Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1035637 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26667842_1.fastq.gz | Fastqsanger.gz | |||
| SRR26667842_2.fastq.gz | Fastqsanger.gz | |||
| SRR26667843_1.fastq.gz | Fastqsanger.gz | |||
| SRR26667843_2.fastq.gz | Fastqsanger.gz | |||
| SRR26667844_1.fastq.gz | Fastqsanger.gz |
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Project description:Iron-sulfur minerals such as pyrite are found in many marine benthic habitats. At deep-sea hydrothermal vent sites they occur as massive sulfide chimneys. Hydrothermal chimneys formed by mineral precipitation from reduced vent fluids upon mixing with cold oxygenated sea water. While microorganisms inhabiting actively venting chimneys and utilizing reduced compounds dissolved in the fluids for energy generation are well studied, only little is known about the microorganisms inhabiting inactive sulfide chimneys. We performed a comprehensive meta-proteogenomic analysis combined with radiometric dating to investigate the diversity and function of microbial communities found on inactive sulfide chimneys of different ages from the Manus Basin (SW Pacific). Our study sheds light on potential lifestyles and ecological niches of yet poorly described bacterial clades dominating inactive chimney communities.
2019-01-02 | PXD010074 | Pride
Project description:Iron- and sulfur-oxidizing bacterium
| PRJNA35415 | ENA
Project description:Iron-oxidizing bacteria are widely found in natural and man-made environments where they influence varied biogeochemical cycles. Despite their prevalence, the mechanisms and Fe(II) substrates used by these organisms remain understudied. To date, there has been limited exploration of the ability of iron-oxidizing bacteria to utilize solid minerals as electron donors. Sideroxydans lithotrophicus ES-1 is a robust, facultative iron oxidizer with multiple enzymatic pathways for iron oxidation, making it a prime candidate for evaluating extracellular electron uptake mechanisms. In this study, S. lithotrophicus ES-1 was grown on dissolved Fe(II)-citrate and three preparations of magnetite that provided different ratios of soluble and solid Fe(II). S. lithotrophicus ES-1 grew equally well on the different batches of magnetite, suggesting it can adapt to the type of iron present during growth. S. lithotrophicus ES-1 oxidized all available dissolved Fe2+ released from magnetite, and continued to build biomass when only solid Fe(II) remained. Quantitative proteomic analyses of S. lithotrophicus ES-1 grown on these substrates revealed proteome remodeling in response to electron donor and growth state, and uncovered potential proteins and metabolic pathways involved in the oxidation of solid magnetite. While the Cyc2 iron oxidases were highly expressed on both dissolved and solid substrates, the MtoAB complex was only expressed during growth on the solid magnetite, suggesting these proteins play a role in oxidation of solid minerals in S. lithotrophicus ES-1. A set of cupredoxin domain-containing proteins were also identified that were specifically expressed during solid iron oxidation. This work confirmed the iron oxidizer, S. lithotrophicus ES-1, utilized distinct extracellular electron transfer pathways when growing on solid mineral electron donors compared to dissolved Fe(II)-citrate. The presence of multiple pathways, and the ability to regulate their expression and use, could benefit iron-oxidizing bacteria that encounter various electron donors in their environments.
2024-01-04 | MSV000093770 | MassIVE
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:Iron- and sulfur-oxidizing acidophilic bacterium
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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:To effectively monitor microbial populations in acidic environments and bioleaching systems, a comprehensive 50-mer-based oligonucleotide microarray was developed based on most of the known genes associated with the acidophiles. This array contained 1,072 probes in which there were 571 related to 16S rRNA and 501 related to functional genes. Acid mine drainage (AMD) presents numerous problems to the aquatic life and surrounding ecosystems. However, little is known about the geographic distribution, diversity, composition, structure and function of AMD microbial communities. In this study, we analyzed the geographic distribution of AMD microbial communities from twenty sites using restriction fragment length polymorphism (RFLP) analysis of 16S rRNA genes, and the results showed that AMD microbial communities were geographically distributed and had high variations among different sites. Then an AMD-specific microarray was used to further analyze nine AMD microbial communities, and showed that those nine AMD microbial communities had high variations measured by the number of detected genes, overlapping genes between samples, unique genes, and diversity indices. Statistical analyses indicated that the concentrations of Fe, S, Ca, Mg, Zn, Cu and pH had strong impacts on both phylogenetic and functional diversity, composition, and structure of AMD microbial communities. This study provides insights into our understanding of the geographic distribution, diversity, composition, structure and functional potential of AMD microbial communities and key environmental factors shaping them. This study investigated the geographic distribution of Acid Mine Drainages microbial communities using a 16S rRNA gene-based RFLP method and the diversity, composition and structure of AMD microbial communities phylogenetically and functionally using an AMD-specific microarray which contained 1,072 probes ( 571 related to 16S rRNA and 501 related to functional genes). The functional genes in the microarray were involved in carbon metabolism (158), nitrogen metabolism (72), sulfur metabolism (39), iron metabolism (68), DNA replication and repair (97), metal-resistance (27), membrane-relate gene (16), transposon (13) and IST sequence (11).
2011-03-08 | E-GEOD-27542 | biostudies-arrayexpress