Browsing by Author "Rojas-Villalobos, Camila"

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    Acidithiobacillia class members originating at sites within the Pacific Ring of Fire and other tectonically active locations and description of the novel genus 'Igneacidithiobacillus'
    (2024) Arisan, Dilanaz; Moya-Beltran, Ana; Rojas-Villalobos, Camila; Issotta, Francisco; Castro, Matias; Ulloa, Ricardo; Chiacchiarini, Patricia A.; Diez, Beatriz; Martin, Alberto J. M.; Nancucheo, Ivan; Giaveno, Alejandra; Johnson, D. Barrie; Quatrini, Raquel
    Recent studies have expanded the genomic contours of the Acidithiobacillia, highlighting important lacunae in our comprehension of the phylogenetic space occupied by certain lineages of the class. One such lineage is 'Igneacidithiobacillus', a novel genus-level taxon, represented by 'Igneacidithiobacillus copahuensis' VAN18-1(T) as its type species, along with two other uncultivated metagenome-assembled genomes (MAGs) originating from geothermally active sites across the Pacific Ring of Fire. In this study, we investigate the genetic and genomic diversity, and the distribution patterns of several uncharacterized Acidithiobacillia class strains and sequence clones, which are ascribed to the same 16S rRNA gene sequence clade. By digging deeper into this data and contributing to novel MAGs emerging from environmental studies in tectonically active locations, the description of this novel genus has been consolidated. Using state-of-the-art genomic taxonomy methods, we added to already recognized taxa, an additional four novel Candidate (Ca.) species, including 'Ca. Igneacidithiobacillus chanchocoensis' (mCHCt20-1(TS)), 'Igneacidithiobacillus siniensis' (S30A2(T)), 'Ca. Igneacidithiobacillus taupoensis' (TVZ-G3 (TS)), and 'Ca. Igneacidithiobacillus waiarikiensis' (TVZ-G4 (TS)). Analysis of published data on the isolation, enrichment, cultivation, and preliminary microbiological characterization of several of these unassigned or misassigned strains, along with the type species of the genus, plus the recoverable environmental data from metagenomic studies, allowed us to identify habitat preferences of these taxa. Commonalities and lineage-specific adaptations of the seven species of the genus were derived from pangenome analysis and comparative genomic metabolic reconstruction. The findings emerging from this study lay the groundwork for further research on the ecology, evolution, and biotechnological potential of the novel genus 'Igneacidithiobacillus'.
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    The phylogeny of Acetobacteraceae: photosynthetic traits and deranged respiratory enzymes
    (2023) Degli Esposti, Mauro; Guerrero, Gabriela; Rogel, Marco A.; Issotta, Francisco; Rojas-Villalobos, Camila; Quatrini, Raquel; Martinez-Romero, Esperanza
    We present here a comprehensive phylogenomic analysis of Acetobacteraceae, a vast group of alphaproteobacteria that has been widely studied for their economic importance. Our results indicate that the ancestor of Acetobacteraceae most likely was photosynthetic and evolved via a progressive transition from versatile photoferrotrophy to the incomplete oxidation of organic substrates defining acetous physiology. Vestigial signs of photosynthetic carotenoid metabolism are present in non-photosynthetic acetous taxa that have lost cytochrome oxidase, while their sister taxa retain such traits. The dominant terminal oxidase of acetous bacteria, the bo(3) ubiquinol oxidase, is derived from duplication and diversification of operons present in Acidocella taxa that have lost photosynthesis. We analyzed the bioenergetic traits that can compensate for the electron transfer function of photosynthetic reaction centers or constitute alternative pathways for the oxidoreduction of c-type cytochromes, such as iron oxidation. The latter pathway bypasses the deranged cytochrome bc(1) complex that is characteristically present in acidophilic taxa due to the loss of conserved ligands in both the Rieske iron-sulfur protein and cytochrome b subunit. The deranged or non-functional bc(1) complex may be retained for its structural role in stabilizing Complex I. The combination of our phylogenetic analysis with in-depth functional evaluations indicates that the order Acetobacterales needs to be emended to include three families: Acetobacteraceae sensu stricto, Roseomonadaceae fam. nov., and Acidocellaceae fam. nov.