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Map of South Africa showing the North West and Gauteng Provinces as well as the sampling locations, that is, Randfontein (Randfontein Local Municipality) and Lichtenburg (Ditsobotla Local Municipality).
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The community of microbes in the rhizosphere region is diverse and contributes significantly to plant growth and crop production. Being an important staple and economic crop, the maize rhizosphere microbiota has been studied in the past using culture-dependent techniques. However, these limited culturing methods often do not help in understanding t...
Contexts in source publication
Context 1
... selected sites for this study were those for maize production, being located in Lichtenburg (25 • 59 40.8 S, 26 • 31 46.6 E) and Randfontein (26 • 11 51.3 S, 27 • 33 18.6 E), South Africa ( Figure 1). The sampling locations are renowned regions for maize cultivation and maximum production of maize in South Africa. ...
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... the beta diversity analysis showed that significant differences exist in the functional categories between the samples (p = 0.01), with the strength of separation between each environment being substantial (R = 0.58). The principal coordinate analysis performed also showed a distinct separation between the samples, as seen in Figure 10. The location of F1 on the PCoA plot was distinctly far from R1, which depicts a clear difference in the functional categories in the samples, with a difference also being observed between F2 and R2, the samples being separated from each other on the PCoA plot. ...
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... (K) correlated positively with clustering-based subsystems, stress response, amino acids and derivatives, metabolism of aromatic compounds, motility and chemotaxis, respiration, sulfur metabolism, potassium metabolism and membrane transport. Likewise, a positive correlation was seen between phosphorus (P) and secondary metabolism, virulence, disease and defense, phosphorus metabolism, cell wall and capsule, nucleosides and nucleotides, iron acquisition and metabolism and protein metabolism ( Figure 11, Table 5). Phosphorus significantly contributed 34.5% of the variation in the samples, and K contributed 38.9% of the total variation, while N-NO 3 explained 26.6% of the variation. ...
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... principal coordinate analysis conducted showed distinct differences between the habitats, which was illustrated by the position of the samples on the PCoA plot ( Figure 10). A significant difference was noted in the rhizosphere soils (F1 and R1) and the bulk soils (F2 and R2). ...
Context 5
... order to determine the relationship between the functional diversities of microbes in the habitats and the soil properties/environmental variables, canonical correspondence analysis was performed (Figure 11). The CCA result shows that K, P and N-NO 3 were the soil properties that best explain the diversities in the functional categories in the samples, where K and P explained 38.9% and 34.5% of the variation, respectively, while N-NO 3 explained 26.6% of the variation (Table 5, Figure 11). ...
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... order to determine the relationship between the functional diversities of microbes in the habitats and the soil properties/environmental variables, canonical correspondence analysis was performed (Figure 11). The CCA result shows that K, P and N-NO 3 were the soil properties that best explain the diversities in the functional categories in the samples, where K and P explained 38.9% and 34.5% of the variation, respectively, while N-NO 3 explained 26.6% of the variation (Table 5, Figure 11). Soil properties are major factors that drive the diversity and structure of soil microbes, thus influencing the functional potentials in the soil ecosystem [8,15]. ...
Citations
... 7 With current technologies, researchers have made tremendous progress in recent years to unravel the genetic, biochemical, and signaling mechanisms associated with plant stress responses. [8][9][10] The complex process that distinguishes resistance and vulnerability within crop species is not well known. 11 Drought stress affects a variety of morphological biochemical parameters, including a decrease in the leaf area, a total reduction in chlorophyll content, leaf wilting, lengthening of the roots, and the formation of reactive oxygen species (ROS). ...
... The usefulness of multiomic approaches in understanding microbial features under drought has been proven in many recent studies 153 Researchers investigated the dynamics of iron metabolism in a drought-induced rhizosphere microbiome using metagenome-guided comparative genomics. 9,154 They discovered a link between drought, iron metabolism, and the plant root microbiome. 154 Michaletti et al 155 looked at some of the critical metabolites that may be used to construct models that show the association between yield-related parameters and different metabolic pathways while analyzing the proteome and metabolomics of spring wheat leaf tissues. ...
