Ontology highlight
ABSTRACT:
PROVIDER: PRJNA971617 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The diversity and environmental distribution of the nosZ gene, which encodes the enzyme responsible for the consumption of nitrous oxide, was investigated in marine and terrestrial environments using a functional gene microarray. The microbial communities represented by the nosZ gene probes showed strong biogeographical separation, with communities from surface ocean waters and agricultural soils significantly different from each other and from those in oceanic oxygen minimum zones. Atypical nosZ genes, usually associated with incomplete denitrification pathways, were detected in all the environments, including surface ocean waters. The abundance of nosZ genes, as estimated by quantitative PCR, was highest in the agricultural soils and lowest in surface ocean waters.
2018-10-19 | GSE121473 | GEO
Project description:An Autonomous Underwater Vehicle (AUV) and large volume underwater pumps were used to collect microbial biomass from offshore waters of the Sargasso Sea, from surface waters and into the deep ocean. Seawater collection was performed along a transect in the western North Atlantic Ocean beginning near Bermuda and ending off the coast of Massachusetts, capturing metabolic signatures from oligotrophic, continental margin, and productive coastal ecosystems.
2023-10-25 | PXD045395 | Pride
Project description:Ammonia-oxidizing archaea (AOA) have been reported at high abundance in much of the global ocean, even in environments such as pelagic oxygen minimum zones (OMZs), where conditions seem unlikely to support aerobic ammonium oxidation. Due to the lack of information on any potential alternative metabolism of AOA, the AOA community composition might be expected to differ between oxic and anoxic environments, indicating some difference in ecology and/or physiology of the AOA assemblage. This hypothesis was tested by evaluating AOA community composition using a functional gene microarray that targets the ammonia monooxygenase gene subunit A (amoA). The relationship between environmental parameters and the biogeography of the Arabian Sea and the Eastern Tropical South Pacific (ETSP) AOA assemblages was investigated using principal component analysis (PCA) and redundancy analysis (RDA). In both the Arabian Sea and the ETSP, AOA communities within the core of the OMZ were not significantly different from those inhabiting the oxygenated surface waters above the OMZ. The AOA communities in the Arabian Sea were significantly different from those in the ETSP. In both oceans, the abundance of archaeal amoA gene in the core of the OMZ was higher than that in the surface waters. Our results indicate that AOA communities are distinguished by their geographic origin. RDA suggested that temperature was the main factor that correlated with the differences between the AOA communities from the Arabian Sea and those from the ETSP. Physicochemical properties that characterized the different environments of the OMZ and surface waters played a less important role than did geography in shaping the AOA community composition.
2013-06-20 | GSE46851 | GEO
Project description:Marine microbial communities are critical for biogeochemical cycles and the productivity of ocean ecosystems. Primary productivity, at the base of marine food webs, is constrained by nutrient availability in the surface ocean, and nutrient advection from deeper waters can fuel photosynthesis. In this study, we compared the transcriptional responses by surface microbial communities after experimental deep water mixing to the transcriptional patterns of in situ microbial communities collected with high-resolution automated sampling during a bloom in the North Pacific Subtropical Gyre. Transcriptional responses were assayed with the MicroTOOLs (Microbiological Targets for Ocean Observing Laboratories) marine environmental microarray, which targets all three domains of life and viruses. The experiments showed that mixing of deep and surface waters substantially affects the transcription of photosystem and nutrient response genes among photosynthetic taxa within 24 hours, and that there are specific responses associated with the addition of deep water containing particles (organisms and detritus) compared to filtered deep water. In situ gene transcription was most similar to that in surface water experiments with deep water additions, showing that in situ populations were affected by mixing of nutrients at the six sampling sites. Together, these results show the value of targeted metatranscriptomes for assessing the physiological status of complex microbial communities.
