Rhizosphere – Definition, Microflora, Structure, Importance


Table of Contents

Rhizosphere Definition

  • The rhizosphere is the localised soil environment around the root of a vascular plant that is impacted by the root.
  • As a result of root exudates that either encourage or hinder rhizosphere organisms, this region is a hotbed of biological activity.
  • The intricacy and dynamic nature of the rhizosphere are defined by the interactions between the soil, the plant, and the creatures that make up the rhizosphere.
  • The rhizosphere is a hotbed of activity between plants and microbes and plants and animals.
  • These partnerships can be beneficial, like in the case of N2 fixation or mycorrhizal connections, or harmful, like in the case of fungi or bacteria.
  • When rhizosphere ecology is taken into account, management measures like bioremediation and biological control have a better chance of succeeding.
  • To improve plant growth and protect the environment, scientists need a deeper understanding of the rhizosphere and its influence on the organisms that live there.
  • Rhizosphere is a term first used by Hiltner in 1904 to define the area of soil where plant roots exert their impact.
  • His research expanded from studying the relationship between symbiotic N2-fixing bacteria and the legume root.
  • The depth of this soil layer varies from only a few hundred micrometres to more than five millimetres below the root zone. Enhanced root exudation and alterations to the soil’s physical and chemical qualities may boost microbial activity and population levels in this area.
  • The rhizosphere is in a continual, dynamic transition.
  • Colonization of the rhizosphere by soil organisms is affected by multiple overlapping gradients in this zone that change with time and distance from the root.
  • The complexity of this region stems from the existence of these gradients and the myriad of interactions taking place inside them.
  • Released nutrients from the root create the most striking gradient in the rhizosphere. Roots of plants secrete a wide range of organic compounds into the rhizosphere, which are then consumed by the resident microbes.
  • Cells that extend themselves and develop lateral roots secrete the most fluid.
  • The concentration of carbon compounds in a plant decreases exponentially as one moves away from the root.
  • Extreme conditions such as high heat, low water, a lack of phosphorus, an overabundance of light, or an overabundance of microbes can all cause an increase in exudation.
  • Factors like as herbicides, pathogens, foliar applications, and symbiotic partnerships may also affect the rate at which exudates are released.
  • N insufficiency and reduced light intensity are both factors that can reduce root exudation.
  • Root surface (rhizoplane) or inner root cell layer microbial colonisation may also be related to exudate pattern (endorhizosphere).
  • Mucilage is a slimy coating that develops on the root’s exterior from high-molecular-weight plant exudates, most of which are secreted by root tips.
  • In contrast, mucigel is made up of plant mucilage and other plant compounds, as well as bacterial cells and their products.
  • These secretions are crucial as they contribute to the formation and upkeep of solid soil aggregates.
  • Root-leaked compounds containing C are crucial to microbial development since soils often contain very little accessible C.
  • Sugars, amino acids, vitamins, tannins, alkaloids, phosphatides, and other chemicals like growth factors, fluorescent substances, nematode cyst or egghatching factors, and fungal growth stimulants and inhibitors are all examples of what can be found in exudates.
  • The two well-studied root exudates, sugars and amino acids, give nutrition to the rhizosphere’s residents and may have a role in determining whether plants are susceptible or resistant to root-infecting fungus.
Rhizosphere | Image Credit:

Rhizosphere effect Definition

  • The rhizosphere effect refers to the impact that plant roots have on the growth of soil microorganisms as a result of the roots’ physical and chemical changes to the soil and the exudation of root secretions and exudates.
  • When the microbial biomass of the rhizosphere is compared to the microbial biomass of the bulk soil, the rhizospheric impact is seen.
  • The “R/ S ratio” is used to quantify the rhizosphere effect on soil microbial population by comparing the population density [colonies forming units (CFU)] of rhizosphere soil (R) and bulk soil (S).
  • Rhizosphere effect is greatest for bacteria, then fungi, then actinomycetes, and finally protozoa.
  • Diversity of microorganisms is greatest close to the rhizoplane and diminishes with distance.
  • The rhizosphere’s microclimate is altered due to the interplay between soil nutrients and plant exudates.
  • Both the plant root and the local microbial community exert mutual influences, leading to the rhizosphere effect.
  • Root secretions from plants can affect the microbial biomass in the rhizosphere, and vice versa.

Structure of Rhizosphere

Based on their proximity to the root system, the rhizosphere structure consists of three zones.

  • Inner zone: It is also referred to as the Endorhizosphere. It is really close to the origin. It consists of the region of the cortex and epidermis that microorganisms are able to occupy within the Apoplastic space.
  • Rhizoplane: Rhizoplane was coined by F.E. Clark. It is the actual root system.
  • Outer zone: It is also known as the Exorhizoshere zone. This layer is located next to the epidermis.
Rhizosphere | Image Source:

Characteristics of Rhizosphere 

  • Plants, soil, bacteria, nutrients, and water all interact in the rhizosphere, making it a highly dynamic habitat. The rhizosphere is distinct from bulk soil due to plant root activities that alter the composition and ecology of soil microbes.
  • The release of organic substances into the soil by plant roots is a defining feature of the rhizosphere. The rhizosphere is distinguished from the bulk soil by the presence of exudates, substances that promote root growth. The exudates boost nutrient availability in the rhizosphere and supply heterotrophic microbes with carbon. The rhizosphere has a much higher microbial density than bulk soil due to the exudates.
  • The ability of plants to take in water and nutrients is another feature of the rhizosphere. Subsequently, the roots are supplied with water from the surrounding soil. Concentrations of water and nutrients in the rhizosphere typically fluctuate greatly from those in the bulk soil due to the delicate balancing act between the uptake of these substances by the roots and their return to the atmosphere. In some cases, this may inhibit the development or function of microorganisms.

