Ontology highlight
ABSTRACT:
PROVIDER: PRJNA777625 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The complete mitochondrial genome of the symbiotic infaunal snapping shrimp Leptalpheus forceps (Decapoda, Alpheidae)
| PRJNA555779 | ENA
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
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 | GSE52225 | 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 | GSE52224 | GEO
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
Project description:Clostridium sp. 'deep sea' isolate:deep sea Genome sequencing
| PRJNA668535 | ENA