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Hassan Z, Westerhoff HV. Arsenic Contamination of Groundwater Is Determined by Complex Interactions between Various Chemical and Biological Processes. TOXICS 2024; 12:89. [PMID: 38276724 PMCID: PMC11154318 DOI: 10.3390/toxics12010089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 01/27/2024]
Abstract
At a great many locations worldwide, the safety of drinking water is not assured due to pollution with arsenic. Arsenic toxicity is a matter of both systems chemistry and systems biology: it is determined by complex and intertwined networks of chemical reactions in the inanimate environment, in microbes in that environment, and in the human body. We here review what is known about these networks and their interconnections. We then discuss how consideration of the systems aspects of arsenic levels in groundwater may open up new avenues towards the realization of safer drinking water. Along such avenues, both geochemical and microbiological conditions can optimize groundwater microbial ecology vis-à-vis reduced arsenic toxicity.
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Affiliation(s)
- Zahid Hassan
- Department of Molecular Cell Biology, A-Life, Faculty of Science, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands;
- Department of Genetic Engineering and Biotechnology, Jagannath University, Dhaka 1100, Bangladesh
| | - Hans V. Westerhoff
- Department of Molecular Cell Biology, A-Life, Faculty of Science, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands;
- School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
- Stellenbosch Institute of Advanced Studies (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch 7600, South Africa
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Yang G, Hou T, Lin A, Xia X, Quan X, Chen Z, Zhuang L. Sub-inhibitory concentrations of ampicillin affect microbial Fe(III) oxide reduction. JOURNAL OF HAZARDOUS MATERIALS 2023; 451:131131. [PMID: 36917911 DOI: 10.1016/j.jhazmat.2023.131131] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/01/2023] [Accepted: 03/01/2023] [Indexed: 06/18/2023]
Abstract
Antibiotics are ubiquitous in the iron-rich environments but their roles in microbial reduction of Fe(III) oxides are still unclear. Using ampicillin and Geobacter soli, this study investigated the underlying mechanism by which antibiotic regulated microbial reduction of Fe(III) oxides. Results showed that sub-minimal inhibitory concentrations (sub-MIC) of ampicillin significantly affected ferrihydrite reduction by G. soli, with a stimulatory effect at 1/64 and 1/32 MIC and an inhibitory effect at 1/8 MIC. Increasing ampicillin concentration resulted in increasing cell length and decreasing bacterial zeta potential that were beneficial for ferrihydrite reduction, and decreasing outer membrane permeability that was unfavorable for ferrihydrite reduction. The respiratory metabolism ability was enhanced by 1/64 and 1/32 MIC ampicillin and reduced by 1/8 MIC ampicillin, which was also responsible for regulation of ferrihydrite reduction by ampicillin. The ferrihydrite reduction showed a positive correlation with the redox activity of extracellular polymeric substances (EPS) which was tied to the cytochrome/polysaccharide ratio and the content of α-helices and β-sheet in EPS. These results suggested that ampicillin regulated microbial Fe(III) oxide reduction through modulating the bacterial morphology, metabolism activity and extracellular electron transfer ability. Our findings provide new insights into the environmental factors regulating biogeochemical cycling of iron.
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Affiliation(s)
- Guiqin Yang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Tiqun Hou
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Annian Lin
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Xue Xia
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Xiaoyun Quan
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Zhili Chen
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Li Zhuang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China.
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Shewanella azerbaijanica sp. nov. a novel aquatic species with high bioremediation abilities. Arch Microbiol 2022; 204:496. [PMID: 35849218 DOI: 10.1007/s00203-022-03112-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 06/22/2022] [Accepted: 06/24/2022] [Indexed: 11/02/2022]
Abstract
A novel Gram-negative, facultative anaerobic, rod-shaped, and non-motile bacterium with bio-degradation potential of polycyclic aromatic hydrocarbons (PAHs) and uranium bio-reduction, designated as RCRI7T, was isolated from Qurugöl Lake water near Tabriz city. Strain RCRI7T can grow in the absence of NaCl and tolerates up to 3% NaCl (optimum, 0-0.5%), at the temperature range of 4-45 °C (optimum, 30 °C) and a pH range of 6-9 (optimum, pH 7 ± 0.5). Results of phylogenetic analysis based on 16S rRNA gene sequence indicated that strain RCRI7T is affiliated with the genus Shewanella, most closely related to Shewanella xiamenensis S4T (99.1%) and Shewanella putrefaciens JCM 20190T (98.9%). The genomic DNA G+C content of strain RCRI7T is 41 mol%. The major fatty acids are C16:1ω9c, C18:1ω9c and iso-C17:1ω5c. The OrthoANI and ANIb values between RCRI7T and Shewanella xiamenensis S4T were 87.4% and 87.7%, and between RCRI7T and Shewanella putrefaciens JCM 20190T were 79.5% and 79.7%, respectively. Strain RCRI7T displayed dDDH values of 30.2% and 39.8% to Shewanella xiamenensis S4T and Shewanella putrefaciens JCM 20190T, respectively. The major polar lipids include phosphatidylglycerol (PG) and phosphatidylethanolamine (PE). The respiratory quinone is Q8. Based on the polyphasic evidence presented in this paper, strain RCRI7T is considered to represent a novel species, with bioremediation potential, in the genus Shewanella, for which the name Shewanella azerbaijanica sp. nov. is proposed. The type strain is RCRI7T (= JCM 17276T) (= KCTC 62476T).
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Salgar-Chaparro SJ, Tarazona J, Machuca LL. Corrosion of Carbon Steel by Shewanella chilikensis DC57 Under Thiosulphate and Nitrate Reducing Conditions. Front Bioeng Biotechnol 2022; 10:825776. [PMID: 35360385 PMCID: PMC8961182 DOI: 10.3389/fbioe.2022.825776] [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] [Received: 11/30/2021] [Accepted: 02/16/2022] [Indexed: 11/13/2022] Open
Abstract
Shewanella chilikensis DC57 is a bacterial strain isolated from a corrosion failure in a floating oil production system. Previous studies have indicated that this microorganism has potential to trigger corrosion of carbon steel through several metabolic pathways identified in its genome. In this study we evaluated the corrosion of carbon steel by S. chilikensis in the presence of thiosulphate or nitrate as terminal electron acceptors of the anaerobic respiration. Electrochemical response of carbon steel to the biofilm formation revealed differences in the corrosion process under the different electron acceptors conditions. Microscopic examination of the metal surface confirmed that S. chilikensis induced corrosion in both scenarios; however, in the presence of thiosulfate S. chilikensis triggered a higher pitting corrosion rate, whereas in presence of nitrate it promoted higher uniform corrosion. This study demonstrates the importance of understanding the metabolic versatility of microbes in order to assess the MIC risk of industrial facilities.
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Zhu F, Huang Y, Ni H, Tang J, Zhu Q, Long ZE, Zou L. Biogenic iron sulfide functioning as electron-mediating interface to accelerate dissimilatory ferrihydrite reduction by Shewanella oneidensis MR-1. CHEMOSPHERE 2022; 288:132661. [PMID: 34699878 DOI: 10.1016/j.chemosphere.2021.132661] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 10/17/2021] [Accepted: 10/23/2021] [Indexed: 06/13/2023]
Abstract
Microbially driven iron and sulfur geochemical cycles co-exist ubiquitously in subsurface environments and are of environmental relevance. Shewanella species (dissimilatory metal-reducing bacteria) are capable of reducing Fe(III)-(oxyhydr)oxide minerals and diverse sulfur sources using corresponding metabolic pathways and producing FeS secondary minerals. In spite of the ability in promoting bacterial extracellular electron transfer (EET), the specific role of FeS in mediating EET between microbe/mineral interface is still unclear. In this work, the electron-mediating function of biogenic FeS on promoting the reduction of ferrihydrite by S. oneidensis MR-1 using thiosulfate as sulfur source was investigated in terms of Fe(III) reduction percentage, X-ray diffraction and scanning electron microscopy. The results showed that the microbial ferrihydrite reduction was pH-dependent and positively correlated with the addition of thiosulfate. In the presence of thiosulfate, biogenic FeS in nano-scale were formed and deposited on the surfaces of S. oneidensis MR-1 and ferrihydrite to build an interfacial electron transfer bridge between them. The addition of either thiosulfate and in-vitro FeS could rescue the entirely inactivated ability of the mutant (△omcA/mtrC) in ferrihydrite reduction to some extent, but which was obviously inferior to the wild-type strain. Meanwhile, the effect of the biogenic FeS in-situ coating on the surfaces of S. oneidensis MR-1 cells on promoting microbial ferrihydrite reduction was significantly superior to the in-vitro ones. Thus, the in-situ formed biogenic FeS secondary minerals were demonstrated to mediate and accelerate interfacial electron transfer from S. oneidensis MR-1 cells to ferrihydrite through interfacing with the bacterial EET routes, especially Mtr pathway. This work provides an insight into the secondary minerals-mediating interfacial electron transfer between microbes and minerals in the presence of biological S (-II), which has important biogeochemical and environmental implications.
