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Wang C, Zheng R, Sun C. Multi-omics analyses provide insights into the sulfur metabolism of a novel deep-sea sulfate-reducing bacterium. iScience 2024; 27:110095. [PMID: 38947506 PMCID: PMC11214288 DOI: 10.1016/j.isci.2024.110095] [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: 01/24/2024] [Revised: 04/02/2024] [Accepted: 05/21/2024] [Indexed: 07/02/2024] Open
Abstract
Sulfate-reducing bacteria (SRB) are ubiquitously distributed across various biospheres and play key roles in global sulfur and carbon cycles. However, few deep-sea SRB have been cultivated and studied in situ, limiting our understanding of the true metabolism of deep-sea SRB. Here, we firstly clarified the high abundance of SRB in deep-sea sediments and successfully isolated a sulfate-reducing bacterium (zrk46) from a cold seep sediment. Our genomic, physiological, and phylogenetic analyses indicate that strain zrk46 is a novel species, which we propose as Pseudodesulfovibrio serpens. We found that supplementation with sulfate, thiosulfate, or sulfite promoted strain zrk46 growth by facilitating energy production through the dissimilatory sulfate reduction, which was coupled to the oxidation of organic matter in both laboratory and deep-sea conditions. Moreover, in situ metatranscriptomic results confirmed that other deep-sea SRB also performed the dissimilatory sulfate reduction, strongly suggesting that SRB may play undocumented roles in deep-sea sulfur cycling.
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Affiliation(s)
- Chong Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Rikuan Zheng
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Chaomin Sun
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- College of Earth Science, University of Chinese Academy of Sciences, Beijing 100049, China
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2
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Stanković S, Schippers A. Goethite dissolution by acidophilic bacteria. Front Microbiol 2024; 15:1360018. [PMID: 38846564 PMCID: PMC11155390 DOI: 10.3389/fmicb.2024.1360018] [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: 12/22/2023] [Accepted: 04/29/2024] [Indexed: 06/09/2024] Open
Abstract
Previous studies have reported the role of some species of acidophilic bacteria in accelerating the dissolution of goethite under aerobic and anaerobic conditions. This has relevance for environments impacted by acid mine drainage and for the potential bioleaching of limonitic laterite ores. In this study, natural well-characterized goethite mineral samples and synthetic goethite were used in aerobic and anaerobic laboratory batch culture incubation experiments with ferric iron-reducing, acidophilic bacteria, including the lithoautotrophic species Acidithiobacillus (At.) thiooxidans, At. ferrooxidans, and At. caldus, as well as two strains of the organoheterotrophic species Acidiphilium cryptum. All bacteria remained alive throughout the experiments and efficiently reduced soluble ferric iron in solution in positive control assays. However, goethite dissolution was low to negligible in all experimental assays with natural goethite, while some dissolution occurred with synthetic goethite in agreement with previous publications. The results indicate that ferric iron-reducing microbial activity at low pH is less relevant for goethite dissolution than the oxidation of elemental sulfur to sulfuric acid. Microbial ferric iron reduction enhances but does not initiate goethite dissolution in very acidic liquors.
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Affiliation(s)
- Srdjan Stanković
- Federal Institute for Geosciences and Natural Resources (BGR), Hannover, Germany
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Axel Schippers
- Federal Institute for Geosciences and Natural Resources (BGR), Hannover, Germany
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3
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Arisan D, Moya-Beltrán A, Rojas-Villalobos C, Issotta F, Castro M, Ulloa R, Chiacchiarini PA, Díez B, Martín AJM, Ñancucheo I, Giaveno A, Johnson DB, Quatrini R. Acidithiobacillia class members originating at sites within the Pacific Ring of Fire and other tectonically active locations and description of the novel genus ' Igneacidithiobacillus'. Front Microbiol 2024; 15:1360268. [PMID: 38633703 PMCID: PMC11021618 DOI: 10.3389/fmicb.2024.1360268] [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: 12/22/2023] [Accepted: 02/21/2024] [Indexed: 04/19/2024] Open
Abstract
Recent studies have expanded the genomic contours of the Acidithiobacillia, highlighting important lacunae in our comprehension of the phylogenetic space occupied by certain lineages of the class. One such lineage is 'Igneacidithiobacillus', a novel genus-level taxon, represented by 'Igneacidithiobacillus copahuensis' VAN18-1T as its type species, along with two other uncultivated metagenome-assembled genomes (MAGs) originating from geothermally active sites across the Pacific Ring of Fire. In this study, we investigate the genetic and genomic diversity, and the distribution patterns of several uncharacterized Acidithiobacillia class strains and sequence clones, which are ascribed to the same 16S rRNA gene sequence clade. By digging deeper into this data and contributing to novel MAGs emerging from environmental studies in tectonically active locations, the description of this novel genus has been consolidated. Using state-of-the-art genomic taxonomy methods, we added to already recognized taxa, an additional four novel Candidate (Ca.) species, including 'Ca. Igneacidithiobacillus chanchocoensis' (mCHCt20-1TS), 'Igneacidithiobacillus siniensis' (S30A2T), 'Ca. Igneacidithiobacillus taupoensis' (TVZ-G3 TS), and 'Ca. Igneacidithiobacillus waiarikiensis' (TVZ-G4 TS). Analysis of published data on the isolation, enrichment, cultivation, and preliminary microbiological characterization of several of these unassigned or misassigned strains, along with the type species of the genus, plus the recoverable environmental data from metagenomic studies, allowed us to identify habitat preferences of these taxa. Commonalities and lineage-specific adaptations of the seven species of the genus were derived from pangenome analysis and comparative genomic metabolic reconstruction. The findings emerging from this study lay the groundwork for further research on the ecology, evolution, and biotechnological potential of the novel genus 'Igneacidithiobacillus'.
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Affiliation(s)
- Dilanaz Arisan
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Santiago, Chile
| | - Ana Moya-Beltrán
- Departamento de Informática y Computación, Facultad de Ingeniería, Universidad Tecnológica Metropolitana, Santiago, Chile
| | - Camila Rojas-Villalobos
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Santiago, Chile
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago, Chile
| | - Francisco Issotta
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Santiago, Chile
- Biological Sciences Faculty, Pontifical Catholic University of Chile, Santiago, Chile
- Millennium Institute Center for Genome Regulation (CGR), Santiago, Chile
| | - Matías Castro
- Instituto Milenio de Oceanografía (IMO), Universidad de Concepción, Concepción, Chile
| | - Ricardo Ulloa
- PROBIEN (CCT Patagonia Confluencia-CONICET, UNCo), Facultad de Ingeniería, Departamento de Química, Universidad Nacional del Comahue, Neuquén, Argentina
| | - Patricia A. Chiacchiarini
- PROBIEN (CCT Patagonia Confluencia-CONICET, UNCo), Facultad de Ingeniería, Departamento de Química, Universidad Nacional del Comahue, Neuquén, Argentina
| | - Beatriz Díez
- Biological Sciences Faculty, Pontifical Catholic University of Chile, Santiago, Chile
- Millennium Institute Center for Genome Regulation (CGR), Santiago, Chile
- Center for Climate and Resilience Research (CR), Santiago, Chile
| | - Alberto J. M. Martín
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Santiago, Chile
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago, Chile
| | - Iván Ñancucheo
- Facultad de Ingeniería y Tecnología, Universidad San Sebastián, Lientur, Concepción, Chile
| | - Alejandra Giaveno
- PROBIEN (CCT Patagonia Confluencia-CONICET, UNCo), Facultad de Ingeniería, Departamento de Química, Universidad Nacional del Comahue, Neuquén, Argentina
| | - D. Barrie Johnson
- College of Natural Sciences, Bangor University, Bangor, United Kingdom
- Faculty of Health and Life Sciences, Coventry University, Coventry, United Kingdom
- Natural History Museum, London, United Kingdom
| | - Raquel Quatrini
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Santiago, Chile
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Luo T, Zheng Q, Yu J, Liang W, Sun Y, Quan G, Zhou F. Roles of nanoparticles in arsenic mobility and microbial community composition in arsenic-enriched soils. J Environ Sci (China) 2024; 138:301-311. [PMID: 38135397 DOI: 10.1016/j.jes.2022.11.001] [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: 10/04/2022] [Revised: 10/28/2022] [Accepted: 11/01/2022] [Indexed: 12/24/2023]
Abstract
Environmental effects of nano remediation engineering of arsenic (As) pollution need to be considered. In this study, the roles of Fe2O3 and TiO2 nanoparticles (NPs) on the microbial mediated As mobilization from As contaminated soil were investigated. The addition of Fe2O3 and TiO2 NPs restrained As(V) release, and stimulated As(III) release. As(V) concentration decreased by 94% and 93% after Fe2O3 addition, and decreased by 89% and 45% after TiO2 addition compared to the Biotic and Biotic+Acetate (amended with sodium acetate) controls, respectively. The maximum values of As(III) were 20.5 and 27.1 µg/L at 48 d after Fe2O3 and TiO2 NPs addition, respectively, and were higher than that in Biotic+Acetate control (12.9 µg/L). The released As co-precipitated with Fe in soils in the presence of Fe2O3 NPs, but adsorbed on TiO2 NPs in the presence of TiO2 NPs. Moreover, the addition of NPs amended with sodium acetate as the electron donor clearly promoted As(V) reduction induced by microbes. The NPs addition changed the relative abundance of soil bacterial community, while Proteobacteria (42.8%-70.4%), Planctomycetes (2.6%-14.3%), and Firmicutes (3.5%-25.4%) were the dominant microorganisms in soils. Several potential As/Fe reducing bacteria were related to Pseudomonas, Geobacter, Desulfuromonas, and Thiobacillus. The addition of Fe2O3 and TiO2 NPs induced to the decrease of arrA gene. The results indicated that the addition of NPs had a negative impact on soil microbial population in a long term. The findings offer a relatively comprehensive assessment of Fe2O3 and TiO2 NPs effects on As mobilization and soil bacterial communities.
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Affiliation(s)
- Ting Luo
- School of Environmental Science and Engineering, Yancheng Institute of Technology, Yancheng 224051, China; Jiangsu Provincial Key Laboratory of Coastal Ecology and Pollution Control, Yancheng 224051, China.
