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PROVIDER: PRJEB37536 | ENA |
REPOSITORIES: ENA
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Project description:Understanding the bacterial community structure, and their functional analysis for active bioremediation process is essential to design better and cost effective strategies. Microarray analysis enables us to simultaneously study the functional and phylogenetic markers of hundreds of microorganisms which are involved in active bioremediation process in an environment. We have previously described development of a hybrid 60-mer multibacterial microarray platform (BiodegPhyloChip) for profiling the bacterial communities and functional genes simultaneously in environments undergoing active bioremediation process (Pathak et al; Appl Microbiol Biotechnol,Vol. 90, 1739-1754). The present study involved profiling the status of bacterial communities and functional (biodegradation) genes using the developed 60-mer oligonucleotide microarray BiodegPhyloChip at five contaminated hotspots in the state of Gujarat, in western India. The expression pattern of functional genes (coding for key enzymes in active bioremediation process) at these sites was studied to understand the dynamics of biodegradation in the presence of diverse group of chemicals. The results indicated that the nature of pollutants and their abundance greatly influence the structure of bacterial communities and the extent of expression of genes involved in various biodegradation pathways. In addition, site specific factors also play a pivotal role to affect the microbial community structure as was evident from results of 16S rRNA gene profiling of the five contaminated sites, where the community structure varied from one site to another drastically.
2012-12-01 | GSE38004 | GEO
Project description:Understanding the bacterial community structure, and their functional analysis for active bioremediation process is essential to design better and cost effective strategies. Microarray analysis enables us to simultaneously study the functional and phylogenetic markers of hundreds of microorganisms which are involved in active bioremediation process in an environment. We have previously described development of a hybrid 60-mer multibacterial microarray platform (BiodegPhyloChip) for profiling the bacterial communities and functional genes simultaneously in environments undergoing active bioremediation process (Pathak et al; Appl Microbiol Biotechnol,Vol. 90, 1739-1754). The present study involved profiling the status of bacterial communities and functional (biodegradation) genes using the developed 60-mer oligonucleotide microarray BiodegPhyloChip at five contaminated hotspots in the state of Gujarat, in western India. The expression pattern of functional genes (coding for key enzymes in active bioremediation process) at these sites was studied to understand the dynamics of biodegradation in the presence of diverse group of chemicals. The results indicated that the nature of pollutants and their abundance greatly influence the structure of bacterial communities and the extent of expression of genes involved in various biodegradation pathways. In addition, site specific factors also play a pivotal role to affect the microbial community structure as was evident from results of 16S rRNA gene profiling of the five contaminated sites, where the community structure varied from one site to another drastically. Agilent one-color CGH experiment and one-color Gene Expresssion expereiment,Organism: Genotypic designed Agilent-17159 Genotypic designed Agilent Multibacterial 8x15k Array , Labeling kits: Agilent Genomic DNA labeling Kit (Part Number: 5190-0453) and Agilent Quick Amp Kit PLUS (Part number: 5190-0442).
2012-12-01 | E-GEOD-38004 | biostudies-arrayexpress
Project description:The study aimed to explore the potential of bacterial biodegradation as a solution to the global problem of plastic pollution, specifically targeting polyethylene (PE), one of the most common types of plastic. The goals of the study were to isolate a bacterial strain capable of breaking down PE, identify the key enzymes responsible for the degradation process, and understand the metabolic pathways involved. By investigating these aspects, researchers sought to gain critical insights that could be used to optimize plastic degradation conditions and inform the development of artificial microbial communities for effective bioremediation strategies. This research has significant relevance, as it addresses the pressing need for innovative and sustainable approaches to tackle the ever-growing issue of plastic waste and its impact on the environment.
2024-01-02 | PXD041981 | Pride
Project description:The study aims essentially at the characterisation of suberin degradation mechanisms by Aspergillus nidulans, at a fundamental level. Suberin is an important protective barrier in plant, thus the study of its biodegradation significantly impacts on phytopatology. In addition, fungal suberin degrading enzymes might provide important insights to develop new waste management, bioremediation and biodeterioration prevention strategies.
2014-07-31 | GSE54427 | GEO
Project description:Enclosure experiments are frequently used to investigate the impact of changing environmental conditions on microbial assemblages. Yet, the question how individual members of bacterial communities respond to challenges posed by the incubation itself remained unanswered. We used metaproteomic profiling, 16S rRNA gene analysis and high nucleic acid content analysis to monitor bacterial communities during long-term incubations (55 days) under marine (M1), mesohaline (M2) and oligohaline (M3) conditions with and without the addition of terrestrial dissolved organic matter. Our results showed that early in the experiment (after one week, T2), bacterial communities were highly diverse and their composition differed significantly between marine, mesohaline and oligohaline conditions. Controls (BS) and tDOM-treated samples (FKB) showed notable differences at this stage. In contrast, in the late phase of the experiment (after 55 days, T6), bacterial communities in both, manipulated and untreated marine and mesohaline enclosures were quite similar to each other and were dominated by gammaproteobacterial Spongiibacter. In the oligohaline enclosure, the actinobacterial hgc-I clade was very abundant in this phase. Our findings suggest that individual capacities, e.g. grazing-resistance, antibiotics production, and the ability to access alternative carbon sources may enable Spongiibacter and hgc-I clade members to successfully prevail during long-term incubations. Bacterial community composition in enclosure experiments thus seems to be strongly influenced by the individual inherent bacterial strategies to cope with the incubation as such. Researchers intending to investigate the effects of manipulation on complex microbial communities may therefore want to use short incubation periods or sophisticated systems that avoid these unspecific effects of long-term experiments.
