The influence of cultivation methods on Shewanella oneidensis physiology and proteome expression
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ORIGINAL PAPER
The inXuence of cultivation methods on Shewanella oneidensis physiology and proteome expression Dwayne A. Elias · Sandra L. Tollaksen · David W. Kennedy · Heather M. Mottaz · Carol S. Giometti · JeVrey S. McLean · Eric A. Hill · Grigoriy E. Pinchuk · Mary S. Lipton · James K. Fredrickson · Yuri A. Gorby
Received: 13 June 2007 / Revised: 31 August 2007 / Accepted: 24 October 2007 / Published online: 21 November 2007 © The Author(s) 2007
Abstract High-throughput analyses that are central to microbial systems biology and ecophysiology research beneWt from highly homogeneous and physiologically welldeWned cell cultures. While attention has focused on the technical variation associated with high-throughput technologies, biological variation introduced as a function of cell cultivation methods has been largely overlooked. This study evaluated the impact of cultivation methods, controlled batch or continuous culture in bioreactors versus shake Xasks, on the reproducibility of global proteome measurements in Shewanella oneidensis MR-1. Variability in dissolved oxygen concentration and consumption rate, metabolite proWles, and proteome was greater in shake Xask than controlled batch or chemostat cultures. Proteins indicative of suboxic and anaerobic growth (e.g., fumarate reductase and decaheme c-type cytochromes) were more abundant in cells from shake Xasks compared to bioreactor
Communicated by Ercko Stackebrandt. D. A. Elias Department of Biochemistry, University of Missouri-Columbia, Columbia, MO 65211, USA S. L. Tollaksen · C. S. Giometti Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA D. W. Kennedy · H. M. Mottaz · J. S. McLean · E. A. Hill · G. E. Pinchuk · M. S. Lipton · J. K. Fredrickson Biological Sciences Division, PaciWc Northwest National Laboratory, Richland, WA 99353, USA Y. A. Gorby (&) J. Craig Venter Institute, 11149 North Torrey Pines Road, Suite 220, La Jolla, CA 92093, USA e-mail: [email protected]; [email protected]
cultures, a Wnding consistent with data demonstrating that “aerobic” Xask cultures were O2 deWcient due to poor mass transfer kinetics. The work described herein establishes the necessity of controlled cultivation for ensuring highly reproducible and homogenous microbial cultures. By decreasing cell to cell variability, higher quality samples will allow for the interpretive accuracy necessary for drawing conclusions relevant to microbial systems biology research. Keywords Controlled cultivation · Systems biology · Proteomics · Shewanella
Introduction The cultivation of microorganisms has been performed for more than a century beginning with Louis Pasteur (1879), Robert Koch (1881) and R. J. Petri (1882) (Sedgwick 1916; Gest 1987), with ever increasingly sophisticated methods becoming available over time. These methods range from using undeWned medium (e.g., boiled meat extracts) in shake Xask cultures where growth rate and substrate utilization (Narang et al. 1997) as well as proteomic proWles (Valentine et al. 2005; Wunschel et al. 2005)
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