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Chen L, Wang Y, Liu H, Zhou Y, Nie Z, Xia J, Shu W. Different fates of Sb(III) and Sb(V) during the formation of jarosite mediated by Acidithiobacillus ferrooxidans. J Environ Sci (China) 2025; 147:342-358. [PMID: 39003052 DOI: 10.1016/j.jes.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/09/2023] [Accepted: 12/10/2023] [Indexed: 07/15/2024]
Abstract
Secondary iron-sulfate minerals such as jarosite, which are easily formed in acid mine drainage, play an important role in controlling metal mobility. In this work, the typical iron-oxidizing bacterium Acidithiobacillus ferrooxidans ATCC 23270 was selected to synthesize jarosite in the presence of antimony ions, during which the solution behavior, synthetic product composition, and bacterial metabolism were studied. The results show that in the presence of Sb(V), Fe2+ was rapidly oxidized to Fe3+ by A. ferrooxidans and Sb(V) had no obvious effect on the biooxidation of Fe2+ under the current experimental conditions. The presence of Sb(III) inhibited bacterial growth and Fe2+ oxidation. For the group with Sb(III), products with amorphous phases were formed 72 hr later, which were mainly ferrous sulfate and pentavalent antimony oxide, and the amorphous precursor was finally transformed into a more stable crystal phase. For the group with Sb(V), the morphology and structure of jarosite were changed in comparison with those without Sb. The biomineralization process was accompanied by the removal of 94% Sb(V) to form jarosite containing the Fe-Sb-O complex. Comparative transcriptome analysis shows differential effects of Sb(III) and Sb(V) on bacterial metabolism. The expression levels of functional genes related to cell components were much more downregulated for the group with Sb(III) but much more regulated for that with Sb(V). Notably, cytochrome c and nitrogen fixation-relevant genes for the A.f_Fe2+_Sb(III) group were enhanced significantly, indicating their role in Sb(III) resistance. This study is of great value for the development of antimony pollution control and remediation technology.
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Affiliation(s)
- Lu Chen
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
| | - Yirong Wang
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
| | - Hongchang Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key Lab of Biometallurgy of Ministry of Education of China, Central South University, Changsha 410083, China.
| | - Yuhang Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
| | - Zhenyuan Nie
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key Lab of Biometallurgy of Ministry of Education of China, Central South University, Changsha 410083, China
| | - Jinlan Xia
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key Lab of Biometallurgy of Ministry of Education of China, Central South University, Changsha 410083, China
| | - Wensheng Shu
- School of Life Sciences, South China Normal University, Guangzhou 510631, China
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2
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Wang Q, Zhang C, Song J, Bamanu B, Zhao Y. Enhancement of bio-promoters on hexavalent chromium inhibited sulfur-driven denitrification: repairing damage, accelerating electron transfer, and reshaping microbial collaboration. BIORESOURCE TECHNOLOGY 2024; 400:130699. [PMID: 38615966 DOI: 10.1016/j.biortech.2024.130699] [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: 01/27/2024] [Revised: 03/13/2024] [Accepted: 04/12/2024] [Indexed: 04/16/2024]
Abstract
Proposing recovery strategies to recover heavy-metal-inhibited sulfur-driven denitrification, as well as disclosing recovery mechanisms, can provide technical support for the stable operation of bio-systems. This study proposed an effective bio-promoter (mediator-promoter composed of L-cysteine, biotin, cytokinin, and anthraquinone-2,6-disulfonate) to recover Cr(VI) inhibited sulfur-driven denitrification, which effectively reduced the recovery time of NO3--N reduction (18-21 cycles) and NO2--N reduction (27-42 cycles) compared with self-recovery. The mediator-promoter repaired microbial damage by promoting intracellular chromium efflux. Moreover, the mediator-promoter reduced the accumulated reactive oxygen species by stimulating the secretion of antioxidant enzymes, reaching equilibrium in the oxidative-antioxidant system. To improve electron transmission, the mediator-promoter restored S2O32- oxidation to provide adequate electron donors and increased electron transfer rate by increasing cytochrome c levels. Mediator-promoter boosted the abundance of Thiobacillus (sulfur-oxidizing bacterium) and Simplicispira (denitrifying bacterium), which were positively correlated, facilitating the rapid denitrification recovery and the long-term stable operation of recovered systems.
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Affiliation(s)
- Qian Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Chenggong Zhang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Jinxin Song
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Bibek Bamanu
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Yingxin Zhao
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China.
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3
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Kanao T. Tetrathionate hydrolase from the acidophilic microorganisms. Front Microbiol 2024; 15:1338669. [PMID: 38348185 PMCID: PMC10859504 DOI: 10.3389/fmicb.2024.1338669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/15/2024] [Indexed: 02/15/2024] Open
Abstract
Tetrathionate hydrolase (TTH) is a unique enzyme found in acidophilic sulfur-oxidizing microorganisms, such as bacteria and archaea. This enzyme catalyzes the hydrolysis of tetrathionate to thiosulfate, elemental sulfur, and sulfate. It is also involved in dissimilatory sulfur oxidation metabolism, the S4-intermediate pathway. TTHs have been purified and characterized from acidophilic autotrophic sulfur-oxidizing microorganisms. All purified TTHs show an optimum pH in the acidic range, suggesting that they are localized in the periplasmic space or outer membrane. In particular, the gene encoding TTH from Acidithiobacillus ferrooxidans (Af-tth) was identified and recombinantly expressed in Escherichia coli cells. TTH activity could be recovered from the recombinant inclusion bodies by acid refolding treatment for crystallization. The mechanism of tetrathionate hydrolysis was then elucidated by X-ray crystal structure analysis. Af-tth is highly expressed in tetrathionate-grown cells but not in iron-grown cells. These unique structural properties, reaction mechanisms, gene expression, and regulatory mechanisms are discussed in this review.
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Affiliation(s)
- Tadayoshi Kanao
- Department of Agricultural and Biological Chemistry, Graduate School of Environment, Life, Natural Science, and Technology, Okayama University, Okayama, Japan
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4
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Li S, Fan S, Peng X, Zheng D, Li D. Using ferrous-oxidizing bacteria to enhance the performance of a pH neutral all-iron flow battery. iScience 2024; 27:108595. [PMID: 38174320 PMCID: PMC10762366 DOI: 10.1016/j.isci.2023.108595] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 11/14/2023] [Accepted: 11/28/2023] [Indexed: 01/05/2024] Open
Abstract
Among various redox flow batteries (RFBs), the all-iron RFBs have greater application potential due to high accessibility of electrolytes. However, the potential of microaerobic ferrous-oxidizing bacteria (FeOB) to improve the performance of RFB has been neglected. Here, several experiments were conducted using Fe2+-diethylenetriaminepentaacetic acid (DTPA)/Na3[Fe(CN)6] as a redox couple for investigating the enhanced performance by FeOB in this RFB. Results showed that the maximum current density of experimental reactors could achieve 22.56 A/m2 at 0.1 M, whereas power density could still maintain 3.42 W/m2(16.96 A/m2 and 1.58 W/m2 for control group); meantime, the polarization impedance of anode increased slower and Fe2+-DTPA oxidation peak emerged maximum 494 mV negative shift. With increased electrolyte concentration in chronopotentiometry experiments, the experimental reactor achieved higher discharging specific capacity at 0.3 M, 10 mA/cm2. Microbial composition analysis showed maximum 75% is Brucella, indicating Brucella has ferrous-oxidizing electroactivity.
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Affiliation(s)
- Sitao Li
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sen Fan
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, China
- Collage of Life Sciences, Sichuan University, Chengdu 610041, China
| | - Xinyuan Peng
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, China
- Collage of Life Sciences, Sichuan University, Chengdu 610041, China
| | - Decong Zheng
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Daping Li
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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5
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Khaleque HN, Nazem-Bokaee H, Gumulya Y, Carlson RP, Kaksonen AH. Simulating compatible solute biosynthesis using a metabolic flux model of the biomining acidophile, Acidithiobacillus ferrooxidans ATCC 23270. Res Microbiol 2024; 175:104115. [PMID: 37572823 DOI: 10.1016/j.resmic.2023.104115] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/14/2023]
Abstract
Halotolerant, acidophilic, bioleaching microorganisms are crucial to biomining operations that utilize saline water. Compatible solutes play an important role in the adaptation of these microorganisms to saline environments. Acidithiobacillus ferrooxidans ATCC 23270, an iron- and sulfur-oxidizing acidophilic bacterium, synthesizes trehalose as its native compatible solute but is still sensitive to salinity. Recently, halotolerant bioleaching bacteria were found to use ectoine as their key compatible solute. Previously, bioleaching bacteria were recalcitrant to genetic manipulation; however, recent advancements in genetic tools and techniques allow successful genetic modification of A. ferrooxidans ATCC 23270. Therefore, this study aimed to test, in silico, the effect of native and synthetic compatible solute biosynthesis by A. ferrooxidans ATCC 23270 on its growth and metabolism. Metabolic network flux modelling was used to provide a computational framework for the prediction of metabolic fluxes during production of native and synthetic compatible solutes by A. ferrooxidans ATCC 23270, in silico. Complete pathways for trehalose biosynthesis by the bacterium are proposed and captured in the updated metabolic model including a newly discovered UDP-dependent trehalose synthesis pathway. Finally, the effect of nitrogen sources on compatible solute production was simulated and showed that using nitrogen gas as the sole nitrogen source enables the ectoine-producing 'engineered' microbe to oxidize up to 20% more ferrous iron in comparison to the native microbe that only produces trehalose. Therefore, the predictive outcomes of the model have the potential to guide the design and optimization of a halotolerant strain of A. ferrooxidans ATCC 23270 for saline bioleaching operations.
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Affiliation(s)
- Himel Nahreen Khaleque
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Environment, 147 Underwood Avenue, Floreat, WA, Australia; Synthetic Biology Future Science Platform, CSIRO, Canberra 2601, ACT, Australia; School of Science, Edith Cowan University, Joondalup, WA, Australia.
| | - Hadi Nazem-Bokaee
- Synthetic Biology Future Science Platform, CSIRO, Canberra 2601, ACT, Australia; Australian National Herbarium, National Research Collections Australia, NCMI, CSIRO, Canberra 2601, ACT, Australia.
| | - Yosephine Gumulya
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Environment, 147 Underwood Avenue, Floreat, WA, Australia; Synthetic Biology Future Science Platform, CSIRO, Canberra 2601, ACT, Australia; Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland, Australia.
| | - Ross P Carlson
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.
| | - Anna H Kaksonen
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Environment, 147 Underwood Avenue, Floreat, WA, Australia; Synthetic Biology Future Science Platform, CSIRO, Canberra 2601, ACT, Australia.
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6
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Jiménez NE, Acuña V, Cortés MP, Eveillard D, Maass AE. Unveiling abundance-dependent metabolic phenotypes of microbial communities. mSystems 2023; 8:e0049223. [PMID: 37668446 PMCID: PMC10654064 DOI: 10.1128/msystems.00492-23] [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: 05/24/2023] [Accepted: 06/21/2023] [Indexed: 09/06/2023] Open
Abstract
IMPORTANCE In nature, organisms live in communities and not as isolated species, and their interactions provide a source of resilience to environmental disturbances. Despite their importance in ecology, human health, and industry, understanding how organisms interact in different environments remains an open question. In this work, we provide a novel approach that, only using genomic information, studies the metabolic phenotype exhibited by communities, where the exploration of suboptimal growth flux distributions and the composition of a community allows to unveil its capacity to respond to environmental changes, shedding light of the degrees of metabolic plasticity inherent to the community.