The future global food security depends on the availability of water for agriculture. Yet, the ongoing rise in nonagricultural uses for water, such as urban and industrial uses, and growing environmental quality concerns have increased pressure of irrigation water demand and posed danger to food security. Nevertheless, its severity and duration are predicted to rise shortly. Drought pressure causes stunted growth, severe damage to photosynthesis activity, loss in crop yield, reduced seed germination, and reduced nutrient intake by plants. To overcome the effects of a devastating drought on plants, it is essential to think about the causes, mechanisms of action, and long-term agronomy management and genetics. As a result, there is an urgent need for long-term medication to deal with the harmful effects of drought pressure. The review focuses on the adverse impact of drought on the plant, physiological, and biochemical aspects, and management measures to control the severity of drought conditions. This article reviews the role of genome editing (GE) technologies such as CRISPR 9 (CRISPR-Cas9) related spaces and short palindromic relapse between proteins in reducing the effects of phytohormones, osmolytes, external compounds, proteins, microbes (plant growth-promoting microorganism [PGPM]), approach omics, and drought on plants that support plant growth. This research is to examine the potential of using the microbiome associated with plants for drought resistance and sustainable agriculture. Researchers also advocate using a mix of biotechnology, agronomic, and advanced GE technologies to create drought-tolerant plant varieties.
... Since the first metagenomic data were published, researchers have begun to analyze the rhizosphere microbial diversity, community structure, interactions, and gene functions based on metagenomic techniques [17][18][19][20]. However, there have been few studies on the rhizosphere microbiome of A. lancea, and a comparative evaluation of the rhizobiome composition in different regions is still lacking [21]. ...
This study aimed to explore the important role of the rhizosphere microbiome in the quality of Atractylodes lancea (Thunb.) DC. (A. lancea). The rhizosphere microbial community of A. lancea at two sampling sites was studied using metagenomic technology. The results of α-diversity analysis showed that the rhizosphere microbial richness and diversity were higher in the Maoshan area. The higher abundance of core microorganisms of the rhizosphere, especially Penicillium and Streptomyces, in the Maoshan area compared with those in the Yingshan area might be an important factor affecting the yield of A. lancea. Redundancy analysis illustrated that the available phosphorus had a significant effect on the rhizosphere microbial community structure of A. lancea. We also showed that the plant–microbe and microbe–microbe interactions were closer in the Maoshan area than in the Yingshan area, and Streptomyces were the main contributors to the potential functional difference between the two regions. A. lancea in the Maoshan area had a high content of atractylodin and atractylon, which might be related to the enhanced abundance of Streptomyces, Candidatus-Solibacter, and Frankia. Taken together, this study provided theoretical insights into the interaction between medicinal plants and the rhizosphere microbiome and provides a valuable reference for studying beneficial microbes of A. lancea.
... Plants release root exudates, such as amino acids, sugars, carboxylic acids, and various secondary metabolites. These exudates are used as energy sources by soil microorganisms, which provide plant growth and sustainability by production of a range of plant-growth-promoting substances [3,4]. In this way, an increased stability of biosystem transformation processes and a balance of biochemical flows between the partners of plant-bacterial association is achieved. ...
Biomodified mineral fertilizers (BMFs) were produced by enriching the ammophos fertilizer with PGPR Bacillus velezensis BS89 with the use of two technologies: BMF 1, the ammophos fertilizer with the addition of spores of Bacillus velezensis BS89 on a dry carrier (diatomite); and BMF2,ammophos granules treated with spores of Bacillus velezensis BS89 in a cell suspension. The effects of BMFs on maize growth and productivity and the rhizosphere bacterial community were assessed. BMFs significantly increased maize growth, dry matter, minerals, starch and protein contents in maize grain. The application of biomodified mineral fertilizers resulted in the significant increase in the yield and some parameters of maize plants such as ear length and number of kernels in the row. The yield was increased by 7.5–7.6%, ear length by 9%, and number of kernels in the rowby 6.7–7%, as compared with ammophos. However, we found no considerable differences in thecomposition of the bacterial community of the maize rhizosphere after the use of BMFs as compared with the use of ammophos at the level of the phyla, which was confirmed by the ecological indices of biodiversity: the Shannon index and the Simpson index. Comparison of the experimental variantswith bulk soil showed differences in the microbiome composition of the dominant bacterial phyla.A greater abundance of Proteobacteria and Bacteroidetes and a lower abundance of Chloroflexi was registered in bulk soil as compared with the other experimental variants where maize plants were present. The highest percentage (5.3%) of unidentified taxonomic phyla was also found in bulk soil.Our studies showed that maize is the main structuring factor during formation of the microbiome composition in the rhizosphere. The application of biomodified fertilizers BMF1 and BMF2 consider-ably increased the abundance of bacteria representing the minority of the community, namely, those from the phyla Verrucomicrobia, Chloroflexi, Planctomycetes, Proteobacteria, Firmicutes and Chlamydiae, as compared with the use of ammophos. Thus, the application of biomodified mineral fertilizers is a promising agronomic and ecological strategy for boosting maize yield and the quality of grain under field conditions.
