Dataset Information

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

ABSTRACT: 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.

SUBMITTER: Babalola OO

PROVIDER: S-EPMC7327808 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

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Shotgun metagenomic data of root endophytic microbiome of maize (<i>Zea mays</i> L.).

Babalola Olubukola Oluranti OO Fadiji Ayomide Emmanuel AE Ayangbenro Ayansina Segun AS

Data in brief 20200620

This dataset represents the root endophytic microbial community profile of maize (<i>Zea mays</i> 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 10,9 ...[more]

PMID: 32637499

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Project description:Background and aimsThe maize lrt1 (lateral rootless1) mutant is impaired in its development of lateral roots during early post-embryonic development. The aim of this study was to characterize, in detail, the influences that the mutation exerts on lateral root initiation and the subsequent developments, as well as to describe the behaviour of the entire plant under variable environmental conditions.MethodsMutant lrt1 plants were cultivated under different conditions of hydroponics, and in between sheets of moist paper. Cleared whole mounts and anatomical sections were used in combination with both selected staining procedures and histochemical tests to follow root development. Root surface permeability tests and the biochemical quantification of lignin were performed to complement the structural data.Key resultsThe data presented suggest a redefinition of lrt1 function in lateral roots as a promoter of later development; however, neither the complete absence of lateral roots nor the frequency of their initiation is linked to lrt1 function. The developmental effects of lrt1 are under strong environmental influences. Mutant primordia are affected in structure, growth and emergence; and the majority of primordia terminate their growth during this last step, or shortly thereafter. The lateral roots are impaired in the maintenance of the root apical meristem. The primary root shows disturbances in the organization of both epidermal and subepidermal layers. The lrt1-related cell-wall modifications include: lignification in peripheral layers, the deposition of polyphenolic substances and a higher activity of peroxidase.ConclusionsThe present study provides novel insights into the function of the lrt1 gene in root system development. The lrt1 gene participates in the spatial distribution of initiation, but not in its frequency. Later, the development of lateral roots is strongly affected. The effect of the lrt1 mutation is not as obvious in the primary root, with no influences observed on the root apical meristem structure and maintenance; however, development of the epidermis and cortex are impaired.

Project description:It is by now well proven that different plant species within their specific root systems select for distinct subsets of microbiota from bulk soil - their individual rhizosphere microbiomes. In maize, root growth advances several centimeters each day, with the locations, quality and quantity of rhizodeposition changing. We investigated the assembly of communities of prokaryotes (archaea and bacteria) and their protistan predators (Cercozoa, Rhizaria) along the longitudinal root axis of maize (Zea mays L.). We grew maize plants in an agricultural loamy soil and sampled rhizosphere soil at distinct locations along maize roots. We applied high-throughput sequencing, followed by diversity and network analyses in order to track changes in relative abundances, diversity and co-occurrence of rhizosphere microbiota along the root axis. Apart from a reduction of operational taxonomic unit (OTU) richness and a strong shift in community composition between bulk soil and root tips, patterns of microbial community assembly along maize-roots were more complex than expected. High variation in beta diversity at root tips and the root hair zone indicated substantial randomness of community assembly. Root hair zone communities were characterized by massive co-occurrence of microbial taxa, likely fueled by abundant resource supply from rhizodeposition. Further up the root where lateral roots emerged processes of community assembly appeared to be more deterministic (e.g., through competition and predation). This shift toward significance of deterministic processes was revealed by low variability of beta diversity, changes in network topology, and the appearance of regular phylogenetic co-occurrence patterns in bipartite networks between prokaryotes and their potential protistan predators. Such patterns were strongest in regions with fully developed laterals, suggesting that a consistent rhizosphere microbiome finally assembled. For the targeted improvement of microbiome function, such knowledge on the processes of microbiome assembly on roots and its temporal and spatial variability is crucially important.

Project description:BackgroundMicroRNAs are a class of small, non-coding RNAs that regulate gene expression by binding target mRNA, which leads to cleavage or translational inhibition. The NAC proteins, which include NAM, ATAF, and CUC, are a plant-specific transcription factor family with diverse roles in development and stress regulation. It has been reported that miR164 negatively regulates NAC1 expression, which in turn affects lateral root development in Arabidopsis; however, little is known about the involvement of the maize NAC family and miR164 in lateral root development.ResultsWe collected 175 maize transcripts with NAC domains. Of these, 7 ZmNACs were putative targets for regulation by miR164. We isolated one gene, called TC258020 (designated ZmNAC1) from 2 maize inbred lines, 87-1 and Zong3. ZmNAC1 had a high expression level in roots and showed higher abundance (1.8 fold) in Zong3 relative to 87-1, which had less lateral roots than Zong3. There was a significant correlation between the expression level of ZmNAC1 and the lateral root density in the recombinant inbred line (RIL) population. Transgenic Arabidopsis that overexpressed ZmNAC1 had increased lateral roots in comparison to the wild type. These findings suggest that ZmNAC1 played a significant role in lateral root development. An allelic expression assay showed that trans-regulatory elements were the dominant mediators of ZmNAC1 differential expression in 87-1 and Zong3, and further analysis revealed that miR164 was a trans-element that guided the cleavage of endogenous ZmNAC1 mRNA. Both mature miR164 and miR164 precursors had higher expression in 87-1 than Zong3, which was the opposite of the expression pattern of ZmNAC1. Additionally, the allelic assay showed that the cis-regulatory element most likely affected Zm-miR164b's expression pattern. A ?-glucuronidase (GUS) assay showed that the Zm-miR164b promoter had higher GUS activity in 87-1 than in Zong3. In addition, we detected miR164b expression in the RIL population, and the results indicated that miR164b had a higher expression level in the RILs containing 87-1 promoter than those containing Zong3 promoter.ConclusionOur results indicate one possible pathway in maize by which differences in miR164b promoter activity resulted in a different expression pattern for mature miR164 which negatively regulates ZmNAC1 expression in 87-1 and Zong3, thereby contributing to a significantly different lateral root phenotype.

Dataset Information

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

Publications

Shotgun metagenomic data of root endophytic microbiome of maize (<i>Zea mays</i> L.).

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