Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Shotgun Metagenomic Survey of the Diseased and Healthy Maize (Zea mays L.) Rhizobiomes.

ABSTRACT: The effective functioning of the rhizosphere microbiome significantly contributes to plant development, disease resistance, and agricultural sustainability. Hence, it is a major predictor of plant health. This study evaluated the microbial diversities and functions associated with healthy and diseased maize rhizosphere at selected farms in North West Province, South Africa.

SUBMITTER: Babalola OO

PROVIDER: S-EPMC9584349 | biostudies-literature | 2022 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Shotgun Metagenomic Survey of the Diseased and Healthy Maize (Zea mays L.) Rhizobiomes.

Babalola Olubukola Oluranti OO Dlamini Siphiwe Prudence SP Akanmu Akinlolu Olalekan AO

Microbiology resource announcements 20220906 10

The effective functioning of the rhizosphere microbiome significantly contributes to plant development, disease resistance, and agricultural sustainability. Hence, it is a major predictor of plant health. This study evaluated the microbial diversities and functions associated with healthy and diseased maize rhizosphere at selected farms in North West Province, South Africa. ...[more]

PMID: 36066249

Similar Datasets

Shotgun metagenomic data of root endophytic microbiome of maize (Zea mays L.).

Project description:This dataset represents the root endophytic microbial community profile of maize (Zea mays L.), one of the largest food crops in South Africa, using a shotgun metagenomic approach. To the best of our understanding, this is the first account showcasing the endophytic microbial diversity in maize plants via the shotgun metagenomics approach. High throughput sequencing of the whole DNA from the community was carried out using NovaSeq 6000 system (Illumina). The data obtained consists of 10,915,268 sequences accounting for 261,906,948 bps with an average length of 153 base pairs and 43% Guanine+Cytosine content. The metagenome data can be accessed at the National Centre for Biotechnology Information SRA registered with the accession number PRJNA607664. Community analysis was done using an online server called MG-RAST, which showed that 0.12% of the sequences were archaeal associated, eukaryotes were 15.06%, while 84.77% were classified as bacteria. A sum of 28 bacterial, 22 eukaryotic and 4 archaeal phyla were identified. The predominant genera were Bacillus (16%), Chitinophaga (12%), Flavobacterium (4%), Chryseobacterium (4%), Paenibacillus (4%), Pedobacter (3%) and Alphaproteobacteria (3%). Annotation using Cluster of Orthologous Group (COG) revealed that 41.47% of the sequenced data were for metabolic function, 24.10% for chemical process and signaling, while 17.43% of the sequences were in the poorly characterized group. Annotation using the subsystem method showed that 18% of the sequences were associated with carbohydrates, 9% were for clustering-based subsystems, and 9% contain genes coding for amino acids and derivatives, which might be beneficial in plant growth and health improvement.

| S-EPMC7327808 | biostudies-literature

Shotgun Metagenomic Survey of Maize Soil Rhizobiome.

Project description:The plant soil rhizobiome induces critical functions in the plant proximal environment. Linkages between soil microbiota and primary functional attributes are underexplored. Here, we present the metagenomes of maize soil rhizosphere organisms with functional diversity associated with farms at two different municipalities in North West and Gauteng provinces of South Africa. We describe a plenteous and diverse microbial community.

| S-EPMC7516154 | biostudies-literature

Shotgun metagenomics dataset of <i>Striga hermonthica</i>-infested maize (<i>Zea mays</i> L.) rhizospheric soil microbiome.

