title: Metagenomic analysis reveals adaptations to a cold-adapted lifestyle in a low-temperature acid mine drainage stream.
abstract: An acid mine drainage (pH 2.5-2.7) stream biofilm situated 250 m below ground in the low-temperature (6-10°C) Kristineberg mine, northern Sweden, contained a microbial community equipped for growth at low temperature and acidic pH. Metagenomic sequencing of the biofilm and planktonic fractions identified the most abundant microorganism to be similar to the psychrotolerant acidophile, Acidithiobacillus ferrivorans. In addition, metagenome contigs were most similar to other Acidithiobacillus species, an Acidobacteria-like species, and a Gallionellaceae-like species. Analyses of the metagenomes indicated functional characteristics previously characterized as related to growth at low temperature including cold-shock proteins, several pathways for the production of compatible solutes and an anti-freeze protein. In addition, genes were predicted to encode functions related to pH homeostasis and metal resistance related to growth in the acidic metal-containing mine water. Metagenome analyses identified microorganisms capable of nitrogen fixation and exhibiting a primarily autotrophic lifestyle driven by the oxidation of the ferrous iron and inorganic sulfur compounds contained in the sulfidic mine waters. The study identified a low diversity of abundant microorganisms adapted to a low-temperature acidic environment as well as identifying some of the strategies the microorganisms employ to grow in this extreme environment.
authors.affiliation: Department of Molecular Biology, Umeå University, S-901 87 Umeå, Sweden.
authors.forename: Maria
authors.initials: M
authors.lastname: Liljeqvist
authors.affiliation: Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida and Depto. de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago 7780272, Chile.
authors.forename: Francisco J
authors.initials: FJ
authors.lastname: Ossandon
authors.affiliation: Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida and Depto. de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago 7780272, Chile Bio-Computing and Applied Genetics Division, Fraunhofer Chile Research Foundation, Center for Systems Biotechnology, Santiago, Piso 14, 7550296, Chile.
authors.forename: Carolina
authors.initials: C
authors.lastname: González
authors.affiliation: Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, 392 31 Kalmar, Sweden.
authors.forename: Sukithar
authors.initials: S
authors.lastname: Rajan
authors.affiliation: Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, 392 31 Kalmar, Sweden.
authors.forename: Adam
authors.initials: A
authors.lastname: Stell
authors.affiliation: Bio-Computing and Applied Genetics Division, Fraunhofer Chile Research Foundation, Center for Systems Biotechnology, Santiago, Piso 14, 7550296, Chile.
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 7780272, Chile.
authors.forename: David S
authors.initials: DS
authors.lastname: Holmes
authors.affiliation: Department of Molecular Biology, Umeå University, S-901 87 Umeå, Sweden Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, 392 31 Kalmar, Sweden mark.dopson@lnu.se.
authors.forename: Mark
authors.initials: M
authors.lastname: Dopson
mesh_terms: D000064:Acclimatization / Q000235:genetics; D042763:Acidithiobacillus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D000595:Amino Acid Sequence; D021301:Antifreeze Proteins / Q000235:genetics; D001483:Base Sequence; D018441:Biofilms / Q000254:growth & development; D052837:Chemoautotrophic Growth; D003080:Cold Temperature; D058639:Cold-Shock Response / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D043372:Gallionellaceae / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D006863:Hydrogen-Ion Concentration; D007501:Iron / Q000378:metabolism; D054892:Metagenome / Q000235:genetics*; D059013:Microbial Consortia; D009586:Nitrogen Fixation / Q000235:genetics; D010084:Oxidation-Reduction; D018384:Oxidative Stress / Q000235:genetics; D010802:Phylogeny; D010933:Plankton / Q000145:classification / Q000235:genetics*; D045483:Rivers; D017422:Sequence Analysis, DNA; D013548:Sweden; D062065:Wastewater / Q000382:microbiology*
chemical_list: D021301:Antifreeze Proteins; D004269:DNA, Bacterial; D007501:Iron; D062065:Wastewater
keywords: Acidithiobacillus ferrivorans; acid mine drainage; low temperature; metagenome; psychrotolerant