MINERIALIZATION IN SOIL AND MICROGANISMS

COURSE CODE MCB 315

1. Introduction

Soil ecosystem is a living and dynamic environment, habitat of thousands of

microbial species, animal organisms and plant roots, integrated all of them in the
food webs, and performing vital functions like organic matter decomposition,
nutrient cycling and release, promote plant growth, receive, hold and release water,
transfer energy in the detritus food chain, and act as an environmental buffer. soil
is also where plant roots productivity represent the main and first trophic level
(producers) [4], the beginning of the soil food

web and of thousands of biological interactions [5, 6]. In Agroecosystems, the

different activities practiced by man will affect all the biological processes carried
out above- and belowground, including soil biodiversity and soil food webs [7],
depending of the kind of

agroecosystem (traditional or intensive), the geographical region, the crop

management, and social and economic interests. Human societies have developed
several kinds of agroecosystems, from traditional/subsistence, multicropping, to
intensive and highly

technified crops [8, 9, 10] however, plant pathogens and pest diseases are a
common component of the agroecosystem, and by some degree all of them are
affected [11]. In this sense, a relevant and unavoidable problem is the soil
degradation and contamination in agroecosystems; plant diseases caused by
soilborne plant pathogens (SBPP) are of great importance because most of the
strategies applied for their control are directed to the soil [12]. Management of
SBPP and diseases require a broader view and a thorough ecological knowledge of
the soil ecosystem, considering the improvement and conservation of the soil
biodiversity and the soil food web structure and function, and studying the soil as a
dynamic ecosystem in time and space. Plant pathologist and agronomist mustknow
about the importance of the soil ecosystem, its biodiversity, the different and
multiple functions soil organisms perform, howevery and all soil organisms are
connected through different relationships established as a result of natural selection
forces, and how

microorganisms such as bacteria and fungi. These microorganisms are omnipresent

and found in various components of earth such aswater and soil. Bacteria and fungi
are also known to improve soil struc-ture by promoting the formation of soil
aggregates and pores within (Degens, 1997; Miller and Jastrow, 2000). Fungal
cellsrelease mucilaginous exudates which are mainly composed of extracellular
surface polysaccharides; cell wall polysaccharide sand somatic or intracellular
polysaccharides located inside the cytoplasmic membrane. Extracellular
polysaccharides are mainly responsible for the formation of aggregates, which are
beneficialfor improving porosity and aeration in soil. Moreover, bacteriarelease
exopolysaccharides that form organo-mineral complexeswhich help to bind soil
particles into aggregates (Degens, 1997).Experimentally it has been proved that
soil structure is not only influenced by the mineral constituents of the soil but also
by the presence of micro-organisms in pores (Gupta and Germida, 2015).On the
other hand, exudates from bacteria, fungi, decomposed cellsas well as plant and
animal residues especially in soils managed byorganic inputs are also responsible
to boost the soil organic matter which in turn improve the soil structure, function
and quality. Reconnoitering the mechanisms of bacterial and fungal inoc-ula
together with organic fertilizer could be very valuable toolfor improving soil
fertility (Song et al., 2015) and aggregation.Such strategy may help in planning a
chemical fertilizer-free, envi-ronmental friendly integrated soil nutrient
management to meetglobal food demand which may further help in reinstating
thefertility of degraded soil. In this regard, various aspects of the bacterial and
fungal-mediated soil nutrient acquisition processe sand aggregate formation have
also been recognized. Co-inoculation of bacteria and fungi with organic
amendments could be an elo-quent approach for sustainable management of soil
fertility andcrop production (Minerdi et al., 2001; Rillig et al., 2002; Mortimeret
al., 2008; Caesar-Tonthat et al., 2014) in strongly degraded soil.In order to avail
maximum benefits from such approaches, thereare still many undeveloped facets
that need to be explored infuture studies. The mechanistic understanding of
bacterial andfungal-mediated soil nutrient enhancement and aggregation is
stillunderdeveloped. Novel field-based studies and experiments undercontrolled
conditions need to be planned to lend better accuracy inthe understanding of
microbial influenced soil fertility and struc-tural attributes. The main objective of
present review is to highlightand discuss current knowledge on the mechanisms
used by bacte-ria and fungi inocula to influence soil nutrient bioavailability (N,
P,K and Fe; other nutrient are not in the scope of this review) andaggregation. We
will discuss the effectiveness of these microbeswhen inoculated solely, as co-
inoculant or in combination withorganic fertilizer in improving fertility and
aggregation stability of degraded soils.

Various species of bacteria and fungi play a key role in improv-ing soil fertility.
These microbes increase organic matter that booststhe availability of N, P, K and
Fe in soil (Egamberdiyeva and Höflich,2004; Caesar-Tonthat et al., 2014; Leifheit
et al., 2015). Additionally,they also produce organic acids for the mobilization of
nutrientsand facilitate their plant uptake from the rhizosphere. The simi-larities or
differences in bacteria and fungi to influence nutrientbioavailability and aggregate
formation are discussed in Table 1.In this manner, the application of chemical
fertilizers in agro-ecosystems can be greatly reduced (Figueiredo et al., 2011a).
Hence,application of microbial inocula would not only help the farmers toreduce
the additional costs of chemical fertilizers but also assistin obtaining high crop
yield. Most of the processes through whichmicrobial inocula promote soil fertility
are not fully understood,however it is believed that microbes use several direct and
indirectmechanisms (Glick, 2012). These are highlighted and reviewed
inforthcoming sections.2.1.1. Nitrogen fixationNitrogen (N) is an essential nutrient
required by plants fortheir growth and metabolism. It is often lost through leaching
oremission thus limiting its availability in most of the cultivatedsoils. Although N
is present abundantly in atmosphere in the formof diatomic (N2)molecule, but its
structure makes N2moleculeinert. However, reduction of N2molecule into N is a
complex pro-cess which requires input of huge amount of energy (Postgate,1982).
Prokaryotic microorganisms known as diazotrophs fix atmo-spheric N2in the form
of ammonia (NH3) through their normalmetabolic process (Riggs et al., 2001;
Galloway et al., 2008). Thesemicrobes are free living organisms present in the bulk
soil (Reedet al., 2011) that mainly includes Cyanobacteria, Proteobacteria,Archaea,
and Firmicutes (Demba Diallo et al., 2004; Duc et al., 2009).Some of these
organisms (Azotobacter and Azoarcus genera) arealso present at comparable
densities in the rhizosphere and bulksoil. However, there are other bacteria from
genera Herbaspirillumand Azospirillum that colonize only in the rhizosphere
(Mrkovackiand Milic, 2001; Malik et al., 2002; Bashan et al., 2004; Bashanand
De-Bashan, 2010). Rhizobia has the capability to infect rootsand induce the
formation of root nodules (Stacey, 2007). There-fore in the field of N fixation,
most of the researchers speciallyfocus on rhizobium-legume symbiosis due to
higher impact onprimary productivity of the agricultural ecosystem (Rengel,
2002).The establishment of this association results in the formation ofhighly
specialized organ called ‘nodules’ that are formed on theintracellular root of
symbionts, on which bacteria colonize. Suchbacteria mainly belong to the family
Rhizobiaceae that develop ahighly specific interaction with the infected root. This
interactionconsists of several stages which involves the exchange of
complexsignals between the bacterium and plant (Sprent et al., 1989). Bac-teria fix
N2 through a complex enzyme system called nitrogenase(Kim and Rees, 1994) and
this enzyme system exists as two sep-arable components; (1) dinitrogenase
reductase (Fe-protein) and(2) dinitrogenase metal cofactor. The former enzyme
serves as anexclusive electron donor with high reducing power whereas thelater
(substrate reduction component) accepts the electrons energyand convert inert
N2molecule into NH3. In order to produce onemole of NH3, 16 moles of
adenosine triphosphate (ATP) is requiredby these microbes (Hubbell and Kidder,
2009), who obtain thisenergy by oxidizing organic molecules. Free-living bacteria
mustobtain this amount of ATP from other organisms, while photo-synthetic
microbes (cyanobacteria) use self-generated energy fromphotosynthesis process.
Other microbes like associative and sym-biotic nitrogen-fixer get these compounds
from the rhizosphereof their host plant (Hubbell and Kidder, 2009). The chemical
reac-tion of microbial N fixation (Postgate, 1998) is shown in followingequation.
N2 + 8 H+ + 8e− + 16MgATP → 2NH3 + H2 + 16MgADP + 16Pi

