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Soil Microbe Diversity and Root Exudates as Important Aspects of Rhizosphere Ecosystem

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Rhisosphere an area of soil surrounding plant roots in which soil’s most reactions takes place. The Rhizosphere word was given by Lorenz Hiltner and it is 1-2 mm wide. Rhizosphere is divided into three zones- endorhizosphere, rhizoplane and ectorhizosphere. The two dynamic properties of soil rhizosphere are root exudates and soil microbes. Root exudates are the chemical compounds that are secreted by roots and act as a source of food for soil microbes and play a pivotal role in soil microbe and plant interaction. These are low and high molecular weight compounds. The root exudates are important for root microbe and root-root communication. The other important aspect of rhizosphere is soil microbes. The soil microbes include bacteria, fungi and actinomycetes. These orgainisms are important for both soil and fungi. The main aspect of this chapter is to give brief information about the underground world and its future perspective is to understand soil microbe and plant interaction for enhancing sustainable agriculture. Studies on gene expression in the rhizosphere and the use of other molecular techniques like m-RNA, Proteomics, labelled root compounds, stable isotope probes and reporter technology will help in exploring underground undiscovered world.
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337
Soil Microbe Diversity and Root Exudates
as Important Aspects of Rhizosphere
Ecosystem
Owais Bashir , Kamran Khan , Khalid Rehman Hakeem , Naseer Ahmed Mir ,
Gh Hassan Rather , and Rehana Mohiuddin
O. Bashir
Division of Soil Sciences , Sher-e-Kashmir University of Agricultural Sciences and
Technology of Kashmir , Srinagar 190025 , India
K. Khan
Division of Plant Pathology , Sher-e-Kashmir University of Agricultural Sciences and
Technology of Kashmir , Srinagar 190025 , India
K. R. Hakeem (*)
Faculty of Forestry , Universiti Putra Malaysia , Serdang , 43400 Selangor , Malaysia
e-mail: kur.hakeem@gmail.com
N. A. Mir
Faculty of Forestry , Sher-e-Kashmir University of Agriculture Science and Technology
of Kashmir , Srinagar , India
G. H. Rather
Division of Fruit Sciences , Sher-e-Kashmir University of Agricultural Sciences
and Technology of Kashmir , Srinagar 190025 , India
R. Mohiuddin
Division of Agronomy , Sher-e-Kashmir University of Agricultural Sciences and Technology
of Kashmir , Srinagar 190025 , India
Abstract The rhizosphere is an area of soil surrounding plant roots in which soil’s
most reactions take place. The term “rhizosphere” was coined by Lorenz Hiltner, and
it is 1–2 mm wide. The rhizosphere is divided into three zones: endorhizosphere, rhi-
zoplane, and ectorhizosphere. The two dynamic properties of soil rhizosphere are root
exudates and soil microbes. Root exudates are the chemical compounds that are
secreted by roots and act as a source of food for soil microbes and play a pivotal role
in soil microbe and plant interaction. These are low- and high-molecular-weight com-
pounds. The root exudates are important for root- microbe and root-root communica-
tion. The other important aspect of rhizosphere is soil microbes. The soil microbes
include bacteria, fungi, and actinomycetes. These organisms are important for both
soil and fungi. The main aspect of this chapter is to give brief information about the
underground world, and its future perspective is to understand soil microbe and plant
interaction for enhancing sustainable agriculture. Studies on gene expression in the
© Springer International Publishing Switzerland 2016
K.R. Hakeem, M.S. Akhtar (eds.), Plant, Soil and Microbes,
DOI 10.1007/978-3-319-29573-2_15
338
rhizosphere and the use of other molecular techniques like m-RNA, proteomics,
labeled root compounds, stable isotope probes, and reporter technology will help in
exploring underground undiscovered world.
Keywords Rhizosphere Roots Exudates Soil microbes Allelochemicals
Ecosystem
1 Introduction
The rhizosphere is the area of soil roots where most of the reactions are affected by
plant roots. The rhizosphere is about 1–2 mm wide with no distinct boundaries
(Brimecombe et al. 2007 ). Lorenz Hiltner is a German scientist who coined the term
“rhizosphere” to explain plant root association. At Munich in 2004, a meeting was
organized in his memory. The term rhizosphere is from the Greek words “ rhiza
which means root and “ sphere ” which means fi eld or area of infl uence (Hartmann
et al. 2008 ). The rhizosphere is broadly classifi ed into the following three zones,
viz., endorhizosphere, rhizoplane, ectorhizosphere (Clark 1949 ; Lynch 1987 ; Pinton
et al. 2001a ). The endorhizosphere consists of root tissues including cortical cells
and the endodermis. Rhizoplane is the area of root surface where soil microbes and
soil particles interact. It comprises of the cortex, epidermis, and mucilage. The third
zone is ectorhizosphere which is formed from soil particles adjacent to roots. In
addition to these three fundamental zones, few other layers are also found which
include the mycorrhizosphere, rhizosheath, and bulk soil (Linderman 1988 ; Curl
and Truelove 1986 ; Gobat et al. 2004 ). Mycorrhizosphere is the mycorrhizal asso-
ciation of plants. Rhizosheath is the strongly adhering dense layer and consists of
root hairs, mucoid layer, soil particles, and soil microbes. Bulk soil is the portion of
soil which is not the component of rhizosphere (Brundrett 2009 ; Lambers et al.
2008 ) (Figs. 1 and 2 ).
The rhizosphere is called the hot spot of soil microbes (Brimecombe et al. 2007 ).
In Kashmiri Language, we may call rhizosphere as Wazwan point for soil microbes.
The rhizosphere is also called as human gut microbiome for plants (Mendes et al.
2011 ). Rhizosphere is considered as the spot where soil genesis actually starts (Pate
et al. 2001 ). To soil microorganisms, rhizosphere is the lush oasis in the desert.
Because it is underground, rhizosphere is considered as the last frontier in agricul-
ture. Soil microbial community also has greater reservoir of biological diversity in
the world (Curtis et al. 2002 ; Chaparro et al. 2013 ; Philippot et al. 2013 ; Buée et al.
2009 ). The rhizosphere soil contains up to 10
11 microbial cells/g (Egamberdiyeva
et al. 2008 ) and over 30,000 prokaryotic species. The combined genome of the rhi-
zosphere is greater than that of plant and thus is called plants’ second genome (Bron
et al. 2012 ). The eelworms are being used to quantify the extent of rhizosphere
because they are highly in peculiar in reacting to chemicals exudated by plant roots
(Bolton et al. 1992 ) (Table 1 ).
O. Bashir et al.
339
Fig. 1 Ectorhizosphere of the soil root ecosystem
Fig. 2 The endorhizosphere and its different components
Soil Microbe Diversity and Root Exudates as Important Aspects of Rhizosphere…
340
Table 1 Similarity between the human gut and rhizosphere
Characters Human gut Rhizosphere References
Important for nutrient uptake Microbes help in the breakdown of food and generate
essential nutrients, such as vitamins B and D. In
reward, microbes of the human gut get the carbon
source from mucin
Soil bacteria, fungi, and actinomycetes assist
plants to the uptake of nitrogen, phosphorus,
potassium, and other important nutrients for their
growth. The microbes also help in genesis and
formation of minerals and degradation of organic
matter. The root exudates and other rhizodeposits
provide the energy source of soil microbes
Bais et al.
(
2006 ), VanDer
et al. (
2008 ),
Derrien et al.
(
2010 ),
Fagundes et al.
(
2012 )
Restricts colonization of
pathogens Certain interactions of benefi cial microorganisms
include nutrient competition, inhibitory protein
production, alteration of receptor sites, and
modifi cation of toxins
Certain soil benefi cial microorganisms suppress
plant pathogens by certain interactions like
nutrient competition, antibiotic and lytic
enzyme production, and consumption of
pathogen stimulatory compounds
Lugtenberg and
Kamilova
(
2009 ),
Doornbos et al.
(
2012 ),
Fagundes et al.
(
2012 )
Modulate host immunity The microbes stimulate host innate immunity system
that not only affect intestinal mucosa but also produce
immune responses in the respiratory tract. Also the
development of microfl ora in the gut of humans during
rst year of life is very important for the development
of the immune system
The rhizobacteria suppress diseases and
systemically boost defense system of plants.
