Ontology highlight
ABSTRACT:
PROVIDER: PRJNA428129 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6435260_1.fastq.gz | Fastqsanger.gz | |||
| SRR6435260_2.fastq.gz | Fastqsanger.gz | |||
| SRR6435261_1.fastq.gz | Fastqsanger.gz | |||
| SRR6435261_2.fastq.gz | Fastqsanger.gz | |||
| SRR6435262_1.fastq.gz | Fastqsanger.gz |
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Project description:Initial attachment to a surface marks the onset of a bacterial life style switch from planktonic to biofilm mode of growth. Among dissimilatory iron reducing bacteria, S. oneidensis MR-1 is notable due to its extensive respiratory versatility. It has been hypothesized that direct interaction of Shewanella cells with, or close proximity to, an appropriate surface facilitates the deposition of electrons. In fact, Shewanella species have been demonstrated to adhere to various surfaces and form biofilms. Global transcriptome profiling was performed on cells in the transition to surface-associated growth using different surfaces and conditions to understand molecular mechanisms underlying the initiation of microbe-surface interactions and the switch from planktonic to sessile life style.
2010-12-07 | GSE25865 | GEO
Project description:Initial attachment to a surface marks the onset of a bacterial life style switch from planktonic to biofilm mode of growth. Among dissimilatory iron reducing bacteria, S. oneidensis MR-1 is notable due to its extensive respiratory versatility. It has been hypothesized that direct interaction of Shewanella cells with, or close proximity to, an appropriate surface facilitates the deposition of electrons. In fact, Shewanella species have been demonstrated to adhere to various surfaces and form biofilms. Global transcriptome profiling was performed on cells in the transition to surface-associated growth using different surfaces and conditions to understand molecular mechanisms underlying the initiation of microbe-surface interactions and the switch from planktonic to sessile life style. In the study presented, expression profiles of two independent replicates of Shewanella oneidensis MR-1 wild type cells attached to glass for 0.25 h and 1 h, respectively, under hydrodynamic conditions were compared to two independent replicates of planktonic grown Shewanella oneidensis MR-1 wild type cells. Furthermore, expression profiles of two independent replicates of Shewanella oneidensis MR-1 wild type cells attached for 1 h to iron surface under hydrodynamic conditions were compared to two independent replicates of Shewanella oneidensis MR-1 wild type cells attached to glass for 1 h. All samples were obtained from aerobically grown cells in LM.
2010-12-07 | E-GEOD-25865 | biostudies-arrayexpress
Project description:Full title: Environmental transcriptome analysis of LfeRT32a in its natural microbial community comparing the biofilm and planktonic modes of life. Extreme acidic environments are characterized among other features by the high metal content and the lack of nutrients (oligotrophy). Macroscopic biofilms and filaments usually grow on the water-air interface or under the stream attached to solid substrates (streamers). In the Tinto River (Spain), brown filaments develop under the water stream where the Gram-negative iron-oxidizing bacteria Leptospirillum ferrooxidans and Acidithiobacillus ferrooxidans are abundant. Both microorganisms play a critical role in bioleaching processes for industrial (biominery) and environmental applications (acid mine drainage, bioremediation). The aim of this study was to investigate the physiological differences between the free living (planktonic) and the sessile (biofilm associated) lifestyles of L. ferrooxidans as part of a natural extremely acidophilic community.
2016-06-23 | GSE20267 | GEO
Project description:Waste decomposition in landfills is a complex and microbe-mediated process. Understanding the microbial community composition and structure is critical for accelerating decomposition and reducing adverse impact on the environment. Here, we examined the microbial communities along with landfill depth and age (LDA) in a sanitary landfill in Beijing, China using 16s rRNA Illumina sequencing and GeoChip 4.6. We found that Clostridiales and Methanofollis were the predominant bacteria and archaea in the present landfill, respectively. Interestingly, in contrast with the decreasing trend of microbial diversity in soil, both phylogenetic and functional diversities were higher in deeper and older refuse in the landfill. Phylogenetic compositions were obviously different in the refuse with the same LDA and such difference is mainly attributed to the heterogeneity of refuse instead of random process. Nevertheless, functional structures were similar within the same LDA, indicating that microbial community assembly in the landfill may be better reflected by functional genes rather than phylogenetic identity. Mantel test and canonical correspondence analysis suggested that environmental variables had significant impacts on both phylogenetic composition and functional structure. Higher stress genes, genes for degrading toxic substances and endemic genes in deeper and older refuse indicated that they were needed for the microorganisms to survive in the more severe environments. This study suggests that landfills are a repository of stress-resistant and contaminant-degrading microorganisms, which can be used for accelerating landfill stabilization and enhancing in situ degradation. Fifteen refuse samples with five landfill depths and ages (6m/2a, 12m/4a, 18m/6a, 24m/8a and 30m/10a) were collected from a sanitary landfill in Beijing, China. Three replicates in every landfill depth and age
2016-06-15 | E-GEOD-68712 | biostudies-arrayexpress
Project description:Iron-reducing bacteria 1 Raw sequence reads
| PRJNA314288 | ENA