Genomic evolution of the class Acidithiobacillia: deep-branching Proteobacteria living in extreme acidic conditions

Ana Moya-Beltrán; Simón  Beard; Camila  Rojas-Villalobos; Francisco Issotta; Yasna  Gallardo; Ricardo  Ulloa; Alejandra  Giaveno; Mauro Degli  Esposti; D. Barrie Johnson; Raquel Quatrini

doi:10.1038/s41396-021-00995-x

Genomic evolution of the class Acidithiobacillia: deep-branching Proteobacteria living in extreme acidic conditions

Ana Moya-Beltrán, Simón Beard, Camila Rojas-Villalobos, Francisco Issotta, Yasna Gallardo, Ricardo Ulloa, Alejandra Giaveno, Mauro Degli Esposti, D. Barrie Johnson, Raquel Quatrini

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Abstract

Members of the genus Acidithiobacillus, now ranked within the class Acidithiobacillia, are model bacteria for the study of chemolithotrophic energy conversion under extreme conditions. Knowledge of the genomic and taxonomic diversity of Acidithiobacillia is still limited. Here, we present a systematic analysis of nearly 100 genomes from the class sampled from a wide range of habitats. Some of these genomes are new and others have been reclassified on the basis of advanced genomic analysis, thus defining 19 Acidithiobacillia lineages ranking at different taxonomic levels. This work provides the most comprehensive classification and pangenomic analysis of this deep-branching class of Proteobacteria to date. The phylogenomic framework obtained illuminates not only the evolutionary past of this lineage, but also the molecular evolution of relevant aerobic respiratory proteins, namely the cytochrome bo3 ubiquinol oxidases.

Original language	English
Pages (from-to)	3221-3238
Number of pages	18
Journal	ISME Journal
Volume	15
Issue number	11
Early online date	18 May 2021
DOIs	https://doi.org/10.1038/s41396-021-00995-x
Publication status	Published - Nov 2021

Bibliographical note

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

Funder

Funding Information: Acknowledgements This work was supported the Agencia Nacional de Investigación y Desarrollo under Grants FONDECYT 1181251 (R.Q.), Programa de Apoyo a Centros con Financiamiento Basal AFB170004 (R.Q.), CONICYT-PFCHA/Doctorado Nacional/ 20171049 (A.M.B.), CONICYT-PFCHA/Doctorado Nacional/ 21160871 (F.I.), the ANID—Millennium Science Initiative Program— NCN17_093, granted by the Ministry of Economy, Development and Tourism from Chile (R.Q.), and Fundación Ciencia and Vida Hinge PostDoc Program (S.B.).

Funding

Acknowledgements This work was supported the Agencia Nacional de Investigaci\u00F3n y Desarrollo under Grants FONDECYT 1181251 (R.Q.), Programa de Apoyo a Centros con Financiamiento Basal AFB170004 (R.Q.), CONICYT-PFCHA/Doctorado Nacional/ 20171049 (A.M.B.), CONICYT-PFCHA/Doctorado Nacional/ 21160871 (F.I.), the ANID\u2014Millennium Science Initiative Program\u2014 NCN17_093, granted by the Ministry of Economy, Development and Tourism from Chile (R.Q.), and Fundaci\u00F3n Ciencia and Vida Hinge PostDoc Program (S.B.). M\u00F3nica Gonzales, Paulo Covarrubias and Hector Carrasco provided assistance with microbiological and molecular biology analyses at early stages of this study. Douglas Rawlings, Violaine Bonnefoy, Patricia Chiacharini, Jiri Kucera, Martin Mandl, Francisco Remonsellez, Pablo Ramirez Roca, and Mario Vera shared strains used in this study. We are grateful to Professor Aharon Oren (Hebrew University of Jerusalem Israel) for his help and advice on the projected names of novel bacterial genera and species. The authors thank the authorities of the Provincial Thermal Baths Agency (EPROTEN) and the Directorate of Protected Natural Areas (ANP) of the province of Neuqu\u00E9n Argentina for allowing access and sampling in the Copahue-Caviahue Provincial Park and Ing. Rub\u00E9n Vargas (alias Caniche) for guidance during ascent to the Copahue volcano.

Funders	Funder number
Agencia Nacional de Investigación y Desarrollo	NCN17_093
Comisión Nacional de Investigación Científica y Tecnológica
Agencia Nacional de Investigación y Desarrollo	21160871
Fundacion Ciencia y Vida
Programa de Apoyo a Centros con Financiamiento Basal	AFB170004
Fondo Nacional de Desarrollo Científico y Tecnológico	1181251

ASJC Scopus subject areas

Microbiology
Ecology, Evolution, Behavior and Systematics

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10.1038/s41396-021-00995-xLicence: CC BY

PublishedFinal published version, 4.8 MBLicence: CC BY

Cite this

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abstract = "Members of the genus Acidithiobacillus, now ranked within the class Acidithiobacillia, are model bacteria for the study of chemolithotrophic energy conversion under extreme conditions. Knowledge of the genomic and taxonomic diversity of Acidithiobacillia is still limited. Here, we present a systematic analysis of nearly 100 genomes from the class sampled from a wide range of habitats. Some of these genomes are new and others have been reclassified on the basis of advanced genomic analysis, thus defining 19 Acidithiobacillia lineages ranking at different taxonomic levels. This work provides the most comprehensive classification and pangenomic analysis of this deep-branching class of Proteobacteria to date. The phylogenomic framework obtained illuminates not only the evolutionary past of this lineage, but also the molecular evolution of relevant aerobic respiratory proteins, namely the cytochrome bo3 ubiquinol oxidases.",

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Genomic evolution of the class Acidithiobacillia: deep-branching Proteobacteria living in extreme acidic conditions

Abstract

Bibliographical note

Funder

Funding

ASJC Scopus subject areas

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