1
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Sun J, He X, LE Y, Al-Tohamy R, Ali SS. Potential applications of extremophilic bacteria in the bioremediation of extreme environments contaminated with heavy metals. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 352:120081. [PMID: 38237330 DOI: 10.1016/j.jenvman.2024.120081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 12/31/2023] [Accepted: 01/07/2024] [Indexed: 02/04/2024]
Abstract
Protecting the environment from harmful pollutants has become increasingly difficult in recent decades. The presence of heavy metal (HM) pollution poses a serious environmental hazard that requires intricate attention on a worldwide scale. Even at low concentrations, HMs have the potential to induce deleterious health effects in both humans and other living organisms. Therefore, various strategies have been proposed to address this issue, with extremophiles being a promising solution. Bacteria that exhibit resistance to metals are preferred for applications involving metal removal due to their capacity for rapid multiplication and growth. Extremophiles are a special group of microorganisms that are capable of surviving under extreme conditions such as extreme temperatures, pH levels, and high salt concentrations where other organisms cannot. Due to their unique enzymes and adaptive capabilities, extremophiles are well suited as catalysts for environmental biotechnology applications, including the bioremediation of HMs through various strategies. The mechanisms of resistance to HMs by extremophilic bacteria encompass: (i) metal exclusion by permeability barrier; (ii) extracellular metal sequestration by protein/chelator binding; (iii) intracellular sequestration of the metal by protein/chelator binding; (iv) enzymatic detoxification of a metal to a less toxic form; (v) active transport of HMs; (vi) passive tolerance; (vii) reduced metal sensitivity of cellular targets to metal ions; and (viii) morphological change of cells. This review provides comprehensive information on extremophilic bacteria and their potential roles for bioremediation, particularly in environments contaminated with HMs, which pose a threat due to their stability and persistence. Genetic engineering of extremophilic bacteria in stressed environments could help in the bioremediation of contaminated sites. Due to their unique characteristics, these organisms and their enzymes are expected to bridge the gap between biological and chemical industrial processes. However, the structure and biochemical properties of extremophilic bacteria, along with any possible long-term effects of their applications, need to be investigated further.
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Affiliation(s)
- Jianzhong Sun
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China.
| | - Xing He
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Yilin LE
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China.
| | - Rania Al-Tohamy
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Sameh S Ali
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China; Botany Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt.
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2
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Sepúlveda-Rebolledo P, González-Rosales C, Dopson M, Pérez-Rueda E, Holmes DS, Valdés JH. Comparative genomics sheds light on transcription factor-mediated regulation in the extreme acidophilic Acidithiobacillia representatives. Res Microbiol 2024; 175:104135. [PMID: 37678513 DOI: 10.1016/j.resmic.2023.104135] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/28/2023] [Accepted: 08/30/2023] [Indexed: 09/09/2023]
Abstract
Extreme acidophiles thrive in acidic environments, confront a multitude of challenges, and demonstrate remarkable adaptability in their metabolism to cope with the ever-changing environmental fluctuations, which encompass variations in temperature, pH levels, and the availability of electron acceptors and donors. The survival and proliferation of members within the Acidithiobacillia class rely on the deployment of transcriptional regulatory systems linked to essential physiological traits. The study of these transcriptional regulatory systems provides valuable insights into critical processes, such as energy metabolism and nutrient assimilation, and how they integrate into major genetic-metabolic circuits. In this study, we examined the transcriptional regulatory repertoires and potential interactions of forty-three Acidithiobacillia complete and draft genomes, encompassing nine species. To investigate the function and diversity of Transcription Factors (TFs) and their DNA Binding Sites (DBSs), we conducted a genome-wide comparative analysis, which allowed us to identify these regulatory elements in representatives of Acidithiobacillia. We classified TFs into gene families and compared their occurrence among all representatives, revealing conservation patterns across the class. The results identified conserved regulators for several pathways, including iron and sulfur oxidation, the main pathways for energy acquisition, providing new evidence for viable regulatory interactions and branch-specific conservation in Acidithiobacillia. The identification of TFs and DBSs not only corroborates existing experimental information for selected species, but also introduces novel candidates for experimental validation. Moreover, these promising candidates have the potential for further extension to new representatives within the class.
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Affiliation(s)
- Pedro Sepúlveda-Rebolledo
- Centro de Genómica y Bioinformática and PhD. Program on Integrative Genomics, Facultad de Ciencias, Universidad Mayor, Santiago (8580745), Chile.
| | - Carolina González-Rosales
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago (8580638), Chile; Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, SE-391 82 Kalmar, Sweden.
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, SE-391 82 Kalmar, Sweden.
| | - Ernesto Pérez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica del Estado de Yucatán, Mérida, Yucatán, Mexico.
| | - David S Holmes
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago (8580638), Chile; Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago (7510156), Chile.
| | - Jorge H Valdés
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago (8370146), Chile.
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3
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Páez-Pérez ED, Hernández-Sánchez A, Alfaro-Saldaña E, García-Meza JV. Disorder and amino acid composition in proteins: their potential role in the adaptation of extracellular pilins to the acidic media, where Acidithiobacillus thiooxidans grows. Extremophiles 2023; 27:31. [PMID: 37848738 DOI: 10.1007/s00792-023-01317-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 09/26/2023] [Indexed: 10/19/2023]
Abstract
There are few biophysical studies or structural characterizations of the type IV pilin system of extremophile bacteria, such as the acidophilic Acidithiobacillus thiooxidans. We set out to analyze their pili-comprising proteins, pilins, because these extracellular proteins are in constant interaction with protons of the acidic medium in which At. thiooxidans grows. We used the web server Operon Mapper to analyze and identify the cluster codified by the minor pilin of At. thiooxidans. In addition, we carried an in-silico characterization of such pilins using the VL-XT algorithm of PONDR® server. Our results showed that structural disorder prevails more in pilins of At. thiooxidans than in non-acidophilic bacteria. Further computational characterization showed that the pilins of At. thiooxidans are significantly enriched in hydroxy (serine and threonine) and amide (glutamine and asparagine) residues, and significantly reduced in charged residues (aspartic acid, glutamic acid, arginine and lysine). Similar results were obtained when comparing pilins from other Acidithiobacillus and other acidophilic bacteria from another genus versus neutrophilic bacteria, suggesting that these properties are intrinsic to pilins from acidic environments, most likely by maintaining solubility and stability in harsh conditions. These results give guidelines for the application of extracellular proteins of acidophiles in protein engineering.
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Affiliation(s)
- Edgar D Páez-Pérez
- Geomicrobiología, Metalurgia, Universidad Autónoma de San Luis Potosí, Sierra Leona 550, 78210, San Luis Potosí, SLP, Mexico.
| | - Araceli Hernández-Sánchez
- Geomicrobiología, Metalurgia, Universidad Autónoma de San Luis Potosí, Sierra Leona 550, 78210, San Luis Potosí, SLP, Mexico.
| | - Elvia Alfaro-Saldaña
- Geomicrobiología, Metalurgia, Universidad Autónoma de San Luis Potosí, Sierra Leona 550, 78210, San Luis Potosí, SLP, Mexico
| | - J Viridiana García-Meza
- Geomicrobiología, Metalurgia, Universidad Autónoma de San Luis Potosí, Sierra Leona 550, 78210, San Luis Potosí, SLP, Mexico
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4
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Ibáñez A, Garrido-Chamorro S, Coque JJR, Barreiro C. From Genes to Bioleaching: Unraveling Sulfur Metabolism in Acidithiobacillus Genus. Genes (Basel) 2023; 14:1772. [PMID: 37761912 PMCID: PMC10531304 DOI: 10.3390/genes14091772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Sulfur oxidation stands as a pivotal process within the Earth's sulfur cycle, in which Acidithiobacillus species emerge as skillful sulfur-oxidizing bacteria. They are able to efficiently oxidize several reduced inorganic sulfur compounds (RISCs) under extreme conditions for their autotrophic growth. This unique characteristic has made these bacteria a useful tool in bioleaching and biological desulfurization applications. Extensive research has unraveled diverse sulfur metabolism pathways and their corresponding regulatory systems. The metabolic arsenal of the Acidithiobacillus genus includes oxidative enzymes such as: (i) elemental sulfur oxidation enzymes, like sulfur dioxygenase (SDO), sulfur oxygenase reductase (SOR), and heterodisulfide reductase (HDR-like system); (ii) enzymes involved in thiosulfate oxidation pathways, including the sulfur oxidation (Sox) system, tetrathionate hydrolase (TetH), and thiosulfate quinone oxidoreductase (TQO); (iii) sulfide oxidation enzymes, like sulfide:quinone oxidoreductase (SQR); and (iv) sulfite oxidation pathways, such as sulfite oxidase (SOX). This review summarizes the current state of the art of sulfur metabolic processes in Acidithiobacillus species, which are key players of industrial biomining processes. Furthermore, this manuscript highlights the existing challenges and barriers to further exploring the sulfur metabolism of this peculiar extremophilic genus.