| | - Qining Zheng
- School of Environmental Science and Engineering, Yancheng Institute of Technology, Yancheng 224051, China; Jiangsu Provincial Key Laboratory of Coastal Ecology and Pollution Control, Yancheng 224051, China
| | - Jie Yu
- School of Environmental Science and Engineering, Yancheng Institute of Technology, Yancheng 224051, China; School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Weihao Liang
- School of Environmental Science and Engineering, Yancheng Institute of Technology, Yancheng 224051, China; Jiangsu Provincial Key Laboratory of Coastal Ecology and Pollution Control, Yancheng 224051, China
| | - Yan Sun
- School of Environmental Science and Engineering, Yancheng Institute of Technology, Yancheng 224051, China; Jiangsu Provincial Key Laboratory of Coastal Ecology and Pollution Control, Yancheng 224051, China
| | - Guixiang Quan
- School of Environmental Science and Engineering, Yancheng Institute of Technology, Yancheng 224051, China; Jiangsu Provincial Key Laboratory of Coastal Ecology and Pollution Control, Yancheng 224051, China
| | - Feng Zhou
- School of Environmental Science and Engineering, Yancheng Institute of Technology, Yancheng 224051, China; Jiangsu Provincial Key Laboratory of Coastal Ecology and Pollution Control, Yancheng 224051, China
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5
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Breuker A, Schippers A. Rates of iron(III) reduction coupled to elemental sulfur or tetrathionate oxidation by acidophilic microorganisms and detection of sulfur intermediates. Res Microbiol 2024; 175:104110. [PMID: 37544391 DOI: 10.1016/j.resmic.2023.104110] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 07/31/2023] [Accepted: 07/31/2023] [Indexed: 08/08/2023]
Abstract
Bioleaching processes and acid mine drainage (AMD) generation are mainly driven by aerobic microbial iron(II) and inorganic sulfur/compound oxidation. Dissimilatory iron(III) reduction coupled to sulfur/compound oxidation (DIRSO) by acidophilic microorganisms has been described for anaerobic cultures, but iron reduction was observed under aerobic conditions as well. Aim of this study was to explore reaction rates and mechanisms of this process. Cell-specific iron(III) reduction rates for different Acidithiobacillus (At.) strains during batch culture growth or stationary phase with iron(III) (∼40 mM) as electron acceptor and elemental sulfur or tetrathionate as electron donor (1% or 5 mM, respectively) were determined. The rates were highest under anaerobic conditions for the At. ferrooxidans type strain with 6.8 × 106 and 1.1 × 107 reduced iron(III) ions per second per cell for growth on elemental sulfur and tetrathionate, respectively. The iron(III) reduction rates were somehow lower for the anaerobically sulfur grown archaeon Ferroplasma acidiphilum, and lowest for the sulfur grown At. caldus type strain under aerobic conditions (1.7 × 106 and 7.3 × 104 reduced iron(III) ions per second per cell, respectively). The rates for five strains of At. thiooxidans (aerobe) were in between those for At. ferrooxidans (anaerobe) and At. caldus (aerobe). There was no pronounced pH dependence of iron(III) reduction rates in the range of pH 1.0-1.9 for the type strains of all species but rates increased with increasing pH for four other At. thiooxidans strains. Thiosulfate as sulfur intermediate was found for At. ferrooxidans during anaerobic growths on tetrathionate and iron(III) but not during anaerobic growths on elemental sulfur and iron(III), and a small concentration was measured during aerobic growths on tetrathionate without iron(III). For the At. thiooxidans type strain thiosulfate was found with tetrathionate grown cells under aerobic conditions in presence and absence of iron(III), but not with sulfur grown cells. Evidence for hydrogen sulfide production at low pH was found for the At. ferrooxidans as well as the At. thiooxidans type strains during microaerophilic growth on elemental sulfur and for At. ferrooxidans during anaerobic growths on tetrathionate and iron(III). The occurrence of sulfur compound intermediates supports the hypothesis that chemical reduction of iron(III) ions takes place by sulfur compounds released by the microbial cells.
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Affiliation(s)
- Anja Breuker
- Federal Institute for Geosciences and Natural Resources (BGR), Stilleweg2, 30655 Hannover, Germany
| | - Axel Schippers
- Federal Institute for Geosciences and Natural Resources (BGR), Stilleweg2, 30655 Hannover, Germany.
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6
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Aerts JW, Sarbu SM, Brad T, Ehrenfreund P, Westerhoff HV. Microbial Ecosystems in Movile Cave: An Environment of Extreme Life. Life (Basel) 2023; 13:2120. [PMID: 38004260 PMCID: PMC10672346 DOI: 10.3390/life13112120] [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: 09/29/2023] [Revised: 10/21/2023] [Accepted: 10/24/2023] [Indexed: 11/26/2023] Open
Abstract
Movile Cave, situated in Romania close to the Black Sea, constitutes a distinct and challenging environment for life. Its partially submerged ecosystem depends on chemolithotrophic processes for its energetics, which are fed by a continuous hypogenic inflow of mesothermal waters rich in reduced chemicals such as hydrogen sulfide and methane. We sampled a variety of cave sublocations over the course of three years. Furthermore, in a microcosm experiment, minerals were incubated in the cave waters for one year. Both endemic cave samples and extracts from the minerals were subjected to 16S rRNA amplicon sequencing. The sequence data show specific community profiles in the different subenvironments, indicating that specialized prokaryotic communities inhabit the different zones in the cave. Already after one year, the different incubated minerals had been colonized by specific microbial communities, indicating that microbes in Movile Cave can adapt in a relatively short timescale to environmental opportunities in terms of energy and nutrients. Life can thrive, diversify and adapt in remote and isolated subterranean environments such as Movile Cave.
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Affiliation(s)
- Joost W. Aerts
- Molecular Cell Biology, A-LIFE, 01-E-57, Faculty of Science, VU University Amsterdam, Van der Boechorstraat 3, 1081 BT Amsterdam, The Netherlands
| | - Serban M. Sarbu
- “Emil Racoviţă” Institute of Speleology, Str. Frumoasă 31, 010986 Bucharest, Romania
- Department of Biological Sciences, California State University, Chico, CA 95929, USA
| | - Traian Brad
- “Emil Racoviţă” Institute of Speleology, Clinicilor 5-7, 400006 Cluj-Napoca, Romania;
| | - Pascale Ehrenfreund
- Laboratory for Astrophysics, Leiden Observatory, Leiden University, 2333 RA Leiden, The Netherlands
- Space Policy Institute, George Washington University, Washington, DC 20052, USA
| | - Hans V. Westerhoff
- Molecular Cell Biology, A-LIFE, 01-E-57, Faculty of Science, VU University Amsterdam, Van der Boechorstraat 3, 1081 BT Amsterdam, The Netherlands
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
- Stellenbosch Institute for Advanced Study, Stellenbosch 7600, South Africa
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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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Liu Y, Gu C, Liu H, Zhou Y, Nie Z, Wang Y, Chen L, Xia J. Fe/S Redox-Coupled Mercury Transformation Mediated by Acidithiobacillus ferrooxidans ATCC 23270 under Aerobic and/or Anaerobic Conditions. Microorganisms 2023; 11:microorganisms11041028. [PMID: 37110452 PMCID: PMC10141921 DOI: 10.3390/microorganisms11041028] [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: 03/04/2023] [Revised: 03/28/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023] Open
Abstract
Bioleaching processes or microbially mediated iron/sulfur redox processes in acid mine drainage (AMD) result in mineral dissolution and transformation, the release of mercury and other heavy metal ions, and changes in the occurrence forms and concentration of mercury. However, pertinent studies on these processes are scarce. Therefore, in this work, the Fe/S redox-coupled mercury transformation mediated by Acidithiobacillus ferrooxidans ATCC 23270 under aerobic and/or anaerobic conditions was studied by combining analyses of solution behavior (pH, redox potential, and Fe/S/Hg ion concentrations), the surface morphology and elemental composition of the solid substrate residue, the Fe/S/Hg speciation transformation, and bacterial transcriptomics. It was found that: (1) the presence of Hg2+ significantly inhibited the apparent iron/sulfur redox process; (2) the addition of Hg2+ caused a significant change in the composition of bacterial surface compounds and elements such as C, N, S, and Fe; (3) Hg mainly occurred in the form of Hg0, HgS, and HgSO4 in the solid substrate residues; and (4) the expression of mercury-resistant genes was higher in earlier stages of growth than in the later stages of growth. The results indicate that the addition of Hg2+ significantly affected the iron/sulfur redox process mediated by A. ferrooxidans ATCC 23270 under aerobic, anaerobic, and coupled aerobic-anaerobic conditions, which further promoted Hg transformation. This work is of great significance for the treatment and remediation of mercury pollution in heavy metal-polluted areas.
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Affiliation(s)
- Yue Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
| | - Chenyun Gu
- 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
| | - Yirong Wang
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
| | - Lu Chen
- School of Minerals Processing and Bioengineering, 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
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9
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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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Roberts M, Srivastava P, Webster G, Weightman AJ, Sapsford DJ. Biostimulation of jarosite and iron oxide-bearing mine waste enhances subsequent metal recovery. JOURNAL OF HAZARDOUS MATERIALS 2023; 445:130498. [PMID: 36459883 DOI: 10.1016/j.jhazmat.2022.130498] [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: 09/24/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Novel resource recovery technologies are required for metals-bearing hazardous wastes in order to achieve circular economy outcomes and industrial symbiosis. Iron oxide and co-occurring hydroxysulphate-bearing wastes are globally abundant and often contain other elements of value. This work addresses the biostimulation of indigenous microbial communities within an iron oxide/ hydroxysulphate-bearing waste and its effect on the subsequent recoverability of metals by hydrochloric, sulphuric, citric acids, and EDTA. Laboratory-scale flow-through column reactors were used to examine the effect of using glycerol (10% w/w) to stimulate the in situ microbial community in an iron oxide/ hydroxysulphate-bearing mine waste. The effects on the evolution of leachate chemistry, changes in microbiological community, and subsequent hydrometallurgical extractability of metals were studied. Results demonstrated increased leachability and selectivity of Pb, Cu, and Zn relative to iron after biostimulation with a total of 0.027 kg of glycerol per kg of waste. Biostimulation, which can be readily applied in situ, potentially opens new routes to metal recovery from globally abundant waste streams that contain jarosite and iron oxides.
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Affiliation(s)
- Mark Roberts
- School of Engineering, Cardiff University, Queen's Building, The Parade, Cardiff CF24 3AA, United Kingdom
| | - Pallavee Srivastava
- School of Engineering, Cardiff University, Queen's Building, The Parade, Cardiff CF24 3AA, United Kingdom.
| | - Gordon Webster
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, United Kingdom
| | - Andrew J Weightman
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, United Kingdom
| | - Devin J Sapsford
- School of Engineering, Cardiff University, Queen's Building, The Parade, Cardiff CF24 3AA, United Kingdom
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11
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Olmsted CN, Ort R, Tran PQ, McDaniel EA, Roden EE, Bond DR, He S, McMahon KD. Environmental predictors of electroactive bacterioplankton in small boreal lakes. Environ Microbiol 2023; 25:705-720. [PMID: 36529539 DOI: 10.1111/1462-2920.16314] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Extracellular electron transfer (EET) by electroactive bacteria in anoxic soils and sediments is an intensively researched subject, but EET's function in planktonic ecology has been less considered. Following the discovery of an unexpectedly high prevalence of EET genes in a bog lake's bacterioplankton, we hypothesized that the redox capacities of dissolved organic matter (DOM) enrich for electroactive bacteria by mediating redox chemistry. We developed the bioinformatics pipeline FEET (Find EET) to identify and summarize predicted EET protein-encoding genes from metagenomics data. We then applied FEET to 36 bog and thermokarst lakes and correlated gene occurrence with environmental data to test our predictions. Our results provide indirect evidence that DOM may participate in bacterioplankton EET. We found a similarly high prevalence of genes encoding putative EET proteins in most of these lakes, where oxidative EET strongly correlated with DOM. Numerous novel clusters of multiheme cytochromes that may enable EET were identified. Taxa previously not considered EET-capable were found to carry EET genes. We propose that EET and DOM interactions are of ecologically important to bacterioplankton in small boreal lakes, and that EET, particularly by methylotrophs and anoxygenic phototrophs, should be further studied and incorporated into methane emission models of melting permafrost.
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Affiliation(s)
- Charles N Olmsted
- Department of Molecular and Environmental Toxicology, University of Wisconsin - Madison, Madison, Wisconsin, USA
- Trout Lake Station, Center for Limnology, University of Wisconsin - Madison, Boulder, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | - Roger Ort
- Trout Lake Station, Center for Limnology, University of Wisconsin - Madison, Boulder, Wisconsin, USA
| | - Patricia Q Tran
- Department of Bacteriology, University of Wisconsin - Madison, Madison, Wisconsin, USA
- Department of Integrative Biology, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | - Elizabeth A McDaniel
- Department of Bacteriology, University of Wisconsin - Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | - Eric E Roden
- Department of Geoscience, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | - Daniel R Bond
- Department of Plant and Microbial Biology and BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
| | - Shaomei He
- Department of Bacteriology, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | - Katherine D McMahon
- Department of Bacteriology, University of Wisconsin - Madison, Madison, Wisconsin, USA
- Department of Civil and Environmental Engineering, University of Wisconsin - Madison, Madison, Wisconsin, USA
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12
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Sun S, Zhang M, Gu X, Yan P, He S, Chachar A. New insight and enhancement mechanisms for Feammox process by electron shuttles in wastewater treatment - A systematic review. BIORESOURCE TECHNOLOGY 2023; 369:128495. [PMID: 36526117 DOI: 10.1016/j.biortech.2022.128495] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/11/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Ammonium oxidation coupled to Fe(III) reduction (Feammox) is a newly discovered iron-nitrogen cycle process of microbial catalyzed NH4+ oxidation coupled with iron reduction. Fe(III) often exists in the form of insoluble iron minerals resulting in reduced microbial availability and low efficiency of Feammox. Electron shuttles(ESs) can be reversibly oxidized and reduced which has the potential to improve Feammox efficiency. This review summarizes the discovery process, electron transfer mechanism, influencing factors and driven microorganisms of Feammox, ang expounds the possibility and potential mechanism of ESs to enhance Feammox efficiency. Based on an in-depth analysis of the current research situation of Feammox for nitrogen removal, the knowledge gaps and future research directions including how to apply ESs enhanced Feammox to promote nitrogen removal in practical wastewater treatment have been highlighted. This review can provide new ideas for the engineering application research of Feammox and strong theoretical support for its development.
