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PXD033692-1

PXD033692 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleMetaexoproteomics identifies active plant-microbe interactions operating in the rhizosphere
DescriptionAdvances 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.
HostingRepositoryPRIDE
AnnounceDate2022-07-01
AnnouncementXMLSubmission_2022-07-01_08:22:06.417.xml
DigitalObjectIdentifierhttps://dx.doi.org/10.6019/PXD033692
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterAndrew Bottrill
SpeciesList scientific name: soil metagenome; NCBI TaxID: 410658;
ModificationListmonohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
InstrumentOrbitrap Fusion
Dataset History
RevisionDatetimeStatusChangeLog Entry
02022-05-05 01:03:30ID requested
12022-07-01 08:22:06announced
Publication List
Dataset with its publication pending
Keyword List
submitter keyword: Metaexoproteomics, LC-MS/MS, Warwick_RTP
Contact List
Dr Ian Liidbury
contact affiliationSchool of Biosciences, University of Sheffield, Sheffield, UK
contact emaili.lidbury@sheffield.ac.uk
lab head
Andrew Bottrill
contact affiliationUniversity of Warwick
contact emaila.r.bottrill@gmail.com
dataset submitter
Full Dataset Link List
Dataset FTP location
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