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David S Holmes - One of the best experts on this subject based on the ideXlab platform.
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draft genome sequence of the type strain of the sulfur oxidizing acidophile Acidithiobacillus albertensis dsm 14366
2017Co-Authors: Matias Castro, Juan Pablo Cárdenas, Paulo C. Covarrubias, Lillian G. Acuña, Harold Nuñez, Ana Moyabeltran, Monica Gonzalez, Francisco Issotta, Gonzalo Encina, David S HolmesAbstract:Acidithiobacillus albertensis is an extremely acidophilic, mesophilic, obligatory autotrophic sulfur-oxidizer, with potential importance in the bioleaching of sulfidic metal ores, first described in the 1980s. Here we present the draft genome sequence of Acidithiobacillus albertensis DSM 14366T, thereby both filling a long-standing gap in the genomics of the acidithiobacilli, and providing further insight into the understanding of the biology of the non iron-oxidizing members of the Acidithiobacillus genus. The assembled genome is 3,1 Mb, and contains 47 tRNAs, tmRNA gene and 2 rRNA operons, along with 3149 protein-coding predicted genes. The Whole Genome Shotgun project was deposited in DDBJ/EMBL/GenBank under the accession MOAD00000000.
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draft genome sequence of the extremely acidophilic bacterium Acidithiobacillus caldus atcc 51756 reveals metabolic versatility in the genus Acidithiobacillus
2009Co-Authors: Jorge Valdés, Mark Dopson, Raquel Quatrini, Kevin B Hallberg, Pablo D T Valenzuela, David S HolmesAbstract:Acidithiobacillus caldus is an extremely acidophilic, moderately thermophilic, chemolithoautotrophic gammaproteobacterium that derives energy from the oxidation of sulfur and reduced inorganic sulfur compounds. Here we present the draft genome sequence of Acidithiobacillus caldus ATCC 51756 (the type strain of the species), which has permitted the prediction of genes for survival in extremely acidic environments, including genes for sulfur oxidation and nutrient assimilation.
Lillian G. Acuña - One of the best experts on this subject based on the ideXlab platform.
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a dna segment encoding the anticodon stem loop of trna determines the specific recombination of integrative conjugative elements in Acidithiobacillus species
2018Co-Authors: Andres Castillo, Lillian G. Acuña, Raquel Quatrini, Mario Tello, Kenneth Ringwald, Omar OrellanaAbstract:ABSTRACTHorizontal gene transfer is crucial for the adaptation of microorganisms to environmental cues. The acidophilic, bioleaching bacterium Acidithiobacillus ferrooxidans encodes an integrative-conjugative genetic element (ICEAfe1) inserted in the gene encoding a tRNAAla. This genetic element is actively excised from the chromosome upon induction of DNA damage. A similar genetic element (ICEAcaTY.2) is also found in an equivalent position in the genome of Acidithiobacillus caldus. The local genomic context of both mobile genetic elements is highly syntenous and the cognate integrases are well conserved. By means of site directed mutagenesis, target site deletions and in vivo integrations assays in the heterologous model Escherichia coli, we assessed the target sequence requirements for site-specific recombination to be catalyzed by these integrases. We determined that each enzyme recognizes a specific small DNA segment encoding the anticodon stem/loop of the tRNA as target site and that specific positi...
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draft genome sequence of the type strain of the sulfur oxidizing acidophile Acidithiobacillus albertensis dsm 14366
2017Co-Authors: Matias Castro, Juan Pablo Cárdenas, Paulo C. Covarrubias, Lillian G. Acuña, Harold Nuñez, Ana Moyabeltran, Monica Gonzalez, Francisco Issotta, Gonzalo Encina, David S HolmesAbstract:Acidithiobacillus albertensis is an extremely acidophilic, mesophilic, obligatory autotrophic sulfur-oxidizer, with potential importance in the bioleaching of sulfidic metal ores, first described in the 1980s. Here we present the draft genome sequence of Acidithiobacillus albertensis DSM 14366T, thereby both filling a long-standing gap in the genomics of the acidithiobacilli, and providing further insight into the understanding of the biology of the non iron-oxidizing members of the Acidithiobacillus genus. The assembled genome is 3,1 Mb, and contains 47 tRNAs, tmRNA gene and 2 rRNA operons, along with 3149 protein-coding predicted genes. The Whole Genome Shotgun project was deposited in DDBJ/EMBL/GenBank under the accession MOAD00000000.
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molecular systematics of the genus Acidithiobacillus insights into the phylogenetic structure and diversification of the taxon
2017Co-Authors: Harold Nuñez, Juan Pablo Cárdenas, Paulo C. Covarrubias, Lillian G. Acuña, Barrie D. Johnson, Ana Moyabeltran, Monica Gonzalez, Francisco Issotta, Joaquin Atavales, Raquel QuatriniAbstract:The 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.
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Architecture and gene repertoire of the flexible genome of the extreme acidophile Acidithiobacillus caldus.
