**5. Endophytic microorganism**

In 1886, Anton de Bary, a German Botanist and father of plant pathology coined the term endophyte and described it as microorganisms that colonize internal tissues of stem and leaves of plants. Endophytic microorganisms are microorganisms that inhabit at least a period of their life cycle in the interior parts of plants especially leaves, branches and stems, showing no apparent harm to the host [54].

**67**

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*DOI: http://dx.doi.org/10.5772/intechopen.89531*

shock, antibiotics and UV radiation [62].

oats and barley under salinity stress [67].

They are also capable in colonizing the roots and shoots of plants and may not remain as endophyte throughout their life cycle [55]. They include both bacteria and fungi that colonize almost every plant species [56]. Endophytic fungal appear to be symbiotically associated with almost all plants in natural ecosystem and constitute important components of plant micro-ecosystems. They have impacts on the composition of plant communities by increasing their tolerance to biotic and abiotic stress, biomass and decreasing water consumption or altering allocation of resources [57]. Endophytic microbes produce a plethora of secondary metabolites, including toxins, enzymes, anti-inflammatory, antibiotics, anticancer and antifungal compounds in order to colonize plants and also compete with other microorganisms [58]. Zhao *et al*. [59] reported that endophytic fungi produce good bioactive compound paclitaxel (taxol) and many other bioactive molecules such as

terpenoids, alkaloids, steroids, lignans, phenols, quinones and lactones.

Endophytic bacteria have been detected inside the stems, leaves and inside the reproductive organs of different host plants [60]. Several endophytic bacteria produce low molecular weight compounds, phytohormones, enzymes, antimicrobial substances and siderophores which support the growth of plants and also increase their nutrient uptake. Endophytic bacteria in combination with the plants they are in association with, produce some metabolites which plants cannot produce alone [61]. *Enterobacter, Pseudomonas, Burkholderia, Bacillus, Erwinia* and *Xanthomonas* are the most commonly isolated genera of endophytic bacteria. Eleven culturable bacterial strains belonging to the genera, *Rahnella, Pseudomonas, Rhodanobacter, Enterobacter, Stenotrophomonas, Phyllobacterium* and *Xanthomonas* have been isolated from the stems of sweet potato. Among these isolates, *Pseudomonas, Enterobacter* and *Rahnella* produced higher amount of indole acetic acid (IAA) which promote plant growth, and *Rahnella sp.* which is resilient to stress like cold

Webber [63] was probably the first researcher to report plant protection given by an endophytic fungus, *Phomopsis oblonga* which protected elm trees against *Physocnemum brevilineum*. He suggested that the endophytic fungus protected elm tree against the Dutch disease caused by *Ceratocystis ulmi* by reducing its spread and controlling the vector, *P. brevilineum*. It was reported by Claydon *et al*. [64] that endophytic fungi belonging to the family *Xylariaceae* synthesize secondary metabolites in the hosts of the genus *Fagus* which affect beetle larvae. Stress-related genes in *Oryza sativa* such as aquaporin, dehydrin and malondialdehyde have been found to be upregulated by *Trichoderma harzianum* responses. *Trichoderma harzianum* used in treating *Brassica juncea* improved oil content affected with sodium chloride was found to increase its vital nutrients uptake, improve aggregation of osmolytes and antioxidants, and also reduces its NaCl uptake [65]. Brotman *et al.* [66] reported that *T. harzianum* synthesize 1-aminocyclopropane-1-carboxylate (ACC) deaminase to ameliorate salinity stress. *Acinetobacter sp.* and *Pseudomonas sp.* have also been reported to increase indole acetic acid and ACC deaminase production in

Beneficial endophytic bacteria and fungi can be used as inoculant in roots and other plant tissues for many tuberous crops to enjoy the mutualist benefits confer to their original host plants. Many growth promoting endophytes can also be applied as a potential bio-fertilizers in tuber crops with minimal environmental risks [56]. Endophytic microorganisms have frequently been reported to be associated with crop plants such as *Triticum aestivum, Glycine max, Zea mays, Hordeum brevisubulatum and Hordeum bogdanii* [68]. The growth of tomato plants in a salinity stress soil have been improved by *Streptomyces sp.* strain PGPA39 by alleviating the salinity stress [69]. PsJN strain of *Burkholderia phytofirmans* have been reported to combat drought stress

in maize and wheat, and also salinity stress in *Arabidopsis thaliana* [70].

