1
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Leung PM, Grinter R, Tudor-Matthew E, Lingford JP, Jimenez L, Lee HC, Milton M, Hanchapola I, Tanuwidjaya E, Kropp A, Peach HA, Carere CR, Stott MB, Schittenhelm RB, Greening C. Trace gas oxidation sustains energy needs of a thermophilic archaeon at suboptimal temperatures. Nat Commun 2024; 15:3219. [PMID: 38622143 PMCID: PMC11018855 DOI: 10.1038/s41467-024-47324-2] [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: 02/03/2023] [Accepted: 03/22/2024] [Indexed: 04/17/2024] Open
Abstract
Diverse aerobic bacteria use atmospheric hydrogen (H2) and carbon monoxide (CO) as energy sources to support growth and survival. Such trace gas oxidation is recognised as a globally significant process that serves as the main sink in the biogeochemical H2 cycle and sustains microbial biodiversity in oligotrophic ecosystems. However, it is unclear whether archaea can also use atmospheric H2. Here we show that a thermoacidophilic archaeon, Acidianus brierleyi (Thermoproteota), constitutively consumes H2 and CO to sub-atmospheric levels. Oxidation occurs across a wide range of temperatures (10 to 70 °C) and enhances ATP production during starvation-induced persistence under temperate conditions. The genome of A. brierleyi encodes a canonical CO dehydrogenase and four distinct [NiFe]-hydrogenases, which are differentially produced in response to electron donor and acceptor availability. Another archaeon, Metallosphaera sedula, can also oxidize atmospheric H2. Our results suggest that trace gas oxidation is a common trait of Sulfolobales archaea and may play a role in their survival and niche expansion, including during dispersal through temperate environments.
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Affiliation(s)
- Pok Man Leung
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.
| | - Rhys Grinter
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Eve Tudor-Matthew
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - James P Lingford
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Luis Jimenez
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Han-Chung Lee
- Monash Proteomics and Metabolomics Platform and Department of Biochemistry, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Michael Milton
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Iresha Hanchapola
- Monash Proteomics and Metabolomics Platform and Department of Biochemistry, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Erwin Tanuwidjaya
- Monash Proteomics and Metabolomics Platform and Department of Biochemistry, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Ashleigh Kropp
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Hanna A Peach
- Geomicrobiology Research Group, Department of Geothermal Sciences, Te Pū Ao | GNS Science, Wairakei, Taupō, 3377, Aotearoa New Zealand
| | - Carlo R Carere
- Geomicrobiology Research Group, Department of Geothermal Sciences, Te Pū Ao | GNS Science, Wairakei, Taupō, 3377, Aotearoa New Zealand
- Te Tari Pūhanga Tukanga Matū | Department of Chemical and Process Engineering, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, 8140, Aotearoa New Zealand
| | - Matthew B Stott
- Geomicrobiology Research Group, Department of Geothermal Sciences, Te Pū Ao | GNS Science, Wairakei, Taupō, 3377, Aotearoa New Zealand
- Te Kura Pūtaiao Koiora | School of Biological Sciences, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, 8140, Aotearoa New Zealand
| | - Ralf B Schittenhelm
- Monash Proteomics and Metabolomics Platform and Department of Biochemistry, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.
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2
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Chang Z, Su B, Zhang C, Zhang C, Song X. Effects of complex sulphur substrates on sludge bioleaching to improve heavy metal removal and microbial community diversity. CHEMOSPHERE 2023; 339:139532. [PMID: 37467854 DOI: 10.1016/j.chemosphere.2023.139532] [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: 03/27/2023] [Revised: 07/08/2023] [Accepted: 07/15/2023] [Indexed: 07/21/2023]
Abstract
In this study, H2S was used as a partial replacement nutrient substrate for sludge bioleaching. The effects of different combinations of H2S/sludge load and monomeric sulphur on heavy metal removal and microbial communities were investigated. Changes in pH, oxidation-reduction potential (ORP), SO42- concentration, heavy metal removal, and the content of heavy metal states during bioleaching were investigated, and community diversity analysis was performed. Daily introduction of H2S three times (at an interval of 8 h) at a gas flow rate of 2 ml/min and an H2S/sludge load of 15 ml/L with 5 g/L FeSO4·7H2O and 2 g/L monomeric sulphur as a nutrient substrate significantly accelerated both the bioleaching process and the pH drop in the sludge system, promoted the production of SO42-, and maintained a higher redox potential. The combination of H2S and monomeric sulphur had a significant effect on the leaching of heavy metals. Compared with the experimental group containing only H2S or monomeric sulphur, the removal rates of Zn, Ni, Pb, and Cr increased by 4.63%/13.8%, 8.5%/20.07%, 3.84%/9.5%, and 4.24%/8.02% respectively, while promoting the transformation of various heavy metal states to labile states, improving heavy metal stability, and reducing sludge ecotoxicity. High-throughput sequencing analysis showed that introducing the H2S gaseous matrix accelerated the decreasing trend of species number, bacterial abundance, and community diversity in the sludge system, promoting Proteobacteria as the dominant phylum, Acidithiobacillus, Metallibacterium, and Thiomonas as the dominant genera, and improving the bioleaching treatment effect.
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Affiliation(s)
- Zhankun Chang
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, 030024, Shanxi, China; Shanxi Municipal Engineering Postgraduate Education Innovation Centre, Taiyuan, 030024, Shanxi, China
| | - Bingqin Su
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, 030024, Shanxi, China; Shanxi Municipal Engineering Postgraduate Education Innovation Centre, Taiyuan, 030024, Shanxi, China.
| | - Chi Zhang
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, 030024, Shanxi, China
| | - Congzheng Zhang
- Shanxi Installation Group Co., Ltd, Taiyuan, 030024, Shanxi, China
| | - Xintong Song
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, 030024, Shanxi, China; Shanxi Municipal Engineering Postgraduate Education Innovation Centre, Taiyuan, 030024, Shanxi, China
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3
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Feng X, Li Y, Tian C, Yang W, Liu X, Zhang C, Zeng Z. Isolation of archaeal viruses with lipid membrane from Tengchong acidic hot springs. Front Microbiol 2023; 14:1134935. [PMID: 37065132 PMCID: PMC10101205 DOI: 10.3389/fmicb.2023.1134935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 03/14/2023] [Indexed: 03/31/2023] Open
Abstract
Archaeal viruses are one of the most mysterious parts of the virosphere because of their diverse morphologies and unique genome contents. The crenarchaeal viruses are commonly found in high temperature and acidic hot springs, and the number of identified crenarchaeal viruses is being rapidly increased in recent two decades. Over fifty viruses infecting the members of the order Sulfolobales have been identified, most of which are from hot springs distributed in the United States, Russia, Iceland, Japan, and Italy. To further expand the reservoir of viruses infecting strains of Sulfolobaceae, we investigated virus diversity through cultivation-dependent approaches in hot springs in Tengchong, Yunnan, China. Eight different virus-like particles were detected in enrichment cultures, among which five new archaeal viruses were isolated and characterized. We showed that these viruses can infect acidophilic hyperthermophiles belonging to three different genera of the family Sulfolobaceae, namely, Saccharolobus, Sulfolobus, and Metallosphaera. We also compared the lipid compositions of the viral and cellular membranes and found that the lipid composition of some viral envelopes was very different from that of the host membrane. Collectively, our results showed that the Tengchong hot springs harbor highly diverse viruses, providing excellent models for archaeal virus-host studies.
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Affiliation(s)
- Xi Feng
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Yanan Li
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Chang Tian
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Wei Yang
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Xinyu Liu
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Changyi Zhang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- *Correspondence: Zhirui Zeng, ; Changyi Zhang,
| | - Zhirui Zeng
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
- *Correspondence: Zhirui Zeng, ; Changyi Zhang,
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4
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Hofmann M, Norris PR, Malik L, Schippers A, Schmidt G, Wolf J, Neumann-Schaal M, Hedrich S. Metallosphaera javensis sp. nov., a novel species of thermoacidophilic archaea, isolated from a volcanic area. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023] Open
Abstract
A novel thermoacidophilic archeaon, strain J1T (=DSM 112778T,=JCM 34702T), was isolated from a hot pool in a volcanic area of Java, Indonesia. Cells of the strain were irregular, motile cocci of 1.0–1.2 µm diameter. Aerobic, organoheterotrophic growth with casamino acids was observed at an optimum temperature of 70 °C in a range of 55–78 °C and at an optimum pH of 3 in a range of 1.5 to 5. Various organic compounds were utilized, including a greater variety of sugars than has been reported for growth of other species of the genus. Chemolithoautotrophic growth was observed with reduced sulphur compounds, including mineral sulphides. Ferric iron was reduced during anaerobic growth with elemental sulphur. Cellular lipids were calditoglycerocaldarchaeol and caldarchaeol with some derivates. The organism contained the respiratory quinone caldariellaquinone. On the basis of phylogenetic and chemotaxonomic comparison with its closest relatives, it was concluded that strain J1T represents a novel species, for which the name Metallosphaera javensis is proposed. Low DNA–DNA relatedness values (16S rRNA gene <98.4%, average nucleotide identity (ANI) <80.1%) distinguished J1T from other species of the genus
Metallosphaera
and the DNA G+C content of 47.3% is the highest among the known species of the genus.
