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Solution structure and dynamics of the outer membrane cytochrome OmcF from Geobacter sulfurreducens. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1858:733-741. [DOI: 10.1016/j.bbabio.2017.03.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 03/24/2017] [Accepted: 03/31/2017] [Indexed: 11/15/2022]
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102
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Dombrowski N, Seitz KW, Teske AP, Baker BJ. Genomic insights into potential interdependencies in microbial hydrocarbon and nutrient cycling in hydrothermal sediments. MICROBIOME 2017; 5:106. [PMID: 28835260 PMCID: PMC5569505 DOI: 10.1186/s40168-017-0322-2] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 08/01/2017] [Indexed: 05/10/2023]
Abstract
BACKGROUND Deep-sea hydrothermal vents are hotspots for productivity and biodiversity. Thermal pyrolysis and circulation produce fluids rich in hydrocarbons and reduced compounds that stimulate microbial activity in surrounding sediments. Several studies have characterized the diversity of Guaymas Basin (Gulf of California) sediment-inhabiting microorganisms; however, many of the identified taxa lack cultures or genomic representations. Here, we resolved the metabolic potential and community-level interactions of these diverse communities by reconstructing and analyzing microbial genomes from metagenomic sequencing data. RESULTS We reconstructed 115 microbial metagenome-assembled genomes comprising 27 distinct archaeal and bacterial phyla. The archaea included members of the DPANN and TACK superphyla, Bathyarchaeota, novel Methanosarcinales (GoM-Arc1), and anaerobic methane-oxidizing lineages (ANME-1). Among the bacterial phyla, members of the Bacteroidetes, Chloroflexi, and Deltaproteobacteria were metabolically versatile and harbored potential pathways for hydrocarbon and lipid degradation and a variety of respiratory processes. Genes encoding enzymes that activate anaerobic hydrocarbons for degradation were detected in Bacteroidetes, Chloroflexi, Latescibacteria, and KSB1 phyla, while the reconstructed genomes for most candidate bacteria phyla (Aminicenantes, Atribacteria, Omnitrophica, and Stahlbacteria) indicated a fermentative metabolism. Newly obtained GoM-Arc1 archaeal genomes encoded novel pathways for short-chain hydrocarbon oxidation by alkyl-coenzyme M formation. We propose metabolic linkages among different functional groups, such as fermentative community members sharing substrate-level interdependencies with sulfur- and nitrogen-cycling microbes. CONCLUSIONS Overall, inferring the physiologies of archaea and bacteria from metagenome-assembled genomes in hydrothermal deep-sea sediments has revealed potential mechanisms of carbon cycling in deep-sea sediments. Our results further suggest a network of biogeochemical interdependencies in organic matter utilization, hydrocarbon degradation, and respiratory sulfur cycling among deep-sea-inhabiting microbial communities.
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Affiliation(s)
- Nina Dombrowski
- Department of Marine Science, Marine Science Institute, University of Texas Austin, Port Aransas, TX USA
| | - Kiley W. Seitz
- Department of Marine Science, Marine Science Institute, University of Texas Austin, Port Aransas, TX USA
| | - Andreas P. Teske
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Brett J. Baker
- Department of Marine Science, Marine Science Institute, University of Texas Austin, Port Aransas, TX USA
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103
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104
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Yang Y, Kong G, Chen X, Lian Y, Liu W, Xu M. Electricity Generation by Shewanella decolorationis S12 without Cytochrome c. Front Microbiol 2017; 8:1115. [PMID: 28676795 PMCID: PMC5476703 DOI: 10.3389/fmicb.2017.01115] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 05/31/2017] [Indexed: 11/24/2022] Open
Abstract
Bacterial extracellular electron transfer (EET) plays a key role in various natural and engineering processes. Outer membrane c-type cytochromes (OMCs) are considered to be essential in bacterial EET. However, most bacteria do not have OMCs but have redox proteins other than OMCs in their extracellular polymeric substances of biofilms. We hypothesized that these extracellular non-cytochrome c proteins (ENCP) could contribute to EET, especially with the facilitation of electron mediators. This study compared the electrode respiring capacity of wild type Shewanella decolorationis S12 and an OMC-deficient mutant. Although the OMC-deficient mutant was incapable in direct electricity generation in normal cultivation, it regained electricity generation capacity (26% of the wide type) with the aid of extracellular electron mediator (riboflavin). Further bioelectrochemistry and X-ray photoelectron spectroscopy analysis suggested that the ENCP, such as proteins with Fe–S cluster, may participate in the falvin-mediated EET. The results highlighted an important and direct role of the ENCP, generated by either electricigens or other microbes, in natural microbial EET process with the facilitation of electron mediators.
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Affiliation(s)
- Yonggang Yang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of MicrobiologyGuangzhou, China
| | - Guannan Kong
- State Key Laboratory of Applied Microbiology Southern ChinaGuangzhou, China
| | - Xingjuan Chen
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of MicrobiologyGuangzhou, China
| | - Yingli Lian
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of MicrobiologyGuangzhou, China
| | - Wenzong Liu
- Key Laboratory of Environmental Biotechnology, Chinese Academy of SciencesBeijing, China
| | - Meiying Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of MicrobiologyGuangzhou, China.,Guangdong Open Laboratory of Applied MicrobiologyGuangzhou, China
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105
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Abstract
Type II secretion (T2S) is one means by which Gram-negative pathogens secrete proteins into the extracellular milieu and/or host organisms. Based upon recent genome sequencing, it is clear that T2S is largely restricted to the Proteobacteria, occurring in many, but not all, genera in the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria classes. Prominent human and/or animal pathogens that express a T2S system(s) include Acinetobacter baumannii, Burkholderia pseudomallei, Chlamydia trachomatis, Escherichia coli, Klebsiella pneumoniae, Legionella pneumophila, Pseudomonas aeruginosa, Stenotrophomonas maltophilia, Vibrio cholerae, and Yersinia enterocolitica T2S-expressing plant pathogens include Dickeya dadantii, Erwinia amylovora, Pectobacterium carotovorum, Ralstonia solanacearum, Xanthomonas campestris, Xanthomonas oryzae, and Xylella fastidiosa T2S also occurs in nonpathogenic bacteria, facilitating symbioses, among other things. The output of a T2S system can range from only one to dozens of secreted proteins, encompassing a diverse array of toxins, degradative enzymes, and other effectors, including novel proteins. Pathogenic processes mediated by T2S include the death of host cells, degradation of tissue, suppression of innate immunity, adherence to host surfaces, biofilm formation, invasion into and growth within host cells, nutrient assimilation, and alterations in host ion flux. The reach of T2S is perhaps best illustrated by those bacteria that clearly use it for both environmental survival and virulence; e.g., L. pneumophila employs T2S for infection of amoebae, growth within lung cells, dampening of cytokines, and tissue destruction. This minireview provides an update on the types of bacteria that have T2S, the kinds of proteins that are secreted via T2S, and how T2S substrates promote infection.
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106
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Use of Bacteria To Stabilize Archaeological Iron. Appl Environ Microbiol 2017; 83:AEM.03478-16. [PMID: 28283522 DOI: 10.1128/aem.03478-16] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 02/15/2017] [Indexed: 11/20/2022] Open
Abstract
Iron artifacts are common among the findings of archaeological excavations. The corrosion layer formed on these objects requires stabilization after their recovery, without which the destruction of the item due to physicochemical damage is likely. Current technologies for stabilizing the corrosion layer are lengthy and generate hazardous waste products. Therefore, there is a pressing need for an alternative method for stabilizing the corrosion layer on iron objects. The aim of this study was to evaluate an alternative conservation-restoration method using bacteria. For this, anaerobic iron reduction leading to the formation of stable iron minerals in the presence of chlorine was investigated for two strains of Desulfitobacterium hafniense (strains TCE1 and LBE). Iron reduction was observed for soluble Fe(III) phases as well as for akaganeite, the most troublesome iron compound in the corrosion layer of archaeological iron objects. In terms of biogenic mineral production, differential efficiencies were observed in assays performed on corroded iron coupons. Strain TCE1 produced a homogeneous layer of vivianite covering 80% of the corroded surface, while on the coupons treated with strain LBE, only 10% of the surface was covered by the same mineral. Finally, an attempt to reduce iron on archaeological objects was performed with strain TCE1, which led to the formation of both biogenic vivianite and magnetite on the surface of the artifacts. These results demonstrate the potential of this biological treatment for stabilizing archaeological iron as a promising alternative to traditional conservation-restoration methods.IMPORTANCE Since the Iron Age, iron has been a fundamental material for the building of objects used in everyday life. However, due to its reactivity, iron can be easily corroded, and the physical stability of the object built is at risk. This is particularly true for archaeological objects on which a potentially unstable corrosion layer is formed during the time the object is buried. After excavation, changes in environmental conditions (e.g., higher oxygen concentration or lower humidity) alter the stability of the corrosion layer and can lead to the total destruction of the object. In this study, we demonstrate the feasibility of an innovative treatment based on bacterial iron reduction and biogenic mineral formation to stabilize the corrosion layer and protect these objects.
