Desulfovibrio vulgaris batch culture was grown at 37 degree C to mid-log phase with hydrogen as the only electron donor and sulfate as the only electron acceptor.
Biomaterial provider
Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Portugal
Treatment protocol
Cells grown with hydrogen as the electron donor
Growth protocol
D. vulgaris (DSM 644) was grown in a modified medium C at 37ºC, under an anoxic atmosphere of N2. The modified medium C contained 25 micromolar FeSO4.7H2O and 1 micromolar NiCl2.6H2O. Medium C-LS contained 40 mM lactate and 40 mM sulfate, and was used as a control. Pyruvate (40 mM) and thiosulfate (40 mM) were used as an alternative electron donor and acceptor, respectively. Fermentative growth was carried out with pyruvate (40 mM). Media (1000-ml) were dispensed in 2000-ml DURAN® SHOTT bottles, flushed with N2 and sealed with butyl rubber stoppers. Cultures with hydrogen as electron donor were grown in a 3L fermentor containing 2L of growth medium with 40 mM acetate, gassed with a mixture of 80 % (vol/vol) H2, 20 % (vol/vol) CO2 at 900 ml/min, stirred at 250 rpm and with a constant pH of 6.8. As a control, D. vulgaris was grown in the same conditions but in Medium C-LS, and gassed with N2. In both procedures a 10% (vol/vol) inoculum of a freshly grown culture of D. vulgaris in the same conditions of the experiment was used, with exception to pyruvate culture where the inoculum was grown in pyruvate/sulfate medium. The optical density of the cultures at 600 nm (OD600) was determined with a Shimadzu UV-1603 spectrophotometer.
Extracted molecule
total RNA
Extraction protocol
He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381. PMID: 16751553, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=16751553
Label
Cy5
Label protocol
He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381. PMID: 16751553, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=16751553
Channel 2
Source name
Cells grown with lactate as the electron donor during sulfate reduction
Desulfovibrio vulgaris batch culture was grown at 37 degree C to mid-log phase with lactate as the only electron donor and sulfate as the only electron acceptor.
Biomaterial provider
Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Portugal
Treatment protocol
Cells grown with lactate as the electron donor
Growth protocol
D. vulgaris (DSM 644) was grown in a modified medium C at 37ºC, under an anoxic atmosphere of N2. The modified medium C contained 25 micromolar FeSO4.7H2O and 1 micromolar NiCl2.6H2O. Medium C-LS contained 40 mM lactate and 40 mM sulfate, and was used as a control. Pyruvate (40 mM) and thiosulfate (40 mM) were used as an alternative electron donor and acceptor, respectively. Fermentative growth was carried out with pyruvate (40 mM). Media (1000-ml) were dispensed in 2000-ml DURAN® SHOTT bottles, flushed with N2 and sealed with butyl rubber stoppers. Cultures with hydrogen as electron donor were grown in a 3L fermentor containing 2L of growth medium with 40 mM acetate, gassed with a mixture of 80 % (vol/vol) H2, 20 % (vol/vol) CO2 at 900 ml/min, stirred at 250 rpm and with a constant pH of 6.8. As a control, D. vulgaris was grown in the same conditions but in Medium C-LS, and gassed with N2. In both procedures a 10% (vol/vol) inoculum of a freshly grown culture of D. vulgaris in the same conditions of the experiment was used, with exception to pyruvate culture where the inoculum was grown in pyruvate/sulfate medium. The optical density of the cultures at 600 nm (OD600) was determined with a Shimadzu UV-1603 spectrophotometer.
Extracted molecule
total RNA
Extraction protocol
He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381. PMID: 16751553, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=16751553
Label
Cy3
Label protocol
He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381. PMID: 16751553, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=16751553
Hybridization protocol
He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381. PMID: 16751553, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=16751553
Scan protocol
He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381. PMID: 16751553, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=16751553
Description
The objective of this study is to identify the genes differentially expressed in dissimilatory sulfate reduction by D. vulgaris using hydrogen as the electron donor as compared to lactate as the electron donor.
Data processing
Lowess intensity-based normalization. He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381. PMID: 16751553, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=16751553
