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^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

32 Scopus citations

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
DOIs	https://doi.org/10.1038/s41396-021-00995-x
State	Published - 2021

Bibliographical note

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.). Mónica 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 Neuquén Argentina for allowing access and sampling in the Copahue-Caviahue Provincial Park and Ing. Rubén Vargas (alias Caniche) for guidance during ascent to the Copahue volcano.

Publisher Copyright:
© 2021, The Author(s).

ASJC Scopus subject areas

Microbiology
Ecology, Evolution, Behavior and Systematics

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

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.",

author = "Ana Moya-Beltr{\'a}n and Sim{\'o}n Beard and Camila Rojas-Villalobos and Francisco Issotta and Yasna Gallardo and Ricardo Ulloa and Alejandra Giaveno and {Degli Esposti}, Mauro and Johnson, {D. Barrie} and Raquel Quatrini",

note = "Funding Information: Acknowledgements This work was supported the Agencia Nacional de Investigaci{\'o}n 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 Fundaci{\'o}n Ciencia and Vida Hinge PostDoc Program (S.B.). M{\'o}nica 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{\'e}n Argentina for allowing access and sampling in the Copahue-Caviahue Provincial Park and Ing. Rub{\'e}n Vargas (alias Caniche) for guidance during ascent to the Copahue volcano. Publisher Copyright: {\textcopyright} 2021, The Author(s).",

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doi = "10.1038/s41396-021-00995-x",

language = "English",

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AU - Issotta, Francisco

AU - Gallardo, Yasna

AU - Ulloa, Ricardo

AU - Giaveno, Alejandra

AU - Degli Esposti, Mauro

AU - Johnson, D. Barrie

AU - Quatrini, Raquel

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AB - 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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ER -

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

Abstract

Bibliographical note

ASJC Scopus subject areas

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