Deep-sea corals
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ABSTRACT:
PROVIDER: PRJNA1328755 | ENA |
REPOSITORIES: ENA
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Project description:Dendrophyllia sp., Eguchipsammia fistula, Rhizotrochus typus Targeted loci environmental
| PRJNA354830 | ENA
Project description:Deep-sea corals are found on hard substrates on seamounts and continental margins worldwide at depths of 300 to approximately 3,000 m. Deep-sea coral communities are hotspots of deep ocean biomass and biodiversity, providing critical habitat for fish and invertebrates. Newly applied radiocarbon age dates from the deep water proteinaceous corals Gerardia sp. and Leiopathes sp. show that radial growth rates are as low as 4 to 35 mum year(-1) and that individual colony longevities are on the order of thousands of years. The longest-lived Gerardia sp. and Leiopathes sp. specimens were 2,742 years and 4,265 years, respectively. The management and conservation of deep-sea coral communities is challenged by their commercial harvest for the jewelry trade and damage caused by deep-water fishing practices. In light of their unusual longevity, a better understanding of deep-sea coral ecology and their interrelationships with associated benthic communities is needed to inform coherent international conservation strategies for these important deep-sea habitat-forming species.
| S-EPMC2663997 | biostudies-literature
Project description:It is usually assumed that metabolic constraints restrict deep-sea corals to cold-water habitats, with 'deep-sea' and 'cold-water' corals often used as synonymous. Here we report on the first measurements of biological characters of deep-sea corals from the central Red Sea, where they occur at temperatures exceeding 20°C in highly oligotrophic and oxygen-limited waters. Low respiration rates, low calcification rates, and minimized tissue cover indicate that a reduced metabolism is one of the key adaptations to prevailing environmental conditions. We investigated four sites and encountered six species of which at least two appear to be undescribed. One species is previously reported from the Red Sea but occurs in deep cold waters outside the Red Sea raising interesting questions about presumed environmental constraints for other deep-sea corals. Our findings suggest that the present understanding of deep-sea coral persistence and resilience needs to be revisited.
| S-EPMC3789407 | biostudies-literature
Project description:The ability of coral reefs to engineer complex three-dimensional habitats is central to their success and the rich biodiversity they support. In tropical reefs, encrusting coralline algae bind together substrates and dead coral framework to make continuous reef structures, but beyond the photic zone, the cold-water coral Lophelia pertusa also forms large biogenic reefs, facilitated by skeletal fusion. Skeletal fusion in tropical corals can occur in closely related or juvenile individuals as a result of non-aggressive skeletal overgrowth or allogeneic tissue fusion, but contact reactions in many species result in mortality if there is no 'self-recognition' on a broad species level. This study reveals areas of 'flawless' skeletal fusion in Lophelia pertusa, potentially facilitated by allogeneic tissue fusion, are identified as having small aragonitic crystals or low levels of crystal organisation, and strong molecular bonding. Regardless of the mechanism, the recognition of 'self' between adjacent L. pertusa colonies leads to no observable mortality, facilitates ecosystem engineering and reduces aggression-related energetic expenditure in an environment where energy conservation is crucial. The potential for self-recognition at a species level, and subsequent skeletal fusion in framework-forming cold-water corals is an important first step in understanding their significance as ecological engineers in deep-seas worldwide.
| S-EPMC5381374 | biostudies-literature
Project description:Despite the importance of deep-sea corals, our current understanding of their ecology and evolution is limited due to difficulties in sampling and studying deep-sea environments. Moreover, a recent re-evaluation of habitat limitations has been suggested after characterization of deep-sea corals in the Red Sea, where they live at temperatures of above 20 °C at low oxygen concentrations. To gain further insight into the biology of deep-sea corals, we produced reference transcriptomes and studied gene expression of three deep-sea coral species from the Red Sea, i.e. Dendrophyllia sp., Eguchipsammia fistula, and Rhizotrochus typus. Our analyses suggest that deep-sea coral employ mitochondrial hypometabolism and anaerobic glycolysis to manage low oxygen conditions present in the Red Sea. Notably, we found expression of genes related to surface cilia motion that presumably enhance small particle transport rates in the oligotrophic deep-sea environment. This is the first study to characterize transcriptomes and in situ gene expression for deep-sea corals. Our work offers several mechanisms by which deep-sea corals might cope with the distinct environmental conditions present in the Red Sea As such, our data provide direction for future research and further insight to organismal response of deep-sea coral to environmental change and ocean warming.
