THE RHIZOSPHERE

• By def., the rhizosphere is that portion of the soil under

the direct influence of the roots of higher plants
whereas the rhizoplane encompasses the root surface
and its adhering soil.
• The soil microbes in the vicinity of the growing roots are
stimulated by the provision of a surface upon which to
grow as well as by the nutrients contained in leachates,
sloughed cells, and decaying roots.
• Microbial colonies develop unevenly along the root
surface, with maximal populations occurring where the
exudates are lost from the root. Therefore, the
occurrence of microcolonies is a good indicator of
carbon and energy source leakage from the root.
• Characteristics that define the rhizosphere are as
follows:
1. The properties of the plant are the predominant
controllers of the ecosystem rather than those of the
soil. The situation results from the fact that the plant
is supplying the nutrient and energy source, plus
space for the microbes to grow, as well as altering
the gaseous regime of the soil.
2. The microbes prevailing in the rhizosphere originate
in the soil and are characteristic of the soil microbial
community. But because of the variation in the nature
of root exudates between plant species, the species
organisms comprising the rhizosphere microbial
community do vary with plant species and soil type.
• Characteristics that define the rhizosphere are as follows (continued):
3. Because of the combination of increased microbial respiration occurring in the root zone
compared to the adjacent non-rhizosphere soil and the root respiration, the gas regime
around the root differs from that of the surrounding soil. Carbon dioxide levels are
generally elevated and molecular oxygen tensions are produced in comparison with the
gaseous content of non-rhizosphere-impacted soil.
• Characteristics that define the rhizosphere are as follows (continued):
4. The influx of carbon and energy in the form of root exudates selects for microbes capable
of using the nutrients most efficiently – the fast-growing microbes. In comparison, non-
rhizosphere microbial communities typically exist in a “feast and famine” state. Nutrients
provided to non-rhizosphere populations primarily result from the influx of nutrients
contained in infiltrated water (a typical source in a non-managed ecosystem is fixed carbon
mobilized by the decay of surface litter) or are carried into the site through the movement
of animal life (including the nutrients contained in the animal body when the organism
expires as well as organic substances translocated by the activity of ants, termites, and
earthworms). It is tempting to consider the rhizosphere community to be continuously bathed
in nutrients. This concept may be of value in developing an overall model of the community,
but it is far from the situation at the microsite. Quantities of root exudates as well as their
chemical composition vary along the root length, change throughout the growing season,
and are dependent upon root density and plant-plant interactions.
• Characteristics that define the rhizosphere are as
follows (continued):
5. Since many of the products of root metabolism are
acids (including carbon dioxide which forms a weak
acid when dissolved in soil water), soil minerals are
solubilized in the rhizosphere. Thus, osmotic impacts
on microbial growth are accentuated in the
rhizosphere, mineral nutrient availability is
modified, and clay mineral transformation may
occur. For example, linkage of potassium
availability and loss of potassium ion from mica
flakes plus transformation of phylogopite into
vermiculite in inoculated pine root (Pinus sylvestris L.)
rhizosphere soils were shown by Leyval and
Verthelin (1991).
THE MICROBIAL COMMUNITY
• The rhizosphere effect or the degree of stimulation of an activity of population
by the energy input of the plant root described by evaluation of the ratio of
activity per unit weight of rhizosphere soil to the activity per unit weight of non-
rhizosphere soil (the R/S value).
• Values greater than 1 indicate selective stimulation in the rhizosphere, equivalence
of the two activities suggests no rhizosphere effect, whereas a R/S ratio of less
than 1 reveals inhibition of the activity in the rhizosphere.
• Rhizosphere bacterial populations: Bacterial populations are stimulated by root
exudates. Populations greater than 109g-1 rhizosphere soil are commonly
detected.
• Selective stimulation of rapidly growing, gram-negative, rod-shaped bacteria (Pseudomonas sp.,
Flavobacterium sp., and Alcaligenes sp. especially and occasionally Agrobacterium sp.) is observed.
