Tephra-Microbiology
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB82440 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR13946631_1.fastq.gz | Fastqsanger.gz | |||
| ERR13946631_2.fastq.gz | Fastqsanger.gz | |||
| ERR13946632_1.fastq.gz | Fastqsanger.gz | |||
| ERR13946632_2.fastq.gz | Fastqsanger.gz | |||
| ERR13946633_1.fastq.gz | Fastqsanger.gz |
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Project description:The weathering of volcanic minerals makes a significant contribution to the global silicate weathering budget, influencing carbon dioxide drawdown and climate control. Basalt rocks may account for over 30% of the global carbon dioxide drawdown in silicate weathering. Yet the genetics of biological rock weathering are unknown. For the first time, we apply a DNA microarray to investigate the genes involved in weathering by the heavy metal resistant organism, Cupriavidus metallidurans CH34; in particular we investigate the sequestering of iron. The results show that the bacterium sequesters iron in the ferrous state (FeII); therefore, not requiring siderophores. Instead an energy efficient process involving upregulation of large porins is employed concomitantly with genes associated with biofilm formation. We hypothesise that rock weathering is induced by changes in chemical equilibrium at the microbe-mineral interface, reducing the saturation state of iron. We also demonstrate that low concentrations of metals in the basalt induce heavy metal resistant genes. Volcanic environments are analogous to some of the earliest environments on Earth. These results not only elucidate the mechanisms by which microorganisms might have sequestered nutrients on the early Earth but they also provide an explanation for the evolution of multiple heavy metal resistance genes long before the creation of contaminated industrial biotopes by human activity. Cultures of Cupriavidus metallidurans CH34 were grown in Tris buffered medium MM284 media (with iron), MM284 without iron and MM284 without iron with sterilized basalt at 25 rpm, 30°C until mid-log phase. RNA was extracted from the cells. Three biological replicates of both samples were differentially labeled (resp. Cy3 and Cy5) and hybridized to three CH34 60-mer oligonucleotide glass-spotted microarray carrying three technical repeats.
2009-12-30 | E-GEOD-12133 | biostudies-arrayexpress
Project description:The weathering of volcanic minerals makes a significant contribution to the global silicate weathering budget, influencing carbon dioxide drawdown and climate control. Basalt rocks may account for over 30% of the global carbon dioxide drawdown in silicate weathering. Yet the genetics of biological rock weathering are unknown. For the first time, we apply a DNA microarray to investigate the genes involved in weathering by the heavy metal resistant organism, Cupriavidus metallidurans CH34; in particular we investigate the sequestering of iron. The results show that the bacterium sequesters iron in the ferrous state (FeII); therefore, not requiring siderophores. Instead an energy efficient process involving upregulation of large porins is employed concomitantly with genes associated with biofilm formation. We hypothesise that rock weathering is induced by changes in chemical equilibrium at the microbe-mineral interface, reducing the saturation state of iron. We also demonstrate that low concentrations of metals in the basalt induce heavy metal resistant genes. Volcanic environments are analogous to some of the earliest environments on Earth. These results not only elucidate the mechanisms by which microorganisms might have sequestered nutrients on the early Earth but they also provide an explanation for the evolution of multiple heavy metal resistance genes long before the creation of contaminated industrial biotopes by human activity.
2009-12-31 | GSE12133 | GEO
Project description:Coal-fired power plant is a major method of electricity generation worldwide with serious concerns relating to air pollution. In recent years, fly ash from coal-fired power plants has become a major target of pollution control by worldwide regulatory agencies. In this present study, fly ash particulate matter (PM) obtained from the electrostatic precipitator of Mae Moh Coal-fired Power Plant (Lampang, Thailand) was selected as a model for determination of physicochemical characteristics and toxicological profiles in mice. The average size of the fly ash PM was 4.29 ± 1.85 µm as determined by electron microscopy. Major heavy metal was iron at 101,067.31 ± 8,246.12 mg/kg as detected by ICPMS. Acenaphthene was the most abundant polyaromatic hydrocarbon at 40.77 ± 0.003 mg/kg as analyzed by GCMS. The toxicological profiles of the characterized fly ash PM were conducted in Balb/c mice by intratracheal instillation at 1 and 10 mg/kg/day for 7 days, compared to vehicle as negative control and standard PM 2.5 as positive control. The fly ash PM and the standard PM induced significant pulmonary inflammation in mice lungs compared to vehicle control. In addition, molecular toxicology of mice lungs investigated by proteomics demonstrated 3 inflammation associated pathways, which include leukocyte transendothelial migration, phagosome, and neutrophil extracellular trap formation. Furthermore, only high dose (10 mg/kg/day) standard PM and high dose fly ash PM showed high expression of NCF2, which potentially promotes cancer in the long run. This study is the first to report on the physicochemical characterization, histopathology, and proteomic-associated toxicological profiles of the fly ash PM obtained from the largest coal-fired power plant in Thailand. Information obtained from this study is useful for academic researchers, electricity enterprises, and policymakers to develop appropriate strategies to manage air pollution from coal-fired power plants worldwide.
