Functional diversity of microbial communities in two contrasting maize rhizosphere soils

Chukwuneme, Chinenyenwa Fortune; Babalola, Olubukola Oluranti; Kutu, Funso Raphael

doi:10.1016/j.rhisph.2020.100282

Cited by 18 publications

(12 citation statements)

References 70 publications

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“…The soil microbiota metabolic categories showed no significant difference (p > 0.05) within the sampling area (i.e., the replicates) (Figure 4). The diversity indices of the samples showed that the functional attributes of various fields were within the same range [22,29]. More so, the combined principal coordinate analysis (PCoA-100%) between rhizosphere soils and the controls described community variation (Figure 4) coupled with clear separations (R = 0.58) among samples.…”

Section: Discussionmentioning

confidence: 90%

“…In the control samples, metabolic hits, such as cell division and cell cycle, nitrogen metabolism, nucleosides and nucleotides, photosynthesis, DNA metabolism, miscellaneous, and respiration were actively involved in Rc and Lc sites. The output of this study is synonymous with the finding of Chukwuneme et al [29] on the functional diversity of maize rhizosphere and bulk soils collected from an intensively cultivated and former grassland in some provinces in South Africa.…”

Section: Discussionmentioning

confidence: 94%

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The Immense Functional Attributes of Maize Rhizosphere Microbiome: A Shotgun Sequencing Approach

Akinola

Babalola

2021

Agriculture

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The northwest (NW) province of South Africa is a semi-arid area, often disturbed by soil extremes such as drought and intense temperature. However, many functions possessed by the rhizosphere microbiome are still required, especially those inhabiting arid and semi-arid soils. This study involves a metagenomic comparison of the major metabolic attributes of two maize rhizosphere soils and their surrounding soils. Here, we hypothesized that there is a considerable difference between the functional diversity of maize rhizosphere and bulk soils and that the rhizosphere soil has distinct functional traits of agricultural importance. A high-throughput sequencing approach was used to assess the metabolic profile of rhizosphere soil microbiota of maize collected from the Gauteng and NW provinces of South Africa. The relative abundance of 13 functional hit categories was significantly different between the sampling sites. The diversity indices showed a considerable difference between the rhizosphere and surrounding soils. The difference in the chemical properties of the sampling sites was responsible for the variation in the microbial functional composition. Nevertheless, the presence of a high relative abundance of functional categories with unknown functions in SEED subsystem-2 coupled with the large number of functional hits conferring a response to soil stressors viz. oxidative stress, heat shock, osmotic stress, and cold shock noticed in the rhizosphere samples may indicate the presence of novel genes at the sampling sites. Exploring the plant growth-promoting traits of microorganisms present at these sites could eliminate the constraint posed by soil stressors on sustainable agriculture.

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Section: Discussionmentioning

confidence: 90%

Section: Discussionmentioning

confidence: 94%

The Immense Functional Attributes of Maize Rhizosphere Microbiome: A Shotgun Sequencing Approach

Akinola

Babalola

2021

Agriculture

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“…The results of the soil chemical analyses of this study have been previously described in Chukwuneme et al [ 41 ]. Briefly, the pH of the GZ samples was between 6.45 and 7.04 (neutral), while that of the AG samples ranged between 4.84 and 5.49 (acidic).…”

Section: Resultsmentioning

confidence: 99%

Metagenomic Analyses of Plant Growth-Promoting and Carbon-Cycling Genes in Maize Rhizosphere Soils with Distinct Land-Use and Management Histories

