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577© The Author(s), under exclusive license to Springer Nature
Switzerland AG 2021
H. I. Mohamed et al. (eds.), Plant Growth-Promoting Microbes
for Sustainable Biotic and Abiotic Stress Management,
https://doi.org/10.1007/978-3-030-66587-6_21
Chapter 21
Rhizosphere, Rhizosphere Biology,
andRhizospheric Engineering
PankajSharma, MayurMukutMurlidharSharma, ArvindMalik,
MedhaviVashisth, DilbagSingh, RakeshKumar, BaljinderSingh,
AnupamPatra, SahilMehta, andVimalPandey
Contents
1 Introduction 578
2 Rhizosphere andRoot Exudates 579
3 Rhizospheric Microbiome 582
4 Plant-Microbe Rhizosphere Interactions 586
4.1 Benecial Interactions: TheGood Microbiome 587
4.2 Harmful Interactions: TheBad Microbiome 591
5 Rhizospheric Engineering 593
5.1 Soil Amendments 594
6 Engineering thePlant 601
7 Engineering ofMicrobial Partners 604
7.1 Rhizosphere Engineering by Microbiome Manipulation 605
7.2 Rhizospheric Engineering by Genetic Manipulation ofMicrobes 607
P. Sharma · R. Kumar
Department of Microbiology, CCS Haryana Agricultural University, Hisar, Haryana, India
M. M. M. Sharma
Department of Agriculture and Life Industry, Kangwon National University,
Chuncheon, Gangwon, Republic of Korea
A. Malik
Department of Zoology, CCS Haryana Agricultural University, Hisar, Haryana, India
M. Vashisth
Department of Molecular Biology, Biotechnology and Bioinformatics, CCS Haryana
Agricultural University, Hisar, Haryana, India
D. Singh
Divison of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
B. Singh · V. Pandey ()
National Institute of Plant Genome Research, New Delhi, India
A. Patra · S. Mehta
International Centre for Genetic Engineering and Biotechnology, New Delhi, India
578
8 Engineering ofInteractions 609
9 Conclusion andFuture Prospects 612
References 613
1 Introduction
The global human population is on a perpetual upsurge, however, at the declining
rates. The human beings inhabiting this planet are now approaching 7.5 billion,
which marks a 100% upturn as compared to that of the early 1960s. This increasing
number of human beings, undoubtedly, requires more food resources to proliferate
and thrive in the existing environments. Therefore, the major challenge for the agri-
cultural systems is to enhance the food crop production in the upcoming era simul-
taneously addressing the hazards as well as inconsistency along with the
eco-efciency (Jeranyama et al. 2020). However, some different strategies are
already being followed for increasing the food crop production, for instance, use of
chemical fertilizers, introduction of genetically modied plants, employment of
agrochemicals, as well as the usage of sophisticated machinery. The explicit appli-
cation of chemical fertilizers has amplied dramatically from 0.5 tons to 23 million
tons from 1960 to 2008 correspondingly (Pandey 2018; FAO 2019a, b). The increas-
ing levels of environmental concerns are laying a pressure on the farming commu-
nity to produce the food crops sustainably (Rani et al. 2019; Singh etal. 2019;
Sharma etal. 2019,2020; Kapoor etal. 2020).
Since the domestication of plants, several strategies have been followed for
enhancing the yield of food crops. The advancements in scientic researches and
innovation of newer technologies introduced the green revolution which proved to
be a milestone in attaining an enhanced food crop production. However, it accounted
for a signicant enhancement in food crop production persistence of the global
monster of hunger coupled with the environmental sustainability concerns requiring
the intervention of novel technologies that can fulll the demands of a higher pro-
duction along with the preservation of environmental sustainability. The quest to
fulll both these demands puts forward the idea of engineering the rhizospheric
portion of plants. The rhizosphere seems to be the most complex habitat of a vast
array of microbial population encompassing an intermingled network of plant roots,
diverse microbial communities, and soil (Ahkami etal. 2017). This narrow zone of
plant-microbe interactions represents the rst plant-prejudiced microbial habitat
which affects the plant growth in a direct as well as indirect manner. The rhizo-
spheric portion is a complex dynamic and compactly inhabited zone of soil that
proves to be an incredible site for the multifaceted set of inter- as well as intraspe-
cies interactions and food web communications which lay a strong effect on the
carbon ow as well as transformation (Dessaux etal. 2016; Walker etal. 2011). The
plant systems have evolved in a realm of microorganisms. The coevolution of plants
with the rhizospheric microbiome has resulted in a state where both these
P. Sharma et al.
579
components start affecting each other from the very rst day of the dawn of plant
life. The roots of plant systems are largely known for altering the physical charac-
teristics of the soil. Plants harbor a vast microbial population by secreting carbon-
rich compounds via roots, where such labile substrates are largely favored by the
members of microbial communities and they swiftly blend them (Doornbos etal.
2012). The alteration of physical as well as chemical environs of the rhizosphere by
the plant systems largely affects the suitability of diverse microbiological clusters
and microbial connections and has also encouraged the evolution of novel microbial
systems that t themselves in the rhizospheric life. The gain of tness sustained by
the microbial systems must overshadow the price to the plants in diverted carbon
and energy (Vandenkoornhuyse etal. 2015). These plants associated with microor-
ganisms largely assist the plant systems under their plant growth promotion attri-
butes. They not only facilitate the plant systems in the uptake of several key nutrients
but also protect them from many biotic as well as abiotic stresses. They are found to
enhance the plant productivity directly by xing the nitrogen, solubilizing the phos-
phate, producing the siderophore, and indirectly increasing the organic carbon pool
of the soil, conferring the plants with the ability to tolerate various biotic as well as
abiotic stresses (Mohanram and Kumar 2019). Numerous indications display that
plants engineer their rhizospheric microbiome. The most primaeval lines of plants
also display a strong capability of altering the comparative richness of different
microbial clusters in the soils neighboring their rhizosphere (Chaparro etal. 2014;
Valverde etal. 2016) that assists the plant systems in their growth. Apart from this
ability of plants to alter their rhizospheric communities, various human practices
have also proven to be key drivers in engineering the microbial population of a rhi-
zospheric portion which strongly favors the establishment of advantageous micro-
bial systems on the plant roots which ultimately results in improved plant health and
upsurged plant productivity. Therefore, the present chapters strongly target different
approaches that are often employed to engineer the plant rhizosphere to bring a
qualitative as well as a quantitative upsurge in the productivity of plant systems.
2 Rhizosphere andRoot Exudates
The rhizosphere seems to be the most composite microbial territory on the earth,
encompassing a cohesive system of plant roots, soil particles, as well as an assorted
microbial conglomerate of archaea, bacteria, virus particles, as well as micro-
eukaryotes. This ne region of contact amid the soil particles and the plant roots
establishes the foremost plant-prompted habitation faced by soil microbiota. The
rhizosphere represents an active and compactly inhabited zone of soil upholding a
multifarious set of inter- as well as intraspecies communications. In addition to this,
it also acts as an active site for the ongoing food web interactions that are known to
have a signicant inuence on the carbon ow and transformation (Ahkami etal.
2017; Dessaux etal. 2016). Adding more to it, the classical description of rhizo-
sphere has described it as a four-dimensional (4D) body: three dimensions for the
21 Rhizosphere, Rhizosphere Biology, andRhizospheric Engineering
580
volume and the fourth dimension representing the time for the rhizospheric func-
tioning (Kuzyakov and Razavi 2019). The assessment of the rhizosphere divulges
that it is a habitat for diverse classes of microorganisms. The total volume of
microbes inhabited in this zone is represented by some good, by some bad, and by
a few ugly microbes. These good, bad, and ugly microorganisms denote at this point
the good microbes, plant pathogenic microbes, and opportunistic human pathogenic
microbes correspondingly (Dutta and Bora 2019). The microbial dwellers of rhizo-
sphere that have sparked the interest in studies targeting rhizosphere and rhizo-
spheric engineering are the microbes having constructive effects on the plant
systems which are largely represented by nitrogen-xing microorganisms, mycor-
rhiza, plant growth-promoting rhizobacteria (PGPR), and the microbes possessing
antagonistic activity toward plant pathogens. However, the rhizospheric inhabitants
that are found to be harmful for the plants take account of the phytopathogenic
fungi, oomycetes, bacteria, and nematodes (Mendes etal. 2013).
This natural environment allows different microbial strains to co-occur and to
form multifarious microbial populations as well as communities. Therefore, the rhi-
zospheric zone has further been divided into three distinct sub-zones: the endorhi-
zosphere which represents the fragment of the root cortex along with the endodermis
where the microorganisms, as well as the mineral ions, exist in the apoplastic space
amid the plant cells; the rhizoplane, which denotes the middle zone after the epider-
mal root cells and mucilage; and the ectorhizosphere, which symbolizes the farthest
zone extending from the rhizoplane out into the bulk soil (McNear 2013). The term
rhizoplane was denoted the direct exterior surface of plant roots along with any
tightly clinging soil particle or debris as well as microbiological populations. The
existence of rhizosphere is not under a section of limited extent or shape but should
rather be considered as an ascent of physical, chemical, as well as biological posses-
sions alongside the plant root. Therefore, the plant rhizospheric portion is of
supreme signicance for several valuable ecosystem amenities, for instance, to
maintain the nutrient as well as water cycle, seizure of vital nutrients, and the
sequestration plus storage of carbon (Adl 2016).
The plant metabolism strongly affects the rhizospheric portion by releasing the
carbon dioxide and by emancipating the photosynthates by way of diverse kinds of
root exudates predominantly via rhizoplane and ectorhizosphere. The importance of
root exudates for plant systems can be understood by the fact that plants discharge
approximately 40% of its photosynthates unswervingly into the soil systems pri-
marily as compounds of higher as well lower molecular masses (McNear 2013).
The plethora of interactions taking place amid rhizosphere and rhizospheric micro-
biome governs the plant growth as well as yield in their natural environments. The
molecular events taking place in the plant rhizosphere precisely shape the plant
rhizospheric microbiome or rhizobiome (Sasse etal. 2018).
The plant roots are the main plant structures that are held accountable for the
acquirement of both water and essential nutrients and the secretion of different pri-
mary and secondary metabolites called as root exudates. The plant’s primary
P. Sharma et al.
581
metabolites oozed through roots are predominantly organic acids, carbohydrates,
and amino acids. In addition to it, plants also exudate a vast range of secondary
metabolites, currently also called plant natural products such as alkaloids, terpe-
noids, and phenolics. In addition to this, these exudates have also been categorized
into two clusters, i.e., low-molecular-weight compounds, for instance, sugars,
amino acids, volatile compounds (VOCs), phenolic compounds, organic acids, and
other secondary metabolites, and high-molecular-weight compounds, like polysac-
charides and proteins. It has also been established that the root exudation is largely
responsible for shaping the plant rhizobiome, and these exudates nd engrossment
in numerous biotic as well as abiotic connections. Several different root exudates
have also been found responsible for the initiation of quorum-sensing mechanisms
in either the repression or stimulation of quorum-sensing rejoinders of correlated
bacterial class. However, the rhizospheric portion has been largely ignored, for its
different possible attributes that can enhance the crop yield, predominantly owing to
the several confronts allied with the sampling within the rhizospheric soil (Oburger
and Schmidt 2016; McCormack etal. 2017; Dutta and Bora 2019). Additionally, the
role of plant-allied rhizospheric microbiome has already been unveiled for its differ-
ent plant growth-promoting attributes. In addition to it, the root exudates, apart from
harboring the rhizobiome, are also known for the maintenance of the rhizospheric
environment by the possession of several key and unique attributes. The root exu-
dates are also acknowledged for enhancing the accessibility of several key nutrients,
for instance, phosphorus, because of the discharge of phosphatases and chelation by
the oozed organic acids that are known to concentrate the available phosphorus for
the plant uptake (Dakora and Phillips 2002). The exudates are also known for del-
eteriously affecting the adjoining plants, for instance, via fabrication of allelochem-
icals (Callaway and Aschehoug 2000) which provides an opportunity for engineering
the trait of weed inhibition in the plant systems. The exudates are also known for
their possession of root-insect communication trait. The root herbivory by numer-
ous pests like aphids can result in noteworthy reductions in produce as well as the
quality of important crops which are known to be inhibited by the root exudates,
thereby demonstrating insecticidal activity. The root exudates are also known for
altering biochemical and physical properties of the soils inevitably. The root exu-
dates are known to stabilize the soil structure along with an enhancement in the
water retention capacity of the soil, thereby indirectly improving the plant growth
by managing the soil health. Moreover, they also play an imperative character in the
elevation of positive interactions among microbes, for instance, by instigating the
colonization with mycorrhizae via releasing strigolactones (Biate et al. 2015).