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107
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Li SW, Zeng RJ, Sheng GP. An excellent anaerobic respiration mode for chitin degradation by Shewanella oneidensis MR-1 in microbial fuel cells. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2016.11.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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108
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Liu T, Wu Y, Li F, Li X, Luo X. Rapid Redox Processes ofc-Type Cytochromes in A Living Cell Suspension ofShewanella oneidensisMR-1. ChemistrySelect 2017. [DOI: 10.1002/slct.201602021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Tongxu Liu
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control; Guangdong Institute of Eco-Environmental and Soil Sciences; Guangzhou 510650 PR China
| | - Yundang Wu
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control; Guangdong Institute of Eco-Environmental and Soil Sciences; Guangzhou 510650 PR China
| | - Fangbai Li
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control; Guangdong Institute of Eco-Environmental and Soil Sciences; Guangzhou 510650 PR China
| | - Xiaomin Li
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control; Guangdong Institute of Eco-Environmental and Soil Sciences; Guangzhou 510650 PR China
| | - Xiaobo Luo
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control; Guangdong Institute of Eco-Environmental and Soil Sciences; Guangzhou 510650 PR China
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109
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Xie Y, Dong H, Zeng G, Tang L, Jiang Z, Zhang C, Deng J, Zhang L, Zhang Y. The interactions between nanoscale zero-valent iron and microbes in the subsurface environment: A review. JOURNAL OF HAZARDOUS MATERIALS 2017; 321:390-407. [PMID: 27669380 DOI: 10.1016/j.jhazmat.2016.09.028] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/26/2016] [Accepted: 09/12/2016] [Indexed: 06/06/2023]
Abstract
Nanoscale zero-valent iron (NZVI) particles, applied for in-situ subsurface remediation, are inevitable to interact with various microbes in the remediation sites directly or indirectly. This review summarizes their interactions, including the effects of NZVI on microbial activity and growth, the synergistic effect of NZVI and microbes on the contaminant removal, and the effects of microbes on the aging of NZVI. NZVI could exert either inhibitive or stimulative effects on the growth of microbes. The mechanisms of NZVI cytotoxicity (i.e., the inhibitive effect) include physical damage and biochemical destruction. The stimulative effects of NZVI on certain bacteria are associated with the creation of appropriate living environment, either through providing electron donor (e.g., H2) or carbon sources (e.g., the engineered organic surface modifiers), or through eliminating the noxious substances that can cause bactericidal consequence. As a result of the positive interaction, the combination of NZVI and some microbes shows synergistic effect on contaminant removal. Additionally, the aged NZVI can be utilized by some iron-reducing bacteria, resulting in the transformation of Fe(III) to Fe(II), which can further contribute to the contaminant reduction. However, the Fe(III)-reduction process can probably induce environmental risks, such as environmental methylation and remobilization of the previously entrapped heavy metals.
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Affiliation(s)
- Yankai Xie
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Haoran Dong
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China.
| | - Guangming Zeng
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Lin Tang
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Zhao Jiang
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Cong Zhang
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Junmin Deng
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Lihua Zhang
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Yi Zhang
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
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110
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Li DB, Huang YX, Li J, Li LL, Tian LJ, Yu HQ. Electrochemical activities of Geobacter biofilms growing on electrodes with various potentials. Electrochim Acta 2017. [DOI: 10.1016/j.electacta.2016.12.146] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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111
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Microbial bioelectrosynthesis of hydrogen: Current challenges and scale-up. Enzyme Microb Technol 2017; 96:1-13. [DOI: 10.1016/j.enzmictec.2016.09.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 08/31/2016] [Accepted: 09/08/2016] [Indexed: 12/18/2022]
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112
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Ali N, Yousaf S, Anam M, Bangash Z, Maleeha S. Evaluating the efficiency of a mixed culture biofilm for the treatment of black liquor and molasses in a mediator-less microbial fuel cell. ENVIRONMENTAL TECHNOLOGY 2016; 37:2815-2822. [PMID: 26984479 DOI: 10.1080/09593330.2016.1166267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 03/10/2016] [Indexed: 06/05/2023]
Abstract
A microbial fuel cell (MFC) is an emerging environment-friendly technology to recover the useful energy available in waste by using microorganisms as catalyst. In this study, double chamber mediator-less MFCs separated by proton exchange membrane (PEM; Nafion) were constructed to determine the efficiency of mixed culture in using complex substrates (molasses and black liquor). It was found that activated sludge can serve as efficient source of electricigens for biofilm development on an anode. Power density of 2.425 W/m² was generated from molasses with chemical oxygen demand (COD) removal efficiency of 67% as compared to power density of 3.55 W/m² produced from black liquor along with COD removal efficiency of 78%. Moreover, it was demonstrated that surface area of PEM has a significant effect on power generation. An almost 5- to 8-fold increase in voltage was observed as the size of PEM was increased from 6.5 to 25 cm².
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Affiliation(s)
- Naeem Ali
- a Department of Microbiology , Quaid-i-Azam University , Islamabad , Pakistan
| | - Sameen Yousaf
- a Department of Microbiology , Quaid-i-Azam University , Islamabad , Pakistan
| | - Maira Anam
- a Department of Microbiology , Quaid-i-Azam University , Islamabad , Pakistan
| | - Zain Bangash
- a Department of Microbiology , Quaid-i-Azam University , Islamabad , Pakistan
| | - Sehrish Maleeha
- a Department of Microbiology , Quaid-i-Azam University , Islamabad , Pakistan
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113
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Wu Y, Li F, Liu T, Han R, Luo X. pH dependence of quinone-mediated extracellular electron transfer in a bioelectrochemical system. Electrochim Acta 2016. [DOI: 10.1016/j.electacta.2016.07.122] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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114
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Nealson KH, Rowe AR. Electromicrobiology: realities, grand challenges, goals and predictions. Microb Biotechnol 2016; 9:595-600. [PMID: 27506517 PMCID: PMC4993177 DOI: 10.1111/1751-7915.12400] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Electromicrobiology is a subdiscipline of microbiology that involves extracellular electron transfer (EET) to (or from) insoluble electron active redox compounds located outside the outer membrane of the cell. These interactions can often be studied using electrochemical techniques which have provided novel insights into microbial physiology in recent years. The mechanisms (and variations) of outward EET are well understood for two model systems, Shewanella and Geobacter, both of which employ multihaem cytochromes to provide an electron conduit to the cell exterior. In contrast, little is known of the intricacies of inward EET, even in these model systems. Given the number of labs now working on EET, it seems likely that most of the mechanistic details will be understood in a few years for the model systems, and the many applications of electromicrobiology will continue to move forward. But emerging work, using electrodes as electron acceptors and donors is providing an abundance of new types of microbes capable of EET inward and/or outward: microbes that are clearly different from our known systems. The extent of this very diverse, and perhaps widely distributed and biogeochemically important ability needs to be determined to understand the mechanisms, importance, and raison d'etre of EET for microbial biology.
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Affiliation(s)
- Kenneth H Nealson
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
| | - Annette R Rowe
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
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115
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Tanzil AH, Sultana ST, Saunders SR, Dohnalkova AC, Shi L, Davenport E, Ha P, Beyenal H. Production of gold nanoparticles by electrode-respiring Geobacter sulfurreducens biofilms. Enzyme Microb Technol 2016; 95:69-75. [PMID: 27866628 DOI: 10.1016/j.enzmictec.2016.07.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 07/19/2016] [Accepted: 07/21/2016] [Indexed: 12/23/2022]
Abstract
The goal of this work was to synthesize gold nanoparticles (AuNPs) using electrode-respiring Geobacter sulfurreducens biofilms. We found that AuNPs are generated in the extracellular matrix of Geobacter biofilms and have an average particle size of 20nm. The formation of AuNPs was verified using TEM, FTIR and EDX. We also found that the extracellular substances extracted from electrode-respiring G. sulfurreducens biofilms reduce Au3+ to AuNPs. From FTIR spectra, it appears that reduced sugars were involved in the bioreduction and synthesis of AuNPs and that amine groups acted as the major biomolecules involved in binding.
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Affiliation(s)
- Abid H Tanzil
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, USA
| | - Sujala T Sultana
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, USA
| | - Steven R Saunders
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, USA
| | - Alice C Dohnalkova
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Liang Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Emily Davenport
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, USA
| | - Phuc Ha
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, USA
| | - Haluk Beyenal
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, USA.