The rhizobacteria trigger plant resistance to the
pathogens. Most important chemicals are
jasmonates
Bron et al.
(
2012 ), Ent et al.
(
2009 ),
Fagundes et al.
(
2012 ), Ichinohe
et al. (
2011 )
O. Bashir et al.
341
Characters Human gut Rhizosphere References
Distinguish friend from foe Pathogens and symbionts have similar molecular
patterns which are perceived by immune system, but
the mechanism of immune system response is still
unknown. Many mechanisms are present to prevent
stimulation of immune system like physical barrier of
mucous and reduced pathogen receptors in epithelial
cells. Regulatory T cells suppress immune response
of commensal gut microbes
Pathogens and symbionts have similar
molecular patterns but are recognized by the
immune system which is still unknown and thus
differentiates friend from foe. Both pathogens
and benefi cial soil microorganisms suppress
plant immune system and promote their own
colonization through secretion of effector
molecules
Chinen and
Rudensky
(
2012 ), Lathrop
et al. (
2011 ),
Zamioudis and
Pieterse (
2012 )
Microbiome density and
diversity Microbial diversity is very high in the human gut
ranging from 10
11 to 10
12 cells per ml of intestinal
uid, but its phylogenetic diversity is very low having
only 7 of 55 described bacterial phyla which mostly
include fi rmicutes and bacteroides. It is seen that
more than 500–1000 sp. of bacteria exist in the
human gut. There occurs stratifi ed type of microbial
variation and certain category of another community
known as enterotypes
The rhizosphere microbial density is higher
than bulk soil, and it ranges from 10
8 to 10
9
cells/g. These microbial communities are
considered most diverse communities in the
world with 10
4 bacterial sps./g of soil.
Rhizosphere microbes vary between plant
species if grown in same soil
Weinert et al.
(
2011 ),
Arumugam et al.
(
2011 ), Roesch
et al. (
2007 ),
Weller et al.
(
2002 )
Soil Microbe Diversity and Root Exudates as Important Aspects of Rhizosphere…
342
2 The Dynamic Properties of Rhizosphere Are Root
Exudates and Soil Microbes
2.1 Root Exudates
The knowledge of roots and its biology, biochemistry, and genetic evolution
has considerably increased during the last few years, but the certain processes
occurring in the rhizosphere by the roots such as root exudates and root border
cells are still unknown (Benfey and Scheres 2000 ; Hawes et al. 2000 ). The
plant roots provide mechanical anchorage to the plants and assist in water and
mineral nutrient uptake. Some special functions including synthesizes, secre-
tion, and accumulation of diverse group of chemical compounds are also per-
formed by the plant roots (Flores et al. 1999 ). These compounds exudated by
the plant roots play a pivotal function as chemical attractants in the soil root
ecosystem (Estabrook and Yoder 1998 ; Bais et al. 2001 ). These chemical com-
pounds are referred as root exudates. A diverse group of these chemical com-
pounds have been found exudating from intact and healthy roots. These
compounds include sugars, amino acids, peptides, vitamins, nucleotides,
organic acids, enzymes, fungal stimulants, and inhabitants and also some
other compounds which help in plant water uptake, plant defense, and stimu-
lation (Pate et al. 2001 ; Pate and Verboom 2009 ; Taylor et al. 2009 ). Sugars,
organic acids, coumarins, lipids, flavonoids, enzymes, amino acids, proteins,
aliphatics, and aromatics are examples of primary substance found within the
roots (Shukla et al. 2011 ). Among these, the organic acids are of considerable
importance because of its role in providing substrate for microorganisms and
also acting as intermediate in biological and chemical reactions in the soil
(Philippe 2006 ; Wutzler and Reichstein 2013 ). The ability of plant roots to
produce a wide range of chemical compounds is the most striking feature of
plant roots with nearly 5–21 % of all photosynthetically fixed carbon being
transferred to rhizosphere through root exudation (Marschner 1995 ). These
root exudates are being classified as low-molecular-weight compounds and
high-molecular-weight compounds. Sugars, amino acids, phenols, organic
acids, and various other secondary metabolites are included in low- molecular-
weight compounds, whereas mucilage and proteins are included in high-
molecular- weight compounds (walker et al. 2003 ). These root exudates are
relatively important in mediating the communication of plants with soil
microbes (Bais et al. 2004 ; 2006 ; Weir et al. 2004 ; Broeckling et al. 2008 ).
Root exudation is an important element of rhizodeposition and is a primary
source of soil organic carbon released by the roots (Hutsch et al. 2000 ; Nguyen
2003 ). Whipps and Lynch ( 1985 ) first coined the term rhizodeposition as
materials lost from roots, which include lysates, insoluble exudates, soluble
material, and certain gases like carbon dioxide and ethylene.
O. Bashir et al.
343
2.1.1 Interaction Studies of Root Exudates
Another important function of root exudates is that it acts as a messenger that
initiates and intimates physical and biological communication between the soil
microbes and plant roots. Root-mediated rhizospheric communication is grouped
into two categories: negative and positive interactions (Weller et al. 2002 ; Mendes
et al. 2011 ; Elsas et al. 2012 ). Positive interactions involve communication of
plant roots with certain plant growth-promoting rhizobacteria (PGPR). These
plant roots produce certain chemicals that act as signals and attract certain
microbes and stimulate chemotaxis (Thimmaraju et al. 2008 ). Positive interac-
tions of root exudates also include growth enhancers that enhance growth of
neighboring plants and help in cross-species signaling. The negative interaction of
root exudates includes secretion of insecticidal and nematicidal compounds, phy-
totoxins, and secretion of antibiotics (Bais et al. 2006 ).
Root Rhizosphere Communication
Performance of plant species depends upon its ability to recognize and receive
changes in environment and to respond to these changes for acclimatization. These
changes are very important for growth and development of plants and microbes
(Chaparro et al. 2014 ). Root exudate is a major food source of soil microbes that
communicate with the plants and is considered most diverse ecosystem on earth
(Vogel et al. 2009 ). These interactions of soil microorganisms and plant roots are
categorized into root-root communication and root-microbe communication.
Root-Root Communication
When roots communicate with neighboring roots of other plant species, they pre-
vent their invadence by release of certain chemical messengers (Ahmed et al. 2007 ).
Allelopathy is the phenomena which involve benefi cial, harmful, direct, and indirect
effect on plants through secretion of secondary metabolites (Li et al. 2010 ).
Allelopathy is known for more than 2000 years with respect to plant interference
(Callaway and Aschehoug 2000 ; Ridenour and Callaway 2001 ; Weston and Duke
2003 ). Allelopathy also has importance in agriculture, because the allelochemicals
produced by the plants control weed population (Haribal and Enwick 1998 ). The
most important allelochemicals in the plant ecosystem include phenolic compounds.
Phenols are the chemical compounds having a hydroxyl group (−OH) attached to an
aromatic hydrocarbon group (Zeng et al. 2008 ). Phenolic compounds which play an
important role in allelopathy are produced from pentose phosphate pathway. 4-
Phosphate erythrose and phosphoenolpyruvic acid undergo certain condensation
reaction with sedoheptulose 7-phosphate and generate phenolic compounds. There
occurs a series of reactions in shikimic and acetic acid metabolic pathway. The
phenolic allelochemicals have adverse impact on the photosynthesis and respiration
Soil Microbe Diversity and Root Exudates as Important Aspects of Rhizosphere…
344
of other plant species by weakening their oxygen absorption capacity and by reduc-
ing their photosynthetic rate by reducing chlorophyll content. Patterson ( 1981 )
reported that 10–30 μmol/l caffeic acid, ferulic acid, vanillic acid, coumaric acid,
and cinnamic acid could considerably reduce growth of soybean. Bais et al. ( 2002 )
reported (+) catechin and (−) catechin as root phytotoxin. + catechin was produced
invasive behavior of knapwood and (−) catechin was inhibitory to the soilborne
bacteria. It has also been seen that certain allelochemicals released by the host roots
stimulate haustoria formation (Estabrook and Yoder 1998 ; Yoder 2001 ).
