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

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

doi:10.1038/s41396-021-00995-x

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.

Highlights

IntroductionMembers of the genus Acidithiobacillus are among the most widely studied extremely acidophilic prokaryotes [1]
Novel results supported the assignment of Acidithiobacillus sulfuriphilus strain CJ-2, A. caldus strains, and Acidithiobacillus-like spp
The functional profile of iron/sulfur-oxidizing acidithiobacilli partially overlaps that of their deepest branching relative, ‘Ambacidithiobacillus sulfuriphilus’, especially in regard to traits of energy conservation, such as the combined presence of type 1 membrane hydrogenases and nitrogenase

Summary

Introduction

Members of the genus Acidithiobacillus are among the most widely studied extremely acidophilic prokaryotes [1]. The genus comprises Gram-negative autotrophic bacteria that are obligate acidophiles. While all Acidithiobacillus spp. can catalyze the dissimilatory oxidation of sulfur compounds, some members of the genus grow by oxidizing ferrous iron, using oxygen as electron acceptor [2]. These combined physiological traits are used extensively in biotechnological applications, including the biomining of metal sulfide ores [3]. The acidithiobacilli are model bacteria for the study of chemolithotrophic energy conversion reactions and pathways under acidic conditions They have provided key insights into the evolution of aerobic respiration [5]

Objectives

Methods

Results

Conclusion