Effects of rhizosphere microbial populations on Plants

Degradation of organic materials, disease suppression, and nutrient conversions within root zones are just a few of the many chemical changes that microorganisms are capable of doing. The development of plants is significantly impacted by microorganisms. Possible stunting of plant development if the rhizosphere lacks the right kinds of microbes. Here are some of the most significant ways in which microbes influence plant life.

  • Rhizosphere microorganisms affect plant access to mineral nutrients. Symbiotic (e.g. mycorrhizal) and other specialised (e.g. nitrogen-fixing) root microbe interactions, as well as rhizobia, can boost plant nutrient intake in nutrient-poor conditions.
  • Organic chemicals produced by rhizosphere organisms have an effect on root growth.
  • Auxins and gibberellin-like substances, both of which are synthesised by microorganisms, promote seed germination and the formation of root hairs.
  • In the rhizosphere of grasses, you can often find the bacterium azospirillum. Hormones produced by certain strains of this microorganism promote plant expansion. The grass can take use of the nitrogen fixed by other Azospirillum strains.
  • There are pathogenic soil organisms that prey on the roots of living plants.
  • Sometimes they can aid in preventing the spread of disease.
  • To help plants grow, Bacillus polymyxa secretes a free phosphate group.

Factors Affecting Rhizosphere Microorganisms

1. Soil type and its moisture

  • When soil moisture is low, the rhizosphere is home to a greater diversity of species, and microbial activity and population are generally higher in sandy soils than in high humus soils.
  • Because of this, sandy soils with a low moisture content see a greater rhizosphere effect.

2. Soil amendments and fertilizers

  • Applied crop residues, animal manure, and chemical fertilisers have no discernible effect on the quantitative or qualitative differences between rhizosphere microorganisms.
  • In general, the nature of plants is more essential than the soil’s fertility.

3. Soil PH/ Rhizosphere PH

  • The rhizosphere microflora’s respiration may alter the ph of the rhizosphere soil.
  • If the activity and population of rhizosphere microflora are greater, then the rhizosphere region will have a lower pH than the surrounding soil or non-rhizosphere soil.
  • For bacteria and protozoa, the rhizosphere effect is greater in slightly alkaline soil, but it is greater in acidic soil for fungus.

4. Proximity of root with Soil

  • The population of bacteria and actinomycetes in soil samples collected closer to the root system increases as the distance and depth from the root system decreases.
  • The rhizosphere effect diminishes dramatically as root distance from soil increases.

5. Plant Species

  • The microflora of the rhizosphere is comprised of numerous plant species and is frequently changeable.
  • Variations in rooting behaviour, tissue composition, and excretory products are responsible for the qualitative and quantitative variances.
  • In general, legumes exhibit a stronger rhizosphere influence than grasses or cereals.
  • Due to their lengthy growth period, biennials stimulate the rhizosphere for a longer duration than annuals.

6. Age of Plant

  • The age of the plant influences the rhizosphere microflora, and the stage of plant maturity determines the extent of the rhizosphere effect and the degree of sensitivity to particular microorganisms.
  • The quantity of rhizosphere microflora rises as a plant ages, reaching a maximum during blooming, the most active period of plant development and metabolism.
  • Consequently, the rhizosphere influence was discovered to be greater during the flowering stage of plants than during their seedling or fully mature stages.
  • The fungal flora (particularly Cellulolytic and Amylolytic) of the rhizosphere (due to accumulation of moribund tissue and sloughed off root parts / tissues) typically increases after fruiting and the onset of senescence, whereas the bacterial flora of the rhizosphere decreases after the flowering period and fruit setting.

7. Root / exudates /excretion

  • Root exudates/excretions are one of the most significant contributors to the rhizosphere effect because they contain a wide range of organic compounds.
  • Root exudates are largely responsible for the quantitative and qualitative variations between the microflora of the rhizosphere and that of the surrounding soil.
  • The chemical composition of root exudates varies widely, and consequently, so does their impact on the microbiota.

Organisms in the Rhizosphere

1. Bacteria

  • Rhizosphere bacteria have crucial functions in plant nutrition, growth stimulation, and contact with pathogens.
  • According to a number of studies, bacteria are the most abundant inhabitants of the rhizosphere, despite their small size, which limits their contribution to the total biomass. Typically, a 1-g sample of rhizosphere soil contains between 108 and 1012 bacterial cells; Gram-negative bacteria predominate in the rhizosphere, with Pseudomonas being the most efficient bacterial root invaders.

2. Actinomycetes

  • Asexual spores are produced by the actinomycetes, which are a type of filamentous chemoorganotrophic bacteria.
  • Soil in the rhizosphere typically has a higher population of these bacteria than soil elsewhere.
  • There is evidence to suggest that in the root zone of some plants, actinomycetes predominate over fluorescent pseudomonads.
  • Many species of actinomycetes have the ability to create antibiotics that could affect plant-microbe interactions like nodulation in legumes or biocontrol efforts against plant pathogens, even if some actinomycetes may cause plant illnesses.

