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 | MassIVE | Wed May 01 07:51:00 BST 2024
REPOSITORIES: MassIVE
Similar Datasets
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.
2024-05-01 | MSV000094652 | GNPS
Project description:<div>Species-rich plant communities can induce unique soil biotic legacy effects through changing the abundance and composition of soil biota. These soil legacy effects can cause feedbacks to influence plant performance. In addition, soil biota can induce (defensive) secondary metabolites in shoots and roots and thus affect plant-herbivore interactions. We hypothesize that plant diversity-driven soil biotic legacy effects elicit changes in the shoot and root metabolome. <br></div><div><br></div><div>We tested this hypothesis by establishing an experiment with four plant species. We grew plants in a sterile substrate inoculated with soil conditioned by different plant species communities: (1) monocultures of either of the four species, (2) the four species in a mixture, (3) an eight species mixture including all four species, or (4) a sterile inoculum. After at least eight weeks in the field, we estimated shoot herbivory. At the same time, we took root and shoot samples for metabolomics analyses by liquid chromatography quadrupole time-of-flight mass spectrometry. <br></div><div><br></div><div>We found that shoot and root metabolomes of all plants grown in sterile soil differed significantly from those grown in living soil. The plant metabolomes in living soils differed by species and tissue. Across all species, shoots displayed a greater richness of secondary metabolites than roots. The richness of secondary metabolites differed by species and among living soils. The conditioning species richness significantly affected the Shannon diversity of secondary metabolites in Centaurea jacea. Shoot herbivory positively correlated with the richness and Shannon diversity of secondary metabolites in Leucanthemum vulgare. We detected multiple metabolites that together explained up to 88% of the variation in herbivory in the shoots of Centaurea jacea and Plantago lanceolata. <br></div><div><br></div><div>Synthesis: Our findings suggest that plant diversity-driven shifts in soil biota elicit changes in the composition and diversity of shoot and root secondary metabolites. However, these plant responses and their effect on shoot herbivores are species-specific. Tracking changes in plant secondary chemistry in response to soil biotic legacy effects will help to understand the mechanisms that govern species-specific plant-plant and plant-herbivore interactions.</div>
2019-05-30 | MTBLS544 | MetaboLights
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.
2020-03-06 | GSE146427 | GEO
Project description:Advances in DNA sequencing technologies has drastically changed our perception of the structure and complexity of the plant microbiome. By comparison, our ability to accurately identify the metabolically active fraction of soil microbiota and its specific functional role in augmenting plant health is relatively limited. Here, we combined our recently developed protein extraction method and an iterative bioinformatics pipeline to enable the capture and identification of extracellular proteins (metaexoproteomics) synthesised in the rhizosphere of Brassica spp. We first validated our method in the laboratory by successfully identifying proteins related to a host plant (Brassica rapa) and its bacterial inoculant, Pseudomonas putida BIRD-1. This identified numerous rhizosphere specific proteins linked to the acquisition of plant-derived nutrients in P. putida. Next, we analysed natural field-soil microbial communities associated with Brassica napus L. (oilseed rape). By combining metagenomics with metaexoproteomics, 1882 proteins were identified across bulk and rhizosphere samples. Meta-exoproteomics identified a clear shift (p<0.001) in the metabolically active fraction of the soil microbiota responding to the presence of B. napus roots that was not apparent in the composition of the total microbial community (metagenome). This metabolic shift was associated with the stimulation of rhizosphere-specialised bacteria, such as Gammaproteobacteria, Betaproteobacteria and Flavobacteriia and the upregulation of plant beneficial functions related to phosphorus and nitrogen mineralisation. Together, our metaproteomic assessment of the ‘active’ plant microbiome at the field-scale demonstrates the importance of moving past a genomic assessment of the plant microbiome in order to determine ecologically important plant-microbe interactions underpinning plant health.
2022-07-01 | PXD033692 | Pride
Project description:Advances in DNA sequencing technologies has drastically changed our perception of the structure and complexity of the plant microbiome. By comparison, our ability to accurately identify the metabolically active fraction of soil microbiota and its specific functional role in augmenting plant health is relatively limited. Here, we combined our recently developed protein extraction method and an iterative bioinformatics pipeline to enable the capture and identification of extracellular proteins (metaexoproteomics) synthesised in the rhizosphere of Brassica spp. We first validated our method in the laboratory by successfully identifying proteins related to a host plant (Brassica rapa) and its bacterial inoculant, Pseudomonas putida BIRD-1. This identified numerous rhizosphere specific proteins linked to the acquisition of plant-derived nutrients in P. putida. Next, we analysed natural field-soil microbial communities associated with Brassica napus L. (oilseed rape). By combining metagenomics with metaexoproteomics, 1882 proteins were identified across bulk and rhizosphere samples. Meta-exoproteomics identified a clear shift (p<0.001) in the metabolically active fraction of the soil microbiota responding to the presence of B. napus roots that was not apparent in the composition of the total microbial community (metagenome). This metabolic shift was associated with the stimulation of rhizosphere-specialised bacteria, such as Gammaproteobacteria, Betaproteobacteria and Flavobacteriia and the upregulation of plant beneficial functions related to phosphorus and nitrogen mineralisation. Together, our metaproteomic assessment of the ‘active’ plant microbiome at the field-scale demonstrates the importance of moving past a genomic assessment of the plant microbiome in order to determine ecologically important plant-microbe interactions underpinning plant health.