... Microbial functions embedded in the rhizosphere of plants occur in the manifold. They involve the breakdown of metabolic substances that improve nutrient production and other needed materials needed for plants' growth [123]. Various functional metabolisms include; protein metabolism, phosphorus, potassium, and sulfur cycling, in the plant rhizosphere that promotes the health condition of the plants [124]. ...
Plant microbiota has a variety of impacts on the plant. Some are beneficial, while some are pathogenic. This study discusses the general metagenomics procedures in processing plant-related metagenomes and focuses on the tomato plants' rhizosphere species. Metagenomics, associated with eventual DNA, is isolated from environmental samples and thus permits absolute microbial population identification. Meanwhile, the genetic content of the DNA sample obtained allows the functional capability identification and biochemical procedure of many microorganisms. This review reveals the recent utilization and application of the potential of Next-Generation Sequencing (NGS) in agriculture. It involves plant-associated microbiota, the factors driving their diversity, and plant metagenome to tackle current challenges experienced in food security. This review provides the newest methods for rapidly identifying the microbial communities inhabiting the rhizosphere soil of tomato plants.
... It can accelerate the decomposition of animal (Araujo et al., 2020) and plant residues in the soil and increase the TN content in the soil with Bacteroidetes (Krishna et al., 2020). In addition, Bacteroidetes also have a phosphorus enrichment effect (Hou et al., 2021), which synergized with Actinobacteria with a phosphorus-dissolving effect (Omotayo et al., 2021) to increase the content of AP in soil. Proteobacteria with increasing relative abundance during decomposition have nitrogen fixation and can adapt to various complex environments (Hou et al., 2019). ...
Introduction
The competitive strategies of plants play a crucial role in their growth. Allelopathy is one of the weapons that plants use to improve their competitive advantage.
Methods
In order to explore the competitive strategy of a poisonous weed Elsholtzia densa Benth. (E. densa) on the Qinghai-Tibet Plateau (QTP), the effects of decomposing substances of E. densa on growth, root border cells (RBCs) characteristics of highland crop highland barley (Hordeum vulgare L.), and soil environment were determined.
Results
The decomposing allelopathic effect of E. densa on the germination and seedling growth of highland barley mainly occurred in the early stage of decomposing. The allelopathic effects were mainly on seed germination and root growth of highland barley. After treatment with its decomposing solution, the RBC’s mucilage layer of highland barley thickened, and the RBC’s activity decreased or even apoptosis compared with the control. However, only the above-ground part of the treatment group showed a significant difference. The effects of E. densa decomposed substances on the soil environment were evaluated from soil physicochemical properties and bacterial community. The results showed that soil bacteria varied greatly in the early stage of decomposion under different concentrations of E. densa. In addition, E. densa decomposing substances increased the soil nutrient content, extracellular enzyme activities, and bacterial community diversity. In the process of decomposition, the bacterial community structure changed constantly, but Actinobacteriota was always the dominant phylum.
Discussion
These results indicated that E. densa might adopt the following two strategies to help it gain an advantage in the competition: 1. Release allelochemicals that interfere with the defense function of surrounding plants and directly inhibit the growth and development of surrounding plants. 2. By changing the physical and chemical properties of soil and extracellular enzyme activity, residual plant decomposition can stimulate soil microbial activity, improve soil nutrition status, and create a more suitable soil environment for growth.
... This is consistent with our findings where Firmicutes was the most abundant bacterial phylum in the maize rhizosphere in this study. Additionally, the core community in this study was integrated mainly by the phylum Firmicutes and in less proportion by the phylum Proteobacteria corresponding well with previous studies that describe the presence of these phyla in the bacterial community of maize rhizosphere (Li et al., 2014;Omotayo et al., 2021;Peiffer et al., 2013). Both, Firmicutes and Proteobacteria have important members with diverse Table 1 Maize rhizosphere bacterial OTU distribution and colonies number in five collection sites in Sinaloa Mexico. ...
... Highlighted in gray: OTUs that were present in all soil samples; N/D: not defined. activities such as carbon, sulfur, nitrogen cycling essential for nutrient cycling and are used in phytoremediation, biocontrol of phytopathogens and as plant biofertilizers (Omotayo et al., 2021). Members of these phyla have been well-described as either plant growth-promoting rhizobacteria (PGPR) or as biocontrol agents (Nagórska et al., 2007). ...