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Affiliation(s)
- Fei Zhu
- Nanchang Key Laboratory of Microbial Resources Exploitation & Utilization from Poyang Lake Wetland, College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Yunhong Huang
- Nanchang Key Laboratory of Microbial Resources Exploitation & Utilization from Poyang Lake Wetland, College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Haiyan Ni
- Nanchang Key Laboratory of Microbial Resources Exploitation & Utilization from Poyang Lake Wetland, College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Jie Tang
- Nanchang Key Laboratory of Microbial Resources Exploitation & Utilization from Poyang Lake Wetland, College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Qi Zhu
- Nanchang Key Laboratory of Microbial Resources Exploitation & Utilization from Poyang Lake Wetland, College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Zhong-Er Long
- Nanchang Key Laboratory of Microbial Resources Exploitation & Utilization from Poyang Lake Wetland, College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China.
| | - Long Zou
- Nanchang Key Laboratory of Microbial Resources Exploitation & Utilization from Poyang Lake Wetland, College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China; Institute of Advanced Cross-field Science, Qingdao University, Qingdao, 200671, China.
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Lherbette M, Regeard C, Marlière C, Raspaud E. Biocorrosion on Nanofilms Induces Rapid Bacterial Motions via Iron Dissolution. ACS CENTRAL SCIENCE 2021; 7:1949-1956. [PMID: 34841065 PMCID: PMC8614109 DOI: 10.1021/acscentsci.1c01126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Indexed: 06/13/2023]
Abstract
Stability and reactivity of solid metal or mineral surfaces in contact with bacteria are critical properties for development of biocorrosion protection and for understanding bacteria-solid environmental interactions. Here, we opted to work with nanosheets of iron nanolayers offering arbitrarily large and stable areas of contact that can be simply monitored by optical means. We focused our study on the sediments' bacteria, the strain Shewanella oneidensis WT MR-1, that served as models for previous research on electroactivity and iron-reduction effects. Data show that a sudden uniform corrosion appeared after an early electroactive period without specific affinities and that iron dissolution induced rapid bacterial motions. By extending the approach to mutant strains and three bacterial species, we established a correlation between corrosion onset and oxygen-depletion combined with iron reduction and demonstrated bacteria's extraordinary ability to transform their solid environments.
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Affiliation(s)
- Marion Lherbette
- Université
Paris-Saclay, CNRS, Laboratoire de Physique des Solides, 91405 Orsay, France
| | - Christophe Regeard
- Institute
for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
| | - Christian Marlière
- Université
Paris-Saclay, CNRS, Laboratoire de Physique des Solides, 91405 Orsay, France
| | - Eric Raspaud
- Université
Paris-Saclay, CNRS, Laboratoire de Physique des Solides, 91405 Orsay, France
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de la Haba RR, López-Hermoso C, Sánchez-Porro C, Konstantinidis KT, Ventosa A. Comparative Genomics and Phylogenomic Analysis of the Genus Salinivibrio. Front Microbiol 2019; 10:2104. [PMID: 31572321 PMCID: PMC6749099 DOI: 10.3389/fmicb.2019.02104] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/27/2019] [Indexed: 12/02/2022] Open
Abstract
In the genomic era phylogenetic relationship among prokaryotes can be inferred from the core orthologous genes (OGs) or proteins in order to elucidate their evolutionary history and current taxonomy should benefits of that. The genus Salinivibrio belongs to the family Vibrionaceae and currently includes only five halophilic species, in spite the fact that new strains are very frequently isolated from hypersaline environments. Species belonging to this genus have undergone several reclassifications and, moreover, there are many strains of Salinivibrio with available genomes which have not been affiliated to the existing species or have been wrongly designated. Therefore, a phylogenetic study using the available genomic information is necessary to clarify the relationships of existing strains within this genus and to review their taxonomic affiliation. For that purpose, we have also sequenced the first complete genome of a Salinivibrio species, Salinivibrio kushneri AL184T, which was employed as a reference to order the contigs of the draft genomes of the type strains of the current species of this genus, as well as to perform a comparative analysis with all the other available Salinivibrio sp. genomes. The genome of S. kushneri AL184T was assembled in two circular chromosomes (with sizes of 2.84 Mb and 0.60 Mb, respectively), as typically occurs in members of the family Vibrionaceae, with nine complete ribosomal operons, which might explain the fast growing rate of salinivibrios cultured under laboratory conditions. Synteny analysis among the type strains of the genus revealed a high level of genomic conservation in both chromosomes, which allow us to hypothesize a slow speciation process or homogenization events taking place in this group of microorganisms to be tested experimentally in the future. Phylogenomic and orthologous average nucleotide identity (OrthoANI)/average amino acid identity (AAI) analyses also evidenced the elevated level of genetic relatedness within members of this genus and allowed to group all the Salinivibrio strains with available genomes in seven separated species. Genome-scale attribute study of the salinivibrios identified traits related to polar flagellum, facultatively anaerobic growth and osmotic response, in accordance to the phenotypic features described for species of this genus.
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Affiliation(s)
- Rafael R. de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
| | - Clara López-Hermoso
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
| | | | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
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Vamshi Krishna K, Venkata Mohan S. Purification and Characterization of NDH-2 Protein and Elucidating Its Role in Extracellular Electron Transport and Bioelectrogenic Activity. Front Microbiol 2019; 10:880. [PMID: 31133996 PMCID: PMC6513898 DOI: 10.3389/fmicb.2019.00880] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 04/05/2019] [Indexed: 11/13/2022] Open
Abstract
In microbial electrochemical systems, transport of electrons from bacteria to an electrode is the key to its functioning. However, the roles of several electron transport proteins, especially the membrane-bound dehydrogenases which link cellular metabolism to EET pathway are yet to be identified. NDH-2 is a non-proton pumping NADH dehydrogenase located in the inner membrane of several bacteria like Bacillus subtilis, Escherichia coli, etc. Unlike NADH dehydrogenase I, NDH-2 is not impeded by a high proton motive force thus helping in the increase of metabolic flux and carbon utilization. In the current study, NADH dehydrogenase II protein (NDH-2) was heterologously expressed from B. subtilis into E. coli BL21 (DE3) for enhancing electron flux through EET pathway and to understand its role in bioelectrogenesis. We found that E. coli expressing NDH-2 has increased the electron flux through EET and has shown a ninefold increase in current (4.7 μA) production when compared to wild strain with empty vector (0.52 μA). Furthermore, expression of NDH-2 also resulted in increased biofilm formation which can be corroborated with the decrease in charge transfer resistance of NDH-2 strain and increased NADH oxidation. It was also found that NDH-2 strain can reduce ferric citrate at a higher rate than wild type strain suggesting increased electron flux through electron transport chain due to NADH dehydrogenase II activity. Purified NDH-2 was found to be ∼42 kDa and has FAD as a cofactor. This work demonstrates that the primary dehydrogenases like NADH dehydrogenases can be overexpressed to increase the electron flux in EET pathway which can further enhance the microbial fuel cells performance.
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Affiliation(s)
- K Vamshi Krishna
- Bioengineering and Environmental Sciences Laboratory, EEFF Centre, CSIR-Indian Institute of Chemical Technology, Hyderabad, India
| | - S Venkata Mohan
- Bioengineering and Environmental Sciences Laboratory, EEFF Centre, CSIR-Indian Institute of Chemical Technology, Hyderabad, India
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Chen R, Liu H, Tong M, Zhao L, Zhang P, Liu D, Yuan S. Impact of Fe(II) oxidation in the presence of iron-reducing bacteria on subsequent Fe(III) bio-reduction. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 639:1007-1014. [PMID: 29929270 DOI: 10.1016/j.scitotenv.2018.05.241] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/18/2018] [Accepted: 05/19/2018] [Indexed: 06/08/2023]
Abstract
The interplay of Fe(II) oxidation and Fe(III) bio-reduction occurs widely in both natural and engineered redox-dynamic systems. This study aimed to unravel the impact of Fe(II) oxidation by O2 in the presence of iron-reducing bacteria on subsequent Fe(III) bio-reduction. Mixed solutions of Fe2+ (0.1-0.5 mM) and Shewanella oneidensis strain MR-1 (MR-1, 2.0 × 107 CFU/mL) at neutral pH were first exposed to laboratory air for Fe(II) oxidation and bacterial inactivation, and then the resultant Fe(III) suspensions were switched to anoxic conditions for bio-reduction by the surviving bacteria. In the oxidation step, the coexisting MR-1 was inactivated by 0.8-1.71 orders of magnitude within 60 min. In the subsequent bio-reduction step, the resultant Fe(III) was bio-reduced by the surviving MR-1. Bio-reduction of the resultant Fe(III) by the surviving MR-1 was 1.8-2.5 times faster than that of the Fe(III) that was produced from Fe2+ oxidation without MR-1 by fresh MR-1 cells at 2.0 × 107 CFU/mL. Although MR-1 inactivation during Fe(II) oxidation may inhibit Fe(III) bio-reduction, the increase in bio-availability of the resultant Fe(III) and the residual reactivity of dead cells led to net enhancement of bio-reduction under the tested conditions. Lepidocrocite was the sole Fe(III) mineral that was produced from Fe2+ oxidation without MR-1, while 19% ferrihydrite was produced from Fe2+ oxidation in the presence of MR-1. The formation of low-crystallinity ferrihydrite accounts for the increase in bio-availability of the Fe(III) minerals. The findings of this study highlight an important but overlooked impact underlying the interplay of Fe(II) oxidation and Fe(III) bio-reduction.
