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The Complex Molecular Signaling Network in Microbe–Plant Interaction

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Soil bacteria living around plants exert neutral, beneficial, or detrimental effects on plant growth and development. These effects are the result of signal exchange in which there is a mutual recognition of diffusible molecules produced by the plant and microbe partners. Understanding the molecular signaling network involved in microbe–plant interaction is a promising opportunity to improve crop productivity and agriculture sustainability. Many approaches have been used to decipher these molecular signals, and the results show that plants and microorganisms respond by inducing the expression of, and releasing, a mixture of molecules that includes flavonoids, phytohormones, pattern recognition receptors, nodulins, lectins, enzymes, lipo-chitooligosaccharides, exopolysaccharides, amino acids, fatty acids, vitamins, and volatiles. This chapter reviews current knowledge of the diverse signaling pathways that are turned on when plants interact with beneficial microbes, with emphasis on bacteria belonging to the genera Rhizobium, Azospirillum, and Pseudomonas.
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169
N.K. Arora (ed.), Plant Microbe Symbiosis: Fundamentals and Advances,
DOI 10.1007/978-81-322-1287-4_6, © Springer India 2013
Chapter 6
The Complex Molecular Signaling Network
in Microbe–Plant Interaction
María A. Morel and Susana Castro-Sowinski
M. A. Morel
Laboratory of Molecular Microbiology , Clemente Estable Institute
of Biological Research , Av. Italia 3318 , CP 11600 Montevideo , Uruguay
S. Castro-Sowinski (*)
Laboratory of Molecular Microbiology , Clemente Estable Institute
of Biological Research , Av. Italia 3318 , CP 11600 Montevideo , Uruguay
Department of Biochemistry and Molecular Biology, Faculty of Science ,
University of the Republic , Igua 4225 , CP 11400 Montevideo , Uruguay
e-mail: s.castro.sow@gmail.com; scs@fcien.edu.uy
Contents
Benefi cial Rhizospheric Microbes ........................................................................................... 170
Rhizobia–Legume Symbiotic Association .......................................................................... 171
Azospirillum–Plant Association .......................................................................................... 172
Other PGPR–Plant Interactions ........................................................................................... 173
Endophytes ..................................................................................................................... 173
Pseudomonas .................................................................................................................. 173
Delftia ............................................................................................................................. 174
Early Signaling Events: The Role of Root Exudates ............................................................... 174
Phytohormones Production ................................................................................................. 176
Other Secondary Metabolites .............................................................................................. 179
Volatile Organic Compounds (VOCs) ............................................................................ 180
Phenolic Compounds ...................................................................................................... 180
Quorum Sensing Responses ........................................................................................... 182
Extracellular Polysaccharides ............................................................................................. 183
PGPR and Plant Root Attachment ...................................................................................... 185
Proteins Involved in Rhizobia–Plant Interaction ................................................................. 186
Rhizobia–Legume Interaction Events ................................................................................. 187
Concluding Remarks ................................................................................................................ 190
Acknowledgements .................................................................................................................. 191
References ................................................................................................................................ 191
170
Abstract Soil bacteria living around plants exert neutral, benefi cial, or detrimental
effects on plant growth and development. These effects are the result of signal
exchange in which there is a mutual recognition of diffusible molecules produced
by the plant and microbe partners. Understanding the molecular signaling network
involved in microbe–plant interaction is a promising opportunity to improve crop
productivity and agriculture sustainability. Many approaches have been used to
decipher these molecular signals, and the results show that plants and microorganisms
respond by inducing the expression of, and releasing, a mixture of molecules that
includes fl avonoids, phytohormones, pattern recognition receptors, nodulins, lectins,
enzymes, lipo-chitooligosaccharides, exopolysaccharides, amino acids, fatty acids,
vitamins, and volatiles.
This chapter reviews current knowledge of the diverse signaling pathways
that are turned on when plants interact with benefi cial microbes, with emphasis on
bacteria belonging to the genera Rhizobium , Azospirillum , and Pseudomonas .
Benefi cial Rhizospheric Microbes
Mutualistic association between microbes and plants brings benefi ts to the interacting
partners. Some mutualistic microbes (plant–arbuscular mycorrhizal fungi interactions
have been excluded from this chapter) are rhizospheric bacteria known as plant growth
promoting rhizobacteria (PGPR) (Glick 1995 ) because they exert a positive infl uence
on plant growth. Over the last decade, several PGPR have been isolated and used as
bio-fertilizers, giving insight into good agronomical practices (Morel et al. 2012 ).
Their contribution to plant growth promotion (PGP) can be exerted through direct
and/or indirect mechanisms. Bacteria that use direct PGP mechanisms secrete metab-
olites such as hormones and polysaccharides, among other molecules, that infl uence
root and shoot development. Indirect PGP effects include the secretion of bacterial
metabolites with deleterious properties against the growth of phytopathogens (Lopez-
Bucio et al. 2007 ). These bacteria are collectively called biocontrol agents.
The best-known microbe–plant mutualistic interaction is the diazotrophic micro-
bial association with plants. Diazotrophs are free-living or symbiotic microbes that
x and reduce atmospheric nitrogen to ammonia. This process, called biological
nitrogen fi xation (BNF), is catalyzed by the bacterial enzyme nitrogenase (Masson-
Boivin et al. 2009 ; Bhattacharjee et al. 2008 ). Examples of bacterial diazotrophs are
Azotobacter (free-living diazotroph), Azospirillum (associative symbiont), Azoarcus
and Gluconacetobacter diazotrophicus (endophytic non-nodular symbionts), and
rhizobia (endophytic nodular symbionts). PGPR also produce phytohormones
(Cassán et al. 2009 ), iron-sequestering siderophores (Yadegari et al. 2010 ), phosphate-
solubilizing molecules (Wani et al. 2007 ), and/or 1-aminocyclopropane- 1-carboxylate
deaminase (Remans et al. 2007 ), among others. Examples of non- diazotrophic PGPR
are Pseudomonas and Bacillus (Parmar and Dufresne 2011 ).
There is an exchange of signaling molecules between both interacting partner
cells in mutualistic PGPR–plant interactions, leading to changes in gene expression.
M.A. Morel and S. Castro-Sowinski
171
This chapter reviews the progress in molecular signaling research involving benefi -
cial microbe–plant interactions reported in recent years.
Rhizobia–Legume Symbiotic Association
The rhizobia–legume association is the best-known endosymbiotic microbe–plant
interaction and, together with plant–mycorrhizal fungi interactions, is recognized
for its importance in sustaining agricultural ecosystems and productivity. Rhizobia
consist of several genera of the subclass Alpha- and Betaproteobacteria that are well
known for their ability to form mutualistic associations, especially (but not exclu-
sively) with leguminous plants ( Fabaceae ). Rhizobia induce the formation of root
nodules where BNF occurs (Bapaume and Reinhardt 2012 ). The rhizobia–legume
association is specifi c (each rhizobium establishes a symbiosis with only a limited
set of host plants and vice versa). Plants mutually compatible with the same species
of Rhizobium are called “cross-inoculation groups” (Morel et al. 2012 ).
Root colonization by rhizobia is accompanied with important changes in root
architecture and gene expression in root and shoot, which lead to the nitrogen-fi xing
phenotype. During the process of BNF, rhizobia provide reduced nitrogen to the
plant in exchange for carbohydrates and a micro-aerobic environment for the effec-
tive functioning of the oxygen-sensitive nitrogenase. Establishment of the symbiosis
requires the reciprocal recognition of partners and the production of various
signaling molecules that are required to regulate nodule initiation and differentiation
and nitrogen fi xation. Briefl y, nitrogen fi xation is preceded by root morphological
changes that include highly coordinated events. Most legumes constitutively release
root-diffusible attractant signal molecules (fl avonoids), which trigger rhizobial
production of specifi c lipo-chitooligosaccharides known as nodulation factors
(Nod Factors or NFs) (Hassan and Mathesius 2012 ) (see section “ Extracellular
Polysaccharides ”). NFs are among the most important molecules in the microbe–
plant dialog, mediating rhizobia recognition by the plant root and nodule organogen-
esis (Masson-Boivin et al. 2009 ). NF recognition is accompanied by curling of root
hairs, where bacteria are entrapped, and formation of plant-derived infection threads
(IT) that carry the rhizobia into the dividing cells of the inner cortex, the nodule
primordium (Fournier et al. 2008 ). Then, rhizobia are released into the nodule
primordium where they differentiate into bacteroids, the symbiotic rhizobial form
that expresses the nitrogen-fi xing enzyme, nitrogenase (Oldroyd et al. 2011 ).
Rhizobia–legume symbiosis is regulated by transcriptional reprogramming of
host cells that ensures the functioning of the nodule. Many reprogrammed genes are
membrane proteins with important roles in signaling, intracellular accommodation,
and nutrient transport (Bapaume and Reinhardt 2012 ; see section “ PGPR and Plant
Root Attachment ”). In addition to BNF, most rhizobia have been found to produce
auxins. The roles of auxins in rhizobia–legume interactions are related to plant
growth and nodule organogenesis (Lambrecht et al. 2000 ; see section “ Phytohormones
Production ”).
6 The Complex Molecular Signaling Network in Microbe–Plant Interaction
172
Azospirillum –Plant Association
Bacteria belonging to the genus Azospirillum are free-living, nitrogen-fi xing,
surface- colonizing, and, sometimes, endophytic diazotroph Alphaproteobacteria
(family Rhodospirillaceae). Azospirillum spp. establish associations that are
benefi cial to plants, but with no apparent preference for specifi c plants, and can be
successfully applied to plants that have never been colonized before by azospirilla
(Bianco and Defez 2011 ; Guerrero-Molina et al. 2011 ; Reis et al. 2011 ). Currently,
there is a limited market for commercial bio-fertilizers for non-legume crops
based on Azospirillum spp., but they have been shown to be effi cient PGPR
(Figueiredo et al. 2010 ).
