title: Architecture and gene repertoire of the flexible genome of the extreme acidophile Acidithiobacillus caldus.
abstract: BACKGROUND
  Acidithiobacillus caldus is a sulfur oxidizing extreme acidophile and the only known mesothermophile within the Acidithiobacillales. As such, it is one of the preferred microbes for mineral bioprocessing at moderately high temperatures. In this study, we explore the genomic diversity of A. caldus strains using a combination of bioinformatic and experimental techniques, thus contributing first insights into the elucidation of the species pangenome.
  
  
  RESULTS
  Comparative sequence analysis of A. caldus ATCC 51756 and SM-1 indicate that, despite sharing a conserved and highly syntenic genomic core, both strains have unique gene complements encompassing nearly 20% of their respective genomes. The differential gene complement of each strain is distributed between the chromosomal compartment, one megaplasmid and a variable number of smaller plasmids, and is directly associated to a diverse pool of mobile genetic elements (MGE). These include integrative conjugative and mobilizable elements, genomic islands and insertion sequences. Some of the accessory functions associated to these MGEs have been linked previously to the flexible gene pool in microorganisms inhabiting completely different econiches. Yet, others had not been unambiguously mapped to the flexible gene pool prior to this report and clearly reflect strain-specific adaption to local environmental conditions.
  
  
  CONCLUSIONS
  For many years, and because of DNA instability at low pH and recurrent failure to genetically transform acidophilic bacteria, gene transfer in acidic environments was considered negligible. Findings presented herein imply that a more or less conserved pool of actively excising MGEs occurs in the A. caldus population and point to a greater frequency of gene exchange in this econiche than previously recognized. Also, the data suggest that these elements endow the species with capacities to withstand the diverse abiotic and biotic stresses of natural environments, in particular those associated with its extreme econiche.
authors.affiliation: Fundación Ciencia & Vida, Santiago, Chile ; Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile.
authors.forename: Lillian G
authors.initials: LG
authors.lastname: Acuña
authors.forename: Juan Pablo
authors.initials: JP
authors.lastname: Cárdenas
authors.forename: Paulo C
authors.initials: PC
authors.lastname: Covarrubias
authors.forename: Juan José
authors.initials: JJ
authors.lastname: Haristoy
authors.forename: Rodrigo
authors.initials: R
authors.lastname: Flores
authors.forename: Harold
authors.initials: H
authors.lastname: Nuñez
authors.forename: Gonzalo
authors.initials: G
authors.lastname: Riadi
authors.forename: Amir
authors.initials: A
authors.lastname: Shmaryahu
authors.forename: Jorge
authors.initials: J
authors.lastname: Valdés
authors.forename: Mark
authors.initials: M
authors.lastname: Dopson
authors.forename: Douglas E
authors.initials: DE
authors.lastname: Rawlings
authors.forename: Jillian F
authors.initials: JF
authors.lastname: Banfield
authors.forename: David S
authors.initials: DS
authors.lastname: Holmes
authors.forename: Raquel
authors.initials: R
authors.lastname: Quatrini
mesh_terms: D042763:Acidithiobacillus / Q000235:genetics* / Q000378:metabolism; D001426:Bacterial Proteins / Q000235:genetics; D019295:Computational Biology; D003227:Conjugation, Genetic; D004251:DNA Transposable Elements / Q000235:genetics*; D016680:Genome, Bacterial; D010957:Plasmids / Q000235:genetics; D013455:Sulfur / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D004251:DNA Transposable Elements; D013455:Sulfur