title: Microbial stratification in low pH oxic and suboxic macroscopic growths along an acid mine drainage.
abstract: Macroscopic growths at geographically separated acid mine drainages (AMDs) exhibit distinct populations. Yet, local heterogeneities are poorly understood. To gain novel mechanistic insights into this, we used OMICs tools to profile microbial populations coexisting in a single pyrite gallery AMD (pH ∼2) in three distinct compartments: two from a stratified streamer (uppermost oxic and lowermost anoxic sediment-attached strata) and one from a submerged anoxic non-stratified mat biofilm. The communities colonising pyrite and those in the mature formations appear to be populated by the greatest diversity of bacteria and archaea (including 'ARMAN' (archaeal Richmond Mine acidophilic nano-organisms)-related), as compared with the known AMD, with ∼44.9% unclassified sequences. We propose that the thick polymeric matrix may provide a safety shield against the prevailing extreme condition and also a massive carbon source, enabling non-typical acidophiles to develop more easily. Only 1 of 39 species were shared, suggesting a high metabolic heterogeneity in local microenvironments, defined by the O2 concentration, spatial location and biofilm architecture. The suboxic mats, compositionally most similar to each other, are more diverse and active for S, CO2, CH4, fatty acid and lipopolysaccharide metabolism. The oxic stratum of the streamer, displaying a higher diversity of the so-called 'ARMAN'-related Euryarchaeota, shows a higher expression level of proteins involved in signal transduction, cell growth and N, H2, Fe, aromatic amino acids, sphingolipid and peptidoglycan metabolism. Our study is the first to highlight profound taxonomic and functional shifts in single AMD formations, as well as new microbial species and the importance of H2 in acidic suboxic macroscopic growths.
authors.affiliation: Departamento de Biología Funcional-IUBA, Universidad de Oviedo, Oviedo, Spain.
authors.forename: Celia
authors.initials: C
authors.lastname: Méndez-García
authors.affiliation: Departamento de Biología Funcional-IUBA, Universidad de Oviedo, Oviedo, Spain.
authors.forename: Victoria
authors.initials: V
authors.lastname: Mesa
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
authors.forename: Richard R
authors.initials: RR
authors.lastname: Sprenger
authors.affiliation: Ribocon GmbH, Bremen, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Richter
authors.affiliation: Chair of Systems and Synthetic Biology, Wageningen University, Wageningen, The Netherlands.
authors.forename: María Suárez
authors.initials: MS
authors.lastname: Diez
authors.affiliation: Department of Bioremediation, Bio-Iliberis R&D, Granada, Spain.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Solano
authors.affiliation: Department of Applied Biocatalysis, Consejo Superior de Investigaciones Científicas (CSIC), Institute of Catalysis, Madrid, Spain.
authors.forename: Rafael
authors.initials: R
authors.lastname: Bargiela
authors.affiliation: School of Biological Sciences, Bangor University, Gwynedd, UK.
authors.forename: Olga V
authors.initials: OV
authors.lastname: Golyshina
authors.affiliation: Departamento de Biología Funcional-IUBA, Universidad de Oviedo, Oviedo, Spain.
authors.forename: Ángel
authors.initials: Á
authors.lastname: Manteca
authors.affiliation: Consejo Superior de Investigaciones Científicas (CSIC), Estación Experimental del Zaidín, Granada, Spain.
authors.forename: Juan Luis
authors.initials: JL
authors.lastname: Ramos
authors.affiliation: Departamento de Explotación y Prospección de Minas-IUBA, Universidad de Oviedo, Oviedo, Spain.
authors.forename: José R
authors.initials: JR
authors.lastname: Gallego
authors.affiliation: Centro Nacional de Investigaciones Metalúrgicas, CSIC, Madrid, Spain.
authors.forename: Irene
authors.initials: I
authors.lastname: Llorente
authors.affiliation: Chair of Systems and Synthetic Biology, Wageningen University, Wageningen, The Netherlands.
authors.forename: Vitor A P
authors.initials: VA
authors.lastname: Martins dos Santos
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
authors.forename: Ole N
authors.initials: ON
authors.lastname: Jensen
authors.affiliation: Departamento de Biología Funcional-IUBA, Universidad de Oviedo, Oviedo, Spain.
authors.forename: Ana I
authors.initials: AI
authors.lastname: Peláez
authors.affiliation: Departamento de Biología Funcional-IUBA, Universidad de Oviedo, Oviedo, Spain.
authors.forename: Jesús
authors.initials: J
authors.lastname: Sánchez
authors.affiliation: Department of Applied Biocatalysis, Consejo Superior de Investigaciones Científicas (CSIC), Institute of Catalysis, Madrid, Spain.
authors.forename: Manuel
authors.initials: M
authors.lastname: Ferrer
mesh_terms: D001105:Archaea / Q000145:classification* / Q000235:genetics / Q000254:growth & development / Q000378:metabolism; D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000254:growth & development / Q000378:metabolism; D018441:Biofilms; D023281:Genomics; D006863:Hydrogen-Ion Concentration; D007501:Iron / Q000032:analysis; D008906:Mining; D020543:Proteome; D045483:Rivers; D013440:Sulfides / Q000032:analysis
chemical_list: D020543:Proteome; D013440:Sulfides; C011342:pyrite; D007501:Iron