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Affiliation(s)
- Natalia E. Jiménez
- Center for Mathematical Modeling, University of Chile, Santiago, Chile
- Center for Genome Regulation, Millennium Institute, University of Chile, Santiago, Chile
| | - Vicente Acuña
- Center for Mathematical Modeling, University of Chile, Santiago, Chile
- Center for Genome Regulation, Millennium Institute, University of Chile, Santiago, Chile
| | - María Paz Cortés
- Center for Mathematical Modeling, University of Chile, Santiago, Chile
| | | | - Alejandro Eduardo Maass
- Center for Mathematical Modeling, University of Chile, Santiago, Chile
- Center for Genome Regulation, Millennium Institute, University of Chile, Santiago, Chile
- Department of Mathematical Engineering, University of Chile, Santiago, Chile
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7
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Li L, Liu Z, Meng D, Liu Y, Liu T, Jiang C, Yin H. Sequence similarity network and protein structure prediction offer insights into the evolution of microbial pathways for ferrous iron oxidation. mSystems 2023; 8:e0072023. [PMID: 37768051 PMCID: PMC10654088 DOI: 10.1128/msystems.00720-23] [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: 07/11/2023] [Accepted: 08/09/2023] [Indexed: 09/29/2023] Open
Abstract
IMPORTANCE Microbial Fe(II) oxidation is a crucial process that harnesses and converts the energy available in Fe, contributing significantly to global element cycling. However, there are still many aspects of this process that remain unexplored. In this study, we utilized a combination of comparative genomics, sequence similarity network analysis, and artificial intelligence-driven structure modeling methods to address the lack of structural information on Fe(II) oxidation proteins and offer a comprehensive perspective on the evolution of Fe(II) oxidation pathways. Our findings suggest that several microbial Fe(II) oxidation pathways currently known may have originated within classes Gammaproteobacteria and Betaproteobacteria.
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Affiliation(s)
- Liangzhi 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
| | - Zhenghua Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Delong Meng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Yongjun Liu
- Hunan Tobacco Science Institute, Changsha, China
| | - Tianbo Liu
- Hunan Tobacco Science Institute, Changsha, China
| | - Chengying Jiang
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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8
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Ibáñez A, Garrido-Chamorro S, Coque JJR, Barreiro C. From Genes to Bioleaching: Unraveling Sulfur Metabolism in Acidithiobacillus Genus. Genes (Basel) 2023; 14:1772. [PMID: 37761912 PMCID: PMC10531304 DOI: 10.3390/genes14091772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Sulfur oxidation stands as a pivotal process within the Earth's sulfur cycle, in which Acidithiobacillus species emerge as skillful sulfur-oxidizing bacteria. They are able to efficiently oxidize several reduced inorganic sulfur compounds (RISCs) under extreme conditions for their autotrophic growth. This unique characteristic has made these bacteria a useful tool in bioleaching and biological desulfurization applications. Extensive research has unraveled diverse sulfur metabolism pathways and their corresponding regulatory systems. The metabolic arsenal of the Acidithiobacillus genus includes oxidative enzymes such as: (i) elemental sulfur oxidation enzymes, like sulfur dioxygenase (SDO), sulfur oxygenase reductase (SOR), and heterodisulfide reductase (HDR-like system); (ii) enzymes involved in thiosulfate oxidation pathways, including the sulfur oxidation (Sox) system, tetrathionate hydrolase (TetH), and thiosulfate quinone oxidoreductase (TQO); (iii) sulfide oxidation enzymes, like sulfide:quinone oxidoreductase (SQR); and (iv) sulfite oxidation pathways, such as sulfite oxidase (SOX). This review summarizes the current state of the art of sulfur metabolic processes in Acidithiobacillus species, which are key players of industrial biomining processes. Furthermore, this manuscript highlights the existing challenges and barriers to further exploring the sulfur metabolism of this peculiar extremophilic genus.
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Affiliation(s)
- Ana Ibáñez
- Instituto de Investigación de la Viña y el Vino, Escuela de Ingeniería Agraria, Universidad de León, 24009 León, Spain; (A.I.); (J.J.R.C.)
- Instituto Tecnológico Agrario de Castilla y León (ITACyL), Área de Investigación Agrícola, 47071 Valladolid, Spain
| | - Sonia Garrido-Chamorro
- Área de Bioquímica y Biología Molecular, Departamento de Biología Molecular, Universidad de León, 24007 León, Spain;
| | - Juan J. R. Coque
- Instituto de Investigación de la Viña y el Vino, Escuela de Ingeniería Agraria, Universidad de León, 24009 León, Spain; (A.I.); (J.J.R.C.)
| | - Carlos Barreiro
- Área de Bioquímica y Biología Molecular, Departamento de Biología Molecular, Universidad de León, 24007 León, Spain;
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9
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Izquierdo-Fiallo K, Muñoz-Villagrán C, Orellana O, Sjoberg R, Levicán G. Comparative genomics of the proteostasis network in extreme acidophiles. PLoS One 2023; 18:e0291164. [PMID: 37682893 PMCID: PMC10490939 DOI: 10.1371/journal.pone.0291164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023] Open
Abstract
Extreme acidophiles thrive in harsh environments characterized by acidic pH, high concentrations of dissolved metals and high osmolarity. Most of these microorganisms are chemolithoautotrophs that obtain energy from low redox potential sources, such as the oxidation of ferrous ions. Under these conditions, the mechanisms that maintain homeostasis of proteins (proteostasis), as the main organic components of the cells, are of utmost importance. Thus, the analysis of protein chaperones is critical for understanding how these organisms deal with proteostasis under such environmental conditions. In this work, using a bioinformatics approach, we performed a comparative genomic analysis of the genes encoding classical, periplasmic and stress chaperones, and the protease systems. The analysis included 35 genomes from iron- or sulfur-oxidizing autotrophic, heterotrophic, and mixotrophic acidophilic bacteria. The results showed that classical ATP-dependent chaperones, mostly folding chaperones, are widely distributed, although they are sub-represented in some groups. Acidophilic bacteria showed redundancy of genes coding for the ATP-independent holdase chaperones RidA and Hsp20. In addition, a systematically high redundancy of genes encoding periplasmic chaperones like HtrA and YidC was also detected. In the same way, the proteolytic ATPase complexes ClpPX and Lon presented redundancy and broad distribution. The presence of genes that encoded protein variants was noticeable. In addition, genes for chaperones and protease systems were clustered within the genomes, suggesting common regulation of these activities. Finally, some genes were differentially distributed between bacteria as a function of the autotrophic or heterotrophic character of their metabolism. These results suggest that acidophiles possess an abundant and flexible proteostasis network that protects proteins in organisms living in energy-limiting and extreme environmental conditions. Therefore, our results provide a means for understanding the diversity and significance of proteostasis mechanisms in extreme acidophilic bacteria.
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Affiliation(s)
- Katherin Izquierdo-Fiallo
- Department of Biology, Faculty of Chemistry and Biology, University of Santiago of Chile (USACH), Santiago, Chile
| | - Claudia Muñoz-Villagrán
- Department of Biology, Faculty of Chemistry and Biology, University of Santiago of Chile (USACH), Santiago, Chile
| | - Omar Orellana
- Programa de Biología Celular y Molecular, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Rachid Sjoberg
- Department of Biology, Faculty of Chemistry and Biology, University of Santiago of Chile (USACH), Santiago, Chile
| | - Gloria Levicán
- Department of Biology, Faculty of Chemistry and Biology, University of Santiago of Chile (USACH), Santiago, Chile
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10
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Li L, Zhou L, Jiang C, Liu Z, Meng D, Luo F, He Q, Yin H. AI-driven pan-proteome analyses reveal insights into the biohydrometallurgical properties of Acidithiobacillia. Front Microbiol 2023; 14:1243987. [PMID: 37744906 PMCID: PMC10512742 DOI: 10.3389/fmicb.2023.1243987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 08/21/2023] [Indexed: 09/26/2023] Open
Abstract
Microorganism-mediated biohydrometallurgy, a sustainable approach for metal recovery from ores, relies on the metabolic activity of acidophilic bacteria. Acidithiobacillia with sulfur/iron-oxidizing capacities are extensively studied and applied in biohydrometallurgy-related processes. However, only 14 distinct proteins from Acidithiobacillia have experimentally determined structures currently available. This significantly hampers in-depth investigations of Acidithiobacillia's structure-based biological mechanisms pertaining to its relevant biohydrometallurgical processes. To address this issue, we employed a state-of-the-art artificial intelligence (AI)-driven approach, with a median model confidence of 0.80, to perform high-quality full-chain structure predictions on the pan-proteome (10,458 proteins) of the type strain Acidithiobacillia. Additionally, we conducted various case studies on de novo protein structural prediction, including sulfate transporter and iron oxidase, to demonstrate how accurate structure predictions and gene co-occurrence networks can contribute to the development of mechanistic insights and hypotheses regarding sulfur and iron utilization proteins. Furthermore, for the unannotated proteins that constitute 35.8% of the Acidithiobacillia proteome, we employed the deep-learning algorithm DeepFRI to make structure-based functional predictions. As a result, we successfully obtained gene ontology (GO) terms for 93.6% of these previously unknown proteins. This study has a significant impact on improving protein structure and function predictions, as well as developing state-of-the-art techniques for high-throughput analysis of large proteomic data.
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Affiliation(s)
- Liangzhi 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
| | - Lei Zhou
- Beijing Research Institute of Chemical Engineering and Metallurgy, Beijing, China
| | - Chengying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhenghua Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Delong Meng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Feng Luo
- School of Computing, Clemson University, Clemson, SC, United States
| | - Qiang He
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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11
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Jones S, Santini JM. Mechanisms of bioleaching: iron and sulfur oxidation by acidophilic microorganisms. Essays Biochem 2023; 67:685-699. [PMID: 37449416 PMCID: PMC10427800 DOI: 10.1042/ebc20220257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/18/2023]
Abstract
Bioleaching offers a low-input method of extracting valuable metals from sulfide minerals, which works by exploiting the sulfur and iron metabolisms of microorganisms to break down the ore. Bioleaching microbes generate energy by oxidising iron and/or sulfur, consequently generating oxidants that attack sulfide mineral surfaces, releasing target metals. As sulfuric acid is generated during the process, bioleaching organisms are typically acidophiles, and indeed the technique is based on natural processes that occur at acid mine drainage sites. While the overall concept of bioleaching appears straightforward, a series of enzymes is required to mediate the complex sulfur oxidation process. This review explores the mechanisms underlying bioleaching, summarising current knowledge on the enzymes driving microbial sulfur and iron oxidation in acidophiles. Up-to-date models are provided of the two mineral-defined pathways of sulfide mineral bioleaching: the thiosulfate and the polysulfide pathway.
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Affiliation(s)
- Sarah Jones
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, WC1E 6BT, U.K
- Institute of Structural and Molecular Biology, Division of Biosciences, Birkbeck, University of London, Malet Street, London, WC1E 7HX, U.K
| | - Joanne M Santini
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, WC1E 6BT, U.K
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12
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Liapun V, Motola M. Current overview and future perspective in fungal biorecovery of metals from secondary sources. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 332:117345. [PMID: 36724599 DOI: 10.1016/j.jenvman.2023.117345] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/09/2023] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Microorganisms are intimately involved in many biogeochemical processes that underpin the transformation of metals and cycling of related substances, such as metalloids and radionuclides. Many processes determine the mobility and bioavailability of metals, thereby influencing their transfer to the environment and living organisms. These processes are closely related to global phenomena such as soil formation and bioweathering. In addition to environmental significance, microbial metal transformations play an essential role in both in situ and ex situ bioremediation processes for solid and liquid wastes. The solubilization of heavy metals from industrial waste and soil is commonly used in bioremediation. Moreover, immobilization processes are applicable to bioremediation of metals and radionuclides from aqueous solutions. This review provides an overview of critical metal extraction and recovery from secondary sources, applied microorganisms and methods, metal-microbe interactions, as well as a detailed description of known metal recovery mechanisms.
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Affiliation(s)
- Viktoriia Liapun
- Department of Inorganic Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 842 15, Bratislava, Slovakia.
| | - Martin Motola
- Department of Inorganic Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 842 15, Bratislava, Slovakia.