3. Fungi

  • Fungal decomposition and organic matter accumulation are mostly attributable to the fungi’s mineralization of cellulose, lignin, and other organic compounds; fungi are eukaryotic, nonphotosynthetic, spore-forming organisms.
  • Symbionts, pathogens, nutrient sinks, and a source of nutrition for other soil microorganisms are just few of the roles that fungi may play in the rhizosphere and rhizoplane.
  • Aggregates can also be formed in soil thanks to the binding effects of fungal mycelia.

4. Fauna

  • The rhizosphere fauna consists of the animals that dwell temporarily or permanently in close proximity to plant roots and have a major impact on the rhizosphere’s physical and functional characteristics.
  • There are three different kinds of soil fauna, and they are all categorised by their size.
    1. Microfauna: Microfauna consists of organisms with only one cell, such protozoa.
    2. Mesofauna: Microarthropods, nematodes, and rotifers are all examples of mesofauna.
    3. Macrofauna: The macrofauna consists of larger animals like worms, millipedes, centipedes, and insects.

a. Microfauna (protozoa) 

  • Most protozoa are quite small, but some can grow to macroscopic proportions.
  • The group’s members have different eating habits, but they all need a water film to be alive.
  • Around 104 to 105 protozoa are found in one gramme of soil, according to estimates.
  • Soil in the rhizosphere (R) typically has a greater protozoa population than bulk soil (S), especially in protozoa “hotspots” like those around decaying plant roots.
  • Protozoa have a role in the mineralization of N because they feed on bacteria and fungi, which in turn increases N uptake by plants.
  • Up to 60% of the surplus N and P is excreted in forms that are readily used by plants when rhizosphere protozoa feast on bacteria.
  • Protozoa in the rhizosphere may help plants by reducing the population of disease-causing bacteria and fungi.
  • Protozoa have been shown to diminish root nodulation in Phaseolus vulgaris by suppressing Rhizobium populations in the rhizosphere.

b. Mesofauna (nematodes and microarthropods)

  • These microscopic nematodes range in size from from 0.5 mm to 2.0 mm and lack any segmentation along their rounded body.
  • They can be classified into five trophic groups based on their diets: bacterivores, who eat bacteria; fungivores, which eat fungal mycelia; predators, which eat other nematodes and small invertebrates; omnivores, which eat a wide variety of foods; and herbivores, which are plant parasites.
  • The importance of nematodes in mineral cycling is substantial. Their diet of bacteria and other organic matter causes an increase in the mineralization of phosphorus and sulphur in some systems, and an increase in the excretion of nitrogen, primarily in the form of ammonia.
  • The importance of nematodes in agriculture stems from the fact that some species feed as parasites on various crops.
  • When these parasitic worms feed on plants, it can cause a variety of issues, including wilting, nutrient shortage symptoms, production losses, and more.
  • Most of the mesofauna in soils consists of microscopic arthropods that pose little threat to plant life, including mites (Acari: Arachnida) and springtails (Collembola: Insecta).
  • Some species of soil mites feed on nematodes and other tiny arthropods, although fungi are their primary food source.
  • Some species actually penetrate the roots of plants to draw out the sap, while others eat the roots themselves or decaying plant detritus.

c. Macrofauna

  • In soil science, the term “macrofauna” refers to organisms that are at least one centimetre in length but are still significantly smaller than an earthworm.
  • Common examples of macrofauna include potworms, myriapods, centipedes, millipedes, slugs, snails, fly larvae, beetles, beetle larvae, and spiders.
  • Many of these animals have burrows in the soil, which helps with drainage and aeration and also allows some organic matter to seep into the soil.
  • Most macrofauna feed on decomposing plant matter and organic detritus, however centipedes, certain insects, and spiders are predators.

Plant Growth Promoting Rhizobacteria (PGPR)

  • Plant Growth Promoting Rhizobacteria (PGPR) are a group of soil bacteria that colonize the rhizosphere (the soil surrounding plant roots) and promote plant growth through various mechanisms. These bacteria have been extensively studied for their potential to enhance crop productivity in a sustainable and eco-friendly manner.
  • PGPR are known to produce plant growth-promoting substances such as auxins, cytokinins, gibberellins, and abscisic acid, which can enhance root and shoot growth, nutrient uptake, and stress tolerance in plants.
  • They can also solubilize and mobilize nutrients such as phosphorus and iron, making them more available to plants. In addition, PGPR can protect plants from various pathogens by producing antibiotics, siderophores, and other biocontrol agents.
  • PGPR can be applied to crops through seed treatment, soil inoculation, or foliar spray. Several commercial products containing PGPR are available in the market for use in agriculture.
  • Overall, the use of PGPR is a promising approach for sustainable agriculture, as it can reduce the use of chemical fertilizers and pesticides while enhancing crop productivity and resilience. However, the effectiveness of PGPR can vary depending on the specific microorganisms and environmental conditions involved, and further research is needed to optimize their use in different cropping systems.
  • The Plant Growth Promoting Rhizobacteria (PGPR), an enigmatic group of bacteria, display fascinating capabilities to enhance plant growth. They achieve this by synthesizing and secreting a variety of biofertilizers and plant growth-promoting substances. PGPR represent a revolutionary approach for sustainable agriculture, promising to increase crop yields while protecting the environment.
  • Their modus operandi entails the colonization of the rhizospheric soil, where they interact with the plant’s roots and release a plethora of growth-promoting substances. These communities of bacteria, which include genera such as Pseudomonas, Azospirillum, Erwinia, and Mycobacterium, play an indispensable role in sustaining the soil’s microbiome and promoting crop growth.
  • PGPR exhibit diverse functions, which range from acting as biofertilizers, biocontrol agents, and biological fungicides. Their biofertilizing role is particularly noteworthy, with their production of phytohormones, such as indole-3-acetic acid (IAA), gibberellic acid (GA3), zeatin, ethylene, and abscisic acid, boosting plant growth.
  • Moreover, PGPR also assist with plant nutrition, acting as phosphate solubilizing bacteria, increasing the efficiency of biological nitrogen fixation, and producing plant growth-promoting substances to make iron and zinc available. PGPR also play a crucial role in protecting plants against pathogens through direct antagonistic interactions and the induction of host resistance.