Consequently, an explicit range of traits associated with the rhizosphere are potent
enough to be targeted for the improvement in crop yields along with a concomitant
reduction in the input of chemical fertilizers and other agrochemicals (Preece and
Peñuelas 2020). Therefore, the highly dynamic and potent attitude of plant rhizo-
sphere makes it a suitable area of interest for its manipulation in the quest to obtain
improved plant health and enhanced crop productivity.
21 Rhizosphere, Rhizosphere Biology, andRhizospheric Engineering
582
3 Rhizospheric Microbiome
The rhizosphere acts as a denite hotspot and provides a platform for numerous
networks in the interior of the bulk soil. It represents an important biological hotspot
where respiration, gaseous altercation, nutrient and moistness usage, and conned
provisions of organic matter are deliberated to be most concerned. On the contrary,
the bulk soil represents an oligotrophic environ, specically on the stock of root-
instigated organic material. Therefore, the rhizosphere, as affected by root exuda-
tion, may encompass up to 1011 microbiological cells per gram root and with 1012
functional genes per gram soil belonging to over and above 30,000 prokaryotic
inhabitants (Mendes etal. 2011; Prosser 2015). The cumulative genome of this rhi-
zospheric microbiome appears to be much greater than the plant genome, and it is,
therefore, denoted as the second genome of the plant. The rhizospheric microbiome
and its role can be considered similar to the human intestinal microbial populations
as they also play a great role in human health maintenance (Berendsen etal. 2012;
Bron et al. 2012). The rhizospheric microbiota control diverse biogeochemical
cycles along with the various other soil processes by inuencing the main rhizo-
sphere progressions, for instance, respiration, nitrication, and denitrication
(Breidenbach etal. 2016; Philippot etal. 2013). They are also known to conspicu-
ously inuence the iron cycle in soils and have also been demonstrated as the essen-
tial drivers of soil organic matter decomposition in the temperate grasslands (Li
etal. 2019). Therefore, total characteristics of the agronomic rehearse demand a
superior considerate of the different rhizospheric progressions that aid plant pro-
gression as well as disease suppression. Consequently, owing to the non-replaceable
role of rhizospheric microbiome, the exploration of the complex connection amid
crop, soil, and microorganisms in the plant rhizosphere has become the fundamental
part for nourishing vigorous as well as high-yielding production structures (Uzoh
and Babalola 2018). Therefore, the term rhizosphere diversity is often employed to
decrypt a vast array of microorganisms residing in the zone of soil, bordering, and
habitually stimulated by plant roots. The intimate interactions of plants with micro-
bial communities in this special zone of soil have made the rhizosphere a place for
extraordinary microbial accomplishments (Huang etal. 2014; Nicolitch etal. 2016).
The major proportion of the diverse microbiota harbored by the plant systems is
picked up throughout their lifespan from the adjacent environs; thereby, it seems
that a considerable part of the plant microbiome nds its origin from the seeds. The
seed-allied microbiota is supposed to play an indispensable part in initial phases of
the plant development, thereby upsetting the germination as well as the subsistence
of the seedling (Pitzschke 2016; Truyens etal. 2015). The soil-based microbes come
later into the play and have to contend alongside the previously established micro-
biota. The microbiota selected in the rhizospheric zone will move to other plant
parts and later inhabit diverse plant tissues especially leaves which later represent a
major part of the phyllosphere microbiome (Hardoim etal. 2015; Mitter etal. 2016;
Sánchez-Cañizares et al. 2017). The plant-originated metabolites known as root
exudates play an indispensable role in the root colonization of rhizospheric
P. Sharma et al.
583
microbiome. These are usually of low molecular weight and accordingly are
straightforwardly easily utilizable, consequently, fashioning an upsurge in the
microbiological population thickness of rhizosphere as equated to the bulk soil. The
most noticeable and earliest work on the “the rhizosphere effect” was done by
Albert Rovira, theresearch provided detailed views of plant-driven microbial colo-
nization of the rhizosphere at the microscopic scale (Burns 2010; White etal. 2017).
This comparative increment in the integer of microbes in plant rhizosphere is usu-
ally articulated as the R/S ratio, where R denotes the numbers per gram of soil in the
rhizosphere and S in the bulk soil. There is a great variation in these ratios which
range between 5 and 50 which may cross 100 also, and this variation is governed by
several factors like microbial members, stage of development of plant systems,
plant species, as well as the nutritional eminence of plant systems. It should also be
taken care of that only a denite percentage of the root surface is shielded by the
microbes, for instance, of the total root surface area of maize, the bacteria cover
only 4% in apical zones, 7% in the root hair zone, and up to 20% in basal zones. The
inhabitation of a root by the rhizospheric microbiome is, however, not limited to
rhizoplane only but can also happen in the apoplast of the cortex to varying degrees
as indicated by the presence of endophytes (Marschner 2012). The growth of roots
into the deeper soil is closely followed by the active colonization of the newer root
just behind the meristematic tissues by the microbes attracted toward the root sur-
face. The exudates oozed in the region directly behind the root tip and in the distal
zone of elongation zone encourage the growth and proliferation of microorganisms
and also appeal additional soil microbes toward the root surface. However, the exu-
dation of metabolites is at a reduced pace and quantity in the root-hair and its neigh-
boring region which furthers marks a decline in the intensity of microbial inhabitants
(Marschner 2012). Thus, the fast-growing roots experience an abrupt variation in
the microbial community of rhizoplane and rhizosphere from apical to basal regions
alongside the root axis (Bowen and Rovira 1991). It is the alteration in category as
well as the amount of carbon accessible as exudates in different root zones which
stimulates the differences in the community structures (Baudoin et al. 2003;
Marschner 2012). However, such differences in the microbial concentration along-
side the root axis are vital for the overall nutrient revenue in the interior of the
microbial load (Marschner etal. 2011). An upsurge in the microbiological density
might lead to an overall nutrient immobilization, while a reduction in microbial load
can lead to a net nutrient release.
The plant largely controls the microbial inhabitation of its root environment by
secreting highly diverse root exudates. Their diversity and complexity can be taken
into account by the fact that the root exudates of even a small plant species may
comprehend more than 100 diverse metabolites (van Dam and Bouwmeester 2016).
Furthermore, the attitude and class of root exudates only happen to be decisive for
the dispersal of bionetworks and niche exactness of denite plant systems (Dakora
and Phillips 2002). The release of these composites by the plant roots proceeds by
as a minimum of two possible mechanisms, for instance, the exudates may be con-
veyed crosswise the cell membrane and then discharged into the adjacent rhizo-
sphere, or the plant produces may also be secreted from the root edge cells and root
21 Rhizosphere, Rhizosphere Biology, andRhizospheric Engineering
584
edge-alike cells, which are known to discrete from the root structures as they mature
(Hawes etal. 2000; Vicré etal. 2005). The root exudates may contain every possible
plant-originated compound excluding some denite composites that nd their key
involvements in the process of photosynthesis. The rhizospheric microbiome is
deliberated as a conglomerate of key engineers that have the potential to be employed
to reconstruct the biodiversity and purposes in the tarnished environments. These
microorganisms owe an imperative part in the management of growth, health, as
well as ecological aptness of their host plant (Buee et al. 2009; Dutta and Bora
2019). Furthermore, these microbial systems have engrossed much attention and
have become a subject for rhizospheric engineering due to their possession of key
role in the management of both natural and accomplished agriculture soil ecosys-
tems as they nd involvement in diverse and signicant progressions referring to
soil structure formation, organic matter disintegration, toxin exclusion, xenobiotic
deterioration, bioremediation, rhizoremediation, nutrient cycling, etc. A plethora of
microbes inhabiting the rhizosphere has the capability of doing these jobs for their
host plants. However, all the microbes inhabiting rhizosphere are not culturable, but
the advances in the techniques of molecular biology and biotechnology have expe-
dited the process of considering the role of other 99% microbes that cannot be cul-
tured in laboratory situations. However, the major plant growth-promoting
rhizobacteria that have been reported so far belong to the genera Azotobacter,
Burkholderia, Arthrobacter, Chromobacterium, Caulobacter, Xanthomonas,
Azospirillum, Enterobacter, Bacillus, Pseudomonas, Serratia, Flavobacterium,
Klebsiella, Erwinia, and Micrococcus (Bal etal. 2013).
The rhizospheric microbiological inhabitants represent a subdivision of the
microbiological society inhabiting the bulk soil. The secretion of exudates by plants
allows the proliferation of some specic microbes in the rhizospheric zone as
equated to the bulk soil. There have been several theories which have tried explain-
ing the relative assembly of microbial communities in the rhizosphere. However,
two main theories have emerged for a possible explanation. The rst one is referred
to as niche theory, which points out the signicance of deterministic progressions,
and the second one is deliberated as the neutral theory, which focuses on stochastic
processes (Dumbrell etal. 2010). The niche-centered theory forecasts that the varia-
tions in the species community conguration are allied to the deviations in the eco-
logical variables because species owe distinctive possessions that reward them the
exploitation of matchless niches. The species copiousness in this theory will follow
pre-emption, broken stick, log-normal, and Zipf-Mandelbrot models. On the other
hand, the neutral theory envisages the structure and conguration of species com-
munities to the geographic remoteness amid the samples on the account of their
dispersal limitation, since several species are functionally comparable based on
their capability to utilize niches. Consequently, their richness will follow a zero-sum
multinomial (ZSM) distribution. Both the theories are well associated with ecologi-
cal aspects, but none can provide any evidence in the favor of the dynamic nature of
microbiological community association in rhizosphere (Mendes etal. 2014).
Since all the members of rhizospheric microbiome are not culturable, however,
the culture-grounded approaches have advocated the supremacy of gram-negative
P. Sharma et al.
585
microbes in rhizosphere. The proper designation of the microbiota to precise groups
requires the use of advanced molecular biology techniques. Since microbial inu-
ences in the rhizospheric portion are repeatedly synergistic, thereby, the understand-
ing of microbial system at the community level seems to be most ecologically
signicant. The community-level depiction of several agriculturally important crops
like corn, pea, potato, rice, alfalfa, avocado, tomato, and corn has revealed that in
most of the studies, but not all, the Proteobacteria was found to be the dominating
group. However, the results varied among different classes of Proteobacteria, but
mostly Gammaproteobacteria were found to overpass the other classes (Hawkes
etal. 2007). Similarly, Urozetal. (2010) also found the dominance of Actinobacteria
and Proteobacteria in the oak rhizosphere soil. Likewise, the exploration of the
rhizospheric community of three different cultivars of potato also revealed the dom-
inance of the phylum Proteobacteria (46%), which was followed by Firmicutes
(18%), Actinobacteria (11%), Bacteroidetes (7%), and Acidobacteria (3%) (Weinert
etal. 2011). The rhizospheric community structure of alfalfa and barley as assessed
by Kumar et al. (2018) was also largely represented by Proteobacteria (45.9%)
which was followed by Bacteroidetes (21.4%) and Actinobacteria (10.4%).
Similarly, the rhizospheric community analysis also proved the dominance of
Proteobacteria with a share of 47% followed by Actinobacteria (23%), Firmicutes
(6%), and Acidobacteria (5%). It also displayed the presence of eukaryote (3%) and
archaea and virus (1%). The comparative analysis of rhizospheric soil as compared
to the bulk soil conrmed the overexpression of phyla Actinobacteria, Acidobacteria,
Chloroexi, Cyanobacteria, Chlamydiae, Tenericutes, Deferribacteres, Chlorobi,
Verrucomicrobia, and Aquicae in the rhizospheric soil (Mendes etal. 2014). The
rhizospheric microbiome of any particular plant is known to be affected by different
factors, and the microbial populations are known to react and acclimatize them-
selves to such factor, for instance, the loss of nitrogen-xing symbiosis in L. japoni-
cus modies the assembly of the community accumulations in the roots as well as
rhizospheric compartments (Zgadzaj etal. 2016; Sánchez-Cañizares et al. 2017).
The patterns of exudates also vary a lot due to plant age, for instance, the GC-MS
analysis of root exudates secreted by gnotobiotically nurtured A. thaliana displayed
that the intensities of sugars and sugar alcohol secretion diminished during the plant
development, although the degrees of amino acid and phenolic secretion augmented
with time. The exudates comprising of sugars, organic acids, and amino acids
intensely shake the conguration of microbiological plant populations, where the
members of Actinobacteria and Proteobacteria represent the principal consumers
of such compounds (Chaparro etal. 2014). The effect of exudates on shaping the
rhizospheric diversity can be taken into consideration by the fact that a mutation of
an ABC transporter, which nds active involvement in the process of exudation,
altered the fungal as well as the populations in the rhizosphere of A. thaliana.
