Ontology highlight
ABSTRACT:
PROVIDER: PRJNA995189 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25293832.fastq.gz | Fastqsanger.gz | |||
| SRR25293833.fastq.gz | Fastqsanger.gz | |||
| SRR25293834.fastq.gz | Fastqsanger.gz | |||
| SRR25293835.fastq.gz | Fastqsanger.gz | |||
| SRR25293836.fastq.gz | Fastqsanger.gz |
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Project description:Ultra-violet (UV) and high-intensity visible (VIS) radiation are environmental stressors known to harm photosynthetic organisms through the generation of reactive intermediates that damage photosynthetic machinery. This study shows the potential of using a thermoacidophilic red alga of the order Cyanidiales to model in situ algal gene expression dynamics as a function of UV exposure and seasonal shifts in UV-VIS intensity. These algae exhibit a dynamic seasonal biomass fluctuation referred to as 'mat decline' where viability drastically decreases as seasonal UV-VIS irradiance intensity increases. In Yellowstone National Park (YNP), temporal experiments coupling UV irradiance manipulations (filtering) with whole-community transcription profiling revealed significant cyanidial gene expression changes occurring as a result of exposure to UV, and that patterns of response adjust across low and high irradiance time periods. Separate analyses examined genes responding to either increasing seasonal UV or VIS intensity, or by the combined effects of both irradiance wavelengths (UV and VIS). Results not only corroborated known physiological changes to solar irradiance, but also suggested the strategies employed to deal with excess VIS and UV intensity may be highly integrated. Finally, a suite of comparative analyses determined the relative utility of environmental transcriptomics technologies in studying ecologically-relevant expression patterns. Results suggest in situ expression profiles will improve understanding of how photosynthetic organisms are responding to environmental stressors as they are observed in nature. 16 samples with 3 biological replicates each.
2014-03-31 | E-GEOD-37673 | biostudies-arrayexpress
Project description:Tibet is one of the most threatened regions by climate warming, thus understanding how its microbial communities function may be of high importance for predicting microbial responses to climate changes. Here, we report a study to profile soil microbial structural genes, which infers functional roles of microbial communities, along four sites/elevations of a Tibetan mountainous grassland, aiming to explore potential microbial responses to climate changes via a strategy of space-for-time substitution. Using a microarray-based metagenomics tool named GeoChip 4.0, we showed that microbial communities were distinct for most but not all of the sites. Substantial variations were apparent in stress, N and C cycling genes, but they were in line with the functional roles of these genes. Cold shock genes were more abundant at higher elevations. Also, gdh converting ammonium into urea was more abundant at higher elevations while ureC converting urea into ammonium was less abundant, which was consistent with soil ammonium contents. Significant correlations were observed between N-cycling genes (ureC, gdh and amoA) and nitrous oxide flux, suggesting that they contributed to community metabolism. Lastly, we found by CCA, Mantel tests and the similarity tests that soil pH, temperature, NH4+–N and vegetation diversity accounted for the majority (81.4%) of microbial community variations, suggesting that these four attributes were major factors affecting soil microbial communities. Based on these observations, we predict that climate changes in the Tibetan grasslands are very likely to change soil microbial community functional structure, with particular impacts on microbial N cycling genes and consequently microbe-mediated soil N dynamics.
2013-07-13 | GSE48820 | GEO
Project description:Ultra-violet (UV) and high-intensity visible (VIS) radiation are environmental stressors known to harm photosynthetic organisms through the generation of reactive intermediates that damage photosynthetic machinery. This study shows the potential of using a thermoacidophilic red alga of the order Cyanidiales to model in situ algal gene expression dynamics as a function of UV exposure and seasonal shifts in UV-VIS intensity. These algae exhibit a dynamic seasonal biomass fluctuation referred to as 'mat decline' where viability drastically decreases as seasonal UV-VIS irradiance intensity increases. In Yellowstone National Park (YNP), temporal experiments coupling UV irradiance manipulations (filtering) with whole-community transcription profiling revealed significant cyanidial gene expression changes occurring as a result of exposure to UV, and that patterns of response adjust across low and high irradiance time periods. Separate analyses examined genes responding to either increasing seasonal UV or VIS intensity, or by the combined effects of both irradiance wavelengths (UV and VIS). Results not only corroborated known physiological changes to solar irradiance, but also suggested the strategies employed to deal with excess VIS and UV intensity may be highly integrated. Finally, a suite of comparative analyses determined the relative utility of environmental transcriptomics technologies in studying ecologically-relevant expression patterns. Results suggest in situ expression profiles will improve understanding of how photosynthetic organisms are responding to environmental stressors as they are observed in nature.
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Project description:Seasonal community dynamics of microbial eukaryotes in freshwater deep lakes
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Project description:Tibet is one of the most threatened regions by climate warming, thus understanding how its microbial communities function may be of high importance for predicting microbial responses to climate changes. Here, we report a study to profile soil microbial structural genes, which infers functional roles of microbial communities, along four sites/elevations of a Tibetan mountainous grassland, aiming to explore potential microbial responses to climate changes via a strategy of space-for-time substitution. Using a microarray-based metagenomics tool named GeoChip 4.0, we showed that microbial communities were distinct for most but not all of the sites. Substantial variations were apparent in stress, N and C cycling genes, but they were in line with the functional roles of these genes. Cold shock genes were more abundant at higher elevations. Also, gdh converting ammonium into urea was more abundant at higher elevations while ureC converting urea into ammonium was less abundant, which was consistent with soil ammonium contents. Significant correlations were observed between N-cycling genes (ureC, gdh and amoA) and nitrous oxide flux, suggesting that they contributed to community metabolism. Lastly, we found by CCA, Mantel tests and the similarity tests that soil pH, temperature, NH4+M-bM-^@M-^SN and vegetation diversity accounted for the majority (81.4%) of microbial community variations, suggesting that these four attributes were major factors affecting soil microbial communities. Based on these observations, we predict that climate changes in the Tibetan grasslands are very likely to change soil microbial community functional structure, with particular impacts on microbial N cycling genes and consequently microbe-mediated soil N dynamics. Twelve samples were collected from four elevations (3200, 3400, 3600 and 3800 m) along a Tibetan grassland; Three replicates in every elevation
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Project description:The increased urban pressures are often associated with specialization of microbial communities. Microbial communities being a critical player in the geochemical processes, makes it important to identify key environmental parameters that influence the community structure and its function.In this proect we study the influence of land use type and environmental parameters on the structure and function of microbial communities. The present study was conducted in an urban catchment, where the metal and pollutants levels are under allowable limits. The overall goal of this study is to understand the role of engineered physicochemical environment on the structure and function of microbial communities in urban storm-water canals. Microbial community structure was determined using PhyoChio (G3) Water and sediment samples were collected after a rain event from Sungei Ulu Pandan watershed of >25km2, which has two major land use types: Residential and industrial. Samples were analyzed for physicochemical variables and microbial community structure and composition. Microbial community structure was determined using PhyoChio (G3)
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