Project description:This dataset includes shotgun metagenomics sequencing of the rhizosphere microbiome of maize infested with Striga hermonthica from Mbuzini, South Africa, and Eruwa, Nigeria. The sequences were used for microbial taxonomic classification and functional categories in the infested maize rhizosphere. High throughput sequencing of the complete microbial community's DNA was performed using the Illumina NovaSeq 6000 technology. The average base pair count of the sequences were 5,353,206 bp with G+C content of 67%. The raw sequence data used for analysis is available in NCBI under the BioProject accession numbers PRJNA888840 and PRJNA889583. The taxonomic analysis was performed using Metagenomic Rapid Annotations using Subsystems Technology (MG-RAST). Bacteria had the highest taxonomic representation (98.8%), followed by eukaryotes (0.56%), and archaea (0.45%). This metagenome dataset provide valuable information on microbial communities associated with Striga-infested maize rhizosphere and their functionality. It can also be used for further studies on application of microbial resources for sustainable crop production in this region.

| S-EPMC10293916 | biostudies-literature

Bacterial Consortium for Improved Maize (Zea mays L.) Production.

Project description:The ever-increasing human population is a major concern for food security. Maize is the third largest most important food crop. The major problems of cultivation arise from urbanization and land pollution. This reduces the amount of land available for agriculture. The use of chemicals in agriculture is not environmentally friendly. Thus, plant growth-promoting bacteria (PGPB) have been proposed as alternatives. This study aims to test the growth-promoting effect of maize inoculated with six indigenous PGPB isolates. These isolates were assayed for various biochemical and plant growth-promoting activities. They were also assayed for biocontrol activities. Based on the results, six isolates viz A1, A18, A29, NWU4, NWU14, and NWU198 were used to inoculate maize seeds. The inoculated seeds were tried out on the field. A randomized block design was used. PGPB used were in single, consortia of two, and three organisms. The length of the leaves, roots, and stem, plant height, numbers of leaves, and weight of 100 seeds were taken at the fourth and eighth weeks after planting. Microbial consortia increased growth parameters compared to single inoculant treatments. Thus, they can be of advantage in the eradication of low yield. They can also serve as reliable alternatives to chemical fertilizers.

| S-EPMC6920993 | biostudies-literature

Maize (Zea mays): control vs cold stress

Project description:Transcriptional profiling of 4 maize varieties comparing genetic root response under control temperature conditions with genetic root response under low temperature conditions

2016-05-24 | GSE72508 | GEO

Contributions of Zea mays subspecies mexicana haplotypes to modern maize.

Project description:Maize was domesticated from lowland teosinte (Zea mays ssp. parviglumis), but the contribution of highland teosinte (Zea mays ssp. mexicana, hereafter mexicana) to modern maize is not clear. Here, two genomes for Mo17 (a modern maize inbred) and mexicana are assembled using a meta-assembly strategy after sequencing of 10 lines derived from a maize-teosinte cross. Comparative analyses reveal a high level of diversity between Mo17, B73, and mexicana, including three Mb-size structural rearrangements. The maize spontaneous mutation rate is estimated to be 2.17?×?10-8 ~3.87?×?10-8 per site per generation with a nonrandom distribution across the genome. A higher deleterious mutation rate is observed in the pericentromeric regions, and might be caused by differences in recombination frequency. Over 10% of the maize genome shows evidence of introgression from the mexicana genome, suggesting that mexicana contributed to maize adaptation and improvement. Our data offer a rich resource for constructing the pan-genome of Zea mays and genetic improvement of modern maize varieties.

| S-EPMC5707364 | biostudies-literature

Iron acquisition in maize (Zea mays L.) using Pseudomonas siderophore.

