PXD033692

PXD033692 is an original dataset announced via ProteomeXchange.

Title	Metaexoproteomics identifies active plant-microbe interactions operating in the rhizosphere
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.
HostingRepository	PRIDE
AnnounceDate	2022-07-01
AnnouncementXML	Submission_2022-07-01_08:22:06.417.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD033692
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Andrew Bottrill
SpeciesList	scientific name: soil metagenome; NCBI TaxID: 410658;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2022-05-05 01:03:30	ID requested
⏵ 1	2022-07-01 08:22:06	announced

Dataset with its publication pending

submitter keyword: Metaexoproteomics, LC-MS/MS, Warwick_RTP

Dr Ian Liidbury
contact affiliation	School of Biosciences, University of Sheffield, Sheffield, UK
contact email	i.lidbury@sheffield.ac.uk
lab head
Andrew Bottrill
contact affiliation	University of Warwick
contact email	a.r.bottrill@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD033692
     1. Label: PRIDE project
     2. Name: Metaexoproteomics identifies active plant-microbe interactions operating in the rhizosphere