N2 fixation in degraded land Phosphorus (P), potassium (K) and sulphur are
generally lim-ited in degraded soils. Under nutrient limited conditions, these
nutrients affect the N2 fixation by reducing the growth of N-fixingbacteria, nodule
formation and functioning, as well as affecting host plant growth. Meta-analysis
study of Divito and Sadras (2014) confirmed that nodule production, activity and
their number arelimited more than plant shoot biomass in response to the
deficiencyof P, K and sulphur. Moreover, P limitation in soil decreases theactivity
of nitrogenase enzyme in N-fixing bacteria, because both autotrophic and
heterotrophic bacteria require high ATP for cellu-lar N2 fixation (Reed et al., 2007,
2011; Pérez et al., 2014). Similar to nutrient deficiency, soil moisture is another
major factor that influ-ences nodule formation or retardation of nodule growth.
Wateravailability in soil is related to water holding capacity which is verylow in
degraded soil (Montgomery, 2007). According to Sinclairet al. (1987) water
limiting conditions severely affect nodule for-mation in soybean crop. Thus in
degraded soils, N2 fixation andother related functions (decomposition,
mineralization, enzymesor organic production) of microbes are severely affected
due to lossof fertility and water holding capacity. Soil microbes adapt vari-ous
strategies to cope with such deficiencies. These strategies are . Mechanisms used
by microbes to reinstate the fertility of degraded soils3.1. Fungi and N2fixationIn
light and moderately degraded soils, AM fungi play an impor-tant role in
N2fixation by providing favorable environment for the bacteria to infect plant root.
As indicated by Puppi et al. (1994) and Nasto et al. (2014), AM colonization can
fulfill high demands of Prequired by nitrogenase enzymes for N2fixation when
inoculated with N2fixer rather than non-N2fixer to increase the growth ofhost
plant. Many studies reported that co-inoculation of bacteria orlegumes with AM
fungi increased N2fixation ability of legumes ortrees (Ibijbijen et al., 1996; Bona
et al., 2014). However, this increasein N2 fixation ability does not necessarily
mean that growth and productivity of host plants will increase. Meta analyses
studies by Larimer et al. (2010) and Kaschuk et al. (2010) have shown that co-
inoculation of AM fungi with rhizobia or free living N-fixingbacteria resulted in a
non-additive effect on the growth of hostplant. However, plant growth responses
were positive when AMfungi or N2fixer were inoculated alone. Extra-radical
hyphae of AMseem to have ability to fix atmospheric N2through N-fixing bacteria
present in mycelia. According to Bianciotto et al. (1996) and Minerdiet al. (2001),
extra-radical hyphae of AM fungi have the poten-tial to protect the intracellular
bacteria of the genus Burkholderia.One of the most important ecological
significance of these bacte-rial genera associated with fungi is to have the potential
abilityto fix atmospheric N2, either in the nodules or as free living form.In this
association, bacteria reside in the thickest host structures(i.e. mycelium) to shelter
the enzyme complex from oxygen and fixatmospheric N2in this structure (Minerdi
et al., 2001). However,the mechanism to fix N2in the mycelium (Kneip et al.,
2007), stillneeds to be determined and need continuous research efforts to focus on
this area especially for the recovery of nutrient depleted degraded soils.

Differences in bacteria and fungi for nutrient bioavailability and aggregate

formation. No. Nutrient/structure Bacteria Fungi 1 Nitrogen (N) Diazotrophs fix
N2 as ammonia through their metabolic process. Bacteria from family
Rhizobiaceae living in the soil infect plant root to form nodules and fix N in this
structure through complex enzymes system. Fungi do not fix N but provide growth
limiting nutrients (i.e., carbon and P) to bacteria for N fixation. Also, in mycelium,
fungi provide shelter to bacterial enzyme system from O2 to fix N. 2 Phosphorous
(P) P solubilization or availability is enhanced by P mineralization as well as well
as production of siderophores and organic acids in the soil. Increase P
bioavailability through mineralization in soil, mycelial transport, P solubilization
by siderophores, N assimilation and CO2 release. 3 Potassium (K) Bacteria release
various types of organic acids to solubilize K in the soil through various processes
such as acidolysis, chelation, complexolysis and exchange reactions. Influence K
mobilization through mycelial transport as well as by K solubilization process that
involves the release of H+, CO2 and organic acid such as citrate, malate and
oxalate. 4 Iron (Fe) Production of siderophores which has affinity to chelate and
solubilize iron from mineral or organic compounds. Translocate Fe from mineral to
organic soil horizon for decomposition and mineralization, and release chelator
(siderophores) for Fe translocation in soil. 5 Aggregate formation Produce
peripheral slime polymers and decompose organic material to form organo-mineral
products that are associated with soil particles to form aggregates. Hyphal network
entrap soil particle and forces them together. Production of mucilages,
polysaccharides and extracellular compounds as well as soil proteins such as
glomalin and hydrophobins.

How do fungi influence N2fixation?As discussed above, fungi indirectly affects

N2fixation through bacteria present in mycelia. During this process, fungi
translocatecarbon and P from the plant roots to the associated bacteria for
N2fixation. In this regard Paul and Kucey (1981) observed a symbiotic association
of bacteria and fungi with legumes, which may indicate a competition between
these microbes for carbon provided bylegume roots. However, this competition is
masked by the associ-ation of AM fungi with Rhizobia who provides a high
amount of Pfor nitrogenase enzyme complex (Puppi et al., 1994). The
enhancedN2fixation ability of the bacteria through AM association is deteriorated
by the depletion of P zone in mycorrhizosphere. AM fungialso provide plant
derived carbon to increase the potential abilityof non-symbiotic N2fixer such as
Herbaspirillum and Azospirillum. During this association, AM fungi decrease the
total amount of sugarand enhance nitrogenous compounds in mycorrhizosphere
(Jonesand Oburger, 2011). The changes occurred in this region strengthen the
carbon limitation of N2 fixer over other microorganisms which could limit their
performance to fix N2(Veresoglou et al., 2012).On the other hand, non-symbiotic
N2fixer are versatile organisms which possess the ability to adapt the carbon and N
limiting conditions (Blaha and Schrank, 2003). Their performance is not
affectedby the changes that occur in rhizosphere due to AM fungi colo-nization
(Veresoglou et al., 2012). Therefore, it is not always truethat AM fungi association
with plant and rhizobia would be benefi-cial for long term recovery of degraded
land as proposed by Chaeret al. (2011). In such condition, carbon limitation could
be replen-ished by organic amendments in addition to the synergistic effectof co-
inoculants such as N-fixing bacteria and AM fungi. Such phe-nomenon needs to be
further investigated for sustainable recovery of degraded soils. In this regard,
efforts are done to figure out thesole inoculation of N-fixing bacteria or AM fungi
with organic fer-tilizers and obtained encouraging results for the rehabilitation of
degraded land under semi-arid environment (Medina et al., 2010; Mengual et al.,
2014a; Mengual et al., 2014b).3.2.

