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Nwachukwu, B.C.;  Ayangbenro, A.S.;  Babalola, O.O. Bacterial Community in The Rhizosphere Soil. Encyclopedia. Available online: https://encyclopedia.pub/entry/39886 (accessed on 08 December 2025).
Nwachukwu BC,  Ayangbenro AS,  Babalola OO. Bacterial Community in The Rhizosphere Soil. Encyclopedia. Available at: https://encyclopedia.pub/entry/39886. Accessed December 08, 2025.
Nwachukwu, Blessing Chidinma, Ayansina Segun Ayangbenro, Olubukola Oluranti Babalola. "Bacterial Community in The Rhizosphere Soil" Encyclopedia, https://encyclopedia.pub/entry/39886 (accessed December 08, 2025).
Nwachukwu, B.C.,  Ayangbenro, A.S., & Babalola, O.O. (2023, January 09). Bacterial Community in The Rhizosphere Soil. In Encyclopedia. https://encyclopedia.pub/entry/39886
Nwachukwu, Blessing Chidinma, et al. "Bacterial Community in The Rhizosphere Soil." Encyclopedia. Web. 09 January, 2023.
Bacterial Community in The Rhizosphere Soil
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This entry is adapted from the peer-reviewed paper 10.3390/agriculture11010075

The rhizosphere is known as the region of the soil that surrounds the root where biological, physical and chemical properties of the soil are modulated by plant processes. The abundance of nutrient accumulation in rhizosphere soils has placed the rhizosphere as an “epicenter” of bacterial concentrations. 

sustainable development goals soil health soil amendment

1. Introduction

The United Nations (UN) have released blueprints for seventeen Sustainable Development Goals (SDGs) to achieve a better and more sustainable life for people globally by 2030. The second goal (Zero hunger) is adopted to end hunger and achieve food security by 2030, ensuring that everyone has sufficient food. This goal seeks sustainable solutions to end hunger in all its forms and to achieve food security. The aim is to ensure that everyone has enough good-quality food to lead a healthy life [1]. Therefore, to achieve this goal, there is a need for better access to food and widespread sustainable agriculture promotion. This entails improving the productivity and income of small-scale farmers by promoting equal access to land, technology and markets, sustainable food production systems and resilient agricultural practices. It also requires increased investments through international cooperation to bolster the productive capacity of agriculture, especially in developing countries [1][2].
Over a decade, the fight against hunger globally has progressively improved, and the proportion of the undernourished population decreased from 15% (2000–2002) to 11% (2014–2016) [3]. Nonetheless, approximately 800 million people do not have constant access to quality and safe food. If prevailing conditions persist, the zero hunger objectives will not be achieved by 2030 [4]. The incessant hunger is no longer the problem of food availability. Still, many countries failed to attain the Millennium Development Goals (MDGs) against hunger and human-induced environmental degradation due to advanced food insecurity, especially in sub-Saharan Africa and southern Asia [2]. Hence, there is a need for novel biotechnological applications of beneficial plant growth-promoting bacteria to improve soil fertility and plant health and, as a result, produce sufficient healthy quality food without having any negative impacts on the environment [1].
In agro-based industry, plant root-associated bacteria have a beneficial effect on the growth and yield of crops and forest trees [5][6]. Plant growth-promoting rhizobacteria (PGPB) are consortia of bacterial species that colonize the plant root region (rhizosphere), impacting plant growth and health advantageously. The PGPB are agricultural bioresources that stimulate plant growth and productivity. They also incite plants’ resistance to different phytopathogens in a wide variety of crops including vegetables, fruits, and some trees [7].
The diversity of bacterial species in the rhizosphere has been used as a biological indicator to estimate soil quality and fertility because they play a critical role in nitrogen fixation, hormone production, and nutrient distribution [8]. Similarly, they have contributed to the production and oxidation of methane and acetone, and have resulted in the enhancement of the soil pH, water composition, organic carbon content, and porosity [9][10].
The rhizosphere soils serve as an exclusive natural niche, which houses myriads of bacterial species and their compositions differ with plant species. The most predominant root-associated bacterial community found in the rhizosphere soil are Betaproteobacteria (e.g., Burkholderia), Bacteroidetes, Alphaproteobacteria (such as Rhizobia), Gammaproteobacteria (like Pseudomonas), and Firmicutes (e.g., Bacillus) [11]. The rhizosphere soil is composed of a high abundance of bacterial population compared to the bulk soil. These bacteria from the rhizosphere soil can be harnessed and used in an ecofriendly approach as promising biotechnology for the production of antimicrobials, and can serve as biocontrol, bioremediation, and biofertilization agents, thereby improving soil health, soil fertility and crop yield, and ensuring environmental sustainability [12].
Environmental sustainability acknowledges the importance of advancing and controlling the biological and physical systems that bolster both the short- and long-term value of all forms of life on earth without jeopardizing the diversity and well-being of natural ecosystems [13]. By virtue of the ecological services rendered by rhizobacteria, Ambrosini, et al. [14] have recommended further research on the factors that aid in the maintenance of the rhizosphere bacterial community and promote practices that advance rhizosphere conservation and protection. Despite the critical role played by rhizobacteria in redressing soil fertility and environmental sustainability, there still remains the need for further understanding of the mechanisms through which rhizobacteria perform their ecological roles and how such roles can be exploited for environmental sustainability.