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Affiliation(s)
- Marika Hofmann
- Biohydrometallurgy & Microbiology, Institute of Bioscience, TU Bergakademie Freiberg, 09599 Freiberg, Germany
| | - Paul R. Norris
- Grinding Solutions, Tresillian Business Park, Tresillian, Truro, Cornwall TR2 4HF, UK
| | - Luise Malik
- Biohydrometallurgy & Microbiology, Institute of Bioscience, TU Bergakademie Freiberg, 09599 Freiberg, Germany
| | - Axel Schippers
- Federal Institute for Geosciences and Natural Resources, 30655 Hannover, Germany
| | - Gert Schmidt
- Keramik, Feuerfest und Verbundstoffe, TU Bergakademie Freiberg, 09599 Freiberg
| | - Jacqueline Wolf
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
| | - Meina Neumann-Schaal
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
| | - Sabrina Hedrich
- Biohydrometallurgy & Microbiology, Institute of Bioscience, TU Bergakademie Freiberg, 09599 Freiberg, Germany
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5
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Zhang X, Li J, Yang W, Chen J, Wang X, Xing D, Dong W, Wang H, Wang J. The combination of aerobic digestion and bioleaching for heavy metal removal from excess sludge. CHEMOSPHERE 2022; 290:133231. [PMID: 34902386 DOI: 10.1016/j.chemosphere.2021.133231] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 12/06/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
In this study, bioleaching is employed for removing heavy metals from excess sludge generated during municipal wastewater treatment. To avoid organic matter impact on bioleaching, aerobic digestion was performed as pretreatment of the bioleaching or accompanied with the bioleaching. The results showed that the leaching amounts of heavy metals from the process of aerobic digestion accompanied with bioleaching was 2.3 times more than that of the process of aerobic digestion followed by bioleaching. The stable-state proportions of Zn, Cu, Ni and Mn increased by 83%, 94%, 96% and 91%, respectively, in the process of aerobic digestion accompanied with bioleaching, and moreover, the reduction rate of MLSS increased by 22.7%. Although the content of ammonia nitrogen and total phosphorus in sludge decreased after bioleaching treatment, they were still much higher than the soil background value. It indicates that the treated sludge still has agricultural value. High throughput sequencing analysis showed that the relative abundance of acid-producing bacteria (Romboutsia, Clostridium, Tricibacter, and Intestinibacter) significantly increased from 0% to 28.6%, 6.9%, 3.9%, and 2.4%. The enrichment of these acidogenic bacteria was the main reason for the pH decrease, which was conducive to the removal of heavy metals from sludge.
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Affiliation(s)
- Xiaolei Zhang
- Department of Civil and Environmental Engineering, Harbin Institute of Technology, Key Laboratory of Water Resource Application and Environmental Pollution Control, Shenzhen, Shenzhen, Shenzhen, 518055, PR China
| | - Ji Li
- Department of Civil and Environmental Engineering, Harbin Institute of Technology, Key Laboratory of Water Resource Application and Environmental Pollution Control, Shenzhen, Shenzhen, Shenzhen, 518055, PR China
| | - Wei Yang
- Department of Civil and Environmental Engineering, Harbin Institute of Technology, Key Laboratory of Water Resource Application and Environmental Pollution Control, Shenzhen, Shenzhen, Shenzhen, 518055, PR China
| | - Jiaxin Chen
- Department of Civil and Environmental Engineering, Shantou University, Shantou, Guangdong, 515063, PR China
| | - Xiaochun Wang
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu, 212013, PR China; Institute of Environmental Health and Ecological Security, Jiangsu University, Zhenjiang, Jiangsu, 212013, PR China.
| | - Dingyu Xing
- Department of Civil and Environmental Engineering, Harbin Institute of Technology, Key Laboratory of Water Resource Application and Environmental Pollution Control, Shenzhen, Shenzhen, Shenzhen, 518055, PR China
| | - Wenyi Dong
- Department of Civil and Environmental Engineering, Harbin Institute of Technology, Key Laboratory of Water Resource Application and Environmental Pollution Control, Shenzhen, Shenzhen, Shenzhen, 518055, PR China
| | - Hongjie Wang
- Department of Civil and Environmental Engineering, Harbin Institute of Technology, Key Laboratory of Water Resource Application and Environmental Pollution Control, Shenzhen, Shenzhen, Shenzhen, 518055, PR China
| | - Jiawen Wang
- Department of Civil and Environmental Engineering, Shantou University, Shantou, Guangdong, 515063, PR China
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6
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Liu LJ, Jiang Z, Wang P, Qin YL, Xu W, Wang Y, Liu SJ, Jiang CY. Physiology, Taxonomy, and Sulfur Metabolism of the Sulfolobales, an Order of Thermoacidophilic Archaea. Front Microbiol 2021; 12:768283. [PMID: 34721370 PMCID: PMC8551704 DOI: 10.3389/fmicb.2021.768283] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 09/22/2021] [Indexed: 11/13/2022] Open
Abstract
The order Sulfolobales (phylum Crenarchaeota) is a group of thermoacidophilic archaea. The first member of the Sulfolobales was discovered in 1972, and current 23 species are validly named under the International Code of Nomenclature of Prokaryotes. The majority of members of the Sulfolobales is obligately or facultatively chemolithoautotrophic. When they grow autotrophically, elemental sulfur or reduced inorganic sulfur compounds are their energy sources. Therefore, sulfur metabolism is the most important physiological characteristic of the Sulfolobales. The functions of some enzymes and proteins involved in sulfur reduction, sulfur oxidation, sulfide oxidation, thiosulfate oxidation, sulfite oxidation, tetrathionate hydrolysis, and sulfur trafficking have been determined. In this review, we describe current knowledge about the physiology, taxonomy, and sulfur metabolism of the Sulfolobales, and note future challenges in this field.
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Affiliation(s)
- Li-Jun Liu
- School of Basic Medical Science, the Xi'an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi'an Medical University, Xi'an, China.,Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Zhen Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Pei Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ya-Ling Qin
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wen Xu
- School of Basic Medical Science, the Xi'an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi'an Medical University, Xi'an, China.,Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Yang Wang
- School of Basic Medical Science, the Xi'an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi'an Medical University, Xi'an, China.,Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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7
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Lewis AM, Recalde A, Bräsen C, Counts JA, Nussbaum P, Bost J, Schocke L, Shen L, Willard DJ, Quax TEF, Peeters E, Siebers B, Albers SV, Kelly RM. The biology of thermoacidophilic archaea from the order Sulfolobales. FEMS Microbiol Rev 2021; 45:fuaa063. [PMID: 33476388 PMCID: PMC8557808 DOI: 10.1093/femsre/fuaa063] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/26/2020] [Indexed: 12/13/2022] Open
Abstract
Thermoacidophilic archaea belonging to the order Sulfolobales thrive in extreme biotopes, such as sulfuric hot springs and ore deposits. These microorganisms have been model systems for understanding life in extreme environments, as well as for probing the evolution of both molecular genetic processes and central metabolic pathways. Thermoacidophiles, such as the Sulfolobales, use typical microbial responses to persist in hot acid (e.g. motility, stress response, biofilm formation), albeit with some unusual twists. They also exhibit unique physiological features, including iron and sulfur chemolithoautotrophy, that differentiate them from much of the microbial world. Although first discovered >50 years ago, it was not until recently that genome sequence data and facile genetic tools have been developed for species in the Sulfolobales. These advances have not only opened up ways to further probe novel features of these microbes but also paved the way for their potential biotechnological applications. Discussed here are the nuances of the thermoacidophilic lifestyle of the Sulfolobales, including their evolutionary placement, cell biology, survival strategies, genetic tools, metabolic processes and physiological attributes together with how these characteristics make thermoacidophiles ideal platforms for specialized industrial processes.
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Affiliation(s)
- April M Lewis
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
| | - Alejandra Recalde
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Christopher Bräsen
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - James A Counts
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
| | - Phillip Nussbaum
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Jan Bost
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Larissa Schocke
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - Lu Shen
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - Daniel J Willard
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
| | - Tessa E F Quax
- Archaeal Virus–Host Interactions, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Eveline Peeters
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Bettina Siebers
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - Sonja-Verena Albers
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
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8
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Distaso MA, Bargiela R, Brailsford FL, Williams GB, Wright S, Lunev EA, Toshchakov SV, Yakimov MM, Jones DL, Golyshin PN, Golyshina OV. High Representation of Archaea Across All Depths in Oxic and Low-pH Sediment Layers Underlying an Acidic Stream. Front Microbiol 2020; 11:576520. [PMID: 33329440 PMCID: PMC7716880 DOI: 10.3389/fmicb.2020.576520] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 10/23/2020] [Indexed: 12/26/2022] Open
Abstract
Parys Mountain or Mynydd Parys (Isle of Anglesey, United Kingdom) is a mine-impacted environment, which accommodates a variety of acidophilic organisms. Our previous research of water and sediments from one of the surface acidic streams showed a high proportion of archaea in the total microbial community. To understand the spatial distribution of archaea, we sampled cores (0-20 cm) of sediment and conducted chemical analyses and taxonomic profiling of microbiomes using 16S rRNA gene amplicon sequencing in different core layers. The taxonomic affiliation of sequencing reads indicated that archaea represented between 6.2 and 54% of the microbial community at all sediment depths. Majority of archaea were associated with the order Thermoplasmatales, with the most abundant group of sequences being clustered closely with the phylotype B_DKE, followed by "E-plasma," "A-plasma," other yet uncultured Thermoplasmatales with Ferroplasma and Cuniculiplasma spp. represented in minor proportions. Thermoplasmatales were found at all depths and in the whole range of chemical conditions with their abundance correlating with sediment Fe, As, Cr, and Mn contents. The bacterial microbiome component was largely composed in all layers of sediment by members of the phyla Proteobacteria, Actinobacteria, Nitrospirae, Firmicutes, uncultured Chloroflexi (AD3 group), and Acidobacteria. This study has revealed a high abundance of Thermoplasmatales in acid mine drainage-affected sediment layers and pointed at these organisms being the main contributors to carbon, and probably to iron and sulfur cycles in this ecosystem.
