Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Metagenomes of deep-sea microorganisms in the South China Sea

PROVIDER: PRJNA1236222 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other
	SRR32696344_1.fastq.gz	Fastqsanger.gz
	SRR32696344_2.fastq.gz	Fastqsanger.gz
	SRR32696348_1.fastq.gz	Fastqsanger.gz
	SRR32696348_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 18

Similar Datasets

Responses to different sulfur sources reveal the complicated and interlinked sulfur metabolism pathways of a deep-sea sulfate reducing bacterium

Project description:Sulfur metabolism in the deep-sea cold seep has been mentioned to have an important contribution to the biogeochemical cycle of sulfur in previous studies. And sulfate reducing bacteria have also been considered to be a dominant microbial population in the deep-sea cold seep and play a crucial role in this process. However, most of sulfate reducing bacteria from cold seep still cannot be purely cultured under laboratory conditions, therefore the actual sulfur metabolism pathways in sulfate reducing bacteria from the deep-sea cold seep have remained unclear. Here, we isolate and pure culture a typical sulfate reducing bacterium Desulfovibrio marinus CS1 from the sediment sample of the deep-sea cold seep in the South China Sea, which provides a probability to understand the sulfur metabolism in the cold seep.

2024-06-16 | PXD023247 | Pride

RNA-Seq of shallow-water mussel Mytilus galloprovincialis under in situ hydrostatic pressure exposure

Project description:Recent studies have unveiled the deep sea as a rich biosphere, populated by species descended from shallow-water ancestors post-mass extinctions. Research on genomic evolution and microbial symbiosis has shed light on how these species thrive in extreme deep-sea conditions. However, early adaptation stages, particularly the roles of conserved genes and symbiotic microbes, remain inadequately understood. This study examined transcriptomic and microbiome changes in shallow-water mussels Mytilus galloprovincialis exposed to deep-sea conditions at the Site-F cold seep in the South China Sea. Results reveal complex gene expression adjustments in stress response, immune defense, homeostasis, and energy metabolism pathways during adaptation. After 10 days of deep-sea exposure, shallow-water mussels and their microbial communities closely resembled those of native deep-sea mussels, demonstrating host and microbiome convergence in response to adaptive shifts. Notably, methanotrophic bacteria, key symbionts in native deep-sea mussels, emerged as a dominant group in the exposed mussels. Host genes involved in immune recognition and endocytosis correlated significantly with the abundance of these bacteria. Overall, our analyses provide insights into adaptive transcriptional regulation and microbiome dynamics of mussels in deep-sea environments, highlighting the roles of conserved genes and microbial community shifts in adapting to extreme environments.

2024-11-24 | GSE263620 | GEO

Metaproteomics and metagenomics analysis reveal distinct metabolic and adaptive functions of euphotic and bathypelagic microbial communities in the South China Sea

Project description:Marine microorganisms inhabiting the bathypelagic zone (1000 m - 4000 m) are pivotal to biogeochemical cycling. However, a comprehensive understanding of microbial community structure and their metabolic activities adaptations to the extreme deep-sea conditions remains elusive. In this study, we employed a metaproteomic approach to investigate the protein profiles of microbial communities spanning the surface and bathypelagic layers of the South China Sea (SCS) and performed a comparative analysis with metagenomic data. The metaproteome and metagenome showed low correlation in functional expression but a high correlation at the phylum level. High-abundance genes were more likely to be translated into proteins, with protein over-representation observed in energy conversion and matter transport processes. Short-chain amide porins facilitate substance exchange and maintain cellular homeostasis, enabling Methylococcales to adapt to deep-sea conditions and actively oxidize methane. Flexible energy utilization strategies, such as CO oxidation, enable Propionibacteriales to thrive in deep-sea environments. This study highlights the significance of microbial enzyme resources and offers valuable insights into the adaptations of deep-sea microorganisms, emphasizing their considerable application potential.

2024-12-02 | PXD058504 |

Metabolic traits of size-fractionated microbial communities at an oceanic deep chlorophyll maximum waters revealed via metaproteomics

Project description:we applied metaproteomic approach to capture proteins from three size-fractionated microbial communities at the DCM in the basin of the South China Sea. The deep recovery of proteomes from a marine DCM plankton assemblage provides the highest resolution of metabolic activities as well as microbial niche differentiation, revealing a spectrum of biological processes carrying out by microbes at DCM of the SCS.

2020-12-21 | PXD016812 | Pride

marine sediment metagenome

Project description:Microbial community of deep sea sediment in South China Sea

| PRJNA360023 | ENA

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

Project description: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.

2024-06-16 | PXD026838 | Pride

Project description:Microbes investigation in deep sea sediment of the South China Sea

| PRJNA659601 | ENA

deep-sea sediments in the South China Sea

Project description:deep-sea sediments in the South China Sea Raw sequence reads

| PRJNA637466 | ENA

A deep-sea bacterium senses and utilizes blue light via a BLUF-dependent pathway

Project description:Light was a ubiquitous environmental stimulus. Deep-sea microorganisms were exposed to a pervasive blue light optical environment. The utilization of blue light by deep-sea microorganisms, especially non-photosynthetic microorganisms, and the downstream pathway after light reception were obscure. Under the enrichment condition surrounded by blue light, a potential novel species named Spongiibacter nanhainus CSC3.9 from the deep-sea cold seep was isolated. Its growth and metabolism under blue light were significantly better than other wavelengths of light. Six blue light sensing proteins, including four BLUF (Blue Light Using Flavin) and two bacteriophytochrome, were annotated in the genome of strain CSC3.9. Then, with the assist of proteomic analysis, we demonstrated that 15960-BLUF was a crucial blue light receptor that interfered with motor behavior through chemotaxis pathway by means of in vivo and in vitro verification. In addition, 15960-BLUF mediated part of the blue light to promote the growth of strain CSC3.9. Further, we summarized the functional BLUF proteins from isolated marine microorganisms, and the high abundance distribution of BLUF similar to the downstream unresponsive domain type in strain CSC3.9 was demonstrated. The widespread distribution of BLUF protein in marine bacteria implied the extensiveness of this regulatory mechanism, and wavelength variation of light was a potential means to isolate uncultured microorganisms. This was the first reported in deep-sea microorganisms that BLUF-dependent physiological response to blue light. It provided a new clue for the blue light adaptation of microorganisms in disphotic zone.

2022-01-18 | PXD028001 | Pride

Metaproteomic analysis of microbial community structure and function in the South China Sea

Project description:In the present study, we studied microbial composition and metabolic activity in the euphotic zone of the South China Sea. 8 samples were collected and subjected to metaproteomic analysis. Our results suggested that mixotrophic phototrophs-driven NDL carbon fixation along with phytoplankton-driven NRL carbon fixation determined primary production in the oligotrophic ocean’s euphotic zone.

2024-06-16 | PXD018513 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data