Examinando por Autor "Issotta, Francisco"
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Ítem Draft genome sequence of chloride-tolerant Leptospirillum ferriphilum Sp-Cl from industrial bioleaching operations in northern Chile(BIOMED CENTRAL, 2016-02) Issotta, Francisco; Galleguillos, Pedro A.; Moya-Beltrán, Ana; Davis-Belmar, Carol S.; Rautenbach, George; Covarrubias, Paulo C.; Acosta, Mauricio; Ossandon, Francisco J.; Contador, Yasna; Holmes, David S.; Marín-Eliantonio, Sabrina; Quatrini, Raquel; Demergasso, CeciliaLeptospirillum ferriphilum Sp-Cl is a Gram negative, thermotolerant, curved, rod- shaped bacterium, isolated from an industrial bioleaching operation in northern Chile, where chalcocite is the major copper mineral and copper hydroxychloride atacamite is present in variable proportions in the ore. This strain has unique features as compared to the other members of the species, namely resistance to elevated concentrations of chloride, sulfate and metals. Basic microbiological features and genomic properties of this biotechnologically relevant strain are described in this work. The 2,475,669 bp draft genome is arranged into 74 scaffolds of 74 contigs. A total of 48 RNA genes and 2,834 protein coding genes were predicted from its annotation; 55 % of these were assigned a putative function. Release of the genome sequence of this strain will provide further understanding of the mechanisms used by acidophilic bacteria to endure high osmotic stress and high chloride levels and of the role of chloride-tolerant iron-oxidizers in industrial bioleaching operations.Ítem Draft genome sequence of the nominated type strain of "Ferrovum myxofaciens," an acidophilic, iron-oxidizing betaproteobacterium(American Society for Microbiology, 2014) Moya-Beltrán, Ana; Cárdenas, Juan Pablo; Covarrubias, Paulo C.; Issotta, Francisco; Ossandon, Francisco J.; Grail, Barry M.; Holmes, David S.; Quatrini, Raquel; Johnson, D. BarrieFerrovum myxofaciens” is an iron-oxidizing betaproteobacterium with widespread distribution in acidic low-temperature en vironments, such as acid mine drainage streams. Here, we describe the genomic features of this novel acidophile and investigate the relevant metabolic pathways that enable its survival in these environments.Ítem Genomic evolution of the class Acidithiobacillia: deep-branching Proteobacteria living in extreme acidic conditions(Springer Nature, 2021-11) Moya-Beltrán, Ana; Beard, Simón; Rojas-Villalobos, Camila; Issotta, Francisco; Gallardo, Yasna; Ulloa, Ricardo; Giaveno, Alejandra; Degli Esposti, Mauro; D. Barrie, Johnson; Quatrini, RaquelMembers 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. © 2021, The Author(s).Ítem Genomic evolution of the class Acidithiobacillia: deep-branching Proteobacteria living in extreme acidic conditions(2021-11) Moya-Beltrán, Ana; Beard, Simón; Rojas-Villalobos, Camila; Issotta, Francisco; Gallardo, Yasna; Ulloa, Ricardo; Giaveno, Alejandra; Degli Esposti, Mauro; Johnson, D. Barrios; Quatrini, RaquelMembers 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.Ítem Insights into the biology of acidophilic members of the Acidiferrobacteraceae family derived from comparative genomic analyses(Elsevier Masson SAS, 2018-12) Issotta, Francisco; Moya-Beltrán, Ana; Mena, Cristóbal; Covarrubias, Paulo C.; Thyssen, Christian; Bellenberg, Sören; Sand, Wolfgangd; Quatrini, Raquel; Vera, MarioThe family Acidiferrobacteraceae (order Acidiferrobacterales) currently contains Gram negative, neutrophilic sulfur oxidizers such as Sulfuricaulis and Sulfurifustis, as well as acidophilic iron and sulfur oxidizers belonging to the Acidiferrobacter genus. The diversity and taxonomy of the genus Acidiferrobacter has remained poorly explored. Although several metagenome and bioleaching studies have identified its presence worldwide, only two strains, namely Acidiferrobacter thiooxydans DSM 2932T, and Acidiferrobacter spp. SP3/III have been isolated and made publically available. Using 16S rRNA sequence data publically available for the Acidiferrobacteraceae, we herein shed light into the molecular taxonomy of this family. Results obtained support the presence of three clades Acidiferrobacter, Sulfuricaulis and Sulfurifustis. Genomic analyses of the genome sequences of A. thiooxydansT and Acidiferrobacter spp. SP3/III indicate that ANI relatedness between the SPIII/3 strain and A. thiooxydansT is below 95–96%, supporting the classification of strain SP3/III as a new species within this genus. In addition, approximately 70% of Acidiferrobacter sp. SPIII/3 predicted genes have a conserved ortholog in A. thiooxydans strains. A comparative analysis of iron, sulfur oxidation pathways, genome plasticity and cell-cell communication mechanisms of Acidiferrobacter spp. are also discussed. © 2018 The AuthorsÍtem Molecular systematics of the Genus Acidithiobacillus: Insights into the phylogenetic structure and diversification of the taxon(Frontiers Media S.A., 2017-01) Nuñez, Harold; Moya Beltrán, Ana; Covarrubias, Paulo C.; Issotta, Francisco; Cárdenas, Juan Pablo; González, Mónica; Atavales, Joaquín; Acuña, Lillian G.; Johnson, D.Barrie; Quatrini, RaquelThe acidithiobacilli are sulfur-oxidizing acidophilic bacteria that thrive in both natural and