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116
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Yuan Y, Guo T, Qiu X, Tang J, Huang Y, Zhuang L, Zhou S, Li Z, Guan BO, Zhang X, Albert J. Electrochemical Surface Plasmon Resonance Fiber-Optic Sensor: In Situ Detection of Electroactive Biofilms. Anal Chem 2016; 88:7609-16. [DOI: 10.1021/acs.analchem.6b01314] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Yong Yuan
- Guangdong
Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, China
| | - Tuan Guo
- Guangdong
Key Laboratory of Optical Fiber Sensing and Communications, Institute
of Photonics Technology, Jinan University, Guangzhou 510632, China
| | - Xuhui Qiu
- Guangdong
Key Laboratory of Optical Fiber Sensing and Communications, Institute
of Photonics Technology, Jinan University, Guangzhou 510632, China
| | - Jiahuan Tang
- Guangdong
Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, China
| | - Yunyun Huang
- Guangdong
Key Laboratory of Optical Fiber Sensing and Communications, Institute
of Photonics Technology, Jinan University, Guangzhou 510632, China
| | - Li Zhuang
- Guangdong
Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, China
| | - Shungui Zhou
- Guangdong
Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, China
| | - Zhaohui Li
- Guangdong
Key Laboratory of Optical Fiber Sensing and Communications, Institute
of Photonics Technology, Jinan University, Guangzhou 510632, China
| | - Bai-Ou Guan
- Guangdong
Key Laboratory of Optical Fiber Sensing and Communications, Institute
of Photonics Technology, Jinan University, Guangzhou 510632, China
| | - Xuming Zhang
- Department
of Applied Physics, Hong Kong Polytechnic University, Hong Kong, People’s Republic of China
| | - Jacques Albert
- Department
of Electronics, Carleton University, Ottawa K1S5B6, Canada
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117
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Marnocha CL, Levy AT, Powell DH, Hanson TE, Chan CS. Mechanisms of extracellular S0 globule production and degradation in Chlorobaculumtepidum via dynamic cell-globule interactions. MICROBIOLOGY (READING, ENGLAND) 2016; 162:1125-1134. [PMID: 27121868 PMCID: PMC5772824 DOI: 10.1099/mic.0.000294] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 04/25/2016] [Indexed: 11/18/2022]
Abstract
The Chlorobiales are anoxygenic phototrophs that produce solid, extracellular elemental sulfur globules as an intermediate step in the oxidation of sulfide to sulfate. These organisms must export sulfur while preventing cell encrustation during S0 globule formation; during globule degradation they must find and mobilize the sulfur for intracellular oxidation to sulfate. To understand how the Chlorobiales address these challenges, we characterized the spatial relationships and physical dynamics of Chlorobaculum tepidum cells and S0 globules by light and electron microscopy. Cba. tepidum commonly formed globules at a distance from cells. Soluble polysulfides detected during globule production may allow for remote nucleation of globules. Polysulfides were also detected during globule degradation, probably produced as an intermediate of sulfur oxidation by attached cells. Polysulfides could feed unattached cells, which made up over 80% of the population and had comparable growth rates to attached cells. Given that S0 is formed remotely from cells, there is a question as to how cells are able to move toward S0 in order to attach. Time-lapse microscopy shows that Cba. tepidum is in fact capable of twitching motility, a finding supported by the presence of genes encoding type IV pili. Our results show how Cba. tepidum is able to avoid mineral encrustation and benefit from globule degradation even when not attached. In the environment, Cba. tepidum may also benefit from soluble sulfur species produced by other sulfur-oxidizing or sulfur-reducing bacteria as these organisms interact with its biogenic S0 globules.
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Affiliation(s)
- C. L. Marnocha
- Department of Geological Sciences, University of Delaware, Newark, DE 19716, USA
- Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
| | - A. T. Levy
- Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
| | - D. H. Powell
- Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
| | - T. E. Hanson
- Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
- School of Marine Science and Policy, University of Delaware, Newark, DE 19716, USA
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - C. S. Chan
- Department of Geological Sciences, University of Delaware, Newark, DE 19716, USA
- Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
- School of Marine Science and Policy, University of Delaware, Newark, DE 19716, USA
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118
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Storck T, Virdis B, Batstone DJ. Modelling extracellular limitations for mediated versus direct interspecies electron transfer. THE ISME JOURNAL 2016; 10:621-31. [PMID: 26545286 PMCID: PMC4817672 DOI: 10.1038/ismej.2015.139] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 06/15/2015] [Accepted: 07/01/2015] [Indexed: 12/21/2022]
Abstract
Interspecies electron transfer (IET) is important for many anaerobic processes, but is critically dependent on mode of transfer. In particular, direct IET (DIET) has been recently proposed as a metabolically advantageous mode compared with mediated IET (MIET) via hydrogen or formate. We analyse relative feasibility of these IET modes by modelling external limitations using a reaction-diffusion-electrochemical approach in a three-dimensional domain. For otherwise identical conditions, external electron transfer rates per cell pair (cp) are considerably higher for formate-MIET (317 × 10(3) e(-) cp(-1) s(-1)) compared with DIET (44.9 × 10(3) e(-) cp(-1) s(-1)) or hydrogen-MIET (5.24 × 10(3) e(-) cp(-1) s(-1)). MIET is limited by the mediator concentration gradient at which reactions are still thermodynamically feasible, whereas DIET is limited through redox cofactor (for example, cytochromes) activation losses. Model outcomes are sensitive to key parameters for external electron transfer including cofactor electron transfer rate constant and redox cofactor area, concentration or count per cell, but formate-MIET is generally more favourable for reasonable parameter ranges. Extending the analysis to multiple cells shows that the size of the network does not strongly influence relative or absolute favourability of IET modes. Similar electron transfer rates for formate-MIET and DIET can be achieved in our case with a slight (0.7 kJ mol(-1)) thermodynamic advantage for DIET. This indicates that close to thermodynamic feasibility, external limitations can be compensated for by improved metabolic efficiency when using direct electron transfer.
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Affiliation(s)
- Tomas Storck
- Advanced Water Management Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Bernardino Virdis
- Advanced Water Management Centre, The University of Queensland, Brisbane, Queensland, Australia
- Centre for Microbial Electrochemical Systems, The University of Queensland, Brisbane, Queensland, Australia
| | - Damien J Batstone
- Advanced Water Management Centre, The University of Queensland, Brisbane, Queensland, Australia
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119
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Otwell AE, Callister SJ, Zink EM, Smith RD, Richardson RE. Comparative Proteomic Analysis of Desulfotomaculum reducens MI-1: Insights into the Metabolic Versatility of a Gram-Positive Sulfate- and Metal-Reducing Bacterium. Front Microbiol 2016; 7:191. [PMID: 26925055 PMCID: PMC4759654 DOI: 10.3389/fmicb.2016.00191] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Accepted: 02/03/2016] [Indexed: 11/30/2022] Open
Abstract
The proteomes of the metabolically versatile and poorly characterized Gram-positive bacterium Desulfotomaculum reducens MI-1 were compared across four cultivation conditions including sulfate reduction, soluble Fe(III) reduction, insoluble Fe(III) reduction, and pyruvate fermentation. Collectively across conditions, we observed at high confidence ~38% of genome-encoded proteins. Here, we focus on proteins that display significant differential abundance on conditions tested. To the best of our knowledge, this is the first full-proteome study focused on a Gram-positive organism cultivated either on sulfate or metal-reducing conditions. Several proteins with uncharacterized function encoded within heterodisulfide reductase (hdr)-containing loci were upregulated on either sulfate (Dred_0633-4, Dred_0689-90, and Dred_1325-30) or Fe(III)-citrate-reducing conditions (Dred_0432-3 and Dred_1778-84). Two of these hdr-containing loci display homology to recently described flavin-based electron bifurcation (FBEB) pathways (Dred_1325-30 and Dred_1778-84). Additionally, we propose that a cluster of proteins, which is homologous to a described FBEB lactate dehydrogenase (LDH) complex, is performing lactate oxidation in D. reducens (Dred_0367-9). Analysis of the putative sulfate reduction machinery in D. reducens revealed that most of these proteins are constitutively expressed across cultivation conditions tested. In addition, peptides from the single multiheme c-type cytochrome (MHC) in the genome were exclusively observed on the insoluble Fe(III) condition, suggesting that this MHC may play a role in reduction of insoluble metals.
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Affiliation(s)
- Anne E Otwell
- Department of Microbiology, Cornell University Ithaca, NY, USA
| | - Stephen J Callister
- Pacific Northwest National Laboratory, Biological Sciences Division Richland, WA, USA
| | - Erika M Zink
- Pacific Northwest National Laboratory, Biological Sciences Division Richland, WA, USA
| | - Richard D Smith
- Pacific Northwest National Laboratory, Biological Sciences Division Richland, WA, USA
| | - Ruth E Richardson
- Department of Civil and Environmental Engineering, Cornell University Ithaca, NY, USA
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120
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Choi O, Sang BI. Extracellular electron transfer from cathode to microbes: application for biofuel production. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:11. [PMID: 27034716 PMCID: PMC4717640 DOI: 10.1186/s13068-016-0426-0] [Citation(s) in RCA: 135] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 01/05/2016] [Indexed: 05/07/2023]
Abstract
Extracellular electron transfer in microorganisms has been applied for bioelectrochemical synthesis utilizing microbes to catalyze anodic and/or cathodic biochemical reactions. Anodic reactions (electron transfer from microbe to anode) are used for current production and cathodic reactions (electron transfer from cathode to microbe) have recently been applied for current consumption for valuable biochemical production. The extensively studied exoelectrogenic bacteria Shewanella and Geobacter showed that both directions for electron transfer would be possible. It was proposed that gram-positive bacteria, in the absence of cytochrome C, would accept electrons using a cascade of membrane-bound complexes such as membrane-bound Fe-S proteins, oxidoreductase, and periplasmic enzymes. Modification of the cathode with the addition of positive charged species such as chitosan or with an increase of the interfacial area using a porous three-dimensional scaffold electrode led to increased current consumption. The extracellular electron transfer from the cathode to the microbe could catalyze various bioelectrochemical reductions. Electrofermentation used electrons from the cathode as reducing power to produce more reduced compounds such as alcohols than acids, shifting the metabolic pathway. Electrofuel could be generated through artificial photosynthesis using electrical energy instead of solar energy in the process of carbon fixation.