Interactions in the Rhizosphere

In the rhizosphere, many interactions are taking place. Nitrogen (N)-fixation, mycorrhizal connections, plant growth promotion, and plant growth inhibition are the most researched. Additionally, bioremediation and biological control have been studied as of late.

Interactions in the Rhizosphere
Interactions in the Rhizosphere | Image Credit:

1. Dinitrogen-Fixation Symbiosis

  • Dinitrogen-fixing bacteria are able to provide N2 to the plant when it would otherwise be unavailable.
  • Nodules are growths on a plant’s roots that are caused by rhizobia and related bacteria.
  • Both parties can benefit from this relationship: the plant can give nutrients and shelter for the bacterium, and the bacteria can provide the plant with nitrogen.
  • N2 fixers from other organisms often partner up with plants.
  • Grass roots, including their inner cells, the intercellular spaces between the cortex and endodermis, and the xylem cells themselves are all colonised by these bacteria.
  • They may also supply chemicals that promote plant growth, in addition to the plant-available nitrogen.

2. Mycorrhizal Associations

  • Mycorrhizal fungi develop a symbiotic relationship with plant roots without causing root disease.
  • These fungi are found in the rhizospheres of the majority of plants and develop relationships with all gymnosperms, more than 83 percent of dicotyledonous plants, and 79 percent of monocotyledonous plants.
  • Mycorrhizal fungus can form structures on the exterior (ectomychorrhizae) or the interior (endomycorrhizae) of plant roots.
  • The hyphae of fungi permit the roots to contact a larger volume of soil.
  • Some mycorrhizal fungi enhance the solubilization of nutrients like phosphorus.
  • They aid the plant in enhancing nutrient absorption, particularly in stressed conditions (such as phosphorus- and water-deficient soils), selective ion uptake, and environmental protection.
  • After colonisation by these fungi, plant exudation patterns may be altered, hence changing the microbial and macrofaunal communities of the rhizosphere.
  • The fungi may also shield plant roots from disease invasion.
  • Endomycorrhizal extraradicle hyphae release glomalin, a glycoprotein that aggregates soil particles, hence enhancing water-stable aggregates and soil structure.
  • This relationship can boost the survival and growth of a plant, particularly in harsh or low-nutrient situations, and may have reforestation potential in damaged areas.

3. Plant Growth-Promoting Organisms

  • Plant growth-promoting organisms are creatures that boost the development of plants in some way.
  • Plant growth-promoting organisms are often particular bacteria or fungi that promote seed germination and plant growth.
  • Many distinct systems are responsible for plant growth promotion.
  • These organisms have been utilised in biological control programmes to defend plants against plant infections, as biofertilizers to fix atmospheric N2, and in phytostimulation, which directly enhances plant growth through the synthesis of plant growth regulators.
  • Some may make nitrogen more available to plants and have the potential to minimise application of inorganic fertilisers.
  • These organisms may create plant growth-stimulating chemicals such as gibberellic and indoleacetic acid.
  • The reduction in pathogen burden may also be a mechanism of plant growth promotion.
  • Iron-chelating chemicals termed siderophores can operate to make iron more available to an organism and less available to the plant pathogen, therefore harming the pathogen. Since iron is a critical nutrient in metabolism and a cofactor in enzyme activity, microbial growth may be regulated by these siderophores.
  • The microbial communities that invade the inside of the root and create intimate relationships with the root are considered endophytes.
  • Endophytic bacteria may boost plant growth, give disease resistance, and aid the plant in withstanding stressors such as drought.
  • The success of endophytes in colonising the rhizosphere may be the ability of the microbe to compete with other bacteria on the exterior or internal sections of plant roots.
  • Introduction of plant growth-promoting organisms may modify the overall composition of the microbial community, notably in the rhizosphere.

4. Plant Growth-Inhibiting Organisms

  • It is possible for the rhizosphere to get colonised by growth-inhibiting organisms, which can then change plant development.
  • Disease signs are not always present when plant growth is stunted.
  • Many harmful organisms, like as fungus and bacteria, are found in the rhizosphere and prey on germinating seeds and young roots.
  • It is possible that pathogens secrete extracellular enzymes that emulsify cell walls, releasing their contents for destruction.
  • Toxins made by some infections alter membrane permeability or enzyme activity, both of which can disrupt a metabolic pathway. These microbe-produced poisons could be host-specific or have a broad range of plant family targets.
  • Some pathogens create polysaccharides that can obstruct vascular tissues, leading to death.
  • Having a tumor-inducing bacterial plasmid integrated into the plant genome causes gall formation in the roots by causing an overabundance of the hormones auxins and cytokinins.
  • Root cell destruction and toxicity from nematode waste reduces the plant’s ability to take up water and nutrients.
  • Other microbial infections may enter the roots through the puncture holes caused by eating.
  • Plant growth can be stunted by deleterious rhizobacteria (DRB) even when there are no outward signs of disease.
  • These organisms have been found on the root surface and maybe in the cortical intercellular spaces.
  • The only food source for DRB is the organic substances generated by plant root cells; they do not parasitize the plant. Phytotoxins, plant growth regulators, volatile compounds, and antibiotics are only some of the metabolites they produce that have negative impacts on plant growth.
  • They are generally found to be species or cultivar specific in their colonisation and inhibition, and root exudates may play a role in some plant-DRB interactions.

