Raquel Quatrini | Fundacion Ciencia para la Vida (original) (raw)
Papers by Raquel Quatrini
Scientific Reports
The recent revision of the Acidithiobacillia class using genomic taxonomy methods has shown that,... more The recent revision of the Acidithiobacillia class using genomic taxonomy methods has shown that, in addition to the existence of previously unrecognized genera and species, some species of the class harbor levels of divergence that are congruent with ongoing differentiation processes. In this study, we have performed a subspecies-level analysis of sequenced strains of Acidithiobacillus ferrooxidans to prove the existence of distinct sublineages and identify the discriminant genomic/genetic characteristics linked to these sublineages, and to shed light on the processes driving such differentiation. Differences in the genomic relatedness metrics, levels of synteny, gene content, and both integrated and episomal mobile genetic elements (MGE) repertoires support the existence of two subspecies-level taxa within A. ferrooxidans. While sublineage 2A harbors a small plasmid related to pTF5, this episomal MGE is absent in sublineage 2B strains. Likewise, clear differences in the occurrence...
<p>Similarities and differences between sequenced <i>A. caldus</i> strains reve... more <p>Similarities and differences between sequenced <i>A. caldus</i> strains revealed by <i>in silico</i> analysis of (A) the chromosome and (B) the megaplasmids. Chromosomes are represented using ACT. Features are color-coded as follows, grey, CDS or coding sequences; light purple, transposases; light orange tRNAs; light green, rRNA; red, prophage <i>Aca</i>ML1; black, ICE or integrative conjugative element; orange, IME or integrative mobilizable element; green, GI or genomic island; purple, ISR or IS rich regions; white, conserved gene modules numbered according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078237#pone.0078237.s003" target="_blank">Table S3a</a>.</p
The CRISPR Journal, 2021
Type IV CRISPR-Cas are a distinct variety of highly derived CRISPR-Cas systems that appear to hav... more Type IV CRISPR-Cas are a distinct variety of highly derived CRISPR-Cas systems that appear to have evolved from type III systems through the loss of the target-cleaving nuclease and partial deterioration of the large subunit of the effector complex. All known type IV CRISPR-Cas systems are encoded on plasmids, integrative and conjugative elements (ICEs), or prophages, and are thought to contribute to competition between these elements, although the mechanistic details of their function remain unknown. There is a clear parallel between the compositions and likely origin of type IV and type I systems recruited by Tn7-like transposons and mediating RNA-guided transposition. We investigated the diversity and evolutionary relationships of type IV systems, with a focus on those in Acidithiobacillia, where this variety of CRISPR is particularly abundant and always found on ICEs. Our analysis revealed remarkable evolutionary plasticity of type IV CRISPR-Cas systems, with adaptation and ancillary genes originating from different ancestral CRISPR-Cas varieties, and extensive gene shuffling within the type IV loci. The adaptation module and the CRISPR array apparently were lost in the type IV ancestor but were subsequently recaptured by type IV systems on several independent occasions. We demonstrate a high level of heterogeneity among the repeats with type IV CRISPR arrays, which far exceed the heterogeneity of any other known CRISPR repeats and suggest a unique adaptation mechanism. The spacers in the type IV arrays, for which protospacers could be identified, match plasmid genes, in particular those encoding the conjugation apparatus components. Both the biochemical mechanism of type IV CRISPR-Cas function and their role in the competition among mobile genetic elements remain to be investigated.
Frontiers in Microbiology, 2019
Moya-Beltrán et al. Second Messenger Based Signaling in Acidithiobacilli respectively. In contras... more Moya-Beltrán et al. Second Messenger Based Signaling in Acidithiobacilli respectively. In contrast, c-di-GMP networks appear diverse and complex, differing both at the species and strain levels. Molecular elements of c-di-GMP metabolism and transduction were mostly found scattered along the flexible genome of the acidithiobacilli, allowing the identification of probable control modules that could be critical for substrate colonization, biofilm development and intercellular interactions. These may ultimately convey increased endurance to environmental stress and increased potential for gene sharing and adaptation to changing conditions.
Solid State Phenomena, 2017
In this work we report the metagenome-derived draft genomic sequence of an enrichment culture dom... more In this work we report the metagenome-derived draft genomic sequence of an enrichment culture dominated by A. ferrooxidans obtained from an airlift bioreactor inoculated with the microbial consortium recovered from the “Relave Viejo” tailing. The genome of this culture was assembled de-novo and by reference, generating a consensus assembly of 3.0 Mb. On the basis of 16S rRNA (100 % identity), average nucleotide identity analysis (99.33% identity) and in silico DNA-DNA hybridization against A. ferrooxidans ATCC 23270T (97.9%), the recovered genome is confirmed to pertain to A. ferrooxidans species. Comparative genomics results are presented to uncover the genetic traits of the variant surviving lime treatment and to further explore the genomic diversity of these model iron oxidizing species.
