Ontology highlight
ABSTRACT:
PROVIDER: PRJNA412618 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6123640.fastq.gz | Fastqsanger.gz | |||
| SRR6123650.fastq.gz | Fastqsanger.gz | |||
| SRR6123660.fastq.gz | Fastqsanger.gz | |||
| SRR6123670.fastq.gz | Fastqsanger.gz | |||
| SRR6123680.fastq.gz | Fastqsanger.gz |
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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: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:integrating metagenomics and metaproteomics to study microbial communities that have undergone long-term P addition experiment
2018-01-08 | PXD005910 | Pride
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:Development of cereal crops with high nitrogen-use efficiency (NUE) is a priority for worldwide agriculture. In addition to conventional plant breeding and genetic engineering, the use of the plant microbiome offers another approach to improve crop NUE. To gain insight into the bacterial communities associated with sorghum lines that differ in NUE, a field experiment was designed comparing 24 diverse sorghum lines under sufficient and deficient nitrogen (N). Amplicon sequencing and untargeted gas chromatography-mass spectrometry (GC-MS) were used to characterize the bacterial communities and the root metabolome associated with sorghum genotypes varying in sensitivity to low N. We demonstrated that N stress and sorghum type (energy, sweet, and grain sorghum) significantly impacted the root-associated bacterial communities and root metabolite composition of sorghum. We found a positive correlation between sorghum NUE and bacterial richness and diversity in the rhizosphere. The greater alpha diversity in high NUE lines was associated with the decreased abundance of a dominant bacterial taxa, Pseudomonas. Multiple strong correlations were detected between root metabolites and rhizosphere bacterial communities in response to low-N stress. This indicates that the shift in the sorghum microbiome due to low-N is associated with the root metabolites of the host plant. Taken together, our findings suggest that host genetic regulation of root metabolites plays a role in defining the root-associated microbiome of sorghum genotypes differing in NUE and tolerance to low-N stress.
2023-08-29 | MSV000092783 | MassIVE
Project description:Amino acid addition experiment Metagenome
| PRJNA295905 | ENA