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Affiliation(s)
- Ana Ibáñez
- Instituto de Investigación de la Viña y el Vino, Escuela de Ingeniería Agraria, Universidad de León, 24009 León, Spain; (A.I.); (J.J.R.C.)
- Instituto Tecnológico Agrario de Castilla y León (ITACyL), Área de Investigación Agrícola, 47071 Valladolid, Spain
| | - Sonia Garrido-Chamorro
- Área de Bioquímica y Biología Molecular, Departamento de Biología Molecular, Universidad de León, 24007 León, Spain;
| | - Juan J. R. Coque
- Instituto de Investigación de la Viña y el Vino, Escuela de Ingeniería Agraria, Universidad de León, 24009 León, Spain; (A.I.); (J.J.R.C.)
| | - Carlos Barreiro
- Área de Bioquímica y Biología Molecular, Departamento de Biología Molecular, Universidad de León, 24007 León, Spain;
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5
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Ibáñez A, Barreiro C, Diez-Galán A, Cobos R, Calvo-Peña C, Coque JJR. Molecular Identification and Acid Stress Response of an Acidithiobacillus thiooxidans Strain Isolated from Rio Tinto (Spain). Int J Mol Sci 2023; 24:13391. [PMID: 37686204 PMCID: PMC10487802 DOI: 10.3390/ijms241713391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/16/2023] [Accepted: 08/26/2023] [Indexed: 09/10/2023] Open
Abstract
Acidithiobacillus thiooxidans is of paramount importance in the development of biomining technologies. Being widely recognized as an extreme acidophile, extensive research has been dedicated to understanding its significant role in the extraction of several ores in recent years. However, there still exist significant molecular uncertainties surrounding this species. This study focuses on developing a taxonomic assignment method based on the sequencing of the 16S-5S rRNA cluster, along with a qPCR-based technology enabling precise growth determination. Additionally, an approach to understanding its response to acid stress is explored through RT-PCR and MALDI-TOF analysis. Our findings indicate that when subjected to pH levels below 1, the cell inhibits central (carbon fixation and metabolism) and energy (sulfur metabolism) metabolism, as well as chaperone synthesis, suggesting a potential cellular collapse. Nevertheless, the secretion of ammonia is enhanced to raise the environmental pH, while fatty acid synthesis is upregulated to reinforce the cell membrane.
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Affiliation(s)
- Ana Ibáñez
- Instituto de Investigación de la Viña y el Vino, Escuela de Ingeniería Agraria, Universidad de León, 24009 León, Spain; (A.I.); (A.D.-G.); (R.C.); (C.C.-P.)
- Instituto Tecnológico Agrario de Castilla y León (ITACYL), 47071 Valladolid, Spain
| | - Carlos Barreiro
- Área de Bioquímica y Biología Molecular, Departamento de Biología Molecular, Universidad de León, 24071 León, Spain
| | - Alba Diez-Galán
- Instituto de Investigación de la Viña y el Vino, Escuela de Ingeniería Agraria, Universidad de León, 24009 León, Spain; (A.I.); (A.D.-G.); (R.C.); (C.C.-P.)
| | - Rebeca Cobos
- Instituto de Investigación de la Viña y el Vino, Escuela de Ingeniería Agraria, Universidad de León, 24009 León, Spain; (A.I.); (A.D.-G.); (R.C.); (C.C.-P.)
| | - Carla Calvo-Peña
- Instituto de Investigación de la Viña y el Vino, Escuela de Ingeniería Agraria, Universidad de León, 24009 León, Spain; (A.I.); (A.D.-G.); (R.C.); (C.C.-P.)
| | - Juan José R. Coque
- Instituto de Investigación de la Viña y el Vino, Escuela de Ingeniería Agraria, Universidad de León, 24009 León, Spain; (A.I.); (A.D.-G.); (R.C.); (C.C.-P.)
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6
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Salwan R, Sharma V. Genomics of Prokaryotic Extremophiles to Unfold the Mystery of Survival in Extreme Environments. Microbiol Res 2022; 264:127156. [DOI: 10.1016/j.micres.2022.127156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 07/30/2022] [Accepted: 07/31/2022] [Indexed: 11/26/2022]
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7
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Accessing Metals from Low-Grade Ores and the Environmental Impact Considerations: A Review of the Perspectives of Conventional versus Bioleaching Strategies. MINERALS 2022. [DOI: 10.3390/min12050506] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Mining has advanced primarily through the use of two strategies: pyrometallurgy and hydrometallurgy. Both have been used successfully to extract valuable metals from ore deposits. These strategies, without a doubt, harm the environment. Furthermore, due to decades of excessive mining, there has been a global decline in high-grade ores. This has resulted in a decrease in valuable metal supply, which has prompted a reconsideration of these traditional strategies, as the industry faces the current challenge of accessing the highly sought-after valuable metals from low-grade ores. This review outlines these challenges in detail, provides insights into metal recovery issues, and describes technological advances being made to address the issues associated with dealing with low-grade metals. It also discusses the pragmatic paradigm shift that necessitates the use of biotechnological solutions provided by bioleaching, particularly its environmental friendliness. However, it goes on to criticize the shortcomings of bioleaching while highlighting the potential solutions provided by a bespoke approach that integrates research applications from omics technologies and their applications in the adaptation of bioleaching microorganisms and their interaction with the harsh environments associated with metal ore degradation.
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8
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González-Rosales C, Vergara E, Dopson M, Valdés JH, Holmes DS. Integrative Genomics Sheds Light on Evolutionary Forces Shaping the Acidithiobacillia Class Acidophilic Lifestyle. Front Microbiol 2022; 12:822229. [PMID: 35242113 PMCID: PMC8886135 DOI: 10.3389/fmicb.2021.822229] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 12/30/2021] [Indexed: 01/22/2023] Open
Abstract
Extreme acidophiles thrive in environments rich in protons (pH values <3) and often high levels of dissolved heavy metals. They are distributed across the three domains of the Tree of Life including members of the Proteobacteria. The Acidithiobacillia class is formed by the neutrophilic genus Thermithiobacillus along with the extremely acidophilic genera Fervidacidithiobacillus, Igneacidithiobacillus, Ambacidithiobacillus, and Acidithiobacillus. Phylogenomic reconstruction revealed a division in the Acidithiobacillia class correlating with the different pH optima that suggested that the acidophilic genera evolved from an ancestral neutrophile within the Acidithiobacillia. Genes and mechanisms denominated as "first line of defense" were key to explaining the Acidithiobacillia acidophilic lifestyle including preventing proton influx that allows the cell to maintain a near-neutral cytoplasmic pH and differ from the neutrophilic Acidithiobacillia ancestors that lacked these systems. Additional differences between the neutrophilic and acidophilic Acidithiobacillia included the higher number of gene copies in the acidophilic genera coding for "second line of defense" systems that neutralize and/or expel protons from cell. Gain of genes such as hopanoid biosynthesis involved in membrane stabilization at low pH and the functional redundancy for generating an internal positive membrane potential revealed the transition from neutrophilic properties to a new acidophilic lifestyle by shaping the Acidithiobacillaceae genomic structure. The presence of a pool of accessory genes with functional redundancy provides the opportunity to "hedge bet" in rapidly changing acidic environments. Although a core of mechanisms for acid resistance was inherited vertically from an inferred neutrophilic ancestor, the majority of mechanisms, especially those potentially involved in resistance to extremely low pH, were obtained from other extreme acidophiles by horizontal gene transfer (HGT) events.
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Affiliation(s)
- Carolina González-Rosales
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Center for Genomics and Bioinformatics, Faculty of Sciences, Universidad Mayor, Santiago, Chile
| | - Eva Vergara
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Jorge H. Valdés
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
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9
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Li M, Wen J. Recent progress in the application of omics technologies in the study of bio-mining microorganisms from extreme environments. Microb Cell Fact 2021; 20:178. [PMID: 34496835 PMCID: PMC8425152 DOI: 10.1186/s12934-021-01671-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 08/30/2021] [Indexed: 11/11/2022] Open
Abstract
Bio-mining microorganisms are a key factor affecting the metal recovery rate of bio-leaching, which inevitably produces an extremely acidic environment. As a powerful tool for exploring the adaptive mechanisms of microorganisms in extreme environments, omics technologies can greatly aid our understanding of bio-mining microorganisms and their communities on the gene, mRNA, and protein levels. These omics technologies have their own advantages in exploring microbial diversity, adaptive evolution, changes in metabolic characteristics, and resistance mechanisms of single strains or their communities to extreme environments. These technologies can also be used to discover potential new genes, enzymes, metabolites, metabolic pathways, and species. In addition, integrated multi-omics analysis can link information at different biomolecular levels, thereby obtaining more accurate and complete global adaptation mechanisms of bio-mining microorganisms. This review introduces the current status and future trends in the application of omics technologies in the study of bio-mining microorganisms and their communities in extreme environments.