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Affiliation(s)
- Shanshan Sun
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Manping Zhang
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Xushun Gu
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Pan Yan
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Shengbing He
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 20092, PR China; Shanghai Engineering Research Center of Landscape Water Environment, Shanghai 200031, PR China.
| | - Azharuddin Chachar
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, PR China
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13
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Yi Q, Wu S, Liu Y, Chan TS, Lu YR, Saha N, Southam G, Huang L. Mineral weathering of iron ore tailings primed by Acidithiobacillus ferrooxidans and elemental sulfur under contrasting pH conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:159078. [PMID: 36179848 DOI: 10.1016/j.scitotenv.2022.159078] [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: 05/16/2022] [Revised: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
The acidophilic sulfur oxidizing bacterium (SOB), Acidithiobacillus ferrooxidans, has been found to stimulate elemental sulfur (S0) oxidation and mineral weathering in alkaline Fe ore tailings. However, A. ferrooxidans growth and activities depend on the pH conditions surrounding their interfaces with minerals. The present study aimed to investigate how pH influences bacterial growth and functions in Fe ore tailings. A simulated aquatic 'homogeneous' incubation system was initially adjusted into acidic (pH 4), neutral (pH 7) and alkaline (pH 9) conditions, which mimicked the microenvironmental conditions of the water-cell-mineral interfaces in the tailings. It was found that A. ferrooxidans grew well and oxidised S0 under the prevailing and initially acidic conditions (pH < 6). These stimulated the weathering of biotite and amphibole-like minerals and the formation of nanosized jarosite and ferrihydrite-like minerals mediated by extracellular polymer substrate (EPS). In contrast, the initially neutral/alkaline pH conditions (i.e., pH > 7) with the presence of the alkaline tailings restricted SOB growth and functions in S0-oxidation and mineral weathering. These findings suggest that it is essential to prime acidic conditions in microenvironments to support SOB growth, activities, and functions toward mineral weathering in tailings, providing critical basis for involving SOB in eco-engineered pedogenesis in tailings.
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Affiliation(s)
- Qing Yi
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane 4072, Australia
| | - Songlin Wu
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane 4072, Australia.
| | - Yunjia Liu
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane 4072, Australia
| | - Ting-Shan Chan
- National Synchrotron Radiation Research Centre, Hsinchu Science Park, Hsinchu 300, Taiwan
| | - Ying-Rui Lu
- National Synchrotron Radiation Research Centre, Hsinchu Science Park, Hsinchu 300, Taiwan
| | - Narottam Saha
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane 4072, Australia
| | - Gordon Southam
- School of Earth & Environmental Sciences, The University of Queensland, Brisbane 4072, Australia
| | - Longbin Huang
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane 4072, Australia.
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14
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Han S, Li Y, Gao H. Generation and Physiology of Hydrogen Sulfide and Reactive Sulfur Species in Bacteria. Antioxidants (Basel) 2022; 11:antiox11122487. [PMID: 36552695 PMCID: PMC9774590 DOI: 10.3390/antiox11122487] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
Sulfur is not only one of the most abundant elements on the Earth, but it is also essential to all living organisms. As life likely began and evolved in a hydrogen sulfide (H2S)-rich environment, sulfur metabolism represents an early form of energy generation via various reactions in prokaryotes and has driven the sulfur biogeochemical cycle since. It has long been known that H2S is toxic to cells at high concentrations, but now this gaseous molecule, at the physiological level, is recognized as a signaling molecule and a regulator of critical biological processes. Recently, many metabolites of H2S, collectively called reactive sulfur species (RSS), have been gradually appreciated as having similar or divergent regulatory roles compared with H2S in living organisms, especially mammals. In prokaryotes, even in bacteria, investigations into generation and physiology of RSS remain preliminary and an understanding of the relevant biological processes is still in its infancy. Despite this, recent and exciting advances in the fields are many. Here, we discuss abiotic and biotic generation of H2S/RSS, sulfur-transforming enzymes and their functioning mechanisms, and their physiological roles as well as the sensing and regulation of H2S/RSS.
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15
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Cantillo-González A, Anguita J, Rojas C, Vargas IT. Winogradsky Bioelectrochemical System as a Novel Strategy to Enrich Electrochemically Active Microorganisms from Arsenic-Rich Sediments. MICROMACHINES 2022; 13:1953. [PMID: 36422381 PMCID: PMC9692521 DOI: 10.3390/mi13111953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/12/2022] [Accepted: 10/28/2022] [Indexed: 06/16/2023]
Abstract
Bioelectrochemical systems (BESs) have been extensively studied for treatment and remediation. However, BESs have the potential to be used for the enrichment of microorganisms that could replace their natural electron donor or acceptor for an electrode. In this study, Winogradsky BES columns with As-rich sediments extracted from an Andean watershed were used as a strategy to enrich lithotrophic electrochemically active microorganisms (EAMs) on electrodes (i.e., cathodes). After 15 months, Winogradsky BESs registered power densities up to 650 μWcm-2. Scanning electron microscopy and linear sweep voltammetry confirmed microbial growth and electrochemical activity on cathodes. Pyrosequencing evidenced differences in bacterial composition between sediments from the field and cathodic biofilms. Six EAMs from genera Herbaspirillum, Ancylobacter, Rhodococcus, Methylobacterium, Sphingomonas, and Pseudomonas were isolated from cathodes using a lithoautotrophic As oxidizers culture medium. These results suggest that the tested Winogradsky BES columns result in an enrichment of electrochemically active As-oxidizing microorganisms. A bioelectrochemical boost of centenarian enrichment approaches, such as the Winogradsky column, represents a promising strategy for prospecting new EAMs linked with the biogeochemical cycles of different metals and metalloids.
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Affiliation(s)
- Angela Cantillo-González
- Departmento de Ingeniería Hidráulica y Ambiental, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- Centro de Desarrollo Urbano Sustentable (CEDEUS), Santiago 6640064, Chile
| | - Javiera Anguita
- Departmento de Ingeniería Hidráulica y Ambiental, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Claudia Rojas
- Laboratory of Soil Microbial Ecology and Biogeochemistry (LEMiBiS), Institute of Agri-Food, Animal and Environmental Sciences (ICA3), Universidad de O’Higgins, San Fernando 3070000, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago 8331150, Chile
| | - Ignacio T. Vargas
- Departmento de Ingeniería Hidráulica y Ambiental, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- Centro de Desarrollo Urbano Sustentable (CEDEUS), Santiago 6640064, Chile
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16
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Deep-Sea
In Situ
Insights into the Formation of Zero-Valent Sulfur Driven by a Bacterial Thiosulfate Oxidation Pathway. mBio 2022; 13:e0014322. [PMID: 35852328 PMCID: PMC9426585 DOI: 10.1128/mbio.00143-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The contribution of microbes to the deep-sea cold seep sulfur cycle has received considerable attention in recent years. In the previous study, we isolated
E. flavus
21-3 from deep-sea cold seep sediments and described a novel thiosulfate oxidation pathway in the laboratorial condition.
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17
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Guo G, Li Z, Chen L, Ling Q, Zan F, Isawi H, Hao T, Ma J, Wang Z, Chen G, Lu H. Advances in elemental sulfur-driven bioprocesses for wastewater treatment: From metabolic study to application. WATER RESEARCH 2022; 213:118143. [PMID: 35149365 DOI: 10.1016/j.watres.2022.118143] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/17/2022] [Accepted: 01/30/2022] [Indexed: 06/14/2023]
Abstract
Elemental sulfur (S0) is known to be an abundant, non-toxic material with a wide range of redox states (-2 to +6) and may serve as an excellent electron carrier in wastewater treatment. In turn, S0-driven bioprocesses, which employ S0 as electron donor or acceptor, have recently established themselves as cost-effective therefore attractive solutions for wastewater treatment. Numerous related processes have, to date, been developed from laboratory experiments into full-scale applications, including S0-driven autotrophic denitrification for nitrate removal and S0-reducing organic removal. Compared to the conventional activated sludge process, these bioprocesses require only a small amount of organic matter and produce very little sludge. There have been great efforts to characterize chemical and biogenic S0 and related functional microorganisms in order to identify the biochemical pathways, upgrade the bioprocesses, and assess the impact of the operating factors on process performance, ultimately aiming to better understand and to optimize the processes. This paper is therefore a comprehensive overview of emerging S0-driven biotechnologies, including the development of S0-driven autotrophic denitrification and S0-based sulfidogenesis, as well as the associated microbiology and biochemistry. Also reviewed here are the physicochemical characteristics of S0 and the effects that environmental factors such as pH, influent sulfur/nitrate ratio, temperature, S0 particle size and reactor configurations have on the process. Research gaps, challenges of process applications and potential areas for future research are further proposed and discussed.
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Affiliation(s)
- Gang Guo
- School of Environmental Science and Engineering, Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Zhaoling Li
- School of Environmental Science and Engineering, Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Lei Chen
- School of Environmental Science and Engineering, Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Qingshan Ling
- School of Environmental Science and Engineering, Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Feixiang Zan
- School of Environmental Science and Engineering, Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Heba Isawi
- Desert Research Center, Water Resources and Desert Soils Division, Egyptian Desalination Research Center of Excellence (EDRC), Cairo, Egypt
| | - Tianwei Hao
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau, China.
| | - Jie Ma
- School of Environmental Science and Engineering, Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Zongping Wang
- School of Environmental Science and Engineering, Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Guanghao Chen
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Hui Lu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China.
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18
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Zhou S, Tong G, Meng X, Wang Y, Gu G, Gan M. Reactive oxygen species formation driven by acidophiles mediated pyrite oxidation and its potential role on 2,4-dichlorophenol transformation. JOURNAL OF HAZARDOUS MATERIALS 2022; 425:127833. [PMID: 34872039 DOI: 10.1016/j.jhazmat.2021.127833] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 11/15/2021] [Accepted: 11/15/2021] [Indexed: 06/13/2023]
Abstract
Researches of reactive oxygen species (ROS) generation from pyrite oxidation and its impact on contaminants transformation has been constrained to abiotic conditions. However, pyrite oxidation by acidophiles is widespread in acidic environments. The potential role of these microorganisms on pyrite-induced ROS formation and pollutants processing is not understood well. Here, ROS production and 2,4-DCP transformation during pyrite oxidation under oxic and anoxic atmospheres by Acidithiobacillus ferrooxidans (A. ferrooxidans) were explored. 2,4-DCP removal was enhanced in biosystem. Under oxic and anoxic conditions, microbially mediated pyrite oxidation resulted in removing 93.66% and 43.77% 2,4-DCP, which were 1.14- and 1.51-fold greater than that without cells. Based on intermediates identified by LC-MS, the transformation pathway of 2,4-DCP was proposed. The trapping experiments demonstrated ROS contributed during 2,4-DCP transformation. The improving effect of A. ferrooxidans on 2,4-DCP degradation was mainly due to ROS increase. A. ferrooxidans was to promote pyrite surface renew, exposing more Fe(II) and Fe(III) sites that facilitated O2 reduction and H2O dissociation for ROS generation. Biogenic ROS and sulfite bio-oxidation with the free radical mechanism provided other ROS sources. ESR revealed A. ferrooxidans-pyrite interaction led to sustainable ROS production, indicating it could be a significant pathway in driving geochemical cycles of elements.
