Ammonia oxidizing archaea in Costa Rica Dome OMZ
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA562607 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10028128.fastq.gz | Fastqsanger.gz | |||
| SRR10028129.fastq.gz | Fastqsanger.gz | |||
| SRR10028130.fastq.gz | Fastqsanger.gz | |||
| SRR10028131.fastq.gz | Fastqsanger.gz | |||
| SRR10028132.fastq.gz | Fastqsanger.gz |
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Similar Datasets
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:Ammonia oxidizing archaea (AOA) are microbes that are widely distributed in the ocean that convert ammonia to nitrite for energy acquisition in the presence of oxygen. Recent study has unraveled highly diverse sublineages within the previously defined AOA ecotypes (i.e., water column A (WCA) and water column B (WCB)), although the eco-physiology and environmental determinants of WCB subclades remain largely unclear. In this study, we examined the AOA communities along the water columns (40-3000 m depth) in the Costa Rica Dome (CRD) upwelling region in the eastern tropical North Pacific Ocean. Highly diverse AOA communities that were significantly different from those in oxygenated water layers were observed in the core layer of the oxygen minimum zone (OMZ), where the dissolved oxygen (DO) concentration was < 2μM. Moreover, a number of AOA phylotypes were found to be enriched in the OMZ core. Most of them were negatively correlated with DO and were also detected in other OMZs in the Arabian Sea and Gulf of California, which suggests low oxygen adaptation. This study provided the first insight into the differential niche partitioning and environmental determinants of various subclades within the ecotype WCB. Our results indicated that the ecotype WCB did indeed consist of various sublineages with different eco-physiologies, which should be further explored.
| S-EPMC6843251 | biostudies-literature
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:Costa Rica subduction zone Metagenome
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Project description:Small RNA was sequenced from banked peripheral blood serum from 1,134 asthmatic children aged 6 to 14 years who participated in the Genetics of Asthma in Costa Rica Study (GACRS). We filtered the participants into high and low bronchodilator response (BDR) quartiles and used DeSeq2 to identify miRNAs with differential expression (DE) in high (N= 277) vs low (N= 278) BDR group. The putative target genes of DE miRNAs were identified, and pathway enrichment analysis was performed. Results: We identified 10 down-regulated miRNAs having odds ratios (OR) between 0.37 and 0.76 for a doubling of miRNA counts and one up-regulated miRNA (OR=2.26) between high and low BDR group. Further, functional annotation of 11 DE miRNAs were performed as well as of two replicated miRs. Target genes of these miRs were enriched in regulation of cholesterol biosynthesis by SREBPs, ESR-mediated signaling, G1/S transition, RHO GTPase cycle, and signaling by TGFB family pathways.
2023-10-09 | GSE244573 | GEO
Project description:Costa Rica subduction zone Targeted loci environmental
| PRJNA797441 | ENA
Project description:ammonia-oxidizing archaea Raw sequence reads
| PRJNA793074 | ENA
Project description:ammonia-oxidizing archaea Raw sequence reads
| PRJNA577974 | ENA