La diversidad de la microbiota asociada a la rizósfera de cultivos en sistemas agrícolas ha sido pobremente estudiada en México y en todo el mundo. El objetivo de este trabajo fue identificar la diversidad de bacterias cultivables en campos de maíz. Se creó una colección de cepas de 11,520 aislados purificados a partir de la rizósfera de maíz. Se procedió a extraer el ADN genómico y secuenciar una región del 16S rADN de cada aislado. Las secuencias fueron analizadas y agrupadas en unidades operacionales taxonómicas (OTU). Esto permitió la agrupación de 7,077 cepas en 185 OTU pertenecientes a 19 géneros dentro de los phyla Firmicutes, Proteobacteria, Actinobacteria y
Bacteroidetes; siendo Firmicutes el phylum más rico, incluyendo 146 OTU y 6 géneros, con Bacillus como el género con más especies. Se identificó la comunidad núcleo de los suelos conteniendo 28 OTU de Firmicutes y 1 OTU de Proteobacteria. Se discute el papel que juegan las diferentes poblaciones bacterianas identificadas en la rizósfera del maíz, su potencial para ser empleadas con propósitos biotecnológicos y la importancia de la conservación de los recursos microbianos empleando colecciones bacterianas.
... Many ecology-based functional activities and nutrient cycling processes of diverse microbial communities can be determined through Illumina MiSeq sequencing of the 16S rRNA gene amplicon (Babalola et al., 2022). These techniques have been used for elucidating microbial structural communities and their functional metabolism (Omotayo et al., 2021). The microbial ecological network is influenced by sudden changes in environmental conditions, which can change microbial world dynamics (Jiao et al., 2022). ...
Aim:
In this study, 16S rRNA amplicon sequencing analyses were performed to determine the diversity of the bacterial community present in the soil, rhizosphere region, root nodules, and seeds of the horse gram plant.
Methods and results:
We observed the dominance of Proteobacteria, Actinobacteria, Firmicutes, Acidobacteria, Bacteroidetes, Planctomycetes, and Gemmatimonadetes across all four domains of the horse gram plant. For community analyses, the significance of the alpha diversity was estimated using the Shannon index, Simpson index, and Chao1 index, which revealed no significant difference among the samples. However, estimation of the beta diversity indicated a significant difference among the samples, with P < 0.001 and R2 = 1. A strong positive correlation was found between the rhizosphere and root nodule samples. Comparative genomics of the 16S rRNA gene showed that ammonium-oxidizing metabolism (amoA), nitrite-reducing metabolism (nirK), and nitrogen-fixing metabolism (nifH) were prominent mechanisms in all samples. The genes involved in the biosynthesis of amino acids, purine metabolism, and nitrogen metabolism were identified as the key genes associated with the functional traits of microbial domains in horse gram.
Conclusion:
The culturable microbes associated with horse gram can be used as a substitute for synthetic fertilizers to maintain soil fertility and ecological health in agricultural practices.
Significance and impact of the study:
Determining the survival strategies of bacterial communities that positively respond to multiple gate selection helps in understanding the structural diversity and functional traits primarily focused on the development of beneficial microbial consortium for promoting plant growth.
... It can accelerate the decomposition of animal(Araujo et al. 2020), and plant residues in the soil and increase the total nitrogen content in the soil with Bacteroidetes(Krishna et al. 2020). In addition, Bacteroidetes also have a phosphorus enrichment effect (Hou et al. 2021), which synergized with Actinobacteria(Omotayo et al. 2021) with a phosphorus-dissolving effect to increase the content of AP in soil. Proteobacteria with increasing relative abundance during decomposition have nitrogen xation and can adapt to various complex environments(Hou et al. 2019). ...
Background The root extracellular trap (RET) comprising root border cells (RBCs) and their secretions are plants' first line of defense to resist external stress. Since soil microorganisms are closely related to nutrient circulation, this study chooses a poisonous weed Elsholtzia densa Benth. (E. densa) in alpine meadows on the Qinghai-Tibet Plateau (QTP) to explore the mechanism of its rapid expansion.
Methods Bioassays and pure agar suspension air culture methods are used to determine the effects of the decomposing substances of E. densa on the RBCs characteristics of the plateau crop highland barley (Hordeum vulgare L.), soil nutrients, soil enzyme activities, and soil bacteria, using microscopic techniques and biochemical analysis techniques.