anthropogenic low pH environments. They contribute to processes that lead to the generation of acid rock drainage in several different geoclimatic contexts, and their properties have long been harnessed for the biotechnological processing of minerals. Presently, the genus is composed of seven validated species, described between 1922 and 2015: Acidithiobacillus thiooxidans, A. ferrooxidans, A. albertensis, A. caldus, A. ferrivorans, A. ferridurans, and A. ferriphilus. However, a large number of Acidithiobacillus strains and sequence clones have been obtained from a variety of ecological niches over the years, and many isolates are thought to vary in phenotypic properties and cognate genetic traits. Moreover, many isolates remain unclassified and several conflicting specific assignments muddle the picture from an evolutionary standpoint. Here we revise the phylogenetic relationships within this species complex and determine the phylogenetic species boundaries using three different typing approaches with varying degrees of resolution: 16S rRNA gene-based ribotyping, oligotyping, and multi-locus sequencing analysis (MLSA). To this end, the 580 16S rRNA gene sequences affiliated to the Acidithiobacillus spp. were collected from public and private databases and subjected to a comprehensive phylogenetic analysis. Oligotyping was used to profile high-entropy nucleotide positions and resolve meaningful differences between closely related strains at the 16S rRNA gene level. Due to its greater discriminatory power, MLSA was used as a proxy for genome-wide divergence in a smaller but representative set of strains. Results obtained indicate that there is still considerable unexplored diversity within this genus. At least six new lineages or phylotypes, supported by the different methods used herein, are evident within the Acidithiobacillus species complex. Although the diagnostic characteristics of these subgroups of strains are as yet unresolved, correlations to specific metadata hint to the mechanisms behind econiche-driven divergence of some of the species/phylotypes identified. The emerging phylogenetic structure for the genus outlined in this study can be used to guide isolate selection for future population genomics and evolutionary studies in this important acidophile model. © 2017 Nuñez, Moya-Beltrán, Covarrubias, Issotta, Cárdenas, González, Atavales, Acuña, Johnson and Quatrini.Ítem Molecular systematics of the Genus Acidithiobacillus: Insights into the phylogenetic structure and diversification of the taxon(Frontiers Media S.A., 2017-01) Nuñez, Harold; Moya-Beltrán; Ana; Covarrubias, Paulo C.; Issotta, Francisco; Cárdenas, Juan Pablo; González, Mónica; Atavales, Joaquín; Acuña, Lillian G.; Johnson, D. Barrie; Quatrini, RaquelThe acidithiobacilli are sulfur-oxidizing acidophilic bacteria that thrive in both natural and anthropogenic low pH environments. They contribute to processes that lead to the generation of acid rock drainage in several different geoclimatic contexts, and their properties have long been harnessed for the biotechnological processing of minerals. Presently, the genus is composed of seven validated species, described between 1922 and 2015: Acidithiobacillus thiooxidans, A. ferrooxidans, A. albertensis, A. caldus, A. ferrivorans, A. ferridurans, and A. ferriphilus. However, a large number of Acidithiobacillus strains and sequence clones have been obtained from a variety of ecological niches over the years, and many isolates are thought to vary in phenotypic properties and cognate genetic traits. Moreover, many isolates remain unclassified and several conflicting specific assignments muddle the picture from an evolutionary standpoint. Here we revise the phylogenetic relationships within this species complex and determine the phylogenetic species boundaries using three different typing approaches with varying degrees of resolution: 16S rRNA gene-based ribotyping, oligotyping, and multi-locus sequencing analysis (MLSA). To this end, the 580 16S rRNA gene sequences affiliated to the Acidithiobacillus spp. were collected from public and private databases and subjected to a comprehensive phylogenetic analysis. Oligotyping was used to profile high-entropy nucleotide positions and resolve meaningful differences between closely related strains at the 16S rRNA gene level. Due to its greater discriminatory power, MLSA was used as a proxy for genome-wide divergence in a smaller but representative set of strains. Results obtained indicate that there is still considerable unexplored diversity within this genus. At least six new lineages or phylotypes, supported by the different methods used herein, are evident within the Acidithiobacillus species complex. Although the diagnostic characteristics of these subgroups of strains are as yet unresolved, correlations to specific metadata hint to the mechanisms behind econiche-driven divergence of some of the species/phylotypes identified. The emerging phylogenetic structure for the genus outlined in this study can be used to guide isolate selection for future population genomics and evolutionary studies in this important acidophile model. © 2017 Nuñez, Moya-Beltrán, Covarrubias, Issotta, Cárdenas, González, Atavales, Acuña, Johnson and Quatrini.