title: Genome Analysis of the Biotechnologically Relevant Acidophilic Iron Oxidising Strain JA12 Indicates Phylogenetic and Metabolic Diversity within the Novel Genus "Ferrovum".
abstract: BACKGROUND
  Members of the genus "Ferrovum" are ubiquitously distributed in acid mine drainage (AMD) waters which are characterised by their high metal and sulfate loads. So far isolation and microbiological characterisation have only been successful for the designated type strain "Ferrovum myxofaciens" P3G. Thus, knowledge about physiological characteristics and the phylogeny of the genus "Ferrovum" is extremely scarce.
  
  
  OBJECTIVE
  In order to access the wider genetic pool of the genus "Ferrovum" we sequenced the genome of a "Ferrovum"-containing mixed culture and successfully assembled the almost complete genome sequence of the novel "Ferrovum" strain JA12.
  The genome-based phylogenetic analysis indicates that strain JA12 and the type strain represent two distinct "Ferrovum" species. "Ferrovum" strain JA12 is characterised by an unusually small genome in comparison to the type strain and other iron oxidising bacteria. The prediction of nutrient assimilation pathways suggests that "Ferrovum" strain JA12 maintains a chemolithoautotrophic lifestyle utilising carbon dioxide and bicarbonate, ammonium and urea, sulfate, phosphate and ferrous iron as carbon, nitrogen, sulfur, phosphorous and energy sources, respectively.
  The potential utilisation of urea by "Ferrovum" strain JA12 is moreover remarkable since it may furthermore represent a strategy among extreme acidophiles to cope with the acidic environment. Unlike other acidophilic chemolithoautotrophs "Ferrovum" strain JA12 exhibits a complete tricarboxylic acid cycle, a metabolic feature shared with the closer related neutrophilic iron oxidisers among the Betaproteobacteria including Sideroxydans lithotrophicus and Thiobacillus denitrificans. Furthermore, the absence of characteristic redox proteins involved in iron oxidation in the well-studied acidophiles Acidithiobacillus ferrooxidans (rusticyanin) and Acidithiobacillus ferrivorans (iron oxidase) indicates the existence of a modified pathway in "Ferrovum" strain JA12. Therefore, the results of the present study extend our understanding of the genus "Ferrovum" and provide a comprehensive framework for future comparative genome and metagenome studies.
authors.affiliation: Institute of Biological Sciences, TU Bergakademie Freiberg, Leipziger Straße 29, Freiberg, Germany.
authors.forename: Sophie R
authors.initials: SR
authors.lastname: Ullrich
authors.affiliation: Georg-August-University Göttingen, Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Grisebachstraße 8, Göttingen, Germany.
authors.forename: Anja
authors.initials: A
authors.lastname: Poehlein
authors.affiliation: Institute of Biological Sciences, TU Bergakademie Freiberg, Leipziger Straße 29, Freiberg, Germany.
authors.forename: Judith S
authors.initials: JS
authors.lastname: Tischler
authors.affiliation: Center for System Biotechnology, Bio-Computing Division and Applied Genetics Division, Fraunhofer Chile Research Foundation, Avenida Mariano Sánchez Fontecilla 310, Santiago, Chile, and Center for Bioinformatics and Genome Biology, Fundación Ciencia y Vida, Zañartu 1482, and Facultad de Ciencias Biologicas, Universidad Andres Bello, Avenida Los Leones 745, Santiago, Chile.
authors.forename: Carolina
authors.initials: C
authors.lastname: González
authors.affiliation: Center for Bioinformatics and Genome Biology, Fundación Ciencia y Vida, Zañartu 1482 and Facultad de Ciencias Biologicas, Universidad Andres Bello, Avenida Los Leones 745, Santiago, Chile.
authors.forename: Francisco J
authors.initials: FJ
authors.lastname: Ossandon
authors.affiliation: Georg-August-University Göttingen, Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Grisebachstraße 8, Göttingen, Germany.
authors.forename: Rolf
authors.initials: R
authors.lastname: Daniel
authors.affiliation: Center for Bioinformatics and Genome Biology, Fundación Ciencia y Vida, Zañartu 1482 and Facultad de Ciencias Biologicas, Universidad Andres Bello, Avenida Los Leones 745, Santiago, Chile.
authors.forename: David S
authors.initials: DS
authors.lastname: Holmes
authors.affiliation: Institute of Biological Sciences, TU Bergakademie Freiberg, Leipziger Straße 29, Freiberg, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Schlömann
authors.affiliation: Institute of Biological Sciences, TU Bergakademie Freiberg, Leipziger Straße 29, Freiberg, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Mühling
mesh_terms: D020562:Betaproteobacteria / Q000235:genetics*; D004269:DNA, Bacterial / Q000235:genetics*; D016680:Genome, Bacterial; D007501:Iron / Q000378:metabolism*; D054892:Metagenome; D008906:Mining; D010802:Phylogeny
chemical_list: D004269:DNA, Bacterial; D007501:Iron