Tall Wheatgrass root exudate metabolipidome V2
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive
ORGANISM(S): Thinopyrum Elongatum (ncbitaxon:4588)
SUBMITTER: 
Kirsten Hofmockel Sneha Couvillion
PROVIDER: MSV000093600 | MassIVE | Thu Dec 07 10:40:00 GMT 2023
REPOSITORIES: MassIVE
Similar Datasets
Project description:<p>This dataset contains 10 Desorption Electrospray Ionization Mass Spectrometry Imaging (DESI-MSI) slides from cross-sections of surgically resected colorectal tissues with cancer and adjacent normal. The data is released with MassVision software platform for exploration and analysis of MSI data. Primary publication for citation: Jamzad et al., Analytical Chemistry 2025. Methods reference for acquisition conditions: Kaufmann et al., Metabolites 2023. Please cite BOTH papers when using this dataset, in whole or in part, in any publications or presentations.</p>
2025-09-19 | MTBLS12868 | MetaboLights
Project description:Raw data files regarding publication titled "Ion Mobility-coupled Mass Spectrometry for Metallophore Detection"
[insert doi here following publication]
2025-01-15 | MSV000096856 | MassIVE
Project description:Raw data files regarding publication titled "Ion Mobility-coupled Mass Spectrometry for Metallophore Detection"
[insert doi here following publication]
2025-01-15 | MSV000096856 | GNPS
Project description:For further details, please refer to the publication.
2018-09-11 | PXD007221 | Pride
Project description:A direct comparison of RNAi in vitro with RNAi in vivo is being performed using RNA interference (RNAi) target sequencing (RIT-Seq) of Trypanosoma brucei to identify all genes specifically required for growth in vivo (the infectome). Assembly of the bloodstream-form T. brucei RNAi library and the RNAi target sequencing (RIT-seq) approach in African trypanosomes were reported previously in Alsford, S. et al. High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome. Genome Res 21, 915-924, 264 doi:gr.115089.110 [pii] 265 10.1101/gr.115089.110 (2011) and Alsford,S et al. High-throughput decoding of antitrypanosomal drug efficacy and resistance. Nature 482, 232236 doi:10.1038/nature10771 (2012). This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
2014-01-21 | E-ERAD-110 | biostudies-arrayexpress
Project description:A PiggyBac transposon based screen in a murine pancreatic cancer model.This data has been described in the following article [doi:10.1038/ng.3164] and its further analysis can be freely submitted for publication. For information on the proper use of data shared by the Wellcome Trust Sanger Institute (including information on acknowledgement), please see http://www.sanger.ac.uk/datasharing/
2016-07-04 | E-ERAD-514 | biostudies-arrayexpress
Project description:Root-knot nematodes (Meloidogyne spp.) have garnered significant attention from researchers owing to the substantial damage they cause to crops and their worldwide distribution. However, controlling these nematodes is challenging because a limited number of chemical pesticides and biocontrol agents are effective against them. Here, we demonstrate that pepper rotation markedly reduces Meloidogyne incognita infection in cucumber and diminishes the presence of p-hydroxybenzoic acid in the soil, a compound known to exacerbate M. incognita infection. Pepper rotation also restructures the rhizobacterial community, leading to the colonization of the cucumber rhizosphere by two Pseudarthrobacter oxydans strains (RH60 and RH97), facilitated by enrichment of palmitic acid in pepper root exudates. Both strains exhibit high nematocidal activity against M. incognita and have the ability to biosynthesize indoleacetic acid and biodegrade p-hydroxybenzoic acid. RH60 and RH97 also induce systemic resistance in cucumber plants and promote their growth. These data suggest that the pepper root exudate palmitic acid alleviates M. incognita infection by recruiting beneficial P. oxydans to the cucumber rhizosphere. Our analyses identify a novel chemical component in root exudates and reveal its pivotal role in crop rotation for disease control, providing intriguing insights into the keystone function of root exudates in plant protection against root-knot nematode infection.