Chukwuneme

Babalola

2021

Genes

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Many studies have shown that the maize rhizosphere comprises several plant growth-promoting microbes, but there is little or no study on the effects of land-use and management histories on microbial functional gene diversity in the maize rhizosphere soils in Africa. Analyzing microbial genes in the rhizosphere of plants, especially those associated with plant growth promotion and carbon cycling, is important for improving soil fertility and crop productivity. Here, we provide a comparative analysis of microbial genes present in the rhizosphere samples of two maize fields with different agricultural histories using shotgun metagenomics. Genes involved in the nutrient mobilization, including nifA, fixJ, norB, pstA, kefA and B, and ktrB were significantly more abundant (α = 0.05) in former grassland (F1) rhizosphere soils. Among the carbon-cycling genes, the abundance of 12 genes, including all those involved in the degradation of methane were more significant (α = 0.05) in the F1 soils, whereas only five genes were significantly more abundant in the F2 soils. α-diversity indices were different across the samples and significant differences were observed in the β diversity of plant growth-promoting and carbon-cycling genes between the fields (ANOSIM, p = 0.01 and R = 0.52). Nitrate-nitrogen (N-NO3) was the most influential physicochemical parameter (p = 0.05 and contribution = 31.3%) that affected the distribution of the functional genes across the samples. The results indicate that land-use and management histories impact the composition and diversity of plant growth-promoting and carbon-cycling genes in the plant rhizosphere. The study widens our understanding of the effects of anthropogenic activities on plant health and major biogeochemical processes in soils.

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“…To address these challenges and ensure sustainable crop production, an understanding of the functional role of the microbial communities that colonize the plant rhizosphere is required. The microbiome functional diversity will aid in the discovery of appropriate and improved methods for increasing plant yield, particularly in nutrient-deficient and semi-arid regions of the world, where chemical inputs are needed to supplement plant growth (Chukwuneme et al, 2021). Rhizosphere microbial communities have been widely investigated using both culture-dependent and culture-independent approaches due to their importance in plant growth and performance (Odelade & Babalola, 2019;Sugiyama et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

“…Metagenomics approaches have simplified the process of taxonomic and functional classification of uncultured microbial populations. This have facilitated a better understanding of microbial behaviours and processes in their environments (Chukwuneme et al, 2021;Ranjan et al, 2016). The technique has been used to obtain detailed information of the specific rhizosphere microorganisms (Lagos et al, 2015), roles, number, and compositions (LeBlanc et al, 2015) ; (Spence et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

Functional Diversity of Microbial Communities in the Soybean (<em>Glycine max</em> L.) Rhizosphere from Free State, South Africa

Ajiboye¹,

Babalola²

2022

Preprint

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The plant microbiome is involved in enhancing nutrient acquisition, plant growth, stress tolerance and reduces chemical inputs. The identification of microbial functional diversity offers the chance to comprehend and engineer them for various agricultural processes. Using a shotgun metagenomics technique, this study examined the functional diversity and metabolic potentials of microbial communities in the rhizosphere soybean. 18 genera were selected out of which six are prominent in sample AB, the prominent genera are Geobacter, Nitrobacter, Burkholderia, Candidatus, Bradyrhizobium and Streptomyces. Twenty-one functional categories were present with 14 of the functions being dominant. The dominant functions include carbohydrates, fatty acids, lipids and isoprenoids, amino acids and derivatives, sulfur metabolism, and nitrogen metabolism. Kruskal- Wallis test was used to test samples’ diversity differences. There was a significant difference in the diversity with p-value of 0.04. ANOSIM was used to analyse the similarities of the samples, p-values and R-values of the samples were 0.01 and 0.5835 respectively. Phosphorus with p-value of0.718 and 64.3% contribution was more prominent among the soil properties that have influence on functional diversity of the samples. Given the functional groups reported in this study, it is clear that soil characteristics had an impact on on the functions role of the rhizospheric microbiome of soybean

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Functional diversity of microbial communities in two contrasting maize rhizosphere soils

Cited by 18 publications

References 70 publications

The Immense Functional Attributes of Maize Rhizosphere Microbiome: A Shotgun Sequencing Approach

The Immense Functional Attributes of Maize Rhizosphere Microbiome: A Shotgun Sequencing Approach

Metagenomic Analyses of Plant Growth-Promoting and Carbon-Cycling Genes in Maize Rhizosphere Soils with Distinct Land-Use and Management Histories

Functional Diversity of Microbial Communities in the Soybean (<em>Glycine max</em> L.) Rhizosphere from Free State, South Africa

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