title: Multi Locus Sequence Typing scheme for Acidithiobacillus caldus strain evaluation and differentiation.
abstract: Phenotypic, metabolic and genetic properties of several Acidithiobacillus caldus strains indicate the existence of as yet undefined levels of variation within the species. Inspite of this, intraspecies genetic diversity has not yet been explored in detail. In this study, the design and implementation of a Multi Locus Sequence Typing (MLST) scheme for At. caldus is described. This represents the first MLST-based study applied to industrial isolates of the species. Seven informative and discriminant MLST markers were selected using a sequence-driven approach and a custom-designed bioinformatic pipeline. The allelic profiles of thirteen At. caldus strains from diverse geographical origins and industrial settings were derived using this scheme. MLST-based population structure analysis indicated only moderate amounts of genetic diversity within the set of strains, further supporting their current assignment to a single species. Also, no clear evidence for geographical isolation could be derived from this study. However, the prevalence of sequence type 1 in heap leaching industrial settings support the view that bioprocess conditions and dynamics may have a strong influence on At. caldus (microbial) microdiversity patterns. The MLST scheme presented herein is a valuable tool for the identification and classification of strains of At. caldus for either ecological or evolutionary studies and possibly also for industrial monitoring purposes.
authors.affiliation: Fundación Ciencia & Vida, Santiago, Chile.
authors.forename: Harold
authors.initials: H
authors.lastname: Nuñez
authors.affiliation: National Center for Genomics, Proteomics and Bioinformatics of Chile, Santiago, Chile.
authors.forename: David
authors.initials: D
authors.lastname: Loyola
authors.affiliation: Fundación Ciencia & Vida, Santiago, Chile; Facultad de Ciencias Biologicas, Andres Bello University, Santiago, Chile.
authors.forename: Juan Pablo
authors.initials: JP
authors.lastname: Cárdenas
authors.affiliation: Fundación Ciencia & Vida, Santiago, Chile; Facultad de Ciencias Biologicas, Andres Bello University, Santiago, Chile.
authors.forename: David S
authors.initials: DS
authors.lastname: Holmes
authors.affiliation: School of Biological Sciences, University of Wales, LL572UW Bangor, UK.
authors.forename: D Barrie
authors.initials: DB
authors.lastname: Johnson
authors.affiliation: Fundación Ciencia & Vida, Santiago, Chile; Facultad de Ciencias Biologicas, Andres Bello University, Santiago, Chile. Electronic address: rquatrini@yahoo.com.ar.
authors.forename: Raquel
authors.initials: R
authors.lastname: Quatrini
mesh_terms: D042763:Acidithiobacillus / Q000145:classification* / Q000235:genetics*; D004783:Environmental Microbiology; D014644:Genetic Variation; D005843:Geography; D007218:Industrial Microbiology; D058885:Multilocus Sequence Typing / Q000379:methods*
keywords: Acidithiobacillus caldus; Industrial isolates; Multi Locus Sequence Typing (MLST); Phylogenetics; SNPs; Sequence types