| S-EPMC11783881 | biostudies-literature
Project description:Certain soil microorganisms can improve plant growth, and practices that encourage their proliferation around the roots can boost production and reduce reliance on agrochemicals. The beneficial effects of the microbial inoculants currently used in agriculture are inconsistent or short-lived because their persistence in soil and on roots is often poor. A complementary approach could use root exudates to recruit beneficial microbes directly from the soil and encourage inoculant proliferation. However, it is unclear whether the release of common organic metabolites can alter the root microbiome in a consistent manner and if so, how those changes vary throughout the whole root system. In this study, we altered the expression of transporters from the ALUMINUM-ACTIVATED MALATE TRANSPORTER and the MULTIDRUG AND TOXIC COMPOUND EXTRUSION families in rice (Oryza sativa L.) and wheat (Triticum aestivum L.) and tested how the subsequent release of their substrates (simple organic anions, including malate, citrate, and γ-amino butyric acid) from root apices affected the root microbiomes. We demonstrate that these exudate compounds, separately and in combination, significantly altered microbiome composition throughout the root system. However, the root type (seminal or nodal), position along the roots (apex or base), and soil type had a greater influence on microbiome structure than the exudates. These results reveal that the root microbiomes of important cereal species can be manipulated by altering the composition of root exudates, and support ongoing attempts to improve plant production by manipulating the root microbiome.
| S-EPMC8644255 | biostudies-literature
Project description:The interactions between plants and rhizosphere microbes mediated by plant root exudates are increasingly being investigated. The root-derived metabolites of medicinal plants are relatively diverse and have unique characteristics. However, whether medicinal plants influence their rhizosphere microbial community remains unknown. How medicinal plant species drive rhizosphere microbial community changes should be clarified. In this study involving high-throughput sequencing of rhizosphere microbes and an analysis of root exudates using a gas chromatograph coupled with a time-of-flight mass spectrometer, we revealed that the root exudate metabolites and microorganisms differed among the rhizosphere soils of five medicinal plants. Moreover, the results of a correlation analysis indicated that bacterial and fungal profiles in the rhizosphere soils of the five medicinal plants were extremely significantly or significantly affected by 10 root-associated metabolites. Furthermore, among the 10 root exudate metabolites, two (carvone and zymosterol) had opposite effects on rhizosphere bacteria and fungi. Our study findings suggest that plant-derived exudates modulate changes to rhizosphere microbial communities.
| S-EPMC11277521 | biostudies-literature
Project description:1. Plant-microbe interactions are critical for ecosystem functioning and drive rhizosphere processes. Root exudates are an important soil carbon (C) input, as well as a mechanism for communication between plants and rhizosphere microbes, but are notoriously difficult to extract and characterise. Common methods produce either substantial noise from the soil or do not mimic natural systems. Optimising methods for root exudate collection in soil is crucial for advancing our understanding of root-microbe interactions under changing environmental conditions. 2. Hybrid root exudate collection methods, where plants are grown in soil and transferred to hydroponics for exudate collection after root washing, might offer an ecologically relevant alternative to existing approaches. However, this method causes potential root damage as well as osmosis and subsequent leaking of cell contents. Here, we assessed different 'root recovery' periods after root washing and before hybrid root exudate collection, by comparing root exudate quantity and quality with both damaged root extracts and with leachates collected from the intact root-soil system. This was done across three common grassland species representing three functional groups. 3. We found that root exudate profiles of the shortest recovery period (0 days) were similar to damaged root extracts and were very high in C. With an increasing period of root recovery, profiles were more similar to leachates collected from the intact root-soil system, and C concentrations decreased. While both hybrid and leachate collection methods separated species by their root exudate profiles, the hybrid method was less variable in terms of the amount of C measured and provided a more diverse and abundant metabolome with better identification of metabolites. 4. Our results show that a recovery period after root washing of at least 3 days is critical to prevent root damage bias in hybrid collection methods, and that our hybrid method yields exudates that discriminate between species. Our data also suggest that exudates collected with this hybrid method are ecologically valid, which is vital for gaining a mechanistic understanding of their role in ecosystem functioning.
| S-EPMC8444088 | biostudies-literature