Allelochemicals produced by the black walnut causes growth inhibition and is one
of the earliest classical examples of allelopathy (Bais et al. 2006 ). The naphthoqui-
none, juglone (5-hydroxy-1, 4- naphthoquinone), is responsible for the walnut tox-
icity. Juglone is generally found in nontoxic form, but when exposed to air it
becomes oxidized and thus becomes toxic. Juglone is extracted from fresh bark of
stripped roots or from fresh fruit hulls (Kocacali et al. 2009 ). Many other close rela-
tive species of black walnut like butternut or white walnut ( Juglans cinerea ) also
produce juglone, but in limited quantities. Wheat is also known to produce root
exudates with allelopathic activity. Due to simple phenolic compounds like
p- coumaric, p-hydroxybenzoic, ferulic acid, vanillic acid, and syringic acid, the
presence of hydroxamic acids is responsible for wheat allelopathy (Yongqing 2006 ).
Sorghum roots also secrete a mixture of hydrophobic substances which are biologi-
cally active and include sorgoleone, characterized as (2-hydroxy-5-methoxy-3-
pentadecatriene)-p-benzoquinone. Sorgoleone is used as an important bioherbicide
which is used for broadleaf and grass weeds at concentrations below 10 μM in
hydroponic bioassays (Xiaohan et al. 2004 ). Some plants also secrete secondary
metabolites that suppress growth of specifi c plants (autotoxicity). Autotoxicity is a
phenomenon mostly applicable in agricultural crops and weeds, as well as in some
plants that inhabit natural systems. Phytotoxic root exudates play an important role
in mediating autoinhibition in some species like Cucumis sativus (garden cucum-
ber), Centaurea maculosa (spotted knapweed) (Perry et al. 2005 ), and Asparagus
offi cinalis (garden asparagus) (Yu et al. 2003 ).
Root Microbiome Communication
In the unseen underground ecosystem, some complex communication occurs which
includes root- root and root-microbe interaction which has both benefi cial and
harmful outcomes (Bais et al. 2006 ). The sophisticated processes include root-
microbe interaction which includes both mutualistic and pathogenic relationship,
metabolic processes including parasitic plants and root secretion, energy transfer
which comprises electric potential, and resource distribution and information trans-
fer which include quorum sensing. These processes play a critical role in terrestrial
ecosystem (Bouwmeester et al. 2007 ; Gewin 2010 ). Some microbial bioactive com-
pounds which function within the belowground ecosystem play a dynamic role in
plant life. Roots of the plants continuously secrete organic compounds which help
in harnessing benefi cial microbes and suppressing plant pathogens (Berg and Smalla
O. Bashir et al.
345
2009 ; Marschner and Timonen 2005 ). Thus, these roots have stimulatory or inhibi-
tory infl uence on soil microbes which help in their community structure develop-
ment as they increase their competition for nutrients and other resources (Cesco
et al. 2010 , 2012 ).
There occurs a dynamic interaction between soil microbes and plants in nature
which is based on coevolutionary pressures (Klironomos 2002 ; Dobbelaere et al.
2003 ; Duffy et al. 2004 ; Morrissey et al. 2004 ; Morgan et al. 2005 ; Reinhart and
Callaway 2006 ). Consequently, the microbial communities in the rhizosphere vary
due to certain factors like different species of plant (Batten et al. 2006 ; Innes et al.
2004 ), their genotypes (Kowalchuk et al. 2006 ), and their different developmental
stages (Mougel et al. 2006 ; Wei et al. 2007 ). Microbial community in soil is closely
related to highly diverse plant communities, but their connecting link is still unclear
and it is believed that their close relationship occurs due to widely occurring habi-
tat heterogeneity or enhanced plant biomass. It may be also due to different carbon
substrates which act as signaling compounds as they are secreted by the plant
roots. These compounds belong to a class called fl avonoids which are responsible
for specifi c microbe-host interactions. These fl avonoids act as signaling molecules
and are highly present in symbiotic and pathogenic microbes; there occur a large
number of fl avonoids in the plants and a greater number of fl avonoids are identifi ed
in legumes. More than 4000 different fl avonoids occur which mediate host speci-
city (Perret et al. 2000 ). In several Fusarium plant interactions, fl avonoids help in
micro- and macroconidia germination but have no effect on hyphal growth during
infection. Certain isofl avonoid compounds are also present in legume crops. Soya
bean ( Glycine max ) produces genistein, daidzein, and, isofl avonoids which effec-
tively stimulate Bradyrhizobiumjaponicum nod genes but have negative effect on
the Sinorhizobium meliloti nod gene expression. S. meliloti nod gene expression
gets stimulated by luteolin (Juan et al. 2007 ). This phenomenon helps rhizobia to
differentiate between hosts and other legumes. The specifi c fl avonoid produced by
the legumes not only stimulates nod gene expression but also has its effect on rhi-
zobial chemotaxis (Bais et al. 2006 ). Strigolactones recently have been identifi ed
as important signaling molecules in the AMF-plant interaction and thus are “hot
issues” in the mycorrhizal study. Ectomycorrhizal fungi are also stimulated by
Brassicaceae (Zeng et al. 2003 ). There occurs a specifi c interaction between rhizo-
bia and legume allowing only few rhizobial strains to nodulate with specifi c host
legumes. Medicago , Melilotus , and Trigonella genera are nodulated with S. meli-
loti , whereas Rhizobium leguminosarum bv. viciae stimulates nodulation in Pisum ,
Vicia , Lens , and Lathyrus genera (Bais et al. 2006 ). Scientists demonstrated that
plant roots secrete L-MA (malic acid) which acts as effective signaling molecule to
establish benefi cial rhizobial communities (Thimmaraju et al. 2008 ). Arabidopsis
thaliana and Medicago truncatula are the two model plant species which are
unable to maintain nonresident soil fungal populations, but maintain resident soil
fungal populations. These phenomena occur largely due to root exudates. In vitro-
generated root exudates applied to the soil fungi show similar results to that of
plants growing in same soil (Yanhong et al. 2009 ) .
Soil Microbe Diversity and Root Exudates as Important Aspects of Rhizosphere…
346
2.2 Rhizosphere Soil Microbes
Someone has rightly said that rhizosphere microorganisms have two faces like
Janus, the Roman god of doors and gates who symbolizes changes and transi-
tions from one condition to another (one part of the face looks at the plant roots
and the other at the soil; the ears and nose sense other gods, and the mouth is
wide open for swallowing). It is also well established that soil is a good medium
for plants and microbes, but the plants and their associated microbes help in
genesis and weathering of soil (Pate et al. 2001 ; Pate and Verboom 2009 ; Taylor
et al. 2009 ; Pausch et al. 2013 ). Soil formation occurs due to weathering process
which primarily occurs due to soil microbes (Raven and Edwards 2001 ; Beerling
and Berner 2005 ; Taylor et al. 2009 ). The soil microfl ora includes bacteria,
fungi, actinomycetes, protozoa, and algae (Raaijmakers and Weller 2001 ; Singh
et al. 2007 ; Grayston et al. 1998 ; Broeckling et al. 2008 ). Recently the nucleic
acid analysis revealed enormous diversity in the soil (Nannipieri et al. 2003 a, b;
Suzuki et al. 2006 ).
2.2.1 Microorganisms and Their Mode of Action
The soil microbes can generally be divided into benefi cial, harmful, and neutral
microbes. The benefi cial soil microbes can further be divided into three categories.
The fi rst category helps in nutrient supply (Ma et al. 2003 ; Robin et al. 2008 ;
Michaud et al. 2008 ). The second group includes those that stimulate plant growth
by suppressing activity of phytopathogens. The third group of microbes directly
promotes growth of plants by secreting phytohormones (Welbaum et al. 2004 ;
Brimecombe et al. 2007 ) (Fig. 3 ).
2.2.2 Nutrient Availability and Plant Growth Promotion
The most population in the rhizosphere is occupied by the bacteria. Those rhizosphere
bacteria which enhance plant growth are called plant growth-promoting rhizobacteria
(PGPR) (Kloepper JW Schroth 1978 ; Lucy et al. 2004 ). The most dynamic function of
PGPR is secretion of phytohormones. A diverse group of PGPR are inoculated on the
crops which include Azospirillum (Cassan and Garcia
2008 ), Bacillus (Jacobsen et al.