Nevertheless, the incorporation of organic acids rather than sugars, even in the
absence of plant systems, encourages bacterial fruitfulness and diversity. Therefore,
the procurement of nutrient in any form acts as a strong driver for the microbial
assemblage (Badri etal. 2009; Shi etal. 2011). The rhizospheric microbiome of a
plant species is also affected by the presence of other plants. Interestingly, the
21 Rhizosphere, Rhizosphere Biology, andRhizospheric Engineering
586
microbial populations of plant systems cultivated in a mixed eld are found to con-
tain an enhanced level of microbial biodiversity, which in turn rewards the plant
with an enlarged plant height and leaf surface area as equated to the plant cultivated
in a monoculture (Lebeis 2015).
4 Plant-Microbe Rhizosphere Interactions
The plant systems have evolved in a realm of tiny microorganisms. The plants
started inuencing their rhizospheric microbiome from the very rst day. The plant
roots brought out numerous changes in the soils which ultimately resulted in the
alteration of the physical conguration of the soil. Plant systems dug out the key
nutrients from the soils, thereby giving a tough competition to the already inhabit-
ing microorganisms. They also took out water from the soils, thereby modifying the
soil moisture that too was faced by microorganisms. The plant debris resulted in the
accretion of organic carbon that was later handled by the heterotrophic microorgan-
isms, which resulted in the materialization of soil organic matter. The beginning of
the process by which plants started releasing their photosynthates via roots favored
the quick assimilation of microorganisms (Cotrufo etal. 2013; Lehmann and Kleber
2015; Doornbos etal. 2012). This further lead to the alterations in the physical as
well as chemical environs of the rhizosphere, which in turn inuenced the tness of
diverse microbial assemblies and communications amid microorganisms and
thereby incited the evolution of new microorganisms that were better suited to the
life in this thin zone of rhizosphere (Lambers etal. 2009). The sum of genotypic as
well as phenotypic deviations in the plant attributes that support the plant-allied
microbiomes responsible for upsurging the plant nutrient accessibility, precluding
pathogenic microbes, or else rening plant aptness coupled with the plant perfor-
mance sustains a tness benet. Therefore, the aptitude of plant systems toward the
sustenance of a constructive microbiota is an attribute under selection. This close
relationship of plant systems with the microorganisms is often regarded as an assim-
ilated ecological entity acknowledged as a holobiont (Vandenkoornhuyse et al.
2015). This holobiont has been the unit under selection for several billions of years,
thereby supervising the evolutionary pathway headed for plant traits supporting
constructive microbiomes.
There is a vast array of microbial systems inhabiting the plant rhizospheric zone,
and they are expected to interact with the plant systems in numerous ways. But most
frequently only three distinctive classes of such host-microorganism associations
are taken into consideration for the activities of the plant-allied microbiome: para-
sitic, which deleteriously affects the health of plant systems; mutualistic, which aids
the plant growth by its growth promotion attributes; and the commensalism, which
does not have any effect on the plant systems. However, these descriptions only take
into account of the direct inuence of the microbial systems on the plant systems
and not the indirect belongings on the other community associates, consequently,
exclusive of the inuence of microbe-microbe communications happening in plant
P. Sharma et al.
587
microbiomes. The microorganisms inhabiting the interior of plant tissues are capa-
ble of producing numerous growth-prompting molecules, improving nutrient pro-
curement, or persuading defense from several biotic and abiotic stresses. While the
benecial and deleterious communications amid hosts and microbial species can be
specically elaborated, the notion targeting commensalism is not dened with much
clarity. A true commensal certainly does not affect the plant health in any form,
therefore, itis discreetly impossible to quantity, since it necessitates witnessing the
absenteeism of a phenotype. In conclusion, the microbial systems can be deceitfully
considered as commensals owing to their transient occurrence, provisional dor-
mancy, or their performance of some formerly uncharacterized roles. Such kind of
perceptions necessitates the performance of community-level investigation at the
multiple time points and ecological situations (Berendsen etal. 2012; Lebeis 2015;
Zapalski 2011). The interactions among numerous microbes inhabiting the rhizo-
sphere also affect the composition of the rhizospheric microbiome. For example,
diverse bacterial and fungal rhizospheric inhabitants act as antagonists for numer-
ous soil-dwelling fungal or nematode phytopathogens by the possession of diverse
mechanisms. These mechanisms may encompass antibiosis, competition, aptitude
of parasitizing the plant pathogens, damage in the phytopathogenic activity via quo-
rum sensing, and initiation of the systemic resistance in plant systems (Ali etal.
2017). However, here, only the account of plant-microbe interactions is taken into
consideration.
4.1 Benecial Interactions: TheGood Microbiome
A major proportion of microbiological populations residing the rhizospheric zone
have a vital part to perform in enhancing the conguration as well as production of
the natural plant systems via safeguarding the persistence and forbearance against
diverse biotic as well as abiotic stresses. This job is done by numerous tools, such
as bio-fertilization, encouragement of root progression, management of stresses,
rhizoremediation, and disease suppression. A large proportion of rhizospheric
microbiomes behave synergistically, promote plant growth as well as development,
expand the nutrient acquirement, enhance their tolerance, and induce different
defense mechanisms in the plant systems. Therefore, these are deliberated as “the
good” of rhizospheric microbiomes (Ali et al. 2017). The bacterial members of
rhizosphere actively engaged in plant health elevation activities are designated as
plant growth-promoting rhizobacteria (PGPR). The plant health and growth promo-
tion trait of rhizosphere-residing bacteria is brought out by maintaining an active
supply of numerous vital nutrients that otherwise are either inaccessible or narrowly
obtainable by the plant systems, for instance, nitrogen, iron, phosphorus, and zinc.
The mechanisms underlying the superior nutrient endorsement encompass phos-
phate solubilization, nitrogen obsession, solubilization of zinc, and iron chelation
via fabrication of siderophores. Additionally, the PGPR also produces several plant
hormones, such as indole acetic acid, cytokinin, and gibberellins. Furthermore, the
21 Rhizosphere, Rhizosphere Biology, andRhizospheric Engineering
588
other mechanisms may comprehend the possession of ACC deaminase activity, bio-
lm materialization, and production of various exopolysaccharides. The active
involvement of rhizospheric dwellers in various nutrient cycles results in recovering
vital nutrients like N, P, K, Zn, and Fe, thus enhancing their bio-obtainability to the
plant systems (Ali et al. 2017; Sharma and Chauhan 2017; Backer et al. 2018).
Broadly, such microbes are classied into three major classes according to their
possession of plant growth promotion trait. First are the microbes that upsurge the
accessibility of the nutrients to plant systems and are designated to be biofertilizers.
The second type of microorganisms is responsible for increasing the plant growth
by various indirect means such as by protecting from different plant pathogenic
attacks. Such organisms are known to be biocontrol agents. The third class com-
prises microbes that are responsible for stimulating plant growth through secretion
of different phytohormones as well as growth regulators, for instance, auxins, gib-
berellins, cytokinins, etc. Such microorganism is best regarded as biostimulants (Ali
etal. 2017).
The PGPRs are also recognized to bring out the accession and assimilation of
nitrogen to the plants which is considered as the succeeding most signicant occur-
rence afterward photosynthesis in the plant systems. The process of biological dini-
trogen xation is extremely important to the global agricultural systems. In this
process, the inactive dinitrogen from the atmosphere is reduced to ammonia in the
occurrence of nitrogenase enzymes and is a doing of diazotrophic microbes
(Sulieman 2011; Dixon and Kahn 2004; Franche etal. 2009). The nitrogen xative
microbial systems are commonly classied as (1) symbiotic nitrogen-xing micro-
bial systems (e.g., rhizobia and Frankia) (Zahran 2001; Ahemad and Khan 2012)
and (2) nonsymbiotic (free-living, associative, and endophytes) nitrogen-xing
microbial systems like Cyanobacteria (Anabaena, Nostoc), Azotobacter,
Azospirillum, Azocarus, etc. The symbiotic association necessitates a multifaceted
communication amid the host microbial partners which may result in creation of
some specialized structures like nodule formation for the intracellular colonization
of bacteria (Bhattacharyya and Jha 2012; Giordano and Hirsch 2004).
PGPR also assist the plant by enhancing the availability of several vital and key
nutrients. The method usually employed is the solubilization of the nutrients fol-
lowed by their enhanced uptake. The solubilization of key nutrients takes place by
secretion of some mild organic acids by the microorganism where the enhanced
uptake proceeds by the secretion of some chelator molecules like iron. The plant
systems usually face a problem which is low phosphate obtainability due to the
occurrence of phosphate in insoluble forms. The phosphate-solubilizing bacterial
strains convert the insoluble phosphate into its monobasic diabasic forms which are
easily available to the plant systems. The phosphate-solubilizing bacteria dwelling
the rhizosphere discharge some mild organic acids and enzymes called as phospha-
tases which facilitate the transformation of inexplicable forms of phosphate to the
plant-accessible forms. The major phosphate-solubilizing bacterial strains are rep-
resented by Azotobacter chroococcum, Bacillus circulans, Cladosporium herbarum,
Enterobacter agglomerans, Pseudomonas chlororaphis, P. putida, Rhizobium sp.,
P. Sharma et al.
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Bradyrhizobium japonicum, Beijerinckia, Burkholderia, Pantoea, Flavobacterium,
and Microbacterium (Ali etal. 2017; Vessey 2003; Lugtenberg and Kamilova 2009).
Iron is another essential nutrient required by the plant systems; however, its com-
parative insolubility in the soils restricts its accessibility to the plants. It plays a key
role by aiding as a cofactor in different enzymes which catalyze numerous biologi-
cal progressions such as nitrogen xation, respiration, and photosynthesis. Plant
roots favor iron absorption in the form of reduced ferrous ion, but the availability of
ferric ion is much common in nely ventilated soils. Several rhizosphere-inhabiting
bacteria have the attribute of siderophore production which functions to bind the
ferric form of iron, and it is evident that plant species have the capability of absorb-
ing bacterial Fe3+-siderophore complexes (Stein etal. 2009; Andrews etal. 2003;
Lemanceau etal. 2009). The siderophores represent some lower molecular mass
complexes possessing excessive empathy toward the chelation of ferric ions which
is shadowed by the shift and its accretion in the bacterial cells. There can be differ-
ent types of siderophores like phenol catecholates, hydroxamates, rhizobactin, and
pyoverdine siderophores which differ in their structure as well as activity. In addi-
tion to this, several fungi are known to produce siderophores which include the
rhodotorulic acids which are di- or tri-hydroxamates, the ferrichrome-type sidero-
phores, and the fusarinines. The siderophore production not only provides the iron
to the plants, but it also restricts the growth of various bacterial and fungal plant
pathogens by restricting the iron availability to those microorganisms. A vast array
of microorganisms have been reported for siderophore production that are largely
represented by Agrobacterium tumefaciens, Erwinia, Bacillus subtilis, Pseudomonas
stutzeri, Mycobacterium, Nocardia, Rhodococcus, Arthrobacter, Azotobacter,
Penicillium, and Aspergillus (Osman etal. 2018; Sheng etal. 2020).
The rhizobacterial members of genera Bacillus and Pseudomonas have been
reported to produce diverse plant growth regulators which further result in the
development of ne root bers by the plant systems, thereby amassing the entire
surface area resulting in enhanced nutrient and water uptake. The different types of
plant growth hormones secreted by microbes are found to be auxins, mainly
indole- 3-acetic acid, cytokinin, and gibberellins. These growth regulators are
acknowledged to enhance the increase in root length, cell division process, seed and
tuber sprouting, movement of water and nutrients, and secondary root development.
Additionally, they also mediate geotropic as well as phototropic reactions and
thereby confer resistance to different stresses. The microbes are also known to
secrete inhibitors like ethylene which inuence the hormonal equilibrium in plant
systems. Ethylene is considered as a senescence hormone acknowledged for inhibit-
ing plant growth during usual circumstances; however, at lower levels (0.05ml/l), it
is known for stimulating plant growth. This gaseous hormone is called as “stress
hormone,” and its level is known to upsurge during the plant exposure to different
stresses. The rhizobacterial members are also known to produce 1- aminocycloprop
ane- 1-carboxylase (ACC) deaminase enzyme which cuts the ethylene production in
plant, thereby assisting the plant systems in stress recovery (Backer etal. 2018;
Ahemad and Kibret 2014).