Phosphorus mobilization Phosphorus (P) is another essential and growth-limiting

nutrient in agro-ecosystems (Smil, 2000). However, this limitation could be
fulfilled by external inputs to the soil in the form of organicas well as synthetic
fertilizers (Fig. 2). The later form of fertilizeris formulated from the rock
phosphate reserves. Therefore, many researchers are concerned about rapid
diminution of the world’sP reserves due to continuous mining for P (Cordell et al.,
2009;van Vuuren et al., 2010). Recently, there is a contradiction in views regarding
the availability of world P reserves. Simulation studies suggested that global P
production will reach to maximum by 2033(Cordell et al., 2009) while other
researchers had concluded that almost 50% of the currently available P reserves
will be mined by2100 (van Vuuren et al., 2010).In most of the agricultural soils
(productive or degraded), hugereserves of inorganic or organic P are present in
immobilized or unavailable form. Fonte et al. (2014) observed no difference in
total P in degraded and productive pasture, however in this study,organic P was
40% higher in latter pasture soil. They explained thisby showing the presence of
higher inorganic P in degraded than productive pasture which was strongly
adsorbed or occluded in this soil. In fact, inorganic P is highly reactive with some
metal com-plexes such as iron, aluminum and calcium (Fig. 2), which lead to75–
90% of P adsorption or precipitation in the soil (Igual et al., 2001;Gyaneshwar et
al., 2002); Fig. 2). Even after the application of P fer-tilizers to the soils, a very low
amount (micromolar) of P is available to plants as most of the P is adsorbed or
becomes sparingly soluble(Gyaneshwar et al., 2002); Fig. 2). Microbial inocula
such as bacteria mobilize native and inherited soil P as wellas any applied
insoluble finely ground rock P. Such type of inocula are now termed as P-
mobilizing microbes (Owen et al., 2015) ratherthan previously referred as
phosphate-solubilizing microorgan-isms (Rodrı´ıguez and Fraga, 1999; Rodriguez
et al., 2004; Dastageret al., 2010; Jones and Oburger, 2011). As these inocula do
not only solubilize P, but they also mobilize its organic form through miner-
alization (enzymatic hydrolysis) and facilitate the translocation ofphosphate (Owen
et al., 2015); Fig. 2). Microbes are responsible formobilizing the soil P unavailable
for plants through their direct andindirect effects. In direct processes, (i) microbes
solubilize P by low-ering the pH (through proton extrusion) of external medium
andproducing low molecular weight organic anions (Fig. 2) like suc-cinic, citric,
gluconic, _-ketogluconic and oxalic acids (Chen et al.,2006). These anions are
exchanged for P on adsorption sites of soil,the process commonly referred to as
ligand exchange (Jones andOburger, 2011; Zhang et al., 2014). Hydroxyl and
carboxyl groupsof these acids chelate the cations bound to phosphate thereby con-
verting it to soluble forms (Miller et al., 2010). (ii) In addition,the inocula
hydrolyze organic P compounds by producing phos-phatases or phytases (Fig. 2).
Besides there are several ways throughwhich indirect mobilization of P can be
carried out by these inoc-ula: (i) Microbes release CO2during respiration which is
dissolvedin water (present in the soil pores) to form carbonic acid, thus sol-
ubilizing P by decreasing the pH of mycorrhizosphere (Marshner,1995) (ii)
Microbes release proton (H+) during assimilation of NH4+as a result of which the
soil pH is lowered and hence solubilize theavailable P (Illmer and Schinner, 1992)
(iii) P solubilizing microbes have the ability to remove and assimilate phosphate
from the soilin order to re-establish the P equilibrium, in this way they stimulatethe
indirect dissolution of Ca–P (Halvorson et al., 1990); (Fig. 2).

Potassium Potassium (K) is another vital nutrient and considered as a key

parameter of soil fertility and plant growth. In most of the soils, Kis present in very
small amount ranging from 0.04 to 3%. Despitebeing in limited amount, 98% of
this K is bound within phyllosili-cates structure (Shelobolina et al., 2014). This is
the layer of silicate minerals found in silt and clay fractions of the soil. The
remaining2% exists in soil solution or on exchange sites to become avail-able for
the plants (Sparks and Huang, 1985). Hence, soil fertility isdecreased due to low
availability of this nutrient which is normallyfulfilled by commercial fertilizer (i.e.,
KCl), thus elevating the inputcost of the farmers. Recently, few microbial strains
were isolatedwho had an ability to oxidize in the first step Fe2+from
primaryphyllosilicates mineral in such a way that they release iron andK from
these minerals (Shelobolina et al., 2014). Bacterial inoc-ula (Neutrophillic
lithotrophs) utilize structural Fe2+in biotite as anelectron donor for their
metabolism in order to produce energyand oxidize biotite (Shelobolina et al.,
2014). The microbes whichoxidized biotite (Fe2+-bearing mica) include
Bradyrhizobium japon-icum, Cupriavidus necator, Ralstonia solanacearum,
Dechloromonasagitate, and Nocardioides sp . In addition to this, Sheng and
He(2006) suggested that inoculation of B. edaphicus NBT strains andits mutants
increase the production of citric, oxalic, tartaric, suc-cinic, and _-ketogluconic
acid. These acids lead to K mobilizationfrom K-containing minerals (e.g. mica,
biotite, kaolinite and smec-tite) and chelation of silicon ions (Han and Lee, 2005;
Sheng andHe, 2006).3.3.1.

Fungi and K mobilization In addition to bacterial strains, mineral form of K is

solubilized byfungi through releasing organic acid anions which mainly
includescitrate, malate and oxalate (Meena et al., 2014). According to Wuet al.
(2005), K uptake was increased in corn crop after inoculationof G. mosseae (now,
Funneliformis mosseae) and G. intraradices (now,Rhizoglomus intraradices)
(Sieverding et al., 2014). In degraded soil(acidic), K solubilization was higher than
calcium and magnesiumafter inoculation of AM fungi compared to un-inoculated
control(Clark et al., 1999). Inoculation of Aspergillus terreus and Aspergillusniger
increased the K level in soil solution by solubilizing K frominsoluble feldspar and
potassium aluminum silicate (Prajapati et al.,2012). This was related to the
production of organic acids espe-cially by A. terreus which shows higher K
solubilization than A.niger . Moreover, other studies have reported that A. niger
also pro-duce organic acids and trace elements during rock
solubilization(Vandenberghe et al., 1999; Mirminachi et al., 2002).3.3.2.

How do bacterial and fungal inocula increase K mobilization?The major processes

involved in mobilizing K are acidolysis andcomplexolysis exchange reactions
(Uroz et al., 2009). During aci-dolysis, soil inocula such as bacteria or fungi
decrease the local pHby producing succinic, citric, gluconic, -ketogluconic and
oxalicacids (Fig. 2). Production of protons (H+) and organic acids anionsnot only
enhances the chelation of cations which are bound to K butalso helps for acidolysis
of surrounding environment of microbes(Uroz et al., 2009; Zarjani et al., 2013;
Parmar and Sindhu, 2013).During the process of acidolysis, rhizospheric microbes
can chelateAl and Si cations associated with K minerals and by doing so theyalso
enhance the exchangeable K in soil solution (Römheld andKirkby, 2010).
Consequently, microbes not only synthesize but alsodischarge H+, inorganic and
organic acids to acidify their own cells,rhizosphere and surroundings of K
minerals. This play an impor-tant role in mobilizing or solubilizing insoluble form
and structuralunavailable forms of K compounds in to soil solution resulting
anincreased K availability in rhizosphere (Goldstein, 1994; Abou-el-Seoud and
Abdel-Megeed, 2012).

3.4. Role of bacteria in Fe mobilizationIron is the fourth most abundant element

available on earthand predominantly exists in nature in ferric (Fe3+) form. It
isconsidered as one of the key micronutrient for soil fertility andis also needed by
all kind of living organisms. It is sparingly soluble, therefore not readily available
for plant or other biota like microbes in aerated soil. Moreover, in soil, ferrous
(Fe2+) is oxi-dized to Fe3+thereby forming insoluble compounds and leaving
avery low amount of iron for microbial or plant assimilation (Ma,2005). Therefore,
to fulfill iron requirement for normal growth,tough competition exists among
bacteria, fungi and plant in the rhi-zosphere. In such circumstances, some strains of
bacteria (Sharmaet al., 2003; Vansuyt et al., 2007) synthesize low-molecular
massproteins known as siderophores. These molecules have high affin-ity to
chelate (Machuca et al., 2007; Miethke and Marahiel, 2007)and solubilize iron
from mineral or organic compounds.

Generally,siderophores have high affinity to form complexes with

Fe3+(1:1).Uptake of the complexes by the cell membrane of both Gram posi-tive
and negative bacteria reduces Fe3+–Fe2+. Later cell membrane expel these ions
from the siderophores into the cell (Boukhalfa andCrumbliss, 2002) by linking its
inner and outer membranes, a mech-anism called “gating”. In this way
siderophores solubilize iron from unavailable minerals or organic compounds in
iron limited con-dition (Indiragandhi et al., 2008). Additionally, bacteria produce
extracellular siderophores which deprive pathogenic organisms produced under Fe
limited condition and form complexes with other heavy metals (Zn, Pb, In, Cu, Ga,
Cd and Al) (Schalk et al.,2011) and radio nuclides including U and Np (Kiss and
Farkas, 1998;Neubauer et al., 2000). Presence of such heavy metals encourages the
bacteria to produce siderophores which chelate the metal to increase Fe availability
in the rhizosphere of these soils (Wang et al.,2002). Such bacteria play a vital role
in elevating heavy metal con-centration by phytoextraction through enhancing the
activity of antioxidants. Hence, siderophores produced by microbial inocula also
play a key role in alleviating the stresses imposed on plants through heavy metals.

