Caminibacter mediatlanticus TB-2
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA19293 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Caminibacter mediatlanticus TB-2 Genome sequencing
| PRJNA543630 | ENA
Project description:Caminibacter mediatlanticus overview
| PRJNA36091 | ENA
Project description:Moderate thermophile isolated from deep sea sediment
| PRJNA13233 | ENA
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
Project description:Despite the fact that deep sea mining is becoming more popular nowadays in terms of obtaining metals ores for daily life purposes, its potential impact to the deep sea habitat, which is originally stable and converse, stills remains uncertain. In order to estimate and regulate the imapct of deep sea mining activities, an in-situ exposure experiment is performed to observe the change in proteomics expression of the deep-sea scvangers, Abyssorchomene distinctus, to copper exposure. This project aims to suggest a potenial protein bio-marker in Abyssorchomene distinctus to assess the impact of mining activities towards deep sea organisms and also discuss the potential application of other deep sea in-situ exposure experiment in the future.
2019-10-30 | PXD012778 | Pride
Project description:The sea cucumber Apostichopus japonicus withstands high water temperatures in the summer by suppressing metabolic rate and entering a state of aestivation. We hypothesized that changes in the expression of miRNAs could provide important post-transcriptional regulation of gene expression during hypometabolism via control over mRNA translation. The present study analyzed profiles of miRNA expression in the sea cucumber respiratory tree using Solexa deep sequencing technology. We identified 279 sea cucumber miRNAs, including 15 novel miRNAs specific to sea cucumber. Animals sampled during deep aestivation (DA; after at least 15 days of continuous torpor) were compared with animals from a non-aestivation (NA) state (animals that had passed through aestivation and returned to an active state). We identified 30 differentially expressed miRNAs ([RPM (reads per million) >10, |FC| (|fold change|) ≥1, FDR (false discovery rate) <0.01]) during aestivation, which were validated by two other miRNA profiling methods: miRNA microarray and real-time PCR. Among the most prominent miRNA species, miR-124, miR-124-3p, miR-79, miR-9 and miR-2010 were significantly over-expressed during deep aestivation compared with non-aestivation animals, suggesting that these miRNAs may play important roles in metabolic rate suppression during aestivation.
2014-10-01 | GSE52224 | GEO
Project description:The sea cucumber Apostichopus japonicus withstands high water temperatures in the summer by suppressing metabolic rate and entering a state of aestivation. We hypothesized that changes in the expression of miRNAs could provide important post-transcriptional regulation of gene expression during hypometabolism via control over mRNA translation. The present study analyzed profiles of miRNA expression in the sea cucumber respiratory tree using Solexa deep sequencing technology. We identified 279 sea cucumber miRNAs, including 15 novel miRNAs specific to sea cucumber. Animals sampled during deep aestivation (DA; after at least 15 days of continuous torpor) were compared with animals from a non-aestivation (NA) state (animals that had passed through aestivation and returned to an active state). We identified 30 differentially expressed miRNAs ([RPM (reads per million) >10, |FC| (|fold change|) ≥1, FDR (false discovery rate) <0.01]) during aestivation, which were validated by two other miRNA profiling methods: miRNA microarray and real-time PCR. Among the most prominent miRNA species, miR-124, miR-124-3p, miR-79, miR-9 and miR-2010 were significantly over-expressed during deep aestivation compared with non-aestivation animals, suggesting that these miRNAs may play important roles in metabolic rate suppression during aestivation.
2014-10-01 | GSE52225 | GEO
Project description:Colonization of deep-sea hydrothermal vents by invertebrates was made efficient through their adaptation to a symbiotic lifestyle with chemosynthetic bacteria, the primary producers of these ecosystems. Anatomical adaptations such as the establishment of specialized cells or organs have been evidenced in numerous deep-sea invertebrates. However, very few studies detailed global inter-dependencies between host and symbionts in these ecosystems. In this study, we proposed to describe, using a proteo-transcriptomic approach, the effects of symbionts on the deep-sea mussel Bathymodiolus azoricus’ molecular biology. We induced an in situ depletion of symbionts and compared the proteo-transcriptome of the gills of mussels in three conditions: symbiotic mussels (natural population), symbiont-depleted mussels and aposymbiotic mussels
2019-02-13 | GSE124699 | GEO
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
Project description:The deep marine subsurface is one of the largest unexplored biospheres on Earth, where members of the phylum Chloroflexi are abundant and globally distributed. However, the deep-sea Chloroflexi have remained elusive to cultivation, hampering a more thorough understanding of their metabolisms. In this work, we have successfully isolated a representative of the phylum Chloroflexi, designated strain ZRK33, from deep-sea cold seep sediments. Phylogenetic analyses based on 16S rRNA genes, genomes, RpoB and EF-tu proteins indicated that strain ZRK33 represents a novel class within the phylum Chloroflexi, designated Sulfochloroflexia. We present a detailed description of the phenotypic traits, complete genome sequence and central metabolisms of the novel strain ZRK33. Notably, sulfate and thiosulfate could significantly promote the growth of the new isolate, possibly through accelerating the hydrolysis and uptake of saccharides. Thus, this result reveals that strain ZRK33 may play a crucial part in sulfur cycling in the deep-sea environments. Moreover, the putative genes associated with assimilatory and dissimilatory sulfate reduction are broadly distributed in the genomes of 27 metagenome-assembled genomes (MAGs) from deep-sea cold seep and hydrothermal vents sediments. Together, we propose that the deep marine subsurface Chloroflexi play key roles in sulfur cycling for the first time. This may concomitantly suggest an unsuspected availability of sulfur-containing compounds to allow for the high abundance of Chloroflexi in the deep sea.
2024-05-22 | PXD023380 | Pride