Results The decomposing allelopathic effect of the E. densa mainly occurs in the early stage of decomposing, with its decomposing solution thickening the RBC’s mucilage layer and decreasing the RBC’s activity and even apoptosis. The decomposed product of the E. densa changes the diversity of the soil bacterial and species composition, affects soil nutrient content, and increases the activities of various extracellular enzymes.
Conclusions During the expansion, the E. densa releases allelochemicals to its surroundings interfering with the surrounding plants' defense function and directly inhibiting their growth. At the same time, the stubble's decomposition changes soil microbial activities, enriches the soil nutrients, and forms a self-interested soil environment. Eventually, the E. densa gains an edge over the competition.
... The metadata obtained from this study showed and supports the notion that maize rhizosphere is a hotspot of genes accountable for converting labile and organic carbon, sulfur, nitrogen, and phosphorus compounds (Li et al., 2014c;Omotayo and Babalola 2020;Omotayo et al., 2021). This can be linked to the release of root exudates into the rhizosphere, as these rhizodeposits have a major influence on the rhizosphere microbiome, thus impacting its microbial diversity and functional profile, consequently affecting the microbial genes (Hu et al., 2018). ...
Genes possessed by microbes in the rhizosphere influence the metabolic activities that occur in this zone. Although the maize rhizosphere has been reported to be a hotspot of genes, these genes remain under-investigated. Hence, this study aimed at identifying putative microbial genes with plant beneficial functions in the underexplored maize rhizosphere microbiome using a shotgun metagenomics approach. Sampling was done at the flowering stage of the maize plants and both the rhizosphere and bulk soils were collected in triplicates. The metagenomes of the examined rhizosphere and bulk soils revealed genes involved in carbon fixation, nitrogen fixation, iron acquisition, heat and cold shock, phosphorus solubilization and utilization, sulfur cycling, and siderophore production. The beta diversity analysis showed significant variations (p < 0.05) in these genes across the examined rhizosphere and bulk soils which was further confirmed by the distinct separations between the samples as seen on the principal coordinate analysis (PCoA) plot. Contrarily, no significant difference was observed in diversity within the habitats (p = 0.99). The predominance of significant genes of agricultural importance such as the nifH, nifA, groES, and cspA in the rhizosphere metagenomes signifies that this region is endowed with beneficial organisms with potential for improving plant growth, mitigating stress, and reducing the effect of extreme temperatures, which can be optimized in developing biofertilizers. Therefore, the development of strategies that will help in cultivating these organisms, which are mostly unculturable, is encouraged. This would make them readily available for use as bio-inoculants and in other biotechnological applications.
... Researchers usually analyze rhizosphere microbial diversity, community structure, interactions, and gene functions based on metagenomics techniques (Sraphet and Javadi. 2022;Wang et al. 2021;Liu et al. 2021;Omotayo et al. 2021). Plant roots release a huge amount of exudates, such as carbohydrates and organic acids, which can provide nutrition and energy to the rhizosphere microbiome and thus stimulate its structural formation (Zhalnina et al. 2018;Weinhold et al. 2020). ...
Rhizoma Alismatis, a commonly used traditional Chinese medicine, is the dried tuber of Alisma orientale and Alisma A. plantago-aquatica, mainly cultivated in Fujian and Sichuan provinces (China), respectively. Studies have shown that the rhizosphere microbiome is a key factor determining quality of Chinese medicinal plants. Here we applied metagenomics to investigate the rhizosphere microbiome of Alisma in Fujian and Sichuan, focusing on its structure and function and those genes involved in protostane triterpenes biosynthesis. The dominant phyla were Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria, and Gemmatimonadetes. Compared with Fujian, the rhizosphere of Sichuan has a greater α diversity and stronger microbial interactions but significantly lower relative abundance of archaea. Microbes with disease-suppressing functions were more abundant in Sichuan than Fujian, but vice versa for those with IAA-producing functions. Gemmatimonas, Anaeromyxobacter, and Pseudolabrys were the main contributors to the potential functional difference in two regions. Genes related to protostane triterpenes biosynthesis were enriched in Fujian. Steroidobacter, Pseudolabrys, Nevskia, and Nitrospira may contribute to the accumulation of protostane triterpenes in Alisma. This work fills a knowledge gap of Alisma’s rhizosphere microbiome, providing a valuable reference for studying its beneficial microorganisms.