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Affiliation(s)
- Rong Chen
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 388 Lumo Road, Wuhan 430074, PR China
| | - Hui Liu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 388 Lumo Road, Wuhan 430074, PR China.
| | - Man Tong
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 388 Lumo Road, Wuhan 430074, PR China
| | - Lei Zhao
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 388 Lumo Road, Wuhan 430074, PR China
| | - Peng Zhang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 388 Lumo Road, Wuhan 430074, PR China
| | - Deng Liu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 388 Lumo Road, Wuhan 430074, PR China
| | - Songhu Yuan
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 388 Lumo Road, Wuhan 430074, PR China.
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Vibrio cholerae VciB Mediates Iron Reduction. J Bacteriol 2017; 199:JB.00874-16. [PMID: 28348025 DOI: 10.1128/jb.00874-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 03/19/2017] [Indexed: 11/20/2022] Open
Abstract
Vibrio cholerae is the causative agent of the severe diarrheal disease cholera. V. cholerae thrives within the human host, where it replicates to high numbers, but it also persists within the aquatic environments of ocean and brackish water. To survive within these nutritionally diverse environments, V. cholerae must encode the necessary tools to acquire the essential nutrient iron in all forms it may encounter. A prior study of systems involved in iron transport in V. cholerae revealed the existence of vciB, which, while unable to directly transport iron, stimulates the transport of iron through ferrous (Fe2+) iron transport systems. We demonstrate here a role for VciB in V. cholerae in which VciB stimulates the reduction of Fe3+ to Fe2+, which can be subsequently transported into the cell with the ferrous iron transporter Feo. Iron reduction is independent of functional iron transport but is associated with the electron transport chain. Comparative analysis of VciB orthologs suggests a similar role for other proteins in the VciB family. Our data indicate that VciB is a dimer located in the inner membrane with three transmembrane segments and a large periplasmic loop. Directed mutagenesis of the protein reveals two highly conserved histidine residues required for function. Taken together, our results support a model whereby VciB reduces ferric iron using energy from the electron transport chain.IMPORTANCEVibrio cholerae is a prolific human pathogen and environmental organism. The acquisition of essential nutrients such as iron is critical for replication, and V. cholerae encodes a number of mechanisms to use iron from diverse environments. Here, we describe the V. cholerae protein VciB that increases the reduction of oxidized ferric iron (Fe3+) to the ferrous form (Fe2+), thus promoting iron acquisition through ferrous iron transporters. Analysis of VciB orthologs in Burkholderia and Aeromonas spp. suggest that they have a similar activity, allowing a functional assignment for this previously uncharacterized protein family. This study builds upon our understanding of proteins known to mediate iron reduction in bacteria.
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Formate Metabolism in Shewanella oneidensis Generates Proton Motive Force and Prevents Growth without an Electron Acceptor. J Bacteriol 2016; 198:1337-46. [PMID: 26883823 DOI: 10.1128/jb.00927-15] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 02/08/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Shewanella oneidensis strain MR-1 is a facultative anaerobe that thrives in redox-stratified environments due to its ability to utilize a wide array of terminal electron acceptors. Conversely, the electron donors utilized by S. oneidensis are more limited and include products of primary fermentation such as lactate, pyruvate, formate, and hydrogen. Lactate, pyruvate, and hydrogen metabolisms inS. oneidensis have been described previously, but little is known about the role of formate oxidation in the ecophysiology of these bacteria. Formate is produced by S. oneidensis through pyruvate formate lyase during anaerobic growth on carbon sources that enter metabolism at or above the level of pyruvate, and the genome contains three gene clusters predicted to encode three complete formate dehydrogenase complexes. To determine the contribution of each complex to formate metabolism, strains lacking one, two, or all three annotated formate dehydrogenase gene clusters were generated and examined for growth rates and yields on a variety of carbon sources. Here, we report that formate oxidation contributes to both the growth rate and yield of S. oneidensis through the generation of proton motive force. Exogenous formate also greatly accelerated growth on N-acetylglucosamine, a carbon source normally utilized very slowly by S. oneidensis under anaerobic conditions. Surprisingly, deletion of all three formate dehydrogenase gene clusters enabled growth of S. oneidensis using pyruvate in the absence of a terminal electron acceptor, a mode of growth never before observed in these bacteria. Our results demonstrate that formate oxidation is a fundamental strategy under anaerobic conditions for energy conservation inS. oneidensis. IMPORTANCE Shewanella species have garnered interest in biotechnology applications for their ability to respire extracellular terminal electron acceptors, such as insoluble iron oxides and electrodes. While much effort has gone into studying the proteins for extracellular electron transport, how electrons generated through the oxidation of organic carbon sources enter this pathway remains understudied. Here, we quantify the role of formate oxidation in the anaerobic physiology of Shewanella oneidensis Formate oxidation contributes to both the growth rate and yield on a variety of carbon sources through the generation of proton motive force. Advances in our understanding of the anaerobic metabolism of S. oneidensis are important for our ability to utilize and engineer this organism for applications in bioenergy, biocatalysis, and bioremediation.
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Soo VWC, McAnulty MJ, Tripathi A, Zhu F, Zhang L, Hatzakis E, Smith PB, Agrawal S, Nazem-Bokaee H, Gopalakrishnan S, Salis HM, Ferry JG, Maranas CD, Patterson AD, Wood TK. Reversing methanogenesis to capture methane for liquid biofuel precursors. Microb Cell Fact 2016; 15:11. [PMID: 26767617 PMCID: PMC4714516 DOI: 10.1186/s12934-015-0397-z] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 12/13/2015] [Indexed: 12/30/2022] Open
Abstract
Background Energy from remote methane reserves is transformative; however, unintended release of this potent greenhouse gas makes it imperative to convert methane efficiently into more readily transported biofuels. No pure microbial culture that grows on methane anaerobically has been isolated, despite that methane capture through anaerobic processes is more efficient than aerobic ones. Results Here we engineered the archaeal methanogen Methanosarcina acetivorans to grow anaerobically on methane as a pure culture and to convert methane into the biofuel precursor acetate. To capture methane, we cloned the enzyme methyl-coenzyme M reductase (Mcr) from an unculturable organism, anaerobic methanotrophic archaeal population 1 (ANME-1) from a Black Sea mat, into M. acetivorans to effectively run methanogenesis in reverse. Starting with low-density inocula, M. acetivorans cells producing ANME-1 Mcr consumed up to 9 ± 1 % of methane (corresponding to 109 ± 12 µmol of methane) after 6 weeks of anaerobic growth on methane and utilized 10 mM FeCl3 as an electron acceptor. Accordingly, increases in cell density and total protein were observed as cells grew on methane in a biofilm on solid FeCl3. When incubated on methane for 5 days, high-densities of ANME-1 Mcr-producing M. acetivorans cells consumed 15 ± 2 % methane (corresponding to 143 ± 16 µmol of methane), and produced 10.3 ± 0.8 mM acetate (corresponding to 52 ± 4 µmol of acetate). We further confirmed the growth on methane and acetate production using 13C isotopic labeling of methane and bicarbonate coupled with nuclear magnetic resonance and gas chromatography/mass spectroscopy, as well as RNA sequencing. Conclusions We anticipate that our metabolically-engineered strain will provide insights into how methane is cycled in the environment by Archaea as well as will possibly be utilized to convert remote sources of methane into more easily transported biofuels via acetate. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0397-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Valerie W C Soo
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802-4400, USA.
| | - Michael J McAnulty
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802-4400, USA.
| | - Arti Tripathi
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802-4400, USA.
| | - Fayin Zhu
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802-4400, USA.
| | - Limin Zhang
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, 16802-4400, USA. .,Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China.
| | - Emmanuel Hatzakis
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802-4400, USA.
| | - Philip B Smith
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802-4400, USA.
| | - Saumya Agrawal
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, 0632, New Zealand.
| | - Hadi Nazem-Bokaee
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802-4400, USA.
| | - Saratram Gopalakrishnan
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802-4400, USA.
| | - Howard M Salis
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802-4400, USA.
| | - James G Ferry
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802-4400, USA.