2018-09-03 | GSE109218 | GEO
Project description:Abstract Hypersaline lakes are of immense ecological value as they niche some of the most exclusive extremophilic communities dominated by bacterial and archaeal domains, with few eukaryotic algal representatives. A handful reports describe Picocystis as a key primary producer with great production rates in extremely saline habitats. An extremely haloalkaliphilic picoalgal strain, Picocystis salinarum SLJS6 isolated from hypersaline lake Sambhar, Rajasthan, India, grew robustly in an enriched soda lake medium containing mainly Na2CO3, 50 g/L; NaHCO3, 50g/L, NaCl, 50 g/L (salinity ≈150 ‰) at pH 10. To elucidate the molecular basis of such tolerance to high inorganic carbon and NaCl concentrations, a high-throughput LFQ (label-free quantitation) based quantitative proteomics approach was applied. Out of the total 383 proteins identified in treated samples, 225 were Differentially abundant proteins (DAPs), of which 150 were statistically significant (p value <0.05) including 70 upregulated and 64 downregulated proteins after 3 days of salt and alkalinity stress. Gene ontology analysis was done to annotate and classify the DAPs into functional groups. The analysis linked most DAPs to photosynthesis, oxidative phosphorylation, glucose metabolism and ribosomal structural components envisaging that photosynthesis and ATP synthesis were central to the alkalinity-salinity response. Key components of photosynthetic machinery like photosystem reaction centres, ATP synthase, Rubisco, Fructose-bisphosphate aldolase were significantly upregulated. Enzymes Peptidylprolyl isomerases (PPIase), important for correct protein folding showed remarkable marked-up regulation along with other chaperon proteins indicating their role in alleviating stress. Enhanced photosynthetic activity exhibited by Picocystis salinarum in highly saline-alkaline condition is noteworthy as photosynthesis is suppressed by salt stress in most photosynthetic organisms. This study provided the first evidence of a tailored regulatory mechanism of alkalinity and salt tolerance in extremophilic alga P. salinarum, potentially unraveling the basis of resilience in this not so known organism and paves the way for a promising future production host and model or¬ganism for deciphering the molecular mechanisms of os¬motic stress responses.
2023-05-10 | PXD037170 | Pride
Project description:Ammonia-oxidizing archaea (AOA) have been reported at high abundance in much of the global ocean, even in environments such as pelagic oxygen minimum zones (OMZs), where conditions seem unlikely to support aerobic ammonium oxidation. Due to the lack of information on any potential alternative metabolism of AOA, the AOA community composition might be expected to differ between oxic and anoxic environments, indicating some difference in ecology and/or physiology of the AOA assemblage. This hypothesis was tested by evaluating AOA community composition using a functional gene microarray that targets the ammonia monooxygenase gene subunit A (amoA). The relationship between environmental parameters and the biogeography of the Arabian Sea and the Eastern Tropical South Pacific (ETSP) AOA assemblages was investigated using principal component analysis (PCA) and redundancy analysis (RDA). In both the Arabian Sea and the ETSP, AOA communities within the core of the OMZ were not significantly different from those inhabiting the oxygenated surface waters above the OMZ. The AOA communities in the Arabian Sea were significantly different from those in the ETSP. In both oceans, the abundance of archaeal amoA gene in the core of the OMZ was higher than that in the surface waters. Our results indicate that AOA communities are distinguished by their geographic origin. RDA suggested that temperature was the main factor that correlated with the differences between the AOA communities from the Arabian Sea and those from the ETSP. Physicochemical properties that characterized the different environments of the OMZ and surface waters played a less important role than did geography in shaping the AOA community composition. Two-color array (Cy3 and Cy5): the universal standard 20-mer oligo is printed to the slide with a 70-mer oligo (an archetype). Environmental DNA sequences (fluoresced with Cy3) within 15% of the 70-mer conjugated to a 20-mer oligo (fluoresced with Cy5) complementary to the universal standard will bind to the oligo probes on the array. Signal is the ratio of Cy3 to Cy5. Three replicate probes were printed for each archetype. Two replicate arrays were run on duplicate targets.
2013-06-20 | E-GEOD-46851 | biostudies-arrayexpress
Project description:Deep Lake is a hypersaline system in Antarctica (68°33’36.8S, 78°11’48.7E) that is so saline it remains liquid at –20°C (DeMaere et al 2013). The lake is dominated by haloarchaea, comprising a low-complexity community that differs greatly to warm-hot latitude hypersaline systems, is hierarchical structured, and supports a high level of intergenera gene exchange. Metaproteomics was performed on biomass that was collected in the austral summer of 2008 by sequential size fractionation (20 – 3 µm, 3 – 0.8 µm, 0.8 – 0.1 µm). The data were integrated to obtain a systems level view of the active host-virus interactions occurring in this novel aquatic Antarctic system. DeMaere MZ, Williams TJ, Allen MA, Brown MV, Gibson JA, Rich J, Lauro FM, Dyall-Smith M, Davenport KW, Woyke T, Kyrpides NC, Tringe SG, Cavicchioli R (2013) High level of intergenera gene exchange shapes the evolution of haloarchaea in an isolated Antarctic lake. Proc Natl Acad Sci USA 110: 16939-16944
2015-07-21 | PXD001436 | Pride
Project description:Variation in gene expression is a fundamental aspect of human phenotypic variation. Several studies have analyzed gene expression levels in populations of different continental ancestry, and concluded that there is variation across populations at a fraction of expressed genes. Here we analyze gene expression levels in African American cell lines, which differ from previously analyzed cell lines in that samples from this population have variable proportions of continental ancestry. We show that for most genes examined, gene expression varies with genetic ancestry. Keywords: Human Gene Expression Study
2008-12-05 | GSE10824 | GEO