title: Genetic variability of psychrotolerant Acidithiobacillus ferrivorans revealed by (meta)genomic analysis.
abstract: Acidophilic microorganisms inhabit low pH environments such as acid mine drainage that is generated when sulfide minerals are exposed to air. The genome sequence of the psychrotolerant Acidithiobacillus ferrivorans SS3 was compared to a metagenome from a low temperature acidic stream dominated by an A. ferrivorans-like strain. Stretches of genomic DNA characterized by few matches to the metagenome, termed 'metagenomic islands', encoded genes associated with metal efflux and pH homeostasis. The metagenomic islands were enriched in mobile elements such as phage proteins, transposases, integrases and in one case, predicted to be flanked by truncated tRNAs. Cus gene clusters predicted to be involved in copper efflux and further Cus-like RND systems were predicted to be located in metagenomic islands and therefore, constitute part of the flexible gene complement of the species. Phylogenetic analysis of Cus clusters showed both lineage specificity within the Acidithiobacillus genus as well as niche specificity associated with an acidic environment. The metagenomic islands also contained a predicted copper efflux P-type ATPase system and a polyphosphate kinase potentially involved in polyphosphate mediated copper resistance. This study identifies genetic variability of low temperature acidophiles that likely reflects metal resistance selective pressures in the copper rich environment.
authors.affiliation: Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida and Depto. de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile; Bio-Computing and Applied Genetics Division, Fraunhofer Chile Research Foundation, Center for Systems Biotechnology, Santiago, Chile. Electronic address: carola.mgr@gmail.com.
authors.forename: Carolina
authors.initials: C
authors.lastname: González
authors.affiliation: Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida and Depto. de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile. Electronic address: mariayanquepe.il@gmail.com.
authors.forename: María
authors.initials: M
authors.lastname: Yanquepe
authors.affiliation: Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida and Depto. de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile. Electronic address: juan.pablo.cardenas@gmail.com.
authors.forename: Juan Pablo
authors.initials: JP
authors.lastname: Cardenas
authors.affiliation: Bio-Computing and Applied Genetics Division, Fraunhofer Chile Research Foundation, Center for Systems Biotechnology, Santiago, Chile. Electronic address: jorge.valdes@fraunhofer.cl.
authors.forename: Jorge
authors.initials: J
authors.lastname: Valdes
authors.affiliation: Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida and Depto. de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile. Electronic address: rquatrini@yahoo.com.ar.
authors.forename: Raquel
authors.initials: R
authors.lastname: Quatrini
authors.affiliation: Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida and Depto. de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile. Electronic address: dsholmes2000@yahoo.com.
authors.forename: David S
authors.initials: DS
authors.lastname: Holmes
authors.affiliation: Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Sweden. Electronic address: mark.dopson@lnu.se.
authors.forename: Mark
authors.initials: M
authors.lastname: Dopson
mesh_terms: D042763:Acidithiobacillus / Q000145:classification* / Q000235:genetics*; D000251:Adenosine Triphosphatases / Q000235:genetics; D016000:Cluster Analysis; D003080:Cold Temperature; D004361:Drug Tolerance; D014644:Genetic Variation; D006863:Hydrogen-Ion Concentration; D020071:Interspersed Repetitive Sequences; D054892:Metagenome; D008670:Metals / Q000633:toxicity; D017856:Phosphotransferases (Phosphate Group Acceptor) / Q000235:genetics; D010802:Phylogeny; D045483:Rivers / Q000382:microbiology*; D017385:Sequence Homology
chemical_list: D008670:Metals; D017856:Phosphotransferases (Phosphate Group Acceptor); C022424:polyphosphate kinase; D000251:Adenosine Triphosphatases
keywords: Copper resistance; Cus; Genome; Heavy metal resistance; Metagenome; Mobilome