Dataset Information

Illuminating the metabolic activities of deep-sea microbes and their functional adaptation to the harsh nutritional conditions with metaproteomics

ABSTRACT: In the present study, we studied microbial composition and metabolic activity in the bathypelagic zone of the South China Sea. 12 samples were collected and subjected to metaproteomic analysis. Our data provide a novel view of the roles of two lifestyle prokaryotes and their link in substrate utilization in dark ocean.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Phytoplankton Environmental Sample

SUBMITTER: keqiang yan

LAB HEAD: Dazhi Wang

PROVIDER: PXD026838 | Pride | 2024-06-16

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

Items per page:

1 - 5 of 245

Publications

Functional vertical connectivity of microbial communities in the ocean.

Chen Shi S Xie Zhang-Xian ZX Yan Ke-Qiang KQ Chen Jian-Wei JW Li Dong-Xu DX Wu Peng-Fei PF Peng Ling L Lin Lin L Dong Chun-Ming CM Zhao Zihao Z Fan Guang-Yi GY Liu Si-Qi SQ Herndl Gerhard J GJ Wang Da-Zhi DZ

Science advances 20240523 21

Sinking particles are a critical conduit for the transport of surface microbes to the ocean's interior. Vertical connectivity of phylogenetic composition has been shown; however, the functional vertical connectivity of microbial communities has not yet been explored in detail. We investigated protein and taxa profiles of both free-living and particle-attached microbial communities from the surface to 3000 m depth using a combined metaproteomic and 16<i>S</i> rRNA amplicon sequencing approach. A ...[more]

PMID: 38781332

Similar Datasets

Project description:Marine viral concentrates (VCs) contains a substantial amount of non-cellular biological particles, e.g. viruses, gene transfer agents (GTAs) and membrane vesicles that are ecological significant. Metagenomic sequencing of VCs has been extensively applied to study the diversity and function potential of natural virions whereas information of nonn-viral components are often excluded for investigation. Here we apply a shotgun proteomic approach to characterize the origin and function of proteins in the VCs collected from the deep chlorophyll maximum (DCM) of the South China Sea. Using a custom database, we identified 636 non-redundant proteins represented by a total of 7220 spectra from the two VC samples. Cyanophages, pelagiphages, Phycodnaviridae and a group of uncultured viruses (previouly collected from DCM of Mediterranean Sea) contributed the most in the viral proteome. Seldom proteins related to RNA viruses and known GTAs were found despites of the presence of their sequences in the protein-searching database, suggested that these particles might be low abundant in the samples. Over 60% of identified spectra could not be assigned to viruses. The non-viral spectra were dominated by microbial groups of SAR324, SAR11, Actinobacteria and picoeukaryotic algae such as prasinophytes.Interestingly, we found that periplasmic proteins such as diverse ABC and TRAP transporters, and 56 kDa selenium-binding proteins, were enriched in this fraction.Together with other detected non-viral proteins,we could identify significant microbial functions, such as the utilization of glycine betaine, 3-dimethylsulphoniopropionate,and taurine by SAR11,and urea by prochlorococcus, nitrous oxide production by ammonia-oxidizing archaea and peroxide detoxification by unkonwn gammaproteobacteria. Our study of marine VCs demonstrates the potential application of metaproteomics to link the nano-size materials to the diversity of virions and interesting microbial functions in the ocean.

			Action	DRS
	P1800820003_F10_1.raw	Raw
	P1800820003_F10_2.raw	Raw
	P1800820003_F1_1.raw	Raw
	P1800820003_F1_2.raw	Raw
	P1800820003_F2_1.raw	Raw