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Agriculture Promises Much From The Endosphere Microbial Communities

by Abdul Rehman
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Agriculture and Endosphere Microbial Communities

Agricultural food production and sustainability need intensification to address the current global food supply to meet human demand. The continuous human population increase and other anthropogenic activities threaten food security.

Agrochemical inputs have long been used in conventional agricultural systems to boost crop productivity, but they are disadvantageous to a safe environment. Towards developing environmentally friendly agriculture, efforts are being directed in exploring biological resources from soil and plant microbes.

The survival of the rhizosphere and endosphere microbiota is influenced by biotic and abiotic factors. Plant microbiota lives interdependently with the host plants. Endophytes are regarded as colonizer microbes inhabiting and establishing microbial communities within the plant tissue.

Their activities are varied and include fixing atmospheric nitrogen, solubilizing phosphate, synthesis of siderophores, secretion of metabolite-like compounds containing active biocontrol agents in the control of phytopathogens, and induced systemic resistance that stimulates plant response to withstand stress.

Exploring beneficial endophyte resources in the formulation of bio-inoculants, such as biofertilizers, as an alternative to agrochemicals (fertilizers and pesticides) in developing environmentally friendly agriculture and for incorporation into crop breeding and disease control program is promising.


Therefore, in this review, endosphere microbial ecology, associating environmental factors, and their roles that contribute to their effectiveness in promoting plant growth for maximum agricultural crop productivity were highlighted.

In this review, various endophytic microbial domains were studied with more emphasis on their roles in ecosystems. Evidence has shown that bacterial and fungal endophytes colonize above (leaves, stems, flowers, flowers, and seeds) and below (root/soil) of plant zones.

Most rhizosphere bacteria and mycorrhiza infiltrating the root tissues can be regarded as root endophytes. Their presence is said to mediate various biological functions and physiological processes in the host plants.

The roles of plant endophytes cannot be overemphasized as some of them have been identified and displayed their relevance in the agricultural, biotechnological, and pharmaceutical industries. Better still, their significance in agriculture is promising but yet to be fully explored.


The coexistence of various microorganisms in the endosphere could either be beneficial or pathogenic depending on the prevailing environmental factors. Plant age, type, developmental stages, soil pH, soil nutrients, and presence or absence of water/moisture, temperature, and pathogens form major factors influencing the activities of endophytes in the host plants.


However, the important roles of endophytes in agricultural crop productivity by secretion of certain metabolites could facilitate their various activities in promoting plant growth through phytohormones synthesis, siderophores production, and secretion of antimicrobial substances, such as antibiotics, ammonia, cyanide, and other volatile compounds, that suppress activities of nematodes, protozoans, and viral, bacterial, and fungal pathogens on plants, thus improving crop productivity.


Many studies have been carried out on plant-root-associated microbes, but harnessing their potential use in agriculture is still limited. Findings have equally established that endophytes possessing growth-promoting traits enhance plant growth by various biological activities, thus are promising in sustainable agricultural production.

The application of endophytes has been employed in various environmental studies, such as for the removal of recalcitrant metals, decaying of organic materials, mineralization, and solubilization of soil nutrients, as well the synthesis of biocontrol agents against plant pathogens.

Also, endophytes exert beneficial effects on plants by enhancing their tolerance to various environmental stresses, such as drought or salinity.

Under crop improvement, harnessing endophyte potential can be employed in the formulation of biofertilizers and biopesticides, on application to improve crop yield and reduce dependence on chemical fertilizers and pesticides that pose a serious threat to ecosystems, the environment, and human health.

Hence, this review provides information on the roles of hidden tiny-big microorganisms living within the tissues of plants, i.e., “microbial endophytes,” their biologically active properties in the formulation of biofertilizers, biopesticides, bioherbicides, and biostimulants to improve crop production in sustainable agriculture; as such, as an alternative in mitigating the menace posed by the use of agrochemicals to the ecosystem.

Consequently, further study on how vital microbial metabolites can be extracted would enhance their potential applications in agriculture. Above all, the study of the endosphere community would revolutionize agriculture if adequately harnessed.

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Endosphere bacteria community

The large community of bacteria colonizing the inner tissue of plants predominantly defends plants against environmental stresses. They elicit strong defense mechanisms in response to the various factors linked with plant growth, survival, and health (Omomowo and Babalola 2019).

The microorganisms penetrating through the soil infiltrated into the plant roots with unique biological functions in sustainable agriculture. Recruitment and exploration of soil endophytes for their ecological and agricultural importance have recently been reported (Fadiji and Babalola 2020b).

The endo-compartment is an environment suitable only for microorganisms with colonizing potential benefits the plant. How endophytes colonize the internal tissue of plants in large numbers and elicit defense mechanisms by protecting plants is a question that has not been answered.

Understanding mechanisms by which microbe-microbe and plant-microbe interactions would be promising in exploring their agricultural and biotechnological importance.

In literature, it has been reported that the ability of microbes to elicit their defense responses in developing a healthy disease-free plant for sustainability depends on their communication pathways, though the actual mechanisms undergone by root endophytes in promoting plant growth have not been clearly defined (Bamisile et al. 2018).

The colonization of the narrow space by endophytes within the plant tissues as well as colonization of endophyte-like pathogens make it suitable in controlling the plant pathogens through the niche exclusion and synthesis of antimicrobials (Fadiji and Babalola 2020a).