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Affiliation(s)
- Min Li
- Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin, China.,Frontier Science Center of Ministry of Education, Tianjin University, Tianjin, China
| | - Jianping Wen
- Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin, China. .,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin, China. .,Frontier Science Center of Ministry of Education, Tianjin University, Tianjin, China.
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10
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Kanao T, Sharmin S, Tokuhisa M, Otsuki M, Kamimura K. Identification of a gene encoding a novel thiosulfate:quinone oxidoreductase in marine Acidithiobacillus sp. strain SH. Res Microbiol 2020; 171:281-286. [PMID: 33031917 DOI: 10.1016/j.resmic.2020.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 09/16/2020] [Accepted: 09/17/2020] [Indexed: 11/30/2022]
Abstract
Sulfur-oxidizing bacteria that are halophilic and acidophilic have gained interest because of their potential use in bioleaching operations in salt-containing environments. Acidithiobacillus sp. strain SH, which was previously identified as Acidithiobacillus thiooxidans based on its 16S rRNA gene sequence, is a chemolithoautotrophic marine bacterium exhibiting sodium chloride-stimulated thiosulfate-oxidizing activities. A novel thiosulfate:quinone oxidoreductase from strain SH (SH-TQO) has been purified from its solubilized membrane fraction. The gene for SH-TQO was determined from the draft genome sequence of the strain SH. Amino acid sequences of peptides generated by the in-gel trypsin digestion of SH-TQO were found in a protein encoded by locus tag B1757_09800 of the genome of the strain SH. The gene encoded 444 amino acids with a signal peptide of 29 amino acids and was annotated to encode a porin. The gene was located in a unique genomic region, not found in A. thiooxidans strains, suggesting that the strain SH acquired this region through a horizontal gene transfer. A protein-protein basic local alignment search revealed that sulfur-oxidizing bacteria, such as Acidithiobacillus species have proteins homologous to SH-TQO, though the degree of homologies was relatively low. The protein, DoxXA, which is homologous to TQO from Acidianus amvibalens, was also found in the genomic region.
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Affiliation(s)
- Tadayoshi Kanao
- Graduate School of Environmental and Life Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan.
| | - Sultana Sharmin
- Graduate School of Environmental and Life Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan.
| | - Mirai Tokuhisa
- Graduate School of Environmental and Life Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan.
| | - Maho Otsuki
- Graduate School of Environmental and Life Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan.
| | - Kazuo Kamimura
- Graduate School of Environmental and Life Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan.
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11
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Cortés MP, Acuña V, Travisany D, Siegel A, Maass A, Latorre M. Integration of Biological Networks for Acidithiobacillus thiooxidans Describes a Modular Gene Regulatory Organization of Bioleaching Pathways. Front Mol Biosci 2020; 6:155. [PMID: 31998751 PMCID: PMC6966769 DOI: 10.3389/fmolb.2019.00155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 12/13/2019] [Indexed: 11/13/2022] Open
Abstract
Acidithiobacillus thiooxidans is one of the most studied biomining species, highlighting its ability to oxidize reduced inorganic sulfur compounds, coupled with its elevated capacity to live under an elevated concentration of heavy metals. In this work, using an in silico semi-automatic genome scale approach, two biological networks for A. thiooxidans Licanantay were generated: (i) An affinity transcriptional regulatory network composed of 42 regulatory family genes and 1,501 operons (57% genome coverage) linked through 2,646 putative DNA binding sites (arcs), (ii) A metabolic network reconstruction made of 523 genes and 1,203 reactions (22 pathways related to biomining processes). Through the identification of confident connections between both networks (V-shapes), it was possible to identify a sub-network of transcriptional factor (34 regulators) regulating genes (61 operons) encoding for proteins involved in biomining-related pathways. Network analysis suggested that transcriptional regulation of biomining genes is organized into different modules. The topological parameters showed a high hierarchical organization by levels inside this network (14 layers), highlighting transcription factors CysB, LysR, and IHF as complex modules with high degree and number of controlled pathways. In addition, it was possible to identify transcription factor modules named primary regulators (not controlled by other regulators in the sub-network). Inside this group, CysB was the main module involved in gene regulation of several bioleaching processes. In particular, metabolic processes related to energy metabolism (such as sulfur metabolism) showed a complex integrated regulation, where different primary regulators controlled several genes. In contrast, pathways involved in iron homeostasis and oxidative stress damage are mainly regulated by unique primary regulators, conferring Licanantay an efficient, and specific metal resistance response. This work shows new evidence in terms of transcriptional regulation at a systems level and broadens the study of bioleaching in A. thiooxidans species.
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Affiliation(s)
- María Paz Cortés
- Center for Mathematical Modeling, Universidad de Chile and UMI CNRS 2807, Santiago, Chile.,Center for Genome Regulation, Universidad de Chile, Santiago, Chile
| | - Vicente Acuña
- Center for Mathematical Modeling, Universidad de Chile and UMI CNRS 2807, Santiago, Chile
| | - Dante Travisany
- Center for Mathematical Modeling, Universidad de Chile and UMI CNRS 2807, Santiago, Chile.,Center for Genome Regulation, Universidad de Chile, Santiago, Chile
| | - Anne Siegel
- IRISA, UMR 6074, CNRS, Rennes, France.,INRIA, Dyliss Team, Centre Rennes-Bretagne-Atlantique, Rennes, France
| | - Alejandro Maass
- Center for Mathematical Modeling, Universidad de Chile and UMI CNRS 2807, Santiago, Chile.,Center for Genome Regulation, Universidad de Chile, Santiago, Chile.,Department of Mathematical Engineering, Universidad de Chile, Santiago, Chile
| | - Mauricio Latorre
- Center for Mathematical Modeling, Universidad de Chile and UMI CNRS 2807, Santiago, Chile.,Center for Genome Regulation, Universidad de Chile, Santiago, Chile.,Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, Santiago, Chile.,Instituto de Ciencias de la Ingeniería, Universidad de O'Higgins, Rancagua, Chile
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12
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Yang L, Zhao D, Yang J, Wang W, Chen P, Zhang S, Yan L. Acidithiobacillus thiooxidans and its potential application. Appl Microbiol Biotechnol 2019; 103:7819-7833. [PMID: 31463545 DOI: 10.1007/s00253-019-10098-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 08/12/2019] [Accepted: 08/21/2019] [Indexed: 11/26/2022]
Abstract
Acidithiobacillus thiooxidans (A. thiooxidans) is a widespread, mesophilic, obligately aerobic, extremely acidophilic, rod-shaped, and chemolithoautotrophic gram-negative gammaproteobacterium. It can obtain energy and electrons from the oxidation of reducible sulfur, and it can fix carbon dioxide and assimilate nitrate, nitrite, and ammonium to satisfy carbon and nitrogen requirement. This bacterium exists as different genomovars and its genome size range from 3.02 to 3.97 Mb. Here, we highlight the recent advances in the understanding of the general biological features of A. thiooxidans, as well as the genetic diversity and the sulfur oxidation pathway system. Additionally, the potential applications of A. thiooxidans were summarized including the recycling of metals from metal-bearing ores, electric wastes, and sludge, the improvement of alkali-salinity soils, and the removal of sulfur from sulfur-containing solids and gases.
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Affiliation(s)
- Lei Yang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, People's Republic of China
| | - Dan Zhao
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, People's Republic of China
| | - Jian Yang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, People's Republic of China
| | - Weidong Wang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, People's Republic of China
| | - Peng Chen
- School of Pharmacy, Lanzhou University, Donggang West Road No. 199, Lanzhou, 730020, People's Republic of China
| | - Shuang Zhang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, People's Republic of China.
| | - Lei Yan
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, People's Republic of China.