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Affiliation(s)
- Shuang Zhou
- School of Minerals Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China; State Environmental Protection Key Laboratory of Mineral Metallurgical Resources Utilization and Pollution Control, Wuhan University of Science and Technology, Wuhan 430081, China
| | - Ge Tong
- School of Minerals Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
| | - Xiaoyu Meng
- School of Minerals Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
| | - Yanhong Wang
- School of Minerals Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
| | - Guohua Gu
- School of Minerals Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China.
| | - Min Gan
- School of Minerals Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China.
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19
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Malik L, Hedrich S. Ferric Iron Reduction in Extreme Acidophiles. Front Microbiol 2022; 12:818414. [PMID: 35095822 PMCID: PMC8790237 DOI: 10.3389/fmicb.2021.818414] [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: 11/19/2021] [Accepted: 12/17/2021] [Indexed: 11/13/2022] Open
Abstract
Biochemical processes are a key element of natural cycles occurring in the environment and enabling life on earth. With regard to microbially catalyzed iron transformation, research predominantly has focused on iron oxidation in acidophiles, whereas iron reduction played a minor role. Microbial conversion of ferric to ferrous iron has however become more relevant in recent years. While there are several reviews on neutrophilic iron reducers, this article summarizes the research on extreme acidophilic iron reducers. After the first reports of dissimilatory iron reduction by acidophilic, chemolithoautotrophic Acidithiobacillus strains and heterotrophic Acidiphilium species, many other prokaryotes were shown to reduce iron as part of their metabolism. Still, little is known about the exact mechanisms of iron reduction in extreme acidophiles. Initially, hypotheses and postulations for the occurring mechanisms relied on observations of growth behavior or predictions based on the genome. By comparing genomes of well-studied neutrophilic with acidophilic iron reducers (e.g., Ferroglobus placidus and Sulfolobus spp.), it became clear that the electron transport for iron reduction proceeds differently in acidophiles. Moreover, transcriptomic investigations indicated an enzymatically-mediated process in Acidithiobacillus ferrooxidans using respiratory chain components of the iron oxidation in reverse. Depending on the strain of At. ferrooxidans, further mechanisms were postulated, e.g., indirect iron reduction by hydrogen sulfide, which may form by disproportionation of elemental sulfur. Alternative scenarios include Hip, a high potential iron-sulfur protein, and further cytochromes. Apart from the anaerobic iron reduction mechanisms, sulfur-oxidizing acidithiobacilli have been shown to mediate iron reduction at low pH (< 1.3) under aerobic conditions. This presumably non-enzymatic process may be attributed to intermediates formed during sulfur/tetrathionate and/or hydrogen oxidation and has already been successfully applied for the reductive bioleaching of laterites. The aim of this review is to provide an up-to-date overview on ferric iron reduction by acidophiles. The importance of this process in anaerobic habitats will be demonstrated as well as its potential for application.
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Affiliation(s)
- Luise Malik
- Research Group Biohydrometallurgy and Microbiology, Institute of Biosciences, TU Bergakademie Freiberg, Freiberg, Germany
| | - Sabrina Hedrich
- Research Group Biohydrometallurgy and Microbiology, Institute of Biosciences, TU Bergakademie Freiberg, Freiberg, Germany
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20
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Genomic evolution of the class Acidithiobacillia: deep-branching Proteobacteria living in extreme acidic conditions. THE ISME JOURNAL 2021; 15:3221-3238. [PMID: 34007059 PMCID: PMC8528912 DOI: 10.1038/s41396-021-00995-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/08/2021] [Accepted: 04/21/2021] [Indexed: 02/04/2023]
Abstract
Members of the genus Acidithiobacillus, now ranked within the class Acidithiobacillia, are model bacteria for the study of chemolithotrophic energy conversion under extreme conditions. Knowledge of the genomic and taxonomic diversity of Acidithiobacillia is still limited. Here, we present a systematic analysis of nearly 100 genomes from the class sampled from a wide range of habitats. Some of these genomes are new and others have been reclassified on the basis of advanced genomic analysis, thus defining 19 Acidithiobacillia lineages ranking at different taxonomic levels. This work provides the most comprehensive classification and pangenomic analysis of this deep-branching class of Proteobacteria to date. The phylogenomic framework obtained illuminates not only the evolutionary past of this lineage, but also the molecular evolution of relevant aerobic respiratory proteins, namely the cytochrome bo3 ubiquinol oxidases.
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21
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Genomic Insights into the Ecological Role and Evolution of a Novel Thermoplasmata Order, " Candidatus Sysuiplasmatales". Appl Environ Microbiol 2021; 87:e0106521. [PMID: 34524897 DOI: 10.1128/aem.01065-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recent omics studies have provided invaluable insights into the metabolic potential, adaptation, and evolution of novel archaeal lineages from a variety of extreme environments. We utilized a genome-resolved metagenomic approach to recover eight medium- to high-quality metagenome-assembled genomes (MAGs) that likely represent a new order ("Candidatus Sysuiplasmatales") in the class Thermoplasmata from mine tailings and acid mine drainage (AMD) sediments sampled from two copper mines in South China. 16S rRNA gene-based analyses revealed a narrow habitat range for these uncultured archaea limited to AMD and hot spring-related environments. Metabolic reconstruction indicated a facultatively anaerobic heterotrophic lifestyle. This may allow the archaea to adapt to oxygen fluctuations and is thus in marked contrast to the majority of lineages in the domain Archaea, which typically show obligately anaerobic metabolisms. Notably, "Ca. Sysuiplasmatales" could conserve energy through degradation of fatty acids, amino acid metabolism, and oxidation of reduced inorganic sulfur compounds (RISCs), suggesting that they may contribute to acid generation in the extreme mine environments. Unlike the closely related orders Methanomassiliicoccales and "Candidatus Gimiplasmatales," "Ca. Sysuiplasmatales" lacks the capacity to perform methanogenesis and carbon fixation. Ancestral state reconstruction indicated that "Ca. Sysuiplasmatales," the closely related orders Methanomassiliicoccales and "Ca. Gimiplasmatales," and the orders SG8-5 and RBG-16-68-12 originated from a facultatively anaerobic ancestor capable of carbon fixation via the bacterial-type H4F Wood-Ljungdahl pathway (WLP). Their metabolic divergence might be attributed to different evolutionary paths. IMPORTANCE A wide array of archaea populate Earth's extreme environments; therefore, they may play important roles in mediating biogeochemical processes such as iron and sulfur cycling. However, our knowledge of archaeal biology and evolution is still limited, since the majority of the archaeal diversity is uncultured. For instance, most order-level lineages except Thermoplasmatales, Aciduliprofundales, and Methanomassiliicoccales within Thermoplasmata do not have cultured representatives. Here, we report the discovery and genomic characterization of a novel order, "Ca. Sysuiplasmatales," within Thermoplasmata in extremely acidic mine environments. "Ca. Sysuiplasmatales" are inferred to be facultatively anaerobic heterotrophs and likely contribute to acid generation through the oxidation of RISCs. The physiological divergence between "Ca. Sysuiplasmatales" and closely related Thermoplasmata lineages may be attributed to different evolutionary paths. These results expand our knowledge of archaea in the extreme mine ecosystem.
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22
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Newsome L, Falagán C. The Microbiology of Metal Mine Waste: Bioremediation Applications and Implications for Planetary Health. GEOHEALTH 2021; 5:e2020GH000380. [PMID: 34632243 PMCID: PMC8490943 DOI: 10.1029/2020gh000380] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 08/17/2021] [Accepted: 08/20/2021] [Indexed: 05/13/2023]
Abstract
Mine wastes pollute the environment with metals and metalloids in toxic concentrations, causing problems for humans and wildlife. Microorganisms colonize and inhabit mine wastes, and can influence the environmental mobility of metals through metabolic activity, biogeochemical cycling and detoxification mechanisms. In this article we review the microbiology of the metals and metalloids most commonly associated with mine wastes: arsenic, cadmium, chromium, copper, lead, mercury, nickel and zinc. We discuss the molecular mechanisms by which bacteria, archaea, and fungi interact with contaminant metals and the consequences for metal fate in the environment, focusing on long-term field studies of metal-impacted mine wastes where possible. Metal contamination can decrease the efficiency of soil functioning and essential element cycling due to the need for microbes to expend energy to maintain and repair cells. However, microbial communities are able to tolerate and adapt to metal contamination, particularly when the contaminant metals are essential elements that are subject to homeostasis or have a close biochemical analog. Stimulating the development of microbially reducing conditions, for example in constructed wetlands, is beneficial for remediating many metals associated with mine wastes. It has been shown to be effective at low pH, circumneutral and high pH conditions in the laboratory and at pilot field-scale. Further demonstration of this technology at full field-scale is required, as is more research to optimize bioremediation and to investigate combined remediation strategies. Microbial activity has the potential to mitigate the impacts of metal mine wastes, and therefore lessen the impact of this pollution on planetary health.
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Affiliation(s)
- Laura Newsome
- Camborne School of Mines and Environment and Sustainability InstituteUniversity of ExeterPenrynUK
| | - Carmen Falagán
- Camborne School of Mines and Environment and Sustainability InstituteUniversity of ExeterPenrynUK
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Kotsyurbenko OR, Cordova JA, Belov AA, Cheptsov VS, Kölbl D, Khrunyk YY, Kryuchkova MO, Milojevic T, Mogul R, Sasaki S, Słowik GP, Snytnikov V, Vorobyova EA. Exobiology of the Venusian Clouds: New Insights into Habitability through Terrestrial Models and Methods of Detection. ASTROBIOLOGY 2021; 21:1186-1205. [PMID: 34255549 PMCID: PMC9545807 DOI: 10.1089/ast.2020.2296] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 04/16/2021] [Indexed: 06/13/2023]
Abstract
The search for life beyond Earth has focused on Mars and the icy moons Europa and Enceladus, all of which are considered a safe haven for life due to evidence of current or past water. The surface of Venus, on the other hand, has extreme conditions that make it a nonhabitable environment to life as we know it. This is in contrast, however, to its cloud layer, which, while still an extreme environment, may prove to be a safe haven for some extreme forms of life similar to extremophiles on Earth. We consider the venusian clouds a habitable environment based on the presence of (1) a solvent for biochemical reactions, (2) appropriate physicochemical conditions, (3) available energy, and (4) biologically relevant elements. The diversity of extreme microbial ecosystems on Earth has allowed us to identify terrestrial chemolithoautotrophic microorganisms that may be analogs to putative venusian organisms. Here, we hypothesize and describe biological processes that may be performed by such organisms in the venusian clouds. To detect putative venusian organisms, we describe potential biosignature detection methods, which include metal-microbial interactions and optical methods. Finally, we describe currently available technology that can potentially be used for modeling and simulation experiments.