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Rakhshani Y, Rahpeyma SS, Tabandeh F, Arabnezhad M, Azimi A, Raheb J. Multi-Objective Optimization of Copper Bioleaching: Comparative Study of Pure and Co-Cultured Cultivation. IRANIAN JOURNAL OF BIOTECHNOLOGY 2023; 21:e3278. [PMID: 37228625 PMCID: PMC10203187 DOI: 10.30498/ijb.2023.328969.3278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 01/09/2023] [Indexed: 05/27/2023]
Abstract
Background Bioleaching is a practical method to recover metals from low-grade mineral sulfides. The most frequent bacteria involved in the bioleaching of metals from ores are Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans. Experimental design is a method through which the optimum activity condition will be obtained, avoiding numerous trials and errors. Objectives This study aimed to optimize the bioleaching condition of two indigenous iron- and sulfur-oxidizing bacteria from the Meydouk mine, Iran, and evaluate their function in a semi-pilot operation in pure and mixed cultures. Material and Methods After treatment with sulfuric acid, the bacterial DNA was extracted, and further 16S rRNA was sequenced to characterize the bacterial species. The cultivation condition of these bacteria was optimized using Design-expert (6.1.1 version) software. The copper recovery rate and the differentiation in the ORP rate in the percolation columns were also investigated. These strains were isolated from the Meydouk mine for the first time. Results 16S rRNA analysis revealed that both bacteria belong to the Acidithiobacillus genus. The factors with the most significant impact on Acidithiobacillus ferrooxidans with their optimum level were temperature=35 °C, pH=2.5, and initial FeSO4 concentration=25 g.L-1. Also, initial sulfur concentration had the most significant impact on Acidithiobacillus thiooxidans with the optimum level of 35 g.L-1. Moreover, the mixed culture determined higher bioleaching efficiency compared with the case of employing the pure cultures. Conclusions Utilizing a mixture of both bacteria, Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans elevated the Cu recovery rate due to the synergetic function of the strains. Also, introducing an initial dosage of sulfur and pre-acidification could elevate metal recovery efficiency.
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Affiliation(s)
- Yasin Rakhshani
- Department of Molecular Medicine, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
- Department of Microbiology, Karaj Branch, Islamic Azad University, Karaj, Iran
| | - Sayyed Shahryar Rahpeyma
- Department of Molecular Medicine, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
- Department of Systems Biotechnology, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Fatemeh Tabandeh
- Department of Energy and Environmental Biotechnology, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | | | - Ali Azimi
- National Iranian Copper Industries Corporation, Tehran, Iran
| | - Jamshid Raheb
- Department of Molecular Medicine, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
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14
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Dopson M, González-Rosales C, Holmes DS, Mykytczuk N. Eurypsychrophilic acidophiles: From (meta)genomes to low-temperature biotechnologies. Front Microbiol 2023; 14:1149903. [PMID: 37007468 PMCID: PMC10050440 DOI: 10.3389/fmicb.2023.1149903] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 02/16/2023] [Indexed: 03/17/2023] Open
Abstract
Low temperature and acidic environments encompass natural milieus such as acid rock drainage in Antarctica and anthropogenic sites including drained sulfidic sediments in Scandinavia. The microorganisms inhabiting these environments include polyextremophiles that are both extreme acidophiles (defined as having an optimum growth pH < 3), and eurypsychrophiles that grow at low temperatures down to approximately 4°C but have an optimum temperature for growth above 15°C. Eurypsychrophilic acidophiles have important roles in natural biogeochemical cycling on earth and potentially on other planetary bodies and moons along with biotechnological applications in, for instance, low-temperature metal dissolution from metal sulfides. Five low-temperature acidophiles are characterized, namely, Acidithiobacillus ferriphilus, Acidithiobacillus ferrivorans, Acidithiobacillus ferrooxidans, “Ferrovum myxofaciens,” and Alicyclobacillus disulfidooxidans, and their characteristics are reviewed. Our understanding of characterized and environmental eurypsychrophilic acidophiles has been accelerated by the application of “omics” techniques that have aided in revealing adaptations to low pH and temperature that can be synergistic, while other adaptations are potentially antagonistic. The lack of known acidophiles that exclusively grow below 15°C may be due to the antagonistic nature of adaptations in this polyextremophile. In conclusion, this review summarizes the knowledge of eurypsychrophilic acidophiles and places the information in evolutionary, environmental, biotechnological, and exobiology perspectives.
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Affiliation(s)
- Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
- *Correspondence: Mark Dopson
| | - Carolina González-Rosales
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastian, Santiago, Chile
| | - Nadia Mykytczuk
- Goodman School of Mines, Laurentian University, Sudbury, ON, Canada
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15
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Zhang X, Shi H, Tan N, Zhu M, Tan W, Daramola D, Gu T. Advances in bioleaching of waste lithium batteries under metal ion stress. BIORESOUR BIOPROCESS 2023; 10:19. [PMID: 38647921 PMCID: PMC10992134 DOI: 10.1186/s40643-023-00636-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 02/09/2023] [Indexed: 03/29/2023] Open
Abstract
In modern societies, the accumulation of vast amounts of waste Li-ion batteries (WLIBs) is a grave concern. Bioleaching has great potential for the economic recovery of valuable metals from various electronic wastes. It has been successfully applied in mining on commercial scales. Bioleaching of WLIBs can not only recover valuable metals but also prevent environmental pollution. Many acidophilic microorganisms (APM) have been used in bioleaching of natural ores and urban mines. However, the activities of the growth and metabolism of APM are seriously inhibited by the high concentrations of heavy metal ions released by the bio-solubilization process, which slows down bioleaching over time. Only when the response mechanism of APM to harsh conditions is well understood, effective strategies to address this critical operational hurdle can be obtained. In this review, a multi-scale approach is used to summarize studies on the characteristics of bioleaching processes under metal ion stress. The response mechanisms of bacteria, including the mRNA expression levels of intracellular genes related to heavy metal ion resistance, are also reviewed. Alleviation of metal ion stress via addition of chemicals, such as spermine and glutathione is discussed. Monitoring using electrochemical characteristics of APM biofilms under metal ion stress is explored. In conclusion, effective engineering strategies can be proposed based on a deep understanding of the response mechanisms of APM to metal ion stress, which have been used to improve bioleaching efficiency effectively in lab tests. It is very important to engineer new bioleaching strains with high resistance to metal ions using gene editing and synthetic biotechnology in the near future.
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Affiliation(s)
- Xu Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Hongjie Shi
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Ningjie Tan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Minglong Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Wensong Tan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Damilola Daramola
- Department of Chemical and Biomolecular Engineering, Institute for Sustainable Energy and the Environment, Ohio University, Athens, Ohio, 45701, USA
| | - Tingyue Gu
- Department of Chemical and Biomolecular Engineering, Institute for Sustainable Energy and the Environment, Ohio University, Athens, Ohio, 45701, USA.
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Kanao T, Kunihisa T, Ohgimoto S, Ito M, Murakami C, Nakayama H, Tamura T, Kamimura K. Recombinant expression using the tetrathionate hydrolase promoter in Acidithiobacillus ferrooxidans. J Biosci Bioeng 2023; 135:176-181. [PMID: 36635106 DOI: 10.1016/j.jbiosc.2022.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 01/12/2023]
Abstract
In the iron- and sulfur-oxidizing acidophilic chemolithoautotrophic bacterium, Acidithiobacillus ferrooxidans, tetrathionate hydrolase gene (Af-tth) is highly expressed during tetrathionate growth. The expression levels of Af-tth were specifically determined by quantitative reverse transcription-polymerase chain reaction and the expression ratios of S0/Fe2+ and S4O62-/Fe2+ were found to be 68 ± 21 and 181 ± 5, respectively. The transcriptional start site was identified by primer extension. Promoter regions of Af-tth were cloned into the expression shuttle vector pMPJC and GFP gene was under the direction of the regions. Green fluorescence was observed by UV irradiation in recombinant A. ferrooxidans harboring the plasmid colonies grown on tetrathionate. Furthermore, His-tagged Af-Tth was synthesized in the recombinant cells grown on tetrathionate. Recombinant, His-tagged Af-Tth in an active form, was rapidly purified through metal-affinity column chromatography, although recombinant Af-Tth was synthesized in the inclusion bodies of Escherichia coli and acid-refolding treatment was necessary to recover the activity. The specific activity of purified Af-Tth from recombinant A. ferrooxidans (2.2 ± 0.37 U mg-1) was similar to that of acid-refolded Af-Tth from recombinant E. coli (2.5 ± 0.18 U mg-1). This method can be applied not only to heterologous expression but also to homologous expression of target genes for modification or specific mutation in A. ferrooxidans cells.
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Affiliation(s)
- Tadayoshi Kanao
- Department of Biofunctional Chemistry, Division of Agricultural and Life Science, Graduate School of Environmental and Life Science, Okayama University, 3-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan.
| | - Tomoki Kunihisa
- Department of Biofunctional Chemistry, Division of Agricultural and Life Science, Graduate School of Environmental and Life Science, Okayama University, 3-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Shuji Ohgimoto
- Department of Biofunctional Chemistry, Division of Agricultural and Life Science, Graduate School of Environmental and Life Science, Okayama University, 3-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Megumi Ito
- Department of Biofunctional Chemistry, Division of Agricultural and Life Science, Graduate School of Environmental and Life Science, Okayama University, 3-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Chisa Murakami
- Department of Biofunctional Chemistry, Division of Agricultural and Life Science, Graduate School of Environmental and Life Science, Okayama University, 3-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Hisayuki Nakayama
- Department of Biofunctional Chemistry, Division of Agricultural and Life Science, Graduate School of Environmental and Life Science, Okayama University, 3-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Takashi Tamura
- Department of Biofunctional Chemistry, Division of Agricultural and Life Science, Graduate School of Environmental and Life Science, Okayama University, 3-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Kazuo Kamimura
- Department of Biofunctional Chemistry, Division of Agricultural and Life Science, Graduate School of Environmental and Life Science, Okayama University, 3-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
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17
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Chen G, Shi H, Ding H, Zhang X, Gu T, Zhu M, Tan W. Multi-scale analysis of nickel ion tolerance mechanism for thermophilic Sulfobacillus thermosulfidooxidans in bioleaching. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130245. [PMID: 36332278 DOI: 10.1016/j.jhazmat.2022.130245] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/11/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Bioleaching is intensively investigated for recovering valuable metals such as Li, Co, Ni and Cu. Nickel ion stress threatens the health of microorganisms when Ni2+ starts to accumulate in the leachate during the bioleaching of materials that are rich in Ni, such as spent lithium-ion batteries. The possible mechanisms underlying the response of S. thermosulfidooxidans to nickel ion stress were analyzed using a multi-scale approach. Under the condition of nickel ion stress, high concentrations of nickel ions were immobilized by extracellular polymeric substances, while concentrations of nickel ions inside the cells remained low. The intracellular adenosine triphosphate (ATP) concentration and H+-ATPase activity increased to maintain normal cell growth and metabolic activities. Scavenging abilities of S. thermosulfidooxidans for hydrogen peroxide and superoxide anion were enhanced to reduce oxidative damage induced by nickel ion stress. There were 734 differentially expressed genes identified by RNA-seq under nickel ion stress. Most of them were involved in oxidative phosphorylation, glutathione metabolism and genetic information processing, responsible for intracellular energy utilization, intracellular antioxidant capacity and DNA damage repair, respectively. The results of this study are of major significance for in-depth understanding of the mechanisms of acidophilic microorganisms' resistance to metal ions.