21 Rhizosphere, Rhizosphere Biology, andRhizospheric Engineering
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Plants being immobile living systems have to confront some abiotic stresses like
drought stress, temperature stress, salinity stress, etc. These stresses cause a consid-
erable decline in plant tness and overall crop produce. The plant-allied valuable
microbes are known to play an important role in stress abatement along with the
expansion of such agricultural systems that are found to be resilient toward the cli-
matic changes. Innumerable studies have proven that numerous rhizospheric
microbes like Rhizobium and Azospirillum possess the trait of plant stress allevia-
tion. The PGPRs are known to secrete several compounds that behave as osmolytes,
for instance, the secretion of glycine-betaine, proline, ectoine, trehalose, polyols,
and sucrose by PGPR actions in harmonization with the composites secreted by
roots in response to various biotic as well as abiotic strains. The bacteria
Pseudomonas pseudoalcaligenes, Bacillus pumilus, Pseudomonas putida,
Enterobacter cloacae, Serratia caria, Pseudomonas uorescence, Dietzianatro
nolimnaea, Bacillus amyloliquefaciens, etc. are reportedly known for alleviating the
salinity stress (Khan and Bano 2019). Similarly, on exposure to drought strain,
plants experience the deposit of numerous stress-induced composites, like proline,
polysugars, abscisic acid, and glycine betaine, along with an increment in the pro-
duction of enzymatic as well as nonenzymatic antioxidants. The soil microbiota
initiate diverse biological contrivances like accrual of compatible solutes, EPS fab-
rication, and spore formation. These mechanisms employed by the microorganisms
assist the plant systems to cope with the drought stress. Similarly microorganisms
employ a variety of stratagems to assist the plant systems in coping with different
abiotic and biotic stresses (Priyanka etal. 2019).
The benecial rhizospheric microora also assists the plant systems to get rid of
different recalcitrant and xenobiotic compounds, which have accreted in soil sys-
tems owing to the rapid pace of anthropogenic activities which further results in the
soil humiliation and sterility. The coevolution of plant and their allied microbiota
has effectively resulted in the reclamation and restoration of the degraded soils
without instigating any detrimental by-products, unlike conventional methods. This
process is often said to be rhizoremediation. Several root exudates secreted by
plants, like linoleic acid, behave as surfactants which enhance the availability of
pollutants to the microbial systems by forming a layer on soil particles which also
upshot improved attachment of bacteria on the pollutant. The bacteria then secrete
several compounds including enzymes and metabolites which function to break-
down the toxic pollutants into their nontoxic forms. The bacteria, namely, Bacillus
licheniformis, Bacillus mojavensis, Achromobacter xylosoxidans, P. aeruginosa,
Ochrobactrum sp., P. uorescence, Microbacterium sp., Microbacterium sp.,
Rhizobium sp., Rhizobium, Pseudomonas, Stenotrophomonas, and Rhodococcus,
have been reported to degrade various pollutants (Mishra and Arora 2019).
Therefore, the possession of numerous and multidisciplinary benecial attributes of
plant-allied rhizospheric microbiota has projected them as an effective substrate for
engineering the plant rhizosphere.
P. Sharma et al.
591
4.2 Harmful Interactions: TheBad Microbiome
The plant systems secrete root exudates for attracting benecial microora, but
some pathogenic microbiota also gets attracted toward plant roots. These microor-
ganisms parasitize the plant systems and result in several severe infections, there-
fore executing damaging effects on various crops of economic importance. This part
of rhizospheric microbiome which affects the health of plant systems and thereby
results in a considerable drop in the plant yield as well as economy represents “the
bad” rhizosphere microbiome. The soil that endured pathogenic microbiota signi-
cantly deteriorates the crops, and among these fungal members of the rhizobiome
are found to be most distressing. Consequently, this portion of rhizobiome seems to
be a notable chronic menace toward global food production as well as economic
steadiness. A vast variety of phytopathogenic fungi nding their origin from the
rhizosphere have been reported; however, the most common pathogenic fungi take
account of members of genera Phytophthora, Aspergillus, Verticillium, Fusarium,
Mucor, Pythium, and Rhizopus. On the other hand, several bacteria have also been
reported as pathogenic which largely belong to the genera Pseudomonas, Ralstonia,
Erwinia, and Xanthomonas. The population and a variety of destructive and con-
structive microbes are interconnected to the measure and eminence of the rhizode-
posits and to the aftermath of the microbiological communications happening in the
rhizospheric zone (Somers etal. 2004; Tournas and Katsoudas 2005).
There are four major classes of phytopathogens, namely, virus, bacteria, fungi,
and nematodes (Agrios 2005); however, only two of these are considered to be key
performers in the soils, namely, fungi and nematodes. Nevertheless, bacterial patho-
gens on a narrow scale are also deliberated to be soil-borne, possibly for the reason
that nonspore formers are not able to endure well in soils for longer times. In addi-
tion to this, bacterial pathogens also necessitate an injury or an indigenous breach
for their penetration into the plants and thereby initiate the infection process.
However, some bacterial pathogens are still able to infect the plant systems, for
instance, Ralstonia solanacearum is responsible for bacterial wilt of tomato and
Agrobacterium tumefaciens for the crown gall disease. A fewer lamentous bacte-
rial pathogens also exist and infect the plant systems and are better adapted for their
survival in soils. However, only fewer viruses are capable of infecting the roots.
Their chances of infection are restricted by their requirement of vector and wound
in the plant tissues for the initiation of infection. However, nematodes and fungi like
Olpidium and Polymyxa act as the vehicles for viral particles (Campbell 1996;
Nester etal. 2005; Raaijmakers etal. 2009). The pathogenic fungal species are caus-
ing major harms to crops in the form of various diseases, thereby affecting the
overall economy of the eld. The major sinks of the crop economy nd their origin
from several genera like Pythium, Fusarium, Verticillium, Rhizoctonia, and
Armillaria (Ali etal. 2017).
The microbiota inhabiting the rhizosphere is also composed of many nematode
species that are found to be parasitic to the plant systems. While a major proportion
of the nematodes inhabiting the soils is free-living, 7% of the overall soil-lodging
21 Rhizosphere, Rhizosphere Biology, andRhizospheric Engineering
592
nematodes are found to be pathogenic to diverse plant species. The plant-parasitic
nematodes have been found to affect different crops of much economic importance
such as wheat, soybean, potato, tomato, and sugar beet. The nematode parasitism
produces different signs in plant systems like leaf chlorosis and patchy, wilting,
arrested growth coupled with the defenselessness against other major pathogens.
The most pathogenic of all these nematodes are said to be root-knot nematodes and
cyst nematodes which belong to the Heteroderidae family due to their broad range
of host plants. The other major category of parasitic nematodes is migratory endo-
parasitic nematodes which migrate through roots and detrimentally feed on the
plant cells, thereby causing substantial necrosis in the plant tissues. These are
largely represented by the rice root nematode (Hirschmanniella), lesion nematode
(Pratylenchus), and burrowing nematodes (Radopholus). These nematodes are
attracted toward the plant roots by several of the root exudates like alcohols, ketones,
organic acids, terpenoids, thiazoles/pyrazidines, cyclic adenosine monophosphate,
esters, ions, amines, amino acids, and other aromatic compounds (Moens and Perry
2009; Jones etal. 2013; Ali etal. 2015; Rasmann etal. 2012).
These soil-originated pathogenic microbes have evolved in very hard situations,
and therefore these are well tted to the rhizospheric zone as equated to other micro-
organisms. They have invented several methodologies in their evolutionary journey
to have hard edices like resting spores, which aid their survival for longer periods
in the nonappearance of the host crop.
The rhizospheric soil encompasses numerous microorganisms, somewhat lesser
in statistics, which are found to be human pathogens. Such unscrupulous microbial
pathogens are “the ugly” ones owing to their most damaging nature by unswerv-
ingly infecting the humans. These ugly microbes may either be native to the soils
and also be dropped by human deeds, for instance, carried by animal as well as the
bird fecal material, manure solicitations, by agricultural machineries, use of slaugh-
terhouse wastes, sewage water, and medical wastes. The major human opportunistic
pathogens dwelling the plant rhizosphere are of dermatological signicance affect-
ing the skin, hair, nails, etc. The opportunistic human pathogens are mainly repre-
sented by fungi like Microsporum canis, Trichophyton mentagrophytes, Aspergillus
spp., Coccidioides, Blastomyces dermatitidis, and Trichophyton rubrum. However,
the human pathogenic bacterial members especially the spore formers also inhabit
the rhizosphere, for instance, Clostridium tetani, C. botulinum, Bacillus anthracis,
Actinomyces israelii, and Clostridium perfringens, and some nonspore formers like
enterotoxigenic strains of E. coli also inhabit rhizosphere (Berg etal. 2005; Chapman
2005; Baumgardner etal. 2011; Blackburn etal. 2007; Ali etal. 2017). The presence
of numerous plant pathogenic microbial systems and unscrupulous human patho-
gens in the rhizospheric zone has prompted a need to engineer the rhizosphere
where only benecial microbiota can thrive by kicking out the plant and human
pathogens so that the release of plant photosynthates via roots can be properly uti-
lized by the plant systems.
P. Sharma et al.
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5 Rhizospheric Engineering
The plant systems regulate the occurrence of microbial populations in the rhizo-
spheric zone. Plants have also advanced several functions and stratagems for the
alteration of rhizosphere and rhizobiome. It has also been proven that both bene-
cial and pathogenic (plant, human) microbes inhabit the rhizosphere. The congura-
tion, comparative copiousness, and spatial and chronological dynamics of the
rhizospheric microbial inhabitants not only affect the plant health and growth but
also lay a strong inuence on the health of human beings (Ryan etal. 2009; Mendes
etal. 2013). The domestication of plant systems was mainly done using articial
selection by selecting crops based on traits excluding reproductive tness, thereby
deviating the whole process from the natural selection. The food crops were mainly
selected based on huge seed size, condensed bitterness which is a principal defense
mechanism, and some other traits, which unintentionally altered the plant traits
regulating the microbiome. Therefore, the domestication process of crops has
resulted in the alteration of the microbiomes conscripted by the plant systems (Leff
etal. 2016; Pérez-Jaramillo etal. 2016). The advent of employing nitrogen-based
fertilizers has also resulted in a paramount deviation from the natural selection. The
application of nitrogen-based fertilizers made it sure that the yield of crops was not
unswervingly associated with a plants’ capability of supporting microbial nutrient
cycling. The N fertilization leads to a sharp reduction in the microbial biomass as
well as their variety (Treseder 2008; Ramirez etal. 2010), concomitantly leading to
the promotion of copiotrophs above oligotrophs (Fierer etal. 2012). The plant selec-
tion following explicit fertilizer establishments has promoted the unlinking of soil
microbiota from the plant health. The application of ammonium-grounded fertiliz-
ers tends to condense the rhizospheric pH, whereas the application of nitrate-based
fertilizers leads to an increase in the pH, thereby resulting in an alkaline rhizo-
sphere. It is evident that alterations in soil pH can modify the soil chemistry in the
zone surrounding the roots and thus impact the progression along with the congu-
ration of microbial societies (Ryan etal. 2009). The selection of plant systems fac-
ing extraordinary fertilization management has resulted in the selection of genotypes
supporting microbial N mineralization (Schmidt et al. 2016). Consequently, the
present varieties may have experienced a loss in their aptitude of supporting micro-
biota responsible for degrading the organic forms of nitrogen and solubilizing the
mineral nutrients like phosphorus (Wallenstein 2017).
Therefore, the major research interest in this eld is precisely leaning toward the
development of different approaches that could reshape the rhizospheric microbiota
in favor of those microbial systems that have the potential of improving plant health
as well as productivity and can also avert the propagation of different plant and
human pathogenic microbiota already inhabiting the rhizosphere. Several research
programs have already proven that plant’s genetic makeup along with soil variety is
an important driver for shaping the rhizospheric microbiota (Berg and Smalla 2009;
Bakker etal. 2012). Moreover, the fascinating roles played by microorganisms in
various natural processes like soil organic materialization, nutrient proclamation,
21 Rhizosphere, Rhizosphere Biology, andRhizospheric Engineering
594
and pathogen burden have projected them for manipulating the microbiome as key
for the rhizosphere engineering (Wallenstein 2017). The impact of soils on the rhi-
zospheric microbiota has already been validated for different plant species (Berg
and Smalla 2009). The soil systems are composed of extremely multifaceted and
assorted environs that considerably affect the physiology of plant systems, a con-
guration of root exudation, and concurrently the rhizospheric microbiome. The pH
of soil systems has also a signicant part to play in determining the rhizospheric
microbiome. The abundance along with a variety of bacterial populations has been
found to uctuate by the ecosystem type where the soil pH is the key driver. The
bacterial variety is utmost in the neutral soils and subordinate in the soils having an
acidic pH (Fierer and Jackson 2006; Mendes etal. 2013). Based on the genetic con-
guration of plant systems also, innumerable methodologies have been suggested
for reshaping the microbial conguration of rhizosphere in the quest to redirect the
microbial movement. The term “rhizosphere engineering” thereby denotes the alter-
ation of plant’s root and adjoining environment in the quest to generate a “biased”
milieu that will unambiguously improve the crop yield as well as the plant endur-
ance. Root exudates play an essential role in enticing different plant pathogenic
microbes and activation of their virulence factors. Therefore, altering the amount of
root exudates through plant breeding experiments or by genetic alteration seems to
be an apparent methodology for redirecting rhizospheric microbiome. The other
strategy for reshaping the rhizosphere involves various soil amendments like the
addition of compost and biochar which favor the colonization by benecial micro-
bial communities. Other strategies include the introduction of benecial microbes
in soil onto seeds and planting materials (Bhattacharyya and Jha 2012; Mendes
etal. 2013). The understanding of the actions involved can help propose the differ-
ent techniques which can allow the modication of the rhizosphere for an improved
plant tness and enhanced soil output. The different methodologies and representa-
tions of rhizospheric engineering are discussed under.
