Ontology highlight
ABSTRACT:
PROVIDER: PRJNA675849 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13019000.fastq.gz | Fastqsanger.gz | |||
| SRR13019001.fastq.gz | Fastqsanger.gz | |||
| SRR13019002.fastq.gz | Fastqsanger.gz | |||
| SRR13019003.fastq.gz | Fastqsanger.gz | |||
| SRR13019004.fastq.gz | Fastqsanger.gz |
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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.
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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.
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Project description:We designed an experimental setup to investigate the transcriptomic and proteomic responses of the hyperthermophilic archaeon Pyrococcus furiosus to heat and cold shock. P. furiosus is a model organism for studying microbial adaptation to extreme environments, including deep-sea hydrothermal vents with temperature gradients ranging from 1°C to 400°C. We aimed to simulate critical conditions where P. furiosus cannot grow and to examine the immediate response to thermal stress as well as the recovery process.
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Project description:Iron-sulfur minerals such as pyrite are found in many marine benthic habitats. At deep-sea hydrothermal vent sites they occur as massive sulfide chimneys. Hydrothermal chimneys formed by mineral precipitation from reduced vent fluids upon mixing with cold oxygenated sea water. While microorganisms inhabiting actively venting chimneys and utilizing reduced compounds dissolved in the fluids for energy generation are well studied, only little is known about the microorganisms inhabiting inactive sulfide chimneys. We performed a comprehensive meta-proteogenomic analysis combined with radiometric dating to investigate the diversity and function of microbial communities found on inactive sulfide chimneys of different ages from the Manus Basin (SW Pacific). Our study sheds light on potential lifestyles and ecological niches of yet poorly described bacterial clades dominating inactive chimney communities.
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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.
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Project description:Bacteria isolated from diverse environments were found to sense blue light to regulate their biological functions. However, this ability of deep-sea bacteria has been studied rarely. In this study, we found serendipitously that blue light stimulated excess zero-valent sulfur (ZVS) production of E. flavus 21-3, which was isolated from the deep-sea cold seep and possessed a novel thiosulfate oxidation pathway. Its ZVS production responding to the blue light was mediated by a light-oxygen-voltage histidine kinase (LOV-1477), a diguanylate cyclase (DGC-2902), a PilZ protein (mPilZ-1753) and the key thiosulfate dehydrogenase (TsdA) in its thiosulfate oxidation pathway. Subsequently, the thiosulfohydrolase (SoxB-277) was found working with another SoxB (SoxB-285) and being as substitute for each other to generate ZVS. This study provided an example of deep-sea bacteria sensing blue light to regulate thiosulfate oxidation. Deep-sea blue light potentially helped these blue-light-sensing bacteria adapt harsh conditions by diversifying their biological processes.
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