Azospirillum is a nitrogen-fi xing microbe, but given that azospirilla promote
plant growth even in nitrogen-rich conditions, PGP by Azospirillum might be
attributed to other mechanisms rather than BNF (Okon and Kapulnik 1986 ),
such as deamination of the ethylene precursor 1-aminocyclopropane-1-carboxylate
and siderophore (Tortora et al. 2011 ), auxin, or nitric oxide production (Baudoin
et al. 2010 ; Spaepen et al. 2007 ). Among these PGP properties, auxin production
is thought to be the main mode of action of Azospirillum brasilense . This assump-
tion was corroborated in experiments using genetically modifi ed azospirilla that
showed enhanced auxin production (Baudoin et al. 2010 ; Spaepen et al. 2007 ,
2008 ). Many other workers have also reported that plant hormone production by
Azospirillum spp. is the main mechanism that explains the PGP effect (Reis
et al. 2011 ; Bashan et al. 2004 ; Lambrecht et al. 2000 ; Okon and Labandera-
Gonzalez 1994 ). Auxin production by azospirilla promotes root development
and proliferation, leading to enhanced nutrient uptake (Lambrecht et al. 2000 )
and increased root exudation of molecules to the rhizosphere. Molecules exuded
by the root act as chemoeffectors that attract azospirilla to the rhizosphere (che-
motaxis), thereby increasing the chance of root–bacterial interactions. This was,
and still is, the mechanism that in fact explains how azospirilla promote plant
growth (Hayat et al. 2010 ).
Azospirilla are considered “helper” bacteria that promote rhizobia–plant interac-
tions (Morel et al. 2012 ). Co-inoculation with azospirilla stimulates nodulation
(early nodulation and more nodules), nodule function, and plant growth and devel-
opment when compared with inoculation with rhizobia alone (Bianco and Defez
2011 ; Remans et al. 2008 ). The evidence supports a mix of molecules secreted to
the rhizosphere being involved in improving rhizobia–legume association. Auxin
production by azospirilla, during co-inoculation, stimulates morphological and
physiological changes in the root system, increasing the number of potential sites
for rhizobial infection, thus leading to a much higher number of nodules (Bianco
and Defez 2011 ). Some direct evidence also suggests that during co-inoculation,
Azospirillum spp. induce the synthesis of chemoattractant fl avonoids by roots of
chickpea, common bean, and alfalfa (Star et al. 2012 ; Dardanelli et al. 2008 ;
Burdman et al. 1996 ; Volpin et al. 1996 ).
M.A. Morel and S. Castro-Sowinski
173
Other PGPR–Plant Interactions
There is a long list of microbes that establish benefi cial interactions with plants, but
some endophytes and Pseudomonas head the list.
Endophytes
Endophytes are bacteria that infect and colonize the plant apoplast, evading or
suppressing the host plant defense system. Many facultative endophytic bacteria
can also survive in the rhizosphere, where they can enter their host plant via the
roots (Badri et al. 2009 ). PGPR are bacteria that live in soil near the root, colonize
the root surface, reside in root tissue, or live inside plant cells in specialized
structures, promoting plant growth; thus, most endophytes might be considered
PGPR. Given the semantic overlap and the difference between PGPR and endo-
phytes, many researchers have adopted two simple terms: intracellular PGPR
(iPGPR), for bacteria residing inside plant cells, and extracellular PGPR (ePGPR)
for those bacteria living outside plant cells, root surface, or rhizosphere (Gray
and Smith 2005 ). However, the defi nition of endophytes is still controversial.
Many authors claim that ePGPR are simply epiphytes and iPGPR are just endophytes
(Ikeda et al. 2010 ).
In endophyte–plant interactions, bacteria are not restricted to a specifi c compart-
ment within the plant but can be found in roots, stems, and leaves. Like rhizobia,
most endophytes commonly used as inoculants are diazotrophs that improve plant
growth. Examples of endophyte–plant interactions are Burkholderia and sugarcane,
Herbaspirillum and a broad range of host plants, and Azospirillum and rice
(Govindarajan et al. 2008 ). It has been shown that crop yield increase after endo-
phyte inoculation is mainly due to BNF. Details about endophytes for non-legumes
can be read in Bhattacharjee et al. ( 2008 ).
Pseudomonas
The genus Pseudomonas includes the most diverse and ecologically signifi cant
group of bacteria, belonging to the class Gammaproteobacteria. They are ubiqui-
tously distributed in terrestrial and marine environments and have been found asso-
ciated with animals and plants (Kiil et al.
2008 ). Their genetic diversity is a
refl ection of their ecological diversity (Silby et al.
2009 ). Many Pseudomonas spp.
have been extensively studied as PGPR. There is evidence that some Pseudomonas
spp. produce siderophores (Rosas et al. 2006 ), phenolic compounds (Combes-
Meynet et al. 2011 ), lytic enzymes (Egamberdieva et al. 2010 ), and phytohormones
(Pallai et al. 2012 ; Khalid et al. 2011 ; Khakipour et al. 2008 ); solubilize phosphate
(Azziz et al. 2012 ); act as biocontrol agents of phytopathogenic microbes
(Quagliotto et al. 2009 ); and induce systemic resistance (Bakker et al. 2007 ), thus
6 The Complex Molecular Signaling Network in Microbe–Plant Interaction
174
promoting plant growth. Moreover, some rhizospheric Pseudomonas spp. interact
synergistically with other PGPR, assisting PGPR–plant colonization and suppress-
ing plant pathogens (Parmar and Dufresne 2011 ). Many studies support the action
of Pseudomonas spp. as “helper” bacteria during the establishment of the rhizobia–
legume interaction, evidenced by the promotion of plant growth during co-inoculation
(Morel et al. 2012 ; Malik and Sindhu 2011 ). This helper effect might be explained
by the production of phytohormones (Malik and Sindhu 2011 ; Egamberdieva et al.
2010 ), a qualitative change in plant-secreted fl avonoids (Parmar and Dadarwal
1999 ), or the solubilization of non-available nutrients (mainly refi xation of exoge-
nously applied phosphorus), among other actions (Medeot et al. 2010 ).
Delftia
Recently, a new genus has emerged as a PGPR. Bacteria belonging to the genus
Delftia have been described as novel PGP microbes (diazotrophic and biocontrol
agents against various plant pathogens). They fi x atmospheric nitrogen, produce the
auxin indole-3-acetic acid and siderophores, promote alfalfa and clover growth under
nitrogen-rich conditions, and assist as a “helper” bacterium during rhizobia–legume
interaction, probably due to auxin production (Ubalde et al. 2012 ; Morel et al. 2011 ;
Han et al. 2005 ).
Early Signaling Events: The Role of Root Exudates
The root system of plants imports water and nutrients from the soil solution but also
releases low- and high-molecular-weight compounds to the rhizosphere. Root exu-
dates are composed of a broad range of root-secreted molecules that act as a com-
plex chemical cocktail that mediates interactions occurring in the rhizosphere and
shapes soil microbial communities (Okumoto and Pilot 2011 ). Their chemical com-
position is infl uenced by environmental conditions, plant genotype, and the multi-
partite interactions occurring in the rhizosphere, among other factors.
Carbon-based compounds are the main constituent of this complex cocktail, but
ions, oxygen, and inorganic acids are also important components with relevant roles
during rhizospheric interactions (Badri and Vivanco 2009 ). Exuded molecules
include low-molecular-weight compounds, such as sugars and phenolics, and
high-molecular- weight compounds such as polysaccharides and proteins, which
often compose a larger proportion of the total mass of the exudate (Cai et al. 2012 ).
Even though these chemicals are root-secreted, many rhizobacteria also secrete
metabolites that contribute to the pool of molecules that mediate rhizospheric
interactions (Badri et al. 2009 ). Table 6.1 summarizes examples of these bacterial-
secreted compounds and their general role in plants. The sections below describe
current knowledge of different plant and bacterial metabolites involved in microbe–
plant interactions.
M.A. Morel and S. Castro-Sowinski
175
Table 6.1 Some bacterial-secreted compounds and their role in plant physiology and architecture
Chemical group
Bacterial
metabolite Plant response Reference
Phytohormones Salicylic acid,
jasmonic
acid, and
ethylene
Immune plant
defense activation
through SAR
a
(mainly) and ISR
b
Bent ( 2010 ), Bakker et al.
(
2007 ), Ping and
Boland (
2004 )
Inhibition of legume
response to NF
and rhizobia
Oldroyd and Downie
(
2008 ), Ramos Solano
et al. (
2009 ), Ding
et al. (
2008 ), Sun et al.
(
2006 )
Cytokinins,
auxins, and
gibberellins
Phyto-stimulation.
Morphogenesis
Morel et al. ( 2011 ),
Cassán et al. (
2009 ),
Ferguson and
Beveridge (
2009 ),
Boiero et al. (
2007 ),
Remans et al. (
2007 ),
(
2008 ), Lopez- Bucio
et al. (
2007 ), Spaepen
et al. (
2007 )
Auxins Pathogenesis (i.e.,
gall induction,
necrotic lesions)
Ding et al. (
2008 ),
Chalupowicz et al.
(
2006 ), Robert-
Seilaniantz et al.
(
2007 ), Lambrecht
et al. (
2000 )
N -acyl- l -homoserine
lactones (AHLs)
and QS
c -related
signals
AHLs Modulation of root
system
architecture
Ortiz-Castro et al.
(
2008a ), von Rad et al.
(
2008 )
Induction of ISR Schuhegger et al. (
2006 )
AHL-degrading
lactonases
Interference with QS
signals required
for virulence in
phytopathogens
Friesen et al. (
2011 )
Volatile organic
compounds
Acetoin,
butanediol,
1-octen- 3-ol,
and
butyrolactone
Modulation of
root system
architecture
Gutierrez-Luna et al.