5.1 Soil Amendments
The alteration of the rhizospheric soil, and in turn its microbial constitution which
has remained the most involuntary concern of the human activities, such as the fre-
quent farming of some denite crops, may bring about the appearance of disease-
oppressive soil systems, and several soil pollutants have also been reported for
radically distressing the conguration of soil as well as plant-allied microbiota. The
expansion of various novel practices in the eld of microbiology and microbial
ecology has delivered several prospects for modifying the soil microora in a way
analogous to the discerning “rhizosphere engineering” that happens in nature (Ryan
etal. 2009). The amendments in soils seem to be the easiest way of engineering the
rhizosphere. A vast array of soil amendments is employed for upsurging the plant
productivity which also proves to be an important tool for shaping the rhizospheric
P. Sharma et al.
595
microbiome (Fig. 21.1). This section takes account of the different types of soil
amendments that are often employed for getting a biased rhizosphere.
5.1.1 Soil Amendments withCompost
The addition of compost to the soils is also known for altering the microbial com-
position of rhizosphere. It increases the soil suppressiveness toward the soil-borne
pathogens. However, the soil suppressiveness is dependent on the type of compost
added. It also enhances the number of antagonists in the rhizosphere (De Brito etal.
1995). It further improves the physical as well as biochemical belongings of the
soil, upsurges the soil water balance, and enhances the nutrient supply to plants,
thus altering the soil properties and making it t for microbial inhabitation. The
short-term application of composts increases the rhizosphere soil carbon mineral-
ization and microbial biomass, and this carbon mineralization increases the progres-
sion of roots and thin root hairs (Zhang etal. 2014) which further allow the plant
systems to harbor benecial microbiota. The compost brings a source of carbon for
the existing rhizospheric microbiota in the form of soil organic matter, and it also
acts as a source of diverse classes of microorganism which later inhabit the plant
rhizosphere. It also alters the soil chemistry as well as soil structure in a substantial
manner and thereby signicantly affects the conguration of plant-allied microbial
communities (Green etal. 2007). The soil organic matter represents a noteworthy
basis of utilizable carbon for different rhizospheric inhabitants (Toal et al. 2000),
Fig. 21.1 Diagram depicting the different types of soil amendments employed for shaping the
rhizospheric microbiome
21 Rhizosphere, Rhizosphere Biology, andRhizospheric Engineering
596
and it has also been advocated that the incorporation of composts to the soil can
upkeep microbes that are not even endured by exudates. This capability for compost-
originated organic matter to endure some microbes advises that the “rhizosphere
effect” does not act similarly on all microbial inhabitants (Boehm etal. 1997). De
Brito et al. (1995) noticed that the compost incorporation to soil augmented the
occurrence of bacteria in the rhizosphere of tomato that exhibited antagonism
against various soil-borne pathogens like Rhizoctonia solani, Pyrenochaeta lycop-
ersici, Fusarium oxysporum f. sp. radicis-lycopersici, and Pythium ultimum. The
suppression of various pathogenic microbes by addition of compost is known to
bring about the recruitment of denite microbes as the suppressive soils tend to lose
their suppressive activity on their pasteurization and sterilization (Weller etal. 2002;
Haas and Défago 2005). The addition of compost and organic matter enhances the
microbial activity in the soil which inhibits the growth of pathogens either directly
by its antagonistic activity or indirectly by the possession of competitive actions of
recruited soil microorganisms. The suppression incurred to the soil systems either
can be general or may also be specic. In case of general suppression, a basal shield
contrary to an extensive collection of pathogenic microbes is established, and the
defeat is not accredited to any precise microbe (Weller etal. 2002). However, the
possession of specic suppression is attributable to the accomplishments of precise
microbes that act contrary to specic pathogens and is found to be more operative
than general suppression. The compost amendments in the soils not only redesign
the structures of a microbial community but also lead to the establishments of new
equilibria (Hadar and Papadopoulou 2012). The composts are also known to contain
various bacterial and fungal biocontrol agents that later inhabit the plant rhizosphere
and are known to advance the regularity of disease control. Antoniou etal. (2017)
assessed the consequence of compost addition on the rhizospheric community of
tomato along with its effect on the suppression of fungal pathogens. The compost
added to the plant was able to suppress the fungus, namely, Fusarium oxysporum f.
sp. lycopersici and Verticillium dahliae. It was also observed that the compost lost
its disease suppression ability upon sterilization. Furthermore, it was found that the
phyla Firmicutes and Ascomycota were dominating the compost, whereas the phyla
Actinobacteria, Proteobacteria, Bacteroidetes, and Mucoromycota were rarely iso-
lated. The addition of compost signicantly altered the microbiological congura-
tion of the rhizospheric zone as experienced by a reduction in the Ascomycota and
Firmicutes, while Actinobacteria, Bacteroidetes, and Proteobacteria were aug-
mented. Surprisingly, the number of Proteobacteria was found to be augmented by
57 times in the rhizosphere samples, while Actinobacteria by 6.1 times as equated
to the unplanted compost sample. Innumerable studies have evidenced that the
incorporation of compost in the agricultural soils protects the plant systems from
some pathogenic microbes such as Pythium ultimum, Pythium irregular,
Phytophthora nicotianae, Sclerotinia minor, and Sclerotinia sclerotiorum. The
mechanisms may include the direct suppression of the pathogens or activation of the
disease resistance genes in plant systems (De Corato 2020). Countless studies have
testied a relative increment in the members of Proteobacteria and Actinobacteria
upon compost addition, thus making it the most dominant group in the rhizosphere.
P. Sharma et al.
597
Proteobacteria are also acknowledged for playing a serious role in the global
cycling of carbon, nitrogen, iron, and sulfur, whereas Actinobacteria are supposed
to subsidize the global carbon cycle by degrading the plant biomass, and because of
their aptitude of decomposing organic matter in the soils, they are also procient for
fabricating several key enzymes like cellulases, hemicellulases, chitinases, gluca-
nases, and amylases (Mickan et al. 2018; Yang et al. 2019). Conclusively, the
amendments of compost in the soils prove to be an effective tool for reshaping the
rhizosphere biology and, in turn, the benecial rhizospheric inhabitants for improved
plant health and yield.
5.1.2 Soil Amendments withBiochar
Biochar is a very steady product of thermal deterioration of organic materials in the
lack of air (pyrolysis) and is distinguished from charcoal by its use as a soil amend-
ment. The temperature of pyrolysis lies in the range from 300 to 1000°C.The bio-
mass employed for pyrolysis is principally composed by organic composites like
cellulose, hemicellulose, and lignin (Kavitha etal. 2018). It has also been desig-
nated as a promising measure to upgrade the soil fertility besides other environmen-
tal amenities such as carbon sequestration for the extenuation of climate changes.
The addition of biochar is acknowledged for the enhancement of the fertility of soil
systems predominantly by uplifting the pH of acidic soils or by enhanced nutrient
retention via cation adsorption and by uplifting the water retention capacity of the
soil. The desired depth for the application of biochar lies in the range of 4–6cm
(Lehmann et al. 2011; Yu et al. 2019). The biochar amendments in the soils are
known to alter the diversity as well as an abundance of the biological community.
The alterations induced by the biochar amendment in the microbial community con-
guration may not only distress nutrient cycling and plant progression but also the
dynamics of organic matter present in the soil systems (Wardle etal. 2008; Kuzyakov
etal. 2009; Liang et al. 2010). The biochar apertures function as a microenviron-
ment for the proliferation of microbial systems. The microorganisms utilize carbon,
nutrients, gases, and water offered by the biochar for growth as well as reproduc-
tion. The soil application of biochar at a proportion of 10t per hectare has resulted
in a noteworthy upsurge in the biological nitrogen xation by red clove as equated
to the control. Its amalgamation in the soil is also known to affect the arbuscular
mycorrhizal fungi in a positive manner (Jaafar 2014; Mia etal. 2014). Biochar also
reduces the tensile strength of the soil, therefore making the root as well as mycor-
rhizal nutrient mining extra operative. The reduced tensile strength also facilitates
the easy seed germination and also simplies the movement of invertebrates through
the soil, thereby modifying the predator/prey dynamic (Lehmann etal. 2011). The
biochar addition supports the growth of PGPRs like Bacillus insolitus, Aeromonas
hydrophila, and A. caviae which are known to mitigate the salinity stress by the
secretion of exopolysaccharide responsible for binding sodium ion that results in a
reduced uptake by the plants along with the production of an enzyme called 1- amin
ocyclopropane1- carboxylate deaminase which also relieves the salinity stress
21 Rhizosphere, Rhizosphere Biology, andRhizospheric Engineering
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(Ashraf and Harris 2004; Ali etal. 2014). In addition to it, the microbial copious-
ness has also been conrmed in the biochar-amended soils by different methods,
like total genomic DNA extraction, plate count, substrate-induced respiration,
fumigation- extraction, phospholipid fatty acid extraction, and staining and direct
surveillance of discrete biochar particles. Furthermore, it also enhances the rate of
reproduction of microbial populations (Lehmann etal. 2011). The microbial com-
munities associated with the nitrogen transformations are known to be altered upon
biochar incorporation indicating a reduced soil nitrogen loss and improved nitrogen
utilization as indicated by a reduction in the number of Nitrososphaera in the rice
elds upon biochar amendment (Liu etal. 2017). Moreover, the biochar addition is
also known to uplift the network of benecial fungi in the rhizospheric zone (Wang
etal. 2019). Win etal. (2020) evaluated the effect of biochar on the rhizospheric
communities using the next-generation sequencing methods and observed that bio-
char augmented the copiousness of Proteobacteria as well as Actinobacteria in the
rhizoplane particularly after 2weeks of transplantation. On the contrary, there was
a decrease in the number of Acidobacteria and Bacteroidetes. The members of
Xanthomonadaceae experienced an increment of 2.8-folds in their numbers after
2 weeks of transplantation followed by Desulfuromonadales (1.8-fold),
Burkholderiales (1.8-fold), and Actinomycetales (1.4-fold) along with a concomi-
tant decline in the relative abundance of Sapropirales (1.8-fold) and Nitrososphaerales
(2-fold). Similarly, Cheng etal. (2018a, b) also observed that the supplementation
of the soils with the biochar augmented the diversity as well as an abundance of
bacteria. The comparative copiousness of Adhaeribacter, Rhodoplanes,
Pseudoxanthomonas, and Candidatus Xiphinematobacter augmented in the biochar-
amended soil; however those of Lacibacter, Pirellula, and Kaistobacter faced a
decline. The addition of biochar is also acknowledged for inuencing the root
metabolome and is known to alter the levels of some amino acids as well as organic
acids. Therefore, it is not only the rhizosphere microbiome that is altered upon soil
amendments with biochar, but the rhizosphere metabolome is also reshaped. Chen
etal. (2017) observed that the biochar addition along with a simultaneous nitrogen
reduction caused a 1.75-fold increase in the levels of isoleucine, a 2.16-fold surge in
malonate, and a 2.15-fold rise in acetate in exudates. Similarly, Bornø etal. (2018)
also observed that the exudates of particularly glucose and fructose were intensely
altered by the biochar application, specifying that the plant reaction to biochar
application can modify the conguration of root exudates discharged into the rhizo-
sphere. This altered exudation process in turn plays a key role in engineering the
rhizospheric microbiome (Fig.21.2).