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Affiliation(s)
- Marco A. Distaso
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
- Centre for Environmental Biotechnology, Bangor University, Bangor, United Kingdom
| | - Rafael Bargiela
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
| | - Francesca L. Brailsford
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
- Centre for Environmental Biotechnology, Bangor University, Bangor, United Kingdom
- School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
| | - Gwion B. Williams
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
- Centre for Environmental Biotechnology, Bangor University, Bangor, United Kingdom
| | - Samuel Wright
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
- Centre for Environmental Biotechnology, Bangor University, Bangor, United Kingdom
| | - Evgenii A. Lunev
- Institute of Living Systems, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | | | - Michail M. Yakimov
- Institute for Biological Resources and Marine Biotechnology, CNR, Messina, Italy
| | - David L. Jones
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
- Centre for Environmental Biotechnology, Bangor University, Bangor, United Kingdom
- School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
| | - Peter N. Golyshin
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
- Centre for Environmental Biotechnology, Bangor University, Bangor, United Kingdom
| | - Olga V. Golyshina
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
- Centre for Environmental Biotechnology, Bangor University, Bangor, United Kingdom
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9
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Srichandan H, Mohapatra RK, Singh PK, Mishra S, Parhi PK, Naik K. Column bioleaching applications, process development, mechanism, parametric effect and modelling: A review. J IND ENG CHEM 2020. [DOI: 10.1016/j.jiec.2020.07.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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10
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Spatial Metagenomics of Three Geothermal Sites in Pisciarelli Hot Spring Focusing on the Biochemical Resources of the Microbial Consortia. Molecules 2020; 25:molecules25174023. [PMID: 32899230 PMCID: PMC7570011 DOI: 10.3390/molecules25174023] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 08/28/2020] [Accepted: 08/28/2020] [Indexed: 12/13/2022] Open
Abstract
Terrestrial hot springs are of great interest to the general public and to scientists alike due to their unique and extreme conditions. These have been sought out by geochemists, astrobiologists, and microbiologists around the globe who are interested in their chemical properties, which provide a strong selective pressure on local microorganisms. Drivers of microbial community composition in these springs include temperature, pH, in-situ chemistry, and biogeography. Microbes in these communities have evolved strategies to thrive in these conditions by converting hot spring chemicals and organic matter into cellular energy. Following our previous metagenomic analysis of Pisciarelli hot springs (Naples, Italy), we report here the comparative metagenomic study of three novel sites, formed in Pisciarelli as result of recent geothermal activity. This study adds comprehensive information about phylogenetic diversity within Pisciarelli hot springs by peeking into possible mechanisms of adaptation to biogeochemical cycles, and high applicative potential of the entire set of genes involved in the carbohydrate metabolism in this environment (CAZome). This site is an excellent model for the study of biodiversity on Earth and biosignature identification, and for the study of the origin and limits of life.
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11
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Wang P, Li LZ, Qin YL, Liang ZL, Li XT, Yin HQ, Liu LJ, Liu SJ, Jiang CY. Comparative Genomic Analysis Reveals the Metabolism and Evolution of the Thermophilic Archaeal Genus Metallosphaera. Front Microbiol 2020; 11:1192. [PMID: 32655516 PMCID: PMC7325606 DOI: 10.3389/fmicb.2020.01192] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 05/11/2020] [Indexed: 01/15/2023] Open
Abstract
Members of the genus Metallosphaera are widely found in sulfur-rich and metal-laden environments, but their physiological and ecological roles remain poorly understood. Here, we sequenced Metallosphaera tengchongensis Ric-A, a strain isolated from the Tengchong hot spring in Yunnan Province, China, and performed a comparative genome analysis with other Metallosphaera genomes. The genome of M. tengchongensis had an average nucleotide identity (ANI) of approximately 70% to that of Metallosphaera cuprina. Genes sqr, tth, sir, tqo, hdr, tst, soe, and sdo associated with sulfur oxidation, and gene clusters fox and cbs involved in iron oxidation existed in all Metallosphaera genomes. However, the adenosine-5'-phosphosulfate (APS) pathway was only detected in Metallosphaera sedula and Metallosphaera yellowstonensis, and several subunits of fox cluster were lost in M. cuprina. The complete 3-hydroxypropionate/4-hydroxybutyrate cycle and dicarboxylate/4-hydroxybutyrate cycle involved in carbon fixation were found in all Metallosphaera genomes. A large number of gene family gain events occurred in M. yellowstonensis and M. sedula, whereas gene family loss events occurred frequently in M. cuprina. Pervasive strong purifying selection was found acting on the gene families of Metallosphaera, of which transcription-related genes underwent the strongest purifying selection. In contrast, genes related to prophages, transposons, and defense mechanisms were under weaker purifying pressure. Taken together, this study expands knowledge of the genomic traits of Metallosphaera species and sheds light on their evolution.
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Affiliation(s)
- Pei Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Liang Zhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Ya Ling Qin
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zong Lin Liang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiu Tong Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Hua Qun 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
| | - Li Jun Liu
- Department of Pathogen Biology, School of Basic Medical Science, Xi’an Medical University, Xi’an, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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Parashar D, Satyanarayana T. An Insight Into Ameliorating Production, Catalytic Efficiency, Thermostability and Starch Saccharification of Acid-Stable α-Amylases From Acidophiles. Front Bioeng Biotechnol 2018; 6:125. [PMID: 30324103 PMCID: PMC6172347 DOI: 10.3389/fbioe.2018.00125] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 08/20/2018] [Indexed: 02/03/2023] Open
Abstract
Most of the extracellular enzymes of acidophilic bacteria and archaea are stable at acidic pH with a relatively high thermostability. There is, however, a dearth of information on their acid stability. Although several theories have been postulated, the adaptation of acidophilic proteins to low pH has not been explained convincingly. This review highlights recent developments in understanding the structure and biochemical characteristics, and production of acid-stable and calcium-independent α-amylases by acidophilic bacteria with special reference to that of Bacillus acidicola.
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Affiliation(s)
- Deepak Parashar
- Functional Genomic Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Tulasi Satyanarayana
- Division of Biological Sciences and Engineering, Netaji Subhas Institute of Technology, New Delhi, India
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Anderson RE, Kouris A, Seward CH, Campbell KM, Whitaker RJ. Structured Populations of Sulfolobus acidocaldarius with Susceptibility to Mobile Genetic Elements. Genome Biol Evol 2018. [PMID: 28633403 PMCID: PMC5554439 DOI: 10.1093/gbe/evx104] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The impact of a structured environment on genome evolution can be determined through comparative population genomics of species that live in the same habitat. Recent work comparing three genome sequences of Sulfolobus acidocaldarius suggested that highly structured, extreme, hot spring environments do not limit dispersal of this thermoacidophile, in contrast to other co-occurring Sulfolobus species. Instead, a high level of conservation among these three S. acidocaldarius genomes was hypothesized to result from rapid, global-scale dispersal promoted by low susceptibility to viruses that sets S. acidocaldarius apart from its sister Sulfolobus species. To test this hypothesis, we conducted a comparative analysis of 47 genomes of S. acidocaldarius from spatial and temporal sampling of two hot springs in Yellowstone National Park. While we confirm the low diversity in the core genome, we observe differentiation among S. acidocaldarius populations, likely resulting from low migration among hot spring “islands” in Yellowstone National Park. Patterns of genomic variation indicate that differing geological contexts result in the elimination or preservation of diversity among differentiated populations. We observe multiple deletions associated with a large genomic island rich in glycosyltransferases, differential integrations of the Sulfolobus turreted icosahedral virus, as well as two different plasmid elements. These data demonstrate that neither rapid dispersal nor lack of mobile genetic elements result in low diversity in the S. acidocaldarius genomes. We suggest instead that significant differences in the recent evolutionary history, or the intrinsic evolutionary rates, of sister Sulfolobus species result in the relatively low diversity of the S. acidocaldarius genome.
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Affiliation(s)
- Rika E Anderson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign.,Biology Department, Carleton College, Northfield, Minnesota
| | - Angela Kouris
- Energy, Bioengineering and Geomicrobiology Group, University of Calgary, Alberta, Canada
| | - Christopher H Seward
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign
| | - Kate M Campbell
- U.S. Geological Survey National Research Program, Boulder, Colorado
| | - Rachel J Whitaker
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign.,Department of Microbiology, University of Illinois at Urbana-Champaign
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Ranawat P, Rawat S. Metal-tolerant thermophiles: metals as electron donors and acceptors, toxicity, tolerance and industrial applications. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:4105-4133. [PMID: 29238927 DOI: 10.1007/s11356-017-0869-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 11/28/2017] [Indexed: 06/07/2023]
Abstract
Metal-tolerant thermophiles are inhabitants of a wide range of extreme habitats like solfatara fields, hot springs, mud holes, hydrothermal vents oozing out from metal-rich ores, hypersaline pools and soil crusts enriched with metals and other elements. The ability to withstand adverse environmental conditions, like high temperature, high metal concentration and sometimes high pH in their niche, makes them an interesting subject for understanding mechanisms behind their ability to deal with multiple duress simultaneously. Metals are essential for biological systems, as they participate in biochemistries that cannot be achieved only by organic molecules. However, the excess concentration of metals can disrupt natural biogeochemical processes and can impose toxicity. Thermophiles counteract metal toxicity via their unique cell wall, metabolic factors and enzymes that carry out metal-based redox transformations, metal sequestration by metallothioneins and metallochaperones as well as metal efflux. Thermophilic metal resistance is heterogeneous at both genetic and physiology levels and may be chromosomally, plasmid or transposon encoded with one or more genes being involved. These effective response mechanisms either individually or synergistically make proliferation of thermophiles in metal-rich habitats possibly. This article presents the state of the art and future perspectives of responses of thermophiles to metals at genetic as well as physiological levels.