2004 ), Pseudomonas (Loper and Gross 2007 ), Rhizobium (Long 2001 ), Serretia (De
Vleeschauwer and Hofte 2007 ), Stenotrophomonas (Ryan et al. 2009 ), and Streptomyces
(Schrey and Tarkka 2008 ). Some fungi belonging to genera Ampelomyces , Coniothyrium ,
and Trichoderma have also benefi cial effects (Harman et al. 2004 ). The mode of action
of PGPR involves complex mechanism which promotes plant growth, development, and
protection. The most versatile functions of PGPR are biofertilization, phytostimulation,
and biocontrol (Morgan et al. 2005 ; Muller et al. 2009 ; Chet and Chernin 2002 ). The
success of plant-microbe interaction depends on colonization (Lugtenberg et al. 2002 ;
O. Bashir et al.
347
Kamilova et al. 2005 ). The steps of colonization include attraction, recognition, adher-
ence, invasion, colonization, and growth (Pinton et al. 2007 ; Berg 2009 ).
Plant growth in the agriculture is enhanced by certain abiotic and biotic fac-
tors. The abiotic factors comprise light, temperature, water, and air. The biotic
factors include PGPR which help in plant growth by secreting enzymes (Lynch
1990 ; Marilley and Aragno 1999 ; Garcia et al. 2001 ). Interestingly the inocula-
tion of PGPR increases the crop yield and plant growth (Farzana et al. 2009 ).
Some plant growth-promoting rhizobacteria have more than one trait (Joseph
et al. 2007 ; Yasmin et al. 2007 ; Egamberdiyeva 2007 ). These PGPR release
volatile compounds like 2,3-butanediol and acetoin that help in growth and
development of Arabidopsis thaliana (Ryu et al. 2003 ). There have also been
reports that diazotrophical bacterial application in the soil increases crop yield,
plant height, and microbial population in the soil (Anjum et al.
2007 ). Due to
certain combination of PGPR, carbohydrates, and IBA (double and triple com-
binations), there occurs increased rooting capacity of apple (Karakurt et al.
2009 ). PGPR are the most effective model organism that can replace pesticides
and other harmful supplements which cause soil and environmental pollutions.
These PGPR also act as biofertilizers and bioenhancers and reduce use of
Rhizosphere
Microbial
Community
Growth promotion N2 fixation
Soil stabilization Biocontrol
Water uptake Antibiosis
Nutrient flow Symbiosis
Free Enzyme Release Disease
Attachment Phytotoxicity
Allelopathy Competition
Fig. 3 Shows role of rhizosphere microbial community and its harmful and benefi cial effects
Soil Microbe Diversity and Root Exudates as Important Aspects of Rhizosphere…
348
chemical fertilizers (Ashrafuzzaman et al. 2009 ). Utilization of PGPR with
alternative use of chemical fertilizers reduces pollution, preserves environ-
ment, and increases agricultural productivity (Ştefa et al. 2008 ). Combination
of PGPR and arbuscular mycorrhizal fungi enhances nutrient use efficiency of
plants and allows low rate of application of fertilizers (Adesemoye et al. 2009 ;
Tanvir et al. 2015 ). The bacteria and archaea are responsible for biological
nitrogen fixation. These include symbiotic nitrogen fixers like rhizobium,
which are obligate symbionts in legume plants and Frankia in nonleguminous
plants and certain free- living forms like cyanobacteria, azospirillum, azoto-
bacter, and diazotroph.
2.2.3 Pathogen Inhibition
Soil microbes live around plant roots and feed on root secretions and dead
root cells. Root colonization not only results in high plant growth-promoting
rhizobacterial population densities but also functions as antagonistic metabo-
lites (Shoda 2000 ; Raaijmakers et al. 2002 ). The different mechanisms
involved are antibiosis, parasitism, and induced systemic resistance.
Antibiosis is the phenomenon where microbial growth gets inhibited by dif-
ferent compounds like antibiotics, toxins, biosurfactants, and volatile organic
compounds. Parasitism is the phenomenon where cell wall-degrading
enzymes such as chitinase and β-1,3-glucanase are secreted which degrade
cell wall (Compant et al. 2005 ; Haas and Defago 2005 ). A wide range of
antifungal metabolites such as zwittermicin-A, kanosamine, and lipopeptides
are secreted by Bacillus subtilis. These antifungal metabolites include surfac-
tin, iturin, and fengycin families (Emmert and Handelsman 1999 ; Ongena
and Thonart 2006 ). Competition for the carbon source of energy is responsi-
ble for fungi inhibition by reducing fungal spore germination (Chin et al.
2003 ; Alabouvette et al. 2006 ). Another mechanism of pathogen inhibition is
induced resistance. The induced resistance involves the use of beneficial bac-
teria that not only reduces the activity of pathogenic microorganisms through
antagonism but also stimulates plant defense mechanism (Shoda 2000 ;
VanLoon 2007 ). In some instances, the mechanism of induced systemic resis-
tance coincides with systemic acquired resistance. Both induced systemic
resistance and systemic acquired resistance enhance the resistance of plant
which depends on signaling compounds like ethylene, jasmonic acid, and
salicylic acid (VanLoon 2007 ).
2.2.4 Rhizosphere Effect
The rhizosphere effect is determined by dividing the number of microorganisms per gram
of rhizosphere soil by the number of microorganisms in a gram of control soil (Wasaki
et al. 2005 ; Herman et al. 2006 ). The rhizosphere effect greatly reduces as we move away
O. Bashir et al.
349
from roots. For bacteria and fungi, R:S value ranges from 5 to 20. Actinomycetes is a less
effected group of soil microorganisms having R:S effect of 2–12 (Curl and Truelove
1986 ; Foster 1986 ; Lynch 1990 ; Rovira 1991 ; Pinton et al. 2001a , b ; Whipps 2001 ).
3 Quorum Sensing: The Bacterial Communication
“Quorum sensing” (QS) is the communication of bacteria which includes cell density.
It is cell-to-cell communication. The bacterial quorum sensing occurs by the binding
of signals with their receptor proteins. When binding occurs, it regulates gene expres-
sion in response to cell density (Gonzalez and Marketon 2003 ; Hong et al. 2012 ). The
signaling molecules involved in quorum sensing are called autoinducers. These auto-
inducers are synthesized at particular stage of life cycle or may be synthesized for
stimulating response, once the signaling molecule has reached at a particular concen-
tration (Gonzalez and Marketon 2003 ). The quorum sensing is a cell density level:
once a particular cell density is achieved, the concentration of quorum-sensing signals
becomes enough to induce gene expression, either directly through transcriptional
regulator or indirectly by signaling cascade activation (Fuqua et al. 2001 ). N -acyl
homoserine lactone (AHL) is the most studied quorum- sensing signal molecule
(Williams et al. 2007 ). AHL signals are highly preserved in nature having same homo-
serine lactone moiety, but differ in length and structure of acyl side chain. The
N -acylated side chains have fatty acids. These chains have varying degrees of satura-
tion, different chain lengths (4–18 carbons), and presence of different groups (hydroxy,
oxo-, or no substituent at the C3 position) (Swift et al. 1997 ; Schuster et al. 2013 ).
LuxI synthase gene using intermediate of fatty acid biosynthesis and S -adenosyl
methionine synthesizes AHL molecules. The AHL molecules will incorporate LuxR
protein and regulate downstream gene expression. Each LuxR protein is specifi c for
its AHL signal molecules (Parsek and Greenberg 2000 ). AHL regulates many target
genes, but basic mechanism of gene regulation and AHL biosynthesis seem to be
specifi c in quorum-sensing bacterial species (Dong et al. 2002 ). QS mechanism with
LuxI/LuxR signal molecules in Agrobacterium tumefaciens causes crown gall disease
of plants. Agrobacterium tumefaciens with tumor-derived opines and transcriptional
factor OccR or AccR regulate gene expression of LuxR homologue TraR (Oger et al.
1998 ; Zhu and Winans 1988 ). Pseudomonas aeruginosa uses LasI/R and RhlI/R to
promote regulation and expression of virulence factors and biofi lm formation
(Glessner et al. 1999 ). Another class of homoserine lactone known as p -coumaroyl-
homoserine lactone (pC-HSL) has been discovered to be produced by the bacteria
Rhodopseudomonas palustris . The intracellular fatty acid is not used as precursor in
the synthesis of pC-HSL molecules, and synthesis occurs due to RpaI and LuxI by
using environmental p -coumaric acid (Schaefer et al. 2008 ). Many bacteria use QS to
gain maximal competition advantages, and to measure the advantages of QS some
organisms use quorum quenching (QQ) (Lin et al. 2003 ; Rodolfo et al. 2015 ). This QS
widely occurs in prokaryotes and eukaryotes and plays an important role in pathogen-
host and microbial interactions (Dong et al. 2002 ).