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13
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Alfaro-Saldaña E, Hernández-Sánchez A, Patrón-Soberano OA, Astello-García M, Méndez-Cabañas JA, García-Meza JV. Sequence analysis and confirmation of the type IV pili-associated proteins PilY1, PilW and PilV in Acidithiobacillus thiooxidans. PLoS One 2019; 14:e0199854. [PMID: 30615628 PMCID: PMC6322766 DOI: 10.1371/journal.pone.0199854] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 11/24/2018] [Indexed: 11/19/2022] Open
Abstract
Acidithiobacillus thiooxidans is an acidophilic chemolithoautotrophic bacterium widely used in the mining industry due to its metabolic sulfur-oxidizing capability. The biooxidation of sulfide minerals is enhanced through the attachment of At. thiooxidans cells to the mineral surface. The Type IV pili (TfP) of At. thiooxidans may play an important role in the bacteria attachment since TfP play a key adhesive role in the attachment and colonization of different surfaces. In this work, we report for the first time the mRNA sequence of three TfP proteins from At. thiooxidans, the adhesin protein PilY1 and the TfP pilins PilW and PilV. The nucleotide sequences of these TfP proteins show changes in some nucleotide positions with respect to the corresponding annotated sequences. The bioinformatic analyses and 3D-modeling of protein structures sustain their classification as TfP proteins, as structural homologs of the corresponding proteins of Ps. aeruginosa, results that sustain the role of PilY1, PilW and PilV in pili assembly. Also, that PilY1 comprises the conserved Neisseria-PilC (superfamily) domain of the tip-associated adhesin, while PilW of the superfamily of putative TfP assembly proteins and PilV belongs to the superfamily of TfP assembly protein. In addition, the analyses suggested the presence of specific functional domains involved in adhesion, energy transduction and signaling functions. The phylogenetic analysis indicated that the PilY1 of Acidithiobacillus genus forms a cohesive group linked with iron- and/or sulfur-oxidizing microorganisms from acid mine drainage or mine tailings.
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Affiliation(s)
- Elvia Alfaro-Saldaña
- Geomicrobiología, Metalurgia, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
- Biofísica Molecular, Instituto de Física, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - Araceli Hernández-Sánchez
- Biofísica Molecular, Instituto de Física, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - O. Araceli Patrón-Soberano
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, San Luis Potosí, México
| | - Marizel Astello-García
- Geomicrobiología, Metalurgia, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - J. Alfredo Méndez-Cabañas
- Biofísica Molecular, Instituto de Física, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - J. Viridiana García-Meza
- Geomicrobiología, Metalurgia, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
- * E-mail:
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14
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Assessment of Bioleaching Microbial Community Structure and Function Based on Next-Generation Sequencing Technologies. MINERALS 2018. [DOI: 10.3390/min8120596] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
It is widely known that bioleaching microorganisms have to cope with the complex extreme environment in which microbial ecology relating to community structure and function varies across environmental types. However, analyses of microbial ecology of bioleaching bacteria is still a challenge. To address this challenge, numerous technologies have been developed. In recent years, high-throughput sequencing technologies enabling comprehensive sequencing analysis of cellular RNA and DNA within the reach of most laboratories have been added to the toolbox of microbial ecology. The next-generation sequencing technology allowing processing DNA sequences can produce available draft genomic sequences of more bioleaching bacteria, which provides the opportunity to predict models of genetic and metabolic potential of bioleaching bacteria and ultimately deepens our understanding of bioleaching microorganism. High-throughput sequencing that focuses on targeted phylogenetic marker 16S rRNA has been effectively applied to characterize the community diversity in an ore leaching environment. RNA-seq, another application of high-throughput sequencing to profile RNA, can be for both mapping and quantifying transcriptome and has demonstrated a high efficiency in quantifying the changing expression level of each transcript under different conditions. It has been demonstrated as a powerful tool for dissecting the relationship between genotype and phenotype, leading to interpreting functional elements of the genome and revealing molecular mechanisms of adaption. This review aims to describe the high-throughput sequencing approach for bioleaching environmental microorganisms, particularly focusing on its application associated with challenges.
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15
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Rouse SL, Matthews SJ, Dueholm MS. Ecology and Biogenesis of Functional Amyloids in Pseudomonas. J Mol Biol 2018; 430:3685-3695. [PMID: 29753779 PMCID: PMC6173800 DOI: 10.1016/j.jmb.2018.05.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/03/2018] [Accepted: 05/04/2018] [Indexed: 12/02/2022]
Abstract
Functional amyloids can be found in the extracellular matrix produced by many bacteria during biofilm growth. They mediate the initial attachment of bacteria to surfaces and provide stability and functionality to mature biofilms. Efficient amyloid biogenesis requires a highly coordinated system of amyloid subunits, molecular chaperones and transport systems. The functional amyloid of Pseudomonas (Fap) represents such a system. Here, we review the phylogenetic diversification of the Fap system, its potential ecological role and the dedicated machinery required for Fap biogenesis, with a particular focus on the amyloid exporter FapF, the structure of which has been recently resolved. We also present a sequence covariance-based in silico model of the FapC fiber-forming subunit. Finally, we highlight key questions that remain unanswered and we believe deserve further attention by the scientific community.
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Affiliation(s)
- Sarah L Rouse
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Stephen J Matthews
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Morten S Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
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16
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Zhang X, Liu Z, Wei G, Yang F, Liu X. In Silico Genome-Wide Analysis Reveals the Potential Links Between Core Genome of Acidithiobacillus thiooxidans and Its Autotrophic Lifestyle. Front Microbiol 2018; 9:1255. [PMID: 29937764 PMCID: PMC6002666 DOI: 10.3389/fmicb.2018.01255] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 05/24/2018] [Indexed: 12/27/2022] Open
Abstract
The coinage “pan-genome” was first introduced dating back to 2005, and was used to elaborate the entire gene repertoire of any given species. Core genome consists of genes shared by all bacterial strains studied and is considered to encode essential functions associated with species’ basic biology and phenotypes, yet its relatedness with bacterial lifestyle of the species remains elusive. We performed the pan-genome analysis of sulfur-oxidizing acidophile Acidithiobacillus thiooxidans as a case study to highlight species’ core genome and its relevance with autotrophic lifestyle of bacterial species. The mathematical modeling based on bacterial genomes of A. thiooxidans species, including a novel strain ZBY isolated from Zambian copper mine plus eight other recognized strains, was attempted to extrapolate the expansion of its pan-genome, suggesting that A. thiooxidans pan-genome is closed. Further investigation revealed a common set of genes, many of which were assigned to metabolic profiles, notably with respect to energy metabolism, amino acid metabolism, and carbohydrate metabolism. The predicted metabolic profiles of A. thiooxidans were characterized by the fixation of inorganic carbon, assimilation of nitrogen compounds, and aerobic oxidation of various sulfur species. Notably, several hydrogenase (H2ase)-like genes dispersed in core genome might represent the novel classes due to the potential functional disparities, despite being closely related homologous genes that code for H2ase. Overall, the findings shed light on the distinguishing features of A. thiooxidans genomes on a global scale, and extend the understanding of its conserved core genome pertaining to autotrophic lifestyle.
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Affiliation(s)
- Xian Zhang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China
| | - Zhenghua Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Guanyun Wei
- College of Life Science, Nanjing Normal University, Nanjing, China
| | - Fei Yang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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17
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Hart A, Cortés MP, Latorre M, Martinez S. Codon usage bias reveals genomic adaptations to environmental conditions in an acidophilic consortium. PLoS One 2018; 13:e0195869. [PMID: 29742107 PMCID: PMC5942774 DOI: 10.1371/journal.pone.0195869] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/30/2018] [Indexed: 11/20/2022] Open
Abstract
The analysis of codon usage bias has been widely used to characterize different communities of microorganisms. In this context, the aim of this work was to study the codon usage bias in a natural consortium of five acidophilic bacteria used for biomining. The codon usage bias of the consortium was contrasted with genes from an alternative collection of acidophilic reference strains and metagenome samples. Results indicate that acidophilic bacteria preferentially have low codon usage bias, consistent with both their capacity to live in a wide range of habitats and their slow growth rate, a characteristic probably acquired independently from their phylogenetic relationships. In addition, the analysis showed significant differences in the unique sets of genes from the autotrophic species of the consortium in relation to other acidophilic organisms, principally in genes which code for proteins involved in metal and oxidative stress resistance. The lower values of codon usage bias obtained in this unique set of genes suggest higher transcriptional adaptation to living in extreme conditions, which was probably acquired as a measure for resisting the elevated metal conditions present in the mine.
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Affiliation(s)
- Andrew Hart
- UMI 2071 CNRS-UCHILE, Facultad de Ciencias Físicas y Matemáticas, Centro de Modelamiento Matemático, Universidad de Chile, Casilla 170, Correo 3, Santiago, Chile
| | - María Paz Cortés
- Mathomics, Centro de Modelamiento Matemático, Universidad de Chile, Santiago, Chile
- Fondap-Center of Genome Regulation, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Mauricio Latorre
- Mathomics, Centro de Modelamiento Matemático, Universidad de Chile, Santiago, Chile
- Fondap-Center of Genome Regulation, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, Macul, Santiago, Chile
- Universidad de O'Higgins, Instituto de Ciencias de la Ingeniería, Rancagua, Chile
- * E-mail: (ML); (SM)
| | - Servet Martinez
- Departamento de Ingeniería Matemática, UMI 2071 CNRS-UCHILE, Facultad de Ciencias Físicas y Matemáticas, Centro de Modelamiento Matemático, Universidad de Chile, Casilla 170, Correo 3, Santiago, Chile
- * E-mail: (ML); (SM)
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18
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Marra A, Cesaro A, Rene ER, Belgiorno V, Lens PNL. Bioleaching of metals from WEEE shredding dust. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2018; 210:180-190. [PMID: 29353112 DOI: 10.1016/j.jenvman.2017.12.066] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 12/12/2017] [Accepted: 12/24/2017] [Indexed: 06/07/2023]
Abstract
A bioleaching process developed in two separate steps was investigated for the recovery of base metals, precious metals and rare earth elements from dusts generated by Waste Electrical and Electronic Equipment (WEEE) shredding. In the first step, base metals were almost completely leached from the dust in 8 days by Acidithiobacillus thiooxidans (DSM 9463) that lowered the pH of the leaching solution from 3.5 to 1.0. During this step, cerium, europium and neodymium were mobilized at high percentages (>99%), whereas lanthanum and yttrium reached an extraction yield of 80%. In the second step, the cyanide producing Pseudomonas putida WSC361 mobilized 48% of gold within 3 h from the A. thiooxidans leached shredding dust. This work demonstrated the potential application of biohydrometallurgy for resource recovery from WEEE shredding dust, destined to landfill disposal, and its effectiveness in the extraction of valuable substances, including elements at high supply risk as rare earths.
