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PROVIDER: PRJNA1122137 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Enrichments with labeled CH4 and NO2 were conducted to test microbial community correlations and constrain potential metabolic interactions between methanotrophs and other one-carbon utilizing microorganisms under low O2 conditions
2023-01-14 | PXD011287 | Pride
Project description:Microbial biofertilizers were investigated for their ability to mitigate drought stress and enhance resilience in Andrographis paniculata. High-performance liquid chromatography (HPLC) analysis revealed that microbial biofertilizer significantly increased andrographolide content, a key bioactive compound, even under drought stress.
2025-06-10 | PXD052952 | JPOST Repository
Project description:Managing tradeoffs through gene regulation is believed to maintain resilience of a microbial community in a fluctuating resource environment. To investigate this hypothesis we imposed a fluctuating environment that required the sulfate-reducing generalist Desulfovibrio vulgaris to manage tradeoffs associated with repeated ecologically-relevant shifts between retaining metabolic independence (active capacity for sulfate respiration) and becoming metabolically specialized to a mutualistic association with the hydrogen consuming Methanococcus maripaludis. Strikingly, the microbial community became progressively less proficient at restoring the environmentally-relevant physiological state after each perturbation. Most cultures collapsed within 3-7 shifts with only a few collapsing later. We demonstrate that the collapse was caused by conditional gene regulation, which drove precipitous decline in intracellular abundance of essential transcripts and proteins, imposing greater energetic burden of regulation to restore function in a fluctuating environment. The microbial community collapse was rescued by a single regulatory mutation that could then potentially serve as a stepping stone for further adaptive evolution in a variable resource environment. Co-culture strains of M. maripaludis wild type and either wild type or DVU0744::Tn5 mutant of D. vulgaris strains were grown anaerobically in replicates. Samples were transitioned between syntrophic and sulfate respiratory growth conditions at early log phases.
2016-03-10 | E-GEOD-79022 | biostudies-arrayexpress
Project description:Despite the global importance of forests, it is virtually unknown how their soil microbial communities adapt at the phylogenetic and functional level to long term metal pollution. Studying twelve sites located along two distinct gradients of metal pollution in Southern Poland revealed that both community composition (via MiSeq Illumina sequencing of 16S rRNA genes) and functional gene potential (using GeoChip 4.2) were highly similar across the gradients despite drastically diverging metal contamination levels. Metal pollution level significantly impacted microbial community structure (p = 0.037), but not bacterial taxon richness. Metal pollution altered the relative abundance of specific bacterial taxa, including Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Planctomycetes and Proteobacteria. Also, a group of metal resistance genes showed significant correlations with metal concentrations in soil, although no clear impact of metal pollution levels on overall functional diversity and structure of microbial communities was observed. While screens of phylogenetic marker genes, such as 16S rRNA, provided only limited insight into resilience mechanisms, analysis of specific functional genes, e.g. involved in metal resistance, appeared to be a more promising strategy. This study showed that the effect of metal pollution on soil microbial communities was not straightforward, but could be filtered out from natural variation and habitat factors by multivariate statistical analysis and spatial sampling involving separate pollution gradients.
2014-07-22 | GSE59620 | GEO
Project description:Analysis of transcript abundance estimates as a function of child soldier status, PTSD symptoms, and psychological resilience. Gene expression profiling was conducted on dried blood spot (DBS) samples collected from community dwelling adolescents and young adults in Nepal. Approximatley half of the sample were former child soldiers in the Nepal People's War and the other half were demographically similiar civilian non-combatants. In addition to basic demographic characteristics (age, sex, ethnic minority status, social caste status, education level), participants were also assessed on syptoms of post-traumatic stress (PTS, assessed by a culturally adapted version of The Child PTSD Symptom Scale; Kohrt BA, et al. (2011) Validation of cross-cultural child mental health and psychosocial research instruments: adapting the Depression Self-Rating Scale and Child PTSD Symptom Scale in Nepal. BMC Psychiatry 11(1):e127, with higher values indicating greater PTSD symptoms) and psychological resilience (assessed by a culturally adapted version of the Resilience Scale; Wagnild GM & Young HM (1993) Development and psychometric evaluation of the Resilience Scale. Journal of Nursing Measurement, with higher values indicating greater resilience). Dichotomous variables were coded 0=no/absent and 1=yes/present. Valid gene expression data are available for 254 samples.