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Affiliation(s)
- Preeti Ranawat
- Department of Botany and Microbiology, Hemvati Nandan Bahuguna Garhwal University, Srinagar (Garhwal), Uttarakhand, India
| | - Seema Rawat
- School of Life Sciences, Central University of Gujarat, Gandhinagar, Gujarat, India.
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How a Genetically Stable Extremophile Evolves: Modes of Genome Diversification in the Archaeon Sulfolobus acidocaldarius. J Bacteriol 2017. [PMID: 28630130 DOI: 10.1128/jb.00177-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In order to analyze in molecular terms how Sulfolobus genomes diverge, damage-induced mutations and natural polymorphisms (PMs) were identified in laboratory constructs and wild-type isolates, respectively, of Sulfolobus acidocaldarius Among wild-type isolates drawn from one local population, pairwise nucleotide divergence averaged 4 × 10-6, which is about 0.15% of the corresponding divergence reported for Sulfolobus islandicus The most variable features of wild-type S. acidocaldarius genomes were homopolymer (mononucleotide) tracts and longer tandem repeats, consistent with the spontaneous mutations that occur under laboratory conditions. Natural isolates, however, also revealed large insertions/deletions and inversions, which did not occur in any of the laboratory-manipulated strains. Several of the large insertions/deletions could be attributed to the integration or excision of mobile genetic elements (MGEs), and each MGE represented a distinct system of site-specific recombination. The mode of recombination associated with one MGE, a provirus related to Sulfolobus turreted icosahedral virus, was also seen in certain chromosomal inversions. Artificially induced mutations, non-MGE insertions/deletions, and small PMs exhibited different distributions over the genome, suggesting that large-scale patterning of Sulfolobus genomes begins early in the divergence process. Unlike induced mutations, natural base pair substitutions occurred in clusters, and one cluster exhibited properties expected of nonreciprocal recombination (gene conversion) between dispersed imperfect repeats. Taken together, the results identify simple replication errors, slipped-strand events promoted by tandem repeats, homologous recombination, and rearrangements promoted by MGEs as the primary sources of genetic variation for this extremely acidophilic archaeon in its geothermal environment.IMPORTANCE The optimal growth temperatures of hyperthermophilic archaea accelerate DNA decomposition, which is expected to make DNA repair especially important for their genetic stability, yet these archaea lack certain broadly conserved types of DNA repair proteins. In this study, the genome of the extreme thermoacidophile Sulfolobus acidocaldarius was found to be remarkably stable, accumulating few mutations in many (though not all) laboratory manipulations and in natural populations. Furthermore, all the genetic processes that were inferred to diversify these genomes also operate in mesophilic bacteria and eukaryotes. This suggests that a common set of mechanisms produces most of the genetic variation in all microorganisms, despite the fundamental differences in physiology, DNA repair systems, and genome structure represented in the three domains of life.
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16
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Counts JA, Zeldes BM, Lee LL, Straub CT, Adams MWW, Kelly RM. Physiological, metabolic and biotechnological features of extremely thermophilic microorganisms. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2017; 9. [PMID: 28206708 DOI: 10.1002/wsbm.1377] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Revised: 11/23/2016] [Accepted: 11/30/2016] [Indexed: 12/12/2022]
Abstract
The current upper thermal limit for life as we know it is approximately 120°C. Microorganisms that grow optimally at temperatures of 75°C and above are usually referred to as 'extreme thermophiles' and include both bacteria and archaea. For over a century, there has been great scientific curiosity in the basic tenets that support life in thermal biotopes on earth and potentially on other solar bodies. Extreme thermophiles can be aerobes, anaerobes, autotrophs, heterotrophs, or chemolithotrophs, and are found in diverse environments including shallow marine fissures, deep sea hydrothermal vents, terrestrial hot springs-basically, anywhere there is hot water. Initial efforts to study extreme thermophiles faced challenges with their isolation from difficult to access locales, problems with their cultivation in laboratories, and lack of molecular tools. Fortunately, because of their relatively small genomes, many extreme thermophiles were among the first organisms to be sequenced, thereby opening up the application of systems biology-based methods to probe their unique physiological, metabolic and biotechnological features. The bacterial genera Caldicellulosiruptor, Thermotoga and Thermus, and the archaea belonging to the orders Thermococcales and Sulfolobales, are among the most studied extreme thermophiles to date. The recent emergence of genetic tools for many of these organisms provides the opportunity to move beyond basic discovery and manipulation to biotechnologically relevant applications of metabolic engineering. WIREs Syst Biol Med 2017, 9:e1377. doi: 10.1002/wsbm.1377 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- James A Counts
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Benjamin M Zeldes
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Laura L Lee
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Christopher T Straub
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
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17
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18
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Donati ER, Castro C, Urbieta MS. Thermophilic microorganisms in biomining. World J Microbiol Biotechnol 2016; 32:179. [PMID: 27628339 DOI: 10.1007/s11274-016-2140-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 09/12/2016] [Indexed: 10/21/2022]
Abstract
Biomining is an applied biotechnology for mineral processing and metal extraction from ores and concentrates. This alternative technology for recovering metals involves the hydrometallurgical processes known as bioleaching and biooxidation where the metal is directly solubilized or released from the matrix for further solubilization, respectively. Several commercial applications of biomining can be found around the world to recover mainly copper and gold but also other metals; most of them are operating at temperatures below 40-50 °C using mesophilic and moderate thermophilic microorganisms. Although biomining offers an economically viable and cleaner option, its share of the world´s production of metals has not grown as much as it was expected, mainly considering that due to environmental restrictions in many countries smelting and roasting technologies are being eliminated. The slow rate of biomining processes is for sure the main reason of their poor implementation. In this scenario the use of thermophiles could be advantageous because higher operational temperature would increase the rate of the process and in addition it would eliminate the energy input for cooling the system (bioleaching reactions are exothermic causing a serious temperature increase in bioreactors and inside heaps that adversely affects most of the mesophilic microorganisms) and it would decrease the passivation of mineral surfaces. In the last few years many thermophilic bacteria and archaea have been isolated, characterized, and even used for extracting metals. This paper reviews the current status of biomining using thermophiles, describes the main characteristics of thermophilic biominers and discusses the future for this biotechnology.
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Affiliation(s)
- Edgardo Rubén Donati
- CINDEFI (CCT LA PLATA-CONICET, UNLP), Facultad de Ciencias Exactas (UNLP), 47 y 115, (1900) La Plata, Buenos Aires, Argentina.
| | - Camila Castro
- CINDEFI (CCT LA PLATA-CONICET, UNLP), Facultad de Ciencias Exactas (UNLP), 47 y 115, (1900) La Plata, Buenos Aires, Argentina
| | - María Sofía Urbieta
- CINDEFI (CCT LA PLATA-CONICET, UNLP), Facultad de Ciencias Exactas (UNLP), 47 y 115, (1900) La Plata, Buenos Aires, Argentina
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Shiers D, Collinson D, Watling H. Life in heaps: a review of microbial responses to variable acidity in sulfide mineral bioleaching heaps for metal extraction. Res Microbiol 2016; 167:576-86. [DOI: 10.1016/j.resmic.2016.05.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 05/24/2016] [Accepted: 05/25/2016] [Indexed: 11/16/2022]
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21
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Role of S-layer proteins in bacteria. World J Microbiol Biotechnol 2015; 31:1877-87. [DOI: 10.1007/s11274-015-1952-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 09/21/2015] [Indexed: 12/30/2022]
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22
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The Confluence of Heavy Metal Biooxidation and Heavy Metal Resistance: Implications for Bioleaching by Extreme Thermoacidophiles. MINERALS 2015. [DOI: 10.3390/min5030397] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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23
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Alex A, Antunes A. Pyrosequencing characterization of the microbiota from Atlantic intertidal marine sponges reveals high microbial diversity and the lack of co-occurrence patterns. PLoS One 2015; 10:e0127455. [PMID: 25992625 PMCID: PMC4439068 DOI: 10.1371/journal.pone.0127455] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 04/15/2015] [Indexed: 11/19/2022] Open
Abstract
Sponges are ancient metazoans that host diverse and complex microbial communities. Sponge-associated microbial diversity has been studied from wide oceans across the globe, particularly in subtidal regions, but the microbial communities from intertidal sponges have remained mostly unexplored. Here we used pyrosequencing to characterize the microbial communities in 12 different co-occurring intertidal marine sponge species sampled from the Atlantic coast, revealing a total of 686 operational taxonomic units (OTUs) at 97% sequence similarity. Taxonomic assignment of 16S ribosomal RNA tag sequences estimated altogether 26 microbial groups, represented by bacterial (75.5%) and archaeal (22%) domains. Proteobacteria (43.4%) and Crenarchaeota (20.6%) were the most dominant microbial groups detected in all the 12 marine sponge species and ambient seawater. The Crenarchaeota microbes detected in three Atlantic Ocean sponges had a close similarity with Crenarchaeota from geographically separated subtidal Red Sea sponges. Our study showed that most of the microbial communities observed in sponges (73%) were also found in the surrounding ambient seawater suggesting possible environmental acquisition and/or horizontal transfer of microbes. Beyond the microbial diversity and community structure assessments (NMDS, ADONIS, ANOSIM), we explored the interactions between the microbial communities coexisting in sponges using the checkerboard score (C-score). Analyses of the microbial association pattern (co-occurrence) among intertidal sympatric sponges revealed the random association of microbes, favoring the hypothesis that the sponge-inhabiting microbes are recruited from the habitat mostly by chance or influenced by environmental factors to benefit the hosts.