5. Bioremediation

  • Over the course of the last few decades, pollution has increased as industrialization and agricultural intensification have both contributed to the release of toxic wastes into the biota of the planet.
  • Due to its poisonous and carcinogenic nature, and tendency to bioaccumulate in people and other species, the prompt and cost-effective clean-up of polluted regions has become a concern.
  • Bioremediation, which makes use of plants’ and microbes’ natural function in the transformation, mineralization, and complexation of organic and inorganic contaminants, can be improved by plant-microbial systems.
  • When compared to more traditional methods of soil remediation, bioremediation is more cost-effective, makes use of less complicated equipment, and has a smaller environmental impact on the contaminated area.
  • Bioremediation may be promoted by plant root exudates that demonstrate strong binding affinities to particular pollutants or by rhizosphere bacteria that mineralize toxins into their harmless derivatives.
  • The microbial populations associated with plant roots may aid in the mineralization of potentially harmful substances in the soil.
  • Several mechanisms have been proposed to account for the “rhizosphere impact” on bioremediation.
  • To begin, it has been hypothesised that elevated populations and activities of xenobiotic degraders are prompted by carbon substrates from root systems.
  • A second factor in the success of soil remediation efforts to eliminate heavy metals like mercury, selenium, and zinc is the presence of abundant populations of microbes.
  • The role of bacteria and bacterial consortiums in bioremediation has received the most attention, but other organisms, such as fungus, actinomycetes, mycorrhizal associations, and even rhizosphere animals, have also demonstrated degradation capabilities.
  • Elucidating the mechanisms involved in the repair of contaminated sites by plants and their related creatures is, without a doubt, the greatest challenge in bioremediation technology.
  • This knowledge will enable for the selection and engineering of the optimal plant–microbe pairings and optimization of the remediation process.

6. Biological Control

  • The rhizosphere is the site of biological control interactions that employ diseases, parasites, or other predators to decrease the population or activity of another organism.
  • The three major biological control tactics are classical, inundative, and integrated management.
  • The traditional method involves the release, diffusion, and self-reproduction of natural enemies against pests.
  • In the rhizosphere, the inundative strategy involves the addition of a virulent strain of a biocontrol agent to inhibit pests. In this instance, the biocontrol agent is not self-sustaining and must be applied annually to the target host.
  • The integrated management method is a comprehensive strategy that incorporates management actions to conserve or improve pests’ natural enemies.
  • Pathogens, nematodes, and weeds can all be managed with biological control.
  • Biological illness management provides alternatives to chemical disease management.
  • The success of biocontrol techniques is aided by the interactions of organisms in the rhizosphere and the ecological significance of these interactions in the root and seed environment.
  • The suppression of plant pathogens such as Fusarium oxysporum, Gaeumannomyces graminis, Pythium, and Phytophthora species by some soils is believed to be the result of physiochemical and microbiological soil variables.
  • The suppression is targeted and may involve multiple methods. Antibiosis, formation of siderophores or volatile chemicals, parasitism, competition for nutrition, competition for ecological niches, and induced disease resistance are some of the mechanisms.
  • Due to the formation of disease-suppressive soils, crop monoculture can, over time, result in a decline in disease.
  • Crop rotation, soil amendments, cover crops, fumigation, and soil solarization are other management techniques that may affect the rhizosphere habitat and be considered as biocontrol methods.
  • Pathogens of protozoa and nematodes that are fungal in nature can be employed for biological control of these plant pests.
  • Mycelial development into cortical cells is believed to aid in the control of protozoa-caused clubroot disease.
  • As they feed, plant-parasitic nematodes modify the exudate patterns of the host plant. This alters the microbial ecology of the rhizosphere at certain places, which influences the colonisation of fungal and bacterial nematode antagonists.
  • Using nematode-trapping fungi to lower nematode populations is one of the most intriguing and extensively studied fungal interactions for biological control.
  • These predatory fungi develop a variety of trapping structures, including constricting rings, sticky knobs, and hyphal meshes.
  • However, the elements that produce major predatory behaviour must be investigated in greater depth.

What is Root Exudation?

  • Due to a phenomenon known as Root exudation, intense microbial activity occurs.
  • The organic and inorganic substances that diffuse out of the root during unfavourable conditions are known as Root exudates.
  • Root exudates thereby create a network between plants and microbes. Root exudates are composed mostly of root secretions and root diffusates.

Classification of Root Exudates

Based on chemical composition, there are three categories of root exudates:

1. Organic compounds

  • Carbon-based compounds are those in which carbon serves as the backbone molecule and is attached to other elements by covalent bonds (hydrogen, nitrogen, etc.).
  • Example: Proteins, organic acids, vitamins, amino acids, sugars, flavonoids, nucleotides, enzymes, etc. are all examples of biomolecules.

2. Inorganic compounds

  • To be more specific, they are compounds that contain either carbon or hydrogen, but not both.
  • Example: Several substances, including water, anions, and the gases carbon, oxygen, nitrogen, etc., serve as examples.