(
2010 ), Lopez- Bucio
et al. (
2007 )
ISR Ryu et al. (
2005 ), Ping and
Boland (
2004 )
Phenolic compounds Flavonoids,
phenolic
acids
nod -gene inducers Mandal et al. (
2010 ),
Parmar and Dadarwal
(
1999 )
Antimicrobial
agents, ISR
Combes-Meynet et al.
(
2011 ), Parmar and
Dufresne (
2011 )
Lipopolysaccharides
(LPS) and
extracellular-
related factors
Siderophores,
LPS
ISR Ping and Boland (
2004 )
a SAR systemic acquired resistance
b ISR induced systemic resistance
c QS quorum sensing
6 The Complex Molecular Signaling Network in Microbe–Plant Interaction
176
Phytohormones Production
Phytohormones are chemical messengers produced by plants and microorganisms,
which coordinate plant cellular activities at low concentrations (Ferguson and
Beveridge 2009 ). Common phytohormones belong to fi ve major classes: auxins,
cytokinins, gibberellins, abscisic acid, and ethylene. Other known phytohormones
are brassinosteroids, salicylic acid, jasmonates, polyamines, nitric oxide, strigolac-
tones, etc. (Pieterse et al. 2009 ). The following microbes are known phytohormone
producers: Pseudomonas (Khakipour et al. 2008 ), Azospirillum (Khalid et al. 2011 ),
rhizobia (Etesami et al. 2009 ), Bacillus (Lim and Kim 2009 ), and Delftia (Morel
et al. 2011 ). Microbial secreted hormones, mainly cytokinins (CKs) and auxins, act
as signaling molecules that coordinate changes in plant cell division and differentia-
tion, affecting root and shoot architecture and functioning (Boiero et al. 2007 ;
Lopez-Bucio et al. 2007 ; Ryu et al. 2005 ). In this section, we review information
concerning phytohormones (auxins and CKs) that positively correlate with PGP
during microbe–plant interaction (Tables 6.2 and 6.3 ).
The information supports the view that a mix of phytohormones, rather than a
single effector, acts to control plant cellular processes at multiple levels (Yoshimitsu
et al. 2011 ), including major effects on plant growth and the induction of plant immune
defenses. During the microbe–plant interaction, bacterial-produced phyto- hormones,
mainly auxins and CKs, also have phyto-stimulation effects (Robert- Seilaniantz et al.
2007 ). Most of the information that supports this affi rmation was gathered working in
the areas of rhizobia–legume and azospirilla–wheat interactions.
CKs are purine derivatives produced in root tips and developing seeds and are
transported via the xylem from roots to shoots (Ortiz-Castro et al. 2009 ). Some
effects of CKs in plants are the induction of root and shoot cell division, cell growth
and dedifferentiation, apical dominance, lateral bud growth, leaf expansion, and
delayed senescence. Zeatin is the most common CK, but other cytokinin-like
substances are known: isopentenyladenine, isopentenyladenosine, zeatin riboside,
and dihydrozeatin riboside (Davies 2010 ). CKs are probably the most studied
phytohormones involved in nodule organogenesis (Ariel et al. 2012 ; Op den Camp
et al. 2011 ; Oldroyd and Downie 2008 ; Murray et al. 2007 ; Tirichine et al. 2007 ).
They have been proposed as secondary signal molecules that perceive NF at the root
epidermis. In response to NF application at roots, a local increase in CK levels is
detected, which induces nodule primordial development in the cortex cells, thus
infl uencing bacterial infection (Heckmann et al.
2011 ; Ding et al. 2008 ; Murray et al.
2007 ; Oldroyd 2007 ; Tirichine et al. 2007 ). For instance, Murray et al. ( 2007 ) and
Tirichine et al. (
2007 ) showed that plant CK signaling pathway activation by rhizo-
bial cells is necessary (and suffi cient) to activate nodule formation in L . japonicum .
CK production by plant-associated bacteria, other than rhizobia, has also been well
documented. Some examples of CK-producing bacteria are Bacillus megaterium and
Azospirillum (Ortiz-Castro et al. 2008b ).
Many plant pathogenic bacteria also secrete CK analogs or activate plant
CK production to form gall structures, leading to delayed senescence activity
and suppression of plant basal defense mechanisms (Chalupowicz et al. 2006 ).
M.A. Morel and S. Castro-Sowinski
177
Table 6.2 Effects of bacterial auxins on microbe–plant interaction: root architecture and/or physiology
PGPR–plant system Strategy used during the study Effect
Possible mechanism of
action Reference
Sinorhizobium meliloti
Medicago truncatula
Proteomics of roots. Effect of
inoculation and exogenous
application of auxin (without
inoculation)
Similar accumulation level in
inoculated and auxin- treated
plants
Auxin is a positive
regulator of nodulation
initiation
Van Noorden
et al. (
2007 )
Azospirillum brasilense
Triticum sp. (wheat)
Plant growth. Inoculation with
overproducing IAA
aA .
brasilense
Increased shoot biomass, thinner
roots, and no signifi cant effect
on root biomass (a month after
inoculation)
Transient positive effect of
bacterial IAA on root
development
Baudoin et al.
(
2010 )
Bacillus subtilis and
B . licheniformisCapsi-
cum sp. (red pepper)
and Solanum lycopersi-
cum (tomato)
Plant growth and seed germina-
tion. Bacillus co-inoculation
and Bacillus purifi ed auxins
exogenous application
Increased root, stem, and leaf
growth and seed germination
Bacterial auxins are major
factors responsible for
plant growth
promotion
Lim and Kim
(
2009 )
Pseudomonas aeruginosa
and A . brasilense –wheat
and rice
Plant growth and yield. Inoculation
under fi eld conditions
Increased number of tiller, straw
and grain yield
Auxin-producing PGPR
positively affect plant
growth
Khalid et al.
(
2011 )
B . japonicum and
A . brasilenseGlycine
max (soybean)
Plant growth and seed
germination. Inoculation
and co-inoculation
Promotion of seed germination
and PGP of soybean seedlings
in co- inoculated plants
PGPR excretion of IAA
(auxin) promotes
young seedlings
Cassán et al.
(
2009 )
Rhizobium galegae and
Pseudomonas
spp.– Galega orientalis
(Galega)
Plant growth and nodulation.
Inoculation and co- inoculation
experiments
Increased shoot and root dry
matter, number of nodules,
and nitrogen content of
co- inoculated plants
Pseudomonas spp.
produce auxin and
cellulase as mechanism
to enhance symbiotic
performance of
rhizobia
Egamberdieva
et al. (
2010 )
Mesorhizobium sp. and
Pseudomonas spp.– Cicer
arietinum (chickpea)
Plant growth and nodulation
parameters. Inoculation and
co- inoculation experiments
Increased shoot and root dry
matter, number, and biomass of
nodules in co- inoculated plants
Enhanced nodulation in
chickpea by auxin
secretion
Malik and Sindhu
(
2011 )
a IAA indol-3-acetic acid
6 The Complex Molecular Signaling Network in Microbe–Plant Interaction
178
Table 6.3 Effects of cytokinins (CKs) on microbe–plant interaction: root architecture and/or physiology
PGPR–plant system Strategy Effect Possible mechanism Reference
Mesorhizobium
lotiLotus
japonicum
Nodule organogenesis. Inoculation
and CK application (without
inoculation) of plant hit1 a
mutants
Hit1 roots are insensitive to
exogenously applied CK
and rhizobia inoculation
A CK receptor (LHK1) is
required for the activation
of Nin b and nodule
organogenesis
Murray et al. (
2007 )
M . lotiL . japonicum Nodule organogenesis in a
L . japonicum snf2 mutant c
Spontaneous development of
root nodules in absence of
rhizobia or rhizobial signal
molecules
CK signaling is required for
nodule initiation and is a key
element in dedifferentiation
of cortical cells
Tirichine et al. (
2007 )
M . lotiL . japonicum Plant growth and nodule
organogenesis. Inoculation and
exogenous CK application to
plant mutants for CK response
Formation of discrete and
easily visible nodule
primordial. Expression of
nodulin genes
Root cortical cell activation
by CK depends on LHK1
Heckmann et al. (
2011 )
B . subtilis
(CK-producing
strain)– Lactuca
sativa (lettuce)
Plant growth and hormone
determination of shoot and root.
Inoculation under drought
stress
Increase of CKs in shoot.
Weight increase in shoots
and roots
Inoculation with CK-producing
bacteria may have a
benefi cial result under
moderate drought
Arkhipova et al. (
2007 )
B . megaterium
Arabidopsis
thaliana
Plant growth. Inoculation of plants
with mutations in three CK
receptors (single, double, and
triple mutants)
Reduced PGP in single and
double mutant. Non-PGP
in triple mutant
PGP can be mediated by
different CK receptor
homologs
Ortiz-Castro et al.
(
2008b )
B . japonicum and
A . brasilense
G . max
Plant growth and seed germination.
Inoculation and co-inoculation
Promotion of seed germina-
tion, PGP of soybean
seedlings
PGPR excrete zeatin (CK) at
suffi cient concentration to
produce PGP in young seed
tissues
Cassán et al. (
2009 )
a Hit1 genetic suppressor of the hyperinfected phenotype; abundant infection threads formation but failed cortical cell division
b Nin nodule inception regulator
c snf2 an allele of a lotus histidine kinase LHK1 gene; spontaneous nodule formation
M.A. Morel and S. Castro-Sowinski
179
The production of CKs enhances pathogenicity and modulates the physiology of
host plants (Choi et al. 2011 ). In contrast, plant-derived CKs may be involved in
plant resistance to pathogen infection (Choi et al. 2011 ). However, the molecular
mechanisms of CK action in disease resistance against a wide spectrum of patho-
gens and the reason for the opposite effects of CKs on plant responses against
pathogens are still unclear.
