PXD051466

PXD051466 is an original dataset announced via ProteomeXchange.

Title	In-depth metaproteome reveals carbon and nitrogen metabolic coupling throughout the water column in the South China Sea using 1-L seawater per sample
Description	Marine microbes drive pivotal transformations in planetary-scale elemental cycles and have crucial impacts on global biogeochemical processes. Metaproteomics is a powerful tool for assessing the metabolic diversity and function of marine microbes. However, hundreds of liters of seawater are required for metaproteomic analysis due to the sparsity of microbial populations in seawater, which poses a substantial challenge to the widespread application of marine metaproteomics, particularly for deep seawater. Herein, a sensitive marine metaproteomics workflow, named SMMP, was developed by integrating polycarbonate filter-assisted microbial enrichment, solid-phase alkylation-based anti-interference metaproteome sample preparation and nanoLC-MS/MS for trace peptide separation and characterization. The method provided more than 8500 proteins from 1 L of bathypelagic seawater samples, which covered diverse microorganisms and crucial functions, e.g. the detection of key enzymes associated with the Wood-Ljungdahl pathway. Then, we applied SMMP to investigate vertical variations in the metabolic expression patterns of marine microorganisms from the euphotic zone to the bathypelagic zone. Methane oxidation and carbon monoxide (CO) oxidation were active processes, especially in the bathypelagic zone, as they provided a remarkable energy supply for the growth and proliferation of heterotrophic microorganisms. In addition, marker protein profiles detected related to ammonia transport, ammonia oxidation, and carbon fixation highlighted that Thaumarchaeota played a critical role in primary production based on the coupled carbon-nitrogen process, contributing to the storage of carbon and nitrogen in the bathypelagic regions. SMMP has low microbial input requirements and yields in-depth metaproteome analysis, making it a prospective approach for comprehensive marine metaproteomic investigations.
HostingRepository	iProX
AnnounceDate	2024-04-16
AnnouncementXML	Submission_2024-04-15_20:12:02.895.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Songduo Wang
SpeciesList	scientific name: Bacillus pacificus; NCBI TaxID: 2026187; scientific name: Pseudomonas abyssi; NCBI TaxID: 170540; scientific name: Erythrobacter marinus; NCBI TaxID: 874156; scientific name: Bacillus infantis; NCBI TaxID: 324767; scientific name: Vibrio azureus; NCBI TaxID: 512649; scientific name: Ruegeria sp. AD91A; NCBI TaxID: 2293862;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ; Orbitrap Exploris 480; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2024-04-15 20:11:34	ID requested
⏵ 1	2024-04-15 20:12:03	announced

Dataset with its publication pending

submitter keyword: metaproteomics, marine microorganism, one-liter seawater, chemoautotrophs, carbon and nitrogen metabolic coupling

Lihua Zhang
contact affiliation	Dalian Institute of chemical physics
contact email	lihuazhang@dicp.ac.cn
lab head
Songduo Wang
contact affiliation	Dalian Institute of chemical physics
contact email	songduowang@dicp.ac.cn
dataset submitter

iProX dataset URI