PXD022897

PXD022897 is an original dataset announced via ProteomeXchange.

Title	Formation and characterization of emergent microbial communities
Description	Microbial communities colonize plant tissues and contribute to host function. How these communities form and how individual members contribute to shaping the microbial community are not well understood. Synthetic microbial communities, where defined individual isolates are combined, can serve as valuable model systems for uncovering the organizational principles of communities. Using genome-defined organisms, systematic analysis by computationally-based network reconstruction can lead to mechanistic insights and the metabolic interactions between species. In this study, 10 bacterial strains isolated from the Populus deltoides rhizosphere were combined and passaged in two different media environments to form a stable microbial community. The membership and relative abundances of the strains stabilized after around 5 growth cycles and resulted in just a few dominant strains. To unravel the underlying metabolic interactions, the KBase platform was used for constructing community-level models and for elucidating the metabolic processes involved in shaping the microbial communities. These analyses were complemented by growth curves of the individual isolates, pairwise interaction screens, and metaproteomics of the community. Flux balance analysis was used to model the metabolic potential in the microbial community and identify potential metabolic exchanges among the component species. Revealing the mechanisms of interaction among plant-associated microorganisms will provide insights into strategies for engineering microbial communities that can potentially increase plant growth and disease resistance. Further, deciphering the membership and metabolic potentials of a bacterial community will enable the design of synthetic co-cultures with desired biological functions.
HostingRepository	MassIVE
AnnounceDate	2022-09-28
AnnouncementXML	Submission_2022-09-28_05:47:33.377.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Paul Abraham
SpeciesList	scientific name: Pseudomonas sp. GM17; NCBI TaxID: 1144323; scientific name: Pantoea sp. YR343; NCBI TaxID: 1144341; scientific name: Rhizobium sp. CF142; NCBI TaxID: 1144314; scientific name: Caulobacter sp. AP07; NCBI TaxID: 1144304; scientific name: Bacillus sp. bc15; NCBI TaxID: 1761758; scientific name: Paraburkholderia sp. BT03; scientific name: Streptomyces mirabilis YR139; scientific name: Variovorax sp. CF313; NCBI TaxID: 1144315; scientific name: Duganella sp. CF402; NCBI TaxID: 1855289; scientific name: Sphingobium sp. AP49; NCBI TaxID: 1144307;
ModificationList	Oxidation; Carbamidomethyl
Instrument	Q Exactive Plus

Revision	Datetime	Status	ChangeLog Entry
0	2020-12-03 13:32:26	ID requested
⏵ 1	2022-09-28 05:47:33	announced

no publication

submitter keyword: microbial community, microbiome, metaproteomics, rhizosphere bacteria

Mitchel J. Doktycz
contact affiliation	Oak Ridge National Laboratory
contact email	doktyczmj@ornl.gov
lab head
Paul Abraham
contact affiliation	ORNL
contact email	pav@ornl.gov
dataset submitter

MassIVE dataset URI

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://massive.ucsd.edu/MSV000086551/