In addition to CKs, auxins also infl uence plant growth. Auxins are compounds
with aromatic ring and carboxylic acid groups. The increasing amount of data about
bacterial strains with the ability to increase the pool of auxins available to plants
leads to the assumption that their production is one of the major direct factors that
promote root and plant growth (Khalid et al. 2011 ; Ali et al. 2009 ). Auxins act on
root architecture increasing the number of lateral roots and root hair elongation. They
are also responsible for apical dominance acting as a signaling molecule in root and
shoot growth (Ferguson and Beveridge 2009 ). As a result of increased root bulk, the
plant may scavenge a larger area for nutrient and water uptake, and the root has a
larger number of potential niches for benefi cial or pathogenic microbial infection.
Tryptophan is an amino acid commonly found in root exudates, and it is the main
precursor of auxin biosynthesis (Etesami et al. 2009 ). Indole-3-acetic acid (IAA) is
the main auxin in plants, controlling cell enlargement and division, tissue differen-
tiation, and responses to light and gravity. Many PGPR, such as Azospirillum ,
Pseudomonas , Delftia , and Rhizobium species, induce root proliferation through IAA
production (Morel et al. 2011 ; Spaepen et al. 2007 , 2008 ; Kapulnik et al. 1985 ).
However, various phytopathogens also have the ability to produce IAA and/or alter
its levels in plants, facilitating host infection and virulence and causing uncontrolled
growth in plant tissues (mainly tumor and gall induction) (Chalupowicz et al. 2006 ;
Robert-Seilaniantz et al. 2007 ). Agrobacterium , Pseudomonas , and Erwinia produce
IAA as part of their pathogenic behavior (Lambrecht et al. 2000 ). Other indolic
compounds with auxin activity are indole-3-butyric acid, indole-3-pyruvic acid,
indoleacetamide and indole-2-carboxylic acid (Lim and Kim 2009 ).
Gibberellins and brassinosteroids also play an important role during nodule for-
mation (Oldroyd and Downie 2008 ). It has been shown that brassinosteroids act
together with auxins on many developmental plant processes (Yoshimitsu et al.
2011 ). Strigolactones are plant hormones that contribute to apical dominance
(Ferguson and Beveridge 2009 ). They are exuded by roots in extremely low concen-
trations (Steinkellner et al. 2007 ). They act as chemical signals for root colonization
by symbiotic arbuscular mycorrhizal fungi and inhibit shoot branching. Even though
there are no reports of microbial production of strigolactones, it has been suggested
that this class of phytohormones has biological signaling functions in the rhizo-
sphere (Tsuchiya and McCourt 2009 ; Steinkellner et al. 2007 ).
Other Secondary Metabolites
Plants produce an extremely diverse array of low molecular mass compounds, often
called secondary metabolites, which include, among others, alkaloids, essential oils
6 The Complex Molecular Signaling Network in Microbe–Plant Interaction
180
or essences, steroids, terpenoids, and phenolic compounds. Some secondary
metabolites are commonly found in plants, but others are specifi c to only a few
related plant species and/or are produced in particular conditions (Pichersky and
Gershenzon 2002 ). Most of them are signaling molecules, and even if their roles in
signaling are unknown, some are strictly necessary, like fl avonoids. Here, we sum-
marize some of the highlights of plant secondary metabolites involved in plant–
microorganism interaction, other than phytohormones, which have been covered in
section “ Phytohormones Production .”
Volatile Organic Compounds (VOCs)
VOCs are molecules that have high vapor pressure and vaporize to the atmosphere
under normal conditions (Ortiz-Castro et al. 2009 ). The fi rst report of a plant VOC
was the plant hormone ethylene in the year 1910 (recognized as cell-to-cell signal
transmission in 1934 by Gane) (Bleecker and Kende 2000 ). Since then, it has been
accepted that plants produce and release a variety of diffusible compounds, includ-
ing low molecular weight compounds, such as terpenoids, modifi ed fatty acids,
benzenoids, and other scented substances (Ortiz-Castro et al. 2009 ; Ping and Boland
2004 ). Improved techniques for the collection and analysis of volatiles, such as gas
chromatography-electroantennographic detection, have allowed the detection of
new plant VOCs (Pichersky and Gershenzon 2002 ). VOCs act as plant growth regu-
lating substances that affect other organisms, acting, for example, as attractants and/
or repellents. Recently, some authors demonstrated that some PGPR can produce
VOCs as signals that stimulate the growth of plants (Gutierrez-Luna et al. 2010 ).
Examples of PGPR-producing VOCs are B . megaterium (acetoin and butanediol
producer) (Lopez-Bucio et al. 2007 ) and Bacillus spp. (1-octen-3-ol and butyrolac-
tone producer) (Gutierrez-Luna et al. 2010 ). Many VOCs have been detected in
rhizospheric soil, but their role in microbe–plant interactions is still uncertain. It has
been suggested that VOCs may have antibiotic functions acting in the control of
plant pathogens, induce different phytohormonal signaling networks (Ortiz-Castro
et al. 2009 ), or activate induced systemic resistance (ISR) via a salicylic acid- and
jasmonic acid-independent pathway (Ping and Boland 2004 ). For example, the
VOCs 2,3-butanediol and acetoin, released by Bacillus spp., trigger growth promo-
tion of Arabidopsis seedlings and induce systemic resistance against Erwinia caro-
tovora (Ryu et al. 2005 ). It was concluded that VOCs activate a CK-dependent
pathway for PGP and an ethylene-dependent signaling pathway for ISR (Ping and
Boland 2004 ).
Phenolic Compounds
Phenolic compounds are produced by plants and microbes as well, but they differ in
chemical structure (Combes-Meynet et al. 2011 ; Mandal et al. 2010 ; Parmar and
Dadarwal
1999 ). Increasing evidence suggests that root-secreted polyphenols initiate
and modulate the dialog between roots and soil microbes (Badri and Vivanco 2009 ).
M.A. Morel and S. Castro-Sowinski
181
Flavonoids are plant phenolic compounds recognized as important signaling
molecules in microbe–plant interaction events. The main subclasses of fl avonoids
include chalcone, fl avone, isofl avone, fl avonol, fl avanone, and isofl avonoid com-
pounds (Cesco et al. 2012 ). The effects of fl avonoids in the rhizosphere depend on
their chemical composition and concentration. In the rhizosphere, they have a criti-
cal role in early stages of the rhizobia–legume symbiotic interaction and in plant
defense. The best-known roles attributed to plant fl avonoids are in chemoattraction
of rhizobia to the legume root and as primary molecular signals for rhizobial nod -
gene induction and NF production (Mandal et al. 2010 ; Badri et al. 2009 ; Oldroyd
and Downie 2008 ; Steinkellner et al. 2007 ). A wide variety of plant fl avonoids have
been shown to induce NF production in different rhizobia–legume interactions
(Table 6.4 ). In the presence of compatible rhizobial strains, the legume host increases
the exudation of a particular set of fl avonoids, e.g., in the presence of Sinorhizobium
strains, alfalfa produces increased amounts of the fl avonoid luteolin. Flavonoids
protect dividing cells from oxidative damage due to their antioxidant properties and
ability to modulate several enzymes (Ariel et al. 2012 ; Cesco et al. 2012 ).
The genome-wide transcriptional response of Bradyrhizobium japonicum to
genistein showed that 100 genes were induced, including all nod box-associated
Table 6.4 Plant-secreted avonoids induce nod genes
PGPR Plant Flavonoid(s) Effect Reference
Sinorhizobium
meliloti
Alfalfa Luteolin(3,4,
5,7- tetrahydroxyfl avone)
nod -gene inducer Peters et al.
(
1986 )
S . meliloti Alfalfa 4,4-dihydroxy-2-
methoxychalcone,
4,7-dihydroxyfl avone,
4-7- dihydroxyfl avanone
Flavonoids, other
than luteolin,
are nod -gene
inducers
Maxwell
et al.
(
1989 )
S . meliloti Alfalfa Chrysoeriol and luteolin nod -gene
induction
Hartwing
et al.
(
1990 )
Azospirillum
brasilense
(co-inoculation
with
Rhizobium
tropici and
Rhizobium etli )
Common
bean
Daidzein, naringenin,
genistein, and
coumestrol
Increased root
hair formation,
nodule number,
nod -gene
induction
Burdman
et al.
(
1996 )
Rhizobium
leguminosarum
Pea and
lentil
Hesperetin and naringenin nod -gene
induction
Begum
et al.
(
2001 )
Bradyrhizobium
japonicum
Soybean Coumestrol Increased number
of nodules,
high degree
of biofi lm
formation.
Weak nod -gene
induction
Lee et al.
(
2012 )
6 The Complex Molecular Signaling Network in Microbe–Plant Interaction
182
genes and fl agellar and transport process genes, suggesting that genistein has a
much broader function than nod -gene induction (Lang et al. 2008 ). Flavonoids (nar-
ingenin and hesperetin) are also factors that infl uence rhizobial competitiveness in
soils, as showed in several biovars of Rhizobium leguminosarum (Maj et al. 2010 ).
Flavonoids also participate in plant host specifi city for few rhizobial species. Plants
secrete a characteristic group of inducing and non-inducing fl avonoids that are rec-
ognized by rhizobial outer membrane protein, NodD (the LysR-type transcriptional
regulator that mediates the expression of nod genes and a key determinant of host
specifi city). Both inducing and non-inducing fl avonoids bind NodD and mediate
conformational changes at nod -gene promoters, but only a few set of fl avonoids are
capable of promoting nod genes. The production of non-inducing fl avonoids may be
a mechanism by which legumes prevent overnodulation (Peck et al. 2006 ). The
rhizospheric microbial community may also alter the amount and composition of
nod -inducing signals secreted by the plant. Many reports showed that the inocula-
tion of leguminous plants with Azospirillum induces the secretion of a particular set
of nod -inducing avonoids that facilitate the establishment of the rhizobia–plant
interaction, even under stress conditions (Burdman et al. 1996 ; Volpin et al. 1996 ;
Dardanelli et al. 2008 ).