5.1.3 Other Soil Amendments
A large number of human practices are known to alter the rhizospheric microbiome
in an unintentional way, for instance, addition of fertilizers, addition of substrates
for fueling bioremediation processes, use of pesticides and other agrochemicals,
etc. The application of glyphosate has been shown to alter the denitrication process
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in the grass sward along with a surprising increment of 20- to 30-fold in the denitri-
cation process as equated to the herbicide-untouched grass. The denitrication
process in the soil is predominantly attributable to the facultative anaerobic bacte-
ria; thereby, any increment in the process suggests a possible alteration in the diver-
sity and number of accountable microbes in the rhizospheric zone (Tenuta and
Beauchamp 1996; Qian etal. 2018). The application of diclofop-methyl leads to a
reduction in the nitrication of urea nitrogen in soils. This weedicide is potent
enough to inhibit the enzyme acetyl-CoA carboxylase activity and thereby can lead
to a reduction in the fatty acid synthesis in the crop. In addition to it, the persistence
of residual DM particles in the soil systems is known to affect an extensive range of
plant metabolic pathways and thus can lead to an augmented exudation of organic
acid (Rensink and Buell 2004; Qian etal. 2012; Chen etal. 2017). The plant root
exudates are the crucial inuencers of rhizospheric microbiota conguration; there-
fore, the testied impact of diclofop-methyl on the exudation nurtures the probabil-
ity that multifaceted plant-microbiome communications could restrain the DM
poisonousness and could also alter the copiousness of specic microbes distressing
the biogeochemical cycles of nutrients. Qian et al. (2018) reported that the
Fig. 21.2 A portrayal depicting a GM plant engineered for the secretion of specic root exudates
which later harbors denite microbial populations and alleviate the heavy metal stress
21 Rhizosphere, Rhizosphere Biology, andRhizospheric Engineering
600
application of DM on rice altered the levels of 28 different exudates in the rice rhi-
zosphere. The altered exudation also affected the rhizospheric microbiome and
resulted in an increase in the fraction of Proteobacteria from 42.1% in the control
to 55.4% after 5days of DM exposure. However, the comparative richness of phyla,
Firmicutes and Acidobacteria, faced a decline from 22.0 and 16.9% in the control
to only 8.9 and 13.9%. Additionally, the comparative richness of the genera
Azospira, Clostridiales, and Rhodocyclaceae increased from 7.1, 0.3, and 1.1% in
the control to 21.0, 2.4, and 2.3% of total rhizospheric microbes.
The wastewater-borne pollutants are also known to alter the rhizospheric con-
guration of the holobiont. The wastewater-borne sulfonamides are known to alter
the microbiome composition in the constructed wetlands planted with Cyperus
alternifolius, Cyperus papyrus, or Juncus effusus. A noteworthy decline in the
microbial diversity has been testied along with a precise inhibition of microbes
involved in the nitrogen and sulfur cycle. However, the microbes like Methylosinus,
Methylotenera, Methylocaldum, and Methylomonas which are potent for degrada-
tion of sulfonamides are found to be increasing in the rhizospheric zones of the
plants (Man etal. 2020). The irrigation with treated wastewater is also known to
alter the composition of rhizobiome. The soil ammonia-oxidizing bacterial popula-
tions are altered irrespective of the ammonium concentration or the presence of
plants. The treated wastewater brings a reduction in the comparative richness of
Actinobacteria along with a simultaneous upsurge in the comparative copiousness
of Gammaproteobacteria (Oved etal. 2011; Frenk etal. 2014). Zolti etal. (2019)
also reported an upsurge in relative copiousness of Gammaproteobacteria and a
decline in Actinobacteria, in the root microbiome receiving irrigation with treated
wastewater. The assessment on more precise levels revealed the abundance of
Pseudomonadales and a reduction in Streptomycetales and Pseudonocardiales.
Similarly, the wastewater efuent containing aged nanoparticles has also been
acknowledged for inuencing rhizospheric microbiota. In a study by Liu et al.
(2018), it has been claimed that the copiousness of cyanobacteria was amplied by
12.5% as demonstrated predominantly by an upsurge of Trichodesmium spp., and
the lavishness of unknown archaea was heightened from 26.7% in the control to
40.5% in the soil watered with wastewater efuent containing aged nanoparticles.
Several other organic amendments, such as seed meal for the control of fungal
pathogens, also alter the rhizospheric microbiome. The soil amendments with
Brassicaceae seed meal preparations for the suppression of apple replant disease
altered the rhizobiome in a signicant way. The amendment not only suppressed the
pathogen Pratylenchus penetrans but also elevated the level of Proteobacteria and
Acidobacteria in the rhizosphere. In addition to it, the microbial genera engaged in
numerous nitrogen-cycling progressions, like Bradyrhizobium, Rhodopseudomonas,
and Nitrospira, were found to exhibit more abundance. Similarly, the fungus
Basidiomycota got reduced in abundance in the apple rhizosphere after the treat-
ment, whereas the abundance of Zygomycota got increased (Mazzola etal. 2015).
The addition of fertilizers also changes the structure of rhizosphere microbiome.
The soil amendments with high levels of nitrogen fertilizers negatively affect the
soil diazotrophs. The discharge of root exudates is reliant on the plant physiological
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status along with the nutrient obtainability. For instance, maize has been reported to
discharge subordinate amounts of amino acids via roots during nitrogen scarcity
(Carvalhais etal. 2011, 2013). Therefore, the application of nitrogenous fertilizers
alters the nutrient status of the soil and thus affects the rhizospheric microbiome.
The analysis of root exudates of maize during nitrogen fertilization has revealed a
tremendous increment of 30-folds in the sugar alcohols, 11-folds in sugars, and
7-folds in phenolics. This altered exudation process affected the rhizospheric micro-
biome by elevating the levels of Bacillales, Nitrosomonadales, and Rhodocyclales
and by reducing the abundance of Chloroexales, Gemmatimonadetes, and
Phycisphaerae (Zhu etal. 2016).
6 Engineering thePlant
The plant systems happen to be the strategic elements for shaping the microbial
populations in the rhizospheric zone. The plant’s ability to employ a diversity of
occupations and stratagems to alter its rhizosphere in the quest to circumvent
environment- associated stresses has attracted the interest of researchers for modify-
ing the rhizosphere by engineering the plant systems. The understanding of the
actions taking place assists in the development of techniques for modifying the
rhizosphere for attaining improved plant healthiness and enhanced soil output ef-
ciency. The plants can be genetically engineered for altering the soil organic anion
efux along with its transference from root cells by altering plants with an inordi-
nate aptitude to produce organic anions coupled with their conveyance outside the
cell. The plants are also potent enough to be genetically amended for the fabrication
of several recombinant proteinaceous molecules, root exudates, and several other
metabolites which target a biased rhizospheric colonization (Ryan et al. 2009;
Mohanram and Kumar 2019). Nevertheless, the engineering of plant systems drives
beyond the presently extensively nurtured, genetically altered plant systems that are
resistant to a few pests or resilient to some herbicides.
The role of root exudates in shaping plant microbiome has attracted the attention
of plant breeders and plant biotechnologists on a global basis for engineering the
plant systems in the quest to get denite root exudates in higher concentration. As
early as 1978, Petit etal. recommended to harness the benet of the close connec-
tion prevailing amid the plants and their accompanying microbiota for framing the
exudation process. This would offer a selective benet to certain microbes which
would help them in their establishment in the rhizospheric zone, a stratagem later
designated “biased rhizosphere” or “articial symbiosis” (Savka etal. 2002). The
earlier reports on engineering plant systems for a biased rhizosphere mainly target
the engineering of plant systems to produce opines. The presence of opines in the
rhizospheric zone powerfully shakes the native microora. To be sure, such opine-
secreting transgenic plants lead to an increment in the population of opine-
consuming associates that may range from 100 to more than 10,000-folds in the
non-sterile soils (Mansouri etal. 2002). This phenomenon can result in alterations
21 Rhizosphere, Rhizosphere Biology, andRhizospheric Engineering
602
of the bacterial members that persist evident even in the nonexistence of the selec-
tive pressure of opines (Oger etal. 2000) which further validate the excellence of
opines as discerning substrates for microbial inhabitants in the rhizospheric zone.
For instance, the transgenic lotus plants genetically altered for the production of two
opines, namely, mannopine and nopaline, altered the composition of rhizospheric
microbiome along with a specic increment in the bacterial communities able to
exploit these molecules as sole carbon source (Oger etal. 2004).
The plant metabolism is redesigned for engineering the plant systems for desir-
able root exudates. The genes directing the synthesis of root exudates are rstly
recognized in the plant systems, and then their expression levels are altered for
redesigning the rhizosphere for upgraded features. For instance, the GM rice and
tomato engineered with the vacuolar H+-pyrophosphatase gene AVP1 from the
Arabidopsis plant displayed almost 50% more citrate as well as malate efux as
compared to their wild types after their treatment with aluminum phosphate. This
was later deduced as a probable mechanism for enhancing resilience toward
aluminum- ion-induced strain and to advance the plant aptitude to consume the
unsolvable phosphorus (Ahkami etal. 2017; Yang etal. 2007). Similarly, a gene
encoding for citrate synthase from Citrus junos plant when cloned and overex-
pressed in Nicotiana benthamiana led to a threefold increment in the enzyme activ-
ity which further supported the accumulation of citrate in a concentration that was
found to be twofolds higher as equated to the wild-type plant systems. Certainly, the
root systems of genetically altered plants were found to be more tolerant to alumi-
num toxicity, and, surprisingly, their roots sustained to lengthen at levels of 100mM
Al, which were enough to constrain growth in wild-type plants (Deng etal. 2009).
Likewise, the citrate synthase gene originating from Pseudomonas aeruginosa
when transferred into papaya also led to an augmented accrual of citrate in the cyto-
plasm (Rengel 2002) which was further complemented by enlarged efux of citrate
into the vicinity of roots along with an improved forbearance of transformed plants
to Al. The secretion of specic root exudates has also been reported for increased
plant tolerance toward the deciency of nutrients. For instance, the transferring of
rye chromosome 5R or only a minor segment of chromatin from the long arm of the
chromosome 5R to wheat upsurges its lenience toward the copper paucity (Schlegel
etal. 1997). The plant’s increased tolerance toward copper deciency after the chro-
mosome transference is also coupled by the fact that genes for mugineic acid syn-
thase and 3-hydroxymugineic acid synthase, the enzymes involved in biosynthesis
of common phytosiderophores, are located on the rye chromosome 5R (Rengel
2002). Furthermore, the root exudates are also supposed to play a signicant role in
the abovementioned process.
The plant systems are evolved with different mechanisms to discharge the exu-
dates into the rhizospheric zone, comprising diverse kinds of passive as well as
active transport systems. Conventionally, the exudation has been deliberated to be a
passive progression, arbitrated via different pathways: the conveyance over the root
membrane by diffusion, ionic channels, and vesicles transport (Baetz and Martinoia
2014). The pitch shaped by their dissimilar levels amid the cytoplasm of root cells
and the rhizosphere is a major factor in shaping the exudation process which is also
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a subject to be affected by the permeability of root membrane, the veracity of root
cells, and the polarity of the compounds to be exuded (Badri and Vivanco 2009).
The presence of ion channels for secretion of several root exudates also provides a
selective prospect for engineering the plants. The ionic channels are held account-
able for discharging the carbohydrates along with some precise carboxylates like
malate and oxalate, which are oozed not by diffusion, but via a transport machinery
facilitated by proteins. Two different anionic channels have been described: SLow
Anion Channels (SLACs), originally named S-type (Slow-type), which need several
seconds to be activated, and QUick Anion Channels (QUACs), originally named
R-type (Rapid type), which can be activated in a few milliseconds (Dreyer etal.
2012). The aluminum-activated malate transporters (ALMT) and multidrug and
toxic compound extrusion (MATE) membrane transporters are extensively studied
among all the transporters (Sharma etal. 2016; Kang etal. 2011; Vives-Peris etal.
2020). The two approaches that have been tried to upsurge the discharge of organic
ions from the roots are engineering the plant systems with an improved ability to
synthesize organic ions and genetically altering the plant systems with a heightened
aptitude to convey organic ions outside the cell (Ryan etal. 2009). The rst approach
targets the expression of genes concerned with the synthesis of particular ions,
whereas the second approach targets the genes encoding proteins facilitating the
movement of organic ions through the plasma membrane. The genetic engineering
of plants grounded based on the second approach takes account of genes encoding
the transport proteins. The foremost gene that was recognized to translate a trans-
port protein facilitating the efux of organic anions from plants is TaALMT1 from
Triticum aestivum (Sasaki etal. 2004). This gene codes for the rst fellow of an
innovative membrane protein family that functions as an anion channel to mediate
Al3+-activated malate efux from roots. Thus, it represents an important tool for
altering the malate release in the plant rhizosphere. Similarly, the MATE genes are
found to efux a vast array of small organic composites comprising secondary
metabolites like avonoids and alkaloids (Omote etal. 2006). They have also been
found to enable citrate efux from the plant cells. The Arabidopsis and tobacco
plants transformed with SbMATE1 and HvMATE genes, respectively, have been
reported to deliberate Al3+-stimulated citrate efux along with an augmented toler-
ance of Al3+ stress (Magalhaes et al. 2007; Furukawa et al. 2007). The examples
have exhibited the key part of transport proteins in engineering the plant systems for
getting a biased rhizospheric zone. Similarly, the plant systems can also be engi-
neered for altering the rhizospheric pH as the plant systems are known to back the
rhizospheric acidication by engendering electrochemical gradient potential cross-
wise the cell membrane of root cells after the efux of H+. This acidication assists
in the augmentation of the plant’s contact to Fe3+ and P which are otherwise not
accessible to plants (Hinsinger etal. 2003). The efux of H+ ions from the plant
cells is principally under the control of a large family of H+-ATPase. Therefore, the
manipulation of plant systems for the overexpression of these genes in the quest to
amend the rhizospheric pH also seems to be an open opportunity. The expression of
the AVP1 pyrophosphatase in Arabidopsis beyond the normal levels persuaded a
highly acidied rhizospheric environ, speciously by increasing the action of the cell
21 Rhizosphere, Rhizosphere Biology, andRhizospheric Engineering
604
membrane H+-ATPase (Yang etal. 2007). Therefore, the involvement of diverse
biotechnological approaches can be utilized to engineer the plant systems for get-
ting a biased rhizosphere owing to the ability of the engineered plants to produce the
desired root exudates, acidify the rhizospheric zone, and therefore harbor the desired
set of microbial systems.
