PXD064252-1

PXD064252 is an original dataset announced via ProteomeXchange.

Title	Differential metaproteomics of bacteria grown in vitro and in planta reveals genes used during growth on maize roots
Description	Plant-associated microbial communities play a crucial role in plant health, yet the metabolism and physiology of bacteria in the rhizosphere remain poorly understood. In this study, we used seven bacterial species (Brucella pituitosa AA2, Chryseobacterium indologenes AA5, Curtobacterium pusillum AA3, Enterobacter ludwigii AA4, Herbaspirillum robiniae AA6, Pseudomonas putida AA7, Stenotrophomonas maltophilia AA1) previously isolated by Niu et al. (2018, PNAS 114(12)) to examine microbial gene expression in the maize root environment (Zea mays cv. Sugar Bun). We conducted differential metaproteomic analyses of these species grown in vitro in a minimal medium and individually in planta on sterile maize roots to identify differentially abundant proteins. We had 3 to 5 biological replicates for each species and condition. For the in vitro condition, we collected cells at mid-log phase and froze the resulting pellet at -80°C prior to protein extraction. For the in planta condition, bacterial species were inoculated individually on sterile maize seeds following the protocol described by Salvato et al. (MPMI, 35(11)) and plants were grown for two weeks. The primary roots were then harvested and vortexed with glass beads; the resulting pellet was frozen at -80°C prior to protein extraction. We identified 1,507-2,159 proteins from each bacterial species, with approximately 30-70% of these proteins significantly differentially abundant between the two conditions. Notably, we found that the differentially abundant functions differed between the seven microbial species, suggesting niche specialization within the rhizosphere. Among the proteins found in increased abundance in planta, many were involved in carbon metabolism, secretion systems, adhesion and motility, and transporters. We are including a table with the submission to help identify which files correspond to which species and condition (OverviewFile.txt).
HostingRepository	PRIDE
AnnounceDate	2026-07-28
AnnouncementXML	Submission_2026-07-28_09:14:24.940.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Simina Vintila
SpeciesList	scientific name: Zea mays (Maize); NCBI TaxID: NEWT:4577; scientific name: Stenotrophomonas maltophilia; NCBI TaxID: NEWT:40324; scientific name: Enterobacter ludwigii; NCBI TaxID: NEWT:299767; scientific name: Curtobacterium pusillum; NCBI TaxID: NEWT:69373; scientific name: Ochrobactrum pituitosum; NCBI TaxID: NEWT:571256; scientific name: Pseudomonas putida; NCBI TaxID: NEWT:303; scientific name: Herbaspirillum robiniae; NCBI TaxID: NEWT:2014887; scientific name: Chryseobacterium indologenes; NCBI TaxID: NEWT:253;
ModificationList	monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2025-05-23 17:21:57	ID requested
⏵ 1	2026-07-28 09:14:25	announced
2	2026-07-28 11:54:36	announced	2026-07-28: Updated project metadata.
3	2026-07-29 09:18:35	announced	2026-07-29: Updated project metadata.

Dataset with its publication pending

submitter keyword: 1D-LC, metaproteome, microbial physiology, maize, differential metaproteomics, plant-microbe interactions, metaproteomics

Manuel Kleiner
contact affiliation	North Carolina State University, department of plant and microbial biology
contact email	manuel.kleiner@ncsu.edu
lab head
Simina Vintila
contact affiliation	North Carolina State University
contact email	svintil@ncsu.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD064252

PRIDE project URI

• PRIDE
  1. PXD064252
     1. Label: PRIDE project
     2. Name: Differential metaproteomics of bacteria grown in vitro and in planta reveals genes used during growth on maize roots