Flavonoids shape rhizosphere microbial community structure because they may
be used as potential carbon sources or may act as toxic substances for microbes that
do not possess fl avonoid biodegradation pathways (Shaw et al. 2006 ). They may also
accelerate the biodegradation of xenobiotics, since the chemical structures of many
avonoids and xenobiotics are similar (Cesco et al. 2012 ; Shaw and Burns 2003 ),
and fl avonoids may have allelopathic effect on other plants (Cesco et al. 2012 ).
The role of phenolic compounds as signaling compounds in pathogenic microbe–
plant interactions is undeniable. Usually, phenolic compounds released from seeds
and roots act against soilborne pathogens and have high antifungal, antibacterial,
and antiviral activities (Mandal et al. 2010 ). For example, Pseudomonas produces
2,4-diacetylphloroglucinol (DAPG), a phenolic compound with antibiotic proper-
ties, and a signal molecule that induces systemic resistance in plants and stimulates
root exudation and branching (Combes-Meynet et al. 2011 ). The secretion of cate-
chin by Combretum albifl orum interferes with the production of virulence factors by
P . aeruginosa (Vandeputte et al. 2010 ).
Quorum Sensing Responses
Quorum sensing (QS) is a phenomenon where microbes communicate and coordi-
nate activities by the accumulation of signal molecules at suffi cient concentration
(Adonizio et al. 2008 ). Both pathogenic and symbiotic bacteria require QS to inter-
act successfully with their hosts (Badri et al. 2009 ). In Gram-negative bacteria, QS
is typically mediated by N -acyl- l -homoserine lactones (AHLs). AHLs are freely
diffused through the bacterial membrane and distributed within the rhizosphere
where they regulate the behavior of rhizospheric bacteria. Increasing evidence
M.A. Morel and S. Castro-Sowinski
183
indicates that higher plants may produce metabolites that mimic AHLs, interfering
with rhizospheric QS behavior (Gao et al. 2003 ). For example, Medicago sativa
produces multiple signal molecules, including l -canavanine, capable of interfering
with QS gene expression in S . meliloti (Keshavan et al. 2005 ). Canavanine is an
arginine analog commonly found in seed and root exudates of a variety of legumes.
Cai et al. ( 2009 ) found that canavanine is toxic to many soil bacteria but not to some
rhizobia and suggest that host legumes may exude canavanine to optimize the bacte-
rial population and select benefi cial rhizobia in their rhizospheres. The role of these
plant AHL-like compounds is still unclear (Ortiz-Castro et al. 2009 ), but some
authors report direct effects on plant development in a similar way to auxins, by
modulating root system architecture (more lateral roots and root hairs) (Ortiz-Castro
et al. 2008a ; von Rad et al. 2008 ). Plant AHL-like compounds are also involved in
protection against pathogens. Vandeputte et al. ( 2010 ) reported the secretion by
Combretum albifl orum of the fl avonoid catechin that interferes in the QS signaling
of Pseudomonas aeruginosa PAO1, as the fi rst line of defense against this patho-
gen. Some PGPR can also protect plants by disrupting the QS signals required for
pathogen–pathogen communication, interfering with the expression of virulence
genes. For example, Bacillus , Arthrobacter , and Klebsiella produce AHL-degrading
lactonases which inactivate AHLs (Friesen et al. 2011 ). Moreover, QS in the rhizo-
sphere can also be disrupted by abiotic factors such as alkaline pH (Reis et al. 2011 ).
Other PGPR secrete AHLs that induce plant systemic resistance to pathogens. For
example, AHL molecules produced by Serratia liquefaciens MG1 and P . putida
IsoF induce ISR in tomato plants against Alternaria alternata via a salicylic acid
and ethylene-dependent pathway (Schuhegger et al. 2006 ). It is important to high-
light the relevance of disrupting bacterial QS signaling as a strategy to fi ght against
phytopathogens. This fi eld is still unexplored.
Extracellular Polysaccharides
Bacterial extracellular polysaccharides (exopolysaccharides, EPSs; lipopolysaccha-
rides, LPSs; capsular polysaccharides, CPSs; and cyclic β-glucans) are usually
accumulated on cell surfaces and/or secreted into the cell surroundings (Gray and
Smith 2005 ). They have multiple roles, such as protection against stress (Qurashi
and Sabri 2012 ; Upadhyay et al. 2011 ), attachment to surfaces (Tsuneda et al. 2003 ),
plant invasion (Fraysse et al. 2003 ; Troch and Vanderleyden 1996 ), and inhibition
of the plant defense response in plant–microbe interactions (Kyungseok et al. 2008 ).
PGPR also produce EPS and other surface polysaccharides as essential components
that promote interaction with plants (Upadhyay et al. 2011 ).
Rhizobial surface polysaccharides are highly important during the early steps of
microbe–legume interaction. They are essential for the formation of infection thread
(IT), for nodule development, and for adaptation and survival of rhizobia under
different environmental conditions (Fischer et al.
2003 ). In rhizobia, surface
6 The Complex Molecular Signaling Network in Microbe–Plant Interaction
184
polysaccharides form a hydrated matrix that contributes to protection against
abiotic factors and plant products secreted as a defense response during the infec-
tion process. Moreover, CPSs may have an active signaling role during benefi cial
infections (Parada et al. 2006 ; Becker et al. 2005 ).
LPSs are anchored to the surface membrane by a lipidic moiety and inserted into the
bacterial phospholipid monolayer, and the saccharidic part is oriented outside. Although
LPS is a constitutive component of the bacterial membrane in Gram- negative bacteria,
it is commonly found in very low concentrations in growth media, being released from
cells in vesicles (Becker et al. 2005 ), and consequently it seems likely that LPSs may
act as long-distance signaling molecules to target cells (Fraysse et al. 2003 ). They play
various roles at different stages of the symbiotic process, act as inhibitors of plant
defense responses, and/or help bacteria to adapt to the endosymbiotic environment.
Experimental evidence demonstrates that root exudates, mainly plant-exuded fl avo-
noids, induce changes in the PGPR-extracellular polysaccharide (EPS, LPS-O antigen,
and CPS) composition, affecting the PGPR–plant interaction (Fischer et al. 2003 ;
Fraysse et al. 2002 , 2003 ; Reuhs et al. 1994 ; Dunn et al. 1992 ).
The importance of bacterial surface polysaccharides during the symbiotic
process has been extensively demonstrated. Azorhizobium caulinodans mutants
with LPS defi ciency (Mathis et al. 2005 ) and LPS with reduced rhamnose content
(Gao et al. 2001 ) established defective interactions with Sesbania rostrata ,
suggesting that both correct LPS amount and composition are required to sustain an
effective rhizobia–legume interaction. In addition, LPS affects competitiveness and
colonization as demonstrated by working with Mesorhizobium loti mutants defec-
tive in LPS and cyclic β-glucans (D’Antuono et al. 2005 ) and LPS mutants of
A . brasilense in maize (Jofre et al. 2004 ), respectively.
EPSs are mostly species-specifi c heteropolysaccharides with an important role
for an effi cient symbiotic process. Bacterial mutants which fail to produce EPS
induce nodules on the roots of the host plant but fail to invade these root nodules.
Rhizobial EPSs are involved in the invasion process, IT formation, bacteroid and
nodule development, and plant defense response and also confer protection to
rhizobia when exposed to environmental stress (Bomfeti et al. 2011 ). EPSs are also
involved in plant colonization and cell aggregation, as widely shown in Azospirillum
species (Bahat-Samet et al. 2004 ; Jofre et al. 2004 ; Fischer et al. 2003 ; Burdman
et al. 2000 ). The data showed that aggregation and root colonization properties of
Azospirillum depend on the concentration and composition of EPS. The infl uence
of EPS during aggregation on rhizospheric soil results in increased water and fertil-
izer availability to inoculated plants (Qurashi and Sabri 2012 ). Some PGPR-EPS
can also bind cations, including Na
+ , suggesting a role in mitigation of salinity
stress by reducing the content of Na
+ available for plant uptake (Upadhyay et al.
2011 ). EPS produced by specifi c rhizobacteria can also elicit plant-induced resis-
tance against biotic stress. For example, inoculation with the EPS-producing
Paenibacillus polymyxa on peanut seeds signifi cantly suppressed crown rot disease
caused by Aspergillus niger (Haggag 2007 ), and the purifi ed EPS from the PGPR
Burkholderia gladioli induced resistance against Colletotrichum orbiculare on
cucumber (Kyungseok et al.
2008 ).
M.A. Morel and S. Castro-Sowinski
185
Among extracellular polysaccharides, the rhizobial lipo-chitooligosaccharide
known as nodulation factor (Nod factor or NF) is the most studied and probably the
“movie star” of rhizobia–legume interaction. NFs have an oligomeric backbone of
β-1,4-linked N -acetyl- d -glucosamine, N-acylated at the nonreducing terminal resi-
due, and trigger the nodule developmental process. Depending on the rhizobial spe-
cies, NFs have different chemical structures (variation in acyl chain, substitutions at
the reducing and nonreducing terminal sugar, and additional decorations) (D’Haeze
and Holsters 2002 ; Geurts and Bisseling 2002 ). Rhizobia perceive plant-secreted
avonoids by binding to NodD, a member of the LysR family of transcriptional
regulators that triggers NF synthesis. NodD binds to conserved DNA sequences,
known as nod boxes, found in the promoter regions of inducible nod genes. NF
synthesis is commanded by the common nodABC genes which encode enzymes
involved in the core structure, and many other nod genes are involved in decora-
tions. Properties and functions of NFs are described throughout the body of the text
of this chapter.