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Affiliation(s)
- Okkyoung Choi
- Department of Chemical Engineering, Hanyang University, 222 Wangshimni-ro, Seongdong-gu, Seoul, 04763 South Korea
| | - Byoung-In Sang
- Department of Chemical Engineering, Hanyang University, 222 Wangshimni-ro, Seongdong-gu, Seoul, 04763 South Korea
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121
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Xia Y, Wang Y, Wang Y, Chin FYL, Zhang T. Cellular adhesiveness and cellulolytic capacity in Anaerolineae revealed by omics-based genome interpretation. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:111. [PMID: 27222666 PMCID: PMC4877987 DOI: 10.1186/s13068-016-0524-z] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 05/09/2016] [Indexed: 05/06/2023]
Abstract
BACKGROUND The Anaerolineae lineage of Chloroflexi had been identified as one of the core microbial populations in anaerobic digesters; however, the ecological role of the Anaerolineae remains uncertain due to the scarcity of isolates and annotated genome sequences. Our previous metatranscriptional analysis revealed this prevalent population that showed minimum involvement in the main pathways of cellulose hydrolysis and subsequent methanogenesis in the thermophilic cellulose fermentative consortium (TCF). RESULTS In further pursuit, five high-quality curated draft genomes (>98 % completeness) of this population, including two affiliated with the inaccessible lineage of SBR1031, were retrieved by sequence-based multi-dimensional coverage binning. Comparative genomic analyses revealed versatile genetic capabilities for carbohydrate-based fermentative lifestyle including key genes catalyzing cellulose hydrolysis in Anaerolinea phylotypes. However, the low transcriptional activities of carbohydrate-active genes (CAGs) excluded cellulolytic capability as the selective advantage for their prevalence in the community. Instead, a substantially active type VI pili (Tfp) assembly was observed. Expression of the tight adherence protein on the Tfp indicated its function for cellular attachment which was further testified to be more likely related to cell aggregation other than cellulose surface adhesion. Meanwhile, this Tfp structure was found not contributing to syntrophic methanogenesis. Members of the SBR1031 encoded key genes for acetogenic dehydrogenation that may allow ethanol to be used as a carbon source. CONCLUSION The common prevalence of Anaerolineae in anaerobic digesters should be originated from advantageous cellular adhesiveness enabled by Tfp assembly other than its potential as cellulose degrader or anaerobic syntrophs.
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Affiliation(s)
- Yu Xia
- />Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China
| | - Yubo Wang
- />Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China
| | - Yi Wang
- />Department of Computer Science, The University of Hong Kong, Hong Kong SAR, China
| | - Francis Y. L. Chin
- />Department of Computer Science, The University of Hong Kong, Hong Kong SAR, China
- />Department of Computing, Hang Seng Management College, Hong Kong SAR, China
| | - Tong Zhang
- />Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, China
- />Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China
- />Environmental Biotechnology Lab, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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122
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Yang Y, Wu Y, Hu Y, Cao Y, Poh CL, Cao B, Song H. Engineering Electrode-Attached Microbial Consortia for High-Performance Xylose-Fed Microbial Fuel Cell. ACS Catal 2015. [DOI: 10.1021/acscatal.5b01733] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Yun Yang
- School
of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, 637457, Singapore
- Singapore
Centre on Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Yichao Wu
- Singapore
Centre on Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
- School
of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, 637798, Singapore
| | - Yidan Hu
- Singapore
Centre on Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Yingxiu Cao
- Key
Laboratory of Systems Bioengineering (Ministry of Education), SynBio
Research Platform, Collaborative Innovation Center of Chemical Science
and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P.R. China
| | - Chueh Loo Poh
- School
of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, 637457, Singapore
| | - Bin Cao
- Singapore
Centre on Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
- School
of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, 637798, Singapore
| | - Hao Song
- Key
Laboratory of Systems Bioengineering (Ministry of Education), SynBio
Research Platform, Collaborative Innovation Center of Chemical Science
and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P.R. China
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123
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Manzella MP, Holmes DE, Rocheleau JM, Chung A, Reguera G, Kashefi K. The complete genome sequence and emendation of the hyperthermophilic, obligate iron-reducing archaeon "Geoglobus ahangari" strain 234(T). Stand Genomic Sci 2015; 10:77. [PMID: 26457129 PMCID: PMC4600277 DOI: 10.1186/s40793-015-0035-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 07/07/2015] [Indexed: 11/10/2022] Open
Abstract
“Geoglobus ahangari” strain 234T is an obligate Fe(III)-reducing member of the Archaeoglobales, within the archaeal phylum Euryarchaeota, isolated from the Guaymas Basin hydrothermal system. It grows optimally at 88 °C by coupling the reduction of Fe(III) oxides to the oxidation of a wide range of compounds, including long-chain fatty acids, and also grows autotrophically with hydrogen and Fe(III). It is the first archaeon reported to use a direct contact mechanism for Fe(III) oxide reduction, relying on a single archaellum for locomotion, numerous curled extracellular appendages for attachment, and outer-surface heme-containing proteins for electron transfer to the insoluble Fe(III) oxides. Here we describe the annotation of the genome of “G. ahangari” strain 234T and identify components critical to its versatility in electron donor utilization and obligate Fe(III) respiratory metabolism at high temperatures. The genome comprises a single, circular chromosome of 1,770,093 base pairs containing 2034 protein-coding genes and 52 RNA genes. In addition, emended descriptions of the genus “Geoglobus” and species “G. ahangari” are described.
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Affiliation(s)
- Michael P Manzella
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI USA
| | - Dawn E Holmes
- Department of Physical and Biological Sciences, Western New England University, Springfield, MA USA
| | - Jessica M Rocheleau
- Department of Physical and Biological Sciences, Western New England University, Springfield, MA USA
| | - Amanda Chung
- Department of Physical and Biological Sciences, Western New England University, Springfield, MA USA
| | - Gemma Reguera
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI USA
| | - Kazem Kashefi
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI USA
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124
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Li Z, Kim DD, Nelson OD, Otwell AE, Richardson RE, Callister SJ, Lin H. Molecular dissection of a putative iron reductase from Desulfotomaculum reducens MI-1. Biochem Biophys Res Commun 2015; 467:503-8. [PMID: 26454174 DOI: 10.1016/j.bbrc.2015.10.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 10/04/2015] [Indexed: 12/01/2022]
Abstract
Desulfotomaculum reducens MI-1 is a Firmicute strain capable of reducing a variety of heavy metal ions and has a great potential in heavy metal bioremediation. We recently identified Dred_2421 as a potential iron reductase through proteomic study of D. reducens. The current study examines its iron-reduction mechanism. Dred_2421, like its close homolog from Escherichia coli (2, 4-dienoyl-CoA reductase), has an FMN-binding N-terminal domain (NTD), an FAD-binding C-terminal domain (CTD), and a 4Fe-4S cluster between the two domains. To understand the mechanism of the iron-reduction activity and the role of each domain, we generated a series of variants for each domain and investigated their iron-reduction activity. Our results suggest that CTD is the main contributor of the iron-reduction activity, and that NTD and the 4Fe-4S cluster are not directly involved in such activity. This study provides a mechanistic understanding of the iron-reductase activity of Dred_2421 and may also help to elucidate other physiological activities this enzyme may have.
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Affiliation(s)
- Zhi Li
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - David D Kim
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Ornella D Nelson
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Anne E Otwell
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Ruth E Richardson
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA
| | | | - Hening Lin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA; Howard Hughes Medical Institute, USA.