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Affiliation(s)
- Guanglin Chen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Hongjie Shi
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Huili Ding
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xu Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Tingyue Gu
- Department of Chemical and Biomolecular Engineering, Institute for Sustainable Energy and the Environment, Ohio University, Athens, OH, United States
| | - Minglong Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Wensong Tan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
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18
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Nguyen PM, Do PT, Pham YB, Doan TO, Nguyen XC, Lee WK, Nguyen DD, Vadiveloo A, Um MJ, Ngo HH. Roles, mechanism of action, and potential applications of sulfur-oxidizing bacteria for environmental bioremediation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 852:158203. [PMID: 36044953 DOI: 10.1016/j.scitotenv.2022.158203] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 06/15/2023]
Abstract
Sulfur (S) is a crucial component in the environment and living organisms. This work is the first attempt to provide an overview and critical discussion on the roles, mechanisms, and environmental applications of sulfur-oxidizing bacteria (SOB). The findings reveal that key enzymes of SOB embarked on oxidation of sulfide, sulfite, thiosulfate, and elemental S. Conversion of reduced S compounds was oxidatively catalyzed by various enzymes (e.g. sulfide: quinone oxidoreductase, flavocytochrome c-sulfide dehydrogenase, dissimilatory sulfite reductase, heterodisulfide reductase-like proteins). Environmental applications of SOB discussed include detoxifying hydrogen sulfide, soil bioremediation, and wastewater treatment. SOB producing S0 engaged in biological S soil amendments (e.g. saline-alkali soil remediation, the oxidation of sulfide-bearing minerals). Biotreatment of H2S using SOB occurred under both aerobic and anaerobic conditions. Sulfide, nitrate, and sulfamethoxazole were removed through SOB suspension cultures and S0-based carriers. Finally, this work presented future perspectives on SOB development, including S0 recovery, SOB enrichment, field measurement and identification of sulfur compounds, and the development of mathematical simulation.
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Affiliation(s)
- Phuong Minh Nguyen
- Faculty of Environmental Sciences, University of Science, Vietnam National University, Hanoi, 334 Nguyen Trai, Thanh Xuan, Hanoi, Vietnam
| | - Phuc Thi Do
- Faculty of Biology, University of Science, Vietnam National University, Hanoi, 334 Nguyen Trai, Thanh Xuan, Hanoi, Vietnam; Key Laboratory of Enzyme and Protein Technology (KLEPT), University of Science, Vietnam National University, Hanoi, 334 Nguyen Trai, Thanh Xuan, Hanoi, Vietnam
| | - Yen Bao Pham
- Key Laboratory of Enzyme and Protein Technology (KLEPT), University of Science, Vietnam National University, Hanoi, 334 Nguyen Trai, Thanh Xuan, Hanoi, Vietnam
| | - Thi Oanh Doan
- Faculty of Environment, Ha Noi University of Natural Resources and Environment, No 41A, Phu Dien Street, Bac Tu Liem, Ha Noi, Vietnam
| | - Xuan Cuong Nguyen
- Center for Advanced Chemistry, Institute of Research and Development, Duy Tan University, Da Nang 550000, Vietnam; Faculty of Environmental Chemical Engineering, Duy Tan University, Da Nang 550000, Vietnam.
| | - Woo Kul Lee
- Department of Chemical Engineering, Dankook University, 152 Jukjeonro, Yongin 16890, South Korea
| | - D Duc Nguyen
- Faculty of Environmental and Food Engineering, Nguyen Tat Thanh University, 300A Nguyen Tat Thanh, District 4, HCM City, 755414, Vietnam; Department of Environmental Energy Engineering, Kyonggi University, Suwon 16227, South Korea
| | - Ashiwin Vadiveloo
- Algae R & D Centre, Environmental and Conservation Sciences, College of Science, Health, Engineering and Education, 90 South Street, Murdoch, WA 6150, Australia
| | - Myoung-Jin Um
- Department of Civil Engineering, Kyonggi University, Suwon 16227, South Korea
| | - Huu Hao Ngo
- School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NWS 2007, Australia.
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Sand W, Schippers A, Hedrich S, Vera M. Progress in bioleaching: fundamentals and mechanisms of microbial metal sulfide oxidation - part A. Appl Microbiol Biotechnol 2022; 106:6933-6952. [PMID: 36194263 PMCID: PMC9592645 DOI: 10.1007/s00253-022-12168-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 11/30/2022]
Abstract
Abstract Bioleaching of metal sulfides is performed by diverse microorganisms. The dissolution of metal sulfides occurs via two chemical pathways, either the thiosulfate or the polysulfide pathway. These are determined by the metal sulfides’ mineralogy and their acid solubility. The microbial cell enables metal sulfide dissolution via oxidation of iron(II) ions and inorganic sulfur compounds. Thereby, the metal sulfide attacking agents iron(III) ions and protons are generated. Cells are active either in a planktonic state or attached to the mineral surface, forming biofilms. This review, as an update of the previous one (Vera et al., 2013a), summarizes some recent discoveries relevant to bioleaching microorganisms, contributing to a better understanding of their lifestyle. These comprise phylogeny, chemical pathways, surface science, biochemistry of iron and sulfur metabolism, anaerobic metabolism, cell–cell communication, molecular biology, and biofilm lifestyle. Recent advances from genetic engineering applied to bioleaching microorganisms will allow in the future to better understand important aspects of their physiology, as well as to open new possibilities for synthetic biology applications of leaching microbial consortia. Key points • Leaching of metal sulfides is strongly enhanced by microorganisms • Biofilm formation and extracellular polymer production influences bioleaching • Cell interactions in mixed bioleaching cultures are key for process optimization
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Affiliation(s)
- Wolfgang Sand
- Institute of Biosciences, TU Bergakademie Freiberg, Freiberg, Germany. .,Faculty of Chemistry, University Duisburg-Essen, Essen, Germany.
| | - Axel Schippers
- Bundesanstalt für Geowissenschaften und Rohstoffe (BGR), Hannover, Germany
| | - Sabrina Hedrich
- Institute of Biosciences, TU Bergakademie Freiberg, Freiberg, Germany
| | - Mario Vera
- Instituto de Ingeniería Biológica y Médica, Escuelas de Ingeniería, Medicina y Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile. .,Departamento de Ingeniería Hidráulica y Ambiental, Escuela de Ingeniería, Pontificia Universidad Católica de Chile, Santiago, Chile.
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20
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Liu D, Shi H, Chen G, Zhang X, Gu T, Zhu M, Tan W. Strategies for anti-oxidative stress and anti-acid stress in bioleaching of LiCoO 2 using an acidophilic microbial consortium. Extremophiles 2022; 26:22. [PMID: 35767155 DOI: 10.1007/s00792-022-01270-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 05/17/2022] [Indexed: 11/04/2022]
Abstract
High metal ion concentrations and low pH cause severely inhibit the activity of an acidophilic microbial consortium (AMC) in bioleaching. This work investigated the effects of exogenous spermine on biofilm formation and the bioleaching efficiency of LiCoO2 by AMC in 9K medium. After the addition of 1 mM spermine, the activities of glutathione peroxidase and catalase increased, while the amount of H2O2, intracellular reactive oxygen species (ROS) and malondialdehyde in AMC decreased. These results indicated that the ability of AMC biofilm to resist oxidative stress introduced by 3.5 g/L Li+ and 30.1 g/L Co2+ was improved by spermine. The activity of glutamate decarboxylase was promoted to restore the intracellular pH buffering ability of AMC. Electrochemical measurements showed that the oxidation rate of pyrite was increased by exogenous spermine. As a result, high bioleaching efficiencies of 97.1% for Li+ and 96.1% for Co2+ from a 5.0% (w v-1) lithium cobalt oxide powder slurry were achieved. This work demonstrated that Tafel polarization can be used to monitor the AMC biofilm's ability of uptaking electrons from pyrite during bioleaching. The corrosion current density increased with 1 mM spermine, indicating enhanced electron uptake by the biofilm from pyrite.
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Affiliation(s)
- Dehong Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Hongjie Shi
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Guanglin Chen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Xu Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Tingyue Gu
- Department of Chemical and Biomolecular Engineering, Ohio University, Athens, OH, USA.
| | - Minglong Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Wensong Tan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
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21
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Morphology, Phase and Chemical Analysis of Leachate after Bioleaching Metals from Printed Circuit Boards. MATERIALS 2022; 15:ma15134373. [PMID: 35806498 PMCID: PMC9267160 DOI: 10.3390/ma15134373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 11/17/2022]
Abstract
The article presents the assessment of solutions and dried residues precipitated from solutions after the bioleaching process of Printed Circuit Boards (PCB) utilizing the Acidithiobacillus ferrooxidans. The obtained dried residues precipitated from bioleaching solution (leachate) and control solution were tested using morphology, phase, and chemical composition analysis, with particular emphasis on the assessment of crystalline and amorphous components. The analysis of the dried residues from leachate after bioleaching as well as those from the sterile control solution demonstrated a difference in the component oxidation—the leachate consisted of mainly amorphous spherical particles in diameter up to 200 nm, forming lacy aggregates. In the specimenform control solution larger particles (up to 500 nm) were observed with a hollow in the middle and crystalline outer part (probably Fe2O3, CuFeS2, and Cu2O). The X-ray diffraction phase analysis revealed that specimen obtained from leachate after bioleaching consisted mainly of an amorphous component and some content of Fe2O3 crystalline phase, while the dried residue from control solution showed more crystalline components. The share of the crystalline and amorphous components can be related to efficiency in dissolving metals during bioleaching. Obtained results of the investigation confirm the activity and participation of the A. ferrooxidans bacteria in the solubilization process of electro-waste components, with their visible degradation–acceleration of the reaction owing to a continuous regeneration of the leaching medium. The performed investigations allowed to characterize the specimen from leachate and showed that the application of complementary cross-check of the micro (SEM and S/TEM) and macro (ICP-OES and XRD) methods are of immense use for complete guidance assessment and obtained valuable data for the next stages of PCBs recycling.
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22
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Zhou H, Zhao D, Zhang S, Xue Q, Zhang M, Yu H, Zhou J, Li M, Kumar S, Xiang H. Metagenomic insights into the environmental adaptation and metabolism of Candidatus Haloplasmatales, one archaeal order thriving in saline lakes. Environ Microbiol 2022; 24:2239-2258. [PMID: 35048500 DOI: 10.1111/1462-2920.15899] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/06/2021] [Indexed: 02/01/2023]
Abstract
The KTK 4A-related Thermoplasmata thrives in the sediment of saline lakes; however, systematic research on its taxonomy, environmental adaptation and metabolism is lacking. Here, we detected this abundant lineage in the sediment of five artificially separated ponds (salinity 7.0%-33.0%) within a Chinese soda-saline lake using culture-independent metagenomics and archaeal 16S rRNA gene amplicons. The phylogenies based on the 16S rRNA gene, and 122 archaeal ubiquitous single-copy proteins and genome-level identity analyses among the metagenome-assembled genomes demonstrate this lineage forming a novel order, Candidatus Haloplasmatales, comprising four genera affiliated with the identical family. Isoelectric point profiles of predicted proteomes suggest that most members adopt the energetically favourable 'salt-in' strategy. Functional prediction indicates the lithoheterotrophic nature with the versatile metabolic potentials for carbohydrate and organic acids as well as carbon monoxide and hydrogen utilization. Additionally, hydrogenase genes hdrABC-mvhADG are linked with incomplete reductive citrate cycle genes in the genomes, suggesting their functional connection. Comparison with the coupling of HdrABC-MvhADG and methanogenesis pathway provides new insights into the compatibility of laterally acquired methanogenesis with energy metabolism in the related order Methanomassiliicoccales. Globally, our research sheds light on the taxonomy, environmental adaptative mechanisms, metabolic potentials and evolutional significance of Ca. Haloplasmatales.