These bacterial species are found as microcolonies covering approximately 4-10% of the root
surface.
• Competition, the primary selective, intermicrobial interaction, is based on growth rate, metabolic
versatility, and growth factor requirements as follows:
• Growth rate: The conditions of the rhizosphere favor those bacteria which have short
generation times. Clearly, organisms that convert the carbon and energy contained in the root
exudates to biomass efficiently and rapidly will achieve greater population densities and
occupy more of the space than the less vigorous and efficient members of the community.
• Nutrients: A variety of fixed carbon compounds are available to the microorganism within the
rhizosphere. Stress of competition may result in exhaustion of a particular growth substrate,
whereas abundant supplies of others remain. Thus, successful bacterial populations are those
capable of using a variety of biochemical growth substrates. Data suggest that, in general,
the organisms in the rhizosphere are not carbon limited, but supplies of specific carbon sources
may become more limiting due to intense competition.
• Growth factor: Root exudates commonly contain a
variety of amino acids and vitamins which may be
used as microbial nutrients or growth factors.
Comparison of the growth factor-synthesizing
capacities of rhizosphere bacteria suggests that some
advantage is conferred on organisms requiring amino
acids and no other growth factors. Interestingly, the
proportion of bacteria in the rhizosphere which
require complex nutritional growth factors declines,
but their actual numbers increase. This somewhat
confusing observation results from the fact that the
number of these organisms in the ecosystem increases
but the total population increases at an even faster
rate. Therefore, although there are more growth
factor-requiring bacteria in the rhizosphere than are
found in non-rhizosphere soil, they make up a smaller
portion of the total population.
• Competition for surface area affects population development primarily at the
microsite where cell-cell interactions are intensified.
• Antibiotic production appears to play a role in amensal interactions in the rhizo-
sphere. With the close proximity of bacteria, the intense competitions occurring,
and the positive impact of inoculation of plant roots with antibiotic-producing
microbial strains.
• Fungi in the rhizosphere: Quantification of the
rhizosphere effect on soil fungal populations is
equivocal at best. This difficulty is derived, to a
large degree, from the inability to separate active
from inactive fungal propagules.
• Fungal population densities may be quantified
through the enumeration of colonial development on
defined media or mycelial strands may be counted
directly in soil samples.
• Colonies growing on defined media may result from
the outgrowth of spores contained in the soil sample
or from mycelial strands. Direct observation of
hyphal strands in soil provides a measure of total
fungal biomass, but not species or genus identity.
• Colonies growing on the defined media can readily be classified into genus and
species, but they may have developed from a quiescent spore serendipitously
existing in the environs of the root or from an actively respiring fungal colony.
Thus, data collected for the evaluation of the rhizosphere effect on fungal
populations are difficult to interpret. Total fungal counts appear not to be
impacted by association with the root, but some individual populations may be
stimulated.
• Plant roots do produce compounds which stimulate the outgrowth of fungal resting
structures and hyphal development. Similarly, zoospores of phycomycetes are
chemotactically attracted to the growing root tip. These observations suggest a
positive rhizosphere effect on fungal populations.
• Other rhizosphere inhabitants: Organisms whose populations
tend not to react to influxes of readily decomposable organic
matter are usually not affected by root growth. This grouping
includes actinomycetes, protozoa, and algal populations. The
actinomycetes generally derive their energy supply from
decomposition of less readily decomposable soil organic
matter components whereas algal populations use solar
energy.
• Protozoan populations are limited by the distribution and
density of prey populations. Because of the high population
density of prey required to support increases in protozoan
cell numbers and the limited precision of the methods used to
quantify protozoa in soil, a slight increase of protozoa in
rhizosphere soil could occur and escape detection.
 RHIZOSPHERE-EFFECT
• “Rhizosphere effect”, a term coined by Starkey (1938), is defined by collective processes occurring at the
root-soil interface of a plant and includes root exudation, microbial activity, genetic exchange, nutrient
transformation and gradient diffusion.
• In living plants, organic carbon released by plant roots is decomposed to CO2 in a mechanism known as
rhizosphere priming effect.