2019-07-09 | PXD011160 | Pride
Project description:Although the biodegradation of biodegradable plastics in soil and compost is well-studied, there is little knowledge on the metabolic mechanisms of synthetic polymers degradation by marine microorganisms. Here, we present a multiomics study to elucidate the biodegradation mechanism of a commercial aromatic-aliphatic copolyester film by a marine microbial enrichment culture. The plastic film and each monomer can be used as sole carbon source. Our analysis showed that the consortium synergistically degrades the polymer, different degradation steps being performed by different members of the community. Analysis of gene expression and translation profiles revealed that the relevant degradation processes in the marine consortium are closely related to poly(ethylene terephthalate) biodegradation from terrestrial microbes. Although there are multiple genes and organisms with the potential to perform a degradation step, only a few of these are active during biodegradation. Our results elucidate the potential of marine microorganisms to mineralize biodegradable plastic polymers and describe the mechanisms of labor division within the community to get maximum energetic yield from a complex synthetic substrate.
2020-09-25 | PXD018391 | Pride
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:Transcriptional response of the photoheterotrophic marine bacterium D. shibea to changing light regimes. Second part of the study analysing the transition from photoheterotrophic light to heterotrophic dark growth. Bacterial aerobic anoxygenic photosynthesis (AAP) is an important mechanism of energy gain in aquatic habitats, accounting for up to 5% of the surface ocean’s photosynthetic electron transport. The dominant AAP bacteria in marine communities belong to the Roseobacter clade. For this reason we used Dinoroseobacter shibae as a model organism to study the transcriptional response of AAP bacteria to changing light regimes. We used continuous cultivation of D. shibae in a chemostat in combination with time series microarray analysis in order to identify gene regulatory patterns after a change in illumination. The change from heterotrophic growth in the dark to photoheterotrophic growth in the light was accompanied by a strong but transient activation of a broad stress response to cope with the formation of harmful singlet oxygen during photophosphorylation, an immediate downregulation of photosynthesis-related genes, fine-tuning of the expression of electron transport chain components and upregulation of the transcriptional and translational apparatus. Furthermore, our data indicate that D. shibae might use the 3-hydroxypropionate cycle for CO2 fixation. Analysis of the transcriptome dynamics after the switch from light to dark demonstrates that only few genes are directly regulated in response to light and other signals such as singlet oxygen concentration, electron flow, redox status and energy charge of the cell must be involved in the regulation of the processes accompanying AAP. Based on the transcriptome data first hypothesis about transcriptional control of AAP could be formulated. This study provides the first analysis of AAP on the level of transcriptome dynamics. Our data allow the formulation of testable hypotheses about the mechanisms involved in the regulation of this important biological process. Samples from light grown cells were used as a reference, 6 timepoints in the dark, biological replicates: 2
2010-12-03 | E-GEOD-25581 | biostudies-arrayexpress
Project description:Transcriptional response of the photoheterotrophic marine bacterium D. shibea to changing light regimes. First part of the study analysing the transition from heterotrophic dark to photoheterotrophic light growth. Bacterial aerobic anoxygenic photosynthesis (AAP) is an important mechanism of energy gain in aquatic habitats, accounting for up to 5% of the surface ocean’s photosynthetic electron transport. The dominant AAP bacteria in marine communities belong to the Roseobacter clade. For this reason we used Dinoroseobacter shibae as a model organism to study the transcriptional response of AAP bacteria to changing light regimes. We used continuous cultivation of D. shibae in a chemostat in combination with time series microarray analysis in order to identify gene regulatory patterns after a change in illumination. The change from heterotrophic growth in the dark to photoheterotrophic growth in the light was accompanied by a strong but transient activation of a broad stress response to cope with the formation of harmful singlet oxygen during photophosphorylation, an immediate downregulation of photosynthesis-related genes, fine-tuning of the expression of electron transport chain components and upregulation of the transcriptional and translational apparatus. Furthermore, our data indicate that D. shibae might use the 3-hydroxypropionate cycle for CO2 fixation. Analysis of the transcriptome dynamics after the switch from light to dark demonstrates that only few genes are directly regulated in response to light and other signals such as singlet oxygen concentration, electron flow, redox status and energy charge of the cell must be involved in the regulation of the processes accompanying AAP. Based on the transcriptome data first hypothesis about transcriptional control of AAP could be formulated. This study provides the first analysis of AAP on the level of transcriptome dynamics. Our data allow the formulation of testable hypotheses about the mechanisms involved in the regulation of this important biological process. Samples from dark grown cells were used as a reference, 6 timepoints in the light, biological replicates: 3 to 4
2010-12-03 | E-GEOD-25579 | biostudies-arrayexpress
Project description:Resuscitation of functional bacterial community for enhanced PCBs biodegradation
| PRJNA496257 | ENA