Ontology highlight
ABSTRACT:
PROVIDER: PRJNA874508 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To study the responses of microbial communities to short-term nitrogen addition and warming,here we examine microbial communities in mangrove sediments subjected to a 4-months experimental simulation of eutrophication with 185 g m-2 year-1 nitrogen addition (N), 3oC warming (W) and nitrogen addition*warming interaction (NW).
2022-03-01 | GSE190739 | GEO
Project description:Monitoring microbial communities can aid in understanding the state of these habitats. Environmental DNA (eDNA) techniques provide efficient and comprehensive monitoring by capturing broader diversity. Besides structural profiling, eDNA methods allow the study of functional profiles, encompassing the genes within the microbial community. In this study, three methodologies were compared for functional profiling of microbial communities in estuarine and coastal sites in the Bay of Biscay. The methodologies included inference from 16S metabarcoding data using Tax4Fun, GeoChip microarrays, and shotgun metagenomics.
2024-04-14 | E-MTAB-13075 | 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: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:Understanding and quantifying the effects of environmental factors influencing the variation of abundance and diversity of microbial communities was a key theme of ecology. For microbial communities, there were two factors proposed in explaining the variation in current theory, which were contemporary environmental heterogeneity and historical events. Here, we report a study to profile soil microbial structure, which infers functional roles of microbial communities, along the latitudinal gradient from the north to the south in China mainland, aiming to explore potential microbial responses to external condition, especially for global climate changes via a strategy of space-for-time substitution. Using a microarray-based metagenomics tool named GeoChip 5.0, we showed that microbial communities were distinct for most but not all of the sites. Using substantial statistical analyses, exploring the dominant factor in influencing the soil microbial communities along the latitudinal gradient. Substantial variations were apparent in nutrient cycling genes, but they were in line with the functional roles of these genes. 300 samples were collected from 30 sites along the latitudinal gradient, with 10 replicates in every site
2015-05-23 | E-GEOD-69171 | 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, 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. sixty-three samples were collected from four elevations (3200,3400,3600 and 3800 m) along a Tibetan alpine meadow; Three replicates in each treatment
2013-11-16 | E-GEOD-52425 | biostudies-arrayexpress
Project description:Understanding and quantifying the effects of environmental factors influencing the variation of abundance and diversity of microbial communities was a key theme of ecology. For microbial communities, there were two factors proposed in explaining the variation in current theory, which were contemporary environmental heterogeneity and historical events. Here, we report a study to profile soil microbial structure, which infers functional roles of microbial communities, along the latitudinal gradient from the north to the south in China mainland, aiming to explore potential microbial responses to external condition, especially for global climate changes via a strategy of space-for-time substitution. Using a microarray-based metagenomics tool named GeoChip 5.0, we showed that microbial communities were distinct for most but not all of the sites. Using substantial statistical analyses, exploring the dominant factor in influencing the soil microbial communities along the latitudinal gradient. Substantial variations were apparent in nutrient cycling genes, but they were in line with the functional roles of these genes.
2015-05-23 | GSE69171 | GEO
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