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125
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Liu Y, Fredrickson JK, Zachara JM, Shi L. Direct involvement of ombB, omaB, and omcB genes in extracellular reduction of Fe(III) by Geobacter sulfurreducens PCA. Front Microbiol 2015; 6:1075. [PMID: 26483786 PMCID: PMC4589669 DOI: 10.3389/fmicb.2015.01075] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Accepted: 09/18/2015] [Indexed: 12/11/2022] Open
Abstract
The tandem gene clusters orfR-ombB-omaB-omcB and orfS-ombC-omaC-omcC of the metal-reducing bacterium Geobacter sulfurreducens PCA are responsible for trans-outer membrane electron transfer during extracellular reduction of Fe(III)-citrate and ferrihydrite [a poorly crystalline Fe(III) oxide]. Each gene cluster encodes a putative transcriptional factor (OrfR/OrfS), a porin-like outer-membrane protein (OmbB/OmbC), a periplasmic c-type cytochrome (c-Cyt, OmaB/OmaC) and an outer-membrane c-Cyt (OmcB/OmcC). The individual roles of OmbB, OmaB and OmcB in extracellular reduction of Fe(III), however, have remained either uninvestigated or controversial. Here, we showed that replacements of ombB, omaB, omcB, and ombB-omaB with an antibiotic gene in the presence of ombC-omaC-omcC had no impact on reduction of Fe(III)-citrate by G. sulfurreducens PCA. Disruption of ombB, omaB, omcB, and ombB-omaB in the absence of ombC-omaC-omcC, however, severely impaired the bacterial ability to reduce Fe(III)-citrate as well as ferrihydrite. These results unequivocally demonstrate an overlapping role of ombB-omaB-omcB and ombC-omaC-omcC in extracellular Fe(III) reduction by G. sulfurreducens PCA. Involvement of both ombB-omaB-omcB and ombC-omaC-omcC in extracellular Fe(III) reduction reflects the importance of these trans-outer membrane protein complexes in the physiology of this bacterium. Moreover, the kinetics of Fe(III)-citrate and ferrihydrite reduction by these mutants in the absence of ombC-omaC-omcC were nearly identical, which suggests that absence of any protein subunit eliminates function of OmaB/OmbB/OmcB protein complex. Finally, orfS was found to have a negative impact on the extracellular reduction of Fe(III)-citrate and ferrihydrite in G. sulfurreducens PCA probably by serving as a transcriptional repressor.
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Affiliation(s)
- Yimo Liu
- Pacific Northwest National Laboratory, Richland, WA USA
| | | | | | - Liang Shi
- Pacific Northwest National Laboratory, Richland, WA USA
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126
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Yu Y, Wu Y, Cao B, Gao YG, Yan X. Adjustable bidirectional extracellular electron transfer between Comamonas testosteroni biofilms and electrode via distinct electron mediators. Electrochem commun 2015. [DOI: 10.1016/j.elecom.2015.07.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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127
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Kondo K, Okamoto A, Hashimoto K, Nakamura R. Sulfur-Mediated Electron Shuttling Sustains Microbial Long-Distance Extracellular Electron Transfer with the Aid of Metallic Iron Sulfides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:7427-7434. [PMID: 26070345 DOI: 10.1021/acs.langmuir.5b01033] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In addition to serving as an energy source for microbial growth, iron sulfides are proposed to act as naturally occurring electrical wires that mediate long-distance extracellular electron transfer (EET) and bridge spatially discrete redox environments. These hypothetical EET reactions stand on the abilities of microbes to use the interfacial electrochemistry of metallic/semiconductive iron sulfides to maintain metabolisms; however, the mechanisms of these phenomena remain unexplored. To obtain insight into EET to iron sulfides, we monitored EET at the interface between Shewanella oneidensis MR-1 cells and biomineralized iron sulfides in an electrochemical cell. Respiratory current steeply increased with the concomitant formation of poorly crystalline mackinawite (FeS) minerals, indicating that S. oneidensis has the ability to exploit extracellularly formed metallic FeS for long-distance EET. Deletion of major proteins of the metal-reduction (Mtr) pathway (OmcA, MtrC, CymA, and PilD) caused only subtle effects on the EET efficiency, a finding that sharply contrasts the majority of studies that report that the Mtr pathway is indispensable for the reduction of metal oxides and electrodes. The gene expression analyses of polysulfide and thiosulfate reductase suggest the existence of a sulfur-mediated electron-shuttling mechanism by which HS(-) ions and water-soluble polysulfides (HS(n)(-), where n ≥ 2) generated in the periplasmic space deliver electrons from cellular metabolic processes to cell surface-associated FeS. The finding of this Mtr-independent pathway indicates that polysulfide reductases complement the function of outer-membrane cytochromes in EET reactions and, thus, significantly expand the number of microbial species potentially capable of long-distance EET in sulfur-rich anoxic environments.
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Affiliation(s)
- Katsuhito Kondo
- †Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Akihiro Okamoto
- †Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kazuhito Hashimoto
- †Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Ryuhei Nakamura
- ‡Biofunctional Catalyst Research Team, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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128
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Kracke F, Vassilev I, Krömer JO. Microbial electron transport and energy conservation - the foundation for optimizing bioelectrochemical systems. Front Microbiol 2015; 6:575. [PMID: 26124754 PMCID: PMC4463002 DOI: 10.3389/fmicb.2015.00575] [Citation(s) in RCA: 318] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 05/25/2015] [Indexed: 12/23/2022] Open
Abstract
Microbial electrochemical techniques describe a variety of emerging technologies that use electrode–bacteria interactions for biotechnology applications including the production of electricity, waste and wastewater treatment, bioremediation and the production of valuable products. Central in each application is the ability of the microbial catalyst to interact with external electron acceptors and/or donors and its metabolic properties that enable the combination of electron transport and carbon metabolism. And here also lies the key challenge. A wide range of microbes has been discovered to be able to exchange electrons with solid surfaces or mediators but only a few have been studied in depth. Especially electron transfer mechanisms from cathodes towards the microbial organism are poorly understood but are essential for many applications such as microbial electrosynthesis. We analyze the different electron transport chains that nature offers for organisms such as metal respiring bacteria and acetogens, but also standard biotechnological organisms currently used in bio-production. Special focus lies on the essential connection of redox and energy metabolism, which is often ignored when studying bioelectrochemical systems. The possibility of extracellular electron exchange at different points in each organism is discussed regarding required redox potentials and effect on cellular redox and energy levels. Key compounds such as electron carriers (e.g., cytochromes, ferredoxin, quinones, flavins) are identified and analyzed regarding their possible role in electrode–microbe interactions. This work summarizes our current knowledge on electron transport processes and uses a theoretical approach to predict the impact of different modes of transfer on the energy metabolism. As such it adds an important piece of fundamental understanding of microbial electron transport possibilities to the research community and will help to optimize and advance bioelectrochemical techniques.
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Affiliation(s)
- Frauke Kracke
- Centre for Microbial Electrochemical Systems, The University of Queensland, Brisbane QLD, Australia ; Advanced Water Management Centre, The University of Queensland, Brisbane QLD, Australia
| | - Igor Vassilev
- Centre for Microbial Electrochemical Systems, The University of Queensland, Brisbane QLD, Australia ; Advanced Water Management Centre, The University of Queensland, Brisbane QLD, Australia
| | - Jens O Krömer
- Centre for Microbial Electrochemical Systems, The University of Queensland, Brisbane QLD, Australia ; Advanced Water Management Centre, The University of Queensland, Brisbane QLD, Australia
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129
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Metabolite-enabled mutualistic interaction between Shewanella oneidensis and Escherichia coli in a co-culture using an electrode as electron acceptor. Sci Rep 2015; 5:11222. [PMID: 26061569 PMCID: PMC4462164 DOI: 10.1038/srep11222] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 05/19/2015] [Indexed: 01/26/2023] Open
Abstract
Mutualistic interactions in planktonic microbial communities have been extensively studied. However, our understanding on mutualistic communities consisting of co-existing planktonic cells and biofilms is limited. Here, we report a planktonic cells-biofilm mutualistic system established by the fermentative bacterium Escherichia coli and the dissimilatory metal-reducing bacterium Shewanella oneidensis in a bioelectrochemical device, where planktonic cells in the anode media interact with the biofilms on the electrode. Our results show that the transfer of formate is the key mechanism in this mutualistic system. More importantly, we demonstrate that the relative distribution of E. coli and S. oneidensis in the liquid media and biofilm is likely driven by their metabolic functions towards an optimum communal metabolism in the bioelectrochemical device. RNA sequencing-based transcriptomic analyses of the interacting organisms in the mutualistic system potentially reveal differential expression of genes involved in extracellular electron transfer pathways in both species in the planktonic cultures and biofilms.