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Affiliation(s)
- Oleg R. Kotsyurbenko
- Yugra State University, The Institute of Oil and Gas, School of Ecology, Khanty-Mansiysk, Russian Federation
- Network of Researchers on the Chemical Evolution of Life, Leeds, UK
| | - Jaime A. Cordova
- Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin, USA
| | - Andrey A. Belov
- Network of Researchers on the Chemical Evolution of Life, Leeds, UK
- Moscow State University, Faculty of Soil Science, Moscow, Russian Federation
| | - Vladimir S. Cheptsov
- Network of Researchers on the Chemical Evolution of Life, Leeds, UK
- Moscow State University, Faculty of Soil Science, Moscow, Russian Federation
- Space Research Institute, Russian Academy of Sciences, Moscow, Russian Federation
| | - Denise Kölbl
- Space Biochemistry Group, Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
| | - Yuliya Y. Khrunyk
- Department of Heat Treatment and Physics of Metal, Ural Federal University, Ekaterinburg, Russian Federation
- M.N. Mikheev Institute of Metal Physics of the Ural Branch of the Russian Academy of Sciences, Ekaterinburg, Russian Federation
| | - Margarita O. Kryuchkova
- Network of Researchers on the Chemical Evolution of Life, Leeds, UK
- Moscow State University, Faculty of Soil Science, Moscow, Russian Federation
| | - Tetyana Milojevic
- Space Biochemistry Group, Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
| | - Rakesh Mogul
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, California, USA
| | - Satoshi Sasaki
- School of Biosciences and Biotechnology/School of Health Sciences, Tokyo University of Technology, Hachioji, Tokyo, Japan
| | - Grzegorz P. Słowik
- Institute of Materials and Biomedical Engineering, Faculty of Mechanical Engineering, University of Zielona Góra, Zielona Góra, Poland
| | - Valery Snytnikov
- Boreskov Institute of Catalysis, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
- Novosibirsk State University, Novosibirsk, Russian Federation
| | - Elena A. Vorobyova
- Network of Researchers on the Chemical Evolution of Life, Leeds, UK
- Moscow State University, Faculty of Soil Science, Moscow, Russian Federation
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24
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Blake RC, Nautiyal A, Smith KA, Walton NN, Pendleton B, Wang Z. Ferrimicrobium acidiphilum Exchanges Electrons With a Platinum Electrode via a Cytochrome With Reduced Absorbance Maxima at 448 and 605 nm. Front Microbiol 2021; 12:705187. [PMID: 34381433 PMCID: PMC8350767 DOI: 10.3389/fmicb.2021.705187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 07/02/2021] [Indexed: 01/22/2023] Open
Abstract
Ferrimicrobium acidiphilum is a Gram-positive member of the Actinobacteria phylum that can respire aerobically or anaerobically with soluble Fe(II) or Fe(III), respectively, in sulfuric acid at pH 1.5. Cyclic voltammetry measurements using intact F. acidiphilum at pH 1.5 produced fully reversible voltammograms that were highly reproducible. The maximum current observed with the anodic peak was considerably less than was the maximum current observed with the cathodic peak. This difference was attributed to the competition between the platinum electrode and the soluble oxygen for the available electrons that were introduced by the cathodic wave into this facultative aerobic organism. The standard reduction potential of the intact organism was determined to be 786 mV vs. the standard hydrogen electrode, slightly more positive than that of 735 mV that was determined for soluble iron at pH 1.5 using the same apparatus. Chronocoulometry measurements conducted at different cell densities revealed that the intact organism remained in close proximity to the working electrode during the measurement, whereas soluble ionic iron did not. When the cyclic voltammetry of intact F. acidiphilum was monitored using an integrating cavity absorption meter, the only small changes in absorbance that were detected were consistent with the participation of a cellular cytochrome with reduced absorbance peaks at 448 and 605 nm. The cytochrome that participated in the exchange of electrons between the intact organism and extracellular solid electrodes like platinum was the same cytochrome whose oxidation was previously shown to be rate-limiting when the organism respired aerobically on extracellular soluble iron.
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Affiliation(s)
- Robert C Blake
- Division of Basic Pharmaceutical Sciences, College of Pharmacy, Xavier University of Louisiana, New Orleans, LA, United States
| | - Amit Nautiyal
- Department of Chemistry, Xavier University of Louisiana, New Orleans, LA, United States
| | - Kayla A Smith
- Division of Basic Pharmaceutical Sciences, College of Pharmacy, Xavier University of Louisiana, New Orleans, LA, United States
| | - Noelle N Walton
- Division of Basic Pharmaceutical Sciences, College of Pharmacy, Xavier University of Louisiana, New Orleans, LA, United States
| | - Brealand Pendleton
- Division of Basic Pharmaceutical Sciences, College of Pharmacy, Xavier University of Louisiana, New Orleans, LA, United States
| | - Zhe Wang
- Department of Chemistry, Oakland University, Rochester, NY, United States
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25
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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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26
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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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27
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Yi Q, Wu S, Southam G, Robertson L, You F, Liu Y, Wang S, Saha N, Webb R, Wykes J, Chan TS, Lu YR, Huang L. Acidophilic Iron- and Sulfur-Oxidizing Bacteria, Acidithiobacillus ferrooxidans, Drives Alkaline pH Neutralization and Mineral Weathering in Fe Ore Tailings. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:8020-8034. [PMID: 34043324 DOI: 10.1021/acs.est.1c00848] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The neutralization of strongly alkaline pH conditions and acceleration of mineral weathering in alkaline Fe ore tailings have been identified as key prerequisites for eco-engineering tailings-soil formation for sustainable mine site rehabilitation. Acidithiobacillus ferrooxidans has great potential in neutralizing alkaline pH and accelerating primary mineral weathering in the tailings but little information is available. This study aimed to investigate the colonization of A. ferrooxidans in alkaline Fe ore tailings and its role in elemental sulfur (S0) oxidation, tailings neutralization, and Fe-bearing mineral weathering through a microcosm experiment. The effects of biological S0 oxidation on the weathering of alkaline Fe ore tailings were examined via various microspectroscopic analyses. It is found that (1) the A. ferrooxidans inoculum combined with the S0 amendment rapidly neutralized the alkaline Fe ore tailings; (2) A. ferrooxidans activities induced Fe-bearing primary mineral (e.g., biotite) weathering and secondary mineral (e.g., ferrihydrite and jarosite) formation; and (3) the association between bacterial cells and tailings minerals were likely facilitated by extracellular polymeric substances (EPS). The behavior and biogeochemical functionality of A. ferrooxidans in the tailings provide a fundamental basis for developing microbial-based technologies toward eco-engineering soil formation in Fe ore tailings.
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Affiliation(s)
- Qing Yi
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane 4072, Australia
- Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang 050061, China
- The Key Laboratory of Groundwater Pollution Mechanism and Remediation, China Geological Survey and Hebei Province, Shijiazhuang 050061, China
| | - Songlin Wu
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane 4072, Australia
| | - Gordon Southam
- School of Earth & Environmental Sciences, The University of Queensland, Brisbane 4072, Australia
| | - Lachlan Robertson
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane 4072, Australia
| | - Fang You
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane 4072, Australia
| | - Yunjia Liu
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane 4072, Australia
| | - Sicheng Wang
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane 4072, Australia
| | - Narottam Saha
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane 4072, Australia
| | - Richard Webb
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane 4072, Australia
| | - Jeremy Wykes
- Australian Synchrotron, Melbourne, Victoria 3168, Australia
| | - Ting-Shan Chan
- National Synchrotron Radiation Research Centre, Hsinchu Science Park, Hsinchu 300, Taiwan
| | - Ying-Rui Lu
- National Synchrotron Radiation Research Centre, Hsinchu Science Park, Hsinchu 300, Taiwan
| | - Longbin Huang
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane 4072, Australia
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28
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Abstract
In recent years, the tree of life has expanded substantially. Despite this, many abundant yet uncultivated microbial groups remain to be explored. Sumerlaeota is a mysterious, putative phylum-level lineage distributed globally but rarely reported. As such, their physiology, ecology, and evolutionary history remain unknown. The 16S rRNA gene survey reveals that Sumerlaeota is frequently detected in diverse environments globally, especially cold arid desert soils and deep-sea basin surface sediments, where it is one dominant microbial group. Here, we retrieved four Sumerlaeota metagenome-assembled genomes (MAGs) from two hot springs and one saline lake. Including another 12 publicly available MAGs, they represent six of the nine putative Sumerlaeota subgroups/orders, as indicated by 16S rRNA gene-based phylogeny. These elusive organisms likely obtain carbon mainly through utilization of refractory organics (e.g., chitin and cellulose) and proteinaceous compounds, suggesting that Sumerlaeota act as scavengers in nature. The presence of key bidirectional enzymes involved in acetate and hydrogen metabolisms in these MAGs suggests that they are acetogenic bacteria capable of both the production and consumption of hydrogen. The capabilities of dissimilatory nitrate and sulfate reduction, nitrogen fixation, phosphate solubilization, and organic phosphorus mineralization may confer these heterotrophs great advantages to thrive under diverse harsh conditions. Ancestral state reconstruction indicated that Sumerlaeota originated from chemotrophic and facultatively anaerobic ancestors, and their smaller and variably sized genomes evolved along dynamic pathways from a sizeable common ancestor (2,342 genes), leading to their physiological divergence. Notably, large gene gain and larger loss events occurred at the branch to the last common ancestor of the order subgroup 1, likely due to niche expansion and population size effects.
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29
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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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30
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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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31
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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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32
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Sajjad W, Zheng G, Ma X, Xu W, Ali B, Rafiq M, Zada S, Irfan M, Zeman J. Dissolution of Cu and Zn-bearing ore by indigenous iron-oxidizing bacterial consortia supplemented with dried bamboo sawdust and variations in bacterial structural dynamics: A new concept in bioleaching. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 709:136136. [PMID: 31884267 DOI: 10.1016/j.scitotenv.2019.136136] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 11/19/2019] [Accepted: 12/14/2019] [Indexed: 06/10/2023]
Abstract
Disposing of low-grade ores involves numerous environmental issues. Bioleaching with acidophilic bacteria is the preferred solution to process these ores for metals recovery. In this study, indigenous iron-oxidizing bacteria Acidithiobacillus ferrooxidans, Leptospirillum ferriphilum, and Leptospirillum ferrooxidans were used in consortia supplemented with acid-treated bamboo sawdust (BSD) for copper and zinc recovery. Findings showed the extreme catalytic response of BSD with the best recovery of metals. Maximum of 92.2 ± 4.0% copper (0.35%) and 90.0 ± 5.4% zinc (0.33%) were recovered after 8 days of processing in the presence of 2 g/L BSD. Significant variations were reported in physicochemical parameters during bioleaching in the presence of a different concentration of BSD. Fourier Transform Infrared spectroscopy results of bioleached residues showed significant variations in spectral pattern and maximum variations were reported in 2.0 g/L BSD, which indicates maximum metals dissolutions. The impact of bacterial consortia and BSD on iron speciation of bioleached ores was analyzed by using Mössbauer spectroscopy and clear variations in iron speciation were reported. Furthermore, the bacterial community structure dynamics revealed significant variations in the individual bacterial proportion in each experiment. This finding shows that the dosage concentration of BSD influenced the microenvironment, which effect the bacterial abundance and these variations in the bacterial structural communities were not associated with the initial proportion of bacterial cells inoculated in the bioleaching process. Moreover, the mechanism of chemical reactions was proposed by explaining the possible role of BSD as a reductant under micro-aerophilic conditions that facilitates the bacterial reduction of ferric iron. This type of bioleaching process with indigenous iron-oxidizing bacteria and BSD has significant potential to further upscale the bioleaching process for recalcitrant ore bodies in an environment friendly and cost-effective way.