2. The Rhizosphere Soil as a Treasure Trove for Bacterial Community Concentration

The rhizosphere is known as the region of the soil that surrounds the root where biological, physical and chemical properties of the soil are modulated by plant processes. The rhizosphere is a hotspot of plant-bacteria interplay within the soil environments [15]. It is colonized by diverse bacterial communities, which are functionally and structurally controlled by soil type and texture, environmental factors and plants [16]. Studies have revealed that the plant root exudates and other rhizodeposits lure beneficial bacteria to the rhizosphere, although uninvited ones are also enticed [1]. The host plant induces selection pressure on the development of the rhizosphere microbiome, which favors and attracts a specific plant microbiota due to variations in the composition of the root exudate [17].
Odelade and Babalola [18] stated that there is a higher bacterial biomass in the rhizosphere soil compared to the bulk (rootless) soil, which is as a result of increased availability of substrates for bacterial growth through root exudates, resulting in greater population density and community structure in the root region that may be different from those in the bulk soil. This was supported by a study by De Luna, et al. [19], who stated that the bacterial cell population in 1g of rhizosphere soils is typically 108–1012, and they surpassed that of the bulk soil, which is due to various root exudates and rhizodepositions in the root region. This high bacterial density in the rhizosphere soils has been ascribed to the high level of available substrate and humidity [20].
Reports have suggested that root exudates and various rhizodeposits perform key roles in the richness and diversity of bacterial communities in the rhizosphere. Root exudates have the most diversified nutritional composition compared to other rhizodeposits. They are also versatile in composition and influenced by the plant host and environmental factors [21]. The root exudates attract beneficial bacterial species to the rhizosphere of plants, while some unwanted bacterial species are also lured [7]. The constituents of root exudates vary between plant species and cultivars, which leads to variation in the rhizosphere bacterial community. These variations can be manipulated to create specific selective effects on the rhizosphere microbiome [22].
Dennis et al. [23] stated that root exudates carry out a limited role in controlling the bacterial communities in the rhizosphere compared to the other rhizodeposits (volatile compounds, mucilages, slough-off root cells, and lysates) due to large variations in exudate composition and dynamics shown by various studies. Collective evidence indicates that bacterial communities are oftentimes distinct from similar plant cultivars and from bulk soil, but not always. The authors classified these plants as having a delicate rhizospheric effect [24][25]. The mechanisms by which hosts winnow the ambient community to form their microbial communities are not fully understood, although plant functional traits, such as the cuticle composition, may be responsible [15]. However, shaping and establishment of the rhizosphere microbiome is a selective and dynamic process that involves several mechanisms such as signal recognition, chemotaxis, biofilm formation and antibiosis [21].
Root exudation includes the secretion of enzymes, oxygen and water, ion, mucilage and diverse carbon-containing metabolites. The plant root system produces various metabolites, while the root tips secrete most of the root exudates, which are low molecular weight organic substances (such as amino acids, amides, organic acids, sugars, enzymes, phenolic acids and coumarin), high-molecular-weight compounds (such as proteins and mucilages) and other substances, including sterols that attract bacteria to the rhizosphere [26][27]. However, the components of the exudates vary in the amount released, molecular weight, and biochemical functions. These exudates act as attraction signals that influence the ability of bacteria to colonize the roots. To proliferate and be established in the rhizosphere, the organisms must be able to use root exudates, colonize the root or rhizosphere effectively and be able to compete with other organisms [23]. Rhizobacteria locate plant roots through cues exuded from the roots and root exudates, which stimulate Plant Growth-Promoting Rhizobacteria PGPR chemotaxis on root surfaces. Root exudates can also stimulate flagella motility in some rhizobacteria [28]. These traits are essential for the colonization of the rhizosphere.
