Data from: The diversity of cellular systems involved in carbonate precipitation by Escherichia coli
Data files
Aug 04, 2025 version files 1.63 MB
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Fig._2_Raw_Data.xlsx
18.47 KB
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Fig._3_Raw_Data.xlsx
14.72 KB
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Fig._4_Raw_Data.xlsx
1.59 MB
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Fig._5_Raw_Data.xlsx
10.29 KB
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README.md
3.18 KB
Abstract
Climate change is increasing the need to limit levels of anthropogenic CO2 released into the atmosphere. One approach being investigated is to generate products based on microbially induced carbonate precipitation (MICP), which can trap CO2 as CaCO3. We recently identified a novel MICP pathway in bacteria that is initiated by Ca2+ toxicity in cells, causing extracellular CO2 to be trapped as CO32- by Escherichia coli, although the yield of precipitated CaCO3 remained low (in the milligram range). In this work, we used the E. coli Keio gene knock-out library to identify 54 genes involved in MICP in E. coli, which could be broadly characterized into four groups: central metabolism, iron metabolism, cell architecture, and transport. The role of central metabolism appears to be crucial in maintaining alkaline conditions surrounding the cell that promote CaCO3 precipitation. The role of iron metabolism was less clear, although the results suggest that growth rate influences the initiation of MICP. While the impact of repeating polymeric structures on cell surfaces promoting MICP is well established, our results suggest that other structural features may play a role, including fimbriae and flagella. Finally, the results confirmed that Ca2+ transport is central to MICP under calcium stress. The results further suggest that the ZntB efflux pump may play a previously unidentified role in Ca2+ transport in E. coli. By overexpressing some of these genes, our work suggests that there are several previously unidentified cellular mechanisms that could serve as a target for enhanced MICP in E. coli. By incorporating these processes into MICP pathways in E. coli, it may be possible to increase the volume of CO2 fixed using this pathway and yield potentially new products that can replace CO2 intensive products, such as precipitated calcium carbonates (PCCs) for industry.
Dataset DOI: 10.5061/dryad.dncjsxmbf
Description of the data and file structure
These are the raw data used to build Figures 2, 3, 4, and 5 in the publication: The diversity of cellular systems involved in carbonate precipitation by Escherichia coli.
Fig._2_Raw_Data.xlsx
Part A. Readings of pH from B4m agar plates containing the indicated calcium salt. Readings from three replicate plates were averaged together for each strain. WT is the K-12 strain of E. coli. The knockouts are from the Keio collection of single gene knockouts in E. coli.
Part B. OD600 readings of B4m containing calcium-propionate media. Time indicates when samples were taken from flasks for OD600 measurements. WT is the K-12 strain of E. coli. The knockouts are from the Keio collection of single gene knockouts in E. coli.
Part C. pH readings of B4m containing calcium-propionate media. Time indicates when samples were taken from flasks for pH measurements. WT is the K-12 strain of E. coli. The knockouts are from the Keio collection of single gene knockouts in E. coli.
Fig._3_Raw_Data.xlsx
ug of insoluble calcium per mL of culture produced by the three tested strains. Three separate tubes of B4m media containing the indicated calcium substrate (2.5 g calcium substrate / L) were inoculated with the indicated strain: WT is the K-12 strain of E. coli. The knockouts are from the Keio collection of single gene knockouts in E. coli. Cultures were harvested after 24 hours to quantify the amount of calcium carbonate present. Three separate tubes were inoculated for each strain, and the* *values were averaged together.
Variables
- ug insoluble calcium / mL of bacterial culture
Fig._4_Raw_Data.xlsx
pH and temperature data were collected from E. coli K-12 cultures grown in B4m containing calcium-succinate. Each table contains data from a single culture, with presence or absence of 0.5 mM FeCl3 and stirring speed of culture indicated to the right of the table.
Variables
- pH and temperature values
- Presence/absence of 0.5 mM FeCl3 (other variables in column H)
Fig._5_Raw_Data.xlsx
ug of insoluble calcium per mL of culture produced by each tested strain. All strains are E. coli DE3. Control indicates a strain containing the pPRO24 plasmid with no insert, all other strains carry a pPRO24 plasmid with the indicated gene cloned into it. "-" indicates uninduced cultures and "+" cultures were induced with 25 mM sodium propionate. Values from three replicates were averaged together.
Variables
- ug insoluble calcium / mL of bacterial culture
- Induction "-" indicates nothing added to culture, "+" indicates addition of 25 mM sodium propionate
Code/software
Excel or some other program that can open .xlsx files.
Access information
Other publicly accessible locations of the data:
- N/A
Data was derived from the following sources:
- N/A
Contact information:
Matthew Jennings
Wilkes University