3.5. Interaction between bacteria and fungi inocula to improve nutrient

bioavailability in soil Fungi and bacterial inocula interact with plant roots to
improve nutrient availability in soil for plant uptake (Glick, 1995; Smith andRead,
2010; Prakamhang et al., 2015); Tables 2 and 3). For this pur-pose, the co-
inoculation between bacteria–bacteria, fungi–fungi orbacteria–fungi species is also
significantly acknowledged in recentstudies (Tytova et al., 2013; Leifheit et al.,
2015; Nguyen and Bruns,2015; Ortiz et al., 2015; Prakamhang et al., 2015). In
these inter-actions, mycelium of AM fungi release carbon compounds whichwill
act as energy source for soil microorganisms in the mycor-rhizosphere, though the
carbon products are in small amount thanalready present in rhizosphere (Andrade
et al., 1997). Similarly, bacteria also exude carbon compounds which increase the
AM fungihyphal growth and its root colonization (Barea et al., 2005).

During the interaction among Rhizobia, AM fungi and legume, AM fungi enhance
the growth and yield of legume by providing waterand nutrients, especially P
which increases Rhizobium N2 fixation through influencing energy production
pathways (Minerdi et al.,2001; Mortimer et al., 2008). Bacteria enhance P
availability foruptake of AM fungi and plant through phosphatase enzyme
andorganic acid production in the soil (Owen et al., 2015). Thus, theirco-
inoculation tends to increase P and N availability in soil (Table 4).Both fungi and
bacterial inocula increase the nutrient availabil-ity in the soil solution through
organic matter decomposition, Nfixation, P, K and Fe mobilization (Fig. 2). For
instant, effect ofco-inoculation of plant growth promoting bacteria and Bradyrhi-
zobium increase the soybean seed yield up to 44% per hectare thantheir lone
(single) inoculant form (Prakamhang et al., 2015). Similarly co-inoculation of B.
thuringiensis or Ps. putida with AM fungiincrease P by 44 and 35% in Trifolium
repens respectively, while Kcontent was increased by 128 and 285%, than their
lone inocula-tion (Oritz et al., 2015; Table 4).

Hence, interactions among soil microbes in the soil rhizosphere positively affect
soil fertility and provide highly valuable ecosystem services. Therefore use of
these inocula can be exploited in order to increase yield, reduce chemicalinputs,
and develop an efficient form of sustainable fertilizer man-agement in agro-
ecosystems (Bhattacharjee et al., 2008; Nguyenand Bruns, 2015; Owen et al.,
2015) especially in degraded soils.In general, it is very clear from the above
mechanistic discus-sion that lone microbial inoculum could not be very effective
ininfluencing the bioavailability of various nutrients (Table 4); there-fore co-
inoculation of microbes could prove to be more beneficial in recovery of degraded
soil. However, some strains of bacteriaor fungi can possess more than one
mechanism and may prove to withstand under water limited or nutrient depleted
condition,therefore could be potential option for reinstating the lost functions of
degraded soils

4. Soil structure Destruction of soil structure is one of the most important indi-
cator of soil degradation which is mainly caused by loss of organicmatter through
intensive soil management practices and land use changes (Oldeman et al., 1990;
Montgomery, 2007).

However, soil structure plays a central role in crops management and thus agri-
cultural ecosystems sustainability (Rillig et al., 2002). This can be defined as size,
shape and three dimensional arrangementsof organic or mineral complexes
(aggregates) and pores in sucha manner that affect pore continuation, water
infiltration andwater holding capacity (Bronick and Lal, 2005). According to
Tisdall(1994), soil structure is an arrangement of individual soil parti-cles formed
from sand, silt and clay. These are bound togetherthrough organic, inorganic or
chemical forces in order to formaggregates. Single particles adhere together more
strongly with surrounding particles to form micro-, (<250 _m) and macroag-
gregates (>250 _m diameter) size fraction (Kemper and Rosenau,1986). Soil
aggregates support root growth, a wide array of soilfunctions and ecosystem
processes. These include carbon storage34 M.I. Rashid et al. / Microbiological
Research 183 (2016) 26–41

Direct Mechanism

4.1.1 Nitrogen Fixation

Nitrogen (N) is most essential for plant growth and development and constitutes 78
of atmosphere. Although it exists in molecular form and not directly available to
plants use, it is available to plant through biological nitrogen fixation to in
ammonia. The process of nitrogen fixation carried out by oxygen sensitive,
nitrogenase enzyme complex. Nitrogenase enzymes convert atmospheric nitrogen
into ammonia using ATP as energy source. Biological nitrogen fixation is an
important growth parameter which affects plant growth and yield. Different
microbial species from various genera have ability of nitrogen fixation such as
Bacillus, Azospirillum, Pseudomonas, Enterobacter, Flavobacterium, Erwinia, and
Rhizobium (Silva et al. 2016).

Nitrogen-fixing microbes are categorized into (1) symbiotic nitrogen fixating

bacteria and (2) non-symbiotic nitrogen-fixing bacteria. The symbiotic
nitrogenfixing microbes include members of rhizobia which form symbiotic
association with leguminous plants. The non-symbiotic bacteria include
Azospirillum, Azotobacter, Gluconacetobacter diazotrophicus, and cyanobacteria.
Most of atmospheric nitrogen is fixed by symbiotic association while non-
symbiotic contributes only little. Some of these microbes for root nodule with their
respective host plant root product play a significant role in communication
between plant and microbes (Yan et al. 2008). Various stress conditions such as
drought and salinity inhibit nodulation, hence nitrogen fixation. Microbes are more
tolerant then host plant for drought and salinity. Nitrogenase enzymes responsible
for nitrogen fixation are highly sensitive to salinity and its activity highly reduced
under stress condition. The microorganism residing soil environment can cause a
dramatic change in plant growth and production through various regulators.
However, various free-living considers as plant growth promoting properties.
Biological nitrogen fixation is environmentally sound and economically viable
alternative of chemical fertilizers.

4.1.2 Phosphate Solubilization

Phosphorus is essential micronutrient and most vital element for plant growth and
development. Plants acquire phosphorus in the form of phosphate ions from soil.
Plant growth promoting rhizobacteria (PGPR) having phosphate solubilization
ability, available phosphorus to plant through mineralization, and solubilization.

Phosphorus solubilizing microbes govern biogeochemical cycle in natural

agriculture system. It is responsible for normal functioning of living organism.
However, most of phosphorus present in soil in insoluble form and unavailable to
plant. It plays a major role in sugar transport and stimulates root development
andphysiological process of plants and animals. The bioavailability of phosphate to
plant depends on plants, microbes, and surrounding environment. The
associationof plant microbes could enhance the mobilization of phosphorus in soil
and The Role of Microbes to Improve Crop Productivity and Soil Health 255
available to plants (Mehta et al. 2013). The phosphate solubilizing rhizobacteria
are ubiquitous in nature and their numbers vary from soil to soil. Phosphate
solubilizing microbes (PSM) such as bacteria and fungi mobilizes it by producing
organic acid and phosphatase. Many genera of bacteria and fungi are described as
phosphate solubilizing microbes (Yadav et al. 2014). The phosphate solubilizing
bacteria are belonging to PGPR and have wide implication in plant growth and
development

(Naseem and Bano 2014). The solubilization of phosphate may result due to either
decrease in PH or cations chelation. The effects of phosphate solubilizing microbes
vary according to soil properties. Majority of plant associated with rhizobacteria
under phosphorus deficient condition improve phosphorus uptake from soil.
Phosphate solubilizing microbes (PSM) as biofertilizer enhancing plant growth and
provide phosphorus in sustainable way to plants (Meena et al. 2015; Naseem and
Bano 2014).The principle mechanism involved in this includes lowering pH,
production of organic acids acid phosphatase. The release of organic acids from
PSB decreases the surrounding pH and release of phosphate ions from H+. Oxalic
acid, succinic acid, malic acid, etc., are important acid produced by plants. These
organic acids compete with binding sites on soil and available phosphorus to
plants. 2-ketogluconic acid is the most potent phosphate solubilizing acid produced
by phosphate solubilizing microbes. A numbers of microbes have capacity to
solubilize phosphate (Istina et al. 2015). Therefore, use of phosphate solubilizing

microbes in agriculture system is may be cost-effective and sustainable approach.

