Sediment metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA263728 | ENA |
REPOSITORIES: ENA
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Project description:Uranium reducing microbial consortia, under alkaline conditions relevent to geological disposal
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Project description:Anthropogenic activities such as urbanization and agriculture can potentially pose a threat to neighboring freshwaters through nitrate and phosphorous contamination, which over time may lead to lake eutrophication. In such nitrogen-polluted environments, oxygen is depleted, and plants die and decompose. This enhances denitrifying microbes that respire under hypoxic/anoxic conditions by reducing nitrate instead of molecular oxygen and using plant remnants (lignocellulose) as carbon source. Microbial lignocellulose degradation has been well-studied for both aerobic- and anaerobic conditions; however, its degradation during denitrification remains largely unknown. Here we have applied a combination of gas kinetics and meta-omics techniques to enrich and analyze microbial communities from 10 eutrophic lakes to identify a set of core microbial metagenome-assembled genomes (MAGs) present in all the eutrophic lakes. We have further investigated their strategies and enzyme profiles for degrading lignocellulose under denitrifying conditions. We identified Pseudomonadota, Bacteroidota, Verrucomicrobiota, and Actinomycetota as the most abundant phyla and they were present in enrichments from all eutrophic lakes having a key role in denitrification and fermentation. Lignocellulose degradation was, however, dominated by species outside the core microbiome, i.e., there were differing key degraders between lakes, suggesting some level of lake-specialization. Among these we observed potential respiratory DNRA pathways, and they expressed a broad range of CAZymes targeting the various lignocellulose subfractions. Interestingly, many of the detected MAGs contained NO dismutases, enzymes postulated to convert NO to molecular oxygen and dinitrogen gas.
2026-04-30 | PXD069160 | Pride
Project description:microbial communities for hexavalent chromium reduction in autotrophic biosystems
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Project description:Gold nanoparticle (AuâNP) oligonucleotide complexes hold considerable promise as an approach for manipulating intracellular gene regulation. We show that the uptake and intracellular fate of AuâNP oligonucleotide complexes is associated with endocytosis and signal transduction. A transcriptomeâwide functional analysis of gene expression implicated multiple signaling pathways specific for AuâNP oligonucleotide complexes. In primary immune cells, the complexes trigger the expression of proâinflammatory nonâchemotactic cytokines rather than the many IFNâstimulated genes critical for induction of the immune response to a microbial challenge. Concordant with these changes, exposure to AuâNP oligonucleotide complexes is also accompanied by marked activation of immune cells. This distinct gene expression profile is not replicated in the lineageârestricted 293T cell line. These findings provide insight into the functional significance of the recruitment of AuâNP oligonucleotide complexes to endocytic structures and highlight the need to study the systems effects of nanomaterials in a biologically relevant model. We investigated the effect of AuâNP antisense EGFP oligonucleotide complexes on the transcriptome by expression profiling of 293T cells under four conditions and PBMCs under six conditions plus HIV infection with the Affymetrix U133 Plus 2.0 microarray. To control for experimental variability, three of the six PBMC conditions (24â and 48âhours after AuâNP oligonucleotide complex treatment, and the negative control) were assayed independently a second time (biological replicates) so that 13 microarrays were hybridized in total. A different batch of AuâNP oligonucleotide complexes was used in the generation of the four 293T and three replicate PBMC samples, and the microarrays for these samples were processed separately.
2010-04-06 | E-GEOD-20677 | biostudies-arrayexpress
Project description:During mammalian colonization and infection, microorganisms must be able to rapidly sense and adapt to changing environmental conditions including alterations in extracellular pH. The fungus-specific Rim/Pal signaling pathway is one process that supports microbial adaptation to alkaline pH. This cascading series of interacting proteins terminates in the proteolytic activation of the highly conserved Rim101/PacC protein, a transcription factor that mediates microbial responses that favor survival in neutral/alkaline pH growth conditions, including many mammalian tissues. We identified the putative Rim pathway proteins Rim101 and Rra1 in the human skin colonizing fungus Malassezia sympodialis. Targeted mutation of these proteins confirmed their role in M. sympodialis growth at higher pH. Additionally, comparative transcriptional analysis of the mutant strains compared to wild-type suggested mechanisms for fungal adaptation to alkaline conditions. These signaling proteins are required for optimal growth in a murine model of atopic dermatitis, a pathological condition associated with increased skin pH. Together these data elucidate both conserved and phylum-specific features of microbial adaptation to extracellular stresses.
2024-02-01 | GSE254653 | GEO
Project description:Xiangjiang River (Hunan, China) has been contaminated with heavy metal for several decades by surrounding factories. However, little is known about the influence of a gradient of heavy metal contamination on the diversity, structure of microbial functional gene in sediment. To deeply understand the impact of heavy metal contamination on microbial community, a comprehensive functional gene array (GeoChip 5.0) has been used to study the functional genes structure, composition, diversity and metabolic potential of microbial community from three heavy metal polluted sites of Xiangjiang River.
2016-08-02 | GSE85064 | GEO
Project description:An improved hot-alkaline DNA extraction method for deep subseafloor microbial communities
| PRJDB2324 | ENA