APPLIED MICROBIAL AND CELL PHYSIOLOGY Chemical characterization of soil extract as growth media for the ecophysiological study of bacteria Manuel Liebeke & Volker S. Brözel & Michael Hecker & Michael Lalk Received: 11 March 2009 / Revised: 11 March 2009 / Accepted: 11 March 2009 / Published online: 24 March 2009 # Springer-Verlag 2009 Abstract We investigated the composition of soil-extracted solubilized organic and inorganic matter (SESOM) pre- pared from three different soils. Growth of various bacterial strains in these soil extracts was evaluated to find appro- priate conditions for ecophysiological approaches. Analysis of SESOM by 1 H-NMR and gas chromatography/mass spectrometry revealed a complex mixture of organic com- pounds. An oak forest SESOM supported the growth of several gram-positive and gram-negative soil-derived het- erotrophic 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 extra- cellular medium can be obtained readily and specific compo- nents 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. Keywords Dissolved organic matter . Gas chromatography/mass spectrometry (GC-MS) . Nuclear magnetic resonance (NMR) . Growth medium . SESOM . Soil bacteria . Metabolomics Introduction Soils support a wide array of bacterial species, so a single gram of soil may contain between 1,000 and 1,000,000 taxa (Torsvik et al. 2002; Gans et al. 2005). The total density may reach 1.5×10 10 bacteria per gram (Torsvik et al. 1990; Torsvik and Øvreås 2002). Key questions in soil microbi- ology are: “who is out there” and “what are they doing” (Urich et al. 2008). Recent molecular approaches allow us to gauge the extent of soil bacterial diversity, but the majority of this diversity remains uncharacterized beyond its 16SrRNA gene pool (Pace 1997; Rappe and Giovannoni 2003; Fierer et al. 2007). While taxa involved in select processes such as the nitrogen cycle and methane produc- tion and consumption have been studied extensively in situ, the ecophysiological characteristics of the majority of soil bacteria are largely unknown (Fierer et al. 2007). This is Appl Microbiol Biotechnol (2009) 83:161–173 DOI 10.1007/s00253-009-1965-0 Journal series publication 3622 from the South Dakota Agricultural Experiment Station. Electronic supplementary material The online version of this article (doi:10.1007/s00253-009-1965-0) contains supplementary material, which is available to authorized users. M. Liebeke : M. Lalk (*) Department of Pharmaceutical Biology, Ernst-Moritz-Arndt University of Greifswald, Friedrich-Ludwig Jahn Street 17, 17487 Greifswald, Germany e-mail: lalk@uni-greifswald.de V. S. Brözel Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA M. Hecker Department of Microbiology, Ernst-Moritz-Arndt University of Greifswald, Friedrich-Ludwig Jahn Street 17, 17487 Greifswald, Germany