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Integrated molecular, physiological and in silico characterization of two Halomonas isolates from industrial brine

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Abstract

Two haloalkaliphilic bacteria isolated from industrial brine solutions were characterized via molecular, physiological, and in silico metabolic pathway analyses. Genomes from the organisms, designated Halomonas BC1 and BC2, were sequenced; 16S ribosomal subunit-based phylogenetic analysis revealed a high level of similarity to each other and to Halomonas meridiana. Both strains were moderate halophiles with near optimal specific growth rates (≥60 % μ max) observed over <0.1–5 % (w/v) NaCl and pH ranging from 7.4 to 10.2. Isolate BC1 was further characterized by measuring uptake or synthesis of compatible solutes under different growth conditions; in complex medium, uptake and accumulation of external glycine betaine was observed while ectoine was synthesized de novo in salts medium. Transcriptome analysis of isolate BC1 grown on glucose or citrate medium measured differences in glycolysis- and gluconeogenesis-based metabolisms, respectively. The annotated BC1 genome was used to build an in silico, genome-scale stoichiometric metabolic model to study catabolic energy strategies and compatible solute synthesis under gradients of oxygen and nutrient availability. The theoretical analysis identified energy metabolism challenges associated with acclimation to high salinity and high pH. The study documents central metabolism data for the industrially and scientifically important haloalkaliphile genus Halomonas.

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Acknowledgments

The authors are grateful for the financial assistance of Procter and Gamble, Inc. and appreciate the contributions of Adam Kennedy and colleagues at Metabolon, Inc. The authors would also like to thank Ryan Jennings, Ashley Beck and Kristopher Hunt for critical reading of the manuscript and 16S rRNA analysis.

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Author notes

  1. Olusegun Oshota

    Present address: Department of Veterinary Medicine, University of Cambridge, Cambridge, UK

  2. Matt Shipman

    Present address: U.S. Navy, Washington, DC, USA

Authors and Affiliations

  1. Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, 59717, USA

    Ross P. Carlson, Olusegun Oshota, Matt Shipman, Zackary J. Jay, Abigail Richards & Brent M. Peyton

  2. Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA

    Ross P. Carlson, Zackary J. Jay, Abigail Richards & Brent M. Peyton

  3. Procter and Gamble Co., Cincinnati, OH, 45202, USA

    Justin A. Caserta, Ping Hu, Charles W. Saunders, Jun Xu, Nancy Reeder & Charles Pettigrew

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  1. Ross P. Carlson
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Correspondence to Ross P. Carlson or Brent M. Peyton.

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Communicated by A. Oren.

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Carlson, R.P., Oshota, O., Shipman, M. et al. Integrated molecular, physiological and in silico characterization of two Halomonas isolates from industrial brine. Extremophiles 20, 261–274 (2016). https://doi.org/10.1007/s00792-015-0806-6

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  • DOI: https://doi.org/10.1007/s00792-015-0806-6

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