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802-4400, USA.
| | - Andrew D Patterson
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, 16802-4400, USA.
| | - Thomas K Wood
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802-4400, USA. .,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802-4400, USA.
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13
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White GF, Edwards MJ, Gomez-Perez L, Richardson DJ, Butt JN, Clarke TA. Mechanisms of Bacterial Extracellular Electron Exchange. Adv Microb Physiol 2016; 68:87-138. [PMID: 27134022 DOI: 10.1016/bs.ampbs.2016.02.002] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The biochemical mechanisms by which microbes interact with extracellular soluble metal ions and insoluble redox-active minerals have been the focus of intense research over the last three decades. The process presents two challenges to the microorganism. Firstly, electrons have to be transported at the cell surface, which in Gram-negative bacteria presents an additional problem of electron transfer across the ~6nm of the outer membrane. Secondly, the electrons must be transferred to or from the terminal electron acceptors or donors. This review covers the known mechanisms that bacteria use to transport electrons across the cell envelope to external electron donors/acceptors. In Gram-negative bacteria, electron transfer across the outer membrane involves the use of an outer membrane β-barrel and cytochrome. These can be in the form of a porin-cytochrome protein, such as Cyc2 of Acidithiobacillus ferrooxidans, or a multiprotein porin-cytochrome complex like MtrCAB of Shewanella oneidensis MR-1. For mineral-respiring organisms, there is the additional challenge of transferring the electrons from the cell to mineral surface. For the strict anaerobe Geobacter sulfurreducens this requires electron transfer through conductive pili to associated cytochrome OmcS that directly reduces Fe(III)oxides, while the facultative anaerobe S. oneidensis MR-1 accomplishes mineral reduction through direct membrane contact, contact through filamentous extensions and soluble flavin shuttles, all of which require the outer membrane cytochromes MtrC and OmcA in addition to secreted flavin.
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Affiliation(s)
- G F White
- School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich, United Kingdom
| | - M J Edwards
- School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich, United Kingdom
| | - L Gomez-Perez
- School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich, United Kingdom
| | - D J Richardson
- School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich, United Kingdom
| | - J N Butt
- School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich, United Kingdom
| | - T A Clarke
- School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich, United Kingdom.
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14
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Baker PW, Högstrand C, Lead J, Pickup RW, Zhang H. Immobilization of Shewanella oneidensis MR-1 in diffusive gradients in thin films for determining metal bioavailability. CHEMOSPHERE 2015; 138:309-315. [PMID: 26093096 DOI: 10.1016/j.chemosphere.2015.06.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 05/26/2015] [Accepted: 06/08/2015] [Indexed: 06/04/2023]
Abstract
Assessing metal bioavailability in soil is important in modeling the effects of metal toxicity on the surrounding ecosystem. Current methods based on diffusive gradient thin films (DGTs) and Gel-Integrated Microelectrode are limited in their availability and sensitivity. To address this, Shewanella oneidensis, an anaerobic iron reducing bacterium, was incorporated into a thin layer of agarose to replace the polyacrylamide gel that is normally present in DGT to form biologically mobilizing DGT (BMDGT). Viability analysis revealed that 16-35% of the cells remained viable within the BMDGTs depending on the culturing conditions over a 20 h period with/without metals. Deployment of BMDGTs in standardized metal solutions showed significant differences to cell-free BMDGTs when cells grown in Luria Broth (LB) were incorporated into BMDGTs and deployed under anaerobic conditions. Deployment of these BMDGTs in hematite revealed no significant differences between BMDGTs and BMDGTs containing heat killed cells. Whether heat killed cells retain the ability to affect bioavailability is uncertain. This is the first study to investigate how a microorganism that was incorporated into a DGT device such as the metal reducing bacteria, S. oneidensis, may affect the mobility of metals.
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Affiliation(s)
- Paul W Baker
- Lancaster Environmental Centre, Lancaster University, Bailrigg, Lancaster LA1 4YQ, UK
| | - Christer Högstrand
- School of Biomedical Sciences, 1.14 Hodgkin Building, Guy's Campus, London LE1 1UL, UK
| | - Jamie Lead
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Roger W Pickup
- Division of Biomedicine and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YQ, UK
| | - Hao Zhang
- Lancaster Environmental Centre, Lancaster University, Bailrigg, Lancaster LA1 4YQ, UK
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15
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Szeinbaum N, Burns JL, DiChristina TJ. Electron transport and protein secretion pathways involved in Mn(III) reduction by Shewanella oneidensis. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:490-500. [PMID: 25646542 DOI: 10.1111/1758-2229.12173] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Soluble Mn(III) represents an important yet overlooked oxidant in marine and freshwater systems. The molecular mechanism of microbial Mn(III) reduction, however, has yet to be elucidated. Extracellular reduction of insoluble Mn(IV) and Fe(III) oxides by the metal-reducing γ-proteobacterium Shewanella oneidensis involves inner (CymA) and outer (OmcA) membrane-associated c-type cytochromes, the extracellular electron conduit MtrCAB, and GspD, the secretin of type II protein secretion. CymA, MtrCAB and GspD mutants were unable to reduce Mn(III) and Mn(IV) with lactate, H2, or formate as electron donor. The OmcA mutant reduced Mn(III) and Mn(IV) at near wild-type rates with lactate and formate as electron donor. With H2 as electron donor, however, the OmcA mutant was unable to reduce Mn(III) but reduced Mn(IV) at wild-type rates. Analogous Fe(III) reduction rate analyses indicated that other electron carriers compensated for the absence of OmcA, CymA, MtrCAB and GspD during Fe(III) reduction in an electron donor-dependent fashion. Results of the present study demonstrate that the S. oneidensis electron transport and protein secretion components involved in extracellular electron transfer to external Mn(IV) and Fe(III) oxides are also required for electron transfer to Mn(III) and that OmcA may function as a dedicated component of an H2 oxidation-linked Mn(III) reduction system.
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16
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Research of Iron Reduction and the Iron Reductase Localization of Anammox Bacteria. Curr Microbiol 2014; 69:880-7. [DOI: 10.1007/s00284-014-0668-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 06/15/2014] [Indexed: 10/24/2022]
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17
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Mu A, Boreham C, Leong HX, Haese RR, Moreau JW. Changes in the deep subsurface microbial biosphere resulting from a field-scale CO2 geosequestration experiment. Front Microbiol 2014; 5:209. [PMID: 24860559 PMCID: PMC4030138 DOI: 10.3389/fmicb.2014.00209] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 04/19/2014] [Indexed: 01/08/2023] Open
Abstract
Subsurface microorganisms may respond to increased CO2 levels in ways that significantly affect pore fluid chemistry. Changes in CO2 concentration or speciation may result from the injection of supercritical CO2 (scCO2) into deep aquifers. Therefore, understanding subsurface microbial responses to scCO2, or unnaturally high levels of dissolved CO2, will help to evaluate the use of geosequestration to reduce atmospheric CO2 emissions. This study characterized microbial community changes at the 16S rRNA gene level during a scCO2 geosequestration experiment in the 1.4 km-deep Paaratte Formation of the Otway Basin, Australia. One hundred and fifty tons of mixed scCO2 and groundwater was pumped into the sandstone Paaratte aquifer over 4 days. A novel U-tube sampling system was used to obtain groundwater samples under in situ pressure conditions for geochemical analyses and DNA extraction. Decreases in pH and temperature of 2.6 log units and 5.8°C, respectively, were observed. Polyethylene glycols (PEGs) were detected in the groundwater prior to scCO2 injection and were interpreted as residual from drilling fluid used during the emplacement of the CO2 injection well. Changes in microbial community structure prior to scCO2 injection revealed a general shift from Firmicutes to Proteobacteria concurrent with the disappearance of PEGs. However, the scCO2 injection event, including changes in response to the associated variables (e.g., pH, temperature and salinity), resulted in increases in the relative abundances of Comamonadaceae and Sphingomonadaceae suggesting the potential for enhanced scCO2 tolerance of these groups. This study demonstrates a successful new in situ sampling approach for detecting microbial community changes associated with an scCO2 geosequestration event.