3. Miscellaneous compounds

  • Other than organic and inorganic compounds, some other substances are also released by the plant, which can impose a negative effect and called as miscellaneous compounds.
  • Example: Auxins, glycosides, saponins, hydrocyanic acids, etc. are all examples of such chemicals.

Role of Root Exudates

  • It’s a food source for the microorganisms.
  • Plants’ roots produce exudates that prevent them from drying out.
  • It helps keep the soil moist, which is essential for the development of soil microbes.
  • It also safeguards the root from biotic stress, or pathogens, by the release of defence proteins and antimicrobial compounds.
  • Systemic defences are bolstered in response to abiotic stresses including those posed by heat, salt, and acidity.
  • It aids in soil aggregation by the release of mucilage.
  • Soil chemistry and physics may be affected by:
    • Osmotic pressure
    • Ionic balance
    • Redox potential

Factors Affecting Root Exudation

  • Temperature and luminosity
  • When a plant wilts, it produces an abundance of amino acids.
  • The production of secondary metabolites by particular bacteria.
  • Rhizospheric microorganisms capable of influencing root permeability and metabolism

Functions of rhizosphere microbiome

Positive effects

1. Effects of rhizosphere microorganisms on nutrient acquisition by plants

  • The rhizosphere microbiome has a substantial impact on the nutritional status of plants.
  • Rhizobia that fix nitrogen and mycorrhizal fungi that enhance phosphorus uptake are well-known examples.
  • Microorganisms in the rhizosphere can also enhance the uptake of trace metals like as iron. Iron is abundant in soil, but under neutral to alkaline conditions, it largely occurs in the insoluble ferric oxide form, which is inaccessible to microbial development.

2. Supporting plant growth under biotic stress

  • The rhizosphere is the first line of defence against soilborne infections for plant roots.
  • Diverse members of the rhizosphere microbiome can combat soil-borne pathogens prior to and during initial infection, as well as during secondary dissemination on and within root tissue.
  • Antibiosis, competition for trace elements, nutrients, and microsites, parasitism, interference with quorum sensing that affects virulence, and induced systemic resistance are the primary methods by which rhizosphere bacteria repel plant diseases.
  • If not all, the vast majority of rhizobacteria produce compounds that limit the growth or activity of rival microbes.
  • Rhizosphere microbiome members can also affect the plant immune system. In many instances, the systemic resistance response elicited in plants by beneficial rhizobacteria is controlled by the phytohormone jasmonic acid.

3. Supporting plant growth under abiotic stress 

  • It has been hypothesised that the rhizosphere microbiome contributes to the ability of certain plant species to survive in harsh environments.
  • For instance, the soil isolate Achromobacter piechaudii ARV8, isolated from an arid and saline environment, dramatically boosted the biomass of tomato and pepper seedlings subjected to transitory drought stress.
  • Rhizobacteria have been demonstrated to promote plant development under conditions of flooding.
  • Low-temperature environments harbour microorganisms evolved to survive in such conditions. Despite the effect of low temperatures on nodule formation and nitrogen fixation, it is fascinating to note that native legumes in the high arctic may nodulate and fix nitrogen at comparable rates to those reported for legumes in temperate climes.
  • pH and excessive concentrations of hazardous chemicals are two additional abiotic variables that may hinder plant growth. In numerous agricultural systems around the globe, low pH or contaminated soils pose significant obstacles. In the instance of pH stress, it was revealed that 2,4-diacetylphloroglucinol (DAPG)-producing Pseudomonas fluorescens strains dramatically decreased foliar lesions generated on corn growing in a low-pH environment.

Negative Effects

1. Fungi and oomycetes

  • The germination, development, and establishment of fungal and oomycete pathogens in the rhizosphere depend on a variety of cues from the host plant.
  • Several factors, including as changes in abiotic conditions (e.g. pH) and root exudates, can activate the dormancy of fungal spores.
  • Low quantities of phenolic substances such as p-hydroxybenzoic, gallic, coumaric, cinnamic, ferulic, salicylic, and sinamic acids in root exudates enhanced conidial germination of pathogenic fungus, whereas higher concentrations had an inhibitory impact.
  • Four phenolic acids from cotton root exudates inhibit Verticillium dahlia spore germination.
  • Also, alkaloids derived from the roots of Veratrum taliense (Liliaceae) prevent the growth of Phytophthora capsici and Rhizoctonia cerealis.
  • The composition of alkaloids in the roots and shoots of Jacobaea vulgaris was significantly influenced by soil type and soil microorganisms, particularly retrorsine and retrorsine N-oxide.
  • Both alkaloids suppress the growth of the mycelium of various plant-associated fungi, including Fusarium oxysporum, Fusarium sambucinum, and Trichoderma sp. The influence of microbes on the alkaloid composition of plants may have additional ecological repercussions, as these modifications may attract specialised herbivores while discouraging generalists.

2. Nematodes

  • The majority of nematodes in soil are free-living, but some feed on the root exterior (migratory ectoparasitic), others penetrate and travel within the root interior (migratory endoparasitic), and others establish a feeding site in the root where they reproduce (sedentary endoparasites).
  • It is essential for plant-parasitic nematodes other than cyst or polyphagous root knot worms to use chemical gradients to locate their host plants.
  • Their sensory equipment allows them to navigate, discover food sources, and orient themselves. In the physicochemically complex soil matrix, volatile and water-soluble chemicals are key nematode feeding cues.
  • It has been postulated that volatile molecules play a significant role in long-range chemotaxis, but water-soluble compounds are more ideal for short-range chemotaxis.