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Affiliation(s)
- Anoop Alex
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas 177, 4050–123, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo, Alegre, 4169–007, Porto, Portugal
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas 177, 4050–123, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo, Alegre, 4169–007, Porto, Portugal
- * E-mail:
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Peng TJ, Liu LJ, Liu C, Yang ZF, Liu SJ, Jiang CY. Metallosphaera tengchongensis sp. nov., an acidothermophilic archaeon isolated from a hot spring. Int J Syst Evol Microbiol 2015; 65:537-542. [DOI: 10.1099/ijs.0.070870-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two novel acidothermophilic archaea, strains Ric-AT and Ric-F, were isolated from muddy water samples of a sulfuric hot spring located in Tengchong County, Yunnan Province, PR China. The strains were aerobic and facultatively chemolithoautotrophic. Both strains could oxidize S0 and K2S4O6 for autotrophic growth, and could use organic materials for heterotrophic growth. Growth was observed at 55–75 °C and pH 1.5–6.5. The strains could oxidize metal sulfide ores, showing their potential in bioleaching. The DNA G+C contents of strains Ric-AT and Ric-F were 41.8 and 41.6 mol%, respectively. Analysis of 16S rRNA gene sequences showed that the two strains shared 99.8 % sequence similarity to each other, but <97 % to other known species of the genus
Metallosphaera
. DNA–DNA hybridization indicated that the isolates were different strains of a novel species of the genus
Metallosphaera
. Strains Ric-AT and Ric-F also shared a number of physiological and biochemical characteristics that distinguished them from recognized species of the genus
Metallosphaera
. On the basis of phenotypic, chemotaxonomic and phylogenetic comparisons with their closest relatives, it was concluded that strains Ric-AT and Ric-F represent a novel species of the genus
Metallosphaera
, for which the name Metallosphaera
tengchongensis sp. nov. is proposed. The type strain is Ric-AT ( = NBRC 109472T = CGMCC 1.12287T).
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Affiliation(s)
- Tang-Jian Peng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, Hunan 410083, PR China
- State Key Laboratory of Microbial Resources, Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Li-Jun Liu
- State Key Laboratory of Microbial Resources, Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Chang Liu
- State Key Laboratory of Microbial Resources, Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Zhi-Fang Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Xinong Road, Yangling, Shanxi 712100, PR China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources, Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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Biomining: metal recovery from ores with microorganisms. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 141:1-47. [PMID: 23793914 DOI: 10.1007/10_2013_216] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Biomining is an increasingly applied biotechnological procedure for processing of ores in the mining industry (biohydrometallurgy). Nowadays the production of copper from low-grade ores is the most important industrial application and a significant part of world copper production already originates from heap or dump/stockpile bioleaching. Conceptual differences exist between the industrial processes of bioleaching and biooxidation. Bioleaching is a conversion of an insoluble valuable metal into a soluble form by means of microorganisms. In biooxidation, on the other hand, gold is predominantly unlocked from refractory ores in large-scale stirred-tank biooxidation arrangements for further processing steps. In addition to copper and gold production, biomining is also used to produce cobalt, nickel, zinc, and uranium. Up to now, biomining has merely been used as a procedure in the processing of sulfide ores and uranium ore, but laboratory and pilot procedures already exist for the processing of silicate and oxide ores (e.g., laterites), for leaching of processing residues or mine waste dumps (mine tailings), as well as for the extraction of metals from industrial residues and waste (recycling). This chapter estimates the world production of copper, gold, and other metals by means of biomining and chemical leaching (bio-/hydrometallurgy) compared with metal production by pyrometallurgical procedures, and describes new developments in biomining. In addition, an overview is given about metal sulfide oxidizing microorganisms, fundamentals of biomining including bioleaching mechanisms and interface processes, as well as anaerobic bioleaching and bioleaching with heterotrophic microorganisms.
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Mukherjee A, Wheaton GH, Blum PH, Kelly RM. Uranium extremophily is an adaptive, rather than intrinsic, feature for extremely thermoacidophilic Metallosphaera species. Proc Natl Acad Sci U S A 2012; 109:16702-7. [PMID: 23010932 PMCID: PMC3478614 DOI: 10.1073/pnas.1210904109] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Thermoacidophilic archaea are found in heavy metal-rich environments, and, in some cases, these microorganisms are causative agents of metal mobilization through cellular processes related to their bioenergetics. Given the nature of their habitats, these microorganisms must deal with the potentially toxic effect of heavy metals. Here, we show that two thermoacidophilic Metallosphaera species with nearly identical (99.99%) genomes differed significantly in their sensitivity and reactivity to uranium (U). Metallosphaera prunae, isolated from a smoldering heap on a uranium mine in Thüringen, Germany, could be viewed as a "spontaneous mutant" of Metallosphaera sedula, an isolate from Pisciarelli Solfatara near Naples. Metallosphaera prunae tolerated triuranium octaoxide (U(3)O(8)) and soluble uranium [U(VI)] to a much greater extent than M. sedula. Within 15 min following exposure to "U(VI) shock," M. sedula, and not M. prunae, exhibited transcriptomic features associated with severe stress response. Furthermore, within 15 min post-U(VI) shock, M. prunae, and not M. sedula, showed evidence of substantial degradation of cellular RNA, suggesting that transcriptional and translational processes were aborted as a dynamic mechanism for resisting U toxicity; by 60 min post-U(VI) shock, RNA integrity in M. prunae recovered, and known modes for heavy metal resistance were activated. In addition, M. sedula rapidly oxidized solid U(3)O(8) to soluble U(VI) for bioenergetic purposes, a chemolithoautotrophic feature not previously reported. M. prunae, however, did not solubilize solid U(3)O(8) to any significant extent, thereby not exacerbating U(VI) toxicity. These results point to uranium extremophily as an adaptive, rather than intrinsic, feature for Metallosphaera species, driven by environmental factors.
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Affiliation(s)
- Arpan Mukherjee
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905; and
| | - Garrett H. Wheaton
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905; and
| | - Paul H. Blum
- Beadle Center for Genetics, University of Nebraska-Lincoln, Lincoln, NE 68588-0666
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905; and
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Survival of the fittest: overcoming oxidative stress at the extremes of Acid, heat and metal. Life (Basel) 2012; 2:229-42. [PMID: 25371104 PMCID: PMC4187130 DOI: 10.3390/life2030229] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 08/14/2012] [Accepted: 08/17/2012] [Indexed: 11/29/2022] Open
Abstract
The habitat of metal respiring acidothermophilic lithoautotrophs is perhaps the most oxidizing environment yet identified. Geothermal heat, sulfuric acid and transition metals contribute both individually and synergistically under aerobic conditions to create this niche. Sulfuric acid and metals originating from sulfidic ores catalyze oxidative reactions attacking microbial cell surfaces including lipids, proteins and glycosyl groups. Sulfuric acid also promotes hydrocarbon dehydration contributing to the formation of black “burnt” carbon. Oxidative reactions leading to abstraction of electrons is further impacted by heat through an increase in the proportion of reactant molecules with sufficient energy to react. Collectively these factors and particularly those related to metals must be overcome by thermoacidophilic lithoautotrophs in order for them to survive and proliferate. The necessary mechanisms to achieve this goal are largely unknown however mechanistics insights have been gained through genomic studies. This review focuses on the specific role of metals in this extreme environment with an emphasis on resistance mechanisms in Archaea.
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Genomic evidence of rapid, global-scale gene flow in a Sulfolobus species. ISME JOURNAL 2012; 6:1613-6. [PMID: 22418622 DOI: 10.1038/ismej.2012.20] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Local populations of Sulfolobus islandicus diverge genetically with geographical separation, and this has been attributed to restricted transfer of propagules imposed by the unfavorable spatial distribution of acidic geothermal habitat. We tested the generality of genetic divergence with distance in Sulfolobus species by analyzing genomes of Sulfolobus acidocaldarius drawn from three populations separated by more than 8000 km. In sharp contrast to S. islandicus, the geographically diverse S. acidocaldarius genomes proved to be nearly identical. We could not link the difference in genome conservation between the two species to a corresponding difference in genome stability or ecological factors affecting propagule dispersal. The results provide the first evidence that genetic isolation of local populations does not result primarily from properties intrinsic to Sulfolobus and the severe discontinuity of its geothermal habitat, but varies with species, and thus may reflect biotic interactions that act after propagule dispersal.
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Kondrat’eva TF, Pivovarova TA, Tsaplina IA, Fomchenko NV, Zhuravleva AE, Murav’ev MI, Melamud VS, Bulayev AG. Diversity of the communities of acidophilic chemolithotrophic microorganisms in natural and technogenic ecosystems. Microbiology (Reading) 2012. [DOI: 10.1134/s0026261712010080] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Acidophilic bacteria and archaea: acid stable biocatalysts and their potential applications. Extremophiles 2011; 16:1-19. [PMID: 22080280 DOI: 10.1007/s00792-011-0402-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Accepted: 10/05/2011] [Indexed: 01/05/2023]
Abstract
Acidophiles are ecologically and economically important group of microorganisms, which thrive in acidic natural (solfataric fields, sulfuric pools) as well as artificial man-made (areas associated with human activities such as mining of coal and metal ores) environments. They possess networked cellular adaptations to regulate pH inside the cell. Several extracellular enzymes from acidophiles are known to be functional at much lower pH than the cytoplasmic pH. Enzymes like amylases, proteases, ligases, cellulases, xylanases, α-glucosidases, endoglucanases, and esterases stable at low pH are known from various acidophilic microbes. The possibility of improving them by genetic engineering and directed evolution will further boost their industrial applications. Besides biocatalysts, other biomolecules such as plasmids, rusticynin, and maltose-binding protein have also been reported from acidophiles. Some strategies for circumventing the problems encountered in expressing genes encoding proteins from extreme acidophiles have been suggested. The investigations on the analysis of crystal structures of some acidophilic proteins have thrown light on their acid stability. Attempts are being made to use thermoacidophilic microbes for biofuel production from lignocellulosic biomass. The enzymes from acidophiles are mainly used in polymer degradation.
