Metallibacterium scheffleri: Genetic data reveal a versatile metabolism

This study describes the physiological properties of a wide spread acidophilic microorganism. Metallibacterium scheffleri DKE6 was described as an acid tolerant, heterotrophic g-proteobacterium living in an acidic biofilm. Casein was reported to be the only growth substrate of the organism. Nevertheless, using a combination of proteomic, genomic and transcriptomic approaches as well as microbiological assays we could identify a rather versatile metabolism. The detected casein hydrolysis was corroborated by the detection of proteases in the supernatant of the organism but also via transcriptome studies. Genomic analysis identified amino acid auxotrophies, which were revealed to be the reason for the observed growth deficiency with other substrates in the absence of casein. Supported by the detection three glycolytic pathways it was verified that glucose could serve as a growth substrate in the presence of amino acids as building blocks. Additionally, genes for sulfur and hydrogen oxidation were found and sulfate formation could be shown during growth with tetrathionate. The organism is acid tolerant. Still, growth with amino acids is accompanied by the release of ammonium and the subsequent increase of the medium pH. The distribution of other Metallibacterium species demonstrates also an adaption to diverse environments with varying pH values. Growth in biofilms or sediments seems to be a preferred habitat . We hypothesize that this supports the ability of the organism to raise the pH in its environment via ammonium production. Overall design: RNA from two biological duplicates under identical conditions was sequenced. Each duplicate sample was obtained by pool three independent cultures that were harvested in exponential phase.