Rhizosphere: its structure, bacterial

diversity and significance

Pratibha Prashar, Neera Kapoor & Sarita

Sachdeva

Reviews in Environmental Science

and Bio/Technology

ISSN 1569-1705

Rev Environ Sci Biotechnol

DOI 10.1007/s11157-013-9317-z

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 Author's personal copy
Rev Environ Sci Biotechnol
DOI 10.1007/s11157-013-9317-z

REVIEW PAPER

Rhizosphere: its structure, bacterial diversity

and significance
Pratibha Prashar • Neera Kapoor •

Sarita Sachdeva

Ó Springer Science+Business Media Dordrecht 2013

Abstract Sustainable agricultural practices are the variety of interactions between themselves as well as
answer to multifaceted problems that have resulted due with the plant. Plant friendly bacteria residing in
to prolonged and indiscriminate use of chemical based rhizosphere which exert beneficial affect on it are
agronomic tools to improve crop productions for the called as plant growth promoting rhizobacteria
last many decades. The hunt for suitable ecofriendly (PGPR). Here we review the structure and bacterial
options to replace the chemical fertilizers and pesti- diversity of the rhizosphere. The major points dis-
cides has thus been aggravated. Owing to their versatile cussed here are: (1) structure and composition of the
and unmatchable capacities microbial agents offer an rhizosphere (2) range of bacteria found in rhizosphere
attractive and feasible option to develop the biological and their interactions with the plant with a particular
tools to replace/supplement the chemicals. Exploring emphasis on PGPR (3) mechanisms of plant growth
the microorganisms that reside in close proximity to promotion by the PGPR (4) rhizosphere competence.
the plant is thus a justified move in the direction to
achieve this target. One of the most lucrative options is Keywords Sustainable agriculture
Rhizosphere

to look into the rhizosphere. Rhizosphere may be Plant growth promoting rhizobacteria
Plant–microbe
defined as the narrow zone of soil that surrounds and interactions
get influenced by the roots of the plants. It is rich in
nutrients compared to the bulk soil and hence exhibit
intense biological and chemical activities. A wide
range of macro and microorganisms including bacte-
ria, fungi, virus, protozoa, algae, nematodes and 1 Introduction
microarthropods co-exist in rhizosphere and show a
Though microbial diversity constitutes most extraor-
dinary and ubiquitous life on earth still they are not
P. Prashar
N. Kapoor
School of Sciences, IGNOU, New Delhi, India uniformly distributed in various habitats across the
e-mail: [email protected] planet. Majority of the microbial populations are
concentrated in nutrient rich niches like the rhizo-
P. Prashar (&)
S. Sachdeva
sphere that have a constant supply of easily utilizable
Department of Biotechnology, FET, MRIU, Sector 43,
Aravalli Hills, Faridabad, India nutrients. Rhizosphere has an enormous pool of soil
e-mail: [email protected]; [email protected] microorganisms and is considered as the ‘hot spot’ for
S. Sachdeva microbial colonization and activity. It is the largest
e-mail: [email protected] ecosystem on earth with huge energy flux (Barriuso

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et al. 2008). Generally regarded as a thin zone

(1–2 mm thick), it holds a large volume of soil in it,
which varies greatly with the plant, soil, root structure
and most importantly the method used to determine it
because it does not have a well defined boundary
(Hinsinger et al. 2005). Due to their close proximity
and/or continuous association with the plant, the
diverse forms of microorganisms found in the rhizo-
sphere influence the host plant in a variety of ways.
These may be broadly classified as beneficial effects
leading to improvement of plant health and growth or
harmful effects, i.e. the pathogenic activities. Thus, it
is very important to understand the composition,
ecology, dynamics and activities of rhizospheric
microbial communities, before we can exploit the
rhizosphere microflora as a tool for developing
sustainable agricultural practices.

