Additional file 1:

Additional figure S1. Interrogation of the apparent second "growth" phase of H. salinarum NRC-1 in rich media. (A) Growth of H. salinarum NRC-1 was tracked by optical density measurements at both 600 nm and 700 nm to determine the contribution of bacteriorhodopsin (a protein whose broad absorption peak centered at 568 nm can contribute to absorption at 600 nm but not at 700 nm) accumulation. The growth curve generated at 700 nm displays similar behavior to the curve generated from measurements taken at 600 nm. In particular, the apparent doubling that occurs during what appears to be stationary phase is apparent in both curves suggesting that this is not due to bacteriorhodopsin accumulation. This increase in optical density is most likely due to an increase in light scattering gas vesicles that are visibly released during this late phase of the growth experiment. (B) Phase-contrast visible light microscopy image of H. salinarum NRC-1 near the end of data collection for the data presented in Figure 1 main text. Three arrows point to examples of small bright bodies (presumably gas vesicles) that populate the field of view. This abundance of gas vesicles only becomes apparent after a significant decrease in CFU following stationary phase.

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Additional file 2:

Potential causes for the apparent second growth phase in H. salinarum NRC-1.

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Additional file 3:

Additional figure S2. Heat maps of genes with significant up or down regulation during growth. Samples from each individual experiments (e.g. MPK407, H. salinarum NRC-1 and H. salinarum NRC-1 + uracil) are organized by increasing optical density moving from left to right. The black volume bar indicates increasing optical density. Genes have been hierarchically clustered to show potential subpatterns of expression. (A) A heatmap showing the changes in expression of 451 genes whose transcript abundance is decreased upon entry into stationary phase. (B) A heatmap showing the changes in expression of 772 genes whose transcript abundance is increased upon entry into stationary phase.

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Additional file 4:

Additional table S1 - Genes whose transcript abundance is decreased during the transition to stationary phase. This table lists ORF name, gene symbol, an estimate fold change in expression between pre-stationary and stationary phase expression, an indicator of significance of change between pre-stationary and stationary phase expression values and the putative gene function (if known). Fold change was calculated by taking the ratio between the average non-logged ratio for the last four samples (replicates included) taken in the growth curve to the average of the first four samples taken in the growth curve. A t-test, computed on logged data, was also used on the same selected sets to (first and last four data points for each strain) to ask whether the changes in expression were statistically significant given an overall p-value threshold = 0.05 and enforcing a false discovery rate of 0.05 or less. 418 genes of the 451 in this clustering derived set were deemed to have significantly different expression levels using this criteria while the remaining 33 genes did not. Genes meeting this criteria are marked with a number one while those not meeting the criteria are marked with a zero. Manual inspection of expression profiles of genes not meeting the above criteria suggest that the t-test in this instance may be too conservative as many gene expression profiles deemed not significant show what seems to be clear decrease in signal between pre-stationary and stationary phases.

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Additional file 5:

Additional table S2 - Genes whose transcript abundance is increased during the transition to stationary phase. This table lists ORF name, gene symbol, an estimate fold change in expression between pre-stationary and stationary phase expression, an indicator of significance of change between pre-stationary and stationary phase expression values and the putative gene function (if known). Fold change was calculated by taking the ratio between the average non-logged ratio for the last four samples (replicates included) taken in the growth curve to the average of the first four samples taken in the growth curve. A t-test, computed on logged data, was also used on the same selected sets to (first and last four data points for each strain) to ask whether the changes in expression were statistically significant given an overall p-value threshold = 0.05 and enforcing a false discovery rate of 0.05 or less. 713 genes of the 772 in this clustering derived set were deemed to have significantly different expression levels using this criteria while the remaining 59 genes did not. Genes meeting this criteria are marked with a number one while those not meeting the criteria are marked with a zero. Manual inspection of expression profiles of genes not meeting the above criteria suggest that the t-test in this instance may be too conservative as many gene expression profiles deemed not significant show what seems to be clear increase in signal between pre-stationary and stationary phases.

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Additional file 6:

Functional KEGG pathway and ontology annotations for those genes reported in Additional tables S1 and S2. Functional assignments are as reported by KEGG, unmodified.

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Additional file 7:

Additional figure S3. Metabolites showing significant changes in abundance during growth. Each panel show a bar chart illustrating the changes in abundance for 51 detected metabolites whose levels change significantly during growth. The numbering scheme at the top of each panel does not have any practical significance and simply serves to identify each MS peak in the experiment. Histogram heights correspond to average counts for each metabolite in the triplicates. Measured levels are not indicative of absolute cellular concentrations. However, relative changes in concentrations between samples derived from different growth states may be inferred the histograms.

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Additional file 8:

Additional figure S4. Spectra of citrulline, phenylalanine, riboflavin and 5-deoxyadenosine. Paired presentation of ion spectra measured from both H. salinarum NRC-1 and from purified metabolite standard for citrulline, phenylalanine, riboflavin and 5-deoxyadenosine. Relative abundance levels are also shown as a histogram.

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