2013Co-Authors: Lillian G. Acuña, Juan Pablo Cárdenas, Paulo C. Covarrubias, Amir Shmaryahu, Juan José Haristoy, Rodrigo Flores, Harold Nuñez, Gonzalo Riadi, Jorge Valdés, Mark DopsonAbstract:CITATION: Acuna, L. G. et al. 2013. Architecture and gene repertoire of the flexible genome of the extreme acidophile Acidithiobacillus caldus. PLoS ONE, 8(11):e78237, doi:10.1371/journal.pone.0078237.
Matias Castro - One of the best experts on this subject based on the ideXlab platform.
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Acidithiobacillus sulfuriphilus sp nov an extremely acidophilic sulfur oxidizing chemolithotroph isolated from a neutral ph environment
2019Co-Authors: Ana Moyabeltran, Matias Castro, Raquel Quatrini, Carmen Falagan, Barrie D. JohnsonAbstract:The genus Acidithiobacillus currently includes seven species with validly published names, which fall into two major groups, those that can oxidize ferrous iron and those that do not. All seven species can use zero-valent sulfur and reduced sulfur oxy-anions as electron donors, are obligately chemolithotrophic and acidophilic bacteria with pH growth optima below 3.0. The 16S rRNA gene of a novel strain (CJ-2T) isolated from circum-neutral pH mine drainage showed 95–97 % relatedness to members of the genus Acidithiobacillus . Digital DNA–DNA hybridization (dDDH) values between strains and whole-genome pairwise comparisons between the CJ-2T strain and the reference genomes available for members of the genus Acidithiobacillus confirmed that CJ-2Trepresents a novel species of this genus. CJ-2T is a strict aerobe, oxidizes zero-valent sulfur and reduced inorganic sulfur compounds but does not use ferrous iron or hydrogen as electron donors. The isolate is mesophilic (optimum growth temperature 25–28 °C) and extremely acidophilic (optimum growth pH 3.0), though its pH optimum and maximum were significantly higher than those of non-iron-oxidising acidithiobacilli with validly published names. The major fatty acids of CJ-2T were C18 : 1ω7c, C:16 : 1ω7c/iso-C15 : 0 2-OH, C16 : 0 and C19 : 0 cyclo ω8c and the major respiratory quinone present was Q8. The name Acidithiobacillus sulfuriphilus sp. nov. is proposed, the type strain is CJ-2T (=DSM 105150T=KCTC 4683T).
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biofilm formation by the acidophile bacterium Acidithiobacillus thiooxidans involves c di gmp pathway and pel exopolysaccharide
2018Co-Authors: Mauricio Diaz, Matias Castro, Sylvia V Copaja, Nicolas GuilianiAbstract:Acidophile bacteria belonging to the Acidithiobacillus genus are pivotal players for the bioleaching of metallic values such as copper. Cell adherence to ores and biofilm formation, mediated by the production of extracellular polymeric substances, strongly favors bioleaching activity. In recent years, the second messenger cyclic diguanylate (c-di-GMP) has emerged as a central regulator for biofilm formation in bacteria. C-di-GMP pathways have been reported in different Acidithiobacillus species; however, c-di-GMP effectors and signal transduction networks are still largely uncharacterized in these extremophile species. Here we investigated Pel exopolysaccharide and its role in biofilm formation by sulfur-oxidizing species Acidithiobacillus thiooxidans. We identified 39 open reading frames (ORFs) encoding proteins involved in c-di-GMP metabolism and signal transduction, including the c-di-GMP effector protein PelD, a structural component of the biosynthesis apparatus for Pel exopolysaccharide production. We found that intracellular c-di-GMP concentrations and transcription levels of pel genes were higher in At. thiooxidans biofilm cells compared to planktonic ones. By developing an At. thiooxidans ΔpelD null-mutant strain we revealed that Pel exopolysaccharide is involved in biofilm structure and development. Further studies are still necessary to understand how Pel biosynthesis is regulated in Acidithiobacillus species, nevertheless these results represent the first characterization of a c-di-GMP effector protein involved in biofilm formation by acidophile species.
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draft genome sequence of the type strain of the sulfur oxidizing acidophile Acidithiobacillus albertensis dsm 14366
2017Co-Authors: Matias Castro, Juan Pablo Cárdenas, Paulo C. Covarrubias, Lillian G. Acuña, Harold Nuñez, Ana Moyabeltran, Monica Gonzalez, Francisco Issotta, Gonzalo Encina, David S HolmesAbstract:Acidithiobacillus albertensis is an extremely acidophilic, mesophilic, obligatory autotrophic sulfur-oxidizer, with potential importance in the bioleaching of sulfidic metal ores, first described in the 1980s. Here we present the draft genome sequence of Acidithiobacillus albertensis DSM 14366T, thereby both filling a long-standing gap in the genomics of the acidithiobacilli, and providing further insight into the understanding of the biology of the non iron-oxidizing members of the Acidithiobacillus genus. The assembled genome is 3,1 Mb, and contains 47 tRNAs, tmRNA gene and 2 rRNA operons, along with 3149 protein-coding predicted genes. The Whole Genome Shotgun project was deposited in DDBJ/EMBL/GenBank under the accession MOAD00000000.