4.1.3

Siderophore Production

Iron (Fe) is a principle nutrient for almost all life form crucial for respiration,
photosynthesis, nitrogen fixation, and DNA biosynthesis. Iron generally
inaccessible to plants because of very low solubility Fe3+, and it forms hydroxides
and oxyhydroxides. Almost all living organism require iron for physiological and
enzymatic activity. Bacteria obtain iron secretion of iron chelating
compoundsiderophore which available to microbes (Schalk et al. 2011).
Siderophore is water soluble and has high oscillation constant for complexing with
iron. Siderophore can be divided into two group extracellular and intracellular
siderophore. Most of iron acquisition by plants occurs through microbial
siderophore. The production of siderophore by microbes depends on immediate
surrounding environment, and microbes may modulate the environment.
Siderophore has higher affinity for iron (Mishra et al. 2011). Siderophore easily
binds with iron and transport inside bacterial cell. The transport of iron begins
through the binding of siderophore–iron complex on material membrane. The
transport of iron from through bacterial membrane involves different transporter.
Once inside, the iron–siderophore complex reduced, ligand exchange to convert
iron (Fe3+) complex on bacterial membrane reduced into soluble Fe2+ species
(Rajkumar et al. 2010). ABC transporter (ATP-binding cassette) is involved in
transport of siderophore–iron complex (Braun and Hantke, 2011) Plant
incorporates iron from the bacterial siderophore through 256 A. Kumar and J. P.
Verma different means either through direct uptake of iron–siderophore or ligand
change reaction. The major effect of siderophore–iron includes chlorophyll a and
chlorophyll

b content of plant leaves. Pseudochelin A, a new siderophore of

Pseudoalteromonas piscicida S2040, shows siderophore activity against
Aspergillus fumigatus.

4.1.4 Phytohormones Production

Abiotic stresses cause change in balance of phytohormones in plants which result

growth inhibition. This change in hormones concentration also leads to

susceptibility to disease occurrences. A major auxin, indole acetic acid (IAA),
controls various physiological aspects such as plant development, cell signaling,
and induction of disease resistance (Sukumar et al. 2013). Indole acetic acid acts as
signaling molecule and affects expression of gene under different conditions

(Egamberdieva et al. 2015, Cassán et al. 2014; Li et al. 2016). The IAA production
varies and depends on microbes and environmental conditions. The growth of

plants depends on concentration gradient of IAA. This results in inhibition,

stimulation, and tissue differentiation. The low level of IAA induces root
elongation while higher level of causes laterals and adventitious root formation
(Ghosh et al. 2013; Tognetti et al. 2012). Phytohormones associated root
colonizing rhizobacteria effectively colonized and supply additional IAA for plant
growth and development (Sukumar et al. 2013). Ethylene is another ubiquitous
phytohormones and plays a crucial role in biotic and abiotic stress tolerance. It
causes cell elongation, root initiation and nodulation, leaf senescence, and fruit
ripening. Under stress condition, ethylene causes inhibition of root elongation and
root hair formation. To overcome this, negative impact bacterial ACC deaminase
hydrolyzes it into a-ketobutyrate and ammonia. It may be a source of nitrogen for
microbes. In addition, physiological process and stress tolerance especially drought
are regulated by another plant hormones abscisic acid. PGPR enhances the
concentration of abscisic acid during drought stress and makes plant to tolerant
stress (Meena et al. 2015; Porcel et al. 2014;). From the above discussion, it is
clear that the presence of phytohormones affects the endogenous mechanism of
plants and stimulates plant growth. The major effects of these phytohormones
include stimulation of lateralroot and root hair formations which facilitate nutrient
acquisition as well as water absorption (Belimov et al. 2014).

4.2 Indirect Mechanism of Plant Growth Promotion

The indirect effect of plant growth promoting bacteria occurs when they either
decrease or inhibit deleterious consequence of pathogen through various
mechanisms. The application of microorganism to control disease in plants is
known as The Role of Microbes to Improve Crop Productivity and Soil Health 257

biocontrol (Kumar et al. 2014). It is an environmentally sustainable and cost-

effective approach to ameliorate deleterious effect of pathogens. Various types of
antifungal and antimicrobial agent secreted by rhizobacteria help in disease
resistance. The major indirect includes competition for nutrient, antifungal
metabolites, induced systemic resistance(ISR) and niche exclusion. Rhizobacteria
have been reported to secrete many metabolites such as 2,4-diacetylphloroglucinol,
HCN, phenazines, pyrrolnitrin are important biocontroling agents.

Biotic Stress

Plants have been evolved various sophisticated (physical and chemical) method to

defense against pathogens. Chemical mechanism involved various chemical

interactions at different steps. However, some plants lake have weak response to
pathogen due to certain reasons. However, PGPR colonizes root surface and has
been showing significant beneficial effect to plants (Salas-Marina et al. 2011).
These PGPR activates plant defense response against pathogen and reduces crop
losses. Plant growth promoting rhizobacteria possess various mechanism of
defense against biotic stress. The mechanism defense against pathogen is trigger
through chemical messengers. The induction of resistance against pathogen is
generally of two kinds: systemic acquired resistance (SAR) and induced systemic
resistance(ISR) (Fig. 1). SAR is induced by pathogenic bacteria and ISR by
reducing disease rate (Nawrocka and Małolepsza 2013; Choudhary and Johri
2009). Both SAR and ISR adopted different signaling mechanism to induced
resistance. SAR involves accumulation of salicylic acid and pathogen-related (PR)
protein while ISR consists of ethylene and jasmonic acid (Dimkpa et al. 2009). The
synergistic effect of pathogen-related (PR) protein and oxidative enzyme causes
high protection against pathogens. Salicylic acid is an essential component for
development of systemic which acquires resistance. Non-pathogenic bacteria
induced systemic resistance in plants and phenotypically similar to systemic
acquired resistance (Wani et al. 2016). These colonizing bacteria cause an increase
in concentration of Chitinase and peroxidase plants leaves and root. The
effectiveness of SAR and ISR is wide spectrum and includes bacterial, fungal, viral
pathogens. The protection of plant to different pathogens includes inhibition of
pathogen growth through competition for nutrient and reduction in disease
symptoms (Ghazalibiglar et al. 2016). It is a highly beneficial, cost-effective, and
sustainable approach to protect plant from pathogens. Once this system of defense
activated increase the activity of enzyme such as peroxidase, catalase, superoxide
dismutase and guaiacol, etc. These enzymes protect cells from oxidative damage
due to reactive oxygen species and pathogen. In addition, several potential
components of bacteria also induced ISR membrane lipopolysaccharides and iron-
regulated siderophore. This defense mechanism provides resistance to pathogen
above-ground part of plants. ISR induced various changes in plant parts including
(1) change in epidermal and cortical cell wall

(2) level of enzyme

peroxidase, chitinase and phenylalanine ammonia lyase, and (3) expression of

stress-related gene (Choudhary and Johri). The effect of ISR and SAR varies from
plant to plant and depends on level of plant and microbes interaction. The
combined effect of ISR and SAR enhances the defense level of protection against
specific pathogens. Chithrashree et al. (2011) reported that PGPR mediate-induced
systemic resistance in rice against bacterial leaf blight caused by Xanthomonas
oryzae pv. oryzae. PGPR causes suppression of disease in plants by various
mechanisms such as competition for space and nutrient, antagonism and induced
systemic resistance

(Beneduzi et al. 2012). Pseudomonas and Bacillus are acted as biocontroling agent
and well known for their antagonistic and induced systemic properties.
Bacteriocins, siderophore, and antibiotics are potential molecule and have
antagonistic properties. Application of PGPR to seed and seedling also results
induced systemic resistance (ISR). So plant growth promoting rhizobacteria play
an important role in defense against various disease-causing agents (Choudhary
and johri 2009). It is a sustainable approach to overcome disease-causing agents in
economic and sustainable way.

