Dataset Information

Bambara groundnut soil metagenomics data.

ABSTRACT: Metagenomics analysis was carried out on extracted DNA of Rhizospheric soil samples from Bambara groundnut. This dataset presented reports on the bacterial communities at the different growth stages of Bambara groundnut and the bulk soil. Paired-end Illumina-Miseq sequencing of 16S rRNA genes was carried on the soil samples of the bacterial community with the phyla dominated by Actinobacteria (30.1%), Proteobacteria (22%), Acidobacteria (20.9%), Bacteroides (8.4%), Chloroflex (4.5%) and Firmicutes (4.4%) in all the soil samples. Samples from the bulk soil had the least average percent phyla, while samples at seed maturity stage had the highest average percent phyla. The alpha diversity at p?=?0.05 was highest at this stage compared to the others and the control. Rubrobacter was the most predominant genera, after which is Acidobacterium and Skermanella. The biodiversity profile generated from the metagenomics analysis is useful in increasing knowledge of the drought-tolerance ability of Bambara groundnut. The data generated can be used to compare bacterial diversity at different growth stages of plants.

SUBMITTER: Ajilogba CF

PROVIDER: S-EPMC7178491 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

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Bambara groundnut soil metagenomics data.

Ajilogba Caroline Fadeke CF Babalola Olubukola Oluranti OO

Data in brief 20200414

Metagenomics analysis was carried out on extracted DNA of Rhizospheric soil samples from Bambara groundnut. This dataset presented reports on the bacterial communities at the different growth stages of Bambara groundnut and the bulk soil. Paired-end Illumina-Miseq sequencing of 16S rRNA genes was carried on the soil samples of the bacterial community with the phyla dominated by Actinobacteria (30.1%), Proteobacteria (22%), Acidobacteria (20.9%), Bacteroides (8.4%), Chloroflex (4.5%) and Firmicut ...[more]

PMID: 32346574

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Project description:Bambara groundnut (BGN) is a drought-tolerant crop majorly cultivated in sub-Saharan Africa. Due to a lack of extensive research, marginalization, lack of awareness, and lack of available fund among others, this crop's improvement has been limited. The development of this crop depends on evaluation and selection of unique and stable breeding lines in different environments. This study aims to estimate genetic diversity using morphological traits at different locations in 95 accessions of BGN collected from the Genebank of the International Institute of Tropical Agriculture (IITA), Ibadan. The experiment was carried out in three replicates at IITA experimental sites in two agroecological zones in Ibadan (7°40'19.62″ N, 3°91'73.13″ E) and Ikenne (6°51'00.873″ N, 3°41'48.528″ E) using a randomized complete block design. Ten vegetative growth traits and eight yield traits were scored. The data was subjected to ANOVA, PCA, correlation, and cluster analysis. Estimations of genetic parameters and broad sense heritability were carried out on the traits. ANOVA revealed significant variation in each trait except for days to emergence. Significant variation was also observed for accession and location interactions (genotype x environment interactions) for plant height, leaf length, leaf width, chlorophyll content, number of petioles, germination count, number of pods, number of seeds, seed length, seed width, and yield. PC1 and PC2 show 42.3% of the total variations observed by the PC, with seed thickness contributing more to PC1 and the number of seeds contributing more to PC2. Cluster analysis categorized the accessions into four distinct groups. The number of pods had the highest genotypic coefficient of variation of 32.55% and the phenotypic coefficient of variation of 97.61%, while seed length (0.63), seed width (0.54), and seed thickness (0.58) have high heritability values. The genetic advance was highest in yield (76.15%) and lowest in days to 50% germination (0.21%). This study can be used to predict appropriate agroecological zones for the planting of BGN while the knowledge of the diversity of the accessions based on the traits could serve a guide in selecting the best trait for the improvement of the crop.

Project description:Bacterial metabolites have been observed to be important in new drug formulation for both plant, animals and human beings. The aim of this study was to identify the different bioactive compounds found in three rhizobacterial isolates (B. amyloliquefaciens, B. thuringiensis and Bacillus sp.) from the rhizosphere of Bambara groundnut and to assay for their antibacterial properties. Gas chromatography mass spectrometry (GC-MS) was used to carry out the analysis using seven extraction solvents. In the GC-MS analysis, 68 compounds were identified based on peak area percentage, retention time and structure. From the bioactive compounds in B. amyloliquefaciens and B. thuringiensis, the peak area percentage shows that dimethylfuvene from ethyl acetate extraction had the highest relative abundance with 89.11% while Formic acid 2-methylpropyl ester from hexane extraction had the lowest with 6.25%. Others are tridecane, acetic acid butyl ester, paraldehyde, s-(+)-1,2 propanediol, tropone, phthalan and p-xylene with relative abundance of 61.72%, 60.41%, 83.79%, 71.53%, 24.06%, 86.72% and 64.33% respectively. These extracts inhibited the growth of the four test organisms, Bacillus cereus, Pseudomonas aeruginosa, Micrococcus cryophilus and Enterococcus feacalis. Butanol extract from B. amyloliquefaciens had 28 mm zone of inhibition against B. cereus compared to 18 mm and 16 mm by Bacillus sp. and B. thuringiensis respectively. Its zone of inhibition was 24 mm zone against M. cryophilus compared to 12 mm and 19 mm by Bacillus sp. and B. thuringiensis respectively. Butanol extract from B. thuringiensis suppressed E. feacalis and P. aeruginosa having 23 mm and 26 mm zones of inhibition respectively. This was higher compared to Bacillus sp. and B. amyloliquefaciens having 18 mm/15 mm and 21 mm/15 mm against E. feacalis and P. aeruginosa respectively. Hexane and ethyl acetate extract from Bacillus sp. suppressed P. aeruginosa with 12 mm and 17 mm inhibition zones respectively compared to no inhibition zones from hexane extract of B. amyloliquefaciens and B. thuringiensis. Zones of inhibition of 2 mm and 6 mm were observed against P. aeruginosa from ethyl acetate extract of B. amyloliquefaciens and B. thuringiensis respectively. These results suggest that the three isolates are quite rich in the production of bioactive compounds that are also very effective antibacterial agents. These volatile organic compounds are promising compounds for more antibacterial bioactivity development.

Dataset Information

Bambara groundnut soil metagenomics data.

Publications

Bambara groundnut soil metagenomics data.

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