#### *Tropical Crops and Microbes DOI: http://dx.doi.org/10.5772/intechopen.89531*

*Microorganisms*

the soil. Soil enzymes play a vital role in the biochemical functioning of soils [32] including nutrients cycling [33], soil structure maintenance [34] and decomposition of organic residue [35]. The activities of soil enzymes are controlled by many factors such as soil microbial community [36], soil physio-chemical properties [37], vegetation type [38] and ecological disturbances [39]. Prior to the utilization of complex organic matter by microorganisms as their source of energy, they produce a quite number of extra cellular enzymes in order to decompose them [40]. Soil enzymes are specific in the types of reactions they participate. For example, a starch hydrolyzing enzyme known as amylase hydrolyses 1-4D glucosidic linkage of amylase and amylopectin and consist of -amylase and β-amylase. -amylase is synthesized by animals, plants and microorganisms while β-amylase is primarily synthesize by plants [41]. To a large extent, soil microbial activities is dependent on the quantity of available carbon and this is shown by dehydrogenase activity [29]. Dehydrogenase is involved in the biological oxidation of soil organic matter, and also responsible in oxidizing organic matter by transferring hydrogens and electrons from substrates to acceptors [42]. Phosphatase originate from root exudates and microorganisms, it cleaves the phosphate from organic substrates and also involved in P cycle in soil [43]. It has been evidently suggested by Ushio *et al.* [44, 45] that plant species significantly have more direct impacts on the composition of soil microbial community and their activities in addition to soil physicochemical properties. Plants' rhizosphere has been reported by Vyas and Gupta [46] to have profound effect on microbial population and activities. From the study of Islam and Borthakur [47], increase in microbial biomass and enzyme activities indicates high

rate of release of nutrients by rice crops which aid microbial activities.

Indigenous microorganisms are naturally occurring microorganisms that have adapted to the environmental conditions where they are found thus being capable of accelerating decomposition of organic materials found in that environment [48]. They contain mainly Lactobacillus and sometimes Rhizobium with a few other species [49]. Effective microorganisms are composed of mixed cultures of beneficial and naturally occurring microorganisms which are applied to the soil in order to increase the soil microbial diversity and the growth of plants [50]. This concept was first discovered by Higa [51]. It is used as a means of improving crops' efficiency in utilizing organic matter. There are three main families of over 80 different species contained in effective microorganisms [52]. In agriculture, microorganisms are of great importance because they promote decomposition, cycling and circulation of plant nutrients and reduce the need for chemical fertilizers [53]. From the study of Desire et al. [53] the use of biofertilizers obtained from indigenous and effective microorganisms significantly improved and maintained the chemical, physical and biological properties of the soil, and thus increased the yield of potato in terms of number and weight

In 1886, Anton de Bary, a German Botanist and father of plant pathology coined

the term endophyte and described it as microorganisms that colonize internal tissues of stem and leaves of plants. Endophytic microorganisms are microorganisms that inhabit at least a period of their life cycle in the interior parts of plants especially leaves, branches and stems, showing no apparent harm to the host [54].

**4. Indigenous microorganisms**

of tubers when compared to untreated (control) soil.

**5. Endophytic microorganism**

**66**

They are also capable in colonizing the roots and shoots of plants and may not remain as endophyte throughout their life cycle [55]. They include both bacteria and fungi that colonize almost every plant species [56]. Endophytic fungal appear to be symbiotically associated with almost all plants in natural ecosystem and constitute important components of plant micro-ecosystems. They have impacts on the composition of plant communities by increasing their tolerance to biotic and abiotic stress, biomass and decreasing water consumption or altering allocation of resources [57]. Endophytic microbes produce a plethora of secondary metabolites, including toxins, enzymes, anti-inflammatory, antibiotics, anticancer and antifungal compounds in order to colonize plants and also compete with other microorganisms [58]. Zhao *et al*. [59] reported that endophytic fungi produce good bioactive compound paclitaxel (taxol) and many other bioactive molecules such as terpenoids, alkaloids, steroids, lignans, phenols, quinones and lactones.