Soil Microbe Diversity and Root Exudates as Important Aspects of Rhizosphere…
350
4 Conclusion
In this chapter, we discussed an overview of ecology of various organisms and the root
exudates. Various microorganisms are present in the rhizosphere, and they form a com-
plex community which is connected with each other and with the external environment.
The genetic and functional diversity of soil microbes is very important for both plant and
soil health. The major challenge ahead of rhizosphere is the discovery of new signaling
molecules that occur between different organisms; these discoveries are very important
to enhance our knowledge to deal with the new pest and disease problems in the sustain-
able manner. There also occurs challenges to adopt new crops and cropping systems
which absorb most of the nutrients from soil particularly nitrogen and phosphorus
because our phosphorus sources are getting diminished. Today rhizosphere is consid-
ered a new research fi eld with many exciting challenges. These challenges can be both
fundamental and applied. There are some major developments in biogeochemistry and
ecology of rhizosphere which need a global consideration. In symbiotic association, a
great achievement has been made, but there still occurs a great lacuna of knowledge in
other biological interactions. Rhizodeposition is considered the central concept in rhizo-
sphere ecosystem and beyond rhizosphere ecology. Rhizodeposition is very important
for terrestrial ecosystem biodiversity and functioning. In rhizosphere studying of gene
expression is used for understanding certain processes like inducing microbial activity,
biological control, nutrient competition, and certain molecular interactions between
roots and roots and roots and microorganisms. Some techniques have been developed to
characterize m-RNA (Nannipieri et al. 2003 a, b), but soil proteomics is still not so devel-
oped (Nannipieri 2006 ; Ogunseitan 2006 ). Stable isotope probe (SIP) has also been used
in understanding functional activity and community structure in soil (Radajewski et al.
2000 ; Manefi eld et al. 2006 ). Labeled root exudate compounds and monitoring micro-
organisms of rhizosphere also involve the use of stable isotope compounds (Manefi eld
et al. 2006 ). At single cell level, reporter technology is to be used to assess functions of
rhizosphere soil including gene expression (Sorensen and Nybroe 2006 ). The increasing
knowledge of the promoter, regulator, and reporter gene insertion techniques shall allow
use of reporter gene technology for regulation, expression, and induction of any gene in
rhizosphere. The methodological improvement of new technology will allow designing
of new reporter bacteria to respond to specifi c root exudates.
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Soil Microbe Diversity and Root Exudates as Important Aspects of Rhizosphere…
... Soil is species rich habitat on earth having diverse and abundant species which help in the formation and development of soil. The soil biodiversity is indicator of soil health, as greater biodiversity means greater soil stability in terms of certain functions, such as maintenance of soil structure, assimilation of organic wastes, and nutrient cycling (Miranda et al. 2019;Oburger and Jones 2018;Conrad et al. 2018;Mahanty et al. 2014;Bashir et al. 2016;Shen et al. 2014;Dijkstra et al. 2013;Wang et al. 2012;. Soil organic matter, soil organic carbon, and soil biodiversity are closely related but distinct. ...
... All these organisms depend on soil organic matter for their energy, nutrients, and habitat. The topmost soil of earth, where concentration of organic matter and roots are higher, forms the largest habitat for these organisms (Bashir et al. 2016). A vast diversity of the organisms is present in the soil but only limited microorganism has been explored (Table 7.4). ...
... Soil enzymes play a key role in organic matter decomposition and its recycling, with their activities being closely related to microbial activity, microbial biomass, soil physical property, and soil organic matter (Oburger and Jones 2018;Mahanty et al. 2014;Bashir et al. 2016;Dijkstra et al. 2013). These enzymes are either intracellular or extracellular, with intracellular being inside the cell in the cytoplasm bound by the cell wall. ...
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The traditional way of monocropping and current strategies of use of inorganic chemical-based pesticides and fertilizers are the main barriers in development of sustainable agriculture. Similarly, sickness is a growing issue because of degradation of agricultural land due to continuous sole cropping. On the other hand, intercropping is an old but efficient and eco-friendly way to get rid of soil sickness and to improve crop production. During intercropping, two or more crops either work symbiotically to facilitate each other or compete on available resources for their survival. These both ways can be utilized for the purpose of reclaiming degraded agricultural soils, utilization of resources, management of disease and pests, and eventually increase in crop production. This chapter explains the mechanisms underlying intercropping facilitating plant acquisition of nitrogen and phosphorus and suppressing insect pest and disease incidence with examples of some effective intercropping systems. Moreover, the phenomenon of soil sickness has been described to understand how intercropping can be manipulated to reclaim agricultural land.
... In the organic farming systems, there is basically the transformation of carbon compounds by macro and microorganisms and plants that provide energy and connects above and below surface energy by the formation of a cycle (Rossiter and Bouma 2018;Wade et al. 2018;Roper et al. 2017;Bonfante and Bouma 2015;Tiquia 2005). The plants assimilate carbon from atmosphere and form glucose and other complex plant biomolecules which, upon plant senescence, enter the soil through roots, litter, and root exudates (Zhang 2013;Zuber et al. 2018;Bashir et al. 2016). The plants supply energy to heterotrophs and, to a less extent, to chemotrophs (microbes, fungi, and earthworms) by the formation of recalcitrant organic matter (Adeniji and Babalola 2019) The carbon source acts as a source of energy and as long as net primary production exceeds respiration the organic carbon will accumulate in the soil (Miranda et al. 2019;Oburger and Jones 2018;Conrad et al. 2018;Mahanty et al. 2014;Dijkstra et al. 2013). ...
... Soil is species rich habitat on earth having diverse and abundant species which help in the formation and development of soil. The soil biodiversity is indicator of soil health, as greater biodiversity means greater soil stability in terms of certain functions, such as maintenance of soil structure, assimilation of organic wastes, and nutrient cycling (Miranda et al. 2019;Oburger and Jones 2018;Conrad et al. 2018;Mahanty et al. 2014;Bashir et al. 2016;Shen et al. 2014;Dijkstra et al. 2013;Wang et al. 2012;Bhatti et al. 2017). Soil organic matter, soil organic carbon, and soil biodiversity are closely related but distinct. ...
... All these organisms depend on soil organic matter for their energy, nutrients, and habitat. The topmost soil of earth, where concentration of organic matter and roots are higher, forms the largest habitat for these organisms (Bashir et al. 2016). A vast diversity of the organisms is present in the soil but only limited microorganism has been explored (Table 7.4). ...
Chapter
In 2050, the population of the world is expected to be 9 billion, which means we have to produce six times more food. With this population explosion and increase in food demand, the agricultural land is depleting at an alarming rate, jeopardizing future progress. In order to overcome this problem, the soil organic matter plays a dynamic role in the maintenance and improvement of soil properties. Organic matter determines larger part of soil and has tremendous ecological significance; it influences ecosystem productivity, soil health, and climate quality. The soil organic matter maintains and improves many physical, chemical, and biological properties. This chapter explicates the effect of organic matter on physical, chemical, and biological properties, including soil structure, water retention, available water capacity, thermal conductivity, erodibility, infiltration, soil aggregate formation, soil color, soil compaction, soil aeration, pH, buffering capacity, CEC, base saturation, zeta potential, exchangeable cations, soil fertility and nutrient release, microbial population, soil microbial biomass carbon, nitrogen transformation, mycorrhizal population, root length and root growth, and soil enzymes. It was concluded that increase in the organic matter enhanced these properties, while reduction in organic matter had a detrimental impact on these properties.
... Soil is species rich habitat on earth having diverse and abundant species which help in the formation and development of soil. The soil biodiversity is indicator of soil health, as greater biodiversity means greater soil stability in terms of certain functions, such as maintenance of soil structure, assimilation of organic wastes, and nutrient cycling (Miranda et al. 2019;Oburger and Jones 2018;Conrad et al. 2018;Mahanty et al. 2014;Bashir et al. 2016;Shen et al. 2014;Dijkstra et al. 2013;Wang et al. 2012;. Soil organic matter, soil organic carbon, and soil biodiversity are closely related but distinct. ...