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130
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Yan H, Catania C, Bazan GC. Membrane-intercalating conjugated oligoelectrolytes: impact on bioelectrochemical systems. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2015; 27:2958-2973. [PMID: 25846107 DOI: 10.1002/adma.201500487] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Indexed: 06/04/2023]
Abstract
Conjugated oligoelectrolytes (COEs), molecules that are defined by a π-delocalized backbone and terminal ionic pendant groups, have been previously demonstrated to effectively reduce charge-injection/extraction barriers at metal/organic interfaces in thin-film organic-electronic devices. Recent studies demonstrate a spontaneous affinity of certain COEs to intercalate into, and align within, lipid bilayers in an ordered orientation, thereby allowing modification of membrane properties and the functions of microbes in bioelectrochemical and photosynthetic systems. Several reports have provided evidence of enhanced current generation and bioproduction. Mechanistic approaches suggest that COEs influence microbial extracellular electron transport to abiotic electrode surfaces via more than one proposed pathway, including direct electron transfer and meditated electron transfer. Molecular dynamics simulations as a function of molecular structure suggest that insertion of cationic COEs results in membrane thinning as the lipid phosphate head groups are drawn toward the center of the bilayer. Since variations in molecular structures, especially the length of the conjugated backbone, distribution of ionic groups, and hydrophobic substitutions, show an effect on their antimicrobial properties, preferential cell localization, and microbial selection, it is promising to further design novel membrane-intercalating molecules based on COEs for practical applications, including energy generation, environmental remediation, and antimicrobial treatment.
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Affiliation(s)
- Hengjing Yan
- Department of Chemistry and Biochemistry, Center for Polymers and Organic Solids, University of California at Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Chelsea Catania
- Department of Materials, University of California at Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Guillermo C Bazan
- Department of Chemistry and Biochemistry, Center for Polymers and Organic Solids, University of California at Santa Barbara, Santa Barbara, CA, 93106, USA
- Department of Materials, University of California at Santa Barbara, Santa Barbara, CA, 93106, USA
- King Abdulaziz University, Jeddah, Saudi Arabia
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131
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Babanova S, Bretschger O, Roy J, Cheung A, Artyushkova K, Atanassov P. Innovative statistical interpretation of Shewanella oneidensis microbial fuel cells data. Phys Chem Chem Phys 2015; 16:8956-69. [PMID: 24691574 DOI: 10.1039/c4cp00566j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The last decade of research has made significant strides toward practical applications of Microbial Fuel Cells (MFCs); however, design improvements and operational optimization cannot be realized without equally considering engineering designs and biological interfacial reactions. In this study, the main factors contributing to MFCs' overall performance and their influence on MFC reproducibility are discussed. Two statistical approaches were used to create a map of MFC components and their expanded uncertainties, principal component analysis (PCA) and uncertainty of measurement results (UMR). PCA was used to identify the major factors influencing MFCs and to determine their ascendency over MFC operational characteristics statistically. UMR was applied to evaluate the factors' uncertainties and estimate their level of contribution to the final irreproducibility. In order to simplify the presentation and concentrate on the MFC components, only results from Shewanella spp. were included; however, a similar analysis could be applied for any DMRB or microbial community. The performed PCA/UMR analyses suggest that better reproducibility of MFC performance can be achieved through improved design parameters. This approach is exactly opposite to the MFC optimization and scale up approach, which should start with improving the bacteria-electrode interactions and applying these findings to well-designed systems.
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Affiliation(s)
- Sofia Babanova
- Chemical and Nuclear Engineering Department, Center for Emerging Energy Technologies, University of New Mexico, Albuquerque, NM 87131, USA.
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132
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Hwang ET, Sheikh K, Orchard KL, Hojo D, Radu V, Lee CY, Ainsworth E, Lockwood C, Gross MA, Adschiri T, Reisner E, Butt JN, Jeuken LJC. A Decaheme Cytochrome as a Molecular Electron Conduit in Dye-Sensitized Photoanodes. ADVANCED FUNCTIONAL MATERIALS 2015; 25:2308-2315. [PMID: 26180522 PMCID: PMC4493899 DOI: 10.1002/adfm.201404541] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 02/05/2015] [Indexed: 06/04/2023]
Abstract
In nature, charge recombination in light-harvesting reaction centers is minimized by efficient charge separation. Here, it is aimed to mimic this by coupling dye-sensitized TiO2 nanocrystals to a decaheme protein, MtrC from Shewanella oneidensis MR-1, where the 10 hemes of MtrC form a ≈7-nm-long molecular wire between the TiO2 and the underlying electrode. The system is assembled by forming a densely packed MtrC film on an ultra-flat gold electrode, followed by the adsorption of approximately 7 nm TiO2 nanocrystals that are modified with a phosphonated bipyridine Ru(II) dye (RuP). The step-by-step construction of the MtrC/TiO2 system is monitored with (photo)electrochemistry, quartz-crystal microbalance with dissipation (QCM-D), and atomic force microscopy (AFM). Photocurrents are dependent on the redox state of the MtrC, confirming that electrons are transferred from the TiO2 nanocrystals to the surface via the MtrC conduit. In other words, in these TiO2/MtrC hybrid photodiodes, MtrC traps the conduction-band electrons from TiO2 before transferring them to the electrode, creating a photobioelectrochemical system in which a redox protein is used to mimic the efficient charge separation found in biological photosystems.
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Affiliation(s)
- Ee Taek Hwang
- School of Biomedical Sciences, University of Leeds Leeds, LS2 9JT, UK E-mail: ; The Astbury Centre for Structural Molecular Biology, University of Leeds Leeds, LS2 9JT, UK
| | - Khizar Sheikh
- School of Biomedical Sciences, University of Leeds Leeds, LS2 9JT, UK E-mail: ; The Astbury Centre for Structural Molecular Biology, University of Leeds Leeds, LS2 9JT, UK
| | - Katherine L Orchard
- Department of Chemistry, University of Cambridge Lensfield Road, Cambridge, CB2 1EW, UK E-mail: ; Advanced Institute for Materials Research, Tohoku University 2-1-1 Katahira Aoba-ku Sendai, Miyagi, 980-8577, Japan E-mail:
| | - Daisuke Hojo
- Advanced Institute for Materials Research, Tohoku University 2-1-1 Katahira Aoba-ku Sendai, Miyagi, 980-8577, Japan E-mail:
| | - Valentin Radu
- School of Biomedical Sciences, University of Leeds Leeds, LS2 9JT, UK E-mail: ; The Astbury Centre for Structural Molecular Biology, University of Leeds Leeds, LS2 9JT, UK
| | - Chong-Yong Lee
- Department of Chemistry, University of Cambridge Lensfield Road, Cambridge, CB2 1EW, UK E-mail:
| | - Emma Ainsworth
- Centre for Molecular and Structural Biochemistry, School of Chemistry and School of Biological Sciences, University of East Anglia Norwich Research Park, Norwich, NR4 7TJ, UK E-mail:
| | - Colin Lockwood
- Centre for Molecular and Structural Biochemistry, School of Chemistry and School of Biological Sciences, University of East Anglia Norwich Research Park, Norwich, NR4 7TJ, UK E-mail:
| | - Manuela A Gross
- Department of Chemistry, University of Cambridge Lensfield Road, Cambridge, CB2 1EW, UK E-mail:
| | - Tadafumi Adschiri
- Advanced Institute for Materials Research, Tohoku University 2-1-1 Katahira Aoba-ku Sendai, Miyagi, 980-8577, Japan E-mail:
| | - Erwin Reisner
- Department of Chemistry, University of Cambridge Lensfield Road, Cambridge, CB2 1EW, UK E-mail:
| | - Julea N Butt
- Centre for Molecular and Structural Biochemistry, School of Chemistry and School of Biological Sciences, University of East Anglia Norwich Research Park, Norwich, NR4 7TJ, UK E-mail:
| | - Lars J C Jeuken
- School of Biomedical Sciences, University of Leeds Leeds, LS2 9JT, UK E-mail: ; The Astbury Centre for Structural Molecular Biology, University of Leeds Leeds, LS2 9JT, UK
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133
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Grobbler C, Virdis B, Nouwens A, Harnisch F, Rabaey K, Bond PL. Use of SWATH mass spectrometry for quantitative proteomic investigation of Shewanella oneidensis MR-1 biofilms grown on graphite cloth electrodes. Syst Appl Microbiol 2015; 38:135-9. [DOI: 10.1016/j.syapm.2014.11.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 11/17/2014] [Accepted: 11/19/2014] [Indexed: 11/27/2022]
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134
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Otwell AE, Sherwood RW, Zhang S, Nelson OD, Li Z, Lin H, Callister SJ, Richardson RE. Identification of proteins capable of metal reduction from the proteome of the Gram-positive bacterium Desulfotomaculum reducens MI-1 using an NADH-based activity assay. Environ Microbiol 2015; 17:1977-90. [PMID: 25389064 DOI: 10.1111/1462-2920.12673] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Accepted: 10/14/2014] [Indexed: 12/14/2022]
Abstract
Understanding of microbial metal reduction is based almost solely on studies of Gram-negative organisms. In this study, we focus on Desulfotomaculum reducens MI-1, a Gram-positive metal reducer whose genome lacks genes with similarity to any characterized metal reductase. Using non-denaturing separations and mass spectrometry identification, in combination with a colorimetric screen for chelated Fe(III)-NTA reduction with NADH as electron donor, we have identified proteins from the D. reducens proteome not previously characterized as iron reductases. Their function was confirmed by heterologous expression in Escherichia coli. Furthermore, we show that these proteins have the capability to reduce soluble Cr(VI) and U(VI) with NADH as electron donor. The proteins identified are NADH : flavin oxidoreductase (Dred_2421) and a protein complex composed of oxidoreductase flavin adenine dinucleotide/NAD(P)-binding subunit (Dred_1685) and dihydroorotate dehydrogenase 1B (Dred_1686). Dred_2421 was identified in the soluble proteome and is predicted to be a cytoplasmic protein. Dred_1685 and Dred_1686 were identified in both the soluble as well as the insoluble protein fraction, suggesting a type of membrane association, although PSORTb predicts both proteins are cytoplasmic. This study is the first functional proteomic analysis of D. reducens and one of the first analyses of metal and radionuclide reduction in an environmentally relevant Gram-positive bacterium.
