Rhizosphere is the region of intense microbial activity, extending several millimeters from the root system of vascular plants. It is where the soil and root of plant make contact. Rhizosphere soil is the thin layer of soil adhering to the root system after shaking and removing the loose soil.
In 1904 the German agronomist and plant physiologist Lorenz Hiltner first coined the term "rhizosphere” [Greek word "rhiza", meaning root]. Hiltner described the rhizosphere as; “The area around a plant root that is inhabited by a unique population of microorganisms, influenced by the chemicals released from plant roots”.
Rhizosphere microflora is quantitatively and qualitatively different from the non-rhizosphere microflora. Also, rhizosphere microflora of one plant differs from that of another. Thus, rhizosphere is a unique subterranean habitat for microorganisms.
Structure of Rhizosphere
It has three zones which are defined based on their relative proximity to, and thus influence from, the root.
1. Endorhizosphere; in close proximity with the plant cortex and endodermis in which microbes can occupy the "free space" between cells
2. Rhizoplane; is the root surface
3. Ectorhizosphere; the outermost zone which extends from the rhizoplane into the adjacent soil.
The direct influence of plant roots on microbes and microbes on plant root within the rhizosphere is known as Rhizosphere effect. The enhancement of the growth of a soil microorganism results from the physical and chemical alteration of the soil by the excretions and organic debris of roots within a rhizosphere. Rhizosphere effect is expressed by R:S ratio, which is the ratio between number of microorganisms in the rhizosphere soil to the number of microorganisms in the non-rhizosphere soil. R: S ratio is different for different plants and changes with the stage of growth of a plant. The values are high for bacteria in rhizosphere region.
During seed germination and seedling growth, the developing plant interacts with microorganisms present in the surrounding soil. As seeds germinate and roots grow through the soil, the release of organic material lead to the development of active microbial populations in rhizosphere region (that includes plant root and surrounding soil in a few mm of thickness).
Root exudation is the release of organic compounds from living plant roots into the surrounding soil. Rates of exudation vary widely among plant species and environmental conditions. It has been estimated that 12-40% of the total amount of carbohydrates produced by photosynthesis is released into the soil surrounding roots. Root exudates are mainly composed of water-soluble sugars, organic acids, and amino acids, but also contain hormones, vitamins, amino compounds, phenolics and sugar phosphate esters. The qualitative and quantitative compositions of root exudates are affected by various environmental factors including; pH, soil type, oxygen status, light intensity, soil temperature, nutrient availability and the presence of microorganisms.
Rhizosphere
microflora
The rhizosphere, is a hot
spot for numerous organisms and is considered as one of the most complex
ecosystems on Earth. Organisms found in the rhizosphere include bacteria, fungi,
oomycetes, nematodes, protozoa, algae, viruses, archaea, and arthropods.
Rhizosphere microorganisms that have been well studied for their beneficial effects
on plant growth and health are; the nitrogen-fixing bacteria, mycorrhizal
fungi, plant growth-promoting rhizobacteria (PGPR), biocontrol microorganisms,
myco parasitic fungi, and protozoa. Rhizosphere organisms that are deleterious
to plant growth and health include the pathogenic fungi, bacteria, and
nematodes. A third group of microorganisms that can be found in the rhizosphere
are the human pathogens.
Plant-Microbe
interactions in the rhizosphere
Microorganisms present in
the rhizosphere play important roles in ecological fitness of their plant host.
Important microbial processes that are expected to occur in the rhizosphere include;
✓ pathogenesis
✓ plant protection/growth promotion,
✓ production of antibiotics,
✓ geochemical cycling of minerals
✓ plant colonization
Plant-microbe
interactions may thus be considered beneficial, neutral, or harmful to the plant,
depending on the specific microorganisms and plants involved and on the
prevailing environmental conditions.
Pathogenic
interactions
Roots exudates can
attract beneficial organisms, but they can also attract pathogenic populations.
Many pathogenic organisms, bacteria as well as fungi, have coevolved with
plants and show a high degree of host specificity. But even though plants are
in permanent contact with potential pathogens such as fungi, bacteria or
viruses, successful infection is rarely established. Such a general resistance
against most pathogens has been named “horizontal resistance” or
“non-host-resistance”. These resistance mechanisms comprise structural barriers
and toxic compounds that are present in the unaffected, healthy plant.
Phytoanticipins; is a toxin which resist the entry and colonization of pathogenic fungi in plants.