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Affiliation(s)
- Alessandra Marra
- SEED - Sanitary Environmental Engineering Division, Department of Civil Engineering, University of Salerno, via Giovanni Paolo II, 84084 Fisciano, SA, Italy.
| | - Alessandra Cesaro
- SEED - Sanitary Environmental Engineering Division, Department of Civil Engineering, University of Salerno, via Giovanni Paolo II, 84084 Fisciano, SA, Italy
| | - Eldon R Rene
- UNESCO-IHE Institute for Water Education, 2611 AX Delft, The Netherlands
| | - Vincenzo Belgiorno
- SEED - Sanitary Environmental Engineering Division, Department of Civil Engineering, University of Salerno, via Giovanni Paolo II, 84084 Fisciano, SA, Italy
| | - Piet N L Lens
- UNESCO-IHE Institute for Water Education, 2611 AX Delft, The Netherlands
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19
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Razmilic V, Castro JF, Marchant F, Asenjo JA, Andrews B. Metabolic modelling and flux analysis of microorganisms from the Atacama Desert used in biotechnological processes. Antonie van Leeuwenhoek 2018; 111:1479-1491. [DOI: 10.1007/s10482-018-1031-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 01/25/2018] [Indexed: 01/16/2023]
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20
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Abstract
As the global population increases, so does the demand for minerals and energy resources. Demand for some of the major global commodities is currently growing at rates of: copper – 1.6% p.a.1; iron ore: 1.4% p.a.2; aluminium – 5% p.a.3; rare earth elements – 7% p.a.4, driven not only by population growth in China, India, and Africa, but also by increasing urbanisation and industrialisation globally. Technological advances in renewable energy production and storage, construction materials, transport, and computing could see demand for some of these resources spike by 2600% over the next 25 years under the most extreme demand scenarios5. Coupled with declining ore grades, this demand means that the global extent of mining environments is set to increase dramatically. Land disturbance attributed to mining was estimated to be 400 000 km2 in 20076, with projected rates of increase of 10 000 km2 per year7. This will increase the worldwide extent of mining environments from around 500 000 km2 at present to 1 330 000 km2 by 2100, larger than the combined land area of New South Wales and Victoria (1 050 000 km2), making them a globally important habitat for the hardiest of microbial life. The extreme geochemical and physical conditions prevalent in mining environments present great opportunities for discovery of novel microbial species and functions, as well as exciting challenges for microbiologists to apply their understanding to solve complex remediation problems.
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21
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Quatrini R, Escudero LV, Moya-Beltrán A, Galleguillos PA, Issotta F, Acosta M, Cárdenas JP, Nuñez H, Salinas K, Holmes DS, Demergasso C. Draft genome sequence of Acidithiobacillus thiooxidans CLST isolated from the acidic hypersaline Gorbea salt flat in northern Chile. Stand Genomic Sci 2017; 12:84. [PMID: 29270251 PMCID: PMC5735861 DOI: 10.1186/s40793-017-0305-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 12/06/2017] [Indexed: 01/16/2023] Open
Abstract
10.1601/nm.2199 CLST is an extremely acidophilic gamma-proteobacteria that was isolated from the Gorbea salt flat, an acidic hypersaline environment in northern Chile. This kind of environment is considered a terrestrial analog of ancient Martian terrains and a source of new material for biotechnological applications. 10.1601/nm.2199 plays a key role in industrial bioleaching; it has the capacity of generating and maintaining acidic conditions by producing sulfuric acid and it can also remove sulfur layers from the surface of minerals, which are detrimental for their dissolution. CLST is a strain of 10.1601/nm.2199 able to tolerate moderate chloride concentrations (up to 15 g L-1 Cl-), a feature that is quite unusual in extreme acidophilic microorganisms. Basic microbiological features and genomic properties of this biotechnologically relevant strain are described in this work. The 3,974,949 bp draft genome is arranged into 40 scaffolds of 389 contigs containing 3866 protein-coding genes and 75 RNAs encoding genes. This is the first draft genome of a halotolerant 10.1601/nm.2199 strain. The release of the genome sequence of this strain improves representation of these extreme acidophilic Gram negative bacteria in public databases and strengthens the framework for further investigation of the physiological diversity and ecological function of 10.1601/nm.2199 populations.
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Affiliation(s)
- Raquel Quatrini
- Fundación Ciencia & Vida, Av. Zañartu 1482, 7780272 Santiago, Chile
| | - Lorena V. Escudero
- Centro de Biotecnología “Profesor Alberto Ruiz”, Universidad Católica del Norte, 1270709 Antofagasta, Chile
- Centro de Investigación Científica y Tecnológica para la Minería, Antofagasta, Chile
| | - Ana Moya-Beltrán
- Fundación Ciencia & Vida, Av. Zañartu 1482, 7780272 Santiago, Chile
| | - Pedro A. Galleguillos
- Centro de Biotecnología “Profesor Alberto Ruiz”, Universidad Católica del Norte, 1270709 Antofagasta, Chile
- Centro de Investigación Científica y Tecnológica para la Minería, Antofagasta, Chile
| | | | - Mauricio Acosta
- Centro de Biotecnología “Profesor Alberto Ruiz”, Universidad Católica del Norte, 1270709 Antofagasta, Chile
| | | | - Harold Nuñez
- Fundación Ciencia & Vida, Av. Zañartu 1482, 7780272 Santiago, Chile
| | | | - David S. Holmes
- Fundación Ciencia & Vida, Av. Zañartu 1482, 7780272 Santiago, Chile
- Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile
| | - Cecilia Demergasso
- Centro de Biotecnología “Profesor Alberto Ruiz”, Universidad Católica del Norte, 1270709 Antofagasta, Chile
- Centro de Investigación Científica y Tecnológica para la Minería, Antofagasta, Chile
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22
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Castro M, Moya-Beltrán A, Covarrubias PC, Gonzalez M, Cardenas JP, Issotta F, Nuñez H, Acuña LG, Encina G, Holmes DS, Johnson DB, Quatrini R. Draft genome sequence of the type strain of the sulfur-oxidizing acidophile, Acidithiobacillus albertensis (DSM 14366). Stand Genomic Sci 2017; 12:77. [PMID: 29255572 PMCID: PMC5731081 DOI: 10.1186/s40793-017-0282-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 11/21/2017] [Indexed: 12/13/2022] Open
Abstract
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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Affiliation(s)
- Matías Castro
- Fundación Ciencia & Vida, Av. Zañartu 1482, Santiago, 7780272 Chile
| | - Ana Moya-Beltrán
- Fundación Ciencia & Vida, Av. Zañartu 1482, Santiago, 7780272 Chile
| | - Paulo C. Covarrubias
- Fundación Ciencia & Vida, Av. Zañartu 1482, Santiago, 7780272 Chile
- Current Address: uBiome Chile, SpA, Santiago, Chile
| | - Mónica Gonzalez
- Fundación Ciencia & Vida, Av. Zañartu 1482, Santiago, 7780272 Chile
| | - Juan Pablo Cardenas
- Fundación Ciencia & Vida, Av. Zañartu 1482, Santiago, 7780272 Chile
- Current Address: uBiome Chile, SpA, Santiago, Chile
| | | | - Harold Nuñez
- Fundación Ciencia & Vida, Av. Zañartu 1482, Santiago, 7780272 Chile
- Current Address: uBiome Chile, SpA, Santiago, Chile
| | - Lillian G. Acuña
- Fundación Ciencia & Vida, Av. Zañartu 1482, Santiago, 7780272 Chile
| | | | - David S. Holmes
- Fundación Ciencia & Vida, Av. Zañartu 1482, Santiago, 7780272 Chile
- Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | | | - Raquel Quatrini
- Fundación Ciencia & Vida, Av. Zañartu 1482, Santiago, 7780272 Chile
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23
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Bull AT, Asenjo JA, Goodfellow M, Gómez-Silva B. The Atacama Desert: Technical Resources and the Growing Importance of Novel Microbial Diversity. Annu Rev Microbiol 2017; 70:215-34. [PMID: 27607552 DOI: 10.1146/annurev-micro-102215-095236] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The Atacama Desert of northern Chile is the oldest and most arid nonpolar environment on Earth. It is a coastal desert covering approximately 180,000 km(2), and together with the greater Atacama region it comprises a dramatically wide range of ecological niches. Long known and exploited for its mineral resources, the Atacama Desert harbors a rich microbial diversity that has only recently been discovered; the great majority of it has not yet been recovered in culture or even taxonomically identified. This review traces the progress of microbiology research in the Atacama and dispels the popular view that this region is virtually devoid of life. We examine reasons for such research activity and demonstrate that microbial life is the latest recognized and least explored resource in this inspiring biome.