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Kinetics of ferrous iron oxidation by batch and continuous cultures of thermoacidophilic Archaea at extremely low pH of 1.1-1.3. Appl Microbiol Biotechnol 2011; 93:1295-303. [PMID: 21751006 PMCID: PMC3264884 DOI: 10.1007/s00253-011-3460-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Revised: 06/20/2011] [Accepted: 06/20/2011] [Indexed: 11/18/2022]
Abstract
The extreme acid conditions required for scorodite (FeAsO4·2H2O) biomineralization (pH below 1.3) are suboptimal for growth of most thermoacidophilic Archaea. With the objective to develop a continuous process suitable for biomineral production, this research focuses on growth kinetics of thermoacidophilic Archaea at low pH conditions. Ferrous iron oxidation rates were determined in batch-cultures at pH 1.3 and a temperature of 75°C for Acidianus sulfidivorans, Metallosphaera prunea and a mixed Sulfolobus culture. Ferrous iron and CO2 in air were added as sole energy and carbon source. The highest growth rate (0.066 h−1) was found with the mixed Sulfolobus culture. Therefore, this culture was selected for further experiments. Growth was not stimulated by increase of the CO2 concentration or by addition of sulphur as an additional energy source. In a CSTR operated at the suboptimal pH of 1.1, the maximum specific growth rate of the mixed culture was 0.022 h−1, with ferrous iron oxidation rates of 1.5 g L−1 d−1. Compared to pH 1.3, growth rates were strongly reduced but the ferrous iron oxidation rate remained unaffected. Influent ferrous iron concentrations above 6 g L−1 caused instability of Fe2+ oxidation, probably due to product (Fe3+) inhibition. Ferric-containing, nano-sized precipitates of K-jarosite were found on the cell surface. Continuous cultivation stimulated the formation of an exopolysaccharide-like substance. This indicates that biofilm formation may provide a means of biomass retention. Our findings showed that stable continuous cultivation of a mixed iron-oxidizing culture is feasible at the extreme conditions required for continuous biomineral formation.
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Terminal oxidase diversity and function in "Metallosphaera yellowstonensis": gene expression and protein modeling suggest mechanisms of Fe(II) oxidation in the sulfolobales. Appl Environ Microbiol 2011; 77:1844-53. [PMID: 21239558 DOI: 10.1128/aem.01646-10] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
"Metallosphaera yellowstonensis" is a thermoacidophilic archaeon isolated from Yellowstone National Park that is capable of autotrophic growth using Fe(II), elemental S, or pyrite as electron donors. Analysis of the draft genome sequence from M. yellowstonensis strain MK1 revealed seven different copies of heme copper oxidases (subunit I) in a total of five different terminal oxidase complexes, including doxBCEF, foxABCDEFGHIJ, soxABC, and the soxM supercomplex, as well as a novel hypothetical two-protein doxB-like polyferredoxin complex. Other genes found in M. yellowstonensis with possible roles in S and or Fe cycling include a thiosulfate oxidase (tqoAB), a sulfite oxidase (som), a cbsA cytochrome b(558/566), several small blue copper proteins, and a novel gene sequence coding for a putative multicopper oxidase (Mco). Results from gene expression studies, including reverse transcriptase (RT) quantitative PCR (qPCR) of cultures grown autotrophically on either Fe(II), pyrite, or elemental S showed that the fox gene cluster and mco are highly expressed under conditions where Fe(II) is an electron donor. Metagenome sequence and gene expression studies of Fe-oxide mats confirmed the importance of fox genes (e.g., foxA and foxC) and mco under Fe(II)-oxidizing conditions. Protein modeling of FoxC suggests a novel lysine-lysine or lysine-arginine heme B binding domain, indicating that it is likely the cytochrome component of a heterodimer complex with foxG as a ferredoxin subunit. Analysis of mco shows that it encodes a novel multicopper blue protein with two plastocyanin type I copper domains that may play a role in the transfer of electrons within the Fox protein complex. An understanding of metabolic pathways involved in aerobic iron and sulfur oxidation in Sulfolobales has broad implications for understanding the evolution and niche diversification of these thermophiles as well as practical applications in fields such as bioleaching of trace metals from pyritic ores.
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Liu LJ, You XY, Guo X, Liu SJ, Jiang CY. Metallosphaera cuprina sp. nov., an acidothermophilic, metal-mobilizing archaeon. Int J Syst Evol Microbiol 2010; 61:2395-2400. [PMID: 21057050 DOI: 10.1099/ijs.0.026591-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel acidothermophilic archaeon, strain Ar-4(T), was isolated from a sulfuric hot spring in Tengchong, Yunnan, China. Cells of strain Ar-4(T) were Gram-staining-negative, irregular cocci and motile by means of flagella. Strain Ar-4(T) grew over a temperature range of 55-75 °C (optimum, 65 °C), a pH range of 2.5-5.5 (optimum, pH 3.5) and a NaCl concentration range of 0-1 % (w/v). The novel strain was aerobic and facultatively chemolithoautotrophic. The strain could extract metal ions from sulfidic ore. It was also able to oxidize reduced sulfur compounds. In addition, it was able to use heterogeneous organic materials for organotrophic growth. The main cellular lipids were calditoglycerocaldarchaeol (CGTE) and caldarchaeol (DGTE). The DNA G+C content of the strain was 40.2 mol%. Analysis of 16S rRNA gene sequences showed that strain Ar-4(T) was phylogenetically related to members of the genus Metallosphaera and had sequence similarities of 97.7 %, 97.0 % and 96.8 % with Metallosphaera hakonensis DSM 7519(T), Metallosphaera sedula DSM 5348(T) and Metallosphaera prunae DSM 10039(T), respectively. Strain Ar-4(T) showed DNA-DNA relatedness values of 47.5 %, 30.8 % and 29.1 % with M. hakonensis DSM 7519(T), M. sedula DSM 5348(T) and M. prunae DSM 10039(T), respectively. The differences in cell motility, the temperature and pH ranges for growth, the ability to utilize carbon sources, the DNA G+C content, and the low DNA-DNA relatedness values distinguished strain Ar-4(T) from recognized species of the genus Metallosphaera. On the basis of these results, it was concluded that strain Ar-4(T) represents a novel species of the genus Metallosphaera, for which the name Metallosphaera cuprina is proposed. The type strain is Ar-4(T) ( = JCM 15769(T) = CGMCC 1.7082(T)).
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Affiliation(s)
- Li-Jun Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Xiao-Yan You
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Xu Guo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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Orell A, Navarro CA, Arancibia R, Mobarec JC, Jerez CA. Life in blue: copper resistance mechanisms of bacteria and archaea used in industrial biomining of minerals. Biotechnol Adv 2010; 28:839-48. [PMID: 20627124 DOI: 10.1016/j.biotechadv.2010.07.003] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Revised: 07/01/2010] [Accepted: 07/02/2010] [Indexed: 10/19/2022]
Abstract
Industrial biomining processes to extract copper, gold and other metals involve the use of extremophiles such as the acidophilic Acidithiobacillus ferrooxidans (Bacteria), and the thermoacidophilic Sulfolobus metallicus (Archaea). Together with other extremophiles these microorganisms subsist in habitats where they are exposed to copper concentrations higher than 100mM. Herein we review the current knowledge on the Cu-resistance mechanisms found in these microorganisms. Recent information suggests that biomining extremophiles respond to extremely high Cu concentrations by using simultaneously all or most of the following key elements: 1) a wide repertoire of Cu-resistance determinants; 2) duplication of some of these Cu-resistance determinants; 3) existence of novel Cu chaperones; 4) a polyP-based Cu-resistance system, and 5) an oxidative stress defense system. Further insight of the biomining community members and their individual response to copper is highly relevant, since this could provide key information to the mining industry. In turn, this information could be used to select the more fit members of the bioleaching community to attain more efficient industrial biomining processes.
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Affiliation(s)
- Alvaro Orell
- Laboratory of Molecular Microbiology and Biotechnology, Department of Biology, and Millennium Institute for Cell Dynamics and Biotechnology, Faculty of Sciences, University of Chile, Santiago, Chile
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Abstract
The dissolution of sulfide minerals such as pyrite (FeS2), arsenopyrite (FeAsS), chalcopyrite (CuFeS2), sphalerite (ZnS), and marcasite (FeS2) yields hot, sulfuric acid-rich solutions that contain high concentrations of toxic metals. In locations where access of oxidants to sulfide mineral surfaces is increased by mining, the resulting acid mine drainage (AMD) may contaminate surrounding ecosystems. Communities of autotrophic and heterotrophic archaea and bacteria catalyze iron and sulfur oxidation, thus may ultimately determine the rate of release of metals and sulfur to the environment. AMD communities contain fewer prokaryotic lineages than many other environments. However, it is notable that at least two archaeal and eight bacterial divisions have representatives able to thrive under the extreme conditions typical of AMD. AMD communities are characterized by a very limited number of distinct species, probably due to the small number of metabolically beneficial reactions available. The metabolisms that underpin these communities include organoheterotrophy and autotrophic iron and sulfur oxidation. Other metabolic activity is based on anaerobic sulfur oxidation and ferric iron reduction. Evidence for physiological synergy in iron, sulfur, and carbon flow in these communities is reviewed. The microbial and geochemical simplicity of these systems makes them ideal targets for quantitative, genomic-based analyses of microbial ecology and evolution and community function.