Endophytic bacteria have been detected inside the stems, leaves and inside the reproductive organs of different host plants [60]. Several endophytic bacteria produce low molecular weight compounds, phytohormones, enzymes, antimicrobial substances and siderophores which support the growth of plants and also increase their nutrient uptake. Endophytic bacteria in combination with the plants they are in association with, produce some metabolites which plants cannot produce alone [61]. *Enterobacter, Pseudomonas, Burkholderia, Bacillus, Erwinia* and *Xanthomonas* are the most commonly isolated genera of endophytic bacteria. Eleven culturable bacterial strains belonging to the genera, *Rahnella, Pseudomonas, Rhodanobacter, Enterobacter, Stenotrophomonas, Phyllobacterium* and *Xanthomonas* have been isolated from the stems of sweet potato. Among these isolates, *Pseudomonas, Enterobacter* and *Rahnella* produced higher amount of indole acetic acid (IAA) which promote plant growth, and *Rahnella sp.* which is resilient to stress like cold shock, antibiotics and UV radiation [62].

Webber [63] was probably the first researcher to report plant protection given by an endophytic fungus, *Phomopsis oblonga* which protected elm trees against *Physocnemum brevilineum*. He suggested that the endophytic fungus protected elm tree against the Dutch disease caused by *Ceratocystis ulmi* by reducing its spread and controlling the vector, *P. brevilineum*. It was reported by Claydon *et al*. [64] that endophytic fungi belonging to the family *Xylariaceae* synthesize secondary metabolites in the hosts of the genus *Fagus* which affect beetle larvae. Stress-related genes in *Oryza sativa* such as aquaporin, dehydrin and malondialdehyde have been found to be upregulated by *Trichoderma harzianum* responses. *Trichoderma harzianum* used in treating *Brassica juncea* improved oil content affected with sodium chloride was found to increase its vital nutrients uptake, improve aggregation of osmolytes and antioxidants, and also reduces its NaCl uptake [65]. Brotman *et al.* [66] reported that *T. harzianum* synthesize 1-aminocyclopropane-1-carboxylate (ACC) deaminase to ameliorate salinity stress. *Acinetobacter sp.* and *Pseudomonas sp.* have also been reported to increase indole acetic acid and ACC deaminase production in oats and barley under salinity stress [67].

Beneficial endophytic bacteria and fungi can be used as inoculant in roots and other plant tissues for many tuberous crops to enjoy the mutualist benefits confer to their original host plants. Many growth promoting endophytes can also be applied as a potential bio-fertilizers in tuber crops with minimal environmental risks [56]. Endophytic microorganisms have frequently been reported to be associated with crop plants such as *Triticum aestivum, Glycine max, Zea mays, Hordeum brevisubulatum and Hordeum bogdanii* [68]. The growth of tomato plants in a salinity stress soil have been improved by *Streptomyces sp.* strain PGPA39 by alleviating the salinity stress [69]. PsJN strain of *Burkholderia phytofirmans* have been reported to combat drought stress in maize and wheat, and also salinity stress in *Arabidopsis thaliana* [70].

## **5.1 Fungi - plants association**

Fungi symbiotic relationship with plants are present in a broad range of terrestrial ecosystems which include a large proportion of plant taxa [71]. It has been established that at least 85% of plant species have been able to establish a symbiotic relationship with fungi, of which those belonging to the phylum Glomeromycota account for 70% of the association [72]. Because of the wide geographical distribution of mycorrhiza and the large proportion of plant taxa involved, mycorrhizal associations are extremely important for terrestrial ecosystem. Due to the development of specialized structures such as proteoid roots, carnivorism or parasitism on other plants, some families of plants have lost their ability to associate with mycorrhizal fungi throughout evolution [71]. For a long time, plant species belonging to the Cyperaceae family was believed not to be able to associate with the mycorrhizal fungi [71] though Bohlen [73] study has evidently shown otherwise. Plant species belonging to the Cyperaceae family are able to associate with arbuscular mycorrhizal fungi and dark septate endophytes (DSE), but the intensity of root colonization intensity may vary depending on the environment in which the samples were collected and phenological stage of the plant [72]. Mycorrhizal associations play an important role in determining the composition of plant communities, since plants that establish this type of association can obtain competitive advantages [74] or facilitate the establishment of other species [75]. van der Heijden *et al*. [76] experimental study evidently suggests the coexistence of different plants. They showed that plants inoculated with AMF grew on the average of 11.8 times more than those not inoculated, and that the distribution of phosphorus and nitrogen between plant species varied depending on the presence of AMF. They further said that AMF can redistribute resources among different species of plant thus allowing their coexistence. The final composition of AMF species varies greatly depending on the plant species cultivated in a soil [77]. The diversity of AMF was much smaller in areas dominated with the invasive species than in areas dominated by native species. Thus, the composition of plant communities and AMF are influenced by feedback interactions in each communities [78, 79].