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Affiliation(s)
- Alan T Bull
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, United Kingdom;
| | - Juan A Asenjo
- Center for Biotechnology and Bioengineering, University of Chile, Santiago, Chile.,Department of Chemical Engineering and Biotechnology, University of Chile, Santiago, Chile;
| | - Michael Goodfellow
- School of Biology, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom;
| | - Benito Gómez-Silva
- Biochemistry Laboratory, Biomedical Department, Faculty of Health Sciences, University of Antofagasta, Chile;
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24
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Nuñez H, Moya-Beltrán A, Covarrubias PC, Issotta F, Cárdenas JP, González M, Atavales J, Acuña LG, Johnson DB, Quatrini R. Molecular Systematics of the Genus Acidithiobacillus: Insights into the Phylogenetic Structure and Diversification of the Taxon. Front Microbiol 2017; 8:30. [PMID: 28154559 PMCID: PMC5243848 DOI: 10.3389/fmicb.2017.00030] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/05/2017] [Indexed: 11/13/2022] Open
Abstract
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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Affiliation(s)
- Harold Nuñez
- Microbial Ecophysiology Laboratory, Fundación Ciencia & VidaSantiago, Chile
| | - Ana Moya-Beltrán
- Microbial Ecophysiology Laboratory, Fundación Ciencia & VidaSantiago, Chile
- Faculty of Biological Sciences, Andres Bello UniversitySantiago, Chile
| | | | - Francisco Issotta
- Microbial Ecophysiology Laboratory, Fundación Ciencia & VidaSantiago, Chile
| | | | - Mónica González
- Microbial Ecophysiology Laboratory, Fundación Ciencia & VidaSantiago, Chile
| | - Joaquín Atavales
- Microbial Ecophysiology Laboratory, Fundación Ciencia & VidaSantiago, Chile
| | - Lillian G. Acuña
- Microbial Ecophysiology Laboratory, Fundación Ciencia & VidaSantiago, Chile
| | | | - Raquel Quatrini
- Microbial Ecophysiology Laboratory, Fundación Ciencia & VidaSantiago, Chile
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González C, Lazcano M, Valdés J, Holmes DS. Bioinformatic Analyses of Unique (Orphan) Core Genes of the Genus Acidithiobacillus: Functional Inferences and Use As Molecular Probes for Genomic and Metagenomic/Transcriptomic Interrogation. Front Microbiol 2016; 7:2035. [PMID: 28082953 PMCID: PMC5186765 DOI: 10.3389/fmicb.2016.02035] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 12/02/2016] [Indexed: 01/06/2023] Open
Abstract
Using phylogenomic and gene compositional analyses, five highly conserved gene families have been detected in the core genome of the phylogenetically coherent genus Acidithiobacillus of the class Acidithiobacillia. These core gene families are absent in the closest extant genus Thermithiobacillus tepidarius that subtends the Acidithiobacillus genus and roots the deepest in this class. The predicted proteins encoded by these core gene families are not detected by a BLAST search in the NCBI non-redundant database of more than 90 million proteins using a relaxed cut-off of 1.0e−5. None of the five families has a clear functional prediction. However, bioinformatic scrutiny, using pI prediction, motif/domain searches, cellular location predictions, genomic context analyses, and chromosome topology studies together with previously published transcriptomic and proteomic data, suggests that some may have functions associated with membrane remodeling during cell division perhaps in response to pH stress. Despite the high level of amino acid sequence conservation within each family, there is sufficient nucleotide variation of the respective genes to permit the use of the DNA sequences to distinguish different species of Acidithiobacillus, making them useful additions to the armamentarium of tools for phylogenetic analysis. Since the protein families are unique to the Acidithiobacillus genus, they can also be leveraged as probes to detect the genus in environmental metagenomes and metatranscriptomes, including industrial biomining operations, and acid mine drainage (AMD).
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Affiliation(s)
- Carolina González
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & VidaSantiago, Chile; Facultad de Ciencias Biologicas, Universidad Andres BelloSantiago, Chile
| | - Marcelo Lazcano
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & VidaSantiago, Chile; Facultad de Ciencias Biologicas, Universidad Andres BelloSantiago, Chile
| | - Jorge Valdés
- Center for Genomics and Bioinformatics, Faculty of Sciences, Universidad Mayor Santiago, Chile
| | - David S Holmes
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & VidaSantiago, Chile; Facultad de Ciencias Biologicas, Universidad Andres BelloSantiago, Chile
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Martínez-Bussenius C, Navarro CA, Jerez CA. Microbial copper resistance: importance in biohydrometallurgy. Microb Biotechnol 2016; 10:279-295. [PMID: 27790868 PMCID: PMC5328820 DOI: 10.1111/1751-7915.12450] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 09/30/2016] [Accepted: 10/03/2016] [Indexed: 11/29/2022] Open
Abstract
Industrial biomining has been extensively used for many years to recover valuable metals such as copper, gold, uranium and others. Furthermore, microorganisms involved in these processes can also be used to bioremediate places contaminated with acid and metals. These uses are possible due to the great metal resistance that these extreme acidophilic microorganisms possess. In this review, the most recent findings related to copper resistance mechanisms of bacteria and archaea related to biohydrometallurgy are described. The recent search for novel metal resistance determinants is not only of scientific interest but also of industrial importance, as reflected by the genomic sequencing of microorganisms present in mining operations and the search of those bacteria with extreme metal resistance to improve the extraction processes used by the biomining companies.
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Affiliation(s)
- Cristóbal Martínez-Bussenius
- Laboratory of Molecular Microbiology and Biotechnology, Department of Biology, Faculty of Sciences, University of Chile, Santiago, Chile
| | - Claudio A Navarro
- Laboratory of Molecular Microbiology and Biotechnology, Department of Biology, Faculty of Sciences, University of Chile, Santiago, Chile
| | - Carlos A Jerez
- Laboratory of Molecular Microbiology and Biotechnology, Department of Biology, Faculty of Sciences, University of Chile, Santiago, Chile
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Latorre M, Cortés MP, Travisany D, Di Genova A, Budinich M, Reyes-Jara A, Hödar C, González M, Parada P, Bobadilla-Fazzini RA, Cambiazo V, Maass A. The bioleaching potential of a bacterial consortium. BIORESOURCE TECHNOLOGY 2016; 218:659-666. [PMID: 27416516 DOI: 10.1016/j.biortech.2016.07.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 07/02/2016] [Accepted: 07/04/2016] [Indexed: 06/06/2023]
Abstract
This work presents the molecular foundation of a consortium of five efficient bacteria strains isolated from copper mines currently used in state of the art industrial-scale biotechnology. The strains Acidithiobacillus thiooxidans Licanantay, Acidiphilium multivorum Yenapatur, Leptospirillum ferriphilum Pañiwe, Acidithiobacillus ferrooxidans Wenelen and Sulfobacillus thermosulfidooxidans Cutipay were selected for genome sequencing based on metal tolerance, oxidation activity and bioleaching of copper efficiency. An integrated model of metabolic pathways representing the bioleaching capability of this consortium was generated. Results revealed that greater efficiency in copper recovery may be explained by the higher functional potential of L. ferriphilum Pañiwe and At. thiooxidans Licanantay to oxidize iron and reduced inorganic sulfur compounds. The consortium had a greater capacity to resist copper, arsenic and chloride ion compared to previously described biomining strains. Specialization and particular components in these bacteria provided the consortium a greater ability to bioleach copper sulfide ores.