. Soil biodiversity

The soil is an ecosystem, a living system where interplay mineral and organic
materials. Soils are built up through millions of years, from the parent rock layer to
the small sand, lime and clay particles derived from physical and chemical
intemperization processes, and from biological activities which perhaps be the
most important factor in the soils formation. Of the total soil components, organic
material represents 5 to 10%, from this percentage 10 to 20% is the active fraction,
from the active organic fraction only 20 to 40% are living organisms, and from
these 50% are fungi, 30% are bacteria and actinomycetes, 10% are yeasts, algae,
protozoa, and nematodes,and 10% are fauna. This means, the active microbial
biomass represents 90% of the soil living organisms. Another essential component
in soil biodiversity is the soil fauna which is divided in function of their size (mm)
into micro-, meso- and macrofauna. Microfauna includes Protozoa, Rotifers from
0.005 to 0.2 mm; mesofauna is composed by nematodes, arthropods, enchytraeids,
mites, springtails from 0.2 to 10 mm; macrofauna include animals like insects from
10 to 20 mm; and megafauna includes earthworm (≥ 20 mm), macroarthropods and
small mammals (cm)

Plant roots are another fundamental component of the soil biodiversity, they
represent the primary source of organic matter in soil, and the amount of root
production is relevant in the process of decomposition and cycling into organic
matter in soils. Roots are the subterranean organ of the plant, and they fix them to
the soil. Plants take water and nutrients from soil through the roots and the root
vascular system transport them to the upper parts of the plant; in some cases, roots
are a storage organ [19]. Root exudates and rhizosphere are relevant components
for root functioning, and they are essential for all the biological and soil microbial
activities like attraction of mutualist symbionts and pathogenic microbes, release
and cycling of nutrients, allelopathic processes [5, 6] and also for physical and
chemical soil characteristics such as soil aggregation and structure, cation
exchange capacity and pH [20]. Plant roots represent the first trophic level
(autotrophs entities) in the soil trophic web, from which microbes and small fauna
obtain their nutrients and energy [18].

Soil-borne plant pathogens (SBPP) are a component of the soil ecosystem, and also
members of the soil biodiversity; these microorganisms live part of their life in soil
and in the plant rhizosphere, but they also infect and damage the plant roots from
which they feed; in some way plant roots are their habitat. SBPP include organisms
from bacteria, fungi, oomycetes, nematode, protozoa groups and mesobiotic
entities like virus and viroids [11, 21].

3. Importance and function of soil biodiversity ¿who are here and what they do?

3.1 Bacteria and fungi

Bacteria and fungi participate in the rock intemperization (degradation) through

their biochemical enzymatic activity; these microorganisms initiate the soil
formation, and with it the important process of mineral transformation and nutrient
liberation [22]. As soil is formed and deeper, it is possible for other
microorganisms and larger organisms like protozoa, rotifers, nematodes, worms,
small arthropods, and also spores of bryophytes, moss, ferns, and mycorrhizal
fungi to arrive and to establish. When soil has enough deep and biological activity
is adequate for higher plant seeds to germinate and their root systems to interact
with the soil microbiome, it begins the formation of a plant community and in
time, with the integration of higher animals and through a successional process, the
establishment of a biome after hundreds and millions of years.

3.2 Soil bacteria

Certain groups of the soil bacteria community participates in the N cycle which
involve four stages or reactions:

a) Nitrogen fixation carried out by nitrogen-fixing bacteria (e.g. Rhizobium,

Azotobacter, Bradyrhizobium),
b) Ammonification performed by ammonifying

bacteria or decomposers bacteria (Bacillus subtilis, Pseudomonas fluorescens),

c) Nitrification accomplished by nitrifying bacteria

(e.g. Nitrosomonas: NO2 nitrite, Nitrobacter: NO3 nitrate), and d) Denitrification

realized by denitrifying bacteria (some species of Serratia and Pseudomonas) .

It must be noted that bacteria also participate in the C biogeochemical cycle, and
they play a crucial role in the regulation of C and N cycles during biological soil
crust succession in arid and semi-arid ecosystems [24].

It is important to indicate that some of these bacteria species besides to participate

in the Nitrogen cycle, like Bacillus subtilis, B. amyloliquefasciens,
Bradyrhizobium (Nod Factors), they also are involved in a complex network of
signaling pathways mediated by plant hormones like jasmonic acid, ethylene and
salicilic acid and in the release of volatile organic compounds which trigger the
induced systemic resistance (ISR) and the acquired systemic resistance (ASR) in
plants, in response to the presence of both beneficial microbes and plant pathogens
invasion and infection, and also to insect attack .

Some bacteria specific strains also produce different antibiotics, e.g., Pseudomonas
fluorescens F113 produces 2,4-diacetyl-phloroglucinol againstPythium spp. [31],
Bacillus amyloliquefasciens FZB42 produces bacillomycin and fengycin against
Fusarium oxysporum [32]; enzymes, and siderophores e.g., Pseudomonas putida
WCS358 against Pseudomonas syringae pv. tomato and Fusarium oxysporum f. sp.
raphani [33], which are important components in their performance as biological
control agents against plant pathogens [7, 34].

Another important activity performed by some soil bacteria is enhancing the plant
growth

a] through the production of growth regulators (hormones) like auxins (Indol

Acetic Acid, IAA), cytokinins, gibberellins, or ethylene, and these bacteria are
known as Plant-Growth Promoting Bacteria (PGPB) examples of bacteria species
involved in this activity are Pseudomonas fluorescens, P. putida, P. gladioli,
Bacillus subtilis, B.cereus, B. circulans, and bacteria in the genre Azospirilum,
Serratia, Flavobacterium, Alcaligenes, Klebsiella and Enterobacter [7].

3.3 Soil fungi

Fungi, organisms in the Kingdom Fungi, perform different and important functions
in soils, they are organic matter decomposers due to their great ability to degrade
complex substrates of plant origin [36]. Fungi participate in the mineral
degradation and in the release and cycling of nutrients; they are also involved in
the C and N cycling . These microorganisms are vital for soil functioning because
most carbon in our planet is stored in rocks and sediments [38]. They also
contribute to the soil particles aggregation and soil structure because of their
filamentous form and exudates [39]. In soils exist a complex and diverse fungal
community widely distributed [40]. This fungal community is composed by
different and important functional groups. One of the most studied is the
mycorrhizal fungi, which exists as mutualist symbionts in most of the plant species
in natural ecosystems and it has a long evolutionary history [41, 42]; some of them
develop a net of hyphae external to the roots and growing intercellularly in the root
cortex, they are ectomycorrhiza; but other mycorrhiza can penetrate the roots and
establish intracellularly in the cortex cells forming small

structures called arbuscules, they are named arbuscular mycorrhiza or

endomycorrhiza. Both kind of mycorrhiza help the plant host in the uptake of
nutrients from soil and protection against pathogens. Arbuscular mycorrhizae play
a central role in the Phosphorus cycle, but they are equally important in the
Nitrogen cycle [43, 44]. Mycorrhiza hyphae link the plants roots with the soil
particles, interconnect directly the root systems of two different individual plants,
and they also interact with different kind of soil microbes (synergistic and
antagonistic); even more, there is evidence of the extra radical mycorrhizal hyphae
associated with symbiont bacteria (hyper
symbionts) for acquisition of C [45]; therefore, ecto and endomycorrhizae fungi
play important functions in the physiology, ecology and evolution of their host
plants.

Fungal Endophytes are other important functional group of fungi, and they enter
and live inside the plants [25, 42]. Here, endophytes are defined as those
microorganisms (bacteria, fungi, virus) which live their life cycle or part of it
inside a plant, within asymptomatic tissues, performing and promoting a beneficial
functioning in the plant host, and enhancing its fitness in plant communities by
conferring abiotic and biotic stress tolerance; therefore, this relationship has
ecological and evolutionary importance .

Endophyte organisms can be found in different plant organs like roots, stems,
leaves, reproductive organs (e.g., vanilla flower ovaries)

and fruits (e.g., vanilla pods) [42, 48]. Endophytic fungi participate in different
plant functions, some of them enhance plant growth and nutrition and are referred
as Plant-Growth Promoting Fungi (PGPF) [25], and they also strengthen plant
defense against pathogens and insects below- and above-ground [46, 47].
Endophyte fungi control plant pathogens attack through different processes: niche
exclusion, antibiosis, predation, mycoparasitism and ISR induction [25]; it is also
possible to find hypovirulent pathogen isolates which will control more virulent
isolates as happens with Monosporascus cannonballus against monosporascus root
rot vine decline [49], or with Fusarium oxysporum strain Fo47 [50, 51]. Endophyte
fungi can express simultaneously more than one control mechanism against

plant pathogens as it was showed with Trichoderma isolates that besides attack
directly Botrytis cinerea, also induced systemic resistance to this pathogen [52].
Other fungal endophytes additionally of increasing plant biomass, confer drought
tolerance, and produce chemicals that are toxic to animals like insects [46, 47],
birds and small mammals and decrease herbivory [53]. Certain endophytic fungi
have an important role in physiological and biochemical aspects during
development of flower and chemical compounds, as is the case of Vanilla
planifolia compound vanillin [48]; researchers have found that fungal endophytes
inoculum from soil get into the roots through rhizosphere, but other endophytes
come from the fungal airborne inoculum and enter into the flower ovaries, and
later in the vanilla pods, participating in the vanillin process and therefore in the
vanilla flavor [48]. Endophyte fungi described as PGPF include important genera
like Fusarium, Trichoderma, Aspergillus, Penicillium, Colletotrichum,
Cylindrocladium, and others; some of them are nonpathogenic or hypovirulent
strains of plant pathogenic fungi .