3. Opportunistic human pathogens in the rhizosphere 

  • In addition to ‘real’ human infections such as Salmonella enterica serovar typhimurium and Escherichia coli O157:H7, the plant environment provides a haven for pathogens that exclusively infect immunocompromised or immunocompromised people.
  • Several wild and cultivated plant species have been documented to harbour opportunistic human infections in the rhizosphere, including Burkholderia (ceno)cepacia, Pseudomonas aeruginosa, and Stenotrophomonas maltophilia.
  • In rhizosphere conditions, however, additional bacterial species that cause skin, wound, and urinary tract infections (such as Bacillus cereus and Proteus vulgaris) can also be detected.

4. Plant colonization by human pathogens 

  • Following attachment, human pathogenic bacteria, specifically Enterobacteriaceae, are able to infiltrate root tissue. For a more exhaustive list of instances of plant internalisation of human diseases.
  • Unlike their invasion of animal hosts, enteric bacteria appear to primarily inhabit the apoplastic regions of plant hosts. At areas of lateral root emergence, human pathogenic bacteria reach the root tissue, according to numerous studies.

5. Soil health status and occurrence of potential human pathogens

  • The rhizosphere of sugar beet seedlings contains various potentially harmful bacteria, including Achromobacter xylosoxidans, Alcaligenes faecalis, A. xylosoxidans, Janthinobacterium lividum, Enterobacter amnigenus, Serratia marcescens, Bacillus cereus, and Staphylococcus aureus.
  • In contrast, Stenotrophomonas maltophilia was much more prevalent in suppressive rhizosphere soil than in supportive soil.

What is Mycorrhiza?

Mycorrhiza is a symbiotic association between plant roots and fungi, where the fungi colonize the roots of the host plant. This relationship benefits both organisms, as the fungi provide the plant with essential nutrients such as phosphorus, while the plant provides the fungi with carbohydrates. Mycorrhizal fungi are ubiquitous in terrestrial ecosystems, and their association with plants is considered essential for sustainable plant growth and ecosystem function. There are two main types of mycorrhiza: ectomycorrhiza, which form a sheath around the plant roots, and endomycorrhiza, which penetrate the root cells. Mycorrhiza is widely used in agriculture to improve crop yields and reduce the use of fertilizers and other inputs.


Mycorrhiza is a mutualistic association between fungi and plant roots that exhibit several unique characteristics. Some of the key features of mycorrhiza include:

  1. Enhanced nutrient uptake: Mycorrhizal fungi are adept at extracting essential nutrients such as phosphorus, nitrogen, and other micronutrients from the soil and making them available to the host plant. This improves plant growth and health.
  2. Improved water absorption: Mycorrhizal fungi can also improve the water-holding capacity of soils, allowing the host plant to access water even in dry conditions.
  3. Symbiotic relationship: Mycorrhizal fungi and plant roots have a mutually beneficial relationship, with the fungi providing nutrients to the plant and receiving carbohydrates in return.
  4. Wide distribution: Mycorrhizal fungi are ubiquitous in terrestrial ecosystems, and nearly all plant species form some type of association with them.
  5. Diverse types: There are two main types of mycorrhiza – ectomycorrhiza, which form a sheath around the plant roots, and endomycorrhiza, which penetrate the root cells. Both types have different characteristics and functions.
  6. Beneficial to ecosystems: Mycorrhiza is considered essential for sustainable plant growth and ecosystem function, as they improve soil fertility and nutrient cycling.

Types of Mycorrhiza

There are two main types of mycorrhiza: ectomycorrhiza and endomycorrhiza.

  • Ectomycorrhiza, as the name suggests, form a sheath around the plant roots and do not penetrate the root cells. Instead, they form a dense network of hyphae, or fungal filaments, around the root system, extending into the soil. Ectomycorrhizal fungi are typically associated with woody plants such as trees and shrubs, and they can be important in nutrient cycling in forest ecosystems.
  • Endomycorrhiza, also known as arbuscular mycorrhiza, form a symbiotic association with the plant roots by penetrating the root cells. They form specialized structures called arbuscules, which allow the fungi to exchange nutrients with the host plant. Endomycorrhizal fungi are widespread in herbaceous plant species and are essential for many agricultural crops.

In addition to these two main types, there are other types of mycorrhiza, such as orchid mycorrhiza, ericoid mycorrhiza, and monotropoid mycorrhiza. Each of these types has unique characteristics and plays a crucial role in the ecology and survival of the host plants.

Understanding the different types of mycorrhiza is important for understanding their functions in ecosystems and agriculture, and for developing strategies to promote their beneficial effects on plant growth and health.


Functions of Mycorrhiza

  • Nutrient uptake: Mycorrhizal fungi enhance the uptake of essential nutrients such as phosphorus, nitrogen, and micronutrients, which can be limited in many soils. The fungi release enzymes that break down organic matter in the soil, making these nutrients available to the host plant.
  • Water uptake: Mycorrhizal fungi can also improve the water-holding capacity of soils, allowing the host plant to access water even in dry conditions.
  • Disease resistance: Mycorrhizal fungi can protect plants from disease by producing antibiotics and stimulating the plant’s immune system.
  • Soil stabilization: Mycorrhizal fungi can help to stabilize soils and prevent erosion, particularly in disturbed ecosystems such as mine sites and construction areas.
  • Carbon sequestration: Mycorrhizal fungi are important in carbon sequestration, or the storage of carbon in the soil. This can help to mitigate climate change by reducing the amount of carbon dioxide in the atmosphere.
  • Ecological relationships: Mycorrhizal fungi form complex ecological relationships with other organisms in the soil, including bacteria, protozoa, and nematodes. These relationships are essential for soil health and nutrient cycling.