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Affiliation(s)
- Andre Mu
- School of Earth Sciences, Faculty of Science, University of Melbourne Melbourne, VIC, Australia ; Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity Melbourne, VIC, Australia ; Cooperative Research Centre for Greenhouse Gas Technologies Canberra, NSW, Australia
| | - Chris Boreham
- Cooperative Research Centre for Greenhouse Gas Technologies Canberra, NSW, Australia ; Geoscience Australia Canberra, NSW, Australia
| | - Henrietta X Leong
- School of Earth Sciences, Faculty of Science, University of Melbourne Melbourne, VIC, Australia ; Cooperative Research Centre for Greenhouse Gas Technologies Canberra, NSW, Australia
| | - Ralf R Haese
- School of Earth Sciences, Faculty of Science, University of Melbourne Melbourne, VIC, Australia ; Cooperative Research Centre for Greenhouse Gas Technologies Canberra, NSW, Australia
| | - John W Moreau
- School of Earth Sciences, Faculty of Science, University of Melbourne Melbourne, VIC, Australia ; Cooperative Research Centre for Greenhouse Gas Technologies Canberra, NSW, Australia
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18
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Dolch K, Danzer J, Kabbeck T, Bierer B, Erben J, Förster AH, Maisch J, Nick P, Kerzenmacher S, Gescher J. Characterization of microbial current production as a function of microbe-electrode-interaction. BIORESOURCE TECHNOLOGY 2014; 157:284-92. [PMID: 24566287 DOI: 10.1016/j.biortech.2014.01.112] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 01/24/2014] [Accepted: 01/27/2014] [Indexed: 05/15/2023]
Abstract
Microbe-electrode-interactions are keys for microbial fuel cell technology. Nevertheless, standard measurement routines to analyze the interplay of microbial physiology and material characteristics have not been introduced yet. In this study, graphite anodes with varying surface properties were evaluated using pure cultures of Shewanella oneidensis and Geobacter sulfurreducens, as well as defined and undefined mixed cultures. The evaluation routine consisted of a galvanostatic period, a current sweep and an evaluation of population density. The results show that surface area correlates only to a certain extent with population density and anode performance. Furthermore, the study highlights a strain-specific microbe-electrode-interaction, which is affected by the introduction of another microorganism. Moreover, evidence is provided for the possibility of translating results from pure culture to undefined mixed species experiments. This is the first study on microbe-electrode-interaction that systematically integrates and compares electrochemical and biological data.
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Affiliation(s)
- Kerstin Dolch
- Institute for Applied Biosciences, Department of Applied Biology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany.
| | - Joana Danzer
- Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany.
| | - Tobias Kabbeck
- Institute for Applied Biosciences, Department of Applied Biology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany.
| | - Benedikt Bierer
- Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany.
| | - Johannes Erben
- Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany.
| | - Andreas H Förster
- Institute for Applied Biosciences, Department of Applied Biology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany.
| | - Jan Maisch
- Botanical Institute, Molecular Cell Biology, Karlsruhe Institute of Technology, Kaiserstrasse 2, 76131 Karlsruhe, Germany.
| | - Peter Nick
- Botanical Institute, Molecular Cell Biology, Karlsruhe Institute of Technology, Kaiserstrasse 2, 76131 Karlsruhe, Germany.
| | - Sven Kerzenmacher
- Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany.
| | - Johannes Gescher
- Institute for Applied Biosciences, Department of Applied Biology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany.
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19
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Graphene oxide as nanogold carrier for ultrasensitive electrochemical immunoassay of Shewanella oneidensis with silver enhancement strategy. Biosens Bioelectron 2014; 52:44-9. [DOI: 10.1016/j.bios.2013.08.022] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 07/26/2013] [Accepted: 08/13/2013] [Indexed: 11/17/2022]
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20
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Furukawa Y, Dale JR. The surface properties of Shewanella putrefaciens 200 and S. oneidensis MR-1: the effect of pH and terminal electron acceptors. GEOCHEMICAL TRANSACTIONS 2013; 14:3. [PMID: 23566080 PMCID: PMC3623883 DOI: 10.1186/1467-4866-14-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 03/26/2013] [Indexed: 05/08/2023]
Abstract
BACKGROUND We investigated the surface characteristics of two strains of Shewanella sp., S. oneidensis MR-1 and S. putrefaciens 200, that were grown under aerobic conditions as well as under anaerobic conditions with trimethylamine oxide (TMAO) as the electron acceptor. The investigation focused on the experimental determination of electrophoretic mobility (EPM) under a range of pH and ionic strength, as well as by subsequent modeling in which Shewanella cells were considered to be soft particles with water- and ion-permeable outermost layers. RESULTS The soft layer of p200 is significantly more highly charged (i.e., more negative) than that of MR-1. The effect of electron acceptor on the soft particle characteristics of Shewanella sp. is complex. The fixed charge density, which is a measure of the deionized and deprotonated functional groups in the soft layer polymers, is slightly greater (i.e., more negative) for aerobically grown p200 than for p200 grown with TMAO. On the other hand, the fixed charge density of aerobically grown MR1 is slightly less than that of p200 grown with TMAO. The effect of pH on the soft particle characteristics is also complex, and does not exhibit a clear pH-dependent trend. CONCLUSIONS The Shewanella surface characteristics were attributed to the nature of the outermost soft layer, the extracellular polymeric substances (EPS) in case of p200 and lypopolysaccharides (LPS) in case of MR1 which generally lacks EPS. The growth conditions (i.e., aerobic vs. anaerobic TMAO) have an influence on the soft layer characteristics of Shewanella sp. cells. Meanwhile, the clear pH dependency of the mechanical and morphological characteristics of EPS and LPS layers, observed in previous studies through atomic force microscopy, adhesion tests and spectroscopies, cannot be corroborated by the electrohydrodynamics-based soft particle characteristics which does not exhibited a clear pH dependency in this study. While the electrohydrodynamics-based soft-particle model is a useful tool in understanding bacteria's surface properties, it needs to be supplemented with other characterization methods and models (e.g., chemical and micromechanical) in order to comprehensively address all of the surface-related characteristics important in environmental and other aqueous processes.
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Affiliation(s)
- Yoko Furukawa
- Naval Research Laboratory, Seafloor Sciences Branch, Stennis Space Center, MS,
39529, USA
| | - Jason R Dale
- Naval Research Laboratory, Seafloor Sciences Branch, Stennis Space Center, MS,
39529, USA
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21
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Kane AL, Bond DR, Gralnick JA. Electrochemical analysis of Shewanella oneidensis engineered to bind gold electrodes. ACS Synth Biol 2013; 2:93-101. [PMID: 23656372 DOI: 10.1021/sb300042w] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Growth in three-electrode electrochemical cells allows quantitative analysis of mechanisms involved in electron flow from dissimilatory metal reducing bacteria to insoluble electron acceptors. In these systems, gold electrodes are a desirable surface to study the electrophysiology of extracellular respiration, yet previous research has shown that certain Shewanella species are unable to form productive biofilms on gold electrodes. To engineer attachment of Shewanella oneidensis to gold, five repeating units of a synthetic gold-binding peptide (5rGBP) were integrated within an Escherichia coli outer membrane protein, LamB, and displayed on the outer surface of S. oneidensis. Expression of LamB-5rGBP increased cellular attachment of S. oneidensis to unpoised gold surfaces but was also associated with the loss of certain outer membrane proteins required for extracellular respiration. Loss of these outer membrane proteins during expression of LamB-5rGBP decreased the rate at which S. oneidensis was able to reduce insoluble iron, riboflavin, and electrodes. Moreover, poising the gold electrode resulted in repulsion of the engineered cells. This study provides a strategy to specifically immobilize bacteria to electrodes while also outlining challenges involved in merging synthetic biology approaches with native cellular pathways and cell surface charge.
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Affiliation(s)
- Aunica L. Kane
- BioTechnology
Institute and ‡Department of Microbiology, University of Minnesota−Twin Cities, St. Paul, Minnesota
55108, United States
| | - Daniel R. Bond
- BioTechnology
Institute and ‡Department of Microbiology, University of Minnesota−Twin Cities, St. Paul, Minnesota
55108, United States
| | - Jeffrey A. Gralnick
- BioTechnology
Institute and ‡Department of Microbiology, University of Minnesota−Twin Cities, St. Paul, Minnesota
55108, United States
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22
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Iyer PR, Liu YA, Deng Y, McManus JB, Kao TH, Tien M. Processing of cellulose synthase (AcsAB) from Gluconacetobacter hansenii 23769. Arch Biochem Biophys 2012; 529:92-8. [PMID: 23232080 DOI: 10.1016/j.abb.2012.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Revised: 11/29/2012] [Accepted: 12/02/2012] [Indexed: 11/28/2022]
Abstract
The cellulose synthase protein (AcsAB) is encoded by a single gene in Gluconacetobacter hansenii ATCC 23769. We have examined the processing pattern of this enzyme and the localization of the cleavage products by heterologously expressing the truncated portions of the AcsAB protein and using specific antibodies generated against these regions. We found that the AcsAB protein is processed into three polypeptide subunits of molecular masses 46kDa, 34kDa and 95kDa. The 46kDa polypeptide (AcsA(cat)) harbors the conserved glycosyltransferase domain and hence contains the catalytic subunit of the enzyme. This polypeptide is localized in the cytoplasmic membrane. The 34kDa polypeptide (AcsA(reg)) is the regulatory subunit with the cyclic diGMP-binding PilZ domain. This polypeptide is largely cytoplasmic. The 95kDa subunit (AcsB) is of unknown function and contains a predicted signal peptide at its N-terminus. This subunit is localized in the outer membrane. In addition to this, we have also localized the AcsC protein in the outer membrane, confirming its predicted localization based on the OM-signal sequence at its N-terminus.