2025-08-21 | PXD058082 | Pride
Project description:How does environmental change drive phenotypic evolution? We addressed this question using Daphnia genotypes separated by ~1600-years of evolution in a Minnesota lake using methods in resurrection ecology (i.e., reviving dormant eggs from sediments) and found substantial genetic and physiological differentiation. These shifts are highly correlated with anthropogenic environmental change, specifically phosphorus (P)-driven eutrophication. Here, we explore transcriptomic changes that may underlie the observed shifts in P use physiology (see poster by Fricsh et al for a detailed explanation). We compared the transcriptomes of two ancient and two contemporary genotypes in ancient (i.e., low P; LP) and contemporary (i.e., high P; HP) conditions using an 11000-gene microarray. Ancient and contemporary genotypes differed in the number of differentially expressed genes in the HP (mean ± SD; 645 ± 112.95) and LP (1071 ± 211.63) treatments. These results indicate considerable transcriptomic variation between ancient and contemporary genotypes in both dietary treatments, with stressful (LP) conditions invoking differential expression of more genes (t= -2.51; P= 0.04). Moreover, ancient and contemporary genotypes exhibited markedly different transcriptomic responses to dietary treatments. Contemporary genotypes upregulated 84.5 ± 28.99 while ancient genotypes upregulated 413.5 ± 26.16 genes (t= 164.5; P= 0.003). Similarly, ancient (127.5 ± 101.1) and contemporary (316 ± 98.99) genotypes differed significantly in the number of genes downregulated between the HP and LP treatments (t= 125.66; P= 0.005). These results indicate substantial regulatory shifts may underlie the striking physiological differences observed. Further analyses of gene families that were differentially expressed (DE) between ancient and contemporary genotypes revealed several gene families already known to be important in mitigating stoichiometric imbalances driven by P availability. Agglomerative hierarchical cluster analyses of DE loci between ancient and contemporary genotypes indicating age-based clustering will be presented. Together, our theoretical framework based on elemental supply, and unique model system enabled a millennial-scale exploration of the environmental contribution to phenotypic evolution.
2015-06-01 | GSE48232 | GEO
Project description:The response of global carbon and nitrogen cycles to future climate change is uncertain. In order to understand the impacts that future changes to climate will have on these cycles, a more detailed understanding of them is essential. This dissertation utilizes a combined approach of molecular biomarkers and proteomic investigations to elucidate historic source material contributions and microbial protein production to contribute to a more thorough understanding of the marine carbon and nitrogen cycles. The examination of molecular organic biomarkers throughout an Arctic sediment core showed the dominant input in the area was from marine sources with lower but steady contributions from terrestrial sources during the Holocene. Attempts to recover proteins from deeper sediments to correlate with lipid biomarkers were unsuccessful but led to the optimization of an extraction protocol for an added protein standard, bovine serum albumin, from sediments. An investigation into the expressed proteome of the heterotrophic marine bacterium, Ruegeria pomeroyi, under environmentally realistic carbon supply conditions during exponential and stationary growth phases identified over 2000 proteins. The most abundant proteins identified were responsible for porins, transport, binding, translation, and protein refolding and could represent potential biomarkers of bacterial processes and/or activity. A parallel study of R. pomeroyi, in which 13C-labeled leucine was added to the culture during exponential growth phase, showed labeled incorporation ranging from 16 to 21% of the total proteins produced depending on growth phase. The widespread distribution of the label among the growth phases indicates active recycling by the bacteria. This study demonstrates a method through which bacterial protein synthesis can be tracked. A study of the marine diatom Thalassiosira pseudonana acclimated to iron replete or iron-limited conditions showed iron-limited organisms increased proteins involved in pathways associated with intracellular protein recycling, the pentose phosphate pathway, lower photosynthetic energy production, enhancement of photorespiration, and increased polysaccharide production. This application of proteomics to the examination of proteins in marine sediments, a marine diatom, and a heterotrophic marine bacterium shows the potential for these techniques to help elucidate the fate of proteins in marine environments and could be used in conjunction with well-established molecular organic marker studies.
2017-07-18 | PXD006689 | Pride
Project description:Iron chlorosis is one of the major abiotic stresses affecting fruit trees and other crops in calcareous soils. The most evident symptoms are connected to a reduction in growth and yield and in the interveinal chlorosis of leaves. A custom CombiMatrix 90K microarray was used to identify candidate genes involved in the citrus response to iron deficiency stress, comparing Tarocco Scirè orange [Citrus sinensis (L.) Osbeck] grafted on two different rootstocks, Swingle citrumelo (C. paradisi × Poncirus trifoliata), high sensitive, and Carrizo citrange (C. sinensis × P. trifoliata), tolerant. RNA was extracted from roots of plants grown in two different soils, one volcanic (0% of active lime) used as control, and the other calcareous (10% of active lime).
2015-06-03 | GSE38667 | GEO
Project description:In recent years, sediments from cave environments have provided invaluable insights into ancient hominids, as well as past fauna and flora. Unfortunately, locations with favourable conditions for ancient DNA (aDNA) preservation in sediments are scarce. In this study we analysed a set of samples obtained from sediments adhered to different human skeletal elements, originating from Neolithic to Medieval sites in England, and performed metagenomics and metaproteomics analysis. From them, we were able to reconstruct a partial human genome. The genetic profile of those human sequences matches the one recovered from the original skeletal element. Additionally, aDNA sequences matching the genomes of endogenous gut and oral microbiome bacteria were identified. We also found the presence of genetic sequences corresponding to animals and plants. In particular we managed to retrieve the partial genome and proteome of a Black Rat (Rattus rattus), sharing close genetic affinities to other medieval Rattus rattus. Our results demonstrate that material usually discarded, as it is sediments adhering to human remains, can be used to get a glimpse of the environmental conditions at the time of the death of an individual.
2025-09-15 | PXD057056 | Pride