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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
Architecture and gene repertoire of the flexible genome of the extreme acidophile Acidithiobacillus caldus
PLoS ONE, Volume 8, No. 11, Article e78237, Year 2013
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Description
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. Principal Findings: 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. Significance: 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. © 2013 Acuña et al.
Available Materials
https://efashare.b-cdn.net/share/pmc/articles/PMC3826726/bin/pone.0078237.s001.xlsx
https://efashare.b-cdn.net/share/pmc/articles/PMC3826726/bin/pone.0078237.s002.xlsx
https://efashare.b-cdn.net/share/pmc/articles/PMC3826726/bin/pone.0078237.s003.xlsx
https://efashare.b-cdn.net/share/pmc/articles/PMC3826726/bin/pone.0078237.s004.xlsx
https://efashare.b-cdn.net/share/pmc/articles/PMC3826726/bin/pone.0078237.s005.xlsx
https://efashare.b-cdn.net/share/pmc/articles/PMC3826726/bin/pone.0078237.s006.xlsx
https://efashare.b-cdn.net/share/pmc/articles/PMC3826726/bin/pone.0078237.s007.xlsx
Authors & Co-Authors
Acuña, Lillian G.
Chile, Santiago
Fundacion Ciencia Para la Vida
Chile, Santiago
Universidad Andrés Bello
Cárdenas, Juan Pablo
Chile, Santiago
Fundacion Ciencia Para la Vida
Chile, Santiago
Universidad Andrés Bello
Covarrubias, Paulo C.
Chile, Santiago
Fundacion Ciencia Para la Vida
Chile, Santiago
Universidad Andrés Bello
Haristoy, Juan José
Chile, Santiago
Fundacion Ciencia Para la Vida
Flores, Rodrigo
Chile, Santiago
Fundacion Ciencia Para la Vida
Nuñez, Harold
Chile, Santiago
Fundacion Ciencia Para la Vida
Riadi, Gonzalo
Chile, Talca
Universidad de Talca
Shmaryahu, Amir
Chile, Santiago
Fundacion Ciencia Para la Vida
Valdés, Jorge
Chile, Santiago
Fraunhofer Chile Research Foundation
Dopson, Mark
Sweden, Kalmar
Linnaeus University, Kalmar
Rawlings, Douglas Eric
South Africa, Stellenbosch
Stellenbosch University
Banfield, Jillian F.
United States, Berkeley
University of California, Berkeley
Holmes, David S.
Chile, Santiago
Fundacion Ciencia Para la Vida
Chile, Santiago
Universidad Andrés Bello
Quatrini, Raquel
Chile, Santiago
Fundacion Ciencia Para la Vida
Chile, Santiago
Universidad Andrés Bello
Statistics
Citations: 58
Authors: 14
Affiliations: 7
Identifiers
Doi:
10.1371/journal.pone.0078237
e-ISSN:
19326203
Research Areas
Genetics And Genomics
Study Design
Cross Sectional Study