• Although the estimate of plant carbon economy is still controversial, approximately one-third to half of total
assimilated carbon is allocated to below-ground, of which 15-25% is exuded from the roots into the soil to
induce fast carbon-turnover in the rhizosphere.
• Due to intensive carbon uptake by the roots, other nutrients in the rhizosphere are strongly limited.
• In contrast, all the nutrients except carbon are unlimited in root-free soil. The surplus of readily available
carbon and substantial nutrient limitation, together, make the rhizosphere milieu strongly different from that
of the root-free zones. The increased microbial number and activity in the rhizosphere compared to those in
bulk soil are mainly due to the release of organic carbon by the plant roots.
• The substances released by plant roots are collectively termed as “rhizodeposits.”
• These compounds include
• (i) water-soluble ions and low-molecular-mass compounds such as mono-saccharides, amino acids and
organic acids which are lost passively along a concentration gradient,
• (ii) high-molecular-mass compounds such as carbohydrates, proteins and lipids which are actively
transported along an electrochemical gradient,
• (iii) insoluble mucilage composed of polysaccharides and polygalacturonic acid,
• (iv) an array of secondary metabolites such as antimicrobial compounds, nematicides and flavonoids and
(v) remnants of the dead and lysed root-cap and border cells.
• Of these, sugars and amino acids are thought to be released in the greatest quantities.
 FACTORS AFFECTING ROOT-EXUDATION
• The quantity and composition of rhizodeposits are influenced by a variety of biotic and abiotic factors and
vary in time and space with respect to the position on the root.
• The host-dependent factors include genotype and age of the plant while the abiotic components include
different environmental factors, grazing activities and anthropometric habits.
• The wide quantitative and qualitative variation in root exudation of different plant species suggests that it is
determined by plant genetic makeup.
• In a study with eight accessions of Arabidopsis thaliana, a unique combination of exudates was found to be
secreted from the plants of different cultivars grown simultaneously under uniform conditions. This gave rise to
genotype-specific rhizobacterial communities at six weeks post-germination.
• The cultivar-specific variation in root exudation is mainly regulated by the root system architecture.
• The zone immediately behind the root tip is considered to be the major site of exudation although different
sites have been recorded to be active in different plant species.
• Different parts of the root system exude different compounds.
• For example, asparagine and threonine are exuded from meristem and root elongation zone;
glutamic acid, valine, leucine and phenylalanine are secreted from root hair zone; while aspartic
acid is exuded from the whole root. Use of 14C to identify the sites of exudation from wheat roots
has shown that non-diffusible materials are released from both primary and lateral root tips and
diffusible materials are released from the whole length of roots.
• In general, apical meristem of plant roots is covered by root cap
which sloughs off as the root tip wends its way through the soil.
These sloughed-off cap cells, known as “border cells”, play a
significant role in determining the rhizosphere chemical
environment.
• Border cells produce polysaccharide mucilages accounting for 2–
12% of the total rhizodeposition and 10% of total carbon
released by roots.
• The number of border cells varies between plant species and this
variability appears to be related to the organization of the root
apical meristem in monocotyledons and dicotyledons.
• Border cells regulate microbial interaction by avoiding
pathogens and favouring association with beneficial microbes.
They also protect against heavy metal toxicity.
• The root cap and hair cells are also involved in
secretion of compounds. Root hairs are the
extensions of single epidermal cells and comprise
as much as 77% of the total root surface area of
cultivated crops, developing a connection between
the plant and the rhizosphere.
• They play an important role in rhizosphere
processes including uptake of water, nutrients and
exudation of different compounds. In addition to
the root cap and hair cells, other cells are also
involved in secretion. For example, citrate secretion
from maize roots in response to aluminium toxicity
predominantly involves cortex and stellar cells
located 5 cm above the root cap.
• Plant age vis-a-vis developmental stages plays a pivotal role in characterizing root-exudation
pattern by its impact on root system architecture.