Solid State Phenomena, 2017
The family Acidiferrobacteraceae (order Acidiferrobacterales) currently contains three genera of ... more The family Acidiferrobacteraceae (order Acidiferrobacterales) currently contains three genera of chemolithoautotrophs: Sulfuricaulis (2016), Sulfurifustis (2015) and Acidiferrobacter (2011). While the two former are neutrophilic sulfur oxidizers isolated from lake sediments in Japan, the latter is an extremely acidophilic, moderately osmophilic, thermotolerant iron/sulfur oxidizer known to occur in macroscopic streamers in Rio Tinto, Spain and in acid waters worldwide. The type strains of both Sulfuricaulis limnicola (HA5T) and Sulfurifustis variabilis (skN76T) have been sequenced, and the draft genome of the ZJ isolate of Acidiferrobacter thiooxydans (MDCF01) has recently been deposited in public databases. Despite this fact, little evidence on the genomic diversity and evolution of this group has been presented so far. Using comparative genomic analyses and phylogenetic reconstruction strategies, we explored the evolutionary information contained in the available genome sequences ...
Acidophiles: Life in Extremely Acidic Environments, 2016
Acidophiles are life-forms that grow preferentially in natural or man-made environments where the... more Acidophiles are life-forms that grow preferentially in natural or man-made environments where the pH is well below seven. Together with other categories of extremophiles, they have greatly expanded our knowledge of the diversity of life, our understanding on how microorganisms can adapt to seemingly hostile situations, and provided scenarios for the possibility that life-forms may be found outside of our solar system. Written by experts in their field, this important volume provides a comprehensive account of acidophilic microbiology from fundamental to applied aspects. The seventeen chapters are arranged in five sections, each dealing with a specific area. The first section looks at the challenges faced by life-forms that grow in extremely acidic environments and how they adapt to meet these challenges. The next section describes the physiological and phylogenetic diversities of acidophilic microorganisms including archaea, bacteria and eukaryotes. Section three covers acidophile community dynamics, quorum sensing and the formation of biofilms. The next section deals with the various omic technologies that are used to study acidophiles including genomic and metagenomic studies, proteomic-, mobilomic-and metabolomic-focused research. The final section considers the ways in which acidophiles are used in established and emerging biotechnologies and describes why these fascinating microorganisms are considered potential candidates for life on other solar bodies, such as Mars, and beyond. This up-to-date and comprehensive book will be indispensable for environmental scientists and microbiologists and is a recommended acquisition for all microbiology libraries. Chapter 1. Acidophile Microbiology in Space and Time (D. Barrie Johnson and Raquel Quatrini) Chapter 2. Energy Acquisition in Low pH Environments (Wolfgang Nitschke and Violaine Bonnefoy) Chapter 3. Adaptation to Extreme Acidity and Osmotic Stress
Genome announcements, Jan 6, 2014
The genomic features of the Leptospirillum ferriphilum type strain DSM 14647 are described here. ... more The genomic features of the Leptospirillum ferriphilum type strain DSM 14647 are described here. An analysis of the predicted genes enriches our knowledge of the molecular basis of iron oxidation, improves our understanding of its role in industrial bioleaching, and suggests how it is adapted to live at extremely low pH.
Advanced Materials Research, 2009
Previous physiological studies of the genus Ferroplasma have indicated that these microorganisms ... more Previous physiological studies of the genus Ferroplasma have indicated that these microorganisms are capable of fixing CO2 in the presence of ferrous iron and low concentrations of yeast extract. Analysis of the gene complement of Ferroplasma acidarmanus fer1 and two partial genomes of Ferroplasma type I and II derived from the Iron Mountain acid mine drainage metagenome revealed the absence of several functional marker genes encoding key enzymes of three know alternative CO2 fixation routes present in archaea, i.e. the 3-hydroxypropionate cycle, the Ljungdahl–Wood pathway and the reverse TCA cycle. It is thus intriguing how these chemoautotrophic archaeal species deal with their requirements for carbon and suggests that they might have a distinct CO2 fixation route, as yet unreported. Using comparative genomics and metabolic reconstruction strategies, a putative pathway was detected for C1 fixation consisting of four main steps: 1) conversion of carbon monoxide to carbon dioxide wi...