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Affiliation(s)
- Mauricio Latorre
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, 7th Floor, Santiago, Chile; Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile; Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, El Líbano 5524, Macul, Santiago, Chile
| | - María Paz Cortés
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, 7th Floor, Santiago, Chile; Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile
| | - Dante Travisany
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, 7th Floor, Santiago, Chile; Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile
| | - Alex Di Genova
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, 7th Floor, Santiago, Chile; Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile
| | - Marko Budinich
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, 7th Floor, Santiago, Chile; Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile
| | - Angélica Reyes-Jara
- Laboratorio de Microbiología y Probióticos, INTA, Universidad de Chile, El Líbano 5524, Macul, Santiago, Chile
| | - Christian Hödar
- Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile; Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, El Líbano 5524, Macul, Santiago, Chile
| | - Mauricio González
- Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile; Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, El Líbano 5524, Macul, Santiago, Chile
| | - Pilar Parada
- BioSigma S.A., Loteo Los Libertadores, Lote 106, Colina, Chile
| | | | - Verónica Cambiazo
- Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile; Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, El Líbano 5524, Macul, Santiago, Chile
| | - Alejandro Maass
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, 7th Floor, Santiago, Chile; Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile; Department of Mathematical Engineering, Universidad de Chile, Beauchef 851, 5th Floor, Santiago, Chile.
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28
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Zhang X, Liu X, Liang Y, Fan F, Zhang X, Yin H. Metabolic diversity and adaptive mechanisms of iron- and/or sulfur-oxidizing autotrophic acidophiles in extremely acidic environments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:738-751. [PMID: 27337207 DOI: 10.1111/1758-2229.12435] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 05/30/2016] [Indexed: 06/06/2023]
Abstract
Many studies have investigated the mechanisms underlying the survival and growth of certain organisms in extremely acidic environments known to be harmful to most prokaryotes and eukaryotes. Acidithiobacillus and Leptospirillum spp. are dominant bioleaching bacteria widely used in bioleaching systems, which are characterized by extremely acidic environments. To survive and grow in such settings, these acidophiles utilize shared molecular mechanisms that allow life in extreme conditions. In this review, we have summarized the results of published genomic analyses, which underscore the ability of iron- and/or sulfur-oxidizing autotrophic acidophiles belonging to the genera Acidithiobacillus and Leptospirillum to adapt to acidic environmental conditions. Several lines of evidence point at the metabolic diversity and multiplicity of pathways involved in the survival of these organisms. The ability to thrive in adverse environments requires versatile activation of structural and functional adaptive responses, including bacterial adhesion, motility, and resistance to heavy metals. We have highlighted recent developments centered on the key survival mechanisms employed by dominant extremophiles, and have laid the foundation for future studies focused on the ability of acidophiles to thrive in extremely acidic environments.
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Affiliation(s)
- Xian Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Fenliang Fan
- Key Laboratory of Plant Nutrition and Fertilizer, Beijing, China
| | - Xiaoxia Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Beijing, China
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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Zhang X, She S, Dong W, Niu J, Xiao Y, Liang Y, Liu X, Zhang X, Fan F, Yin H. Comparative genomics unravels metabolic differences at the species and/or strain level and extremely acidic environmental adaptation of ten bacteria belonging to the genus Acidithiobacillus. Syst Appl Microbiol 2016; 39:493-502. [PMID: 27712915 DOI: 10.1016/j.syapm.2016.08.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 07/22/2016] [Accepted: 08/11/2016] [Indexed: 01/17/2023]
Abstract
Members of the Acidithiobacillus genus are widely found in extreme environments characterized by low pH and high concentrations of toxic substances, thus it is necessary to identify the cellular mechanisms needed to cope with these harsh conditions. Pan-genome analysis of ten bacteria belonging to the genus Acidithiobacillus suggested the existence of core genome, most of which were assigned to the metabolism-associated genes. Additionally, the unique genes of Acidithiobacillus ferrooxidans were much less than those of other species. A large proportion of Acidithiobacillus ferrivorans-specific genes were mapped especially to metabolism-related genes, indicating that diverse metabolic pathways might confer an advantage for adaptation to local environmental conditions. Analyses of functional metabolisms revealed the differences of carbon metabolism, nitrogen metabolism, and sulfur metabolism at the species and/or strain level. The findings also showed that Acidithiobacillus spp. harbored specific adaptive mechanisms for thriving under extreme environments. The genus Acidithiobacillus had the genetic potential to resist and metabolize toxic substances such as heavy metals and organic solvents. Comparison across species and/or strains of Acidithiobacillus populations provided a deeper appreciation of metabolic differences and environmental adaptation, as well as highlighting the importance of cellular mechanisms that maintain the basal physiological functions under complex acidic environmental conditions.
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Affiliation(s)
- Xian Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China; Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, China.
| | - Siyuan She
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China; Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, China.
| | - Weiling Dong
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China; Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, China.
| | - Jiaojiao Niu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China; Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, China.
| | - Yunhua Xiao
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China; Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, China.
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China; Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, China.
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China; Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, China.
| | - Xiaoxia Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Beijing, China; Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Fenliang Fan
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China; Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, Beijing, China.
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China; Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, China.
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A Multi-Serotype Approach Clarifies the Catabolite Control Protein A Regulon in the Major Human Pathogen Group A Streptococcus. Sci Rep 2016; 6:32442. [PMID: 27580596 PMCID: PMC5007534 DOI: 10.1038/srep32442] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 08/04/2016] [Indexed: 12/20/2022] Open
Abstract
Catabolite control protein A (CcpA) is a highly conserved, master regulator of carbon source utilization in gram-positive bacteria, but the CcpA regulon remains ill-defined. In this study we aimed to clarify the CcpA regulon by determining the impact of CcpA-inactivation on the virulence and transcriptome of three distinct serotypes of the major human pathogen Group A Streptococcus (GAS). CcpA-inactivation significantly decreased GAS virulence in a broad array of animal challenge models consistent with the idea that CcpA is critical to gram-positive bacterial pathogenesis. Via comparative transcriptomics, we established that the GAS CcpA core regulon is enriched for highly conserved CcpA binding motifs (i.e. cre sites). Conversely, strain-specific differences in the CcpA transcriptome seems to consist primarily of affected secondary networks. Refinement of cre site composition via analysis of the core regulon facilitated development of a modified cre consensus that shows promise for improved prediction of CcpA targets in other medically relevant gram-positive pathogens.
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31
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Nuñez H, Covarrubias PC, Moya-Beltrán A, Issotta F, Atavales J, Acuña LG, Johnson DB, Quatrini R. Detection, identification and typing of Acidithiobacillus species and strains: a review. Res Microbiol 2016; 167:555-67. [DOI: 10.1016/j.resmic.2016.05.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/19/2016] [Accepted: 05/23/2016] [Indexed: 01/10/2023]
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32
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Comparative Genomics of the Extreme Acidophile Acidithiobacillus thiooxidans Reveals Intraspecific Divergence and Niche Adaptation. Int J Mol Sci 2016; 17:ijms17081355. [PMID: 27548157 PMCID: PMC5000751 DOI: 10.3390/ijms17081355] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Revised: 08/05/2016] [Accepted: 08/11/2016] [Indexed: 11/17/2022] Open
Abstract
Acidithiobacillus thiooxidans known for its ubiquity in diverse acidic and sulfur-bearing environments worldwide was used as the research subject in this study. To explore the genomic fluidity and intraspecific diversity of Acidithiobacillus thiooxidans (A. thiooxidans) species, comparative genomics based on nine draft genomes was performed. Phylogenomic scrutiny provided first insights into the multiple groupings of these strains, suggesting that genetic diversity might be potentially correlated with their geographic distribution as well as geochemical conditions. While these strains shared a large number of common genes, they displayed differences in gene content. Functional assignment indicated that the core genome was essential for microbial basic activities such as energy acquisition and uptake of nutrients, whereas the accessory genome was thought to be involved in niche adaptation. Comprehensive analysis of their predicted central metabolism revealed that few differences were observed among these strains. Further analyses showed evidences of relevance between environmental conditions and genomic diversification. Furthermore, a diverse pool of mobile genetic elements including insertion sequences and genomic islands in all A. thiooxidans strains probably demonstrated the frequent genetic flow (such as lateral gene transfer) in the extremely acidic environments. From another perspective, these elements might endow A. thiooxidans species with capacities to withstand the chemical constraints of their natural habitats. Taken together, our findings bring some valuable data to better understand the genomic diversity and econiche adaptation within A. thiooxidans strains.
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Cárdenas JP, Quatrini R, Holmes DS. Genomic and metagenomic challenges and opportunities for bioleaching: a mini-review. Res Microbiol 2016; 167:529-38. [PMID: 27394987 DOI: 10.1016/j.resmic.2016.06.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 06/28/2016] [Accepted: 06/29/2016] [Indexed: 12/19/2022]
Abstract
High-throughput genomic technologies are accelerating progress in understanding the diversity of microbial life in many environments. Here we highlight advances in genomics and metagenomics of microorganisms from bioleaching heaps and related acidic mining environments. Bioleaching heaps used for copper recovery provide significant opportunities to study the processes and mechanisms underlying microbial successions and the influence of community composition on ecosystem functioning. Obtaining quantitative and process-level knowledge of these dynamics is pivotal for understanding how microorganisms contribute to the solubilization of copper for industrial recovery. Advances in DNA sequencing technology provide unprecedented opportunities to obtain information about the genomes of bioleaching microorganisms, allowing predictive models of metabolic potential and ecosystem-level interactions to be constructed. These approaches are enabling predictive phenotyping of organisms many of which are recalcitrant to genetic approaches or are unculturable. This mini-review describes current bioleaching genomic and metagenomic projects and addresses the use of genome information to: (i) build metabolic models; (ii) predict microbial interactions; (iii) estimate genetic diversity; and (iv) study microbial evolution. Key challenges and perspectives of bioleaching genomics/metagenomics are addressed.