• Seedlings produce the lowest amounts of root exudates which gradually increases until flowering
and decreases again at maturity. Secretion of phenolic compounds and defense-related proteins
by Arabidopsis roots at flowering stage has been correlated with the age-related resistance of
the plant.
• The environmental factors affecting root exudation include soil characteristics such as soil texture,
pH, and moisture content in addition to climate, temperature, light and humidity.
• High soil moisture leads to hypoxia which may cause an increased anaerobic respiration rate,
accumulation of ethanol, lactic acid and alanine in the rhizosphere.
• The presence or absence of particular minerals or toxic metals in the soil affects the composition of
root-exudation. For example, citric, malic and oxalic acids are secreted to detoxify aluminium;
secretion of phenolic compounds is increased in phosphorus deficient soils.
• Secretion of signalling molecules like flavanones and flavones is enhanced in nitrogen limiting
conditions.
• Mineral-deficiency enhances the production of elicitors that influence root-exudation. Potassium
deficiency increases jasmonic acid mediated defense responses.
• Lower temperatures and light reduce the secretion of root exudates. For example, the exudation
of tannins and phenolic compounds in Vicia faba was greatly reduced at 4 °C.
• The presence of neighbouring plant species and the rhizosphere microflora also affect the root
exudation. Outcome of glucosinolates activation in Arabidopsis was regulated by the presence of
neighbouring plants. Production of glucosinolates is increased in a high-density environment having
large number of Arabidopsis plants grown together compared with a low-density range.
 ROOT EXUDATES AND MICROBIAL COLONIZATION
• The structural and functional diversities of rhizosphere microbial communities of a wide variety of
plants including Arabidopsis, Medicago, maize, pea, wheat and sugar beet are shaped by plant
developmental stages.
• For example, rhizosphere microbial communities in early development of Arabidopsis were
different from that observed in the bulk soil and this difference decreased with plant age.
• Carbohydrates, organic acids and amino acids stimulate positive chemotactic responses in
bacteria. The capacities of different microbial species to compete for these substrates and utilize
vary. In the rhizosphere of maize, exudation of the benzoxazinone DIMBOA (2,4-dihydroxy-7-
methoxy-1,4-benzoxazin-3-one) resulted in an increase of population density of Pseudomonas
putida strain with plant beneficial characteristics.
• Many soil-borne organisms follow the concentration gradients of sugars and amino acids towards
the root. This leads to differential proliferation of microorganisms along different compartments of
rhizosphere.
• Since quantity and composition of root exudates respond rapidly to subtle environmental changes,
the selective pressure exerted on microbial communities varies spatiotemporally.
• Rhizosphere pH also shapes microbial ecology in the root environment. Root-induced pH changes
have a dramatic impact on key biogeochemical processes such as (i) dissolution/precipitation of
soil minerals and (ii) adsorption/desorption of ions, and hence bioavailability of either anions (e.g.
phosphate) or cations (e.g. copper).
• Further understanding of rhizosphere biogeochemistry is required to quantify the driving role of
higher plants in ecosystem services such as soil formation and nutrient cycling.

Role of microbial biomass in the cycling of nutrients in

rhizosphere
 PLANT-MICROBE AND MICROBE-MICROBE INTERACTIONS
• The plant–microbe interaction in the rhizosphere may be categorized as associative, symbiotic,
neutralistic, or parasitic.
• The positive interactions include symbiotic and associative interactions with beneficial microbes,
such as endo- and ecto-mycorrhizal fungi, nitrogen-fixing bacteria and plant growth-promoting
rhizobacteria (PGPR) whereas negative interactions include association with parasitic plants,
pathogenic bacteria, fungi, oomycetes, nematodes and invertebrate herbivores.
• Symbiosis between legume plants and Rhizobia in the soil is of particular importance in
agriculture. Legume-Rhizobia interactions are mediated by host-specific flavonoids secreted in the
root-exudates (Table 1).
• These molecules belong to a diverse family of aromatic compounds derived from plant’s secondary
metabolism.