2 Rhizosphere Fig. 1 A simplistic diagram of rhizosphere

The term ‘‘rhizosphere’’ has been derived from the hairs, mucoid material, microbes and soil particles
Greek word ‘rhiza’, meaning root, and ‘sphere’, (Curl and Truelove 1986). The root itself is a part of
meaning field of influence. It was first defined by the rhizosphere as endophytic microorganisms colo-
German scientist Hiltner (1904) as ‘‘the zone of soil nize the inner root tissues as well (Bowen and Rovira
immediately adjacent to legume roots that supports 1999). The volume of the soil which is not a part of the
high levels of bacterial activity’’. However, over the rhizosphere, i.e. which is not influenced by the root is
period of time, it has been redefined many times to known as bulk soil (Gobat et al. 2004). The dead root
include the volume of soil influenced by the root and is transformed into soil by rhizospheric activity but it
parts of root tissues as well as the soil surrounding the is different from the bulk soil. Thus, rhizosphere may
root in which physical, chemical and biological be considered as a unique region distinct from the bulk
properties have been changed by root growth and soil.
activity (Pinton et al. 2001). Rhizosphere has been
broadly subdivided into the following three zones 2.1 Rhizosphere effect
(Clark 1949; Lynch 1987; Pinton et al. 2001) (Fig. 1):
In the due course of its growth and development, plant
1. Endorhizosphere: that consists of the root tissue
passes through the early stages of seed germination
including the endodermis and cortical layers.
and seedling growth. During this process a variety of
2. Rhizoplane: is the root surface where soil particles
organic compounds are released from the roots by
and microbes adhere. It consists of epidermis,
exudation, secretion and deposition (Curl and True-
cortex and mucilaginous polysaccharide layer.
love 1986) making the rhizosphere rich in nutrients as
3. Ectorhizosphere: that consists of soil immediately
compared to the bulk soil. This acts as a driving force
adjacent to the root.
for the set up of active and enhanced microbial
Apart from these three basic zones, certain other populations in root zone, much higher as compared to
layers may be defined in some cases e.g. in plants with the bulk soil (Grayston et al. 1996). This phenomenon
mycorrhizal association, there is a zone termed as the of establishment of rich microflora in the rhizosphere
mycorrhizosphere (Linderman 1988) while in some under the influence of root-secreted nutrients is
other plants another, strongly adhering dense layer referred as the rhizosphere effect or plant effect
termed as ‘‘rhizosheath’’, is found. It consists of root (Morgan and Whipps 2001; Antoun and Prevost

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2005). It is calculated in terms of rhizosphere ratio, i.e. insoluble materials, lysates, dead fine roots and gases
R: S by dividing the total number of microorganisms like CO2 and ethylene’’. In simple terms it is defined as
in the rhizosphere (R) by the corresponding number in ‘‘the organic compounds released by living plant roots
the bulk soil (S) (Aneja 2003). Rhizosphere effect is into their surrounding environment’’ (Whipps 1990;
reflected by the noticeable difference in the structure Nguyen 2003) and may also include the inorganic ions
of microbial populations of uncultivated and culti- (Uren 2001). It is equivalent to almost 15–60 % of the
vated soils (Antoun and Prevost 2005) and the total photosynthetic production of the plant and leads
variations in bacterial and fungal community struc- to the accumulation of substantial carbon and energy
tures with rhizosphere related factors such as the crop reserves in the rhizosphere for the microflora (Curl and
variety (Berg et al. 2006), plant growth developmental Truelove 1986; Lynch and Whipps 1990). The plant-
stages (Gomes et al. 2003) and soil characteristics (Nie derived carbon allocated belowground via roots,
et al. 2009). consists of three main components (Cheng and
Though greater rhizosphere effect has been Gershenson 2007):
reported for bacteria that show R: S values ranging
1. Roots mass: that may be living or dead.
between 10 and 100 or even more (Katznelson et al.
2. Rhizodeposit: materials of plant origin localized
1948) than with fungi (Buyer et al. 2002) however
in the rhizosphere or the surrounding soil which
recent studies utilizing cultivation-independent anal-
are utilized and transformed by rhizosphere biota
ysis of soil microflora have revealed significant
and mixed with soil organic materials.
rhizosphere effect for soil fungi as well (Gomes
3. Carbon dioxide: released as a result of respiration
et al. 2003; Berg et al. 2005). For certain classes of soil
of roots and root symbionts or microbial
bacteria like ammonifying and denitrifying bacteria
respiration.
(Rouatt et al. 1960) an even more pronounced
rhizosphere effect has been observed whereas it is Rhizodeposition is a significant process in terms of
almost negligible for algae (Aneja 2003). Though studying the carbon fluxes in the rhizosphere. Rhizo-
some reports have been obtained on stimulating deposit is subdivided into various parts, i.e. root cap
effects of root exudates of plants like tea and pea on cells and root tissues (sloughed root hairs and epider-
algal populations under controlled conditions (Had- mal cells) (Rovira 1956), mucilage and root exudates
field 1960; Cullimore and Woodbine 1963) such (Nguyen 2003) (Fig. 2). Root exudates are the most
effects have not been found very significant in natural important part of the rhizodeposit and are classified
soil habitats and higher algal populations are generally into two types depending on their molecular weight.
recorded in the bulk soils. Soil protozoa form an First class comprises of the low molecular weight
important part of the plant–bacteria–protozoa interac- components like water soluble compounds including
tions which are critical in nutrient recycling and simple carbohydrates, amino acids, organic acids,
selective set-up of beneficial bacterial populations in plant hormones, vitamins, phenolics, sugar phosphate
the rhizosphere (Kreuzer et al. 2006). Due to the effect esters, ions and many other carbon-containing sec-
of root derived carbon and large bacterial populations ondary metabolites (Uren 2001; Farrar et al. 2003;
in the rhizosphere, protozoan population may increase Bais et al. 2006; Cheng and Gershenson 2007). High
as much as 35-fold (Zwart et al. 1994) in this zone. molecular weight exudates form the second class and
Hence, it may be concluded that owing to the nutrient these are generally enzymes, proteins and mucilage
richness of rhizosphere and excellent substrate utili- (polysaccharides). High molecular weight exudates
zation capacities of bacteria, larger bacterial popula- are more significant in terms of total mass of the root
tions can be encountered in rhizosphere as compared exudates but have comparatively lesser variety than
to other forms of soil microbes. the first class (Bais et al. 2006).
Exudates may also be classified as active and
2.2 Rhizodeposition passive exudates on the basis of their role and mode of
secretion from the roots (Rougier and Chaboud 1989;
The term rhizodeposition was first defined by Whipps Bais et al. 2006). Passive exudates have unknown
and Lynch (1985) as ‘‘the material lost from plant functions and are diffused from the roots as basal
roots, including water-soluble exudates, secretions of exudation (output of waste materials) depending on