7 Engineering ofMicrobial Partners
The particular aim of microbiome engineering is to inuence the microbiota in the
direction of an assured type of microbial community that owes the potential of opti-
mizing plant functions of interest. Furthermore, the engineering of microbial part-
ners is always motivated to harnessing the advantage of naturally evolved
plant-microbiome communication networks (Quiza etal. 2015). The directing force
toward the alteration of rhizospheric microbiome in the quest to upsurge the plant
functioning and productivity is the plenty of evidence that has unveiled the critical
role of plant-microorganism connection to the healthiness, output-efciency, and
the complete situation of plant systems. Therefore, the only objective of modifying
the plant microbiome is to drive the plethora of rhizospheric interactions in the
direction of enhanced constructive aftermaths for the plant systems. The plant root
exudation-mediated microbial colonization of rhizospheric microbiome is largely
explored, but what is of more interest is that the presence of specic microbes in the
rhizosphere is also identied to amend and shape the exudation process, for instance,
antimicrobial-resistant Pseudomonas is potent enough to block the fabrication of
plant antimicrobial compounds (Bais etal. 2008; Hartmann et al. 2009; Oburger
etal. 2013). Thus, the parameter dealing with the engineering of microbial partners
requires a prompt knowledge of rhizospheric interactions. However, the efforts for
revealing rhizospheric communications are predominantly focused toward the apti-
tude of a single plant root exudate to touch the single bacterial or fungal rhizo-
spheric inhabitant. The unblemished constraint tackling this kind of attitude is the
removal of the microorganism from any environment that would surely pot the exis-
tence of interspecies interactions into ignorance (Ziegler et al. 2013). The other
major restrain in this approach is the inability of several rhizospheric microbes to
grow in the laboratory and the inadequacy of the culture-dependent approaches for
the qualitative scrutiny of rhizosphere microbiome. Interestingly, in spite of these
several methodologies, targeting rhizosphere microbiome engineering necessitates
the involvement of microbial isolates at hand, thereby pointing the requirement for
the escalation of cultivability of rhizospheric microbes. Therefore, the possession of
a distinct functional capacity by several microbial isolates puts forward the approach
of inoculating these microbial cultures in the plant rhizosphere in the quest to engi-
neer the plant microbiome for improved plant well-being and output (Ryan etal.
2009; Quiza etal. 2015). However, the perseverance, as well as the serviceability of
the inoculated isolates, needs to be further measured to ascertain positive inuences
when used as a denite stratagem for manipulating the rhizospheric microbiome
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(Stefani et al. 2015). In addition to this, the inoculation with genetically altered
microbial strains also represents an important strategy for manipulating the rhizo-
spheric microbiome. The recombinant strains are genetically altered for any particu-
lar desired trait, and in several circumstances, the recombinant strains have the
potential to address complications allied with the swift diminution of the population
density coupled with their undersized persistence. The recombinant strains may
bring out the augmentation of several inhabitants of the endogenous community by
the transferal of genetic material via horizontal gene transfer. However, the release
of GM strains in the environs necessitates a thorough assessment to appraise the
impending risks associated (Ryan etal. 2009). However, the disruption of existing
microbial communities of the rhizosphere before the inoculation favors the estab-
lishment of biological functions in the rhizosphere. The different approaches for
altering the rhizosphere by targeting the microbial partner of the holobiont are
explained in detail in the subsequent paragraphs.
7.1 Rhizosphere Engineering by Microbiome Manipulation
The manipulation of rhizospheric microbiome in a direct manner seems to be an
easy and more feasible method for engineering the rhizosphere. The inoculation of
potent microbial strains seems to be an imperative choice for altering the rhizo-
spheric microbiota. The existence of several novel tactics is potent enough to aug-
ment the competence as well as perseverance of the newly introduced microorganism
into the soil systems (Bakker etal. 2012). The inoculation process follows some
screens and selection perimeters along with a precise evaluation of the different
plant health elevation attributes of the retrieved microbial isolates. Furthermore,
their survival and growth in the carrier and their efcacy to perform in the natural
environments are also assessed before the inoculation (Okafor 2016). The coloniza-
tion followed by dominance in the rhizospheric zone by the microorganisms is very
critical for both benecial and pathogenic microbes (Bakker etal. 2012). The apti-
tude of PGPR is being harnessed from several decades as amendments in the form
of attributable to their employment as eco-friendly substitute to chemicals, thereby
acting as protecting shield against the long-lasting negative impact on different
chemicals on the environmental health. However, the employment of this technique
has not picked up the anticipated pace regardless of having numerous proven ben-
ets. Therefore, the farming community has lost interest in this technology and thus
still relies on the usage of chemical fertilizers (Dubey and Sharma 2019). Several
limitations in the abovementioned process came across either with the monoinocu-
lation or even with a consortium assembled with a group of two or more bioinocu-
lants. The direct inoculation of any microbial culture in the rhizosphere is estimated
to tackle a substantial degree of competition from the surroundings. It may also alter
the already prevailing equipoise in the rhizospheric zone and, thus, can upset the
plethora of valuable natural connections (plant-microbe and microbe-microbe inter-
actions) prevailing in the soils. However, some strategies for enhancing the
21 Rhizosphere, Rhizosphere Biology, andRhizospheric Engineering
606
rhizosphere microbiome focusing on the co-inoculation with numerous microbial
strains or mixed cultures of arbuscular mycorrhizal fungi (AMF), ectomycorrhizal
fungi (ECM), PGPR, and endophytes, enabling combined niche exploitation, cross-
feeding, enhancement of one organism’s colonization ability, modulating plant
growth, and achieving niche saturation and competitive exclusion of pathogens have
become successful also (Satyanarayana etal. 2019). The inoculation of microbial
culture along with some organic amendment like compost has also proven to be suc-
cessful and has produced desirable results. The microbial strains that are to be inoc-
ulated are the result of the study of any particular plant’s microbiome as the plant
microbiome consists of several energetic microorganisms that have the potential to
alter the plant physiology as well as development and can also prompt the resistance
systems against pathogenic microbes along with the elicitation of diverse tolerance
mechanisms against numerous plant stresses (Santoyo etal. 2017; Yaish etal. 2017;
Yuan et al. 2016). The whole plant microbiome is not capable of assisting plant
growth as only a few microbial strains possess these benecial attributes and the
synergistic effects between two strains or more have also been reported for their
plant growth supportive attributes (Rojas-Solís et al. 2018; Timm et al. 2016).
Therefore, the desired microbial strains are maintained in the form of bioformula-
tions for preserving their viability by shielding them from hostile environmental
situations. There are different modes of applications of bioformulations in the eld
such as biopriming of seeds, foliar spray, seedling dip, and soil drenching. However,
the inoculation of the desired microorganisms in the rhizosphere not only increases
the number of the inoculated microbes but results in the alteration in the rhizo-
spheric environmental conditions, and therefore the change in the diverse array of
communications taking place in the rhizosphere brings out an overall change in the
rhizospheric microbiome. For instance, Wan etal. (2017) reported that the inocula-
tion of tomato rhizosphere with the biocontrol agent Bacillus amyloliquefaciens
altered the rhizospheric composition and increased the abundance of Pseudomonas
and Massilia. Similarly, Bacillus amyloliquefaciens when inoculated in the sor-
ghum rhizosphere signicantly enhanced the yield and also affected the rhizosphere
microbiology as the proportion of Tremellomycetes was reduced by 8.87% in the
continuous cropping soil (Wu etal. 2019). Likewise, the inoculation of Pseudomonas
putida Rs-198in the pepper rhizosphere increased the abundance of Blastococcus,
AKYG587, Pseudomonas, Cyanobacteria, and Chloroexi (He et al. 2019). The
PGPR Paenibacillus mucilaginosus when co-inoculated with the rhizobia
Sinorhizobium meliloti in the rhizosphere of Medicago sativa also altered the rhizo-
biome as displayed by a relative increment in the abundance of Firmicutes as well
as Acidobacteria (Ju etal. 2020). The inoculation with AMF also changes the pro-
les of rhizospheric microbial community, for instance, the rhizosphere of Prosopis
juliora when inoculated with Glomus intraradices and a mix of G. intraradices
and G. deserticola also signicantly affected the bacterial and fungal community
structure (Solís-Domínguez etal. 2011). Similarly, the inoculation of the AMF in
the rhizospheres of Salvia ofcinalis L., Lavandula dentata L., Thymus vulgaris L.,
and Santolina chamaecyparissus also altered the bacterial and fungal communities
of rhizosphere. Moreover, the ability of the AM fungus to shape the rhizosphere
P. Sharma et al.
607
bacterial community structure was independent of the host plant species (Rodríguez-
Caballero et al. 2017). Similarly the inoculation of maize with the phosphate-
solubilizing fungi, namely, Aspergillus niger P39 and Penicdlium ozalzcum P66,
also lead to an increased bacterial diversity in the rhizospheric zone as assessed
using DGGE ngerprinting (Guang-Hua etal. 2007). Therefore, it can be concluded
that the members of rhizospheric microbiota which are often selected from the core
microbiome on the basis of their several growth promotion attributes not only
directly benet the plant systems by their valuable possessions but also serve the
plant systems by creating a unique environment in the plant rhizosphere. The inocu-
lated microbes assist the growth of plant systems by reshaping the microbial com-
munity of the rhizosphere where some genera face a relative increment in their
proportion, while the others have to bear a concomitant decline. Thus, this approach
inoculating desirable microbes proves to be an important tool for engineering the
rhizosphere.
7.2 Rhizospheric Engineering by Genetic Manipulation
ofMicrobes
The microbial strains used for inoculation in the quest to engineer the rhizosphere
must be established in the rhizosphere and should uphold biologically active popu-
lations to outcompete the already adapted occupant microbial systems. However,
microbial systems employ a lot of stratagems for successfully inhabiting the new
environment, for instance, synthesis of cell surface molecules; at various times the
colonization process is not found to be much effective (Ryan etal. 2009). Therefore,
the genetic engineering of several microbial strains for various desired traits seems
to be a viable option for enhancing their tness before their inoculation (Fig.21.3).
The genes responsible for the growth promotion attributes of microbial systems
have demonstrated to be effective targets for strain enhancement, either by amend-
ing the timing or degree of their expression or by transferring and expressing them
in alternate hosts with other desirable attributes (Ryan etal. 2009). However, the
early efforts comprise the insertion of a heterologous gene encoding a siderophore
receptor into a Pseudomonas uorescens strain to render it more competitive in soil
(Dessaux etal. 2016). This methodology targets the gene insertion tactic for increas-
ing the number of outer membrane siderophore receptors in microbial strains for
making them more efcient on iron acquisition and therefore inhabiting the rhizo-
sphere, for instance, the insertion of the siderophore receptor for ferric pseudobactin
358 into P. uorescens WCS374 resulted in a strain that was found to be more com-
petitive than the WCS374 parental strain for the occupation of the radish rhizo-
sphere (Geetha and Joshi 2013; Raaijmakers etal. 1995). The rhizobacteria are also
genetically engineered for the production of several key enzymes and have demon-
strated improved plant growth promotion attributes, for instance, Pseudomonas
uorescens CHA0 altered with the acdS gene coding for the enzyme ACC
21 Rhizosphere, R hizosphere Biology, andRhizospheric Engineering
608
deaminase signicantly improved the root length in canola seedlings and also pro-
vided enhanced defense against the phytopathogen Pythium (Wang et al. 2000).
Similarly, the genetically altered B. subtilis OKBHF signicantly increased the
height, fresh weight, and ower along with the fruit number in tomato plants along
with a concomitant reduction in the disease rigorousness due to Cucumber mosaic
virus. The Bacillus strain was genetically engineered for the gene coding for the
HpaGXooc which is a member of the harpin group of proteins and is responsible for
the biocontrol activity (Wang etal. 2011).