• Depending on the host and the bacterium, flavonoids activate a series of transcriptional events
culminating in the production of main rhizobial nodulation signals called Nod factors (NF) or lipo-
chito oligosaccharides.
• Nod factors induce diverse developmental processes in the plant partner leading to morphological
changes in legume root hairs, infection thread formation, nodule development and symbiotic
nitrogen fixation. Rhizobium sp. is a vast group of soil-borne rhizobia with other plant growth
promoting activities such as siderophore production and disease suppression.
• Rhizosphere microbial populations communicate among themselves in
addition to interacting with the plant root system. Based on their
primary effects, the beneficial rhizosphere organisms are generally
classified into two broad groups (i) biological control agents (BCA) that
indirectly assist with plant productivity through the control of plant
pathogens and (ii) plant growth promoting microorganisms (PGPM) with
direct effects on plant growth promotion.
• BCA adversely affect the population density, spatio-temporal dynamics
and metabolic activities of soil borne pathogens via three types of
interactions. These include competition, antagonism by producing
secondary antimicrobial metabolites, lytic enzymes, effectors and
hyperparasitism.
• Trichoderma sp. is the most studied fungal BCA which has been proved
to reduce plant diseases by multifarious modes of action.
• Bacillus amyloliquefaciens SQR9, isolated from cucumber rhizosphere,
could protect the host from invasion by Fusarium oxysporum f.sp.
cucumerinum through competition for nutrients and space.
• Hyperparasitism among BCA involves the secretion of chitinases and cellulases which degrade
pathogen’s cell-wall. This has been documented for Trichoderma, Gliocladium and Pasteuria
penetrans.
• The pathogens in the rhizosphere also exert diverse array of mechanisms to counteract
antagonism. These include active degradation of antimicrobial compounds detoxification of
oxygen radicals resulting from the oxidative stress generated by the antimicrobial compounds,
conversion of antimicrobial metabolite into less toxic derivatives and interference with the
regulation and biosynthesis of enzymes and antimicrobial metabolites produced by antagonistic
microorganisms.
• Studies on bacteria in the legume rhizosphere have shown that indigenous Rhizobia compete via
either antagonism or synergism not only with diazotrophs such as Azotobacter and Azospirillum but
with Pseudomonas and Bacillus species for nodulation and nitrogen fixation.
• The diazotrophs manage important biological functions by symbiotically interacting with Rhizobium
populations within the rhizosphere to form a beneficiary region where interacting microorganisms
benefit from nutrient resources. Synergistic effects of PGPR and Rhizobium enhance nodulation,
rate of nitrogen fixation and better yield of crops such as pea, chickpea and pigeon pea.
• PGPMs may act as biofertilizer and/or phytostimulators. The activity and effects of beneficial
rhizosphere microorganisms on plant growth and health are well documented for bacteria
belonging to the Proteobacteria noticeably Pseudomonas and Burkholderia, Firmicutes,
Actinobacteria and fungi viz. Trichoderma, Gliocladium and nonpathogenic Fusarium oxysporum.
• Pseudomonads are common colonizers of plant tissues and traditionally known to be the major
component of many rhizosphere communities. Pseudomonas sp. have been broadly studied for their
ability to reduce the development of various soil-borne plant pathogens through production of
different antimicrobial compounds, competition for the nutrients in the root exudates and induction
of the plant defense mechanisms.
• Bacillus species offer several advantages over fluorescent Pseudomonads and other Gram-
negative bacteria as seed inoculants by protecting against root pathogens by virtue of their ability
to form endospores and producing broad-spectrum antibiotics.
• There is a growing list of reports demonstrating rhizosphere colonization and root disease control
by B. cereus UW85, B. megaterium B153-2-2 and B. subtilis GB03 which are involved in controlling
damping-off in alfalfa and cotton and Rhizoctonia root-rot disease in soybean.

Wheat plants amended with TCP and rhizobacterial strains (A) without Glomus
etunicatum (B) rhizobacterial strains with Glomus etunicatum at 45 DAS.