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Affiliation(s)
- Brett J Baker
- Departments of Earth and Planetary Sciences and Environment Sciences Policy and Management, University of California Berkeley, Berkeley, CA 94720, USA
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Beblo K, Rabbow E, Rachel R, Huber H, Rettberg P. Tolerance of thermophilic and hyperthermophilic microorganisms to desiccation. Extremophiles 2009; 13:521-31. [DOI: 10.1007/s00792-009-0239-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Accepted: 03/16/2009] [Indexed: 11/27/2022]
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Karakashev D, Kotay SM, Trably E, Angelidaki I. A strict anaerobic extreme thermophilic hydrogen-producing culture enriched from digested household waste. J Appl Microbiol 2009; 106:1041-9. [DOI: 10.1111/j.1365-2672.2008.04071.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Xiao S, Xie X, Liu J. Microbial communities in acid water environments of two mines, China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2009; 157:1045-1050. [PMID: 18976840 DOI: 10.1016/j.envpol.2008.09.035] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2008] [Revised: 09/11/2008] [Accepted: 09/12/2008] [Indexed: 05/27/2023]
Abstract
To understand the compositions and structures of microbial communities in different acid-aqueous environments, a PCR-based cloning approach was used. A total of five samples were collected from two mines in China. Two samples, named as G1 and G2, were acid mine drainage (AMD) samples and from Yunfu sulfide mine in Guangdong province, China. The rest of the three samples named as D1, DY and D3, were from three sites undertaking bioleaching in Yinshan lead-zinc mine in Jiangxi province, China. Phylogenetic analysis revealed that bacteria in the five samples fell into six putative divisions, which were alpha-Proteobacteria, beta-Proteobacteria, gamma-Proteobacteria, Firmicutes, Actinobacteria and Nitrospira. Archaea was only detected in the three samples from Yinshan lead-zinc mine, which fell into two phylogenentic divisions, Thermoplsma and Ferroplasma. In addition, the results of principal component analysis (PCA) suggested that more similar the geochemical properties in samples were, more similar microbial community structures in samples were.
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Affiliation(s)
- Shengmu Xiao
- College of Environmental Science and Engineering, Donghua University, Shanghai, China
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Isolation and distribution of a novel iron-oxidizing crenarchaeon from acidic geothermal springs in Yellowstone National Park. Appl Environ Microbiol 2007; 74:942-9. [PMID: 18083851 DOI: 10.1128/aem.01200-07] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Novel thermophilic crenarchaea have been observed in Fe(III) oxide microbial mats of Yellowstone National Park (YNP); however, no definitive work has identified specific microorganisms responsible for the oxidation of Fe(II). The objectives of the current study were to isolate and characterize an Fe(II)-oxidizing member of the Sulfolobales observed in previous 16S rRNA gene surveys and to determine the abundance and distribution of close relatives of this organism in acidic geothermal springs containing high concentrations of dissolved Fe(II). Here we report the isolation and characterization of the novel, Fe(II)-oxidizing, thermophilic, acidophilic organism Metallosphaera sp. strain MK1 obtained from a well-characterized acid-sulfate-chloride geothermal spring in Norris Geyser Basin, YNP. Full-length 16S rRNA gene sequence analysis revealed that strain MK1 exhibits only 94.9 to 96.1% sequence similarity to other known Metallosphaera spp. and less than 89.1% similarity to known Sulfolobus spp. Strain MK1 is a facultative chemolithoautotroph with an optimum pH range of 2.0 to 3.0 and an optimum temperature range of 65 to 75 degrees C. Strain MK1 grows optimally on pyrite or Fe(II) sorbed onto ferrihydrite, exhibiting doubling times between 10 and 11 h under aerobic conditions (65 degrees C). The distribution and relative abundance of MK1-like 16S rRNA gene sequences in 14 acidic geothermal springs containing Fe(III) oxide microbial mats were evaluated. Highly related MK1-like 16S rRNA gene sequences (>99% sequence similarity) were consistently observed in Fe(III) oxide mats at temperatures ranging from 55 to 80 degrees C. Quantitative PCR using Metallosphaera-specific primers confirmed that organisms highly similar to strain MK1 comprised up to 40% of the total archaeal community at selected sites. The broad distribution of highly related MK1-like 16S rRNA gene sequences in acidic Fe(III) oxide microbial mats is consistent with the observed characteristics and growth optima of Metallosphaera-like strain MK1 and emphasizes the importance of this newly described taxon in Fe(II) chemolithotrophy in acidic high-temperature environments of YNP.
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He Z, Xiao S, Xie X, Zhong H, Hu Y, Li Q, Gao F, Li G, Liu J, Qiu G. Molecular diversity of microbial community in acid mine drainages of Yunfu sulfide mine. Extremophiles 2006; 11:305-14. [PMID: 17177020 DOI: 10.1007/s00792-006-0044-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2006] [Accepted: 10/16/2006] [Indexed: 10/23/2022]
Abstract
Two acid mine drainage (AMD) samples were studied by a PCR-based cloning approach, which were from Yunfu sulfide mine in Guangdong province, China. A total of 15 operational taxonomic units (OTUs) were obtained from the two AMD samples. The percentage of overlapped OTUs in two AMD samples was 42.1%. Phylogenetic analysis revealed that the bacterium in the two samples fell into four putative divisions, which were Nitrospira, alpha-Proteobacteria, beta-Proteobacteria, and gamma-Proteobacteria four families. Organisms of genuses Acidithiobacillus and Gallionella, which were in gamma-Proteobacteria family and beta-Proteobacteria family, respectively, were dominant in two samples. The proportions of clones affiliated with Gallionella in each sample were 47.2% (G2) and 16.9% (G1). The result suggested that organisms of Gallionella were a very important composition in microbial communities of the two AMD samples we studied. In addition, the PCR amplification of archaeal 16S rDNA genes form these two AMD samples have been performed with two sets of archaea-specific primers, but no PCR product found.
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Affiliation(s)
- Zhiguo He
- School of Resources Processing and Bioengineering, Central South University, Changsha, 410083, China
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Näther DJ, Rachel R, Wanner G, Wirth R. Flagella of Pyrococcus furiosus: multifunctional organelles, made for swimming, adhesion to various surfaces, and cell-cell contacts. J Bacteriol 2006; 188:6915-23. [PMID: 16980494 PMCID: PMC1595509 DOI: 10.1128/jb.00527-06] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pyrococcus furiosus ("rushing fireball") was named for the ability of this archaeal coccus to rapidly swim at its optimal growth temperature, around 100 degrees C. Early electron microscopic studies identified up to 50 cell surface appendages originating from one pole of the coccus, which have been called flagella. We have analyzed these putative motility organelles and found them to be composed primarily (>95%) of a glycoprotein that is homologous to flagellins from other archaea. Using various electron microscopic techniques, we found that these flagella can aggregate into cable-like structures, forming cell-cell connections between ca. 5% of all cells during stationary growth phase. P. furiosus cells could adhere via their flagella to carbon-coated gold grids used for electron microscopic analyses, to sand grains collected from the original habitat (Porto di Levante, Vulcano, Italy), and to various other surfaces. P. furiosus grew on surfaces in biofilm-like structures, forming microcolonies with cells interconnected by flagella and adhering to the solid supports. Therefore, we concluded that P. furiosus probably uses flagella for swimming but that the cell surface appendages also enable this archaeon to form cable-like cell-cell connections and to adhere to solid surfaces.
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Affiliation(s)
- Daniela J Näther
- Lehrstuhl für Microbiology, University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany
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Karavaiko GI, Dubinina GA, Kondrat’eva TF. Lithotrophic microorganisms of the oxidative cycles of sulfur and iron. Microbiology (Reading) 2006. [DOI: 10.1134/s002626170605002x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Abstract
The domain Archaea represents a third line of evolutionary descent, separate from Bacteria and Eucarya. Initial studies seemed to limit archaea to various extreme environments. These included habitats at the extreme limits that allow life on earth, in terms of temperature, pH, salinity, and anaerobiosis, which were the homes to hyper thermo philes, extreme (thermo)acidophiles, extreme halophiles, and methanogens. Typical environments from which pure cultures of archaeal species have been isolated include hot springs, hydrothermal vents, solfataras, salt lakes, soda lakes, sewage digesters, and the rumen. Within the past two decades, the use of molecular techniques, including PCR-based amplification of 16S rRNA genes, has allowed a culture-independent assessment of microbial diversity. Remarkably, such techniques have indicated a wide distribution of mostly uncultured archaea in normal habitats, such as ocean waters, lake waters, and soil. This review discusses organisms from the domain Archaea in the context of the environments where they have been isolated or detected. For organizational purposes, the domain has been separated into the traditional groups of methanogens, extreme halophiles, thermoacidophiles, and hyperthermophiles, as well as the uncultured archaea detected by molecular means. Where possible, we have correlated known energy-yielding reactions and carbon sources of the archaeal types with available data on potential carbon sources and electron donors and acceptors present in the environments. From the broad distribution, metabolic diversity, and sheer numbers of archaea in environments from the extreme to the ordinary, the roles that the Archaea play in the ecosystems have been grossly underestimated and are worthy of much greater scrutiny.Key words: Archaea, methanogen, extreme halophile, hyperthermophile, thermoacidophile, uncultured archaea, habitats.