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Affiliation(s)
- Prashanti R Iyer
- Department of Biochemistry and Molecular Biology, 305 South Frear, University Park, The Pennsylvania State University, PA 16802, USA
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23
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Rosenbaum MA, Bar HY, Beg QK, Segrè D, Booth J, Cotta MA, Angenent LT. Transcriptional analysis of Shewanella oneidensis MR-1 with an electrode compared to Fe(III)citrate or oxygen as terminal electron acceptor. PLoS One 2012; 7:e30827. [PMID: 22319591 PMCID: PMC3271074 DOI: 10.1371/journal.pone.0030827] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Accepted: 12/29/2011] [Indexed: 11/19/2022] Open
Abstract
Shewanella oneidensis is a target of extensive research in the fields of bioelectrochemical systems and bioremediation because of its versatile metabolic capabilities, especially with regard to respiration with extracellular electron acceptors. The physiological activity of S. oneidensis to respire at electrodes is of great interest, but the growth conditions in thin-layer biofilms make physiological analyses experimentally challenging. Here, we took a global approach to evaluate physiological activity with an electrode as terminal electron acceptor for the generation of electric current. We performed expression analysis with DNA microarrays to compare the overall gene expression with an electrode to that with soluble iron(III) or oxygen as the electron acceptor and applied new hierarchical model-based statistics for the differential expression analysis. We confirmed the differential expression of many genes that have previously been reported to be involved in electrode respiration, such as the entire mtr operon. We also formulate hypotheses on other possible gene involvements in electrode respiration, for example, a role of ScyA in inter-protein electron transfer and a regulatory role of the cbb3-type cytochrome c oxidase under anaerobic conditions. Further, we hypothesize that electrode respiration imposes a significant stress on S. oneidensis, resulting in higher energetic costs for electrode respiration than for soluble iron(III) respiration, which fosters a higher metabolic turnover to cover energy needs. Our hypotheses now require experimental verification, but this expression analysis provides a fundamental platform for further studies into the molecular mechanisms of S. oneidensis electron transfer and the physiologically special situation of growth on a poised-potential surface.
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Affiliation(s)
- Miriam A. Rosenbaum
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York, United States of America
| | - Haim Y. Bar
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Qasim K. Beg
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Daniel Segrè
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - James Booth
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Michael A. Cotta
- Bioenergy Research Unit, United States Department of Agriculture, Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Peoria, Illinois, United States of America
| | - Largus T. Angenent
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York, United States of America
- * E-mail:
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Qian Y, Shi L, Tien M. SO2907, a putative TonB-dependent receptor, is involved in dissimilatory iron reduction by Shewanella oneidensis strain MR-1. J Biol Chem 2011; 286:33973-80. [PMID: 21813652 DOI: 10.1074/jbc.m111.262113] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Shewanella oneidensis strain MR-1 utilizes soluble and insoluble ferric ions as terminal electron acceptors during anaerobic respiration. The components of respiratory metabolism are localized in the membrane fractions which include the outer membrane and cytoplasmic membrane. Many of the biological components that interact with the various iron forms are proposed to be localized in these membrane fractions. To identify the iron-binding proteins acting either as an iron transporter or as a terminal iron reductase, we used metal-catalyzed oxidation reactions. This system catalyzed the oxidation of amino acids in close proximity to the iron binding site. The carbonyl groups formed from this oxidation can then be labeled with fluoresceinamine (FLNH(2)). The peptide harboring the FLNH(2) can then be proteolytically digested, purified by HPLC and then identified by MALDI-TOF tandem MS. A predominant peptide was identified to be part of SO2907 that encodes a putative TonB-dependent receptor. Compared with wild type (wt), the so2907 gene deletion (ΔSO2907) mutant has impaired ability to reduce soluble Fe(III), but retains the same ability to respire oxygen or fumarate as the wt. The ΔSO2907 mutant was also impacted in reduction of insoluble iron. Iron binding assays using isothermal titration calorimetry and fluorescence tryptophan quenching demonstrated that a truncated form of heterologous-expressed SO2907 that contains the Fe(III) binding site, is capable of binding soluble Fe(III) forms with K(d) of approximate 50 μm. To the best of our knowledge, this is the first report of the physiological role of SO2907 in Fe(III) reduction by MR-1.
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Affiliation(s)
- Yufeng Qian
- Department of Biochemistry and Molecular Biology, the Pennsylvania State University, University Park, Pennsylvania 16802, USA
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Abstract
Some bacterial species are able to utilize extracellular mineral forms of iron and manganese as respiratory electron acceptors. In Shewanella oneidensis this involves decaheme cytochromes that are located on the bacterial cell surface at the termini of trans-outer-membrane electron transfer conduits. The cell surface cytochromes can potentially play multiple roles in mediating electron transfer directly to insoluble electron sinks, catalyzing electron exchange with flavin electron shuttles or participating in extracellular intercytochrome electron exchange along "nanowire" appendages. We present a 3.2-Å crystal structure of one of these decaheme cytochromes, MtrF, that allows the spatial organization of the 10 hemes to be visualized for the first time. The hemes are organized across four domains in a unique crossed conformation, in which a staggered 65-Å octaheme chain transects the length of the protein and is bisected by a planar 45-Å tetraheme chain that connects two extended Greek key split β-barrel domains. The structure provides molecular insight into how reduction of insoluble substrate (e.g., minerals), soluble substrates (e.g., flavins), and cytochrome redox partners might be possible in tandem at different termini of a trifurcated electron transport chain on the cell surface.
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Partial functional replacement of CymA by SirCD in Shewanella oneidensis MR-1. J Bacteriol 2011; 193:2312-21. [PMID: 21378180 DOI: 10.1128/jb.01355-10] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The gammaproteobacterium Shewanella oneidensis MR-1 utilizes a complex electron transfer network composed primarily of c-type cytochromes to respire under anoxic conditions a variety of compounds, including fumarate, nitrate, and dimethyl sulfoxide (DMSO), in addition to the minerals Fe(III) and Mn(IV). Central to several respiratory pathways is CymA, a cytoplasmic membrane-bound tetraheme c-type cytochrome that functions as the major hydroquinone dehydrogenase. To investigate functional redundancy and plasticity in S. oneidensis MR-1 electron transport, we isolated ΔcymA suppressor mutants and characterized one biochemically and genetically. Interestingly, in the characterized ΔcymA suppressor mutant, respiration of fumarate, ferric citrate, and DMSO was restored but that of nitrate was not. The suppression was found to be due to transcriptional activation of sirC and sirD, encoding a periplasmic iron sulfur protein and an integral membrane hydroquinone dehydrogenase, respectively. Biochemical in vitro reconstitution experiments confirmed electron transport between formate and fumarate via fumarate reductase by suppressor membrane fractions. The suppression was found to be caused by insertion of an ISSod1 element upstream of the sirCD transcriptional start site, generating a novel, constitutively active hybrid promoter. This work revealed that adaptation of an alternative electron transfer pathway from quinol to terminal oxidoreductases independent of CymA occurs rapidly in S. oneidensis MR-1.
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Firer-Sherwood MA, Bewley KD, Mock JY, Elliott SJ. Tools for resolving complexity in the electron transfer networks of multiheme cytochromes c. Metallomics 2011; 3:344-8. [PMID: 21327265 DOI: 10.1039/c0mt00097c] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Examining electron transfer between two proteins with identical spectroscopic signatures is a challenging task. It is supposed that several multiheme cytochromes in Shewanella oneidensis form a molecular "wire" through which electrons are transported across the cellular space and a direct study of this transient protein-protein interaction has not yet been reported. In this study, we present variations on catalytic protein film voltammetry and an anaerobic affinity chromatography assay to demonstrate unidirectional electron transfer between proposed protein pairs. Through use of these techniques, we are able to confirm the transient interactions between these cytochromes, supporting the model of electron transfer that is present in the literature.
