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Carbon Source Influence on Extracellular pH Changes along Bacterial Cell-Growth
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The effect of initial pH on bacterial cell-growth and its change over time was studied under aerobic heterotrophic conditions by using three bacterial strains: Escherichia coli ATCC 25922, Pseudomonas putida KT2440, and Pseudomonas pseudoalcaligenes CECT 5344. In Luria-Bertani (LB) media, pH evolved by converging to a certain value that is specific for each bacterium. By contrast, in the buffered Minimal Medium (MM), pH was generally more stable along the growth curve. In MM with glucose as carbon source, a slight acidification of the medium was observed for all strains. In the case of E. coli, a sudden drop in pH was observed during exponential cell growth that was later recovered at initial pH 7 or 8, but was irreversible below pH 6, thus arresting further cell-growth. When using other carbon sources in MM at a fixed initial pH, pH changes depended mainly on the carbon source itself. While glucose, glycerol, or octanoate slightly decreased extracellular pH, more oxidized carbon sources, such as citrate, 2-furoate, 2-oxoglutarate, and fumarate, ended up with the alkalinization of the medium. These observations are in accordance with pH change predictions using genome-scale metabolic models for the three strains, thus revealing the metabolic reasons behind pH change. Therefore, we conclude that the composition of the medium, specifically the carbon source, determines pH change during bacterial growth to a great extent and unravel the main molecular mechanism behind this phenotype. These findings pave the way for predicting pH changes in a given bacterial culture and may anticipate the interspecies interactions and fitness of bacteria in their environment.
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pH variation during bacterial growth is greatly influenced by the medium composition, particularly the carbon source.
“pH variation during bacterial growth is greatly influenced by the medium composition, particularly the carbon source.”
From Optimization of Bacillus subtilis PW12 biomass production using RSM: a preliminary study towards single-cell protein production for aquaculture (2024) · cites this paper as [50]
Since glucose is a reduced carbon source, more energy may be derived from its oxidation, leading to greater bacterial proliferative potential, and there might be an increased proton flux causing acidification of the medium during the exponential phase of bacterial growth.
“Since glucose is a reduced carbon source, more energy may be derived from its oxidation, leading to greater bacterial proliferative potential, and there might be an increased proton flux causing acidification of the medium during the exponential phase of bacterial growth [50].”
From Optimization of Bacillus subtilis PW12 biomass production using RSM: a preliminary study towards single-cell protein production for aquaculture (2024) · cites this paper as [50]
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Research works printed but not linked: 48
- Davies, 2016, Rotary ATPases: A New Twist to an Ancient Machine, Trends Biochem. Sci., 41, 106, 10.1016/j.tibs.2015.10.006 · DOI
- Casey, 2009, Sensors and regulators of intracellular pH, Nat. Rev. Mol. Cell Biol., 11, 50, 10.1038/nrm2820 · DOI · Paper page
- Krulwich, 2011, Molecular aspects of bacterial pH sensing and homeostasis, Nat. Rev. Microbiol., 9, 330, 10.1038/nrmicro2549 · DOI
- Pao, 1998, Major facilitator superfamily, Microbiol. Mol. Biol. Rev., 62, 1, 10.1128/MMBR.62.1.1-34.1998 · DOI · Paper page
- Noinaj, 2010, TonB-dependent transporters: Regulation, structure, and function, Annu. Rev. Microbiol., 64, 43, 10.1146/annurev.micro.112408.134247 · DOI · Paper page
- Nirody, 2017, The biophysicist’s guide to the bacterial flagellar motor, Adv. Phys. X, 2, 324
- Smith, 2018, The Culture Environment Influences Both Gene Regulation and Phenotypic Heterogeneity in Escherichia coli, Front. Microbiol., 9, 1739, 10.3389/fmicb.2018.01739 · DOI
- Hayes, E.T., Wilks, J.C., Sanfilippo, P., Yohannes, E., Tate, D.P., Jones, B.D., Radmacher, M.D., BonDurant, S.S., and Slonczewski, J.L. (2006). Oxygen limitation modulates pH regulation of catabolism and hydrogenases, multidrug transporters, and envelope composition in Escherichia coli K-12. BMC Microbiol., 6. · DOI