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Affiliation(s)
- Wasim Sajjad
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; Key Laboratory of Petroleum Resources, Gansu Province, Lanzhou 730000, China; State Key Laboratory of Cryosphere Science, Northwest Institute of Eco-Environment and Resources, University of Chinese Academy of Sciences, Lanzhou, China
| | - Guodong Zheng
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; Key Laboratory of Petroleum Resources, Gansu Province, Lanzhou 730000, China.
| | - Xiangxian Ma
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; Key Laboratory of Petroleum Resources, Gansu Province, Lanzhou 730000, China
| | - Wang Xu
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; Key Laboratory of Petroleum Resources, Gansu Province, Lanzhou 730000, China
| | - Barkat Ali
- State Key Laboratory of Cryosphere Science, Northwest Institute of Eco-Environment and Resources, University of Chinese Academy of Sciences, Lanzhou, China
| | - Muhammad Rafiq
- Department of Microbiology, Faculty of Life Sciences and Informatics, Balochistan University of IT, Engineering and Management Sciences, Quetta, Pakistan
| | - Sahib Zada
- Department of Biology, College of Science, Shantou University, Shantou, China
| | - Muhammad Irfan
- Department of Microbiology and Cell Science Genetics Institute and Institute of Food and Agricultural Science, University of Florida, Gainesville, FL, United States of America
| | - Josef Zeman
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; Key Laboratory of Petroleum Resources, Gansu Province, Lanzhou 730000, China; Department of Geological Sciences, Faculty of Science, Masaryk University, Kotlářská 267/2, 611 37 Brno, Czech Republic
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Molecular Mechanisms Underpinning Aggregation in Acidiphilium sp. C61 Isolated from Iron-Rich Pelagic Aggregates. Microorganisms 2020; 8:microorganisms8030314. [PMID: 32106516 PMCID: PMC7142476 DOI: 10.3390/microorganisms8030314] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/21/2020] [Accepted: 02/23/2020] [Indexed: 12/04/2022] Open
Abstract
Iron-rich pelagic aggregates (iron snow) are hot spots for microbial interactions. Using iron snow isolates, we previously demonstrated that the iron-oxidizer Acidithrix sp. C25 triggers Acidiphilium sp. C61 aggregation by producing the infochemical 2-phenethylamine (PEA). Here, we showed slightly enhanced aggregate formation in the presence of PEA on different Acidiphilium spp. but not other iron-snow microorganisms, including Acidocella sp. C78 and Ferrovum sp. PN-J47. Next, we sequenced the Acidiphilium sp. C61 genome to reconstruct its metabolic potential. Pangenome analyses of Acidiphilium spp. genomes revealed the core genome contained 65 gene clusters associated with aggregation, including autoaggregation, motility, and biofilm formation. Screening the Acidiphilium sp. C61 genome revealed the presence of autotransporter, flagellar, and extracellular polymeric substances (EPS) production genes. RNA-seq analyses of Acidiphilium sp. C61 incubations (+/− 10 µM PEA) indicated genes involved in energy production, respiration, and genetic processing were the most upregulated differentially expressed genes in the presence of PEA. Additionally, genes involved in flagellar basal body synthesis were highly upregulated, whereas the expression pattern of biofilm formation-related genes was inconclusive. Our data shows aggregation is a common trait among Acidiphilium spp. and PEA stimulates the central cellular metabolism, potentially advantageous in aggregates rapidly falling through the water column.
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Panyushkina AE, Babenko VV, Nikitina AS, Selezneva OV, Tsaplina IA, Letarova MA, Kostryukova ES, Letarov AV. Sulfobacillus thermotolerans: new insights into resistance and metabolic capacities of acidophilic chemolithotrophs. Sci Rep 2019; 9:15069. [PMID: 31636299 PMCID: PMC6803676 DOI: 10.1038/s41598-019-51486-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 09/23/2019] [Indexed: 11/09/2022] Open
Abstract
The first complete genome of the biotechnologically important species Sulfobacillus thermotolerans has been sequenced. Its 3 317 203-bp chromosome contains an 83 269-bp plasmid-like region, which carries heavy metal resistance determinants and the rusticyanin gene. Plasmid-mediated metal resistance is unusual for acidophilic chemolithotrophs. Moreover, most of their plasmids are cryptic and do not contribute to the phenotype of the host cells. A polyphosphate-based mechanism of metal resistance, which has been previously unknown in the genus Sulfobacillus or other Gram-positive chemolithotrophs, potentially operates in two Sulfobacillus species. The methylcitrate cycle typical for pathogens and identified in the genus Sulfobacillus for the first time can fulfill the energy and/or protective function in S. thermotolerans Kr1 and two other Sulfobacillus species, which have incomplete glyoxylate cycles. It is notable that the TCA cycle, disrupted in all Sulfobacillus isolates under optimal growth conditions, proved to be complete in the cells enduring temperature stress. An efficient antioxidant defense system gives S. thermotolerans another competitive advantage in the microbial communities inhabiting acidic metal-rich environments. The genomic comparisons revealed 80 unique genes in the strain Kr1, including those involved in lactose/galactose catabolism. The results provide new insights into metabolism and resistance mechanisms in the Sulfobacillus genus and other acidophiles.
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Affiliation(s)
- Anna E Panyushkina
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, 119071, Russia.
| | - Vladislav V Babenko
- Federal Medical Biological Agency, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia
| | - Anastasia S Nikitina
- Federal Medical Biological Agency, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia
| | - Oksana V Selezneva
- Federal Medical Biological Agency, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia
| | - Iraida A Tsaplina
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, 119071, Russia
| | - Maria A Letarova
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, 119071, Russia
| | - Elena S Kostryukova
- Federal Medical Biological Agency, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia
| | - Andrey V Letarov
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, 119071, Russia
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Slobodkin AI, Slobodkina GB. Diversity of Sulfur-Disproportionating Microorganisms. Microbiology (Reading) 2019. [DOI: 10.1134/s0026261719050138] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Tan S, Liu J, Fang Y, Hedlund BP, Lian ZH, Huang LY, Li JT, Huang LN, Li WJ, Jiang HC, Dong HL, Shu WS. Insights into ecological role of a new deltaproteobacterial order Candidatus Acidulodesulfobacterales by metagenomics and metatranscriptomics. THE ISME JOURNAL 2019; 13:2044-2057. [PMID: 30962514 PMCID: PMC6776010 DOI: 10.1038/s41396-019-0415-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 02/15/2019] [Accepted: 03/24/2019] [Indexed: 12/21/2022]
Abstract
Several abundant but yet uncultivated bacterial groups exist in extreme iron- and sulfur-rich environments, and the physiology, biodiversity, and ecological roles of these bacteria remain a mystery. Here we retrieved four metagenome-assembled genomes (MAGs) from an artificial acid mine drainage (AMD) system, and propose they belong to a new deltaproteobacterial order, Candidatus Acidulodesulfobacterales. The distribution pattern of Ca. Acidulodesulfobacterales in AMDs across Southeast China correlated strongly with ferrous iron. Reconstructed metabolic pathways and gene expression profiles showed that they were likely facultatively anaerobic autotrophs capable of nitrogen fixation. In addition to dissimilatory sulfate reduction, encoded by dsrAB, dsrD, dsrL, and dsrEFH genes, these microorganisms might also oxidize sulfide, depending on oxygen concentration and/or oxidation reduction potential. Several genes with homology to those involved in iron metabolism were also identified, suggesting their potential role in iron cycling. In addition, the expression of abundant resistance genes revealed the mechanisms of adaptation and response to the extreme environmental stresses endured by these organisms in the AMD environment. These findings shed light on the distribution, diversity, and potential ecological role of the new order Ca. Acidulodesulfobacterales in nature.
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Affiliation(s)
- Sha Tan
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Jun Liu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
- Department of Geology and Environmental Earth Science, Miami University, Oxford, OH, 45056, USA
| | - Yun Fang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Zheng-Han Lian
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
- Guangdong Magigene Biotechnology Co. Ltd., 510000, Guangzhou, China
| | - Li-Ying Huang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Jin-Tian Li
- School of Life Sciences, South China Normal University, 510631, Guangzhou, China
| | - Li-Nan Huang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Hong-Chen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
| | - Hai-Liang Dong
- Department of Geology and Environmental Earth Science, Miami University, Oxford, OH, 45056, USA.
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 100083, Beijing, China.
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, 510631, Guangzhou, China.
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Osorio H, Mettert E, Kiley P, Dopson M, Jedlicki E, Holmes DS. Identification and Unusual Properties of the Master Regulator FNR in the Extreme Acidophile Acidithiobacillus ferrooxidans. Front Microbiol 2019; 10:1642. [PMID: 31379789 PMCID: PMC6659574 DOI: 10.3389/fmicb.2019.01642] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/02/2019] [Indexed: 12/28/2022] Open
Abstract
The ability to conserve energy in the presence or absence of oxygen provides a metabolic versatility that confers an advantage in natural ecosystems. The switch between alternative electron transport systems is controlled by the fumarate nitrate reduction transcription factor (FNR) that senses oxygen via an oxygen-sensitive [4Fe-4S]2+ iron-sulfur cluster. Under O2 limiting conditions, FNR plays a key role in allowing bacteria to transition from aerobic to anaerobic lifestyles. This is thought to occur via transcriptional activation of genes involved in anaerobic respiratory pathways and by repression of genes involved in aerobic energy production. The Proteobacterium Acidithiobacillus ferrooxidans is a model species for extremely acidophilic microorganisms that are capable of aerobic and anaerobic growth on elemental sulfur coupled to oxygen and ferric iron reduction, respectively. In this study, an FNR-like protein (FNRAF) was discovered in At. ferrooxidans that exhibits a primary amino acid sequence and major motifs and domains characteristic of the FNR family of proteins, including an effector binding domain with at least three of the four cysteines known to coordinate an [4Fe-4S]2+ center, a dimerization domain, and a DNA binding domain. Western blotting with antibodies against Escherichia coli FNR (FNREC) recognized FNRAF. FNRAF was able to drive expression from the FNR-responsive E. coli promoter PnarG, suggesting that it is functionally active as an FNR-like protein. Upon air exposure, FNRAF demonstrated an unusual lack of sensitivity to oxygen compared to the archetypal FNREC. Comparison of the primary amino acid sequence of FNRAF with that of other natural and mutated FNRs, including FNREC, coupled with an analysis of the predicted tertiary structure of FNRAF using the crystal structure of the related FNR from Aliivibrio fisheri as a template revealed a number of amino acid changes that could potentially stabilize FNRAF in the presence of oxygen. These include a truncated N terminus and amino acid changes both around the putative Fe-S cluster coordinating cysteines and also in the dimer interface. Increased O2 stability could allow At. ferrooxidans to survive in environments with fluctuating O2 concentrations, providing an evolutionary advantage in natural, and engineered environments where oxygen gradients shape the bacterial community.
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Affiliation(s)
- Héctor Osorio
- Center for Bioinformatics and Genome Biology, Fundación Ciencia y Vida, Santiago, Chile
| | - Erin Mettert
- Department of Biomolecular Chemistry, University of Wisconsin–Madison, Madison, WI, United States
| | - Patricia Kiley
- Department of Biomolecular Chemistry, University of Wisconsin–Madison, Madison, WI, United States
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Eugenia Jedlicki
- Center for Bioinformatics and Genome Biology, Fundación Ciencia y Vida, Santiago, Chile
| | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Fundación Ciencia y Vida, Santiago, Chile
- Universidad San Sebastian, Santiago, Chile
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
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Esparza M, Jedlicki E, González C, Dopson M, Holmes DS. Effect of CO 2 Concentration on Uptake and Assimilation of Inorganic Carbon in the Extreme Acidophile Acidithiobacillus ferrooxidans. Front Microbiol 2019; 10:603. [PMID: 31019493 PMCID: PMC6458275 DOI: 10.3389/fmicb.2019.00603] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 03/11/2019] [Indexed: 02/01/2023] Open
Abstract
This study was motivated by surprising gaps in the current knowledge of microbial inorganic carbon (Ci) uptake and assimilation at acidic pH values (pH < 3). Particularly striking is the limited understanding of the differences between Ci uptake mechanisms in acidic versus circumneutral environments where the Ci predominantly occurs either as a dissolved gas (CO2) or as bicarbonate (HCO3 -), respectively. In order to gain initial traction on the problem, the relative abundance of transcripts encoding proteins involved in Ci uptake and assimilation was studied in the autotrophic, polyextreme acidophile Acidithiobacillus ferrooxidans whose optimum pH for growth is 2.5 using ferrous iron as an energy source, although they are able to grow at pH 5 when using sulfur as an energy source. The relative abundance of transcripts of five operons (cbb1-5) and one gene cluster (can-sulP) was monitored by RT-qPCR and, in selected cases, at the protein level by Western blotting, when cells were grown under different regimens of CO2 concentration in elemental sulfur. Of particular note was the absence of a classical bicarbonate uptake system in A. ferrooxidans. However, bioinformatic approaches predict that sulP, previously annotated as a sulfate transporter, is a novel type of bicarbonate transporter. A conceptual model of CO2 fixation was constructed from combined bioinformatic and experimental approaches that suggests strategies for providing ecological flexibility under changing concentrations of CO2 and provides a portal to elucidating Ci uptake and regulation in acidic conditions. The results could advance the understanding of industrial bioleaching processes to recover metals such as copper at acidic pH. In addition, they may also shed light on how chemolithoautotrophic acidophiles influence the nutrient and energy balance in naturally occurring low pH environments.
