PCR protocol- and inulin catabolism-based differentiation of inulinolytic soil bacteria

Bacteria collected from rotting dahlia tubers, instead of degrading inulin to D-fructose, preferentially formed the known DFA III (beta-2.1': alpha-2',3 difructofuranose anhydride), inulobiose, higher inulo-oligosaccharides, and exoheteropolysaccharides. Owing to the morphological and Gram staining variability, the bacterial isolates designated YLW and CRM were examined to differentiate them from a reference strain Arthrobacter ureafaciens. The comparative analyses were whole DNA random amplification by Taq polymerase (RAPD-PCR protocol), culture media DFA III content in culture media, chromatographic profile of oligosaccharides formed, and exopolysaccharide fractionation/fragmentation. A comparative study in liquid shake cultures showed that the isolate YLW was faster than the reference strain in the production of DFA III when the inulin/yeast extract ratio was maintained at 10 in the medium, although a similar maximum yield was displayed with both bacteria (13-14 mg of DFA/mL cell free media from the initial 30 mg/mL of inulin load). Doubling the yeast extract input, an even faster onset of DFA III production occurred with YLW but with no further improvement in the maximum yield. Both strains further degraded the resulting DFA during the stationary growth phase. The main ability of CRM when grown on inulin was the production of exopolysaccharides, although culture condition variation also allowed DFA III production, which was accompanied by somewhat lower amounts of its reducing analog, inulobiose.