PGPR and Plant Root Attachment
Successful colonization and persistence in the rhizosphere are required for PGPR to
exert their benefi cial effect on plants. Many studies have shown that rhizobacteria
are attracted to seed and root (chemotaxis) by plant-exuded molecules, the “rhizo-
sphere effect” (Bais et al. 2006 ). Plant roots provide a carbon-rich environment and
produce signals that are recognized by microbes which in turn produce others sig-
nals that initiate colonization. What are the most important traits in root–microbe
interaction events? Motility, chemotaxis, and electrotaxis (the ability to use electric
potentials produced at the root surface which act as attractants) enhance competi-
tiveness during root colonization. Many microbe–plant interactions are mediated by
the fl agella which modulate attachment of the microbial cell to the root system. This
process is well known in root colonization by azospirilla. Azospirilla undergo a
biphasic attachment process, with an initial fl agella-dependent adsorption phase,
followed by an irreversible anchoring of the bacterium to the surface, and then the
formation of bacterial aggregates embedded within the fi brillar material (Reis et al.
2011 ; Troch and Vanderleyden 1996 ).
A model described by Genre and Bonfante ( 2007 ) suggests alternative routes to
biotrophy in interactions between plants and PGPR, endophytes, and pathogens,
where precontact signaling contributes to the recognition of rhizobacteria as benefi -
cial or pathogenic. A weak, nonspecifi c, and reversible fi rst contact occurs mediated
by lectins, bacterial surface proteins, CPS, and/or fl agella (Rodriguez-Navarro et al.
2007 ). Then, a direct contact occurs characterized by a rapid translocation of the
cytosolic and subcellular elements to the contact site (localized secretion). In ben-
efi cial interactions, this secretion leads directly to (1) epiphyte–bacterial aggregates
on the plant surface or (2) a preemptive assembly of an intracellular apoplastic
compartment to host the endophyte (Genre and Bonfante
2007 ). In this step,
6 The Complex Molecular Signaling Network in Microbe–Plant Interaction
186
extracellular polysaccharides are the main determinants, required for tight and
irreversible binding of bacteria (Rodriguez-Navarro et al. 2007 ).
In the rhizobia–legume interaction, the endophytes access the root by the ITs, tubu-
lar structures derived from plant plasma membranes that act as “tourist guides” to the
root cortex. The process of rhizobia accommodation into the nodule primordium may
be explained by a sequence of events described by Held et al. ( 2010 ). The extracellular
colonization of roots by rhizobia leads to the uptake of cells through an intracellular
(through root hairs) or intercellular (“crack-entry”) infection (Held et al. 2010 ). The
latter is thought to be the ancestral mechanism of root infection and involves the for-
mation of transcellular ITs within the root cortex (Downie 2010 ). The next section
gives a brief but more detailed description of rhizobia–legume interaction events.
Proteins Involved in Rhizobia–Plant Interaction
Proteomics, the identifi cation of a set of proteins under specifi c conditions, is a
valuable tool to decipher part of the complex network involved in plant and microbe
communication. Most works dealing with plant–microbe exchange of information
through a proteomic approach have been performed on plant tissues after bacterial
inoculation, bacteroids, or nodules. Additional information has also been achieved
by transcriptomic and metabolomic analysis (Stacey et al. 2006 ).
It has been shown that rhizobia inoculation induces or increases the level of
several proteins in soybean root hairs (calcium/calmodulin kinase, lipoxygenases,
phospholipase D, ascorbate peroxidase, phosphoglucomutase, lectin), roots (enzymes
involved in energy, carbohydrate, amino acid, and fl avonoid metabolism), and bacte-
roids (proteins involved in carbon and nitrogen metabolism, stress response and
detoxifi cation, ABC transporters and receptors) (Mathesius 2009 ). In addition, large
amount of information has been generated about the regulation of signal transduction
involved in bacterial infection and nodule organogenesis and long-distance signaling
to control nodule number (Oka-Kira and Kawaguchi 2006 ; Popp and Ott 2011 ).
However, few experiments have analyzed proteins secreted in the rhizosphere or
those that are associated with the bacterial outer membrane. These experiments
involve plant growth in liquid media, protein concentration by lyophilization or pre-
cipitation, desalting, two-dimensional gel electrophoresis, and protein identifi cation
by mass spectrometry (Jayaraman et al. 2012 ). In addition, proteins secreted by bac-
teria or associated with their outer membrane have been found using a classical
approach, by the analysis of culture medium after adding plant-secreted molecules, or
a genomic approach through the study of mutants. Using different approaches, many
proteins secreted to the rhizosphere and involved in plant–microbe communication
have been identifi ed.
Rhizobial proteins are secreted by general secretion (Sec) and two-arginine (Tat)
systems of general use (NodO, adhesins, PlyA and PlyB polysaccharide lyases,
ExoK and ExsH succinoglycan depolymerases, calsymin, cellulose, etc.) and by
specialized secretion systems (Nops or nodulation outer proteins secreted by the
M.A. Morel and S. Castro-Sowinski
187
type III secretion system, Msi059 and Msi061 by the type IV secretion system,
ribose-binding protein-like by the type V and VI secretion systems) (Downie 2010 ;
Deakin and Broughton 2009 ; Tseng et al. 2009 ; Fauvart and Michiels 2008 ). Plant
roots secrete compounds mainly by passive process mediated diffusion, ion chan-
nels, and vesicle transport. But excretion of high-molecular weight compounds by
roots, including proteins, generally involves vesicular transport. Rhizobial cells
secrete adhesins such as rhicadhesin that plays an important role in attachment to
root hairs (Smit et al. 1992 ), hydrolytic proteins such as cellulase that erodes the
noncrystalline cellulose in the root hair cell wall allowing rhizobial penetration
(Robledo et al. 2008 ), and glycanases that cut emerging EPS produced by rhizobia
and are required for biofi lm formation (Russo et al. 2006 ). Many extracellular gly-
canases, involved in nodulation and EPS modifi cation, have been identifi ed and
characterized in rhizobia: PlyA and PlyB of R . leguminosarum bv. viciae and ExoK
and ExsH of S . meliloti . The secreted nodulation-signaling protein NodO was puri-
ed from the supernatant of cultures of R . leguminosarum bv. viciae supplemented
with fl avonoids (Sutton et al. 1994 ). NodO is a calcium-binding protein that forms
cation-selective channels in membranes and may complement NF function by pro-
moting the movement of cations across the root hair membrane (Downie 2010 ).
M . sativa inoculation with S . meliloti caused an increase in the secretion of plant
hydrolases (chitinases that use NFs as substrates, glycosidases, and peptidases),
peroxidase precursors, pathogenesis-related proteins (thaumatin-like protein), lectins,
bacterial superoxide dismutase, glycine betaine-binding ABC transporter, and a
putative outer membrane lipoprotein transmembrane (De la Peña et al. 2008 ).
Rhizobia–Legume Interaction Events
Rhizobia–legume signaling strategies are mainly based on sugars such as the NFs,
EPSs, lipopolysaccharides and capsular polysaccharides, as well as cyclic β-glucans.
However, roots and microorganisms also produce diverse proteins that play a
dynamic role in the process of signaling and recognition that occurs during their
interaction. A picture of events implicated in legume–rhizobia interaction involving
carbohydrates, fl avonoids, phytohormones, and proteins may be summarized as
follows (Fig. 6.1 ).
Plant roots release species-specifi c mixtures of molecules, such as phytohor-
mones and fl avonoids (that act as bacterial attractants), that initiate the symbiotic
chemical dialog. Rhizobial cells recognize fl avonoids by their binding to NodD, an
extracellular membrane protein that works as an environmental sensor and master
transcriptional activator of genes downstream of promoters known as nod boxes.
In response to nod -gene activation, rhizobia produce and release the signaling
molecule NF that is identifi ed by plant root receptor-like kinases (NFR-LKs).
Many NFR-LKs have been identifi ed, e.g., LysM-type RLKs NFR5/NFR1 of
L . japonicus , NFP/LYK3/LYK4 of M . truncatula , SYM10/SYM2 of Pisum
sativum , and NFR5αβ/NFR1β of G . max . After the NFR-LK-ligand recognition,
6 The Complex Molecular Signaling Network in Microbe–Plant Interaction
188
many physiological events are turned on, such as root hair deformation and IT
initiation, depolarization of the plasma membrane, rhizosphere alkalinization, Ca
spiking by a calcium-dependent calmodulin kinase (CCaMK), cytoskeletal rear-
rangement, early nodulin gene expression, and fi nally nodule formation.
In addition to NF, some rhizobia secrete proteins involved in host specifi city and
symbiotic effi ciency by a type III secretion system or T3SS. T3SS delivers viru-
lence proteins called effectors directly into the host cells. Rhizobial effector proteins
are known as Nops (nodulation outer proteins). Rhizobial NopL and NopP interfere
with plant signaling pathways acting as positive effectors that enhance nodule
formation. These and other Nops effectors might contribute to suppression of plant
innate immune response or modulate cytoskeletal rearrangements in root cells dur-
ing nodule formation. Thus, rhizobial effectors could facilitate bacterial release
from IT, initiate symbiosis, and/or promote or maintain persistence of bacteroids
(Saeki 2011 ; Deakin and Broughton 2009 ).
The invading bacteria move through the IT and are taken into the plant cell by a
type of endocytosis in which they are surrounded by a plant-derived peribacteroid
membrane. Nodule organogenesis, cell proliferation and dedifferentiation, and bac-
teroid differentiation are driven by plant hormones and systemic signaling peptides
(ENOD40, CLE, NCR) (Ding et al. 2008 ; Batut et al. 2011 ). Ethylene, jasmonic
Fig. 6.1 Overview of rhizobia–legume interaction events. ( a ) Induction of nod genes by root-
exuded fl avonoids and NF production; ( b ) NF perception by NFR-LK elicits calcium signaling that
leads to localized CK biosynthesis. CK induces the ENOD40 production and downstream signal-
ing for activation of symbiotic response and nodule organogenesis; ( c ) deformation of root hair and
formation of IT. Bacteria move through the IT; ( d ) rhizobia penetrate cortical cells via IT. They are
released from unwalled IT into the host cell cytoplasm as membrane-delimited symbiosome into
bacteroids; ( e ) CLE peptide synthesis in the nodule and recognition by shoot-specifi c receptor
kinase (LRR-RLK). Production of shoot-derived inhibitor ( SDI ) that regulates nodule number
( AON ); ( f ) indeterminated nodule produces NCRs that induce bacteroid differentiation
M.A. Morel and S. Castro-Sowinski
189
acid, and abscisic acid (ABA) regulate NF signaling and affect the nature of
NF-induced calcium spiking, with ABA being capable of coordinating regulation of
diverse development pathways associated with nodule formation (Ding et al. 2008 ).
