Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Using data from microarray experiments, we investigated the transcriptional changes in evolved and ancestor D. vulgaris strains.

ABSTRACT: Using data from microarray experiments, we investigated the transcriptional changes in evolved and ancestor D. vulgaris strains. gene expression changes in evolved salt-stressed DvH strain (ES, evolved in LS4D + 100 mM NaCl for 1200 generations), evolved control DvH strain (EC, evolved in LS4D for 1200 generations) and ancestor DvH strain grown in non-stress (LS4D), low salt stress (LS4D + 100 mM NaCl) or high salt stress (LS4D + 250 mM NaCl) conditions Comparison of gene expression in evolved salt-stressed strain (ES, 1200g) to ancestor (An) or evolved control (EC, 1200g) strains at mid-logarithmic phase under standard growth condition with defined medium LS4D, salt stress conditions LS4D+100 mM NaCl or LS4D+250 mM NaCl.

ORGANISM(S): Desulfovibrio vulgaris str. Hildenborough

SUBMITTER: Adam Arkin

PROVIDER: E-GEOD-39675 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Background. Desulfovibrio vulgaris Hildenborough is a sulfate-reducing bacterium (SRB) that is intensively studied in the context of metal corrosion and heavy-metal bioremediation, and SRB populations are commonly observed in pipe and subsurface environments as surface-associated populations. In order to elucidate physiological changes associated with biofilm growth at both the transcript and protein level, transcriptomic and proteomic analyses were done on mature biofilm cells and compared to both batch and reactor planktonic populations. The biofilms were cultivated with lactate and sulfate in a continiouslly fed biofilm reactor, and compared to both batch and reactor planktonic populations. The functional genomic analysis demonstrated that biofilm cells were different compared to planktonic cells, and the majority of altered abundances for genes and proteins were annotated as hypothetical (unknown function), energy conservation, amino acid metabolism, and signal transduction. Genes and proteins that showed similar trends in detected levels were particularly involved in energy conservation such as increases in an annotated ech hydrogenase, formate dehydrogenase, pyruvate:ferredoxin oxidoreductase, and rnf oxidoreductase, and the biofilm cells had elevated formate dehydrogenase activity. Several other hydrogenases and formate dehydrogenases also showed an increased protein level, while decreased transcript and protein levels were observed for putative coo hydrogenases as well as a lactate permease and hyp hydrogenases for biofilm cells. Genes annotated for amino acid synthesis and nitrogen utilization were also predominant changers within the biofilm state. Ribosomal transcripts and proteins were notably decreased within the biofilm cells compared to exponential-phase cells but were not as low as levels observed in planktonic, stationary-phase cells. Several putative, extracellular proteins (DVU1012, 1545) were also detected in the extracellular fraction from biofilm cells. Even though both the planktonic and biofilm cells were oxidizing lactate and reducing sulfate, the biofilm cells were physiologically distinct compared to planktonic growth states due to altered abundances of genes/proteins involved in carbon/energy flow and extracellular structures. In addition, average expression values for multiple rRNA transcripts and respiratory activity measurements indicated that biofilm cells were metabolically more similar to exponential-phase cells although biofilm cells are structured differently. The characterization of physiological advantages and constraints of the biofilm growth state for sulfate-reducing bacteria will provide insight into bioremediation applications as well as microbially-induced metal corrosion. Biofilms grown in reactors were compared to reference samples of reactor, planktonic and batch, planktonic. Each sample had a biological triplicate.

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Using data from microarray experiments, we investigated the transcriptional changes in evolved and ancestor D. vulgaris strains.

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