DOI: 10.5061/dryad.dncjsxmbf
title: Data from: The diversity of cellular systems involved in carbonate precipitation by Escherichia coli

description: 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.
description: # Data from: The diversity of cellular systems involved in carbonate
 precipitation by Escherichia coli Dataset DOI:
 [10.5061/dryad.dncjsxmbf](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
 [matthew.jennings@wilkes.edu](mailto:matthew.jennings@wilkes.edu)