Pseudomonas putida F1 strain:F1
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA13909 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR253120.fastq.gz | Fastqsanger.gz | |||
| SRR9434170.fastq.gz | Fastqsanger.gz | |||
| SRR9434180.fastq.gz | Fastqsanger.gz | |||
| SRR9434171.fastq.gz | Fastqsanger.gz | |||
| SRR9434181.fastq.gz | Fastqsanger.gz |
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Project description:The genus Pseudomonas is a very versatile and heterogeneous group whose members regularly serve as model system of various applications. These include pathogens and rhizospheric strains as well as organisms with exceptional broad substrate ranges. Nevertheless, when it comes to physiological adaptation due to cell density and growth, on transcript- or proteome level, our knowledge is rather limited. The few existing studies so far focused mainly on B. subtilis and E. coli. In this study Pseudomonas putida F1, a model for the degradation of aromatic compounds, and its adaptation to stationary growth was investigated by label-free proteome quantification. The data unveiled that entrance to the stationary phase does not involve an abrupt switch within the P. putida F1 proteome, but is rather an ongoing adaptation which starts during exponential growth which is illustrated by principle component and functional enrichment analysis. These changes were especially metabolic adaptations, which involved a clear increase in amino acid degradation capabilities and a loss of transcription as well as translation capacity. The final entrance to the stationary phase was accompanied by increased oxidative stress protection, although the stress and stationary sigma factor RpoS increased in abundance already during mid-exponential growth. Finally, the data supports previous observations that phenylacetic acid concentrations might play an important role in growth and pathogenicity regulation within Pseudomonades.
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Project description:Degradation of polycyclic aromatic hydrocarbons (PAHs) such as naphthalene by anaerobic microorganisms is poorly understood. Strain NaphS2, an anaerobic sulfate reducing marine delta-proteobacterium is capable of using naphthalene and the aromatic compound benzoate, as well as pyruvate, as an electron donors in the presence of sulfate. In order to identify genes involved in the naphthalene degradation pathway, we compared gene expression in NaphS2 during growth on benzoate vs. pyruvate, naphthalene vs. pyruvate, and naphthalene vs benzoate.
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Project description:A soil-borne bacteria capable of metabolizing aromatic hydrocarbons.
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Project description:Soil bacteria are generally capable of growth on a wide range of organic chemicals, and pseudomonads are particularly adept at utilizing aromatic compounds. Pseudomonads are motile bacteria that are capable of sensing a wide range of chemicals, using both energy taxis and chemotaxis. Whilst the identification of specific chemicals detected by the ?26 chemoreceptors encoded in Pseudomonas genomes is ongoing, the functions of only a limited number of Pseudomonas chemoreceptors have been revealed to date. We report here that McpC, a methyl-accepting chemotaxis protein in Pseudomonas putida F1 that was previously shown to function as a receptor for cytosine, was also responsible for the chemotactic response to the carboxylated pyridine nicotinic acid.
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Project description:iJN1462 (i) incorporates several hundred additional genes and associated reactions resulting in new predictive capabilities, including new nutrients supporting growth; (ii) was validated by in vivo growth screens that included previously untested carbon (48) and nitrogen (41) sources; (iii) yielded gene essentiality predictions showing large accuracy when compared with a knock-out library and Bar-seq data; and (iv) allowed mapping of its network to 82 P. putida sequenced strains revealing functional core that reflect the large metabolic versatility of this species, including aromatic compounds derived from lignin.
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Project description:The efficacy of inoculation of single pure bacterial cultures into complex microbiomes, for example, in order to achieve increased pollutant degradation rates in contaminated material (i.e., bioaugmentation), has been frustrated by insufficient knowledge on the behaviour of the inoculated bacteria under the specific abiotic and biotic boundary conditions. Here we present a comprehensive analysis of global gene expression of the bacterium Sphingomonas wittichii RW1 in contaminated sand, compared to regular suspended batch growth in liquid culture. RW1 is a well-known bacterium capable of mineralizing polycyclic aromatic hydrocarbons such as dioxins, dibenzofurans and other chlorinated congeners. We tested the reactions of the cells both during the immediate transition phase from liquid culture to sand with or without dibenzofuran, as well during growth and stationary phase in sand. Cells during transition resemble going through stationary phase, showing evidence of stress responses and nutrient scavenging, and even of major adjustments in their primary metabolism if they were not pre-cultured on the same contaminant as found in the soil. Cells growing and surviving in soil show very different signatures as in liquid or in liquid culture exposed to chemicals inducing drought stress, and we obtain evidence for numerous soil-specific expressed genes. We conclude that studies focusing on inoculation efficacy should test behavior under conditions as closely as possible mimicking the intended microbiome conditions. We were interested to study the global reactions of bacteria with biodegradative properties under near-environmental as compared to laboratory culture conditions. We compared here the genome-wide responses of RW1 between regular laboratory batch growth on the aromatic substrates DBF and salicylate with growth in sandy soil with or without the same aromatic compounds. We analysed the cellular reactions immediately after introduction into the sand, during exponential growth and at stationary phase, all in carefully controlled and replicated experimental conditions.
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Project description:The efficacy of inoculation of single pure bacterial cultures into complex microbiomes, for example, in order to achieve increased pollutant degradation rates in contaminated material (i.e., bioaugmentation), has been frustrated by insufficient knowledge on the behaviour of the inoculated bacteria under the specific abiotic and biotic boundary conditions. Here we present a comprehensive analysis of global gene expression of the bacterium Sphingomonas wittichii RW1 in contaminated sand, compared to regular suspended batch growth in liquid culture. RW1 is a well-known bacterium capable of mineralizing polycyclic aromatic hydrocarbons such as dioxins, dibenzofurans and other chlorinated congeners. We tested the reactions of the cells both during the immediate transition phase from liquid culture to sand with or without dibenzofuran, as well during growth and stationary phase in sand. Cells during transition resemble going through stationary phase, showing evidence of stress responses and nutrient scavenging, and even of major adjustments in their primary metabolism if they were not pre-cultured on the same contaminant as found in the soil. Cells growing and surviving in soil show very different signatures as in liquid or in liquid culture exposed to chemicals inducing drought stress, and we obtain evidence for numerous soil-specific expressed genes. We conclude that studies focusing on inoculation efficacy should test behavior under conditions as closely as possible mimicking the intended microbiome conditions We were interested to study the global reactions of bacteria with biodegradative properties under near-environmental as compared to laboratory culture conditions. we compared here the genome-wide responses of RW1 between regular laboratory batch growth on the aromatic substrates DBF and salicylate with growth in sandy soil with or without the same aromatic compounds. We analysed the cellular reactions immediately after introduction into the sand, during lag phase, all in carefully controlled and replicated experimental conditions.
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