| S-EPMC5526985 | biostudies-literature
Project description:Coral reefs around the world are under threat due to anthropogenic impacts on the environment. It is therefore important to develop methods to monitor the status of the reefs and detect changes in the health condition of the corals at an early stage before severe damage occur. In this work, we evaluate underwater hyperspectral imaging as a method to detect changes in health status of both orange and white color morphs of the coral species Lophelia pertusa. Differing health status was achieved by exposing 60 coral samples to the toxic compound 2-methylnaphthalene in concentrations of 0 mg L-1 to 3.5 mg L-1. A machine learning model was utilized to classify corals according to lethal concentration (LC) levels LC5 (5% mortality) and LC25 (25% mortality), solely based on their reflectance spectra. All coral samples were classified to correct concentration group. This is a first step towards developing a remote sensing technique able to assess environmental impact on deep-water coral habitats over larger areas.
| S-EPMC6392237 | biostudies-literature
Project description:A total 10 mitochondrial genomes from deep-sea corals in the South China Sea Genome sequencing and assembly
| PRJNA795264 | ENA
Project description:BackgroundNumerous studies have shown that bacteria form stable associations with host corals and have focused on identifying conserved "core microbiomes" of bacterial associates inferred to be serving key roles in the coral holobiont. Because studies tend to focus on only stony corals (order Scleractinia) or soft corals (order Alcyonacea), it is currently unknown if there are conserved bacteria that are shared by both. A meta-analysis was done of 16S rRNA amplicon data from multiple studies generated via identical methodology to allow direct comparisons of bacterial associates across seven deep-sea corals, including both stony and soft species: Anthothela grandiflora, Anthothela sp., Lateothela grandiflora, Lophelia pertusa, Paramuricea placomus, Primnoa pacifica, and Primnoa resedaeformis.ResultsTwenty-three operational taxonomic units (OTUs) were consistently present in greater than 50% of the coral samples. Seven amplicon sequence variants (ASVs), five of which corresponded to a conserved OTU, were consistently present in greater than 30% of the coral samples including five or greater coral species. A majority of the conserved sequences had close matches with previously identified coral-associated bacteria. While known to dominate tropical and temperate coral microbiomes, Endozoicomonas were extremely rare or absent from these deep-sea corals. An Endozoicomonas OTU associated with Lo. pertusa in this study was most similar to those from shallow-water stony corals, while an OTU associated with Anthothela spp. was most similar to those from shallow-water gorgonians.ConclusionsBacterial sequences have been identified that are conserved at the level of class Anthozoa (i.e., found in both stony and soft corals, shallow and deep). These bacterial associates are therefore hypothesized to play important symbiotic roles and are highlighted for targeted future study. These conserved bacterial associates include taxa with the potential for nitrogen and sulfur cycling, detoxification, and hydrocarbon degradation. There is also some overlap with kit contaminants that need to be resolved. Rarely detected Endozoicomonas sequences are partitioned by whether the host is a stony coral or a soft coral, and the finer clustering pattern reflects the hosts' phylogeny.