CLE (CLAVATA3/endosperm surrounding region) are peptides that have been
identifi ed in a wide variety of plants. They are key molecules in the regulation of
nodulation acting as a root-derived ascending signal to the shoot. This peptide is
probably recognized as a ligand for a leucine-rich repeat (LRR) autoregulation
receptor kinase that controls multiple aspects of shoot development, jasmonate sig-
naling, and the production of a shoot-derived inhibitor (produced in leaves) that
regulates root nodule number. These LRR receptor kinases (GmNARK, Glycine
max nodule autoregulation receptor kinase of soybean; HAR1, hypernodulation and
aberrant root of Lotus japonicus ; SYM29, symbiosis of pea; and SUNN, super
numeric nodules of alfalfa) are key regulators of the autoregulation of nodulation
(AON) signaling pathway that controls a hypernodulated unproductive phenotype
(Staehelin et al. 2011 ; Popp and Ott 2011 ; Miyazawa et al. 2010 ; Kinkema and
Gresshoff 2008 ; Oka-Kira and Kawaguchi 2006 ). AON is the major pathway that
controls nodulation events acting through the inhibition of nodule development in a
long-distance signaling fashion between root and shoot. NF is also involved in the
expression of several early nodulin (ENOD) genes (ENOD12 y ENOD40).
It has been suggested that CK is an epidermal cell synthesized secondary signal,
which after translocation to cortex cells triggers the initiation of nodule primordial
ahead of the upcoming IT (see section “ Phytohormones Production ”). CK induces
the expression of the enod40 gene serving as an amplifi cation mechanism, thus trig-
gering a localized hormone imbalance, a state that initiates cell divisions in the root
cortex (Fang and Hirsch 1998 ). The enod40 gene codes for two short conserved
peptides, A and B, which strongly bind the cytosolic sucrose synthase (SuSy)
enzyme-stimulating sucrose breakdown activity. The data support the view that
Enod40 peptide may participate in phloem uploading, increasing the carbon sink
strength in pre-dividing root cortical cells and in mature nodule tissues (Batut et al.
2011 ). CK induces the expression of the Nin transcriptional regulator within the
root cortex through the activation of the LHK1 cytokinin receptor, subjected to
HAR1-mediated autoregulation (Heckmann et al. 2011 ).
Some legumes such as Medicago , Pisum , Vicia , and Trifolium maintain active
apical meristems that produce indeterminate nodules. This type of nodule under-
goes an irreversible differentiation mediated by nodule-specifi c cysteine-rich (NCR)
peptides. NCRs are produced by the host cells and targeted to bacteroids where they
interfere with the rhizobial cell cycle affecting terminal bacterial differentiation. In
addition, NCRs resemble antimicrobial peptides (Batut et al. 2011 ; Van de Velde
et al. 2010 ). Findings suggest that after the root epidermal cell recognition of NF,
several kinase receptors are activated, working as a signal transduction cascade
responsible for the control and progression of IT, nodule organogenesis, and nitro-
gen fi xation (activation of downstream common nod and sym genes). These kinase
receptors are regulated by E3-ubiquitin ligases that act as dynamic modulators of
cellular reprogramming during rhizobial infections (Popp and Ott
2011 ; Mathesius
2009 ). Hundreds of proteins from nodule, xylem, root, and shoot have been
6 The Complex Molecular Signaling Network in Microbe–Plant Interaction
190
implicated in rhizobia–legume interaction (Mathesius 2009 ), but insuffi cient work
has been done on proteins secreted in the soil by roots and bacteria during microbe–
plant interaction.
A large variety of regulatory molecules, including kinases, transcriptional factors,
and other regulatory molecules, are involved in symbiotic nodule organogenesis,
and recent reports showed that sRNAs, especially microRNAs (miRNAs), are also
key regulatory factors of this process. Thus, miRNAs are emerging as riboregulators
that control gene networks in plant cells through interactions with specifi c target
mRNAs. Only a few nodulation-responsive miRNAs have been linked to nodule
formation: among other miRNAs, miR169 and miR166 overexpression in M . trun-
catula led to lower densities of lateral roots and nodules, and they might be respon-
sible for nodule meristematic zone regulation during nodule differentiation into
nitrogen-fi xing cells; soybean miR482 targets the resistance gene receptor kinase
involved in the defense response, playing a role during nodule initiation; miR1511
and miR1512 target transcripts encoding signaling proteins, including a calmodu-
lin-binding protein (Bazin et al. 2012 ; Khan et al. 2011 ; Voinnet 2008 ). In addition,
there is strong evidence that there is a connection between miRNA regulation and
hormone response. Some miRNAs facilitate hormone-induced responses, e.g., the
miRNAs miR160, 167, and 393 that are implicated in the regulation of auxin signal-
ing target transcripts to reduce lateral root production and are potentially involved
in nodulation (Simon et al. 2009 ; Bazin et al. 2012 ).
Concluding Remarks
Compounds exuded by plants and microbes provide a cocktail of molecules (carbo-
hydrates, phytohormones, fl avonoids, amino acids, and proteins) that constitute the
words of a chemical dialog between plants and microbes in the rhizosphere
(Fig. 6.2 ). The massive variety of metabolites released by plants suggests that they
provide a specifi c language for communication. Researchers are deciphering the
content and signifi cance of the cells’ signaling and responses. Recent advances in
analytical skills and biochemical and molecular approaches have provided new
tools for evaluating the natural roles of these substances and for investigating the
mechanisms underlying their regulation.
In brief, the picture of microbe–plant interaction events involves a huge number
of molecules that span our imagination. Every year a new signaling molecule is
found, and the overall scene is getting much bigger and more complex. The new
information on proteins involved in two-component signal transduction systems
that allow sensing and responding to different stimuli, transcriptional regulators,
and plant-derived peptides is far from completing the picture of the microbe–plant
interaction. In this chapter, only some recent and relevant earlier information related
to molecules involved in microbe–plant interaction have been used to present a
partial panorama.
M.A. Morel and S. Castro-Sowinski
191
Acknowledgements We thank Programa de Desarrollo de las Ciencias Básicas (PEDECIBA).
The work of M. Morel was supported by Agencia Nacional de Investigación e Innovación (ANII).
Dr. Valerie Dee revised linguistic aspects of this manuscript.
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6 The Complex Molecular Signaling Network in Microbe–Plant Interaction
... The rhizobia-Delftia co-inoculation of leguminous plants improves the agronomic expectations compared with a single-rhizobial inoculation, mainly because Delftia strains produce auxins (indole-3-acetic acid, IAA) and induce the secretion of plant flavonoids (Morel et al. 2015;Cagide et al. 2018). While IAA promotes the development of the root system, flavonoids are fundamental for the establishment of the nitrogen-fixing symbiosis between nodulating rhizobia and leguminous roots (Morel and Castro-sowinski 2013). As a consequence, we detected an increase in total nitrogen and the content of ureides in co-inoculated soybean plants, including an important beneficial effect on the main productive parameter of soybean, the grain yield (Cagide et al. 2018). ...
... Briefly, the events taking place during the rhizobial-plant interaction are: plant secretion of flavonoids; rhizobial recognition of flavonoids and induction of nod genes (production and secretion of the Nodulation Factor; NF); plant recognition of NF molecules followed by the induction of the symbiotic response and nodule organogenesis; deformation of root hair and formation of the infection thread (IT); rhizobial invasion through the IT towards the cortical cells; release of rhizobial cells (differentiated into bacteroids) to the host cell cytoplasm; formation of the membrane-delimited symbiosome containing bacteroids; and nitrogen fixation (Morel and Castro-Sowinski 2013). The symbiotic nodule is the plant organ that contains the symbiosomes formed by bacteroids (nitrogen-fixing rhizobia), the peribacteroid membrane (of plant origin, and some proteins synthesized by the bacteroids), and the peribacteroid space (Tsyganova et al. 2017). ...
... Genistein also induces the chemotaxis towards the plant in both microbes, Bradyrhizobium and Delftia strains (v). On the left side of the figure -The NF induces the formation of root nodules, where the bradyrhizobial cells differentiate into bacteroids with the establishment of the symbiosome (Morel and Castro-Sowinski 2013). As a consequence of rhizoplane colonization by JD2 cells (epiphytic behavior) (Morel et al. 2015), the soybean symbiosomes have an upregulation of proteins involved in stress tolerance and, iron storage and homeostasis (see Table 2). ...
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The effect of plant-produced flavonoids in rhizobial cells is well-known, and flavonoids are considered the first signals in the rhizobia-plant communication. We previously reported that Delftia strains increase the performance (nodulation and nitrogen fixation) of leguminous plants in co-inoculation experiments, as compared with the single rhizobial inoculation. By using an approach based on quantitative shotgun proteomics, we explored the response of Delftia sp. JD2 cells to the presence of the flavonoid genistein (nod gene-inducer of Bradyrhizobium cells). We found that genistein up-regulates the production of regulatory proteins associated with the epiphytic habit (TetR and diguanylate cyclase), proteins involved in the formation of flagella, iron acquisition, resistance to several drugs, the rhizoplane colonization (biofilm establishment), and the rearrangement of the peptidoglycan structure and membrane proteins. These results indicate that genistein induces chemotaxis, mobility and prepares JD2 strain for an epiphytic lifestyle. We also analyzed the effect of the co-inoculation on the proteome of symbiosome-enriched fractions from soybean nodules. The fractions from co-inoculated plants showed an up-regulation of proteins involved in stress endurance (“stem 31 kDa glycoprotein”, “Kunitz trypsin protease inhibitor”, proteasome subunits) and ferritin (involved in iron storage and homeostasis), suggesting that co-inoculation with JD2 prepares the soybean plants to deal with unfriendly environmental conditions. In summary, the plant-secreted genistein functions as a chemical signal in the communications between soybean plants and Delftia sp. JD2, while the presence of JD2 would prepare the plant to cope with abiotic stresses in co-inoculation experiments.