The impact of plant roots was examined on rhizosphere and bacterial communities, and it was deduced that root length, biomass, density, volume, and surface area create distinct ecological niches for some bacterial species to improve advantageous interactions in the rhizosphere [29]. It has been established that since the root tips make the initial connection with the bulk soil, the bacterial communities and rhizodeposits are notable in maintaining the rhizosphere [4][30].
Despite variations in the dynamics and composition of root exudates, a subset of the bacterial population is designated as the core rhizosphere microbiome, which are ubiquitous across plant species and environment [17]. The microbiota uses the root exudates as a source of energy, and the common genera in the rhizosphere include Burkholderia, Bacillus, Microbacterium, Azospirillum, Serratia, Pseudomonas, Erwinia, Aeromonas, Mesorhizobium, Rahnella, Acinetobacter, Enterobacter and Acinetobacter [31][32]. Conventionally, bacterial species in the rhizosphere were isolated and identified using the traditional or culture-based method for isolating and classifying microorganisms. This method’s main inadequacy is that it cannot identify the entire microorganism in a sample, making approximately 99% of the microorganism unknown [6]. Thus, only a few bacterial populations has been identified from the rhizosphere soils using conventional techniques, but not until the advent of next-generation sequencing techniques [33]. High-throughput sequencing has made the identification of most rhizobacteria possible and also lends credence to their functional role in the rhizosphere (Table 1).
Table 1. Bacteria present in rhizosphere soil and the techniques used in identifying them.
Technique Used Bacteria Reported Plant Reference
Denaturing Gradient Gel Electrophoresis (DGGE) Sphingobacteriales, Flavobacteriaceae, Xanthomonadaceae, Cyanobacteria Lettuce, soybean, potato, maize [34][35]
Quantitative PCR (qPCR) analysis Bacillus velezensis NJAU-Z9 Pepper [36]
G3 PhyloChip microarray analyses Atribacteria, Dependentiae, TM6, Latescibacteria WS3 Marinimicrobia, SAR406; Omnitrophica, OP3; BRC1. Acidobacteria, Gemmatimonadetes, and Tenericutes Wheat, barley [31]
Restriction Fragment Length Polymorphism (RFLP) Azospirillum, Pseudomonas chlororaphis, P. frederiksbergensis, Bacillus aryabhattai, and Paenibacillus peoriae Maize [27]
DNA-Stable Isotope Probing (DNA-SIP) Nostocales, Stigonematales, Streptomyces Bacillus, Alicyclobacillus, Clostridium. Rhizobiales, Rhodospirillale, Myxococcales, and Actinomycetales Rice [20][37]
16S amplicon sequencing Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria, Firmicutes, Verrucomicrobia, Planctomycetes, Actinobacteria, Cyanobacteria, and Gemmatimonadetes Wheat, maize, potato, soybean [38][39]
Shotgun sequencing Stenotrophomonas, Rahnella, Sphingomonas, Janthinobacterium Luteibacter, Arthrobacter, Streptomyces, Bradyrhizobium, Methylobacterium, Ramlibacter, Nitrospira, Nocardioides, Geodermatophilus, and Burkholderia Soybean, sunflower, sugar beet [26]
Culture-based Bacillus, Pseudomonas, Ochrobactrium, Providencia, Achromobacter, Burkholderia, and Enterobacter Wheat [40]
Bacterial communities from the rhizosphere have been implicated in synthesizing extracellular hydrolytic enzymes responsible for biodegradation into the soil. Therefore, they are viewed as the leading force manipulating the terrestrial ecosystems. The abundance of nutrients in the rhizosphere not only contributes to plant growth and development but also maintains the beneficial soil bacterial community inhabiting the rhizosphere soil [1]. Some studies conducted on rhizosphere soils have reported the presence of beneficial bacterial communities essential for biotechnological applications (Table 1). Methanotrophic bacteria capable of producing methane from NH4+ were identified from rice paddy rhizosphere soil [41].

References

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Contributors MDPI registered users' name will be linked to their SciProfiles pages. To register with us, please refer to https://encyclopedia.pub/register : Blessing Chidinma Nwachukwu , Ayansina Segun Ayangbenro , Olubukola Oluranti Babalola
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Update Date: 10 Jan 2023
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