Metagenomic insights into the bacterial community structure and functional potentials in the rhizosphere soil of maize plants

Molefe, Rebaona R.; Amoo, Adenike Eunice; Babalola, Olubukola Oluranti

doi:10.1080/17429145.2021.1936228

Cited by 13 publications

(12 citation statements)

References 61 publications

(60 reference statements)

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“…Each site harbors distinct functional signatures with hits mined from the study represented as Ls >Rs >Rc >Lc. The inference from this study echoes the research of Molefe et al [63] on the bacterial community structure and functions at the rhizosphere of maize plant, but the outcome differs from the findings of Taffner et al [43] that compared results from both shotgun and 16S rRNA-metagenomic analysis of archaeal functions associated with soil, rhizosphere and phyllosphere habitats of Eruca sativa Mill.…”

Section: Discussionsupporting

confidence: 51%

Metagenomic Insight into the Community Structure of Maize-Rhizosphere Bacteria as Predicted by Different Environmental Factors and Their Functioning within Plant Proximity

Akinola

Babalola

2021

Microorganisms

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The rhizosphere microbiota contributes immensely to nutrient sequestration, productivity and plant growth. Several studies have suggested that environmental factors and high nutrient composition of plant’s rhizosphere influence the structural diversity of proximal microorganisms. To verify this assertion, we compare the functional diversity of bacteria in maize rhizosphere and bulk soils using shotgun metagenomics and assess the influence of measured environmental variables on bacterial diversity. Our study showed that the bacterial community associated with each sampling site was distinct, with high community members shared among the samples. The bacterial community was dominated by Proteobacteria, Actinobacteria, Acidobacteria, Gemmatimonadetes, Bacteroidetes and Verrucomicrobia. In comparison, genera such as Gemmatimonas, Streptomyces, Conexibacter, Burkholderia, Bacillus, Gemmata, Mesorhizobium, Pseudomonas and Micromonospora were significantly (p ≤ 0.05) high in the rhizosphere soils compared to bulk soils. Diversity indices showed that the bacterial composition was significantly different across the sites. The forward selection of environmental factors predicted N-NO3 (p = 0.019) as the most influential factor controlling the variation in the bacterial community structure, while other factors such as pH (p = 1.00) and sulfate (p = 0.50) contributed insignificantly to the community structure of bacteria. Functional assessment of the sampling sites, considering important pathways viz. nitrogen metabolism, phosphorus metabolism, stress responses, and iron acquisition and metabolism could be represented as Ls > Rs > Rc > Lc. This revealed that functional hits are higher in the rhizosphere soil than their controls. Taken together, inference from this study shows that the sampling sites are hotspots for biotechnologically important microorganisms.

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Section: Discussionsupporting

confidence: 51%

Metagenomic Insight into the Community Structure of Maize-Rhizosphere Bacteria as Predicted by Different Environmental Factors and Their Functioning within Plant Proximity

Akinola

Babalola

2021

Microorganisms

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“…1). This result contradicts the result of Molefe et al (2021), who reported 10.9% bacterial similarity between maize rhizosphere and bulk soils obtained from Ventersdorp, and 17.2% bacterial similarity between maize rhizosphere and bulk soils obtained from Mafikeng in South Africa. The contradiction between the results of the two studies could be due to the different sampling locations and plant type.…”

Section: Discussioncontrasting

confidence: 98%

“…Increase in carbon substrate utilization is directly proportional to increase in CO 2 released or produced (respiration rate) (Creamer et al 2016). Carbon substrates have huge ability to distinguish diverse soil bacterial communities through carbon mineralization capacity (Amoo et al 2021). Bacterial communities of R1, B1, R2 and B2 soils were found to use the different carbon substrates as an energy source, but significant differences were only observed in tryptophan and methionine amended soils.…”

Section: Discussionmentioning

confidence: 99%

Effects of soil properties and carbon substrates on bacterial diversity of two sunflower farms

