GNPS - Rhizosphere-associated metabolites of four wetland plant species
Ontology highlight
ABSTRACT:
INSTRUMENT(S): 6510 Quadrupole Time-of-Flight LC/MS
ORGANISM(S): Phragmites Australis (ncbitaxon:29695) Schoenoplectus Americanus (ncbitaxon:46335) Spartina Patens Ncbitaxon:180100 Spartina Alterniflora Var. Glabra (ncbitaxon:198030)
SUBMITTER: 
Katherine Haviland
PROVIDER: MSV000094652 | GNPS | Wed May 01 07:51:00 BST 2024
REPOSITORIES: GNPS
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Project description:This dataset contains raw files for metabolites collected from the soil and roots of four wetland plant species under non-sterile conditions, both in soil and hydroponically, during the day and night time periods.
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Project description:There are both financial and environmental reasons for optimising the use of phosphorus (P) fertilisers in potato production. One strategy to effect this is to develop genotypes with greater P use efficiency (PUE), which is generally defined as yield divided by the P available to the crop. In this article we report that potato (Solanum tuberosum L.) genotypes differ in their PUE, expressed both as yield in the field and as shoot biomass when grown hydroponically. When grown hydroponically, PUE was strongly correlated with P uptake efficiency (PUpE, defined as shoot P content), but not with physiological P utilisation efficiency (PUtE, defined as shoot biomass divided by shoot P content). Gene expression in roots differed between potato genotypes, and changed with P supply. A common transcriptional response to reduced P supply was determined in roots of four potato genotypes. This response comprised genes encoding enzymes involved in increasing rhizosphere P availability, phosphate transport, P-sparing metabolism, replacement of phospholipids in cell membranes, and various transcription factors. A specific transcriptional response associated only with roots of genotypes with high yields in the absence of P-fertiliser application in the field (Maris Piper and Stirling) was also identified. Genes involved in this response encoded various transcription factors, proteins facilitating water, solute and auxin transport, and enzymes involved in polyamine metabolism and the biosynthesis of tropane alkaloids.
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Project description:Background: The soil environment is responsible for sustaining most terrestrial plant life on earth, yet we know surprisingly little about the important functions carried out by diverse microbial communities in soil. Soil microbes that inhabit the channels of decaying root systems, the detritusphere, are likely to be essential for plant growth and health, as these channels are the preferred locations of new root growth. Understanding the microbial metagenome of the detritusphere and how it responds to agricultural management such as crop rotations and soil tillage will be vital for improving global food production. Methods: The rhizosphere soils of wheat and chickpea growing under + and - decaying root were collected for metagenomics sequencing. A gene catalogue was established by de novo assembling metagenomic sequencing. Genes abundance was compared between bulk soil and rhizosphere soils under different treatments. Conclusions: The study describes the diversity and functional capacity of a high-quality soil microbial metagenome. The results demonstrate the contribution of the microbiome from decaying root in determining the metagenome of developing root systems, which is fundamental to plant growth, since roots preferentially inhabit previous root channels. Modifications in root microbial function through soil management, can ultimately govern plant health, productivity and food security.
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Project description:Transcriptome analysis of root development related genes in terrestrial and hydroponic ramie. Ramie seedlings were cultivated in soil, and in hydroponic with the shoot-cutting propagation method. The root samples from hydrophonic ramie were collected from the early stage (5-day-old seedling) and the late stage (30-day-old seedling) of acquatic roots induction. The roots of ramie seedling cultivated in soil were also collected for comparative analysis. Our study represents the detailed analysis of ramie root transcriptomes with biologic replicates.
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Project description:Plant-parasitic nematodes and especially the root-knot nematodes are ubiquitous pathogens. Eggs of root-knot nematodes (Meloidogyne javanica) were extracted from greenhouse cultures and second-stage juveniles (J2) were hatched in tap, sterile water on 30 µm sieves. Solanum tubersum cv. Desiree explants, i.e., stem including an axillary bud, were sectioned, under sterile conditions from in vitro growing seedlings and transferred to Magenta boxes containing Gamborg's media. Seedlings, 4 weeks post transferring to Gamborg's media were planted in pots containing autoclaved quartz sand. Three weeks later the plants were infected with 3000 M. javanica infective juveniles, applied to the soil in tap, sterile water. Control uninfected plants were mock-inoculated with tap, sterile water. Roots from 6 infected and 6 mock-inoculated plants were collected at a series of time points, including 5, 10 and 15 days post nematode infection/mock inoculation. Roots were observed under the microscope, and nematode feeding sites were selectively dissected, from young lateral roots. To control for the effect of tissue sectioning on gene expression, young lateral roots of the mock inoculated roots were dissected similarly to the infected roots, and collected. Dissected roots were snapped-freeze in liquid nitrogen and immediately stored in -80 C freezer. Total RNA was extracted using Qiagen RNAEasy kit. The experiment for each time point was duplicated, each duplicate derived from independent biological repeat. All RNA samples were amplified using the Ambion kit Message Amp catalog no. 1750, using as starting material 2.5 to 5 µg of total RNA. Keywords: Reference design
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