2022-07-01 | PXD033803 | Pride
Project description:Advances in DNA sequencing technologies has drastically changed our perception of the structure and complexity of the plant microbiome. By comparison, our ability to accurately identify the metabolically active fraction of soil microbiota and its specific functional role in augmenting plant health is relatively limited. Here, we combined our recently developed protein extraction method and an iterative bioinformatics pipeline to enable the capture and identification of extracellular proteins (metaexoproteomics) synthesised in the rhizosphere of Brassica spp. We first validated our method in the laboratory by successfully identifying proteins related to a host plant (Brassica rapa) and its bacterial inoculant, Pseudomonas putida BIRD-1. This identified numerous rhizosphere specific proteins linked to the acquisition of plant-derived nutrients in P. putida. Next, we analysed natural field-soil microbial communities associated with Brassica napus L. (oilseed rape). By combining metagenomics with metaexoproteomics, 1882 proteins were identified across bulk and rhizosphere samples. Meta-exoproteomics identified a clear shift (p<0.001) in the metabolically active fraction of the soil microbiota responding to the presence of B. napus roots that was not apparent in the composition of the total microbial community (metagenome). This metabolic shift was associated with the stimulation of rhizosphere-specialised bacteria, such as Gammaproteobacteria, Betaproteobacteria and Flavobacteriia and the upregulation of plant beneficial functions related to phosphorus and nitrogen mineralisation. Together, our metaproteomic assessment of the ‘active’ plant microbiome at the field-scale demonstrates the importance of moving past a genomic assessment of the plant microbiome in order to determine ecologically important plant-microbe interactions underpinning plant health.
2022-07-01 | PXD033802 | Pride
Project description:We have analyzed the effect of high temepratures in roots and shoots of Arabidopsis using a novel approach, since we cultivate the seedlings with the root system in a temeprature gradient, simulatinfg the soil.
2023-05-31 | GSE214280 | GEO
Project description:Increased root H+ secretion is known as a strategy of plant adaption to low phosphorus (P) stress by enhancing mobilization of sparingly soluble P-sources. However, it remains fragmentarywhether enhanced H+ exudation could reconstruct the plant rhizosphere microbial community under low P stress. The present study found that P deficiency led to enhanced H+ exudation from soybean (Glycine max) roots. Three out of all eleven soybean H+-pyrophosphatases (GmVP) geneswere up-regulated by Pi starvation in soybean roots. Among them, GmVP2 showed the highest expression level under low P conditions. Transient expression of a GmVP2-green fluorescent protein chimera in tobacco (Nicotiana tabacum) leaves, and functional characterization of GmVP2 in transgenic soybean hairy roots demonstrated that GmVP2 encoded a plasma membrane transporter that mediated H+ exudation. Meanwhile, GmVP2-overexpression in Arabidopsis thaliana resulted in enhanced root H+ exudation, promoted plant growth, and improved sparingly soluble Ca-P utilization. Overexpression of GmVP2 also changed the rhizospheric microbial community structures, as reflected by a preferential accumulation of acidobacteria in the rhizosphere soils. These results suggested that GmVP2 mediated Pi-starvation responsive H+ exudation,which is not only involved in plant growth and mobilization of sparingly soluble P-sources, but also affects microbial community structures in soils.
2023-06-01 | GSE205273 | GEO
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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Project description:The medicinal value of the Ferula L. has been recognized for more than a thousand years. Wild stocks of Ferula have declined dramatically because high economic value has led to overharvesting. The objective of this study was to compare the rhizosphere microbial community of four Ferula species [F. syreitschikowii K.-Pol., F. gracilis (Ledeb.) Ledeb., F. ferulaeoides (Steud.) Korov., and F. lehmannii Boiss.] in the northern part of Xinjiang, China. The 16S rRNA sequences of rhizosphere bacteria were obtained with an Illumina paired-end sequence platform. Analysis was conducted to determine the richness and diversity of the rhizosphere bacterial communities. Two-way ANOVA indicated that plant species and soil depth had no significant effect on the alpha diversity of rhizobacteria. Linear discriminant analysis effect size showed that F. lehmannii followed by F. ferulaeoides had the most biomarkers and the highest taxon level, F. syreitschikowii and F. gracilis the least, while F. syreitschikowii and F. gracilis had the least property. This trend is consistent with reports that the medicinal value of F. lehmannii and F. ferulaeoides is greater than that of F. gracilis and F. syreitschikowii. The results of this study provide information that could be used for the commercial cultivation of Ferula spp.
| S-EPMC5871818 | biostudies-other