Nwachukwu

Babalola

2022

AMB Expr

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The sustainable production of sunflower (Helianthus annuus) is crucial and one way to accomplish this feat is to have an understanding of the beneficial bacteria of sunflower rhizosphere. Similarly, the respiratory response of these bacteria needs to be studied to understand their roles in the ecosystem. This study was therefore conceptualized to gain insights into the effects of soil properties and carbon substrate utilization on bacterial community diversity of sunflower rhizosphere grown in Ditsobottla and Kraaipan, North West Province, South Africa. Extracted DNA from sunflower rhizosphere and bulk soils was subjected to 16S amplicon sequencing. Significant differences were observed in the alpha and beta diversities of the soil bacterial communities (p < 0.05). At the order level, among all the bacterial taxa captured in the farms, Bacillales were the most dominant. The abundance of Lactobacillales, Bacillales, Rhizobiales, Enterobacteriales, Burkholderiales, Flavobacteriales, Sphingomonadales, Myxococcales, and Nitrosomonadales obtained from Ditsobottla rhizosphere soil (R1) was positively influenced by organic matter (OM), while the abundance of Planctomycetales, Cytophagales, Gemmatimonadales, Nitrospirales and Caulobacteriales from Kraaipan rhizosphere soil (R2) was positively influenced by total N and pH. Bacterial communities of all the soil samples utilized the different carbon substrates (three amino acids, six carbohydrates, and three carboxylic acids) as an energy source. Significant differences (p < 0.05) were only observed in tryptophan and methionine amended soils. Unclassified bacteria were also captured in this study, such bacteria can further be harnessed for sustainable production of sunflower and other agricultural crops.

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“…The soil is a rich source of microorganisms, but when it comes to crops, the rhizosphere is like the coral reef of the soil where all the significant microbial species reside. We discuss further in the review metagenomic studies on rhizosphere and its respective crops [ 5 ] (Table 1 ).…”

Section: Introductionmentioning

confidence: 99%

Analysis and Interpretation of metagenomics data: an approach

et al. 2022

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Advances in next-generation sequencing technologies have accelerated the momentum of metagenomic studies, which is increasing yearly. The metagenomics field is one of the versatile applications in microbiology, where any interaction in the environment involving microorganisms can be the topic of study. Due to this versatility, the number of applications of this omics technology reached its horizons. Agriculture is a crucial sector involving crop plants and microorganisms interacting together. Hence, studying these interactions through the lenses of metagenomics would completely disclose a new meaning to crop health and development. The rhizosphere is an essential reservoir of the microbial community for agricultural soil. Hence, we focus on the R&D of metagenomic studies on the rhizosphere of crops such as rice, wheat, legumes, chickpea, and sorghum. These recent developments are impossible without the continuous advancement seen in the next-generation sequencing platforms; thus, a brief introduction and analysis of the available sequencing platforms are presented here to have a clear picture of the workflow. Concluding the topic is the discussion about different pipelines applied to analyze data produced by sequencing techniques and have a significant role in interpreting the outcome of a particular experiment. A plethora of different software and tools are incorporated in the automated pipelines or individually available to perform manual metagenomic analysis. Here we describe 8–10 advanced, efficient pipelines used for analysis that explain their respective workflows to simplify the whole analysis process.

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Metagenomic insights into the bacterial community structure and functional potentials in the rhizosphere soil of maize plants

Cited by 13 publications

References 61 publications

Metagenomic Insight into the Community Structure of Maize-Rhizosphere Bacteria as Predicted by Different Environmental Factors and Their Functioning within Plant Proximity

Metagenomic Insight into the Community Structure of Maize-Rhizosphere Bacteria as Predicted by Different Environmental Factors and Their Functioning within Plant Proximity

Effects of soil properties and carbon substrates on bacterial diversity of two sunflower farms

Analysis and Interpretation of metagenomics data: an approach

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