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Affiliation(s)
- Heng Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Dahe Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shengjie Zhang
- 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
| | - Qiong Xue
- 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
| | - Manqi Zhang
- 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
| | - Haiying Yu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jian Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ming Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Sumit Kumar
- Enzyme and Microbial Biochemistry Lab, Department of Chemistry, Indian Institute of Technology, Delhi, India
| | - Hua Xiang
- 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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23
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Expression, purification, characterization and direct electrochemistry of two HiPIPs from Acidithiobacillus caldus SM-1. Anal Biochem 2022; 650:114724. [DOI: 10.1016/j.ab.2022.114724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 04/15/2022] [Accepted: 05/05/2022] [Indexed: 11/18/2022]
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24
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Cortez D, Neira G, González C, Vergara E, Holmes DS. A Large-Scale Genome-Based Survey of Acidophilic Bacteria Suggests That Genome Streamlining Is an Adaption for Life at Low pH. Front Microbiol 2022; 13:803241. [PMID: 35387071 PMCID: PMC8978632 DOI: 10.3389/fmicb.2022.803241] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/07/2022] [Indexed: 01/04/2023] Open
Abstract
The genome streamlining theory suggests that reduction of microbial genome size optimizes energy utilization in stressful environments. Although this hypothesis has been explored in several cases of low-nutrient (oligotrophic) and high-temperature environments, little work has been carried out on microorganisms from low-pH environments, and what has been reported is inconclusive. In this study, we performed a large-scale comparative genomics investigation of more than 260 bacterial high-quality genome sequences of acidophiles, together with genomes of their closest phylogenetic relatives that live at circum-neutral pH. A statistically supported correlation is reported between reduction of genome size and decreasing pH that we demonstrate is due to gene loss and reduced gene sizes. This trend is independent from other genome size constraints such as temperature and G + C content. Genome streamlining in the evolution of acidophilic bacteria is thus supported by our results. The analyses of predicted Clusters of Orthologous Genes (COG) categories and subcellular location predictions indicate that acidophiles have a lower representation of genes encoding extracellular proteins, signal transduction mechanisms, and proteins with unknown function but are enriched in inner membrane proteins, chaperones, basic metabolism, and core cellular functions. Contrary to other reports for genome streamlining, there was no significant change in paralog frequencies across pH. However, a detailed analysis of COG categories revealed a higher proportion of genes in acidophiles in the following categories: "replication and repair," "amino acid transport," and "intracellular trafficking". This study brings increasing clarity regarding the genomic adaptations of acidophiles to life at low pH while putting elements, such as the reduction of average gene size, under the spotlight of streamlining theory.
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Affiliation(s)
- Diego Cortez
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - Gonzalo Neira
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - Carolina González
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - Eva Vergara
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastian, Santiago, Chile
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25
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Jung H, Inaba Y, Jiang V, West AC, Banta S. Engineering Polyhistidine Tags on Surface Proteins of Acidithiobacillus ferrooxidans: Impact of Localization on the Binding and Recovery of Divalent Metal Cations. ACS APPLIED MATERIALS & INTERFACES 2022; 14:10125-10133. [PMID: 35170950 DOI: 10.1021/acsami.1c23682] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Metal processing using microorganisms has many advantages including the potential for reduced environmental impacts as compared to conventional technologies.Acidithiobacillus ferrooxidansis an iron- and sulfur-oxidizing chemolithoautotroph that is known to participate in metal bioleaching, and its metabolic capabilities have been exploited for industrial-scale copper and gold biomining. In addition to bioleaching, microorganisms could also be engineered for selective metal binding, enabling new opportunities for metal bioseparation and recovery. Here, we explored the ability of polyhistidine (polyHis) tags appended to two recombinantly expressed endogenous proteins to enhance the metal binding capacity of A. ferrooxidans. The genetically engineered cells achieved enhanced cobalt and copper binding capacities, and the Langmuir isotherm captures their interaction behavior with these divalent metals. Additionally, the cellular localization of the recombinant proteins correlated with kinetic modeling of the binding interactions, where the outer membrane-associated polyHis-tagged licanantase peptide bound the metals faster than the periplasmically expressed polyHis-tagged rusticyanin protein. The selectivity of the polyHis sequences for cobalt over copper from mixed metal solutions suggests potential utility in practical applications, and further engineering could be used to create metal-selective bioleaching microorganisms.
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Affiliation(s)
- Heejung Jung
- Department of Chemical Engineering, Columbia University, 500 West 120th Street, New York, New York 10027, United States
| | - Yuta Inaba
- Department of Chemical Engineering, Columbia University, 500 West 120th Street, New York, New York 10027, United States
| | - Virginia Jiang
- Department of Chemical Engineering, Columbia University, 500 West 120th Street, New York, New York 10027, United States
| | - Alan C West
- Department of Chemical Engineering, Columbia University, 500 West 120th Street, New York, New York 10027, United States
| | - Scott Banta
- Department of Chemical Engineering, Columbia University, 500 West 120th Street, New York, New York 10027, United States
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26
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Lovley DR. Electrotrophy: Other microbial species, iron, and electrodes as electron donors for microbial respirations. BIORESOURCE TECHNOLOGY 2022; 345:126553. [PMID: 34906705 DOI: 10.1016/j.biortech.2021.126553] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/06/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
Electrotrophy, the growth of microbes on extracellular electron donors, drives important biogeochemical cycles and has practical applications. Studies of Fe(II)-based electrotrophy have provided foundational cytochrome-based mechanistic models for electron transport into cells. Direct electron uptake from other microbial species, Fe(0), or cathodes is of intense interest due to its potential roles in the production and anaerobic oxidation of methane, corrosion, and bioelectrochemical technologies. Other cells or Fe(0) can serve as the sole electron donor supporting the growth of several Geobacter and methanogen strains that are unable to use H2 as an electron donor, providing strong evidence for electrotrophy. Additional evidence for electrotrophy in Geobacter strains and Methanosarcina acetivorans is a requirement for outer-surface c-type cytochromes. However, in most instances claims for electrotrophy in anaerobes are based on indirect inference and the possibility that H2 is actually the electron donor supporting growth has not been rigorously excluded.
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Affiliation(s)
- Derek R Lovley
- Electrobiomaterials Institute, Key Laboratory for Anisotropy and Texture of Materials (Ministry of Education), Northeastern University, Shenyang 110819, China; Department of Microbiology and Institute for Applied Life Sciences (IALS), University of Massachusetts, Amherst, MA, USA.
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27
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Harnessing electrical-to-biochemical conversion for microbial synthesis. Curr Opin Biotechnol 2022; 75:102687. [PMID: 35104718 DOI: 10.1016/j.copbio.2022.102687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/18/2021] [Accepted: 01/10/2022] [Indexed: 11/23/2022]
Abstract
Electrical-to-biochemical conversion (E2BC) drives cell metabolism for biosynthesis and has become a promising way to realize green biomanufacturing. This review discusses the following aspects: 1. the natural E2BC processes and their underlying E2BC mechanism; 2. development of artificial E2BC for tunable microbial electrosynthesis; 3. design of electrobiochemical systems using self-powered, light-assisted, and nano-biohybrid approaches; 4. synthetic biology methods for efficient microbial electrosynthesis. This review also compares E2BC with electrocatalysis-biochemical conversion (EC2BC), as both strategies may lead to future carbon negative green biomanufacturing.
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28
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Lin L, Tsou CH, Dou B, Yan S, Zeng Y, Gong M. Electrochemical corrosion behavior and mechanism of iron-oxidizing bacteria Thiobacillus ferrooxidans from acid mine drainage on Q235 carbon steel. NEW J CHEM 2022. [DOI: 10.1039/d2nj04013a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Bread or steel! Is it true that some microbes can eat steel as bread? Dear friends, come and have a look!
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Affiliation(s)
- Li Lin
- College of Materials and Chemistry and Chemical Engineering, Chengdu University of Technology, Chengdu, 610059, China
- Sichuan Provincial Key Lab of Process Equipment and Control, Zigong, 643000, China
- Vanadium and Titanium Resource Comprehensive Utilization Key Laboratory of Sichuan Province, China
| | - Chi-Hui Tsou
- School of Materials Science and Engineering, Sichuan University of Science & Engineering, Zigong, 643000, China
| | - Baojie Dou
- School of Materials Science and Engineering, Sichuan University of Science & Engineering, Zigong, 643000, China
| | - Shisen Yan
- Sichuan Provincial Key Lab of Process Equipment and Control, Zigong, 643000, China
| | - Ying Zeng
- College of Materials and Chemistry and Chemical Engineering, Chengdu University of Technology, Chengdu, 610059, China
- Vanadium and Titanium Resource Comprehensive Utilization Key Laboratory of Sichuan Province, China
| | - Min Gong
- School of Materials Science and Engineering, Sichuan University of Science & Engineering, Zigong, 643000, China
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29
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Narayanan M, Natarajan D, Kandasamy S, Chinnathambi A, Ali Alharbi S, Karuppusamy I, Kathirvel B. Pyrite biomining proficiency of sulfur dioxygenase (SDO) enzyme extracted from Acidithiobacillus thiooxidans. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.09.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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30
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Jung H, Inaba Y, Banta S. Genetic engineering of the acidophilic chemolithoautotroph Acidithiobacillus ferrooxidans. Trends Biotechnol 2021; 40:677-692. [PMID: 34794837 DOI: 10.1016/j.tibtech.2021.10.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 12/21/2022]
Abstract
There are several natural and anthropomorphic environments where iron- and/or sulfur-oxidizing bacteria thrive in extremely acidic conditions. These acidophilic chemolithautotrophs play important roles in biogeochemical iron and sulfur cycles, are critical catalysts for industrial metal bioleaching operations, and have underexplored potential in future biotechnological applications. However, their unique growth conditions complicate the development of genetic techniques. Over the past few decades genetic tools have been successfully developed for Acidithiobacillus ferrooxidans, which serves as a model organism that exhibits both iron- and sulfur-oxidizing capabilities. Conjugal transfer of plasmids has enabled gene overexpression, gene knockouts, and some preliminary metabolic engineering. We highlight the development of genetic systems and recent genetic engineering of A. ferrooxidans, and discuss future perspectives.
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Affiliation(s)
- Heejung Jung
- Department of Chemical Engineering, Columbia University, 500 West 120th Street, New York, NY 10027, USA
| | - Yuta Inaba
- Department of Chemical Engineering, Columbia University, 500 West 120th Street, New York, NY 10027, USA
| | - Scott Banta
- Department of Chemical Engineering, Columbia University, 500 West 120th Street, New York, NY 10027, USA.
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31
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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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32
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Mo S, Li J, Li B, Kashif M, Nie S, Liao J, Su G, Jiang Q, Yan B, Jiang C. L-Cysteine Synthase Enhanced Sulfide Biotransformation in Subtropical Marine Mangrove Sediments as Revealed by Metagenomics Analysis. WATER 2021; 13:3053. [DOI: 10.3390/w13213053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/24/2023]
Abstract
High sulfides concentrations can be poisonous to environment because of anthropogenic waste production or natural occurrences. How to elucidate the biological transformation mechanisms of sulfide pollutants in the subtropical marine mangrove ecosystem has gained increased interest. Thus, in the present study, the sulfide biotransformation in subtropical mangroves ecosystem was accurately evaluated using metagenomic sequencing and quantitative polymerase chain reaction analysis. Most abundant genes were related to the organic sulfur transformation. Furthermore, an ecological model of sulfide conversion was constructed. Total phosphorus was the dominant environmental factor that drove the sulfur cycle and microbial communities. We compared mangrove and non-mangrove soils and found that the former enhanced metabolism that was related to sulfate reduction when compared to the latter. Total organic carbon, total organic nitrogen, iron, and available sulfur were the key environmental factors that effectively influenced the dissimilatory sulfate reduction. The taxonomic assignment of dissimilatory sulfate-reducing genes revealed that Desulfobacterales and Chromatiales were mainly responsible for sulfate reduction. Chromatiales were most sensitive to environmental factors. The high abundance of cysE and cysK could contribute to the coping of the microbial community with the toxic sulfide produced by Desulfobacterales. Collectively, these findings provided a theoretical basis for the mechanism of the sulfur cycle in subtropical mangrove ecosystems.