#### *5.1.1 Arbuscular mycorrhizal fungi (AMF)*

Arbuscular mycorrhizae are formed by non-septate phycomycetous fungi belonging to the genera Glomus, Acaulospora and Sclerocystics in the family Endogonaceae of the order Mucorales which are not specialized in host range [80]. The arbuscular mycorrhizal (AM) symbiosis is the association between fungi of the order Glomales (Zygomycetes) and the roots of terrestrial plants [81]. Arbuscular Mycorrhizal Fungi (AMF) also known as Vesicular Arbuscular Mycorrhizal (VAM) are widespread in terrestrial ecosystems and form mutually beneficial association with nearly 80% of higher plants [82]. According to Voko *et al*. [83], the population of AMF, frequency of occurrence and distribution varied with site.

During the formation of AM symbiosis, the fungus forms a haustoria-like structure (arbuscules) that interface with the host cytoplasm by penetrating the cortical cell wall of the root [84]. They penetrate the living cells of plants without harming them and their hyphae can range far into the bulk soil establishing equally intimate contact with the microbiota of soil aggregates and micro-sites [85]. From the fixed photosynthates of the plant, it supplies carbon to the fungus while the fungus in turn assist the plant in the uptake of phosphorus and other mineral nutrients from the soil [86]. It has been demonstrated that plants can receive up to 100% of the phosphorus through mycorrhizal pathway, and 4 to 20% of plant carbon can be transferred to fungi [87].

**69**

between plants [99].

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*DOI: http://dx.doi.org/10.5772/intechopen.89531*

thetic potential and enhanced growth [94].

*5.1.2 Dark septate endophytes and crop plants*

**5.2 Beneficial soil bacteria and crop production**

plant growth and development [102].

*5.2.1 Root colonization by bacteria*

The transference of these resources between plants and fungi have profound effect on plant nutrition, growth and ecology [88]. The activities of AMF improve crop growth and yield by increasing nutrients availability and increasing root proliferation [82] as well as altering some physiological processes in the plant that result in increased yield [89]. This might also be as a result of modification of host hormonal relations [90] and soil structure [91]. AMF can alter the pattern of gene expression, cellular programming and organ development of the host crop [92]. AMF can improve both plant growth under low fertility conditions, improve plant water balance and help in the establishment of plants in new environment [93]. AMF are useful in the cultivation of cassava in the tropics where rainfall is erratic and may seize for 2–3 months giving rise to drought-prone water deficit-stress condition [94]. AMF enhances plant resistance to drought by building up macroporous structure in soil that allows water and air to penetrate and also prevent erosion thus improving photosynthesis and reducing micropropagation stresses [95]. The mutualistic association between AMF and cassava in AMF-inoculated cassava stimulated the production of more leaf chlorophyll which increased their photosyn-

Dark Septate Endophytes (DSEs) are another important group of soil microorganism that have the capacity to associate with the roots of several plant species [96]. They sometimes colonize roots containing AMF [96]. The increasing severity of environmental conditions increase the importance of DSE. The associations of plants with DSE in high-stress environment is more frequent than their associations with AMF [97]. AMF and DSE have appeared to have similar and complimentary roles in various terrestrial ecosystem [98]. Grunig *et al*. [99] said that since DSEs can alter the performance of colonized plants, they can also play a vital role in determining the composition of plant communities. In the study of Barrow and Osuna [100], some plants colonized by DSE were more advantageous in the absorption of phosphorus from the soil and production of biomass when compared to those not inoculated. Though DSE is advantageous to plants, its colonization of roots can be of disadvantage to plants, such as decreases in the production of biomass [99]. Thus, the interaction of DSEs with plants seems to vary from mutualism to parasitism and may alter the competitive relations

Apart from fungi, there are several groups of soil bacteria that are important to plant growth. Some bacteria have the ability to fix atmospheric nitrogen and form symbiotic relationship with plants [101]. In tropical soils, phosphate-solubilizing microorganisms indirectly provide phosphorus for plants by solubilizing phosphorus precipitated with iron, aluminum and calcium thus making it important for

Root colonization is the microbial attachment to and proliferation on roots. It is an essential factor in the beneficial interactions used for biofertilization, microbiological control, phytoremediation and phytostimulation as well as in plant pathogenesis of soil borne microbes [103]. PGPR may colonize the rhizosphere, root surface, or even superficial intercellular spaces [104].