Project description:Siderophore facilitates iron availability in soil, but its assistance in iron transportation to different plant parts is not reported till date. Therefore, it is worthwhile to study the effect of siderophore produced by Pseudomonas for iron acquisition in the presence and absence of iron. To study these effects, two siderophore-producing Pseudomonas aeruginosa strains RSP5 and RSP8 were selected. RSP5 and RSP8 produced the highest and lowest amounts of siderophore, respectively. Iron (Fe) concentration of stem, leaf, seed, and shoot length, root length, cob length, and number of grains parameters were analysed. It was observed that the plants treated with RSP5 were sturdier and taller than RSP5 + Fe > RSP8 > RSP8 + Fe > Fe > Control plants. Iron content of RSP8 vs. RSP8 + Fe, RSP8 + Fe vs. Control, and RSP8 + Fe vs. RSP5 + Fe was significantly different (P < 0.01). Analysis of variance (ANOVA) proves that RSP5 was able to transport higher amount of iron to maize plant than other treatments. Increase in shoot length, root length, cob length, grain number and iron content of stem, and leaf and seed of maize plant inoculated with RSP5 suggests that the strain can be used as an inoculant for increasing iron transportation in maize plant. (Indian Patent Filed: 40163/DEL/2016).

| S-EPMC5451364 | biostudies-literature

Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.).

Project description:We measured sequence diversity in 21 loci distributed along chromosome 1 of maize (Zea mays ssp. mays L.). For each locus, we sequenced a common sample of 25 individuals representing 16 exotic landraces and nine U.S. inbred lines. The data indicated that maize has an average of one single nucleotide polymorphism (SNP) every 104 bp between two randomly sampled sequences, a level of diversity higher than that of either humans or Drosophila melanogaster. A comparison of genetic diversity between the landrace and inbred samples showed that inbreds retained 77% of the level of diversity of landraces, on average. In addition, Tajima's D values suggest that the frequency distribution of polymorphisms in inbreds was skewed toward fewer rare variants. Tests for selection were applied to all loci, and deviations from neutrality were detected in three loci. Sequence diversity was heterogeneous among loci, but there was no pattern of diversity along the genetic map of chromosome 1. Nonetheless, diversity was correlated (r = 0.65) with sequence-based estimates of the recombination rate. Recombination in our sample was sufficient to break down linkage disequilibrium among SNPs. Intragenic linkage disequilibrium declines within 100-200 bp on average, suggesting that genome-wide surveys for association analyses require SNPs every 100-200 bp.

| S-EPMC55390 | biostudies-literature

Low nitrogen availability inhibits the phosphorus starvation response in maize (Zea mays ssp. mays L.).

Project description:BackgroundNitrogen (N) and phosphorus (P) are macronutrients essential for crop growth and productivity. In cultivated fields, N and P levels are rarely sufficient, contributing to the gap between realized and potential production. Fertilizer application increases nutrient availability, but is not available to all farmers, nor are current rates of application sustainable or environmentally desirable. Transcriptomic studies of cereal crops have revealed dramatic responses to either low N or low P single stress treatments. In the field, however, levels of both N and P may be suboptimal. The interaction between N and P starvation responses remains to be fully characterized.ResultsWe characterized growth and root and leaf transcriptomes of young maize plants under nutrient replete, low N, low P or combined low NP conditions. We identified 1555 genes to respond to our nutrient treatments, in one or both tissues. A large group of genes, including many classical P starvation response genes, were regulated antagonistically between low N and P conditions. An additional experiment over a range of N availability indicated that a mild reduction in N levels was sufficient to repress the low P induction of P starvation genes. Although expression of P transporter genes was repressed under low N or low NP, we confirmed earlier reports of P hyper accumulation under N limitation.ConclusionsTranscriptional responses to low N or P were distinct, with few genes responding in a similar way to the two single stress treatments. In combined NP stress, the low N response dominated, and the P starvation response was largely suppressed. A mild reduction in N availability was sufficient to repress the induction of P starvation associated genes. We conclude that activation of the transcriptional response to P starvation in maize is contingent on N availability.

| S-EPMC8178920 | biostudies-literature

An Interactome Map of Maize (Zea mays L.)

Project description:These data include RNA-seq, circRNA-seq, and small RNA-seq of transcriptome, Ribo-seq of translatome and protein protein binary interactions by recombination-based library vs. library yeast-2-hybrid throughout the lifecycle of the maize inbred line B73.

2022-12-25 | GSE160288 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data