However,
in some instances, pathogens can overcome the pre-formed barriers and develop virulent
infection processes leading to plant disease. soil-borne pathogens cause
important losses in agriculture, fungi being the most aggressive. The extent of
their harmful effects ranges from mild symptoms to catastrophes where large fields
planted with agricultural crops are destroyed. Thus, they are major and chronic
threats to food production and ecosystem stability worldwide.
Common and well
investigated bacterial agents include;
• Gram negative bacteria Erwinia carotovora, Pseudomonas,
Ralstonia spp.
• Gram positive bacterium
like Streptomyces.
• The fungal phytopathogens
include members of; Fusarium,
Phytophthora, Pythium, Rhizopus, Rhizoctonia and Verticillium.
Beneficial
microorganisms and modes of action
Plant-beneficial
microbial interactions can be roughly divided into three categories.
First, those
microorganisms that, in association with plants, are responsible for its nutrition (i.e., microorganisms that
can increase the supply of mineral nutrients to the plant). While most may not
directly interact with the plant, their effects on soil biotic and abiotic parameters
have an impact on plant growth. e.g. Microbes involved in biogeochemical cycles.
Second, there is a group
of microorganisms that stimulate plant growth indirectly by preventing the
growth or activity of pathogens. Such microorganisms are referred to as biocontrol agents.
A third group involves
those microorganisms responsible for direct growth promotion by production of
phytohormones etc
Neutral
interactions
Saprophytic
microorganisms are responsible for many vital soil processes, such as decomposition
of organic residues in soil and associated soil nutrient mineralization or turnover
processes. Whereas these organisms do not appear to benefit or harm the plant directly
(hence the term neutral), their presence is vital for soil dynamics,
and their absence would clearly influence plant health and productivity.
Beneficial
effects of Rhizosphere Microbes
1. Plant growth
promotion; by PGPR (plant growth promoting rhizobacteria) which improve
plant growth.
Diverse PGPR strains have been used successfully for crop inoculations, such as; Azospirillum, Bacillus, Pseudomonas, Rhizobium, Serratia and Streptomyces.
Some fungi belonging to the
genera; Ampelomyces, Coniothyrium, and Trichoderma have also been described to
be beneficial for the host plant.
The modes of action of
PGPR to promote plant growth, development and protection are,
1. Biofertilization (directly, by helping to provide nutrient to the host plant, or indirectly by positively influencing root growth and morphology or by aiding other beneficial symbiotic relationships). Rhizobium, Azospirillum, Burkholderia etc
2. Phyto stimulation (plant growth promoting, usually by the production of phytohormones phytohormones [indole-3-acetic acid (IAA), auxins, cytokinins, and gibberellins). Azospirillum, Pseudomonas etc
3. Biocontrol (controlling diseases, mainly by the production of antibiotics and antifungal metabolites, lytic enzymes and induction of plant defense responses). Bacillus spp.
Pathogen inhibition; Bacteria and fungi live around roots and feed on root exudates and dead root cells.
Competition between
microbial species in this area is stiff. In the battle for establishment and persistence
in the niche, bacteria use several strategies.
a. Antagonism
b. Competition
c. Induced resistance
a.
Antagonism, including;
Antibiosis
i.e. the inhibition of microbial growth by diffusible antibiotics and volatile organic
compounds, toxins, and biosurfactants,
Parasitism
that may involve production of extracellular cell wall-degrading enzymes such as
chitinases and β-1,3-glucanase.
Degradation of
pathogenicity factors of the pathogen such as toxins by the beneficial organism
has also been reported as protective mechanism
b.
Competition, Competition for resources such as
nutrients and oxygen occur generally in soil between soil-inhabiting organisms.
For biocontrol purpose, it occurs when the antagonist directly competes with
pathogens for these resources.
E.g. Competition for
nutrients, especially for carbon, is assumed to be responsible for the wellknown phenomenon of fungistasis
characterizing the inhibition of fungal spore germination in soil
c.
Induced resistance
Plant-associated bacteria
can reduce the activity of pathogenic microorganisms by activating the plant to
better defend itself, a phenomenon termed “induced systemic resistance”, “ISR”.
Phyllosphere
The above-ground parts of plants, including the stems, leaves, flower and fruits are normally colonized by a variety of bacteria, yeasts, and fungi. The aerial habitat colonized by these microbes is termed the phyllosphere, and the inhabitants are called epiphytes.
The phyllosphere can be further subdivided into the caulosphere (stems), phylloplane (leaves), anthosphere (flowers), and carposphere (fruits). Even though the Phyllosphere comprises stems, leaves, flower and fruits, most work on phyllosphere microbiology has focused on leaves, which is the most dominant aerial plant structure.