Harold Nuñez - One of the best experts on this subject based on the ideXlab platform.
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draft genome sequence of the type strain of the sulfur oxidizing acidophile Acidithiobacillus albertensis dsm 14366
2017Co-Authors: Matias Castro, Juan Pablo Cárdenas, Paulo C. Covarrubias, Lillian G. Acuña, Harold Nuñez, Ana Moyabeltran, Monica Gonzalez, Francisco Issotta, Gonzalo Encina, David S HolmesAbstract:Acidithiobacillus albertensis is an extremely acidophilic, mesophilic, obligatory autotrophic sulfur-oxidizer, with potential importance in the bioleaching of sulfidic metal ores, first described in the 1980s. Here we present the draft genome sequence of Acidithiobacillus albertensis DSM 14366T, thereby both filling a long-standing gap in the genomics of the acidithiobacilli, and providing further insight into the understanding of the biology of the non iron-oxidizing members of the Acidithiobacillus genus. The assembled genome is 3,1 Mb, and contains 47 tRNAs, tmRNA gene and 2 rRNA operons, along with 3149 protein-coding predicted genes. The Whole Genome Shotgun project was deposited in DDBJ/EMBL/GenBank under the accession MOAD00000000.
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molecular systematics of the genus Acidithiobacillus insights into the phylogenetic structure and diversification of the taxon
2017Co-Authors: Harold Nuñez, Juan Pablo Cárdenas, Paulo C. Covarrubias, Lillian G. Acuña, Barrie D. Johnson, Ana Moyabeltran, Monica Gonzalez, Francisco Issotta, Joaquin Atavales, Raquel QuatriniAbstract:The 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.
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Architecture and gene repertoire of the flexible genome of the extreme acidophile Acidithiobacillus caldus.
2013Co-Authors: Lillian G. Acuña, Juan Pablo Cárdenas, Paulo C. Covarrubias, Amir Shmaryahu, Juan José Haristoy, Rodrigo Flores, Harold Nuñez, Gonzalo Riadi, Jorge Valdés, Mark DopsonAbstract:CITATION: Acuna, L. G. et al. 2013. Architecture and gene repertoire of the flexible genome of the extreme acidophile Acidithiobacillus caldus. PLoS ONE, 8(11):e78237, doi:10.1371/journal.pone.0078237.
Paulo C. Covarrubias - One of the best experts on this subject based on the ideXlab platform.
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draft genome sequence of the type strain of the sulfur oxidizing acidophile Acidithiobacillus albertensis dsm 14366
2017Co-Authors: Matias Castro, Juan Pablo Cárdenas, Paulo C. Covarrubias, Lillian G. Acuña, Harold Nuñez, Ana Moyabeltran, Monica Gonzalez, Francisco Issotta, Gonzalo Encina, David S HolmesAbstract:Acidithiobacillus albertensis is an extremely acidophilic, mesophilic, obligatory autotrophic sulfur-oxidizer, with potential importance in the bioleaching of sulfidic metal ores, first described in the 1980s. Here we present the draft genome sequence of Acidithiobacillus albertensis DSM 14366T, thereby both filling a long-standing gap in the genomics of the acidithiobacilli, and providing further insight into the understanding of the biology of the non iron-oxidizing members of the Acidithiobacillus genus. The assembled genome is 3,1 Mb, and contains 47 tRNAs, tmRNA gene and 2 rRNA operons, along with 3149 protein-coding predicted genes. The Whole Genome Shotgun project was deposited in DDBJ/EMBL/GenBank under the accession MOAD00000000.
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molecular systematics of the genus Acidithiobacillus insights into the phylogenetic structure and diversification of the taxon
2017Co-Authors: Harold Nuñez, Juan Pablo Cárdenas, Paulo C. Covarrubias, Lillian G. Acuña, Barrie D. Johnson, Ana Moyabeltran, Monica Gonzalez, Francisco Issotta, Joaquin Atavales, Raquel QuatriniAbstract:The 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.
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Architecture and gene repertoire of the flexible genome of the extreme acidophile Acidithiobacillus caldus.
2013Co-Authors: Lillian G. Acuña, Juan Pablo Cárdenas, Paulo C. Covarrubias, Amir Shmaryahu, Juan José Haristoy, Rodrigo Flores, Harold Nuñez, Gonzalo Riadi, Jorge Valdés, Mark DopsonAbstract:CITATION: Acuna, L. G. et al. 2013. Architecture and gene repertoire of the flexible genome of the extreme acidophile Acidithiobacillus caldus. PLoS ONE, 8(11):e78237, doi:10.1371/journal.pone.0078237.