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Affiliation(s)
- Bonnie Chaban
- Department of Microbiology and Immunology, Queen's University, Kingston, ON, Canada
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Okabayashi A, Wakai S, Kanao T, Sugio T, Kamimura K. Diversity of 16S ribosomal DNA-defined bacterial population in acid rock drainage from Japanese pyrite mine. J Biosci Bioeng 2005; 100:644-52. [PMID: 16473774 DOI: 10.1263/jbb.100.644] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2005] [Accepted: 08/25/2005] [Indexed: 11/17/2022]
Abstract
Four acidophilic bacteria (YARDs1-4) were isolated from an acid rock drainage (ARD) from Yanahara mine, Okayama prefecture, Japan. The physiological and 16S rDNA sequence analyses revealed that YARD1 was closely affiliated with Acidithiobacillus ferrooxidans, YARD2 was an Acidiphilium-like bacterium, and YARD3 and YARD4 were sulfur-oxidizing bacteria with a relatively close relationship to A. ferrooxidans in the phylogenetic analysis. A molecular approach based on the construction of a 16S rDNA clone library was used to investigate the microbial population of the ARD. Small-subunit rRNA genes were PCR amplified, subsequently cloned and screened for variation by a restriction fragment length polymorphism (RFLP) analysis. A total of 284 clones were grouped into 133 operational taxonomic units (OTUs) by the RFLP analysis. Among them, an OTU showing the same RFLP pattern as those of the isolates from the ARD was not detected. The phylogenetic analysis based on the 16S rDNA sequences from 10 major OTUs and their close relatives revealed that 4 OTUs containing 32.1% of the total clones were loosely affiliated with Verrucomicrobia, 2 OTUs containing 6.6% of the total clones were loosely affiliated with Chloribi, and other OTUs were affiliated with Actinobacteria, Nitrospirae, and beta-Proteobacteria.
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Affiliation(s)
- Ai Okabayashi
- Department of Botany and Microbiology, Division of Bioscience, Graduate School of Natural Science and Technology, Okayama University, Japan
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Valenzuela L, Chi A, Beard S, Orell A, Guiliani N, Shabanowitz J, Hunt DF, Jerez CA. Genomics, metagenomics and proteomics in biomining microorganisms. Biotechnol Adv 2005; 24:197-211. [PMID: 16288845 DOI: 10.1016/j.biotechadv.2005.09.004] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2005] [Indexed: 10/25/2022]
Abstract
The use of acidophilic, chemolithotrophic microorganisms capable of oxidizing iron and sulfur in industrial processes to recover metals from minerals containing copper, gold and uranium is a well established biotechnology with distinctive advantages over traditional mining. A consortium of different microorganisms participates in the oxidative reactions resulting in the extraction of dissolved metal values from ores. Considerable effort has been spent in the last years to understand the biochemistry of iron and sulfur compounds oxidation, bacteria-mineral interactions (chemotaxis, quorum sensing, adhesion, biofilm formation) and several adaptive responses allowing the microorganisms to survive in a bioleaching environment. All of these are considered key phenomena for understanding the process of biomining. The use of genomics, metagenomics and high throughput proteomics to study the global regulatory responses that the biomining community uses to adapt to their changing environment is just beginning to emerge in the last years. These powerful approaches are reviewed here since they offer the possibility of exciting new findings that will allow analyzing the community as a microbial system, determining the extent to which each of the individual participants contributes to the process, how they evolve in time to keep the conglomerate healthy and therefore efficient during the entire process of bioleaching.
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Affiliation(s)
- Lissette Valenzuela
- Laboratory of Molecular Microbiology and Biotechnology, Department of Biology, Faculty of Sciences, University of Chile, Santiago, Chile
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48
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Prokofeva MI, Kublanov IV, Nercessian O, Tourova TP, Kolganova TV, Lebedinsky AV, Bonch-Osmolovskaya EA, Spring S, Jeanthon C. Cultivated anaerobic acidophilic/acidotolerant thermophiles from terrestrial and deep-sea hydrothermal habitats. Extremophiles 2005; 9:437-48. [PMID: 15970992 DOI: 10.1007/s00792-005-0461-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2004] [Accepted: 05/25/2005] [Indexed: 11/27/2022]
Abstract
Metabolic and phylogenetic diversity of cultivated anaerobic microorganisms from acidic continental hot springs and deep-sea hydrothermal vents was studied by molecular and microbiological methods. Anaerobic organotrophic enrichment cultures growing at pH 3.5-4.0 and 60 or 85 degrees C with organic energy sources were obtained from samples of acidic hot springs of Kamchatka Peninsula (Pauzhetka, Moutnovski Volcano, Uzon Caldera) and Kunashir Island (South Kurils) as well as from the samples of chimneys of East Pacific Rise (13 degrees N). The analyses of clone libraries obtained from terrestrial enrichment cultures growing at 60 degrees C revealed the presence of archaea of genus Thermoplasma and bacteria of genus Thermoanaerobacter. Bacterial isolates from these enrichments were shown to belong to genera Thermoanaerobacter and Thermoanaerobacterium, being acidotolerant with the pH optimum for growth at 5.5-6.0 and the pH minimum at 3.0. At 85 degrees C, domination of thermoacidophilic archaea of genus Acidilobus in terrestrial enrichments was found by both molecular and microbiological methods. Five isolates belonging to this genus possessed some phenotypic features that were new for this genus, such as flagellation or the ability to grow on monosaccharides or disaccharides. Analyses of clone libraries from the deep-sea thermoacidophilic enrichment cultures showed that the representatives of the genus Thermococcus were present at both 60 and 85 degrees C. From the 60 degrees C deep-sea enrichment, a strain belonging to Thermoanaerobacter siderophilus was isolated. It grew optimally at pH 6.0 with the minimum pH for growth at 3.0 and with salinity optimum at 0-2.5% NaCl and the maximum at 7%, thus differing significantly from the type strain. These data show that fermentative degradation of organic matter may occur at low pH and wide temperature range in both terrestrial and deep-sea habitats and can be performed by acidophilic or acidotolerant thermophilic prokaryotes.
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Affiliation(s)
- Maria I Prokofeva
- Institute of Microbiology, Russian Academy of Sciences, Prospect 60-Letya Oktyabrya 7/2, 117312 Moscow, Russia.
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49
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Kurosawa N, Itoh YH, Itoh T. Reclassification of Sulfolobus hakonensis Takayanagi et al. 1996 as Metallosphaera hakonensis comb. nov. based on phylogenetic evidence and DNA G+C content. Int J Syst Evol Microbiol 2003; 53:1607-1608. [PMID: 13130056 DOI: 10.1099/ijs.0.02716-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic status of Sulfolobus hakonensis Takayanagi et al. 1996 was re-evaluated by fresh determinations of the 16S rDNA sequence and G+C content of the genomic DNA of the type strain, HO1-1(T). The 16S rDNA sequence of strain HO1-1(T) showed 98 % similarity to those of two Metallosphaera species and only </=92 % similarity to those of other Sulfolobus species. The DNA G+C content (46.2 mol%) is in accordance with those of Metallosphaera species. In addition, strain HO1-1(T) shares some phenotypic properties with Metallosphaera species; however, it can be differentiated from them by its capacity to utilize FeS and tetrathionate and the absence of flagella. Therefore, it is proposed that Sulfolobus hakonensis should be transferred to the genus Metallosphaera as Metallosphaera hakonensis comb. nov.
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Affiliation(s)
- Norio Kurosawa
- Departments of Environmental Engineering for Symbiosis, Faculty of Engineering, Soka University, 1-236 Tangi-cho, Hachioji, Tokyo 192-8577, Japan
| | - Yuko H Itoh
- Departments of Bioinformatics, Faculty of Engineering, Soka University, 1-236 Tangi-cho, Hachioji, Tokyo 192-8577, Japan
| | - Takashi Itoh
- Japan Collection of Microorganisms, RIKEN (The Institute of Physical and Chemical Research), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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50
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Itoh T, Suzuki K, Sanchez PC, Nakase T. Caldisphaera lagunensis gen. nov., sp. nov., a novel thermoacidophilic crenarchaeote isolated from a hot spring at Mt Maquiling, Philippines. Int J Syst Evol Microbiol 2003; 53:1149-1154. [PMID: 12892143 DOI: 10.1099/ijs.0.02580-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four novel, thermoacidophilic, crenarchaeotic cocci that grew anaerobically and heterotrophically were isolated from an acidic hot spring in the Philippines; two representative strains were characterized in detail. Most cells were regular cocci, 0.8-1.1 microm in width, which occurred singly or in pairs. They were non-motile and grew at 45-80 degrees C (optimum 70-75 degrees C) and pH 2.3-5.4 (optimum 3.5-4.0). They utilized starch, glycogen, gelatin, beef extract, yeast extract and peptone as carbon and energy sources. Growth was stimulated by the presence of sulfur as an electron acceptor. The lipid fraction contained cyclic and acyclic tetraether core lipids. The DNA G + C content was 31 mol%; phylogenetic analysis based on 16S rDNA sequences showed that the novel cocci represent an independent lineage in the phylum Crenarchaeota, distantly related to Acidilobus aceticus and an allied strain, NC12. Caldisphaera lagunensis gen. nov., sp. nov. is proposed to accommodate the four strains. The type strain is IC-154T (=JCM 11604T=MCC-UPLB 1331T=ANMR 0165T).
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Affiliation(s)
- T Itoh
- Japan Collection of Microorganisms, RIKEN (Institute of Physical and Chemical Research), Wako-shi, Saitama 351-0198, Japan
| | - K Suzuki
- Biological Resource Center, Biotechnology Center, National Institute of Technology and Evaluation, Kazusa-Kamatari, Kisarazu, Chiba 292-0812, Japan
- Japan Collection of Microorganisms, RIKEN (Institute of Physical and Chemical Research), Wako-shi, Saitama 351-0198, Japan
| | - P C Sanchez
- Museum of Natural History, University of the Philippines Los Baños College, Laguna 4031, Philippines
| | - T Nakase
- Laboratory of Microbiology, Department of Applied Biology and Chemistry, Faculty of Applied Bioscience, Tokyo University of Agriculture, Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
- Japan Collection of Microorganisms, RIKEN (Institute of Physical and Chemical Research), Wako-shi, Saitama 351-0198, Japan
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