The greater the number of active microorganisms, the more effective they are in the environment via various microbial activities beneficial to plants through the following processes: Plant growth promotion by the production of plant growth factors, such as growth hormones (e.g., auxin, gibberellin, and cytokinins), suppression of biosynthetic environmental stress-related plant hormones such as ethylene under stress, bio-fixation of atmospheric nitrogen, potassium mineralization, phosphate solubilization and a draft of systemic induced plant resistance (Igiehon and Babalola 2017).

The need for plant-microbe interactions is essential in establishing a mutual relationship in supporting plant growth. In an ecosystem, the plants shield and secrete exudates that supply nutrients to the microorganisms while the microorganisms produce growth stimulators and biocontrol agents needed for plant growth and control of phytopathogens for improved crop productivity (Olanrewaju et al. 2019).

Endophytes bacteria are the common microbial domains found associating with plants, stimulating plant growth, and conferring stress tolerance, owing to their firm establishment with the host plant. The allelopathic actions of endophytic bacteria that improve plant growth have been reported (Polyak and Sukcharevich 2019).

Studies on bacterial endophytes characterization from different parts of plants, which include roots, seeds, stems, leaves, and flowers have been reported (Tyc et al. 2020; Wolfe and Ballhorn 2020; Xie et al. 2020) (Table 2). The bacteria population is more pronounced in the root zone than the aerial parts of the plant above the ground level i.e., flowers, stems, and leaves.

The screening of plant growth-promoting bacterial endophytes isolated from crop plants, which include maize, rice, tomato, and other essential crops, has been well documented (Liu et al. 2020; Zhou et al. 2020).

The exploration of bacterial endophyte resources in the formulation of bio-inoculants and application in agriculture would help sustainably in achieving the desired agriculture productivity.

The endophytic bacteria species isolated from various plants include Bradyrhizobium, Enterobacter, Pseudomonas (rice—Oryza sativa), Pantoea, Pseudomonas, Enterobacter (sugar cane—Saccharum officinarum), Bacillus (millet—Pennisetum glaucum and Citrus spp.), and Curtobacterium (soybean—Glycine max) that promote plant growth, induced plant tolerance to abiotic stress, stimulation of biocontrol agents against plant pathogens in controlling their infestation have been reported (De Silva et al. 2019; Sheirdil et al. 2019; Shen et al. 2019).

In the endosphere, a large population of microorganisms interacts with each other, most notably the bacteria species, and till today, little information has been documented about their isolation. In contrast, some have not been cultured at all.

The culturable bacterial endophytes are suspected to be Gram-positive and Gram-negative (Alawiye and Babalola 2019). Studies on the bacterial endophytes from various plants have been successfully carried out by many researchers, which include Pantoea sp., Kosakonia sacchari, Herbaspirillum sp., Enterobacter ludwigii EnVs6, etc., and Variovorax paradoxus S110 (Liotti et al. 2018; Pinto-Carbó et al. 2018; Eke et al. 2019).

The bacterial community in the endosphere thrives well, due to low competition that occurs in the zone with other microbes.

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Factors influencing microbial diversity in the endosphere

The colonization, abundance, and diversity of microorganisms in the endo-rhizosphere regions are affected by many factors (physical, chemical, and biological).

The physical factors include the temperature, soil pH, light intensity, geographical locations, time, water availability (rainfall), chemical factors including exudates, mineral elements, other organic substances, and biological factors including pathogens, nematodes, viruses, protozoans, and beneficial plant growth promoter (Ojuederie et al. 2019).

All these factors positively or negatively influence the survival of microorganisms in the endosphere. The adaptation strategies of microbes to strive well in an econiche depend on their ability to tolerate or resist environmental stresses (Enebe and Babalola 2018).

The erratic rainfall, abnormal high temperatures leading to the release of toxic gasses (CO2) to the atmosphere due to human activities have resulted in the greenhouse effect causing global warming, and this affects the ecosystem, hence, making it unfriendly for both plants and microorganisms to inhabit.

As stated in the previous endosphere bacteria community that rhizosphere microbes form a premise in establishing endosphere community in the plant roots because of the high rhizodeposits and exudation secretion containing nutrients which provide nutrients for the microorganism to stimulate growth factors that enhance plant growth and health.

The availability of abundant organic substrates can influence the abundance and performance of diverse endophytic microbes in the root zone, unlike endophytes found in the leaves and stems that are affected by physical factors (Li et al. 2019).

Moreover, soil mineral compositions such as iron, phosphorus, and nitrogen affect the microbial population found in the rhizosphere, thus causing a change in the microbial community both outside and in the internal root environment.

The nitrogen fixer, as well as phosphate solubilizer microbes, make nutrients more abundant in the soil by enhancing nitrogen, potassium, and phosphorus uptake by the resident roots microflora, in response to the improvement in crop yield (Maheshwari et al. 2019; Ramakrishna et al. 2019).

The microbial population in the endosphere often stems from the growing plant seeds or rhizoplane or bulk soil and strives under different environmental conditions.

Factors, such as plant age, type, soil pH, plant developmental stages, excess or limited organic compounds, and nutrient availability, are known to influence the microbial competence and activities in the root zone (Shymanovich and Faeth 2019).

It has been affirmed that the plant growth stage, soil physicochemical parameters, and plant species attest to be the principal factors influencing the rhizosphere and endosphere microbial communities (Ojuederie et al. 2019).

Source: Adeleke, B. S., & Babalola, O. O. (2021). The endosphere microbial communities, a great promise in agriculture. International Microbiology, 24(1), 1-17.

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