Project description:Desulfovibrio vulgaris has been studied extensively for its potential in the bioremediation of heavy metals and radionuclides. Hydrocarbons and solvents, as frequent environmental co-contaminants, have been reported to inhibit microbial activities and thereby pose a limitation on bioremediation efficiency. As a part of the Genomes: GTL project to deduce the stress response pathways in metal/radionuclide reducing bacteria, we studied the responses of D. vulgaris to ethanol, which is a solvent and co-contaminant frequently encountered at contaminated DOE sites. Growth experiments in closed vessels at 37 Â°C indicated that D. vulgaris could maintain normal growth with 1%(v/v) ethanol. The growth rates were reduced with increasing ethanol concentrations at 2% and 5%. Growth ceased when ethanol concentration was raised to 5%(v/v). Cell lysis was apparent with decreasing optical density following 10% ethanol addition. To assess the mechanism of ethanol inhibition, genome-wide transcriptional profiles were analyzed from D. vulgaris cultures following ethanol (5% v/v) treatment using whole-genome microarrays. The ethanol treatment altered the expression of a large number of genes in the D. vulgaris genome, of which 354 were up-regulated greater than 2 fold and 217 were down-regulated by over 2 fold. As expected, changes in the transcriptional profile were similar to those of the stress response to acetone, which is also a solvent. Transcripts highly up-regulated included genes encoding the flagella structural subunits, suggesting motility as a mechanism of solvent stress response. Another group of genes highly induced were chaperones, such as dnaJ, groES, and hsp20, indicating the importance of maintaining proper protein folding under ethanol stress. Down-regulated genes included two groups of genes, ribosomal proteins and amino acid transporters, consistent with the growth inhibition by ethanol observed in growth studies. These results were interpreted that D. vulgaris responds to elevated solvent levels by increased motility and maintenance of proper protein functions. Current work is focused on the analysis of regulatory pathways based on temporal transcriptional dynamics. Keywords: Stress response Desulfovibrio vulgaris from our laboratory culture collection was cultured at 37Â°C in Lactate-Sulfate medium to mid-log phase. Subsequently, ethanol (5% v/v) was added into triplicate cultures. Gene expression profiles 30 and 100 minutes following ethanol exposure were compared with those of the control cultures without ethanol treatment. Total RNA was harvested from three replicate control and treated cultures at two time points following ethanol addition. RNA extraction, purification, and labeling were performed independently on each cell sample.Two samples of each total RNA preparation were labeled, one with Cy3-dUTP and another with Cy5-dUTP for microarray hybridization (Dye swap).

Project description:Desulfovibrio vulgaris has been studied extensively for its potential in the bioremediation of heavy metals and radionuclides. Hydrocarbons and solvents, as frequent environmental co-contaminants, have been reported to inhibit microbial activities and thereby pose a limitation on bioremediation efficiency. As a part of the Genomes: GTL project to deduce the stress response pathways in metal/radionuclide reducing bacteria, we studied the responses of D. vulgaris to acetone, which is a ketone solvent frequently observed at contaminated DOE sites. Growth experiments in closed vessels at 37 °C indicated that D. vulgaris could maintain normal growth with 3%(v/v) acetone following a 1-h lag phase. When the acetone concentration was raised to 5%(v/v), we observed a 2-h lag phase followed by a growth rate which was only 15% that of normal. At an acetone concentration of 8%(v/v), no active growth was observed following 10 hours of incubation. To assess the mechanism of acetone inhibition, genome-wide transcriptional profiles were analyzed from D. vulgaris cultures following acetone (5% v/v) treatment using whole-genome microarrays. This acetone shock altered the expression of a large number of genes in the D. vulgaris genome, of which 309 were up-regulated greater than 2 fold and 199 were down-regulated by over 2 fold. Transcripts highly up-regulated included genes encoding the flagella structural subunits, flgB (15 fold), fliE (11 fold), and flgH (10 fold). Another group of genes highly induced were chaperones, such as dnaJ (11 fold), groES (8 fold), and hsp20 (8 fold). Down-regulated genes included two groups of genes, ribosomal proteins and amino acid transporters, suggesting a state of growth arrest upon acetone addition. These results were interpreted to mean that D. vulgaris responds to elevated solvent levels by increased motility and maintenance of proper protein functions. Current work is focused on the analysis of regulatory pathways based on temporal transcriptional dynamics. Keywords: Stress response