| S-EPMC6558771 | biostudies-literature
Project description:Today, nanoparticles are used in various commercial products. One of the most common nanoparticles is titanium dioxide (TiO2). It has a catalytic activity and UV absorption (λ<400 nm), and it generates reactive oxygen species (ROS). The catalytic activity of TiO2 nanoparticle is capable of killing a wide range of microorganisms. In the environment, nanoparticles form structures consisting of primary particles, and their aggregates and agglomerates. These compounds are defined NOAA (nano-objects, and their aggregates and agglomerates greater than 100 nm). The unique properties of TiO2 nanoparticles can be maintained in the environment, thus, the growing use of TiO2 nanoparticles is raising concerns about the environmental risks. The assessment of biological and ecological effects of TiO2-NOAA is necessary. In our previous study, we assessed the effect of TiO2-NOAA on microbes by using Saccharomyces cerevisiae and Escherichia coli. It was shown that TiO2-NOAA decomposed methylene blue under UV irradiation. It suggested that TiO2-NOAA generated ROS under UV irradiation. However, TiO2-NOAA did not show growth inhibition in minimal agar medium under UV irradiation. By adding TiO2-NOAA in medium, colony formation was observed with UV intensity that inactivates microbes. Moreover, TiO2-NOAA adsorbed microbes. These results suggested that the amount of ROS generated by TiO2-NOAA was not enough to inactivate microbes, and TiO2-NOAA might protect microbes from UV. In this study, we assessed the effect of TiO2-NOAA in more detail by using S. cerevisiae. We used DNA microarray analysis for qualitative assessment. Further, we carried out quantitative assessment by using Real Time RT-PCR method for characteristic genes in DNA microarray analysis. To compare yeast cells in various conditions, six kinds of treatment conditions were prepared (Condition 1. adsorbed fraction to TiO2-NOAA under UV, 2. non-adsorbed fraction to TiO2-NOAA under UV, 3. adsorbed fraction to TiO2-NOAA without UV, 4. non-adsorbed fraction to TiO2-NOAA without UV, 5. irradiated UV and 6. negative control). From the result of DNA microarray analysis, the most number of genes was altered in Condition 1, followed by Condition 3 and 5. The genes related to oxidative stress, and the genes related to synthesis of trehalose and glycogen were significantly up-regulated of yeast cells in Condition 1 and 5, and Condition 1 and 3, respectively. These results suggest that yeast cells suffer oxidative stress by TiO2-NOAA under UV, and they also suffer membrane damage by TiO2-NOAA itself, as a result, they reserve energy sources. From the result of Real Time RT-PCR, genes related to oxidative stress (GRE2, SOD2) were up-regulated in Condition 1 and 3, however, these expression levels in each condition were not significant. And genes related to synthesis of trehalose and glycogen (GSY1, TPS2) were up-regulated in Condition 1 and 3. These results suggest that oxidative stress is caused not by TiO2-NOAA but by UV. It is also suggested that yeast cells were damaged at their membranes by TiO2-NOAA, as a result, genes related to synthesis of trehalose and glycogen were up-regulated. Thus, we suggest that the effect of TiO2-NOAA on yeast cells under UV irradiation is greater due to TiO2-NOAA itself than due to ROS generated by TiO2-NOAA.
2017-06-06 | GSE99660 | GEO
Project description:The deep sea (>200 m) is home to a surprisingly rich biota, which in some cases compares to that found in shallow areas. Scleractinian corals are an example of this - they are key species in both shallow and deep ecosystems. However, what evolutionary processes resulted in current depth distribution of the marine fauna is a long-standing question. Various conflicting hypotheses have been proposed, but few formal tests have been conducted. Here, we use global spatial distribution data to test the bathymetric origin and colonization trends across the depth gradient in scleractinian corals. Using a phylogenetic approach, we infer the origin and historical trends in directionality and speed of colonization during the diversification in depth. We also examine how the emergence of photo-symbiosis and coloniality, scleractinian corals' most conspicuous phenotypic innovations, have influenced this process. Our results strongly support an offshore-onshore pattern of evolution and varying dispersion capacities along depth associated with trait-defined lineages. These results highlight the relevance of the evolutionary processes occurring at different depths to explain the origin of extant marine biodiversity and the consequences of altering these processes by human impact, highlighting the need to include this overlooked evolutionary history in conservation plans.
| S-EPMC10656505 | biostudies-literature