Some soil fungi are pathogens of other microorganisms like bacteria [54], fungi
and nematodes [55], plants [11], insects and arthropods [47]; for instance,
Metarhizium anisopliae and Beauveria bassiana are endophytic and pathogenic in
insects, while Paecelomyces lilacinus is endophytic and pathogenic in nematodes
[55]; these fungi take part in the regulation of their hosts populations and they are
of relevance in the biological control and management of agroecosystems [46]. As
mentioned above soil fungi are included in several functional groups:
decomposers, mutualists (mycorrhiza), endophytes, pathogens, parasites, and
everyone of these activities are of great relevance for the soil ecosystem function.

3.4 Soil virus

Viruses are considered entities between living and non-living state,

quasiorganisms; they are composed by RNA or DNA molecules contained within
protein capsids, and they are mainly known as pathogens in plants, animal, and the
human being, causing important diseases. However, and fortunately, with the help
of the molecular biology methods, in the last 10 years there has been an
unprecedent interest and research about virus diversity and functions in different
environments: marine and soils [56, 57]. Knowledge about soil viruses are just
beginning, very little is known about their ecology in soils [2, 56, 58]. However, it
is suggested they participate in the biogeochemical cycling of Carbon [59], as well
as in short-term adaptation and long-term evolution of microbes [2], through their
infection like bacteriophage on beneficial bacteria (Rhizobia) and soilborne plant
pathogens (bacteria, fungi, virus, nematodes and

other soil organisms) [56]; they also perform horizontal gene transfer
(transduction) among bacteria [60]. Viruses impact the evolution and ecology of
their plant hosts, and they seem to have a mutualistic relationship rather than a
pathogenic one under experimental laboratory conditions [57]. On the other hand,
plant pathogen viruses cause great economic and yield losses in agroecosystems
where they are vectored by insects (aphids, white flies, trips, etc.), but they also are
transmitted by mechanical ways. There are just few soil borne plant pathogenic
viruses known so far, and they are transmitted by fungi and nematodes [61, 62].

3.5 Soil protozoa

Protozoa are other important component in the soil ecosystem and in the food web.
The free-living protozoa feed from microbes like bacteria and fungi (non-
pathogenic and pathogenic) [63], and also from algae; they are included in four
groups: flagellates, naked amoebae, testacea amoebae and ciliates. They contribute
to the regulation of these microbes population densities and dynamic. Protozoa
also play an important role in the nutrient turnover [64].

3.6 Soil nematodes

Soil nematodes are some of the most abundant invertebrate animals in soils, they
often reach densities of 1 million/m2; they are worm-like microorganisms and live
in water films or water-filled pore spaces in soils [64]. Many kinds of nematodes
are found in the rhizosphere of roots and root hairs because of the rich exudates.
They help to accelerate organic matter decomposition when they graze on bacteria,
fungi, and plant residues [18]. Nematodes biological characteristics like structure,
physiology, diverse reproductive patterns, and adaptability help them to inhabit
many and different environments [65].

3.7 Earthworms

Earthworms participate in the fragmentation, breakdown, and incorporation of the

soil organic matter, affecting its physical and chemical characteristics, and in turn
other soil biota organisms [2]. They also affect positively soil structure helping in
pores formation and particles aggregation, contributing to the soil aeration and
better water distribution. Earthworms play an important role in C and N cycling
[66]. Ecologically, earthworms promote diversity of fungal species and oribatid
mites through their casts from where they feed, and through reducing competition
between fungal species [67].

3.8 Soil arthropods

Arthropods in soil, are other important component in soil biodiversity. After

microbes and Protozoa, microarthropods play a very important role in soil
activities, they participate in the organic soil matter decomposition, nutrient release
and cycling, but they also enhance plant growth and the expression of induced
systemic resistance to pests in plants [68]; participate in the secondary seed
dispersal of higher plants and dispersal of sperm in lower plants like mosses [69];
they are involved in the regulations of population densities of bacteria and fungi
including plant pathogenic organisms and decomposition of agrochemicals [17,
70]. Micro arthropods like collembola, protura, diplura, isopoda and others are also
components in the soil food web, and they have been included as indicators of soil
health and soil disturbance because they live a sedentary life and express the
habitat conditions better than those organisms with a high dispersal capacity.

3.9 Soil-borne plant pathogens (SBPP)

Different groups of soil microorganisms bacteria, fungi, nematodes, protozoa and

entities like virus and viroids may also act as plant root pathogens, and they
received the name of soil-borne plant pathogens. These plant pathogens damage all
kind of plants in the different botanical taxa in both natural and worldwide
managed ecosystems; however, in agroecosystems their damages have economical
relevance due to the resulted crop yield losses [73, 74]. However, SBPP like other
plant pathogens play important roles in the structure, function, and diversity of
natural plant communities they also are important in the evolution of the plant
host-pathogen relationship [13, 79].

We can see, microorganisms have developed multiple, diverse and vital

relationships through time and space with all other organisms in the soil ecosystem
including plant roots, insects, and animals, and maybe most of these relationships
have been developed in response to nature selection forces throughout an
evolutionary time. It is necessary to mention that soil type [80] and soil
management [81] have an important influence on the diversity and structure of soil
microbial diversity, and in other soil microorganisms such as protozoa, rotifers,
nematodes, microarthropods, mites, and of course in worms, ants, termites and
small mammals [18]. However, plant roots, the principal C source in soils, and
their rhizosphere exudates determine in relevant way, the spatial structure and
diversity of the soil microbial and microorganisms community [82].

4. Trophic webs and complementary or interference interactions in soil “not

everything in life is food”

Since the beginning of soil formation from the parental rock, biological activity is
fundamental, many biological interactions are

established, and they initiate the soil trophic web. At the beginning, trophic webs
may be simple and with few components, but as root

biomass and their exudates increase in amount and different types, the soil trophic
webs are more complex in their biological diversity,

structure and functions. Plant roots are key components in soil function, they
provide most of the organic matter to the soils [4], they are the first trophic level in
the soil food web and represent the autotroph organisms (photosynthesizers) from
which heterotrophs organisms in the next trophic levels obtain their food and
energy [83]. Plant roots and specifically the rhizosphere region have a

transcendental role in the dynamic of soil microbial activities through the

development and release of rhizodeposits [6, 84]. Rhizodeposits include sloughed-
off root cap and border cells, mucilage, and exudates. The exudates are made up of
organic acids, amino acids, proteins, fatty acids, enzymes, sugars, phenolic
metabolites and other metabolites which are used by microorganisms

[84, 85]. Most of the root exudates are released at the root cap and the meristematic
zone behind the root cap; therefore, these regions are considered important for
determining the temporal and spatial activity and distribution of the microbial
communities [82, 84, 85].

Bacteria and fungi together with protozoa, plant pathogenic nematodes and fungi,
are in the second trophic level of the soil food web,

they are heterotrophs and they may function as decomposers, mutualists,

pathogens, parasites and root-feeders, and they are food for the third trophic level
(heterotrophs) that includes also nematodes and protozoa (bacterivorous and
fungivorous), and micro arthropods which work as shredders, predators and
grazers; organisms from this level are food for the fourth and fifth trophic levels
(heterotrophs)

which include higher level predators like arthropods, small mammals, birds [83].

Soil protozoa is a group of microorganisms which has not been studied so deep and
frequently like bacteria or fungi, and their role in the soil food web is sometimes
considered only like predators and grazers of microbes; however, they interact with
the root systems and bacteria in several and particularly important modes.
Bonkowski and Brandt [86] worked with an Amoebae, specifically with

Acanthamoebae sp. which is considered the most common soil free-living

protozoon, and they found this amoebae have a positive effect on root elongation
and branching in interaction with rhizobacteria, and mention that “Protozoa
function as bacteria-mediated mutualists promoting plant growth by hormonal
feed-back mechanisms and nutrient effects based on nutrient release from grazed

bacterial biomass”; these bacteria may also be involved in the different phases of
the soil nitrogen cycle. All these activities occur in the soil microbial loop [87], as
a relevant component of the soil food web.

