502-1520. 10.21474/IJAR01/7960. 
  • Balasubramanian, A.. (2017). Soil Microorganisms. 10.13140/RG.2.2.27925.12008. 
  • Gupta, R., Mohapatra, H. (2002). Soil Microflora : Isolation, Enumeration and Identification. In: Mukerji, K.G., Manoharachary, C., Chamola, B.P. (eds) Techniques in Mycorrhizal Studies. Springer, Dordrecht.
  • Baxi SN, Portnoy JM, Larenas-Linnemann D, Phipatanakul W; Environmental Allergens Workgroup. Exposure and Health Effects of Fungi on Humans. J Allergy Clin Immunol Pract. 2016 May-Jun;4(3):396-404. doi: 10.1016/j.jaip.2016.01.008. Epub 2016 Mar 3. PMID: 26947460; PMCID: PMC4861659.
  • Gupta, R. K., Abrol, I. P., Finkl, C. W., Kirkham, M. B., Arbestain, M. C., Macías, F., … Feng, Y. (2008). Soil Microbiology. Encyclopedia of Earth Sciences Series, 673–678. doi:10.1007/978-1-4020-3995-9_544 

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