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Involvement of the Shewanella oneidensis decaheme cytochrome MtrA in the periplasmic stability of the beta-barrel protein MtrB. Appl Environ Microbiol 2010; 77:1520-3. [PMID: 21169449 DOI: 10.1128/aem.01201-10] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Shewanella oneidensis outer membrane β-barrel protein MtrB is part of a membrane-spanning protein complex (MtrABC) which is necessary for dissimilatory iron reduction. Quantitative PCR, heterologous gene expression, and mutant studies indicated that MtrA is required for periplasmic stability of MtrB. DegP depletion compensated for this MtrA dependence.
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Rosenbaum M, Cotta MA, Angenent LT. Aerated Shewanella oneidensis in continuously fed bioelectrochemical systems for power and hydrogen production. Biotechnol Bioeng 2010; 105:880-8. [PMID: 19998276 DOI: 10.1002/bit.22621] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We studied the effects of aeration of Shewanella oneidensis on potentiostatic current production, hydrogen production in a microbial electrolysis cell, and electric power generation in a microbial fuel cell (MFC). The potentiostatic performance of aerated S. oneidensis was considerably enhanced to a maximum current density of 0.45 A/m(2) or 80.3 A/m(3) (mean: 0.34 A/m(2), 57.2 A/m(3)) compared to anaerobically grown cultures. Biocatalyzed hydrogen production rates with aerated S. oneidensis were studied within the applied potential range of 0.3-0.9 V and were highest at 0.9 V with 0.3 m(3) H(2)/m(3) day, which has been reported for mixed cultures, but is approximately 10 times higher than reported for an anaerobic culture of S. oneidensis. Aerated MFC experiments produced a maximum power density of 3.56 W/m(3) at a 200-Omega external resistor. The main reasons for enhanced electrochemical performance are higher levels of active biomass and more efficient substrate utilization under aerobic conditions. Coulombic efficiencies, however, were greatly reduced due to losses of reducing equivalents to aerobic respiration in the anode chamber. The next challenge will be to optimize the aeration rate of the bacterial culture to balance between maximization of bacterial activation and minimization of aerobic respiration in the culture.
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Affiliation(s)
- Miriam Rosenbaum
- Department of Biological and Environmental Engineering, Cornell University, 214 Riley-Robb Hall, Ithaca, New York 14853, USA
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Comparative analysis of membranous proteomics of Shewanella decolorationis S12 grown with azo compound or Fe (III) citrate as sole terminal electron acceptor. Appl Microbiol Biotechnol 2010; 86:1513-23. [DOI: 10.1007/s00253-010-2475-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Revised: 01/23/2010] [Accepted: 01/25/2010] [Indexed: 02/06/2023]
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Periplasmic electron transfer via the c-type cytochromes MtrA and FccA of Shewanella oneidensis MR-1. Appl Environ Microbiol 2009; 75:7789-96. [PMID: 19837833 DOI: 10.1128/aem.01834-09] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Dissimilatory microbial reduction of insoluble Fe(III) oxides is a geochemically and ecologically important process which involves the transfer of cellular, respiratory electrons from the cytoplasmic membrane to insoluble, extracellular, mineral-phase electron acceptors. In this paper evidence is provided for the function of the periplasmic fumarate reductase FccA and the decaheme c-type cytochrome MtrA in periplasmic electron transfer reactions in the gammaproteobacterium Shewanella oneidensis. Both proteins are abundant in the periplasm of ferric citrate-reducing S. oneidensis cells. In vitro fumarate reductase FccA and c-type cytochrome MtrA were reduced by the cytoplasmic membrane-bound protein CymA. Electron transfer between CymA and MtrA was 1.4-fold faster than the CymA-catalyzed reduction of FccA. Further experiments showing a bidirectional electron transfer between FccA and MtrA provided evidence for an electron transfer network in the periplasmic space of S. oneidensis. Hence, FccA could function in both the electron transport to fumarate and via MtrA to mineral-phase Fe(III). Growth experiments with a DeltafccA deletion mutant suggest a role of FccA as a transient electron storage protein.
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Ziegler S, Ackermann S, Majzlan J, Gescher J. Matrix composition and community structure analysis of a novel bacterial pyrite leaching community. Environ Microbiol 2009; 11:2329-38. [DOI: 10.1111/j.1462-2920.2009.01959.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Baron D, LaBelle E, Coursolle D, Gralnick JA, Bond DR. Electrochemical measurement of electron transfer kinetics by Shewanella oneidensis MR-1. J Biol Chem 2009; 284:28865-73. [PMID: 19661057 DOI: 10.1074/jbc.m109.043455] [Citation(s) in RCA: 176] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Shewanella oneidensis strain MR-1 can respire using carbon electrodes and metal oxyhydroxides as electron acceptors, requiring mechanisms for transferring electrons from the cell interior to surfaces located beyond the cell. Although purified outer membrane cytochromes will reduce both electrodes and metals, S. oneidensis also secretes flavins, which accelerate electron transfer to metals and electrodes. We developed techniques for detecting direct electron transfer by intact cells, using turnover and single turnover voltammetry. Metabolically active cells attached to graphite electrodes produced thin (submonolayer) films that demonstrated both catalytic and reversible electron transfer in the presence and absence of flavins. In the absence of soluble flavins, electron transfer occurred in a broad potential window centered at approximately 0 V (versus standard hydrogen electrode), and was altered in single (DeltaomcA, DeltamtrC) and double deletion (DeltaomcA/DeltamtrC) mutants of outer membrane cytochromes. The addition of soluble flavins at physiological concentrations significantly accelerated electron transfer and allowed catalytic electron transfer to occur at lower applied potentials (-0.2 V). Scan rate analysis indicated that rate constants for direct electron transfer were slower than those reported for pure cytochromes (approximately 1 s(-1)). These observations indicated that anodic current in the higher (>0 V) window is due to activation of a direct transfer mechanism, whereas electron transfer at lower potentials is enabled by flavins. The electrochemical dissection of these activities in living cells into two systems with characteristic midpoint potentials and kinetic behaviors explains prior observations and demonstrates the complementary nature of S. oneidensis electron transfer strategies.
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Affiliation(s)
- Daniel Baron
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota 55108, USA
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Kinetic characterization of OmcA and MtrC, terminal reductases involved in respiratory electron transfer for dissimilatory iron reduction in Shewanella oneidensis MR-1. Appl Environ Microbiol 2009; 75:5218-26. [PMID: 19542342 DOI: 10.1128/aem.00544-09] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have used scaling kinetics and the concept of kinetic competence to elucidate the role of hemeproteins OmcA and MtrC in iron reduction by Shewanella oneidensis MR-1. Second-order rate constants for OmcA and MtrC were determined by single-turnover experiments. For soluble iron species, a stopped-flow apparatus was used, and for the less reactive iron oxide goethite, a conventional spectrophotometer was used to measure rates. Steady-state experiments were performed to obtain molecular rate constants by quantifying the OmcA and MtrC contents of membrane fractions and whole cells by Western blot analysis. For reduction of soluble iron, rates determined from transient-state experiments were able to account for rates obtained from steady-state experiments. However, this was not true with goethite; rate constants determined from transient-state experiments were 100 to 1,000 times slower than those calculated from steady-state experiments with membrane fractions and whole cells. In contrast, addition of flavins to the goethite experiments resulted in rates that were consistent with both transient- and steady-state experiments. Kinetic simulations of steady-state results with kinetic constants obtained from transient-state experiments supported flavin involvement. Therefore, we show for the first time that OmcA and MtrC are kinetically competent to account for catalysis of soluble iron reduction in whole Shewanella cells but are not responsible for electron transfer via direct contact alone with insoluble iron-containing minerals. This work supports the hypothesis that electron shuttles are important participants in the reduction of solid Fe phases by this organism.
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Gescher JS, Cordova CD, Spormann AM. Dissimilatory iron reduction in Escherichia coli: identification of CymA of Shewanella oneidensis and NapC of E. coli as ferric reductases. Mol Microbiol 2008; 68:706-19. [PMID: 18394146 DOI: 10.1111/j.1365-2958.2008.06183.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Over geological time scales, microbial reduction of chelated Fe(III) or Fe(III) minerals has profoundly affected today's composition of our bio- and geosphere. However, the electron transfer reactions that are specific and defining for dissimilatory iron(III)-reducing (DIR) bacteria are not well understood. Using a synthetic biology approach involving the reconstruction of the putative electron transport chain of the DIR bacterium Shewanella oneidensis MR-1 in Escherichia coli, we showed that expression of cymA was necessary and sufficient to convert E. coli into a DIR bacterium. In intact cells, the Fe(III)-reducing activity was limited to Fe(III) NTA as electron acceptor. In vitro biochemical analysis indicated that CymA, which is a cytoplasmic membrane-associated tetrahaem c-type cytochrome, carries reductase activity towards Fe(III) NTA, Fe(III) citrate, as well as to AQDS, a humic acid analogue. The in vitro specific activities of Fe(III) citrate reductase and AQDS reductase of E. coli spheroplasts were 10x and 30x higher, respectively, relative to the specific rates observed in intact cells, suggesting that access of chelated and insoluble forms of Fe(III) and AQDS is restricted in whole cells. Interestingly, the E. coli CymA orthologue NapC also carried ferric reductase activity. Our data support the argument that the biochemical mechanism of Fe(III) reduction per se was not the key innovation leading to environmental relevant DIR bacteria. Rather, the evolution of an extension of the electron transfer pathway from the Fe(III) reductase CymA to the cell surface via a system of periplasmic and outer membrane cytochrome proteins enabled access to diffusion-impaired electron acceptors.