... All these organisms depend on soil organic matter for their energy, nutrients, and habitat. The topmost soil of earth, where concentration of organic matter and roots are higher, forms the largest habitat for these organisms (Bashir et al. 2016). A vast diversity of the organisms is present in the soil but only limited microorganism has been explored (Table 7.4). ...
... Soil enzymes play a key role in organic matter decomposition and its recycling, with their activities being closely related to microbial activity, microbial biomass, soil physical property, and soil organic matter (Oburger and Jones 2018;Mahanty et al. 2014;Bashir et al. 2016;Dijkstra et al. 2013). These enzymes are either intracellular or extracellular, with intracellular being inside the cell in the cytoplasm bound by the cell wall. ...
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Full-text available
Cyanobacteria (blue-green algae) are the photosynthetic organisms that are widely grown in all sorts of habitats including aquatic and terrestrial environments. Today, the agricultural sector is highly dependent on chemical fertilizers to enhance the crop production in order to meet the demand for food around the globe which have severe negative effects on both mankind and environment. Due to its pool of properties that are beneficial for sustainable agroecosystem, cyanobacterial biofertilizers are eco-friendly and can be an effective and economical alternative for synthetic fertilizers with less input of cost and energy. They can be explored for producing natural fertilizers, which provide positive alterations for both biotic and abiotic components. Cyanobacteria are potential sources of nitrogen fixation, cost-effective, and a major component of the nitrogen-fixing biomass. They have become paramount microbes for producing natural fertilizers, plant growth-promoting hormones, bioactive compounds, etc. These properties enable them in boosting soil fertility, control the activity of other microorganisms, and also can play a role in bioremediation of pesticides, herbicides, and combating pollution attributed to heavy metals and other toxicants as well. The agricultural importance of cyanobacterial biofertilizers is directly related to their nitrogen fixation ability and other effects for plants and enhances soil fertility. This chapter emphasizes on the use of cyanobacteria as a sustainable microbiome and biofertilizer in agriculture sector to enhance crop production and yield.
... The highest population and biodiversity of organisms are found in the area of the root system, known as rhizosphere and the bacteria that occupy the rhizosphere are called the rhizobacteria, the community of organisms being called the rhizomicrobiome (Mendes et al. 2013;Bashir et al. 2016). The term rhizosphere is from the Greek words "rhiza" which means root and "sphere" which means field or area of influence (Hiltner 1904;.The rhizosphere as the key habitat of soil organisms is a rich zone of highly available nutrients, acting as a junction for nutrient exchange between plants, soil, and microbes Bashir et al. 2016) and as the hot spot and harbor for the beneficially microbial community. ...
... The highest population and biodiversity of organisms are found in the area of the root system, known as rhizosphere and the bacteria that occupy the rhizosphere are called the rhizobacteria, the community of organisms being called the rhizomicrobiome (Mendes et al. 2013;Bashir et al. 2016). The term rhizosphere is from the Greek words "rhiza" which means root and "sphere" which means field or area of influence (Hiltner 1904;.The rhizosphere as the key habitat of soil organisms is a rich zone of highly available nutrients, acting as a junction for nutrient exchange between plants, soil, and microbes Bashir et al. 2016) and as the hot spot and harbor for the beneficially microbial community. The activity and biodiversity of the microbial community composition of the rhizosphere are highly dependent on root exudates (Dias et al. 2012;Aranda et al. 2013).The rhizosphere as an effective root zone may contain up to 10 11 microbes cells per gram of root and more than 30,000 prokaryotic species (Manoharachary and Mukerji 2006;Parmar and Dufresne 2011). ...
... The zone of ectorhizosphere is formed from soil particles adjacent to the roots (Figure 9.1). Bulk soil is the portion of soil which is not the component of the rhizosphere (Lambers et al. 2008;Bashir et al. 2016) (Figure 9.1). In addition, the rhizoplane is referred to as the surface of the plant tissues in contact with the soil (i.e. ...
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Full-text available
In a context of a changing environment, it is crucial to maximize our knowledge on all the mechanisms involved in plant microbiome interactions at the genetic, physiological, and ecological levels. This chapter reviews some recent advances in plant microbiome investigations and describes potential applications of such associations for the mitigation of both abiotic and biotic stresses to improve crop health and productivity. Understanding the full potential of microbes in the ecosystem functioning in general and their complex beneficial interactions in improving agriculture productivity in particular requires the development and improvement of compatible tools that can be verified in biological assays, always bearing in mind their reproducibility in situ on different scales. Progress in the engineering microbiome have made it possible to show how meta‐omics (metataxonomic, metagenomics, metatranscriptomics, and metaproteomics) can be potentially powerful tools to gain deeper knowledge of the functional capabilities of the microbiome and how they can shape ecosystems.
... Nannipieri et al., (2008). Soil microbial activity and its diversity in the rhizosphere have been extensively studied, Bashir et al., (2016); ; ; Kumar et al., (2016a);Swamy et al., (2016);de Medeiros et al., (2017), depending on the interaction between cultivated plants and rhizosphere properties Fig. (57), which include: -Effects of applied pesticides e.g., Álvarez-Martín et al., (2016);Franco-Andreu et al., (2016);Lv et al., (2017); Mauffret et al., (2017) -Effects of soil earthworm in presence of plants, Aghababaei et al., (2014); Aghababaei and Raiesi (2015); Lv et al., (2016);Zhang et al., (2016a); Kim et al., (2017;Liu et al., (2017b) -Effects of soil pollution including organic and inorganic pollutants, Parelho et al., (2016); Hansda et al., (2017); Tong et al., (2017); Wang et al., (2017b) -Effects of different soil characterizations like soil organic matter, soil redox potential, etc., ; Su et al., (2017);Xiao et al., (2017) -Effects of climate change, Bojko and Kabala (2017); Zhang et al., (2016b), (2017b) -Effects of plant characterization, ; Mohammadi et al., (2017);Zhang et al., (2017c) -Effects of application of soil amendments and fertilizers, Meena et al., (2016); Abad-Valle et al., (2017); Wang et al., (2017c, d) -Effects of applied nanomaterials, Nogueira et al., (2012); Oyelami and Semple (2015); Schlich and Hund-Rinke (2015); Schlich et al., (2016);Liang et al., (2017) -Effects of different stresses, Cheng et al., (2016); ; Xue et al., (2017); Wu et al., (2017) -Effects of tillage and other agricultural practices, Kabiri et al., (2016); Tautges et al., (2016); León et al., (2017); Yuan et al., (2017) -Effects of transgenic plants on microbial diversity in the rhizosphere soil, Chaudhry et al., (2012); Canfora et al., (2014); Sahoo et al., (2015); Turrini et al., (2015); Guan et al., (2016);Arpaia et al., (2017). Therefore, there is a crucial understanding for the principles of interaction among microbes-plants and microbes-microbes. ...
... Generally, there is close relationship between plant roots, their exudations and plant nutrition. There are direct and indirect effects of plant root exudates on plants nutrition including uptake, transformation, translocation and accumulation of different soluble compounds in the rhizosphere, Fig.(59), Neumann (2007); Nannipieri et al., (2008); Doornbos et al., (2012); Bashir et al., (2016);Liu et al., (2017c);Meier et al., (2017). Agric. ...
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Global climatic has been changed and will continue to change because of the activity of unreasonable controlled of human activities, which gradually increase the concentrations of greenhouse gases in the atmosphere. Population is gradually increased at the same time and due to climate change, soil and water resources is threastened due to natural resource degradation. Many reports, by IPCC has clearly stated that warming of the climate system is unmistakable and it is very likely caused by natural and human activities. Climatic changes always affect hydrological cycle components, such as precipitation, evapotranspiration, temperature, stream flow, ground water and finally surface runoff, and may have stronger or weaker, permanent or periodical, favorable or unfavorable, harmful, direct or indirect impact on soil processes. Climatic changes will result in stimulated floods and drought, which will have significant impacts on the soil and the availability of water resource availability. Soils are linked to the climatic system through cycles of nitrogen, the carbon, and hydrologic. Because of climatic changes, soil processes and their characteristics will gradually be affected, by changing in temperature, that causing changes in global amounts of rainfall and their distribution patterns. Temperature and water are very important factors influencing the processes of soils, which causing changes in the soils throughout the world. Managements of water resources can affect on the counter balance of climatic changes on stream flow and water availability at certain level. This review studies the impacts of climate change on soil, water resources. Studies also dealing on hydrological responses to climate change, and possible adaptation options in the realm of climate change impacts on soil and water resources. Deficit of soil moisture affects crop productivity through its influence on the availability and transportation of nutrients which gradually increases vulnerability to nutrient losses from the rhizosphere soil by erosion. Nutrient elements are carried by soil moisture to the roots. Decreasing moisture in root zone resulted in decreasing nutrient diffusion and their availability, consequently decreasing mass flow of water-soluble nutrients such as nitrate, sulfate Ca, Mg and Si over longer distances. Roots extend their length, gradually increase their surface area and alter their architecture in an effort to capture less mobile nutrients such as phosphorus. Reduction of root under drought conditions reduces the nutrient acquisition capacity of root systems. Also reduce both carbon and oxygen fluxes, furthermore minimize the accumulation of nitrogen in root nodules particularly, in legume crops, furthermore, alters the composition and activity of soil microbial communities like the reduction of soil nitrifying bacteria.