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Affiliation(s)
- Mario Esparza
- Laboratorio de Biominería, Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Eugenia Jedlicki
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago, Chile
| | - Carolina González
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago, Chile
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago, Chile
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
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Song X, Yang W, Lin Z, Huang L, Quan X. A loop of catholyte effluent feeding to bioanodes for complete recovery of Sn, Fe, and Cu with simultaneous treatment of the co-present organics in microbial fuel cells. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 651:1698-1708. [PMID: 30317169 DOI: 10.1016/j.scitotenv.2018.10.089] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 09/25/2018] [Accepted: 10/07/2018] [Indexed: 06/08/2023]
Abstract
A loop of catholyte effluent feeding to the bioanodes of air-cathode microbial fuel cells (MFCs) achieved complete recovery of mixed Sn(II), Fe(II) and Cu(II), with simultaneous treatment of the co-present organics in synthetic wastewater of printed circuit boards (PrCBs). This in-situ utilization of caustic in the cathodes and the neutralization of acid in the anodes achieved superior metal recovery performance at an optimal hydraulic retention time (HRT) of 24 h. Cathode chambers primarily removed Sn of 91 ± 4% (bottom: 74 ± 3%; electrode: 17 ± 1%), Fe of 89 ± 8% (bottom: 64 ± 4%; electrode: 25 ± 2%), and Cu of 92 ± 7% (electrode: 63 ± 5%; bottom: 29 ± 1%), compared to Sn of 9 ± 3% (electrode: 7 ± 1%; bottom: 2 ± 1%), Fe of 9 ± 3% (electrode: 8 ± 3%; bottom: 1 ± 0%), and Cu of 7 ± 3% (electrode: 4 ± 1%; bottom: 3 ± 1%) in the bioanodes. Bacterial communities on the anodes were well evolutionarily developed after the feeding of catholyte effluent, with the increase in abundance of Rhodopseudomonas and Geobacter, and the shift from Thiobacillus and Acinetobacter to Pseudomonas, Comamonas, Aeromonas and Azospira. This loop of cathodic effluent feeding to the bioanodes of MFCs may represent a unique method for complete metal recovery with simultaneous extraction of renewable electrical energy from the co-present organics. This study also offers new insights into the development of compact microbial electro-metallurgical processes for simultaneous recovery of value-added products from PrCBs processing wastewaters and accomplishing the national wastewater discharge standard for both metals and organics.
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Affiliation(s)
- Xu Song
- Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Wulin Yang
- Department of Civil and Environmental Engineering, The Pennsylvania State University, University Park, PA 16802, United States of America
| | - Zheqian Lin
- Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Liping Huang
- Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China.
| | - Xie Quan
- Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
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Tanabe TS, Leimkühler S, Dahl C. The functional diversity of the prokaryotic sulfur carrier protein TusA. Adv Microb Physiol 2019; 75:233-277. [PMID: 31655739 DOI: 10.1016/bs.ampbs.2019.07.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Persulfide groups participate in a wide array of biochemical pathways and are chemically very versatile. The TusA protein has been identified as a central element supplying and transferring sulfur as persulfide to a number of important biosynthetic pathways, like molybdenum cofactor biosynthesis or thiomodifications in nucleosides of tRNAs. In recent years, it has furthermore become obvious that this protein is indispensable for the oxidation of sulfur compounds in the cytoplasm. Phylogenetic analyses revealed that different TusA protein variants exists in certain organisms, that have evolved to pursue specific roles in cellular pathways. The specific TusA-like proteins thereby cannot replace each other in their specific roles and are rather specific to one sulfur transfer pathway or shared between two pathways. While certain bacteria like Escherichia coli contain several copies of TusA-like proteins, in other bacteria like Allochromatium vinosum a single copy of TusA is present with an essential role for this organism. Here, we give an overview on the multiple roles of the various TusA-like proteins in sulfur transfer pathways in different organisms to shed light on the remaining mysteries of this versatile protein.
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Sajjad W, Zheng G, Ma X, Rafiq M, Irfan M, Xu W, Ali B. Culture-dependent hunt and characterization of iron-oxidizing bacteria in Baiyin Copper Mine, China, and their application in metals extraction. J Basic Microbiol 2018; 59:323-336. [DOI: 10.1002/jobm.201800433] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 11/01/2018] [Accepted: 11/30/2018] [Indexed: 11/07/2022]
Affiliation(s)
- Wasim Sajjad
- Key Laboratory of Petroleum Resources; Gansu Province/Key Laboratory of Petroleum Resources Research; Institute of Geology and Geophysics; Chinese Academy of Sciences; Lanzhou PR China
- University of Chinese Academy of Sciences; Beijing PR China
| | - Guodong Zheng
- Key Laboratory of Petroleum Resources; Gansu Province/Key Laboratory of Petroleum Resources Research; Institute of Geology and Geophysics; Chinese Academy of Sciences; Lanzhou PR China
| | - Xiangxian Ma
- Key Laboratory of Petroleum Resources; Gansu Province/Key Laboratory of Petroleum Resources Research; Institute of Geology and Geophysics; Chinese Academy of Sciences; Lanzhou PR China
| | - Muhammad Rafiq
- Bristol Glaciology Centre; School of Geographical Sciences; Faculty of Sciences; University of Bristol; Bristol United Kingdom
| | - Muhammad Irfan
- Department of Microbiology and Cell Science Genetics Institute and Institute of Food and Agricultural Science University of Florida; Gainesville Florida
| | - Wang Xu
- Key Laboratory of Petroleum Resources; Gansu Province/Key Laboratory of Petroleum Resources Research; Institute of Geology and Geophysics; Chinese Academy of Sciences; Lanzhou PR China
- University of Chinese Academy of Sciences; Beijing PR China
| | - Barkat Ali
- University of Chinese Academy of Sciences; Beijing PR China
- State Key Laboratory of Cryosphere Science; Northwest Institute of Eco-Environment and Resources; University of Chinese Academy of Sciences; Lanzhou PR China
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42
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Ni G, Simone D, Palma D, Broman E, Wu X, Turner S, Dopson M. A Novel Inorganic Sulfur Compound Metabolizing Ferroplasma-Like Population Is Suggested to Mediate Extracellular Electron Transfer. Front Microbiol 2018; 9:2945. [PMID: 30568637 PMCID: PMC6289977 DOI: 10.3389/fmicb.2018.02945] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 11/16/2018] [Indexed: 11/13/2022] Open
Abstract
Mining and processing of metal sulfide ores produces waters containing metals and inorganic sulfur compounds such as tetrathionate and thiosulfate. If released untreated, these sulfur compounds can be oxidized to generate highly acidic wastewaters [termed ‘acid mine drainage (AMD)’] that cause severe environmental pollution. One potential method to remediate mining wastewaters is the maturing biotechnology of ‘microbial fuel cells’ that offers the sustainable removal of acid generating inorganic sulfur compounds alongside producing an electrical current. Microbial fuel cells exploit the ability of bacterial cells to transfer electrons to a mineral as the terminal electron acceptor during anaerobic respiration by replacing the mineral with a solid anode. In consequence, by substituting natural minerals with electrodes, microbial fuel cells also provide an excellent platform to understand environmental microbe–mineral interactions that are fundamental to element cycling. Previously, tetrathionate degradation coupled to the generation of an electrical current has been demonstrated and here we report a metagenomic and metatranscriptomic analysis of the microbial community. Reconstruction of inorganic sulfur compound metabolism suggested the substrate tetrathionate was metabolized by the Ferroplasma-like and Acidithiobacillus-like populations via multiple pathways. Characterized Ferroplasma species do not utilize inorganic sulfur compounds, suggesting a novel Ferroplasma-like population had been selected. Oxidation of intermediate sulfide, sulfur, thiosulfate, and adenylyl-sulfate released electrons and the extracellular electron transfer to the anode was suggested to be dominated by candidate soluble electron shuttles produced by the Ferroplasma-like population. However, as the soluble electron shuttle compounds also have alternative functions within the cell, it cannot be ruled out that acidophiles use novel, uncharacterized mechanisms to mediate extracellular electron transfer. Several populations within the community were suggested to metabolize intermediate inorganic sulfur compounds by multiple pathways, which highlights the potential for mutualistic or symbiotic relationships. This study provided the genetic base for acidophilic microbial fuel cells utilized for the remediation of inorganic sulfur compounds from AMD.
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Affiliation(s)
- Gaofeng Ni
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Domenico Simone
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Daniela Palma
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Elias Broman
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Xiaofen Wu
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Stephanie Turner
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
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Ni G, Canizales S, Broman E, Simone D, Palwai VR, Lundin D, Lopez-Fernandez M, Sleutels T, Dopson M. Microbial Community and Metabolic Activity in Thiocyanate Degrading Low Temperature Microbial Fuel Cells. Front Microbiol 2018; 9:2308. [PMID: 30323799 PMCID: PMC6172326 DOI: 10.3389/fmicb.2018.02308] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 09/10/2018] [Indexed: 11/25/2022] Open
Abstract
Thiocyanate is a toxic compound produced by the mining and metallurgy industries that needs to be remediated prior to its release into the environment. If the industry is situated at high altitudes or near the poles, economic factors require a low temperature treatment process. Microbial fuel cells are a developing technology that have the benefits of both removing such toxic compounds while recovering electrical energy. In this study, simultaneous thiocyanate degradation and electrical current generation was demonstrated and it was suggested that extracellular electron transfer to the anode occurred. Investigation of the microbial community by 16S rRNA metatranscriptome reads supported that the anode attached and planktonic anolyte consortia were dominated by a Thiobacillus-like population. Metatranscriptomic sequencing also suggested thiocyanate degradation primarily occurred via the ‘cyanate’ degradation pathway. The generated sulfide was metabolized via sulfite and ultimately to sulfate mediated by reverse dissimilatory sulfite reductase, APS reductase, and sulfate adenylyltransferase and the released electrons were potentially transferred to the anode via soluble electron shuttles. Finally, the ammonium from thiocyanate degradation was assimilated to glutamate as nitrogen source and carbon dioxide was fixed as carbon source. This study is one of the first to demonstrate a low temperature inorganic sulfur utilizing microbial fuel cell and the first to provide evidence for pathways of thiocyanate degradation coupled to electron transfer.
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Affiliation(s)
- Gaofeng Ni
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Sebastian Canizales
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Elias Broman
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Domenico Simone
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Viraja R Palwai
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Daniel Lundin
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Margarita Lopez-Fernandez
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Tom Sleutels
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, Netherlands
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
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44
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Vuillemin A, Horn F, Friese A, Winkel M, Alawi M, Wagner D, Henny C, Orsi WD, Crowe SA, Kallmeyer J. Metabolic potential of microbial communities from ferruginous sediments. Environ Microbiol 2018; 20:4297-4313. [PMID: 29968357 DOI: 10.1111/1462-2920.14343] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/22/2018] [Accepted: 06/25/2018] [Indexed: 01/22/2023]
Abstract
Ferruginous (Fe-rich, SO4 -poor) conditions are generally restricted to freshwater sediments on Earth today, but were likely widespread during the Archean and Proterozoic Eons. Lake Towuti, Indonesia, is a large ferruginous lake that likely hosts geochemical processes analogous to those that operated in the ferruginous Archean ocean. The metabolic potential of microbial communities and related biogeochemical cycling under such conditions remain largely unknown. We combined geochemical measurements (pore water chemistry, sulfate reduction rates) with metagenomics to link metabolic potential with geochemical processes in the upper 50 cm of sediment. Microbial diversity and quantities of genes for dissimilatory sulfate reduction (dsrAB) and methanogenesis (mcrA) decrease with increasing depth, as do rates of potential sulfate reduction. The presence of taxa affiliated with known iron- and sulfate-reducers implies potential use of ferric iron and sulfate as electron acceptors. Pore-water concentrations of acetate imply active production through fermentation. Fermentation likely provides substrates for respiration with iron and sulfate as electron donors and for methanogens that were detected throughout the core. The presence of ANME-1 16S and mcrA genes suggests potential for anaerobic methane oxidation. Overall our data suggest that microbial community metabolism in anoxic ferruginous sediments support coupled Fe, S and C biogeochemical cycling.