Nucleic Acids Research, 2007
The c-proteobacterium Acidithiobacillus ferrooxidans lives in extremely acidic conditions (pH 2) ... more The c-proteobacterium Acidithiobacillus ferrooxidans lives in extremely acidic conditions (pH 2) and, unlike most organisms, is confronted with an abundant supply of soluble iron. It is also unusual in that it oxidizes iron as an energy source. Consequently, it faces the challenging dual problems of (i) maintaining intracellular iron homeostasis when confronted with extremely high environmental loads of iron and (ii) of regulating the use of iron both as an energy source and as a metabolic micronutrient. A combined bioinformatic and experimental approach was undertaken to identify Fur regulatory sites in the genome of A. ferrooxidans and to gain insight into the constitution of its Fur regulon. Fur regulatory targets associated with a variety of cellular functions including metal trafficking (e.g. feoPABC, tdr, tonBexbBD, copB, cdf), utilization (e.g. fdx, nif), transcriptional regulation (e.g. phoB, irr, iscR) and redox balance (grx, trx, gst) were identified. Selected predicted Fur regulatory sites were confirmed by FURTA, EMSA and in vitro transcription analyses. This study provides the first model for a Fur-binding site consensus sequence in an acidophilic iron-oxidizing microorganism and lays the foundation for future studies aimed at deepening our understanding of the regulatory networks that control iron uptake, homeostasis and oxidation in extreme acidophiles.
Hydrometallurgy, 2006
Acidithiobacillus ferrooxidans is a well known acidophilic, chemolithoautotrophic, Gram negative,... more Acidithiobacillus ferrooxidans is a well known acidophilic, chemolithoautotrophic, Gram negative, bacterium involved in bioleaching and acid mine drainage. In aerobic conditions, it gains energy mainly from the oxidation of ferrous iron and/or reduced sulfur compounds present in ores. After initial oxidation of the substrate, electrons from ferrous iron or sulfur enter respiratory chains and are transported through several redox proteins to oxygen. However, the oxidation of ferrous iron and reduced sulfur compounds has also to provide electrons for the reduction of NAD(P) that is subsequently required for many metabolic processes including CO 2 fixation. To help unravel the enzymatic pathways and the electron transfer chains involved in these processes, a genome-wide microarray transcript profiling analysis was carried out. Oligonucleotides corresponding to approximately 3000 genes of the A. ferrooxidans type strain ATCC23270 were spotted onto glass-slides and hybridized with cDNA retrotranscribed from RNA extracted from ferrous iron and sulfur grown cells. The genes which are preferentially transcribed in ferrous iron conditions and those preferentially transcribed in sulfur conditions were analyzed. The expression of a substantial number of these genes has been validated by real-time PCR, Northern blot hybridization and/or immunodetection analysis. Our results support and extend certain models of iron and sulfur oxidation and highlight previous observations regarding the possible presence of alternate electron pathways. Our findings also suggest ways in which iron and sulfur oxidation may be coordinately regulated. An accompanying paper (Appia-Ayme et al.) describes results pertaining to other metabolic functions.
Hydrometallurgy, 2010
A comparison of the metabolic potential of 20 bioleaching microorganisms and their close relative... more A comparison of the metabolic potential of 20 bioleaching microorganisms and their close relatives from the Eubacteria and Archaea kingdoms permits the prediction of inter-and intra-species physiological interactions (ecophysiology) during spatial and temporal changes that are known to occur within industrial bioleaching heaps. Genome analysis has allowed preliminary models to be built for genes and pathways involved in key processes such as nitrogen and carbon cycling, sulfur and iron uptake and homeostasis, extra-cellular polysaccharide biosynthesis, heavy metal resistance and energy metabolism. This paper will focus on the diverse ways that bioleaching microorganisms obtain carbon from their environment with a particular emphasis on elucidating how these processes might be expected to vary over space and time during the lifetime of a bioleaching operation. It is anticipated that this knowledge will improve our understanding of fundamental biological processes in extremely acidic environments.
Hydrometallurgy, 2008
This article appeared in a journal published by Elsevier. The attached copy is furnished to the a... more This article appeared in a journal published by Elsevier. The attached copy is furnished to the author for internal non-commercial research and education use, including for instruction at the authors institution and sharing with colleagues. Other uses, including reproduction and distribution, or selling or licensing copies, or posting to personal, institutional or third party websites are prohibited. In most cases authors are permitted to post their version of the article (e.g. in Word or Tex form) to their personal website or institutional repository. Authors requiring further information regarding Elsevier's archiving and manuscript policies are encouraged to visit: http://www.elsevier.com/copyright
Hydrometallurgy, 2006
Acidithiobacillus ferrooxidans is a chemolithoautotrophic bacterium that uses iron or sulfur as a... more Acidithiobacillus ferrooxidans is a chemolithoautotrophic bacterium that uses iron or sulfur as an energy and electron source. Bioinformatic analysis of the A. ferrooxidans draft genome sequence was used to identify putative genes and potential metabolic pathways involved in CO 2 ...
