PXD008780

PXD008780 is an original dataset announced via ProteomeXchange.

Title	Functional Response of Polar Bacterial Communities under Variable Organic Inputs Revealed with Metaproteomic, 16S rRNA and Organic Compositional Analysis
Description	Organic matter recycling in marine systems is largely driven by microbial processes, particularly in the Arctic where primary production and inputs can be temporally offset from upper trophic level consumption. This study followed bacterial dynamics in the chlorophyll maximum of the Bering Strait and sediment-water interface of the Chukchi Sea using metaproteomic and 16S rRNA methods to measure cellular function and taxonomic composition under low and high marine-derived particulate organic matter (POM) treatments at 0°C. Parallel analysis of major organic components (lipids and amino acids) allowed a comparison of microbial-POM interactions. Over the 10 day experimental period, bacteria under both treatments showed rapid community responses and changes in proteomic expression, accompanied by small changes in the concentration and distributions of organic components. In the Bering Strait community, protein translation was an important immediate cellular response under both POM scenarios while specific metabolic processes were more distinct between treatments. For example, under both conditions, evidence for carboxylic acid metabolism increased at day 6 while carbohydrate utilization as an energy source showed unique patterns as the experiments progressed. With POM additions to the Bering Strait community, nitrogen transport and regulation went up, including nitrogen fixation and ammonia assimilation, by day 6. In addition, a number of vitamin enzymatic cofactors were enriched by this day, providing evidence for an increase in C1 metabolism at that time. Low POM conditions stimulated the cycling and synthesis of amino acids, which was not as pronounced under the high POM treatment. In the Chukchi Sea community, nitrate reduction and substrate-specific transporter activity was statistically higher than in the Bering Strait, especially under low POM conditions. Taxonomic inference revealed that a wide range of bacterial classes were associated with the shifting cellular functions, but that Alphaproteobacteria, Gammaproteobacteria and Flavobacteria controlled most of these protein abundances. Activities of all classes were highly variable, with less dominant bacterial groups exhibiting a particularly strong degree of niche separation.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:01:13.636.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Emma Timmins-Schiffman
SpeciesList	scientific name: marine metagenome; NCBI TaxID: 408172;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-01-29 01:30:14	ID requested
1	2018-06-20 02:27:23	announced
2	2019-08-19 02:46:51	announced	Updated publication reference for DOI(s): 10.25777/p8gg-tr58.
⏵ 3	2023-11-14 09:01:15	announced	2023-11-14: Updated project metadata.

Mikan MP, Harvey HR, Timmins-Schiffman E, Riffle M, May DH, Salter I, Noble WS, Nunn BL, Metaproteomics reveal that rapid perturbations in organic matter prioritize functional restructuring over taxonomy in western Arctic Ocean microbiomes. ISME J, 14(1):39-52(2020) [pubmed]

curator keyword: Metaproteomics, Biological

submitter keyword: metaproteomics, metagenomics, bacteria, Arctic, organic matter

Brook L. Nunn
contact affiliation	University of Washington Department of Genome Sciences
contact email	brookh@uw.edu
lab head
Emma Timmins-Schiffman
contact affiliation	University of Washington
contact email	emsie25@gmail.com
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/2019/02/PXD008780

PRIDE project URI

• PRIDE
  1. PXD008780
     1. Label: PRIDE project
     2. Name: Functional Response of Polar Bacterial Communities under Variable Organic Inputs Revealed with Metaproteomic, 16S rRNA and Organic Compositional Analysis