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Affiliation(s)
- Johannes S Gescher
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
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Ross DE, Ruebush SS, Brantley SL, Hartshorne RS, Clarke TA, Richardson DJ, Tien M. Characterization of protein-protein interactions involved in iron reduction by Shewanella oneidensis MR-1. Appl Environ Microbiol 2007; 73:5797-808. [PMID: 17675441 PMCID: PMC2074908 DOI: 10.1128/aem.00146-07] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The interaction of proteins implicated in dissimilatory metal reduction by Shewanella oneidensis MR-1 (outer membrane [OM] proteins OmcA, MtrB, and MtrC; OM-associated protein MtrA; periplasmic protein CctA; and cytoplasmic membrane protein CymA) were characterized by protein purification, analytical ultracentrifugation, and cross-linking methods. Five of these proteins are heme proteins, OmcA (83 kDa), MtrC (75 kDa), MtrA (32 kDa), CctA (19 kDa), and CymA (21 kDa), and can be visualized after sodium dodecyl sulfate-polyacrylamide gel electrophoresis by heme staining. We show for the first time that MtrC, MtrA, and MtrB form a 198-kDa complex with a 1:1:1 stoichiometry. These proteins copurify through anion-exchange chromatography, and the purified complex has the ability to reduce multiple forms of Fe(III) and Mn(IV). Additionally, MtrA fractionates with the OM through sucrose density gradient ultracentrifugation, and MtrA comigrates with MtrB in native gels. Protein cross-linking of whole cells with 1% formaldehyde show new heme bands of 160, 151, 136, and 59 kDa. Using antibodies to detect each protein separately, heme proteins OmcA and MtrC were shown to cross-link, yielding the 160-kDa band. Consistent with copurification results, MtrB cross-links with MtrA, forming high-molecular-mass bands of approximately 151 and 136 kDa.
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Affiliation(s)
- Daniel E Ross
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
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Bretschger O, Obraztsova A, Sturm CA, Chang IS, Gorby YA, Reed SB, Culley DE, Reardon CL, Barua S, Romine MF, Zhou J, Beliaev AS, Bouhenni R, Saffarini D, Mansfeld F, Kim BH, Fredrickson JK, Nealson KH. Current production and metal oxide reduction by Shewanella oneidensis MR-1 wild type and mutants. Appl Environ Microbiol 2007; 73:7003-12. [PMID: 17644630 PMCID: PMC2074945 DOI: 10.1128/aem.01087-07] [Citation(s) in RCA: 361] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Shewanella oneidensis MR-1 is a gram-negative facultative anaerobe capable of utilizing a broad range of electron acceptors, including several solid substrates. S. oneidensis MR-1 can reduce Mn(IV) and Fe(III) oxides and can produce current in microbial fuel cells. The mechanisms that are employed by S. oneidensis MR-1 to execute these processes have not yet been fully elucidated. Several different S. oneidensis MR-1 deletion mutants were generated and tested for current production and metal oxide reduction. The results showed that a few key cytochromes play a role in all of the processes but that their degrees of participation in each process are very different. Overall, these data suggest a very complex picture of electron transfer to solid and soluble substrates by S. oneidensis MR-1.
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Affiliation(s)
- Orianna Bretschger
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089, USA
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Chatfield CH, Cianciotto NP. The secreted pyomelanin pigment of Legionella pneumophila confers ferric reductase activity. Infect Immun 2007; 75:4062-70. [PMID: 17548481 PMCID: PMC1951983 DOI: 10.1128/iai.00489-07] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The virulence of Legionella pneumophila is dependent upon its capacity to acquire iron. To identify genes involved in expression of its siderophore, we screened a mutagenized population of L. pneumophila for strains that were no longer able to rescue the growth of a ferrous transport mutant. However, an unusual mutant was obtained that displayed a strong inhibitory effect on the feoB mutant. Due to an insertion in hmgA that encodes homogentisate 1,2-dioxygenase, the mutant secreted increased levels of pyomelanin, the L. pneumophila pigment that is derived from secreted homogentisic acid (HGA). Thus, we hypothesized that L. pneumophila-secreted HGA-melanin has intrinsic ferric reductase activity, converting Fe(3+) to Fe(2+), but that hyperpigmentation results in excessive reduction of iron that can, in the case of the feoB mutant, be inhibitory to growth. In support of this hypothesis, we demonstrated, for the first time, that wild-type L. pneumophila secretes ferric reductase activity. Moreover, whereas the hyperpigmented mutant had increased secreted activity, an lly mutant specifically impaired for pigment production lacked the activity. Compatible with the nature of HGA-melanins, the secreted ferric reductase activity was positively influenced by the amount of tyrosine in the growth medium, resistant to protease, acid precipitable, and heterogeneous in size. Together, these data represent the first demonstration of pyomelanin-mediated ferric reduction by a pathogenic bacterium.
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Affiliation(s)
- Christa H Chatfield
- Department of Microbiology-Immunology, Northwestern University Medical School, 320 East Superior Street, Chicago, IL 60611-3010, USA
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Tang X, Yi W, Munske GR, Adhikari DP, Zakharova NL, Bruce JE. Profiling the membrane proteome of Shewanella oneidensis MR-1 with new affinity labeling probes. J Proteome Res 2007; 6:724-34. [PMID: 17269728 PMCID: PMC2527595 DOI: 10.1021/pr060480e] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The membrane proteome plays a critical role in electron transport processes in Shewanella oneidensis MR-1, a bacterial organism that has great potential for bioremediation. Biotinylation of intact cells with subsequent affinity-enrichment has become a useful tool for characterization of the membrane proteome. As opposed to these commonly used, water-soluble commercial reagents, we here introduce a family of hydrophobic, cell-permeable affinity probes for extensive labeling and detection of membrane proteins. When applied to S. oneidensis cells, all three new chemical probes allowed identification of a substantial proportion of membrane proteins from total cell lysate without the use of specific membrane isolation method. From a total of 410 unique proteins identified, approximately 42% are cell envelope proteins that include outer membrane, periplasmic, and inner membrane proteins. This report demonstrates the first application of this intact cell biotinylation method to S. oneidensis and presents the results of many identified proteins that are involved in metal reduction processes. As a general labeling method, all chemical probes we introduced in this study can be extended to other organisms or cell types and will help expedite the characterization of membrane proteomes.
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Affiliation(s)
| | | | | | | | | | - James E. Bruce
- *Corresponding author: James E. Bruce, (E-mail): , (Phone): 509-335-2116, (Fax): 509-335-8867
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Xu M, Guo J, Kong X, Chen X, Sun G. Fe(III)-enhanced Azo Reduction by Shewanella decolorationis S12. Appl Microbiol Biotechnol 2007; 74:1342-9. [PMID: 17216448 DOI: 10.1007/s00253-006-0773-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2006] [Revised: 11/16/2006] [Accepted: 11/17/2006] [Indexed: 10/23/2022]
Abstract
Shewanella decolorationis S12 is capable of high rates of azo dye decolorization and dissimilatory Fe(III) reduction. Under anaerobic conditions, when Fe(III) and azo dye were copresent in S12 cultures, dissimilatory Fe(III) reduction and azo dye biodecolorization occurred simultaneously. Furthermore, the dye decolorization was enhanced by the presence of Fe(III). When 1 mM Fe(III) was added, the methyl red decolorizing efficiency was 72.1% after cultivation for 3 h, whereas the decolorizing efficiency was only 60.5% in Fe(III)-free medium. The decolorizing efficiencies increased as the concentration of Fe(III) was increased from 0 to 6 mM. Enzyme activities, which mediate the dye decolorization and Fe(III) reduction, were not affected by preadaption of cells to Fe(III) and azo dye nor by the addition of chloramphenicol. Both the Fe(III) reductase and the azo reductase were membrane associated. The respiratory electron transport chain inhibitors metyrapone, dicumarol, and stigmatellin showed significantly different effects on Fe(III) reduction than on azo dye decolorization.
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Affiliation(s)
- Meiying Xu
- Guangdong Institute of Microbiology, 100 Central Xianlie Road, Guangzhou 510070, People's Republic of China
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