... The concentration of heavy metals may affect the bacteria by reducing their number, size, biochemical activity, diversity, and change in the community structure (Pająk et al. 2016). The high concentration of bacteria in the rhizosphere occurs due to the presence of high levels of nutrients that are exuded from the roots that support bacterial growth and metabolism (Chandran 2014;Bashir et al. 2016). The occurrence of bacteria on sterilized Hoagland solution is due to the dissolution of inoculated bacterial cells from the rhizosphere to the culturing solution (So 2003). ...
Article
The role of multi-heavy metal tolerant bacteria isolated from the rhizosphere of Eichhornia crassipes in the phytoremediation of Cu and Pb under laboratory conditions was investigated. The heavy metal tolerant rhizosphere bacteria were identified as Bacillus cereus, Paenibacillus alvei, Aeromonas caviae, Paenibacillus taiwanensis, and Achromobacter spanius. Results showed a significant variation in wet weight, Heterotrophic Plate Count (HPC) of the rhizosphere, HPC of water, removal and uptake of Cu and Pb by E. crassipes, either alone or in association with the rhizosphere bacteria. The removal of Cu by E. crassipes in different experimental conditions showed that OTC (Oxytetracycline) untreated E. crassipes with rhizosphere bacteria has maximum removal with 95%, followed by E. crassipes alone with 84%. The OTC treated E. crassipes with rhizosphere bacteria could remove 81% of Cu. The maximum Pb removal efficiency of 93.4% was shown by OTC untreated E. crassipes with rhizosphere bacteria, followed by E. crassipes alone with 86.8%. The OTC treated E. crassipes with rhizosphere bacteria showed the least removal efficiency with 82.32%. The translocation factor (TF) values for Cu and Pb were lower than 1 indicated that the absorption was mainly accomplished in the roots of E. crassipes. The order of accumulation of Cu and Pb in E. crassipes was noted as root > leaf > petiole.
Chapter
Rhizosphere is the busiest part where a series of interactions occur between plants and microbes that include both beneficial and harmful interactions. Beneficial rhizobacteria improve plant growth by mobilizing nutrients, producing growth regulators, or inhibiting phytopathogens. For performing such benefits, collective working strategies are required, which are fulfilled by exploiting the complex intracellular communication systems called quorum sensing (QS). Extensive research works suggested strong correlation between QS systems and the plant growth-promoting (PGP) traits of rhizobacteria. Additionally, QS system is also associated with the virulent properties of soil-borne pathogens. Based on accumulated knowledge, bacterial QS system operating in the rhizosphere is regarded as a suitable target for improving crop plant growth and development. In this chapter, we have discussed about the involvement of QS systems with different PGP traits of rhizobacteria and regarding the further strategies, which will be taken by targeting such systems for improving plant growth.
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Nitrogen fixing bacteria (NFB) plays an important role in increasing N availability for plants. Research to examine the ability of nitrogen fixing bacteria isolates to produce nitrogenase, phytohormone and the ability of nitrogen fixing bacteria isolates in the biological test process using the corn plant indicator as an indicator has been carried out from September 2018 to February 2019 in laboratories and greenhouses. The ability of nitrogen fixing bacteria was tested by the ARA method, while the phytohormone testing of nitrogen fixing bacteria was tested using the HPLC method. Bioassays using Murphy media and corn plants as indicators were performed using a randomized block design consisting of six treatments (one control and five selected NFB isolates from the selection results) and given five replications. Measurement of root length, plant height, and dry weight of plants were carried out every 2 days for 14 days. The results showed that the nitrogen fixing bacteria isolates used from North Sangattarhizobiome, East Kalimantan had different nitrogenase and differentphytohormone test results, and obtained five selected isolates based on the selection results. The results of the bioassay did not show any significant differences based on the Duncan test at the level of 5%. However, it can be seen visually the significant difference in which plants in the biological test using nitrogen fixing bacterial isolates have relatively higher plant growth and dry weight of plants than plants that are not given treatment or control.
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Intensive agricultural practices have led to a decline in soil health, thereby affecting environmental sustainability. To feed the ever-increasing global population in a sustainable manner, shifting to eco-friendly agricultural practices is of paramount importance. In this respect organic farming, which excludes chemicals, has been widely popularised. However, the effect of such an intervention on microbial communities that are the major drivers of soil processes, is yet to be conclusively determined. Such an understanding is important for the maintenance of soil health and improvisations for enhancing the efficiency of the practice. A general belief is that organic farming results in a more diverse microbiota. But the information available is inconsistent and fragmented. Besides, limited efforts have been made to link the structure of microbial communities to soil functionality. The review is an attempt to critically re-look into the decade-old question of how organic farming shapes the microbial diversity of arable land, as well as the diversity of plant-associated microbial communities, especially in light of the popularization of the technique of next generation sequencing. Based on the available knowledge, the review aims to pave the way for future studies in the area by identifying the research gaps.
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Rhizomicrobiome composed of high diversity of microbial community is act like a gut to plant genome as ascribed to microbial communities in the human gut. It is an excellence habitat and shelter to highly diversified of microbial community with specific functions and characterize by sophisticate interaction and relationship among the organismsin soil food web and energy. It influences the plant growth, plant health and the health of soils ecosystem significantly. The health of rhizomicrobiome as a part of soil food web or energy are highly depend on rhizodeposits released by the plant (exudates, border cells, mucilage, etc.) and the soil organic matter supply as fuel or source of energy. They play an extremely important role in regulating of microbial diversity and activity on rhizosphere ecosystem. The rhizomicrobiome enhance the soil health, plant growth and health by releasing the major nutrients (macroand micro elemental) from non‐useable form to useable form, decomposing organic residues, contributing to soil humus formation, improving plant health through symbiotic or mutualistic association, (maintaining soil stability through biogeochemical cycling and biological control of plant pathogens, insects and weeds. A comprehensive and holistic study for better understanding of dynamic of microbial community (soil microbiome diversity and function), and its traits under different plants or soils ecosystem are urgently require to the develop the new technologies and product such as biofertilizers and biopesticides. Moreover, the research to optimize soil management, crop management (crop rotation, intercropping) are needs to enhance beneficial soil microbiome diversity and function in rhizomicrobiome and as well as to develop the methods for the assessment health of the rhizomicrobiome using the physical, chemical and biological indicators which can be used as key tools of soils and crop health management in sustainable ways.