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Affiliation(s)
- Aurèle Vuillemin
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3: Geomicrobiology, Potsdam, Germany.,Department of Earth & Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Fabian Horn
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3: Geomicrobiology, Potsdam, Germany
| | - André Friese
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3: Geomicrobiology, Potsdam, Germany
| | - Matthias Winkel
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3: Geomicrobiology, Potsdam, Germany
| | - Mashal Alawi
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3: Geomicrobiology, Potsdam, Germany
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3: Geomicrobiology, Potsdam, Germany.,University of Potsdam, Faculty of Mathematics and Natural Sciences, Institute of Earth and Environmental Sciences, Potsdam, Germany
| | - Cynthia Henny
- Research Center for Limnology (LIPI), Indonesian Institute of Sciences, Division of Inland Waterways Dynamics, Cibinong-Bogor, Indonesia
| | - William D Orsi
- Department of Earth & Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany.,Geobio-CenterLMU, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sean A Crowe
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada.,Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, Canada
| | - Jens Kallmeyer
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3: Geomicrobiology, Potsdam, Germany
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45
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Morrison C, Heitmann E, Armiger W, Dodds D, Koffas M. Electrochemical Bioreactor Technology for Biocatalysis and Microbial Electrosynthesis. ADVANCES IN APPLIED MICROBIOLOGY 2018; 105:51-86. [PMID: 30342723 DOI: 10.1016/bs.aambs.2018.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Two seemingly distinct fields, industrial biocatalysis and microbial electrosynthesis, can be viewed together through the lens of electrochemical bioreactor technology in order to highlight the challenges that exist in creating a versatile platform technology for use in chemical and biological applications. Industrial biocatalysis applications requiring NAD(P)H to perform redox transformations often necessitate convoluted coupled-enzyme regeneration systems to regenerate reduced cofactor, NAD(P)H from oxidized cofactor, NAD(P). Renewed interest in continuously recycling the cofactor via electrochemical reduction is motivated by the low cost of performing electrochemical reactions, easy monitoring of the reaction progress, and straightforward product recovery. However, electrochemical cofactor regeneration methods invariably produce adventitious reduced cofactor side products which result in unproductive loss of input NAD(P). Microbial electrosynthesis is a form of microbially driven catalysis in which electricity is supplied to living microorganisms for the production of industrially relevant chemical products at higher carbon efficiencies and yields compared with traditional, nonelectrically driven, fermentations. The fundamental biochemistry of these organisms as related to selected biochemical redox processes will be explored in order to highlight opportunities to devise strategies for taking advantage of these biochemical processes in engineered systems.
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Affiliation(s)
- Clifford Morrison
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Elizabeth Heitmann
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, United States
| | | | - David Dodds
- BioChemInsights, Inc., Malvern, PA, United States
| | - Mattheos Koffas
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, United States; Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, United States
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46
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Tufo AE, Porzionato NF, Curutchet G. Effects of pollution and bioleaching process on the mineral composition and texture of contaminated sediments of the Reconquista River, Argentina. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:21368-21384. [PMID: 29090439 DOI: 10.1007/s11356-017-0484-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 10/16/2017] [Indexed: 06/07/2023]
Abstract
In this work, we report on the structural and textural changes in fluvial sediments from Reconquista River´s basin, Argentina, due to processes of contamination with organic matter and remediation by bioleaching. The original uncontaminated matrix showed quartz and phyllosilicates as the main primary mineral constituents and phases of interstratified illite-montmorillonite as secondary minerals. It was found that in contaminated sediments, the presence of organic matter in high concentration causes changes in the specific surface area, particle size distribution, size and distribution of micro and meso, and the morphology of the particles with respect to the uncontaminated sediment. After the bioleaching process, there were even greater changes in these parameters at the level of secondary mineral formation and the appearance of nanoparticles, which were confirmed by SEM. Especially, we found the formation of cementing substances such as gypsum, promoting the formation of macroporous aggregates and the weathering of clay components. Our results indicate that the bioleaching not only decreases the content of metals but also favors the formation of a material with improved characteristics for potential future applications.
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Affiliation(s)
- Ana E Tufo
- Instituto de Investigación e Ingeniería Ambiental, and Escuela de Ciencia y Tecnología, Universidad Nacional de San Martín, Campus Miguelete 25 de Mayo y Francia, San Martín, Provincia de Buenos Aires, Argentina
| | - Natalia F Porzionato
- Instituto de Investigación e Ingeniería Ambiental, and Escuela de Ciencia y Tecnología, Universidad Nacional de San Martín, Campus Miguelete 25 de Mayo y Francia, San Martín, Provincia de Buenos Aires, Argentina
| | - Gustavo Curutchet
- Instituto de Investigación e Ingeniería Ambiental, and Escuela de Ciencia y Tecnología, Universidad Nacional de San Martín, Campus Miguelete 25 de Mayo y Francia, San Martín, Provincia de Buenos Aires, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas, Rivadavia, 1917, Buenos Aires, Argentina.
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47
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Bioleaching of copper- and zinc-bearing ore using consortia of indigenous iron-oxidizing bacteria. Extremophiles 2018; 22:851-863. [DOI: 10.1007/s00792-018-1042-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 07/09/2018] [Indexed: 11/25/2022]
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48
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Cao X, Koch T, Steffens L, Finkensieper J, Zigann R, Cronan JE, Dahl C. Lipoate-binding proteins and specific lipoate-protein ligases in microbial sulfur oxidation reveal an atpyical role for an old cofactor. eLife 2018; 7:e37439. [PMID: 30004385 PMCID: PMC6067878 DOI: 10.7554/elife.37439] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/12/2018] [Indexed: 01/02/2023] Open
Abstract
Many Bacteria and Archaea employ the heterodisulfide reductase (Hdr)-like sulfur oxidation pathway. The relevant genes are inevitably associated with genes encoding lipoate-binding proteins (LbpA). Here, deletion of the gene identified LbpA as an essential component of the Hdr-like sulfur-oxidizing system in the Alphaproteobacterium Hyphomicrobium denitrificans. Thus, a biological function was established for the universally conserved cofactor lipoate that is markedly different from its canonical roles in central metabolism. LbpAs likely function as sulfur-binding entities presenting substrate to different catalytic sites of the Hdr-like complex, similar to the substrate-channeling function of lipoate in carbon-metabolizing multienzyme complexes, for example pyruvate dehydrogenase. LbpAs serve a specific function in sulfur oxidation, cannot functionally replace the related GcvH protein in Bacillus subtilis and are not modified by the canonical E. coli and B. subtilis lipoyl attachment machineries. Instead, LplA-like lipoate-protein ligases encoded in or in immediate vicinity of hdr-lpbA gene clusters act specifically on these proteins.
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Affiliation(s)
- Xinyun Cao
- Department of BiochemistryUniversity of IllinoisUrbanaUnited States
| | - Tobias Koch
- Institut für Mikrobiologie and BiotechnologieRheinische Friedrich-Wilhelms-Universität BonnBonnGermany
| | - Lydia Steffens
- Institut für Mikrobiologie and BiotechnologieRheinische Friedrich-Wilhelms-Universität BonnBonnGermany
| | - Julia Finkensieper
- Institut für Mikrobiologie and BiotechnologieRheinische Friedrich-Wilhelms-Universität BonnBonnGermany
| | - Renate Zigann
- Institut für Mikrobiologie and BiotechnologieRheinische Friedrich-Wilhelms-Universität BonnBonnGermany
| | - John E Cronan
- Department of BiochemistryUniversity of IllinoisUrbanaUnited States
- Department of MicrobiologyUniversity of IllinoisUrbanaUnited States
| | - Christiane Dahl
- Institut für Mikrobiologie and BiotechnologieRheinische Friedrich-Wilhelms-Universität BonnBonnGermany
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49
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Koch T, Dahl C. A novel bacterial sulfur oxidation pathway provides a new link between the cycles of organic and inorganic sulfur compounds. ISME JOURNAL 2018; 12:2479-2491. [PMID: 29930335 DOI: 10.1038/s41396-018-0209-7] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 05/16/2018] [Accepted: 06/01/2018] [Indexed: 12/16/2022]
Abstract
Dimethylsulfide (DMS) plays a globally significant role in carbon and sulfur cycling and impacts Earth's climate because its oxidation products serve as nuclei for cloud formation. While the initial steps of aerobic DMS degradation and the fate of its carbon atoms are reasonably well documented, oxidation of the contained sulfur is largely unexplored. Here, we identified a novel pathway of sulfur compound oxidation in the ubiquitously occurring DMS-degrader Hyphomicrobium denitrificans XT that links the oxidation of the volatile organosulfur compound with that of the inorganic sulfur compound thiosulfate. DMS is first transformed to methanethiol from which sulfide is released and fully oxidized to sulfate. Comparative proteomics indicated thiosulfate as an intermediate of this pathway and pointed at a heterodisulfide reductase (Hdr)-like system acting as a sulfur-oxidizing entity. Indeed, marker exchange mutagenesis of hdr-like genes disrupted the ability of H. denitrificans to metabolize DMS and also prevented formation of sulfate from thiosulfate provided as an additional electron source during chemoorganoheterotrophic growth. Complementation with the hdr-like genes under a constitutive promoter rescued the phenotype on thiosulfate as well as on DMS. The production of sulfate from an organosulfur precursor via the Hdr-like system is previously undocumented and provides a new shunt in the biogeochemical sulfur cycle. Furthermore, our findings fill a long-standing knowledge gap in microbial dissimilatory sulfur metabolism because the Hdr-like pathway is abundant not only in chemoheterotrophs, but also in a wide range of chemo- and photolithoautotrophic sulfur oxidizers acting as key players in global sulfur cycling.
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Affiliation(s)
- Tobias Koch
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Meckenheimer Allee 168, 53115, Bonn, Germany
| | - Christiane Dahl
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Meckenheimer Allee 168, 53115, Bonn, Germany.
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50
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An electrochemical sensing approach for scouting microbial chemolithotrophic metabolisms. Bioelectrochemistry 2018; 123:125-136. [PMID: 29747131 DOI: 10.1016/j.bioelechem.2018.04.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 04/25/2018] [Accepted: 04/29/2018] [Indexed: 11/21/2022]
Abstract
The present study was aimed to test an electrochemical sensing approach for the detection of an active chemolithotrophic metabolism (and therefore the presence of chemolithotrophic microorganisms) by using the corrosion of pyrite by Acidithiobacillus ferrooxidans as a model. Different electrochemical techniques were combined with adhesion studies and scanning electron microscopy (SEM). The experiments were performed in presence or absence of A. ferrooxidans and without or with ferrous iron in the culture medium (0 and 0.5 g L-1, respectively). Electrochemical parameters were in agreement with voltammetric studies and SEM showing that it is possible to distinguish between an abiotically-induced corrosion process (AIC) and a microbiologically-induced corrosion process (MIC). The results show that our approach not only allows the detection of chemolithotrophic activity of A. ferrooxidans but also can characterize the corrosion process. This may have different kind of applications, from those related to biomining to life searching missions in other planetary bodies.
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