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33
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Mo S, Li J, Li B, Kashif M, Nie S, Liao J, Su G, Jiang Q, Yan B, Jiang C. L-Cysteine Synthase Enhanced Sulfide Biotransformation in Subtropical Marine Mangrove Sediments as Revealed by Metagenomics Analysis. WATER 2021; 13:3053. [DOI: https:/doi.org/10.3390/w13213053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/24/2023]
Abstract
High sulfides concentrations can be poisonous to environment because of anthropogenic waste production or natural occurrences. How to elucidate the biological transformation mechanisms of sulfide pollutants in the subtropical marine mangrove ecosystem has gained increased interest. Thus, in the present study, the sulfide biotransformation in subtropical mangroves ecosystem was accurately evaluated using metagenomic sequencing and quantitative polymerase chain reaction analysis. Most abundant genes were related to the organic sulfur transformation. Furthermore, an ecological model of sulfide conversion was constructed. Total phosphorus was the dominant environmental factor that drove the sulfur cycle and microbial communities. We compared mangrove and non-mangrove soils and found that the former enhanced metabolism that was related to sulfate reduction when compared to the latter. Total organic carbon, total organic nitrogen, iron, and available sulfur were the key environmental factors that effectively influenced the dissimilatory sulfate reduction. The taxonomic assignment of dissimilatory sulfate-reducing genes revealed that Desulfobacterales and Chromatiales were mainly responsible for sulfate reduction. Chromatiales were most sensitive to environmental factors. The high abundance of cysE and cysK could contribute to the coping of the microbial community with the toxic sulfide produced by Desulfobacterales. Collectively, these findings provided a theoretical basis for the mechanism of the sulfur cycle in subtropical mangrove ecosystems.
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34
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Beaver RC, Engel K, Binns WJ, Neufeld JD. Microbiology of barrier component analogues of a deep geological repository. Can J Microbiol 2021; 68:73-90. [PMID: 34648720 DOI: 10.1139/cjm-2021-0225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Canada is currently implementing a site selection process to identify a location for a deep geological repository (DGR) for the long-term storage of Canada's used nuclear fuel, wherein used nuclear fuel bundles will be sealed inside copper-coated carbon steel containers, encased in highly compacted bentonite clay buffer boxes, and sealed deep underground in a stable geosphere. Because a DGR must remain functional for a million years, it is important to examine ancient natural systems that serve as analogues for planned DGR components. Specifically, studying the microbiology of natural analogue components of a DGR is important for developing an understanding of the types of microorganisms that may be able to grow and influence the long-term stability of a DGR. This study explored the abundance, viability, and composition of microorganisms in several ancient natural analogues using a combination of cultivation and cultivation-independent approaches. Samples were obtained from the Tsukinuno bentonite deposit (Japan) that formed ∼10 mya, the Opalinus Clay formation (Switzerland) that formed ∼174 mya, and Canadian shield crystalline rock from Northern Ontario that formed ∼2.7 bya. Analysis of 16S rRNA gene amplicons revealed that three of the ten Tsukinuno bentonite samples analyzed were dominated by putative aerobic heterotrophs and fermenting bacteria from the phylum Actinobacteria, whereas five of the Tsukinuno bentonite samples were dominated by sequences associated with putative acidophilic chemolithoautotrophs capable of sulfur reduction. The remaining Tsukinuno bentonite samples, the Northern Ontario rock samples, and the Opalinus Clay samples generated inconsistent replicate 16S rRNA gene profiles and were associated primarily with contaminant sequences, suggesting that the microbial profiles detected were not sample-specific but spurious. Culturable aerobic heterotroph abundances were relatively low for all Tsukinuno bentonite samples, culturable anaerobic heterotrophs were only detected in half of the Tsukinuno samples, and sulfate-reducing bacteria (SRB) were only detected in one Tsukinuno sample by cultivation. Culture-specific 16S rRNA gene profiles from Tsukinuno clay samples demonstrated the presence of phyla Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes among aerobic heterotroph cultures and additional bacteria from the phyla Actinobacteria and Firmicutes from anaerobic heterotroph plate incubations. Only one nucleic acid sequence detected from a culture was also associated with its corresponding clay sample profile, suggesting that nucleic acids from culturable bacteria were relatively rare within the clay samples. Sequencing of DNA extracted from the SRB culture revealed that the taxon present in the culture was affiliated with the genus Desulfosporosinus, which has been found in related bentonite clay analyses. Although the crystalline rock and Opalinus Clay samples were associated with inconsistent, likely spurious 16S rRNA gene profiles, we show evidence for viable and detectable microorganisms within several Tsukinuno natural analogue bentonite samples.
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Affiliation(s)
- Rachel C Beaver
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
| | - Katja Engel
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
| | - W Jeffrey Binns
- Nuclear Waste Management Organization, Toronto, Ontario, Canada
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
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35
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Wu B, Liu F, Fang W, Yang T, Chen GH, He Z, Wang S. Microbial sulfur metabolism and environmental implications. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 778:146085. [PMID: 33714092 DOI: 10.1016/j.scitotenv.2021.146085] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/19/2021] [Accepted: 02/20/2021] [Indexed: 06/12/2023]
Abstract
Sulfur as a macroelement plays an important role in biochemistry in both natural environments and engineering biosystems, which can be further linked to other important element cycles, e.g. carbon, nitrogen and iron. Consequently, the sulfur cycling primarily mediated by sulfur compounds oxidizing microorganisms and sulfur compounds reducing microorganisms has enormous environmental implications, particularly in wastewater treatment and pollution bioremediation. In this review, to connect the knowledge in microbial sulfur metabolism to environmental applications, we first comprehensively review recent advances in understanding microbial sulfur metabolisms at molecular-, cellular- and ecosystem-levels, together with their energetics. We then discuss the environmental implications to fight against soil and water pollution, with four foci: (1) acid mine drainage, (2) water blackening and odorization in urban rivers, (3) SANI® and DS-EBPR processes for sewage treatment, and (4) bioremediation of persistent organic pollutants. In addition, major challenges and further developments toward elucidation of microbial sulfur metabolisms and their environmental applications are identified and discussed.
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Affiliation(s)
- Bo Wu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China
| | - Feifei Liu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, China
| | - Wenwen Fang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China
| | - Tony Yang
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK S9H 3X2, Canada
| | - Guang-Hao Chen
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China
| | - Shanquan Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China.
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36
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Potential application of a knowledgebase of iron metabolism of Acidithiobacillus ferrooxidans as an alternative platform. ELECTRON J BIOTECHN 2021. [DOI: 10.1016/j.ejbt.2021.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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37
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Inaba Y, Kernan T, West AC, Banta S. Dispersion of sulfur creates a valuable new growth medium formulation that enables earlier sulfur oxidation in relation to iron oxidation in Acidithiobacillus ferrooxidans cultures. Biotechnol Bioeng 2021; 118:3225-3238. [PMID: 34086346 DOI: 10.1002/bit.27847] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 01/19/2023]
Abstract
Acidithiobacillus ferrooxidans is an acidophilic chemolithoautotroph that is commonly reported to exhibit diauxic population growth behavior where ferrous iron is oxidized before elemental sulfur when both are available, despite the higher energy content of sulfur. We have discovered sulfur dispersion formulations that enables sulfur oxidation before ferrous iron oxidation. The oxidation of dispersed sulfur can lower the culture pH within days below the range where aerobic ferrous iron oxidation can occur. Thus, ferric iron reduction can be observed quickly which had previously been reported over extended incubation periods with untreated sulfur. Therefore, we demonstrate that this substrate utilization pattern is strongly dependent on the cell loading in relation to sulfur concentration, sulfur surface hydrophobicity, and the pH of the culture. Our dispersed sulfur formulation, lig-sulfur, can be used to support the rapid antibiotic selection of plasmid-transformed cells, which is not possible in liquid cultures where ferrous iron is the main source of energy for these acidophiles. Furthermore, we find that media containing lig-sulfur supports higher production of green fluorescent protein compared to media containing ferrous iron. The use of dispersed sulfur is a valuable new tool for the development of engineered A. ferrooxidans strains and it provides a new method to control iron and sulfur oxidation behaviors.
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Affiliation(s)
- Yuta Inaba
- Department of Chemical Engineering, Columbia University, New York, USA
| | - Timothy Kernan
- Department of Chemical Engineering, Columbia University, New York, USA
| | - Alan C West
- Department of Chemical Engineering, Columbia University, New York, USA
| | - Scott Banta
- Department of Chemical Engineering, Columbia University, New York, USA
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38
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Degli Esposti M, Moya-Beltrán A, Quatrini R, Hederstedt L. Respiratory Heme A-Containing Oxidases Originated in the Ancestors of Iron-Oxidizing Bacteria. Front Microbiol 2021; 12:664216. [PMID: 34211444 PMCID: PMC8239418 DOI: 10.3389/fmicb.2021.664216] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/12/2021] [Indexed: 11/13/2022] Open
Abstract
Respiration is a major trait shaping the biology of many environments. Cytochrome oxidase containing heme A (COX) is a common terminal oxidase in aerobic bacteria and is the only one in mammalian mitochondria. The synthesis of heme A is catalyzed by heme A synthase (CtaA/Cox15), an enzyme that most likely coevolved with COX. The evolutionary origin of COX in bacteria has remained unknown. Using extensive sequence and phylogenetic analysis, we show that the ancestral type of heme A synthases is present in iron-oxidizing Proteobacteria such as Acidithiobacillus spp. These bacteria also contain a deep branching form of the major COX subunit (COX1) and an ancestral variant of CtaG, a protein that is specifically required for COX biogenesis. Our work thus suggests that the ancestors of extant iron-oxidizers were the first to evolve COX. Consistent with this conclusion, acidophilic iron-oxidizing prokaryotes lived on emerged land around the time for which there is the earliest geochemical evidence of aerobic respiration on earth. Hence, ecological niches of iron oxidation have apparently promoted the evolution of aerobic respiration.
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Affiliation(s)
- Mauro Degli Esposti
- Center for Genomic Sciences, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Mexico
| | - Ana Moya-Beltrán
- Fundación Ciencia & Vida, Santiago, Chile
- ANID–Millennium Science Initiative Program–Millennium Nucleus in the Biology of the Intestinal Microbiota, Santiago, Chile
| | - Raquel Quatrini
- Fundación Ciencia & Vida, Santiago, Chile
- ANID–Millennium Science Initiative Program–Millennium Nucleus in the Biology of the Intestinal Microbiota, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastian, Santiago, Chile
| | - Lars Hederstedt
- The Microbiology Group, Department of Biology, Lund University, Lund, Sweden
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Jiang V, Khare SD, Banta S. Computational structure prediction provides a plausible mechanism for electron transfer by the outer membrane protein Cyc2 from Acidithiobacillus ferrooxidans. Protein Sci 2021; 30:1640-1652. [PMID: 33969560 DOI: 10.1002/pro.4106] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/30/2021] [Accepted: 05/03/2021] [Indexed: 12/14/2022]
Abstract
Cyc2 is the key protein in the outer membrane of Acidithiobacillus ferrooxidans that mediates electron transfer between extracellular inorganic iron and the intracellular central metabolism. This cytochrome c is specific for iron and interacts with periplasmic proteins to complete a reversible electron transport chain. A structure of Cyc2 has not yet been characterized experimentally. Here we describe a structural model of Cyc2, and associated proteins, to highlight a plausible mechanism for the ferrous iron electron transfer chain. A comparative modeling protocol specific for trans membrane beta barrel (TMBB) proteins in acidophilic conditions (pH ~ 2) was applied to the primary sequence of Cyc2. The proposed structure has three main regimes: Extracellular loops exposed to low-pH conditions, a TMBB, and an N-terminal cytochrome-like region within the periplasmic space. The Cyc2 model was further refined by identifying likely iron and heme docking sites. This represents the first computational model of Cyc2 that accounts for the membrane microenvironment and the acidity in the extracellular matrix. This approach can be used to model other TMBBs which can be critical for chemolithotrophic microbial growth.