Article
en The soil organic matter plays a key role in ecological soil functions, and has to be considered as an important CO2 sink on a global scale. Apart from crop residues (shoots and roots), left over on the field after harvest, carbon and nitrogen compounds are also released by plant roots into the soil during vegetation, and undergo several transformation processes. Up to now the knowledge about amount, composition, and turnover of these root‐borne compounds is still very limited. So far it could be demonstrated with different plant species, that up to 20 % of photosynthetically fixed C are released into the soil during vegetation period. These C amounts are ecological relevant. Depending on assimilate sink strength during ontogenesis, the C release varies with plant age. A large percentage of these root‐borne substances were rapidly respired by microorganisms (64—86 %). About 2—5 % of net C assimilation was kept in soil. The root exudates of maize were mainly water‐soluble (79 %), and in this fraction about 64 % carbohydrates, 22 % amino acids/amides and 14 % organic acids could be identified. Plant species and in some cases also plant cultivars varied strongly in their root exudation pattern. Under non‐sterile conditions the exuded compounds were rapidly stabilized in water‐insoluble forms and bound preferably to the soil clay fraction. The binding of root exudates to soil particles also improved soil structure by increasing aggregate stability. Future research should focus on quantification and characterization of root‐borne C compounds during the whole plant ontogenesis. Apart from pot experiments with ¹⁴CO2 labeling, it is necessary to conduct model field experiments with ¹³CO2 labeling in order to be able to distinguish between CO2 originating from the soil C pool and rhizosphere respiration, originating from plant assimilates. Such a separation is necessary to assess if soils are sources or sinks of CO2. The incorporation of root‐borne C (¹⁴C, ¹³C) into soil organic matter of different stability is also of particular interest. Abstract de Pflanzliche Rhizodeposition — eine wichtige Quelle für den Kohlenstoffumsatz in Böden Die organische Bodensubstanz (OBS) nimmt eine Schlüsselrolle bei den ökologischen Bodenfunktionen ein und stellt global betrachtet eine wichtige CO2‐Senke dar. Neben den auf dem Feld verbleibenden Ernte‐ und Wurzelrückständen werden C‐ und N‐Verbindungen auch während des Pflanzenwachstums in den Boden abgegeben und unterliegen dort vielfältigen Umsetzungsprozessen. Der Kenntnisstand über die Menge, Zusammensetzung und den Umsatz dieser wurzelbürtigen Verbindungen im Boden ist noch sehr begrenzt. Daher beschäftigt sich die vorliegende Publikation mit der Rhizodeposition als wichtiger Quelle des C‐Umsatzes in Böden, insbesondere mit den mobilen Wurzelabscheidungen. Bisher konnte anhand verschiedener Pflanzenarten gezeigt werden, dass bis zu 20 % des photosynthetisch fixierten C während der Vegetation durch die Wurzeln freigesetzt werden. Es handelt sich dabei um ökologisch relevante C‐Mengen. In Abhängigkeit von der Stärke des Assimilatsinks während der Ontogenese variiert die C‐Freisetzung mit dem Pflanzenalter. Ein hoher Anteil dieser wurzelbürtigen Verbindungen (64—86 %) wurde schnell durch Mikroorganismen veratmet. 2—5 % der Netto‐C‐Fixierung blieben im Boden zurück. Dieser Bodenrückstand war bei Wurzelabscheidungen von Mais hauptsächlich wasserlöslich (79 %), und in dieser Fraktion wurden 64 % Kohlenhydrate, 22 % Aminosäuren/Amide und 14 % organische Säuren identifiziert. Pflanzenarten und teilweise auch ‐sorten variierten stark in der Zusammensetzung ihrer Wurzelexsudate. Unter insterilen Bedingungen wurden die exsudierten Verbindungen schnell in nichtwasserlöslicher Form stabilisiert und vor allem an die Tonfraktion des Bodens gebunden. Die Bindung an Bodenpartikel verbesserte die Bodenstruktur durch erhöhte Aggregatstabilität. Zukünftige Forschungsarbeiten sollten sich auf die Quantifizierung und Charakterisierung wurzelbürtiger C‐Verbindungen während der gesamten pflanzlichen Ontogenese konzentrieren. Abgesehen von Gefäßversuchen mit ¹⁴CO2‐Applikation ist es erforderlich, Feldmodellversuche mit ¹³CO2‐Applikation durchzuführen, um zwischen der CO2‐Emission aus dem Boden‐C‐Pool und derjenigen aus der Rhizosphärenatmung (Ursprung sind Pflanzenassimilate) unterscheiden zu können. Eine solche Trennung ist zur Beurteilung, ob Böden eine Quelle oder Senke für CO2 darstellen, zwingend erforderlich. Von besonderem Interesse ist auch der Einbau des wurzelbürtigen C (¹⁴C, ¹³C) in OBS‐Fraktionen unterschiedlicher Stabilität.
Book
An understanding of the mineral nutrition of plants is of fundamental importance in both basic and applied plant sciences. The Second Edition of this book retains the aim of the first in presenting the principles of mineral nutrition in the light of current advances. This volume retains the structure of the first edition, being divided into two parts: Nutritional Physiology and Soil-Plant Relationships. In Part I, more emphasis has been placed on root-shoot interactions, stress physiology, water relations, and functions of micronutrients. In view of the worldwide increasing interest in plant-soil interactions, Part II has been considerably altered and extended, particularly on the effects of external and interal factors on root growth and chapter 15 on the root-soil interface. The second edition will be invaluable to both advanced students and researchers.
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This paper reviews the major steps which have contributed to our knowledge of rhizosphere biology since 1904. The progress made has been very considerable, and the frustrations limited. Prospects are bright for improving our understanding of the biology of the rhizosphere and for managing the rhizosphere microflora to increase plant growth.
Book
History.- Historical Examples of Allelopathy and Ethnobotany from the Mediterranean Region.- Allelopathy: Advances, Challenges and Opportunities.- Allelopathy in Chinese Ancient and Modern Agriculture.- Allelochemicals and Allelopathic Mechanisms.- Allelochemicals in Plants.- Allelopathy: Full Circle from Phytotoxicity to Mechanisms of Resistance.- Allelopathic Mechanisms and Experimental Methodology.- Indirect Effects of Phenolics on Plant Performance by Altering Nitrogen Cycling: Another Mechanism of Plant-Plant Negative Interactions.- Genomic Approaches to Understanding Allelochemical Effects on Plants.- Allelopathy from a Mathematical Modeling Perspective.- Application of Allelopathy in Agriculture and Forestry.- Progress and Prospect of Rice Allelopathy Research.- Rice Allelopathy Research in China.- Recent Advances in Wheat Allelopathy.- Sorghum Allelopathy for Weed Management in Wheat.- Allelochemicals in Pre-cowing Soils of Continuous Soybean Cropping and Their Autointoxication.- Autotoxicity in Agriculture and Forestry.- Black Walnut Allelopathy: Implications for Intercropping.- Plant Growth Promoting Rhizobacteria and Mycorrhizal Fungi in Sustainable Agriculture and Forestry.- Utilization of Stress Tolerant, Weed Suppressive Groundcovers for Low Maintenance Landscape Settings.- Allelopathy in Forested Ecosystems.
Article
The effects of caffeic acid, chlorogenic acid, t -cinnamic acid, p -coumaric acid, ferulic acid, gallic acid, p -hydroxybenzaldehyde, 5-sulfosalicylic acid, vanillic acid, and vanillin on growth, photosynthesis, water relations, and chlorophyll content of 3-week-old soybeans [ Glycine max (L.) Merr. ‘Tracy’] grown in aerated nutrient solution were determined. At concentrations of 10 ⁻³ M, caffeic, t -cinnamic, p -coumaric, ferulic, gallic, and vanillic acids significantly reduced dry matter production, leaf expansion, height, leaf production, net assimilation rate (rate of dry matter production per unit leaf area), and leaf area duration (total leaf area present during treatment interval). Chlorogenic acid, p -hydroxybenzaldehyde, 5-sulfosalicylic acid, and vanillin at 10 ⁻³ M did not inhibit growth. None of the 10 compounds at 10 ⁻⁴ M inhibited growth. At concentrations of 10 ⁻³ M, caffeic, t -cinnamic, p -coumaric, ferulic, gallic, and vanillic acids severely reduced net photosynthetic rate and stomatal conductance of single, fully expanded leaves. These same compounds also caused marked reductions in leaf chlorophyll content, with net losses of chlorophyll occurring over an 86-h period after treatment.
Article
Root exudate is one of the ways for plant communication to the neighboring plant and adjoining of microorganisms present in the rhizosphere of the root. The chemicals ingredients of the root exudates are specific to a particular plant species and also depend on the nearby biotic and abiotic environment. The chemical ingredient exuded by plant roots include amino acids, sugars, organic acids, vitamins, nucleotides, various other secondary metabolites and many other high molecular weight substances as primarily mucilage and some unidentified substances. Through the exudation of a wide variety of compounds, roots may regulate the soil microbial community in their immediate vicinity, cope with herbivores, encourage beneficial symbioses, change the chemical and physical properties of the soil and inhibit the growth of competing plant species. Root exudates mediate various positive and negative interactions like plant-plant and plant-microbe interactions. The present review has been undertaken to examine the possible role of root exudates on the removal of the polluted matter and nourishing the neighboring microorganisms present in the rhizosphere of the root.