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Affiliation(s)
| | - Robert W Sherwood
- Department of Proteomics and Mass Spectrometry Facility, Cornell University, Ithaca, NY, USA
| | - Sheng Zhang
- Department of Proteomics and Mass Spectrometry Facility, Cornell University, Ithaca, NY, USA
| | - Ornella D Nelson
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Zhi Li
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Hening Lin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | | | - Ruth E Richardson
- Department of Civil and Environmental Engineering, Cornell University, Ithaca, NY, USA
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135
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DENG X, NAKAMURA R, HASHIMOTO K, OKAMOTO A. Electron Extraction from an Extracellular Electrode by Desulfovibrio ferrophilus Strain IS5 Without Using Hydrogen as an Electron Carrier. ELECTROCHEMISTRY 2015. [DOI: 10.5796/electrochemistry.83.529] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Xiao DENG
- Department of Applied Chemistry, University of Tokyo
| | - Ryuhei NAKAMURA
- Biofunctional Catalyst Research Team, RIKEN Center for Sustainable Resource Science
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136
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Venkidusamy K, Megharaj M, Schröder U, Karouta F, Mohan SV, Naidu R. Electron transport through electrically conductive nanofilaments in Rhodopseudomonas palustris strain RP2. RSC Adv 2015. [DOI: 10.1039/c5ra08742b] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The study demonstrates the physiological induction of electrically conductive nanofilaments from a metabolically versatile, iron(iii) respiring, photosynthetic bacteriumRhodopseudomonas palustrisstrain RP2.
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Affiliation(s)
- Krishnaveni Venkidusamy
- Centre for Environmental Risk Assessment and Remediation (CERAR)
- University of South Australia
- Mawson Lakes
- Australia
- CRC for Contamination Assessment and Remediation of the Environment (CRCCARE)
| | - Mallavarapu Megharaj
- Centre for Environmental Risk Assessment and Remediation (CERAR)
- University of South Australia
- Mawson Lakes
- Australia
- CRC for Contamination Assessment and Remediation of the Environment (CRCCARE)
| | - Uwe Schröder
- Institute of Environmental and Sustainable Chemistry
- Technische
- Universitat Braunschweig
- 38106 Braunschweig
- Germany
| | - Fouad Karouta
- Australian National Fabrication Facility, ACT Node
- Australian National University
- Canberra
- Australia
| | - S. Venkata Mohan
- Bioengineering and Environmental Sciences (BEES)
- CSIR-Indian Institute of Chemical Technology (CSIR-IICT)
- Hyderabad 500 007
- India
| | - Ravi Naidu
- Centre for Environmental Risk Assessment and Remediation (CERAR)
- University of South Australia
- Mawson Lakes
- Australia
- CRC for Contamination Assessment and Remediation of the Environment (CRCCARE)
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137
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Semenec L, E Franks A. Delving through electrogenic biofilms: from anodes to cathodes to microbes. AIMS BIOENGINEERING 2015. [DOI: 10.3934/bioeng.2015.3.222] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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138
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Shi L, Fredrickson JK, Zachara JM. Genomic analyses of bacterial porin-cytochrome gene clusters. Front Microbiol 2014; 5:657. [PMID: 25505896 PMCID: PMC4245776 DOI: 10.3389/fmicb.2014.00657] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 11/13/2014] [Indexed: 11/13/2022] Open
Abstract
The porin-cytochrome (Pcc) protein complex is responsible for trans-outer membrane electron transfer during extracellular reduction of Fe(III) by the dissimilatory metal-reducing bacterium Geobacter sulfurreducens PCA. The identified and characterized Pcc complex of G. sulfurreducens PCA consists of a porin-like outer-membrane protein, a periplasmic 8-heme c-type cytochrome (c-Cyt) and an outer-membrane 12-heme c-Cyt, and the genes encoding the Pcc proteins are clustered in the same regions of genome (i.e., the pcc gene clusters) of G. sulfurreducens PCA. A survey of additionally microbial genomes has identified the pcc gene clusters in all sequenced Geobacter spp. and other bacteria from six different phyla, including Anaeromyxobacter dehalogenans 2CP-1, A. dehalogenans 2CP-C, Anaeromyxobacter sp. K, Candidatus Kuenenia stuttgartiensis, Denitrovibrio acetiphilus DSM 12809, Desulfurispirillum indicum S5, Desulfurivibrio alkaliphilus AHT2, Desulfurobacterium thermolithotrophum DSM 11699, Desulfuromonas acetoxidans DSM 684, Ignavibacterium album JCM 16511, and Thermovibrio ammonificans HB-1. The numbers of genes in the pcc gene clusters vary, ranging from two to nine. Similar to the metal-reducing (Mtr) gene clusters of other Fe(III)-reducing bacteria, such as Shewanella spp., additional genes that encode putative c-Cyts with predicted cellular localizations at the cytoplasmic membrane, periplasm and outer membrane often associate with the pcc gene clusters. This suggests that the Pcc-associated c-Cyts may be part of the pathways for extracellular electron transfer reactions. The presence of pcc gene clusters in the microorganisms that do not reduce solid-phase Fe(III) and Mn(IV) oxides, such as D. alkaliphilus AHT2 and I. album JCM 16511, also suggests that some of the pcc gene clusters may be involved in extracellular electron transfer reactions with the substrates other than Fe(III) and Mn(IV) oxides.
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Affiliation(s)
- Liang Shi
- Pacific Northwest National Laboratory Richland, WA, USA
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139
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Melton ED, Swanner ED, Behrens S, Schmidt C, Kappler A. The interplay of microbially mediated and abiotic reactions in the biogeochemical Fe cycle. Nat Rev Microbiol 2014; 12:797-808. [DOI: 10.1038/nrmicro3347] [Citation(s) in RCA: 503] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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140
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Ding DW, Xu J, Li L, Xie JM, Sun X. Identifying the potential extracellular electron transfer pathways from a c-type cytochrome network. MOLECULAR BIOSYSTEMS 2014; 10:3138-46. [PMID: 25227320 DOI: 10.1039/c4mb00386a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Extracellular electron transfer (EET) is the key feature of some bacteria, such as Geobacter sulfurreducens and Shewanella oneidensis. Via EET processes, these bacteria can grow on electrode surfaces and make current output of microbial fuel cells. c-Type cytochromes can be used as carriers to transfer electrons, which play an important role in EET processes. Typically, from the inner (cytoplasmic) membrane through the periplasm to the outer membrane, they could form EET pathways. Recent studies suggest that a group of c-type cytochromes could form a network which extended the well-known EET pathways. We obtained the protein interaction information for all 41 c-type cytochromes in Shewanella oneidensis MR-1, constructed a large-scale protein interaction network, and studied its structural characteristics and functional significance. Centrality analysis has identified the top 10 key proteins of the network, and 7 of them are associated with electricity production in the bacteria, which suggests that the ability of Shewanella oneidensis MR-1 to produce electricity might be derived from the unique structure of the c-type cytochrome network. By modularity analysis, we obtained 5 modules from the network. The subcellular localization study has shown that the proteins in these modules all have diversiform cellular compartments, which reflects their potential to form EET pathways. In particular, combination of protein subcellular localization and operon analysis, the well-known and new candidate EET pathways are obtained from the Mtr-like module, indicating that potential EET pathways could be obtained from such a c-type cytochrome network.
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Affiliation(s)
- De-Wu Ding
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, P.R. China.
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141
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Liebensteiner MG, Tsesmetzis N, Stams AJM, Lomans BP. Microbial redox processes in deep subsurface environments and the potential application of (per)chlorate in oil reservoirs. Front Microbiol 2014; 5:428. [PMID: 25225493 PMCID: PMC4150442 DOI: 10.3389/fmicb.2014.00428] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Accepted: 07/29/2014] [Indexed: 12/15/2022] Open
Abstract
The ability of microorganisms to thrive under oxygen-free conditions in subsurface environments relies on the enzymatic reduction of oxidized elements, such as sulfate, ferric iron, or CO2, coupled to the oxidation of inorganic or organic compounds. A broad phylogenetic and functional diversity of microorganisms from subsurface environments has been described using isolation-based and advanced molecular ecological techniques. The physiological groups reviewed here comprise iron-, manganese-, and nitrate-reducing microorganisms. In the context of recent findings also the potential of chlorate and perchlorate [jointly termed (per)chlorate] reduction in oil reservoirs will be discussed. Special attention is given to elevated temperatures that are predominant in the deep subsurface. Microbial reduction of (per)chlorate is a thermodynamically favorable redox process, also at high temperature. However, knowledge about (per)chlorate reduction at elevated temperatures is still scarce and restricted to members of the Firmicutes and the archaeon Archaeoglobus fulgidus. By analyzing the diversity and phylogenetic distribution of functional genes in (meta)genome databases and combining this knowledge with extrapolations to earlier-made physiological observations we speculate on the potential of (per)chlorate reduction in the subsurface and more precisely oil fields. In addition, the application of (per)chlorate for bioremediation, souring control, and microbial enhanced oil recovery are addressed.