- Cama, 2014, A label-free microfluidic assay to quantitatively study antibiotic diffusion through lipid membranes, Lab Chip, 14, 2303, 10.1039/C4LC00217B · DOI
- Cama, 2015, Quantification of Fluoroquinolone Uptake through the Outer Membrane Channel OmpF of Escherichia coli, J. Am. Chem. Soc., 137, 13836, 10.1021/jacs.5b08960 · DOI
- Prieto, 2001, Biodegradation of Aromatic Compounds by Escherichia coli, Microbiol. Mol. Biol. Rev., 65, 523, 10.1128/MMBR.65.4.523-569.2001 · DOI
- Clarke, 1982, The metabolic versatility of pseudomonads, Antonie Van Leeuwenhoek, 48, 105, 10.1007/BF00405197 · DOI
- Bishop, 2006, The Core and Most Useful Molecules in Organic Chemistry, Angew. Chem. Int. Ed., 45, 5348, 10.1002/anie.200600881 · DOI
- Ratzke, C., and Gore, J. (2018). Modifying and reacting to the environmental pH can drive bacterial interactions. PLoS Biol., 16. · DOI
- Huertas, 2010, Alkaline cyanide degradation by Pseudomonas pseudoalcaligenes CECT5344 in a batch reactor. Influence of pH, J. Hazard. Mater., 179, 72, 10.1016/j.jhazmat.2010.02.059 · DOI
- Villano, 2010, Effect of pH on the production of bacterial polyhydroxyalkanoates by mixed cultures enriched under periodic feeding, Process Biochem., 45, 714, 10.1016/j.procbio.2010.01.008 · DOI
- Vylkova, S. (2017). Environmental pH modulation by pathogenic fungi as a strategy to conquer the host. PLoS Pathog., 13. · DOI
- Farber, 1991, Listeria monocytogenes, a food-borne pathogen, Microbiol. Rev., 55, 476, 10.1128/mr.55.3.476-511.1991 · DOI
- Glover, 2019, Bacterial ageing in the absence of external stressors, Philos. Trans. B, 374, 20180442, 10.1098/rstb.2018.0442 · DOI
- Nogales, 2020, High-quality genome-scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities, Environ. Microbiol., 22, 255, 10.1111/1462-2920.14843 · DOI
- Orth, 2011, A comprehensive genome-scale reconstruction of Escherichia coli metabolism-2011, Mol. Syst. Biol., 7, 535, 10.1038/msb.2011.65 · DOI · Paper page
- Sambrook, J., and Russell, D.W. (2012). Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press. [3rd ed.].
- Elbing, 2002, Media Preparation and Bacteriological Tools, Curr. Protoc. Mol. Biol., 59, 1.1.1, 10.1002/0471142727.mb0101s59 · DOI
- Nogales, J., and Agudo, L. (2015). A Practical Protocol for Integration of Transcriptomics Data into Genome-Scale Metabolic Reconstructions, Humana Press. · DOI
- Nogales, J., Gudmundsson, S., Duque, E., Ramos, J.L., and Palsson, B.O. (2017). Expanding the Computable Reactome in Pseudomonas putida Reveals Metabolic Cycles Providing Robustness. bioRxiv. · DOI
- Nogales, 2012, Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis, Proc. Natl. Acad. Sci. USA, 109, 2678, 10.1073/pnas.1117907109 · DOI · Paper page
- Huertas, 2005, Bacterial degradation of cyanide and its metal complexes under alkaline conditions, Appl. Environ. Microbiol., 71, 940, 10.1128/AEM.71.2.940-947.2005 · DOI
- Haynes, W.M., Lide, D.R., and Bruno, T.J. (2017). CRC Handbook of Chemistry and Physics, CRC Press. [97th ed.]. · DOI
- Escapa, 2013, The role of GlpR repressor in Pseudomonas putida KT2440 growth and PHA production from glycerol, Environ. Microbiol., 15, 93, 10.1111/j.1462-2920.2012.02790.x · DOI
- Gahlawat, 2017, Valorization of waste glycerol for the production of poly (3-hydroxybutyrate) and poly (3-hydroxybutyrate-co-3-hydroxyvalerate) copolymer by Cupriavidus necator and extraction in a sustainable manner, Bioresour. Technol., 243, 492, 10.1016/j.biortech.2017.06.139 · DOI
- Randriamahefa, 2003, Fourier Transform Infrared Spectroscopy for Screening and Quantifying Production of PHAs by Pseudomonas Grown on Sodium Octanoate, Biomacromolecules, 4, 1092, 10.1021/bm034104o · DOI
- Igeño, M.I., Macias, D., and Blasco, R. (2019). A Case of Adaptive Laboratory Evolution (ALE): Biodegradation of Furfural by Pseudomonas pseudoalcaligenes CECT 5344. Genes, 10. · DOI
- Manson, M.D. (2020). pH Sensing in Bacillus subtilis: A New Path to a Common Goal. J. Bacteriol., 202. · DOI
- Tohidifar, P., Plutz, M.J., Ordal, G.W., and Rao, C.V. (2020). The Mechanism of Bidirectional pH Taxis in Bacillus subtilis. J. Bacteriol., 202. · DOI
- Derek, J., and Chadwick, G.C. (2007). Bacterial Responses to Ph, John Wiley & Sons.