BMC Molecular Biology, 2009
Background Normalization is a prerequisite for accurate real time PCR (qPCR) expression analysis ... more Background Normalization is a prerequisite for accurate real time PCR (qPCR) expression analysis and for the validation of microarray profiling data in microbial systems. The choice and use of reference genes that are stably expressed across samples, experimental conditions and designs is a key consideration for the accurate interpretation of gene expression data. Results Here, we evaluate a carefully selected set of reference genes derived from previous microarray-based transcriptional profiling experiments performed on Acidithiobacillus ferrooxidans and identify a set of genes with minimal variability under five different experimental conditions that are frequently used in Acidithiobacilli research. Suitability of these and other previously reported reference genes to monitor the expression of four selected target genes from A. ferrooxidans grown with different energy sources was investigated. Utilization of reference genes map, rpoC, alaS and era results in improved interpretatio...
Extremophiles, 2020
Strain MG, isolated from an acidic pond sediment on the island of Milos (Greece), is proposed as ... more Strain MG, isolated from an acidic pond sediment on the island of Milos (Greece), is proposed as a novel species of ferrous iron- and sulfur-oxidizing Acidithiobacillus. Currently, four of the eight validated species of this genus oxidize ferrous iron, and strain MG shares many key characteristics with these four, including the capacities for catalyzing the oxidative dissolution of pyrite and for anaerobic growth via ferric iron respiration. Strain MG also grows aerobically on hydrogen and anaerobically on hydrogen coupled to ferric iron reduction. While the 16S rRNA genes of the iron-oxidizing Acidi-thiobacillus species (and strain MG) are located in a distinct phylogenetic clade and are closely related (98–99% 16S rRNA gene identity), genomic relatedness indexes (ANI/dDDH) revealed strong genomic divergence between strain MG and all sequenced type strains of the taxon, and placed MG as the first cultured representative of an ancestral phylotype of iron oxidizing acidithiobacilli. ...
BMC Genomics, 2008
Background Acidithiobacillus ferrooxidans is a major participant in consortia of microorganisms u... more Background Acidithiobacillus ferrooxidans is a major participant in consortia of microorganisms used for the industrial recovery of copper (bioleaching or biomining). It is a chemolithoautrophic, γ-proteobacterium using energy from the oxidation of iron- and sulfur-containing minerals for growth. It thrives at extremely low pH (pH 1–2) and fixes both carbon and nitrogen from the atmosphere. It solubilizes copper and other metals from rocks and plays an important role in nutrient and metal biogeochemical cycling in acid environments. The lack of a well-developed system for genetic manipulation has prevented thorough exploration of its physiology. Also, confusion has been caused by prior metabolic models constructed based upon the examination of multiple, and sometimes distantly related, strains of the microorganism. Results The genome of the type strain A. ferrooxidans ATCC 23270 was sequenced and annotated to identify general features and provide a framework for in silico metabolic ...
Revista Chilena de Historia Natural, 2001
Se estudió morfología y dieta de dos poblaciones de Liolaemus elongatus del noroeste de la Patago... more Se estudió morfología y dieta de dos poblaciones de Liolaemus elongatus del noroeste de la Patagonia, una de ambiente de estepa y otra de bosque. Ambas poblaciones se encuentran separadas por una distanciada de 30 km. Se evaluó la variación entre poblaciones y entre sexos de la coloración y patrón de diseño corporal, los parámetros métricos más relevantes (longitud hocico-cloaca, longitud y ancho de la cabeza y longitud del maxilar), así como de la composición y diversidad de los contenidos digestivos de 22 ejemplares adultos de estepa y 25 de bosque. Las poblaciones difirieron en la coloración, el patrón de diseño y en el tamaño corporal promedio (mayor en la zona de estepa). La variación en la coloración podría estar relacionada con factores genéticos o selectivos. Los valores mayores de tamaño corporal en la estepa podrían representar una disminución de tamaño a mayor altitud. No se encontró dimorfismo sexual en la coloración ni en la longitud hocico-cloaca en ninguna de las dos ...
Amino acid sequence alignments for predicted proteins and domains proteins of nucleotide-second m... more Amino acid sequence alignments for predicted proteins and domains proteins of nucleotide-second messengers in a acidithiobacilli genomes. Files are in FASTA format.
