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Chemical characterization of soil extract as growth media for the ecophysiological study of bacteria


We investigated the composition of soil-extracted solubilized organic and inorganic matter (SESOM) prepared from three different soils. Growth of various bacterial strains in these soil extracts was evaluated to find appropriate conditions for ecophysiological approaches. Analysis of SESOM by 1H-NMR and gas chromatography/mass spectrometry revealed a complex mixture of organic compounds. An oak forest SESOM supported the growth of several gram-positive and gram-negative soil-derived heterotrophic bacteria, whereas beech forest and grassland soil extracts did not. A metabolomic approach was performed by determining the extracellular metabolite profile of Bacillus licheniformis in SESOM. The results demonstrated that determination of the organic composition of SESOM during batch culturing is feasible. This makes SESOM amenable to studying the ecophysiology of a range of soil bacteria growing on soil-dissolved organic matter under more defined laboratory conditions. SESOM may also increase success in isolating previously uncultured or novel soil bacteria. Cell populations and the corresponding extracellular medium can be obtained readily and specific components extracted, paving the way for proteomic, transcriptomic, and metabolomic analyses. The synthetic carbon mixture based on SESOM, which mimics soil abilities, shows a positive impact on higher cell yields and longer cultivation time for biotechnological relevant bacteria.

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We are grateful to S. Seefeld for performing the ICP and IC. We thank K. Surmann for the assistance and Dr. M. Sadowsky for donating the bacterial strains. This research was funded by a grant from the Apotheker-Paul-Marschall-Stiftung to M. Liebeke and by the South Dakota Agricultural Experiment Station and the State of South Dakota. VSB was the recipient of a fellowship from the Stiftung Alfried Krupp Kolleg Greifswald.

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Correspondence to Michael Lalk.

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Journal series publication 3622 from the South Dakota Agricultural Experiment Station.

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Fig. S1

Growth of Bacillus licheniformis DSM 13 in synthetic media and appending metabolite concentrations [in millimolars] of culture supernatants (determined by 1H-NMR measurements) for M9 medium with a carbon source cocktail in low concentrations (a) and high concentrations (b). Also displayed is growth in M9 medium with glucose in low concentrations (c) and high concentrations (d) as carbon source. All experiments were done in triplicate and a representative experiment is shown (DOC 221 kb)

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Liebeke, M., Brözel, V.S., Hecker, M. et al. Chemical characterization of soil extract as growth media for the ecophysiological study of bacteria. Appl Microbiol Biotechnol 83, 161–173 (2009).

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  • Dissolved organic matter
  • Gas chromatography/mass spectrometry (GC-MS)
  • Nuclear magnetic resonance (NMR)
  • Growth medium
  • Soil bacteria
  • Metabolomics