Project description:Desulfovibrio vulgaris has been studied extensively for its potential in the bioremediation of heavy metals and radionuclides. Hydrocarbons and solvents, as frequent environmental co-contaminants, have been reported to inhibit microbial activities and thereby pose a limitation on bioremediation efficiency. As a part of the Genomes: GTL project to deduce the stress response pathways in metal/radionuclide reducing bacteria, we studied the responses of D. vulgaris to acetone, which is a ketone solvent frequently observed at contaminated DOE sites. Growth experiments in closed vessels at 37 Â°C indicated that D. vulgaris could maintain normal growth with 3%(v/v) acetone following a 1-h lag phase. When the acetone concentration was raised to 5%(v/v), we observed a 2-h lag phase followed by a growth rate which was only 15% that of normal. At an acetone concentration of 8%(v/v), no active growth was observed following 10 hours of incubation. To assess the mechanism of acetone inhibition, genome-wide transcriptional profiles were analyzed from D. vulgaris cultures following acetone (5% v/v) treatment using whole-genome microarrays. This acetone shock altered the expression of a large number of genes in the D. vulgaris genome, of which 309 were up-regulated greater than 2 fold and 199 were down-regulated by over 2 fold. Transcripts highly up-regulated included genes encoding the flagella structural subunits, flgB (15 fold), fliE (11 fold), and flgH (10 fold). Another group of genes highly induced were chaperones, such as dnaJ (11 fold), groES (8 fold), and hsp20 (8 fold). Down-regulated genes included two groups of genes, ribosomal proteins and amino acid transporters, suggesting a state of growth arrest upon acetone addition. These results were interpreted to mean that D. vulgaris responds to elevated solvent levels by increased motility and maintenance of proper protein functions. Current work is focused on the analysis of regulatory pathways based on temporal transcriptional dynamics. Keywords: Stress response Desulfovibrio vulgaris from our laboratory culture collection was cultured at 37Â°C in Lactate-Sulfate medium to mid-log phase. Subsequently, acetone (5% v/v) was added into triplicate cultures. Gene expression profiles 30 and 100 minutes following acetone exposure were compared with those of the control cultures without acetone treatment. Total RNA was harvested from three replicate control and treated cultures at two time points following acetone addition. RNA extraction, purification, and labeling were performed independently on each cell sample.Two samples of each total RNA preparation were labeled, one with Cy3-dUTP and another with Cy5-dUTP for microarray hybridization (Dye swap).

Project description:Purpose: Free nitrous acid (FNA) has recently been demonstrated as an antimicrobial agent to a range of microorganisms. However, its antimicrobial mechanism is largely unknown. For this study Desulfovibrio vulgaris Hildenborough was selected to gain a systematic understanding of the antimicrobial mechanism of FNA. Methods: D. vulgaris was grown under anaerobic denitrifying conditions and when FNA was added (4 Î¼g-N/L) growth temporarily stopped. From cultures with and without added FNA, RNA was extracted and the abundance of gene transcripts was detected by sequencing. Transcripts exhibiting â¥1 or â¤-1 fold abundance change in the presence of FNA were designated as differentially expressed. Results:The results imply that FNA exerted multiple antimicrobial effects. Growth of the culture was inhibited by FNA and significant proportions of the cells were killed during the exposure. Respiration by sulfate reduction and lactate oxidation was shut down along with ATP production when exposed to FNA. Correspondingly, decreased transcript levels of genes involved in these metabolic pathways were detected. Detoxification of FNA was evident by nitrite reduction and the genes coding both nitrite reductase (NrfA) and hydroxylamine reductase were highly up regulated. During the FNA induced energy depleted state, there was evidence that D. vulgaris lowered both ribosome activity and protein production. Conditions within the cells were more oxidizing and genes coding for proteins providing resistance to oxidative stress were up regulated. Culture thiol levels increased during the exposure, suggesting that FNA had caused protein structures to alter. Furthermore, genes for motility were up regulated possibly as an attempt to avoid FNA stress. These findings provide new insight for understanding the response of D. vulgaris to FNA exposure. Conclusion: In this study, we performed genome-wide high throughput RNA sequencing (RNA-Seq) analysis on D. vulgaris in the absence and presence of a bacteriostatic-level of FNA (4 Î¼g-N/L). By combining the global activated/suppressed gene profiles and detected physiological responses, we detected the microbial response to FNA exposure and revealed potential antimicrobial mechanisms of FNA on this prevalent model sulfate reducing bacteria. mRNA profiles of D. vulgaris Hildenborough towards FNA stress were generated by next generation sequencing in triplicate via Illumina 2000.

Project description:Purpose: Free nitrous acid (FNA) has recently been demonstrated as an antimicrobial agent to a range of microorganisms. However, its antimicrobial mechanism is largely unknown. For this study Desulfovibrio vulgaris Hildenborough was selected to gain a systematic understanding of the antimicrobial mechanism of FNA. Methods: D. vulgaris was grown under anaerobic denitrifying conditions and when FNA was added (4 μg-N/L) growth temporarily stopped. From cultures with and without added FNA, RNA was extracted and the abundance of gene transcripts was detected by sequencing. Transcripts exhibiting ≥1 or ≤-1 fold abundance change in the presence of FNA were designated as differentially expressed. Results:The results imply that FNA exerted multiple antimicrobial effects. Growth of the culture was inhibited by FNA and significant proportions of the cells were killed during the exposure. Respiration by sulfate reduction and lactate oxidation was shut down along with ATP production when exposed to FNA. Correspondingly, decreased transcript levels of genes involved in these metabolic pathways were detected. Detoxification of FNA was evident by nitrite reduction and the genes coding both nitrite reductase (NrfA) and hydroxylamine reductase were highly up regulated. During the FNA induced energy depleted state, there was evidence that D. vulgaris lowered both ribosome activity and protein production. Conditions within the cells were more oxidizing and genes coding for proteins providing resistance to oxidative stress were up regulated. Culture thiol levels increased during the exposure, suggesting that FNA had caused protein structures to alter. Furthermore, genes for motility were up regulated possibly as an attempt to avoid FNA stress. These findings provide new insight for understanding the response of D. vulgaris to FNA exposure. Conclusion: In this study, we performed genome-wide high throughput RNA sequencing (RNA-Seq) analysis on D. vulgaris in the absence and presence of a bacteriostatic-level of FNA (4 μg-N/L). By combining the global activated/suppressed gene profiles and detected physiological responses, we detected the microbial response to FNA exposure and revealed potential antimicrobial mechanisms of FNA on this prevalent model sulfate reducing bacteria.

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Ethanol stress response in Desulfovibrio vulgaris

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