- Sánchez-Clemente, R., Igeño, M.I., Población, A.G., Guijo, M.I., Merchán, F., and Blasco, R. (2018). Study of pH Changes in Media during Bacterial Growth of Several Environmental Strains. Proceedings, 2. · DOI
- Gale, 1942, The effect of the pH of the medium during growth on the enzymic activities of bacteria (Escherichia coli and Micrococcus lysodeikticus) and the biological significance of the changes produced, Biochem. J., 36, 600, 10.1042/bj0360600 · DOI
- Bartek, I.L., Reichlen, M.J., Honaker, R.W., Leistikow, R.L., Clambey, E.T., Scobey, M.S., Hinds, A.B., Born, S.E., Covey, C.R., and Schurr, M.J. (2016). Antibiotic Bactericidal Activity Is Countered by Maintaining pH Homeostasis in Mycobacterium smegmatis. mSphere, 1. · DOI
- Zarkan, 2019, Indole Pulse Signalling Regulates the Cytoplasmic pH of E. coli in a Memory-Like Manner, Sci. Rep., 9, 3868, 10.1038/s41598-019-40560-3 · DOI
- Ventola, 2015, The antibiotic resistance crisis: Part 1: Causes and threats, Pharm. Ther., 40, 277
- Molina, 2019, Pseudomonas putida KT2440 metabolism undergoes sequential modifications during exponential growth in a complete medium as compounds are gradually consumed, Environ. Microbiol., 21, 2375, 10.1111/1462-2920.14622 · DOI
- Wolfe, 2005, The Acetate Switch, Microbiol. Mol. Biol. Rev., 69, 12, 10.1128/MMBR.69.1.12-50.2005 · DOI · Paper page
- Losen, 2004, Effect of Oxygen Limitation and Medium Composition on Escherichia coli Fermentation in Shake-Flask Cultures, Biotechnol. Prog., 20, 1062, 10.1021/bp034282t · DOI
- Palsson, B.O. (2015). Systems Biology. Constraint-Based Reconstruction and Analysis, Cambridge University Press. · DOI · Paper page
- Nikel, 2018, Pseudomonas putida as a functional chassis for industrial biocatalysis: From native biochemistry to trans-metabolism, Metab. Eng., 50, 142, 10.1016/j.ymben.2018.05.005 · DOI
- Feist, 2010, The biomass objective function, Curr. Opin. Microbiol., 13, 344, 10.1016/j.mib.2010.03.003 · DOI
- Naresh, 2012, The chemical formula of a magnetotactic bacterium, Biotechnol. Bioeng., 109, 1205, 10.1002/bit.24403 · DOI
- Popovic, M. (2019). Thermodynamic properties of microorganisms: Determination and analysis of enthalpy, entropy, and Gibbs free energy of biomass, cells and colonies of 32 microorganism species. Heliyon, 5. · DOI
Cited by
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Gracious, M., & Nandakumar, S. (2024) · Journal of Applied Biology & Biotechnology · doi:10.7324/jabb.2024.177031 · Cited by 2
“Since glucose is a reduced carbon source, more energy may be derived from its oxidation, leading to greater bacterial proliferative potential, and there might be an increased proton flux causing acidification of the medium during the exponential phase of bacterial growth [50].”
Metadata
- Authors
- Sánchez-Clemente, R., Guijo, M. I., Nogales, J., & Blasco, R.
- Affiliations
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Veterinaria, Universidad de Extremadura, 10003 Cáceres, Spain
- Universidad de Extremadura (ES)
- Consejo Superior de Investigaciones Científicas (ES)
- Corresponding author
- Blasco, Rafael
- Venue
- Genes
- Publisher
- MDPI AG
- Published
- 2020-10-30
- Volume
- 11
- Issue
- 11
- Pages
- 1292
- ISSN
- 2073-4425 (ISSN-L)
- PMC
- PMC7693008
- OpenAlex
- W3097458860
- Cited by
- 63
- References
- 0
- Citations by year
- 2026: 10 · 2025: 19 · 2024: 14 · 2023: 12 · 2022: 6 · 2021: 2
- FWCI
- 1.62
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Genes (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Consejería de Educación y Empleo, Junta de Extremadura (IB16062)
- European Regional Development Fund (GR18031)
- European Commission (PID2019-108458RB-I00)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial metabolism and enzyme function
- Keywords
- extracellular pH, carbon source, bacterial growth, Escherichia coli, Pseudomonas putida, Pseudomonas pseudoalcaligenes, glucose, glycerol, citrate, fumarate, alpha-ketoglutarate, octanoate, genome-scale metabolic models, acidification, alkalization
- MeSH terms
- Bacteria, Bacterial Proteins, Carbon, Culture Media, Escherichia coli, Hydrogen-Ion Concentration, Gene Expression Regulation, Bacterial, Pseudomonas putida, Pseudomonas pseudoalcaligenes
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