The plant systems also face several abiotic stresses, and it is an unhidden fact that
several PGPR strains have got unique abilities to aid plant systems during their
exposure to different stresses. The competent microbial strains which prove to be
effective in coping with the abiotic stresses are isolated and identied, and the
molecular cascade of events taking place during the microbial elimination of plant
stress is unveiled in the quest to engineer microbial strains with an improved capa-
bility of assuaging the plant stress responses. A cadmium-resistant Pseudomonas
aeruginosa transformed with metallothionein gene has been validated for its tre-
mendous capability of adsorbing cadmium ions via extracellular accrual and was
also found to owe an improved aptitude for the immobilization of cadmium divalent
ions from the external source. The inoculation of this genetically altered microor-
ganism in cadmium-polluted soil considerably heightened the plant biomass as well
as the chlorophyll content in leaf (Huang etal. 2016; Jishma etal. 2019).
The colonization of plant root by the inoculated microorganism represents an
important parameter to be considered for genetically altering the microbial systems.
The colonization of root surfaces is driven by a molecular cascade of events and also
Fig. 21.3 Effect of inoculating plants with GM microorganisms altered for various traits on the
plant health
P. Sharma et al.
609
depends on various factors like phenomenon of chemotaxis and biolm formation
(Yaryura et al. 2008). The disruption of gene abrB created a genetically altered
strain of Bacillus amyloliquefaciens SQR9 which resulted in enhanced root coloni-
zation therefore with enhanced biocontrol ability (Weng etal. 2013).
The plants facing insect attacks can also be inoculated with the genetically engi-
neered endophytic microbes transformed with the genes coding for precise insecti-
cidal proteins. Such endophytes are also designated as living vectors meant for the
expression of anti-pest proteins in plant systems. The rst attempt to insert a heter-
ologous gene into an endophytic microbe was made by Fahey (1988). The other
endophyte Clavibacter xyli subsp. cynodontis was also genetically manipulated
with an endotoxin gene originating from Bacillus thuringiensis. The genetically
improved bacterium was capable of secreting toxin inside the plant that protected
the plant systems from insect attacks with a specic reduction in the attacks of
Ostrinia nubilalis (Tomasino etal. 1995; Lampel etal. 1994). The nitrogen-xing
bacterium Bradyrhizobium has also been transformed with the endotoxin gene from
B. thuringiensis and was later inoculated into the roots of Cajanus cajan, where it
not only upgraded the nitrogen xation process but also provided protection to the
plant systems against Rivelia angulata larvae (Nambiar etal. 1990). Similarly, the
endophytic Bacillus subtilis WH2 which was genetically engineered to express anti-
pest Pinellia ternata agglutinin by insertion of PTA gene into plasmid pP43NMK
displayed insecticidal activity against white-backed planthopper Sogatella furcifera
when inoculated in the rice rhizosphere (Qi etal. 2013). Thus, the genetically altered
microbes represent an important candidature to be considered for engineering the
plant rhizosphere owing to their enhanced performance as compared to their wild
relatives. They can be genetically altered for improved colonization of the plant
roots as well as for other plant-growth-aiding traits. Moreover, the employment of
GM microorganisms could result in the enhancement of many members of the
endogenous population by the transmission of genetic information via horizontal
gene transfer.
8 Engineering ofInteractions
The involvement of root-associated microbiome makes the holobiont a single and
complete unit. The association of microorganisms to the plant tissues is a complex
process which happens in the soil by way of chemical interactions that takes place
with the active involvement of both the partners (Farrar etal. 2014). Taking into
account the complication of these communications, a ne understanding of these
chemical networks amid all members is indispensable to untangle how microbial
inhabitants harmonize their activities and intermingle with the plant roots. Therefore,
the portrayal of these interactions is an essential step for understanding the connota-
tions as well as occupations of microbial populations (Kumar etal. 2016). However,
many molecules along with the mechanisms involved that synchronize the founda-
tion of precise rhizospheric interactions have already been unveiled and explored in
21 Rhizosphere, R hizosphere Biology, andRhizospheric Engineering
610
literature. The understanding of such interactions is staggering as the signaling mol-
ecules owe the aptitude of upsurging plant functions of interest and provide a unique
methodology to access control over the microbial inhabitants if properly understood
and harnessed (Guttman etal. 2014; Quiza etal. 2015). The plant’s sole purpose of
shaping the rhizospheric microbiome is to fascinate favored microbial associates
and to deter the pathogens along with the undesirable contestants. These activities
happen as a result of different signaling molecules secreted by the plant systems in
the form of root exudates. In addition to plant systems, numerous microbes also
discharge different signaling compounds in the rhizosphere. These signaling mole-
cules play important roles not only in the life cycles of these organisms but also in
their evolution as well as complexity of life (Cornforth etal. 2014; Parks etal. 2014;
West et al. 2015). Furthermore, the successful colonization of plant roots by the
competent rhizobacteria is possible only due to this bidirectional signaling.
Consequently, the collective interests of both the donor and the recipient in the quest
to disseminate the unswerving information prompt an operative signaling arrange-
ment to procure numerous health benets (Kumar etal. 2016). Thus, this bidirec-
tional signaling which accounts for ecological interaction between plant and
microbial systems also provides a platform for rhizospheric engineering by manipu-
lating the interaction taking place in the rhizospheric zone. The plant-allied micro-
bial partners yield and exploit diffusible quorum-sensing molecules (e.g.,
N-acyl-homoserine lactones, AHLs) for signaling each other and thus to order their
gene expression (Berendsen etal. 2012). The AHLs of bacterial origin have also
been reported to affect root development in the plant systems (Ortíz-Castro etal.
2008) along with the elicitation of the phenomenon acknowledged as induced sys-
temic resistance (ISR) which permits the plant systems to withstand the pathogenic
attacks that possibly will be disastrous without the occurrence of such factors of
bacterial origin. The plant systems have also developed the ability to utilize the
microbial communication systems for manipulating the gene expression in their
accompanying microbial populations, such as various plant-allied bacterial mem-
bers, which owe some LuxR-like proteinaceous molecules which are motivated
from different signals originating from plant systems (Ferluga and Venturi 2009). A
small proportion of bacterial communities is diverse owing to their ability to quench
the signaling process by deteriorating numerous compounds of plant as well as
microbial origin in the rhizosphere, thereby leading to the disruption of quorum-
sensing process (Tarkka etal. 2009), and other members have also been reported for
degrading the compounds, like ethylene, that negatively affect the plant health (Bais
etal. 2008). Such members of microbiological community provide an ostensible
opportunity for engineering the rhizospheric interactions in the hunt to shape a per-
fect rhizosphere supporting healthy plant systems. For instance, the members of
genus Pectobacterium are highly plant pathogenic, and their pathogenicity depends
on the fabrication of enzymes that degrade the plant cell wall and are popularly
known as macerating enzymes (Liu et al. 2008). The microbe produces these
enzymes at great cell density via quorum-sensing mechanisms. The bacterial cell
synthesizes a signal molecule, and the concentration of that molecule upturns with
the cell density. The quorum-sensing signal is professed after attaining a threshold
P. Sharma et al.
611
cell concentration which further prompts the production of the macerating enzymes
and in turn the humiliation of the plant tissues. The biocontrol of this plant pathogen
is usually based on the alteration of the interactions, i.e., by inhibiting the quorum-
sensing mechanism (Faure and Dessaux 2007). Several soil microbes having the
potential to degrade the QS signal, for instance, Bacillus cereus, Bacillus thuringi-
ensis, and Rhodococcus erythropolis, have been reported to condense the macera-
tion signs under laboratory conditions (Uroz etal. 2003). It has been found that the
bacterium R. erythropolis does not hinder the progression of the pathogen, but pro-
ciently averts the accretion of the QS signal and henceforth the deliquescence of
the plant tissues (Cirou etal. 2007, 2011, 2012).
Another example of successful engineering of interactions is the successful
transformation of soil bacterium Burkholderia cepacia with a plasmid encoding
toluene degradation (Fig.21.4). The reinoculation of yellow lupine plants with the
transformed bacterial strain sustained the plant growth that too without the appear-
ance of any symptoms of phytotoxicity even at the elevated levels (1000mg/l) of
toluene, contrary to the control plants that displayed symptoms of phytotoxicity at
the toluene intensities above 100mg/l. Some PGPRs are known to aid the plant
growth by forming a biolm around the plant root cells. This biolm formation hap-
pens as a result of microbial response toward the plant root exudates. The addition
of root exudates responsible for prompting biolm formation along with the inocu-
lation of microbial culture is known to enhance plant-microbe interactions and
therefore also encourage the biolm formation (Zhang etal. 2015). Furthermore,
Fig. 21.4 Inoculation of a stressed plant with the genetically engineered microbial partners of
holobiont for improved plant-microbe interactions
21 Rhizosphere, R hizosphere Biology, andRhizospheric Engineering
612
the combinatorial addition of several microbial strains has also been reported for
their improved efcacy as well as improved plant growth assessment parameters. In
addition to it, the combinatorial addition has also been proven for supporting greater
microbial diversity in plant rhizosphere (Gupta etal. 2019) which probably has hap-
pened due to reshaping of the biotic interactions happening in the rhizospheric
hotspot. The plant-microbe interactions especially the symbiotic association
between plant systems and the rhizospheric microbiota are also engineered for in
situ bioremediation of an extensive array of organic pollutants like parathion, tri-
chloroethylene, toluene, and PCBs using genetically altered rhizobacteria or endo-
phytic bacteria (Wu etal. 2006). In a study, the Arabidopsis thaliana phytochelatin
synthase gene (PCSAT) was expressed in a micro-symbiont, Mesorhizobium huakuii
subsp. rengei, which lives in the nodules of Astragalus sinicus. The symbiont
expressing the PC synthase possessed the ability to upsurge the cadmium accretion
by 1.5-fold in the nodules (Sriprang etal. 2003). Similarly, an antifungal bacterium
Pseudomonas putida 06909 engineered for plant-microbe symbiotic relationship
also exhibited enhanced cadmium-binding properties. The genetic engineering-
mediated expression of a metal-binding peptide (EC20) not only upgraded cad-
mium binding but also alleviated the cellular toxicity of cadmium (Wu etal. 2006).
Thus it can be concluded that the interval of interactions between plants and
microbes happens to be very critical as it is the process of interaction only which
kicks the plant systems as well as microbial systems toward a state of interdepen-
dence where both the members can harness the benecial attributes of each other.
Therefore, the engineering of interactions can reshape the plant-microbe interac-
tions for enhanced plant productivity as well as superior plant health.
9 Conclusion andFuture Prospects
The rhizosphere is one among the most complex microbial habitats. Plants have
evolved into a microbial world where they extended their ne network of roots into
the soil already inhabited by a diverse community of microbes. The rapid coloniza-
tion of the plant roots by the microbes followed by the plant-mediated release of
photosynthates via its roots has put both the life forms in a state of interdependence
where both these survive as a single unit called as holobiont. Plants are largely
known for engineering their rhizospheric microbiomes which differ by the cultivar,
age, and variety of plants. However, a large proportion of the rhizospheric microbi-
ome is still represented by the Proteobacteria and Actinobacteria, and the microbial
population varies at the genus and species levels. Plants secrete root exudates to
harbor a great diversity of microorganisms. The rhizospheric microbiota responds
to these exudates by the phenomenon of chemotaxis and actively colonizes the plant
roots. But the prevalence of bad and ugly microbiome proves to be problematic at
different times and puts the plant systems in a state of stress. However, the valuable
possessions of the benecial rhizospheric microbiota, for instance, their ability to
own plant growth promotion traits and xenobiotic degradation, improve soil
P. Sharma et al.
613
structure, and sustain the plant health and productivity, have attracted the attention
of researchers to create a “rhizosphere bias”. Where only the microbiota benecial
to the plant systems can thrive and aid the plant growth. The rhizosphere can be
engineered for the benecial microbiota by several soil amendments and by direct
inoculation of the selected PGPR isolates. However, only a little proportion of rhi-
zospheric microbiome is culturable; therefore, the development of novel processes
which can study the valuable microbial possessions in its natural habitat should be
a point of major concern. The amendments should be decided after unveiling the
requirements of unculturable microbiota. The articial addition of root exudates is
also known to be the important soil amendment, but on the ip side, all the root
exudates secreted by the plants at different times haven’t been unveiled yet. The
interactive effect of all the root exudates should be worked out along with their
precise effect on both culturable and non-culturable rhizospheric microbiota. The
plant systems are genetically engineered for the production of the desired root exu-
dates, ion efux, and other metabolites. The advancement in techniques for cheaper
production of such metabolites is the need of the hour. Moreover, the articial pro-
duction of root exudates at an industrial scale could save a lot of money in the agri-
cultural sector by boosting the overall production. The identication of different
biotic and abiotic parts of rhizosphere can also unveil some hidden rhizospheric
interactions which can further prove to be an important asset for the agricultural
sector. The genetic engineering experiments in the plants have proven to be of only
a little success; therefore, the development of robust methodologies which can
reveal some novel pathways for metabolic engineering of the plant systems should
be addressed. Ultimately, the rhizosphere is a highly dynamic habitat where predic-
tions work the least; thus, this dynamic microbial habitat is a subject to dynamic
research.
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