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Affiliation(s)
| | | | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University Wageningen, Netherlands ; Center of Biological Engineering, University of Minho Braga, Portugal
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142
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Dalla Vecchia E, Shao PP, Suvorova E, Chiappe D, Hamelin R, Bernier-Latmani R. Characterization of the surfaceome of the metal-reducing bacterium Desulfotomaculum reducens. Front Microbiol 2014; 5:432. [PMID: 25191310 PMCID: PMC4137172 DOI: 10.3389/fmicb.2014.00432] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 07/31/2014] [Indexed: 11/13/2022] Open
Abstract
Desulfotomaculum reducens strain MI-1 is a Gram-positive, sulfate-reducing bacterium also capable of reducing Fe(III). Metal reduction in Gram-positive bacteria is poorly understood. Here, we investigated Fe(III) reduction with lactate, a non-fermentable substrate, as the electron donor. Lactate consumption is concomitant to Fe(III) reduction, but does not support significant growth, suggesting that little energy can be conserved from this process and that it may occur fortuitously. D. reducens can reduce both soluble [Fe(III)-citrate] and insoluble (hydrous ferric oxide, HFO) Fe(III). Because physically inaccessible HFO was not reduced, we concluded that reduction requires direct contact under these experimental conditions. This implies the presence of a surface exposed reductase capable of transferring electrons from the cell to the extracellular electron acceptor. With the goal of characterizing the role of surface proteins in D. reducens and of identifying candidate Fe(III) reductases, we carried out an investigation of the surface proteome (surfaceome) of D. reducens. Cell surface exposed proteins were extracted by trypsin cell shaving or by lysozyme treatment, and analyzed by liquid chromatography-tandem mass spectrometry. This investigation revealed that the surfaceome fulfills many functions, including solute transport, protein export, maturation and hydrolysis, peptidoglycan synthesis and modification, and chemotaxis. Furthermore, a few redox-active proteins were identified. Among these, three are putatively involved in Fe(III) reduction, i.e., a membrane-bound hydrogenase 4Fe-4S cluster subunit (Dred_0462), a heterodisulfide reductase subunit A (Dred_0143) and a protein annotated as alkyl hydroperoxide reductase but likely functioning as a thiol-disulfide oxidoreductase (Dred_1533).
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Affiliation(s)
- Elena Dalla Vecchia
- Environmental Microbiology Laboratory, Environmental Engineering Institute, École Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | - Paul P Shao
- Environmental Microbiology Laboratory, Environmental Engineering Institute, École Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | - Elena Suvorova
- Environmental Microbiology Laboratory, Environmental Engineering Institute, École Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | - Diego Chiappe
- Proteomics Core Facility, Core Facility PTECH, École Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | - Romain Hamelin
- Proteomics Core Facility, Core Facility PTECH, École Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | - Rizlan Bernier-Latmani
- Environmental Microbiology Laboratory, Environmental Engineering Institute, École Polytechnique Fédérale de Lausanne Lausanne, Switzerland
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143
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Okamoto A, Nakamura R, Nealson KH, Hashimoto K. Bound Flavin Model Suggests Similar Electron-Transfer Mechanisms inShewanellaandGeobacter. ChemElectroChem 2014. [DOI: 10.1002/celc.201402151] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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144
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Membrane permeabilization underlies the enhancement of extracellular bioactivity in Shewanella oneidensis by a membrane-spanning conjugated oligoelectrolyte. Appl Microbiol Biotechnol 2014; 98:9021-31. [DOI: 10.1007/s00253-014-5973-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 07/01/2014] [Accepted: 07/19/2014] [Indexed: 01/29/2023]
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145
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Type II secretion system: A magic beanstalk or a protein escalator. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:1568-77. [DOI: 10.1016/j.bbamcr.2013.12.020] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 12/13/2013] [Accepted: 12/23/2013] [Indexed: 12/12/2022]
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146
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Cell-secreted flavins bound to membrane cytochromes dictate electron transfer reactions to surfaces with diverse charge and pH. Sci Rep 2014; 4:5628. [PMID: 25012073 PMCID: PMC4092373 DOI: 10.1038/srep05628] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 06/18/2014] [Indexed: 11/08/2022] Open
Abstract
The variety of solid surfaces to and from which microbes can deliver electrons by extracellular electron transport (EET) processes via outer-membrane c-type cytochromes (OM c-Cyts) expands the importance of microbial respiration in natural environments and industrial applications. Here, we demonstrate that the bifurcated EET pathway of OM c-Cyts sustains the diversity of the EET surface in Shewanella oneidensis MR-1 via specific binding with cell-secreted flavin mononucleotide (FMN) and riboflavin (RF). Microbial current production and whole-cell differential pulse voltammetry revealed that RF and FMN enhance EET as bound cofactors in a similar manner. Conversely, FMN and RF were clearly differentiated in the EET enhancement by gene-deletion of OM c-Cyts and the dependency of the electrode potential and pH. These results indicate that RF and FMN have specific binding sites in OM c-Cyts and highlight the potential roles of these flavin-cytochrome complexes in controlling the rate of electron transfer to surfaces with diverse potential and pH.
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147
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Tang J, Liu Y, Yuan Y, Zhou S. Humic acid-enhanced electron transfer of in vivo cytochrome c as revealed by electrochemical and spectroscopic approaches. J Environ Sci (China) 2014; 26:1118-1124. [PMID: 25079642 DOI: 10.1016/s1001-0742(13)60518-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 10/31/2013] [Accepted: 11/07/2013] [Indexed: 06/03/2023]
Abstract
Out-membrane cytochrome c (Cyt c) plays an important role carrying electrons from the inside of microbes to outside electron acceptors. However, the active sites of Cyt c are wrapped by nonconductive peptide chains, hindering direct extracellular electron transfer (EET). Humic acids (HA) have been previously proven to efficiently facilitate EET. However, the inherent mechanism of HA-stimulated EET has not been well interpreted. Here, to probe the mechanism behind HA-stimulated EET, we studied the interaction between Cyt c and HA. The attachment of active in vivo Cyt c on a graphite electrode was achieved when MR-1 cells were self-assembled on the electrode surface. Pure horse-heart Cyt c was covalently immobilized on an electrode via 4-aminobenzoic acid to create an active in vitro Cyt c-enriched surface. Cyclic voltammetric measurements and scanning electron microscopy confirmed the immobilization of bacterial cells and pure Cyt c protein. Electrochemical methods revealed that HA could enhance the electrocatalytic current of both in vitro and in vivo Cyt c towards oxygen and thiosulfate, suggesting enhanced EET. The blue-shifted soret band in the UV-Vis spectra and changes in the excitation/emission matrix fluorescence spectra demonstrated that Cyt c interacted with HA to form organic complexes via electrostatic or hydrogen-bonding interactions. The results will help understand electron shuttle-stimulated EET and develop bacteria-based bioremediation and bioenergy technologies.
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Affiliation(s)
- Jiahuan Tang
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; Guangdong Institute of Eco-environmental and Soil Sciences, Guangzhou 510650, China.
| | - Yi Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Yong Yuan
- Guangdong Institute of Eco-environmental and Soil Sciences, Guangzhou 510650, China
| | - Shungui Zhou
- Guangdong Institute of Eco-environmental and Soil Sciences, Guangzhou 510650, China.
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148
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Liu J, Chakraborty S, Hosseinzadeh P, Yu Y, Tian S, Petrik I, Bhagi A, Lu Y. Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. Chem Rev 2014; 114:4366-469. [PMID: 24758379 PMCID: PMC4002152 DOI: 10.1021/cr400479b] [Citation(s) in RCA: 560] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Jing Liu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Saumen Chakraborty
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Parisa Hosseinzadeh
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yang Yu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shiliang Tian
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Igor Petrik
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ambika Bhagi
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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Nanostructured Graphene/TiO2Hybrids as High-Performance Anodes for Microbial Fuel Cells. Chemistry 2014; 20:7091-7. [DOI: 10.1002/chem.201400272] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Indexed: 11/07/2022]
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Comparison of flavins and a conjugated oligoelectrolyte in stimulating extracellular electron transport from Shewanella oneidensis MR-1. Electrochem commun 2014. [DOI: 10.1016/j.elecom.2014.01.025] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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