Scientific Reports
The recent revision of the Acidithiobacillia class using genomic taxonomy methods has shown that,... more The recent revision of the Acidithiobacillia class using genomic taxonomy methods has shown that, in addition to the existence of previously unrecognized genera and species, some species of the class harbor levels of divergence that are congruent with ongoing differentiation processes. In this study, we have performed a subspecies-level analysis of sequenced strains of Acidithiobacillus ferrooxidans to prove the existence of distinct sublineages and identify the discriminant genomic/genetic characteristics linked to these sublineages, and to shed light on the processes driving such differentiation. Differences in the genomic relatedness metrics, levels of synteny, gene content, and both integrated and episomal mobile genetic elements (MGE) repertoires support the existence of two subspecies-level taxa within A. ferrooxidans. While sublineage 2A harbors a small plasmid related to pTF5, this episomal MGE is absent in sublineage 2B strains. Likewise, clear differences in the occurrence...
<p>Similarities and differences between sequenced <i>A. caldus</i> strains reve... more <p>Similarities and differences between sequenced <i>A. caldus</i> strains revealed by <i>in silico</i> analysis of (A) the chromosome and (B) the megaplasmids. Chromosomes are represented using ACT. Features are color-coded as follows, grey, CDS or coding sequences; light purple, transposases; light orange tRNAs; light green, rRNA; red, prophage <i>Aca</i>ML1; black, ICE or integrative conjugative element; orange, IME or integrative mobilizable element; green, GI or genomic island; purple, ISR or IS rich regions; white, conserved gene modules numbered according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078237#pone.0078237.s003" target="_blank">Table S3a</a>.</p
The CRISPR Journal, 2021
Type IV CRISPR-Cas are a distinct variety of highly derived CRISPR-Cas systems that appear to hav... more Type IV CRISPR-Cas are a distinct variety of highly derived CRISPR-Cas systems that appear to have evolved from type III systems through the loss of the target-cleaving nuclease and partial deterioration of the large subunit of the effector complex. All known type IV CRISPR-Cas systems are encoded on plasmids, integrative and conjugative elements (ICEs), or prophages, and are thought to contribute to competition between these elements, although the mechanistic details of their function remain unknown. There is a clear parallel between the compositions and likely origin of type IV and type I systems recruited by Tn7-like transposons and mediating RNA-guided transposition. We investigated the diversity and evolutionary relationships of type IV systems, with a focus on those in Acidithiobacillia, where this variety of CRISPR is particularly abundant and always found on ICEs. Our analysis revealed remarkable evolutionary plasticity of type IV CRISPR-Cas systems, with adaptation and ancillary genes originating from different ancestral CRISPR-Cas varieties, and extensive gene shuffling within the type IV loci. The adaptation module and the CRISPR array apparently were lost in the type IV ancestor but were subsequently recaptured by type IV systems on several independent occasions. We demonstrate a high level of heterogeneity among the repeats with type IV CRISPR arrays, which far exceed the heterogeneity of any other known CRISPR repeats and suggest a unique adaptation mechanism. The spacers in the type IV arrays, for which protospacers could be identified, match plasmid genes, in particular those encoding the conjugation apparatus components. Both the biochemical mechanism of type IV CRISPR-Cas function and their role in the competition among mobile genetic elements remain to be investigated.
Frontiers in Microbiology, 2019
Moya-Beltrán et al. Second Messenger Based Signaling in Acidithiobacilli respectively. In contras... more Moya-Beltrán et al. Second Messenger Based Signaling in Acidithiobacilli respectively. In contrast, c-di-GMP networks appear diverse and complex, differing both at the species and strain levels. Molecular elements of c-di-GMP metabolism and transduction were mostly found scattered along the flexible genome of the acidithiobacilli, allowing the identification of probable control modules that could be critical for substrate colonization, biofilm development and intercellular interactions. These may ultimately convey increased endurance to environmental stress and increased potential for gene sharing and adaptation to changing conditions.
Solid State Phenomena, 2017
In this work we report the metagenome-derived draft genomic sequence of an enrichment culture dom... more In this work we report the metagenome-derived draft genomic sequence of an enrichment culture dominated by A. ferrooxidans obtained from an airlift bioreactor inoculated with the microbial consortium recovered from the “Relave Viejo” tailing. The genome of this culture was assembled de-novo and by reference, generating a consensus assembly of 3.0 Mb. On the basis of 16S rRNA (100 % identity), average nucleotide identity analysis (99.33% identity) and in silico DNA-DNA hybridization against A. ferrooxidans ATCC 23270T (97.9%), the recovered genome is confirmed to pertain to A. ferrooxidans species. Comparative genomics results are presented to uncover the genetic traits of the variant surviving lime treatment and to further explore the genomic diversity of these model iron oxidizing species.
