TIDE 16S
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB12902 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Salt marshes provide many key ecosystem services that have tremendous ecological and economic value. One critical service is the removal of fixed nitrogen from coastal waters, which limits the negative effects of eutrophication resulting from increased nutrient supply. Nutrient enrichment of salt marsh sediments results in higher rates of nitrogen cycling and, commonly, a concurrent increase in the flux of nitrous oxide, an important greenhouse gas. Little is known, however, regarding controls on the microbial communities that contribute to nitrous oxide fluxes in marsh sediments. To address this disconnect, we generated microbial community profiles as well as directly assayed nitrogen cycling genes that encode the enzymes responsible for overall nitrous oxide flux from salt marsh sediments. We hypothesized that communities of microbes responsible for nitrogen transformations will be structured by nitrogen availability. Taxa that respond positively to high nitrogen inputs may be responsible for the elevated rates of nitrogen cycling processes measured in fertilized sediments. Our data show that, with the exception of ammonia-oxidizing archaea, the community composition of organisms responsible for production and consumption of nitrous oxide was altered under nutrient enrichment. These results suggest that elevated rates of nitrous oxide production and consumption are the result of changes in community structure, not simply changes in microbial activity.
2018-01-13 | GSE108888 | GEO
Project description:Functional redundancy in bacterial communities is expected to allow microbial assemblages to survive perturbation by allowing continuity in function despite compositional changes in communities. Recent evidence suggests, however, that microbial communities change both composition and function as a result of disturbance. We present evidence for a third response: resistance. We examined microbial community response to perturbation caused by nutrient enrichment in salt marsh sediments using deep pyrosequencing of 16S rRNA and functional gene microarrays targeting the nirS gene. Composition of the microbial community, as demonstrated by both genes, was unaffected by significant variations in external nutrient supply, despite demonstrable and diverse nutrient–induced changes in many aspects of marsh ecology. The lack of response to external forcing demonstrates a remarkable uncoupling between microbial composition and ecosystem-level biogeochemical processes and suggests that sediment microbial communities are able to resist some forms of perturbation. nirS gene diversity from two salt marsh experiments, GSM (4 treatments, 8 samples, duplicate arrays, four replicate blocks per array, 8 arrays per slide) and PIE (2 treatments, 16 samples, duplicate arrays four replicate blocks per array, 8 arrays per slide)
2010-11-13 | E-GEOD-25227 | biostudies-arrayexpress
Project description:Functional redundancy in bacterial communities is expected to allow microbial assemblages to survive perturbation by allowing continuity in function despite compositional changes in communities. Recent evidence suggests, however, that microbial communities change both composition and function as a result of disturbance. We present evidence for a third response: resistance. We examined microbial community response to perturbation caused by nutrient enrichment in salt marsh sediments using deep pyrosequencing of 16S rRNA and functional gene microarrays targeting the nirS gene. Composition of the microbial community, as demonstrated by both genes, was unaffected by significant variations in external nutrient supply, despite demonstrable and diverse nutrient–induced changes in many aspects of marsh ecology. The lack of response to external forcing demonstrates a remarkable uncoupling between microbial composition and ecosystem-level biogeochemical processes and suggests that sediment microbial communities are able to resist some forms of perturbation.
2010-11-13 | GSE25227 | GEO
Project description:Vibrio natriegens is a rapidly growing salt marsh bacterium that is being developed as a synthetic biology chassis. We characterized its physiological response to different salinities and temperatures in order to optimize culturing conditions and understand its adaptations to a salt marsh environment. Using metabolomics, transcriptomics, and proteomics we determined what pathways respond to these environmental parameters. We found that organic osmolyte synthesis and membrane transporters were most responsive to changes in salinity. The primary osmolytes were glutamate, glutamine, and ectoine, responding to salinity across temperature treatments. However, when media was supplemented with choline, glycine betaine seemed to mostly replace ectoine. These results provide a baseline dataset of metabolic activity under a variety of conditions that will inform decisions made about culturing and genome engineering for future applications.
2021-09-15 | PXD027874 | Pride
Project description:Salt marsh sediment microbial community
| PRJEB66381 | ENA
Project description:Relatively little is known about the presence and regulation of pathways involved in nutrient acquisition in the brown tide forming alga, Aureococcus anophagefferens. In this study, Long-SAGE (Serial Analysis of Gene Expression) was used to profile the A. anophagefferens transcriptome under nutrient replete (control), and nitrogen (N) and phosphorus (P) deficiency with the goal of understanding how this organism responds at the transcriptional level to varying nutrient conditions. This approach has aided A. anophagefferens genome annotation efforts and identified a suite of genes up-regulated by N and P deficiency, some of which have known roles in nutrient metabolism. Genes up-regulated under N deficiency include an ammonium transporter, an acetamidase/formamidase, and two peptidases. This suggests an ability to utilize reduced N compounds and dissolved organic nitrogen, supporting the hypothesized importance of these N sources in A. anophagefferens bloom formation. There are also a broad suite of P-regulated genes, including an alkaline phosphatase, and two 5’-nucleotidases, suggesting A. anophagefferens may use dissolved organic phosphorus under low phosphate conditions. These N- and P-regulated genes may be important targets for exploring nutrient controls on bloom formation in field populations.
2010-11-05 | GSE21465 | GEO
Project description:Salt marsh cyanobacteria
| PRJNA19325 | ENA
Project description:Bacterial 16S rRNA sequencing data from salt marsh soil samples (n=60) (454 sequencing platform)
| PRJEB22178 | ENA