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Fig. 2 Rhizodeposit. It consists of material of plant origin that is released by the roots and is localized in the rhizosphere. It contributes
significantly towards the total plant-derived carbon in soil as well as developing rich microbial diversity in the rhizosphere

the gradient (Bais et al. 2006). They constitute about Rhizodeposition is affected qualitatively as well as
3–5 % of the total carbon fixed during photosynthesis quantitatively by a number of biotic and abiotic factors
(Pinton et al. 2001). The active exudates are secreted associated with plant and soil (Rovira 1956; Lynch
through open membrane pores of the plants and have a and Whipps 1990; Nguyen 2003; Jones et al. 2004) as
specific function such as lubrication and defense summarized in the Table 1.
(Jones et al. 2004; Bais et al. 2006). Exudation and plant health are mutually related.
Another classification of the exudates can be made The quality and quantity of exudates affects the
on the basis of their biological activity and accordingly microbial diversity including the beneficial and dele-
they may be the signaling molecules, phytoalexins, terious microorganisms as well as the related ecolog-
phytohormones, enzymes or allelochemicals (Nanni- ical processes in the rhizosphere (Bolton et al. 1993;
pieri et al. 2007). Jaeger et al. 1999; Paterson et al. 2007) which in turn
Chemical composition of the rhizodeposit is an influence the plant processes like the rooting patterns,
important determinant of the functions and ecological nutrient availability and pathogen persistence in the
consequences of rhizodeposition (Cheng and Ger- rhizosphere (Bolton et al. 1993; Bowen and Rovira
shenson 2007). The composition, rate and extent of 1999; Barea 2000). At the same time microbial
exudations depend on genetic factors and vary widely activities in the rhizosphere modify the root exudation
among plant species and environmental conditions process and pattern. Thus, it may be said that
(Kochian et al. 2005). Persistence of root exudates in rhizodeposition strongly influence the structural and
the rhizosphere is governed by their chemical prop- functional aspects of microbial communities in the
erties, their stability and the soil volume through rhizosphere.
which they diffuse. They may loose their properties
and hence get inactivated as a result of processes like
adsorption, biodegradation, volatilization, chemical 3 Rhizosphere bacterial diversity
degradation, etc. (Nannipieri et al. 2007).
Exudation provides various kinds of physical and Though majority of the soil microorganisms (approx-
chemical benefits to the plant like reduction of friction imately 99 %) are not culturable, recent advances in
between root tips and soil, reduction in root desicca- biochemical and molecular genetics techniques for
tion process and improving the structural stability of isolation of unculturable bacterial strains has enabled
soil (Rougier and Chaboud 1989). Rhizodeposition is the scientists to generate vital information pertaining
expressed in terms of C release by the roots (CdfR) by to the rhizosphere bacterial communities. Most com-
measuring the production of labeled CO2 in the monly used tools for studying the diversity of uncul-
rhizosphere of 14C-labelled plants (Nguyen 2003). trable microbes include phospholipid fatty acid
However, apart from carbon compounds, various analysis (PLFA), nucleic acid extraction and hybrid-
kinds of nitrogen containing substances are also ization, polymerase chain reaction (PCR) based
released by the plant roots like nitrates (Wacquant methods, rRNA sequencing, G ? C percentages and
et al. 1989), ammonium ions (Brophy and Heichel DNA re-association between bacteria in the commu-
1989) and amino acids (Rovira 1956; Phillips et al. nity, restriction fragment length polymorphism
2004, 2006). (RFLP), amplified ribosomal DNA restriction analysis

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