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Affiliation(s)
| | | | - David S Holmes
- Fundación Ciencia & Vida, Santiago, Chile; Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile.
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Biogeography of sulfur-oxidizing Acidithiobacillus populations in extremely acidic cave biofilms. ISME JOURNAL 2016; 10:2879-2891. [PMID: 27187796 PMCID: PMC5148195 DOI: 10.1038/ismej.2016.74] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Revised: 03/17/2016] [Accepted: 03/24/2016] [Indexed: 02/01/2023]
Abstract
Extremely acidic (pH 0–1.5) Acidithiobacillus-dominated biofilms known as snottites are found in sulfide-rich caves around the world. Given the extreme geochemistry and subsurface location of the biofilms, we hypothesized that snottite Acidithiobacillus populations would be genetically isolated. We therefore investigated biogeographic relationships among snottite Acidithiobacillus spp. separated by geographic distances ranging from meters to 1000s of kilometers. We determined genetic relationships among the populations using techniques with three levels of resolution: (i) 16S rRNA gene sequencing, (ii) 16S–23S intergenic transcribed spacer (ITS) region sequencing and (iii) multi-locus sequencing typing (MLST). We also used metagenomics to compare functional gene characteristics of select populations. Based on 16S rRNA genes, snottites in Italy and Mexico are dominated by different sulfur-oxidizing Acidithiobacillus spp. Based on ITS sequences, Acidithiobacillus thiooxidans strains from different cave systems in Italy are genetically distinct. Based on MLST of isolates from Italy, genetic distance is positively correlated with geographic distance both among and within caves. However, metagenomics revealed that At. thiooxidans populations from different cave systems in Italy have different sulfur oxidation pathways and potentially other significant differences in metabolic capabilities. In light of those genomic differences, we argue that the observed correlation between genetic and geographic distance among snottite Acidithiobacillus populations is partially explained by an evolutionary model in which separate cave systems were stochastically colonized by different ancestral surface populations, which then continued to diverge and adapt in situ.
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35
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Latorre M, Ehrenfeld N, Cortés MP, Travisany D, Budinich M, Aravena A, González M, Bobadilla-Fazzini RA, Parada P, Maass A. Global transcriptional responses of Acidithiobacillus ferrooxidans Wenelen under different sulfide minerals. BIORESOURCE TECHNOLOGY 2016; 200:29-34. [PMID: 26476161 DOI: 10.1016/j.biortech.2015.09.110] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 09/28/2015] [Accepted: 09/29/2015] [Indexed: 06/05/2023]
Abstract
In order to provide new information about the adaptation of Acidithiobacillus ferrooxidans during the bioleaching process, the current analysis presents the first report of the global transcriptional response of the native copper mine strain Wenelen (DSM 16786) oxidized under different sulfide minerals. Microarrays were used to measure the response of At. ferrooxidans Wenelen to shifts from iron supplemented liquid cultures (reference state) to the addition of solid substrates enriched in pyrite or chalcopyrite. Genes encoding for energy metabolism showed a similar transcriptional profile for the two sulfide minerals. Interestingly, four operons related to sulfur metabolism were over-expressed during growth on a reduced sulfur source. Genes associated with metal tolerance (RND and ATPases type P) were up-regulated in the presence of pyrite or chalcopyrite. These results suggest that At. ferrooxidans Wenelen presents an efficient transcriptional system developed to respond to environmental conditions, namely the ability to withstand high copper concentrations.
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Affiliation(s)
- Mauricio Latorre
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, 7th Floor, Santiago, Chile; Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile; Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, El Líbano 5524, Macul, Santiago, Chile
| | - Nicole Ehrenfeld
- BioSigma S.A., Loteo Los Libertadores, Lote 106, Colina, Chile; Austral Biotech S.A., Francisco Noguera 41, Santiago, Chile
| | - María Paz Cortés
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, 7th Floor, Santiago, Chile; Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile
| | - Dante Travisany
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, 7th Floor, Santiago, Chile; Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile
| | - Marko Budinich
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, 7th Floor, Santiago, Chile; Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile
| | - Andrés Aravena
- Department of Molecular Biology and Genetics, Istanbul University, Istanbul, Turkey
| | - Mauricio González
- Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile; Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, El Líbano 5524, Macul, Santiago, Chile
| | | | - Pilar Parada
- BioSigma S.A., Loteo Los Libertadores, Lote 106, Colina, Chile
| | - Alejandro Maass
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, 7th Floor, Santiago, Chile; Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile; BioSigma S.A., Loteo Los Libertadores, Lote 106, Colina, Chile; Department of Mathematical Engineering, Universidad de Chile, Beauchef 851, 5th Floor, Santiago, Chile.
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Martinez P, Vera M, Bobadilla-Fazzini RA. Omics on bioleaching: current and future impacts. Appl Microbiol Biotechnol 2015; 99:8337-50. [PMID: 26278538 PMCID: PMC4768214 DOI: 10.1007/s00253-015-6903-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 07/27/2015] [Accepted: 07/30/2015] [Indexed: 11/28/2022]
Abstract
Bioleaching corresponds to the microbial-catalyzed process of conversion of insoluble metals into soluble forms. As an applied biotechnology globally used, it represents an extremely interesting field of research where omics techniques can be applied in terms of knowledge development, but moreover in terms of process design, control, and optimization. In this mini-review, the current state of genomics, proteomics, and metabolomics of bioleaching and the major impacts of these analytical methods at industrial scale are highlighted. In summary, genomics has been essential in the determination of the biodiversity of leaching processes and for development of conceptual and functional metabolic models. Proteomic impacts are mostly related to microbe-mineral interaction analysis, including copper resistance and biofilm formation. Early steps of metabolomics in the field of bioleaching have shown a significant potential for the use of metabolites as industrial biomarkers. Development directions are given in order to enhance the future impacts of the omics in biohydrometallurgy.
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Affiliation(s)
- Patricio Martinez
- BioSigma 'S.A.', Parque Industrial Los Libertadores, Lote 106, Colina, Chile
| | - Mario Vera
- Biofilm Centre, Aquatische Biotechnologie, Universität Duisburg-Essen, Universitätstraße 5, 45141, Essen, Germany
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Sharmin S, Yoshino E, Kanao T, Kamimura K. Characterization of a novel thiosulfate dehydrogenase from a marine acidophilic sulfur-oxidizing bacterium, Acidithiobacillus thiooxidans strain SH. Biosci Biotechnol Biochem 2015; 80:273-8. [PMID: 26393925 DOI: 10.1080/09168451.2015.1088377] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
A marine acidophilic sulfur-oxidizing bacterium, Acidithiobacillus thiooxidans strain SH, was isolated to develop a bioleaching process for NaCl-containing sulfide minerals. Because the sulfur moiety of sulfide minerals is metabolized to sulfate via thiosulfate as an intermediate, we purified and characterized the thiosulfate dehydrogenase (TSD) from strain SH. The enzyme had an apparent molecular mass of 44 kDa and was purified 71-fold from the solubilized membrane fraction. Tetrathionate was the product of the TSD-oxidized thiosulfate and ferricyanide or ubiquinone was the electron acceptor. Maximum enzyme activity was observed at pH 4.0, 40 °C, and 200 mM NaCl. To our knowledge, this is the first report of NaCl-stimulated TSD activity. TSD was structurally different from the previously reported thiosulfate-oxidizing enzymes. In addition, TSD activity was strongly inhibited by 2-heptyl-4-hydroxy-quinoline N-oxide, suggesting that the TSD is a novel thiosulfate:quinone reductase.
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Affiliation(s)
- Sultana Sharmin
- a Division of Agricultural and Life Science, Graduate School of Environmental and Life Science , Okayama University , Okayama , Japan
| | - Eriko Yoshino
- a Division of Agricultural and Life Science, Graduate School of Environmental and Life Science , Okayama University , Okayama , Japan
| | - Tadayoshi Kanao
- a Division of Agricultural and Life Science, Graduate School of Environmental and Life Science , Okayama University , Okayama , Japan
| | - Kazuo Kamimura
- a Division of Agricultural and Life Science, Graduate School of Environmental and Life Science , Okayama University , Okayama , Japan
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