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Affiliation(s)
- Virginia Jiang
- Department of Chemical Engineering, Columbia University in the City of New York, New York, New York, USA
| | - Sagar D Khare
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Scott Banta
- Department of Chemical Engineering, Columbia University in the City of New York, New York, New York, USA
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40
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Barragán CE, Márquez MA, Dopson M, Montoya D. RNA transcript response by an Acidithiobacillus spp. mixed culture reveals adaptations to growth on arsenopyrite. Extremophiles 2021; 25:143-158. [PMID: 33616780 DOI: 10.1007/s00792-021-01217-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/25/2021] [Indexed: 11/26/2022]
Abstract
Biooxidation of gold-bearing refractory mineral ores such as arsenopyrite (FeAsS) in stirred tanks produces solutions containing highly toxic arsenic concentrations. In this study, ferrous iron and inorganic sulfur-oxidizing Acidithiobacillus strain IBUN Ppt12 most similar to Acidithiobacillus ferrianus and inorganic sulfur compound oxidizing Acidithiobacillus sp. IBUNS3 were grown in co-culture during biooxidation of refractory FeAsS. Total RNA was extracted and sequenced from the planktonic cells to reveal genes with different transcript counts involved in the response to FeAsS containing medium. The co-culture's response to arsenic release during biooxidation included the ars operon genes that were independently regulated according to the arsenopyrite concentration. Additionally, increased mRNA transcript counts were identified for transmembrane ion transport proteins, stress response mechanisms, accumulation of inorganic polyphosphates, urea catabolic processes, and tryptophan biosynthesis. Acidithiobacillus spp. RNA transcripts also included those encoding the Rus and PetI proteins involved in ferrous iron oxidation and gene clusters annotated as encoding inorganic sulfur compound metabolism enzymes. Finally, mRNA counts of genes related to DNA methylation, management of oxidative stress, chemotaxis, and motility during biooxidation were decreased compared to cells growing without mineral. The results provide insights into the adaptation of Acidithiobacillus spp. to growth during biooxidation of arsenic-bearing sulfides.
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Affiliation(s)
- Carlos Eduardo Barragán
- Bioprocesses and Bioprospecting Group, Biotechnology Institute (IBUN), Universidad Nacional de Colombia, Bogotá D.C., Colombia
- Applied Mineralogy and Bioprocesses Research Group, Facultad de Minas, Universidad Nacional de Colombia, Medellín, Colombia
| | - Marco Antonio Márquez
- Applied Mineralogy and Bioprocesses Research Group, Facultad de Minas, Universidad Nacional de Colombia, Medellín, Colombia
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems EEMiS, Linnaeus University, Kalmar, Sweden
| | - Dolly Montoya
- Bioprocesses and Bioprospecting Group, Biotechnology Institute (IBUN), Universidad Nacional de Colombia, Bogotá D.C., Colombia.
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41
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Kucera J, Lochman J, Bouchal P, Pakostova E, Mikulasek K, Hedrich S, Janiczek O, Mandl M, Johnson DB. A Model of Aerobic and Anaerobic Metabolism of Hydrogen in the Extremophile Acidithiobacillus ferrooxidans. Front Microbiol 2020; 11:610836. [PMID: 33329503 PMCID: PMC7735108 DOI: 10.3389/fmicb.2020.610836] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 11/04/2020] [Indexed: 12/12/2022] Open
Abstract
Hydrogen can serve as an electron donor for chemolithotrophic acidophiles, especially in the deep terrestrial subsurface and geothermal ecosystems. Nevertheless, the current knowledge of hydrogen utilization by mesophilic acidophiles is minimal. A multi-omics analysis was applied on Acidithiobacillus ferrooxidans growing on hydrogen, and a respiratory model was proposed. In the model, [NiFe] hydrogenases oxidize hydrogen to two protons and two electrons. The electrons are used to reduce membrane-soluble ubiquinone to ubiquinol. Genetically associated iron-sulfur proteins mediate electron relay from the hydrogenases to the ubiquinone pool. Under aerobic conditions, reduced ubiquinol transfers electrons to either cytochrome aa 3 oxidase via cytochrome bc 1 complex and cytochrome c 4 or the alternate directly to cytochrome bd oxidase, resulting in proton efflux and reduction of oxygen. Under anaerobic conditions, reduced ubiquinol transfers electrons to outer membrane cytochrome c (ferrireductase) via cytochrome bc 1 complex and a cascade of electron transporters (cytochrome c 4, cytochrome c 552, rusticyanin, and high potential iron-sulfur protein), resulting in proton efflux and reduction of ferric iron. The proton gradient generated by hydrogen oxidation maintains the membrane potential and allows the generation of ATP and NADH. These results further clarify the role of extremophiles in biogeochemical processes and their impact on the composition of the deep terrestrial subsurface.
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Affiliation(s)
- Jiri Kucera
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czechia
| | - Jan Lochman
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czechia
| | - Pavel Bouchal
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czechia
| | - Eva Pakostova
- School of Biological Sciences, College of Natural Sciences, Bangor University, Bangor, United Kingdom
| | - Kamil Mikulasek
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Brno, Czechia
| | - Sabrina Hedrich
- Institute of Biosciences, Technische Universität (TU) Bergakademie Freiberg, Freiberg, Germany
| | - Oldrich Janiczek
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czechia
| | - Martin Mandl
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czechia
| | - D Barrie Johnson
- School of Biological Sciences, College of Natural Sciences, Bangor University, Bangor, United Kingdom
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42
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Defosset A, Kress A, Nevers Y, Ripp R, Thompson JD, Poch O, Lecompte O. Proteome-Scale Detection of Differential Conservation Patterns at Protein and Subprotein Levels with BLUR. Genome Biol Evol 2020; 13:5991441. [PMID: 33211099 PMCID: PMC7851591 DOI: 10.1093/gbe/evaa248] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2020] [Indexed: 11/23/2022] Open
Abstract
In the multiomics era, comparative genomics studies based on gene repertoire comparison are increasingly used to investigate evolutionary histories of species, to study genotype–phenotype relations, species adaptation to various environments, or to predict gene function using phylogenetic profiling. However, comparisons of orthologs have highlighted the prevalence of sequence plasticity among species, showing the benefits of combining protein and subprotein levels of analysis to allow for a more comprehensive study of genotype/phenotype correlations. In this article, we introduce a new approach called BLUR (BLAST Unexpected Ranking), capable of detecting genotype divergence or specialization between two related clades at different levels: gain/loss of proteins but also of subprotein regions. These regions can correspond to known domains, uncharacterized regions, or even small motifs. Our method was created to allow two types of research strategies: 1) the comparison of two groups of species with no previous knowledge, with the aim of predicting phenotype differences or specializations between close species or 2) the study of specific phenotypes by comparing species that present the phenotype of interest with species that do not. We designed a website to facilitate the use of BLUR with a possibility of in-depth analysis of the results with various tools, such as functional enrichments, protein–protein interaction networks, and multiple sequence alignments. We applied our method to the study of two different biological pathways and to the comparison of several groups of close species, all with very promising results. BLUR is freely available at http://lbgi.fr/blur/.
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Affiliation(s)
- Audrey Defosset
- Complex Systems and Translational Bioinformatics, ICube UMR 7357, Université de Strasbourg, France
| | - Arnaud Kress
- Complex Systems and Translational Bioinformatics, ICube UMR 7357, Université de Strasbourg, France
| | - Yannis Nevers
- Complex Systems and Translational Bioinformatics, ICube UMR 7357, Université de Strasbourg, France.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Department of Computational Biology, University of Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, Switzerland
| | - Raymond Ripp
- Complex Systems and Translational Bioinformatics, ICube UMR 7357, Université de Strasbourg, France
| | - Julie D Thompson
- Complex Systems and Translational Bioinformatics, ICube UMR 7357, Université de Strasbourg, France
| | - Olivier Poch
- Complex Systems and Translational Bioinformatics, ICube UMR 7357, Université de Strasbourg, France
| | - Odile Lecompte
- Complex Systems and Translational Bioinformatics, ICube UMR 7357, Université de Strasbourg, France
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43
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Gupta D, Guzman MS, Bose A. Extracellular electron uptake by autotrophic microbes: physiological, ecological, and evolutionary implications. ACTA ACUST UNITED AC 2020; 47:863-876. [DOI: 10.1007/s10295-020-02309-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/07/2020] [Indexed: 02/05/2023]
Abstract
Abstract
Microbes exchange electrons with their extracellular environment via direct or indirect means. This exchange is bidirectional and supports essential microbial oxidation–reduction processes, such as respiration and photosynthesis. The microbial capacity to use electrons from insoluble electron donors, such as redox-active minerals, poised electrodes, or even other microbial cells is called extracellular electron uptake (EEU). Autotrophs with this capability can thrive in nutrient and soluble electron donor-deficient environments. As primary producers, autotrophic microbes capable of EEU greatly impact microbial ecology and play important roles in matter and energy flow in the biosphere. In this review, we discuss EEU-driven autotrophic metabolisms, their mechanism and physiology, and highlight their ecological, evolutionary, and biotechnological implications.
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Affiliation(s)
- Dinesh Gupta
- grid.4367.6 0000 0001 2355 7002 Department of Biology Washington University in St. Louis One Brookings Drive 63130 St. Louis MO USA
| | - Michael S Guzman
- grid.250008.f 0000 0001 2160 9702 Biosciences and Biotechnology Division Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory Livermore CA USA
| | - Arpita Bose
- grid.4367.6 0000 0001 2355 7002 Department of Biology Washington University in St. Louis One Brookings Drive 63130 St. Louis MO USA
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44
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Huynh D, Kaschabek SR, Schlömann M. Effect of inoculum history, growth substrates and yeast extract addition on inhibition of Sulfobacillus thermosulfidooxidans by NaCl. Res Microbiol 2020; 171:252-259. [PMID: 32916217 DOI: 10.1016/j.resmic.2020.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 08/25/2020] [Accepted: 08/28/2020] [Indexed: 10/23/2022]
Abstract
This study reports on the effect of inoculum history, growth substrates, and yeast extract on sodium chloride tolerance of Sulfobacillus thermosulfidooxidans DSM 9293T. The concentrations of NaCl for complete inhibition of Fe2+ oxidation by cells initially grown with ferrous iron sulfate, or tetrathionate, or pyrite as energy sources were 525 mM, 725 mM, and 800 mM, respectively. Noticeably, regardless of NaCl concentrations, oxygen consumption rates of S. thermosulfidooxidans with 20 mM tetrathionate were higher than with 50 mM FeSO4. NaCl concentrations of higher than 400 mM strongly inhibited the iron respiration of S. thermosulfidooxidans. In contrast, the presence of NaCl was shown to stimulate tetrathionate oxidation. This trend was especially pronounced in NaCl-adapted cells where respiration rates at 200 mM NaCl were threefold of those in the absence of NaCl. In NaCl-adapted cultures greater respiration rates for tetrathionate were observed than in non-NaCl-adapted cultures, especially at concentrations ≥ 200 mM NaCl. At concentrations of ≤ 200 mM NaCl, cell growth and iron oxidation were enhanced with the addition of increasing concentrations of yeast extract. Thus, cell numbers in cultures with 0.05% yeast extract were ∼5 times higher than without yeast extract addition. At NaCl concentration as high as 400 mM, however, iron oxidation rates improved compared to control assays without yeast extract, but there was no clear dependence on yeast extract concentrations. The initial growth of bacteria with and without yeast extract in the presence of different NaCl concentrations was shown to impact leaching of copper from chalcopyrite. Copper dissolution was enhanced in the presence of 200 mM NaCl and absence of yeast extract, while the addition of 0.02% yeast extract was shown to promote copper solubilization in the presence of 500 mM NaCl.
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Affiliation(s)
- Dieu Huynh
- Environmental Microbiology, Institute of Biosciences, Technische Universität Bergakademie Freiberg, 09599 Freiberg, Germany.
| | - Stefan R Kaschabek
- Environmental Microbiology, Institute of Biosciences, Technische Universität Bergakademie Freiberg, 09599 Freiberg, Germany.
| | - Michael Schlömann
- Environmental Microbiology, Institute of Biosciences, Technische Universität Bergakademie Freiberg, 09599 Freiberg, Germany.