Soil nematodes are considered important component in the soil food web; their soil
communities are usually large and species-rich, with different functional groups
(bacterivores, fungivores, herbivores, omnivores, predators, parasites and
pathogens), located in different trophic levels: root feeders nematodes in second
trophic level (decomposers), fungi and bacterial feeder nematodes in third
trophic level (grazers), nematode and protozoa predators in fourth trophic level
(higher level predators), in this way nematodes participate in the regulation of soil
microbial communities and indirectly in the flux of plant nutrients. Because of
their biological characteristics (they are ubiquitous, abundant and diverse), they
respond soon to changes in the soil environment, and for this reason

they have been considered as important indicators of the soil health [18, 70, 88,
89].

Plant pathogens and therefore soilborne plant pathogens are also an important
component inside the soil food web and the

ecosystems [90, 91]. They can be considered as microherbivores because they feed
over root systems, and later they are food for the

next trophic level, protozoa, nematode, rotifers, mites, and microarthropods.

4.1 Plant root diversity and their effects in soil diversity and soil food web

Plant roots are the principal biomass and C source in soils; as roots and their
exudates grow, they die and are decomposed by soil microorganisms and
incorporated into the soil organic matter [4]. Plant roots are of many different
types, lengths and architecture with a main and secondary roots and root hairs [92].
Roots produce different kind of exudates, and this is influenced by the plant
species,

soil physical and chemical conditions, soil temperature and moisture [82, 93];
however, root exudates are also affected by the rhizosphere microbial community
[82]. Root exudates supply nutrients, they prevent invasion by other plant species
(allelopathy), they function also like especially important chemical signals for
attracting symbionts (chemotaxis) e.g., rhizobia and legume, and other beneficial
organisms as plant-growth promoter bacteria and fungi [94, 95, 96]. With all the
diversity of plant roots, exudates, microbes, and other soil organisms it is expected
that in soil occur different interactions and responses which will be reflected in the
soil food web structure, diversity, and function [87].

Complexity of soil food web involves the species number and the number of
different kind of species (trophic and functional groups);
other characteristics as connectedness, interactions strength and length of chains
are important in the food web stability [97]. Throughout the soil food web the main
relationship is the vital need to obtain food and energy to accomplish the life
functions and the species survival; however this relationship acquire different
tonalities when each microbe or protozoa; or arthropod species in the soil,

develops different life strategies in response to specific natural selection forces,

and they establish inter- and intraspecific biological interactions like mutualism,
competition, parasitism, predation, pathogenism, fungistasis, antibiosis,
allelopathy, herbivory. These‘complementary’ interactions among species are of
ecological relevance because throughout them is built up the structure, function
and diversity of the soil community; Wardle [67], talks about some of these kind of
interactions as ‘interference interactions’ and he indicates that apply primarily to
interactions among fungi, among bacteria, and between bacteria and fungi.

Microbial symbionts (endosymbionts) play vital roles inside plants, fungi,

nematodes, protozoa, insects (termites, ants), etc. they are interactions inside
interactions and are “complementary interactions” that biological species have
been developed and evolved throughout time and space, improving their fitness
[25, 45, 56]; without them the host species would be unable to live. All kind

of symbionts are also components in the soil foo web; some of these relationships
are obligate or facultative, and others are intermediate between an obligate and
facultative behavior, depending on the press of natural selection forces and the
evolutionary time through which these species have been related [101]. What about
the role pathogens play in the soil food-web, and the role plant pathogens have in
different important functions for plant life: seed germination [77], seedlings and
young plant establishment [76], plant sexual reproduction and sexuality expression
[102, 103] and their role in plant community successional process? Ecological

functions of pathogens and specifically of plant pathogens, have received few

attention in the plant communities of wild ecosystems, even though Dinoor and
Eshed [105] drew the attention about the importance of studying plant pathogens
and disease

they cause in natural ecosystems, to better understand plant diseases in

agroecosystems and applied the best management
strategies.

To this point, we have seen that soil organisms play multiple and different
activities in the soil ecosystem and all of them are relevant for the soil dynamic
functioning (Table 1); in fact, the FAO Report of 2020 talks about “The
Multifunctionality of Soil Biodiversity” [107].

But what drives soil microbial diversity? Soil ecologists suggest that innate soil
spatial heterogeneity, or patchiness, would be a main environmental factor to
explain soil biodiversity at different spatial and temporal scales, arguing that soil
heterogeneity ‘provides unrivaled potential for niche partitioning, or resource and
habitat specialization, leading to avoidance of competition and hence coexistence

of species’ [1]. At the same time, the knowledge of the multiple and diverse
biological intra- and interspecies interactions that happen in the soil environment at
all levels of biological organization, and taking as a fundamental basis the structure
and complexity of the soil food web, we reason that these two factors: soil spatial
heterogeneity and ecological interactions (trophic and

complementary interactions) working together through evolutionary processes and

time, at the population and community levels, have

resulted in the immense soil biodiversity.

Table 1.

Multiple and different functions performed by the soil organisms at the individual,
population and community organization levels in the

soil ecosystem and soil food web, considering the ecosystem services.

Pathogens affect all groups of organisms: plants, microbes, protozoa, nematodes,

insects, etc.

Food webs, and therefore soil food webs, are biological systems organized with
different subsystems (trophic levels), and subsubsystems

(functional groups in each trophic level). Food webs are also open systems, with a
spatio-temporal dynamic of the whole,
in which each subsystem and each subsystem component has also its own dynamic
function but interrelated with other components

in the web-system. Food webs are open systems with energy and material flow,
and in some cases there is also a flow of genetic

information (e.g., fungi endophytes maybe transmitted through vertical or

horizontal gene transfer, [47]). In this sense, ecologists have

mentioned that “The analysis of energy and material flow is considered to be

fundamental to understanding the patterns and dynamics

in ecosystems and the way ecosystems are organized.” [97].

With all the information presented here, it is argued that most of the trophic
relationships in the soil trophic web has been established

through evolutionary processes, and this is an important basis to understand that

disturbances (e.g., plant disease epidemics) in the

soil food web can have irreparable consequences in the ecosystem functions, e.g.,
natural or managed systems. Disturbances that

occur in the soil environment will cause changes at different physical and
biological levels; these perturbations will affect the

ecological interactions and depending on the strength and duration of the

perturbation, soil ecosystem will be able to recover through

its resilience and resistance capacities, expressed at the individual (e.g., dormancy),
population (temporal and spatial population

density and dynamics) and community (regulation throughout mutualistic vs.

antagonistic relations) levels [108]. These processes will

be evidenced in the complexity of the structure and diversity [108, 109] and in the
stability of the soil food web [97]; However, we must

also keep in mind that all the multiple and different soil organisms since plant roots
to microorganisms and to animals, all together as
a whole, participate in vital soil processes such as biogeochemical and nutrients
cycling, soil formation and conservation, and climate

regulation [2] (Table 1). In this sense De Ruiter and Moore [110], indicated that
‘soil food webs are thought to govern major components

in the global cycling of materials, energy and nutrients’.

Soil ecologists indicate that soil food web complexity improves the turnover of
nutrients, enhance soil structure, water holding capacity

and infiltration, promotes disease suppressiveness, pollutants degradation and

biodiversity [18, 110]. All the different interactions that

soil fungi and bacteria have established with other soil microorganisms like
protozoa, nematodes, rotifers, microarthropods, mites,

ants, and root plants, establish the foundations for a complex soil food web with
direct and indirect biological and ecological

relationships. Complexity and performance of the soil food web is also affected by
physical and chemical soil factors; soil structure,

particles aggregation, pore size [111], soil texture, pH [22], amount of organic
matter, all of them affect direct and indirectly the soil

biological species diversity, their interactions, their population densities and their
spatio-temporal dynamics. At the same time, every

biological activity performed by the soil community will transcend and affect some
physical and chemical characteristics in soil. It is

important to mention that trophic and non-trophic relationships in the soil

community and ecosystems have been developed through

time and they are ruled by natural selection forces, which mean, trophic food webs
have evolutionary and ecological basis [101].