Solid State Phenomena, 2017
The family Acidiferrobacteraceae (order Acidiferrobacterales) currently contains three genera of ... more The family Acidiferrobacteraceae (order Acidiferrobacterales) currently contains three genera of chemolithoautotrophs: Sulfuricaulis (2016), Sulfurifustis (2015) and Acidiferrobacter (2011). While the two former are neutrophilic sulfur oxidizers isolated from lake sediments in Japan, the latter is an extremely acidophilic, moderately osmophilic, thermotolerant iron/sulfur oxidizer known to occur in macroscopic streamers in Rio Tinto, Spain and in acid waters worldwide. The type strains of both Sulfuricaulis limnicola (HA5T) and Sulfurifustis variabilis (skN76T) have been sequenced, and the draft genome of the ZJ isolate of Acidiferrobacter thiooxydans (MDCF01) has recently been deposited in public databases. Despite this fact, little evidence on the genomic diversity and evolution of this group has been presented so far. Using comparative genomic analyses and phylogenetic reconstruction strategies, we explored the evolutionary information contained in the available genome sequences ...
Acidophiles: Life in Extremely Acidic Environments, 2016
Acidophiles are life-forms that grow preferentially in natural or man-made environments where the... more Acidophiles are life-forms that grow preferentially in natural or man-made environments where the pH is well below seven. Together with other categories of extremophiles, they have greatly expanded our knowledge of the diversity of life, our understanding on how microorganisms can adapt to seemingly hostile situations, and provided scenarios for the possibility that life-forms may be found outside of our solar system. Written by experts in their field, this important volume provides a comprehensive account of acidophilic microbiology from fundamental to applied aspects. The seventeen chapters are arranged in five sections, each dealing with a specific area. The first section looks at the challenges faced by life-forms that grow in extremely acidic environments and how they adapt to meet these challenges. The next section describes the physiological and phylogenetic diversities of acidophilic microorganisms including archaea, bacteria and eukaryotes. Section three covers acidophile community dynamics, quorum sensing and the formation of biofilms. The next section deals with the various omic technologies that are used to study acidophiles including genomic and metagenomic studies, proteomic-, mobilomic-and metabolomic-focused research. The final section considers the ways in which acidophiles are used in established and emerging biotechnologies and describes why these fascinating microorganisms are considered potential candidates for life on other solar bodies, such as Mars, and beyond. This up-to-date and comprehensive book will be indispensable for environmental scientists and microbiologists and is a recommended acquisition for all microbiology libraries. Chapter 1. Acidophile Microbiology in Space and Time (D. Barrie Johnson and Raquel Quatrini) Chapter 2. Energy Acquisition in Low pH Environments (Wolfgang Nitschke and Violaine Bonnefoy) Chapter 3. Adaptation to Extreme Acidity and Osmotic Stress
Genome announcements, Jan 6, 2014
The genomic features of the Leptospirillum ferriphilum type strain DSM 14647 are described here. ... more The genomic features of the Leptospirillum ferriphilum type strain DSM 14647 are described here. An analysis of the predicted genes enriches our knowledge of the molecular basis of iron oxidation, improves our understanding of its role in industrial bioleaching, and suggests how it is adapted to live at extremely low pH.
Advanced Materials Research, 2009
Previous physiological studies of the genus Ferroplasma have indicated that these microorganisms ... more Previous physiological studies of the genus Ferroplasma have indicated that these microorganisms are capable of fixing CO2 in the presence of ferrous iron and low concentrations of yeast extract. Analysis of the gene complement of Ferroplasma acidarmanus fer1 and two partial genomes of Ferroplasma type I and II derived from the Iron Mountain acid mine drainage metagenome revealed the absence of several functional marker genes encoding key enzymes of three know alternative CO2 fixation routes present in archaea, i.e. the 3-hydroxypropionate cycle, the Ljungdahl–Wood pathway and the reverse TCA cycle. It is thus intriguing how these chemoautotrophic archaeal species deal with their requirements for carbon and suggests that they might have a distinct CO2 fixation route, as yet unreported. Using comparative genomics and metabolic reconstruction strategies, a putative pathway was detected for C1 fixation consisting of four main steps: 1) conversion of carbon monoxide to carbon dioxide wi...