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45
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Ernst C, Kayastha K, Koch T, Venceslau SS, Pereira IAC, Demmer U, Ermler U, Dahl C. Structural and spectroscopic characterization of a HdrA-like subunit from Hyphomicrobium denitrificans. FEBS J 2020; 288:1664-1678. [PMID: 32750208 DOI: 10.1111/febs.15505] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 07/03/2020] [Accepted: 07/31/2020] [Indexed: 02/01/2023]
Abstract
Many bacteria and archaea employ a novel pathway of sulfur oxidation involving an enzyme complex that is related to the heterodisulfide reductase (Hdr or HdrABC) of methanogens. As a first step in the biochemical characterization of Hdr-like proteins from sulfur oxidizers (sHdr), we structurally analyzed the recombinant sHdrA protein from the Alphaproteobacterium Hyphomicrobium denitrificans at 1.4 Å resolution. The sHdrA core structure is similar to that of methanogenic HdrA (mHdrA) which binds the electron-bifurcating flavin adenine dinucleotide (FAD), the heart of the HdrABC-[NiFe]-hydrogenase catalyzed reaction. Each sHdrA homodimer carries two FADs and two [4Fe-4S] clusters being linked by electron conductivity. Redox titrations monitored by electron paramagnetic resonance and visible spectroscopy revealed a redox potential between -203 and -188 mV for the [4Fe-4S] center. The potentials for the FADH•/FADH- and FAD/FADH• pairs reside between -174 and -156 mV and between -81 and -19 mV, respectively. The resulting stable semiquinone FADH• species already detectable in the visible and electron paramagnetic resonance spectra of the as-isolated state of sHdrA is incompatible with basic principles of flavin-based electron bifurcation such that the sHdr complex does not apply this new mode of energy coupling. The inverted one-electron FAD redox potentials of sHdr and mHdr are clearly reflected in the different FAD-polypeptide interactions. According to this finding and the assumption that the sHdr complex forms an asymmetric HdrAA'B1C1B2C2 hexamer, we tentatively propose a mechanism that links protein-bound sulfane oxidation to sulfite on HdrB1 with NAD+ reduction via lipoamide disulfide reduction on HdrB2. The FAD of HdrA thereby serves as an electron storage unit. DATABASE: Structural data are available in PDB database under the accession number 6TJR.
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Affiliation(s)
- Corvin Ernst
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | | | - Tobias Koch
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Sofia S Venceslau
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Ulrike Demmer
- Max-Planck-Institut für Biophysik, Frankfurt, Germany
| | - Ulrich Ermler
- Max-Planck-Institut für Biophysik, Frankfurt, Germany
| | - Christiane Dahl
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
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46
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Gao XY, Fu CA, Hao L, Gu XF, Wang R, Lin JQ, Liu XM, Pang X, Zhang CJ, Lin JQ, Chen LX. The substrate-dependent regulatory effects of the AfeI/R system in Acidithiobacillus ferrooxidans reveals the novel regulation strategy of quorum sensing in acidophiles. Environ Microbiol 2020; 23:757-773. [PMID: 32656931 PMCID: PMC7984328 DOI: 10.1111/1462-2920.15163] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/05/2020] [Indexed: 12/22/2022]
Abstract
A LuxI/R‐like quorum sensing (QS) system (AfeI/R) has been reported in the acidophilic and chemoautotrophic Acidithiobacillus spp. However, the function of AfeI/R remains unclear because of the difficulties in the genetic manipulation of these bacteria. Here, we constructed different afeI mutants of the sulfur‐ and iron‐oxidizer A. ferrooxidans, identified the N‐acyl homoserine lactones (acyl‐HSLs) synthesized by AfeI, and determined the regulatory effects of AfeI/R on genes expression, extracellular polymeric substance synthesis, energy metabolism, cell growth and population density of A. ferrooxidans in different energy substrates. Acyl‐HSLs‐mediated distinct regulation strategies were employed to influence bacterial metabolism and cell growth of A. ferrooxidans cultivated in either sulfur or ferrous iron. Based on these findings, an energy‐substrate‐dependent regulation mode of AfeI/R in A. ferrooxidans was illuminated that AfeI/R could produce different types of acyl‐HSLs and employ specific acyl‐HSLs to regulate specific genes in response to different energy substrates. The discovery of the AfeI/R‐mediated substrate‐dependent regulatory mode expands our knowledge on the function of QS system in the chemoautotrophic sulfur‐ and ferrous iron‐oxidizing bacteria, and provides new insights in understanding energy metabolism modulation, population control, bacteria‐driven bioleaching process, and the coevolution between the acidophiles and their acidic habitats.
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Affiliation(s)
- Xue-Yan Gao
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, China
| | - Chang-Ai Fu
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, China
| | - Likai Hao
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, No. 99 Lincheng West Road, Guiyang, 550081, China.,CAS Center for Excellence in Quaternary Science and Global Change, Xi'an, 710061, China
| | - Xiu-Feng Gu
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, China
| | - Rui Wang
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, China
| | - Jian-Qiang Lin
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, China
| | - Xiang-Mei Liu
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, China
| | - Xin Pang
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, China
| | - Cheng-Jia Zhang
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, China
| | - Jian-Qun Lin
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, China
| | - Lin-Xu Chen
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, China
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47
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Inaba Y, West AC, Banta S. Enhanced microbial corrosion of stainless steel by
Acidithiobacillus ferrooxidans
through the manipulation of substrate oxidation and overexpression of
rus. Biotechnol Bioeng 2020; 117:3475-3485. [DOI: 10.1002/bit.27509] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/24/2020] [Accepted: 07/10/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Yuta Inaba
- Department of Chemical Engineering Columbia University New York New York
| | - Alan C. West
- Department of Chemical Engineering Columbia University New York New York
| | - Scott Banta
- Department of Chemical Engineering Columbia University New York New York
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48
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Vargas-Straube MJ, Beard S, Norambuena R, Paradela A, Vera M, Jerez CA. High copper concentration reduces biofilm formation in Acidithiobacillus ferrooxidans by decreasing production of extracellular polymeric substances and its adherence to elemental sulfur. J Proteomics 2020; 225:103874. [PMID: 32569817 DOI: 10.1016/j.jprot.2020.103874] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/04/2020] [Accepted: 06/06/2020] [Indexed: 12/14/2022]
Abstract
Acidithiobacillus ferrooxidans is an acidophilic bacterium able to grow in environments with high concentrations of metals. It is a chemolithoautotroph able to form biofilms on the surface of solid minerals to obtain its energy. The response of both planktonic and sessile cells of A. ferrooxidans ATCC 23270 grown in elemental sulfur and adapted to high copper concentration was analyzed by quantitative proteomics. It was found that 137 proteins varied their abundance when comparing both lifestyles. Copper effllux proteins, some subunits of the ATP synthase complex, porins, and proteins involved in cell wall modification increased their abundance in copper-adapted sessile lifestyle cells. On the other hand, planktonic copper-adapted cells showed increased levels of proteins such as: cupreredoxins involved in copper cell sequestration, some proteins related to sulfur metabolism, those involved in biosynthesis and transport of lipopolysaccharides, and in assembly of type IV pili. During copper adaptation a decreased formation of biofilms was measured as determined by epifluorescence microscopy. This was apparently due not only to a diminished number of sessile cells but also to their exopolysaccharides production. This is the first study showing that copper, a prevalent metal in biomining environments causes dispersion of A. ferrooxidans biofilms. SIGNIFICANCE: Copper is a metal frequently found in high concentrations at mining environments inhabitated by acidophilic microorganisms. Copper resistance determinants of A. ferrooxidans have been previously studied in planktonic cells. Although biofilms are recurrent in these types of environments, the effect of copper on their formation has not been studied so far. The results obtained indicate that high concentrations of copper reduce the capacity of A. ferrooxidans ATCC 23270 to form biofilms on sulfur. These findings may be relevant to consider for a bacterium widely used in copper bioleaching processes.
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Affiliation(s)
- M J Vargas-Straube
- Laboratory of Molecular Microbiology and Biotechnology, Department of Biology, Faculty of Sciences, University of Chile, Santiago, Chile
| | - S Beard
- Fundación Ciencia y Vida, Santiago, Chile
| | - R Norambuena
- Laboratory of Molecular Microbiology and Biotechnology, Department of Biology, Faculty of Sciences, University of Chile, Santiago, Chile
| | - A Paradela
- Proteomics Laboratory, National Biotechnology Center, CSIC, Madrid, Spain
| | - M Vera
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile.; Department of Hydraulic and Environmental Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - C A Jerez
- Laboratory of Molecular Microbiology and Biotechnology, Department of Biology, Faculty of Sciences, University of Chile, Santiago, Chile..
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49
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Jafarpour R, Fatemi F, Eidi A, Mehrnejad F. Effect of the Met148Leu mutation on the structure and dynamics of the rusticyanin protein from Acidithiobacillus sp. FJ2. J Biomol Struct Dyn 2020; 39:4122-4132. [PMID: 32462978 DOI: 10.1080/07391102.2020.1775119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The rusticyanin protein, a blue monomeric copper protein type-1, is one of the main components in the iron-electron transfer chain of the Acidithiobacillus ferrooxidans, and is the product of the rus gene expression. Herein, first the bacterial DNA of Acidithiobacillus sp. FJ2 was extracted. Then, the rus gene sequence and the sequence amino acid rusticyanin protein were determined. The Met148Leu mutation increased the oxidase activity of the rusticyanin protein, thereby enhancing the efficiency of the bioleaching process by bacteria Acidithiobacillus ferroxidans. Met148Leu mutation was created in the rusticyanin protein, then molecular dynamics (MD) simulations and structural analysis were performed. The MD analysis of the wild-type and mutant protein demonstrated a slight instability in the mutant protein and significant instability in the active site of the mutant protein. The usefulness of this study is the genetic manipulation of the native Acidithiobacillus sp. FJ2 bacterium, which can boost the bioleaching efficiency of the bacterium to some extent, and investigating its effects on the structure of a mutant protein using computational methods.
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Affiliation(s)
- Roghayeh Jafarpour
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Faezeh Fatemi
- Materials and Nuclear Fuel Research School, Nuclear Science and Technology Research Institute, Tehran, Iran
| | - Akram Eidi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Faramarz Mehrnejad
- Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
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Mechanism for the Bio-Oxidation and Decomposition of Pentlandite: Implication for Nickel Bioleaching at Elevated pH. MINERALS 2020. [DOI: 10.3390/min10030289] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
This work investigated the effects of Fe3+, H+ and adsorbed leaching bacteria on the bioleaching of pentlandite. Collectively, an integrated model for the oxidation and decomposition of pentlandite was built to describe the behaviors of different components in a bioleaching system. Proton ions and ferric ions could promote the break and oxidation of Ni-S and Fe-S bonds. The iron-oxidizing microorganisms could regenerate ferric ions and maintain a high Eh value. The sulfur-oxidizing microorganisms showed significant importance in the oxidation of polysulfide and elemental sulfur. The atoms in pentlandite show different modification pathways during the bioleaching process: iron transformed through a (Ni,Fe)9S8 → Fe2+ → Fe3+ → KFe3(SO4)2(OH)6 pathway; nickel experienced a transformation of (Ni,Fe)9S8 → NiS → Ni2+; sulfur modified through the pathway of S2−/S22− → Sn2− → S0 → SO32− → SO42−. During bioleaching, a sulfur-rich layer and jarosite layer formed on the mineral surface, and the rise of pH value accelerated the process. However, no evidence for the inhibition of the layers was shown in the bioleaching of pentlandite at pH 3.00. This study provides a novel method for the extraction of nickel from pentlandite by bioleaching at elevated pH values.
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