Ontology highlight
ABSTRACT:
PROVIDER: PRJNA598854 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10994600.fastq.gz | Fastqsanger.gz | |||
| SRR10994601.fastq.gz | Fastqsanger.gz | |||
| SRR10994602.fastq.gz | Fastqsanger.gz | |||
| SRR10994603.fastq.gz | Fastqsanger.gz | |||
| SRR10994604.fastq.gz | Fastqsanger.gz |
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Project description:We established simple synthetic microbial communities in a microcosm model system to determine the mechanisms that underlay cross-feeding in microbial methane-consuming communities. Co-occurring strains from Lake Washington sediment were used that are involved in methane consumption, a methanotroph and two non-methanotrophic methylotrophs.
2016-12-26 | GSE85736 | GEO
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:The increased urban pressures are often associated with specialization of microbial communities. Microbial communities being a critical player in the geochemical processes, makes it important to identify key environmental parameters that influence the community structure and its function.In this proect we study the influence of land use type and environmental parameters on the structure and function of microbial communities. The present study was conducted in an urban catchment, where the metal and pollutants levels are under allowable limits. The overall goal of this study is to understand the role of engineered physicochemical environment on the structure and function of microbial communities in urban storm-water canals. Water and sediment samples were collected after a rain event from Sungei Ulu Pandan watershed of >25km2, which has two major land use types: Residential and industrial. Samples were analyzed for physicochemical variables and microbial community structure and composition. Functional gene abundance was determined using GeoChip.
2014-12-22 | E-GEOD-64286 | biostudies-arrayexpress
Project description:The increased urban pressures are often associated with specialization of microbial communities. Microbial communities being a critical player in the geochemical processes, makes it important to identify key environmental parameters that influence the community structure and its function.In this proect we study the influence of land use type and environmental parameters on the structure and function of microbial communities. The present study was conducted in an urban catchment, where the metal and pollutants levels are under allowable limits. The overall goal of this study is to understand the role of engineered physicochemical environment on the structure and function of microbial communities in urban storm-water canals. Microbial community structure was determined using PhyoChio (G3) Water and sediment samples were collected after a rain event from Sungei Ulu Pandan watershed of >25km2, which has two major land use types: Residential and industrial. Samples were analyzed for physicochemical variables and microbial community structure and composition. Microbial community structure was determined using PhyoChio (G3)
2014-12-22 | E-GEOD-64368 | 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. 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:Plastid Encoded RNA Polymerase (PEP) is a bacterial type multisubunit RNA polymerase responsible for the bulk of transcription in chloroplasts. It contains four core subunits, which are orthologs of their cyanobacterial counterparts. In Arabidopsis thaliana PEP associates with 12 PEP-associated proteins (PAPs), which serve as peripheral subunits of the RNA polymerase. The exact contributions of PAPs to PEP function remain poorly understood. We show that a peripheral subunit of PEP, PAP1 (pTAC3), binds the same genomic loci as RpoB, a core subunit of PEP. PAP1 (pTAC3) and another peripheral PEP subunit, PAP7 (pTAC14), are required for RpoB binding to DNA. RpoB and another core PEP subunit, RpoC1, are expressed in pap1 (ptac3) and pap7 (ptac14) mutants. We propose that the peripheral subunits of PEP are required for the recruitment of core PEP subunits to DNA. pTAC3, binds the same genomic loci as RpoB, a core subunit of PEP. PAP1 pTAC3 and another peripheral PEP subunit, PAP7
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2018-12-19 | PXD004328 | Pride
Project description:Volatilization of lower-chlorinated polychlorinated biphenyls (LC-PCBs) from sediment poses health threats to nearby communities and ecosystems. Biodegradation combined with black carbon (BC) materials is an emerging approach to remove PCBs from sediment, but development of aerobic biofilms on BC for long-term, sustained LC-PCBs remediation is poorly understood. This work aimed to characterize cell enrichment and activity of biphenyl- and benzoate-grown Paraburkholderia xenovorans strain LB400 on various BCs. Biphenyl dioxygenase gene (bphA) abundance on four BC types demonstrated corn kernel biochar hosted at least four orders of magnitude more attached cells per gram than other feedstocks, and microscopic imaging revealed the attached live cell fraction was >1.5X more on corn kernel biochar than GAC. BC characteristics (i.e., sorption potential, surface area, pH) drove cell attachment differences. Reverse transcription qPCR indicated BC feedstocks significantly influenced bphA expression in attached cells. The bphA transcript-per-gene ratio of attached cells was >10-fold more than suspended cells, confirmed by transcriptomics. RNA-seq also demonstrated significant upregulation of biphenyl and benzoate degradation pathways on attached cells, revealing biofilm formation potential and cell-cell communication pathway connections. These novel findings demonstrate aerobic PCB-degrading cell abundance and activity could be tuned by adjusting BC feedstocks/ attributes to improve LC-PCBs biodegradation.
2023-11-03 | GSE246487 | GEO
Project description:The catalytic core of the RNA polymerase of most eubacteria is composed of two α subunits and β, β’ and ω subunits. In Escherichia coli, the ω subunit (encoded by the rpoZ gene) has been suggested to assist β’ during RNA polymerase core assembly. The function of the ω subunit is particularly interesting in cyanobacteria because the cyanobacterial β’ is split to N-terminal γ and C-terminal β’ subunits. The ∆rpoZ strain of the cyanobacterium Synechocystis sp. PCC 6803 grew well in standard conditions although the mutant cells showed low light-saturated photosynthetic activity, low Rubisco content and accumulated high quantities of protective carotenoids and α-tocopherol. The ∆rpoZ strain contained 15% less of the primary σ factor, SigA, than the control strain, and recruitment of SigA to the RNA polymerase core was inefficient in ∆rpoZ. Thus, a cyanobacterial RNA polymerase holoenzyme lacking the ω subunit contains less frequently the primary σ factor. A DNA microarray analysis revealed that this leads to specific down-regulation of highly expressed genes, like genes encoding subunits for Rubisco, ATP synthase, NADH-dehydrogenase and carbon concentrating mechanisms. On the contrary, many genes showing only low or moderate expression in the control strain were up-regulated in ∆rpoZ. A conserved -10 region was detected in promoters showing up or down-regulation in ∆rpoZ, but -35 regions of down-regulated genes completely differed from -35 regions of up-regulated genes.
2014-01-30 | GSE51647 | GEO