#### *Tropical Crops and Microbes DOI: http://dx.doi.org/10.5772/intechopen.89531*

*Microorganisms*

**5.1 Fungi - plants association**

interactions in each communities [78, 79].

*5.1.1 Arbuscular mycorrhizal fungi (AMF)*

Fungi symbiotic relationship with plants are present in a broad range of terrestrial ecosystems which include a large proportion of plant taxa [71]. It has been established that at least 85% of plant species have been able to establish a symbiotic relationship with fungi, of which those belonging to the phylum Glomeromycota account for 70% of the association [72]. Because of the wide geographical distribution of mycorrhiza and the large proportion of plant taxa involved, mycorrhizal associations are extremely important for terrestrial ecosystem. Due to the development of specialized structures such as proteoid roots, carnivorism or parasitism on other plants, some families of plants have lost their ability to associate with mycorrhizal fungi throughout evolution [71]. For a long time, plant species belonging to the Cyperaceae family was believed not to be able to associate with the mycorrhizal fungi [71] though Bohlen [73] study has evidently shown otherwise. Plant species belonging to the Cyperaceae family are able to associate with arbuscular mycorrhizal fungi and dark septate endophytes (DSE), but the intensity of root colonization intensity may vary depending on the environment in which the samples were collected and phenological stage of the plant [72]. Mycorrhizal associations play an important role in determining the composition of plant communities, since plants that establish this type of association can obtain competitive advantages [74] or facilitate the establishment of other species [75]. van der Heijden *et al*. [76] experimental study evidently suggests the coexistence of different plants. They showed that plants inoculated with AMF grew on the average of 11.8 times more than those not inoculated, and that the distribution of phosphorus and nitrogen between plant species varied depending on the presence of AMF. They further said that AMF can redistribute resources among different species of plant thus allowing their coexistence. The final composition of AMF species varies greatly depending on the plant species cultivated in a soil [77]. The diversity of AMF was much smaller in areas dominated with the invasive species than in areas dominated by native species. Thus, the composition of plant communities and AMF are influenced by feedback

Arbuscular mycorrhizae are formed by non-septate phycomycetous fungi belonging to the genera Glomus, Acaulospora and Sclerocystics in the family Endogonaceae of the order Mucorales which are not specialized in host range [80]. The arbuscular mycorrhizal (AM) symbiosis is the association between fungi of the order Glomales (Zygomycetes) and the roots of terrestrial plants [81]. Arbuscular Mycorrhizal Fungi (AMF) also known as Vesicular Arbuscular Mycorrhizal (VAM) are widespread in terrestrial ecosystems and form mutually beneficial association with nearly 80% of higher plants [82]. According to Voko *et al*. [83], the population

During the formation of AM symbiosis, the fungus forms a haustoria-like structure (arbuscules) that interface with the host cytoplasm by penetrating the cortical cell wall of the root [84]. They penetrate the living cells of plants without harming them and their hyphae can range far into the bulk soil establishing equally intimate contact with the microbiota of soil aggregates and micro-sites [85]. From the fixed photosynthates of the plant, it supplies carbon to the fungus while the fungus in turn assist the plant in the uptake of phosphorus and other mineral nutrients from the soil [86]. It has been demonstrated that plants can receive up to 100% of the phosphorus through mycorrhizal pathway, and 4 to 20% of plant carbon can be

of AMF, frequency of occurrence and distribution varied with site.

**68**

transferred to fungi [87].

The transference of these resources between plants and fungi have profound effect on plant nutrition, growth and ecology [88]. The activities of AMF improve crop growth and yield by increasing nutrients availability and increasing root proliferation [82] as well as altering some physiological processes in the plant that result in increased yield [89]. This might also be as a result of modification of host hormonal relations [90] and soil structure [91]. AMF can alter the pattern of gene expression, cellular programming and organ development of the host crop [92]. AMF can improve both plant growth under low fertility conditions, improve plant water balance and help in the establishment of plants in new environment [93]. AMF are useful in the cultivation of cassava in the tropics where rainfall is erratic and may seize for 2–3 months giving rise to drought-prone water deficit-stress condition [94]. AMF enhances plant resistance to drought by building up macroporous structure in soil that allows water and air to penetrate and also prevent erosion thus improving photosynthesis and reducing micropropagation stresses [95]. The mutualistic association between AMF and cassava in AMF-inoculated cassava stimulated the production of more leaf chlorophyll which increased their photosynthetic potential and enhanced growth [94].