2016-07-27 | E-GEOD-77164 | biostudies-arrayexpress
Project description:Managing tradeoffs through gene regulation is believed to maintain resilience of a microbial community in a fluctuating resource environment. To investigate this hypothesis we imposed a fluctuating environment that required the sulfate-reducing generalist Desulfovibrio vulgaris to manage tradeoffs associated with repeated ecologically-relevant shifts between retaining metabolic independence (active capacity for sulfate respiration) and becoming metabolically specialized to a mutualistic association with the hydrogen consuming Methanococcus maripaludis. Strikingly, the microbial community became progressively less proficient at restoring the environmentally-relevant physiological state after each perturbation. Most cultures collapsed within 3-7 shifts with only a few collapsing later. We demonstrate that the collapse was caused by conditional gene regulation, which drove precipitous decline in intracellular abundance of essential transcripts and proteins, imposing greater energetic burden of regulation to restore function in a fluctuating environment. The microbial community collapse was rescued by a single regulatory mutation that could then potentially serve as a stepping stone for further adaptive evolution in a variable resource environment.
2016-03-10 | GSE79022 | GEO
Project description:Despite the global importance of forests, it is virtually unknown how their soil microbial communities adapt at the phylogenetic and functional level to long term metal pollution. Studying twelve sites located along two distinct gradients of metal pollution in Southern Poland revealed that both community composition (via MiSeq Illumina sequencing of 16S rRNA genes) and functional gene potential (using GeoChip 4.2) were highly similar across the gradients despite drastically diverging metal contamination levels. Metal pollution level significantly impacted microbial community structure (p = 0.037), but not bacterial taxon richness. Metal pollution altered the relative abundance of specific bacterial taxa, including Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Planctomycetes and Proteobacteria. Also, a group of metal resistance genes showed significant correlations with metal concentrations in soil, although no clear impact of metal pollution levels on overall functional diversity and structure of microbial communities was observed. While screens of phylogenetic marker genes, such as 16S rRNA, provided only limited insight into resilience mechanisms, analysis of specific functional genes, e.g. involved in metal resistance, appeared to be a more promising strategy. This study showed that the effect of metal pollution on soil microbial communities was not straightforward, but could be filtered out from natural variation and habitat factors by multivariate statistical analysis and spatial sampling involving separate pollution gradients. 12 samples were collected from two long-term polluted areas (Olkusz and Miasteczko M-EM-^ZlM-DM-^Eskie) in Southern Poland. In the study presented here, a consecutively operated, well-defined cohort of 50 NSCLC cases, followed up more than five years, was used to acquire expression profiles of a total of 8,644 unique genes, leading to the successful construction of supervised
2014-07-22 | E-GEOD-59620 | biostudies-arrayexpress
Project description:Co-culture of methanotrophs and microalgae
| PRJNA637452 | ENA
Project description:This experiment aimed to understand stress responses of microbial communities differing in chronic exposure to the photosynthesis inhibitor diuron, combining untargeted metatranscriptomics (RNA-seq) and dose-response design. First, river microbial communities were incubated for 5-weeks in microcosms 1/ under constant exposure to 4µg/L of diuron (stressed community) or 2/ without contamination (non-stressed community). Then, both communities were exposed for 1 hour to a gradient of diuron concentrations to investigate differences in stress responses after chronic exposure. This experimental design enabled the determination of contig response trends as well as sensitivity thresholds.
2025-04-01 | GSE201034 | 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