Maximizing microbial degradation of perchlorate using a genetic algorithm: Media optimization

• Published in: Journal of biotechnology 2012-01, Vol.157 (1), p.189-197
• Main Authors: Kucharzyk, Katarzyna H., Crawford, Ronald L., Paszczynski, Andrzej J., Soule, Terence, Hess, Thomas F.
• Format: Article
• Language: English
• Subjects: Algorithms; Bacterial ecology; biodegradation; Biodegradation, Environmental; Biological and medical sciences; Biotechnology; carbon; Culture Media - chemistry; Culture Media - metabolism; Dechloromonas; Dechlorosoma; ecosystems; environmental factors; Fundamental and applied biological sciences. Psychology; Genetic algorithm; Hydrogen-Ion Concentration; Kinetics; microbial communities; Microbial Consortia; Models, Genetic; Perchlorate degradation; Perchlorates - metabolism; Principal Component Analysis; Resazurin; Rhodocyclaceae - metabolism; temperature
• ISSN: 0168-1656; 1873-4863
• DOI: 10.1016/j.jbiotec.2011.10.011

► Genetic algorithms can optimize experiments with large numbers of variables (>5). ► 15-fold increase in perchlorate degradation rate from GA-optimized growth media. ► The GA increased perchlorate degradation mainly by optimizing pH in microbial medium. Microbial communities are under constant influence of physical and chemical components in ecosystems. Shifts in conditions such as pH, temperature or carbon source concentration can translate into shifts in overall ecosystem functioning. These conditions can be manipulated in a laboratory setup using evolutionary computation methods such as genetic algorithms (GAs). In work described here, a GA methodology was successfully applied to define sets of environmental conditions for microbial enrichments and pure cultures to achieve maximum rates of perchlorate degradation. Over the course of 11 generations of optimization using a GA, we saw a statistically significant 16.45 and 16.76-fold increases in average perchlorate degradation rates by Dechlorosoma sp. strain KJ and Dechloromonas sp. strain Miss R, respectively. For two bacterial consortia, Pl6 and Cw3, 5.79 and 5.75-fold increases in average perchlorate degradation were noted. Comparison of zero-order kinetic rate constants for environmental conditions in GA-determined first and last generations of all bacterial cultures additionally showed marked increases.