Nucleic Acids Research, 2007
The c-proteobacterium Acidithiobacillus ferrooxidans lives in extremely acidic conditions (pH 2) ... more The c-proteobacterium Acidithiobacillus ferrooxidans lives in extremely acidic conditions (pH 2) and, unlike most organisms, is confronted with an abundant supply of soluble iron. It is also unusual in that it oxidizes iron as an energy source. Consequently, it faces the challenging dual problems of (i) maintaining intracellular iron homeostasis when confronted with extremely high environmental loads of iron and (ii) of regulating the use of iron both as an energy source and as a metabolic micronutrient. A combined bioinformatic and experimental approach was undertaken to identify Fur regulatory sites in the genome of A. ferrooxidans and to gain insight into the constitution of its Fur regulon. Fur regulatory targets associated with a variety of cellular functions including metal trafficking (e.g. feoPABC, tdr, tonBexbBD, copB, cdf), utilization (e.g. fdx, nif), transcriptional regulation (e.g. phoB, irr, iscR) and redox balance (grx, trx, gst) were identified. Selected predicted Fur regulatory sites were confirmed by FURTA, EMSA and in vitro transcription analyses. This study provides the first model for a Fur-binding site consensus sequence in an acidophilic iron-oxidizing microorganism and lays the foundation for future studies aimed at deepening our understanding of the regulatory networks that control iron uptake, homeostasis and oxidation in extreme acidophiles.
Hydrometallurgy, 2006
Acidithiobacillus ferrooxidans is a well known acidophilic, chemolithoautotrophic, Gram negative,... more Acidithiobacillus ferrooxidans is a well known acidophilic, chemolithoautotrophic, Gram negative, bacterium involved in bioleaching and acid mine drainage. In aerobic conditions, it gains energy mainly from the oxidation of ferrous iron and/or reduced sulfur compounds present in ores. After initial oxidation of the substrate, electrons from ferrous iron or sulfur enter respiratory chains and are transported through several redox proteins to oxygen. However, the oxidation of ferrous iron and reduced sulfur compounds has also to provide electrons for the reduction of NAD(P) that is subsequently required for many metabolic processes including CO 2 fixation. To help unravel the enzymatic pathways and the electron transfer chains involved in these processes, a genome-wide microarray transcript profiling analysis was carried out. Oligonucleotides corresponding to approximately 3000 genes of the A. ferrooxidans type strain ATCC23270 were spotted onto glass-slides and hybridized with cDNA retrotranscribed from RNA extracted from ferrous iron and sulfur grown cells. The genes which are preferentially transcribed in ferrous iron conditions and those preferentially transcribed in sulfur conditions were analyzed. The expression of a substantial number of these genes has been validated by real-time PCR, Northern blot hybridization and/or immunodetection analysis. Our results support and extend certain models of iron and sulfur oxidation and highlight previous observations regarding the possible presence of alternate electron pathways. Our findings also suggest ways in which iron and sulfur oxidation may be coordinately regulated. An accompanying paper (Appia-Ayme et al.) describes results pertaining to other metabolic functions.
Hydrometallurgy, 2010
A comparison of the metabolic potential of 20 bioleaching microorganisms and their close relative... more A comparison of the metabolic potential of 20 bioleaching microorganisms and their close relatives from the Eubacteria and Archaea kingdoms permits the prediction of inter-and intra-species physiological interactions (ecophysiology) during spatial and temporal changes that are known to occur within industrial bioleaching heaps. Genome analysis has allowed preliminary models to be built for genes and pathways involved in key processes such as nitrogen and carbon cycling, sulfur and iron uptake and homeostasis, extra-cellular polysaccharide biosynthesis, heavy metal resistance and energy metabolism. This paper will focus on the diverse ways that bioleaching microorganisms obtain carbon from their environment with a particular emphasis on elucidating how these processes might be expected to vary over space and time during the lifetime of a bioleaching operation. It is anticipated that this knowledge will improve our understanding of fundamental biological processes in extremely acidic environments.
Hydrometallurgy, 2008
This article appeared in a journal published by Elsevier. The attached copy is furnished to the a... more This article appeared in a journal published by Elsevier. The attached copy is furnished to the author for internal non-commercial research and education use, including for instruction at the authors institution and sharing with colleagues. Other uses, including reproduction and distribution, or selling or licensing copies, or posting to personal, institutional or third party websites are prohibited. In most cases authors are permitted to post their version of the article (e.g. in Word or Tex form) to their personal website or institutional repository. Authors requiring further information regarding Elsevier's archiving and manuscript policies are encouraged to visit: http://www.elsevier.com/copyright
Hydrometallurgy, 2006
Acidithiobacillus ferrooxidans is a chemolithoautotrophic bacterium that uses iron or sulfur as a... more Acidithiobacillus ferrooxidans is a chemolithoautotrophic bacterium that uses iron or sulfur as an energy and electron source. Bioinformatic analysis of the A. ferrooxidans draft genome sequence was used to identify putative genes and potential metabolic pathways involved in CO 2 ...
