Ontology highlight
ABSTRACT:
PROVIDER: PRJNA521526 | ENA |
REPOSITORIES: ENA
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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:Microbial communities in deep eastern Mediterranean Sea surface sediments
| PRJNA270910 | ENA
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: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:A significant part of the heavier petroleum fraction resulting from offshore oil-spills sinks to the deep-sea. Its fate and biodegradation by microbial communities is unclear. In particular, the physiological and metabolic features of hydrostatic pressure (HP) adapted oil-degraders have been neglected. In this study, hydrocarbon-free sediment from 1km below surface water (bsl) was incubated at 0.1, 10 and 20MPa (equivalent to surface waters, 1 and 2km bsl) using triacontane (C30) as sole carbon source for a 3-month enrichment period. HP strongly impacted biodegration, as it selected for microbial communities with small cells, high O2 respiration and nutrients requirements, but low biomass and C30-degradation yields. The alkane-degrading metaproteome linked to β-oxidation was detected but its expression was reduced under HP contrary to several housekeeping genes. This was reflected in the enriched communities, as atmospheric pressure was dominated by hydrocarbonoclastic bacteria while non-specialized or previously unrecognized oil-degrading genera were enriched under HP.
2018-12-19 | PXD004328 | Pride
Project description:Zero-valent sulfur (ZVS) distributes widely in the deep-sea cold seep, which is important immediate in the active sulfur cycle of cold seep. In our preview work, a novel ZVS formation pathway discovered in the deep-sea cold weep bacterium Erythrobacter flavus 21-3 was described. However, whether this pathway worked and what function roles it played in the cold seep were unknown. In this study, E. flavus 21-3 was verified to produce zero-valent sulfur in the cold seep using genes soxB and tsdA as our preview report described. Based on proteomic data, stoichiometric methods and microscopic observation, this ZVS formation pathway benefited E. flavus 21-3 in the deep-sea cold seep. Notably, 30% metagenomes contained these two genes in the shallow sediments, which present the most abundant sulfur genes and active sulfur cycle in the cold seep sediments. It suggested that this sulfur formation pathway exist across many bacteria in the cold seep. This strongly indicates that this novel pathway might be frequently used by microbes and plays an important role in the biogeochemical sulfur cycle in cold seep.
2022-07-09 | PXD029383 | Pride
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:Viral metagenomes in deep-sea surface sediments
| PRJDB199 | ENA
Project description:we applied metaproteomic approach to capture proteins from three size-fractionated microbial communities at the DCM in the basin of the South China Sea. The deep recovery of proteomes from a marine DCM plankton assemblage provides the highest resolution of metabolic activities as well as microbial niche differentiation, revealing a spectrum of biological processes carrying out by microbes at DCM of the SCS.
2020-12-21 | PXD016812 | Pride