Positive effect of Rhizospheric microorganisms on Plants

Rhizospheric microorganisms, or microorganisms that inhabit the soil surrounding plant roots, can have many positive effects on plant growth and health. Some of these effects include:

  • Nutrient cycling: Microorganisms in the rhizosphere can break down organic matter and release nutrients such as nitrogen, phosphorus, and potassium, making them available to the plant.
  • Nutrient uptake: Some microorganisms can help plants take up nutrients more efficiently by increasing root surface area or producing enzymes that break down nutrients into forms that the plant can absorb.
  • Disease suppression: Certain microorganisms can protect plants from pathogens by producing antibiotics or competing with harmful microbes for resources.
  • Stress tolerance: Some microorganisms can help plants tolerate stress caused by factors such as drought, high salinity, or extreme temperatures.
  • Growth promotion: Some microorganisms produce plant growth-promoting substances such as auxins and cytokinins, which can stimulate plant growth and development.
  • Improved soil structure: Microorganisms can improve soil structure by creating aggregates and increasing water-holding capacity.

Negative effect of Rhizospheric microorganisms on Plants

While rhizospheric microorganisms can have many positive effects on plant growth and health, they can also have negative effects under certain circumstances. Some of these negative effects include:

  • Disease promotion: Some microorganisms can cause plant diseases or contribute to their spread by producing harmful toxins or weakening the plant’s immune system.
  • Nutrient immobilization: Some microorganisms can immobilize nutrients in the soil, making them unavailable to the plant and leading to nutrient deficiencies.
  • Competition for resources: Microorganisms can compete with plants for nutrients and other resources, potentially reducing plant growth and productivity.
  • Allelopathy: Some microorganisms produce chemicals that inhibit the growth of other plants or interfere with their ability to take up nutrients.
  • Soil degradation: Certain microorganisms can degrade soil quality by producing toxins or degrading soil structure, leading to soil erosion and reduced plant productivity.


What is the rhizosphere?

The rhizosphere is the soil region surrounding the plant roots that is influenced by the plant’s root exudates and microbial activity.

What is the role of microorganisms in the rhizosphere?

Microorganisms in the rhizosphere play a crucial role in nutrient cycling, plant growth promotion, disease suppression, and overall soil health.

How do plants influence the rhizosphere microbial community?

Plants influence the rhizosphere microbial community through root exudation and by providing a source of carbon and other nutrients.

What is root exudate?

Root exudates are organic compounds secreted by plant roots into the surrounding soil that can influence the rhizosphere microbial community.

What is the difference between rhizosphere and bulk soil?

Rhizosphere is the soil region immediately surrounding the plant roots, while bulk soil refers to the soil farther away from the roots.

How do rhizosphere microorganisms promote plant growth?

Rhizosphere microorganisms can promote plant growth by fixing nitrogen, solubilizing nutrients, producing plant growth hormones, and suppressing plant pathogens.

What factors influence the rhizosphere microbial community?

Factors that influence the rhizosphere microbial community include plant species, soil type, nutrient availability, and environmental conditions.

Can the rhizosphere microbial community vary between different plant species?

Yes, the rhizosphere microbial community can vary between different plant species due to differences in root exudation and other factors.

How can we study the rhizosphere microbial community?

The rhizosphere microbial community can be studied using a variety of methods, including DNA sequencing, microbial culturing, and functional gene analysis.

Can we manipulate the rhizosphere microbial community to improve plant growth?

Yes, manipulating the rhizosphere microbial community through practices like crop rotation, cover cropping, and inoculation with beneficial microorganisms can improve plant growth and soil health.


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  • Broeckling, C. D., Manter, D. K., Paschke, M. W., & Vivanco, J. M. (2008). Rhizosphere Ecology. Encyclopedia of Ecology, 3030–3035. doi:10.1016/b978-008045405-4.00540-1
  • Koo, B.-. J., Adriano, D. C., Bolan, N. S., & Barton, C. D. (2005). ROOT EXUDATES AND MICROORGANISMS. Encyclopedia of Soils in the Environment, 421–428. doi:10.1016/b0-12-348530-4/00461-6 
  • Mendes, R., Garbeva, P., & Raaijmakers, J. M. (2013). The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiology Reviews, 37(5), 634–663. doi:10.1111/1574-6976.12028
  • Huang, X.-F., Chaparro, J. M., Reardon, K. F., Zhang, R., Shen, Q., & Vivanco, J. M. (2014). Rhizosphere interactions: root exudates, microbes, and microbial communities. Botany, 92(4), 267–275. doi:10.1139/cjb-2013-0225
  • Dotaniya, M. & Meena, Vasudev. (2015). Rhizosphere Effect on Nutrient Availability in Soil and Its Uptake by Plants: A Review. Proceedings of the National Academy of Sciences, India Section B: Biological Sciences. 85. 10.1007/s40011-013-0297-0. 
  • Qu, Q., Zhang, Z., Peijnenburg, W. J. G. M., Liu, W., Lu, T., Hu, B., … Qian, H. (2020). Rhizosphere microbiome assemble and its impact on plant growth. Journal of Agricultural and Food Chemistry. doi:10.1021/acs.jafc.0c00073

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