BMC Molecular Biology, 2009
Background Normalization is a prerequisite for accurate real time PCR (qPCR) expression analysis ... more Background Normalization is a prerequisite for accurate real time PCR (qPCR) expression analysis and for the validation of microarray profiling data in microbial systems. The choice and use of reference genes that are stably expressed across samples, experimental conditions and designs is a key consideration for the accurate interpretation of gene expression data. Results Here, we evaluate a carefully selected set of reference genes derived from previous microarray-based transcriptional profiling experiments performed on Acidithiobacillus ferrooxidans and identify a set of genes with minimal variability under five different experimental conditions that are frequently used in Acidithiobacilli research. Suitability of these and other previously reported reference genes to monitor the expression of four selected target genes from A. ferrooxidans grown with different energy sources was investigated. Utilization of reference genes map, rpoC, alaS and era results in improved interpretatio...
Extremophiles, 2020
Strain MG, isolated from an acidic pond sediment on the island of Milos (Greece), is proposed as ... more Strain MG, isolated from an acidic pond sediment on the island of Milos (Greece), is proposed as a novel species of ferrous iron- and sulfur-oxidizing Acidithiobacillus. Currently, four of the eight validated species of this genus oxidize ferrous iron, and strain MG shares many key characteristics with these four, including the capacities for catalyzing the oxidative dissolution of pyrite and for anaerobic growth via ferric iron respiration. Strain MG also grows aerobically on hydrogen and anaerobically on hydrogen coupled to ferric iron reduction. While the 16S rRNA genes of the iron-oxidizing Acidi-thiobacillus species (and strain MG) are located in a distinct phylogenetic clade and are closely related (98–99% 16S rRNA gene identity), genomic relatedness indexes (ANI/dDDH) revealed strong genomic divergence between strain MG and all sequenced type strains of the taxon, and placed MG as the first cultured representative of an ancestral phylotype of iron oxidizing acidithiobacilli. ...
BMC Genomics, 2008
Background Acidithiobacillus ferrooxidans is a major participant in consortia of microorganisms u... more Background Acidithiobacillus ferrooxidans is a major participant in consortia of microorganisms used for the industrial recovery of copper (bioleaching or biomining). It is a chemolithoautrophic, γ-proteobacterium using energy from the oxidation of iron- and sulfur-containing minerals for growth. It thrives at extremely low pH (pH 1–2) and fixes both carbon and nitrogen from the atmosphere. It solubilizes copper and other metals from rocks and plays an important role in nutrient and metal biogeochemical cycling in acid environments. The lack of a well-developed system for genetic manipulation has prevented thorough exploration of its physiology. Also, confusion has been caused by prior metabolic models constructed based upon the examination of multiple, and sometimes distantly related, strains of the microorganism. Results The genome of the type strain A. ferrooxidans ATCC 23270 was sequenced and annotated to identify general features and provide a framework for in silico metabolic ...
Revista Chilena de Historia Natural, 2001
Se estudió morfología y dieta de dos poblaciones de Liolaemus elongatus del noroeste de la Patago... more Se estudió morfología y dieta de dos poblaciones de Liolaemus elongatus del noroeste de la Patagonia, una de ambiente de estepa y otra de bosque. Ambas poblaciones se encuentran separadas por una distanciada de 30 km. Se evaluó la variación entre poblaciones y entre sexos de la coloración y patrón de diseño corporal, los parámetros métricos más relevantes (longitud hocico-cloaca, longitud y ancho de la cabeza y longitud del maxilar), así como de la composición y diversidad de los contenidos digestivos de 22 ejemplares adultos de estepa y 25 de bosque. Las poblaciones difirieron en la coloración, el patrón de diseño y en el tamaño corporal promedio (mayor en la zona de estepa). La variación en la coloración podría estar relacionada con factores genéticos o selectivos. Los valores mayores de tamaño corporal en la estepa podrían representar una disminución de tamaño a mayor altitud. No se encontró dimorfismo sexual en la coloración ni en la longitud hocico-cloaca en ninguna de las dos ...
Amino acid sequence alignments for predicted proteins and domains proteins of nucleotide-second m... more Amino acid sequence alignments for predicted proteins and domains proteins of nucleotide-second messengers in a acidithiobacilli genomes. Files are in FASTA format.