... The establishment of the symbiotic process between rhizobia and legumes is precisely and highly regulated, where chemical signals are exchanged between both symbionts and trigger cellular and molecular responses with consequences at the physiological level (Morel and Castro-sowinski 2013). Flavonoid exudation by the legumes' roots towards the rhizosphere is one of the first signals exchanged between the symbionts (Badri and Vivanco 2009). ...
... These compounds represent a potential source of carbon, and they act as strong chemoattractants and screening bacteria by the ability to degrade them (Chan 1986;Seneviratne and Jayasinghearachchi 2003). In legumerhizobia symbiosis, flavonoids also play a vital role inducing the expression of rhizobial nod genes, affecting the production of the Nod Factor and, subsequently, inducing the nodule formation (Shaw et al. 2006;Morel and Castro-sowinski 2013). Interestingly, we recently reported that genistein upregulates proteins from JD2 cells involved in chemotaxis (Riviezzi et al. 2021). ...
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Delftia sp. strain JD2 is a soil bacterium that produces auxins and acts as a nodulation-assisting bacterium in legumes inoculated with rhizobia. The co-inoculation of soybean (Glycine max) seeds with Bradyrhizobium elkanii and JD2 enhances plant growth, nitrogen fixation, and grain yield. This work aimed to characterize bioactive compounds in soybean plants under different inoculation treatments. Metabolomic profiling by Ultra-High-Performance Liquid Chromatography coupled with High-Resolution Mass Spectrometry (UHPLC-HRMS) was carried out on freeze-dried rhizospheric exudates and root extracts from hydroponic or greenhouse plants experiments, respectively. The differential metabolomic profiling between treatments was analyzed by pair-wise comparisons. Statistical results showed that both root and rhizospheric samples clustered according to the inoculation treatment and the sampling time of plants. This classification derives from the different production of cinnamic acids, coumarins, benzoic acids, and flavonoids, among other discriminant compounds between treatments. We observed the over-production of nod genes inducers in roots from plants inoculated with JD2. In contrast, a reduction in the discriminant flavonoids occurred in co-inoculated plants. JD2 positively influences the production of auxins. These changes in the composition of flavonoids and auxins are likely to explain the differences observed in the growth and nodulation of co-inoculated plants. This study emphasizes some metabolic changes that positively affect the co-inoculation of soybean seeds with bradyrhizobia and JD2.
... Second, plants and soil microbes compete for amino acids because their metabolism and growth require adequate N [24,25,[28][29][30]; on the other hand, plants and microbes can benefit from each other through substance (e.g., carbohydrate and phosphorus) exchange [26,27,31]. Additionally, plants exhibit versatile strategies to cope with changes in amino acids and microbes [24,32,33]. Therefore, it might be valuable to consider plants, soil microbes, and amino acids together. ...
... In this experiment, two Solidago species grew well on amino acids in the absence of AMF (Fig. 1a), not supporting the traditional notion that plant species are unable to grow on organic N without their mycorrhizal symbiont [10] but being consistent with our previous finding [14]. Overall, the AMF-enhanced amino acid effects might be partly attributable to complex networks among plants, AMF, and amino acids [16,32,33,50]. Amino acid N sources enabled invasive Solidago to grow larger than native Solidago, regardless of inoculation (Fig. 1). ...
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Arbuscular mycorrhizal fungi (AMF) and soil amino acids both affect plant performance. However, little is known about how AMF compete for amino acids with native and invasive congeners. We conducted a factorial experiment (inoculation, native and invasive species, and amino acids) to examine the competition for amino acids between soil microbes and both native and invasive congeners. The competition for amino acids between AMF and invasive Solidago canadensis was weaker than that observed between AMF and native S. decurrens. This asymmetric competition increased the growth advantage of S. canadensis over S. decurrens. The efficacy (biomass production per unit of nitrogen supply) of amino acids compared to ammonium was smaller in S. canadensis than in S. decurrens when both species were grown without inoculation, but the opposite was the case when both species were grown with AMF. AMF and all microbes differentially altered four phenotypic traits (plant height, leaf chlorophyll content, leaf number, and root biomass allocation) and the pathways determining the effects of amino acids on growth advantages. These findings suggest that AMF could enhance plant invasiveness through asymmetric competition for amino acids and that amino acid-driven invasiveness might be differentially regulated by different microbial guilds.
... The composition of this microfauna is influenced by deposition of mucilaginous substances and root exudates (Kent and Triplett 2002). Root exudates not only govern the composition of phytomicrobiome but also determine the physical and chemical properties of soil, prevent herbivory and alleviate symbiotic associations (Ping and Boland 2004;Badri et al. 2009;Morel and Castro-Sowinski 2013). Interestingly, Bhatt et al. (2020) observed that the microbiome composition of a plant species remains same even if it is grown in diverse soil conditions. ...
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Harnessing the phytomicrobiome offers a great opportunity to improve plant productivity and quality of food. In the recent past, several phytomicrobiome microbes have been explored for their potential involvement in increasing crop yield. This review strategically targets to harness the various dimensions of phytomicrobiome for biotic stress management of crop plants. The tripartite interaction involving plant-microbiome-pathogen has been discussed. Positive interventions in this system so as to achieve disease tolerant plants has been forayed upon. The different signalling molecules sent out by interacting partners of phytomicrobiome have also been analysed. The novel concept of artificial microbial consortium in mitigation of pathogenic stress has also been touched upon. The aim of this review is to explore the hidden potential of phytomicrobiome diversity as a potent tool against phytopathogens, thereby improving crop health and productivity in a sustainable way.
... But the mobile DNA elements, phages, and the transfer of genes horizontally make the microbial genomes highly dynamic and are difficult to characterize also (Darmon and Leach, 2014). The major goals of the desired microbiome in the rhizosphere are to benefit from the microbial associations that facilitate nutrient acquisition and uptake, promote plant growth and development, inhibit, or suppress pathogenic organisms and other competing plant species, and alter the physico-chemical properties for the common good (Morel and Castro-Sowinski, 2013). ...
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Pesticides are becoming a significant transnational pollutant in agricultural production environments. This review presents the interconnectedness and interaction effects of pesticides with the microbiomes in the environments of plant rhizosphere and animal (limited to insect and human) guts. The metabolic growth and functions of rhizosphere microbiomes are altered by complex mechanisms involving redox reactions and preferential substrate utilization. The rhizospheres of crop plants with the assemblies of microbiota and other biotic components are sensitive to the deliberate introduction of pesticides. Pesticides become one of the major drivers for the metabolic processes, which rely on the evolutionary mechanisms, including the genetic exchange events within the rhizosphere microbiomes. Pesticides, even at the below detection levels, in the rhizosphere enable the plant uptake which can be up to 1% of the dose applied and trophic transfers involving the animal gut environments. To overcome the metabolic constraints due to the nutrient-poor plant diets contaminated with pesticides, insects gain the resistance traits, mainly due to the pesticide-degrading members of the gut microbiomes. Such evolved microbiome members and their genes can increase their spread of resistance in the environment. Like the insect gut microbiomes, the human gut microbiomes get modulated by the pesticide-laden plant foods, leading to dysbiosis. The confounding effects of pesticides on the gut microbiomes which include mutational and genetic exchange events can upsurge many health disorders. The evolutionary and microbiome perspectives on the rhizosphere and animal guts as the hotspots of metabolic and horizontal gene transfer (HGT) events need careful considerations to mitigate the risks and health hazards due to extensive and intensive application of synthetic chemical pesticides in the modern agriculture.
... Diazotrophs convert environmental nitrogen to alkali. Certain diazotrophs and different PGPBs (Pseudomonas and Bacillus) likewise yield phytohormones, siderophores, and phosphate-solubilizing atoms, among different edifices (Morel and Castro-Sowinski 2013). Added substances and metabolites assume crucial jobs in making bioformulations progressively solid and powerful. ...
Chapter
A growing worldwide population, urbanization and industrialization are expanding the pace of transformation of arable land into no-man’s land. Providing food to an ever-expanding populace is perhaps the greatest test that agriculturalists and plant researchers are now facing. Ecological anxieties make this circumstance much graver. In spite of the enlistment of a few resilience components, touchy plants regularly neglect to make due under natural limits. New mechanical methodologies are basic. Customary rearing techniques have a restricted potential to improve plant genomes against ecological pressure. As of late, hereditary building has contributed hugely to the advancement of hereditarily altered assortments of various harvests, for example, cotton, maize, rice, canola and soybean. The distinguishing proof of pressure responsive qualities and their resulting introgression or overexpression inside delicate yield species is presently being broadly done by plant researchers. The design of significant resilience pathways, similar to cell reinforcement chemicals, osmolyte amassing, layer limited transporters for effective compartmentation of harmful particles and aggregation of fundamental components and opposition against irritations or microorganisms is additionally a territory that has been seriously investigated. In this chapter, the role of microbial biotechnology for mitigation of heat stress in plants are discussed.
... Flavonoids, coumarins (phytoalexins), benzoxazinoids, strigolactones, terpenoids, malic acid, camalexin, and ethylene are important chemical mediators in the beneficial plant-microbe interaction (Stringlis et al., 2019). The plant exudates are either actively produced or elicited when exposed to certain threats and environmental conditions (Morel and Castro-Sowinski, 2013). These rhizodeposits generate quorum sensing response in microbial communities and also secrete various signaling compounds such as antibiotics, volatile molecules, phytohormones, organic acids, amino acids, sugars, and surface receptors (pattern-recognition receptors) (Zhang et al., 2015;Arif et al., 2020). ...
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