The microbial communities of leaves are diverse and include many different genera of bacteria, filamentous fungi, yeasts, algae, and, less frequently, protozoa and nematodes.
Filamentous fungi are considered transient inhabitants of leaf surfaces, with rapidly sporulating species and yeasts colonizing this habitat more actively.
Bacteria are the most abundant inhabitants of the phyllosphere. Epiphytic bacterial populations differ in size among and within plants of the same species, and over time as well as over the growing season. These variations in population sizes are caused by the large fluctuations in the physical and nutritional conditions characteristic of the phyllosphere.
Factors influencing microbial growth and distribution on Phyllosphere
- Growth on the leaf surface is frequently limited by both water and nutrients, as well as exposure to high levels of ultraviolet (UV) radiation.
- Variation in the physical and chemical landscape of the leaf itself and patchiness of nutrients on the leaf surface impose additional constraints for colonizing microorganisms.
- Leaf topography changes as the leaf ages, so that plant–microbial interactions are dependent on time as well as the specific characteristics of the host plant.
- Abiotic stress including adverse environmental conditions also limit microbial growth on phyllosphere. Denser populations of bacteria are found in the grooves between plant cells, at the base of trichomes, and near leaf veins and stomatal openings. This is a protective measure from abiotic stress.
- Moisture availability is a key limitation to microbial growth on the leaf surface. The cuticle prevents moisture from leaving the inside of the leaf and limits how much water remains on the leaf surface. To overcome this challenge, bacteria may form aggregates and biofilms, producing extracellular polymeric substances (EPS), which can resist desiccation. Some bacteria produce surfactants to increase the wettability of the leaf and lessen the ability of the cuticle to limit water accumulation.
- The leaf surface has a boundary layer with a microclimate that typically has higher humidity than the broader phyllosphere, and this reduces some of the desiccation pressure for microbiota that are in that layer.
Microbial populations typically increase following precipitation, when there can be substantial changes in the diversity and composition of the phyllosphere microbiome. Microorganisms on the leaf surface are generally oligotrophs that can tolerate low-nutrient conditions or are microorganisms that can interact with the host plant to obtain more nutrients. Although cuticular waxes are generally resistant to chemical movement, some plant metabolites can move to the leaf surface, supporting microbial growth. These compounds may arrive on the leaf surface by excretion from leaf cells, or due to osmotic pressure when the leaf is wet.
Plants also release volatile organic compounds, which support specific populations of microorganisms; for example, methylotrophic bacteria that metabolize plant-derived single-carbon compounds are abundant constituents of the phyllosphere of many plant species.
Phyllosphere microorganisms may obtain nitrogen from plant produced amino acids, which leach to the leaf surface or by inorganic forms of nitrogen.
Bacterial nitrogen fixation can occur on the leaf surface. Exposure to UV radiation poses a particular challenge to leaf epiphytes, and bacterial and fungal populations that have been isolated from the phyllosphere are typically more pigmented than those from soil. This pigmentation can increase survival in the phyllosphere environment. Sphingomonas is an abundantly occuring bacteria in phyllosphere which produce yellow or orange pigments.
The Nature and Composition of the Phyllosphere Microbiome
Phyllosphere microbiota represent a diverse array of microorganisms, but they are typically dominated by bacteria. Phyllosphere bacterial are generally less species rich than the rhizosphere or soil. Alpha proteobacteria are particularly well represented on the leaf surface, and these bacteria play many ecological roles. Gamma proteobacteria have also commonly been reported in surveys of phyllosphere bacterial community composition.
Proteobacteria are metabolically diverse, and the phyllosphere bacteria that carry out methyltrophy, nitrification, nitrogen fixation, or anoxygenic photosynthesis are typically representatives of this phylum.
Bacteroidetes and Actinobacteria are generally the next most dominant bacterial lineages in phyllosphere communities. Bacteroidetes are often aerobic and pigmented, suggesting that they are well adapted to the leaf surface.
The phylum Actinobacteria includes members that are plant pathogens, nitrogen-fixing symbionts, and fungal antagonists, as well as decomposers. Many of these roles have not been explored in the phyllosphere environment, but the Actinobacteria Corynebacterium has been used as a foliar-applied plant growth promoter (Nitrogen fixer).
The fungal community is composed of organisms with a wide variety of ecological roles whose population sizes fluctuate in distinct seasonal trends based on the growing season and, ultimately, leaf senescence.
Moulds belonging to the Ascomycota are often the dominant fungi on the leaf surface before senescence. Other important fungi are yeasts belonging to the Ascomycota and Basidiomycota.
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